January 27, 2020 -Advancements in genomics and precision medicine have improved healthcares understanding of human disease, but stakeholders will need to address disparities and increase data sharing in order to leverage the full potential of genomic medicine, according to a study published in Nature.

Over the past two decades, technological advancements, as well as the collection and analysis of genetic and clinical data, have enhanced the use of genomics in healthcare. With these industry-wide changes, genomic medicine is poised to go mainstream, researchers noted.

The future of medicine will increasingly focus on delivering care that is tailored to an individual's genetic makeup and patterns, said Judy H. Cho, MD, Dean of Translational Genetics at the Icahn School of Medicine at Mount Sinai, Director of The Charles Bronfman Institute for Personalized Medicine, and a co-author of the report.

Applying this knowledge will help us to enhance personalized health and medicine for patients at The Mount Sinai Hospital now and for years to come.

Despite the progress the industry has made in genomic medicine, researchers stated that there are still several barriers to overcome, including deeply entrenched disparities and limited genomic knowledge.

READ MORE: Genetic Variant Reveals Disparities in Heart Failure Diagnosis

The absence of evidence-based guidelines to support healthcare recommendations continues to hinder the clinical applications of genetic data. In some countries, this is compounded by confusion over reimbursement and disparities in testing across society, researchers said.

Many healthcare professionals lack experience in genomic medicine and need education and guidance to practice in the rapidly evolving space of genetic and genomic testing.

In addition, researchers noted that concerns about data sharing and a lack of strong infrastructure are limiting the industrys ability to advance genomic medicine.

There are also concerns about the consequences of unfettered release of genetic data of dubious or inflated clinical relevance, and limited infrastructure to pull these results into mainstream medical systems, the team said.

To overcome these challenges, the group recommended that the industry take proactive measures to address disparities in scientific research, and to identify clinical opportunities that will benefit individuals and societies around the world.

READ MORE: Evaluating the Benefits and Challenges of Genomics in Healthcare

It will be particularly important to include populations historically under-represented in genomic research. As over time, clinically sequenced genomes will outnumber those collected in academia, research and healthcare communities will need to develop a harmonized approach to genomics to transcend historical boundaries, researchers stated.

Progress will be critically dependent on platforms and governance that lower barriers to the integration of genetic and phenotypic data across studies and countries, along with technical standards that are reliable, secure and compatible with the international regulatory landscape.

The industry should also increase data sharing and access in order to develop comprehensive inventories of genomic information across populations and environments.

Research access to functional data, generated at scale, should lower the barriers to mechanistic inference, provide system-wide context, and enable researchers to focus wet-laboratory validation on the most critical experiments, researchers said.

Collectively, these efforts will support compilation of a systematic catalogue of key networks and processes that influence normal physiology and disease development and inform a revised molecular taxonomy of disease.

READ MORE: Over 70% of Orgs Say Precision Medicine Meets or Tops Expectations

Finally, stakeholders will need to transform basic knowledge into fully developed physiological and molecular models of disease development. Researchers will have to apply biological insights to facilitate new treatment and preventive options, the group stated.

Ultimately, barriers to genomic medicine are most directly overcome by demonstrating clinical utility in disease management and therapeutic decision-making, with evidence for improved patient outcomes, the team said.

Given the clinical importance of slowing disease progression, target-discovery efforts will increasingly need to embrace the genetics of disease progression and treatment response, as these may involve processes distinct from those captured by studies of disease onset.

With these recommendations, the researchers believe the industry will be able to leverage the promise of genomics and precision medicine to deliver more personalized, targeted care.

Collectively, these developments can be expected to accelerate personalization of healthcare delivery. Provided costs are sustainable, a more preventative perspective on health could emerge, managed through proactive genomic, clinical and lifestyle surveillance using risk scores, complex biomarkers, liquid biopsies and wearables, researchers concluded.

For the full potential of genomic medicine to be realized, there will need to be sustained collaborative endeavor on several fronts to ensure that the capacity to generate ever more detailed maps of the relationships between sequence variation and biomedical phenotypes delivers a comprehensive understanding of disease mechanisms that can be translated into the medicines of tomorrow.

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Addressing Disparities Will Advance Genomics, Precision Medicine - HealthITAnalytics.com

Physiology

Breeding Every Color of the Rainbow – Seed World

January 28, 2020 medical

What started as a hobby turned into a breeding program. Now, Texas A&M AgriLife plant physiologist and breeder Dariusz Malinowski is being recognized for his work in winter-hardy hibiscus.

in the north-central part of Texas, almost as close to Oklahoma as you can get, theres a little town called Vernon. About three hours away from Oklahoma City and Dallas, Vernon, Texas isnt known for being large in the last census, the population of Vernon listed 11,000 people but, it is known for being vibrant for a slew of reasons.

Most recently? Hundreds of winter hardy hibiscuses line Vernons streets as well as businesses. Now, you might expect these winter-hardy hibiscuses to be in the usual colors: white, red and pink. However, Vernon has some special varieties of hibiscuses lining the streets colors ranging from blue to silver and from maroon to lavender.

The Drag, Vernons mainstreet, is usually known for hosting festivals, including the Summers Last Blast, which is a large antique car show for that lasts four to five days, Mayor Doug Jeffrey says. However, theyre working on a new idea.

Were excited to see new varieties come out of the Texas A&M Agrilife Center, Jeffrey says. When you think of tulips, you think of Holland. Well, I want Vernon to be the place people think of when they think of hibiscuses.

These colorful hibiscuses didnt come out of nowhere they were bred with meticulous care, not by a breeder, but by a plant physiologist.

I had the opportunity to come to Texas A&M Agrilife on a postdoctoral position in forage agronomy and physiology, says Dariusz Malinowski, a plant physiologist and breeder at Texas A&M Agrilife. By profession, Im not a plant breeder, but I could use my knowledge in plant physiology in my cool-season forage grass breeding program. Hibiscus breeding was actually something that I started in my backyard.

Malinowski says his initial desire to breed hibiscus came from the idea that he wanted some colorful flowers in his backyard. He thought there was potential in making a winter-hardy hibiscus with a color other than red, pink and white.

One of my colleagues, the late Steve Brown who was the former director of the Texas A&M AgriLife Foundation Seed, saw a photo of my flowers in my office, he says. I jokingly said I have very nice flowers, right? Brown thought that my winter-hardy hibiscuses could have huge value as a breeding program.

But this joke led to something bigger than Malinowski had imagined.

From there, Malinowski met with Brown and learned how breeding programs worked in the United States and at Texas A&M Agrilife, and if hed be willing to add hibiscus breeding as a part of his program.

Initially, I expanded the amateur hibiscus breeding to backyards of my friends, Steve Brown and Dr. William Pinchak of Texas AgriLife, he says. It became a part of my program in 2010, and we planted the official plots in Vernon.

Every year since then, we plant about 2,000 hybrid winter hardy hibiscuses, and every fall we pick around 30-40 hybrids.

From there, the hybrids are disclosed to the Texas A&M Office of Technology Commercialization. Malinowski says in 2018, J Berry Nursery of Grand Saline, Texas, commercialized the first eight cultivars under the series trademark name Summer Spice Hibiscus, and theyve found some good success with it. Currently, there are 30-40 lines in evaluation for potential commercialization.

However, Malinowski says getting to this point only seemed easy because of how much access theyve had to the germplasm he created.

In 2010, I wanted to create new colors for winter-hardy hibiscus, he says. My dream was of a blue hibiscus, and within three years, we were able to breed a purple-blue hibiscus. Based on that plant, we were able to develop around 20 blue flowering lines.

He says these flowers range anywhere from silver to blue to dark purple.

Two are on the market as of 2018, Bleu Brulee and Cordon Bleu, and there are plenty of other blue lines in evaluation, Malinowski says. The first blue cultivar we developed was in 2012 called the Blue Angel. It was blue in shade, but in the sunlight, it was more purple-ish.

While working toward this blue color, Malinowski says the first different color they actually hit was a really light purple.

When I first saw Fantasia (a lavender-colored) and Plum Crazy (a plum-colored) winter-hardy hibiscus cultivars on the market, I brought them into the breeding program because I thought we could get into the blue color, he says. Eventually by repeated crossing them with our hybrids, we were able to get the blue color.

Malinowski says it took crossing four winter-hardy hibiscus species to get the first variation, and then he started adding new genetic materials. By adding new genetic materials and getting new variations, the program saw new colors develop.

An easier color they were able to develop was a maroon color perfect for Texas A&M.

We have shades of magenta, silver colors, dark purple colors and any shade of red that you could ever want, he says.

Despite the success Malinowski has found in breeding so many different colors of winter-hardy hibiscus, hes found that color isnt always the biggest things companies look for when marketing winter-hardy hibiscus.

We started working with commercial partners, and eventually, we had to shift our view of how to breed new varieties, he says. We learned that commercial partners dont necessarily care about the new colors we made. Instead, they look for different characteristics like plant growth habit, foliage color, shape and flower petal appearance.

While focusing on color, Malinowski says they had to start considering other characteristics and different traits, such as making the plants dwarf or compact.

Our first hybrids had beautiful novel flower colors, but their shapes and appearances other than the color werent fantastic, he says. We had to shorten the plants about two to three feet to make them compact.

Now, most of the hybrids they produce are compact and able to grow in a pot.

After we adjusted the size, we could introduce the color, Malinowski says.

From there, he learned commercial partners wanted more: new foliage colors and flower petal shapes.

They want to see different leaf color, ranging from purple to red leaves, Malinowski says. Were starting to consider adding that into our program, which means well focus on flower and foliage color.

In the meantime, he says theyve been working hard to come up with new colors and petal shapes.

Were working now on a new series, where the flowers will have different colors, but theyll have serrated edges on the petals, Malinowski says. We dont have those in blue yet, but were working on it.

Besides the serrated petals, theyve been working on a trait to make the winter-hardy hibiscus flowers seem like it has more petals.

The winter-hardy hibiscus flower only has five petals, he says. Tropical hibiscus can have many more petals, but not winter hardy. Were trying to intensify the trait so that there are different levels to the petals. That way, it makes the impression that there are more petals inthe winter-hardy hibiscus flower. So instead, theyll look more like a peony flower.

As the program continues, well start having a hibiscus that looks completely different and new!

As for new colors, Malinowski has his eyes set on orange.

Its not impossible, but its certainly more difficult than developing the blue color, he says. We probably wont ever have a completely orange color, but well get close. After that, wed really like to create a yellow-ish color, which is also difficult to create. Once we get the pigment, we can try to establish it.

At the beginning, it took around three to four years to come close to whatever we wanted, Malinowski says. Its much easier now because we have thousands of hybrids with different traits. We usually have the potential patterns to get a new trait easier, rather than at the beginning when we had nothing. But it depends!

Malinowski says one reason his program comes out with novel colors is because at the beginning of his program, he just worked on creating as many hybrids as he could.

Now, theres a lot of work every year for this, but we arent putting as much work as we had to 10 years ago, he says.

Now, the only restrictor he has: space.

Weve just about used all of our space, Malinowski says. We dont want to slow down and quit producing new hybrids, but were going to start making fewer but more focused crosses every year.

Now, with the excitement of so many new varieties of winter-hardy hibiscus popping out, Vernon wants to celebrate it.

This year, Mayor Jeffrey is working to put together a festival similar to their Summers Last Blast festival; however, this one is specifically only around the winter-hardy hibiscus.

If you think about a diamond in the rough, these winter-hardy hibiscuses are ours, he says.

Mayor Jeffrey uses an analogy of a farmer whos not making any headway on a farm and decides to sell it to find other solutions. But, the next farmer who buys it finds a diamond.

Thats the hibiscus, he says. We have something that was born and bred in Vernon, and it kind of represents a person from Vernon in a way. We often have droughts here, and were used to a tough climate. All those things make people tough, and you cant get more Texan than that. The hibiscus is tough and its able to stand a harsher climate If it can grow here, it can grow anywhere.

Were excited that Vernon is promoting itself as the hibiscus capital of the world, Malinowski says. The rose capital of the world is in Tyler, Texas, and Vernon wants to do something similar.

Malinowski says Texas A&M AgriLife gave them around 600 seedlings of the hibiscus this past spring, that were extra plants from the growing season.

Its so fun getting flower donations from Texas A&M Agrilife, because its a mystery, Mayor Jeffery says. You never know what color youre going to get.

Vernon planted them in parks, museums, churches, outside of businesses and all along the Drag, Malinowski says. We had so many visitors over the summer to see the plants blooming, it was so intense, but its good to meet a different audience.

One reason Malinowski believes people gravitate to the hibiscus is because they see the fields blooming in the summer, and they want to know what it is that looks so good.

Once established, the winter-hardy hibiscus grows great, he says. I have some at my house that I planted between 2008-2009 that I dont water because theyre outside my fenced area, but theyre still surviving and prospering. Theyre really good at growing in drought.

As the festival, Mayor Jeffrey is excited.

During Summers Last Blast, we shut down the Drag, and all of our hotels and restaurants are full, he says. We shoot from a population of 11,000 to a population of 30,000 during those days. I want to take that model and build a hibiscus festival around it.

Mayor Jeffrey says to think about a fun festival right before school starts back.

I dont think itll start as large as Summers Last Blast, but I want to build it up, he says. Im thinking it would be great to have a parade with a winter-hardy hibiscus queen and king.

Agritourism speaks to people, Mayor Jeffrey says. A lot of rural communities are shriveling up, and if you dont have anything to highlight a town, itll disappear. I think the hardy hibiscus can do so much for us.

Physiology

Life in the Balance – HSC Newsbeat

January 28, 2020 medical

Harshini Mukundan, PhD, juggles a dizzying number of responsibilities while somehow making it all look effortless.

As an administrator in the Chemistry Division at Los Alamos National Laboratory, she serves as Deputy Group Leader for Physical Chemistry and Applied Spectroscopy and Team Leader in Chemistry for Biomedical Applications. The 2003 graduate from UNM's Biomedical Sciences Graduate Program is also a teacher, as well as a devoted parent and spouse, who, in her spare time, participates in traditional Indian dance.

But in her role as a research scientist, Mukundan is laser-focused on finding solutions to some of the most urgent health concerns facing humanity. At LANL she has developed diagnostic assays for tuberculosis and helped create technology to detect breast cancer and influenza. Her current highly ambitious research agenda centers on finding a universal method for identifying infectious disease.

Munkundans lab has unraveled some of the common methods by which disease-causing organisms interact with a human host in hopes of creating a mechanism to mimic what the body already does naturally.

All pathogens support or secrete biomarkers that are recognized by our innate immune system, she says, adding that many of these molecules are highly conserved. The body recognizes conserved signatures. It looks at the commonality and uses that to mount a response.

These molecules are not easily detected in the bloodstream, but they are carried throughout the body by hitchhiking on HDL and LDL cholesterol proteins (My buzzword for them is the biological taxi service, she says).

Mukundan and her collaborators are working on sensor technology that can liberate these biomarkers from their cholesterol hosts and measure them, providing a rapid readout of what type of infection theyre signaling.

While the labs work has national defense applications, it also has obvious relevance in clinical health care and is already being assessed for its use in diagnosing disease in the field. It has been tested in South Korea, Uganda and Kenya, Mukundan says, and could provide a quick way to distinguish a bacterial from a viral infection.

Mukundans path to a leadership role at the nations premier national laboratory started in a small town in the Indian state of Tamil Nadu, where her father was in banking and her mother was a teacher.

She earned her undergraduate degree in microbiology from the University of Delhi in 1995. It seemed cool, she says. I liked biology and I always wanted to do medicine or biology. She went on to complete a masters in microbiology at Barkatullah University in Bhopal, with her thesis research conducted at Indias National Institute of Immunology.

Her lab work there centered on drug-resistant cancer cell lines. There were pretty awesome researchers working at NII, Mukundan says. I got to meet a lot of really cool people. Essentially, it was just the exposure, and then I decided I wanted to do a PhD.

She and her husband, LANL staff scientist Rangachary Mukundan, came to the U.S. for their doctoral work. He earned his PhD in materials science at the University of Pennsylvania and joined LANL as a postdoctoral fellow in 1997.

Harshini initially was accepted at Penn for her PhD, but transferred to The University of New Mexico when her husband got his job at Los Alamos. As a late arrival in UNMs Biomedical Sciences Graduate Program, she started by rotating through several labs, where she met Nancy Kanagy, PhD, now chair of the Department of Cell Biology & Physiology.

I really liked Nancy, Mukundan says. I liked her work ethic and approach to balance. She has this way of making you feel very welcome.

At the time, Kanagy was working on alpha adrenergic receptors and their role in cardiovascular disease, which Mukundan found interesting. Mukundan started by exploring a hypothesis involving the movement of calcium ions in cells that soon turned out to be incorrect.

I definitely proved that the hypothesis was wrong, she says. We got a paper out of it, but that research was at a dead end. We had to make a project change.

With Kanagy and fellow Cell Biology professor Thomas Resta, Mukundan devised a new project. It was looking at gender differences in hypertension and the role of estrogen in erythropoietin regulation, she says.

In putting together the research proposal that would lead to her dissertation on how estrogen regulates of erythropoietin gene expression during hypoxia. Nan and Tom were heavily involved and helped a lot, obviously, and we got it, she says, adding that the setback taught her a valuable lesson.

It looks like a big bummer when your original project doesnt work, but in retrospect, I learned how to write, she says. It made me altogether much more confident. Sometimes you have what appears to be a big tragedy but it actually works out for the better.

Mukundan says she experienced some reactions when she first came to the U.S. that were a little bit racist, she sometimes felt she was treated differently because she was a woman. But at UNM she felt supported.

In Nan and Toms team I found acceptance, Mukundan says. Kanagy, who was starting a family, became a friend and mentor. I think it kind of subconsciously does teach you that women can be great scientists, good mothers and perpetually tired.

Mukundan and her husband lived in Santa Fe while she was doing her lab research, requiring a daily commute to the UNM campus in Albuquerque. She stayed at my house, Kanagy recalls. Sometimes it was really late to drive back to Santa Fe.

Mukundan showed an aptitude for research, Kanagy says. Harshini was unafraid of challenges, she recalls. Early on, she was not daunted by having a hard problem to solve and taking this on. She used very creative approaches.

Mukundan was unflappable in the face of the failure of her first research project, Kanagy says. Courageous might be the right word or at least unintimidated by difficulty, she says. When we she had to switch gears she was very resilient. She developed a whole bunch of new methods to answer this question.

Kanagy also appreciates her friends ability to keep the many commitments in her life in balance.

Shes very human and cared very deeply about her family and cared about my family, she says. Even then, she was doing traditional Indian dance while commuting an hour each way. When I think of Harshini, she has a great smile and she just invites people in shes just a pleasure to have around.

When Mukundan defended her dissertation in 2002, soon after having her first child, Kanagy urged her to pursue postdoctoral research at another university, but Mukundan instead took a job at QTL Biosystems, Santa Fe a biotech startup, where she worked for two years on biosensor technology.

In 2006 Mukundan won a postdoctoral position at LANL in the lab of Dr. Basil Swanson, where she wrote a National Institutes of Health grant for research on developing a diagnostic tool for tuberculosis. We got that proposal and I still work on TB today, she says. Thats how we got started.

After graduating to become a full member of the LANL faculty, Mukundan has become a mentor in her own right. Earlier this year, she was recognized as one of 125 IF/THEN Ambassadors by the American Association for the Advancement of Science for her support of young women in science, technology, engineering and math (STEM) at LANL.

IF/THEN is a national initiative of Lyda Hill Philanthropies that seeks to further women in STEM fields by recognizing innovators and inspiring the next generation of researchers.

Although scientific careers can be incredibly demanding, Mukundan says she learned from her UNM colleagues you can have a good career and have a family and have work-life balance. That makes people want to go into science.

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Life in the Balance - HSC Newsbeat

Genetics

Massive effort to document the genetics of European forests bears fruit – Science Magazine

January 28, 2020 medical

A power drill helps a researcher extract a core from a tree included in the GenTree project.

By Elizabeth PennisiJan. 27, 2020 , 3:15 PM

Faced with deforestation, climate change, invasive pests, and new diseases, many trees are in trouble. Foresters and conservationists are scrambling to save them, but cant protect every stand of woods. And prioritizing which placesand even which individual treeswarrant preservation has been a challenge. For example, You want a lot of genetic diversity in a conservation area. The higher the diversity, the more the chances that the population will survive, says F. A. (Phil) Aravanopoulos, a forest geneticist at Aristotle University of Thessaloniki. But robust data on the genetic diversity of trees can be scarce.

Now, a 4-year, $7.7 million effort to document the genetic diversity of forests in Europe is helping fill that gap. In a project dubbed GenTree, researchers from 14 countries measured, cored, and took DNA samples from 12 important tree species across Europe. No other continents forests have been documented so broadly and so comprehensively, says Nathalie Israel, a forest geneticist and forester with Natural Resources Canada. The sampling is amazing.

The results, reported at a forest genetics conference this week in Avignon, France, could help conservationists, tree breeders, forest managers, and researchers trying to understand how forests will cope with climate change. The data trove will provide a solid base for a better understanding of the links between genetic diversity and increased adaptation and resilience of the European forests, says forest researcher Hernn Serrano-Len, who worked at the recently disbanded European Forest Institute Planted Forests Facility.

More than 42% of the European Unions land area is covered by forests and other wooded land. These areas provide wood, food, energy, and ecosystem services such as clean water and flood control, and are enjoyed by hunters, hikers, and birdwatchers. In a bid to improve forest management, in 2016 the European Unions Horizons 2020 program funded GenTree to document tree species of both economic and ecological importance. It is the first project to consider genetic diversity not only from the breeding side, but also from the conservation side, says project leader Bruno Fady, a forest geneticist at the French National Institute for Agricultural Research.

To assemble the data set, research teams looked at about 20 trees from each of the dozen tree species, which included maritime pine, Norway spruce, sessile oak, stone pine, and European beech. They took samples from 10 to 25 populations of each species, working to include individuals from across the trees range, and that survived in places with extreme environmental conditions, such as drought or late frosts. The researchers then sequenced active genes, as well as other DNA from across the genomes, to determine the range of genetic variation both within and between tree populations. The researchers also measured key traits such as annual growth, leaf surface area, seed germination rate, and resistance to disease, and analyzed the degree to which these traits were linked to specific gene variants.

A core that GenTree researchers extracted from a black poplar inthe Drmeregion ofFrancein 2017

Such data helped reveal how trees coped with their local environments; for example, identifying populations and individuals that were better adapted to drought or frost than others. A key revelation was just how much genetic variation exists in some populations. Theres a huge within-species diversity, which is rarely acknowledged in forestry and rarely used in management, Fady says. A single population of beech, for example, might contain high- and low-elevation trees that are as different genetically as trees living in forests that are hundreds of kilometers apart.

Such genetic insights can be very helpful in planning conservation programs, Israel says. I wish we could have a North American project like that, she says.

The data might also come in handy for researchers thinking about how to help forests survive climate change. One possible strategy is to transplant trees from warmer climates into cooler areas undergoing warming, a process called assisted migration. In some cases, the genetic data could be key in deciding which seeds to plant in new areas, or how to breed hardier trees. But in others, the genetic data might indicate dont bother with assisted migration, Fady explains. You have enough seeds [with enough variation], and natural selection will play the role of the breeder, so the trees will be able to adapt to warming on their own.

The work also drives home the need for tree breeders to focus more on genetics, says David Neale, a forest geneticist at the University of California, Davis. They need to understand the genetic composition of the individual [tree], he says. Its not enough to say [the tree] came from this place in the world. Thats the level the foresters are working with right now.

Other results at the meeting suggest better genetic data can benefit commercial foresters. In onemodeling study, researchers found that pine forests grown from relatively expensive improved seed developed by breeders are likely to be worth the added cost, because the bred trees mature quickly and produce more wood. Its a negligible extra seedling cost, says Serrano-Leon, who predicts that tree breeding programs all over Europe will benefit from the [GenTree] data. It is an extraordinary resource.

Genetics

Genetics research at BYU may not be what you think – Universe.byu.edu

January 28, 2020 medical

See also BYU researchers contribute toward finding a cure for Alzheimers disease

Genetics and Alzheimers researchers at BYU have made far-reaching contributions to their fields through two valuable campus resources: the DNA Sequencing Center (DNASC) and the Office of Research Computing. These resources generate data that is used by BYU faculty researchers, students and collaborators from other universities in their research.

Although many people approach the DNASC requesting sequencing for family history and genealogy related samples, these services are currently not offered. The DNASC, along with the Office of Research Computing, is centered on the primary focus of providing support for academic research.

DNA Sequencing Center

Inside the Life Sciences Building (LSB) on the BYU campus is a collection of small rooms that make up what is known as the BYU DNASC. This center is vital to researchers and houses DNA sequencing machines that are dedicated to efficiently and economically processing DNA samples.

Edward Wilcox, managing director of the sequencing center, has worked as a full-time research faculty member since 2005. He manages everything from the DNA sequencing machines to student employees who help prepare samples.

The process of preparing DNA samples involves isolating them, shearing them down to the right size, making libraries and cleaning them.

A library is just pieces of DNA with adapters on the ends, Wilcox said. The adapters are what allows us to sequence in since its a known sequence. From there, we can sequence into the unknown.

After the libraries are prepared, they are ready to be placed in the sequencing machines. The DNASC currently has three machines the Illumina, PacBio I and PacBio II. The 2015 Illumina will retire at some point and be replaced by a new machine called the NovaSeq. This machine will cost about a million dollars but is essential for the work and is expected to generate more data at less of a cost.

Handling all this expensive equipment requires great care. Wilcox admits he may come off as overbearing to student employees at times, but thats because everything needs to be done just right.

Thats $20,000 of reagent (a substance or compound added to a system to cause a chemical reaction) were putting on the machines right now. If we dont do things right, and the run fails, were out $20,000, Wilcox said. Its a little concerning, and we cannot afford to lose a run.

BYU junior Miranda Johnson has been working at the DNASC since September 2018. The neuroscience major said the job is stressful and requires a lot of multitasking.

But its less stressful than customer service in my opinion, Johnson said.

The DNASC receives a variety of different samples from all across the United States and the world, including recent samples from Russia, the Czech Republic and Italy. The samples can come from any living organism, including fish, plants, insects, sunflowers and blood.

Its pretty random what we get, Johnson said. Thats the fun part of the DNA Sequencing lab! Its familiar enough you dont get lost, but its always a little bit different.

BYU biology professor and Alzheimers researcher John Kauwe said the DNASC is an important resource that nearly everyone doing genetics research at BYU relies on for some aspects of their data generation.

Its great to have that resource right down the hall, where we know we can get high quality data, Kauwe said.

The Office of Research Computing

Another vital resource for research at BYU is the Office of Research Computing. With over a thousand computer servers and 24,000 processor cores, this valuable resource is utilized by hundreds of users, including BYU faculty researchers, students and a few dozen collaborators from other universities.

Nothing I do would be possible without it, said Perry Ridge, an Alzheimers researcher and biology professor at BYU. Every analysis that we run for every project is on the supercomputer.

Director of research computing Ryan Cox oversees the entire works, running everything from the servers to the employees. His team does everything from maintaining the hardware and software that researchers use and purchasing new equipment to staying on top of industry trends and helping people with code optimizations.

The servers that make up the supercomputer are located in three separate rooms across BYU campus, the biggest being in the James E. Talmage building. Several departments on campus rely on this resource especially the engineering, physical, mathematical and life sciences colleges.

The DNASC in the life sciences college sends terabyte-sized files to the servers on a weekly basis. Wilcox, the managing director of the sequencing center, said not having enough computer space has been one of their biggest challenges.

Were dealing with some big files here, Wilcox said. The computer center at BYU limits you to 15 terabytes; thats a weeks worth of data and its hard to distribute everyones data in that time.

Realizing this was an issue, Cox said the Office of Research Computing recently started renting out storage space to accommodate those who need the extra space.

Some people use 80 to a 100 times more storage than the allocation we give people, Cox said.

Generally the research computing sources are freely available to everyone, but the limited storage space makes it difficult to satisfy everyones needs. But according to Ridge, Cox and his team are always finding ways to accommodate those in the research community.

The Office of Research Computing is service-oriented and they go out of their way to help faculty and students in doing research, Ridge said. They really make a lot of what we do here at BYU possible, and make it possible for BYU to stand out in positive ways.

Kauwe agrees and added that these campus resources help him and his colleagues make a positive impact in their fields of research.

Its been wonderful coming here and having a DNA sequencing center and a high quality research computing center to analyze the scale of data were generating, Kauwe said. Its allowed us to be competitive on a national scale and to make research progress that is meaningful in our field. They are incredible resources that are key to genetics research at BYU.

Genetics

Advancement in genetics, husbandry and more help animal ag – AberdeenNews.com

January 28, 2020 medical

JAMESTOWN, N.D. Travis Bell knew exactly how many pounds of feed each pen of cattle in his 1,500 head feedlot in Fordville, N.D., got on Monday, Jan. 20. That wouldnt seem like much of a feat unless you consider that Bell was more than two hours away, in Jamestown at the Precision Ag Summit.

Bell could see exactly how much of each component of his calves ration his employees had put down, using the Performance Beef app on his phone. The app has been a game changer for Bells Edgewood Ranch. Unlike in the old days, when mixing feed meant half a scoop of this and half a scoop of that, Bell could keep track of exactly how much feed each pen got, enabling him to better track profitability. The app also allows him to keep tabs on cattle intake and health.

Performance Beef has probably been my biggest asset, he said.

He can compare how different cattle perform as well as keeping track of his true costs rather than just estimates.

Were knowing exactly what all of our costs are now versus before it was just pen and paper, he said.

Bell joined North Dakota State University Extension veterinarian and livestock stewardship specialist Gerald Stokka and North Dakota Farmers Union Vice President Jason McKenney on a panel about precision agriculture in livestock at the ninth annual Precision Ag Summit.

While the Summit typically focuses more on farming than ranching, livestock operators have adopted technological advancements, too, Stokka explained. For instance, he compared development of genetics in cattle using techniques like artificial insemination and embryo transfer to development of seed genetics in farming. Both have enabled the industry to move toward more desirable traits.

For Bell, those genetic advancements mean he can use Simmental bulls to breed Angus cows, something that many ranchers avoided in the past due to concerns about pulling calves. He also raises registered Simmental cattle to propagate the genetics he wants to see in cattle.

Besides the genetics and the Performance Beef app, Bell said he also benefits from advancements in feed and medication. He feeds a product with probiotics and ionophores to try to keep cattle healthy and reduce the amount of antibiotics he has to use to treat sick calves.

McKenney, who serves on the board of the North Dakota Livestock Alliance, said the dairy and swine industries also have found many uses for technology in modern operations. From animal identification to heating and cooling and waste management, the industries have used technology not just to improve herds but also to keep animals comfortable and keep operations sustainable, he said.

A happy cow is a cow that makes the money, or in this case, produces milk, he said.

As much as livestock operators use technology now, Stokka sees future development that could help some of the main problems operations face. He sees even better genetic data, looking at things like cow longevity and resistance to disease. He can see applications in imagery, whether drones or satellite or cameras in remote places, to check cattle on pasture. He can see thermal imaging used to help determine spikes in temperature and respiratory problems, even before cattle show signs of illness. He sees stations in pens or pastures where cameras and scales can give updates on cattle, identified by tracking devices. Some of those things already are in the works, and others dont seem as far-fetched as they once would have.

But can technology revitalize a livestock industry that has seen many people in recent generations leave?

Id sure like to think so, Stokka said.

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Advancement in genetics, husbandry and more help animal ag - AberdeenNews.com

Genetics

My ‘Tiredness’ Turned Out to Be a Genetic Condition That Raises Cancer Risk – msnNOW

January 28, 2020 medical

Courtesy Jen B.

In 2012, Bev Michel found a large lump in her breast. This discovery started a medical odyssey that led to a cancer diagnosis and ultimately unraveled the mystery of a variety of health issues that had plagued her for more than eight years.

Following up on the lump with a mammogram and biopsy, Michel got the startling news that she had cancer. The West Chester, Pennsylvania resident immediately jumped into a chemotherapy regimen, undergoing six sessions of chemo and two lumpectomiesonly to find later after genetic testing that her type of cancer, lobular breast cancer, doesn't respond to chemotherapy. She then requested and underwent a double mastectomy, hoping to ensure the cancer was gone for good. But the cancer recurred in 2016near the nodes. So she again had surgery, this time to remove lymph nodes that she later learned were benign.

Michel felt there had to be more to her troubles, and she went to her general practitioner for guidance. "I told her how I was always tired, and how much my joints ached," Michel recalls. "She ran a couple of blood tests, and when she received the results she didn't believe them. She said my iron levels were sky-high, so she retested them. They were even higher." Michel's doctor diagnosed her with hemochromatosis, a metabolic disorder that leads to abnormally high iron levels in the body.

The mineral deposits itself into organs like the heart, liver, and pancreas, and in the joints; it can raise the risk of cancer and other diseases. A normal human absorbs about 8 to 10 percent of the iron they get from their diet; people with hemochromatosis absorb four times as much. The condition is inherited, and people with northern European ancestry have an elevated risk, according to the Genetics Home Reference. Experts estimate that 16 million Americans have elevated iron levels. Michel's diagnosis helped shed light on her family's medical history. "My mom died of breast cancer, had macular degeneration, and heart issueswhich are all signs of the disorder. When I had genetic testing, my results showed that both of my parents had the gene mutation, so of course, I would, too." (Here, doctors reveal the rarest conditions they've ever diagnosed.)

About one in 227 of people of Northern European descent have the condition, and about 10% of white people in the U.S. are carriers, according to National Organization for Rare Disorders. That means they have one copy of the gene mutation that causes hemochromatosis. You need to inherit two copies of the gene, one from each parent, to have the condition, although not everyone with both genes develops it. It's most often diagnosed in men after age 40 and in women after 60, in the postmenopausal years. While it's one of the most common genetic diseases in the U.S., it's less common in African Americans, and people who are of Hispanic, Asian, or Native American descent.

Michel was told she would need to donate blood every few weeks for the rest of her life, as giving blood regularly helps reduce iron levels. The prospect of this sent her to the internet to research other possible treatments. "What I found was that high iron is correlated to cancer, and I'm convinced it's what caused cancer for both my mom and me," she says."I found a doctor at the University of Maryland, Abulkalam M. Shamsuddin, MB, BS, PhD, who had studied the use of something called IP6 for treatment of cancer and iron overload." IP6 stands for inositol hexaphosphate: It's basically a carbohydrate substance that behaves like a vitamin, and it binds with extra iron in the body, explains Michael. "Once I began taking it, I haven't had a blood draw in two years, and my cancer has not recurred. My doctors are amazed."

Through her journey, Michel has found a passion for educating others about this relatively common yet underdiagnosed disorder. "I think there needs to be more open-mindedness among the medical community regarding treatments for conditions like this. Instead of treating only symptoms, look for the cause," she says.

If you have suspicious symptoms and you're not finding answers, Michel advises you be direct: "Ask to be tested for hemochromatosis. It's not an expensive test. If you have cancer, look for a possible correlation to your iron levels. If you test positive, then consider genetic testing for your children's sake. If you have it, they might, too."

Don't miss the 50 everyday habits that reduce your risk of breast cancer.

Gallery: 50 everyday habits that can reduce your risk of breast cancer

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My 'Tiredness' Turned Out to Be a Genetic Condition That Raises Cancer Risk - msnNOW

Genetics

Is the consumer genetics fad over? – MIT Technology Review

January 28, 2020 medical

The CEO of 23andMe told CNBC her company will lay off 100 people as sales of its direct-to-consumer gene tests slump.

This has been slow and painful for us, CEO Anne Wojcicki told the website, which estimated the cuts would pare about 15% of the company's staff.

Boom times: Sales of DNA tests that tell people their ancestry and health facts started booming a few years ago, propelled by TV and Internet ads hawking the promise that people could gain unique insights from their genes.

During 2018, the total number of people who had ever bought the tests doubled, swelling the databases of 23andMe, Ancestry, and several smaller companies to over 26 million people altogether.

The bust: Now, all signs are that sales of the $99 consumer tests slowed dramatically in 2019.

Our own calculations suggest the largest companies sold only four to six million of them, meaning the databases would have grown by just 20% during the year. That would have been the slowest growth rate for the DNA test industry ever.

Uncertain causes: It's not clear why consumers stopped buying tests in droves. It could be that the market is tapped out, and there aren't many people left curious to learn what percent French or Nigerian they are, or whether they are at risk for going bald.

Others may have concerns about their DNA data staying private, since police have started accessing smaller ancestry databases to carry out genetic manhunts.

Ancestry, which maintains the largest database with more than 16 million people, did not answer questions about whether it had seen a sales slowdown. Last year, Ancestry introduced new health offerings in what some analysts saw as a bid spark a "re-testing" market, or coaxing consumers to pay for an additional test.

Genetics

Local News Doctors weigh in on pros and cons of genetic testing kits Brooke Hafs 5 – WGBA-TV

January 28, 2020 medical

APPLETON, Wis. (NBC26) -- Genetic testing kits have grown in popularity.

Doctors say there's a time where it is appropriate to use them and a time when the information might not be sufficient.

At 59-years-old, Robin Vandermoss was diagnosed with cancer.

"It has tracked through my father and his father," said Vandermoss. "I just kind of want to put the puzzle together."

Now more than 6 months later he's undergoing genetic testing at ThedaCare.

"Hopefully we end up with some results that can be useful for my children and their children going on," said Vandermoss.

He's taking a route that doctors say is best under his circumstances.

As direct-to-consumer genetic testing kits grow in demand, doctors are informing people there are times to use them and times to seek an alternate route.

"If anybody has a strong personal or family history of cancer, heart disease or other conditions running in their family, then they really need a more formal evaluation," said Bobby McGivern, a Genetic Counselor with ThedaCare Regional Cancer Center.

Here's how these tests work.

You send a saliva sample in the mail. Your sample is tested in a lab and you receive your results revealing a plethora of new information about yourself.

Some examples of traits you can learn from a direct-to-consumer kit are:

Doctors say if you choose to use a gene testing kit that you've ordered online it's best to read the fine print.

Make sure you understand the capabilities of the test and look closely at the privacy information so you know what the lab is doing with your DNA.

Overall doctors say direct-to-consumer genetic testing kits have inspired a valuable trend.

"Families are talking more about family history," said McGivern. "They're asking some of the older relatives what is in the family, or maybe they're initiating some conversations with primary care doctors that they wouldn't have otherwise."

Use the kits wisely and seek a genetics referral from your primary care doctor if you have risk factors or a family history.

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Local News Doctors weigh in on pros and cons of genetic testing kits Brooke Hafs 5 - WGBA-TV

Neuroscience

Reflections on the Culturally Responsive Campus Community (CRCC) Conference – News – Illinois State University News

January 28, 2020 medical

The Culturally Responsive Campus Community Conference drew big crowds of Redbirds looking to learn more about activism and solidarity.

The fourth annual Culturally Responsive Campus Community (CRCC) Conference was held on November 18 and 19 at Illinois State University. The overall mission of the annual CRCC Conference is to enlighten, educate, and ignite conversation around creating a more equitable and just campus environment for all. This years conference theme was Building Solidarity Across Movements.

With over 700 students, staff, and community members registered to attend, participants chose from 60 presentations, workshops, and discussions during the conference. Topics over the two days included working with international students, cultivating social justice learning through art and creative writing, anti-Blackness, Trans advocacy, diverse learning environments, fighting racial inequity, and challenging the norms of sexual violence.

There is something unspeakably beautiful about spending two days learning and connecting with passionate, intelligent, and caring people whose life work is that of justice. Unsurprisingly, many of the National Center for Urban Education (NCUE) staff, affiliated faculty, students, and community partners had a hand in various aspects of the conference.

CRCC Program Chair and NCUE-affiliated faculty Dr. Shamaine Bertrand and others questioned: What if we begin to build a sustainable movement across campus? Dr. April Mustian, CRCC Chair and Director of Faculty Development and INFUSE Coordinator for NCUE, stated the conference was aimed to be clear and honest about what is still standing in the way of reaching solidarity.

CTEP Director Jennifer OMalley speaks during the Neuroscience presentation at the CRCC conference.

NCUE staff and community partners heard this call and led two workshops during the conference. The first session was titled Cultivating an Understanding of Neuroscience to Empower Urban School Communities. Jennifer OMalley, Director of the Chicago Teacher Education Pipeline (CTEP) at NCUE along with Chicago community partners: Brienne Ahearn of North River Commission, Carlos Millan of The Resurrection Project, Ana Mosqueda of Latinos Progresando, and Gynger Garcia of Breakthrough shared how an understanding of fundamental concepts in brain development can empower educators. They affirmed that when neuroscience concepts are partnered with community knowledge, educators can bring empathy to any learning space to be truly culturally responsive.

The second NCUE workshop, led by CTEP Induction & Mentoring Director Apryl Riley, Melanie Christion of Greater Auburn Gresham Development Corporation, and Jose Guerrero, former CTEP staff and current Chicago Public Schools teacher, centered on restorative practices. Titled Promoting Equity and Teaching Empathy Through Restorative Circle Practices, the presentation showed how restorative practices are transformative ways to communicate with others and are intended to support and keep people accountable. Specifically, this presentation asserted that restorative circle practices are profound tools to integrate into urban education environments, K-12 classrooms and beyond. Restorative practices, characterized by awareness and intentionality, allow teachers and students to communicate more effectively with each other, and ultimately achieve a more equitable classroom.

Junior Genesis Robinson speaks at the main stage of the CRCC Conference, November 19.

The CRCC conference serves to ensure ISU and the surrounding community continues to commit to an inclusive, equitable, and culturally responsive campus. Genesis Robinson, a junior education major and two-time NCUE STEP-UP program alum, echoed this sentiment during her remarks to the conference audience attending the student-led session The Roots of Anti-blackness.

The way some people experience an institution is not the same as how others experience an institution. I think events like this shed light on that fact and how we need to see things from different perspectives, Robinson said.

NCUE is proud to be associated with such great leaders across our communities. Together, we aim to create a more just and equitable world for all.

Originally posted here:
Reflections on the Culturally Responsive Campus Community (CRCC) Conference - News - Illinois State University News