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https://www.readbyqxmd.com/read/28330916/climate-warming-and-humans-played-different-roles-in-triggering-late-quaternary-extinctions-in-east-and-west-eurasia
#1
Xinru Wan, Zhibin Zhang
Climate change and humans are proposed as the two key drivers of total extinction of many large mammals in the Late Pleistocene and Early Holocene, but disentangling their relative roles remains challenging owing to a lack of quantitative evaluation of human impact and climate-driven distribution changes on the extinctions of these large mammals in a continuous temporal-spatial dimension. Here, our analyses showed that temperature change had significant effects on mammoth (genus Mammuthus), rhinoceros (Rhinocerotidae), horse (Equidae) and deer (Cervidae)...
March 29, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28327635/the-evolutionary-and-phylogeographic-history-of-woolly-mammoths-a-comprehensive-mitogenomic-analysis
#2
Dan Chang, Michael Knapp, Jacob Enk, Sebastian Lippold, Martin Kircher, Adrian Lister, Ross D E MacPhee, Christopher Widga, Paul Czechowski, Robert Sommer, Emily Hodges, Nikolaus Stümpel, Ian Barnes, Love Dalén, Anatoly Derevianko, Mietje Germonpré, Alexandra Hillebrand-Voiculescu, Silviu Constantin, Tatyana Kuznetsova, Dick Mol, Thomas Rathgeber, Wilfried Rosendahl, Alexey N Tikhonov, Eske Willerslev, Greg Hannon, Carles Lalueza-Fox, Ulrich Joger, Hendrik Poinar, Michael Hofreiter, Beth Shapiro
Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28277493/genomics-gene-time-bomb-hurt-mammoths
#3
(no author information available yet)
No abstract text is available yet for this article.
March 8, 2017: Nature
https://www.readbyqxmd.com/read/28253255/excess-of-genomic-defects-in-a-woolly-mammoth-on-wrangel-island
#4
Rebekah L Rogers, Montgomery Slatkin
Woolly mammoths (Mammuthus primigenius) populated Siberia, Beringia, and North America during the Pleistocene and early Holocene. Recent breakthroughs in ancient DNA sequencing have allowed for complete genome sequencing for two specimens of woolly mammoths (Palkopoulou et al. 2015). One mammoth specimen is from a mainland population 45,000 years ago when mammoths were plentiful. The second, a 4300 yr old specimen, is derived from an isolated population on Wrangel island where mammoths subsisted with small effective population size more than 43-fold lower than previous populations...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28157639/distinguishing-real-from-fake-ivory-products-by-elemental-analyses-a-bayesian-hybrid-classification-method
#5
Kittisak Buddhachat, Janine L Brown, Chatchote Thitaram, Sarisa Klinhom, Korakot Nganvongpanit
As laws tighten to limit commercial ivory trading and protect threatened species like whales and elephants, increased sales of fake ivory products have become widespread. This study describes a method, handheld X-ray fluorescence (XRF) as a noninvasive technique for elemental analysis, to differentiate quickly between ivory (Asian and African elephant, mammoth) from non-ivory (bones, teeth, antler, horn, wood, synthetic resin, rock) materials. An equation consisting of 20 elements and light elements from a stepwise discriminant analysis was used to classify samples, followed by Bayesian binary regression to determine the probability of a sample being 'ivory', with complementary log log analysis to identify the best fit model for this purpose...
January 21, 2017: Forensic Science International
https://www.readbyqxmd.com/read/28127429/machine-learning-and-systems-genomics-approaches-for-multi-omics-data
#6
REVIEW
Eugene Lin, Hsien-Yuan Lane
In light of recent advances in biomedical computing, big data science, and precision medicine, there is a mammoth demand for establishing algorithms in machine learning and systems genomics (MLSG), together with multi-omics data, to weigh probable phenotype-genotype relationships. Software frameworks in MLSG are extensively employed to analyze hundreds of thousands of multi-omics data by high-throughput technologies. In this study, we reviewed the MLSG software frameworks and future directions with respect to multi-omics data analysis and integration...
2017: Biomarker Research
https://www.readbyqxmd.com/read/28125603/relation-between-the-macroscopic-pattern-of-elephant-ivory-and-its-three-dimensional-micro-tubular-network
#7
Marie Albéric, Mason N Dean, Aurélien Gourrier, Wolfgang Wagermaier, John W C Dunlop, Andreas Staude, Peter Fratzl, Ina Reiche
Macroscopic, periodic, dark and bright patterns are observed on sections of elephant tusk, in the dentin part (ivory). The motifs-also called Schreger pattern-vary depending on the orientation in the tusk: on sections perpendicular to the tusk axis, a checkerboard pattern is present whereas on sections longitudinal to it, alternating stripes are observed. This pattern has been used to identify elephant and mammoth ivory in archeological artifacts and informs on the continuous tissue growth mechanisms of tusk...
2017: PloS One
https://www.readbyqxmd.com/read/28033530/mini-snapshot-multiplex-assays-authenticate-elephant-ivory-and-simultaneously-identify-the-species-origin
#8
Thitika Kitpipit, Kantima Thongjued, Kitichaya Penchart, Kanita Ouithavon, Wilaiwan Chotigeat
Illegal trading of ivory is mainly responsible for the dramatic decline in elephant populations. Thailand is one of the largest laundering hotspots for African ivory, as the domestic Asian elephant ivory can be legally traded. So, to help combat ivory poaching and smuggling, an efficient method is needed to identify the elephant species from its ivory and ivory products. In this study, a mini-SNaPshot(®) multiplex assay was developed and fully validated for the identification of confiscated ivory and low DNA template ivory products...
December 21, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27997045/dynamics-of-escherichia-coli-type-i-e-crispr-spacers-over-42-000-years
#9
Ekaterina Savitskaya, Anna Lopatina, Sofia Medvedeva, Mikhail Kapustin, Sergey Shmakov, Alexey Tikhonov, Irena I Artamonova, Maria Logacheva, Konstantin Severinov
CRISPR-Cas are nucleic acids-based prokaryotic immune systems. CRISPR arrays accumulate spacers from foreign DNA and provide resistance to mobile genetic elements containing identical or similar sequences. Thus, the set of spacers present in a given bacterium can be regarded as a record of encounters of its ancestors with genetic invaders. Such records should be specific for different lineages and change with time, as earlier acquired spacers get obsolete and are lost. Here, we studied Type I-E CRISPR spacers of Escherichia coli from extinct pachyderm...
December 20, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/27587336/drivers-of-bacterial-genomes-plasticity-and-roles-they-play-in-pathogen-virulence-persistence-and-drug-resistance
#10
REVIEW
Seema Patel
Despite the advent of next-generation sequencing (NGS) technologies, sophisticated data analysis and drug development efforts, bacterial drug resistance persists and is escalating in magnitude. To better control the pathogens, a thorough understanding of their genomic architecture and dynamics is vital. Bacterial genome is extremely complex, a mosaic of numerous co-operating and antagonizing components, altruistic and self-interested entities, behavior of which are predictable and conserved to some extent, yet largely dictated by an array of variables...
August 30, 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27509852/postglacial-viability-and-colonization-in-north-america-s-ice-free-corridor
#11
Mikkel W Pedersen, Anthony Ruter, Charles Schweger, Harvey Friebe, Richard A Staff, Kristian K Kjeldsen, Marie L Z Mendoza, Alwynne B Beaudoin, Cynthia Zutter, Nicolaj K Larsen, Ben A Potter, Rasmus Nielsen, Rebecca A Rainville, Ludovic Orlando, David J Meltzer, Kurt H Kjær, Eske Willerslev
During the Last Glacial Maximum, continental ice sheets isolated Beringia (northeast Siberia and northwest North America) from unglaciated North America. By around 15 to 14 thousand calibrated radiocarbon years before present (cal. kyr bp), glacial retreat opened an approximately 1,500-km-long corridor between the ice sheets. It remains unclear when plants and animals colonized this corridor and it became biologically viable for human migration. We obtained radiocarbon dates, pollen, macrofossils and metagenomic DNA from lake sediment cores in a bottleneck portion of the corridor...
September 1, 2016: Nature
https://www.readbyqxmd.com/read/27426005/an-overview-of-the-regulation-of-influenza-vaccines-in-the-united-states
#12
Jerry P Weir, Marion F Gruber
Influenza virus vaccines are unique among currently licensed viral vaccines. The vaccines designed to protect against seasonal influenza illness must be updated periodically in an effort to match the vaccine strain with currently circulating viruses, and the vaccine manufacturing timeline includes multiple, overlapping processes with a very limited amount of flexibility. In the United States (U.S.), over 150 million doses of seasonal trivalent and quadrivalent vaccine are produced annually, a mammoth effort, particularly in the context of a vaccine with components that usually change on a yearly basis...
September 2016: Influenza and Other Respiratory Viruses
https://www.readbyqxmd.com/read/27326379/phosphorus-mobilizing-consortium-mammoth-p-%C3%A2-enhances-plant-growth
#13
Peter Baas, Colin Bell, Lauren M Mancini, Melanie N Lee, Richard T Conant, Matthew D Wallenstein
Phosphorus (P) is a critical nutrient used to maximize plant growth and yield. Current agriculture management practices commonly experience low plant P use efficiency due to natural chemical sorption and transformations when P fertilizer is applied to soils. A perplexing challenge facing agriculture production is finding sustainable solutions to deliver P more efficiently to plants. Using prescribed applications of specific soil microbial assemblages to mobilize soil bound-P to improve crop nutrient uptake and productivity has rarely been employed...
2016: PeerJ
https://www.readbyqxmd.com/read/27252584/ascribing-functions-to-genes-journey-towards-genetic-improvement-of-rice-via-functional-genomics
#14
Ananda Mustafiz, Sumita Kumari, Ratna Karan
Rice, one of the most important cereal crops for mankind, feeds more than half the world population. Rice has been heralded as a model cereal owing to its small genome size, amenability to easy transformation, high synteny to other cereal crops and availability of complete genome sequence. Moreover, sequence wealth in rice is getting more refined and precise due to resequencing efforts. This humungous resource of sequence data has confronted research fraternity with a herculean challenge as well as an excellent opportunity to functionally validate expressed as well as regulatory portions of the genome...
June 2016: Current Genomics
https://www.readbyqxmd.com/read/27143688/changes-in-variation-at-the-mhc-class-ii-dqa-locus-during-the-final-demise-of-the-woolly-mammoth
#15
Patrícia Pečnerová, David Díez-Del-Molino, Sergey Vartanyan, Love Dalén
According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27113442/the-maintaining-musculoskeletal-health-mammoth-study-protocol-for-a-randomised-trial-of-cognitive-behavioural-therapy-versus-usual-care-for-the-prevention-of-chronic-widespread-pain
#16
RANDOMIZED CONTROLLED TRIAL
Gary J Macfarlane, Marcus Beasley, Gordon Prescott, Paul McNamee, Philip Keeley, Majid Artus, John McBeth, Philip Hannaford, Gareth T Jones, Neil Basu, John Norrie, Karina Lovell
BACKGROUND: Cognitive behavioural therapy (CBT) has been shown to improve outcomes for patients with fibromyalgia, and its cardinal feature chronic widespread pain (CWP). Prediction models have now been developed which identify groups who are at high-risk of developing CWP. It would be beneficial to be able to prevent the development of CWP in these people because of the high cost of symptoms and because once established they are difficult to manage. We will test the hypothesis that among patients who are identified as at high-risk, a short course of telephone-delivered CBT (tCBT) reduces the onset of CWP...
April 26, 2016: BMC Musculoskeletal Disorders
https://www.readbyqxmd.com/read/27051865/climate-co2-and-the-history-of-north-american-grasses-since-the-last-glacial-maximum
#17
Jennifer M Cotton, Thure E Cerling, Kathryn A Hoppe, Thomas M Mosier, Christopher J Still
The spread of C4 grasses in the late Neogene is one of the most important ecological transitions of the Cenozoic, but the primary driver of this global expansion is widely debated. We use the stable carbon isotopic composition (δ(13)C) of bison and mammoth tissues as a proxy for the relative abundance of C3 and C4 vegetation in their grazing habitat to determine climatic and atmospheric CO2 controls on C4 grass distributions from the Last Glacial Maximum (LGM) to the present. We predict the spatial variability of grass δ(13)C in North America using a mean of three different methods of classification and regression tree (CART) machine learning techniques and nine climatic variables...
March 2016: Science Advances
https://www.readbyqxmd.com/read/26946579/mammoth-order-for-singapore-project
#18
(no author information available yet)
Two new hospitals in Singapore that form a new integrated healthcare hub, that feature a range of innovations in patient treatment and care, and are reportedly the country's first such healthcare facilities built together as an integrated development to complement each other's capabilities and services, were officially opened by Singapore's Prime Minister, Lee Hsien Loong, last October. Operated by Jurong Health, a public healthcare 'cluster' formed to facilitate the integration of healthcare services in the west of Singapore, the Ng Teng Fong Hospital and Jurong Community Hospital feature an extensive array of Gerflor flooring, selected, as the company explains in this article, for a combination of outstanding aesthetics, durability, safety, and hard wear...
January 2016: Health Estate
https://www.readbyqxmd.com/read/26868396/draft-genome-sequence-of-enterococcus-faecium-strain-58m-isolated-from-intestinal-tract-content-of-a-woolly-mammoth-mammuthus-primigenius
#19
Artemiy Goncharov, Semyon Grigorjev, Alena Karaseva, Viktoria Kolodzhieva, Daniil Azarov, Yana Akhremenko, Lidia Tarasova, Alexei Tikhonov, Alexey Masharskiy, Lyudmila Zueva, Alexander Suvorov
Enterococcus faecium 58m is a putative ancient nonpathogenic strain isolated from the intestinal content of an adult woolly mammoth (Mammuthus primigenius). Here, we report its draft genome sequence, consisting of 60 contigs. In silico genomic analysis was performed to determine the genetic features and pathogenic potential of this microorganism.
2016: Genome Announcements
https://www.readbyqxmd.com/read/26840445/was-frozen-mammoth-or-giant-ground-sloth-served-for-dinner-at-the-explorers-club
#20
Jessica R Glass, Matt Davis, Timothy J Walsh, Eric J Sargis, Adalgisa Caccone
Accounts of woolly mammoths (Mammuthus primigenius) preserved so well in ice that their meat is still edible have a long history of intriguing the public and influencing paleontological thought on Quaternary extinctions and climate, with some scientists resorting to catastrophism to explain the instantaneous freezing necessary to preserve edible meat. Famously, members of The Explorers Club purportedly dined on frozen mammoth from Alaska, USA, in 1951. This event, well received by the press and general public, became an enduring legend for the Club and popularized the notorious annual tradition of serving rare and exotic food at Club dinners that continues to this day...
2016: PloS One
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