love bet 爱博官网 - love bet 爱博官网 //www.abewal.com A blog from the Genetics Society of America Tue, 02 Jun 2020 17:04:42 +0000 en-US hourly 1 https://wordpress.org/?v=4.9.2 74327306 Racism is everyone’s problem //www.abewal.com/racism-is-everyones-problem/ //www.abewal.com/racism-is-everyones-problem/#respond Tue, 02 Jun 2020 13:05:58 +0000 //www.abewal.com/?p=68005 As yet another Black man suffocates under a policeman’s knee, cities burn, and the coronavirus spreads a disproportionate burden of suffering and death to communities of color, we are in a moment that calls for action. It would be heartfelt and true for White scientists like me to say to our colleagues and fellow citizens […]]]>

Frameshifts LogoAs yet another Black man suffocates under a policeman’s knee, cities burn, and the coronavirus spreads a disproportionate burden of suffering and death to communities of color, we are in a moment that calls for action. It would be heartfelt and true for White scientists like me to say to our colleagues and fellow citizens of color that we hear you, we stand with you, and we want to help make things better. But it would not be enough.

We can and should read the many heartbreaking accounts of innocent Black men like LZ Granderson who have been repeatedly traumatized by encounters with police who regularly mistake them for a fugitive criminal. But it is not enough. It is too easy to conclude that this is someone else’s problem, a problem between Black men and police.

We can and should read the eloquent words of Kareem Abdul-Jabbar putting current events in the context of the ubiquitous and inescapable racism that permeates this country. “Racism in America is like dust in the air,” he says. “It seems invisible — even if you’re choking on it — until you let the sun in. Then you see it’s everywhere. As long as we keep shining that light, we have a chance of cleaning it wherever it lands.”

Acknowledging pervasive racism gets us closer, but it is still not enough. Only when White people understand our own complicity in the system that holds people of color in this country down, can we really begin to change course. I learned this truth by reading the book “White Fragility,” and I urge you to read it too. The author, Robin DiAngelo, opened my mind to an idea that was and still is abhorrent to me: I have come to realize that I, as a White person, was born into privileges that have propelled me upward at someone else’s expense. More cutting still, I have perpetuated racism in this country—albeit unconsciously—by accepting those privileges. Once we truly and deeply understand these facts, it becomes unbearable not to act.

This moment is a call to each one of us to take action against the institutional racism and inequality that are woven into the very fabric of our society. It is not enough to watch and comment from the sidelines as people revolt against the outrageous murder of George Floyd—and so many before him. This is not just a problem caused by racist and overly zealous police officers and their enablers. This is not someone else’s problem. Racism is everyone’s problem.

So what can we do? We can start by listening to our colleagues to uncover the racism in academia that is hiding in plain sight. We can learn what they experience. We can begin every lab meeting with a statement of commitment to a more just and equal lab, society, and world. We can acknowledge painful ongoing events that may be affecting some of us more directly than others. We can educate ourselves about movements for racial justice. I am sure there is much more we can do. I am just a beginning student in this endeavor. But it has become unbearable not to act.


This week the GSA Board of Directors will be discussing what actions the Society should take to confront racism within scientific communities. While acknowledging the historical role genetics and geneticists have played in promoting racist thinking and actions, we hope going forward to provide support for Black scientists and all others affected by racism in science. With the help of the GSA Equity and Inclusion Committee, we will provide an update on our ideas and plans within the next two weeks. In the meantime, we welcome your feedback and suggestions via email: society@genetics-gsa.org.

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Principal investigators on how COVID-19 is affecting their labs //www.abewal.com/principal-investigators-on-how-covid-19-is-affecting-their-labs/ //www.abewal.com/principal-investigators-on-how-covid-19-is-affecting-their-labs/#respond Thu, 21 May 2020 21:23:23 +0000 //www.abewal.com/?p=67772 As COVID-19 spreads across the world, members of the GSA community have had to face unprecedented challenges in their professional and personal lives. To stay connected during this socially distant time, GSA invites the scientists in our community to share how they are meeting these challenges, as well as their questions and worries.  If you […]]]>

As COVID-19 spreads across the world, members of the GSA community have had to face unprecedented challenges in their professional and personal lives. To stay connected during this socially distant time, GSA invites the scientists in our community to share how they are meeting these challenges, as well as their questions and worries. 

If you would like to contribute to this series, please contact Communications Assistant Jacqueline Treboschi.


PI members of the GSA community share how they are adjusting to the remote teaching, lab shutdowns, and isolation caused by COVID-19.


Michael Buszczak, Professor, UT Southwestern

“I think establishing a routine is important for staying sane and productive during this unprecedented time. Towards this goal, my lab meets online on Mondays and Fridays. The Monday meeting is usually pretty quick and provides an opportunity for everyone to touch base with one another. I have also been asking each person to come up with a set of modest goals for the week. I realize none of us is going to be as productive as we are under normal conditions. But I still think it’s important to keep the members of the lab engaged in their research. Their goals for a given week can be as simple as reading a paper a day. On Fridays, one person presents [in] journal club. With all this reading, I hope, at the very least, that our group becomes much more familiar with the literature by the end of all this.”

Susan Dutcher, Professor, Washington University

“At Washington University in St. Louis, as at many other universities, we moved to online courses. I moderate one of the discussion groups for our Advanced Genetics course for graduate students. We had our first Zoom discussion group [in March]. I will admit that I was very worried about a discussion group online. The students rose to the occasion and were amazing. Everyone contributed; they were more interactive than [when] we meet in a room. I applaud them for their discussion of QTLs and their great questions and thoughts. My lab is sheltering at home. We had our first lab meeting yesterday and invited a colleague from Emory University to join us. It was so much fun to have an outside person with other insights. I would highly recommend inviting colleagues to join. The discussion was lively and we came up [with] more experiments to do when we can come back to [the] lab.”

Pam Geyer, Professor, University of Iowa

On keeping in touch with lab members: “The lab is small, so we don’t go over the 10-person limit. We have organized so that members come into [the] lab at different times to decrease contact. We have agreed that any member that is feeling ill must remain home. We feel it is important for members to come into work because they need to maintain their fly stocks and keep the multi-generation crosses going. We have not had [a] lab meeting yet—but I expect to start lab meetings up using Zoom.” 
On teaching duties: “I am only teaching two small workshop classes, and these are continuing using Zoom. Since last week was spring break, we did not have either class. The first class is tomorrow—so we will see how that goes. 
On lab ramp-downs: “To minimize duties for management of our stock collection, I went through and culled the collection greatly.”
On manuscript progress: “The work slowdown has both positive and negative consequences on manuscript preparation. We are benefitting from an increased attention to data analysis, but we are somewhat frustrated by our inability to respond to questions that arise from these analyses. We have also experienced delays in an editorial decision of a submitted manuscript—with the review greatly overdue.”
On mental health: “This is a major concern. Many of our trainees report extra stress, especially because it remains unclear how long this situation will continue. I co-direct the MD-PhD program here, and those trainees are particularly affected. Trainees in the clinical phase are being told that their clinical rotations will be virtual—no patient contact. They are all concerned about whether the needed skills will be obtained in such a fashion. Another consequence of COVID-19 is the shutdown of national testing services, which impacted trainees who were about ready to take the Step 1 licensing exam. National match day for graduating medical students was canceled this year, as well as any graduation ceremonies—this is hard for a group of trainees who have worked so hard. Our community has a wellness group [that] has posted links for their peers. They have also started a group chat through GroupMe—we will see how that goes. We plan to have bi-weekly informational meetings using Zoom, so that we can connect as a group.”

Thomas Merritt, Professor, Laurentian University

“Like, I think, many PIs, I’m not generally allowed in the lab and definitely not in the fly kitchen (OK, I do sneak in to make ramen for my lunch on occasion). I haven’t made fly food in a decade or been in charge of stock transfers for about as long. With the COVID-19 changes, faculty have been asked to take on any necessary tasks, like maintaining stocks, so that students do not need to travel. So this afternoon I had a Zoom meeting to organize my training. Two students have volunteered to show me where everything is and remind me, gently, how to make food. I think I’ve got this. My students, and my daughter eavesdropping on the conversation, were more skeptical.”

Detlef Weigel, Director, Max Planck Institute for Developmental Biology

“When discussing how to best reassure students and postdocs, my friend Jeff Dangl gave me some sage advice: Time is slowing down for everybody right now. Thus, everybody else’s papers, theses, preliminary data for grants, etc. are delayed. As a counterpoint to this, I’ve told my lab that we will do our best to accommodate delayed graduation dates as well as delayed lab departures because of delays in the conclusion of projects, difficulties in obtaining visas for the next job, or a drying up of new job openings. Because we are saving on consumables now, and because the arrival of new lab members will be inevitably delayed, there should be funds for extending contracts.”

Mariana Wolfner, Professor, Cornell University

On keeping in touch with lab members: “As situations changed around us, we continued our weekly lab meetings (by Zoom). We discuss our science, and recent papers that we’ve seen. It’s interesting and exciting, and also lends some normalcy to these stressful times. We added two additional Zoom meetings each week for all who wish to attend to talk, catch up personally, see each other’s families and pets, and encounter some levity like trying out new virtual backgrounds for Zoom. I continue to meet with each person in the lab individually at our normal weekly time, but now by Zoom. Lab members also meet with each other by Zoom for collaborative projects, and to touch base.”
On teaching duties: “Learning technical and pedagogical methods for remote teaching and rapidly modifying lectures, discussions and assignments, has been intense. But we’re getting there, with lots of help from an awesome TA (and this comforting song from M. Bruening). Cornell provides many helpful resources, though some days it’s a lot to watch so many instructional webinars. [The] most stressful [part] has been to have to turn on a dime whenever the landscape suddenly changes, and concerns about students who are widely dispersed, stressed, and may be facing health, family-health, or connectivity issues.
On lab ramp-downs: “This has been challenging. Experiments had to stop abruptly, including one that was the last thing needed to address a reviewer’s comments on a paper. It will take time to get everything back up once the shutdown ends. Terminating experiments caused a lot of stress to our students, postdocs, and staff (and me); everyone has been pretty shell-shocked. Despite this, lab members have been amazing in pulling together to make the shutdown as non-disruptive as possible. Different people took on different tasks—making sure essential flystocks would be transferred, generating to-do lists and shift-schedules, making sure that equipment was in stable shutdown states, and doing kind and supportive things for each other. Each person focused on one task, knowing that their colleagues were covering the others. Lab members are understandably worried about how the shutdown will affect the duration of their training. I’ve been trying hard to reassure them that although times are uncertain, we will all make it through this. We are only allowed into [the] lab to transfer our flies. We do this with a shift schedule of essential personnel, maintained via a Google calendar. Only one person is in [the] lab at any time, and the lab is sanitized at the end of each shift. Other than this, we work remotely: reading, writing, doing (or learning) bioinformatics, meeting in lab meetings, etc.”

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Early career scientists on how COVID-19 is affecting them //www.abewal.com/early-career-scientists-on-how-covid-19-is-affecting-them/ //www.abewal.com/early-career-scientists-on-how-covid-19-is-affecting-them/#respond Wed, 13 May 2020 18:51:29 +0000 //www.abewal.com/?p=67632 As COVID-19 spreads across the world, members of the GSA community have had to face unprecedented challenges in their professional and personal lives. To stay connected during this socially distant time, GSA invites the scientists in our community to share how they are meeting these challenges, as well as their questions and worries.  If you […]]]>

As COVID-19 spreads across the world, members of the GSA community have had to face unprecedented challenges in their professional and personal lives. To stay connected during this socially distant time, GSA invites the scientists in our community to share how they are meeting these challenges, as well as their questions and worries. 

If you would like to contribute to this series, please contact Communications Assistant Jacqueline Treboschi.


Early career members of the GSA community share how they are adjusting to the career uncertainty, lab shutdowns, and isolation caused by COVID-19.


“The COVID-19 shutdown has greatly slowed the progression of our work, which, unfortunately, is aging focused. Our institution has taken appropriate steps in closing down the university for all but non-essential work. Luckily, I am able to continue to feed colonies, however, the delay of experiments make me and others in my position worried about how this delay in progress will be viewed by hiring committees.”
—Balint Kacsoh, Postdoc at University of Pennsylvania

“One of my favorite things about my lab is our camaraderie, and its absence has made it particularly hard to adjust to working remotely. After just five days of social distancing, I found myself unable to focus meaningfully on any work-related task, and my daily schedule slowly devolved into an amorphous mess. To counteract loneliness and keep up motivation, my lab and I established Write Club. We meet in our virtual Zoom cafe, where we spend 15-30 minutes chatting, 90 minutes writing, and a final 15 minutes sharing our progress (or even the lack thereof). We initially agreed to meet for Write Club on Mondays, Wednesdays, and Fridays, but it’s been so effective that you’ll find us there most days of the work week. Having a daily bit of interaction with my labmates has helped enormously – we all help keep each other accountable for making progress on our projects. But more importantly, we can re-capture a little of our lab’s magic by catching up, commiserating, and lending emotional support when we most need it.”
—Teresa Lee, Postdoc at Emory University

“I am struggling with productivity during this time. With not being able to go to lab anymore, many things I felt were almost finished now feel much further off. I am doing my best to remember that we are all going through this and to break up my goals into smaller pieces.”
—Gavin Rice, Postdoc at University of Pittsburgh

“Being a non-citizen during quarantine has a negative impact on mental health because you feel constantly anxious about family and friends living in another country; whether you’ll keep getting paid while you’re working from home; visa renewals; and job continuation.”
—Seyma Katrinli, Postdoc at Emory University

“Most of our laboratory’s work has shifted to working from home. Online meetings are working well so far. Students have been asked to move out of the university’s residences in several cities. While some universities are making it mandatory, others are allowing some of the residents to stay if they do not have anywhere else to go. In my case, I am going to move out because I had started planning to do so before the pandemic started, but this is likely not the case for everybody. Some friends have defended their theses in online meetings; at least one of them faced technical difficulties.”
—Angel Fernando Cisneros Caballero, Graduate Student at Université Laval

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Finding positivity during COVID-19 lockdown //www.abewal.com/finding-positivity-during-covid-19-lockdown/ //www.abewal.com/finding-positivity-during-covid-19-lockdown/#respond Mon, 04 May 2020 18:28:35 +0000 //www.abewal.com/?p=67468 As COVID-19 spreads across the world, members of the GSA community have had to face unprecedented challenges in their professional and personal lives. To stay connected during this socially distant time, GSA invites the scientists in our community to share how they are meeting these challenges, as well as their questions and worries.  If you […]]]>

As COVID-19 spreads across the world, members of the GSA community have had to face unprecedented challenges in their professional and personal lives. To stay connected during this socially distant time, GSA invites the scientists in our community to share how they are meeting these challenges, as well as their questions and worries. 

If you would like to contribute to this series, please contact Communications Assistant Jacqueline Treboschi.


Guest post by Madhumala K. Sadanandappa, Ph.D. and Shivaprasad H. Sathyanarayana, Ph.D.


The authors’ five-year-old daughter drew a picture of their life in quarantine.

“Mamma, Papa, when we go back home, I would like to invite my friends for a playdate. I would like to have a family movie night. I want to go to the swimming pool, bowling alley, Montshire museum.” Our five-year-old daughter has been making this extensive list of plans for when COVID-19 is over, but, for now, no one seems to know when that will be.

Before travel restrictions and national quarantines began, our family of three took a trip to our home country, India. During our trip, we enjoyed family get-togethers, college reunions, tropical winters, savored delicacies, festive occasions, and memories that we created all through our visit. When it was almost time to say adieu to our families, friends, and our home country, everything seemed to be in order. Our passports had arrived on time, along with renewed visa stamps. Excluding the sweets and snacks that we had planned to bring back to the lab, we had checked off all the items on our to-do list; our luggage was partially packed, and our flights were on schedule.

Shortly before our planned departure, we received an email from the airline saying that they had canceled our flight. We also received several emails from our host institution and advisor about the preparation for on-campus research ramp down. Then, India announced a temporary ban on all the commercial passenger flights, leaving us only three days to depart before the restrictions were enforced. After several attempts (151!) to contact the airlines and more than an hour waiting on the phone, the customer care executive offered limited options for rebooking our flight. We initially chose to fly out on the day before the international travel ban was set to begin, but after weighing the travel-associated risks, we decided that it would be in our family’s best interest to stay. It was not an easy call, but the thought of enduring flight delays, crowded airports, and being stranded in an airport with a kid was dreadfully unimaginable. A few days later, India officially declared a complete nationwide lockdown for 21 days to fight COVID-19.

India during COVID-19 lockdownAround the clock, we were busy catching up with the news updates, keeping tabs on the infection rates, and discussing facts about the virus and the government’s actions. We worried about our experimental animals, projects, and return to our host institution; we failed to make daily routines, stopped all physical activities, and reduced our interactions with our daughter, who was enjoying unlimited screen time. We halted our productivity in terms of manuscript writing, data analysis, literature review, attending the webinars, and networking. In many ways, it felt like the virus had hijacked our lives.

A few weeks after we initially decided to stay in India, the country extended its lockdown period, and flights remained suspended. The reality of living through such a historic and unprecedented situation was challenging. While we were dealing with anxiety, helplessness, uncertainty, and social distancing, we also felt our early-career-researcher clocks ticking!

Eventually, we came up with reasonable solutions to reduce the impact that negativity was having on our physical and mental health as well as on our careers. In these trying times, we set up realistic goals and achievable plans for the coming weeks to support each other. First and foremost, we consciously avoided COVID-19 related conversations, unless it was especially important. We talked about our stress, anxiety, and gloom, and we sought advice from trusted friends and our PI. Every day, we held each other accountable for work as well as for leisurely activities that restored our energies. We diverted our obsession over virus-related news to learning new skills, attending virtual seminars, updating our social media profiles, engaging in professional networking, and supporting COVID-19-related causes.Girl in India

Instead of focusing on what we can’t control, we have shifted our attention to what’s good about COVID-19 life. For instance, staying at home means being with our families during difficult times and spending quality time creating memories with our daughter. We choose to focus on thoughtful words from a supportive advisor, who said, “Be safe and healthy. We will happily welcome you when you return.” We are thankful to our lab members, who are taking care of our experimental animals, and we appreciate the scientific community and our institution in their efforts to keep us all engaged, motivated, and productive.

As we write this, longing to see each other, our daughter is still planning a family dinner, birthday celebration, and playdates with her friends. Her positive outlook is unaffected by the rate of infection, vaccine research, the new proclamations, the lockdown extensions, or the travel bans. Her innocence and trust reassure us that this time will pass, and sooner or later, we will all return to our normal life. Until then, stay safe, stay healthy, and be positive.

 

About the Authors

Madhumala Sadanandappa and Shivaprasad Sathyanarayana are Postdoctoral Research Associates in the Bosco Lab at the Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH. Madhu is a member of the GSA’s Conference Childcare Committee.

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In Memoriam: Gordon Lark //www.abewal.com/in-memoriam-gordon-lark/ //www.abewal.com/in-memoriam-gordon-lark/#respond Mon, 04 May 2020 01:39:10 +0000 //www.abewal.com/?p=67448 We are sad to report that Dr. Karl Gordon Lark died on April 10th, 2020 from an aggressive form of prostate cancer. Karl Gordon Lark was born on December 13th, 1930 in Lafayette, Indiana to Karl and Betty Lark-Horovitz. His father was a physicist with an interest in biology. Gordon entered the University of Chicago […]]]>

We are sad to report that Dr. Karl Gordon Lark died on April 10th, 2020 from an aggressive form of prostate cancer. Karl Gordon Lark was born on December 13th, 1930 in Lafayette, Indiana to Karl and Betty Lark-Horovitz. His father was a physicist with an interest in biology. Gordon entered the University of Chicago in 1945. Following a course in physical chemistry in 1948, his professor, Leo Szilard, recommended the newly emerging field of molecular biology and, as a good introduction, Gordon took the phage course at Cold Spring Harbor taught by Marc Adams. Subsequently, Gordon enrolled at New York University to obtain his PhD with Marc as his mentor. He became a member of the “Phage Group”  of scientists under the guidance of Max Delbrück, using bacterial viruses as a model organism for genetics. This group included the likes of not only Delbrück, but also Luria, Hershey, Meselson, Stahl, Watson and Crick. Gordon obtained his PhD in 1952 and began a lifelong career in molecular biology with his companion and wife, Cynthia Thompson. Gordon Lark emerged as a remarkable scientist not only with an illustrious career in the molecular biology of bacteria and bacteriophages, but he then ventured into new territories including soybean and dog genetics. In each of these fields a hallmark of Gordon’s pursuits were clarity, passion and creativity.  How he managed, with only a modest-sized laboratory, to significantly contribute to such a diverse set of fields was, and still is, truly amazing.

In 1970 Gordon Lark was recruited to the University of Utah to assemble a new Department of Biology that would include all of the biological sciences, from molecular biology to ecology and evolutionary biology. In the first six years he hired seventeen new tenure-track faculty. His energy was boundless, his formula simple. He looked for excellence, creativity and synergy. The latter he interpreted as having passion for science and the need to share that passion, particularly with the next generation of scientists. In a few years, Gordon’s vision, tenacity and impeccable taste established a world class Biology department that was particularly well-recognized for its excellence in genetics. New recruits learned so much from Gordon, who taught by example. His rigor, diligence and attention to detail were unparalled.  He set very high bars for himself and his science, with those around him sometimes struggling to keep up. But, perhaps surprisingly given his boundless energy, Gordon was in some ways a very patient man. Before every critical faculty vote Gordon would take time to personally discuss this issue with every member of the department. When the vote came, there were no surprises.

The dog genetics community owes a special thanks to Gordon for his seminal contributions. His PNAS paper in 2002 with Kevin Chase revolutionized the field, demonstrating for the first time that seemingly complex morphologic traits were controlled by a small number of genes, thus nominating the dog as a genetic system for the identification of genes controlling breed-specific differences in morphology and behavior. That paper also provided a key impetus to select the dog as a mammal for early whole genome sequencing in 2005, which in turn allowed canine genetics to blossom as a system of interest to medical geneticists, anthropologists, behavioral scientists and physiologists.

Gordon was unique in his ability to make connections where no one else saw them. He frequently drew parallels between his soybean and dog work, pointing out that interactions between quantitative trait loci in soybeans were key for understanding phenotypic variation. He argued, correctly, that the same must be true in dogs, likely explaining some of the nuanced changes observed between breeds.  The “Georgie Project,” an effort to fully sample large numbers of living Portuguese Water dogs is just one example that can be pointed to when a trainee says “…I can’t possibly…,” reminding them that if Gordon could do it, they can at least try.

Gordon Lark created a space of trust and synergy, rather than competition, a place that inspired, was rigorous but also joyful. The surrounding environment in Utah is magnificent, and its splendor matched the environment Gordon built in his department. It is doubtful that any achievements which we have been fortunate to accrue could have been attained in any other environment. Utah was and is a place where people like Gordon could think big, and then bigger still, with unfettered creativity. Those of us living in other places found reasons to visit Gordon frequently, believing that our collaborations with him would somehow make us heirs to his success.

Our final mental pictures of Gordon are not of him at the bench, but of him with Mopsa, his all-time favorite dog, sitting beside him in his messy office as Gordon talked with unbridled enthusiasm about the achievements of his family, and his love of music, literature, and history. We will all miss Gordon. In these very strange times of social distancing, it is difficult to grieve together. However, such grieving, in Gordon’s eyes, would likely be displaced. What would please Gordon most is for us as scientists to continue our endless quests for the joy of doing science and, most of all, to share that joy with the next generation of scientists.

 

Mario R. Capecchi

University of Utah School of Medicine

 

Elaine A. Ostrander

National Human Genome Research Institute/NIH

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GSA Journals Spotlight 2019 //www.abewal.com/gsajournalsspotlight2019/ //www.abewal.com/gsajournalsspotlight2019/#respond Fri, 01 May 2020 18:32:52 +0000 //www.abewal.com/?p=67364 The GSA Journals, GENETICS and G3: Genes|Genomes|Genetics, are proud to present our annual Spotlight booklets for research published in 2019. Each Spotlight is a showcase of the excellent research and scholarship published over the course of the year, along with a selection of striking images submitted by our authors. Browse the 2019 GENETICS Spotlight. Browse the 2019 G3 Spotlight.]]>

The GSA Journals, GENETICS and G3: Genes|Genomes|Genetics, are proud to present our annual Spotlight booklets for research published in 2019. Each Spotlight is a showcase of the excellent research and scholarship published over the course of the year, along with a selection of striking images submitted by our authors.

Browse the 2019 GENETICS Spotlight.

Browse the 2019 G3 Spotlight.

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Three GENETICS articles from 2019 recognized with Editors’ Choice Awards //www.abewal.com/three-genetics-articles-from-2019-recognized-with-editors-choice-awards/ //www.abewal.com/three-genetics-articles-from-2019-recognized-with-editors-choice-awards/#respond Tue, 28 Apr 2020 19:56:22 +0000 //www.abewal.com/?p=67334 Congratulations to the winners of the Editors’ Choice Awards for outstanding articles published in GENETICS in 2019! The journal’s Editorial Board considered a diverse range of articles, finding many papers worthy of recognition. After much deliberation, they settled on one exceptional article for each of the three award categories: molecular genetics, population and evolutionary genetics, and quantitative genetics. […]]]>

Congratulations to the winners of the Editors’ Choice Awards for outstanding articles published in GENETICS in 2019! The journal’s Editorial Board considered a diverse range of articles, finding many papers worthy of recognition. After much deliberation, they settled on one exceptional article for each of the three award categories: molecular genetics, population and evolutionary genetics, and quantitative genetics. Check out some of the best GENETICS had to offer in 2019!


EDITORS’ CHOICE AWARD IN MOLECULAR GENETICS

Coupling of Human Rhodopsin to a Yeast Signaling Pathway Enables Characterization of Mutations Associated with Retinal Disease

Benjamin M. Scott, Steven K. Chen, Nihar Bhattacharyya, Abdiwahab Y. Moalim, Sergey V. Plotnikov, Elise Heon, Sergio G. Peisajovich, and Belinda S. W. Chang

Editor’s Note

G protein-coupled receptors (GPCRs) are crucial sensors of extracellular signals in eukaryotes, and direct measurement of GPCR mediated signaling is useful for high-throughput mutational studies; however, this is particularly difficult for the light-activated GPCR rhodopsin. Here, Scott et al. report a fluorescence-based reporter assay in which human rhodopsin is activated in the yeast mating pathway. Their novel yeast-based assay shows similar characteristics as more traditional methods, demonstrating that their engineered yeast strain can be useful in classifying rhodopsin mutants that are consistent with clinical phenotypes.


EDITORS’ CHOICE AWARD IN POPULATION AND EVOLUTIONARY GENETICS

A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution

Scott G. Foy, Benjamin A. Wilson, Jason Bertram, Matthew H. J. Cordes, and Joanna Masel

GENETICS April 2019 211: 1345–1355

Editor’s Note

The current consensus among biologists is that evolution does not have a direction. Here, Foy et al. compare recently-born gene families to genes that are chronologically “more evolved,” finding a striking directionality in the evolution of the structural properties of proteins, which must balance the need to fold in a functional manner against the need to avoid misfolding. Young genes use a primitive strategy to avoid protein misfolding, while old genes use a much more subtle strategy, suggesting a progressive shift in protein folding strategy over billions of years.


 EDITORS’ CHOICE AWARD IN QUANTITATIVE GENETICS

The Genetics of Mating Song Evolution Underlying Rapid Speciation: Linking Quantitative Variation to Candidate Genes for Behavioral Isolation

Mingzi Xu and Kerry L. Shaw

GENETICS March 2019 211: 1089–1104

Editor’s Note

A common component of divergence in mating behavior is the distinctive mating songs of insects, and identifying genes underlying natural variation in acoustic behavior is important for understanding targets of selection during speciation. Here, Xu and Shaw examine the largest quantitative trait locus underlying an interspecific difference in the male mating song of two closely related species of Hawaiian crickets, characterize its genetic and phenotypic effects, and refine its map location. They identify an ion channel gene as a promising candidate underlying behavioral isolation between the two cricket species.

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GSA awards 2020 Edward Novitski Prize to Welcome Bender //www.abewal.com/gsa-awards-2020-edward-novitski-prize-to-welcome-bender/ //www.abewal.com/gsa-awards-2020-edward-novitski-prize-to-welcome-bender/#respond Thu, 23 Apr 2020 20:20:50 +0000 //www.abewal.com/?p=67265 Today it’s easy to take for granted that geneticists can identify a mutation, find its gene, and map it to the expressed protein. But just a few decades ago, this problem remained a thorny one. Welcome Bender of Harvard Medical School—with his work teasing out the function of the bithorax complex in Drosophila—made key advances […]]]>

Welcome BenderToday it’s easy to take for granted that geneticists can identify a mutation, find its gene, and map it to the expressed protein. But just a few decades ago, this problem remained a thorny one. Welcome Bender of Harvard Medical School—with his work teasing out the function of the bithorax complex in Drosophila—made key advances in this area. For the development of positional cloning approaches and his creative, in-depth exploration of the function of the bithorax complex, Bender has received the Genetics Society of America’s 2020 Edward Novitski Prize for extraordinary creativity and intellectual ingenuity in solving significant problems in genetics research.

“Welcome Bender opened up the fields of developmental and disease genetics for years to come,” says Mark Peifer of the University of North Carolina, Bender’s former graduate student and one of the scientists who nominated him for the award. “Working in Dave Hogness’s lab, where molecular biology was first applied to Drosophila, Welcome invented a simple but conceptually ingenious idea for positional cloning: Look for a clone in the rough region of the genome and use this as a toehold. Then isolate a larger genomic region overlapping this original clone and use the most distal sequences in that region to iteratively repeat the process.”

Bender’s interest in Drosophila genetics started during his final year as a Harvard undergraduate, which he spent at the MRC Laboratory, working down the hall from Francis Crick and Sydney Brenner. At the time, Crick was excited about fruit flies and the notion of one-band, one-gene, Bender recalls. “When I then began graduate work, I, I imagined that I was going to figure out how to do a transformation into fruit flies.” That idea crashed and burned, he notes. “I was ahead of my time in ideas and behind my time in capabilities.”

Bender completed his PhD at Caltech with Norman Davidson while focusing on RNA tumor viruses, but his interest in Drosophila genetics continued. For his postdoc, he chose to work on recombinant DNA in fruit flies with David Hogness at Stanford. At the time, he says, the biggest challenge was getting access to interesting genes with a history, such as the rosy locus studied by Art Chovnick or the bithorax complex studied by Ed Lewis.

When he started working on positional cloning in the Hogness lab, Bender thought he could divide the Drosophila genome into restriction fragments and separate them with 2-D gel electrophoresis, comparing wild-type fly strains with those that had deletions in an interesting region. “It was a disaster,” Bender says. “At the time we didn’t appreciate that there were so many mobile elements in flies and that every strain had a distinct collection of them.” Plan B involved “walking” along a chromosome with overlapping recombinant clones. (It was a close collaboration with Pierre Spierer, another postdoc.) The walk quickly bumped into a mobile element, which had also inserted into many other places in the genome. This repeat blocked the recovery of a unique overlap. That’s where using different genetic libraries from distinct Drosophila strains—one developed by Elliot Meyerowitz in the Hogness lab and another developed by Joyce Lauer in the Maniatis lab—proved fruitful. The mobile element blockage in one library was absent in the other. Bender also harnessed his knowledge of electron microscopy with nucleic acids, a technique he’d learned in Davidson’s lab. Because they could use heteroduplexing to follow overlaps between two clones, they could unravel tricky genetic problems, including a rearrangement within the bithorax complex that would have been difficult to identify by other methods.

After Bender had launched his own lab at Harvard Medical School, he, Peifer and postdoc François Karch published an influential 1987 review article in Genes & Development outlining the layout and logic of the bithorax complex. “The notion was that the bithorax complex is made up of a series of domains of DNA segments, each of which is responsible for the regulation of a different segment. It’s not that you turn on a gene everywhere in a segment,” he says. Instead each domain is a group of cis regulatory elements that elaborate a pattern in time and space of the small number of transcription factors encoded within the complex. “So the pattern gets richer as you go further back in the animal.” Bender’s lab would then validate this model, initially by characterizing many spontaneous and induced mutations from Ed Lewis’ collection.

Bender’s team and many other labs used the P element to make transgenic flies, and many of these P element insertions landed within the bithorax complex. P elements carrying a reporter gene, like beta galactosidase, were restricted in their expression to particular segments, depending on the position of the insertion within the complex. By following gene expression patterns, they could outline the layout and logic of this complex regulatory network. P elements could also be mobilized by the P transposase, leaving a double stranded break at the insertion site. Bill Engels had shown that such breaks could be used for gene conversion. The Bender lab used that strategy to patch in sequences of interest, a strategy that gave them CRISPR-like gene editing capabilities years before CRISPR was developed. This permitted a series of elegant experiments, many in collaboration with Karch’s group at the University of Geneva.

Bender’s team has gone on to use these tools to map the topology of the bithorax complex, looking at the way that the Polycomb system of repression restricts access to silenced genes. “Bender envisioned that chromosomal structure or chromosomal domains played a fundamental role in the regulation of the BX-C cluster more than a decade before the proposed histone code hypothesis,” adds Karch, who also nominated Bender for the award.

Bender takes a focused research approach, modeled after Ed Lewis. He says, “I think you want to find a problem, a gene, where you have a lot of information on a small amount of biology and grind down until you’re sure you understand it.”


The Edward Novitski Prize recognizes an extraordinary level of creativity and intellectual ingenuity in the solution of significant problems in genetics research. The prize honors scientific achievement that stands out from other innovative work, that is deeply impressive to creative masters in the field, and that solves a difficult problem in genetics. It also recognizes the beautiful and intellectually ingenious experimental design and execution involved in genetics scientific discovery. Bender will accept the award at TAGC 2020 Online.

The next nomination period will open in May 2020.

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GSA awards 2020 George W. Beadle Award to Julie Ahringer //www.abewal.com/gsa-awards-2020-george-w-beadle-award-to-julie-ahringer/ //www.abewal.com/gsa-awards-2020-george-w-beadle-award-to-julie-ahringer/#respond Mon, 20 Apr 2020 16:46:08 +0000 //www.abewal.com/?p=67134 Julie Ahringer has focused her career on understanding development and transcriptional regulation in Caenorhabditis elegans. Along the way her lab has built invaluable tools, including a genome-wide RNAi library, that have supported a huge range of discoveries across biology. In recognition of this work, Ahringer has been awarded the 2020 George W. Beadle Award from […]]]>

Julie AhringerJulie Ahringer has focused her career on understanding development and transcriptional regulation in Caenorhabditis elegans. Along the way her lab has built invaluable tools, including a genome-wide RNAi library, that have supported a huge range of discoveries across biology. In recognition of this work, Ahringer has been awarded the 2020 George W. Beadle Award from the Genetics Society of America for individuals who make outstanding contributions to the community of genetics researchers.

“Ahringer has distinguished herself in the areas of transcriptional regulation and genome architecture by posing insightful questions and producing groundbreaking publications,” says Judith Kimble of the University of Wisconsin-Madison, Ahringer’s PhD advisor and one of the researchers who nominated her for the award. “Her community contributions have focused on C. elegans research, but her impact reaches far beyond.”

Ahringer originally thought she’d become an engineer, but after two years of coursework at Lafayette College, she was struggling to choose an undergraduate major. To take her mind off the decision, she read a magazine article about Barbara McClintock and her discovery of DNA transposition, and she immediately decided to turn her problem-solving skills toward making new biological discoveries. Ahringer majored in chemistry, pursued a PhD in biochemistry, and has never looked back.

Her engineer-like approach to detail and methods have served her well in genetics. She started working on C. elegans with Kimble at the University of Wisconsin. “It’s a beautiful and simple animal, having just 1000 somatic cells. It grows from an egg to an adult in three days and is transparent, so you can watch it develop. It’s a great system for studying nearly any aspect of biology.” she says.

As a postdoc she moved to the MRC Laboratory for Molecular Biology in Cambridge UK, where she studied embryogenesis by making 4D videos of C. elegans mutants using techniques developed in her advisor John White’s group. Working on a mutant of a heterotrimeric G-protein developed by Ronald Plasterk, she helped to uncover the role of the protein in spindle orientation. Her independent lab at the Gurdon Institute launched with studies of spindle orientation and cell polarity and has evolved to focus on chromatin and gene expression in worms.

The C. elegans RNAi feeding library developed out of the Ahringer lab’s search for genes involved in early embryo development and cell polarity. The original plan was to use RNAi to silence thousands of genes by injection in pools and then assess phenotypes of embryonic lethals using 4D videorecordings. “Then postdoc Andrew Fraser had the idea: ‘What if we could make an RNAi library, with a feeding clone for every gene?” The idea seemed a bit crazy and would need money, but Ahringer wrote a letter to the Wellcome Trust and within a week received a supplementary award of £70,000 to support the work. A three-person team set to work on protocols to make the library. After nine months, at the end of 1999, all procedures worked, and they churned out Chromosome I within a month, Ahringer recalls. “Initially, we thought this was mainly for our lab.” But then her group presented the work at conferences in 2000 and were mobbed with library requests. To finish the library, PhD student Ravi Kamath organized the work, and all eight lab members pitched in to make 16,757 RNAi clones.
“Her vision accelerated a stunning swath of C. elegans research. This accomplishment is simple to state but has had (and continues to have) huge impact on the community,” says Paul Sternberg of Caltech, who also nominated Ahringer for the award. “What’s been really rewarding is seeing all the great science that’s been done with the library and across every kind of biology,” Ahringer says.

More recently Ahringer’s group has focused on chromatin and gene expression regulation in C. elegans. They started working on genome-wide mapping of different types of chromatin and where different proteins are binding. They then needed to figure out exactly where promoters were located. This wasn’t yet known because in worms, unlike many other organisms, messenger RNAs are trans-spliced, meaning that promoter locations can’t be inferred from the beginning of the mRNA sequence. That led to painstaking work to identify 45,000 regulatory elements and annotate them. “That is essential because you can’t study transcription if you don’t know where the promoters and enhancers are,” says Ahringer. With those tools they have been studying tissue-specific activities, and they’re now studying how the genome is regulated on a cell-by-cell basis through specific developmental trajectories to understand how cell-type specific gene expression is achieved.

But as with the RNAi library, these datasets are supporting research outside Ahringer’s laboratory. “Her datasets defining regulatory elements, mapping histone modifications, and chromatin binding proteins have become crucial community resources,” Kimble adds. Ahringer has also produced software including BEADS to normalize ChIP-seq data and SeqPlots to visualize diverse genomic data. “Together, these contributions have provided critical tools and key datasets used worldwide,” Kimble says.

In addition to her problem-solving mindset, Ahringer says that watching the work on the worm and human genomes develop when she was a postdoc inspired her to pursue ambitious questions. Conversations at the pub on Friday evenings with John Sulston and other colleagues tossed around interesting ideas and how they might be achieved. “You can do anything if you can work out how to do it: You work out a procedure; you develop your methods; you apply them; and you can do it.” she says.


The George W. Beadle Award honors individuals who have made outstanding contributions to the community of genetics researchers. Ahringer will accept the award at TAGC 2020 Online.

The next nomination period will open in May 2020.

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The chaos of parenting and doing science during a pandemic //www.abewal.com/the-chaos-of-parenting-and-doing-science-during-a-pandemic/ //www.abewal.com/the-chaos-of-parenting-and-doing-science-during-a-pandemic/#respond Fri, 17 Apr 2020 21:03:37 +0000 //www.abewal.com/?p=67152 As COVID-19 spreads across the world, members of the GSA community have had to face unprecedented challenges in their professional and personal lives. To stay connected during this socially distant time, GSA invites the scientists in our community to share how they are meeting these challenges, as well as their questions and worries.  If you […]]]>

As COVID-19 spreads across the world, members of the GSA community have had to face unprecedented challenges in their professional and personal lives. To stay connected during this socially distant time, GSA invites the scientists in our community to share how they are meeting these challenges, as well as their questions and worries. 

If you would like to contribute to this series, please contact Communications Assistant Jacqueline Treboschi.


Guest post by Elisabeth Marnik, Ph.D.


As I write this, I can hear my one-year-old son screaming in delight as he pushes his walker around the house. I can also hear the echoes of my husband’s fifteenth conference call of the day. Our house is nowhere big enough for the three of us right now. I long for the solitude of days in the lab where I could listen to things of my choosing or just bask in the quiet with a cup of coffee and my computer. I am a postdoc who works with C. elegans, and luckily, I was able to bring home a microscope and incubator to finish some ongoing experiments while minimizing physical lab presence. I am grateful for this option, but now most of my day is spent juggling barely controlled chaos—and it is hard and exhausting.

I am new at managing parenting and science in general. I had just started being comfortable in my new rhythm of science and motherhood when the pandemic hit and daycares closed. Life is now upside down as my husband and I try balancing two full-time jobs with childcare. I am also navigating the intense and overwhelming anxiety I feel for everyone I love, and the world in general, as COVID-19 explodes. Even in my moments of quiet, I often find myself struggling between organizing data for a figure, trying to entertain my son, crying, or obsessing over the newest COVID-19 news and research. It is all impossible. At the end of the day, I am often left feeling like an utter failure as a mother and as a scientist.

I’ve finally realized that this is not sustainable. We are three and a half weeks into a process that has no end in sight yet. It is impossible for me to get as much work done as I did before. No one can be both a stay at home parent and a full-time working parent. There are just not enough hours in the day. Thus, I have started making long to-do lists for the work I need to accomplish. I tell myself that even if I only check off the bare minimum that day, it is OK. I also keep telling myself that a little extra baby music videos aren’t going to ruin my son, and that as long as he is healthy and fed, my husband and I are doing a good job. I don’t need to be doing crafts with him every day to be a good mom.

I am also trying (with mixed success) to make time for self-care. For me this means running, lessening my media consumption, attending virtual therapy appointments, and enjoying weekly Zoom meetings with friends and family. I know that I am a better mom and scientist when I make time for these things, even if they are often the first things I want to cut when time is short.

I also recognize my privilege, even in this situation. I am lucky to have an equal partner, two paychecks, a supportive PI, and my own funding that makes many of my productivity worries internally, rather than externally, motivated . I know this is not universally the case. We are all struggling in our own ways, but some struggles are undoubtedly greater than others. I see you, and I wish I could help more.

Ultimately, I keep reminding myself that we are all living through a historic and unprecedented situation. We cannot hold ourselves to normal standards of parenting or science productivity. If you’re keeping your kids fed and safe, you’re winning. The rest is just a bonus. You are not alone if you feel like a failure or are struggling. I am there with you every single day. But one day this will be over. One day we will return to our labs, and our children will return to their schools and daycares.

In the meanwhile, please consider joining the GSA’s Parents in Science Slack channel so that we can start a community of support to help each other through this difficult time.


About the Author

Elisabeth MarnikElisabeth Marnik is a postdoctoral researcher in the Updike Lab at The MDI Biological Laboratory. Marnik is a member of the GSA’s Conference Childcare Committee and a GSA Early Career Scientist Leader (Communication and Outreach Subcommittee).

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