Monthly Archives: August 2021

NEW YORK An international team of researchers has used transcriptomic data from ulcerative colitispatients to develop a predicted polygenic transcriptional risk score, or PPTRS,that can identify UC-affected individuals at fivefold elevated risk of progressing to surgical resection of the large bowel.

In a paper published on Thursday in the American Journal of Human Genetics, the Georgia Institute of Technology-led team noted that 5 percent to 10 percent of people with UC require bowel resection, or colectomy, within five years of diagnosis, but that polygenic risk scores based on genome-wide association studies generally don't provide meaningful prediction of progression to surgery. However, studies of Crohn's disease have shown that gene expression profiling of GWAS-significant genes provides some stratification of risk of progression to complicated disease through transcriptional risk scoring, or TRS.

In their paper, the researchers demonstrated that a measured TRS based on bulk rectal gene expression in a cohort of UC patients had a positive predictive value approaching 50 percent for colectomy. Single-cell profiling demonstrated that the disease-associated genes were active in multiple diverse cell types from both the epithelial and immune compartments, and expression quantitative trait locusanalysis identified genes with differential effects at baseline and the one-year follow-up, the researchers said. But for the most part, they found that differential expression associated with colectomy risk was independent of local genetic regulation.

Overall, their data suggested that prediction of gene expression from relatively small transcriptome datasets can be used in conjunction with transcriptome-wide association studies for stratification of risk of disease complications.

The researchers began by performing differential expression analysis between baseline rectal RNA-seq biopsies of individuals in the PROTECT multicenter pediatric inception cohort study of response to standardized colitis therapy. Analyses were done on 21 affected individuals who progressed to colectomy and 310 who did not. They identified downregulation of 783 transcripts in the individuals who underwent colectomy and upregulation of 1,405 transcripts overall.

They also obtained rectal biopsy RNA-seq data for 92 affected individuals at week 52 and observed a marked shift in gene expression at follow-up, prompting them to ask whether local regulation of the gene expression might contribute to this effect. They found that there were 72 SNPs that were significantly regulating 308 genes at both time points.

Further examination of the expression of colectomy-associated genes in a single-cell RNA-seq dataset obtained from rectal biopsies provided strong evidence that both epithelial and immune cells contributed to the risk of disease progression, the researchers said.

The researchers then performed a TWAS to capture the effects of all polymorphisms within 1 Mb of each transcript expressed in the PROTECT rectal biopsies and then used the weights to predict gene expression in a validation cohort from the UK Biobank. They tested for differential predicted gene expression in 70 percent of the validation samples and discovered about 800 genes either upregulated or downregulated in UC-affected individuals relative to non-IBD control individuals. They then derived a PPTRS for UC based on the effect sizes of the minor alleles and applied it to the remaining 30 percent of the validation samples, as well as to the PROTECT genotypes, and found that the PPTRS efficiently discriminated UC-affected individuals from non-IBD control individuals.

Significantly, it also discriminated the individuals who underwent colectomy versus those who didn't in both the UK Biobank and PROTECT.

"More extensive single-cell profiling, combined with cell-type-specific genetic analysis of gene expression, is likely to lead to the development of even better transcriptional risk signatures," the authors concluded. "It is also likely that such focused and personalized analysis may highlight specific pathological mechanisms active in particular affected individuals."

They did note, however, that these results were limited by the relatively small sample size of colectomies in the PROTECT study, and that validation of cross-ancestry assessments and the evaluation of the consistency of gene expression prediction across populations should be a high priority.

In an email, corresponding author and GIT researcher Greg Gibson noted that while the study's multiple layers of replication show that transcriptional profiling of the rectum greatly enhances risk stratification for risk of colectomy, this was not a clinical trial, so the approach is not yet approved for evaluation of patients.

"We hope that it will progress to implementation in the near future," he added."The prediction from genotypes alone is less likely to have clinical utility since the precision is still quite low, so that aspect is more research oriented."

He further noted that the approach he and his colleagues used could also be applied to a wide range of diseases, and that they are pursuing that research.

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Ulcerative Colitis Study Analyzes Gene Expression to Measure Risk of Progression to Surgery - GenomeWeb

SAN DIEGO, Aug. 26, 2021 (GLOBE NEWSWIRE) -- Bionano Genomics, Inc. (Nasdaq: BNGO) today announced the European Society of Human Genetics (ESHG) conference lineup featuring 11 customer presentations of optical genome mapping (OGM) data spanning three major clinical areas of application from 10 institutions and six countries. The clinical application areas represented below cover hematological malignancies, inherited genetic disorders and solid tumor analysis. The presentations are expected to cover the clinical utility of OGM across these application areas, along with the unique capabilities of Bionanos Saphyr system to detect all classes of structural variants, across the genome, at a superior resolution relative to traditional techniques. The ESHG conference is being held virtually starting this Saturday from August 28 - 31, 2021.

More than 3,400 participants are registered for this years ESHG meeting, which provides a platform for the dissemination of the most exciting advancements in the field of human genetics. The upcoming customer presentations featuring OGM data are listed below along with the associated clinical areas of application:

OGM Application Area

Presenter

Affiliation

Presentation/Poster Title

Hematological Malignancies

Dr. Anna Puiggros

Hospital del Mar, Barcelona, Spain

Analysis of genomic complexity in patients with chronic lymphocytic leukemia (CLL) using optical genome mapping

Dr. Jonathan L. Lhmann

Hannover Medical School, Hannover, Germany

The clinical utility of optical genome mapping for the assessment of genomic aberrations in acute lymphoblastic leukemia

Inherited Genetic Disorders

Dr. Caroline Schluth-Bolard

Universite Hospital de Lyon, France

What is the best solution to manage failures of chromosomal structural variations detection by short-read strategy?

Dr. Kornelia Neveling

Radboud University Medical Centre, Netherlands

Long-read technologies identify a hidden inverted duplication in a family with choroideremia

Dr. Valrie Race

Univ. Hosp. of Leuven, Leuven, Belgium

Bionano optical genome mapping and southern blot analysis for FSHD detection

Dr. Romain Nicolle

Hospital Necker-Enfants Malades, Paris, France

16p13.11p11.2 triplication syndrome: a new recognizable genomic disorder characterized by Bionano optical genome mapping and WGS

Dr. Jenny Schiller

MVZ Martinsried, Martinsried, Germany

Characterization of breakpoint regions of apparently balanced translocations by optical genome mapping

Dr. Viola Alesi

Bambino Ges Children's Hospital, Rome, Italy,

Optical Genome Mapping: where molecular techniques give up

Dr. Valeria Orlando

Bambino Ges Children's Hospital, Rome, Italy

Optical genome mapping: a cytogenetic revolution

Solid Tumor Analysis

Dr. Florentine Scharf

Medical Genetics Center Munich, Germany

Germline chromothripsis of the APC locus in a patient with adenomatous polyposis

Dr. Mariangela Sabatella

Princess Maxima Center for Pediatric Oncology, Utrecht, Netherlands

Optical Genome Mapping Identifies Germline Retrotransportation Insertion in SMARCB1 in Two Siblings with Atypical Teratoid Rhabdoid Tumor

We believe our progress in Europe, with the increased awareness of OGM and the development of the market there, has been outstanding, commented Erik Holmlin, PhD, CEO of Bionano Genomics. Thanks to key sites like Radboud, Leuven and Cochin, the OGM footprint has now expanded in Germany, Spain and Italy. With the growing installed base of Saphyr in Europe, we have seen these institutions and their research teams conduct ground-breaking research to help demonstrate the potential utility of OGM as an alternative to traditional cytogenetics methods for the identification of genome structural variations that can be more sensitive, give a faster time to results and be less expensive to implement when compared to traditional methods. We believe the momentum of research that has been building will continue as more supporting data, like the data that we expect the researchers to show this week at ESHG, are released from around the world.

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For more details and to register for this online event please go to https://vmx.m-anage.com/home/release/eshg2021/en-GB

About Bionano Genomics

Bionano is a genome analysis company providing tools and services based on its Saphyr system to scientists and clinicians conducting genetic research and patient testing, and providing diagnostic testing for those with autism spectrum disorder (ASD) and other neurodevelopmental disabilities through its Lineagen business. Bionanos Saphyr system is a research use only platform for ultra-sensitive and ultra-specific structural variation detection that enables researchers and clinicians to accelerate the search for new diagnostics and therapeutic targets and to streamline the study of changes in chromosomes, which is known as cytogenetics. The Saphyr system is comprised of an instrument, chip consumables, reagents and a suite of data analysis tools. Bionano provides genome analysis services to provide access to data generated by the Saphyr system for researchers who prefer not to adopt the Saphyr system in their labs. Lineagen has been providing genetic testing services to families and their healthcare providers for over nine years and has performed over 65,000 tests for those with neurodevelopmental concerns. For more information, visit http://www.bionanogenomics.com or http://www.lineagen.com.

Forward-Looking Statements

This press release contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Words such as may, will, expect, plan, anticipate, estimate, intend and similar expressions (as well as other words or expressions referencing future events, conditions or circumstances) convey uncertainty of future events or outcomes and are intended to identify these forward-looking statements. Forward-looking statements include statements regarding our intentions, beliefs, projections, outlook, analyses or current expectations concerning, among other things: the timing, content and significance of the presentations identified in this press release; our assessments regarding our progress in the European market, including our expectations with respect to the continued adoption of OGM throughout Europe; the benefits of OGM relative to traditional cytogenetic testing methods and its potential to replace traditional cytogenetic methods; our assessments regarding current and future research by the institutions identified in this press release; and the execution of Bionanos strategy. Each of these forward-looking statements involves risks and uncertainties. Actual results or developments may differ materially from those projected or implied in these forward-looking statements. Factors that may cause such a difference include the risks and uncertainties associated with: potential inaccuracies in presentations given at the ESHG Conference or subsequently published data that may minimize the impact of OGM in human genetics; the impact of the COVID-19 pandemic on our business and the global economy; general market conditions; changes in the competitive landscape and the introduction of competitive products; changes in our strategic and commercial plans; our ability to obtain sufficient financing to fund our strategic plans and commercialization efforts; the ability of medical and research institutions to obtain funding to support adoption or continued use of our technologies; the loss of key members of management and our commercial team; and the risks and uncertainties associated with our business and financial condition in general, including the risks and uncertainties described in our filings with the Securities and Exchange Commission, including, without limitation, our Annual Report on Form 10-K for the year ended December 31, 2020 and in other filings subsequently made by us with the Securities and Exchange Commission. All forward-looking statements contained in this press release speak only as of the date on which they were made and are based on management's assumptions and estimates as of such date. We do not undertake any obligation to publicly update any forward-looking statements, whether as a result of the receipt of new information, the occurrence of future events or otherwise.

CONTACTSCompany Contact:Erik Holmlin, CEOBionano Genomics, Inc.+1 (858) 888-7610eholmlin@bionanogenomics.com

Investor Relations and Media Contact:Amy ConradJuniper Point+1 (858) 366-3243amy@juniper-point.com

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Bionano Genomics Announces ESHG Lineup Featuring 11 Customer Presentations of OGM Data Spanning Three Major Clinical Research Areas of Application...

By Brian McNeill

An analysis of data from 1.5 million people has identified 579 locations in the genome associated with a predisposition to different behaviors and disorders related to self-regulation, including addiction and child behavioral problems.

With these findings, researchers have constructed a genetic risk score a number reflecting a persons overall genetic propensity based on how many risk variants they carry that predicts a range of behavioral, medical and social outcomes, including education levels, obesity, opioid use disorder, suicide, HIV infections, criminal convictions and unemployment.

[This study] illustrates that genes dont code for a particular disorder or outcome; there are no genes for substance use disorder, or for behavior problems, said joint senior authorDanielle Dick, Ph.D., Distinguished Commonwealth Professor of Psychology and Human and Molecular Genetics at Virginia Commonwealth University. Instead, genes influence the way our brains are wired, which can make us more at risk for certain outcomes. In this case, we find that there are genes that broadly influence self-control or impulsivity, and that this predisposition then confers risk for a variety of life outcomes.

The study, Multivariate Analysis of 1.5 Million People Identifies Genetic Associations with Traits Related to Self-Regulation and Addiction, was published today in the journal Nature Neuroscience and was conducted by a consortium of 26 researchers at 17 institutions in the United States and the Netherlands.

It was led by Dick;Philipp Koellinger, Ph.D., professor of social science genetics at the University of Wisconsin Madison and Vrije Universiteit Amsterdam;Kathryn Paige Harden, Ph.D., professor of psychology at the University of Texas at Austin; andAbraham A. Palmer, Ph.D., professor of psychiatry at the University of California, San Diego.

The study is one of the largest genome-wide association studies ever conducted, pooling data from an effective sample size of 1.5 million people of European descent. The researchers genetic risk score has one of the largest effect sizesa measurement of the prediction powerof any genetic risk score for a behavioral outcome to date.

It demonstrates the far-reaching effects of carrying a genetic liability toward lower self-control, impacting many important life outcomes, said Dick, a professor in the Department of Psychology in the College of Humanities and Sciences and the Department Human and Molecular Genetics in the School of Medicine at VCU. We hope that a greater understanding of how individual genetic differences contribute to vulnerability can reduce stigma and blame surrounding many of these behaviors, such as behavior problems in children and substance use disorders.

The identification of the more than 500 genetic loci is important, the researchers said, because it provides new insight into our understanding of behaviors and disorders related to self-regulation, collectively referred to as externalizing and that have a shared genetic liability.

We know that regulating behavior is a critical component of many important life outcomesfrom substance use and behavioral disorders, like ADHD, to medical outcomes ranging from suicide to obesity, to educational outcomes like college completion, Dick said.

Characterizing the genetic contributions to self-regulation can be helpful in myriad ways, she said.

It allows us to better understand the biology behind why some people are more at risk, which can assist with medication development, and it can allow us to know who is more at risk, so we can put early intervention and prevention programs in place, she said. Identifying genetic risk factors is a critical component of precision medicine, which has the goal of using information about an individuals genetic and environmental risk factors to deliver more tailored, effective intervention specific to that individuals risk profile.

The researchers noted, however, that having a higher risk profile isnt necessarily a bad thing.

For example, CEOs, entrepreneurs and fighter pilots are often higher on risk taking, Dick said. DNA is not destiny. We all have unique genetic codes, and were all at risk for something; but understanding ones predisposition can be empoweringit can help individuals understand their strengths, and their potential challenges, and act accordingly.

For more information about the study and its findings, please visit thisFAQ.

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Excerpt from:
Study identifies 579 genetic locations linked to anti-social behavior, alcohol use, opioid addiction and more - VCU News

A $2 million grant from the Mass Life Sciences Center has helped launch the Comparative Pathology and Genomics Shared Resource at Cummings School of Veterinary Medicine, a shared resource with state-of-the-art equipment that fills newly renovated laboratory space. For Cheryl London, a veterinary oncologist and Associate Dean for Research and Graduate Education, it represents a long-time vision becoming reality.

Understanding the pathology of infectious diseases is more critical than ever, said London, who added that the resource will lead to improvements in the treatment and prevention of diseases in humans through detailed genetic characterization of model systems and the associated pathology across species.

London tapped two Cummings School faculty members to lead the effort: assistant professorAmanda Martinot, a veterinary pathologistwho focuses on infectious diseases such as SARS CoV-2 and tuberculosis, and assistant research professor Heather Gardner, GBS20, a veterinary oncologist and geneticist.

Cummings School has been investing in this goal for quite some time. In 2020, the 7,500-square-foot Peabody Pavilion was renovated into modern, flexible lab space designed to support multidisciplinary teams. In addition, the resource will leverage Tufts resources such as the New England Regional Biosafety Laboratory (RBL).

When fully operational, this resource will offer advanced capacities for credentialling and analyzing animal models of disease that will help to grow collaborative opportunities among regional academic and industry entities; provide training opportunities for students, fellows, scientists and clinicians; and ultimately support job growth through expansion of the research enterprise in Central Massachusetts, said London.

Martinots research has focused on tuberculosis (TB). When the Martinot Lab and her collaboratorsCummings School associate professor Gillian Beamer, Tufts University School of Medicineassociate professor Bree Aldridge, and Harvard University professor Peter Sorger, head of the Harvard Program in Therapeutic Sciencesidentified some rare lung biopsies and archived lung specimens from tuberculosis patients that were taken during autopsies many years ago, Martinot thought they were a natural pilot project for the Comparative Pathology and Genomics Shared Resource.

We're trying to understand the biology of tuberculosis in human tissue, what helps the body clear TB, and what fuels TB progression, said Martinot. We use a lot of animal models to try to understand these processes, but there's no animal model that perfectly mimics human TB disease.

The resources new technology can extract meaningful genetic information from the immune cells surrounding and within granulomas, a hallmark pathologic feature of tuberculosissomething they haven't been able to do before. This technology also will allow them to obtain similar information from a variety of pathology samples.

Another pilot project aims to advance research by London and Gardner in canine osteosarcoma, an aggressive bone cancer that affects more than 25,000 dogs each year. In 2019, they published findingsof a study that detailed the landscape of genetic mutations in canine osteosarcoma, and more recently completed a clinical trial to test a new immunotherapy treatment on dogs diagnosed with this type of cancer. TheClinical Trials Officeat Cummings School has treated a number of canine osteosarcoma patients, allowing banking of associated biologic samples for further investigation. With these tissue samples, investigators can ask questions about the molecular and genomic features of cancer over time and identify clinical and pathologic correlates.

Animals get a lot of the same diseases that people do, and the information we learn from animals with these diseases can inform investigation of novel research opportunities across species, said Gardner.

We can start to interrogate the combination of pathology with genetics and follow how the cancer is mutating, Martinot said. And we can look at where these cancer cells live to try to understand how the microenvironment might be supporting the progression of the cancer. That information could lead to potential treatment options.

Paul Mathew, anoncologist at Tufts Medical Center and an associate professor at Tufts School of Medicine, is interested in using the resources technology to ask similar questions about prostate cancer using biopsies from human patients. He wants to understand the tumor and how the microenvironment changes over time in prostate cancer patients. The School of Medicineis one of many potential users of the resourceothers include UMass Medical School and Medical Center, which has plans for a new Veterans Administration outpatient clinic and Institute for Human Genetics.

The resource is home to cutting edge new technology that integrates pathology and genomics, said Martinot. With the help of this grant, we can do whole genome sequencing for genetic analysis of pathogens, tumors, and anything imaginable where the DNA sequence might make a difference.

The goal is to help drive discovery, adds Gardner. We have equipment to support next generation sequencing projects, such as a liquid handler robot to help automate sample processing and an Illumina sequencer. We also have a suite of NanoString equipment, which is a platform that will allow increased use of samples historically considered difficult to work with, including formalin-fixed samples, which are often very degraded.

The new technology that will power this effort falls into two main categories:

Everyone involved with the shared resource is excited about its future potential and the opportunity to see it grow. As Gardner said, The opportunities to impact research, in all areas, are limited by the investigators imagination.

Angela Nelson can be reached atangela.nelson@tufts.edu.

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Investing in the Power of Pathology and Genomics - Tufts Now

NEW YORK A suite of new studies has examined how one cell develops into all the tissues of the human body by tracing and investigating the mutations they acquire over time.

As cells divide, they acquire mutations that are then passed on to their daughter cells. The resulting patterns of mutations can be used to trace back a cell's family tree, possibly all the way to the first cell. In four new studies appearing Wednesday in Nature, teams of researchers from across the world used this approach to study the earliest stages of human development as well as the later accumulation of somatic mutations, including ones linked to cancer.

"Exploring the human body via the mutations cells acquire as we age is as close as we can get to studying human biology in vivo," Luiza Moore, a researcher at the Wellcome Sanger Institute and first author of one of the studies, said in a statement. "Our life history can be found in the history of our cells, but these studies show that this history is more complex than we might have assumed."

Tracing these mutations back in time revealed differences in mutation rates very early in embryonic development. Researchers led by the Sanger Institute's Michael Stratton uncovered a pattern of mutations that indicated a high initial mutation rate that then fell in a study that combined laser capture microdissections with whole-genome sequencing of samples from three individuals. A team led by the Korea Advanced Institute of Science and Technology's Young Seok Ju similarly found a high mutational rate during the early stages of development that then declined, using a capture-recapture approach.

The Stratton-led team estimated that the first two cell divisions had mutation rates of 2.4 per cell per generation, which then fell to 0.7 per cell per generation. This dip, they said, is likely due to the activation of the zygotic genome that increases the ability to repair DNA.

These early cells also contributed unequally to the development of subsequent lineages, though the degree of asymmetry varied from person to person. Ju and his colleagues reported, for instance, that for one individual in their analysis, 112 early lineages split at a ratio of 6.5:1, rather than the expected 1:1.

Stratton and his colleagues, meanwhile, reported that one individual in their study had a 69:31 contribution of the initial daughter cells to subsequent lineages, while another had a 93:7 ratio based on bulk brain samples, but an 81:19 ratio based on colon samples.

This, they said, indicates that the lineage commitment of cells is not fixed. Ju and his colleagues likewise said their finding suggested a stochasticity of clonal segregation in humans, unlike the deterministic embryogenesis observed in C. elegans.

These analyses also shed light on the development of somatic mutations later in life. KAIST's Ju and his colleagues, for instance, found most mutations are specific to certain clones, while in a separate study, the Sanger's Moore and her colleagues, who examined the mutational landscape of 29 cell types from three individuals through sequencing, found mutationrates varied by cell type and were very low in spermatogonia.

Ju and his colleagues also reported that normal tissues harbored known mutational signatures, including UV-mediated DNA damage and endogenous clock-like mutagenesis. Similarly, Moore and her colleagues noted known mutational signatures within normal tissues. They found, for instance, the aging-related SBS1 and SBS5 mutational signatures to be the most common signatures across all cell types, while other signatures were more prominent in certain cell types but not others. The SBS88 signature, which is due to a strain of E. coli, for example, was present among colorectal and appendiceal crypts.

Chen Wu, an investigator at the Chinese Academy of Medical Sciences, and her colleagues also found the aging-related SBS1 and SBS5 mutational signatures to be common among normal tissues, based on their sequencing analysis of microbiopsies from five individuals. Other tissues, like the liver and lung, also harbored other mutational signature like SBS4, which is associated with tobacco smoking.

Some of the mutations present in normal somatic tissues are typically associated with cancer, Wu and her colleagues added. They found mutations in 32 cancer driver genes were widespread among their normal tissue samples, though varied by organ. For instance, driver mutations were present in 6.5 percent of pancreas parenchyma samples and in 73.8 percent of esophageal samples.

Additionally, many normal tissue samples harbored as many as three cancer driver mutations. This, Harvard Medical School's Kamila Naxerova noted in a related commentary in Nature, begins to blur the line between what is normal and what is cancer. "Indeed, if cells with three driver mutations can easily be found in a small tissue sample, cells with four or five drivers probably exist in that tissue as well without necessarily giving rise to cancer," she wrote. "These new insights invite us to reconsider how we genetically define cancer."

Overall, she added that "the four studies provide an impressive demonstration of the power of modern genetics to decode the cellular dynamics that unfold in our bodies over time."

See the article here:
Genetic Analyses Trace How Mutations Accumulate in Cells of the Human Body Over Time - GenomeWeb

The Roman Catholics of Goa-- Kumta and Mangalore regions, are the remnants of very early lineages of Brahmin community of India, majorly with Indo-European-specific genetic composition, according to a study conducted by the Centre for Cellular and Molecular Biology (CCMB)

The study throws vital light on the genetic history of the Roman Catholic populations of West Coast India.

This multi-disciplinary study, using history, anthropology and genetics information, has helped us in understanding the population history of Roman Catholics from one of the most diverse and multicultural region of our country, said Dr. Vinay K Nandikoori, Director, CCMB, Hyderabad.

The west coast of India harbours a rich diversity of various ethno-linguistic human population groups. The Roman Catholic is one such distinct group, whose origin is much debated. Some historians and anthropologists relate them to ancient group of Gaud Saraswat. Others believe they are members of the Jews Lost Tribes in the first century migration to India.

Till date, no genetic study was done on this group to infer their origin and genetic history.

The first high throughput study was conducted by Dr Kumarasamy Thangaraj, Chief Scientist, CSIR-Centre for Cellular and Molecular Biology (CCMB) & Director, Centre for DNA Fingerprinting and Diagnostics, Hyderabad and Dr. Niraj Rai, Senior Scientist, DST-Birbal Sahni Institute of Palaeosciences (BSIP), Lucknow.

Researchers analysed DNA of 110 individuals from Roman Catholic community of Goa-- Kumta and Mangalore. They compared the genetic information of the Roman Catholic group with previously published DNA data from India and West Eurasia. They put this information alongside archaeological, linguistic, and historical records. All of these helped the researchers fill in many of the key details about the demographic changes and history of the Roman Catholic population of South West of India since the Iron Age (until around 2,500 years ago), and how they relate to the contemporary Indian population.

It found that consequences of Portuguese inquisition in Goa on the population history of Roman Catholics. They also found some indication of Jewish component. This finding has been published in Human Genetics on August 23.

Our genetic study revealed that majority of the Roman Catholics are genetically close to an early lineage of Gaur Saraswat community, Dr. Kumarasamy Thangaraj, senior author of the study, said in a statement.

He further added, More than 40 percent of their paternally inherited Y chromosomes can be grouped under R1a haplogroup. Such a genetic signal is prevalent among populations of north India, middle East and Europe, and unique to this population in Konkan region.

This study strongly suggests profound cultural transformations in ancient South West of India. This has mostly happened due to continuous migration and mixing events since last 2500 years, according to Dr. Niraj Rai, co- corresponding author of the paper.

The origins of many population groups in India like the Jews and Parsis are not well-understood. These are gradually unfolding with advances in modern and ancient population genetics. Roman Catholics is one of them with much debated history of origin based on inferences of anthropologists and historians,said Lomous Kumar, first author of the paper.

The other institutes involved in this study are Mangalore University, Canadian Institute for Jewish Research, and Institute of Advanced Materials, Sweden.

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Roman Catholics of west coast of India have Brahmin lineages: CCMB Study - BusinessLine

Credit: Pixabay.

On the face of it, homosexual behavior and Darwins theory of evolution dont match. Genes have to be passed to offspring otherwise they die out, hence any genes that will make an animal more likely to engage in same-sex mating ought to quickly be eliminated from the population. Yet same-sex behavior is quite prevalent among human populations across the globe.

In a new study published in Nature Human Behavior, researchers led by Brendan Zietsch, Associate Professor at the School of Psychology at the University of Queensland, have found compelling clues in our genomes that may resolve this paradox. According to the findings, the same genes that may drive homosexuality in some individuals may enhance the reproductive success of heterosexual individuals.

In other words, genes that offer evolutionary advantageous effects to some people may result in homosexual offspring in subsequent generations as an unintended effect.

For their study, the researchers analyzed the genetic effects associated with same-sex sexual behavior in a dataset of 477,522 people from the UK and the US that contains a wealth of genetic and health information. They performed the same analysis for opposite-sex sexual behavior in a sample of 358,426 people from the same countries.

Participants in the opposite-sex dataset reported how many sexual partners they had in their lifetime. The number of opposite-sex sexual partners is an indicator of mating success, which during evolution would have led to more children

The researchers scoured millions of individual genetic variants that were associated with two variables: whether people ever had a same-sex partner and how many partners they had in their lifetime.

Each variable had many associated genetic variants spread through the genome. And although each of these variants had a tiny effect, in aggregate their effects were substantial.

Ultimately, this analysis showed that the genetic effects associated with ever having had a same-sex partner were also associated with having had more opposite-sex partners among people who never engaged in same-sex behavior.

In order to verify the confidence of their results, the researchers replicated their findings by narrowing the study conditions. Specifically, they performed the same analysis on a sample of individuals with predominantly or exclusively same-sex partners. The results remained largely consistent.

Lastly, the researchers tested whether physical attractiveness, risk-taking propensity, and openness to experience may also influence the results.

In other words, could genes associated with these variables be associated with both same-sex sexual behavior and with opposite-sex partners in heterosexuals? In each case, we found evidence supporting a significant role for these variables, but most of the main results remained unexplained. So we still dont have a solid theory on exactly how these genes confer an evolutionary advantage. But it might be a complex mix of factors that generally make someone more attractive in broad terms, explained Zietsch in an article.

These findings were also validated by an evolutionary computer simulation that crunched the numbers and found that in the lack of any countervailing benefits to genes associated with same-sex sexual behavior, these genes disappear from the gene pool.

Of course, this isnt the last word on the matter. Important limitations include samples involving Western white participants which may not be representative of the general population. Secondly, the number of opposite-sex sexual partners reported in individuals today may not necessarily reflect the same reproductive advantage in our evolutionary past.

Even so, this hypothesis seems like the most solid explanation for same-sex behavior in humans proposed thus far.

I am aware some people believe it is inappropriate to study sensitive topics such as the genetics and evolution of same-sex sexual behavior. My perspective is that the science of human behavior aims to shine a light on the mysteries of human nature and that this involves understanding the factors that shape our commonalities and our differences, Zietsch wrote. Were we to avoid studying sexual preference or other such topics due to political sensitivities, we would be leaving these important aspects of normal human diversity in the dark.

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Whats the evolutionary explanation for homosexuality? Ironically, genes that help people make more babies may be involved - ZME Science

Brain development that occurs after birth is also important. Rebecca Saxe at MIT is working to understand the brain structures and activities responsible for social cognition, which allows us to consider the mental states of other people.

Saxe has discovered a particular brain region that is key; by studying how activity in this region and others changes over the course of childhood, she may be able to understand how social abilities develop. She has also found that these brain activity patterns are altered in people with autism spectrum disorders.

Even though researchers are starting to understand some of the processes that govern development and have identified things that can derail it, were far from being able to intervene when such problems occur. But as we gain insights, we could someday test therapies or other ways to address these developmental issues.

Computational neuroscientists use mathematical models to better understand how networks of brain cells help us interpret what we see and hear, integrate new information, create and store memories, and make decisions.

Understanding how the activity of neurons governs cognition and behavior could lead to ways to improve memory or understand disease processes.

Terry Sejnowski, a computational neurobiologist at the Salk Institute, has built a computer model of the prefrontal cortex and analyzed its performance on a task in which a person (or machine) has to sort cards according to a rule thats always changing. While humans are great at adapting, machines generally struggle. But Sejnowskis computer, which imitates information flow patterns observed in the brain, performed well on this task. This research could help machines think more like humans and adapt more quickly to new conditions.

Aude Oliva, the MIT director of the MIT-IBM Watson AI Lab, uses computational tools to model and predict how brains perceive and remember visual information. Her research shows that different images result in certain patterns of activity both in the monkey cortex and in neural network models, and that these patterns predict how memorable a certain image will be.

Research like Sejnowskis may inspire smarter machines, but it could also help us understand disorders in which the function of the prefrontal cortex is altered, including schizophrenia, dementia, and the effects of head trauma.

Researchers are trying to determine the genetic and environmental risk factors for neurodegenerative diseases, as well as the diseases underlying mechanisms.

NHUNG LE

Improving prevention, early detection, and treatment for diseases like Alzheimers, Parkinsons, Huntingtons, chronic traumatic encephalopathy, and ALS would benefit millions of people around the world.

Yakeel Quiroz, at Massachusetts General Hospital, studies changes in brain structure and function that occur before the onset of Alzheimers symptoms. Shes looking for biomarkers that could be used for early detection of the disease and trying to pinpoint potential targets for therapeutics. One potential biomarker of early-onset Alzheimers that shes founda protein called NfLis elevated in the blood more than two decades before symptoms appear. Quiroz has also identified a woman with a protective genetic mutation that kept her from developing cognitive impairments and brain degeneration even though her brain showed high levels of amyloid, a protein implicated in Alzheimers development. Studying the effects of this beneficial mutation could lead to new therapies.

Researchers at the Early Detection of Neurodegenerative Diseases initiative in the United Kingdom are analyzing whether digital data collected by smartphones or wearables could give early warnings of disease before symptoms develop. One of the initiatives projectsa partnership with Boston Universitywill collect data using apps, activity tracking, and sleep tracking in people with and without dementia to identify possible digital signatures of disease.

As we learn more about the underlying causes of neurodegenerative diseases, researchers are trying to translate this knowledge into effective treatments. Advanced clinical trials targeting newly understood mechanisms of disease are currently under way for many neurodegenerative disorders, including Alzheimers, Parkinsons, and ALS.

Connectomics researchers map and analyze neuronal connections, creating a wiring diagram for the brain.

Understanding these connections will shed light on how the brain functions; many projects are exploring how macro-scale connections are altered during development, aging, or disease.

Mapping these connections isnt easythere may be as many as 100 trillion connections in the human brain, and theyre all tiny. Researchers need to find the best ways to label specific neurons and track the connections they make to other neurons in remote parts of the brain, refine the technology to collect these images, and figure out how to analyze the mountains of data that this process produces.

Link:
Eight ways scientists are unwrapping the mysteries of the human brain - MIT Technology Review

Changing your diet to improve your health is nothing newpeople with diabetes, obesity, Crohns disease, celiac disease, food allergies, and a host of other conditions have long done so as part of their treatment. But new and sophisticated knowledge about biochemistry, nutrition, and artificial intelligence has given people more tools to figure out what to eat for good health, leading to a boom in the field of personalized nutrition.

Personalized nutrition, often used interchangeably with the terms precision nutrition or individualized nutrition is an emerging branch of science that uses machine learning and omics technologies (genomics, proteomics, and metabolomics) to analyze what people eat and predict how they respond to it. Scientists, nutritionists, and health care professionals take the data, analyze it, and use it for a variety of purposes, including identifying diet and lifestyle interventions to treat disease, promote health, and enhance performance in elite athletes.

Increasingly, its being adopted by businesses to sell products and services such as nutritional supplements, apps that use machine learning to provide a nutritional analysis of a meal based on a photograph, and stool-sample tests whose results are used to create customized dietary advice that promises to fight bloat, brain fog, and a myriad of other maladies.

Nutrition is the single most powerful lever for our health, says Mike Stroka, CEO of the American Nutrition Association, the professional organization whose mandate includes certifying nutritionists and educating the public about science-based nutrition for health care practice. Personalized nutrition will be even bigger.

In 2019, according to ResearchandMarkets.Com, personalized nutrition was a $3.7 billion industry. By 2027, it is expected to be worth $16.6 billion. Among the factors driving that growth are consumer demand, the falling cost of new technologies, a greater ability to provide information, and the increasing body of evidence that there is no such thing as a one-size-fits-all diet.

The sequencing of the human genome, which started in 1990 and concluded 13 years later, paved the way for scientists to more easily and accurately find connections between diet and genetics.

When the term personalized nutrition first appeared in the scientific literature, in 1999, the focus was on using computers to help educate people about their dietary needs. It wasnt until 2004 that scientists began to think about the way genes affect how and what we eat, and how our bodies respond. Take coffee, for instance: Some people metabolize caffeine and the other nutrients in coffee in a productive, healthy way. Others dont. Which camp you fall into depends on a host of factors including your genetics, age, environment, gender, and lifestyle.

More recently, researchers have been studying connections between the health of the gut microbiome and conditions including Alzheimers, Parkinsons, and depression. The gut microbiome, the bodys least well-known organ, consists of more than 1000 species of bacteria and other microbes. Weighing in at almost a pound, it produces hormones, digests food that the stomach cant, and sends thousands of different diet-derived chemicals coursing through our bodies every day. In many respects the microbiome is key to understanding nutrition and is the basis of the growth in personalized nutrition.

Blood, urine, DNA, and stool tests are part of the personalized nutrition toolkit that researchers, nutritionists, and health care professionals use to measure the gut microbiome and the chemicals (known as metabolites) it produces. They use that data, sometimes in conjunction with self-reported data collected via surveys or interviews, as the basis for nutrition advice.

Link:
The Poop About Your Gut Health and Personalized Nutrition - WIRED

As anyone who has ever lived with a dog will know, it often feels like we dont get enough time with our furry friends. Most dogs only live around ten to 14 years on average though some may naturally live longer, while others may be predisposed to certain diseases that can limit their lifespan.

But what many people dont know is that humans and dogs share many genetic similarities including a predisposition to age-related cancer. This means that many of the things humans can do to be healthier and longer lived may also work for dogs.

Here are just a few ways that you might help your dog live a longer, healthier life.

One factor thats repeatedly linked with longevity across a range of species is maintaining a healthy bodyweight. That means ensuring dogs arent carrying excess weight, and managing their calorie intake carefully. Not only will a lean, healthy bodyweight be better for your dog in the long term, it can also help to limit the impact of certain health conditions, such as osteoarthritis.

Carefully monitor and manage your dogs bodyweight through regular weighing or body condition scoring where you look at your dogs physical shape and score them on a scale to check whether theyre overweight, or at a healthy weight. Using both of these methods together will allow you to identify weight changes and alter their diet as needed.

Use feeding guidelines as a starting point for how much to feed your dog, but you might need to change food type or the amount you feed to maintain a healthy weight as your dog gets older, or depending on how much activity they get. Knowing exactly how much you are feeding your dog is also a crucial weight-management tool so weigh their food rather than scooping it in by eye.

More generally, good nutrition can be linked to a healthy ageing process, suggesting that what you feed can be as important as how much you feed. Good nutrition will vary for each dog, but be sure to look for foods that are safe, tasty and provide all the nutrients your dog needs.

Exercise has many physiological and psychological benefits, both for our dogs (and us). Physical activity can help to manage a dogs bodyweight, and is also associated with anti-ageing effects in other genetically similar species.

While exercise alone wont increase your dogs lifespan, it might help protect you both from carrying excess bodyweight. And indeed, research suggests that happy dog walks lead to both happy dogs and people.

Ageing isnt just physical. Keeping your dogs mind active is also helpful. Contrary to the popular adage, you can teach old dogs new tricks and you might just keep their brain and body younger as a result.

Even when physical activity might be limited, explore alternative low-impact games and pursuits, such as scentwork that you and your dog can do together. Using their nose is an inherently rewarding and fun thing for dogs to do, so training dogs to find items by scent will exercise them both mentally and physically.

Other exercise such as hydrotherapy a type of swimming exercise might be a good option especially for dogs who have conditions which affect their ability to exercise as normal.

Like many companion animals, dogs develop a clear attachment to their caregivers. The human-dog bond likely provides companionship and often, dog lovers describe them as a family member.

A stable caregiver-dog bond can help maintain a happy and mutually beneficial partnership between you and your dog. It can also help you recognise subtle changes in your dogs behaviour or movement that might signal potential concerns.

Where there is compatability between caregiver and dog, this leads to a better relationship and even benefits for owners, too, including stress relief and exercise. Sharing positive, fun experiences with your dog, including playing with them, are great for cementing your bond.

Modern veterinary medicine has seen substantial improvements in preventing and managing health concerns in dogs. Successful vaccination and parasite management programmes have effectively reduced the incidence of disease in both dogs and humans including toxocariasis, which can be transmitted from dog faeces to humans, and rabies, which can be transmitted dog-to-dog or dog-to-human.

Having a good relationship with your vet will allow you to tailor treatments and discuss your dogs needs. Regular health checks can also be useful in identifying any potential problems at a treatable stage such as dental issues or osteoarthritis which can cause pain and negatively impact the dogs wellbeing.

At the end of the day, its a combination of our dogs genetics and the environment they live in that impacts their longevity. So while we cant change their genetics, there are many things we can do to improve their health that may just help them live a longer, healthier life.

See the original post:
Five ways to help your dog live a longer, healthier life - The Conversation UK