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https://www.readbyqxmd.com/read/28959177/ancient-permafrost-staphylococci-carry-antibiotic-resistance-genes
#1
Elena Kashuba, Alexey A Dmitriev, Shady Mansour Kamal, Ojar Melefors, Gennady Griva, Ute Römling, Ingemar Ernberg, Vladimir Kashuba, Anatoli Brouchkov
Background: Permafrost preserves a variety of viable ancient microorganisms. Some of them can be cultivated after being kept at subzero temperatures for thousands or even millions of years. Objective: To cultivate bacterial strains from permafrost. Design: We isolated and cultivated two bacterial strains from permafrost that was obtained at Mammoth Mountain in Siberia and attributed to the Middle Miocene. Bacterial genomic DNA was sequenced with 40-60× coverage and high-quality contigs were assembled. The first strain was assigned to Staphylococcus warneri species (designated MMP1) and the second one to Staphylococcus hominis species (designated MMP2), based on the classification of 16S ribosomal RNA genes and genomic sequences...
2017: Microbial Ecology in Health and Disease
https://www.readbyqxmd.com/read/28916375/bacterial-community-in-ancient-permafrost-alluvium-at-the-mammoth-mountain-eastern-siberia
#2
Anatoli Brouchkov, Marsel Kabilov, Svetlana Filippova, Olga Baturina, Victor Rogov, Valery Galchenko, Andrey Mulyukin, Oksana Fursova, Gennady Pogorelko
Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa...
December 15, 2017: Gene
https://www.readbyqxmd.com/read/28875067/high-incidence-of-cervical-ribs-indicates-vulnerable-condition-in-late-pleistocene-woolly-rhinoceroses
#3
Alexandra A E van der Geer, Frietson Galis
Mammals as a rule have seven cervical vertebrae, a number that remains remarkably constant. Changes of this number are associated with major congenital abnormalities (pleiotropic effects) that are, at least in humans, strongly selected against. Recently, it was found that Late Pleistocene mammoths (Mammuthus primigenius) from the North Sea have an unusually high incidence of abnormal cervical vertebral numbers, approximately ten times higher than that of extant elephants. Abnormal numbers were due to the presence of large cervical ribs on the seventh vertebra, indicating a homeotic change from a cervical rib-less vertebra into a thoracic rib-bearing vertebra...
2017: PeerJ
https://www.readbyqxmd.com/read/28754955/isotopic-analyses-suggest-mammoth-and-plant-in-the-diet-of-the-oldest-anatomically-modern-humans-from-far-southeast-europe
#4
Dorothée G Drucker, Yuichi I Naito, Stéphane Péan, Sandrine Prat, Laurent Crépin, Yoshito Chikaraishi, Naohiko Ohkouchi, Simon Puaud, Martina Lázničková-Galetová, Marylène Patou-Mathis, Aleksandr Yanevich, Hervé Bocherens
Relatively high (15)N abundances in bone collagen of early anatomically modern humans in Europe have often been interpreted as a specific consumption of freshwater resources, even if mammoth is an alternative high (15)N prey. At Buran-Kaya III, access to associated fauna in a secured archaeological context and application of recently developed isotopic analyses of individuals amino acids offer the opportunity to further examine this hypothesis. The site of Buran-Kaya III is located in south Crimea and has provided a rich archaeological sequence including two Upper Palaeolithic layers, from which human fossils were retrieved and directly dated as from 37...
July 28, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28746760/de-extinction-and-conservation-genetics-in-the-anthropocene
#5
Ronald Sandler
One interesting feature of de-extinction-particularly with respect to long-extinct species such as the passenger pigeon, thylacine, and mammoth-is that it does not fit neatly into the primary rationales for adopting novel ecosystem-management and species-conservation technologies and strategies: efficiency and necessity. The efficiency rationale is that the new technology or strategy enables conservation biologists to do what they already do more effectively. Why should researchers embrace novel information technologies? Because they allow scientists to better track, monitor, map, aggregate, and analyze species behaviors, biological systems, and human-environment interactions...
July 2017: Hastings Center Report
https://www.readbyqxmd.com/read/28706989/inactivation-of-thermogenic-ucp1-as-a-historical-contingency-in-multiple-placental-mammal-clades
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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...
August 1, 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
#14
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
#15
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
#16
(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
#17
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
#18
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
#19
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
#20
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
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