Marcus Harrell Receives the Dean's Award for Best Dissertation in Mathematics and Science

Marcus Harrell, Ph.D., of the Das Lab has been selected to receive the Dean's Award for Best Dissertation in Mathematics and Science. Marcus' dissertation, titled "Spatiotemporal Regulation of Cdc42 GEF, Scd1, for Multiple Sites of Cellular Growth", was defended on November 22, 2024.

The award is an annual feature of the Graduate Degree Ceremony taking place at Boston College's Commencement on May 19 at 12 pm, where Marcus will be recognized for this accomplishment. 

New paper by Sean Keeley and Miriam Fernández-Lajarín of the González-Rosa Lab is published on the front cover of the Cell Reports Methods journal

Sean Keeley and Miriam Fernández-Lajarín of the González-Rosa Lab have a recent paper published on the front cover of the Cell Reports Methods journal. The paper is titled "Optimization of methods for rapid and robust generation of cardiomyocyte-specific crispants in zebrafish using the cardiodeleter system". The Abstract of the paper reads as follows: 

CRISPR/Cas9 has massively accelerated the generation of gene loss-of-function models in zebrafish. However, establishing tissue-specific mutant lines remains a laborious and time-consuming process. Although a few dozen tissue-specific Cas9 zebrafish lines have been developed, the lack of standardization of some key methods, including gRNA delivery, has limited the implementation of these approaches in the zebrafish community. To tackle these limitations, we have established a cardiomyocyte-specific Cas9 line, the cardiodeleter , which efficiently generates biallelic mutations in combination with gene-specific gRNAs. We have also optimized the development of transposon-based guide shuttles that carry gRNAs targeting a gene of interest and permanently label the cells susceptible to becoming mutant. We validated this modular approach by deleting five genes ( ect2 , tnnt2a , cmlc2 , amhc , and erbb2 ), all resulting in the loss of the corresponding protein or phenocopying established mutants. Additionally, we provide detailed protocols describing how to generate guide shuttles , which will facilitate the dissemination of these techniques in the zebrafish community. Our approach enables the rapid generation of tissue-specific crispants and analysis of mosaic phenotypes, bypassing limitations such as embryonic lethality, making it a valuable tool for cell-autonomous studies and genetic screenings.

The full article can be accessed on Cell Press here. 

Helena Ebeling '25, Biology major and current senior at Boston College, publishes new paper in the American Medical Writers Association Journal

A new paper by Helena Ebeling, Biology major and current senior at Boston College, has been chosen for publication by the American Medical Writers Association Journal. The paper is titled, "The XYY Story as a Cautionary Tale: How Scientific Misinformation and Common Biases Can Negatively Impact Lives and Opinions".

The Abstract reads as follows:

In recent decades, huge strides have been made in the field of genetics. Genomic analysis technology has enabled sci-entists to explore how genetics affect every aspect of human life and development. Genetic testing is poised to be at theforefront of contemporary medicine. Parents often grapplewith the correlation of their child’s genetic mutations andserious diseases. At a time when misinformation spreadsthrough the popular press like wildfire, we are recounting the XYY story as a cautionary tale to highlight the impor-tance of scientists speaking up and standing against the misuse of genetic information.

The full article can be viewed on the AMWA Journal website. 

DOI: https://doi.org/10.55752/amwa.2024.393

Madisen Caferro of the Folker Lab Presents at Cell Bio 2024 in San Diego, CA

Graduate student Madisen Caferro of the Folker Lab presented her research at Cell Bio 2024, the joint meeting of the American Society for Cell Biology (ASCB) and the European Molecular Biology Organization (EMBO). The abstract to Madisen's research, titled "Microtubule Organizing Proteins Contribute to Drosophila Muscle Patterning", is included below: 

Drosophila muscles are acentrosomal, multinucleated cells, formed through a multi-step developmental process known as myogenesis. Myogenesis in Drosophila requires the specification of founder cells that program the size, shape, and orientation of each eventual muscle, as well as the fusion of myoblasts with founder cells to donate nuclei and increase myotube size. At the conclusion of myogenesis, multiple nuclei are evenly spaced throughout the large muscle cell. Because the muscle cell microtubule network is organized by multiple acentrosomal microtubule organizing centers (MTOCs), including the nuclei and the Golgi bodies, we hypothesized that these distinct populations of microtubules regulate unique features of myogenesis. To test our hypothesis, we compared the developmental effects of depleting centrosomin (Cnn), a MTOC protein localized to the nuclear envelope, or GM130, a MTOC protein that anchors the essential microtubule nucleator 𝛄-tubulin to the Golgi bodies. Specifically, we tested whether muscle specific depletion of Cnn or GM130 affected nuclear spacing, cell fusion, muscle identity, or muscle patterning in both embryos and larvae. Surprisingly, although nuclear spacing is microtubule-dependent, no significant effects on nuclear spacing were observed. However, a variety of other phenotypes were observed. In the Cnn-depleted larvae, we observed a decreased average number of nuclei per muscle. In the Cnn-depleted embryos, we observed the development of an increased number of myotubes. In addition, the GM130 depleted embryos contained increased and mislocalized expression of apterous, a Drosophila identity gene. These preliminary data suggest that while Cnn and GM130 do not contribute to nuclear spacing, the nucleus-organized microtubules and the Golgi-organized microtubules do play two distinct roles in muscle patterning. The nucleus-organized microtubules contribute to muscle number, while the Golgi-organized microtubules contribute to muscle identity. These findings open exciting new directions for the field, as a role for microtubule organizing proteins in general muscle identity and development, let alone distinct roles for different populations of microtubules, has yet to be characterized.

For more information about Cell Bio 2024, see the conference's website here.

Biology Major Emma Su Recognized for "Outstanding Trainee Poster Award" at the American Thyroid Association Annual Meeting

Emma Su '26, a Biology major and Math minor on the pre-health track at Boston College, was recognized at the American Thyroid Association Annual Meeting. Emma is an undergraduate researcher at Dana Farber, and her research project is investigating changes in the immune programs that drive thyroid cancer progression through single-nuclei RNA-seq analysis. 

For more information regarding the conference, held in Chicago from October 30th to November 2nd, 2024, please see the 2024 ATA Annual Meeting website. 

Professor Peter Clote's First Volume of "RNA: Computational Methods for Structure, Kinetics, and Rational Design" is Now Available

Comprising two volumes, Biology Professor Peter Clote's RNA: Computational Methods for Structure, Kinetics, and Rational Design is a comprehensive treatment of computational methods concerning the secondary structure, folding kinetics and rational design of RNA.

RNA computational biology is an interdisciplinary research field, involving contributions from physical chemistry (determination of free energy parameters), polymer physics (calculation of entropy by Gaussian integrals and enumeration of self-avoiding walks), mathematics (combinatorics that leads to dynamic programming algorithms) and computer science (efficient algorithm design and implementation). Volume 1 of this new ~400 page monograph describes how energy parameters are determined, and how effficient structure prediction algorithms are designed that use such parameters. These algorithms have ubiquitous applications in molecular biology, ranging from prediction of microRNA targets in messenger RNA to the design of RNA thermoswitches, a topic in synthetic biology. The forthcoming Volume 2 describes folding kinetics and the rational design of RNA molecules. The focus of the monograph is not on tool use, but rather tool design: figuratively, the reader is given a chisel, hammer, design plans of the Notre Dame and provided the wherewithal to reconstruct the cathedral.

This publication is available for pre-order on October 30, 2024. Item will ship after November 20, 2024

Biology Majors Present Research at Annual Biomedical Engineering Sciences Convention

Boston College undergraduate researchers presented their work at the annual Biomedical Engineering Sciences Convention in Baltimore, MD. Hear from one Biology student below:

"My name is Nick Reilly and I am a Senior majoring in Biology on the Pre-Medical Track with a minor in Medical Humanities. I work on the 5th floor of 245 Beacon Street in Professor Gaudette’s Cell Agriculture Laboratory. I perform research that analyzes the behavior of decellularized plant scaffolds within a fluidized bed bioreactor system. Fluidized bed bioreactors are engineered systems that offer a continuous flow of media, nutrient replenishment, and reduced water usage, allowing for a more environmentally friendly and efficient mechanism to culture laboratory-grown meat. By incubating a fresh plant in solutions of SDS and bleach, the internal cellular components are degraded leaving behind a scaffold consisting solely of extracellular matrix. These scaffolds function as potential carriers of satellite cells allowing for an environmentally friendly and edible alternative to culturing laboratory-grown meat compared to plastic scaffolds commonly used in industry. As of this moment, I have adhered quail myogenic cells to the scaffolds within the bioreactor system allowing me to actively analyze how well these cells adhere to the decellularized plant scaffolds and any production of metabolic byproducts throughout continuous media flow. I am presenting this research at the annual Biomedical Engineering Sciences convention on October 24th in Baltimore, MD."

Dasha Perminova Wins Best Image at 2024 Biology Department Retreat

Dasha Perminova of the González-Rosa Lab won Best Image at the 2024 Biology Department Retreat, voted by her peers and Biology Faculty members.

Dasha writes: "The image is of a transgenic larval zebrafish under brightfield and is part of my work trying to understand and manipulate immune cells, especially T-cells, during zebrafish heart regeneration. This is further part of the overarching goal of the Gonzalez-Rosa lab to understand the molecular processes that facilitate regeneration and how these mechanisms differ from mammalian hearts, which do not regenerate. We hope that our work can eventually facilitate the development of novel therapies for heart disease and myocardial infarctions ("heart attacks"), which are becoming an increasingly prevalent global problem."

Marcus Harrell Wins Best Poster at 2024 Biology Department Retreat

Marcus Harrell of the Das Lab won Best Poster at the 2024 Biology Department Retreat, voted by his peers and Biology Faculty members.

The abstract to Marcus' poster is included:

Title: The Cdc42 GEF, Scd1, localizes to cell ends via Diffusion to promote bipolar growth in S. pombe

Abstract: The Rho GTPase Cdc42 is highly conserved and a major regulator of polarized growth in most eukaryotes. In the bipolar yeast S. pombe, Cdc42 activity periodically oscillates between the two ends to promote growth. Both ends do not simultaneously remain active, and the active end must lose Cdc42 activation for the other end to gain Cdc42 activity. This suggests the two ends must compete for resources that activate Cdc42. However, the underlying mechanisms that coordinate the precise spatiotemporal activation of Cdc42 are not fully understood. One outstanding question is what resource do the two ends compete for? We previously found that disruption of branched actin (required for endocytosis) but not actin cables (required for exocytosis), impedes Scd1 localization (Cdc42 activator) which disrupts active Cdc42 dynamics. We further found that Scd1 localization was disrupted because endocytosis is required to remove the PAK kinase Pak1 (Scd1 inhibitor). These results suggest that Scd1 localization is essential for competition, but Scd1 is not directly localized by actin. Thus, we hypothesize that growing ends compete for Scd1 which diffuses between both ends. We tested this by quantifying the impact of increasing the mass of Scd1 on cell morphology and protein dynamics. We find that heavier Scd1 leads to more monopolar cells and slower Scd1 localization. Thus, we propose that the Cdc42 activator Scd1 diffuses along a concentration gradient between the two ends to promote periodic spatiotemporal activation of Cdc42.

First Demonstration of In Vivo PDE11A4 Target Engagement for Potential Treatment of Age-Related Memory Disorders

PDE11A4 is a target of interest for the treatment of age-related memory disorders. A previous report from our laboratories described an amide series of potent, selective PDE11A4 inhibitors that was metabolically unstable. Investigation of heterocyclic amide isosteres for the labile amide moiety revealed distinct structure-activity relationships and identified several compounds with potency comparable to the amide series. This manuscript describes the characterization of structure-activity and structure-property relationships in this set, leading to the identification of an orally bioavailable, brain-penetrant, selective and potent PDE11A4 inhibitor. Target engagement experiments demonstrated PDE11A4 inhibition in the hypothalamus of mice that was absent in PDE11A4 knock out animals.

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Single cell expression and chromatin accessibility of the Toxoplasma gondii lytic cycle identifies AP2XII-8 as an essential ribosome regulon driver

Sequential lytic cycles driven by cascading transcriptional waves underlie pathogenesis in the apicomplexan parasite Toxoplasma gondii. This parasite’s unique division by internal budding, short cell cycle, and jumbled up classically defined cell cycle stages have restrained in-depth transcriptional program analysis. Here, unbiased transcriptome and chromatin accessibility maps throughout the lytic cell cycle are established at the single-cell level. Correlated pseudo-timeline assemblies of expression and chromatin profiles maps transcriptional versus chromatin level transition points promoting the cell division cycle. Sequential clustering analysis identifies functionally related gene groups promoting cell cycle progression. Promoter DNA motif mapping reveals patterns of combinatorial regulation. Pseudo-time trajectory analysis reveals transcriptional bursts at different cell cycle points. The dominant burst in G1 is driven largely by transcription factor AP2XII-8, which engages a conserved DNA motif, and promotes the expression of 44 ribosomal proteins encoding regulon. Overall, the study provides integrated, multi-level insights into apicomplexan transcriptional regulation.

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Growth patterns of caudal fin rays are informed by both external signals from the regenerating organ and remembered identity autonomous to the local tissue

Regenerating tissues must remember or interpret their spatial position, using this information to restore original size and patterning. The external skeleton of the zebrafish caudal fin is composed of 18 rays; after any portion of the fin is amputated, position-dependent regenerative growth restores each ray to its original length. We tested for transcriptional differences during regeneration of proximal versus distal tissues and identified 489 genes that differed in proximodistal expression. Thyroid hormone directs multiple aspects of ray patterning along the proximodistal axis, and we identified 364 transcripts showing a proximodistal expression pattern that was dependent on thyroid hormone context. To test what aspects of ray positional identity are directed by extrinsic environental cues versus remembered identity autonomous to the tissue, we transplanted distal portions of rays to proximal environments and evaluated regeneration within the new location. Native regenerating proximal tissue showed robust expression of scpp7, a transcript with thyroid-regulated proximal enrichment; in contrast, regenerating rays originating from transplanted distal tissue showed reduced (distal-like) expression during outgrowth. These distal-to-proximal transplants regenerated far beyond the length of the graft itself, indicating that cues from the proximal environment promoted additional growth. Nonetheless, these transplants initiated regeneration at a much slower rate compared to controls, suggesting memory of distal identity was retained by the transplanted tissue. This early growth retardation caused rays that originated from transplants to grow noticeably shorter than neighboring native rays. While several aspects of fin ray morphology (bifurcation, segment length) were found to be determined by the environment, we found that both regeneration speed and ray length are remembered autonomously by tissues, and that persist through multiple rounds of amputation and regeneration.

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Development of a hepatic cryoinjury model to study liver regeneration

The liver is a remarkable organ that can regenerate in response to injury. Depending on the extent of injury, the liver can undergo compensatory hyperplasia or fibrosis. Despite decades of research, the molecular mechanisms underlying these processes are poorly understood. Here, we developed a new model to study liver regeneration based on cryoinjury. To visualise liver regeneration at cellular resolution, we adapted the CUBIC tissue-clearing approach. Hepatic cryoinjury induced a localised necrotic and apoptotic lesion characterised by inflammation and infiltration of innate immune cells. After this initial phase, we observed fibrosis, which resolved as regeneration re-established homeostasis in 30 days. Importantly, this approach enables the comparison of healthy and injured parenchyma within an individual animal, providing unique advantages to previous models. In summary, the hepatic cryoinjury model provides a fast and reproducible method for studying the cellular and molecular pathways underpinning fibrosis and liver regeneration.

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Toxoplasma FER1 is a versatile and dynamic mediator of differential microneme trafficking and microneme exocytosis

Toxoplasma gondii is a polarized cell concentrating several secretory organelles at the apical pole. The secretory micronemes come in two sub-populations differentiated by dependence on the Rab5A/C in their biogenesis. Calcium-dependent exocytosis of micronemes occurs at the very apical tip and is critical for parasite egress from its host cell, adhesion and invasion of the next cell. Ferlins represent a protein family with roles in exocytosis containing multiple Ca2+-sensing C2 domains. We determined that T. gondii’s ferlin 1 (FER1) localized dynamically to the parasite’s secretory pathway. FER1 function was dissected by dominant negative overexpression strategies. We demonstrated that FER1 traffics microneme organelles along the following trajectories:1. From the trans-Golgi-endosomes network to the subpellicular cortex; 2. Along the cortex to the apical end; 3. To the apical tip for fusion with the plasma membrane; 4. Retrograde transport allowing microneme recycling from mother to daughter; 5. Differential microneme sub-population traffic. Finally, FER1 overexpression triggers a microneme exocytosis burst, supporting the notion that the radially organized micronemes at the apical tip comprise a readily-releasable microneme pool. In summary, FER1 is pivotal for dynamic microneme trafficking, acts differently on the two microneme subpopulations, and acts on the plasma membrane fusion step during microneme exocytosis.

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Hamilton Symposium 2024 Held at Boston College

The Hamilton Symposium featured a panel discussion highlighting the current Narratives and Discoveries surrounding Rare Genetic diseases. Conversations addressed the barriers and challenges for those with rare genetic disease and the impact on families. The Department of Biology sponsored this event on May 3rd, 2024.

Panelists offered perspectives on the broad range of factors that influence societal behavior, education, therapeutic approaches and advancement, humanities and research and development which affect an estimated 300 million people with rare disorders. This year's panel featured Kenna Sullivan of the BC School of Social Work, Jessica Pugliesi of the Lynch School of Education & Human Development, and Ravi Balasubramanian, Physician-Scientist at Massachusetts General Hospital. 

Featured in this photo (left to right) are: Kenna Sullivan, Ravi Balasubramanian, and Jessica Pugliesi. Andrew Dwyer (right) of the Connell School of Nursing at Boston College moderated the panel discussion. 

Associate Professor of the Practice Christopher Kenaley Discovers a New Species

Christopher Kenaley, Associate Professor of the Practice in the Department of Biology, has discovered a new species: Eustomias (Nominostomias) robertsi. Only two of these dragonfish have been found in the western South Pacific Ocean. The full article can be accessed from the Miami Herald here. 

Dynamics of collagen oxidation and cross linking in regenerating and irreversibly infarcted myocardium

In mammalian hearts myocardial infarction produces a permanent collagen-rich scar. Conversely, in zebrafish a collagen-rich scar forms but is completely resorbed as the myocardium regenerates. The formation of cross-links in collagen hinders its degradation but cross-linking has not been well characterized in zebrafish hearts. Here, a library of fluorescent probes to quantify collagen oxidation, the first step in collagen cross-link (CCL) formation, was developed. Myocardial injury in mice or zebrafish resulted in similar dynamics of collagen oxidation in the myocardium in the first month after injury. However, during this time, mature CCLs such as pyridinoline and deoxypyridinoline developed in the murine infarcts but not in the zebrafish hearts. High levels of newly oxidized collagen were still seen in murine scars with mature CCLs. These data suggest that fibrogenesis remains dynamic, even in mature scars, and that the absence of mature CCLs in zebrafish hearts may facilitate their ability to regenerate.

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2024 Northeastern Nuclear Envelope meeting sponsored by Boston College and Yale University

NENE 2024 will be the fifth iteration of The Northeastern Nuclear Envelope meeting, bringing together laboratories in the Northeast that share a common interest in the nuclear envelope and related biology.

The meeting will take place at Yale University on May 17th. NENE 2024 is sponsored by Yale University and Boston College. The organizers are trainees from the biology departments of these two institutions. The NENE meeting provides a unique opportunity for researchers who share a common interest in the biology of the nucleus, the nuclear envelope, and nuclear transport to share their work, discover new biology, and develop professional networks. We're thrilled to have Dr. Abby Buchwalter as our NENE 2024 keynote speaker. Dr. Buchwalter is an Assistant Professor at UCSF and a Chan Zuckerberg Biohub Investigator.

Induction of durable remission by dual immunotherapy in SHIV-infected ART-suppressed macaques

The eradication of the viral reservoir represents the major obstacle to the development of a clinical cure for established HIV-1 infection. Here, we demonstrate that the administration of N-803 (brand name Anktiva) and broadly neutralizing antibodies (bNAbs) results in sustained viral control after discontinuation of antiretroviral therapy (ART) in simian-human AD8 (SHIV-AD8)-infected, ART-suppressed rhesus macaques. N-803+bNAbs treatment induced immune activation and transient viremia but only limited reductions in the SHIV reservoir. Upon ART discontinuation, viral rebound occurred in all animals, which was followed by durable control in approximately 70% of all N-803+bNAb-treated macaques. Viral control was correlated with the reprogramming of CD8+ T cells by N-803+bNAb synergy. Thus, complete eradication of the replication-competent viral reservoir is likely not a prerequisite for the induction of sustained remission after discontinuation of ART.

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Plastics, Fossil Carbon, and the Heart

Plastics have enabled extraordinary advances in virtually every area of medicine and have made our lives immeasurably more convenient. Multiple lines of evidence now indicate, however, that plastics are neither as safe nor as inexpensive as they seem. The benefits of plastics come at great and increasingly visible costs to human health and the environment.

Plastics are manufactured chemical materials.Fossil fuels — gas, oil, and coal — are the main feedstocks of plastics, and fossil carbon corporations such as ExxonMobil are their principal producers. Plastics comprise a polymer matrix plus thousands of chemical additives that impart such properties as color, stability, flexibility, flame resistance, and water repellency. Many additives are toxic; these include carcinogens, neurotoxicants, and endocrine disruptors such as bisphenols and perfluorinated and polyfluorinated substances that can disrupt lipid metabolism and increase the risk of diabetes, cardiovascular disease, and stroke.

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RNA cis-regulators are important for Streptococcus pneumoniae in vivo success

Bacteria have evolved complex transcriptional regulatory networks, as well as many diverse regulatory strategies at the RNA level, to enable more efficient use of metabolic resources and a rapid response to changing conditions. However, most RNA-based regulatory mechanisms are not well conserved across different bacterial species despite controlling genes important for virulence or essential biosynthetic processes. Here, we characterize the activity of, and assess the fitness benefit conferred by, twelve cis-acting regulatory RNAs (including several riboswitches and a T-box), in the opportunistic pathogen Streptococcus pneumoniae TIGR4. By evaluating native locus mutants of each regulator that result in constitutively active or repressed expression, we establish that growth defects in planktonic culture are associated with constitutive repression of gene expression, while constitutive activation of gene expression is rarely deleterious. In contrast, in mouse nasal carriage and pneumonia models, strains with either constitutively active and repressed gene expression are significantly less fit than matched control strains. Furthermore, two RNA-regulated pathways, FMN synthesis/transport and pyrimidine synthesis/transport display exceptional sensitivity to mis-regulation or constitutive gene repression in both planktonic culture and in vivo environments. Thus, despite lack of obvious phenotypes associated with constitutive gene expression in vitro, the fitness benefit conferred on bacteria via fine-tuned metabolic regulation through cis-acting regulatory RNAs is substantial in vivo, and therefore easily sufficient to drive the evolution and maintenance of diverse RNA regulatory mechanisms.

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Biology BS Major & Studio Art Minor Joanna Folta Displays Work In Higgins Hall

Joanna Folta '24 and Biology Professor David Burgess, PhD, stand beside Joanna's work titled The Study of Life (2023), displayed in Higgins Hall at Boston College. She writes, "This installation is a reflection of my passion for trying to understand life - both through scientific and artistic perspectives. Borders of handmade hanji (Korean traditional paper) depict cross-sections of six unique organelle-packed cells sitting in an extracellular matrix of hanji fibers. The artwork is a continuation of a series on a reflection of who I am". Joanna was a student in Professor Burgess's Cell Biology course, and some of the construction of this piece is handmade paper consisting of pieces of Joanna's cellular biology class notes.

A viral insulin-like peptide inhibits IGF-1 receptor phosphorylation and regulates IGF1R gene expression

Objective: The insulin/IGF superfamily is conserved across vertebrates and invertebrates. Our team has identified five viruses containing genes encoding viral insulin/IGF-1 like peptides (VILPs) closely resembling human insulin and IGF-1. This study aims to characterize the impact of Mandarin fish ranavirus (MFRV) and Lymphocystis disease virus-Sa (LCDV-Sa) VILPs on the insulin/IGF system for the first time.

Methods: We chemically synthesized single chain (sc, IGF-1 like) and double chain (dc, insulin like) forms of MFRV and LCDV-Sa VILPs. Using cell lines overexpressing either human insulin receptor isoform A (IR-A), isoform B (IR-B) or IGF-1 receptor (IGF1R), and AML12 murine hepatocytes, we characterized receptor binding, insulin/IGF signaling. We further characterized the VILPs' effects of proliferation and IGF1R and IR gene expression, and compared them to native ligands. Additionally, we performed insulin tolerance test in CB57BL/6 J mice to examine in vivo effects of VILPs on blood glucose levels. Finally, we employed cryo-electron microscopy (cryoEM) to analyze the structure of scMFRV-VILP in complex with the IGF1R ectodomain.

Results: VILPs can bind to human IR and IGF1R, stimulate receptor autophosphorylation and downstream signaling pathways. Notably, scMFRV-VILP exhibited a particularly strong affinity for IGF1R, with a mere 10-fold decrease compared to human IGF-1. At high concentrations, scMFRV-VILP selectively reduced IGF-1 stimulated IGF1R autophosphorylation and Erk phosphorylation (Ras/MAPK pathway), while leaving Akt phosphorylation (PI3K/Akt pathway) unaffected, indicating a potential biased inhibitory function. Prolonged exposure to MFRV-VILP led to a significant decrease in IGF1R gene expression in IGF1R overexpressing cells and AML12 hepatocytes. Furthermore, insulin tolerance test revealed scMFRV-VILP's sustained glucose-lowering effect compared to insulin and IGF-1. Finally, cryo-EM analysis revealed that scMFRV-VILP engages with IGF1R in a manner closely resembling IGF-1 binding, resulting in a highly analogous structure.

Conclusions: This study introduces MFRV and LCDV-Sa VILPs as novel members of the insulin/IGF superfamily. Particularly, scMFRV-VILP exhibits a biased inhibitory effect on IGF1R signaling at high concentrations, selectively inhibiting IGF-1 stimulated IGF1R autophosphorylation and Erk phosphorylation, without affecting Akt phosphorylation. In addition, MFRV-VILP specifically regulates IGF-1R gene expression and IGF1R protein levels without affecting IR. CryoEM analysis confirms that scMFRV-VILP' binding to IGF1R is mirroring the interaction pattern observed with IGF-1. These findings offer valuable insights into IGF1R action and inhibition, suggesting potential applications in development of IGF1R specific inhibitors and advancing long-lasting insulins.

Keywords: Biased signaling; IGF-1; IGF1 receptor; IGF1 receptor inhibition; Insulin; Iridoviridae; Viral insulin/IGF-1 like peptides (VILPs).

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Students and Faculty Attend 2023 SACNAS Conference

Boston College Biology students and faculty attended the 2023 SACNAS National Conference in Portland, Oregon. Students presented individual research in poster sessions spanning October 26-28. 

BC Biology Major Attends 2023 ABRCMS Conference in Phoenix

Thanks to the BC Biology department, I was fortunate enough to be given the opportunity to attend the 2023 ABRCMS conference in Phoenix, Arizona as an undergraduate poster presenter. Being able to present my research from my summer research program at the Keck School of Medicine of USC was a wonderful and exciting experience. Attending scientific and career-orientated talks was also enriching as well. I am very thankful for this experience!

Caleb Alebachew, Boston College Biology B.S. 2024

Biology PhD Candidates Attend Keystone Symposia Conference

Boston College Biology PhD Candidates Kristina Kelley (left) and Audrey Randall (right) attend the Keystone Symposia Conference. Kristina and Audrey presented their research as members of the Altindis Lab at Boston College. 

Revised fission yeast gene and allele nomenclature guidelines for machine readability

Standardized nomenclature for genes, gene products, and isoforms is crucial to prevent ambiguity and enable clear communication of scientific data, facilitating efficient biocuration and data sharing. Standardized genotype nomenclature, which describes alleles present in a specific strain that differ from those in the wild-type reference strain, is equally essential to maximize research impact and ensure that results linking genotypes to phenotypes are Findable, Accessible, Interoperable, and Reusable (FAIR). In this publication, we extend the fission yeast clade gene nomenclature guidelines to support the curation efforts at PomBase (www.pombase.org), the Schizosaccharomyces pombe Model Organism Database. This update introduces nomenclature guidelines for noncoding RNA genes, following those set forth by the Human Genome Organisation Gene Nomenclature Committee. Additionally, we provide a significant update to the allele and genotype nomenclature guidelines originally published in 1987, to standardize the diverse range of genetic modifications enabled by the fission yeast genetic toolbox. These updated guidelines reflect a community consensus between numerous fission yeast researchers. Adoption of these rules will improve consistency in gene and genotype nomenclature, and facilitate machine-readability and automated entity recognition of fission yeast genes and alleles in publications or datasets. In conclusion, our updated guidelines provide a valuable resource for the fission yeast research community, promoting consistency, clarity, and FAIRness in genetic data sharing and interpretation.

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2023 Sophomore and Dean's Scholars Named for students within the Biology Department

The Dean's Office of Boston College has named the 2023 Sophomore and Dean's Scholars for academically distinguished students of the Sophomore and Junior classes respectively. Sophomores Daniel Akinremi, Andrew Keenan, Michelle Kim, Nick Reilly, Kevin Tang, Jackson Yates, and Xingyan Wang have been named Sophomore Scholars. Juniors Isabel Craven, David Koo, Kristi Liivak, David Wang, Allison Pelligrino, Mehdi Kayi, Bonnie Stewart, Julianna Barbaro, Jeramiah Bravo, Andrew Joyal, Jonah Kotzen, Maria Louis, and Julie Satterthwaite have been named Dean's Scholars. 

For your reference, the details for these awards can be found here. 

Sophomore Scholars: Academically distinguished members of the Sophomore Class who have achieved an academic ranking, placing them in the top three percent of their class, are selected by the Dean of the College of Arts and Sciences. Most have also received the recognition and nomination of their major departments. 
Dean's Scholars: The Dean of the Morrissey College of Arts and Sciences selects the brightest scholars from the Junior Class to be chosen for this honor. Students are selected on the basis of their overall academic performance, recommendations from their departmental faculty, co-curricular initiatives, and their sense of purpose in how they approach their future.

Sarah McMenamin hosts BAZaR: Boston Area Zebrafish Researchers Meeting

Sarah McMenamin and the McMenamin Lab helped to organize and host BAZaR: Boston Area Zebrafish Researchers Meeting on March 18th, 2023. Nearly 90 Boston area researchers, scientists, postdoctoral fellows, graduate students, and undergrad researchers who utilize zebrafish in research gathered to share in an exciting full-day conference at Boston College. 

For those interested in more information, the abstract book is available online to view the day's agenda with the invited speakers and the titles of their talks. A poster session was held after the talks and three exhibition tables from daniolab, ACD Biotechne, and Leica Microsystems joined for the event. Information regarding the talks and posters is also available online.

Hamilton Symposium Panelists Announced

Boston College is excited to announce the panelists of the 2023 Hamilton Symposium on Rare Genetic Diseases. The Hamilton Symposium will feature a panel discussion highlighting the current Discoveries and Narrative of Rare Genetic diseases. Amy Boesky, Professor in the English Department at BC and Program Director of Medical Humanities will be the Moderator of this year's Hamilton Symposium. This year's panelists include: Dr. Elizabeth O'Day '06, CEO and Founder of Olaris, Inc. Andrea Vicini, SJ, Professor in the Theology Department, Chairperson, and Michael P. Walsh Professor of Bioethics. Patricia Weltin P'24, CEO/Founder Beyond the Diagnosis.        

Conversations will address the barriers and challenges for those with rare genetic disease and the impact on families. The Department of Biology will sponsor this event on May 5th, 2023, beginning at 1pm.

Panelists will offer perspectives on the broad range of factors that influence societal behavior, education, therapeutic approaches and advancement, humanities and research and development which affect an estimated 300 million people with rare disorders.

Named in honor of Annie Hamilton and the CUREFA Foundation, the Symposium’s purpose is to promote research, advocacy, and treatment of people living with rare disorders. More information to come can be viewed on the BC Event Calendar. 

Altindis Lab Wins D-Challenge 2022 Award for Novel Type 1 Diabetes Research

Congratulations to Postdoctoral Fellow Khyati Girdhar and Ph.D. candidates Dogus Dogru and Audrey Randall for winning first place in the 2022 D-Challenge, awarded to teams for novel research pertaining to Type 1 Diabetes. 

These three members of the Altindis Lab were awarded for their project, titled "Uncovering the Role of Microbiome-Derived Autoantigen Mimics in Type 1 Diabetes".  Girdhar, Dogru, and Randall will meet in June of 2023 to present their continued work on this project. 

Victoria Hogan and Welkin Johnson Publish New Review

Ph.D. Candidate Victoria Hogan and Biology Department Chair Welkin E. Johnson recently published a new article in Viruses. This article, titled "Unique Structure and Distinctive Properties of the Ancient and Ubiquitous Gamma-Type Envelope Glycoprotein", is now available online.

Biology DEI Committee's Statement On Incidents in Xavier Hall

Statement Issued Saturday, Feb 20, 2021: At Boston College, we strive to create an inclusive community of excellence. How can students in our community learn, engage and thrive when they feel threatened, harassed and targeted in the very places where they live? We are disappointed, sad and angry about the racist harassment that has been occurring in the MLE floor of Xavier Hall. This is unfortunately just one particularly egregious example of the agressions, exclusions and inequities that occur far too frequently within our community. Such events have disproportionately negative effects on our students who are Black, Indigenous and People of Color (BIPoC), and the toll of overt and systemic racism within our community is substantial and unacceptable. As a committee and a department, we extend our support and stand with everyone affected, directly and indirectly by this incident. The members of the DEI committee, and many members of the Biology administration and Faculty are available to talk with students and all community members about any concerns. We will work together to create a safe and welcoming environment. Faculty have put together resources for addressing racism on campus, which may be found here. Bias motivated behavior and incidence can always be reported here, and the Office of Student Conduct may be reached at 617-552-3470 and our Biology Diversity and Outreach homepage may be found here.

The Biology DEI Committee

(Sarah McMenamin, Emrah Altindis, Kari Jensen, David Burgess, Suyen Espinoza Miranda)

Human Health and Ocean Pollution

December 3, 2020 - Philip J. Landrigan & Bret Judson

Philip J. Landrigan , John J. Stegeman, Lora E. Fleming, Denis Allemand, Donald M. Anderson, Lorraine C. Backer, Françoise Brucker-Davis, Nicolas Chevalier, Lilian Corra, Dorota Czerucka, Marie-Yasmine Dechraoui Bottein, Barbara Demeneix, Michael Depledge, Dimitri D. Deheyn, Charles J. Dorman, Patrick Fénichel, Samantha Fisher, Françoise Gaill, François Galgani, William H. Gaze, Laura Giuliano, Philippe Grandjean, Mark E. Hahn, Amro Hamdoun, Philipp Hess, Bret Judson, Amalia Laborde, Jacqueline McGlade, Jenna Mu, Adetoun Mustapha, Maria Neira, Rachel T. Noble, Maria Luiza Pedrotti, Christopher Reddy, Joacim Rocklöv, Ursula M. Scharler, Hariharan Shanmugam, Gabriella Taghian, Jeroen A. J. M. van de Water, Luigi Vezzulli, Pál Weihe, Ariana Zeka, Hervé Raps, Patrick Rampal
Annals of Global Health

Abstract
Background: Pollution – unwanted waste released to air, water, and land by human activity – is the largest environmental cause of disease in the world today. It is responsible for an estimated nine million premature deaths per year, enormous economic losses, erosion of human capital, and degradation of ecosystems. Ocean pollution is an important, but insufficiently recognized and inadequately controlled component of global pollution. It poses serious threats to human health and well-being. The nature and magnitude of these impacts are only beginning to be understood.

Goals: (1) Broadly examine the known and potential impacts of ocean pollution on human health. (2) Inform policy makers, government leaders, international organizations, civil society, and the global public of these threats. (3) Propose priorities for interventions to control and prevent pollution of the seas and safeguard human health.

Methods: Topic-focused reviews that examine the effects of ocean pollution on human health, identify gaps in knowledge, project future trends, and offer evidence-based guidance for effective intervention.

Environmental Findings: Pollution of the oceans is widespread, worsening, and in most countries poorly controlled. It is a complex mixture of toxic metals, plastics, manufactured chemicals, petroleum, urban and industrial wastes, pesticides, fertilizers, pharmaceutical chemicals, agricultural runoff, and sewage. More than 80% arises from land-based sources. It reaches the oceans through rivers, runoff, atmospheric deposition and direct discharges. It is often heaviest near the coasts and most highly concentrated along the coasts of low- and middle-income countries. Plastic is a rapidly increasing and highly visible component of ocean pollution, and an estimated 10 million metric tons of plastic waste enter the seas each year. Mercury is the metal pollutant of greatest concern in the oceans; it is released from two main sources – coal combustion and small-scale gold mining. Global spread of industrialized agriculture with increasing use of chemical fertilizer leads to extension of Harmful Algal Blooms (HABs) to previously unaffected regions. Chemical pollutants are ubiquitous and contaminate seas and marine organisms from the high Arctic to the abyssal depths.

Ecosystem Findings: Ocean pollution has multiple negative impacts on marine ecosystems, and these impacts are exacerbated by global climate change. Petroleum-based pollutants reduce photosynthesis in marine microorganisms that generate oxygen. Increasing absorption of carbon dioxide into the seas causes ocean acidification, which destroys coral reefs, impairs shellfish development, dissolves calcium-containing microorganisms at the base of the marine food web, and increases the toxicity of some pollutants. Plastic pollution threatens marine mammals, fish, and seabirds and accumulates in large mid-ocean gyres. It breaks down into microplastic and nanoplastic particles containing multiple manufactured chemicals that can enter the tissues of marine organisms, including species consumed by humans. Industrial releases, runoff, and sewage increase frequency and severity of HABs, bacterial pollution, and anti-microbial resistance. Pollution and sea surface warming are triggering poleward migration of dangerous pathogens such as the Vibrio species. Industrial discharges, pharmaceutical wastes, pesticides, and sewage contribute to global declines in fish stocks.

Human Health Findings: Methylmercury and PCBs are the ocean pollutants whose human health effects are best understood. Exposures of infants in utero to these pollutants through maternal consumption of contaminated seafood can damage developing brains, reduce IQ and increase children’s risks for autism, ADHD and learning disorders. Adult exposures to methylmercury increase risks for cardiovascular disease and dementia. Manufactured chemicals – phthalates, bisphenol A, flame retardants, and perfluorinated chemicals, many of them released into the seas from plastic waste – can disrupt endocrine signaling, reduce male fertility, damage the nervous system, and increase risk of cancer. HABs produce potent toxins that accumulate in fish and shellfish. When ingested, these toxins can cause severe neurological impairment and rapid death. HAB toxins can also become airborne and cause respiratory disease. Pathogenic marine bacteria cause gastrointestinal diseases and deep wound infections. With climate change and increasing pollution, risk is high that Vibrio infections, including cholera, will increase in frequency and extend to new areas. All of the health impacts of ocean pollution fall disproportionately on vulnerable populations in the Global South – environmental injustice on a planetary scale.

Conclusions: Ocean pollution is a global problem. It arises from multiple sources and crosses national boundaries. It is the consequence of reckless, shortsighted, and unsustainable exploitation of the earth’s resources. It endangers marine ecosystems. It impedes the production of atmospheric oxygen. Its threats to human health are great and growing, but still incompletely understood. Its economic costs are only beginning to be counted.

Ocean pollution can be prevented. Like all forms of pollution, ocean pollution can be controlled by deploying data-driven strategies based on law, policy, technology, and enforcement that target priority pollution sources. Many countries have used these tools to control air and water pollution and are now applying them to ocean pollution. Successes achieved to date demonstrate that broader control is feasible. Heavily polluted harbors have been cleaned, estuaries rejuvenated, and coral reefs restored.

Prevention of ocean pollution creates many benefits. It boosts economies, increases tourism, helps restore fisheries, and improves human health and well-being. It advances the Sustainable Development Goals (SDG). These benefits will last for centuries.

Recommendations: World leaders who recognize the gravity of ocean pollution, acknowledge its growing dangers, engage civil society and the global public, and take bold, evidence-based action to stop pollution at source will be critical to preventing ocean pollution and safeguarding human health.

Prevention of pollution from land-based sources is key. Eliminating coal combustion and banning all uses of mercury will reduce mercury pollution. Bans on single-use plastic and better management of plastic waste reduce plastic pollution. Bans on persistent organic pollutants (POPs) have reduced pollution by PCBs and DDT. Control of industrial discharges, treatment of sewage, and reduced applications of fertilizers have mitigated coastal pollution and are reducing frequency of HABs. National, regional and international marine pollution control programs that are adequately funded and backed by strong enforcement have been shown to be effective. Robust monitoring is essential to track progress.

Further interventions that hold great promise include wide-scale transition to renewable fuels; transition to a circular economy that creates little waste and focuses on equity rather than on endless growth; embracing the principles of green chemistry; and building scientific capacity in all countries. Read more

Biology Graduate Program of Boston College is Recruiting for Fall 2021

The Boston College Biology Department Graduate Program is excited to announce its Fall 2021 recruiting initiative.  Research concentrations, key features of our program, and the benefits of our Ph.D. candidates are outlined in this flyer.  Additional information of our graduate program may be found here: bit.ly/37KiOhe

Join an inclusive, professional STEM society!

The BC SACNAS Regional Chapter would like to officially welcome and invite Boston College students in STEM to join!

SACNAS is a nationwide society of innovative scientists dedicated to fostering the success of underrepresented students in STEM. It is a bridge connecting opportunities, resources, and information to underrepresented students and professionals.

SACNAS was created as the Society for Advancement of Chicanos/Hispanics and Native Americans in Science. As an inclusive organization, membership is open to all underrepresented scientists, including but not limited to women, LGBTQ, those financially underserved in STEM, and allies.

We invite all to attend our first virtual information session:

Wednesday, October 7th

7:00 PM

RSVP and SACNAS Mailing List: https://forms.gle/LyEktCQdwPk34zbdA

Meeting Zoom Link: https://bccte.zoom.us/j/5921502573

Our first initiative during the upcoming fall semester will be attending the 2020 SACNAS National Diversity in Stem Virtual Conference on October 19-24. Those interested can learn more here. More information will be provided at the information session.

Feel free to email with questions and comments at ivanovaf@bc.edu.

Undergraduate Thesis and Research Day 2020

Each year at Undergraduate Research Day the Biology Department takes a moment to recognize the hard work of our students. Every year there is a group of exceptional students who undertake the process of writing an undergraduate thesis. An outline of the day and a list of our 2020 participating students, including the Grant Balkema award recipient can be found here.

Zooming with a Scientist Seminar Series

Beginning two summers ago (2018), the Biology Department started a summer Dinner with a Scientist series where we invited a local scientist to speak to a small group of summer students over dinner.  In the spirit of this series we continued with the series this summer in the form of a Zooming with a Scientist series.  This series of Zoom seminars are intended to help students explore the fields available to them with a degree in biology.  This summers guests included the following speakers:

Sara Patti '18 - Senior Associate Scientist at Pfizer

Seth D. Robertson - Assistant Director of Undergraduate Programs -Boston College Biology Department

Alexander Lorestani '09 - CEO/Founder of Geltor, Inc.

Brian Harris - CEO/Founder of MedRhythms, Inc.

Laura Shelton '10G - Manager, Scientific Project Development at Human Metabolome Technologies America

Heather Gudejko '13G - Global Technical Support Manager at Cell Signaling Technology

Laura Burk - Pharmacist in Charge at Katahdin Valley Health Center

NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and Xenopus laevis models

February 2020
Mayanglambam Dhruba Singh, Matthew Jensen, Micaela Lasser, Emily Huber, Tanzeen Yusuff, Lucilla Pizzo, Brian Lifschutz, Inshya Desai, Alexis Kubina, Sneha Yennawar, Sydney Kim, Janani Iyer, Diego E. Rincon-Limas, Laura Anne Lowery, Santhosh Giriajan
PLOS GENETICS

Abstract
The 1.6 Mbp deletion on chromosome 3q29 is associated with a range of neurodevelopmental disorders, including schizophrenia, autism, microcephaly, and intellectual disability. Despite its importance towards neurodevelopment, the role of individual genes, genetic interactions, and disrupted biological mechanisms underlying the deletion have not been thoroughly characterized. Here, we used quantitative methods to assay Drosophila melanogaster and Xenopus laevis models with tissue-specific individual and pairwise knockdown of 14 homologs of genes within the 3q29 region. We identified developmental, cellular, and neuronal phenotypes for multiple homologs of 3q29 genes, potentially due to altered apoptosis and cell cycle mechanisms during development. Using the fly eye, we screened for 314 pairwise knockdowns of homologs of 3q29 genes and identified 44 interactions between pairs of homologs and 34 interactions with other neurodevelopmental genes. Interestingly, NCBP2 homologs in Drosophila (Cbp20) and X. laevis (ncbp2) enhanced the phenotypes of homologs of the other 3q29 genes, leading to significant increases in apoptosis that disrupted cellular organization and brain morphology. These cellular and neuronal defects were rescued with overexpression of the apoptosis inhibitors Diap1 and xiap in both models, suggesting that apoptosis is one of several potential biological mechanisms disrupted by the deletion. NCBP2 was also highly connected to other 3q29 genes in a human brain-specific interaction network, providing support for the relevance of our results towards the human deletion. Overall, our study suggests that NCBP2-mediated genetic interactions within the 3q29 region disrupt apoptosis and cell cycle mechanisms during development.  Read more

The Role of Gut Microbiota and Environmental Factors in Type 1 Diabetes Pathogenesis

February 2020
Sandra Dedrick, Bhrathi Sundaresh, Qian Huang, Claudi Brady, Tessa Yoo, Catherine Cronin, Caitlin Rudnicki, Michael Flood, Babak Momeni, Johnny Ludvigsson and Emrah Altindis
Frontiers in Endocrinology

AbstractType 1 Diabetes (T1D) is regarded as an autoimmune disease characterized by insulin deficiency resulting from destruction of pancreatic β-cells. The incidence rates of T1D have increased worldwide. Over the past decades, progress has been made in understanding the complexity of the immune response and its role in T1D pathogenesis, however, the trigger of T1D autoimmunity remains unclear. The increasing incidence rates, immigrant studies, and twin studies suggest that environmental factors play an important role and the trigger cannot simply be explained by genetic predisposition. Several research initiatives have identified environmental factors that potentially contribute to the onset of T1D autoimmunity and the progression of disease in children/young adults. More recently, the interplay between gut microbiota and the immune system has been implicated as an important factor in T1D pathogenesis. Although results often vary between studies, broad compositional and diversity patterns have emerged from both longitudinal and cross-sectional human studies. T1D patients have a less diverse gut microbiota, an increased prevalence of Bacteriodetes taxa and an aberrant metabolomic profile compared to healthy controls. In this comprehensive review, we present the data obtained from both animal and human studies focusing on the large longitudinal human studies. These studies are particularly valuable in elucidating the environmental factors that lead to aberrant gut microbiota composition and potentially contribute to T1D. We also discuss how environmental factors, such as birth mode, diet, and antibiotic use modulate gut microbiota and how this potentially contributes to T1D. In the final section, we focus on existing recent literature on microbiota-produced metabolites, proteins, and gut virome function as potential protectants or triggers of T1D onset. Overall, current results indicate that higher levels of diversity along with the presence of beneficial microbes and the resulting microbial-produced metabolites can act as protectors against T1D onset. However, the specifics of the interplay between host and microbes are yet to be discovered. Read more

Notochord vacuoles absorb compressive bone growth during zebrafish spine formation

January 29, 2020
Jennifer Bagwell, James Norman, Kathryn Ellis, Brianna Peskin, James Hwang, Xiaoyan Ge, Stacy V. Nguyen, Sarah K. McMenamin, Didier YR Stainier, Michel Bagnat
eLIFE

Abstract
The vertebral column or spine assembles around the notochord rod which contains a core made of large vacuolated cells. Each vacuolated cell possesses a single fluid-filled vacuole, and loss or fragmentation of these vacuoles in zebrafish leads to spine kinking. Here, we identified a mutation in the kinase gene dstyk that causes fragmentation of notochord vacuoles and a severe congenital scoliosis-like phenotype in zebrafish. Live imaging revealed that Dstyk regulates fusion of membranes with the vacuole. We find that localized disruption of notochord vacuoles causes vertebral malformation and curving of the spine axis at those sites. Accordingly, in dstyk mutants the spine curves increasingly over time as vertebral bone formation compresses the notochord asymmetrically, causing vertebral malformations and kinking of the axis. Together, our data show that notochord vacuoles function as a hydrostatic scaffold that guides symmetrical growth of vertebrae and spine formation. Read more

Ernest Violet, Biology '20 Presents Poster at SICB Annual Meeting

Ernest Violet, Biology ‘20 and member of the Kenaley Lab, just returned from the annual meeting of the Society for Intergrative and Comparative Biology (SICB) held in Austin, TX.  Ernie presented a poster outlining his research on the function of teeth in deep-sea fishes. 

Regulatory context drives conservation of glycine riboswitch aptamers

December 20, 2019
Matt Crum, Nikhil Ram-Mohan, Michelle M. Meyer
PLOS Computational Biology

Abstract
In comparison to protein coding sequences, the impact of mutation and natural selection on the sequence and function of non-coding (ncRNA) genes is not well understood. Many ncRNA genes are narrowly distributed to only a few organisms, and appear to be rapidly evolving. Compared to protein coding sequences, there are many challenges associated with assessment of ncRNAs that are not well addressed by conventional phylogenetic approaches, including: short sequence length, lack of primary sequence conservation, and the importance of secondary structure for biological function. Riboswitches are structured ncRNAs that directly interact with small molecules to regulate gene expression in bacteria. They typically consist of a ligand-binding domain (aptamer) whose folding changes drive changes in gene expression. The glycine riboswitch is among the most well-studied due to the widespread occurrence of a tandem aptamer arrangement (tandem), wherein two homologous aptamers interact with glycine and each other to regulate gene expression. However, a significant proportion of glycine riboswitches are comprised of single aptamers (singleton). Here we use graph clustering to circumvent the limitations of traditional phylogenetic analysis when studying the relationship between the tandem and singleton glycine aptamers. Graph clustering enables a broader range of pairwise comparison measures to be used to assess aptamer similarity. Using this approach, we show that one aptamer of the tandem glycine riboswitch pair is typically much more highly conserved, and that which aptamer is conserved depends on the regulated gene. Furthermore, our analysis also reveals that singleton aptamers are more similar to either the first or second tandem aptamer, again based on the regulated gene. Taken together, our findings suggest that tandem glycine riboswitches degrade into functional singletons, with the regulated gene(s) dictating which glycine-binding aptamer is conserved.
Read more

Biology Graduate Students from Folker and Lowery Labs attend the 2019 ASCB/EMBO Meeting.

Members of the Boston College Ph.D. program from the Dr. Eric Folker and Dr. Laura Anne Lowery labs are taking a break from sharing their science and enjoy a networking event at the Smithsonian National Museum of Natural History during their trip to Washington DC for 2019 ASCB.

Yinan Hu Image part of special evo devo issue of Developmental Dynamics Magazine???

Drosophila emerins control LINC complex localization and transcription to regulate myonuclear position

September 16, 2019
Torrey R. Mandigo, Blake D. Turcich, Alyssa J. Anderson, Michael R. Hussey and Eric S. Folker
Journal of Cell Science

Abstract
Mispositioned nuclei are a hallmark of skeletal muscle disease. Many of the genes that are linked to Emery–Dreifuss muscular dystrophy (EDMD) encode proteins that are critical for nuclear movement in various cells, suggesting that disruptions in nuclear movement and position may contribute to disease progression. However, how these genes are coordinated to move nuclei is not known. Here, we focussed on two different emerin proteins in Drosophila, Bocksbeutel and Otefin, and their effects on nuclear movement. Although nuclear position was dependent on both, elimination of either Bocksbeutel or Otefin produced distinct phenotypes that were based in differential effects on the KASH-domain protein Klarsicht. Specifically, loss of Bocksbeutel reduced Klarsicht localization to the nucleus and resulted in a disruption in nuclear separation. Loss of Otefin increased the transcription of Klarsicht and led to premature separation of nuclei and their positioning closer to the edge of the muscle. Consistent with opposing functions, nuclear position is normal in otefin; bocksbeutel double mutants. These data indicate emerin-dependent regulation of Klarsicht levels in the nuclear envelope is a critical determinant of nuclear position. Read more

Complex Problems Require Ternary Solutions: Another Lesson from SIV Nef

September 11, 2019
Welkin E. Johnson and Kevin R. McCarthy
Cell Host & Microbe

Abstract
In this issue of Cell Host & Microbe, Buffalo et al. describe a cryo-EM structure of SIV Nef complexed with AP-2 and tetherin. The structure helps explain why human tetherin is Nef-resistant and why lentiviruses that successfully emerged in humans (HIV-1 and HIV-2) had to evolve novel anti-tetherin strategies. Read more
 

Designing a bioremediator: mechanistic models guide cellular and molecular specialization

September 6, 2019
Marco Zaccaria, William Dawson, Vivianan Cristiglio, Massimo Reverberi, Laura E Ratcliff, Takahito Nakajima, Luidi Genovese and Babak Momeni
ScienceDirect

Abstract
Bioremediators are cells or non-living subcellular entities of biological origin employed to degrade target pollutants. Rational, mechanistic design can substantially improve the performance of bioremediators for applications, including waste treatment and food safety. We highlight how such improvements can be informed at the cellular level by theoretical observations especially in the context of phenotype plasticity, cell signaling, and community assembly. At the molecular level, we suggest enzyme design using techniques such as Small Angle Neutron Scattering and Density Functional Theory. To provide an example of how these techniques could be synergistically combined, we present the case-study of the interaction of the enzyme laccase with the food contaminant aflatoxin B₁. In designing bioremediators, we encourage interdisciplinary, mechanistic research to transition from an observation-oriented approach to a principle-based one.  Read more

The apical annuli of Toxoplasma gondii are composed of coiled‐coil and signalling proteins embedded in the inner membrane complex sutures

August 30, 2019
Klemens Engelberg, Chun-Ti Chen, Tyler Bechtel, Victoria Sanchez Guzman, Allison A. Drozda, Suyog Chavan, Eranthie Weerapana, Marc-Jan Gubbels
Cellular Microbiology

Abstract
The apical annuli are among the most intriguing and understudied structures in the cytoskeleton of the apicomplexan parasite Toxoplasma gondii. We mapped the proteome of the annuli in Toxoplasma by reciprocal proximity biotinylation (BioID), and validated five apical annuli proteins (AAP1–5), Centrin2, and an apical annuli methyltransferase. Moreover, inner membrane complex (IMC) suture proteins connecting the alveolar vesicles were also detected and support annuli residence within the sutures. Super‐resolution microscopy identified a concentric organisation comprising four rings with diameters ranging from 200 to 400 nm. The high prevalence of domain signatures shared with centrosomal proteins in the AAPs together with Centrin2 suggests that the annuli are related and/or derived from the centrosomes. Phylogenetic analysis revealed that the AAPs are conserved narrowly in coccidian, apicomplexan parasites that multiply by an internal budding mechanism. This suggests a role in replication, for example, to provide pores in the mother IMC permitting exchange of building blocks and waste products. However, presence of multiple signalling domains and proteins are suggestive of additional functions. Knockout of AAP4, the most conserved compound forming the largest ring‐like structure, modestly decreased parasite fitness in vitro but had no significant impact on acute virulence in vivo. In conclusion, the apical annuli are composed of coiled‐coil and signalling proteins assembled in a pore‐like structure crossing the IMC barrier maintained during internal budding. Read more

Viral Hormones: Expanding Dimensions in Endocrinology

July 16, 2019
Qian Huang, C. Ronald Kahn, Emrah Altindis
Endocrinology

Abstract
Viruses have developed different mechanisms to manipulate their hosts, including the process of viral mimicry in which viruses express important host proteins. Until recently, examples of viral mimicry were limited to mimics of growth factors and immunomodulatory proteins. Using a comprehensive bioinformatics approach, we have shown that viruses possess the DNA/RNA with potential to encode 16 different peptides with high sequence similarity to human peptide hormones and metabolically important regulatory proteins. We have characterized one of these families, the viral insulin/IGF-1–like peptides (VILPs), which we identified in four members of the Iridoviridae family. VILPs can bind to human insulin and IGF-1 receptors and stimulate classic postreceptor signaling pathways. Moreover, VILPs can stimulate glucose uptake in vitro and in vivo and stimulate DNA synthesis. DNA sequences of some VILP-carrying viruses have been identified in the human enteric virome. In addition to VILPs, sequences with homology to 15 other peptide hormones or cytokines can be identified in viral DNA/RNA sequences, some with a very high identity to hormones. Recent data by others has identified a peptide that resembles and mimics α-melanocyte-stimulating hormone’s anti-inflammatory effects in in vitro and in vivo models. Taken together, these studies reveal novel mechanisms of viral and bacterial pathogenesis in which the microbe can directly target or mimic the host endocrine system. These findings also introduce the concept of a system of microbial hormones that provides new insights into the evolution of peptide hormones, as well as potential new roles of microbial hormones in health and disease. Read more

Therapeutic benefit of combining calorie-restricted ketogenic diet and glutamine targeting in late-stage experimental glioblastoma

May 29, 2019
Purna Mukherjee, Zachary M. Augur, Mingyi Li, Collin Hill, Bennett Greenwood, Marek A. Domin, Gramoz Kondakci, Niven R. Narain, Michael A. Kiebish, Roderick T. Bronson, Gabriel Arismendi-Morilla, Christos Chinopoulos & Thomas N. Seyfried
Communications Biology

Abstract
Glioblastoma (GBM) is an aggressive primary human brain tumour that has resisted effective therapy for decades. Although glucose and glutamine are the major fuels that drive GBM growth and invasion, few studies have targeted these fuels for therapeutic management. The glutamine antagonist, 6-diazo-5-oxo-L-norleucine (DON), was administered together with a calorically restricted ketogenic diet (KD-R) to treat late-stage orthotopic growth in two syngeneic GBM mouse models: VM-M3 and CT-2A. DON targets glutaminolysis, while the KD-R reduces glucose and, simultaneously, elevates neuroprotective and non-fermentable ketone bodies. The diet/drug therapeutic strategy killed tumour cells while reversing disease symptoms, and improving overall mouse survival. The therapeutic strategy also reduces edema, hemorrhage, and inflammation. Moreover, the KD-R diet facilitated DON delivery to the brain and allowed a lower dosage to achieve therapeutic effect. The findings support the importance of glucose and glutamine in driving GBM growth and provide a therapeutic strategy for non-toxic metabolic management. Read more

Thyroid Hormone Coordinates Developmental Trajectories But Does Not Underlie Developmental Truncation in Danionins

May 18, 2019
Yinan Hu, Angela Mauri, Joan Donahue, Rajendra Singh, Benjamin Acosta, Sarah McMenamin

Developmental Dynamics - Wiley

Abstract
Background Differences in postembryonic developmental trajectories can profoundly alter adult phenotypes and life histories. Thyroid hormone (TH) regulates metamorphosis in many vertebrate taxa with multiphasic ecologies, and alterations to TH metabolism underlie notable cases of paedomorphosis in amphibians. We tested the requirement for TH in multiple postembryonic developmental processes in zebrafish, which has a monophasic ecology, and asked if TH production was compromised in paedomorphic Danionella.

Results We showed that TH regulates allometric growth in juvenile zebrafish, and inhibits relative head growth. The lateral line system showed differential requirements for TH: the hormone promotes canal neuromast formation and inhibits neuromast numbers in the head, but causes expansion of the neuromast population in the trunk. While Danionella morphology resembled that of larval zebrafish, the two Danionella species analyzed were not similar to hypothyroid zebrafish in their shape or neuromast distribution, and both possessed functional thyroid follicles. Read more

Schlumberger Foundation Award Recipient Suyen Espinoza Miranda

A hearty congratulations to Suyen Espinoza Miranda of the Tim van Opijnen Lab, on being awarded a Faculty for the Future grant for the 2019-2020 academic year, following a competitive selection process. A total of 38 new grants were awarded this year out of 526 applications originally submitted, and 93 grants were renewed.

The Schlumberger Foundation is pleased to welcome her into the community of Fellows & Alumnae, now totaling 721 women scientists originating from 80 countries having enrolled or completed PhD or Post-Doctoral research with top universities worldwide.

The program’s long-term goal is to generate conditions that result in more women pursuing scientific careers by removing the barriers women face when entering STEM disciplines, thus reducing the gender gap. Faculty for the Future Fellows are expected to return to their home countries after completion of their studies to contribute to economic, social and technological advancement by strengthening the STEM teaching and research faculties of their home institutions, and to pursue positions in the public sector where their newly acquired technical and scientific skills can help provide evidence-based support for STEM policy making. In so doing, they become powerful role models and help to inspire other girls and women to pursue scientific careers.

Comparative Functional and Phylogenomic Analyses of Host Association in the Remoras (Echeneidae), a Family of Hitchhiking Fishes

May 10, 2019
C P Kenaley, A Stote, W B Ludt, P Chakrabarty
Integrative Organismal Biology

Abstract
The family Echeneidae consists of eight species of marine fishes that hitchhike by adhering to a wide variety of vertebrate hosts via a sucking disc. While several studies have focused on the interrelationships of the echeneids and the adhesion performance of a single species, no clear phylogenetic hypothesis has emerged and the morphological basis of adhesion remains largely unknown. We first set out to resolve the interrelationships of the Echeneidae by taking a phylogenomic approach using ultraconserved elements. Then, within this framework, we characterized disc morphology through µ-CT analysis, evaluated host specificity through an analysis of host phylogenetic distance, and determined which axes of disc morphological variation are associated with host diversity, skin surface properties, mean pairwise phylogenetic distance (MPD obs.), and swimming regime. We recovered an extremely well-supported topology, found that the specificity of host choice is more variable in a pelagic group and less variable in a reef-generalist group than previously proposed, and that axes of disc morphospace are best explained by models that include host skin surface roughness, host MPD obs., and maximum host Reynolds number. This suggests that ecomorphological diversification was driven by the selection pressures of host skin surface roughness, host specialization, and hydrodynamic regime.
Read more

Microbial coexistence through chemical-mediated interactions

May 3, 2019
Lori Niehaus, Ian Boland, Minghao Liu, Kevin Chen, David Fu, Catherine Henckel, Kaitlin Chaung, Suyen Espinoza Miranda, Samantha Dyckman, Matthew Crum, Sandra Dedrick, Wenying Shou, Babak Momeni
Nature Communications

Abstract
Many microbial functions happen within communities of interacting species. Explaining how species with disparate growth rates can coexist is important for applications such as manipulating host-associated microbiota or engineering industrial communities. Here, we ask how microbes interacting through their chemical environment can achieve coexistence in a continuous growth setup (similar to an industrial bioreactor or gut microbiota) where external resources are being supplied. We formulate and experimentally constrain a model in which mediators of interactions (e.g. metabolites or waste-products) are explicitly incorporated. Our model highlights facilitation and self-restraint as interactions that contribute to coexistence, consistent with our intuition. When interactions are strong, we observe that coexistence is determined primarily by the topology of facilitation and inhibition influences not their strengths. Importantly, we show that consumption or degradation of chemical mediators moderates interaction strengths and promotes coexistence. Our results offer insights into how to build or restructure microbial communities of interest. Read more

A fission yeast platform for heterologous expression of mammalian adenylyl cyclases and high throughput screening

April 2019
Rachel A. Getz, Grace Kwak, Stacie Cornell, Samuel Mbugua, Jeremy Eberhard, Sheng Xiang Huang, Zainab Abbasi, Anna Santos de Medeiros, Rony Thomas, Brett Bukowski, Patricia K. Dranchak, James Inglese, Charles S. Hoffman
Cellular Signalling

Abstract
The fission yeast Schizosaccharomyces pombe uses a cAMP signaling pathway to link glucose-sensing to Protein Kinase A activity in order to regulate cell growth, sexual development, gluconeogenesis, and exit from stationary phase. We previously used a PKA-repressed fbp1-ura4 reporter to conduct high throughput screens (HTSs) for inhibitors of heterologously-expressed mammalian cyclic nucleotide phosphodiesterases (PDEs). Here, we describe the successful expression of all ten mammalian adenylyl cyclase (AC) genes, along with the human GNAS Gα_s gene. By measuring expression of an fbp1-GFP reporter together with direct measurements of intracellular cAMP levels, we can detect both basal AC activity from all ten AC genes as well as GNAS-stimulated activity from eight of the nine transmembrane ACs (tmACs; AC2-AC9). The ability to use this platform to conduct HTS for novel chemical probes that reduce PKA activity was demonstrated by a pilot screen of the LOPAC®¹²⁸⁰ library, leading to the identification of diphenyleneiodonium chloride (DPI) as an inhibitor of basal AC activity. This screening technology could open the door to the development of therapeutic compounds that target GNAS or the ACs, an area in which there is significant unmet need.
Read more

The role of an overlooked adductor muscle in the feeding mechanism of ray-finned fishes: Predictions from simulations of a deep-sea viperfish

April 18, 2019
Christopher P. Kenaley, Mikhaila C. Marecki, George V. Lauder
Zoology

Abstract
In a majority of ray-finned fishes (Actinopterygii), effective acquisition of food resources is predicated on rapid jaw adduction. Although the musculoskeletal architecture of the feeding system has been the subject of comparative research for many decades, individual contributions of the major adductor divisions to closing dynamics have not been elucidated. While it is understood that the dorsal divisions that arise from the head and insert on the posterior of the lower jaw are major contributors to closing dynamics, the contribution of the ventral components of the adductor system has been largely overlooked. In many ray-finned fishes, the ventral component is comprised of a single division, the A_ω, that originates on an intersegmental aponeurosis of the facialis divisions and inserts on the medial face of the dentary, anterior to the Meckelian tendon. This configuration resembles a sling applied at two offset points of attachment on a third-order lever. The goal of this study was to elucidate the contributions of the A_ω to jaw adduction by modeling jaw closing in the deep-sea viperfish Chauliodus sloani. To do this, we simulated adduction with a revised computational model that incorporates the geometry of the A_ω. By comparing results between simulations that included and excluded A_ω input, we show that the A_ω adds substantially to lower-jaw adduction dynamics in C. sloani by acting as a steering motor and displacing the line of action of the dorsal facialis adductor muscles and increasing the mechanical advantage and input moment arms of the jaw lever system. We also explored the effect of the A_ω on muscle dynamics and found that overall facialis muscle shortening velocities are higher and normalized force production is lower in simulations including the A_ω. The net effect of these changes in muscle dynamics results in similar magnitudes of peak power in the facialis divisions between simulations, however, peak power is achieved earlier in adduction Modifications of muscle mechanics and posture result in significant increases in closing performance, including static bite force, angular velocity, and adduction time. We compare this configuration to a similar design in crocodilians and suggest that the A_ω configuration and similar sling configurations across the vertebrate tree of life indicate the importance of this musculoskeletal design in feeding. Read more

Phylogenomics clarifies biogeographic and evolutionary history, and conservation status of West Indian tremblers and thrashers (Aves: Mimidae)

April 14, 2019
Jeffrey M. DaCosta, Matthew J. Miller, Jennifer L. Mortensen, J. Michael Reed, Robert L. Curry, Michael D. Sorenson
Molecular Phylogenetics and Evoloution

Abstract
The West Indian avifauna has provided fundamental insights into island biogeography, taxon cycles, and the evolution of avian behavior. Our interpretations, however, should rely on robust hypotheses of evolutionary relationships and consistent conclusions about taxonomic status in groups with many endemic island populations. Here we present a phylogenetic study of the West Indian thrashers, tremblers, and allies, an assemblage of at least 5 species found on 29 islands, including what is considered the Lesser Antilles’ only avian radiation. We improve on previous phylogenetic studies of this group by using double-digest restriction site-associated DNA sequencing (ddRAD-seq) to broadly sample loci scattered across the nuclear genome. A variety of analyses, based on either nucleotide variation in 2223 loci recovered in all samples or at 13,282 loci confidently scored as present or absent in all samples, converged on a single well-supported phylogenetic hypothesis. Results indicate that the resident West Indian taxa form a monophyletic group, exclusive of the Neotropical–Nearctic migratory Gray Catbird Dumetella carolinensis, which breeds in North America; this outcome differs from earlier studies suggesting that Gray Catbird was nested within a clade of island resident species. Thus, our findings imply a single colonization of the West Indies without the need to invoke a subsequent ‘reverse colonization’ of the mainland by West Indian taxa. Additionally, our study is the first to sample both endemic subspecies of the endangered White-breasted Thrasher Ramphocinclus brachyurus. We find that these subspecies have a long history of evolutionary independence with no evidence of gene flow, and are as genetically divergent from each other as other genera in the group. These findings support recognition of R. brachyurus (restricted to Martinique) and the Saint Lucia Thrasher R. sanctaeluciae as two distinct, single-island endemic species, and indicate the need to re-evaluate conservation plans for these taxa. Our results demonstrate the utility of phylogenomic datasets for generating robust systematic hypotheses.
Read more

Wolf-Hirschhorn Syndrome-Associated Genes Are Enriched in Motile Neural Crest Cells and Affect Craniofacial Development in Xenopus laevis

April 2019
Alexandra Mills, Elizabeth Bearce, Rachael Cella, Seung Woo Kim, Megan Selig, Sangmook Lee and Laura Anne Lowery
Frontiers in Physiology

Abstract
Wolf-Hirschhorn Syndrome (WHS) is a human developmental disorder arising from a hemizygous perturbation, typically a microdeletion, on the short arm of chromosome four. In addition to pronounced intellectual disability, seizures, and delayed growth, WHS presents with a characteristic facial dysmorphism and varying prevalence of microcephaly, micrognathia, cartilage malformation in the ear and nose, and facial asymmetries. These affected craniofacial tissues all derive from a shared embryonic precursor, the cranial neural crest (CNC), inviting the hypothesis that one or more WHS-affected genes may be critical regulators of neural crest development or migration. To explore this, we characterized expression of multiple genes within or immediately proximal to defined WHS critical regions, across the span of craniofacial development in the vertebrate model system Xenopus laevis. This subset of genes, whsc1, whsc2, letm1, and tacc3, are diverse in their currently-elucidated cellular functions; yet we find that their expression demonstrates shared tissue-specific enrichment within the anterior neural tube, migratory neural crest, and later craniofacial structures. We examine the ramifications of this by characterizing craniofacial development and neural crest migration following individual gene depletion. We observe that several WHS-associated genes significantly impact facial patterning, cartilage formation, neural crest motility in vivo and in vitro, and can separately contribute to forebrain scaling. Thus, we have determined that numerous genes within and surrounding the defined WHS critical regions potently impact craniofacial patterning, suggesting their role in WHS presentation may stem from essential functions during neural crest-derived tissue formation. Read more

Origins and evolutionary consequences of ancient endogenous retroviruses

April 8, 2019
Welkin E. Johnson
Nature Reviews Microbiology

Abstract
Retroviruses infect a broad range of vertebrate hosts that includes amphibians, reptiles, fish, birds and mammals. In addition, a typical vertebrate genome contains thousands of loci composed of ancient retroviral sequences known as endogenous retroviruses (ERVs). ERVs are molecular remnants of ancient retroviruses and proof that the ongoing relationship between retroviruses and their vertebrate hosts began hundreds of millions of years ago. The long-term impact of retroviruses on vertebrate evolution is twofold: first, as with other viruses, retroviruses act as agents of selection, driving the evolution of host genes that block viral infection or that mitigate pathogenesis, and second, through the phenomenon of endogenization, retroviruses contribute an abundance of genetic novelty to host genomes, including unique protein-coding genes and cis-acting regulatory elements. This Review describes ERV origins, their diversity and their relationships to retroviruses and discusses the potential for ERVs to reveal virus–host interactions on evolutionary timescales. It also describes some of the many examples of cellular functions, including protein-coding genes and regulatory elements, that have evolved from ERVs. Read more

From Diagnosis To Survival, A Story of Childhood Cancer

April 10th, 2019 from 7:30-9:00 p.m. in Higgins 310, two time cancer survivor and bone marrow transplant recipient, Christine Song, Boston College Class of 2019 shares her story of cancer treatment from a child's perspective. Hosted by Drs. Phillip Landrigan and Rosemary Byrne. Q & A to follow.

Dr. Heather Olins awarded Teaching, Advising and Mentoring (TAM) grant by B.C.’s University Council on Teaching

Congratulations to Dr. Heather Olins on being awarded the Teaching, Advising, and Mentoring (TAM) grant by B.C.’s University Council on Teaching. With this award, Dr. Olins will expand an existing “Scientist Spotlight” video interview series (publicly available here) and more deeply integrate the work of these scientists in to the curriculum of her introductory course (BIOL2010: Introduction to Ecology & Evolution). The goal of the project is to create an easily accessible resource for introductory biology students to see examples of the fantastic variety of career trajectories in ecology and evolutionary biology, and hear about them from a diverse set of scientists. Dr. Olins hopes that sharing these scientist’s stories will help students, and in particular underrepresented minority students, more easily envision themselves in STEM fields in the future, and provide inspirational examples of a variety of paths forward in biology.

Dr. Klemens Engelberg Awarded Knights Templar Eye Foundation Grant

The Biology Department is pleased to announce that Dr. Klemens Engelberg, a postdoctoral researcher in the Gubbels lab, has been awarded a Knights Templar Eye Foundation Career Starter grant. This fellowship will allow Dr. Engelberg (featured here) to investigate cell division of Toxoplasma gondii. Toxoplasma is a widespread parasite that can cause severe disease in humans, which in children can manifest in eye disorders and progressive blindness. A better understanding of parasite biology will allow the design of new treatments to combat this disease.

Dr. Sarah McMenamin awarded an NSF CAREER: Faculty Early Career Development Grant

ddRAD‐seq ata eveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America

March 2019
Philip Lavretsky, Jeffrey M. DaCosta, Michael D. Sorenson, Kevin G. McCracken, Jeffrey L. Peters
Molecular Ecology

Abstract

Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi‐locus data requires substantial genomic coverage. In this study, we used ddRAD‐seq to sample the genomes of five recently diverged, New World “mallards” (Anas spp.), a group of dabbling duck species characterized by diagnosable phenotypic differences but minimal genetic differentiation. With increased genomic sampling, we aimed to characterize population structure within this group and identify genomic regions that may have experienced divergent selection during speciation. We analyzed 3,017 autosomal ddRAD‐seq loci and 177 loci from the Z‐chromosome. In contrast to previous studies, the ddRAD‐seq data were sufficient to assign individuals to their respective species or subspecies and to generate estimates of gene flow in a phylogenetic framework. We find limited evidence of contemporary gene flow between the dichromatic mallard and several monochromatic taxa, but find evidence for historical gene flow between some monochromatic species pairs. We conclude that the overall genetic similarity of these taxa likely reflects retained ancestral polymorphism rather than recent and extensive gene flow. Thus, despite recurring cases of hybridization in this group, our results challenge the current dogma predicting the genetic extinction of the New World monochromatic dabbling ducks via introgressive hybridization with mallards. Moreover, ddRAD‐seq data were sufficient to identify previously unknown outlier regions across the Z‐chromosome and several autosomal chromosomes that may have been involved in the diversification of species in this recent radiation. Read more

Botanical Careers Panel, Hosted By Dr. Helen Kurkjian of the Biology Dept.

Thursday, March 21, 2019 at 9:00 am in Higgins Hall, Rm. 310; Plant Biology Professor, Dr. Helen Kurkjian will host four guest speakers from plant-related professions for a panel-style Q&A. We will discuss our guests' backgrounds, career paths, and current positions, the role that plants play in their jobs and lives, and the importance of this work to solving some of the challenges we face as humans, including global climate change, food shortages, and nutritional deficits. Our speakers will be:

Julie Coop: Urban & Community Forestry Coordinator, Department of Conservation & Recreation, MA
Spencer Debenport: Scientist at Indigo Agricultural, a Boston-based biotechnology company, specializing in altering crop microbiomes to improve yield
Michael Piantedosi: Seed Bank Coordinator, New England Wild Flower Society
Paul Strother: Visiting Professor, Earth & Environmental Sciences, Boston College, who specializes in paleobotany and palynology

Women in STEM keynote speaker Dr. Joan Roughgarden will present. Talk title: Holobiont Evolution: Model with Vertical vs. Horizontal Microbiome Transmission.

Tuesday, March 19th @ 4:30-6:00 pm. in Devlin Hall, Rm. 101, Dr. Joan Roughgarden will be presenting. Hosted by Dr. Sarah McMenamin, Boston College Biology Dept.. Dr. Roughgarden received her undergraduate degrees from University of Rochester and a Ph.D. in biology from Harvard University.  She has taught at Stanford University since 1972 as Professor of Biology and Geophysics. She transitioned in 1998.  Dr. Roughgarden has published more than 180 papers and 8 books, including Evolution's Rainbow (2004) which won the 2005 Stonewall Prize for nonfiction from the American Library Association. Her current research pertains to the evolution of holobionts, or composite organisms such as corals where the host contains a symbiotic microbial community called its microbiome.

2019 Northeast Regional Meeting of the Society for Developmental Biology.

Hosted by Dr. Sarah McMenamin, of the Boston College Biology Dept. & Marcos Simoes-Costa, Cornell University, Dept. of Molecular Biology and Genetics.

April 5-7, Woods Hole, MA. - Dr. Elaine Fuchs and Dr. Cassandra Extavour, Keynote Speakers
Deadline for abstract submissions: March 15th and Registration deadline is March 29th

Dr. Sarah McMenamin, Biology Dept., Hosting Women in Stem Lecture Series. Featured speaker is Dr. Joan Roughgarden.

TgCep250 is dynamically processed through the division cycle and essential for structural integrity of the Toxoplasma centrosome

March 5, 2019
Chun-Ti Chen, Marc-Jan Gubbels
Molecular Biology of the Cell

Abstract
The Toxoplasma centrosome is a unique bipartite structure comprising an inner- and outer-core responsible for the nuclear cycle (mitosis) and budding cycles (cytokinesis), respectively. These two cores remain associated during the cell cycle but have been proposed to function independently. Here, we describe the function of a large coiled-coil protein, TgCep250, in connecting the two centrosomal cores and promoting their structural integrity. Throughout the cell cycle TgCep250 localizes to the centrosome inner-core but resides on both inner- and outer-cores during the onset of cell division. This dynamic localization pattern is associated with proteolysis: the processed version residing on the inner-core. In the absence of TgCep250, stray centrosome inner- and outer-core foci were observed; detachment of the inner-outer-core connection resulted in nuclear partitioning defects. The detachment between centrosome inner- and outer-core was found in only one of the centrosomes during cell division, indicating distinct states of mother and daughter centrosomes. We further dissected the hierarchical organization of centrosome and kinetochore complex through depletion of kinetochore component TgNuf2, which resulted in dissociation of the intact bipolar centrosome from the nuclear periphery. Together, these data suggest that TgCep250 bridges the interaction between the centrosome cores but not between the inner-core and kinetochore.

On-Chip Electrochemical Detection of Cholera Using a Polypyrrole-Functionalized Dendritic Gold Sensor

February 18, 2019
Amy E. Valera, Nathan T. Nesbitt, Michelle M. Archibald, Michael J. Naughton, Thomas C. Chiles
ACS Sensors

Abstract
Rapid diagnosis of an infectious disease outbreak in the field is critical for limiting the escalation of an outbreak into an epidemic. Devices suited to point-of-care (POC) diagnosis of cholera must not only demonstrate clinical laboratory levels of sensitivity and specificity but do so in a portable and low-cost manner, with a simplistic readout. We report work toward an on-chip electrochemical immunosensor for the detection of cholera toxin subunit B (CTX), based on a dendritic gold architecture biofunctionalized via poly(2-cyanoethyl)pyrrole (PCEPy). The dendritic electrode has an ∼18× greater surface area than a planar gold counterpart, per electrochemical measurements, allowing for a higher level of detection sensitivity. A layer of PCEPy polymer generated on the dendritic surface facilitated the performance of an electrochemical enzyme-linked immunosorbant assay (ELISA) for CTX on-chip, which demonstrated a detection limit of 1 ng mL^–1, per a signal-to-noise ratio of 2.6. This was more sensitive than detection using a simple planar gold electrode (100 ng mL^–1) and also matched the diagnostic standard optical ELISA, but on a miniaturized platform with electrical readout. The ability to meet POC demands makes biofunctionalized gold dendrites a promising architecture for on-chip detection of cholera. Read more

Alex Hung, MCAS '20, recently presented a poster at the annual meeting of the Society Integrative and Comparative Biology

Alex Hung, MCAS '20 and BC Biology major, recently presented a poster at the annual meeting of the Society Integrative and Comparative Biology (SICB) in Tampa, FL, January 3-7. A student in Professor Chris Kenaley's lab, Alex spoke about his work on the mechanics and material properties of fish vertebrae and how they contribute to swimming behavior. Alex received competitive awards from both BC's University Fellowships Committee and SICB to fund travel to Tampa.

The Amazon rain forest plant Uncaria tomentosa (cat's claw) and its specific proanthocyanidin constituents are potent inhibitors and reducers of both brain plaques and tangles

January 24, 2019
Snow AD, Castillo GM, Nguyen BP, Choi PY, cummings JA, Cam J, Hu Q, Lake T, Pan W, Kastin AJ, Kirschner DA, Wood SG, Rockenstine E, Masliah E, Lorimer S, Tanzi RE, Larsen L
Scientific Reports

Abstract
Brain aging and Alzheimer's disease both demonstrate the accumulation of beta-amyloid protein containing "plaques" and tau protein containing "tangles" that contribute to accelerated memory loss and cognitive decline. In the present investigation we identified a specific plant extract and its constituents as a potential alternative natural solution for preventing and reducing both brain "plaques and tangles". PTI-00703 cat's claw (Uncaria tomentosa from a specific Peruvian source), a specific and natural plant extract from the Amazon rain forest, was identified as a potent inhibitor and reducer of both beta-amyloid fibrils (the main component of "plaques") and tau protein paired helical filaments/fibrils (the main component of "tangles"). PTI-00703 cat's claw demonstrated both the ability to prevent formation/aggregation and disaggregate preformed Aβ fibrils (1-42 and 1-40) and tau protein tangles/filaments. The disaggregation/dissolution of Aβ fibrils occurred nearly instantly when PTI-00703 cat's claw and Aβ fibrils were mixed together as shown by a variety of methods including Thioflavin T fluorometry, Congo red staining, Thioflavin S fluorescence and electron microscopy. Sophisticated structural elucidation studies identified the major fractions and specific constituents within PTI-00703 cat's claw responsible for both the observed "plaque" and "tangle" inhibitory and reducing activity. Specific proanthocyanidins (i.e. epicatechin dimers and variants thereof) are newly identified polyphenolic components within Uncaria tomentosa that possess both "plaque and tangle" reducing and inhibitory activity. One major identified specific polyphenol within PTI-00703 cat's claw was epicatechin-4β-8-epicatechin (i.e. an epicatechin dimer known as proanthocyanidin B2) that markedly reduced brain plaque load and improved short-term memory in younger and older APP "plaque-producing" (TASD-41) transgenic mice (bearing London and Swedish mutations). Proanthocyanidin B2 was also a potent inhibitor of brain inflammation as shown by reduction in astrocytosis and gliosis in TASD-41 transgenic mice. Blood-brain-barrier studies in Sprague-Dawley rats and CD-1 mice indicated that the major components of PTI-00703 cat's claw crossed the blood-brain-barrier and entered the brain parenchyma within 2 minutes of being in the blood. The discovery of a natural plant extract from the Amazon rain forest plant (i.e. Uncaria tomentosa or cat's claw) as both a potent "plaque and tangle" inhibitor and disaggregator is postulated to represent a potential breakthrough for the natural treatment of both normal brain aging and Alzheimer's disease. Read more

Anatomical Assessment of the Adult Skeleton of Zebrafish Reared Under Different Thyroid Hormone Profiles

January 2019
Stephanie Keer, Karly Cohen, Catherine May, Yinan Hu, Sarah McMenamin and Luz Patricia Hernandez
The Anatomical Record

Abstract

Thyroid hormone (TH) directs the growth and maintenance of tissues throughout the body during development and into adulthood, and plays a particularly important role in proper ossification and homeostasis of the skeleton. To better understand the roles of TH in the skeletogenesis of a vertebrate model, and to define areas of the skeleton that are particularly sensitive to developmental TH, we examined the effects of hypo- and hyperthyroidism on skeletal development in zebrafish. Performing a bone-by-bone anatomical assessment on the entire skeleton of adult fish, we found that TH is required for proper ossification, growth, morphogenesis, and fusion of numerous bones. We showed that the pectoral girdle, dermatocranium, Weberian apparatus, and dentary are particularly sensitive to TH, and that TH affects development of skeletal element regardless of bone type and developmental origin. Indeed, the hormone does not universally promote ossification: we found that developmental TH prevents ectopic ossification in multiple thin bones and within connective tissue of the jaw. In all, we found that TH regulates proper morphogenesis and ossification in the majority of zebrafish bones, and that the requirement for the hormone extends across bone types and developmental profiles. Read more

The Transcriptional landscape of Streptococcus pneumoniae TIGR4 reveals a complex operon architecture and abundant riboregulation critical for growth and virulence

December 5, 2018
Indu Warrier, Nikhil Ram-Mohan, Zeyu Zhu, Ariana Hazery, Haley Echlin, Jason Rosch, Michelle M. Meyer, Tim van Opijnen
PLOS Pathogens

Abstract
Efficient and highly organized regulation of transcription is fundamental to an organism’s ability to survive, proliferate, and quickly respond to its environment. Therefore, precise mapping of transcriptional units and understanding their regulation is crucial to determining how pathogenic bacteria cause disease and how they may be inhibited. In this study, we map the transcriptional landscape of the bacterial pathogen Streptococcus pneumoniae TIGR4 by applying a combination of high-throughput RNA-sequencing techniques. We successfully map 1864 high confidence transcription termination sites (TTSs), 790 high confidence transcription start sites (TSSs) (742 primary, and 48 secondary), and 1360 low confidence TSSs (74 secondary and 1286 primary) to yield a total of 2150 TSSs. Furthermore, our study reveals a complex transcriptome wherein environment-respondent alternate transcriptional units are observed within operons stemming from internal TSSs and TTSs. Additionally, we identify many putative cis-regulatory RNA elements and riboswitches within 5’-untranslated regions (5’-UTR). By integrating TSSs and TTSs with independently collected RNA-Seq datasets from a variety of conditions, we establish the response of these regulators to changes in growth conditions and validate several of them. Furthermore, to demonstrate the importance of ribo-regulation by 5’-UTR elements for in vivo virulence, we show that the pyrR regulatory element is essential for survival, successful colonization and infection in mice suggesting that such RNA elements are potential drug targets. Importantly, we show that our approach of combining high-throughput sequencing with in vivo experiments can reconstruct a global understanding of regulation, but also pave the way for discovery of compounds that target (ribo-)regulators to mitigate virulence and antibiotic resistance. Read more

A Member of the Ferlin Calcium Sensor Family Is Essential for Toxoplasma gondii Rhoptry Secretion

September/October 2018
Bradley I. Coleman, Sudeshna Saha, Seiko Sato, Klemens Engelberg, David J. P. Ferguson, Isabelle Coppens, Melissa B. Lodoen, Marc-Jan Gubbels
American Society for Microbiology
Abstract

Invasion of host cells by apicomplexan parasites such as Toxoplasma gondii is critical for their infectivity and pathogenesis. In Toxoplasma, secretion of essential egress, motility, and invasion-related proteins from microneme organelles is regulated by oscillations of intracellular Ca²⁺. Later stages of invasion are considered Ca²⁺ independent, including the secretion of proteins required for host cell entry and remodeling from the parasite’s rhoptries. We identified a family of three Toxoplasma proteins with homology to the ferlin family of double C2 domain-containing Ca²⁺ sensors. In humans and model organisms, such Ca²⁺ sensors orchestrate Ca²⁺-dependent exocytic membrane fusion with the plasma membrane. Here we focus on one ferlin that is conserved across the Apicomplexa, T. gondii FER2 (TgFER2). Unexpectedly, conditionally TgFER2-depleted parasites secreted their micronemes normally and were completely motile. However, these parasites were unable to invade host cells and were therefore not viable. Knockdown of TgFER2 prevented rhoptry secretion, and these parasites failed to form the moving junction at the parasite-host interface necessary for host cell invasion. Collectively, these data demonstrate the requirement of TgFER2 for rhoptry secretion in Toxoplasma tachyzoites and suggest a possible Ca²⁺ dependence of rhoptry secretion. These findings provide the first mechanistic insights into this critical yet poorly understood aspect of apicomplexan host cell invasion.

IMPORTANCE Apicomplexan protozoan parasites, such as those causing malaria and toxoplasmosis, must invade the cells of their hosts in order to establish a pathogenic infection. Timely release of proteins from a series of apical organelles is required for invasion. Neither the vesicular fusion events that underlie secretion nor the observed reliance of the various processes on changes in intracellular calcium concentrations is completely understood. We identified a group of three proteins with strong homology to the calcium-sensing ferlin family, which are known to be involved in protein secretion in other organisms. Surprisingly, decreasing the amounts of one of these proteins (TgFER2) did not have any effect on the typically calcium-dependent steps in invasion. Instead, TgFER2 was essential for the release of proteins from organelles called rhoptries. These data provide a tantalizing first look at the mechanisms controlling the very poorly understood process of rhoptry secretion, which is essential for the parasite’s infection cycle. Read more

Pollution and Global Health - An Agenda for Prevention

August 2018
Philip J. Landrigan, Richard Fuller, Howard Hu, Jack Caravanos, Maureen L. Cropper, David Hanrahan, Karti Sandilya, Thomas C. Chiles, Pushpam Kumar and Williams A. Suk
Environmental Health Perspectives

Abstract
Pollution is a major, overlooked, global health threat that was responsible in 2015 for an estimated 9 million deaths and great economic losses. To end neglect of pollution and advance prevention of pollution-related disease, we formed the Lancet Commission on Pollution and Health. Despite recent gains in understanding of pollution and its health effects, this Commission noted that large gaps in knowledge remain. To close these gaps and guide prevention, the Commission made research recommendations and proposed creation of a Global Observatory on Pollution and Health. We posit that successful pollution research will be translational and based on transdisciplinary collaborations among exposure science, epidemiology, data science, engineering, health policy, and economics. We envision that the Global Observatory on Pollution and Health will be a multinational consortium based at Boston College and the Harvard T.H. Chan School of Public Health that will aggregate, geocode, and archive data on pollution and pollution-related disease; analyze these data to discern trends, geographic patterns, and opportunities for intervention; and make its findings available to policymakers, the media, and the global public to catalyze research, inform policy, and assist cities and countries to target pollution, track progress, and save lives. Read more

Graduate Student Mary Ann Collins of Dr. Eric Folker's lab, Presents at the Boston Area Drosophila Meeting.

Mary Ann Collins, a graduate student in Dr. Eric Folker's lab, presents her research, entitled "Mispositioned nuclei: Distinct mechanisms drive similar phenotypes" at the Boston Area Drosophila Meeting held at Harvard Medical School. She also met keynote speaker and Nobel Laurette, Michael Rosbash, who was awarded the 2017 Nobel Prize in Physiology or Medicine for his scientific contributions to the discovery of the molecular mechanisms that regulate circadian rhythm.

Dr. Heather Olins Deep-Sea Biology Class Is Selected To Be Part of the NOAA Expedition Team

Dr. Heather Olins's Deep Sea Biology Class recently had a visit from Nick Pawlenko....

of the National Oceanographic and Atmospheric Administration Office of Ocean Education & Research (OER). Nick was joined via video by OER's science lead Dr. Scott France of the University of Louisiana at Lafayette.

They are helping the class remotely participate in an upcoming research expedition in the Gulf of Mexico being carried out by NOAA's Okeanos Explorer. To plan this expedition, a call went out to the scientific community to suggest specific sites of interest to potentially explore on the April expedition.

The class was invited to propose two potential sites to be considered along side sites proposed by scientists. Students worked in groups to examine bathymetric data from the Gulf, and researched previous discoveries at sites nearby to help select their sites. Ultimately, the class chose two locations where we think deep sea corals may be present. In the next few weeks a committee will discuss all of the proposed sites, and if we are lucky enough to have one of ours chosen, it will happen towards the end of April, and will be live streamed online (along with all the other dives of the expedition) for all to watch!

Department faculty member, Dr. Ben Fofana's recent publication in Frontiers in Immunology.

Dr. Fofana's paper on Coupling of Single Molecule, Long Read Sequencing with IMGT/HighV-QUEST Analysis Expedites Identification of SIV gp140-Specific Antibodies from scFv Phage Display Libraries can be read here.

Coupling of Single Molecule, Long Read Sequencing with IMGT/HighV-QUEST Analysis Expedites Identification of SIV gp140-Specific Antibodies from scFv Phage Display Libraries

March 1, 2018
Seung Yub Han, Alexia Antoine, David Howard, Bryant Chang, Woo Sung Chang, Matthew Slein, Gintaras Deikus, Sofia Kossida, Patrice Duroux, Marie-Paule Lefranc, Robert P. Sebra, Melissa L. Smith, and Ismael Ben F. Fofana
Frontiers in Immunology

Abstract
The simian immunodeficiency virus (SIV)/macaque model of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome pathogenesis is critical for furthering our understanding of the role of antibody responses in the prevention of HIV infection, and will only increase in importance as macaque immunoglobulin (IG) gene databases are expanded. We have previously reported the construction of a phage display library from a SIV-infected rhesus macaque (Macaca mulatta) using oligonucleotide primers based on human IG gene sequences. Our previous screening relied on Sanger sequencing, which was inefficient and generated only a few dozen sequences. Here, we re-analyzed this library using single molecule, real-time (SMRT) sequencing on the Pacific Biosciences (PacBio) platform to generate thousands of highly accurate circular consensus sequencing (CCS) reads corresponding to full length single chain fragment variable. CCS data were then analyzed through the international ImMunoGeneTics information system^® (IMGT^®)/HighV-QUEST (www.imgt.org) to identify variable genes and perform statistical analyses. Overall the library was very diverse, with 2,569 different IMGT clonotypes called for the 5,238 IGHV sequences assigned to an IMGT clonotype. Within the library, SIV-specific antibodies represented a relatively limited number of clones, with only 135 different IMGT clonotypes called from 4,594 IGHV-assigned sequences. Our data did confirm that the IGHV4 and IGHV3 gene usage was the most abundant within the rhesus antibodies screened, and that these genes were even more enriched among SIV gp140-specific antibodies. Although a broad range of VH CDR3 amino acid (AA) lengths was observed in the unpanned library, the vast majority of SIV gp140-specific antibodies demonstrated a more uniform VH CDR3 length (20 AA). This uniformity was far less apparent when VH CDR3 were classified according to their clonotype (range: 9–25 AA), which we believe is more relevant for specific antibody identification. Only 174 IGKV and 588 IGLV clonotypes were identified within the VL sequences associated with SIV gp140-specific VH. Together, these data strongly suggest that the combination of SMRT sequencing with the IMGT/HighV-QUEST querying tool will facilitate and expedite our understanding of polyclonal antibody responses during SIV infection and may serve to rapidly expand the known scope of macaque V genes utilized during these responses. Read more

Dr. Laura Anne Lowery, Beckman Foundation Grant Recipient

The Biology Department is pleased to congratulate Dr. Laura Anne Lowery on being a recipient of the 2018 Beckman Program Scholar Award.  In collaboration with Dr. Jeff Byers of the Chemistry Dept., their science has been chosen for this highly competitive award.  Six Boston College students will have the multi-faceted opportunity to work with Drs. Lowery and Byers in this exciting endeavor; outlined in this BC News article. 

Assistant Professor Babak Momeni receives the Smith Family Award for Excellence in Biomedical Research

Dr. Momeni is granted the award, worth $300,000 to perform research on identifying molecular mechanisms of inter-bacterial interactions.  This award program (https://hria.org/tmf/smith/), presented by the Smith Family Foundation, supports biomedical innovation and discovery by early-career investigators. To learn more about Dr. Momeni's lab and research activities, please visit http://www.momenilab.org/.

Lowery Helps Students Learn About Biology and Beyond

A feature article on Dr. Laura Anne Lowery. Spotlighting her teaching, mentoring and science and the positive impact she has on her students here at Boston College.  

Folker Lab Graduate Students Present at 2017 ASCB Meeting

Members of Dr. Eric Folker's Lab take their science on the road to the 2017 ASCB meeting in Philadelphia.

Presenters and talk titles are as follows:

B393/P1834: Mary Ann Collins - Attractive and repulsive nuclear interactions are regulated by distinct genes linked to EmeryDreifuss Muscular Dystrophy and Centronuclear Myopathy. M.A. Collins, J.M. Camuglia, M. Gutierrez, T. Shu, E.S. Folker; Department of Biology, Boston College, Chestnut Hill, MA.

B394/P1385: Torrey Mandigo - Bocksbeutel regulates nuclear positioning by a klarsicht-dependent mechanism. T.R. Mandigo, A.J. Anderson, B.D. Turcich, E.S. Folker; Department of Biology, Boston College, Boston, MA.

B104/P2826: Alexander Auld - Aplip1 (Drosophila JIP1) regulates myonuclear positioning and muscle stability. A.L. Auld, S.A. Roberts, C.B. Murphy, J.M. Camuglia, E.S. Folker; Biology, Boston College, Chestnut Hill, MA.

American Society for Cell Biology (ASCB) features Bret Judson in career perspectives article

An informative interview on Bret Judson's career path; from specializing in light and electron microscopy to teaching here at Boston College.  See this article on the ASCB website. 

Identification and characterization of a potent and biologically-active PDE4/7 inhibitor via fission yeast-based assays

December 2017
Medeiros, A.S., Wyman, A., Alaamery, M., Allain, C., Ivey, F.D., Wang, L., Le, H., Morken, J., Habara, A., Le, C., Cui, S., Lerner, A., Hoffman, C.S.
Cellular Signalling

Abstract
We previously constructed a collection of fission yeast strains that express various mammalian cyclic nucleotide phosphodiesterases (PDEs) and developed a cell-based high throughput screen (HTS) for small molecule PDE inhibitors. Here we describe a compound, BC54, that is a selective inhibitor of enzymes from the cAMP-specific PDE4 and PDE7 families. Consistent with the biological effect of other PDE4 and PDE7 inhibitors, BC54 displays potent anti-inflammatory properties and is superior to a combination of rolipram (a PDE4 inhibitor) and BRL50481 (a PDE7A inhibitor) for inducing apoptosis in chronic lymphocytic leukemia (CLL) cells. We further exploited PKA-regulated growth phenotypes in fission yeast to isolate two mutant alleles of the human PDE4B2 gene that encode enzymes possessing single amino acid changes that confer partial resistance to BC54. We confirm this resistance to both BC54 and rolipram via yeast-based assays and, for PDE4B2T407A, in vitro enzyme assays. Thus, we are able to use this system for both chemical screens to identify biologically-active PDE inhibitors and molecular genetic studies to characterize the interaction of these molecules with their target enzymes. Based on its potency, selectivity, and effectiveness in cell culture, BC54 should be a useful tool to study biological processes regulated by PDE4 and PDE7 enzymes. Read more

Two Phosphoglucomutase Paralogs Facilitate Ionophore-Triggered Secretion of the Toxoplasma Micronemes

November/December 2017
Sudeshna Saha, Bradley I. Coleman, Rashmi Dubey, Ira J. Blader, Marc-Jan Gubbels
mSphere

Abstract
Paralogs of the widely prevalent phosphoglucomutase (PGM) protein called parafusin function in calcium (Ca²⁺)-mediated exocytosis across eukaryotes. In Toxoplasma gondii, the parafusin-related protein 1 (PRP1) has been associated with Ca²⁺-dependent microneme organelle secretion required for essential processes like host cell invasion and egress. Using reverse genetics, we observed PRP1 to be dispensable for completion of the lytic cycle, including host cell invasion and egress by the parasite. However, the absence of the gene affected increased microneme release triggered by A23187, a Ca²⁺ ionophore used to raise the cytoplasmic Ca²⁺ concentration mimicking the physiological role of Ca²⁺ during invasion and egress. The basal levels of constitutive microneme release in extracellular parasites and phosphatidic acid-triggered microneme secretion were unaffected in the mutant. The phenotype of the deletion mutant of the second PGM-encoding gene in Toxoplasma, PGM2, was similar to the phenotype of the PRP1 deletion mutant. Furthermore, the ability of the tachyzoites to induce acute infection in the mice remained normal in the absence of both PGM paralogs. Our data thus reveal that the microneme secretion upon high Ca²⁺ flux is facilitated by the Toxoplasma PGM paralogs, PRP1 and PGM2. However, this protein-mediated release is neither essential for lytic cycle completion nor for acute virulence of the parasite.

IMPORTANCE Ca²⁺-dependent exocytosis is essential for the life cycle of apicomplexan parasites. Toxoplasma gondii harbors a phosphoglucomutase (PGM) ortholog, PRP1, previously associated with Ca²⁺-dependent microneme secretion. Here it is shown that genetic deletion of either PRP1, its PGM2 ortholog, or both genes is dispensable for the parasite’s lytic cycle, including host cell egress and invasion. Depletion of the proteins abrogated high Ca²⁺-mediated microneme secretion induced by the ionophore A23187; however, the constitutive and phosphatidic acid-mediated release remained unaffected. Secretion mediated by the former pathway is not essential for tachyzoite survival or acute in vivo infection in the mice. Read more

Thyroid Hormone Stimulates the Onset of Adult Feeding Kinematics in Zebrafish

December 1, 2017
Sarah McMenamin, Casey Carter, and Wiliam James Cooper
Zebrafish

Abstract
The physical demands for swimming and feeding change dramatically over the course of development for many aquatic animals. Indeed, in teleosts, the transition from larva to adult involves major shifts in both trophic morphology and feeding behavior. A spike in thyroid hormone (TH) coordinates many developmental processes that occur during this adult transition in numerous vertebrate species. Using mutant and transgenic zebrafish, we tested the hypothesis that TH is essential for the transition from larval to adult feeding kinematic profiles. We found that every measured kinematic variable that distinguished larvae from adults also differentiated hypothyroid from wild-type (WT) euthyroid adults, suggesting that TH is indeed necessary for the onset of mature feeding behaviors. In contrast, feeding kinematics in hyperthyroid adults were extremely similar to those measured in euthyroid adults. Altered TH signaling underlies pedomorphosis in some amphibian species, and Danionella is a pedomorphic danionin genus. We therefore tested whether feeding kinematics of adult Danionella would more closely match larval zebrafish (and hypothyroid adults) than WT adult zebrafish. We found Danionella feeding kinematics resemble those of larval (and hypothyroid) zebrafish in multiple respects. Overall, we conclude that TH is essential in stimulating the onset of adult feeding kinematics in zebrafish, and that some of the underlying developmental pathways may have been lost in Danionella.  Read more

Does Context Matter? Convergent and Divergent Findings in the Cross-Institutional Evaluation of Graduate Teaching Assistant Professional Development Programs

November 8, 2017
Todd D. Reeves, Laura E. Hake, Xinnian Chen, Jennifer Frederick, Kristin Rudenga, Larry H. Ludlow, Clare M. O'Connor
CBE-Life Sciences Education

Abstract
Graduate teaching assistants (GTAs) play important instructional roles in introductory science courses, yet they often have little training in pedagogy. The most common form of teaching professional development (PD) for GTAs is a presemester workshop held at the course, department, or college level. In this study, we compare the effectiveness of presemester workshops at three northeastern research universities, each of which incorporated scientific teaching as the pedagogical content framework. The comparison of GTA PD program outcomes at three different institutions is intended to test theoretical assertions about the key role of contextual factors in GTA PD efficacy. Pretest and posttest surveys were used to assess changes in GTA teaching self-efficacy and anxiety following the workshops, and an objective test was used to assess pedagogical knowledge. Analysis of pretest/posttest data revealed statistically significant gains in GTA teaching self-efficacy and pedagogical knowledge and reductions in teaching anxiety across sites. Changes in teaching anxiety and self-efficacy, but not pedagogical knowledge, differed by training program. Student ratings of GTAs at two sites showed that students had positive perceptions of GTAs in all teaching dimensions, and relatively small differences in student ratings of GTAs were observed between institutions. Divergent findings for some outcome variables suggest that program efficacy was influenced as hypothesized by contextual factors such as GTA teaching experience.  Read more

Professor Jeffrey DaCosta encourages students to 'leaf peep' during the fall season

Students in Biology Professor Jeffrey DaCosta's Ecology and Evolution class have been studying the phenology of the trees on campus. As Professor DaCosta explains, phenology is the study of the timing of biological events, such as trees stopping the maintenance of chlorophyll in the fall. Students in his class are each assigned two trees on campus to observe, take photos of, and record an estimated percentage of foliage change and leaf loss. The hope is to create a long-term data set that will one day serve as an authentic and nearby testament to the effects of climate change on the environment. Read more in The Environmental Eagle, a newsletter from BC's EcoPledge and the Office of Sustainability.

Tenure-track faculty position available

The Boston College Biology Department seeks outstanding candidates for a tenure-track faculty position in the area of Microbial Systems/Synthetic Biology with a special emphasis on host-microbe interactions. Applicants are sought at the Assistant Professor level; however, exceptionally strong candidates will be considered at the Associate Professor level. The university provides competitive start-up funds and research space with the expectation that the successful candidate will establish, or bring to the university, a vigorous, funded research program. The successful candidate will join an active and expanding department with current strengths in microbial systems biology, evolutionary virology, HIV pathology, Toxoplasma genetics, immunology, microbial communities and regulatory RNA-structure and function prediction and analyses, as well as non-microbial fields including developmental and cancer biology.

The university is situated on a beautiful campus dating back to the beginning of the twentieth century and is closely located to downtown Boston and Cambridge. The Biology Department has strong ongoing collaborative efforts with other departments including Chemistry and Physics, surrounding institutes including BU, Harvard, MIT, Northeastern University, and Tufts University, and has state of the art (core-)facilities including next-gen sequencing, cleanrooms for nanofabrication, multi-colored FACS, microscopy (including TIRF), microfluidics, robotics, NMR, and mass-spec. Moreover, the university has recently announced its decision to establish an interdisciplinary Institute for Integrated Science and Society, www.bc.edu/strategicplan.

QUALIFICATIONS

We especially encourage applicants whose research is focused on biomedically relevant host-microbe interactions with the goals of:

a) understanding the behavior of microbes in their complex host-environment and developing predictive models or approaches to control or intervene into that behavior or;

b) applying novel approaches from fields including synthetic biology, computer science, or biophysics to develop new methods or technology aimed at measuring, controlling, or intervening into host-microbe interactions.

Candidates working in areas with clear relevance to human health, and those who combine cutting-edge wet-lab experimentation with computational modeling will be given priority. Special consideration will be given to candidates whose research program synergizes with current faculty interests in computational biology and/or microbiology (see http://www.bc.edu/biology for profiles of the Biology Department’s current research programs).

APPLICATION INSTRUCTIONS

Applicants should submit a cover letter, curriculum vitae, a statement of research plans, a statement of teaching interests, and arrange for three letters of reference. All application materials should be submitted via Interfolio at http://apply.interfolio.com/45021

Review of applications will begin on November 1, 2017, and continue until the position is filled.

High postural costs and anaerobic metabolism during swimming support the hypothesis of a U-shaped metabolism–speed curve in fishes

October 2017
Valentina DiSanto, Christopher Kenaley and George V. Lauder
PNAS

Abstract
Swimming performance is considered a key trait determining the ability of fish to survive. Hydrodynamic theory predicts that the energetic costs required for fishes to swim should vary with speed according to a U-shaped curve, with an expected energetic minimum at intermediate cruising speeds and increasing expenditure at low and high speeds. However, to date no complete datasets have shown an energetic minimum for swimming fish at intermediate speeds rather than low speeds. To address this knowledge gap, we used a negatively buoyant fish, the clearnose skate Raja eglanteria, and took two approaches: a classic critical swimming speed protocol and a single-speed exercise and recovery procedure. We found an anaerobic component at each velocity tested. The two approaches showed U-shaped, though significantly different, speed–metabolic relationships. These results suggest that (i) postural costs, especially at low speeds, may result in J- or U-shaped metabolism–speed curves; (ii) anaerobic metabolism is involved at all swimming speeds in the clearnose skate; and (iii) critical swimming protocols might misrepresent the true costs of locomotion across speeds, at least in negatively buoyant fish. 

Read more        

Differential Roles for Inner Membrane Complex Proteins across Toxoplasma gondii and Sarcocystis neurona Development

September/October 2017
Dubey R, Harrison B, Dangoudoubiyam S, Bandini, Cheng K, Kosber A, Aqop-Nersesian C, Howe DK, Samuelson J, Ferguson DJP, Gubbels MJ
mSphere

Abstract
The inner membrane complex (IMC) of apicomplexan parasites contains a network of intermediate filament-like proteins. The 14 alveolin domain-containing IMC proteins in Toxoplasma gondii fall into different groups defined by their distinct spatiotemporal dynamics during the internal budding process of tachyzoites. Here, we analyzed representatives of different IMC protein groups across all stages of the Toxoplasma life cycle and during Sarcocystis neurona asexual development. We found that across asexually dividing Toxoplasma stages, IMC7 is present exclusively in the mother’s cytoskeleton, whereas IMC1 and IMC3 are both present in mother and daughter cytoskeletons (IMC3 is strongly enriched in daughter buds). In developing macro- and microgametocytes, IMC1 and -3 are absent, whereas IMC7 is lost in early microgametocytes but retained in macrogametocytes until late in their development. We found no roles for IMC proteins during meiosis and sporoblast formation. However, we observed that IMC1 and IMC3, but not IMC7, are present in sporozoites. Although the spatiotemporal pattern of IMC15 and IMC3 suggests orthologous functions in Sarcocystis, IMC7 may have functionally diverged in Sarcocystis merozoites. To functionally characterize IMC proteins, we knocked out IMC7, -12, -14, and -15 in Toxoplasma. IMC14 and -15 appear to be involved in switching between endodyogeny and endopolygeny. In addition, IMC7, -12, and -14, which are all recruited to the cytoskeleton outside cytokinesis, are critical for the structural integrity of extracellular tachyzoites. Altogether, stage- and development-specific roles for IMC proteins can be discerned, suggesting different niches for each IMC protein across the entire life cycle.

IMPORTANCE The inner membrane complex (IMC) is a defining feature of apicomplexan parasites key to both their motility and unique cell division. To provide further insights into the IMC, we analyzed the dynamics and functions of representative alveolin domain-containing IMC proteins across developmental stages. Our work shows universal but distinct roles for IMC1, -3, and -7 during Toxoplasma asexual division but more specialized functions for these proteins during gametogenesis. In addition, we find that IMC15 is involved in daughter formation in both Toxoplasma and Sarcocystis. IMC14 and IMC15 function in limiting the number of Toxoplasma offspring per division. Furthermore, IMC7, -12, and -14, which are recruited in the G₁ cell cycle stage, are required for stress resistance of extracellular tachyzoites. Thus, although the roles of the different IMC proteins appear to overlap, stage- and development-specific behaviors indicate that their functions are uniquely tailored to each life stage requirement.  Read more

"We should never have to poison and burn patients to treat cancer" - Thomas Seyfried

Biology Professor Thomas Seyfried was recently featured in a Business Day article, "Cancer treatments undergo a rethink as fasting and diet studies deepen." He argues that cancer is a simple disease that has been made complex, and is an industry with crippling costs for treatment - treatments which in some cases, can cause additional cancers. Seyfried has developed a "press-pulse" model, which is a nontoxic, therapeutic strategy based on paleobiology and the Warburg effect. It includes ketogenic diets, drugs and hyperbaric oxygen therapy to deprive cancer cells of the fuel needed to survive. Read more. 

Kif2 localizes to a subdomain of cortical endoplasmic reticulum that drives asymmetric spindle position

October 2017
Vlad Costache, Celine Hebras, Gerard Pruliere, Lydia Besnardeau, Margaux Failla,
Richard R. Copley, David Burgess, Janet Chenevert and Alex McDougall
Nature Communications

Abstract
Asymmetric positioning of the mitotic spindle is a fundamental process responsible for creating sibling cell size asymmetry; however, how the cortex causes the depolymerization of astral microtubules during asymmetric spindle positioning has remained elusive. Early ascidian embryos possess a large cortical subdomain of endoplasmic reticulum (ER) that causes asymmetric spindle positioning driving unequal cell division. Here we show that the microtubule depolymerase Kif2 localizes to this subdomain of cortical ER. Rapid live-cell imaging reveals that microtubules are less abundant in the subdomain of cortical ER. Inhibition of Kif2 function prevents the development of mitotic aster asymmetry and spindle pole movement towards the subdomain of cortical ER, whereas locally increasing microtubule depolymerization causes exaggerated asymmetric spindle positioning. This study shows that the microtubule depolymerase Kif2 is localized to a cortical subdomain of endoplasmic reticulum that is involved in asymmetric spindle positioning during unequal cell division. Read more

Learn Who is on the Current E-Board for the Boston College Chapter of SACNAS

SACNAS, or the Society for Advancement of Chicanos/Hispanics and Native Americans in Science, is focused on training and supporting the next generation of diverse STEM talent. Boston College has a SACNAS chapter - below is the run-down of their current e-board:

Benjamin Acosta is the new president of the SACNAS Boston College Chapter; his role involves organizing events and dealing with administrative duties, such as planning methods to connect the student body with the professional world of science.

Hung Tran is the vice president; he assists in creating and hosting events as well as department outreach.

Mary Ann Collins is the secretary; she records the group's minutes during meetings and aids with coordinating events.

Raj Singh is the national liaison; his role is to provide a report to the national SACNAS organization with an update on our local chapter every semester.

Elise Gray is the former chapter president and has moved on to the treasurer role; she is in charge of managing the budget.

In Vivo Behavior of the Tandem Glycine Riboswitch in Bacillus subtilis

October 2017
Arianne M. Babina, Nicholas E. Lea, Michelle M. Meyer
American Society for Microbiology

Abstract
In many bacterial species, the glycine riboswitch is composed of two homologous ligand-binding domains (aptamers) that each bind glycine and act together to regulate the expression of glycine metabolic and transport genes. While the structure and molecular dynamics of the tandem glycine riboswitch have been the subject of numerous in vitro studies, the in vivo behavior of the riboswitch remains largely uncharacterized. To examine the proposed models of tandem glycine riboswitch function in a biologically relevant context, we characterized the regulatory activity of mutations to the riboswitch structure in Bacillus subtilis using β-galactosidase assays. To assess the impact disruptions to riboswitch function have on cell fitness, we introduced these mutations into the native locus of the tandem glycine riboswitch within the B. subtilis genome. Our results indicate that glycine does not need to bind both aptamers for regulation in vivo and mutations perturbing riboswitch tertiary structure have the most severe effect on riboswitch function and gene expression. We also find that in B. subtilis, the glycine riboswitch-regulated gcvT operon is important for glycine detoxification.

IMPORTANCE The glycine riboswitch is a unique cis-acting mRNA element that contains two tandem homologous glycine-binding domains that act on a single expression platform to regulate gene expression in response to glycine. While many in vitro experiments have characterized the tandem architecture of the glycine riboswitch, little work has investigated the behavior of this riboswitch in vivo. In this study, we analyzed the proposed models of tandem glycine riboswitch regulation in the context of its native locus within the Bacillus subtilis genome and examined how disruptions to glycine riboswitch function impact organismal fitness. Our work offers new insights into riboswitch function in vivo and reinforces the potential of riboswitches as novel antimicrobial targets.    Read more       

Biology students Katya Van Anderlecht and Lauren Havens win prestigious undergraduate fellowships

Katya Van Anderlecht was selected to participate in the Amgen Foundation’s Amgen Scholars Program this past summer. Van Anderlecht, a junior who is also a pre-med student, spent the summer conducting developmental biology research at CalTech. This year, Van Anderlecht will work in the cellular biology lab of Assistant Professor of Biology Laura Anne Lowery.

Biology major Lauren Havens has been awarded a 2017 American Society for Microbiology Undergraduate Research Fellowship. Haven, a senior, is one of 19 awardees out of 128 applications, according to the society. The ASM fellowship supports undergraduate students in work in their home institution with a faculty mentor. Haven, who will conduct research into the genome of the deadly bacteria streptococcus pneumoniae, will be mentored by Associate Professor of Biology Tim van Opijnen.

To read more about the fellowships, see this BC news article. 

Biology Graduate Student Elise Gray Wins the Reverend Donald J. Plocke, S.J. Award

Elise Gray, a Biology graduate student in Professor Michelle Meyer's lab, was honored with the Reverend Donald J. Plocke, S.J. Award at the Biology Department Annual Scientific Meeting. Her talk was entitled, "The rplU-ysxB-rpmA operon in Bacillus subtilis is auto-regulated by ribosomal protein L21 via an RNA cis-regulatory element."

In 2016, the award for best speaker at the Biology Department annual scientific retreat was renamed the Father Plocke Award in honor of the late former Chair of the Biology Department. Fr. Plocke was a member of the department for 43 years, and served as the Chairperson from 1971-1980. His research activities focused on the biological role of metal ions - especially zinc - and cellular responses to toxic levels of metals. He was a dedicated researcher and teacher, whose work and ministry affected thousands of students over the years.

Last year's recipient was Alexander Auld, a graduate student in Professor Eric Folker's lab, for his talk, "Nucleus-dependent sarcomere assembly is mediated by the LINC complex."

Postdoctoral Research Fellow Marco Zaccaria Wins Best Poster

Marco Zaccaria, a Postdoctoral Research Fellow in Professor Babak Momeni's lab, won the honor of "Best Poster" at the Biology Department Annual Scientific Meeting. Marco's talk was entitled, "Engineering an applicable bacterial bioremediator through Artificial Selection."

A biorobotic adhesive disc for underwater hitchhiking inspired by the remora suckerfish

September 2017
Yueping Wang, Xingbang Yang, Yufeng Chen, Dylan K. Wainwright, Christopher P. Kenaley, Zheyuan Gong, Zemin Liu, Huan Liu, Juan Guan, Tianmiao Wang, James C. Weaver, Robert J. Wood3, and Li Wen
Science Robotics

Abstract
Remoras of the ray-finned fish family Echeneidae have the remarkable ability to attach to diverse marine animals using a highly modified dorsal fin that forms an adhesive disc, which enables hitchhiking on fast-swimming hosts despite high magnitudes of fluid shear. We present the design of a biologically analogous, multimaterial biomimetic remora disc based on detailed morphological and kinematic investigations of the slender sharksucker (Echeneis naucrates). We used multimaterial three-dimensional printing techniques to fabricate the main disc structure whose stiffness spans three orders of magnitude. To incorporate structures that mimic the functionality of the remora lamellae, we fabricated carbon fiber spinules (270 μm base diameter) using laser machining techniques and attached them to soft actuator–controlled lamellae. Our biomimetic prototype can attach to different surfaces and generate considerable pull-off force—up to 340 times the weight of the disc prototype. The rigid spinules and soft material overlaying the lamellae engage with the surface when rotated, just like the discs of live remoras. The biomimetic kinematics result in significantly enhanced frictional forces across the disc on substrates of different roughness. Using our prototype, we have designed an underwater robot capable of strong adhesion and hitchhiking on a variety of surfaces (including smooth, rough, and compliant surfaces, as well as shark skin). Our results demonstrate that there is promise for the development of high-performance bioinspired robotic systems that may be used in a number of applications based on an understanding of the adhesive mechanisms used by remoras. Read more

Biology Alumni Seminar - Alexander Lorestani '09

On October 18th, the biology department will be hosting its first alumni seminar at 3:30 pm in Devlin 008. The seminar speaker will be Alexander Lorestani '09. Alex is the CEO of Geltor Inc. based out of San Leandro, CA. Geltor's primary focus is on the production of vegan gelatin. Alex's seminar will focus on his time here at Boston College and how it helped prepare him for his current role of leading a company that is solving a current economic and environmental need through biology. We hope to see you all there!  

MicroCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system

September 2017
Matthew Hur, Charlotte A Gistelinck, Philippe Huber, Jane Lee, Marjorie H Thompson, Adrian T Monstad-Rios, Claire J Watson, Sarah K McMenamin, Andy Willaert, David M Parichy, Paul Coucke, Ronald Y Kwon
eLIFE

Abstract
Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of phenotypic measures comprised of morphological and densitometric traits at a large number of sites within the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes associated with human brittle bone disease and thyroid stimulating hormone receptor hyperactivity. Finally, we develop allometric models and show their potential to aid in the discrimination of mutant phenotypes masked by alterations in growth. Our studies demonstrate virtues of deep phenotyping in a spatially distributed organ system. Analyzing phenotypic patterns may increase productivity in genetic screens, and facilitate the study of genetic variants associated with smaller effect sizes, such as those that underlie complex diseases.  Read more

MAGenTA: a Galaxy implemented tool for complete Tn-Seq analysis and data visualization

September 2017
McCoy KM, Antonio ML, van Opijnen T
Bioformatics

Abstract

Motivation: Transposon insertion sequencing (Tn-Seq) is a microbial systems-level tool, that can determine on a genome-wide scale and in high-throughput, whether a gene, or a specific genomic region, is important for fitness under a specific experimental condition.

Results: Here, we present MAGenTA, a suite of analysis tools which accurately calculate the growth rate for each disrupted gene in the genome to enable the discovery of: (i) new leads for gene function, (ii) non-coding RNAs; (iii) genes, pathways and ncRNAs that are involved in tolerating drugs or induce disease; (iv) higher order genome organization; and (v) host-factors that affect bacterial host susceptibility. MAGenTA is a complete Tn-Seq analysis pipeline making sensitive genome-wide fitness (i.e. growth rate) analysis available for most transposons and Tn-Seq associated approaches (e.g. TraDis, HiTS, IN-Seq) and includes fitness (growth rate) calculations, sliding window analysis, bottleneck calculations and corrections, statistics to compare experiments and strains and genome-wide fitness visualization.

Read more

Analysis of SIVmac Envelope-Specific Antibodies Selected Through Phage Display

September 2017
Ita S, Agostinho MR, Sullivan K, Yub Han S, Akleh R, Johnson WE, Fofana IBF
AIDS Research and Human Retroviruses

Abstract
We have constructed a single chain fragment variable (scFv) phage display library from a simian immunodeficiency virus (SIV)-infected rhesus macaque that developed unusually high-titer neutralizing antibody responses against tier-3, neutralization-resistant SIVmac239. The library was screened using trimeric (gp140) and monomeric (gp120) forms of the SIVmac239 envelope (Env) glycoprotein. We also cloned variable-heavy and variable-light (VH-VL) antibody fragments from seven previously described rhesus macaque B-cell lines (BLCLs) that produce SIV gp120-specific monoclonal antibodies (mAbs). Thirty-two gp140-specific mAbs were selected along with 20 gp120-specific ones. gp120-specific mAbs were only from the VH4 family, while gp41-specific mAbs were primarily from VH1, followed by VH4 and VH3. Rhesus macaque BLCL-derived mAbs belonged primarily to the VH4 family of antibodies followed by VH3 and a smaller number of VH1s. A preferential VH combination with Vλ light chain was observed with phage display-selected SIV Env-specific mAbs (gp120 and gp140), but not with BLCL-derived antibodies or the unpanned library. None of the tested antibodies had detectable neutralizing activity against tier-3 SIVmac239. The majority of gp120-specifc mAbs potently neutralized tier-1 SIVmac316 with 50% inhibitory concentration (IC50) values below 1 μg/ml. For gp140-specific antibodies, which were all specific for the gp41-subunit, 2 out of 11 tested neutralized SIVmac316 (IC50 of 7 and 5 μg/ml, respectively). These data suggest an order of preferential VH segment usage for SIV-specific antibodies in rhesus macaques. These antibodies will be useful in assessing the contribution of non-neutralizing antibodies to inhibition of SIV infection in vitro and in vivo. Read more

Biology Student Zach Augur presents at the St. Jude's National Symposium for Undergraduate Research

The National Symposium for Undergraduate Research is a competitive academic event hosted by the St. Jude Graduate School of Biomedical Sciences. The symposium allows U.S. undergraduate students to showcase their research work in poster and oral platform settings, improve their presentations skills, and learn about the cutting-edge research and facilities at St. Jude Children's Research Hospital. Biology student Zach Augur was among just 40 students selected to present at this event over the summer. The title of his presentation was "Diet/drug combinatorial approach to target energy metabolism in preclinical glioblastoma multiforme."

2017 Biology Retreat held in August

Each year the Biology Department hosts a scientific retreat for its research faculty and graduate students. The retreat features presentations by both professors and graduate students highlighting their research as well as a poster session for the graduate students to present their own projects. This year, Marco Zaccaria, a Postdoctoral Research Fellow in Professor Babak Momeni's lab, won the honor of "Best Poster" and Elise Gray, a Biology graduate student in Professor Michelle Meyer's lab, was honored with the Reverend Donald J. Plocke, S.J. Award for the best talk. To learn more about featured speakers and posters presented please read the descriptions featured in the Retreat Booklet. 

NSF funding used to purchase super resolution Zeiss microscope

The Biology Department received NSF funding to purchase a $1.1 million super resolution Zeiss Microscope. This new microscope is the latest addition to a well-equipped imaging core facility in Higgins Hall managed by Imaging Facility Manager Bret Judson. The system was delivered in late January 2017 and came on-line in February 2017, extending the range of experiments that can be conducted at Boston College. The microscope provides cutting-edge imaging capabilities to researchers that were previously only available at other institutions, and serves as an excellent teaching tool for undergraduate and graduate students in Bret’s microscopy course: Advanced Lab in Cell Imaging.

A brief description of the microscope follows:

Zeiss LSM 880-AS-FAST Elyra S1: This system combines several technologies into one flexible platform. At the base level, the system is the latest laser scanning confocal microscope from Zeiss capable of imaging samples at multiple wavelengths from 405nm to 633nm and from magnifications of 10x to 100x.  Included on this new system are two “super-resolution” modalities – the Airyscan unit with the FAST module and the Elyra S1 unit.  The Airyscan technology improves resolution down to 140 nm laterally and 400 nm axially while also enhancing sensitivity from 4-8x. In addition, the Airyscan module can be run in the “FAST” mode for live samples. The FAST module re-shapes the Airyscan beam, resulting in a 4-fold enhancement in speed while still remaining up to 4x more sensitive than a standard detector. For users requiring better resolution than the Airyscan can provide, the system has the Elyra unit which can provide resolution of 120 nm laterally and 300 nm axially.  Depending on experimental needs, users can freely change between any of these technologies. In contrast to some other super-resolution technologies, the Airyscan and the Elyra do not require special fluorophores and both work well with most standard mounting medias. This makes using either technology easier, as most standard microscope samples are inherently imaged well by either technique.

Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria

August 2017
Paul A. Jensen, Zeyu Zhu, Tim van Opijnen
Cell Reports

Abstract
Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude. Moreover, a gene expression meta-analysis reveals that genes with large fitness changes during stress have low transcriptional variation across hundreds of other conditions, and vice versa. Our work suggests that cellular responses can be understood through network models that incorporate regulatory and genetic relationships, which could aid drug target predictions and genetic network engineering. Read more

Emery-Dreifuss muscular dystrophy-linked genes and centronuclear myopathy-linked genes regulate myonuclear movement by distinct mechanisms

August 15, 2017
Collins, MA, Mandigo TR, Camuglia JM, Vazquez GA, Anderson AJ, Hudson CH, Hanron JL, Folker ES
Molecular Biology of the Cell

Abstract
Muscle cells are a syncytium in which the many nuclei are positioned to maximize the distance between adjacent nuclei. Although mispositioned nuclei are correlated with many muscle disorders, it is not known whether this common phenotype is the result of a common mechanism. To answer this question, we disrupted the expression of genes linked to Emery–Dreifuss muscular dystrophy (EDMD) and centronuclear myopathy (CNM) in Drosophila and evaluated the position of the nuclei. We found that the genes linked to EDMD and CNM were each necessary to properly position nuclei. However, the specific phenotypes were different. EDMD-linked genes were necessary for the initial separation of nuclei into distinct clusters, suggesting that these factors relieve interactions between nuclei. CNM-linked genes were necessary to maintain the nuclei within clusters as they moved toward the muscle ends, suggesting that these factors were necessary to maintain interactions between nuclei. Together these data suggest that nuclear position is disrupted by distinct mechanisms in EDMD and CNM.  Read more

Harry Cheung Wins Balkema Award

Harry Cheung wins the Balkema Award during the 2017 Undergraduate Research Day! The title of his research is "Sexual motivation is mediated by vasopressin in the brain, but does so differently in males than in females." 

The Balkema Award is presented to the undergraduate student who has presented the most outstanding senior thesis based on original research. The winner is judged to have written the thesis possessing the best overall balance of several attributes, including rigor of analysis, quality of results, and clarity of presentation. A panel of faculty judges makes the selection at the end of each academic year.

Prof. Grant Balkema was a tenured member of the Biology Department of Boston College, whose research interests concerned the physiology of vision. He was a very strong supporter of undergraduate research, and worked closely with the students in his laboratory. Following his death in 2004, the Balkema Award was established and named in his honor.

Professor Danielle Taghian earns Phi Beta Kappa Award

Congratulations to Professor Danielle Taghian on her Phi Beta Kappa Award! Professor Taghian has been with the Biology department since 2002 and has been known to keep close relationships with her students. It is these relationships that earned her the prestigious honor, awarded by students in the Honors Society. For more information about Professor Taghian and the Phi Beta Kappa Award, please visit the official Boston College Press Release.

BC researchers reveal new clues to the emergence of antibiotic-resistant bacteria.

Boston College biologist Tim van Opijnen and computer scientist José Bento reveal how different strains of bacteria use different groups of genes to resist antibiotics. Their approach maps, ranks, and identifies where antibiotic sensitivity functions reside in the genome of strains of S. pneumoniae. Read BC News article

Myelin structure in unfixed, single nerve fibers: Scanning X-ray microdiffraction with a beam size of 200 nm

July 2017
Hideyo Inouye, Fong-Hsu Kuo, Andrew R. Denninger, Britta Weinhausen, Manfred Burghammer, Daniel A. Kirschner
Journal of Structural Biology

Abstract
Previous raster-scanning with a 1 μm X-ray beam of individual, myelinated fibers from glutaraldehyde-fixed rat sciatic nerve revealed a spatially-dependent variation in the diffraction patterns from single fibers. Analysis indicated differences in the myelin periodicity, membrane separations, distribution of proteins, and orientation of membrane lamellae. As chemical fixation is known to produce structural artifacts, we sought to determine in the current study whether the structural heterogeneity is intrinsic to unfixed myelin. Using a 200 nm-beam that was about five-fold smaller than before, we raster-scanned individual myelinated fibers from both the peripheral (PNS; mouse and rat sciatic nerves) and central (CNS; rat corpus callosum) nervous systems. As expected, the membrane stacking in the internodal region was nearly parallel to the fiber axis and in the paranodal region it was perpendicular to the axis. A myelin lattice was also frequently observed when the incident beam was injected en face to the sheath. Myelin periodicity and diffracted intensity varied with axial position along the fiber, as did the calculated membrane profiles. Raster-scanning with an X-ray beam at sub-micron resolution revealed for the first time that the individual myelin sheaths in unfixed nerve are heterogeneous in both membrane structure and packing. Read more

Genetic fossil hunter

Welkin Johnson combs through ancient history for clues to help fight modern viruses. Read Article

Modeling Microbial Communities: A Call for Collaboration between Experimentalists and Theorists

June 2017
Marco Zaccaria, Sandra Dedrick and Babak Momeni 
Processes

Abstract
With our growing understanding of the impact of microbial communities, understanding how such communities function has become a priority. The influence of microbial communities is widespread. Human-associated microbiota impacts health, environmental microbes determine ecosystem sustainability, and microbe-driven industrial processes are expanding. This broad range of applications has led to a wide range of approaches to analyze and describe microbial communities. In particular, theoretical work based on mathematical modeling has been a steady source of inspiration for explaining and predicting microbial community processes. Here, we survey some of the modeling approaches used in different contexts. We promote classifying different approaches using a unified platform, and encourage cataloging the findings in a database. We believe that the synergy emerging from a coherent collection facilitates a better understanding of important processes that determine microbial community functions. We emphasize the importance of close collaboration between theoreticians and experimentalists in formulating, classifying, and improving models of microbial communities. Read more

Viral Family Tree

Scientists in the lab of Professor of Biology Welkin Johnson, shown above with then-undergraduate researcher Nirali Patel '15, study viruses ranging from HIV/AIDs to those that affected modern mammals' ancesters 15-30 million years ago. A team including Patel, who majored in both biology and English, has generated "a family tree" of ancient retroviruses. Read Article on BC News

Co-registered Geochemistry and Metatranscriptomics Reveal Unexpected Distributions of Microbial Activity within a Hydrothermal Vent Field

June 2017
Olins HC, Rogers DR, Preston C, Ussler W 3rd, Pargett D, Jensen S, Roman B, Birch JM, Scholin CA, Haroon MF, Girguis PR
Frontiers in Microbiology

Abstract
Despite years of research into microbial activity at diffuse flow hydrothermal vents, the extent of microbial niche diversity in these settings is not known. To better understand the relationship between microbial activity and the associated physical and geochemical conditions, we obtained co-registered metatranscriptomic and geochemical data from a variety of different fluid regimes within the ASHES vent field on the Juan de Fuca Ridge. Microbial activity in the majority of the cool and warm fluids sampled was dominated by a population of Gammaproteobacteria (likely sulfur oxidizers) that appear to thrive in a variety of chemically distinct fluids. Only the warmest, most hydrothermally-influenced flows were dominated by active populations of canonically vent-endemic Epsilonproteobacteria. These data suggest that the Gammaproteobacteria collected during this study may be generalists, capable of thriving over a broader range of geochemical conditions than the Epsilonproteobacteria. Notably, the apparent metabolic activity of the Gammaproteobacteria-particularly carbon fixation-in the seawater found between discrete fluid flows (the intra-field water) suggests that this area within the Axial caldera is a highly productive, and previously overlooked, habitat. By extension, our findings suggest that analogous, diffuse flow fields may be similarly productive and thus constitute a very important and underappreciated aspect of deep-sea biogeochemical cycling that is occurring at the global scale. Read more

The Road to a Cure: Characterization of a New HIV Antibody

Undergraduate students in Dr. Ismael Ben Fofana’s advanced lab course, Vaccine Development and Public Health, have published an article in Elements, the undergraduate research journal of Boston College. The article was entitled, “The Road to a Cure: Characterization of a New HIV Antibody.” This article was a version of the final paper submitted by undergraduate student Zachary Park. 

The lab course is research-based and is built on Dr. Fofana’s research, which focuses on understanding antibody responses to HIV infection and immunization using the SIV/macaque model of HIV/AIDS pathogenesis and vaccine.

The work presented in the BC journal was further developed in the lab and published in the Aids Research and Human Retroviruses journal under the title “Analysis of SIVmac Envelope-Specific Antibodies Selected Through Phage Display.” This work included BC undergraduates Seung Yub Han and Katherine Sullivan. Katherine Sullivan is currently a Research Associate I at MassBiologics, UMass Medical School. Seung Yub Han is currently a research technician in the lab of Prof Junhyong Kim in the Department of Biology and Department of Computer and Information Science, University of Pennsylvania.

The work presented in both journals will improve our ability to induce protective antibodies during anti-HIV vaccination.

Laura Anne Lowery receives "Ever to Excel" Award

Congratulations to Dr. Laura Anne Lowery for receiving an "Ever to Excel" award here at Boston College, given to "a faculty member that expanded the horizons, skills, and value systems of students outside the classroom." She was nominated by 5 of her own students for this well-deserved honor. 

For more information about the Ever to Excel awards, please visit bc.edu/awards.

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

March 2017
Babak Momeni, Li Xie, Wenying Shou
eLIFE

Abstract
Pairwise models are commonly used to describe many-species communities. In these models, an individual receives additive fitness effects from pairwise interactions with each species in the community ('additivity assumption'). All pairwise interactions are typically represented by a single equation where parameters reflect signs and strengths of fitness effects ('universality assumption'). Here, we show that a single equation fails to qualitatively capture diverse pairwise microbial interactions. We build mechanistic reference models for two microbial species engaging in commonly-found chemical-mediated interactions, and attempt to derive pairwise models. Different equations are appropriate depending on whether a mediator is consumable or reusable, whether an interaction is mediated by one or more mediators, and sometimes even on quantitative details of the community (e.g. relative fitness of the two species, initial conditions). Our results, combined with potential violation of the additivity assumption in many-species communities, suggest that pairwise modeling will often fail to predict microbial dynamics. Read more

The microtubule plus-end-tracking protein TACC3 promotes persistent axon outgrowth and mediates responses to axon guidance signals during development

February 2017
Burcu Erdogan, Garrett M. Cammarata, Eric J. Lee, Benjamin C. Pratt, Andrew F. Franci, Erin L. Rutherford and Laura Anne Lowery
Neural Development

Abstract

Background: Formation of precise neuronal connections requires proper axon guidance. Microtubules (MTs) of the growth cone provide a critical driving force during navigation of the growing ends of axons. Pioneer MTs and their plus-end tracking proteins (+TIPs) are thought to play integrative roles during this navigation. TACC3 is a + TIP that we have previously implicated in regulating MT dynamics within axons. However, the role of TACC3 in axon guidance has not been previously explored.

Results: Here, we show that TACC3 is required to promote persistent axon outgrowth and prevent spontaneous axon retractions in embryonic Xenopus laevis neurons. We also show that overexpressing TACC3 can counteract the depolymerizing effect of low doses of nocodazole, and that TACC3 interacts with MT polymerase XMAP215 to promote axon outgrowth. Moreover, we demonstrate that manipulation of TACC3 levels interferes with the growth cone response to the axon guidance cue Slit2 ex vivo, and that ablation of TACC3 causes pathfinding defects in axons of developing spinal neurons in vivo.

Conclusion: Together, our results suggest that by mediating MT dynamics, the + TIP TACC3 is involved in axon outgrowth and pathfinding decisions of neurons during embryonic development.

Read more

The A2V mutation as a new tool for hindering Aβ aggregation: A neutron and x-ray diffraction study

July 14, 2017
Laura Cantu, Laura Colombo, Tatiana Stoilova, Bruno Deme, Hideyo Inouye, Rachel Booth, Valeria Rondelli, Giuiseppe Di Fede, Fabrizio Tagliavini, Elena Del Favero, Daniel A. Kirschner & Mario Salmona
Scientific Reports

Abstract
We have described a novel C-to-T mutation in the APP gene that corresponds to an alanine to valine substitution at position 673 in APP (A673V), or position 2 of the amyloid-β (Aβ) sequence. This mutation is associated with the early onset of AD-type dementia in homozygous individuals, whereas it has a protective effect in the heterozygous state. Correspondingly, we observed differences in the aggregation properties of the wild-type and mutated Aβ peptides and their mixture. We have carried out neutron diffraction (ND) and x-ray diffraction (XRD) experiments on magnetically-oriented fibers of Aβ1-28WT and its variant Aβ1-28A2V. The orientation propensity was higher for Aβ1-28A2V suggesting that it promotes the formation of fibrillar assemblies. The diffraction patterns by Aβ1-28WT and Aβ1-28A2V assemblies differed in shape and position of the equatorial reflections, suggesting that the two peptides adopt distinct lateral packing of the diffracting units. The diffraction patterns from a mixture of the two peptides differed from those of the single components, indicating the presence of structural interference during assembly and orientation. The lowest orientation propensity was observed for a mixture of Aβ1-28WT and a short N-terminal fragment, Aβ1-6A2V, which supports a role of Aβ’s N-terminal domain in amyloid fibril formation.
Read more

Annual Clote Summer School

Dr. Professor Clote hosted the annual Clote Summer School, a one week course intended for Ph.D. students and Postdoctoral fellows with an interest in RNA research. The course teaches the computational methods necessary for performing RNA research. See the Clote Lab web page. 

Biology student Grace Lisius wins 2016 McCarthy Prize in Natural Sciences

Graduating senior and Biology major Grace Lisius won the 2016 McCarthy Prize in Natural Sciences for her Scholar of the College thesis titled "Vegetation Community Response to Hydrologic and Geomorphic Changes Following Dam Removal in a New England River." The award is given to those that exemplify academic excellence and substantial independent study in their undergraduate fields. Grace will start at the University of Pittsburgh School of Medicine in the fall of 2016.

Professor Tim van Opijnen awarded $10 million NIH grant

National Institutes of Health (NIH) Awards $10 million grant to Assistant Professor of Biology Tim van Opijnen, Assistant Professor of Computer Science Jose Bento, and colleagues to study how the immune system, bacteria, and antibiotics interact, and develop tools to help researchers to forecast resistant bacteria and optimal treatments. See BC news release for more details. 

Professor Thomas Seyfried featured in NPR article

Comments by Dr. Thomas Seyfried lead a piece that explores limitation of fuels available for fermentation—sugar glucose and the amino acid glutamine—as an overlooked approach to aid cancer treatment NPR "Your Health."

Professor Laura Anne Lowery receives an R03 from the National Institute of Dental and Craniofacial Research

Dr. Laura Anne Lowery received an R03 from the National Institute of Dental and Craniofacial Research, worth $234,000, to perform research on the role of microtubule dynamics in embryonic cell migration. To learn more about Dr. Lowery's research, visit her website at https://www2.bc.edu/laura-anne-lowery/. 

Professor Thomas Seyfried in Scientific American article

An article in Scientific American explores the connections between cancer and fermentation and includes comments by Biology Professor Thomas Seyfried, who has written extensively on cancer as a mitochondrial metabolic disease rather than a genetic disease. 

Biology student Margaret Antonio receives molecular and computational biology award

Margaret Antonio, a senior biology major conducting thesis research in Dr. Tim van Opijnen's lab, received the molecular and computational biology award for her poster presentation entitled: "MAGenTA: A bioinformatics pipeline for genome-wide Tn-Seq analysis of microbial pathogens" at the 15th Annual Biomedical Research Conference for Minority Students in Seattle, WA where over 1,700 abstracts were presented. The conference hosts notable speakers, including NIH and NIGMS director Jon Lorsch, HHMI investigator and Nobel Prize winner Linda Buck, and social activist Naomi Tutu. The 350 exhibitors from graduate programs, national laboratories, professional societies, and research companies also provided a rich opportunity for networking.

Biology postdoctoral fellow Federico Rosconi wins prestigious PEW Charitable Trust Latin American Fellowship

Dr. Federico Rosconi is the first postdoctoral fellow at Boston College to receive a prestigious PEW Charitable Trust Latin American Fellowship. Dr. Rosconi performs research in the van Opijnen lab and focuses on how bacterial pathogens make people sick. 

Biology Professors Michelle Meyer and Tim van Opijnen receive a joint R01 from NIH worth $1.5 million

Biology Professors Dr. Michelle Meyer and Dr. Tim van Opijnen received a joint R01 from the National Institute of Allergy and Infectious Diseases worth $1,500,000 to perform research on RNA regulators and their possible application as antibiotic targets. To learn more about their research, visit their lab websites at http://bioinformatics.bc.edu/meyerlab/ and www.vanopijnenlab.com.

Professor Tim van Opijnen receives R01 of $2 million from NIH

Biology Professor, Dr. Tim van Opijnen, receives an R01 from the National Institute of Allergy and Infectious Diseases worth $2,000,000 to perform research on antibiotics and antibiotic resistance. To learn more about Dr. van Opijnen’s research, visit his website at www.vanopijnenlab.com.

Imaging Facility Manager Bret Judson wrote piece for Bioprobes magazine

The Biology department's Imaging Facility Manager, Bret Judson, recently wrote a piece for Bioprobes magazine entitled The EVOS FL Cell Imaging System: A key component of an imaging core facility (see page 9). The article features images taken by Biology students in Dr. Judson's Advanced Cell Imaging Lab.

Biology Professor Dr. Tim van Opijnen Publishes Book

Dr. Tim van Opijnen published his 4th popular-science book (in Dutch) in November. This book, with a title that translates into “This is the most beautiful thing ever”, is the third in an annual series Dr. van Opijnen started together with a colleague in 2013. Each year they find an influential person to help them develop a question that they then put forward to 100 scientists, entrepreneurs, writers and artists. For this year’s edition they found the world famous designer duo Viktor&Rolf willing to help them formulate the question: ”What is the most beautiful thing you’ve ever seen?”

But what is beauty? After all, what is beautiful for one person may be trivial for another. With such a question you cannot expect anything less than a book with extremely diverse and often surprising essays. For instance, the former commander in chief of the Royal Dutch Army writes in moving poetic style about camaraderie amongst his troops, while a famous Dutch novelist writes about a black and white photo from Sebastião Salgado and the rawness of life it depicts, and how that can still be immensely beautiful. Dr. van Opijnen had a long interview on national TV and received raving reviews in the biggest national Newspaper deVolkskrant. The book will no doubt become a bestseller, and is possibly a great reason for you to brush up on your Dutch.

Biology student Beth Bearce featured in BC ad campaign

Biology graduate student Beth Bearce in Dr. Laura Anne Lowery's lab was recently featured in Boston College's new ad campaign: Ever to Excel: The Power of Resilience.

Members of Dr. Laura Anne Lowery's lab featured in BC Magazine

Assistant Professor of Biology Dr. Laura Anne Lowery investigates the cellular mechanisms that guide development of the nervous system. She assigns small teams of undergraduates responsibility for discrete pieces of her research. Undergraduates (Eric Lee ’18, Alexandra Mills ’18, Jessica Tiber ’18, Kelly Hawkins ’18, Laurie Hayrapetian ’17, Lowery, Jackson Bowers ’17, Erin Rutherford ’16, Leslie Carandang ’16, and Claire Stauffer ’16) conducting research in Dr. Laura Anne Lowery's lab are featured in the fall 2015 issue of Boston College Magazine.

Todd Gaines receives 2015 John F Zucker Animal Technician Award

Boston College Veterinary Technician, Todd Gaines received the 2015 John F Zucker Animal Technician Award from the New England Branch of the American Association for Laboratory Animal Science for his work in BC's Animal Care Facility.

Dr. Charles Hoffman receives praise for article in Genetics

Dr. Charles Hoffman's article for the journal Genetics helps to educate students on the value of Schizosaccharomyces pombe as a model organism and has received much praise from the scientific community. You can read his piece here: An Ancient Yeast for Young Geneticists: A Primer on the Schizosaccharomyces pombe Model System

Thomas Chiles Named to Global Commission on Pollution, Health and Development

DeLuca Professor of Biology and Vice Provost for Research Thomas Chiles is among influential leaders, researchers and practitioners named to the Global Commission on Pollution, Health and Development, an initiative of The Lancet, The Global Alliance on Health and Pollution, and Mount Sinai's Icahn School of Medicine, along with the U.N. and World Bank. The commission will detail the health and economic costs of pollution globally and provide a plan of action to policy makers. See the GAHP's interview with Thomas Chiles. 

Dr. Babak Momeni featured as a Freshman Faculty member

Biology Professor, Dr. Babak Momeni, is featured in BC's Freshman Faculty highlights. Professor Momeni has joined BC in this 2015-2016 academic year as an Assistant Professor. His research interests are quantitative and systems-biology approaches to the ecology and evolution of microbial communities.