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.