A new associate editor is joining GENETICS. We’re excited to welcome Xin Li to the editorial team.

Xin Li
Associate Editor

Xin Li is the Qiushi Distinguished Professor at Zhejiang University and serves as the Executive Director of the Center for RNA Medicine. He completed his undergraduate studies at Tsinghua University in the Department of Biological Sciences and Technology, followed by a PhD from Cornell University under the mentorship of John Schimenti and Bik Tye. His postdoctoral training was conducted at the RNA Therapy Institute at University of Massachusetts Medical School/Howard Hughes Medical Institute with Phillip Zamore and Melissa Moore. Prior to his return to China, he held positions as Assistant Professor and Associate Professor at the RNA Center of the University of Rochester. Throughout his career, Professor Li has been the recipient of numerous prestigious awards recognizing his contributions to the field. These include the Liu Memorial Award, the Hsien Wu and Daisy Yen Wu Scholarship, the Lalor Foundation Postdoctoral Fellowship, the Jane Coffin Childs Memorial Foundation for Medical Research Fellowship, the NIH Pathway to Independence Award, the AFRI Award, the MIRA, the Kun Peng Award, and the Zhejiang Talent Award.

The primary objective of the Li Lab is to elucidate the regulatory mechanisms governing the fate of cytoplasmic RNA. This includes why some RNA molecules in the cell last longer and are more active than others, and why the same RNA can behave differently in different types of cells. These variations play a pivotal role in molecular mechanism underlying development and pathogenesis and the conceptualization of RNA-targeted pharmacological interventions.

Employing an integrative methodology that combines wet lab techniques with in silico (dry lab) analysis and comparative genomic studies across a spectrum of animal models, the Li Lab seeks to decode the cell-specific principles underlying cytosolic RNA translation and degradation. The ultimate goal is to harness these insights for the innovation of RNA-based therapeutic modalities.

In the Paths to Science Policy series, we talk to individuals who have a passion for science policy and are active in advocacy through their various roles and careers. The series aims to inform and guide early career scientists interested in science policy. This series is brought to you by the GSA Early Career Scientist Policy and Advocacy Subcommittee.

Today, as part of the ECLP Policy and Advocacy Interview Series, I’m with Maria Elena Bottazzi, current Senior Associate Dean of the National School of Tropical Medicine at Baylor College of Medicine.

Could you tell us a little bit more about your career path and your current work at Baylor?

I am an Italian-born, Honduran-raised microbiologist. I received a microbiology and clinical chemistry degree from the National Autonomous University of Honduras. In Honduras, as is the case with most Latin American countries and other low-middle income settings, training at the bachelor’s-in-science level rarely involves experience within molecular biology. So, in order to further understand the molecular and biochemical basis of host-pathogen interactions, I moved to the United States to complete my PhD at the University of Florida, [studying the] molecular basis of pathogenic disease. As I was completing my postdoctoral work at University of Pennsylvania, I realized that my true calling was using all I have learned in the biomedical field to create solutions and develop new interventions for tropical and emerging diseases. So, I decided to enroll in a Master of Business Administration program to hone my business management and organizational skills. Shortly after, I met Peter Hotez (the current Dean of the National School of Tropical Medicine) and realized we were both interested in the same goal: developing global health technologies and translating them from the academic laboratory to the world. We have since worked together with an emphasis on vaccine development and accessibility for developing countries and for diseases that are typically ignored.

You have worked with vaccines and neglected tropical diseases for a while. What has been your own level of involvement in the policy area around these issues? Do you have any advice for young scientists interested in science policy?   

I have been around tropical diseases my whole life. Growing up in Honduras and studying microbiology there, I have always been observing the devastating effects they have on people. But to be fair, my interest peaked around the time I was finishing my higher education. This coincided with the turn of the century, when there was a re-emerging interest in global and tropical health. As I started my professional career, I saw all these policy frameworks being developed around poverty, hunger, education, and other health factors. Yet, as I moved forward with my scientific path, we started seeing how several diseases were being ignored, especially those that affected only tropical countries. I found myself part of a drive towards open science and creating partnerships and collaborations that would make research in tropical diseases accessible and transparent. Very early on, Peter Hotez and I realized that we needed to go beyond the bench: we had to be capable of developing robust products, like vaccines, that would be able to directly help people. Besides our scientific language, we also had to learn policy, business, ethics, and legal languages to serve the community in the best way possible. As scientists, it is difficult to be properly trained on these other dimensions: you are usually focused on the science and presentation skills. Peter Hotez was a great role model for me. He was really interested in the behind-the-scenes of policy making, so I ended up tagging along for the ride. Eventually, I realized I was very interested in scientific policy, so I applied to and got selected for a fellowship with the Leshner Leadership Institute in the American Association for the Advancement of Science. There I got formal training on how to integrate academic sciences and business practices. It is not all about the formal training, however. During my personal time, I also took several courses and met with different people to learn more about pharmaceutical economics, licensing and intellectual property laws, and even how to write legal contracts. This is something I recommend to every early career scientist: make sure that you take advantage of all the resources out there. Branch out from your bench, and learn about things that will help you engage the community and your own science in a much more efficient way! In the real world, you are always surrounded by so many more things than just your science. Always try a holistic approach when it comes to preparing your own career path.

You and Peter Hotez developed a COVID vaccine. Can you tell us more about it and how any regulations impacted your work?

As Peter and I started working on neglected tropical disease vaccine programs, we realized a pattern: funding for these programs dramatically increases when the disease emerges, but then it rapidly decreases as other priorities arise. We decided to take advantage of all the knowledge created during the “golden years” of funding for these rare diseases, and in 2011, we were awarded a grant to tackle a Severe Acute Respiratory Syndrome (SARS) vaccine in case of future outbreaks. Between 2011–2014, we were incredibly successful: we developed and manufactured a candidate for a SARS vaccine and were close to moving into human trials. Then, the 2015 Middle Eastern Respiratory Syndrome (MERS) outbreak happened; the NIH asked us to use the rest of the funding to develop a MERS vaccine instead of moving the SARS vaccine into toxicology trials. By the end of 2016, we had already come up with a prototype vaccine for SARS and for MERS as well; we were ready to start a pathway towards the clinic for these vaccines. Then, suddenly, coronaviruses were not that important anymore; our direct funding for these vaccines stopped as the agencies believed they had other diseases to deal with at that point. Internally, we decided to keep the program alive with some intramural money so all the scientific knowledge wouldn’t be wasted.  

To our surprise, the 2020 pandemic was being caused by a coronavirus family virus with a sequence similar to the SARS virus: we were ready to hit the ground running! Instead of 4 years, it only took us a few months to figure out the COVID-19 prototype vaccine. Since the world was in a state of urgency, we decided to not patent our COVID-19 vaccine technology and offered it as open source for manufacturing to different companies. Sadly, no company in the US or Europe was interested. This was mainly due to both scientific and policy misunderstandings. Our vaccine was based on the spike protein’s receptor binding domain and was produced in yeast, so it was easily scalable. At the time, both pharmaceutical companies and policy makers worked under the false assumption that the whole spike protein must be used, and they would rather fund new technologies such as mRNA-based vaccines because of their perceived speed to develop although they were not nearly as scalable at that time. Although we had pre-clinical trial data proving the high efficiency of our vaccine prototype, big pharmaceutical companies had no interest in it due to both policy and scientific mishaps. Eventually, we received interest from companies in India and Indonesia since they were having a hard time getting access to the mRNA vaccine technologies. These manufacturers shared our same vision to make scalable, affordable, and equitable vaccines for the public. We now have administered more than 100 million doses, making our vaccine one of the most accessible ones out there. Thankfully, we were able to surpass initial hurdles and make the vaccine accessible to those who needed it the most.

As a vaccine expert, do you think we are prepared for the next pandemic? What do you think needs to change regarding current vaccine policies?

One of the main issues during this pandemic was how countries with lots of resources decided to over-stock vaccine doses and disregard the needs of other countries. Nationalism plays a big part in this; everyone wants what is best for their own people first. Yet, as we clearly saw with the failed response to this pandemic, this is not the correct way to go about public health. Even if you vaccinate all your citizens, you will still suffer the downsides of a pandemic if your neighbors and trade partners cannot do the same. We learned the hard way that to get completely out of a pandemic, we need the whole world to work together and help each other.  

I think we learned a lot during this pandemic that will be useful in the future. For example, regulators around the world realized that many steps of the process could be done in parallel instead of sequentially, so we now know that the pipeline to create and manufacture vaccines, or other drugs, can be shorter and more efficient. Yet, we still face a terrible monster: inequality. With high-income countries overstocking vaccine doses, many low-income countries were left without the opportunity to order vaccines. Even after some countries started donating doses for children and senior adults, many low-income countries had their whole health system collapse due to how long it took to access vaccines. In the long run, this deeply affected high-income countries since the world was not able to truly go “back to normal” until most countries had regained control over their health systems. By not making vaccines equitable, we kind of shot ourselves in the foot and prolonged the pandemic far beyond what it could have been if we had made vaccines readily accessible to everyone since the beginning. We learned some lessons from this pandemic; however, we still have much work to do if we want to be prepared for another one. It is not only vaccine accessibility that needs to be more equitable but also vaccine research and regulation. There is a common belief that anything that is manufactured in middle- or low-income countries is, by default, of poor or dubious quality. If we want to be ready, we need to trash that old mentality. Worldwide regulators, like the World Health Organization, should work harder to improve vaccine research, manufacturing, and regulatory enterprises in low-income countries. With COVID, we clearly saw how economic power bought you a ticket to the discussion table. We need to move forward and show that you do not need economic power to have a voice regarding the world’s public health.

Thanks for being with us today. Do you have any final words for prospective scientists in developing countries who think their dream of being a researcher is far-fetched?

No dream is too far-fetched. I would like to tell them that, although it can be hard, they need to leave the impostor syndrome behind. It does not matter if you graduate from your country’s national university or from Harvard. You don’t need a prestigious degree to do great science. You need dedication, passion, courage, and consistency. You have been exposed to very different life stories than the average scientist. You need to take advantage of that cultural intelligence and let it propel you to success. I believe those of us who come from low-income countries are well suited for science; we are accustomed to surviving crisis after crisis, and our resilience is beyond that of anyone else. Our culture, our language, and all our lived experiences are strengths that prepare us for a bright future. Be proud of who you are and where you come from and leverage that to increase your skills. Do a self-evaluation, identify your weak spots, and use all that resilience to move forward. You have all the potential to become successful scientists. Never stop working hard and aiming for the top!

One of life’s great mysteries is how a single egg cell can contain all the information needed to create a fully specialized complex organism, including more egg cells.

Ruth Lehmann, director of the Whitehead Institute at MIT, has done a tremendous amount to solve that mystery. Beginning in her graduate student days, she uncovered a pathway that controls germ cell specification within the embryo. Since then, her work has continued to illuminate many unique facets of germ cell biology, providing a deep foundation from which to understand how the germline lineage carries genetic and cytoplasmic information from generation to generation.

For her achievements, Lehmann has been awarded the 2021 Thomas Hunt Morgan Medal for lifetime achievement in the field of genetics from the Genetics Society of America.

“Her work became textbook material, not just for developmental biology books, but biology books in general,” says Alexander Schier of Biozentrum, the University of Basel and Harvard University, one of the scientists who nominated Lehmann for the award. 

Embryos gain a clear polarity early on, ensuring that the animal’s head and tail develop on opposite ends. As a graduate student at the University of Tübingen, working with Christiane Nüsslein-Volhard, Lehmann went looking for Drosophila mutants that lacked proper patterning. 

Researchers had already observed that fly egg cells had a specialized cytoplasm with the instruction for germ cells located at the posterior pole. Lehmann wanted to find the germ cell determinants, those genes that told the germ plasm what to do. In her screening, she found a number of mutations that produced embryos with no abdomen, that were also missing their germ cells.

It was during these experiments that Lehmann first discovered oskar, nanos, and pumilio, genes she would continue to study throughout her career. As she characterized more and more genes with the same ‘posterior group’ phenotype, she realized that oskar acted as an important organizer of the pathway, and that all the other genes are needed downstream. Take out any individual member of the pathway, and no abdomen and in most cases no germ plasm nor germ cells.

“I had a very good genetically-based idea of how that pathway worked. Then molecular tools became available, which allowed us to study genes at the DNA, RNA, and protein level and ultimately to uncover their mechanisms of action,” she says. “I was at a crossroads. I realized I could not continue as a pure geneticist, but really had to become a molecular geneticist as well.”

She spent a year working at the MRC Laboratory of Molecular Biology in Cambridge to learn how to ‘clone’ genes with the goal to identify their DNA sequence and study their molecular function. At the end of her year at MRC, she had a position waiting for her on the faculty of the Whitehead Institute and the MIT Biology department, where she remained for eight years before moving to the Skirball Institute at NYU School of Medicine in 1996. 

Once she cloned oskar and other genes, such as nanos, pumilio and egalitarian in the pathway, she found that the RNA of some of these genes are deposited by the mother to a specific location, at the posterior pole, of the egg. Control over the distribution of the protein product comes from spatially controlled translation of these localized RNAs, rather than localized transcription, as was commonly expected.

“This idea of RNA localization and translational control, that was quite revolutionary at the time,” says Schier. “This was a whole level of control that people hadn’t anticipated at the time. She always stumbles across these strange and intriguing mechanisms.”

Her pursuit of the mechanics of germ cell migration led her into lipid biosynthesis, perhaps somewhat unusual territory for a geneticist. She discovered that flies lacking the enzyme HMG-CoA reductase, which synthesizes cholesterol in humans (But not in flies—they have to take it up from their diet.), developed germ cells that looked normal, but were scattered around the egg. Somehow the enzyme was acting as the rate-limiting step for a homing signal for germ cells, but how it did so remained a mystery. Now, it appears that HMG-CoA regulates the production of a hormone that attracts the germ cells to the correct location in the egg. 

“She sees things that others haven’t seen,” says Alex Schier. “She doesn’t follow fashion; she carves out her own niche and makes really interesting discoveries that then are followed up by many others.”

For her part, Lehmann describes her philosophy as “follow the phenotype.” Rather than focusing on a single molecule and studying it in different organisms or cell types, she’s chosen to stick with the problem and explore the entire panoply of molecules involved in the germline life cycle. So she and her group have studied how germ cells are initially set aside from the other cells in the body, how they remain “naïve” during larval stages until they eventually, in the adult, develop into gametes, egg, and sperm so that the life cycle can start anew.   

“I’ve always been lucky to make these discoveries, and I think it’s because I’m not prejudiced,” she says. “I start from the mutant phenotype, which tells me about the normal role of the gene that was hit by the mutation. And if this defective gene leads to a protein that is novel or unexpected for the process we study, I’m not afraid to study something new and learn about the function of this gene, that has allowed us to discover novel pathways or placed known pathways into a novel context.”

That strategy hasn’t been easy. Following the phenotype has meant learning to work with a wide variety of biochemical processes, from RNA transport, localization, and translation to lipid phosphorylation, hormone signaling, and transposon-mediated chromatin regulation. “It’s a hard way, it’s true,” she says. “It only works when you get really good people in your lab, because the people in my lab become the experts in a variety of fields.”

Eventually, those experts leave and start their own labs, taking their projects with them.  Attracting early career scientists who bring their own expertise in new techniques and fields is part of the process for Lehmann. “The projects grow as the technologies grow,” she says. 

These days, she’s developing new cell biology methods to understand how the cell physically brings together the molecules that make up the membraneless germ granules. Traditional biochemical methods involve grinding up the cell, and that’s no use when you’re studying condensates that only form in a tiny region of the egg. Recent innovations in visualizing liquid-liquid phase separations are enabling more research in this area. 

“I really want to understand how these molecules come together in germ granules to create activities only there, so that germ cells attain and maintain the special ability to create the next generation,” she says. “And that’s why I am still working on this.”

More than half of her postdocs have gone on to secure faculty positions, an indication of her leadership strategy, which she says emphasizes independence. “While they are in my lab, they can see whether they like being a scientist, whether they are good at being a scientist, because I’m not telling them every day what to do,” she says. “I don’t think that’s my role. I see the training in my lab as a pathway to independence.” 

Alex Schier describes her as “a generous mentor,” ready and willing to go to bat for her students, postdocs, and colleagues against administrators who might be tempted to undervalue basic research. “She really is a great defender of fundamental research of discovery,” he says, “as well as a defender of research driven by individuals with creative ideas.”

The T.H. Morgan Medal recognizes extraordinary achievement in the field of genetics. Lehmann’s work spans many disciplines, including cell biology, developmental biology, and molecular biology, and her contributions have been recognized by various professional societies. Still, she firmly considers herself a geneticist.

“People ask, ‘What are you?’ At heart, I’m really a geneticist,” she says. “The problem always starts with genetics. That’s the discovery phase.”

The Thomas Hunt Morgan Medal recognizes lifetime achievement in the field of genetics. It recognizes the full body of work of an exceptional geneticist. Lehmann accepted the award at the 62^nd Annual Drosophila Research Conference (#Dros21) and will present an Award Seminar online on April 28, 2021 from 1-2 p.m. EDT.

Analysis of insulin-like signaling in C. elegans reveals extensive positive and negative feedback regulation.

The insulin-like signaling system of nematode worms is comparable to that of more complex organisms; it helps regulate a wide range of the animal’s biology, including metabolism, growth, and development. This system is remarkably flexible, with the ability to maintain a physiological steady-state (homeostasis) while also controlling switches between quite different developmental fates (developmental plasticity). A report published in GENETICS reveals the pervasive involvement of both positive and negative feedback in regulating this master pathway in the model nematode Caenorhabditis elegans.

The C. elegans genome encodes one insulin-like receptor and 40 insulin-like signaling proteins. The activity of insulin-like peptides can, in turn, affect the expression of these peptides themselves, yet exactly how this signaling network is regulated remains ambiguous. Kaplan et al. explored the extent of the feedback mechanisms of insulin-like signaling, along with their dependence on nutrient availability.

The worm insulin-like receptor, DAF-2, signals through antagonizing the activity of the transcription factor DAF-16, the nematode ortholog of mammalian FoxO. Because of these opposing functions, daf-2– and daf-16-mutant nematodes were employed to observe how changes in insulin-like signaling affect the expression of insulin-like genes.

Using these mutants under multiple conditions, such as fed vs. starved larval worms, the authors analyzed the expression of insulin-like genes, along with other genes involved in insulin-like signaling, like those in the PI3K pathway.

The authors found extensive feedback regulations within insulin-like signaling; the expression of nearly all detectable insulin-like genes was affected by altering insulin-like signaling, as were some components of the PI3K pathway. These feedback mechanisms were extensive and complex; for example, the well-studied insulin-like protein DAF-28, an agonist of DAF-2, seems to be repressed by DAF-16—thus, DAF-28 is a positive regulator of its own transcription, since activating DAF-2 represses DAF-16.

Overall, considerable evidence for both negative and positive feedback of insulin-like signaling was found; the authors write that this is likely to allow for rapid response to stimuli—like food availability—while still maintaining homeostasis. Further studies will be needed to delve into the precise molecular mechanisms of such feedback systems and to explore similar regulation in other organisms.

CITATION:

Pervasive Positive and Negative Feedback Regulation of Insulin-Like Signaling in Caenorhabditis elegans

Rebecca E. W. Kaplan, Colin S. Maxwell, Nicole Kurhanewicz Codd, L. Ryan Baugh

GENETICS  January 2019 211: 349-361; https://doi.org/10.1534/genetics.118.301702

https://www.genetics.org/content/211/1/349

Apoptotic pathway promotes asymmetric cell division during C. elegans development.

Cell division doesn’t always produce identical daughter cells; often, the demands of multicellular development require cells to split into two quite different daughters with quite different fates. These “asymmetric” divisions are needed so that cells can differentiate and specialize, and some cells are even programmed to die shortly after their creation to ensure the proper function of the organism as a whole. In GENETICS, Mishra et al. found that the apoptotic cell death pathway regulates asymmetric division in the nematode worm Caenorhabditis elegans.

C. elegans is an exceptionally useful model organism for studying development because the fate of each of its relatively few cells can be precisely mapped. Many of the cells destined for death in the worm are actually the product of unequal division into a larger cell that differentiates and a smaller cell that undergoes apoptosis. The authors of the new report had previously studied the parent of one such uneven division, a cell known as the embryonic neurosecretory motor neuron neuroblast. They found that in the parental neuroblast, there is a gradient of activated CED-3 caspase, an executioner of apoptosis. This gradient leads to more active CED-3 caspase in the smaller daughter cell, which helps facilitate its death.

The authors wondered whether this CED-3 caspase gradient might be a general phenomenon in asymmetric divisions, so in the GENETICS report they studied another cell that divides into a large cell that survives and a smaller cell that dies: the QL.p neuroblast. The authors identified a similar CED-3 caspase gradient in these cells, showing that the phenomenon is indeed somewhat general.

Then, the authors used loss-of-function mutants to explore the role of the CED-3 caspase and its related pathways in the asymmetric division of QL.p. They found that disrupting the cell death pathway impaired the ability of QL.p to divide asymmetrically and could impact the fate of the daughter cells—often giving rise to two living cells, rather than one that lives and one that dies. Mutations in other genes associated with asymmetric division, like pig-1, also affected the fate of the daughter cells but did not change the CED-3 caspase gradient.

The authors explain that, in QL.p, two molecular gradients are simultaneously created: one of “mitotic potential,” which is normally passed on to the larger daughter to facilitate its differentiation, and one of “apoptotic potential,” which is passed on to the smaller daughter and promotes its death. Although the details of these “potentials” are not yet understood, this separation within the parental cell seems crucial for ensuring that each cell reaches its proper endpoint.

Although caspases are well-known for their role in apoptosis, it is particularly noteworthy that mutations in CED-3 caspase do not only affect the ability of the small daughter cell to die. CED-3 caspase also appears to function in the division of the parental cell, suggesting a more complicated role of this molecular executioner during development.

CITATION:

Caenorhabditis elegans ced-3 Caspase Is Required for Asymmetric Divisions That Generate Cells Programmed To Die

Nikhil Mishra, Hai Wei, Barbara Conradt

GENETICS November 1, 2018 vol. 210 no. 3 983-998; https://doi.org/10.1534/genetics.118.301500

A Wnt protein involved in the formation of the human ovary plays an important role in female zebrafish sex development.   

Even though zebrafish are a well-studied research model, how these fish develop into males or females remains rather obscure—in part because the sex of lab strains is not determined by sex chromosomes. Research published in GENETICS reveals that one of the genes critical for proper development of mammalian ovaries seems to play a related role in zebrafish, providing insight into this major difference between fish and mammals.

In humans and other mammals, Wnt4 encodes a signaling molecule that antagonizes the male-promoting signal FGF9 and is crucial to the proper development of the ovaries. Though they lack an Fgf9 ortholog, zebrafish have two Wnt4-like genes—wnt4a and wnt4b—so Kossack et al. investigated whether these genes might play a role in zebrafish sexual development.

The authors first performed a phylogenetic analysis to better understand how the Wnt4-like genes have changed over evolutionary time. Zebrafish have two such genes, while mammals only have one, so two evolutionary scenarios are possible: either fish gained an extra copy of the gene, or mammals lost a copy that was originally present. The authors found that the latter scenario is more likely; both reptiles and birds have two such genes, making it more likely that  mammals lost one of their copies. Further analysis revealed that wnt4a is likely the ortholog of mammalian Wnt4, whereas wnt4b was lost in mammals after they split from birds.

The authors next used RT-PCR to examine the expression patterns of the two genes. They detected wnt4a, but not wnt4b, in the ovaries of female zebrafish. In contrast, only wnt4b was detected in the testis of male fish. They also found that wnt4a was dynamically expressed in gonads during development in a non-sex-specific manner.

Fish mutant for wnt4a develop predominantly—though not exclusively—as males, which supports the idea that wnt4a is involved in either differentiation into a female or the maintenance of a female phenotype throughout development. Analysis of mutant embryos during development suggests that wnt4a likely promotes female development since most mutant embryos developed as males rather than “reverting” to males from an initially female phenotype.

Interestingly, wnt4a mutants were unable to produce progeny when mated to each other or to  wild-type. Closer inspection revealed that wnt4a-mutant fish of both sexes had malformed reproductive tracts. Even though viable eggs and sperm could be obtained from their gonads, mutant fish were unable to release their gametes, preventing them from reproducing.

These findings suggest that Wnt4-like genes have been involved in female development of a diverse array of animals—including our fishy ancestors that swam the oceans some 450 millions year ago.

CITATION:

Female Sex Development and Reproductive Duct Formation Depend on Wnt4a in Zebrafish

Michelle E. Kossack, Samantha K. High, Rachel E. Hopton, Yi-lin Yan, John H. Postlethwait, Bruce W. Draper

GENETICS January 2019 211: 219-233; https://doi.org/10.1534/genetics.118.301620

http://www.genetics.org/content/211/1/219

Holes in the plasma membrane trigger the activation of the Torso receptor tyrosine kinase.

As a general rule, cells don’t do well when holes are poked in their plasma membranes. That’s why many immune cells use enzymes like perforin to puncture the membranes of pathogenic cells, dysregulating and often killing them. However, a new report in GENETICS by Mineo et al. suggests that creating holes in the plasma membrane might be a normal and necessary process during development.

The authors were interested in whether membrane hole-punching could play a role in activation of a receptor tyrosine kinase known as Torso. Torso is crucial for development of the fruit fly Drosophila melanogaster and is activated at both poles of the developing embryo. Torso activation depends on the polar accumulation of Torso-like (Tsl), which is the only Drosophila protein known to have a Membrane Attack Complex/Perforin domain. This domain is often present in proteins that perforate cell membranes, so the authors hypothesized that Tsl’s function might be to create membrane pores and, therefore, that simply pricking holes in the cell membrane might substitute for its function.

To test their hypothesis, Mineo et al. studied mutant embryos that either lacked the Tsl protein entirely or carried a non-functional version; both mutants exhibit several easily observable developmental defects. At this stage of development, the embryos are syncytial, which means all the dividing nuclei share a common cytoplasm and are surrounded by a single cell membrane. The researchers poked holes in the membrane at the poles of the embryo using sharpened capillaries of the type sometimes used to inject DNA for genetic engineering. Remarkably, embryos that had holes poked in them had fewer defects than their un-poked counterparts, suggesting that the mechanical formation of holes partially compensate for Tsl function.

To determine whether the rescue was due to mechanical stress on the membrane—but not necessarily the holes themselves—the authors then prodded membranes but did not puncture them. Prodded embryos showed the same developmental defects as their untreated counterparts, showing that an actual rupture in the membrane was required to rescue the developmental phenotype in Tsl-deficient fly embryos.

The authors also demonstrated that Torso signaling is required for the rescue effect of these membrane holes; fly embryos lacking Torso or its ligand, Trunk, did not show any change in developmental phenotypes when they were mechanically punctured. The location of the holes also mattered; the rescue was greatly diminished when the holes were created in the middle of the embryos, rather than at their poles.

Overall, the results suggest that Tsl spatiotemporally regulates Torso signaling by puncturing the cell membrane. These punctures are presumably needed for the exchange of a molecular signal between the interior of the embryo and its extracellular surroundings; it remains to be seen exactly how activation by Tsl works. What is clear is that, sometimes, all that’s needed to keep development on track is a sharp punch in the membrane.

CITATION:

Holes in the Plasma Membrane Mimic Torso-Like Perforin in Torso Tyrosine Kinase Receptor Activation in the Drosophila Embryo

Alessandro Mineo, Esther Fuentes, Marc Furriols, Jordi Casanova

Genetics September 2018 210: 257-262; https://doi.org/10.1534/genetics.118.301397

http://www.genetics.org/content/210/1/257

A fruit fly model of fetal alcohol spectrum disorder reveals a Cyclin E-centric network modifies developmental sensitivity.

Alcohol exposure in utero can lead to a wide range of developmental problems, even causing fetal death in some cases. But since this exposure doesn’t always have the same outcome, is it more likely to be a problem for some than others? Exploring the genetic factors that influence susceptibility to fetal alcohol effects is extremely challenging in humans because both exposure levels and the spectrum of phenotypic outcomes are inherently difficult to quantify. In a report in G3: Genes|Genomes|Genetics, Morozova et al. turned to fruit flies to investigate genes that might be involved in prenatal sensitivity to alcohol.

Alcohol is a familiar hazard to the rotten-fruit-loving fly. However, like humans, fruit flies are susceptible to the effects of too much booze, especially during development. When fly larvae are exposed to alcohol, the outcome can be developmental delays and even death. Morozova et al. looked for genes that influence the developmental response to alcohol by using a population of over 200 wild-derived inbred fly lines called the Drosophila melanogaster Genetic Reference Panel (DGRP). The DGRP lines capture a great deal of genetic diversity while also allowing for replication within a line, and the lines have fully-sequenced, well-annotated genomes. The authors compared the effects of alcohol exposure on viability (how many of the flies survived) and development time (how long it takes for flies to reach adulthood) in the DGRP lines. They also examined how ethanol exposure affected locomotion in a subset of the lines.

Unsurprisingly, ethanol exposure in this experiment increased development time, decreased viability, and impaired locomotion in most of the lines tested. However, there was a lot of variation between lines, and a few lines actually developed faster when reared on ethanol-supplemented food.

The authors performed genome-wide association analyses to identify the genetic variants associated with different sensitivities to alcohol exposure. The genes identified were involved in a wide range of biological processes, including cytoskeleton organization, egg laying, and mitosis regulation. The authors validated the function of a number of these genes using RNAi-mediated knockdown or transposon-tagged mutational insertions.

They then constructed an interaction network using the genes associated with viability and development time, revealing that Cyclin E (CycE) was a highly connected hub gene. Since CycE is associated with cell cycle regulation and is highly expressed in Drosophila ovaries, it makes sense that it might play a key role in determining an organism’s sensitivity to developmental alcohol exposure. Their results may one day help researchers narrow the search for human gene variants that influence fetal sensitivity to this most common of drugs.

CITATION:

A Cyclin E Centered Genetic Network Contributes to Alcohol-Induced Variation in Drosophila Development

Tatiana V. Morozova, Yasmeen Hussain, Lenovia J. McCoy, Eugenea V. Zhirnov, Morgan R. Davis, Victoria A. Pray, Rachel A. Lyman, Laura H. Duncan, Anna McMillen, Aiden Jones, Trudy F. C. Mackay, R. H. Anholt

G3: GENES|GENOMES|GENETICS August 2018 8: 2643-2653;

https://doi.org/10.1534/g3.118.200260

http://www.g3journal.org/content/8/8/2643

Fruit fly mutants can sometimes be grisly. Ecdysteroid hormones control aspects of fly development, including molting and metamorphosis; because aberrations in these genes lead to embryos with a ghastly appearance, they have been collectively dubbed “Halloween genes.”

In a study published in GENETICS, Uryu et al. investigated how the expression of these genes is regulated. Halloween genes, such as spookier and neverland, are expressed in specific parts of the developing fly at specific times, suggesting that precise transcriptional programming is at play. Since some Halloween genes are regulated by zinc finger transcription factors like Ouija board and Molting defective, the authors explored whether other, structurally similar transcription factors in the Drosophila genome could also play a role.

Uryu et al. identified the novel transcription factor Séance as a regulator of Halloween genes. They found that Seance, Ouija board, and Molting defective collectively control the expression of spookier and neverland, which in turn regulate ecdysteroid synthesis. The cooperation of three transcription factors to modulate expression of just two genes underscores the critical importance of spatiotemporal regulation of gene expression.

As developmental genes are characterized and studied, our understanding of them continues to increase, hopefully making these sinister-sounding genes a little less scary. However, one burning question still looms: why do Drosophila genes get all the cool names?

CITATION

Cooperative Control of Ecdysone Biosynthesis in Drosophila by Transcription Factors Séance, Ouija board, and Molting Defective

Outa Uryu, Qiuxiang Ou, Tatsuya Komura-Kawa, Takumi Kamiyama, Masatoshi Iga, Monika Syrzycka, Keiko Hirota, Hiroshi Kataoka, Barry M. Honda, Kirst King-Jones and Ryusuke Niwa. 

Genetics February 2018 208: 605-62

https://doi.org/10.1534/genetics.117.300268

http://www.genetics.org/content/208/2/605

Why study human diseases in frogs? For starters, 79% of genes implicated in human disease have orthologs in the African clawed frog Xenopus laevis. Frogs also produce hundreds of embryos that can be grown in a dish, meaning they can be manipulated in ways that are impractical on a large scale in mammals. For example, scientists can microinject specific cells in the developing frog embryo as a way to alter the genes in particular organs in the adult. This is particularly useful since disruption of many important developmental genes is lethal, which prevents detailed investigation into these genes’ functions.

Though frogs as a model system allow for scales not easily achieved in other species, there are limitations to the genetic tools available. Current knockout techniques, like the use of morpholinos, are expensive and often toxic. In a report in GENETICS, DeLay et al. showed how CRISPR technology can be used for tissue-specific gene editing in X. laevis.

CRISPR is a gene editing technique which is quickly revolutionizing many aspects of genetics, and DeLay et al. used it to knock out lhx1 in the kidneys of developing frogs. Lhx1 is important for development of the kidney, head, spine, and other structures in both frogs and mice. Embryos lacking functional lhx1 rarely survive, and if they do, they have severe defects. The researchers used CRISPR to functionally knock out lhx1 in a targeted manner by microinjecting different cells in the frog embryo. For example, injection of one of the cells in a  two-cell embryo knocks out lhx1 in half of the frog, leaving the other half undisturbed. These frogs then develop with one normal, unaffected kidney and one deformed kidney. This method will be especially useful for genetic screens because the unaffected kidney serves as a near-perfect internal control.

The researchers hope that this relatively inexpensive technique will be used to further study the role of different genes in organogenesis and development. It will also make frogs a better model for studying human disease, since CRISPR sidesteps many of the problems of other knockout methods. Discoveries in frogs can help us better understand what the human counterparts of these genes do and, hopefully, pave the way for advances in combating human disease.

CITATION
Tissue-Specific Gene Inactivation in Xenopus laevis: Knockout of lhx1 in the Kidney with CRISPR/Cas9

Bridget D. DeLay,  Mark E. Corkins, Hannah L. Hanania, Matthew Salanga, Jian Min Deng, Norihiro Sudou, Masanori Taira, Marko E. Horb and Rachel K. Miller

Genetics February 2018, 208: 673-686;

https://doi.org/10.1534/genetics.117.300468 

http://www.genetics.org/content/208/2/673