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Bottle Gourd Genome Sequence Provides Insights into Cucurbitaceae Evolution and Facilitates Mapping of a Papaya Ring-Spot Virus Resistance Locus

Researchers from the Boyce Thompson Institute (BTI), the United States Department of Agriculture (USDA), and collaborators in China and France have produced the first high-quality genome sequence for the bottle gourd (Lagenaria siceraria) and a reconstructed genome of the most recent Cucurbitaceae ancestor. Also known as calabash, the bottle gourd is valued for its numerous practical and culturally-significant uses in food, medicine, and novelties such as musical instruments, utensils, containers, and decorations. As a rootstock for other cucurbit crops, the bottle gourd also serves as a target for genomic research interests. Despite this, a high-quality sequence of the bottle gourd genome has not been available and much of the evolutionary history of modern cucurbits and their genetic relationships has remained largely unknown. In their findings, researchers compared the sequenced bottle gourd genome to those of other cucurbit species, allowing them to reconstruct the ancient genomic history of the Cucurbitaceae family. "Using this genome and other available genomes of cucurbit species including watermelon, melon, cucumber and pumpkin, we reconstructed the genome of the most recent common ancestor of Cucurbitaceae, which provides insights into the paleohistory of the Cucurbitaceae genome evolution," according to Dr. Zhangjun Fei, Associate Professor at BTI. The high-quality bottle gourd genome sequence also provides a comprehensive collection of the genetic relationships between the bottle gourd and other Cucurbitaceae species, which can be used to accelerate improvements in cucurbit quality and tolerance to stressors such as disease and cold.

Pigeons Can Discriminate Both Space and Time

New research at the University of Iowa (UI) shows that pigeons can discriminate the abstract concepts of space and time--and seem to use a different region of the brain than humans and primates to do so. In experiments, pigeons were shown on a computer screen a static horizontal line and had to judge its length or the amount of time it was visible to them. Pigeons judged longer lines to also have longer duration and judged lines longer in duration to also be longer in length. What that means, says Dr. Edward Wasserman, Stuit Professor of Experimental Psychology in the Department of Psychological and Brain Sciences at UI, is that pigeons use a common area of the brain to judge space and time, suggesting that these abstract concepts are not processed separately. Similar results have been found with humans and other primates. The finding adds to growing recognition in the scientific community that lower-order animal species -- such as birds, reptiles, and fish -- are capable of high-level, abstract decision-making. "Indeed, the cognitive prowess of birds is now deemed to be ever closer to that of both human and nonhuman primates," says Dr. Wasserman, who has studied intelligence in pigeons, crows, baboons, and other animals for more than four decades. "Those avian nervous systems are capable of far greater achievements than the pejorative term 'bird brain' would suggest." Humans are able to perceive space and time, even without the aid of inventions such as a watch or a ruler. The region of the brain that helps humans make those abstract concepts more tangible is the parietal cortex, part of the cerebral cortex and the outermost layer of the brain.

Zika Vaccine Using DNA-Based Platform Is Safe and Induces an Immune Response in Two Phase 1 Trials

Results from two Phase 1 clinical trials show an experimental Zika vaccine developed by government scientists at the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health, is safe and induces an immune response in healthy adults. The findings were published online on December 4, 2017 in The Lancet. The article is titled “Zika Virus DNA Vaccine Candidates Are Safe and Immunogenic in Healthy Adults.” NIAID is currently leading an international effort to evaluate the investigational vaccine in a Phase 2/2b safety and efficacy trial. "Following early reports that Zika infection during pregnancy can lead to birth defects, NIAID scientists rapidly created one of the first investigational Zika vaccines using a DNA-based platform and began initial studies in healthy adults less than one year later," said NIAID Director Anthony S. Fauci, MD. "NIAID has begun Phase 2 testing of this candidate to determine if it can prevent Zika virus infection, and the promising Phase 1 data published today support its continued development." Investigators from NIAID's Vaccine Research Center (VRC) and Laboratory of Viral Diseases, part of the Division of Intramural Research, developed the investigational vaccine, which includes a small, circular piece of DNA called a plasmid. Scientists inserted genes into the plasmid that encode two proteins found on the surface of the Zika virus. After the vaccine is injected into muscle, the body produces proteins that assemble into particles that mimic the Zika virus and trigger the body to mount an immune response.

Zika Purified Inactivated Virus (ZPIV) Vaccine Is Safe and Immunogenic in Three Phase 1 Trials

The investigational Zika purified inactivated virus (ZPIV) vaccine was well-tolerated and induced an immune response in participants, according to initial results from three Phase 1 clinical trials. Scientists at the Walter Reed Army Institute of Research (WRAIR), part of the U.S. Department of Defense, are developing the vaccine as well as leading one of the trials. WRAIR is also co-funding the trials together with the National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH). The results appeared online on December 4, 2017 in The Lancet. The open-access article is titled “Preliminary Aggregate Safety and Immunogenicity Results from Three Trials of a Purified Inactivated Zika Virus Vaccine Candidate: Phase 1, Randomised, Double-Blind, Placebo-Controlled Clinical Trials.” "A vaccine is urgently needed to help prevent Zika infection, which can cause birth defects and other developmental abnormalities in babies born to infected women, as well as a constellation of other health problems in infected adults and children," says NIAID Director Anthony S. Fauci, MD. "We are encouraged by initial clinical trial results that indicate the ZPIV vaccine is safe and immunogenic, data that support additional clinical testing of the vaccine to determine its ability to prevent Zika virus infection." The ZPIV vaccine candidate contains whole Zika virus particles that have been inactivated and therefore cannot replicate and cause disease in humans. However, because the protein shell of the inactivated virus remains intact, it can be recognized by the immune system.

Kidney Disease Diagnosis May Benefit from DNA Sequencing

DNA sequencing could soon become part of the routine diagnostic workup for patients with chronic kidney disease, suggests a new study from Columbia University Medical Center (CUMC). The researchers found that DNA sequencing could identify the genetic cause of the disease and influence treatment for many patients with chronic kidney disease. The study was published online on December 4, 2017 in the Annals of Internal Medicine. The article is titled "Whole Exome Sequencing in Adults with Chronic Kidney Disease: A Pilot Study." An estimated 14 percent of people in the United States have chronic kidney disease, and between 10 and 25 percent of these individuals have a family history of kidney problems. Diagnosis typically relies on clinical, rather than genetic, evidence. Even with a kidney biopsy, it can be difficult to identify different subtypes of the disease. As a result, the precise cause of kidney failure often remains unknown. "Because CKD is usually silent in the early stages, it may not be detected until an individual develops severe kidney problems," said Ali G. Gharavi, MD, Professor of Medicine and Chief of the Division of Nephrology at CUMC. "At that stage, the patient may be sent to a variety of specialists in order to identify the type and cause of the disease and determine the best treatment. In this study, we hypothesized that genomic testing would help us answer these questions, without sending patients on a time-consuming, and often frustrating diagnostic odyssey." The researchers performed whole exome sequencing--a technique used to analyze DNA from the protein-coding portion of the genome--in 92 adults with kidney disease. More than half had a family history of kidney problems. Most had been given a clinical diagnosis, but 16 individuals did not know the cause of their disease.

Belowground Fungal Interactions with Trees Help Explain Non-Native Plant Invasions

New research published by a team of scientists from the USDA Forest Service and Purdue University suggests that tiny soil fungi that help and are helped by trees may influence a forest's vulnerability to invasion by non-native plants. Research published on December 1, 2017 in the online edition of Ecology Letters suggests that the invasion of nonnative plants is strongly related to what type of mycorrhizal fungi are dominant in forest ecosystems. Mycorrhizal fungi are a type of fungi that help trees feed on minerals in the soil and, in turn, feed off sugars in tree roots. Lead author Dr. Insu Jo of Purdue University and his co-authors, including Dr. Grant Domke, a research forester with the Forest Service's Northern Research Station, explored how dominant forest tree mycorrhizal type affects understory plant invasions. Researchers found that arbuscular mycorrhizal (AM) tree-dominant forests are more vulnerable to nonnative plant invasions than ectomycorrhizal (ECM) tree-dominant forests, likely because nutrients in the soil are consumed and recycled back into the soil more frequently in AM- dominant -forests, creating more nutrition for trees. Understory plant cover for both native and nonnative invasive species was positively associated with the AM fungi, however, invasive species cover increased at a rate 12 times greater than native species as AM-tree-dominance increased. The study, titled "Dominant Forest Tree Mycorrhizal Type Mediates Understory Plant Invasions," is available at: https://www.nrs.fs.fed.us/pubs/55479.

Earlobe Attachment Characteristic Involves at Least 49 Genes, University of Pittsburgh-Led Study Including 23andMe Data Shows

A common, hands-on method for teaching genetics in grade school encourages students to compare their earlobes with those of their parents: Are they attached and smoothly mesh with the jawline? Or are they detached and dangly? The answer is meant to teach students about dominant and recessive genes. Simple, right? Not so fast. New research led by the University of Pittsburgh (Pitt) Graduate School of Public Health and School of Dental Medicine, and published online on November 30, 2017 in the American Journal of Human Genetics, reveals that the lesson is much more complicated, with an interplay of at least 49 genes contributing to earlobe attachment. "Sometimes the genetics of a fairly simple trait are actually quite complex," said lead author John R. Shaffer, Ph.D., Assistant Professor in Pitt Public Health's Department of Human Genetics and the Department of Oral Biology in Pitt's School of Dental Medicine. "By understanding that complexity, we can work toward treatments for genetic conditions, several of which have distinct facial features that involve the earlobe, including Mowat-Wilson Syndrome, which can cause cupped ears with protruding lobes." The study was an international collaboration involving investigators in the United Kingdom and China, and included data from the U.S.-based personal genetics company 23andMe Inc. "The great thing about these collaborations is that we not only had a large sample size, but we also had participants from different ethnicities, giving us a greater depth of genetic information," said senior author Seth M. Weinberg, PhD, Associate Professor in Pitt's Departments of Oral Biology and Human Genetics. The open-access AJHG article is titled “Multiethnic GWAS Reveals Polygenic Architecture of Earlobe Attachment.”

2017 Nobel Prize in Physiology or Medicine Awarded for Discoveries of Molecular Mechanisms Controlling Circadian Rhythm

On October 2, 2017, The Nobel Assembly at Karolinska Institutet decided to award the 2017 Nobel Prize in Physiology or Medicine jointly to Jeffrey C. Hall, Michael Rosbash, and Michael W. Young “for their discoveries of molecular mechanisms controlling the circadian rhythm.” Jeffrey C. Hall was born 1945 in New York, USA. He received his doctoral degree in 1971 at the University of Washington in Seattle and was a postdoctoral fellow at the California Institute of Technology in Pasadena from 1971 to 1973. He joined the faculty at Brandeis University in Waltham in 1974. In 2002, he became associated with University of Maine. Michael Rosbash was born in 1944 in Kansas City, USA. He received his doctoral degree in 1970 at the Massachusetts Institute of Technology in Cambridge. During the following three years, he was a postdoctoral fellow at the University of Edinburgh in Scotland. Since 1974, he has been on faculty at Brandeis University in Waltham, USA. Michael W. Young was born in 1949 in Miami, USA. He received his doctoral degree at the University of Texas in Austin in 1975. Between 1975 and 1977, he was a postdoctoral fellow at Stanford University in Palo Alto. From 1978, he has been on faculty at the Rockefeller University in New York. Life on Earth is adapted to the rotation of our planet. For many years we have known that living organisms, including humans, have an internal, biological clock that helps them anticipate and adapt to the regular rhythm of the day. But how does this clock actually work? Dr. Hall, Dr. Rosbash, and Dr. Young were able to peek inside our biological clock and elucidate its inner workings.

Skin Pigmentation Far More Genetically Complex Than Previously Thought

Many studies have suggested that the genetics of skin pigmentation are simple. A small number of known genes, it is thought, account for nearly 50 percent of pigment variation. However, these studies rely on datasets consisting almost entirely of information from northern Eurasian populations--those that reside mostly in higher latitude regions. Reporting in the November 30, 2017 issue of Cell, researchers from the Broad Institute of MIT and Harvard, Stanford University, and Stony Brook University report that while skin pigmentation is nearly 100 percent heritable, it is hardly a straightforward, Mendelian trait. The article is titled “An Unexpectedly Complex Architecture for Skin Pigmentation in Africans.” By working closely with the KhoeSan, a group of populations indigenous to southern Africa, the researchers have found that the genetics of skin pigmentation become progressively complex as populations reside closer to the equator, with an increasing number of genes--known and unknown--involved, each making a smaller overall contribution. "Africa has the greatest amount of phenotypic variability in skin color, and yet it's been underrepresented in large scale endeavors," said Dr. Alicia Martin, a postdoctoral scientist in the lab of Broad Institute member Dr. Mark Daly. "There are some genes that are known to contribute to skin pigmentation, but by and large there are many more new genes that have not been discovered." "We need to spend more time focusing on these understudied populations in order to gain deeper genetic insights," said Dr. Brenna Henn, Assistant Professor in the Department of Ecology and Evolution at Stony Brook University who, along with Dr. Martin, is a co-corresponding author.

New Approach Enables ID of Human DNA in Minutes Using Portable MinION Sequencer and New Algorithm; Correct Identification of Misidentified or Contaminated Cell Lines Seen As One Application

In the science-fiction movie Gattaca, visitors only clear security if a blood test and readout of their genetic profile matches the sample on file. Now, inexpensive DNA sequencers and custom software could make real-time DNA-authentication a reality. Researchers at Columbia University and the New York Genome Center have developed a method to quickly and accurately identify people and cell lines from their DNA. The technology could have multiple applications, from identifying victims in a mass disaster to analyzing crime scenes. But its most immediate use could be to flag mislabeled or contaminated cell lines in cancer experiments, a major reason that studies are later invalidated. The discovery is described in an article published online on November 28, 2017 in eLife. The article is titled “Rapid Re-Identification of Human Samples Using Portable DNA Sequencing.” "Our method opens up new ways to use off-the-shelf technology to benefit society," said the study's senior author Yaniv Erlich, a computer science professor at Columbia Engineering, an adjunct core member at NYGC, and a member of Columbia's Data Science Institute. "We're especially excited about the potential to improve cell-authentication in cancer research and potentially speed up the discovery of new treatments." The software is designed to run on the MinION (Oxford Nanopore Technologies), an instrument the size of a credit card that pulls in strands of DNA through its microscopic pores and reads out sequences of nucleotides, or the DNA letters A, T, C, G. The device has made it possible for researchers to study bacteria and viruses in the field, but its high error-rate and large sequencing gaps have, until now, limited its use on human cells with their billions of nucleotides.

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