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July 2nd, 2018

First Complete High-Quality Genome Sequence Determined for Koala

The koala is one of the world's most fascinating and iconic mammals. Not only is the koala synonymous with Australia, it is also a powerful international symbol for the preservation and conservation of our natural world. "The Koala Genome Consortium has been an ambitious journey affording us great insights into the genetic building blocks that make up a koala - one of Australia's, as well as the world's, most charismatic and iconic mammals," Professor Rebecca Johnson, Director of the Australian Museum Research Institute, said. "The expert contributions from the teams at the Earlham Institute (UK) were a critical component of this study. I'm so proud of the work this great collaboration has produced and thrilled it will be assisting future koala conservation efforts." The Australian-led consortium of scientists comprised 54 scientists from 29 different institutions across seven countries. The scientists have sequenced over 3.4 billion base pairs and more than 26,000 genes in the koala genome - which makes it slightly larger than the human genome. Unlocking the genomic sequence gives scientists unprecedented insights into the unique biology of the koala. Dr. Katherine Belov, co-lead author at the University of Sydney, Professor of Comparative Genomics, and member of Earlham Institute's Scientific Advisory Board, said: "The genome provides a springboard for the conservation of this biologically unique species." The kaola genome sequencing was reported online on July 2, 2018 in an open-access article in Nature Genetics.

Scientists ID Gene That Regulates Production of Certain Cytokines

Australia's national science agency CSIRO has identified a gene that plays a critical role in regulating the body's immune response to infection and disease. The discovery could lead to the development of new treatments for influenza, arthritis, and even cancer. The gene, called C6orf106 or "C6," controls the production of proteins involved in infectious diseases, cancer, and diabetes. The gene has existed for 500 million years, but its potential is only now understood. The article is titled “C6orf106 Is A Novel Inhibitor of the Interferon-Regulatory Factor 3-Dependent Innate Antiviral Response.” "Our immune system produces proteins called cytokines that help fortify the immune system and work to prevent viruses and other pathogens from replicating and causing disease," CSIRO researcher Dr. Cameron Stewart said. "C6 regulates this process by switching off the production of certain cytokines to stop our immune response from spiraling out of control. The cytokines regulated by C6 are implicated in a variety of diseases including cancer, diabetes and inflammatory disorders such as rheumatoid arthritis." The discovery helps improve our understanding of our immune system, and it is hoped that this understanding will enable scientists to develop new, more targeted therapies. "Even though the human genome was first fully sequenced in 2003, there are still thousands of genes that we know very little about," Dr. Rebecca Ambrose, a former CSIRO researcher, now based at the Hudson Institute of Medical Research said. Dr. Ambrose was part of the CSIRO team that discovered the C6 gene, and co-authored the recent paper announcing the discovery, published online on May 25, 2018 in the Journal of Biological Chemistry.

Mayo Researchers Find Off/On Switch for DNA Repair Protein; Work May Lead to Development of New Therapies for Ovarian Cancer

Damage to DNA is a daily occurrence, but one that human cells have evolved to manage. Now, in work reported in a new paper published on July 2, 2018 in Nature Structural & Molecular Biology, Mayo Clinic researchers have determined how one DNA repair protein gets to the site of DNA damage. The article is titled “Mechanism of 53BP1 activity regulation by RNA-binding TIRR and a designer protein.” The authors say they hope this discovery research will help identify new therapies for ovarian cancer. While the human genome is constantly being damaged, cells have proteins that detect and repair the damage. One of those proteins is called 53BP1. It is involved in the repair of DNA when both strands break. In the publication, Georges Mer, PhD, a Mayo Clinic structural biologist, and his team report on how 53BP1 relocates to chromosomes to do its job. Dr. Mer explains that, in the absence of DNA damage, 53BP1 is inactive -- blocked by a protein called "TIRR." Using X-ray crystallography, the authors show that TIRR obstructs an area on 53BP1 that 53BP1 uses to bind chromosomes. But what shifts TIRR away from 53BP1, so the repair protein can work? The scientists theorized that RNA was responsible for this shift. To test their theory, they engineered a protein that would bind to the 53BP1 repair protein and the RNA molecules released when DNA is damaged. This effort, plus other work detailed in the paper, provides evidence that their idea was sound. The authors report that when DNA damage occurs, RNA molecules produced at that time can bind to TIRR, displacing it from 53BP1 and allowing 53BP1 to swing into action. "Our study provides a proof-of-principle mechanism for how RNA molecules can trigger the localization of 53BP1 to DNA damage sites," says Dr. Mer.

May 30th

Exosome Diagnostics’ Second Prospective Validation Study of Its Urine/Exosome-Based Prostate Cancer Liquid Biopsy Test (EPI) Highlighted at American Urological Association Annual Meeting Press Briefing

Exosome Diagnostics’ novel urine-based prostate cancer liquid biopsy biomarker test, ExoDx™ Prostate(IntelliScore) or EPI, was selected from among 3,000 abstracts for presentation at the Press Sessions during the American Urological Association (AUA) annual meeting. This elite group of abstracts undergoes a rigorous review and selection process to ensure the abstract is not only newsworthy, but also scientifically sound and ready for presentation to the general public. The study findings in over 500 men were to be presented by the study’s Lead Investigator, James McKiernan, MD, John K. Lattimer Professor and Chair, Department of Urology at New York-Presbyterian Hospital/Columbia University, during the AUA’s Press Session on Friday May 18, 2018. EPI is designed to reduce the number of unnecessary initial prostate biopsies in men 50 years of age or older, with a PSA (Prostate Specific Antigen) value between 2-10 ng/ml. The PSA blood test lacks specificity as a screening test for prostate cancer and does not discriminate between high- and low-grade cancer. The EPI urine liquid biopsy genomic test has been previously validated (JAMA Oncology 2016) as a “follow-on” test after PSA that identifies men at high risk of high-grade aggressive prostate cancer on prostate biopsy. This second prospective Validation Study, two years later, confirms the diagnostic value of the test in a contemporary population. Up to 2 million prostate biopsies are performed annually in the United States and Europe, and it is estimated that more than 75 percent of these biopsies are unnecessary because the patient has benign or low-grade/indolent prostate cancer. Use of the EPI test reduces the number of these unnecessary biopsies.

Iron-Sulfur Cluster Research Offers New Avenues for Investigating Disease

Many important proteins in the human body need iron-sulfur clusters, tiny structures made of iron and sulfur atoms, in order to function correctly. Researchers at the National Cancer Institute (NCI), the National Institutes of Health (NIH), and the University of Kentucky have discovered that disruptions in the construction of iron-sulfur clusters can lead to the buildup of fat droplets in certain cells. These findings, which were published in the May 25, 2018 issue of the Journal of Biological Chemistry, provide clues about the biochemical causes of conditions like nonalcoholic fatty liver disease and clear cell renal carcinoma. The article, which was an Editor’s Pick of the May 25 issue, is titled “Acute loss of Iron–Sulfur Clusters Results in Metabolic Reprogramming and Generation of Lipid Droplets in Mammalian Cells.” "Iron-sulfur clusters are delicate and susceptible to damage within the cell," said Daniel Crooks, PhD, the postdoctoral fellow who led the new study. "For this reason, the cells in our body are constantly building new iron-sulfur clusters." Dr. Crooks began studying the enzymes that build iron-sulfur clusters during his graduate studies in Dr. Tracey Rouault's lab at the Eunice Kennedy Shriver National Institute of Child Health and Human Development of the NIH. Mutations in one of these enzymes can cause ISCU (i.e., iron-sulfur cluster assembly enzyme deficiency) myopathy, a hereditary condition in which patients, despite seeming strong and healthy, cannot exercise for more than a short time without feeling pain and weakness. Therefore, it was clear to Dr. Crooks that lifelong deficiency of iron-sulfur clusters caused profound changes in how cells processed energy. But he wondered exactly what happened in a cell in the first moments after something went wrong with iron-sulfur cluster production.

May 28th

Homeless Populations at High Risk to Develop Cardiovascular Disease; Review Calls for Clinicians to Adjust Practices to Meet Needs of This Vulnerable Population

Among homeless individuals, cardiovascular disease remains one of the major causes of death due to challenges in predicting initial risk, limited access to health care, and difficulties in long-term management, according to a review published online on May 28, 2018 in the Journal of the American College of Cardiology. In the U.S., roughly 550,000 people are homeless on any given night, and an estimated 2.3 million to 3.5 million people experience homelessness over the course of a year. The median age of the homeless population is 50 years, approximately 60 percent are male and 39 percent are African-American. These demographic groups experience high cardiovascular disease mortality rates, highlighting the need for proper prevention and treatment. While the prevalence of hypertension and diabetes among homeless individuals is similar to that of the general population, it often goes untreated, leading to worse blood pressure and blood sugar control. Smoking remains the largest contributor to cardiovascular disease mortality in homeless populations, with an estimated 60 percent of ischemic heart disease deaths attributable to tobacco. Although, according to the review, most homeless individuals have a desire to quit smoking, quit rates are only one-fifth the national average. Homeless populations are more likely to drink heavily and have a history of cocaine use, which have been linked to congestive heart failure, atherosclerosis, heart attack, and sudden cardiac death. Twenty-five percent of homeless people have a chronic mental illness, contributing to cardiovascular disease risk and complicating diagnoses by impacting motivation to seek care.

Young Mongooses Learn Life-Long Habits from Role Models Not Their Parents

Young mongooses learn life-long habits from role models rather than inheriting them from genetic parents, new research shows. Banded mongooses live in social groups where pups are consistently cared for one-to-one by a single adult known as an "escort" - not their mother or father. The young mongooses develop "niche" diets and, by studying these diets, University of Exeter researchers showed that pups inherit the behavior of their escort, rather than parents. The findings offer a fascinating insight into one of the great puzzles of evolution - how diversity persists rather than disappearing with passing generations. "It was a big surprise to discover that foraging behavior learned in the first three months of life lasts a lifetime," said Professor Michael Cant, of the Centre for Ecology and Conservation on the University of Exeter's Penryn Campus in Cornwall. "This is pretty remarkable, because we have no evidence that pups and escorts preferentially hang out together after pups become independent. "Cultural inheritance, the transmission of socially learned information across generations, is a huge influence on human behavior: we behave the way we do, not just because of our genes, but also because of what we learn from parents, teachers and cultural role models. "It is less well appreciated that cultural inheritance is a major force shaping behavior in a wide range of non-human animals, from insects to apes - and mongooses." To explore the influence of escorts on eating habits, the researchers chemically analyzed the whiskers of individual mongooses. The findings help explain how diverse behavior persists in nature. Early critics of Darwin's theory of natural selection argued that, if his theory was correct, the result should be the erosion of the very variation he suggested as the engine of evolution.

May 23rd

Muscles Thought to Be “Uniquely Human” Have Been Discovered in Apes

Muscles once thought “uniquely human” have been discovered in several ape species, challenging long-held theories on the origin and evolution of human soft tissues. The findings question the anthropocentric view that certain muscles evolved for the sole purpose of providing special adaptations for human traits, such as walking on two legs, tool use, vocal communication, and facial expressions. Published on April26, 2018 in Frontiers in Ecology and Evolution, the study highlights that thorough knowledge of ape anatomy is necessary for a better understanding of human evolution. The article is titled “First Detailed Anatomical Study of Bonobos Reveals Intra-Specific Variations and Exposes Just-So Stories of Human Evolution, Bipedalism, and Tool Use.” "This study contradicts key dogmas about human evolution and our distinct place on the 'ladder of nature,'" says Rui Diogo, PhD, an Associate Professor in the Department of Anatomy at Howard University in Washington, DC. "Our detailed analysis shows that, in fact, every muscle that has long-been accepted as 'uniquely human' and providing 'crucial singular functional adaptations' for our bipedalism, tool use, and vocal and facial communications is actually present in the same or similar form in bonobos and other apes, such as common chimpanzees and gorillas." Long-standing evolutionary theories are largely based on the bone structures of prehistoric specimens -- and, according to Dr. Diogo, also on the idea that humans are necessarily more special and complex than other animals. These theories suggest that certain muscles evolved in humans only, giving us our unique physical characteristics.

Researchers Set Sights on Exosome-Based Early-Detection Blood Test for Pancreatic Cancer

A team of researchers from the University of California, San Diego (UCSD), published a study on March 23, 2018, evaluating a new strategy to analyze blood samples to search for clues indicating the presence of pancreatic cancer. The article, published in ACS Nano, is titled “Integrated Analysis of Exosomal Protein Biomarkers on Alternating Current Electrokinetic Chips Enables Rapid Detection of Pancreatic Cancer in Patient Blood.” Patients whose pancreatic cancer is diagnosed early have a higher chance of long-term survival and increased access to treatment options, including surgery. However, there is currently no standard screening program or effective early detection strategy for pancreatic cancer. Researchers and organizations like the Pancreatic Cancer Action Network (PanCAN) are dedicated to identifying ways to effectively diagnose the disease earlier and improve patient outcomes. The new study from the UCSD team analyzed blood samples from people who had been diagnosed with pancreatic cancer, and compared them to blood from healthy individuals. Specifically, they isolated small particles, called exosomes, from the blood samples. Exosomes are tiny fluid-filled sacs that can contain protein and genetic material called RNA, which can provide information signifying the presence of disease. Previous work, such as a project conducted at MD Anderson Cancer Center (https://www.pancan.org/news/blood-test-could-potentially-diagnose-pancre...), has also focused on exosomes as a biomarker, or detectable and measurable substance that can indicate what’s happening inside a person’s body.

May 20th

Giraffes Surprise Biologists Yet Again; Increased Understanding Much Needed to Aid Conservation Efforts for This “Vulnerable” Species

New research from the University of Bristol in the UK has highlighted how little we know about giraffe behavior and ecology. It is commonly accepted that group sizes of animals increase when there is a risk of predation, because larger group sizes reduce the risk of individuals being killed, and there are “many eyes” to spot any potential predation risk. Now, however, in the first study of its kind, Bristol PhD student Zoe Muller from the School of Biological Sciences has found that this is not true for giraffes, and that the size of giraffe groups is not influenced by the presence of predators. Muller said, "This is surprising, and highlights how little we know about even the most basic aspects of giraffe behavior." This study investigates how the grouping behavior of giraffes differed in response to numerous factors, such as predation risk, habitat type, and the characteristics of individuals. Habitat type had some effect on group size, but the main effect on group size was in the behavior of adult females, who were found to be in smaller groups when they had calves. This is contrary to another popular belief that female giraffes form large groups to communally care for their young - this study, published recently in the Journal of Zoology presents the first evidence to show that, actually, the opposite is true. Giraffe populations have declined by 40 percent in the last 30 years, and there are now thought to be fewer than 98,000 individuals remaining in the wild. In recognition of their drastic decline in the wild, giraffes have recently been listed as "Vulnerable" on the International Union for Conservation in Nature's Red List of Threatened Species.