There is no simple way to make a brain, even in a creature as small as a fruit fly. As an embryonic fly develops into adulthood, its central nervous system (CNS) expands almost 100-fold in mass. Neuronal, glial, immune, and vascular cells—in both the CNS and the peripheral nervous system (PNS)—must work in harmony to build the structures responsible for controlling movement and behavior. Since structure dictates function, the size and shape of the CNS must be tightly regulated, but the genes and pathways involved in the process have yet to be fully described.

In a recent study published in the September issue of G3: Genes|Genomes|Genetics, Lacin et al. use the power of forward genetics in Drosophila larvae to identify genes controlling nervous system shape. Using the robust genetic manipulation toolkit available in Drosophila, they further identify a glial subtype-specific molecular profile that functionally subdivides glia along the peripheral-central axis.

Their screen used the classic mutagenesis agent ethyl methanesulfonate (EMS) to randomly introduce mutations, generating more than 12,000 mutant lines that carried mutations specifically on the second chromosome. The authors screened for larval mutants with dramatically altered CNS shapes, sorting them into three categories: widened, elongated, or misshapen. Through a combination of genetic mapping, complementation analysis, and whole genome sequencing, they identified 50 mutant alleles across 17 genes that encode transcription factors, enzymes, signaling receptors, tumor suppressors, and basement membrane proteins.

Four of the mutant alleles were found in the senseless-2 (sens-2) gene, which encodes a zinc-finger domain transcription factor; these alleles caused massive elongation of the ventral nerve cord (the Drosophila equivalent to the spinal cord) that manifested very early in the first-instar larvae (see Figure 1). To understand the cellular basis for the mutant sens-2 CNS elongation phenotype, the authors generated an antibody against the Sens-2 protein and found it localized to most glia on peripheral nerves—but not in any CNS glial cells.

To determine whether sens-2’s role in determining ventral nerve cord length was specific to its presence in peripheral glia, the authors selectively knocked down its expression in those cells using the Gal4-UAS system. They found that sens-2 expression in peripheral glia is necessary to control CNS structure, and loss in those cells accounted for the observed elongation phenotype. Restoration of sens-2 expression rescued the elongation phenotype.

Lacin et al. were able to establish sens-2 as a marker distinguishing specific glial subtypes along the CNS-PNS axis with a profound impact on gross nervous system structure. In the future, the authors aim to investigate transcriptional targets of sens-2, which could help illuminate mechanisms governing glial development and differentiation in the PNS.

In recent years, the use of expensive -omics technologies to discover cellular heterogeneity at scale has become quite popular in neuroscience research, and the genes identified in these studies need validation and characterization. Here, Lacin et al. present a powerful demonstration that classical genetic studies in invertebrate model systems are still effective at powering neurogenetics and cellular heterogeneity research—at a fraction of the cost.

Biodegradation is currently the most eco-friendly approach to breaking down complex plastic into less harmful products. Luckily, a number of insects and microorganisms have the capability to digest plastic polymers, and several studies have shown that insect guts can biodegrade plastics faster than environmental microbes. To tackle the global—and mounting—plastic waste problem, researchers look to these critters in hopes of adapting their enzymatic capabilities into efficient systems that can degrade plastic waste at scale.

In a recent study published in the June issue of G3: Genes, Genomes, Genetics, Young et al. report an improved reference genome for the greater wax moth Galleria mellonella as a tool to identify enzymatic pathways with plastic biodegradation properties.

Well-known as a honeybee pest, greater wax moth larvae feed on beeswax, which contains long-chain hydrocarbons. Since long-chain hydrocarbons are also the major constituent in polyethylene (PE), researchers are quite interested in the enzymes responsible for beeswax degradation; in fact, the hexamerin and arylphorin proteins, found in larval saliva, have demonstrated PE-degrading abilities. Evidence suggesting wax moth larvae can degrade other plastics like polystyrene and polypropylene makes them attractive for plastic biodegradation research. The extent to which moth larvae possess plastic catabolizing enzymes is unclear; however, since both the larvae themselves and their gut microbiota have been implicated in PE biodegradation.

Since the existing reference genome for G. mellonella was fragmented, Young et al. combined short- and long-read sequencing approaches to generate a new assembly with improved continuity, identifying an additional 3,000 mRNA sequences. This new reference genome also supported phylogenetic comparisons with other Lepidoptera members such as moths, butterflies, and silkworms, allowing the authors to begin constructing an understanding of the evolutionary history of PE-degrading enzymes in winged insects.

Secreted proteins have a much better chance of playing a role in long-chain hydrocarbon degradation than intracellular proteins, so the authors investigated 3,865 proteins identified as secreted in their assembly, finding numerous hydrolases, transferases, oxidoreductases, ligases, lyases, and isomerases. They propose that these secretory enzymes, which may have evolved to catabolize a variety of exogenous and insoluble polymers, must also be capable of processing long-chain polymers like polyethylene. Several of the identified hydrolases and oxidoreductases are members of enzyme classes known to degrade plastic. They also found 135 hydrolases and 10 oxidoreductases that are predicted to act on ester bonds and peroxide, which may make them capable of breaking polyethylene. This genome is one of many sequenced by the Applied Genomics Initiative at the Commonwealth Scientific and Industrial Research Organisation in Australia. The initiative aims to sequence the genomes of a variety of organisms of interest to enable translational research in areas such as conservation, biosecurity, and health. The improved reference genome for the greater wax moth will continue to aid researchers in uncovering the molecular mechanisms behind its ability to degrade long-chain hydrocarbons; hopefully, these larvae can become a powerhouse for developing industrial and bioremediation applications in reducing plastic waste.

Genome-wide prediction and association studies offer a powerful approach to connecting genotype to phenotype at a large scale, but performing genomic analyses in humans invokes genomic privacy concerns that complicate the sharing of data. In a study published in the March issue of GENETICS, Zhao and colleagues expand an existing encryption approach, offering a secure avenue to perform genomic analysis without compromising confidentiality.

In whole-genome analysis, such as genomic prediction and genome-wide association studies (GWAS), researchers use statistical methods to compare genetic variants across many genomes to calculate genetic effects and estimate heritability. Linear mixed models allow testing for associations in both continuous traits, such as height, blood pressure, and body mass index, and binary phenotypes, such as disease status. Information about covariates like age, sex, and family origin is critical to assess confounding effects originating from demographic factors. In these cases, linear mixed model analysis helps account for genetic relatedness among individuals, which is necessary to strengthen statistical inference for discoveries made from the genomics data.

Because of the inherent privacy and intellectual property concerns, direct sharing of raw genotype and phenotype data is often prohibited, for example in human research; researchers first anonymize sensitive information like individual ID numbers, sex, disease status, family relations between individuals, and other covariates before performing any calculations.

So then, in a research landscape that values open-access data principles like FAIR (findable, accessible, interoperable, and reusable), how can population geneticists make their data widely available without compromising the privacy of the individuals in question?

Several data encryption approaches that obscure sensitive information have been developed; the homomorphic encryption method for genotype and phenotype (HEGP) methodology encrypts genotype, phenotype, and covariate data in a way that cannot be linked back to original identifiers, thus maintaining data privacy. However, the HEGP methodology has only been proposed for single-marker regression in GWAS using linear mixed models. Thus, Zhao et al. extended the HEGP methodology for wider application in genome-to-phenome analyses and demonstrated that HEGP can be effectively applied to many popular mixed models for genomic analyses of quantitative traits, beyond single-marker regression.

The authors used the HEGP scheme to perform linear mixed model analysis without the need for data decryption before the analysis. They successfully measured random effects originating from covariates that matched the original sample data.

They also demonstrated the HEGP method’s usefulness in analyzing genotype-phenotype characterization from multiple studies. In genomics, certain traits are difficult and expensive to measure, which often leads to studies with lower sample sizes. Researchers usually need to analyze multiple underpowered studies together to increase statistical power. Zhao et al. showed their HEGP expansion can combine multiple datasets for joint genomic analyses while preserving data confidentiality.

In conclusion, geneticists have an encryption method available for genomic analyses that allows them to perform necessary statistical analyses without disclosing sensitive information, thereby avoiding privacy concerns altogether. 

Falling in love with bacterial genetics

Marraffini was obsessed with space, astrophysics, and science fiction from a young age while growing up in Argentina. After reading about the advent and promise of recombinant DNA technology in a popular science magazine, his interest shifted toward biology. “During my undergraduate degree in biotechnology in Argentina, I did a lot of DNA manipulation and generated recombinant proteins. This experimental knowledge in molecular biology motivated me to follow a research path,” recollects Marraffini. Because the research opportunities were better in North America compared to Argentina, Marraffini uprooted his young family to pursue a PhD at the University of Chicago.

As part of the PhD curriculum, Marraffini recounts, “I took a class on bacterial pathogenesis and found molecular mechanisms by which bacteria cause diseases fascinating. I found bacteria a great experimental system because many tools were available to mutate and overexpress almost anything. There were also a lot of possibilities to purify proteins of interest using in vitro assays. This is why I fell in love with the bacterial experimental system and ended up joining the laboratory of the course teacher Olaf Schneewind for my PhD.” 

Dissecting CRISPR mechanisms in bacterial immunity

Bacteria are numerous but they are outnumbered by viruses that infect them. CRISPR-Cas is a major immune defense system that evolved in bacteria to fight viruses. Marraffini was interested in how bacteria employ CRISPR mechanisms to interact with and nullify infiltrating DNA and RNA. As a postdoc, Marraffini worked with Eric Sondheimer to experimentally demonstrate for the first time how CRISPR works against conjugative plasmids containing antibiotic resistance. “We showed that CRISPR can prevent the dissemination of antibiotic resistance among bacteria by directly targeting plasmid DNA,” explains Marraffini. This milestone in the CRISPR field was important later for gene editing technology development in mammalian cells. “I collaborated with Feng Zhang at the Massachusetts Institute of Technology. We transplanted a CRISPR-Cas9 system from Streptococcus pyogenes into human hepatocytes and showed that CRISPR cleaves DNA and can be repurposed for gene editing in cells,” shares Marraffini.

Over the years, Marraffini’s group gained mechanistic insights into how CRISPR systems contribute to bacterial immunity. When a phage or a plasmid invades bacteria, the CRISPR system captures a 30- to 40-nucleotides long sequence from the invader DNA called a spacer and incorporates it into the chromosome. This spacer DNA transcribed into the guide RNA gives Cas9—an enzyme that cuts DNA—the target specificity towards invading DNA. This is how bacteria acquire a memory of infection to then fight future infections.

Marraffini also discovered that phage DNA cleavage by Cas9 generates additional DNA fragments, resulting in the acquisition of new spacers for the CRISPR locus. More spacers and guide RNAs against the same-phage DNA are advantageous for bacteria as phages can escape Cas9 cleavage by mutating the target site, offering greater fitness to bacteria. According to Marraffini, “That’s one of our major contributions, showing how spacers acquisition determines infection memory. In addition, we also found that the CRISPR machinery uses free DNA ends, which is a way of diminishing autoimmunity since the bacterial chromosome is circular without a free end.”

Fostering curiosity and boldness

Joshua Modell, Assistant Professor of Molecular Biology and Genetics at Johns Hopkins University School of Medicine, describes his former postdoctoral mentor as “a rare scientist and an intellectual heavyweight who makes the laboratory a stimulating and fun place to do science.” Modell adds, “His ability to interact with and inspire scientists at any career stage, from the greenest summer intern to a long-tenured professor, is what makes him truly special. When I started my postdoc, he explained how much we still had to learn about CRISPR biology and how the work we do could end up in the textbooks. I still try to use that textbook standard with my trainees.”

“My mentors were extremely supportive of my interest in CRISPR despite CRISPR being unknown when I started my academic career,” says Marraffini. He champions the same generosity in his mentorship style, supporting projects his trainees want to pursue. 

“I wanted to investigate a new type of CRISPR that targeted RNA exclusively. No one understood how it worked. While everyone in the laboratory worked on Staphylococcus, I worked on a Listeria strain that naturally carried this RNA-targeting CRISPR system and developed it into a model system,” says Alex Meeske, Assistant Professor in the Department of Microbiology at the University of Washington, who did his postdoctoral training with Marraffini. “He encouraged me to be bold and try new methodologies, even if they were outside his expertise. He taught me to focus, keep my eyes on the prize, and investigate the most significant and testable questions.”

Join us in congratulating Luciano Marraffini, who received the Genetics Society of America Medal at The Allied Genetics Conference 2024 in Metro Washington, DC.

2024 GSA Awards Seminar Series

On September 9, at 1:00 p.m. EDT, Luciano Marraffini will join us to discuss CRISPR-CARF immunity and sacrificing the host for the benefit of the population. Save the date and register here!

Sejal Davla, PhD, is a neuroscientist, science writer, and data scientist with expertise in research in a variety of life sciences. She has more than a decade of experience studying the brain by using cutting-edge methodologies in microscopy, molecular biology, genetics, and biochemistry, and is a motivated storyteller and science communicator.

Parental chromosomes separate during meiosis and segregate into sex cells, like sperm or egg, transferring genetic information to the next generation. For successful inheritance to occur, chromosomes must communicate with each other to ensure they remain intact throughout the process. Ofer Rog, who is Associate Professor of Biological Sciences at the University of Utah, employed cutting-edge genetics and high-resolution microscopy to probe local and chromosome-wide physical changes during meiosis to understand their function in chromosome inheritance.

Unraveling chromosome biology  

Rog considers himself privileged to be doing science. Since he started college, he was surrounded by people who were doing research, allowing him to envision a career in academia. “I had crucial connections that helped me land a PhD position in a top-notch research institute in the UK,” says Rog. Since then, Rog has been dedicated to understanding chromosome biology. 

As a PhD student in Julie Cooper’s laboratory at the University College London, Rog showed that a DNA-binding protein is required for replication forks to pass through telomeres. This was a dogma-shattering observation since the prevailing view was that DNA-binding proteins are barriers to replication. Continuing his work in chromosome biology as a postdoc with Abby Dernburg at the University of California, Berkeley, Rog embraced cell biological approaches and dissected molecular mechanisms of chromosome interactions. He first developed tools for high-resolution live imaging of chromosome dynamics in C. elegans and visualized the structure-function relationship between protein complexes that latch onto chromosomes. He provided the first direct observation of a protein network assembly onto parental chromosomes, where many proteins form a railroad-like zipper structure between parental (homologous) chromosomes to regulate exchanges during sexual reproduction. He further discovered that this structure is not static and rigid, as was widely assumed based on electron microscopy images, but rather a liquid-like dynamic compartment.

“Rog developed a cytological method to measure exchanges between sister chromatids in meiosis using pulse-chase experiments. Before his work, exchanges between sister chromatids were effectively invisible since sister chromatids are genetically identical,” explains Lisa Kursel, a Research Assistant Professor working in Rog’s laboratory at the University of Utah.

Launching his independent research group on the back of these remarkable discoveries, Rog now investigates the broader implications of the liquid-like state of the chromosomal-protein complex structure on genetic exchanges during meiosis and on cellular health. “We are interested in why the structure of the protein-chromosome complex behaves as a liquid. We hypothesize that the structure allows communication between different molecules in a very controlled way where the molecular signal diffuses inside a compartment instead of spreading to all directions at once. We are also interested in how this liquid structure can bring and hold chromosomes together to exert force on the genome and shape it into chromosomes,” says Rog. He is now combining powerful stimulated emission depletion (STED) microscopy and cryogenic electron tomography to look at molecular structures and how they manifest in the complex organization of chromosomes.

A terrific role model with a passion for science communication

Rog is the first openly gay faculty in the College of Science at the University of Utah, and he deeply values inclusion. “It is important to have visibility and have everyone’s voices heard. I have made sure to provide space for members of the LGBTQ community,” he shares. Rog used his position and influence to create changes within his research community, founding an LGBTQ+ STEM group at the University of Utah where he invites LGBTQ+ speakers to campus and discusses their inspiring research journey with students. Rog is also advocating for diversifying science along other axes as an early career researcher. “I think we currently have a lot of walls, such as people coming into a biology PhD from a non-R01 university or non-western countries. We want to hear how people in leadership positions can make science inclusive and bring down walls in the scientific community,” says Rog.

Lisa Kursel describes Rog as an excellent teacher and mentor. “His teaching and mentoring style is welcoming and inclusive. He manages to get undergraduate students excited about genetics. My undergrad mentee told me his dream is to become a genetics professor because of Rog’s influence,” says Kursel. Rog is also deeply involved in the graduate program, where he serves as an advisor on the graduate program committee.

Another of Rog’s passions is to improve science communication. As far as his research is concerned, he believes that the tools to communicate the dynamic chromosome movement are limited. “Anything you draw will look like two separate things and will not convey the dynamic nature. Static images also fail to convey that the molecules are constantly rearranging during sexual reproduction,” he explains. In coordination with Janet Iwasa, a molecular animator and Assistant Professor in the Department of Biochemistry at the University of Utah, Rog organized a conference bringing together scientists and experts in visualization technologies, such as animators, illustrators, and developers to build virtual reality platforms that communicate his work on dynamic chromosome biology. He also created an intensive fellowship writing course for graduate students to address an unmet need in formal training for science writing.

Join us in congratulating Ofer Rog, who received the Genetics Society of America Early Career Medal at The Allied Genetics Conference 2024 in Metro Washington, DC.

2024 GSA Awards Seminar Series

In a recent seminar, Ofer Rog joined us to discuss two unpublished stories from his lab–the first documenting the unexpected de-mixing of sister chromatids during meiotic prophase and the mechanisms that mediate it, and the second describing a new genomic technique his lab developed to characterize large-scale chromatin organization and its application to meiotic chromosomes. Watch the recording here!

Sejal Davla, PhD, is a neuroscientist, science writer, and data scientist with expertise in research in a variety of life sciences. She has more than a decade of experience studying the brain by using cutting-edge methodologies in microscopy, molecular biology, genetics, and biochemistry, and is a motivated storyteller and science communicator.

“How do genes control physical, behavioral, and disease traits?” is a perennial question for geneticist Elaine Ostrander, Chief and Distinguished Senior Investigator of the Cancer Genetics and Comparative Genomics Branch at the National Human Genome Research Institute of the National Institutes of Health and Section Head of Comparative Genetics. Ostrander, who is known for her seminal discoveries in trait heritability in dogs and humans, tracked the history of dog breeds to address questions in morphology, behavior, and disease variation. She also mapped important cancer genes in canines and humans, advancing the knowledge of how complex diseases are inherited. 

Developing a canine genetic model from scratch

Ostrander started her scientific journey by investigating the relationship between the DNA structure and transcription in yeast during her PhD and postdoctoral years. Learning about the discovery of microsatellites steered her into mammalian research. “It became immediately clear that microsatellites were polymorphic in a population that they were useful for studying variation, but they were also stable enough to track inheritance of sections of DNA within a family. Suddenly, it became possible to make a genetic map of any mammal you cared about,” she recalls.

For Ostrander and Jasper Rine, that choice of mammal was a dog. While other scientists studying genetics were mapping genes in flies, worms, yeast, and humans, Ostrander, working in Jasper Rine’s research group at the University of California, Berkeley, began to construct a genetic map of the dog genome, with a long-term goal of using the map to find genes that distinguish breed appearance and behavior as well as genes associated with disease susceptibility. Continuing this work in her own research group at Fred Hutchinson Cancer Center, Ostrander created the first linkage maps in dogs in the early 90s. A decade later, her foundational work snowballed into a modern canine genetics project establishing dogs as a genetic model system. “Ostrander’s work built the stage and collected, in collaboration with several institutions, the first whole genome sequence of a domestic dog, the Boxer, in 2005. The subsequent decade was populated by an explosion of publications and genome developments led by her research group and collaborators,” says Bridgett vonHoldt, Associate Professor of Ecology and Evolutionary Biology at Princeton University and a long-time collaborator of Ostrander.

According to Leonid Kruglyak, Professor of Human Genetics and Biological Chemistry at the University of California, Los Angeles and Howard Hughes Medical Institute Investigator who nominated Ostrander for this honor, “Ostrander is without a doubt the leader in the field of canine genetics and genomics.” Leading an international consortium, Ostrander helped generate a global public repository consisting of genomes from 2,000 individual canids—including 1,611 dogs of known breeds (321 breeds), 309 village dogs, 63 wolves, and 4 coyotes—to address questions surrounding domestication, behavior, morphology, and disease susceptibility.

“Dogs were an obvious choice because the dog breed structure makes it easier to find genes responsible for traits. To be a member of a breed, parents and grandparents must be members of the same breed, making each breed a closed population,” explains Ostrander. Tapping into breed structure, where breed appearance and behavior remain intact generation after generation, Ostrander’s group identified genes responsible for the remarkable differences in size and shape between breeds. Her work showed that a single allele of IGF-1 is a major determinant of size in small breeds and that coat variation is determined by variants in just three genes. By identifying the time when variants first showed up in ancient DNA, her work takes a holistic view of morphology and behavior across different canid species.

Studying man’s best friend to understand humans

In addition to genes in dogs, Ostrander extensively studied human cancer genes in her laboratory at the Fred Hutchinson Cancer Research Center, focusing on human breast and prostate cancer. Her group was one of the first to describe a role for BRCA1 and BRCA2 mutations in women from the general population at risk for breast and ovarian cancer. Her expertise in dog genetics dovetailed well with this work, as she ended up discovering cancer-causing DNA variants in both humans and dogs. “Most things that dogs get, humans also get—they get the same cancers and diabetes; they also get many of the same neuromuscular, kidney and heart diseases. Some breeds are at an extraordinary risk for certain types of cancer. For instance, a Scottish Terrier is at 20-fold higher risk of getting bladder cancer than any mixed breed dog. Therefore, the underlying genetics must be really strong and profound,” explains Ostrander.

In an effort to explore the history between the dog and cancer genomes, her group used a multi-omics approach that was largely unexplored in the canine model to create the largest catalog of canine whole-genome, transcriptome, and chromatin immunoprecipitation sequencing. Such resources allow scientists today to identify common cancer-causing alleles in dog breeds and link them to human malignancies. For example, Ostrander identified two regions in the canine genome that explain a risk for developing a lethal histiocytic sarcoma, which also occurs in humans. By understanding genes in these risk regions in cancer-related pathways, her work empowered new diagnostics and therapeutic strategies for human cancers.

Ostrander’s group also studies aging and survival-related genes. “Big dogs do not live as long as little dogs. We would like to know why that happens,” she says. To solve this puzzle, Ostrander collaborated with international researchers looking for dog samples in the most unlikely places. “We are studying DNA samples from over 400 dogs, sampled by collaborators, from the exclusion zone around the Chernobyl nuclear power plant. We are looking for changes in DNA that dogs have accumulated over 15 generations which allows them to survive in this radioactive environment,” says Ostrander.  

A champion in all walks of life

Ostrander has contributed greatly to the scientific community through making her cutting-edge research in dog genetics accessible to the general public. A big proponent of community outreach, she takes pride in regularly engaging with dog groups, breed clubs, professional dog trainers’ associations, and families to help answer questions about behavior and diseases.

In addition to being a pioneer in science, Ostrander is also at the top of her game in powerlifting. She is a nationally ranked powerlifter, competing as a Masters lifter for five years. With a growing accumulation of first- and second-place medals, Ostrander looks forward to a time when she trains Masters lifters herself.  

Join us in congratulating Elaine Ostrander, who received the Edward Novitski Prize at The Allied Genetics Conference 2024 in Metro Washington, DC.

2024 GSA Awards Seminar Series

In a recent seminar, Elaine Ostrander discussed how domestic dogs are among the most variable mammalian land-based species on earth and the genetic underpinnings of that variation, including breed-associated morphology, behavior, and disease susceptibility. Watch the recording here.

Sejal Davla, PhD, is a neuroscientist, science writer, and data scientist with expertise in research in a variety of life sciences. She has more than a decade of experience studying the brain by using cutting-edge methodologies in microscopy, molecular biology, genetics, and biochemistry, and is a motivated storyteller and science communicator.

Build-a-Genome (BAG) course 

Boeke studied transposable elements in yeast and mammalian cells. Along the way, he decided to synthesize transposon DNA from scratch. “I was impressed with the power of being able to do that, which led me to synthesize first a synthetic chromosome arm and eventually the entire yeast genome with people around the world,” he describes. Using this first synthetic eukaryotic genome project, Boeke developed a unique laboratory component for his class that allowed students to contribute to this mammoth research endeavor.

“We built the genome from scratch, starting with oligonucleotides to entire genomes worth of synthetic chromosomes, piece by piece. In the early phases, we involved a lot of undergraduate students,” he explains. For Boeke, the course had two essential components. “One was to use the manpower needed to build such an enormous genome. The other was that it’s a fantastic way to teach molecular biology and genetics to undergraduate students, for whom it was new. They were doing original research as part of a course, learning about how to do a PCR reaction,” he shares. Because students were synthesizing genome fragments that were never created before, they faced several setbacks and performed extensive troubleshooting. This integral component of the course provided an authentic research experience to students.

Eventually, the course evolved as the technologies advanced. In the early years, students would generate 750 base pairs (bp) of synthetic fragments using PCR reactions on overlapping oligos. They would run gels to get clean bands and regularly present their observations in lab meetings. However, as the cost of synthesizing synthetic DNA fragments rapidly decreased, the course shifted from fundamental molecular biology in E. coli to yeast genetics. “The students started assembling medium-sized DNA pieces into bigger pieces using homologous recombination in yeast. After successfully running the course for 20 years and using work from undergraduate students, they are now helping combine sixteen fully man-made synthetic chromosomes and put them into a single strain,” says Boeke.

“Running the course wasn’t always easy,” describes Patrick Cai, Professor of Synthetic Genomics at the Manchester Institute of Biotechnology and former course instructor. “Boeke was running the course on a very limited budget, so we did a lot of work ourselves. One night, he drove his pickup truck and two of us moved all the chairs across the campus to a new course location. He was that dedicated and serious about the course,” says Cai.

With Boeke’s steadfast commitment and exceptional planning, the course eventually culminated in a global research and teaching consortium. Researchers from across the globe came to Boeke’s laboratory and learned teaching modules to build their parallel courses. “For example, Yingjin Yuan, Professor of Biochemical Engineering at Tianjin University, came to us and we helped him set up this course in China. He and colleagues focused on turning the course into a production machine and developed a landmark project by finishing one whole synthetic yeast chromosome in just a year,” says Boeke.

Teaching how to teach

Boeke involved his graduate students and postdoctoral researchers in teaching the course. According to Lisa Scheifele, Associate Professor in the Department of Biology at Loyola University Maryland, “The number of postdoctoral fellows and graduate students who have been empowered to learn the art of teaching, mentoring students, and developing course structure and content is notable and impressive.” She adds, “Boeke has been incredibly supportive of trainees who wanted to include a significant teaching aspect in their future careers. The Build-a-Genome course was my first teaching experience that ‘lit the fire’ for a future career where I’ve been able to blend teaching and cutting-edge research as we have done in Build-a-Genome.” Plus, the fact that this course inspired several of Boeke’s trainees in pivoting to a teaching career is something he’s quite proud of.

Harnessing the power of designer yeast

The synthetic yeast genome built through this innovative laboratory course offered a major paradigm shift in genetics and biotechnology, showcasing how to design and assemble synthetic DNA at scale. These synthetic chromosomes further facilitate testing genome fundamentals traditionally difficult to dissect in laboratory yeast strains. “Our knowledge about yeast genetics is largely based on our observation of the natural yeast genomes, which sometimes can be difficult to study. The synthetic yeast genome allows us to engineer the genomes to address societal challenges,” explains Cai. For example, Boeke made a bold choice to remove all the tRNA genes from the synthetic chromosomes and put them all on a new chromosome, allowing researchers to engineer it independently of all the other chromosomes. Now, Cai is testing yeast strains with tRNAs adapted to human codon usage to better express human proteins that can in turn be used in therapeutic applications to increase product yield.

Join us in congratulating Jef Boeke, who received the Elizabeth W. Jones Award for Excellence in Education, on behalf of Build-A-Genome, at The Allied Genetics Conference 2024 in Metro Washington, DC. And congratulations to the Build-a-Genome team whose members include Jessica Dymond of In-Q-Tel; Lisa Z. Scheifele of Loyola University Maryland; Eric Cooper of Hartwick College; Robert Newman of North Carolina Agricultural and Technical State University; Franziska Sandmeier of Colorado State University, Pueblo; Yu (Jeremy) Zhao of NYU Langone Health; Stephanie Lauer of St. Thomas Aquinas College; and Raquel Ordoñez of NYU Langone Health.

2024 GSA Awards Seminar Series

In a recent seminar, Jef Boeke, who received this award on behalf of Build-a-Genome, described how the course teaches students fundamental principles of genetics and how to perform, interpret, and troubleshoot an experiment when the outcome is unknown. He also touched on the history of the course and the resultant Network of Build-a-Genome courses, how it has affected students and instructors, and the course’s impact on the overarching International Sc2.0 project. Watch the recording here.

Sejal Davla, PhD, is a neuroscientist, science writer, and data scientist with expertise in research in a variety of life sciences. She has more than a decade of experience studying the brain by using cutting-edge methodologies in microscopy, molecular biology, genetics, and biochemistry, and is a motivated storyteller and science communicator.

Just like Thomas Hunt Morgan, Paul Sternberg’s scientific legacy dominates many fields of biology, including embryology, evolution, genetics, neuroscience, and systems biology. Sternberg, who is Professor of Biology at California Institute of Technology and Investigator Emeriti at Howard Hughes Medical Institute, studied parasitic nematode worms to make important discoveries in comparative development across different worm species and their behavior. 

Unraveling fundamentals of worm biology

During his undergraduate studies, Sternberg wasn’t particularly interested in science, but classes in quantum mechanics and microbiology attracted him to logic and exploration. He enrolled in mathematics and economics with the hope of applying relevant lessons to complex systems, but “…then I realized you can’t really do experiments in economics. I thought there is an interesting complexity in biology too, so I chose biology,” says Sternberg. As an undergraduate, Sternberg was looking at cell cycle control in slime molds. “By the time I was a graduate student, the worm appealed to me, and I wanted to understand everything about the organism. That is the goal,” he shares enthusiastically.

During his PhD, Sternberg contributed to groundbreaking work in the evolution of cellular lineages and developmental mechanisms for the induction and patterning of worm vulva. “When he was a student, his interest in the evolution of development was way ahead of his time. In the cell lineage paper by John Sulston and colleagues that reported the first comprehensive embryonic lineage analysis in 1983, they cited papers from Sternberg as a student in the Horvitz laboratory, identifying evolutionary changes in nematode cell lineages and cell fate. While Horvitz and Sulston received the Nobel Prize for their lineage work, Sternberg was also dissecting lineages in another genus and investigating how lineages would evolve. In that sense, he was prescient and visionary,” says Ryan Baugh who did his Postdoctoral training with Sternberg and is now a Professor of Biology at Duke University. 

Continuing the vulva development paradigm in his independent research group, Sternberg cloned and mapped numerous receptors and ligands, determining their functions in the signal transduction pathway. This pioneering work is taught today in introductory genetics and developmental biology courses to illustrate intercellular signaling, transcriptional regulation, and genetic epistasis mechanisms in coordinated organ development. Additionally, his students showed the importance of vulva development genes in the male mating structure called hook formation, further demonstrating conserved gene function in different organ patterning.

Sternberg also solved the mystery of the chemotaxis of males to the hermaphrodites, which many believed had no specificity. “People would say, male worms mate with chunks of agar. We looked at different species and found specificity. Hermaphrodites in a conditioned media would give pheromone signals that the males would respond to,” explains Sternberg. He collaborated with chemists to assess the chemical nature of purified mating attractants and discovered nematode-specific chemicals called ascarosides. Over the years, he made discoveries surrounding how males sensed ascarosides and nutrients in their environment to determine whether they should reproduce or wait. Using transcriptomics and CRISPR to knock out multiple genes, he continues to identify neuronal signaling in the pheromone sensing process.

In his quest to understand the worm, Sternberg studied multiple nematode species. His major interest is identifying lineage differences in species different from C. elegans, a commonly studied worm species. “We collected a lot of nematodes from soil and worked with a professional taxonomist, who figured out whether they are a diverse set of worms. Over the years, my students performed numerous comparative developmental analyses and started their research programs,” says Sternberg. 

Behavioral genetics is another field where Sternberg has made a huge impact. “What is the most complicated thing the worm does in the neuroscience sphere? The male mating behavior seemed pretty complicated to me,” shares Sternberg on how he focused his research. Sternberg’s student ablated each male-specific neuron using the knowledge from lineage maps and identified neuron-specific mating behavior defects. Observations from male mating behavior led him to investigate complex behavior like sleep, where he discovered several neuropeptides and signaling molecules controlling sleep in worms. To further strengthen the idea of sleep in invertebrate model organisms, Sternberg says, “I thought to push the defensive perimeter out in phylogenetic evolution in some primitive organisms. We studied jellyfish and found sleep-like states in them.”

According to Baugh, “It is really impressive that he went into neuroscience and behavior in addition to the evolution and development and trained important leaders in that field. I am seeing whole swaths of biology that are monumental as most people would hope to accomplish in their careers. He has just done it many times over.”

A community builder and a problem solver

Sternberg is also a visionary when it comes to building a scientific community and solving problems related to resource sharing and knowledge dissemination as well as developing new tools. “He sees a problem, and he fixes it,” says Maureen Barr, Professor in the Department of Genetics at Rutgers University, who did her postdoctoral research with Sternberg. “The C. elegans genome database was difficult and frustrating to navigate. Sternberg wanted to fix it, so he made WormBase. There are just too many papers – it’s not humanly possible to read them all, so he made Textpresso, which provides detailed information based on a few keywords. There are negative results in science that others might be interested in knowing, so he created microPublication where researchers can publish brief, novel findings and negative results that may not fit a traditional research article,” says Barr. Sternberg actively runs and supports these irreplaceable tools that make science accessible.  

Join us in congratulating Paul Sternberg, who received the Thomas Hunt Morgan Medal at The Allied Genetics Conference 2024 in Metro Washington, DC.

2024 GSA Awards Seminar Series

On July 30, at 1:00 p.m. EDT, Paul Sternberg will join us to describe how C. elegans as an extensively-studied research organism holds out the promise of achieving comprehensive understanding of an organism. He will also discuss the status of our knowledge of how a genome sequence specifies the properties of an organism in the context of state-of-the-art technology and cool biology. Save the date and register here!

Sejal Davla, PhD, is a neuroscientist, science writer, and data scientist with expertise in research in a variety of life sciences. She has more than a decade of experience studying the brain by using cutting-edge methodologies in microscopy, molecular biology, genetics, and biochemistry, and is a motivated storyteller and science communicator.

Deborah Andrew’s journey from a first-generation college student to a leader in fruit fly genetics is nothing short of inspiring. She began her undergraduate studies in freshwater ecology; during that time, she took a genetics class taught by fruit fly geneticist David Kuhn that changed the course of her career. She worked in fruit fly genetics laboratories throughout her academic training to understand the role of homeotic genes in organ formation. Andrew, now the Bayard Halsted Professor of Cell Biology at the Johns Hopkins University School of Medicine, is still dedicated to studying organogenesis, particularly in uncovering genetic mechanisms governing tubular structures in Drosophila.

Mapping tubular structures from birth to morphogenesis

“I have always been interested in the questions about how a relatively nondescript fertilized egg turns into the multitude of specialized cell types found in the mature organism. Interested in organ formation, I began addressing the following questions: How is organ fate specified? How do organs specialize? How do they achieve their normal morphologies?” explains Andrew. Harnessing the power of genetic tractability in Drosophila, her pioneering work addressed fundamental mysteries in the salivary gland (digestive system) and trachea (respiratory system) development.

Andrew’s group made considerable strides toward understanding how an organ develops in its primordial state and achieves a final functional morphology by identifying the major transcription factors that control these processes at different stages of embryonic development. The major regulators of organ specification and function are known for only a small handful of organs in even fewer organisms. Remarkably, Andrew’s work identified major regulatory genes for salivary gland and trachea development and their interactions with downstream target genes. 

The salivary gland contains specialized cells with very high levels of secretion. The discovery of a conserved bZip-family transcription factor CrebA as the major regulator of increased secretory capacity is one of the most important findings from Andrew’s research group. “CrebA upregulates nearly all secretory pathway component genes, including genes encoding the protein components of the ER, Golgi, and secretory vesicles, as well as the genes that encode the proteins that transport nascent polypeptides to secretory organelles. This single transcription factor—CrebA—upregulates all of those,” emphasizes Andrew.

From fundamental biology to a direct impact on human health

Discovering conserved positive regulators of tube formation and secretion processes, Andrew’s work showed tremendous potential in developing artificial salivary glands and conferring secretory abilities to non-secretory cells. Her lab showed that each of the five human orthologues of CrebA could also induce the expression of secretory pathway component genes in fly embryos, highlighting the functional conservation of this gene family. Indeed, by expressing the closest mammalian ortholog of CrebA in HeLa cells, her group showed a similar upregulation in human secretory pathway gene expression. Such strategies could help ramp up the production of secretory products in biotherapeutic applications.

Andrew used her expertise in the Drosophila salivary gland to study the orthologous structure in Anopheles mosquitoes. The malaria-causing parasite Plasmodium migrates to the salivary gland ready to be injected into the vertebrate host at the time of feeding. Her group identified another transcription factor Sage that expresses only in the salivary gland. When knocked out from the Drosophila salivary gland cells, cells die massively via apoptosis. Now, her lab is using CRISPR technology to knockdown Sage from mosquito salivary glands in the hope of achieving cell death. “Moreover, Andrew has shown that the polarized architecture of the salivary gland acts as a natural barrier for parasite transmission. This line of investigation is likely to generate new targets for transmission-blocking strategies,” says Geraldine Seydoux, Professor of Molecular Biology and Genetics at Johns Hopkins University and long-time colleague and collaborator of Andrew.

A beloved mentor and community leader

Throughout her career at the Johns Hopkins School of Medicine, Andrew considered herself privileged to work with young scientists, and her trainees returned the feeling. Andrew’s former trainee Caitlin Hanlon described her as an incredible mentor who always showed confidence in what her trainees could achieve. “Her dedication to helping train people and showing up for them created a wonderful and meaningful work culture not just in the laboratory but also in the department,” says Hanlon, who is now an Associate Professor at Quinnipiac University. Andrew also contributed to teaching efforts at Johns Hopkins. She dedicated countless hours teaching medical and graduate students the fundamentals of cell biology and physiology, keenly elucidating how things really work at the basic level in any cell. 

In addition to being a leader in her research field, Andrew generously offered her time and expertise to build fly genetics and development biology communities. She served as a representative to the Drosophila Board (“Fly Board”) from 1996 to 1999, as treasurer from 2013 to 2016, and president in 2017. She has organized major conferences over the years, including the Annual Drosophila Research Conference, the Santa Cruz Developmental Biology Meeting, and a Gordon Research Conference. She has been a long-term member of the Drosophila Genetics Resource Center Advisory Board.

Beyond her exemplary research and community work, Andrew is a fierce advocate of fundamental research and the fruit fly model system. “I would like more people to enter the Drosophila field. While we can do so many things in other systems, such as humans and mice, I strongly believe you get more bang for your buck in fly research,” emphasizes Andrew for scientists in training, encouraging them with a firm belief that what can be discovered in flies cannot easily be discovered anywhere else.

Join us in congratulating Deborah Andrew, who received the George W. Beadle Award at The Allied Genetics Conference 2024 in Metro Washington, DC.

2024 GSA Awards Seminar Series

In the first installment of the 2024 GSA Awards seminar series, Deborah Andrew described her lab’s findings on how the Drosophila salivary gland is first specified and maintained, and how early and continuously expressed transcription factors control both secretory capacity and specificity. She also shared recent efforts using genome-wide approaches to discover how functional enhancers of downstream target genes are organized. Watch the recording here!

Sejal Davla, PhD, is a neuroscientist, science writer, and data scientist with expertise in research in a variety of life sciences. She has more than a decade of experience studying the brain by using cutting-edge methodologies in microscopy, molecular biology, genetics, and biochemistry, and is a motivated storyteller and science communicator.