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Dave Jackson. Photo from CSHL

By Daniel Dunaief

Just as humans have competing impulses — should we eat or exercise, should we wait outside in the rain to meet a potential date or seek shelter, should we invest in a Spanish tutor or a lacrosse coach — so, too, do plants, albeit not through the same deliberate abstract process.

Working with corn, Dave Jackson, a professor at Cold Spring Harbor Laboratory, has discovered that the gene Gß, (pronounced Gee-Beta,) balances between the competing need to grow and to defend itself against myriad potential threats.

By looking at variations in the gene, Jackson and his postdoctoral fellows, including Qingyu Wu and Fang Xu, have found that some changes in Gß can lead to corn ears with more kernels. The results of this work, which were published in the Proceedings of the National Academy of Sciences last month, suggest that altering this gene may eventually increase the productivity of agricultural crops.

Indeed, the study of this gene included an analysis of why some mutations are lethal. An overactive Gß gene turns the corn brown and kills it. This occurs because the gene cranks up the immune system, causing the plant to attack itself.

Other scientists have found mutations in this gene in plants including arabodopsis and rice.

“We are the first to figure out why the mutations are lethal in corn,” Jackson said. “That’s also true in rice. Rice mutations were made over a decade ago and they also caused the plants to die. Nobody knew why. The main puzzle was solved.”

Dialing back this immune response, however, can encourage the plant to dedicate more resources to growth, although Jackson cautions that the research hasn’t reached the point where scientists or farmers could fine tune the balance between growth and defense.

“We are not there yet,” he said. “That’s what would be possible, based on this knowledge.”

Even in the safer environment of an agricultural field, however, plants can’t abandon all efforts at defense.

“Plants need some defense, but probably much less than if they were growing in the wild,” he said.

By altering the balance toward growth, Jackson is looking at mutations that make more stem cells, which can produce flowers and, eventually kernels. The next steps in this research will not likely include scientists in Jackson’s lab. Qingyu Wu plans to move on to a research position in China. 

Penelope Lindsay. Photo by Patricia Waldron

A prolific plant scientist and mentor, Jackson has seen several of his lab members leave CSHL to pursue other opportunities. Recently, he has added three new postdoctoral researchers to his team: Thu Tran, Jae Hyung Lee and Penelope Lindsay.

Jackson plans to use single-cell sequencing in his future research. Using this technique, scientists can find regulatory relationships between genes and monitor cell lineages in development. Jackson described this approach as an “amazing new technology” that’s only been around for a few years. He hopes to use this technique to find new leads into genes that control growth.

Lindsay, who is joining the lab this month, would like to build on her experience as a plant biologist by adding computational expertise. A graduate of the Boyce Thompson Institute in upstate Ithaca, where she was working on the symbiotic relationship between some plants and a specific type of fungi in the soil, Lindsay would also like to work on single-cell sequencing. She plans to continue to study “how specific genotypes produce a phenotype” or how its genes affect what it becomes.

Jackson’s lab’s focus on the undifferentiated cells of the meristem appealed to Lindsay.

Lindsay first met Jackson a few years ago, when he was giving a talk at Cornell University. It was there, fittingly enough, that she had learned about the work that led to the current paper in the Proceedings of the National Academy of Sciences about growth versus defense.

“I was really impressed with the techniques and with the connection to basic research,” Lindsay said. She was excited to learn how Jackson and his students took biochemical approaches to understand how this signaling pathway affected development.

Cold Spring Harbor Laboratory also intrigued Lindsay, who was interested to join a facility that encouraged collaborations among labs.

Born in New York City, Lindsay spent some of her time in upstate New York before moving to Florida, where she also attended college.

Surrounded by family members who have found outlets for their creativity through art — her mother, Michelle Cartaya, is an artist who takes nature photos and her father, Ned Lindsay, remodels homes — she initially attended New College of Florida in Sarasota expecting to pursue a degree in English. Once in college, however, she found excellent scientific mentors, who encouraged her to pursue research.

As a graduate student, Lindsay was greatly intrigued by the signaling pathway between plants and the symbiotic relationship with arbuscular mycorrhizal fungi. During her graduate work, she studied a mutated version of a plant that lacked a signaling protein that encourages this collaboration. When she added considerable amount of the protein to the plant, she expected to restore the symbiosis, but she found the exact opposite.

“The amount of the protein is critical,” she said. “If you have too much, that’s a bad thing. If you don’t have enough, it’s also bad. It’s like Goldilocks.”

A new resident of Huntington, Lindsay, who was a disc jockey for a community radio station in Ithaca and makes electronic music using synthesizers and computers, is looking forward to starting her work at Cold Spring Harbor Laboratory and to living near New York City.

Lindsay continues to find plants fascinating because they “get everything they need” while living in one place their entire lives. “They have so many sophisticated biochemical pathways to protect themselves,” she said.

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Saket Navlakha

By Daniel Dunaief

Plants have to solve challenges in their environment – without a brain or the kind of mobility mammals rely on to survive – through strategies and computations that keep them alive and allow them to reproduce.

Intrigued by plants and by the neurobiology that affect decisions or behavior in a range of other organisms, Associate Professor Saket Navlakha recently joined Cold Spring Harbor Laboratory to study the processes a range of organisms use.

“Biological systems have to solve problems to survive,” said Navlakha. “The hope is that by studying these algorithms, we can inspire new methods for computer science and engineering and, at the same time, come up with new ways to predict and model behaviors of these systems.”

Navlakha, who has a doctorate in computer science from the University of Maryland College Park and conducted postdoctoral research at Carnegie Mellon University’s Machine Learning Department, focuses on the “algorithms of nature,” in which organisms evolved ways to solve problems that enhance the likelihood of their survival.

In his first three months at CSHL, Navlakha plans to do an interview tour, speaking with researchers who study cancer, molecular biology, neurology and plants.

While his primary areas of focus have been on plants and neurobiology, he appreciates that the internationally recognized research facility presents “new opportunities” for him and a lab in which he intends to hire four to six scientists over the next two years.

Adam Siepel, the chair of the Simons Center for Quantitative Biology and professor at the Watson School of Biological Sciences at Cold Spring Harbor Laboratory, led the recruitment of Navlakha.

In an email, Siepel wrote that Navlakha “immediately struck us as an ideal candidate for the center” in part because he is a “free thinker with an eye for interesting and important problems in biology.”

Navlakha believes processes and strategies that foster survival spring from a set of principles that helps them thrive and adapt. In 2018, when he was at the Salk Center for Integrative Biology, he wrote a piece for Wired magazine about species extinction. “By not preserving [species that become extinct], we are losing out on interesting ideas that evolution gave them to survive,” he said.

Even amid these losses, however, Navlakha recognizes the lessons computer scientists and engineers like him can learn. Through losses and failures, humans can understand the limitations of algorithms that only allowed a species to survive up to a point, as conditions pushed its algorithms past a tipping point.

At its core, Navlakha’s approach to these algorithms includes the idea that biological systems perform computations. He originally studied brains because they are “such an elegant computer, doing all kinds of things that modern, human-made computers can’t do,” he said.

When he was at the Salk Institute, he spoke with colleagues in plant biology who told him about research that examined how plants modify their shape amid a changing environment, which is what triggered his interest in plants.

One of the themes of his work involves understanding trade-offs. Doing well in one task typically means doing worse in another. He likened this analysis to investing in stocks. An investor can put considerable funds into one stock, like Apple, or diversify a portfolio, investing less money per stock in a variety of companies from different sectors.

“We’ve been studying how plants hedge” their bets, he said. The hedge in this description bears no relation to a collection of plants at the edge of a property.

A plant can create one huge seed that might survive a drought or other environmental threat, or it can diversify the types of seeds. “We’re really interested in understanding these trade-offs, how they hedge, and what kind of strategies” they employ, he said.

Ziv Bar-Joseph, a professor of computer science at Carnegie Mellon University who has known Navlakha for over eight years, suggested Navlakha has “deep insights.” 

In an email, Bar-Joseph described Navlakha’s biggest achievement as his work that shows how the brain uses a computational method to store and retrieve smells. 

“This work both solved an important mystery about how the brain functions and informed us on novel usages of an important computational method, thus contributing to both areas,” Bar-Joseph explained.

Navlakha doesn’t have a typical laboratory filled with beakers, pipettes or plants growing under various conditions. He relies on wet labs to provide data that he then interprets and analyzes as a part of the Simons Center for Quantitative Biology. While his training is in computer science, he has shown a talent for experimental research as well. 

Bar-Joseph recalled how Navlakha performed experiments and analysis. In a short time, Navlakha “was able to master very involved techniques and obtained very good results.” 

Navlakha explained that the work he does colors the way he sees the world. “People walk by plants without paying attention to the incredible computations that they’re doing to keep us on this planet,” he said. “Computation is the basis of life.”

A resident of Great Neck, Navlakha recently married Sejal Morjaria, an infectious disease physician at Sloan Kettering, who works with patients who have cancer. The couple met through an online dating app when he was in San Diego and she lived in New York. They chatted for a while without any expectation of seeing each other, until he traveled to Washington, D.C                                 for a conference.

Navlakha enjoys playing numerous sports, including tennis and basketball. He also played hockey. He and Morjaria participate in yoga classes together.

Navlakha, who grew up in Miami, Florida, said he had to readjust to life on Long Island after living in Southern California for several years. “San Diego makes you weak,” he joked.

In his work, Navlakha hopes to bring together two fields in a different way.

Given the importance of computations, Navlakha appreciates a corollary to the concept proposed by Rene Descartes’ “I think, therefore I am.” For Navlakha, “I compute, therefore I am” describes processes he studies among animals and plants.

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the U.S. Department of Energy awarded a 10-year multi-billion project to build a new electron-ion collider at Brookhaven National Laboratory in Upton. Provide photo from Brookhaven National Lab

By Daniel Dunaief

Through answers to basic questions, scientists develop new technology that changes the world, leading to medical breakthroughs, energy applications and national security devices.

That’s the theory behind the U.S. Department of Energy’s decision last week to award a 10-year project that will cost between $1.6 billion and $2.6 billion to build a new electron-ion collider at Brookhaven National Laboratory in Upton. 

For the scientists, the discoveries will flow from answers to questions about the nature of visible matter.

“The big science we’re excited about, the hundred-year-old questions, are things like where does the mass of a proton come from,” said Robert Tribble, the deputy director for science and technology at Brookhaven National Laboratory and a nuclear physicist. The EIC is like a microscope to look at quarks and gluons, he explained.

With support from numerous New York State and Long Island leaders, BNL recently won a competition against Thomas Jefferson National Accelerator in Virginia to build an electron-ion collider. Members of the Jefferson Accelerator, as well as over 1,000 scientists from 30 nations, will partner with BNL staff to conceptualize and build the new collider, which will be the most advanced ever constructed.

In addition to understanding atomic nuclei, we will be able to generate a better view of the universe writ large [with discoveries from the EIC].”

– Robert Tribble

“We do not understand very dense matter that exists in the universe in objects like neutron stars and black holes,” Tribble explained in an email. “In addition to understanding atomic nuclei, we will be able to generate a better view of the universe writ large [with discoveries from the EIC].”

Over the next decade, the construction of the new EIC will employ 4,000 people, said Doon Gibbs, the laboratory director at BNL. That number represents the workforce that will, at one time or another, contribute to the construction of this new facility. 

The new EIC will expand on the technology of the Relativistic Heavy Ion Collider, which has been operating since 2000 and will stop running experiments in 2024. Indeed, part of the appeal of BNL as a site for this new facility arose out of the ability to extend the resources by building a new electron storage ring and electron accelerator elements.

Researchers will collide electrons and protons and numerous atomic nuclei to study the strong nuclear force. These collisions will reveal how the subunits of protons and neutrons in the nucleus, namely the quarks and gluons, come together to help generate mass in visible matter.

The staff at BNL is “delighted and excited” that the site for the EIC will be on Long Island, said Gibbs. “Our design has the capability of using many existing technologies and extending them farther than they’ve been before.”

Indeed, even the conception of the EIC has led to some new scientific breakthroughs, some of which the lab and its partners will share with the public in the next few weeks.

While the application of research at the EIC will likely lead to breakthroughs in fields including materials science, researchers at BNL are excited about basic questions about the nature of nuclear matter.

A typical experiment at the EIC will likely follow the same pattern as it has with RHIC, in which hundreds of researchers from around the world collaborate to understand physics properties. In the next few years, researchers will develop a detailed design before they start construction.

“We love challenges at BNL, we like building big machines. We’re good at it. We have a whole class of staff who, in particular, are experts at this kind of activity and they are pretty excited.”

– Doon Gibbs

Gibbs said the facility has a strong handle on the safety features of the new collider, which will build on the protocols and designs developed at the RHIC as well as with the National Synchrotron Light Source II, also at the lab in Upton.

“We love challenges at BNL,” Gibbs said. “We like building big machines. We’re good at it. We have a whole class of staff who, in particular, are experts at this kind of activity and they are pretty excited.”

Area politicians are also excited about discoveries in basic science, translational benefits in areas like medicine and the expected boost to the local economy.

“Establishing the electron-ion collider on Long Island might be focused on particles, but it will add some serious mass — nearly $1 billion worth — to the local economy,” U.S. Sen. Chuck Schumer (D) said in a statement. BNL has the “talent, the technology and the track record to make the most of this national project.”

Schumer believes this project will guarantee that BNL continues to be a “world class research facility for the next generation.”

U.S. Rep. Lee Zeldin (R-Shirley) praised the leadership at BNL.

“I congratulate BNL Director Doon Gibbs for leading this exceptional organization and all of its scientists who have worked incredibly hard every step of the way to make this possible, and can’t wait to see what they do next,” Zeldin said in a statement.

 

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Donghui Zhu

By Daniel Dunaief

About 5 percent of people who suffer from Alzheimer’s disease have a genetic mutation that likely contributed to a condition that causes cognitive declines.

That means the vast majority of people with Alzheimer’s have other risk factors.

Donghui Zhu, an associate professor of biomedical engineering in the Institute for Engineering-Driven Medicine who joined Stony Brook University this summer, believes that age-related decline in the presence of the element magnesium in the brain may exacerbate or contribute to Alzheimer’s.

Donghui Zhu

The National Institutes of Health believes the former associate professor at the University of North Texas may be on the right track, awarding Zhu $3.5 million in funding. Zhu believes magnesium helps prevent the loss of neurons, in part because of the connection between this element, inflammation and the development of Alzheimer’s.

Numerous other factors may also contribute to the development of Alzheimer’s. Diabetes, lifestyle, a specific sleep cycle and low exercise levels may all play a role in leading to cognitive declines associated with Alzheimer’s, Zhu said.

According to some prior research, people with Alzheimer’s have a lower level of free magnesium in their body and in their serum levels than people who don’t suffer from this disease, he added.

In the short term, he aspires to try to link the magnesium deficiency to neuronal inflammation and Alzheimer’s disease.

Zhu plans to use some of the funds from the grant, which will run for the next five years, on animal models of Alzheimer’s. If his study shows that a lower level of magnesium contributes to inflammation and the condition, he would like to add magnesium back to their systems. Magnesium acts as an antioxidant and an anti-inflammatory agent.

“If we supply a sufficient amount of magnesium, can we slow down or reverse the process of this disease?” Zhu asked. “We hope it would.”

Any potential cognitive improvement in animal models might offer a promising alternative to current treatments, which often only have limited to moderate effects on patient symptoms.

In the longer term, Zhu would like to contribute to an understanding of why Alzheimer’s disease develops in the first place. Knowing that would lead to other alternative treatments as well.

“I don’t think my group or we alone can solve this puzzle,” he said. “We are all trying to chip in so the scientific community can have an answer or solution for the public.”

Like people with many other diseases or disorders, any two people with an Alzheimer’s diagnosis don’t necessarily have the same causes or type of the progressive disorder.

Women represent two-thirds of the Alzheimer’s population. Zhu said this isn’t linked to the longer life span for women, but may be more of a by-product of the change in female hormones over time.

In his research, he plans to study female and male animal models separately, as he looks to understand how the causes and progression of the disease may differ by gender.

In the human population, scientists have linked drug addiction or alcoholism with a higher risk of developing Alzheimer’s. He plans to perform additional studies of this connection as well.

“It’s the consensus in the community that alcohol addiction will increase the risk of developing Alzheimer’s disease,” Zhu said. People who consume considerable alcohol have reduced blood flow to the brain that can endanger or threaten the survival of blood vessels.

“This is another topic of interest to us,” he added.

Zhu is collaborating with other experts in drug addiction studies to explore the link with Alzheimer’s. 

In his research, he hopes to link his background in biology and engineering to tackle a range of translational problems. 

Stefan Judex, a professor and interim chair in the Department of Biomedical Engineering at Stony Brook, is excited about the potential for Zhu’s work.

Zhu is “a fast rising star in the field of biomaterials and fills a gap in our department and the university,” Judex explained in an email. “He is well-equipped to apply his unique research skills to a number of diseases, ultimately aiding in preventing and treating those conditions.”

In addition to his work on Alzheimer’s, Zhu also pursues studies in several other areas, including nano-biomaterials, biodegradable or bio-resorbable materials, regenerative medicine for cardiovascular and orthopedic applications, and drug delivery device and platforms

During his doctoral studies and training at the University of Missouri in Columbia, he focused on dementia and neuron science, while his postdoctoral research at the University of Rochester involved engineering, where he did considerable work on tissue engineering and biomaterials.

Zhu decided he had the right training and experience to do both, which is how he picked up on tissue engineering, regenerative medicine and neuroscience.

“They are not totally exclusive to each other,” he said. “There are many common theories or technologies, methods and models we can share.”

Adults don’t generate or create new neurons. He hopes in the future that an engineering approach may help to reconnect neurons that may have lost their interaction with their neighbors, in part through small magnesium wires that can “help guide their reconnection,” which is, he said, a typical example of how to use biomaterials to promote neuro-regeneration.

In his lab, he works on the intersection between engineering and medicine. The interdisciplinary and translational nature of the research attracted him to the new Institute for Engineering-Driven Medicine at Stony Brook.

He described Stony Brook as the “total package for me” because it has a medical school and hospital, as well as an engineering department and entrepreneurial support.

He has already filed numerous patents and would like to form start-up companies to apply his research.

Judex wrote that he is “incredibly pleased and proud that Dr. Zhu joined” Stony Brook and that it is “incredible that he received this large grant within the first few months since his start.”

In his career, Zhu would like to contribute to new treatments.

“Some day,” he said, he hopes to “put a real product on the market.”

 

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Nicholas Gladman with a harvest of sorghum at Cornell University’s Long Island Horticultural Research Lab in Riverhead. Photo by Sendi Mejia

By Daniel Dunaief

When people buy a bag of potato chips, they often find that half of the bag is filled with air. The same is true of a sorghum plant, which produces livestock feed and is converted into ethanol, part of many gases that power cars.

Nicholas Gladman

In a typical sorghum plant, half of the flowers become grain, while the other half remain infertile. As the world grapples with food shortages and scientists seek ways to increase the yield of a wide array of plants, researchers at Cold Spring Harbor Laboratory wondered whether they could increase that yield.

Building on previous work done in the lab of Doreen Ware, an adjunct professor at CSHL, postdoctoral fellow Nicholas Gladman characterized a mutation for a single gene that lowered the level of a hormone. The effect of the lower hormone, or jasmonic acid, at a specific time and place within plant development doubled the fertility of the sorghum plant.

“When we don’t have a functional version of this enzyme, it releases this form of development that wouldn’t normally occur,” Gladman said. “You get increased fertility in flowers.”

The gene they studied is called MSD2. The researchers published their work in International Journal of Molecular Sciences. Another gene, MSD1, which Ware’s lab characterized in 2018, is a likely regulator for MSD2. Other genes may also serve as regulators of MSD2, Gladman said. Disruptions in either gene leads to altered flower development and seed production.

Gladman’s postdoctoral research adviser Zhanguo Xin collaborated on the work. Xin, who is a research molecular biologist at the United States Department of Agriculture’s Agricultural Research Service, explained that Gladman characterized the mutants, identified the interaction between MSD1 and MSD2 and identified the regulatory sequences of MSD1.

This research could extend to other cereal crops, which have the same conserved sets of genes that affect their growth and fertility.

A concern in altering any gene resides in the overall effect on the health of the plant. Creating a super plant that falls over and dies in a slight wind, can’t fend off common infections, or requires a perfect blend of soil would likely offset the benefit of the increased fertility. Plant geneticists would like to ensure any mutation doesn’t make the plant less viable in the long run.

“Sometimes there can be a trade off between an agriculturally beneficial genetic change by introducing other detrimental effects,” Gladman explained in an email. “Optimally, plant geneticists will try to ensure the side effects of any mutation are insignificant to farmers; sometimes, this is more difficult and the downsides may not always present themselves at the early stages of lab investigation.”

This particular gene is narrowly and spatially expressed within the plant, Gladman said, and the researchers haven’t been able to identify or quantify the effect of this gene on anything else other than flowers and floral architecture.

The gene and the hormone would be a concern if it were expressed more broadly and at high levels throughout other plant tissues, but that doesn’t seem to be the case, he said.

The researchers have looked at other tissues, such as the leaf and stem, and have found that MSD2 is expressed in low levels in these other areas. Plants that have the MSD2 mutation do not demonstrate any noticeable differences in growth compared to nonmutants in the field or in greenhouse conditions. If this mutated gene had an agricultural benefit, farmers would likely crossbreed a plant that had this gene with an elite sorghum hybrid line

Ideally, the benefits of the increased fertility would combine with benefits of all the genetic components of the hybrid lines as well. The way the researchers involved in this study produced this more fertile version of sorghum is an “acceptable type of breeding for organic or conventional farming,” Gladman said.

While the plant increases the grain number per seed head, it doesn’t necessarily produce greater overall yield in part because the seeds are smaller. Researchers haven’t been able to confirm that yet in a field condition, although they hope that’s the case.

Gladman was grateful for the opportunity to work in Ware’s lab and to collaborate with Xin. The effects of disrupting similar genes in maize and Arabidopsis, which is a plant in the mustard family that scientists often use in genetic studies, influences flower fertility.

He said researchers in Ware’s lab can perform additional developmental analysis. The researchers in Ware’s lab may seek additional collaborators for other analyses down the road as well.

“How this particular pathway is triggered and cross-communicates with other developmental pathways is very complex, but influences so much about traits that control grain production and yield that it is essential for further investigations,” he explained.

Gladman arrived at Cold Spring Harbor Laboratory in 2017. Prior to conducting research on Long Island, he finished his doctorate at the University of Wisconsin at Madison, where he worked on Arabidopsis. He decided he wanted to get more involved with crop species and explored research opportunities at United States Department of Agriculture labs. He was working with Xin in Lubbock, Texas, before transitioning to Cold Spring Harbor Laboratory.

Gladman has been delighted by the “wonderful place to learn,” where he is surrounded by “people who are always willing to talk and engage and collaborate.”

A resident of Greenlawn, Gladman enjoys hiking along the Hudson and in the Adirondacks. He credits a high school biology class he took in Grandview Heights High School in Columbus, Ohio, with instilling in him and his three brothers an appreciation and love of science. He particularly enjoyed a unit on the “genetics of disease” that inspired him to pursue a career in the sciences.

As for his work, Gladman is excited to be a part of research that may, one day, increase the productivity of crop species. He said thoughts about food shortages are “a constant concern and driver of our research.”

 

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Interns Nylette Lopez (rear) and Stephanie Taboada characterize catalysts as they attempt to convert carbon dioxide and methane into synthesis gas this past summer at Brookhaven National Laboratory. Photo from BNL.

By Daniel Dunaief

This article is part two in a two-part series.

Local medical and research institutions are aware of the challenges women face in science and are taking steps to ensure that women receive equal opportunities for success in science, technology, engineering and mathematics (or STEM). Times Beacon Record News Media reached out to members of each institution and received an overview of some initiatives.

Brookhaven National Laboratory 

The Department of Energy-funded research facility has created a number of opportunities for women, including Brookhaven Women in Science. This effort has been active for over four decades and its mission, according to Peter Genzer, a BNL spokesman, is to support the development of models, policies and practices that enhance the quality of life for BNL employees and emphasize the recruitment, hiring, promotion and retention of women.

BWIS offers annual awards, outreach events and various networking opportunities in the lab and community, while the lab’s Talent Management Group partners with BWIS to bring classes and speakers to discuss issues specific to women.

In October, the group hosted Kimberly Jackson, a vice chair and associate professor of chemistry and biochemistry at Spelman College, who gave a talk titled “Realigning the Crooked Room in STEM.”

The Leona Woods Distinguished Postdoctoral Lectureship Award at BNL, meanwhile, celebrates the scientific accomplishments of female physicists, physicists from under-represented minority groups and LGBTQ physicists and to promote diversity and inclusion. BNL awarded the lectureship this year to Kirsty Duffy, a fellow at Fermi National Accelerator Laboratory.

For the past five years, BNL has also partnered with a local chapter of Girls Inc., which helps to “encourage young women towards careers” in STEM, Genzer explained in an email.

BNL has also collaborated with the Girl Scouts of Suffolk County to organize a new patch program that encourages Girl Scouts to work in scientific fields. As of September, county Girl Scouts can earn three new Brookhaven Lab patches, and the lab hopes to extend the program nationwide across the Department of Energy complex.

BNL also provides six weeks of paid time off at 100 percent of base pay for a primary caregiver after birth or adoption and one week of full pay for a secondary caregiver. BNL is exploring plans to enhance support for primary and secondary caregivers, Genzer said.

Cold Spring Harbor Laboratory

Cold Spring Harbor Laboratory has taken several recent steps as part of an ongoing effort to encourage gender diversity.

In October, a group of four CSHL administrators traveled to the University of Wisconsin in Madison to discuss mentoring. The goal was to train them on how to design and deliver mentoring training regularly to the faculty, postdocs and graduate students on campus, said Charla Lambert, the diversity, equity and inclusion officer for research at CSHL. The first version of the training will occur next spring. The ultimate goal is to ensure the research environment at CSHL emphasizes good mentoring practices and is more inclusive for all mentees.

CSHL has also hosted a three-day workshop in leadership practices for postdoctoral researchers and junior faculty since 2011. The workshop, which is run through the Meetings & Courses Program, trains about 25 postdoctoral researchers and junior faculty each year and has about one per year from CSHL, addresses how to hire and motivate people, while providing constructive feedback.

Lambert said family-friendly policies were already a part of CSHL policies, which include a child care facility. Members of the faculty receive extra funding when they travel to conferences to provide additional child care.

Lambert, who is a program manager for extramural Meetings & Courses overseeing diversity initiatives, has worked to get the demographic data for participants centralized, analyzed and used in developing policies. She believes this kind of data centralization is an area for potential improvement in the research division, where she is working to ensure an equitable distribution of resources among CSHL scientists.

Throughout her nine-year career at CSHL, Lambert said she has worked with the meetings and courses division to make sure the 9,000 scientists who visit the facility each year include women as invited speakers. She also works to reach course applicants from a wide range of institutions, including outside of prestigious research schools.

Ultimately, Lambert is hoping to help change the culture of science among the researchers with whom she interacts from a wide range of institutions. She feels that those people who leave the STEM fields because something about the culture of science didn’t work for them represent a “huge loss” to the field and creates a “survivorship bias.”

Stony Brook University 

For Stony Brook, gender diversity is “very important,” said Latha Chandran, the vice dean for Academic and Faculty Affairs at the Stony Brook University Renaissance School of Medicine. 

Chandran said more men entered the field of medicine 14 years ago. That has completely changed, as women have outnumbered their male counterparts in medicine for the last three or four years.

Chandran cited a number of statistics to indicate changes at the medical school. For starters, women faculty constituted 38 percent of the total in 2011. This April, that number climbed to 48.1 percent. That puts Stony Brook in the top 79th percentile of medical schools in terms of female representation.

While the overall numbers are higher, women are still underrepresented in the top tiers of the medical school, as 18 percent of the department chairs are women. She hopes more women can lead departments and that they can serve as role models that others can aspire to follow.

As for harassment, Chandran said Stony Brook was above the national mean in 2011. For almost all categories, Stony Brook is now below the national mean.

In 2011, Stony Brook created We Smile, which stands for We can Eradicate Student Mistreatment in the Learning Environment. The goal of this program is to educate people about harassment and to ensure that any mistreatment is reported. Through this effort, Stony Brook medical students are aware of the policies and procedures surrounding reporting.

Stony Brook is also addressing any bias in admission procedures by prospective applicants, who receive a standardized scenario to address with an admissions officer. In 2025, admissions officers will not have any information about the qualifications of the individual and will evaluate his or her response during interviews only based on response to scenarios.

Stony Brook University has almost finalized its search for a chief diversity candidate. Chandran expects that the medical school will “continue to make progress.”

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Photo by ©Constance Brukin, 2018/ CSHL

By Daniel Dunaief

This article is part one in a two-part series.

Women have made great strides in science, but they haven’t yet found equal opportunity or a harassment-free work environment.

After the National Academy of Sciences published a study in 2018 that highlighted sexual harassment and unconscious bias, a team of scientists came together at Cold Spring Harbor Laboratory last December to discuss ways to improve the work environment.

Led by Carol Greider, an alumni of CSHL and the director of molecular biology and genetics at Johns Hopkins and a Nobel Laureate, and Jason Sheltzer, a fellow at CSHL, the group recently released its recommendations in the journal Science.

While the atmosphere and opportunities have changed, “It’s not a clear-cut enlightenment and everybody is on board,” said Leemor Joshua-Tor, a professor at CSHL and a member of the group that discussed the challenges women face in science at the Banbury Center last year.

The Science article highlights earlier work that estimates that 58 percent of women experienced unwanted sexual attention or advances at some point in their careers. The authors write that this harassment is often ignored or excused, which can cause talented and capable women to leave the field of scientific research.

A member of the group that came together to discuss how to continue to build on the progress women have made in the STEM fields, Nancy Hopkins, an Amgen Inc. professor of biology emerita at the Massachusetts Institute of Technology, helped bring attention to the disparity between opportunities for men and women in science in the 1990s.

“My generation pushed [opportunities for women] forward and got through the door,” Hopkins said. “We found out that when you get through the door, the playing field wasn’t level.”

Hopkins said the progress is “still not enough” and that leaders like Greider and Sheltzer, whom she praised for tackling this nettlesome issue, “are now identifying problems that we accepted.”

For starters, the group agrees with the National Academy of Sciences, Engineering and Medicine, which believes treating sexual harassment in the same way as scientific misconduct would help. 

The scientists, which include CSHL’s CEO Bruce Stillman, recommend creating institutional and government offices to address substantiated claims of sexual misconduct and to educate institutions on harassment policy, using the same structures for research misconduct as models. 

An office that verified these claims could offer reporting chains, consistent standards of evidence and defined protocols.

Additionally, the scientists believe researchers should have to answer questions from funding agencies about whether they have been found responsible for gender-based harassment at any point in the prior 10 years, as well as whether they have been a part of a settlement regarding a claim of professional misconduct, research misconduct or gender-based harassment in the same time period. 

This policy, they urge, could prevent institutions from tolerating serial offenders who have generated a high level of research funding over the years.

“People that go through a complete investigation and have been found to have committed egregious harassment [can] get a job somewhere else, where nobody knows and everything happens again,” Joshua-Tor said. This policy of needing to answer questions about harassment in the previous decade would prevent that scenario.

The dependence scientists have on lab leaders creates professional risk for students who report harassment. The fortunes of the trainees are “very much dependent on the principal investigator in an extreme way,” explained Joshua-Tor. Senior faculty members affect the future of their staff through letters of recommendation.

“There’s a lot at stake,” said Joshua-Tor, especially if these lab leaders lose their jobs. Indeed, their students may suffer from a loss of funding. The authors recommend finding another researcher with a proven track record of mentorship to manage the lab.

Even though many senior scientists have considerable responsibilities, Joshua-Tor said principal investigators have assumed mentorship duties for others in unusual circumstances. 

“There were cases where people died,” so other scientists in neighboring labs took over their staff, she explained.

If, however, the institution can’t find another researcher who is available to take on these additional responsibilities, the authors recommend that the funding agency make bridge funding available to these researchers.

In addition to claims of harassment, the scientists discussed the difficulty women face from conscious and unconscious bias.

Joshua-Tor recalls an experience in a physics lab when she was an undergraduate. She was a lab partner with a man who was a “fantastic theoretician,” but couldn’t put together an experiment, so she connected the circuits. “The professor would come and talk” to her lab partner about the experimental set up while ignoring her and treating her as if she were “air.”

The scientists cited how male postdoctoral researchers tend to receive higher salaries than their female counterparts, while male faculty also receive larger salaries and start-up offers. Men may also get a larger share of internal funding, as was alleged with a $42 million donation to the Salk Institute.

To provide fair salaries, institutions could create anonymized salary data to an internal committee or to an external advisory committee for regular review, the scientists suggested.

Additionally, the researchers urged work-life balance through family-friendly policies, which include encouraging funding agencies to consider classifying child care as an acceptable expense on federal grants. Conferences, they suggest, could also attempt to provide on-site childcare and spaces for lactation.

While these extra efforts would likely cost more money, some groups have already addressed these needs.

“The American Society for Cell Biology has a fantastic child care program, where, if you are traveling, they have funds to alleviate extra child care services at home,” Joshua-Tor said. “If this is something we need and it’s in everybody’s psyche that it has to be taken care of for a meeting, it will be commonplace.”

Finally, the group addressed the challenge of advancing the careers of women in science. Female authors are often underrepresented in high-impact journals. Women also tend to dedicate more time to teaching and mentorship. The group encouraged holistic evaluations, which focus on an analysis of a candidate’s scientific and institutional impact.

Hopkins suggested that the solutions to these challenges at different institutions will vary. “You have to pick solutions that work in your culture” and that involve the administration. Ultimately, leveling the playing field doesn’t happen just once. “You’ve got to solve it and stay on it,” she urged.

Next week’s article explores some of the efforts of Stony Brook University, Brookhaven National Lab and Cold Spring Harbor Laboratory to provide an inclusive environment that ensures women have an equal opportunity to succeed in the STEM fields.

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Mirna Kheir Gouda

By Daniel Dunaief

Mirna Kheir Gouda arrived in Commack from Cairo, Egypt, in 2012, when she was entering her junior year of high school. She dealt with many of the challenges of her junior year, including taking the Scholastic Aptitude Test, preparing for college and adjusting to life in the United States.

Her high school counselor at Commack High School, Christine Natali, suggested she apply to Stony Brook University. Once she gained admission, she commuted by train to classes, where she planned to major in biology on the road to becoming a doctor.

She did not know much about research and wanted to be involved in it to learn, especially because Stony Brook is so active in many fields.

“After some time conducting research, I came to be passionate about it and it was no longer just another piece of my resume, but rather, part of my career,” she explained in an email.

She reached out to Gábor Balázsi, a relatively new faculty member at the time, who suggested she consider joining a lab.

Balázsi uses synthetic gene circuits to develop a quantitative knowledge of biological processes such as cellular decision making and the survival and evolution of cell populations.

Balázsi knew Kheir Gouda from the 2015 international Genetically Engineered Machine team, which consisted of 14 members selected from 55 undergraduate students.

“Having this iGEM experience,” which included deciding on a project, raising funds, carrying out the project and preparing a report in nine months, was a “very promising indication” that Kheir Gouda would be an “excellent student,” Balázsi explained in an email.

Kheir Gouda chose Balázsi’s laboratory, where she worked with him and his former postdoctoral fellow Harold Bien, who offered her guidance, direction and encouragement.

As a part of the honors program, Kheir Gouda had to conduct an independent research project.

She wanted to “work on a project that involved adaptations and I always thought, ‘What happens when the environment changes? How do cells adapt?’”

She started her project by working with a mutant gene circuit that was not functioning at various levels, depending on the mutation. She wanted to know how cells adapt after beneficial but costly function loss.

An extension of this research, as she and Balázsi discussed, could involve a better understanding of the way bacterial infections become resistant to drugs, which threaten their survival.

“The idea for the research was hers,” Balázsi explained in an email. Under Bien’s mentorship skills, Kheir Gouda’s knowledge “developed quickly,” Balázsi said.

Balázsi said he and Kheir Gouda jointly designed every detail of this project.

Kheir Gouda set up experiments to test whether a yeast cell could overcome various mutations to an inducer, which regains the function of the genetic gene circuit.

Seven different mutations caused some type of loss of function of the inducible promoter of the gene circuit function. Some caused severe but not complete function loss, while others led to total function loss. Some were more able to “reactivate the circuit” rescuing its function, while others used an alternative pathway to acquire a resistance.

The presence of the resistance gene was necessary for cell survival, while the circuit induction was not necessary. At the end of the experiment, cells were resistant to the drug even in the absence of an inducer.

“This synthetic gene circuit in yeast cells can provide a model for the role of positive feedback regulation in drug resistance in yeast and other cell types,” Balázsi explained.

Kheir Gouda said she and Balázsi worked on the mathematical modeling toward the end of her research.

“What our work suggests is that slow growth can turn on quiescent genes if they are under positive feedback regulation within a gene network,” Balázsi wrote.

This mathematical model of limited cellular energy could also apply to cancer, which might slow its own growth to gain access to a mechanism that would aid its survival, Balázsi suggested. 

Recently, Kheir Gouda, who graduated from Stony Brook in 2018, published a paper about her findings in the journal Proceedings of the National Academy of Sciences, which is a prestigious and high-profile journal for any scientist.

“Because PNAS has a lot of interdisciplinary research, we thought it would be a good fit,” Kheir Gouda said. The work she did combines evolutionary biology with applied math and synthetic biology.

The next steps in this research could be verifying how evolution restores the function of other synthetic gene circuits or the function of natural network modules in various cell types, Balázsi suggested.

Kheir Gouda’s experience proved positive for her and for Balázsi, who now has eight undergraduates working in his lab. “The experience of mentoring a successful undergraduate might help make me a better mentor for other undergraduates and for other graduate students or postdoctoral researchers, because it helps set goals based on a prior example,” Balázsi said.

He praised Kheir Gouda’s work, appreciating how she learned new techniques and methods while also collaborating with a postdoctoral fellow in Switzerland, Michael Mahart, who is an author on the paper.

“It is unusual for an undergraduate to see a research project all the way through to completion, including a publication in PNAS,” marveled Balázsi in an email. He said he was excited to have mentored a student of Kheir Gouda’s character.

Kheir Gouda has continued on a research path. After she graduated from Stony Brook, she worked for a year on cancer research in David Tuveson’s lab at Cold Spring Harbor Laboratory. She then transitioned to working at the Massachusetts Institute of Technology for Assistant Professor of Chemical Engineering Kate Galloway. Kheir Gouda, who started working at MIT in October, plans to continue contributing to Galloway’s effort until she starts a doctoral program next fall.

Kheir Gouda said her parents have been supportive throughout her education.

“I want to take this opportunity to thank them for all the sacrifices they made for me,” Kheir Gouda said.

She is also grateful for Balázsi’s help.

He has “always been a very supportive mentor,” she explained. She would like to build on a career in which she “hopes to answer basic biology questions but also build on research and clinical tools.”

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Stock photo

By Elof Axel Carlson

Elof Axel Carlson

Most of us would say that our sense of self exists in our head, more specifically in our brain, and for those with some memory of high school or college biology, in the frontal lobes of our cerebral hemispheres of the brain where memory, language and sense perceptions are stored and coordinated. 

That is a 20th-century view of where we are. 

If you asked that question earlier, you would get a variety of answers in, let us say, ancient Rome, the golden age of Greece, the Middle East at the time of the rise of Christianity or even before there were written histories. 

Vestiges of these beliefs exist in our language. We say we have “gut feelings” about issues that are central to our beliefs. We say we give heartfelt thanks for things that touch us deeply or spiritually. 

Our ancestors a millennium or so ago also believed that our brains cooled the blood and terms like “hot-headed” or “cold-blooded” reflected the differences in brain heated or chilled states. These phrases reflect the belief that our soul or being was in our intestines or in our heart. How did we shift our self from the gut or the heart to the brain? 

The heart was known to beat, and it responded to emotions by racing and thumping. Galen in ancient Rome believed the blood entered the right ventricle and passed through invisible pores into the left ventricle where it was “vitalized.”

Servetus in the 1550s believed blood entered the right ventricle and then passed into the lungs from the pulmonary artery and returned aerated, into the left ventricle. Thus, he identified the role of the lungs as air exchange and established there was a pulmonary circulation.

William Harvey in 1628 did experimental work to prove that the circulatory system was more complex. He showed veins had valves and arteries did not. He argued (and demonstrated) that the heart is a pump and the blood from the body enters the right atrial chamber, goes into the lungs through the pulmonary artery, exchanges air in the lungs through microscopic vessels (later seen and called capillaries) and returns to the left atrial chamber, goes into the left ventricle, and then gets pumped through the aorta to the rest of the body. 

What neither Servetus nor Harvey knew was that they were scooped by Ibn al Nafis (1213-1288) who was born in Damascus and died in Cairo. He was a celebrated Arab physician and rejected Galen’s views of the role of the heart and claimed there was a pulmonary circulation that went into the right chambers and entered the lungs and returned to the left chambers with refreshed blood. 

The history of science is a wonderful field because it teaches us that knowledge is gained piecemeal and often each generation has an incomplete understanding of the most important parts of who we are and how we work and what composes our body and our understanding of the universe. 

We tend to drop out of memory the predecessors whose partial insights were a mixture of valid insights and false interpretations. We make do with what we know and guess at what we think is complex and reduce it to our understanding, and later generations fix our errors and drop out conclusions. 

I like to think of this analysis with “heartfelt” thanks for the pleasure it gives to have this insight. I also feel, “deep in my gut,” that reason, and not my bowels, is the basis of my success as a scientist in my career. That reason I associate with my brain and the neurons whose connections and synaptic associations (most still to be worked out by future generations of scientists) which allow my “cool-headed” capacity to think and to suppress my “hot-headed” or fevered brain saturated with emotion to be subdued. 

Elof Axel Carlson is a distinguished teaching professor emeritus in the Department of Biochemistry and Cell Biology at Stony Brook University.

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Ellen Pikitch, left, with Christine Sanora, taken in 2015 while the two scientists were researching Shinnecock Bay. Photo by Peter Thompson

By Daniel Dunaief

It’s one thing to make a commitment to a good idea; it’s another to follow through. Ellen Pikitch, endowed professor of ocean conservation science in the School of Marine and Atmospheric Sciences at Stony Brook University, is making sure countries around the world know where and how they can honor their commitment to protect the ocean.

In 2015, the United Nations had agreed to designate at least 10 percent of the oceans as Marine Protected Areas, which would restrict fishing and foster conservation. The goal of the proposal is to reach that figure by next year. 

Three years ago, with the support of the Italian Ministry of Environment and private donations, Pikitch started the labor-intensive process of finding ocean regions that countries could protect. 

Ellen Pikitch, right, with Natasha Gownaris at the United Nations Ocean Conference in June of 2017. Photo Courtesy of IOCS

She published the results of her analysis in the journal Frontiers in Marine Science. Her research could help countries move from the current 7.8 percent of oceans protected to the 10 percent target, and beyond that figure in the ensuing years.

The United States has met its target, although most of its marine protected ares are far from human population centers, so the coverage is uneven, Pikitch explained. The rest of the world has some gaps in high priority areas.

“I’m hoping that the study will light a fire under the policymakers so that they do meet their commitment,” said Pikitch. “It’s quite feasible for them to meet the goal. We’ve given [policymakers] advice in this paper about how exactly it could be done.”

The maps in the paper show areas that are within the current jurisdiction that are priority areas and are unprotected.

“There is quite a bit of area that meets this description — more than 9 percent — so there is flexibility in how countries can use the results and reach or exceed” the 10 percent target by next year, Pikitch explained in an email.

To determine where nations can enhance their ocean protection, Pikitch, Assistant Professor Christina Santora at the Institute for Ocean Conservation Science at Stony Brook University and Stony Brook graduate Natasha Gownaris, who is now an assistant professor in environmental studies at Gettysburg College, pulled together information from 10 internationally recognized maps indicating the location of global marine priority areas.

“We are standing on the shoulders of giants, capitalizing or leveraging all the hard work that has gone into other maps,” said Gownaris. 

One of the most unexpected findings from the study for Pikitch is that 14 percent of the ocean was considered important by two to seven maps, but over 90 percent of those areas remained unprotected. A relatively small part of this area is on the high seas, while most is within exclusive economic zones, which nations can control.

To preserve this resource that continues to remove carbon dioxide from the atmosphere while serving a critical role in the world’s food chain, conservationists have focused on marine protected areas because they provide the “one thing we felt was going to be the most effective single step,” said Mark Newhouse, the executive vice president for newspapers at Advance Publications and president of the Ocean Sanctuary Alliance. “It could happen overnight. A country could say, ‘This area is off limits to fishing,’ and it is.”

Countries can protect areas within their exclusive economic zones “more quickly than figuring out a way to solve global warming,” Newhouse added.

Santora explained the urgency to take action. “The situation in the ocean is worsening and we can’t wait to have perfect information to act,” Santora wrote in an email. “What we can do is put strong, effectively managed MPAs in the right places, with a high level of protection, that are well managed and enforced.”

Members of the Ocean Sanctuary Alliance, which counts Pikitch as its scientific officer, recognize that the 7.8 percent figure includes areas where countries have announced their intention to protect a region, but that doesn’t necessarily include any enforcement or protection.

“Intentions don’t protect the environment,” Newhouse said.

Ambassadors from several nations have reached out to OSA to discuss the findings. 

These diplomats are “exactly the people we want paying attention” to the research Pikitch and her team put together, Newhouse said.

Pikitch also plans to reach out proactively.

According to Pikitch’s recent analysis, the largest gaps in policy coverage occurred in the Caribbean Sea, Madagascar and the southern tip of Africa, the Mediterranean Sea and the Coral Triangle area, although they found additional widespread opportunities as well.

Pikitch calculated that an additional 9.34 percent of areas within exclusive economic zones would join the global marine protected area network if all the unprotected area identified as important by two or more initiatives joined the MPA network. 

“When effectively managed, when strong protections are put in place, they work,” Pikitch said.

Indeed, one such example is in Cabo Pulmo, Mexico, where establishing a marine protected area resulted in an 11-fold increase in the biomass of top predators within a decade. Many MPAs become sites for ecotourism, which can bring in hefty sums as people are eager to see the endemic beauty in their travels.

Pikitch hopes this kind of study spreads the word about the benefit of protecting the ocean and that policymakers and private citizens recognize that protecting sensitive regions also benefits fisheries, refuting the notion that environmentally driven policy conflicts with the goal of economic growth.

The groups involved in this study are already discussing the new goal for the ocean. Several diplomats and scientists would like to see the bar raised to 30 percent by 2030, although the United Nations hasn’t committed to this new target yet.

“Studies show that 10 percent is insufficient — it is a starting point,” Santora wrote. “I do think that targets beyond 2020 will increase.”

Pikitch said the ocean has always been one of her passions. Her goal is to “leave the world in better shape than I found it” for her children and six grandchildren.

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