Category Archives: Genetics

Genetics

The same genetic mutations behind gorillas’ small penises may hinder fertility in men – Livescience.com

Silverback gorillas are famous for their impressive, bulging physiques and their rather modest genitalia. Now, scientists have uncovered a potential genetic link between these apes' small members and infertility problems in male humans.

Coming in at just 1.1 inches (3 centimeters) long, on average, the penis of the adult male gorilla (Gorilla) is the smallest phallus of all apes. The gorilla's genital size comes with other deficits in its reproductive capacity, such as low sperm count compared to other primates, and sperm with poor motility and a diminished ability to bind to eggs.

Given that these are reproductive issues that can also affect humans, it may seem surprising that all male gorillas share these traits. However, this can be explained by gorillas' mating system, said Jacob Bowman, lead author of the new study and a postdoctoral researcher at the University at Buffalo.

Gorillas operate in a polygynous system, in which a dominant male has near-exclusive access to females in his troop. The silverback's unwieldy physique means it has no problem securing mates, and thus, its sperm doesn't have to compete with that of other males and it can produce offspring without many, highly motile swimmers. The theory is that this lack of sperm competition led to the evolution of gorillas' small genitalia.

Related: Move over, Viagra this spider's boner-inducing venom could treat people let down by the blue pill

This got researchers "wondering if, at a genetic level, we can find genes associated with spermatogenesis [sperm production] or that we see leading to poor-quality sperm," Bowman told Live Science. Gorillas and humans share the vast majority of the same genes so if the researchers could pinpoint suspect genes in gorillas, they could next turn their attention to the human genome.

Roughly 15% of U.S. couples have trouble conceiving, according to Yale Medicine, and more than half of those cases involve male infertility. Around 30% of infertility cases have a genetic basis, said Vincent Straub, a doctoral student in population health at the University of Oxford who was not involved in the new study. However, the genes involved in male infertility are poorly understood.

Get the worlds most fascinating discoveries delivered straight to your inbox.

To help unravel those genetics, Bowman and colleagues combed through a database of more than 13,000 genes across 261 mammals. This involved looking at genes' underlying sequences, to see how they changed over time in related animals. The aim was to see if certain genes in the gorilla branch of the tree of life were evolving at dramatically reduced rates, Bowman said.

This can happen when there isn't strong pressure to get rid of genetic mutations that could hinder a population's survival such as those related to gorillas' low-quality sperm. This process, called "relaxed purifying selection," can result in seemingly harmful mutations becoming common in a species.

The data turned up 578 genes in the gorilla lineage that underwent this type of selection. An analysis and existing data suggested that many of these genes are involved in making sperm. However, not all the flagged genes had known roles in male fertility.

To better understand these genes' functions, the team turned to the fruit fly (Drosophila melanogaster), a commonly used genetic model in biology. They systematically silenced each of the genes in male flies to see if they affected the insects' ability to reproduce. In this way, they uncovered 41 new genes that hadn't previously been tied to male fertility.

The researchers then connected the dots back to humans using a genetic database with data from 2,100 men with infertility, who either had very low amounts or a lack of sperm in their semen. They also looked at data from fertile men, focusing on the genes they'd flagged in gorillas. They found that, in 109 of relaxed gorilla genes, the infertile men carried more loss-of-function mutations than did fertile men; loss-of-function mutations reduce a gene's ability to make the protein it codes for.

While it's likely these genes are involved in human male fertility, more research is needed to learn exactly how they work in the body. Straub emphasized that infertility is very complex, and that not all of it comes down to genetics. To fully understand it, scientists need to account for how different genes interact with one another and with an organism's environment and its behavior.

The findings drawn from gorillas open the door to future explorations about how these genes, and others closely associated with them, might influence fertility in people, Straub said. The study was published May 9 in the journal eLife.

Ever wonder why some people build muscle more easily than others or why freckles come out in the sun? Send us your questions about how the human body works to community@livescience.com with the subject line "Health Desk Q," and you may see your question answered on the website!

See the rest here:
The same genetic mutations behind gorillas' small penises may hinder fertility in men - Livescience.com

Genetics

Genetics reveals surprising origin of the German cockroach – Cosmos

The German cockroach lurks in human homes, cities, and structures worldwide. You wont find it crawling through natural habitats its entirely domesticated.

The pest species, Blattella germanica, was first recorded in central Europe about 250 years ago. But its origin and spread has remained a mystery until now.

But a team of researchers has now confirmed the species evolved from the Asian cockroach Blattella asahinaiabout 2,100 years ago and probably did this by adapting to human settlements in India or Myanmar.

We found that the sequence for the German cockroach was almost identical to that of B. asahinai, a species native to the Bay of Bengal, from east India to Bangladesh and into Myanmar, says Theo Evans of the University of Western Australia, who co-authored the study published inProceedings of the National Academy of Sciences.

Genomic analysis of DNA collected from 281 cockroaches, from 17 countries across 6 continents, revealed 2 routes through which the species spread across the globe.

We found an early spread route around 1,200 years ago, which was from eastern India westwards, likely from increasing trade and military activities of the Islamic Umayyad or Abbasid Caliphates, says Evans.

The next spread route was eastwards around 390 years ago into the Indonesia archipelago, likely facilitated by various European East India Companies.These companies traded spices, tea, cotton and other products within South and Southeast Asia, and back to Europe.

We estimated that German cockroaches arrived in Europe about 270 years ago, which matches the historical records from the Seven Years War. From Europe the German cockroach spread to the rest of the world, around 120 years ago, probably from faster transportation on steam ships.

B. germanica grows to about 1.1-1.6 centimetres long and varies in colouration from tan to almost black. They are omnivorous scavengers attracted to meats, starches, sugars and fatty foods.

To survive, cockroaches have to avoid being seen by humans. German cockroaches have evolved to be nocturnal, avoid open spaces, and although it retained its wings it has stopped flying, says Evans.

Originally posted here:
Genetics reveals surprising origin of the German cockroach - Cosmos

Genetics

Optimizing genetics to advance controlled environment agriculture – AgriLife Today – AgriLife Today

Texas A&M AgriLife is adding crucial expertise to help guide future innovations in controlled environment horticulture as the burgeoning field continues to evolve.

Krishna Bhattarai, Ph.D., Texas A&M AgriLife Research plant breeder for controlled environment horticulture and assistant professor, has joined the Texas A&M College of Agriculture and Life Sciences Department of Horticultural Sciences. His research uses genetics and genomics to develop new horticulture crop cultivars specifically for controlled environment production.

Bhattarais research will be performed at the Texas A&M AgriLife Research and Extension Center in Dallas.

Amit Dhingra, Ph.D., head of the Department of Horticultural Sciences, said Bhattarais hiring is a major step forward for the controlled environment horticulture program. He said technological advances have spurred much of the burgeoning fields momentum, and Bhattarais arrival and focus on optimization of plant genetics in these systems comes at a critical time.

Dhingra said he believes the next step in the evolution of controlled environment horticulture is cohesion between plant genetics and the grow systems they support. The idea is not only to optimize yields but also focus on other cultivar characteristics like nutritional density and growth habit as well as aesthetics and flavor.

Daniel Leskovar, Ph.D., director at the Dallas center, said Bhattarais hire resulted from the strategic plan and vision of the controlled environment horticulture program at Texas A&M AgriLife.

His expertise in plant breeding and phenotyping tools will provide very valuable synergy to our growing CEH multidisciplinary programs at Texas A&M University, he said.

Specifically, his expertise in plant breeding and genetics focused on developing new fruits and vegetable cultivars with improved resource use of efficient traits, disease and abiotic stress resistance, and with high nutritional and sensorial quality will ultimately benefit consumers, as well as the controlled environment growers and industry.

The controlled environment program at the Dallas center includes small-acreage/urban horticulturists, Joe Masabni, Ph.D., and Genhua Niu, Ph.D., both professors in the Department of Horticultural Sciences; Azlan Zahid, agriculture engineer from the Department of Biological and Agricultural Engineering and entomologist, Arash Kheirodin, Ph.D., in the Department of Entomology. The team also includes Shuyang Zhen, Ph.D., assistant professor in the Department of Horticultural Sciences, College Station.

Dhingra said Bhattarais arrival provides important expertise for the programs holistic approach, making Texas A&M an innovator and leader in the field.

Researchers in the controlled environment horticulture program are experimenting with plants in a range of technologies that include long-standing methods like high tunnels and greenhouses and aquaponic and hydroponic systems.

They are also engaged in concepts like precision agriculture that rely on innovative technologies such as remote sensors to collect a range of data related to environmental and plant conditions. Sensing technology allows growers to incorporate other cutting-edge advancements like automation, robotics and artificial intelligence to manage plants.

The next frontier in controlled environment production of horticultural crops is plant genetics, Dhingra said. We hope to increase the efficiency, sustainability and profitability for controlled environment growers by harnessing the genetic potential in plant material so that crops perform at optimal levels in these systems.

Bhattarai said he is aware of only one other plant breeder conducting public research dedicated to controlled environment production.

A lot of research has been done on the structural and software programming side of controlled environment horticulture, but plant breeding specifically for those systems is lagging, he said. Cultivar development dedicated to controlled environment production is a field where there is a lot of opportunity to explore and contribute.

Bhattarais previous research covered a broad range of horticultural crops, including flowers, fruits and vegetables.

Bacterial leaf spot resistance was the focal point of his research as a graduate research assistant in the North Carolina State University tomato breeding program. The disease is problematic for open-field tomato production.

In 2014, while a masters student at the University of Florida, his focus shifted to ornamental plants, including the prevention of powdery mildew in cut flowers like Gerbera daisies.

Bhattarais research took another turn as a postdoctorate researcher at the University of California, Davis. Instead of breeding for plant disease resistance, he started analyzing genomic regions of strawberries in search of improved aroma and flavor.

Since I have experience in all three of these important commodities, I thought I could deliver some good research that could impact plant breeding for controlled environment production in Texas, he said. We have seen tremendous growth of controlled environment production in Texas, and that makes Texas A&M an ideal place to be.

Controlled environment horticulture is emerging as a sustainable production method that can supplement traditional field production. As agriculture grapples with the potential impacts of climate change, water scarcity, land fragmentation and other challenges, systems that optimize resources, operate within small footprints and are not subject to the whims of Mother Nature continue to gain momentum.

Bhattarai said Texas is rapidly becoming a leader in controlled environment production, which puts Texas A&M AgriLife in a position to help the industry and producers navigate challenges. Breeding plants to optimize their uptake of water and fertilizer is a focus, but he is also looking at genes that determine plant structure and inflorescence to maximize yields in limited space.

According to grower surveys, he said many of these systems are dedicated to leafy green production, but Bhattarai wants to expand grower options and crop variety.

Producers have to be profitable, and the ability to harness traits in cultivars for these targeted environments will be a critical part of the industrys evolution, he said. The genetic side of innovation in this field will optimize technological innovations in these systems.

Using genetic tools to identify and harness traits for specific growing systems will drive system optimization and industry sustainability, Bhattarai said.

For instance, in hydroponic systems, plants do not need high root biomass because nutrients are readily available. Bhattarai will select for cultivars producing higher volumes of the consumable products, whether fruit, shoots or leaves, for hydroponic growers. Genetics influencing inflorescence could also be chosen to optimize the systems ability to automate the crop harvest.

Identifying and expressing plant genes that open pathways to better flavors, better nutrition and other distinct characteristics will help controlled environment producers grow premium produce, Bhattarai said. Plant breeding programs will also help create high-value fruit and vegetables that are distinct in the marketplace.

The idea is to give controlled environment growers options and to optimize those options, Bhattarai said.

Visit link:
Optimizing genetics to advance controlled environment agriculture - AgriLife Today - AgriLife Today

Genetics

Genetics help combat illegal movement of feral swine – The Wildlife Society

May 21, 2024 by Gail Keirn and Tim Smyser, USDA Wildlife Services

Most wild pigs are hybrids, offering clues to distinguish them from domestic pigs

When the gate swings open on a trailer, it doesnt take long for wild pigs to pour out into their new environment. Experts are not sure how often people move wild pigs, but they know it is contributing to the spread of invasive wild pigs (Sus scrofa) across the United States.

The illegal transportation of wild pigs (also known as feral swine) for hunting purposes has contributed to the rapid expansion of this invasive species across to the United States over the past 40 years. They are now reported in at least 35 states. To help curb the spread of these invasive animals, multiple states have passed laws prohibiting their possession or transport. However, the similarities between domestic pigs and invasive wild pigs pose a challenge to enforcing these regulations.

Sometimes it can be difficult to distinguish a domestic pig from an invasive wild pig just by looking at them, said NWRC geneticist Dr. Tim Smyser. But genetic analysis shows that about 97% of invasive wild pigs (Sus scrofa) in the U.S. are hybrids of wild boars and domestic pigs, Smyser said.

That has allowed NWRC researchers and partners to exploit the wild boar ancestry found in most invasive pigs to differentiate them from domestic pigs. Approximately 1,400 samples from 33 domestic breeds and 16 wild boar populations were genotyped and sorted into five genetically cohesive reference groups: mixed-commercial breeds, Durocs, heritage breeds, primitive breeds and wild boars.

Then, researchers used well-established genetic clustering techniques to evaluate the likelihood that some level of wild boar hybridization took place.

The technique we developed basically allows wildlife managers and law enforcement officials to collect a genetic sample from a captured pig, genotype it and determine how likely it is that the pig descended from one of the domestic breed lineages, a pure wild boar lineage or a hybrid of the two, Smyser said.

Researchers evaluated the discriminatory power of this approach using simulated genotypes and real data from an additional 29 breeds of domestic pigs and more than 6,500 invasive wild pig samples. All the simulated and real data from domestic pigs fell within the statistical distribution of the domestic pig reference groups, while 74% of the wild pig data exceeded the maximum threshold for the domestic pig reference groups and could be statistically classified as having wild boar ancestry.

The ability to curtail illegal translocations of invasive wild pigs is an important part of reducing their spread and damage to the economy and the environment, Smyser said. This new genetic and statistical approach will aid in the enforcement of prohibitions on wild pig movement and introduction.

Wildlife Services is a Strategic Partner of TWS.

See the article here:
Genetics help combat illegal movement of feral swine - The Wildlife Society

Genetics

Tracking the cellular and genetic roots of neuropsychiatric disease – Yale News

A new analysis has revealed detailed information about genetic variation in brain cells that could open new avenues for the targeted treatment of diseases such as schizophrenia and Alzheimers disease.

The findings, reported May 23 in Science, were the result of a multi-institutional collaboration known as PsychENCODE, founded in 2015 by the National Institutes of Health, which seeks new understandings of genomic influences on neuropsychiatric disease. The study was published alongside related studies in Science, Science Advances, and Science Translational Medicine.

Previous research has established a strong link between a persons genetics and their likelihood of developing neuropsychiatric disease, saysMark Gerstein, the Albert L. Williams Professor of Biomedical Informatics at Yale School of Medicine and senior author of the new study.

The correlations between genetics and your susceptibility to disease are much higher for brain diseases than for cancer or heart disease, said Gerstein. If your parents have schizophrenia, youre much more likely to get it than you are to get heart disease if your parents have the disease. There is a very large heritability for these brain-related conditions.

Whats less clear, however, is how this genetic variation leads to disease.

We want to understand the mechanism, said Gerstein. What is that gene variantdoingin the brain?

For the new study, researchers set out to better understand the genetic variation across individual cell types in the brain. To do so, they performed several types of single-cell experiments on more than 2.8 million cells taken from the brains of 388 people, including healthy individuals and others with schizophrenia, bipolar disorder, autism spectrum disorder, post-traumatic stress disorder, and Alzheimers disease.

From that pool of cells, the researchers identified 28 different cell types. Then they examined gene expression and regulation within those cell types.

In one analysis, the researchers were able to link gene expression to variants in upstream regulatory regions, bits of genetic code situated before the gene in question that can increase or decrease the genes expression.

Thats useful because if you have a variant of interest, you can now link it to a gene, said Gerstein. And thats really powerful because it helps you interpret the variants. It helps you understand what effect theyre having in the brain. And because we looked across cell types, our data also allow you to connect that variant to an individual cell type of action.

The researchers also assessed how particular genes, such as those associated with neurotransmitters, varied across individuals and cell types, finding variability was usually higher across cell types than across individuals. This pattern was even stronger for genes that code for proteins targeted for drug treatment.

And thats generally good for a drug, Gerstein said. It means that those drugs are homing in on particular cell types and not affecting your whole brain or body. It also means those drugs are more likely to be unaffected by genetic variants and work in many people.

Using the data generated by the analysis, the researchers were able to map out within-cell type genetic regulatory networks and between-cell communication networks, and then plug those networks into a machine learning model. Then, using an individuals genetic information, the model could predict whether they had a brain disease.

Because these networks were hard coded in the model, when the model made a prediction we could see which parts of the network contributed to it, said Gerstein. So we could identify which genes and cell types were important for that prediction. And that can suggest candidate drug targets.

In one example, the model predicted an individual with a particular genetic variant might have bipolar disorder, and the researchers could see that prediction was based on two genes in three cell types. In another, the researchers identified six genes in six cell types that contributed to a schizophrenia prediction.

The model also worked in the opposite direction. The researchers could introduce a genetic perturbation and see how that might affect the network and an individuals health. This, Gerstein says, is useful for drug design or previewing how well drugs or drug combinations might fare as treatments.

Together, the findings could help facilitate precision-medicine approaches for neuropsychiatric disease, said the researchers.

To further this work, the consortium hasmade its results and model availableto other researchers.

Our vision is that researchers interested in a particular gene or variant can use our resources to better understand what its doing in the brain or to perhaps identify new candidate drug targets to investigate more, said Gerstein.

View post:
Tracking the cellular and genetic roots of neuropsychiatric disease - Yale News

Genetics

Seedling root system adaptation to water availability during maize domestication and global expansion – Nature.com

Meyer, R. S. & Purugganan, M. D. Evolution of crop species: genetics of domestication and diversification. Nat. Rev. Genet. 14, 840852 (2013).

Article CAS PubMed Google Scholar

Hake, S. & Ross-Ibarra, J. Genetic, evolutionary and plant breeding insights from the domestication of maize. eLife 4, e05861 (2015).

Article PubMed PubMed Central Google Scholar

Yang, N. et al. Two teosintes made modern maize. Science 382, 1013 (2023).

Article Google Scholar

Ross-Ibarra, J. & Piperno, D. Maize moving. Figshare https://doi.org/10.6084/m9.figshare.12781307.v1 (2020).

Romero Navarro, J. A. et al. A study of allelic diversity underlying flowering-time adaptation in maize landraces. Nat. Genet. 49, 476480 (2017).

Article CAS PubMed Google Scholar

Swarts, K. et al. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 357, 512515 (2017).

Article CAS PubMed Google Scholar

Ma, Z. et al. Evolutionary history resolves global organization of root functional traits. Nature 555, 9497 (2018).

Article CAS PubMed Google Scholar

Eshel, A. & Beeckman, T. (eds) Plant roots: the hidden half (CRC Press, 2013).

Hochholdinger, F., Yu, P. & Marcon, C. Genetic control of root system development in maize. Trends Plant Sci. 23, 7988 (2018).

Article CAS PubMed Google Scholar

Lopez-Valdivia, I. et al. Gradual domestication of root traits in the earliest maize from Tehuacn. Proc. Natl Acad. Sci. USA 119, e2110245119 (2022).

Article CAS PubMed PubMed Central Google Scholar

Yu, P., Gutjahr, C., Li, C. & Hochholdinger, F. Genetic control of lateral root formation in cereals. Trends Plant Sci. 21, 951961 (2016).

Article CAS PubMed Google Scholar

Golan, G., Hendel, E., Mndez Espitia, G. E., Schwartz, N. & Peleg, Z. Activation of seminal root primordia during wheat domestication reveals underlying mechanisms of plant resilience. Plant Cell Environ. 41, 755766 (2018).

Article CAS PubMed Google Scholar

Perkins, C. & Lynch, J. P. Increased seminal root number associated with domestication improves nitrogen and phosphorus acquisition in maize seedlings. Ann. Bot. 128, 453468 (2021).

Article CAS PubMed PubMed Central Google Scholar

Hochholdinger, F., Woll, K., Sauer, M. & Dembinsky, D. Genetic dissection of root formation in maize (Zea mays) reveals roottype specific developmental programmes. Ann. Bot. 93, 359368 (2004).

Article CAS PubMed PubMed Central Google Scholar

Burton, L., Brown, K. M. & Lynch, J. P. Phenotypic diversity of root anatomical and architectural traits in Zea species. Crop Sci. 53, 10421055 (2013).

Article Google Scholar

Taramino, G. et al. The maize (Zea mays L.) RTCS gene encodes a LOB domain protein that is a key regulator of embryonic seminal and postembryonic shootborne root initiation. Plant J. 50, 649659 (2007).

Article CAS PubMed Google Scholar

Merrill, W. L. et al. The diffusion of maize to the southwestern United States and its impact. Proc. Natl Acad. Sci. USA 106, 2101921026 (2009).

Article CAS PubMed PubMed Central Google Scholar

da Fonseca, R. R. et al. The origin and evolution of maize in the Southwestern United States. Nat. Plants 1, 14003 (2015).

Article PubMed Google Scholar

Doebley, J. F., Goodman, M. & Stuber, C. W. Exceptional genetic divergence of northern flint corn. Am. J. Bot. 73, 6469 (1986).

Article PubMed Google Scholar

Rebourg, C. et al. Maize introduction into Europe: the history reviewed in the light of molecular data. Theor. Appl. Genet. 106, 895903 (2003).

Article CAS PubMed Google Scholar

Hu, Y. et al. Genome assembly and population genomic analysis provide insights into the evolution of modern sweet corn. Nat. Commun. 12, 1227 (2021).

Article CAS PubMed PubMed Central Google Scholar

Salvi, S. et al. Genetic dissection of maize phenology using an intraspecific introgression library. BMC Plant Biol. 11, 4 (2011).

Article CAS PubMed PubMed Central Google Scholar

Osthoff, A. et al. Transcriptomic reprogramming of barley seminal roots by combined water deficit and salt stress. BMC Genom. 20, 325 (2019).

Article Google Scholar

Zhou, X. et al. CPlantBox, a whole-plant modelling framework for the simulation of water- and carbon-related processes. in silico Plants 2, diaa001 (2020).

Article CAS Google Scholar

Ahmed, M. A., Zarebanadkouki, M., Kaestner, A. & Carminati, A. Measurements of water uptake of maize roots: the key function of lateral roots. Plant Soil 398, 5977 (2016).

Article CAS Google Scholar

Abdalla, M. et al. Stomatal closure during water deficit is controlled by below-ground hydraulics. Ann. Bot. 129, 161170 (2022).

Article PubMed Google Scholar

Cai, G., Ahmed, M. A., Abdalla, M. & Carminati, A. Root hydraulic phenotypes impacting water uptake in drying soils. Plant Cell Environ. 45, 650663 (2022).

Article CAS PubMed PubMed Central Google Scholar

Li, C. et al. Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding. Nat. Plants 8, 750763 (2022).

Article CAS PubMed Google Scholar

Marcon, C. et al. BonnMu: a sequence-indexed resource of transposon-induced maize mutations for functional genomics studies. Plant Physiol. 184, 620631 (2020).

Article CAS PubMed PubMed Central Google Scholar

Qiu, X. et al. Genome-wide identification of HD-ZIP transcription factors in maize and their regulatory roles in promoting drought tolerance. Physiol. Mol. Biol. Plants 28, 425437 (2022).

Article CAS PubMed PubMed Central Google Scholar

Salvi, S. et al. Registration of Gasp Flint 1.1.1, a small-size early-flowering maize inbred line. J. Plant Registrat. 16, 152161 (2021).

Article Google Scholar

Giehl, R. F. & von Wirn, N. Root nutrient foraging. Plant Physiol. 166, 509517 (2014).

Article PubMed PubMed Central Google Scholar

Tenaillon, M. I. & Charcosset, A. A European perspective on maize history. Biologies 334, 221228 (2011).

Article PubMed Google Scholar

Liu, Y. et al. Genomic basis of geographical adaptation to soil nitrogen in rice. Nature 590, 600605 (2021).

Article CAS PubMed Google Scholar

Jgermeyr, J. et al. Climate impacts on global agriculture emerge earlier in new generation of climate and crop models. Nat. Food 2, 873885 (2021).

Article PubMed Google Scholar

Yuan, X. et al. A global transition to flash droughts under climate change. Science 380, 187191 (2023).

Article CAS PubMed Google Scholar

Schneider, H. M. et al. Multiseriate cortical sclerenchyma enhance root penetration in compacted soils. Proc. Natl Acad. Sci. USA 118, e2012087118 (2021).

Article CAS PubMed PubMed Central Google Scholar

Wang, X. et al. Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings. Nat. Genetics 48, 12331241 (2016).

Article CAS PubMed Google Scholar

Grando, S. & Ceccarelli, S. Seminal root morphology and coleoptile length in wild (Hordeum vulgare ssp. spontaneum) and cultivated (Hordeum vulgare ssp. vulgare) barley. Euphytica 86, 7380 (1995).

Article Google Scholar

Orosa-Puente, B. et al. Root branching toward water involves posttranslational modification of transcription factor ARF7. Science 362, 14071410 (2018).

Article CAS PubMed Google Scholar

Mehra, P. et al. Hydraulic flux-responsive hormone redistribution determines root branching. Science 378, 762768 (2022).

Article CAS PubMed Google Scholar

Maurel, C. & Nacry, P. Root architecture and hydraulics converge for acclimation to changing water availability. Nat. Plants 6, 744749 (2020).

Article PubMed Google Scholar

Liu, K. et al. Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites. Genetics 165, 21172128 (2003).

Article CAS PubMed PubMed Central Google Scholar

Gouesnard, B. et al. Genotyping-by-sequencing highlights original diversity patterns within a European collection of 1191 maize flint lines, as compared to the maize USDA genebank. Theor. Appl. Genet. 130, 21652189 (2017).

Article CAS PubMed Google Scholar

Yu, P. et al. Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation. Nat. Plants 7, 481499 (2021).

Article CAS PubMed Google Scholar

Metzner, R. et al. In vivo imaging and quantification of carbon tracer dynamics in nodulated root systems of pea plants. Plants 11, 632 (2022).

Article CAS PubMed PubMed Central Google Scholar

Streun, M. et al., PhenoPET: a dedicated PET scanner for plant research based on digital SiPMs (DPCs). In IEEE Medical Imaging Conference (IEEE, 2014).

Hinz, C. Accurate quantitative and dynamic PET imaging with the phenoPET Scanner for plant studies. PhD dissertation, University of Wuppertal (2021).

Scheins, J. J. et al. High performance volume-of-intersection projectors for 3D-PET image reconstruction based on polar symmetries and SIMD vectorisation. Phys. Med. Biol. 60, 93499375 (2015).

Article CAS PubMed Google Scholar

Bauer, F. M. et al. Development and validation of a deep learning based automated minirhizotron image analysis pipeline. Plant Phenoics 2022, 9758532 (2022).

Google Scholar

Smith, A. G. et al. RootPainter: deep learning segmentation of biological images with corrective annotation. New Phytol. 236, 774791 (2022).

Article CAS PubMed PubMed Central Google Scholar

Leitner, D. et al. Recovering root system traits using image analysis exemplified by two-dimensional neutron radiography images of lupine. Plant Physiol. 164, 2435 (2014).

Article CAS PubMed Google Scholar

Read more:
Seedling root system adaptation to water availability during maize domestication and global expansion - Nature.com

Genetics

Class of 2024: After completing the human genetics certificate program, Alanna Varca Gentile is translating personal … – VCU News

By Grace McOmber School of Medicine

Medicine had been the plan since high school for Alanna Varca Gentile. Motivated by her own experiences as a patient, she enrolled at Virginia Commonwealth University in VCU Acceleration, a program for incoming freshmen interested in health care, and confidently began the pre-medical track.

But when the COVID-19 pandemic hit during Varca Gentiles junior year, she began questioning whether medical school was the right fit.

I really enjoyed my time in the Acceleration program, Varca Gentile said. But I think the pandemic really made me start to ask a lot of questions about what I really wanted and what I was mentally prepared for.

Still interested in medicine but unsure of her plan, Varca Gentile said she confided in a professor only days before graduating with her bachelors degree in psychology from the College of Humanities and Sciences in 2021. The professor suggested genetic counseling a field shed never heard of.

I didnt even know what clinical genetic counseling was before that, Varca Gentile said. I went on an internet deep dive and attended phone call informational interviews. I had a really good gut feeling about this path.

In 2023, she enrolled in the Certificate in Clinical Genetics program, one of five certificate programs offered by the VCU School of Medicine to enhance students qualifications for advanced degrees, continued education and highly specialized fields. Varca Gentile said the academic exposure and networking opportunities solidified her interest in the niche, competitive field and helped her get into the genetic counseling M.S. program at VCU, which shell begin in the fall. Many of her credits from the certificate program will count toward her masters.

She also received the Genetic Counseling Equity Scholarship, which is awarded to a qualified applicant who demonstrates a commitment to serving populations that are historically underprivileged or underserved by the field of genetic counseling.

Im hoping to get involved in outreach for genetic counseling, Varca Gentile said. I want to help bring more diversity to the field, mentor students from underrepresented backgrounds and work towards making the field a more accessible service to patients.

Genetic counseling, according to the National Society of Genetic Counselors, is a relatively young field at a little over 50 years old. The practice combines the scientific analysis of human genetics with patient consultations. Counselors assess patients risk for inherited diseases, educate families about genetic disorders like sickle cell and Huntingtons and present options on how to adapt to findings. This combination of science and psychosocial work was what attracted Varca Gentile to the field.

It's a very empathy-heavy role, Varca Gentile said. Youre taking the time, establishing a relationship and walking patients through some really scary topics.

As she prepares to become a genetic counselor, Varca Gentile draws on her own experiences as a patient. A concussion during high school caused a traumatic brain injury with long-lasting effects she still deals with today. Despite following typical concussion protocols, she has experienced regular headaches and migraines since the injury. She also developed postural orthostatic tachycardia syndrome, which is also known as POTS, from the injury, which affects the autonomic nervous system, causing heart rate and blood pressure dysregulation and resulting in dizziness, light-headedness and heart palpitations.

My brain processes very differently than it did before my TBI, Varca Gentile said, noting that the chronic pain impacts her capabilities as a student, and shes grateful for the disability services and accommodations through the Division of Student Affairs and Division for Academic Success. POTS is sort of a daily struggle, and it adds a lot of fatigue and brain fog to my life.

Over the past nine years, Varca Gentiles interactions with medical professionals have been mixed, inspiring her to be a counselor who leads with empathy and advocates for her patients. Her POTS and vertigo diagnoses came after a long string of appointments with different specialists, which she said gives her a unique perspective on the diagnostic odyssey many patients go through. When the headaches became a nearly daily occurrence, she said it took longer than it should have to be referred to a neurologist, which made her feel unheard by her doctor.

A lot of people are dismissive of pain and struggle, especially when it comes to young women, Varca Gentile said. Im excited to be a female provider and be a voice for my patients, especially for people who often go dismissed.

Varca Gentiles empathy doesnt stop with her future patients. After graduate school, she hopes to work at a university-affiliated hospital, such as VCU Health, to pay forward the support she received during the certificate program. The Association of Genetic Counseling Program Directors reports that only 59% of applicants matched into genetic counseling M.S. programs in 2024, making it one of the most competitive fields in health care.

I know how hard getting into genetic counseling school is, and I want to help in the way people helped me, Varca Gentile said. Its a small field, but its a great community.

Heather Creswick, the clinical genetics certificate advisor, said the genetic counseling faculty is excited to have Varca Gentile join the program in the fall. Creswick described her as a driven, curious hard worker who connects well with those around her.

I hope Alanna finds joy in engaging with her patients and that she is surrounded by colleagues who inspire and guide her, Creswick said. I hope that she will embrace learning, stay open-minded and get involved with the profession. She has great potential to be a leader in this field.

For now, Varca Gentile said she is excited to become a four-time Ram and continue her education at VCU, learning under many of the same instructors she did during her certificate program.

I made great connections during the program that I am so incredibly grateful for, Varca Gentile said. I wouldnt have gotten in without them.

This article was originally published on the VCU School of Medicines website.

Subscribe to VCU News at newsletter.vcu.edu and receive a selection of stories, videos, photos, news clips and event listings in your inbox.

Excerpt from:
Class of 2024: After completing the human genetics certificate program, Alanna Varca Gentile is translating personal ... - VCU News

Genetics

New Research Demonstrates the Importance of Genetic Testing for Many Cancers Not Currently Covered by Clinical … – PR Newswire

Study findings to be presented at the 2024 ASCO Annual Meeting find hereditary risk for gastric and lung cancers, among others, underscoring the need for broader genetic testing

SAN FRANCISCO, May 23, 2024 /PRNewswire/ -- Invitae (OTC:NVTAQ), a leading medical genetics company, today announced eight studies to be presented at the 2024 American Society of Clinical Oncology (ASCO) Annual Meeting held in Chicago from May 31-June 4, 2024. The clinical data being presented demonstrate the importance of genetic testing for patients with various different types of cancers, including breast, gastric, prostate and lung, to better inform management and treatment decisions.

Genetic testing guidelines need to be inclusive of more cancer types, with new data finding gastric, lung and prostate cancer patients with inherited genes linked to increased cancer risk

Gastric cancer is the fourth leading cause of cancer-related deaths worldwide, and the role of pathogenic (disease causing) variants in cancer predisposition genes is not well understood for this disease. One study looked at genetic testing results in 3,706 gastric cancer patients the largest study of its kind to better understand the prevalence of disease causing variants in cancer associated genes. The results found the percentage of patients with disease causing variants to be 13.4%, about 1 in 8 patients. This shows the value of genetic testing in all gastric cancer patients, as the prevalence of pathogenic variants is similar to other cancer types for which guidelines recommend universal genetic testing.

"Current guidelines haven't met the needs for patients across cancer types, gastric cancer included," said Dr. Ophir Gilad, University of Chicago and a co-author of this study. "The prevalence of actionable gene variants found in this study of gastric cancer patients is on par with other cancer types for which guidelines recommend universal genetic testing. We're increasingly seeing evidence for germline genetic testing to help guide treatment plans and familial testing for various cancer types."

Additionally, in a study of 14,317 patients with lung cancer, 12.6% had pathogenic germline variants -- regardless of smoking history. The study results suggest these inherited genes are not only independently associated with lung cancer, but also additive to smoking risk for lung cancer. These data reinforce prior studies supporting consideration of germline genetic testing for all patients with lung cancer, independent of age or reported smoking history.

Genetic testing is similarly underutilized for prostate cancer. In a large study of 15,000 prostate cancer patients that received genetic testing, results showed that of the patients with genetic variants that increase risk of prostate cancer, 3 in 4 patients had no reported family history of prostate cancer and more than 1 in 3 patients had no reported family history of any cancer. The findings underscore the importance of genetic testing for all prostate cancer patients, regardless of age, stage or family history.

Breast cancer data in Rwanda demonstrates need for more genetic testing in underrepresented populations

Despite the observation that cancers are often diagnosed at young ages and take an aggressive course in Sub-Saharan Africa (SSA), genetic data that could inform treatment are limited for this population group.

In a recent study, patients undergoing cancer treatment in hospitals in Rwanda for female breast, male breast and prostate cancer underwent multigene panel testing (Invitae), and the results found a large proportion of the patients had inherited pathogenic variants that could help inform their treatment (18.3% of female breast cancer, 16.7% of male breast cancer, and 4.3% of prostate cancer patients). The findings suggest that genetic testing should be more routinely implemented into cancer care and prevention strategies in this population.

Underrepresented race, ethnicity, and ancestry (REA) groups face these challenges across geographies. In another recent study being presented at ASCO that included more than one million people over an eight-year period who underwent genetic testing for hereditary cancer syndromes, it was found that underrepresented REA groups are disproportionately impacted by variants of uncertain significance (VUS) in genetic testing, which are uncertain results that are not clinically actionable. With more representation of these groups in clinical studies, there will be more data that could uncover life-saving discoveries. Clinical evidence was the most significant source of information leading to VUS resolution, underscoring the importance of the clinician-lab partnership and communication.

"Germline genetic testing should be the standard of cancer care across many types of cancers. In underrepresented populations, this is especially crucial as more information needs to be collected to better inform care and improve population health overall," said Dr. Michael Korn, chief medical officer at Invitae. "Each year, ASCO presents us with an opportunity to share compelling research to help propel cancer treatment forward, and we're proud of the clinical insights our tests are able to provide across cancer types."

Study offers reassurance that variants of uncertain significance in genetic testing results among patients with breast cancer do not lead to overuse of treatment or surveillance interventions, such as mastectomies

It's common for patients with breast cancer undergoing germline genetic testing to have uncertain results, but it's previously been unclear if these results impact clinical management. However, a recent study being presented at ASCO presents new evidence indicating that variants of uncertain significance (VUS) identified through germline genetic testing do not result in guideline-discordant management in real-world settings. Specifically, patients with breast cancer and VUS results demonstrated similar rates of treatment, prevention and surveillance interventions compared to those with negative results. This offers reassurance that VUS results do not lead to overuse of mastectomies or other interventions for patients with breast cancer.

2024 ASCO presentations and posters:

About InvitaeInvitae (OTC: NVTAQ) is a leading medical genetics company trusted by millions of patients and their providers to deliver timely genetic information using digital technology. We aim to provide accurate and actionable answers to strengthen medical decision-making for individuals and their families. Invitae's genetics experts apply a rigorous approach to data and research, serving as the foundation of their mission to bring comprehensive genetic information into mainstream medicine to improve healthcare for billions of people.

To learn more, visit invitae.comand follow for updates on LinkedIn, X, Instagram, and Facebook@Invitae.

Safe Harbor StatementThis press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995, including statements relating to the company's beliefs regarding its new research; the company's belief that its new research demonstrates the importance of genetic testing for many cancers not currently covered by clinical guidelines; the company's belief that its new research demonstrates the need for more research in underrepresented populations; and the company's belief that its research helps move cancer treatment forward.. Forward-looking statements are subject to risks and uncertainties that could cause actual results to differ materially, and reported results should not be considered as an indication of future performance. These risks and uncertainties include, but are not limited to: the applicability of clinical results to actual outcomes; the company's ability to use rapidly changing genetic data to interpret test results accurately and consistently; risks and uncertainties regarding the company's ability to successfully consummate and complete a plan under chapter 11 or any strategic or financial alternative as well as the company's ability to implement and realize any anticipated benefits associated with its sale of assets to Labcorp and the any alternative that may be pursued, including the asset sales and wind down of operations; the company's public securities' potential liquidity and trading; and any impact resulting from the delisting of the company's common stock from the New York Stock Exchange and trading instead on the OTC Pink Marketplace; and the other risks set forth in the company's filings with the Securities and Exchange Commission, including the risks set forth in the company's Quarterly Report on Form 10-Q for the quarter ended September 30, 2023. These forward-looking statements speak only as of the date hereof, and Invitae Corporation disclaims any obligation to update these forward-looking statements.

Invitae PR contact: Renee Kelley [emailprotected]

SOURCE Invitae Corporation

Continued here:
New Research Demonstrates the Importance of Genetic Testing for Many Cancers Not Currently Covered by Clinical ... - PR Newswire

Genetics

Sequencing of the developing human brain uncovers hundreds of thousands of new gene transcripts – UCLA Newsroom

Key takeaways

A team led by researchers at UCLA and the University of Pennsylvania has produced a first-of-its kind catalog of gene-isoform variation in the developing human brain. This novel dataset provides crucial insights into the molecular basis of neurodevelopmental and psychiatric brain disorders and paves the way for targeted therapies.

The research, published in Science, also details how transcript expression varies by cell type and maturity, finding that changing gene-isoform expression levels can help us better understand how the human brain develops.

Every cell in our body contains the same genetic information encoded in DNA, but it is the expression of different proteins, encoded in mRNA transcripts, that give cells their distinct functions. These varied proteins, or isoforms, mostly arise from alternative splicing a process that is highly prevalent in the brain and contributes to its wide range of proteins and characteristics.

We knew, based on our previous research, that isoform regulation is a key molecular feature for understanding brain development and genetic risk for neuropsychiatric disorders, said Dr. Luis de la Torre-Ubieta of the Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, who co-led the study alongside Dr. Michael Gandal, an associate professor of psychiatry and genetics in the Perelman School of Medicine at the University of Pennsylvania.

Previously, despite its prevalence, the role of cell-type-specific splicing and transcript-isoform diversity in the developing human brain had not been systematically investigated due to limitations in prior generations of sequencing technologies. Here, the researchers were able to leverage new third-generation long-read sequencing technologies to capture complete RNA molecules and profile the full-length transcriptome of two major regions of the developing neocortex: the germinal zone, which contains stem cells, and the cortical plate, which houses newly generated neurons.

This technology allowed the researchers to uncover 214,516 unique isoforms over 70% of which have never been previously studied. They then compared the two regions of the developing brain and observed that changes in isoform expression levels are important for neurogenesis, differentiation and cell fate in essence, the maturation of the brain.

The researchers found thousands of isoform switches that occur during brain development, implicating previously uncharacterized RNA-binding proteins in cellular identity and cellular fate decisions. Their findings also elucidate genetic risk mechanisms for neurodevelopmental and neuropsychiatric disorders, including a reassessment of the significance and clinical relevance of thousands of rare genetic variants.

We found that high-confidence risk genes for autism or neurodevelopmental disorders tend to be genes that have more isoforms, and those isoforms are expressed differently during neurogenesis, said de la Torre-Ubieta, an assistant professor of psychiatry and behavioral sciences. This implies that dysregulation of the expression of specific isoforms is a potential mechanism underlying these disorders.

Scientists studying the brain often rely on publicly available catalogs of genes and gene transcripts. However, human brain tissue, particularly embryonic tissue, is difficult to access, restricting the comprehensiveness of these datasets. For this study, the researchers obtained six developing human neocortex tissue samples representing the mid-gestation period, or 15 to 17 weeks post-conception. This developmental time point in the human brain is a critical window during which the complexity of our brain the most sophisticated organ in our body begins to emerge.

These tissue samples enabled a striking level of novel transcript discovery, Gandal said. And because these databases havent incorporated or represented these critical time points, we can dramatically expand our understanding of how genes are regulated in the context of human brain development.

The findings from the study have strong therapeutic implications and could be clinically actionable, the researchers said. Uncovering new transcripts could pave the way for identifying novel treatment approaches in gene therapy trials or targeted therapeutic trials for individuals harboring rare mutations associated with psychiatric or neurodevelopmental disorders.

In the nearer term, the data also has direct implications in improving our ability to make genetic diagnoses of neurodevelopmental disorders. Because the study found several thousand genetic variants that are more impactful than previously thought, families or individuals carrying those variants can better understand how their children might be predisposed to certain disorders.

Gandal has shared the dataset with several colleagues at the Childrens Hospital of Philadelphia, which has a large population of children with rare neurodevelopmental disorders or undiagnosed disorders in development. Physicians there are already using this resource to help better interpret neurogenetics diagnostically.

Im really excited to leverage this resource to help patients, said Gandal, who is also a practicing psychiatrist. Having this knowledge brings us one step closer to being able to develop targeted treatments and understand genetic mechanisms in a much more specific way.

Other UCLA authors include Ashok Patowary, Pan Zhang, Celine K. Vuong, Xinzhou Ge, Kangcheng Hou, Minsoo Kim, Michael Margolis, Bogdan Pasaniuc and Jingyi Jessica Li. Connor Jops, Naihua Gong, Daniel Vo, Xusheng Wang and Chunyu Liu contributed to this study.

The research was supported by the Simons Foundation Autism Research Initiative, the National Institute of Mental Health, the National Science Foundation and the UCLA Medical Scientist Training Program.

Read more:
Sequencing of the developing human brain uncovers hundreds of thousands of new gene transcripts - UCLA Newsroom