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https://www.readbyqxmd.com/read/28706989/inactivation-of-thermogenic-ucp1-as-a-historical-contingency-in-multiple-placental-mammal-clades
#1
Michael J Gaudry, Martin Jastroch, Jason R Treberg, Michael Hofreiter, Johanna L A Paijmans, James Starrett, Nathan Wales, Anthony V Signore, Mark S Springer, Kevin L Campbell
Mitochondrial uncoupling protein 1 (UCP1) is essential for nonshivering thermogenesis in brown adipose tissue and is widely accepted to have played a key thermoregulatory role in small-bodied and neonatal placental mammals that enabled the exploitation of cold environments. We map ucp1 sequences from 133 mammals onto a species tree constructed from a ~51-kb sequence alignment and show that inactivating mutations have occurred in at least 8 of the 18 traditional placental orders, thereby challenging the physiological importance of UCP1 across Placentalia...
July 2017: Science Advances
https://www.readbyqxmd.com/read/28698111/phylogeny-and-biogeography-of-maclura-moraceae-and-the-origin-of-an-anachronistic-fruit
#2
Elliot M Gardner, Paya Sarraf, Evelyn W Williams, Nyree J C Zerega
BACKGROUND AND AIMS: Maclura (ca. 12 spp., Moraceae) is a widespread genus of trees and woody climbers found on five continents. Maclura pomifera, the Osage orange, is considered a classic example of an anachronistic fruit. Native to the central USA, the grapefruit-sized Osage oranges are unpalatable and have no known extant native dispersers, leading to speculation that the fruits were adapted to extinct megafauna. Our aim was to reconstruct the phylogeny, estimate divergence dates, and infer ancestral ranges of Maclura in order to test the monophyly of subgeneric classifications and to understand evolution and dispersal patterns in this globally distributed group...
July 8, 2017: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/28657198/family-science-talk-in-museums-predicting-children-s-engagement-from-variations-in-talk-and-activity
#3
Maureen A Callanan, Claudia L Castañeda, Megan R Luce, Jennifer L Martin
Children's developing reasoning skills are better understood within the context of their social and cultural lives. As part of a research-museum partnership, this article reports a study exploring science-relevant conversations of 82 families, with children between 3 and 11 years, while visiting a children's museum exhibit about mammoth bones, and in a focused one-on-one exploration of a "mystery object." Parents' use of a variety of types of science talk predicted children's conceptual engagement in the exhibit, but interestingly, different types of parent talk predicted children's engagement depending on the order of the two activities...
June 28, 2017: Child Development
https://www.readbyqxmd.com/read/28649261/the-role-of-sink-strength-and-nitrogen-availability-in-the-down-regulation-of-photosynthetic-capacity-in-field-grown-nicotiana-tabacum-l-at-elevated-co2-concentration
#4
Ursula M Ruiz-Vera, Amanda P De Souza, Stephen P Long, Donald R Ort
Down-regulation of photosynthesis is among the most common responses observed in C3 plants grown under elevated atmospheric CO2 concentration ([CO2]). Down-regulation is often attributed to an insufficient capacity of sink organs to use or store the increased carbohydrate production that results from the stimulation of photosynthesis by elevated [CO2]. Down-regulation can be accentuated by inadequate nitrogen (N) supply, which may limit sink development. While there is strong evidence for down-regulation of photosynthesis at elevated [CO2] in enclosure studies most often involving potted plants, there is little evidence for this when [CO2] is elevated fully under open-air field treatment conditions...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28463978/molecular-docking-studies-of-3-bromopyruvate-and-its-derivatives-to-metabolic-regulatory-enzymes-implication-in-designing-of-novel-anticancer-therapeutic-strategies
#5
Saveg Yadav, Shrish Kumar Pandey, Vinay Kumar Singh, Yugal Goel, Ajay Kumar, Sukh Mahendra Singh
Altered metabolism is an emerging hallmark of cancer, as malignant cells display a mammoth up-regulation of enzymes responsible for steering their bioenergetic and biosynthetic machinery. Thus, the recent anticancer therapeutic strategies focus on the targeting of metabolic enzymes, which has led to the identification of specific metabolic inhibitors. One of such inhibitors is 3-bromopyruvate (3-BP), with broad spectrum of anticancer activity due to its ability to inhibit multiple metabolic enzymes. However, the molecular characterization of its binding to the wide spectrum of target enzymes remains largely elusive...
2017: PloS One
https://www.readbyqxmd.com/read/28432954/fully-automatic-left-ventricular-segmentation-from-long-axis-cardiac-cine-mr-scans
#6
Rahil Shahzad, Qian Tao, Oleh Dzyubachyk, Marius Staring, Boudewijn P F Lelieveldt, Rob J van der Geest
With an increasing number of large-scale population-based cardiac magnetic resonance (CMR) imaging studies being conducted nowadays, there comes the mammoth task of image annotation and image analysis. Such population-based studies would greatly benefit from automated pipelines, with an efficient CMR image analysis workflow. The purpose of this work is to investigate the feasibility of using a fully-automatic pipeline to segment the left ventricular endocardium and epicardium simultaneously on two orthogonal (vertical and horizontal) long-axis cardiac cine MRI scans...
April 13, 2017: Medical Image Analysis
https://www.readbyqxmd.com/read/28400493/a-virus-induced-assay-for-functional-dissection-and-analysis-of-monocot-and-dicot-flowering-time-genes
#7
Cheng Qin, Weiwei Chen, Jiajia Shen, Linming Cheng, Femi Akande, Ke Zhang, Chen Yuan, Chunyang Li, Pengcheng Zhang, Nongnong Shi, Qi Cheng, Yule Liu, Stephen Jackson, Yiguo Hong
Virus-induced flowering (VIF) uses virus vectors to express Flowering Locus T (FT) to induce flowering in plants. This approach has recently attracted wide interest for its practical applications in accelerating breeding in crops and woody fruit trees. However, the insight into VIF and its potential as a powerful tool for dissecting florigenic proteins remained to be elucidated. Here, we describe the mechanism and further applications of Potato virus X (PVX)-based VIF in the short-day Nicotiana tabacum cultivar Maryland Mammoth...
June 2017: Plant Physiology
https://www.readbyqxmd.com/read/28369217/evolutionary-adaptation-revealed-by-comparative-genome-analysis-of-woolly-mammoths-and-elephants
#8
Sean D Smith, Joseph K Kawash, Spyros Karaiskos, Ian Biluck, Andrey Grigoriev
Comparative genomics studies typically limit their focus to single nucleotide variants (SNVs) and that was the case for previous comparisons of woolly mammoth genomes. We extended the analysis to systematically identify not only SNVs but also larger structural variants (SVs) and indels and found multiple mammoth-specific deletions and duplications affecting exons or even complete genes. The most prominent SV found was an amplification of RNase L (with different copy numbers in different mammoth genomes, up to 9-fold), involved in antiviral defense and inflammasome function...
March 22, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28330916/climate-warming-and-humans-played-different-roles-in-triggering-late-quaternary-extinctions-in-east-and-west-eurasia
#9
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
#10
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
#11
(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
#12
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
#13
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
#14
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
#15
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
#16
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...
March 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27997045/dynamics-of-escherichia-coli-type-i-e-crispr-spacers-over-42%C3%A2-000%C3%A2-years
#17
Ekaterina Savitskaya, Anna Lopatina, Sofia Medvedeva, Mikhail Kapustin, Sergey Shmakov, Alexey Tikhonov, Irena I Artamonova, Maria Logacheva, Konstantin Severinov
CRISPR-Cas are nucleic acid-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...
April 2017: Molecular Ecology
https://www.readbyqxmd.com/read/27587336/drivers-of-bacterial-genomes-plasticity-and-roles-they-play-in-pathogen-virulence-persistence-and-drug-resistance
#18
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
#19
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
#20
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
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