Category Archives: Genetics

Genetics

Coffee habits are partly linked to genetics, UC San Diego researchers say – NBC San Diego

L.L. Bean has just added a third shift at its factory in Brunswick, Maine, in an attempt to keep up with demand for its iconic boot.

Orders have quadrupled in the past few years as the boots have become more popular among a younger, more urban crowd.

The company says it saw the trend coming and tried to prepare, but orders outpaced projections. They expect to sell 450,000 pairs of boots in 2014.

People hoping to have the boots in time for Christmas are likely going to be disappointed. The bootsare back ordered through February and even March.

"I've been told it's a good problem to have but I"m disappointed that customers not getting what they want as quickly as they want," said Senior Manufacturing Manager Royce Haines.

Customers like, Mary Clifford, tried to order boots on line, but they were back ordered until January.

"I was very surprised this is what they are known for and at Christmas time you can't get them when you need them," said Clifford.

People who do have boots are trying to capitalize on the shortage and are selling them on Ebay at a much higher cost.

L.L. Bean says it has hired dozens of new boot makers, but it takes up to six months to train someone to make a boot.

The company has also spent a million dollars on new equipment to try and keep pace with demand.

Some customers are having luck at the retail stores. They have a separate inventory, and while sizes are limited, those stores have boots on the shelves.

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Coffee habits are partly linked to genetics, UC San Diego researchers say - NBC San Diego

Genetics

Advanced genetic tools help researchers ID new neurodevelopmental syndrome – Yale News

In a recent study, a Yale-led research team described for the first time a rare neurodevelopmental syndrome that begins affecting patients during infancy, and typically causes developmental delays, severe seizures, cardiac dysrhythmia, and recurring infection.

After conducting a genetic analysis on 18 individuals with similar symptoms but for whom there was no established diagnosis and comparing the results with other findings, the research team, led by Yales Saquib Lakhani and Lauren Jeffries, was able to discern the genetic roots of what they determined was a syndrome shared by all of the patients.

According to their findings, published in the journal Genetics in Medicine, the newly defined syndrome now known as Jeffries-Lakhani Neurodevelopment Syndrome, or JELANS arises when patients have variants in a gene called CRELD1, which has known roles in the cardiac and immune systems but had never before been characterized in patients with neurodevelopmental symptoms.

It may be surprising to know that while over 7,000 rare genetic disorders are already defined, the majority of our 20,000 genes are still not well understood.

Lauren Jeffries

The discovery would not have been possible, researchers say, without next-generation DNA sequencing, a tool refined within the past decade that can rapidly sequence thousands of genes or even entire genomes.

The advancements in DNA sequencing have completely transformed how we approach patients, said Lakhani, clinical director of Yale School of Medicines Pediatric Genomics Discovery Program and senior author of the study.

With next-generation sequencing, researchers can uncover alterations in genes also known as variants shared by people around the world with similar symptoms. That allows them to draw connections that may have been missed when relying on symptoms alone.

In this case, and in a growing number of others, it means a disorder that had gone undiscovered is now named and defined, giving those affected by it much-needed answers and researchers a clearer route to treatment development.

Lakhani and Jeffries, an associate research scientist and medical geneticist with the Pediatric Genomics Discovery Program and lead author of the study, recently sat down with Yale News to discuss JELANS and the process of identifying a new syndrome, how the programs gene-centric approach to care yielded this discovery, and how it benefits families facing these rare disorders.

This interview has been edited and condensed.

Lauren Jeffries:It may be surprising to know that, even in 2024, while over 7,000 rare genetic disorders are already defined, the majority of our 20,000 genes are still not well understood. So, while comparing clinical notes across patients is still critical to our work, in the Pediatric Genomics Discovery Programwe utilize a gene-centric approach, meaning that instead of comparing symptoms, we look for genetic differences as our first step.

In this particular case, GeneDx a commercial lab headquartered in Connecticut that we collaborate with had genetically screened 10 patients who had compound heterozygous variants for theCRELD1gene. That means that the patients had two variants in this gene, one coming from their mom and one from their dad. GeneDx then asked if we wanted to look into this further. Most of the patients in our full cohort ended up sharing the exact same change, which was remarkably suspicious.

Knowing a syndrome name and the underlying genetic cause can be so powerful by bringing a sense of closure and relief to families.

Saquib Lakhani

Saquib Lakhani: In general, you need a certain number of patients and consistency in the characteristics of those patients. You also typically need basic science evidence which could be biochemical, cell system, or animal model testing that corroborates that the variation in the gene in question is associated with the condition in the patients youve identified, and that it causes some changes or abnormalities in the scientific testing. And ultimately you need to be able to get a paper describing the syndrome published, indicating that your peers have accepted the evidence defining the syndrome.

Jeffries: We worked with an incredible team of researchers to find 18 patients from 14 families in the U.S., Canada, and the U.K., including one who we cared for in our pediatric ICU here at Yale. When no established diagnoses were identified for them, their genetic data was analyzed under the research lens. From this deeper analysis of genetic data, the CRELD1 gene emerged as the candidate to study.

We also looked through their clinical data to see what patterns might exist. All of the patients had low muscle tone at birth. In the majority of cases, epilepsy developed by around five months of age, and all patients had seizures at some point in time. Cardiac dysrhythmias and recurrent infections were also common, and we noticed that several patients had shared facial features such as large-appearing eyes.

Lakhani: We then studied the gene in frogs. We first wanted to see what happened when we removed the gene, because that can give us a clue as to what the gene is important for. When we fully knocked out the gene, the frog embryos did not survive. But when the gene was partially knocked out, we found that there were a lot of developmental defects in these frogs. Interestingly, surviving tadpoles with the gene significantly knocked out were more susceptible to developing seizures. That showed us that CRELD1 is important for the development of the embryo overall and that if its limited in function, it can also increase the susceptibility to seizures.

However, these patients arent missing CRELD1, they have variations in it: letter changes in the gene that result in changes to the CRELD1 protein but do not cause the protein to completely disappear. When we tested the patient forms of the protein in tadpoles, we found that they did not function the same way as the normal form of CRELD1. Taken together, the clinical and basic science data provides solid evidence that JELANS is a new syndrome caused by variants in the CRELD1 gene.

Jeffries: As more patients are identified to have JELANS, I think well further refine the clinical syndrome and begin to uncover the molecular mechanisms underlying the symptoms. For instance, well get a better sense of whether the immune system is affected, leading to the increased risk of infection, and how common cardiac dysrhythmias are and whats the underlying cause.

Lakhani: The families of children with undiagnosed diseases frequently go through wandering medical diagnostic odysseys doctor after doctor, test after test without ever reaching an answer. Parents can go their entire lives wondering what happened to their child, whether their other children can get the disease, whether they did something to cause it. Knowing a syndrome name and the underlying genetic cause can be so powerful by bringing a sense of closure and relief to families.

We now have a tool that allows us to see if theres a genetic explanation for a childs condition. We no longer have to just do the best we can with limited information.

Saquib Lakhani

Jeffries: Its validating. Its clarifying. With a syndrome name, families can find a community and move forward. Especially for rare disorders, in syndrome support groups families can share their stories, discuss what treatments have worked and what treatments havent, and just talk to other parents who understand.

Lakhani: And in some countries, it can be hard to get resources without a specific diagnosis. With a diagnosis, families may qualify for support services, so it can have practical implications even beyond the knowledge.

Jeffries: Understanding this syndrome at the molecular level is essential for the ultimate goal of finding treatment thats targeted and specific to this disorder and that is meaningful in helping patients thrive.

Lakhani: Everyone who cares for patients should be thinking about this. For many years, as physicians we would look at certain patients and say, Theyve got something underlying. But we could never put our finger on it because we didnt have a robust way to test broadly for genetic conditions; we had to just do the best we could. But we now have a tool that allows us to see if theres a genetic explanation for a childs condition. We no longer have to just do the best we can with limited information. We can actually try to find answers. Its something that has had an incredible impact and its something we regularly encourage others to pursue.

Jeffries: And while the discovery of JELANS was through a research endeavor, we want to be clear that DNA sequencing is not just for uncovering new syndromes. Genetic testing can be ordered by a doctor and is available for patients with all sorts of descriptive diagnoses, such as autism, intellectual disability, epilepsy, and cerebral palsy, where symptoms determine the diagnosis.

A patients genes may reveal a more specific diagnosis than any constellation of symptoms can define; understanding the molecular cause can ultimately give patients clearer answers and, hopefully, more targeted treatments.

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Advanced genetic tools help researchers ID new neurodevelopmental syndrome - Yale News

Genetics

Nutritious diet may protect against type 2 diabetes, regardless of genetics – News-Medical.Net

A healthy diet that adheres to nutrition recommendations is associated with better blood glucose levels and a lower risk of prediabetes and type 2 diabetes, a new study from the University of Eastern Finland shows. This association was observed also in individuals with a high genetic predisposition to type 2 diabetes.

Type 2 diabetes is a strongly genetic disease that can be prevented and delayed with a healthy lifestyle, such as diet and exercise.

However, we havent really known whether a healthy diet is equally beneficial to all, i.e., to those with a low genetic risk and to those with a high genetic risk.

Ulla Tolonen, Doctoral Researcher, University of Eastern Finland

The cross-sectional study examined food consumption and blood glucose levels in more than 1,500 middle-aged and elderly men participating in the broader Metabolic Syndrome in Men Study, METSIM. Food consumption was measured using a food frequency questionnaire, and blood glucose levels were measured using a two-hour glucose tolerance test. In addition, study participants genetic risk of type 2 diabetes was scored based on 76 genetic variants associated with type 2 diabetes risk.

The researchers identified two dietary patterns based on food consumption. A dietary pattern termed as healthy included, among other things, vegetables, berries, fruits, vegetable oils, fish, poultry, potatoes, unsweetened and low-fat yogurt, low-fat cheese and whole grain products, such as porridge, pasta and rice. This diet was associated with, e.g., lower blood glucose levels and a lower risk of prediabetes and type 2 diabetes.

The study also explored the effect of the genetic risk of type 2 diabetes on the associations with diet and glucose metabolism. The associations of a healthy diet with better glucose metabolism seemed to hold true for individuals with both a low and a high genetic risk of diabetes.

"Our findings suggest that a healthy diet seems to benefit everyone, regardless of their genetic risk," Tolonen concludes.

The findings were published inEuropean Journal of Nutrition.

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Nutritious diet may protect against type 2 diabetes, regardless of genetics - News-Medical.Net

Genetics

Genome-wide association study identifies host genetic variants influencing oral microbiota diversity and metabolic … – Nature.com

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Genome-wide association study identifies host genetic variants influencing oral microbiota diversity and metabolic ... - Nature.com

Genetics

Unlock the Secrets of Your DNA with Advanced Genetic Testing – North Forty News

Photo by RODNAE Productions from Pexels

The field of testing has made progress in recent times, transforming our understanding of our bodies and well-being. These advancements have empowered individuals to delve into the details hidden within their genetic code, enabling them to make informed choices regarding their health. In this guest contribution, we will delve into the rising trend of testing and its ability to offer valuable insights.

Not long ago, genetic testing was a sophisticated and expensive process mainly utilized in academic circles and by those with financial means. However, rapid advancements in technology have opened doors to cost-effective options. Specialized companies focusing on testing have emerged, providing individuals with direct access to their genetic data. To know more, click here: https://myriad.com/.

A key benefit of testing lies in its capacity to unveil potential health vulnerabilities encoded in an individuals DNA. By examining genes associated with illnesses like cancer, diabetes, or heart conditions, these tests can pinpoint whether an individual carries a risk compared to those lacking such gene variations.

Equipped with this information, individuals have the opportunity to collaborate proactively with healthcare providers to create treatment plans that focus on preventing diseases or intervening early if needed. Utilizing the information gathered from testing, healthcare professionals can customize approaches explicitly tailored to each patients requirements. This targeted method improves the effectiveness of treatments while reducing reactions and unnecessary procedures.

In addition to identifying predispositions for diseases, advanced genetic testing provides insights into optimizing fitness and nutrition routines. These tests reveal how individuals may react differently to various exercise regimens or dietary plans by analyzing genes for factors such as metabolism or nutrient absorption.

Advanced genetic testing can offer reassurance for couples contemplating starting a family and worried about conditions in their family history. These tests can pinpoint risks and help make informed decisions regarding family planning and potential interventions to safeguard the health of future offspring.

Furthermore, knowledge of an individuals composition enables the prediction of age-related conditions or chronic illnesses. With this information, individuals can seek advice from healthcare professionals to devise strategies.

While genetic testing is a tool, addressing concerns about privacy related to using genetic data is crucial. Individuals must conduct research. Carefully choose a reputable company that values data security and follows strict guidelines regarding using and sharing genetic information.

Ethical issues arise when dealing with testing. Companies providing these services must ensure the validity and transparency of their methods, safeguarding consumers from unverified assertions. Service providers and consumers need to take action and understand the ramifications, including potential implications for health or life insurance policies based on genetic test findings.

While advanced genetic testing offers potential, it is essential to acknowledge its limitations. Genetic testing cannot precisely predict the future. Instead, it provides insights into an individuals predispositions without guaranteeing disease outcomes. Recognizing that genetic factors interact with lifestyle factors underscores the significance of an approach to well-being.

Furthermore, research and evolving knowledge in genetics shape our understanding of genetic test results over time as scientists uncover more about our genes and their implications. Hence, its vital for people to keep themselves informed and seek guidance from healthcare experts specializing in genetics.

To sum up, recent advancements in testing have allowed everyday individuals to explore hidden insights within their DNA. Embracing this technology provides benefits, such as lowering health risks through treatment plans, optimizing fitness routines, and even planning for fertility.

Nevertheless, its essential for consumers to approach these tests carefully by selecting companies that prioritize privacy regulations and uphold standards throughout their processes. As we progress into this era, increased accessibility and use will unlock more opportunities as we continue unraveling our distinct genetic codes.

By cautiously yet enthusiastically embracing these innovations, we set forth on a path toward a future driven by the analysis of genomic data for all individuals seeking answers from within themselves.

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Unlock the Secrets of Your DNA with Advanced Genetic Testing - North Forty News

Genetics

Modern and precise: Using gene editing to change the blueprint of an organism – Beef Magazine

Gene editing is the use of modern molecular technology to precisely change the DNA sequence of an organism. And the key words here are modern and precisely, said Dr. Jon Beever from the University of Tennessee during his presentation titled Biotechnology 101: A practical guide to gene editing and vaccinology at the Beef Improvement Federation (BIF) Symposium June 10 in Knoxville, Tennessee.

The methodology used to edit an organisms genome in this precise manner involves the use of nucleases including Zinc finger nucleases, Transcription activator-like effector nucleases [TALENs], or CRISPR-Cas9 systems. All three tools facilitate a double-stranded break at a precise location in the DNA sequence. Gene editing leverages the cells own DNA repair machinery to generate either a non-homology directed repair, which often results in a disruption in the gene and its function, or a homology directed repair which allows for correction or insertion in the gene of interest. This methodology works in both somatic and gametic cell types.

Beever shared examples of gene edits in livestock, to date, including Myostatin edits in sheep and cattle using TALEN technology. Myostatin suppresses muscle development and thus, disruption of this gene generates more heavily muscled animals. In 2016, Shanthalingam leveraged gene editing technology to generate Mannheimia haemolytica leukotoxin-resistant cattle. More recently, the SLICK gene variant, which naturally occurs in Senepol cattle, has been edited in several breeds of cattle to increase their thermotolerance. Another example of using this technology to address disease resistance includes disruption of the CD163 gene in pigs to generate pigs that are resistant to Porcine Reproductive and Respiratory Syndrome (PRRS).

There are obvious animal health and animal welfare concerns that can be addressed using gene editing technology. Similarly, mRNA vaccines offer advantages that can increase animal health and welfare. There are thousands of information and educational resources online about mRNA vaccines in livestock available. Half of these are ridiculous claims about being mRNA free, Beever explained.

We vaccinate because pathogenic organisms cause loss through disease and death in our cattle, Beever said. The vaccines that we administer stimulate an immune response to specific antigens. This immune response leads to the production of antibodies that protect our cattle.

Traditional vaccines that contain live attenuated virus or killed bacteria or viruses contain the antigen (proteins) themselves. The mRNA vaccines contain the genetic code, or roadmap, such that the immunized body can create the protein itself. The generated protein or antigen sits on the cell surface and the body raises an immune response and creates protective antibodies.

The advantage of mRNA vaccines is that they are faster to produce and to customize as the virus mutates. Because of this, we can protect ourselves, and our cattle, more effectively, Beever summarized.

To learn more about the molecular genetics driving gene editing and mRNA vaccines, watch Dr. Beevers full presentation at https://youtu.be/swvhXXjFxgs. To learn more about the Beef

Improvement Federation, or watch other presentations from the 2024 Symposium, visit BIFSymposium.com.

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Modern and precise: Using gene editing to change the blueprint of an organism - Beef Magazine

Genetics

The ‘gene deserts’ unravelling the mysteries of disease – BBC.com

Mutations in these regions of so-called "junk" DNA are increasingly being linked to a range of diseases, from Crohn's to cancer.

Ever since the Human Genome Project was declared complete in 2003, scientists have sought to pinpoint new regions among the three billion letters of our genetic code which may play a critical role in disease.

With the help of technologies which can analyse whole genome samples faster and more cheaply than ever before, vast numbers of genome-wide association studies dubbed GWAS have been published, identifying genetic variants linked to different chronic illnesses.

Frustratingly for many geneticists, this has turned out to be the easy bit. The much harder part is understanding how they are relevant. For example, while GWAS have identified segments of DNA associated with inflammatory bowel disease at 215 different chromosomal sites , scientists have only been able to pinpoint the exact mechanisms involved for four of them.

One of the biggest challenges is that many of these pieces of DNA lie in so-called gene deserts, swathes of the genome that initially appeared to contain nothing of relevance genetic "junk" that could be disregarded. After all, less than 2% percent of the human genome is dedicated to coding for genes which produce proteins, while much of the remaining 98% has no obvious meaning or purpose.

"You'll go, 'Oh here's a really important association and it increases your risk of many different diseases'," says James Lee, a clinician-scientist who runs a research group at the Francis Crick Institute in London. "But when you actually go and look at that bit of DNA, there's just nothing there."

For many years, gene deserts have been one of the most perplexing areas of medical science, but scientists are slowly managing to accrue information about their apparent purpose and why they exist.

Recently, Lee and colleagues at the Crick Institute published a new investigation into a particular gene desert known as chr21q22. Geneticists have known about this gene desert for more than a decade, because it is associated with at least five different inflammatory diseases from inflammatory bowel disease (IBD) to a form of spinal arthritis known as ankylosing spondylitis. Yet deciphering its function has always proven elusive.

However, for the first time, the Crick scientists were able to show that chr21q22 contains an enhancer, a segment of DNA which can regulate nearby or distant genes, capable of cranking up the amount of proteins they make. Lee refers to this behaviour as "a volume dial". Delving deeper, they found that this enhancer is only active in white blood cells called macrophages where it can ramp up the activity of a previously little-known gene called ETS2.

While macrophages play a vital role in clearing dead cells or fighting off harmful micro-organisms, when the body produces too many they can wreak havoc in inflammatory or autoimmune diseases, flooding into affected tissues and secreting damaging chemicals which attack them. The new study demonstrated that when ETS2 is boosted in macrophages, it heightens virtually all their inflammatory functions.

Lee describes it as "the central orchestrator of inflammation". "We've known for a while that there must be something at the top of the pyramid that is telling the macrophages to behave like this," he says. "But we've never known what it was. The most exciting bit of this, is if we can target it in some way, we might have a new way to treat these diseases."

But if gene deserts are capable of causing us so much harm, why are they in our DNA?

Tracing back in time, Lee's colleagues at the Crick's Ancient Genomics Laboratory were able to show that the disease-causing mutation in chr21q22 first entered the human genome somewhere between 500,000 and one million years ago. This particular DNA change is so ancient that it was even present in the genomes of Neanderthals as well as some ancestors of Homo sapiens.

It turns out that its original purpose was to help the body fight off foreign pathogens. After all, before antibiotics were invented, being able to rapidly switch on a heightened inflammatory response through ETS2 was extremely useful. "Within the first couple of hours of seeing bacteria, it ramps up your macrophage responses," says Lee.

As a result, blocking ETS2 completely could leave IBD patients vulnerable to future infections. However, Lee says when its activity is turned down by between 25 to 50%, it seems to be capable of eliciting a profound anti-inflammatory effect, without risking making the patient too immunosuppressed. While this theory has yet to be tested in clinical trials, the researchers showed that MEK inhibitors a class of cancer drugs which can dampen ETS2 signalling were capable of reducing inflammation not just in macrophages but in gut samples taken from people with IBD.

This appears to represent a new pathway to a completely novel class of treatments for IBD patients. "Some of these MEK inhibitor drugs do have side effects, and what we're trying to do now is to make them more targeted and safer, so that for lifelong diseases like IBD, we would actually be able to offer patients a drug that could switch off the inflammatory process and actually make them a lot better," says Lee.

Now the Crick's researchers are turning their attention to the other four diseases which have been linked to the chr21q22 gene desert, to see whether altering ETS2 activity can also help alleviate the excess inflammation which seems to be driving the condition.

"One of the most significant ones is an inflammatory liver disease called primary sclerosing cholangitis," says Lee. "It's a particularly nasty disease because it can cause liver failure leaving people needing transplants. It can also have a much higher risk of causing liver cancers, and this can happen in young people. And at the moment, there's not a single drug that has been shown to work, there's very little to offer patients," he says.

Scientists also predict that studying gene deserts will yield vital information which will help to improve our understanding of the variouspathways involved in tumour development.

As an example, cancer researchers havepinpointed a gene desert called 8q24.21 which is known to contribute to cervical cancer as the human papilloma virus, the main cause of the disease, embeds itself in this part of the genome. In doing so, the virus enhances a gene called Myc which is a well-known driver of cancer. Studies are suggesting that the connection between 8q24.21 and Myc may also play a role in a number of ovarian, breast, prostate and colorectal cancers.

RichardHoulston, of the Institute of Cancer Research in London, says that various genetic variants which have been identified as contributing to the heritable risk of many common cancers have been found in gene deserts. Knowledge of these target genes will provide opportunities for drug discovery as well as for cancer prevention.

HoweverHoulstonpoints out it is harder to translate this knowledge into new therapeutics for cancer compared to IBD, because tumours are not static targets, but continuously evolve over time. "This is the challenge, whereas with something like Crohn's disease and other bowel conditions, it's not evolving," he says.

Lee is optimistic that the Crick's work on IBD will provide a template for how researchers can find new ways of understanding the pathways involved in all kinds of autoimmune and inflammatory diseases. The institute's scientists are now investigating other gene deserts which have been associated with conditions such as lupus, a disease in which the immune system damages the body's tissues, leading to symptoms such as skin rashes and tiredness.

Other research centres around the world such as the University of Basel in Switzerland are also examining how single inherited mutations in gene deserts could lead to some rare genetic diseases. Three years ago, Basel scientists discovered how one of these mutations could lead to babies being born with limb malformation due to its regulatory effects on a nearby gene.

Lee predicts that understanding the roles of gene deserts will ultimately help improve the notoriously inefficient drug development process. "Making new drugs for these diseases is terribly unsuccessful," he says. "Only about 10% of the drugs going into clinical studies are ever approved at the end, so 90% of them fail because they don't make people better. But if you know that your drug going into development is actually targeting a pathway supported by genetics, the chances of that drug actually being approved is at least somewhere between three- and five-fold higher."

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The 'gene deserts' unravelling the mysteries of disease - BBC.com

Genetics

UGA plant geneticists are tackling the climate crisis – Longview News-Journal

Plant genetics research at the University of Georgia spans schools, departments, disciplines, and centers. From the College of Agricultural and Environmental Sciences (CAES) to Franklin College of Arts and Sciences, the Plant Center to the Institute of Plant Breeding, Genetics & Genomics and more, UGA faculty with genetics expertise are seeking plant-based solutions to societal challenges. (Photo by Andrew Davis Tucker)

ATHENS -- With record-breaking temperatures and extreme weather escalating, the threats posed by climate change are intensifying. But the plants of tomorrow small and humble though they might be could help us meet the massive challenges of our warming planet.

Plant genetics research at the University of Georgia spans schools, departments, disciplines, and centers. From the College of Agricultural and Environmental Sciences to Franklin College of Arts and Sciences; from the Plant Center to the Institute of Plant Breeding, Genetics & Genomics and more, UGA faculty with genetics expertise are seeking plant-based solutions to societal challenges.

Some of these faculty are conducting studies at the cellular level, while others investigate plants as whole organisms. Still others are exploring how epigenetics shape entire ecosystems. And while a number of UGA geneticists prioritize fundamental discovery, others are partnering with breeders or with industry to bring new crops and plant-based products to market.

Were spread out all over campus, Bob Schmitz, UGA Foundation Professor of Plant Sciences and the Lars G. Ljungdahl Distinguished Investigator of Genetics, said. But we all speak the same language."

Growing up in Minnesota, Distinguished Research Professor John Burke took an interest in the outdoors, collecting snakes, salamanders, and turtles with his two older brothers. Years later, he earned his Ph.D. in genetics from UGA and returned as a faculty member in 2006. Among his many studies, he has put particular focus on sunflowers.

Schmitz likes to tell people that hell work on any plant that has DNA which is all of them, of course. Our questions are broader than any particular plant, he said.

A member of the Department of Genetics in the Franklin College of Arts and Sciences, Schmitz studies the mechanisms of epigenetic inheritance in plants, or how a plants environment influences the way its genes operate.

Members of the Schmitz Lab, working in partnership with international researchers, discovered that rare changes to DNA methylation can spuriously occur over generations of plants. They then found that they could use those multigenerational changes, which tick at a constant rate, to determine plant divergence time.

The information provided by this epigenetic clock, Schmidtz says, includes data relevant to the timing of invasive species introduction and the impact of human activity on native environments. These insights could prove useful for understanding how plant populations migrate, expand, or contract due to a changing climate.

Passing along fundamental genetic discoveries to research partners along the basic-to-applied continuum is something UGA does well, John Burke, a distinguished research professor and head of the Department of Plant Biology in the Franklin College of Arts and Sciences, said. He notes that the broad intersectionality of plant research has become a signature strength of the university.

There are intentional mechanisms in place to help bridge gaps between units, Burke said. We have ways to work together here. Thats critically important.

While some UGA plant geneticists pursue fundamental discovery, others are bridging the gap between basic and applied research. From Crop & Soil Sciences to Plant Pathology and Horticulture within the College of Agricultural and Environmental Sciences, these faculty members are helping transform crop plants, native species, and the future of bioenergy for a changing global climate.

As the Georgia Research Alliance Eminent Scholar Chair in Crop Genomics, Robin Buell uses comparative genomics, bioinformatics, and computational biology to investigate the genome biology of plants and plant pathogens. While her subjects have ranged from rice and potatoes to maize, switchgrass, and medicinal plants, she currently studies poplar. Buell is the principal investigator on a $15.8 million Department of Energy grant to genetically engineer poplar trees (Populus sp. and hybrids) for biofuel production and other uses.

Poplar has strong potential to provide an alternative to petroleum-based products, Buell explains.

Its so fast-growing, its almost a weed," she said. "You can grow it almost everywhere. You dont have to grow it on prime land. Weve been able to do genetic engineering for the last 20 years, active breeding for even longer. But those developments have been incremental, not substantial.

This project has a more audacious goal.

Lets reinvent this tree, she said. Lets take Humpty Dumpty, lets break him, and lets put him back together again, but in a more intelligent way and faster.

The redesigned poplars will be fabricated through an intensive process that begins with measuring mRNA transcripts and includes mapping gene function throughout the tree. The end result could provide an alternative fuel for jet engines, among other sustainable products.

Wayne Parrott, distinguished research professor of crop and soil sciences, calls his area of investigation Biotechnology 2.0. An internationally renowned geneticist, Parrott has spent more than 35 years at UGA leveraging tools to help new soybean varieties and investigating the environmental and human safety of genetically modified crops.

My lab focuses on the development and use of biotechnology applications to help out with conventional plant breeding and plant improvement, he said. But theres a lag between what people want to do and what people are able to do.

His team is closing that gap by developing biotechnology applications to help strengthen conventional crop plant breeding and improvement.

Parrott directs the Institute for Plant Breeding, Genetics & Genomics, where researchers from multiple disciplines develop new crop varieties and conduct studies to understand the genetic traits of plants important to agriculture and humankind. He credits the institute with helping bring together plant genetics experts from all positions along the research pipeline.

Esther van der Knaap is a distinguished research professor of horticulture in the College of Agricultural and Environmental Sciences. She describes Integrated Plant Sciences as a central access point for prospective students to plant and fungal research across UGA. The curriculum allows students to undertake rotations in their first year to determine the best fit for their research interests, whether bioinformatics, ecology, genetics, breeding, biochemistry or some combination.

This type of program is something I dreamed about at my previous institution, but it wouldnt have been possible, van der Knaap said. At UGA, it was possible.

Van der Knaaps own research involves tomato foodshed. At the Center for Applied Genetic Technologies, which supports the development, application, and commercialization of new technologies to genetically improve crops, the van der Knaap lab studies variations in tomato fruit quality, from shape and size to taste. The latter trait is closely connected to aroma and especially important for fresh market tomatoes.

Van der Knaaps team is collaborating with food scientists, breeders, and biochemists at UGA and at the University of Florida to identify genes that cause variations in the flavor profile of tomato as they became domesticated over time, from fully wild to what we buy in grocery stores today. The resulting information about genes that improve flavor can be used by breeders to develop tastier tomatoes for the market.

Our focus is on capturing the genes that control fruit quality traits in tomato, she said. We also investigate the genetic diversity of these genes that, collectively, offer knowledge to breeders in both public and private sectors.

A new frontier in plant genetics research is high-throughput phenotyping, a type of genetic screening that uses cutting-edge technologies to generate data about large plant populations such as a crop field or forest. Guoyu Lu, an assistant professor in the School of Electrical and Computer Engineering and a specialist in high-throughput phenotyping, says that these new technologies could help researchers, breeders, farmers, and forestry officials make decisions in real time to support and protect the plants they oversee.

Lu comes to this work with a track record of engineering innovation. Before joining the UGA faculty in 2022, his career included positions as a research scientist on autonomous driving at Ford and a computer vision engineer at the Disney ESPN Advanced Technology Group. His projects have attracted the interest and investment of Ford, GM, Qualcomm, Tencent, Mackinac and more.

I work on the AI side, Lu said. Im an AI scientist, but Im developing algorithms for plant scientists.

Using computer vision and robotics, including unmanned aerial vehicles, Lu and his team are capturing and generating data on specific genetic traits within large plant populations. The information they gather includes root structure, height, disease state, and more all collected without harming the plants themselves.

Currently, Lu is working to build an AI algorithm that is one-size-fits-all a multipurpose tool suitable for gathering genetic data on many different plants across multiple populations. He wants that tool to be accessible to anyone who needs it in the field, especially as extreme weather patterns intensify.

My work uses UAV to estimate the 3D structure models of both crops and forests, he said. The 3D structures can provide height, coverage, and other information. This data can be used to estimate growth, carbon dioxide absorption, impact on the environment, and more.

Plant genetics at UGA begins and ends with partnerships. Researchers have forged ties across disciplines and schools, with strong collaboration from field sites and with sustained support from leaders and partners across Georgia and beyond.

We have some of the top researchers in the world right here at UGA, Burke said. And the work is going on across the spectrum.

The race to adapt to a changing climate is on and these scientists are leading the way, with bold inquiry and deep appreciation for the plants they have dedicated their professional lives to understanding and championing.

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UGA plant geneticists are tackling the climate crisis - Longview News-Journal

Genetics

Genetic Tests for Predicting Clopidogrel Response Gain Traction: AHA – TCTMD

Its time for genetic testing of clopidogrel response to move into the mainstream, suggests a new scientific statement from the American Heart Association (AHA) that outlines the supporting evidence but also acknowledges the obstacles that still stand in the way of wider adoption.

Clopidogrel, the mainstay oral P2Y12 inhibitor, is a prodrug thats metabolized by the enzyme CYP2C19 before becoming biologically active. But a substantial part of the populationthe prevalence varies by race/ethnicityhas a loss-of-function variation in the CYP2C19 gene. For decades, its been known that patients with this allele have more platelet aggregation and ischemic events than noncarriers while on clopidogrel therapy.

Still, US and European guidelines addressing antiplatelet therapy in CAD havent gone so far as to recommend routine genetic testing, though a few of these documents did give a nod to selective use in situations like dual antiplatelet therapy (DAPT) de-escalation after PCI for ACS.

Writing group chair Naveen L. Pereira, MD (Mayo Clinic, Rochester, MN), told TCTMD that one driver of their new AHA statement is the fact that the guidelines havent yet addressed the latest published clinical trials (POPular Genetics, TAILOR-PCI, PHARMCLO, and IAC-PCI), observational studies, and meta-analyses.

We felt that incorporating data from these studies and providing some guidance to clinicians by interpreting the data, which can be pretty complicated sometimes, would be helpful, said Pereira, who served as a co-principal investigator for the TAILOR-PCI trial.

Beyond this, the authors also collected information on the pharmacology and pharmacokinetics of P2Y12 inhibitors, both genetic and nongenetic determinants of patients response to the drugs, as well as practicalities like reimbursement and how to choose among assays.

Our conclusion was that the evidence to date supports genetic testing, Pereira noted. But in an AHA statement, we cannot directly say, You should do genetic testing. That's up to the guidelines.

As the document points out, many clinicians have positive perceptions about pharmacogenetic testing and its clinical implications, [but fewer than] 10% adopt pharmacogenetic testing in their routine clinical practice, primarily because of a lack of clinical guidelines and pharmacogenetic education.

Indeed, only a very small fraction of practices preemptively genotype, said Pereira. For patients who go on clopidogrel only to fare poorly and experience an event, genetic testing is moot by that point, he explained, since the answer would be to simply give an alternative antiplatelet drug.

Why Clopidogrel Shouldnt Be Skipped

Increasingly, the oral P2Y12 inhibitor of choice isnt clopidogrel but ticagrelor or prasugrelneither of which are dependent on CYP2C19. Some clinicians wonder, why not just avoid the problem of clopidogrel response entirely?

There are physicians who say, I know that having a loss-of-function genotype is a problem when I give clopidogrel, but if I give ticagrelor or prasugrel to all my patients, I don't have to worry about genetic testing, Pereira commented. The problem with this blanket approach is that these drugs are more potent antiplatelets, so on the whole there will be an increase in bleeding incidence. If you want to balance the ischemic and bleeding event risk, it appears that genetic-guided therapy [from the outset] would be an optimal strategy, he added.

Pereira pointed out that multiple studies have shown the cost-effectiveness of using genetic testing to guide antiplatelet therapy. Both clopidogrel and prasugrel are now generic, but not ticagrelor (Brilinta; AstraZeneca), which is considerably more expensive. Medicare considers genetic testing for CYP2C19 loss-of-function alleles to be medically necessary in certain situations, such as when an ACS patient is undergoing PCI, and thus covers its cost. Some commercial payers also offer reimbursement for the testing.

With the availability of point-of-care assays, the logistical hurdles to widespread adoption are also less high. Previously, it could take 2 or 3 days to get results after sending a blood sample for analysis, he noted, but now the testing can be done at bedside with a buccal swab, producing results within an hour.

Naturally, the field loves to see data, Pereira said. While it would be ideal to have a clinical trial comparing genetic-guided therapy versus no testing, with that design, there would be a lot of overlap, since perhaps 70% of patients in the testing arm and 100% of those in the control arm would be taking clopidogrelwith any difference driven by the 30% in the testing arm on another P2Y12 inhibitor. You're going to need tens of thousands of patients to show a difference, so I think doing a trial like that is very difficult at this point, he said. Its easier to see the impact of testing when, as he pointed out was done in a prespecified analysis of TAILOR-PCI, only patients found to have a loss-of-function variant are compared: those given clopidogrel versus those given ticagrelor or prasugrel.

In an AHA statement, we cannot directly say, You should do genetic testing. That's up to the guidelines. Naveen L. Pereira

Overall, Pereira urged, I think it's important to pay attention to evidence in a holistic way. . . . All the data, even though there's not that one big trial showing a difference, really points to [the need] to be careful giving loss-of-function patients clopidogrel. This is especially true when talking about the monotherapy thats happening with newer stents after DAPT de-escalation.

What hed like to see next, said Pereira, is for guidelines to give specific advice on how to use CYP2C19 testing. Clinicians in the meantime should consider looking at [point-of-care] platforms and see how they can incorporate that in their practices so it becomes easy and intuitive. Implementation, the statement adds, depends on the ease not only of performing the tests but also of interpreting their results, as well as knowledge about how to adjust therapy accordingly and the ability to integrate each patients genetic status into the electronic health record for care teams to access.

But What About Platelet Function?

In a commentary published on the AHAs Professional Heart Daily website, Mark B. Effron, MD (John Ochsner Heart and Vascular Institute, New Orleans, LA), highlights the fact that platelet function testing (PFT) is another option for predicting who will benefit from a more-potent antiplatelet agent versus clopidogrel, or from de-escalation of therapy.

In most institutions in the United States, it is easier to obtain results of a platelet aggregation test using VerifyNow than it is to obtain genomics on the patient, he writes. Until . . . there are studies evaluating the benefit of an all-comers genomic strategy versus a directed PFT, there will still be controversy as to which is more appropriate in the management of patients receiving P2Y12 inhibitor therapy.

In their statement, Pereira and colleagues point out that platelet function testing and genetic testing each has advantages and disadvantages.

The key advantage of PFT lies in directly defining the intermediate phenotype of interest (ie, levels of on-treatment platelet reactivity) for which studies have shown an association with clinical outcomes (ie, increased thrombotic and bleeding risks with high and low platelet reactivity, respectively), they say. Nevertheless, its clinical implementation has been challenging given the need for multiple repeated assessments due to potential of variability of results over time and the need for a patient to be on treatment for a certain length of time with a given antiplatelet agent (eg, for at least 12 weeks with clopidogrel) to be able to assess antiplatelet effects and define responsiveness adequately.

Effron agrees that a tailored approach is the way forward, though the exact strategy is still being debated. Whether directed P2Y12 therapy is accomplished through genotype-guided antiplatelet therapy or through PFT, he says, it is becoming clear that patient profiling is needed to determine the best therapy for the patient.

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Genetic Tests for Predicting Clopidogrel Response Gain Traction: AHA - TCTMD

Genetics

Bringing Gene Therapy to the Brain – The Scientist

This webinar will be hosted live and available on-demand

Thursday, August 8, 2024 2:30 - 4:00 PMET

The blood-brain barrier (BBB) is a semi-permeable membrane between the blood and the interstitium of the brain that regulates molecule and ion movement between the circulation and the brain. This barrier poses an obstacle to gene therapy delivery, as strategies that work for other organs may not necessarily be able to cross the BBB. In this webinar brought to you by The Scientist, Douglas Marchuk and Viviana Gradinaru will explain the obstacles posed by the BBB, as well as how overcoming the BBB allows them to investigate new approaches for combatting neurological disease.

Topics to be covered

Douglas A. Marchuk, PhD James B. Duke Distinguished Professor Department of Molecular Genetics and Microbiology Duke University School of Medicine

Viviana Gradinaru, PhD Lois and Victor Troendle Professor of Neuroscience and Biological Engineering Director, Molecular and Cellular Neuroscience Center of the Tianqiao and Chrissy Chen Institute for Neuroscience Director and Allen V.C. and Lenabelle Davis Leadership Chair Merkin Institute for Translational Research California Institute of Technology

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Bringing Gene Therapy to the Brain - The Scientist