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May 30th, 2020

Fearful Great Danes Provide New Insights to Genetic Causes of Fear

A novel genomic region on chromosome 11 has been associated with fearfulness in dogs in a study of Great Danes by researchers at the University of Helsinki and the University of Oahu, both in Finland. The identified genomic region includes several candidate genes associated with brain development and function, as well as anxiety, whose further analysis may reveal new neural mechanisms related to fear. For the purposes of the study, led by the University of Helsinki’s Professor Hannes Lohi's (https://researchportal.helsinki.fi/en/persons/hannes-lohi) research group (https://www.koirangeenit.fi/english/) and published online on May 28, 2020 in Translational Psychiatry, data from a total of 120 Great Danes was collected. The article is titled “A Novel Genomic Region on Chromosome 11 Associated with Fearfulness in Dogs.” [Editor’s Note: Dogs have 38 pairs of somatic chromosomes, and the X and Y sex chromosomes, compared to the human complement of 22 pairs of somatic chromosomes and the X and Y sex chromosomes.] The Great Dane breed is among the largest breeds of dog in the world. The project was launched after a number of Great Dane owners approached the research group to tell them about their dogs' disturbing fearfulness towards unfamiliar human beings in particular. "Fear in itself produces a natural and vital reaction, but excessive fear can be disturbing and results in behavioral disorders. Especially in the case of large dogs, strongly expressed fearfulness is often problematic, as it makes it more difficult to handle and control the dog," says Riika Sarviaho, PhD, from the University of Helsinki. In dogs, behavioral disorders associated with anxiety and fearfulness include generalized anxiety disorder and a range of phobias.

May 29th

Eight-Protein Blood Test Can ID Those at Risk of Carrying Hidden Malaria Parasites (Hypnozoites) within Nine Months of Active Infection with Plasmodium vivax; Test Offers Possibility of Reducing P. vivax Prevalence by As Much As 69%; 2 Billion Now at Risk

Plasmodium vivax is the most widespread malaria parasite worldwide, with up to 2,000,000,000 people at risk of infection. As well as causing illness and death in its “active” stage of infection, the parasite can hide as hypnozoites, a dormant stage, in the liver, and is a significant cause of “relapsing” malaria. These hypnozoites, undetectable with current diagnostics, can be responsible for >80% of all blood-stage infections. Identifying and targeting individuals with hypnozoites is thus essential for accelerating and achieving malaria elimination. A major gap in the P. vivax elimination toolkit is the identification of individuals carrying clinically silent and undetectable hypnozoites. The current study developed a panel of serological exposure markers capable of classifying individuals with P. vivax infections within the previous nine months who have a high likelihood of harboring hypnozoites. Using the Perkin-Elmer AlphaScreen system (https://www.perkinelmer.com/Content/RelatedMaterials/Brochures/BRO_Alpha...), the researchers measured IgG antibody responses to 342 P. vivax proteins expressed by a wheat germ cell-free system, invented at Ehime University in Japan, in longitudinal clinical cohorts conducted in Thailand and Brazil, and identified 60 candidate serological markers of exposure. Candidate markers were then validated using samples from year-long observational cohorts conducted in Thailand, Brazil, and the Solomon Islands and antibody responses to eight P. vivax proteins classified P. vivax infections in the previous 9 months with 80% sensitivity and specificity. Mathematical models demonstrate that a serological testing and treatment strategy based on testing for responses to these eight P.

Przewalski’s Horse: The Long Way Home

Przewalski’s Horse (Equus ferus przewalskii) (see also photos at end) is the last surviving species of wild horse – however, since 1969, it has been considered extinct in the wild. Because it was possible to continue breeding the remaining animals in captivity, the species could be preserved until today. “The current population goes back to a mere twelve horses that produced offspring while kept in zoos--a genetic bottleneck that carries the risk of diseases caused by inbreeding, such as a reduced resistance or shortened life expectancy,” explains Professor Hermann Ansorge, PhD, of the Senckenberg Research Institute and Natural History Museum in Görlitz, Germany, and he continues, “Under these conditions, attempts to reintroduce the Przewalski’s Horses into the wild pose a serious challenge. A species can only react to environmental changes if it has a high level of genetic variability!” In 1992, the first successful attempts began to reintroduce the Przewalski’s Horse into its former home, the Mongolian steppe. Today, about 746 individual horses can be found there in the wild again. In recent years, an international team took a closer look at the reintroduced Przewalski’s Horses and at historic collection materials. The researchers examined a total of 130 skulls from a period of 110 years. The comparison of non-metric characteristics revealed insights into the genetic variability. “This involves defined manifestations on the skull whose appearance can be differentiated qualitatively,” explains Dr. Ansorge, and he adds, “For example, these can be small natural openings that serve as passageways for blood vessels or nerves.

One in Three British Women Have Inherited Neandertal Variant of Gene for Progesterone—Variant Associated with More Siblings, Fewer Bleedings in Early Pregnancy, and Fewer Miscarriages, Suggesting Neandertal Variant Promotes Fertility

New data analysis indicates that almost one in three women in the UK Biobank have inherited the gene variant receptor for progesterone from Neandertals—and that this gene variant is associated with greater number of siblings, fewer bleedings during early pregnancy, and fewer miscarriages—suggesting increased fertility. This is according to a study published online on May 21, 2020 in Molecular Biology and Evolution by researchers at the Max Planck Institute for Evolutionary Anthropology in Germany and Karolinska Institutet in Sweden. The article is titled “The Neandertal Progesterone Receptor.” "The progesterone receptor is an example of how favorable genetic variants that were introduced into modern humans by mixing with Neandertals can have effects in people living today," says Hugo Zeberg, PhD, Assistant Professor in the Department of Neuroscience at Karolinska Institutet and researcher with the Max Planck Institute for Evolutionary Anthropology, who performed the study with colleagues Janet Kelso, PhD, Group leader of the Minerva Research Group for Bioinformatics at the Max Planck Institute for Evolutionary Anthropology, and Svante Pääbo (photo), PhD, Director, Max Planck Institute for Evolutionary Anthropology. Progesterone is a hormone that plays an important role in the menstrual cycle and in pregnancy. Analyses of biobank data from more than 450,000 participants--among them 244,000 women--show that almost one in three women in Europe have inherited the progesterone receptor from Neandertals. 29 percent carry one copy of the Neandertal receptor and three percent have two copies. "The proportion of women who inherited this gene is about ten times greater than for most Neandertal gene variants," says Dr. Zeberg.

May 28th

First Human Trial of COVID-19 Vaccine Finds It Is Safe and Induces Rapid Immune Response; Results from China Published in The Lancet

The first COVID-19 vaccine to reach phase 1 clinical trial has been found to be safe, well-tolerated, and able to generate an immune response against SARS-CoV-2 in humans, according to new research published online on May 22, 2020 in The Lancet. The open-access article is titled “Safety, Tolerability, and Immunogenicity of a Recombinant Adenovirus Type-5 Vectored COVID-19 Vaccine: A Dose-Escalation, Open-Label, Non-R andomised, First-In-Human Trial.” The open-label trial in 108 healthy adults demonstrates promising results after 28 days--the final results will be evaluated in six months. Further trials are needed to determine whether the immune response the vaccine elicits effectively protects against SARS-CoV-2 infection. "These results represent an important milestone. The trial demonstrates that a single dose of the new adenovirus type 5 vectored COVID-19 (Ad5-nCoV) vaccine produces virus-specific antibodies and T cells in 14 days, making it a potential candidate for further investigation,” says Professor Wei Chen from the Beijing Institute of Biotechnology in Beijing, China, who is responsible for the study. "However, these results should be interpreted cautiously. The challenges in the development of a COVD-19 vaccine are unprecedented, and the ability to trigger these immune responses does not necessarily indicate that the vaccine will protect humans from COVID-19. This result shows a promising vision for the development of COVID-19 vaccines, but we are still a long way from this vaccine being available to all." The creation of an effective vaccine is seen as the long-term solution to controlling the COVID-19 pandemic. Currently, there are more than 100 candidate COVID-19 vaccines in development worldwide.

Oldest Connection with Native Americans Identified Near Lake Baikal in Siberia; Newly Sequenced Genomes from Prehistoric Hunter-Gatherers in Region of Lake Baikal Reveal Connections with First Americans and Across Eurasia

Using human population genetics, ancient pathogen genomics, and isotope analysis, a team of researchers assessed the population history of the Lake Baikal region (image), finding the deepest connection to date between the peoples of Siberia and of the Americas. The current study, published online on May 20, 2020 in Cell, also demonstrates human mobility, and hence connectivity, across Eurasia during the Early Bronze Age. The article is titled “Paleolithic to Bronze Age Siberians Reveal Connections with First Americans and Across Eurasia.” Modern humans have lived near Lake Baikal since the Upper Paleolithic, and have left behind a rich archaeological record. Ancient genomes from the region have revealed multiple genetic turnovers and admixture events, indicating that the transition from the Neolithic to the Bronze Age was facilitated by human mobility and complex cultural interactions. The nature and timing of these interactions, however, remains largely unknown. The new study published in Cell reports the findings of 19 newly sequenced ancient human genomes from the region of Lake Baikal, including one of the oldest reported from that region. Led by the Department of Archaeogenetics at the Max Planck Institute for the Science of Human History in Germany, the study illuminates the population history of the region, revealing deep connections with the First Peoples of the Americas, dating as far back as the Upper Paleolithic period, as well as connectivity across Eurasia during the Early Bronze Age. "This study reveals the deepest link between Upper Paleolithic Siberians and First Americans," says He Yu, PhD, first author of the Cell article.

Scientists ID Gene for Which Variants Are Associated with Thinness; Thinness-Associated Variants of ALK Gene Found in GWAS Study of Over 47,000 in Estonian Biobank; Results Highlight Important Therapeutic Potential of ALK Inhibition

A noticeable impact on the waistline of many people is a side-effect of the quarantine due to the global COVID19 outbreak. Reduced activity and lack of sports while consuming the same, or even elevated, amounts of calories can quickly cause a substantial weight gain. Strikingly, some individuals can make it through this period without gaining any weight--we all know these people who can eat what they want, but do not appear to gain weight. A consortium of international researchers including scientists from the IMBA (Institute of Molecular Biotechnology of the Austrian Academy of Sciences), the University of British Columbia, the Medical University of Vienna, and the Estonian Biobank have now taken a unique approach: thus far, the regulation of fat metabolism has mainly focused on finding genes linked to obesity. This team, however, went on a quest to discover genes linked to thinness, or the resistance to weight gain. In order to identify candidate thinness genes, the research team conducted genome-wide association studies (GWAS) in an Estonian population cohort, profiling over 47,000 people. The researchers compared thin to control individuals and were thereby able to determine that variants in the ALK (anaplastic lymphoma kinase) gene (image of ALK protein shown below) were associated with thinness. ALK is mainly known due to its involvement in cancer, as it is frequently mutated in multiple cancers. However, its physiological function has been largely elusive. The article describing the new thinness research was published online on May 21, 2020 in Cell, and it is titled “Identification of ALK in Thinness.” To test the hypothesis of ALK variants being involved in thinness, the researchers inactivated the Alk gene in mice.

Genome Aggregation Database (gnomAD) Consortium Releases Its First Major Studies of Human Genetic Variation Simultaneously in Seven Articles—Four in Nature, Two in Nature Communications, One in Nature Medicine

Analyses of the largest publicly available catalog of human genomic data reveal new details on rare types of genetic variation and provide better tools for genetic disease diagnosis and drug development. For the last eight years, the Genome Aggregation Database (gnomAD) Consortium (and its predecessor, the Exome Aggregation Consortium, or ExAC), has been working with geneticists around the world to compile and study more than 125,000 exomes and 15,000 whole genomes from populations around the world. Now, on May 27, 2020, in seven open-access papers published in Nature, Nature Communications, and Nature Medicine, gnomAD Consortium scientists describe their first set of discoveries from the database, showing the power of this vast collection of data. Together the studies: (1) present a more complete catalog and understanding of a class of rare genetic variation called loss-of-function (LoF) variants, which are thought to disrupt genes' encoded proteins; (2) introduce the largest comprehensive reference map of an understudied yet important class of genetic variation called structural variants; (3) show how tools that account for unique forms of variation and variants' biological context can help clinical geneticists when trying to diagnose patients with rare genetic diseases; and (4) illustrate how population-scale datasets like gnomAD can help evaluate proposed drug targets. Researchers at the Broad Institute of MIT and Harvard and Massachusetts General Hospital (MGH) served as co-first or co-senior authors on all of the studies, with scientists from Imperial College London in the United Kingdom, the direct-to-consumer genetics company 23andMe, and other institutions contributing to individual papers.

Scientists Develop Tool to Sequence Circular DNA; New Method Will Provide Insight into Genomes of Bacteria and Viruses, As Well As Extrachromosomal Circular DNA (eccDNA) in Humans; SMRT Long-Range Sequencing from Pacific Biosciences Employed

University of Alberta (Canada) biologists have invented a new way for sequencing circular DNA, according to a new study. The tool, called CIDER-Seq, will give other scientists rich, accurate data on circular DNA in any type of cell. The article describing the new method was published online on April 3, 2020 in Nature Protocols. The article is titled “Full-Length Sequencing of Circular DNA Viruses and Extrachromosomal Circular DNA Using CIDER-Seq.” While our own DNA is linear, circular DNA is common in the genomes of bacteria and viruses. Scientists have also discovered circular DNA within the nuclei of human and plant cells, called extrachromosomal circular DNA (eccDNA). Recently, research has begun to investigate the role of eccDNA in human cancer--but progress has been hampered due to the lack of effective methods for studying and sequencing eccDNA. "Our key advance is that, through our method, scientists can finally gain an unbiased, high-resolution understanding of circular DNA in any type of cell," explained Devang Mehta, PhD, postdoctoral fellow in the Department of Biological Sciences at the University of Alberta and lead author. "With our invention of CIDER-Seq, we can start to begin to understand the function of these mysterious circular DNAs in human and plant cells." CIDER-Seq uses DNA sequencing technology called single-molecule real-time (SMRT) long-read sequencing from Pacific Biociences to obtain full-length sequences without the need for PCR or restriction digestion. The method includes a web-lab protocol, as well as a new computational pipeline. It is optimized to examine both viral genomes and eccDNA and is made accessible to other scientists online.

May 27th

New Evidence for Blood-Based Biomarker (Neurofilament Light Chain) (NfL) for Alzheimer's Disease; Findings Made in MGH-Led Study of Over 2,000 Members of Colombian Kindred with Familial Alzheimer’s Due to Same Mutation (PSEN1 E280A)

A potential blood-based biomarker for Alzheimer's and other neurodegenerative diseases seems even more promising thanks to new research from a Massachusetts General Hospital (MGH)-led study. According to this team's work, neurofilament light chain (NfL) has great potential as a biomarker for early detection of Alzheimer's disease and could be also useful for monitoring treatment response for that condition. The study was carried out by a team co-led by Yakeel T. Quiroz, PhD, Assistant Professor at Harvard Medical School, and Director of the Familial Dementia Neuroimaging Lab at MGH. Their work was published in the June 1, 2020 issue of The Lancet Neurology. The article is titled “Plasma Neurofilament Light Chain in the Presenilin 1 E280A Autosomal Dominant Alzheimer's Disease Kindred: A Cross-Sectional and Longitudinal Cohort Study.” Additional co-first authors were Henrik Zetterberg, PhD, of Sahlgrenska University Hospital in Sweden, and Eric Reiman, MD, from the University of Arizona. "We wanted to determine the earliest age at which plasma NfL levels could distinguish individuals at high risk of Alzheimer's," says Dr. Quiroz, who is also an MGH Research Scholar 2020-2025. The researchers found that NfL levels increased with age among people at genetic risk because of a specific mutation (PSEN1 E280A) and began to differentiate carriers from noncarriers at age 22, an average of 22 years before their estimated age of cognitive impairment (age 44). Neurofilament light chain (NfL) is a biomarker of neurodegeneration-- damage to neurons. Measures of NfL concentrations in cerebral spinal fluid (CSF) and blood have been used to detect and track neurodegeneration in individuals with Alzheimer's disease and other brain disorders.