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https://www.readbyqxmd.com/read/28650986/evolutionary-history-and-phylogeographic-relationships-of-shrews-from-sorex-araneus-group
#1
Paweł Mackiewicz, Magdalena Moska, Heliodor Wierzbicki, Przemysław Gagat, Dorota Mackiewicz
Shrews of the Sorex genus are an evolutionarily successful group that includes more than 77 species widely distributed in Eurasia and North America. The genus is one of the rare cases where karyotypic changes reflect well the evolutionary relationships among its species. The taxa showing the greatest variation in karyotype are usually classified into the Sorex araneus group. Its evolution was associated with chromosomal rearrangements, which could have promoted fast diversification of this group into many chromosomal races and species...
2017: PloS One
https://www.readbyqxmd.com/read/28649328/spatiotemporal-variation-in-mechanisms-driving-regional-scale-population-dynamics-of-a-threatened-grassland-bird
#2
Danielle M Ethier, Nicola Koper, Thomas D Nudds
To achieve national population targets for migratory birds, landscape-level conservation approaches are increasingly encouraged. However, knowledge of the mechanisms that drive spatiotemporal patterns in population dynamics are needed to inform scale-variant policy development. Using hierarchical Bayesian models and variable selection, we determined by which mechanism(s), and to what extent, changes in quantity and quality of surrogate grassland habitats contributed to regional variation in population trends of an obligatory grassland bird, Bobolink (Dolichonyx oryzivorous)...
June 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28647735/uniparental-disomy-of-chromosome-15-in-two-cases-by-chromosome-microarray-a-lesson-worth-thinking
#3
Shu Liu, Kaihui Zhang, Fengling Song, Yali Yang, Yuqiang Lv, Min Gao, Yi Liu, Zhongtao Gai
Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are neurogenetic disorders caused by loss of function of the imprinted genes at 15q11q13. A 5-7 Mb paternal/maternal deletion of chromosomal region 15q11.2q13 is the major genetic cause of PWS/AS, but in a small group of patients, the PWS/AS phenotype can result from maternal/paternal uniparental disomy (UPD) of chromosome 15. Various mechanisms leading to UPD include gametic complementation, trisomy rescue, and compensatory UPD, which can be inferred from the pattern of uniparental heterodisomy (heteroUPD) or uniparental isodisomy (isoUPD)...
June 24, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28646918/diurnal-cycling-of-rhizosphere-bacterial-communities-is-associated-with-shifts-in-carbon-metabolism
#4
Christopher Staley, Abigail P Ferrieri, Malak M Tfaily, Yaya Cui, Rosalie K Chu, Ping Wang, Jared B Shaw, Charles K Ansong, Heather Brewer, Angela D Norbeck, Meng Markillie, Fernanda do Amaral, Thalita Tuleski, Tomás Pellizzaro, Beverly Agtuca, Richard Ferrieri, Susannah G Tringe, Ljiljana Paša-Tolić, Gary Stacey, Michael J Sadowsky
BACKGROUND: The circadian clock regulates plant metabolic functions and is an important component in plant health and productivity. Rhizosphere bacteria play critical roles in plant growth, health, and development and are shaped primarily by soil communities. Using Illumina next-generation sequencing and high-resolution mass spectrometry, we characterized bacterial communities of wild-type (Col-0) Arabidopsis thaliana and an acyclic line (OX34) ectopically expressing the circadian clock-associated cca1 transcription factor, relative to a soil control, to determine how cycling dynamics affected the microbial community...
June 24, 2017: Microbiome
https://www.readbyqxmd.com/read/28645249/comparative-transcriptomic-analysis-of-the-evolution-and-development-of-flower-size-in-saltugilia-polemoniaceae
#5
Jacob B Landis, Douglas E Soltis, Pamela S Soltis
BACKGROUND: Flower size varies dramatically across angiosperms, representing innovations over the course of >130 million years of evolution and contributing substantially to relationships with pollinators. However, the genetic underpinning of flower size is not well understood. Saltugilia (Polemoniaceae) provides an excellent non-model system for extending the genetic study of flower size to interspecific differences that coincide with variation in pollinators. RESULTS: Using targeted gene capture methods, we infer phylogenetic relationships among all members of Saltugilia to provide a framework for investigating the genetic control of flower size differences via RNA-Seq de novo assembly...
June 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28645168/genomic-reconstruction-of-the-history-of-native-sheep-reveals-the-peopling-patterns-of-nomads-and-the-expansion-of-early-pastoralism-in-east-asia
#6
Yong-Xin Zhao, Ji Yang, Feng-Hua Lv, Xiao-Ju Hu, Xing-Long Xie, Min Zhang, Wen-Rong Li, Ming-Jun Liu, Yu-Tao Wang, Jin-Quan Li, Yong-Gang Liu, Yan-Ling Ren, Feng Wang, EEr Hehua, Juha Kantanen, Johannes Arjen Lenstra, Jian-Lin Han, Meng-Hua Li
China has a rich resource of native sheep (Ovis aries) breeds associated with historical movements of several nomadic societies. However, the history of sheep and the associated nomadic societies in ancient China remains poorly understood. Here, we studied the genomic diversity of Chinese sheep using genome-wide SNPs, mitochondrial and Y-chromosomal variations in more than 1,000 modern samples. Population genomic analyses combined with archaeological records and historical ethnic demographics data revealed genetic signatures of their origins, secondary expansions and admixtures, thereby revealing the peopling patterns of nomads and the expansion of early pastoralism in East Asia...
June 22, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/28637861/epidemic-and-endemic-pathogen-dynamics-correspond-to-distinct-host-population-microbiomes-at-a-landscape-scale
#7
Andrea J Jani, Roland A Knapp, Cheryl J Briggs
Infectious diseases have serious impacts on human and wildlife populations, but the effects of a disease can vary, even among individuals or populations of the same host species. Identifying the reasons for this variation is key to understanding disease dynamics and mitigating infectious disease impacts, but disentangling cause and correlation during natural outbreaks is extremely challenging. This study aims to understand associations between symbiotic bacterial communities and an infectious disease, and examines multiple host populations before or after pathogen invasion to infer likely causal links...
June 28, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28636089/geographic-substructure-in-craniometric-estimates-of-admixture-for-contemporary-american-populations
#8
Bridget F B Algee-Hewitt
OBJECTIVES: This study investigates heterogeneity in craniometrically-derived estimates of admixture in order to reveal population substructure in a sample of Black, White, Hispanic, and Native American individuals from the FDB. It reports evidence of spatial trends in population-specific patterns of admixture and contextualizes its results in terms of demographic diversity in the United States. MATERIALS AND METHODS: The FDB was sampled to capture the population variation within forensic casework, skeletal collections, and the U...
June 21, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28634295/population-genomic-inference-of-the-strength-and-timing-of-selection-against-gene-flow
#9
Simon Aeschbacher, Jessica P Selby, John H Willis, Graham Coop
The interplay of divergent selection and gene flow is key to understanding how populations adapt to local environments and how new species form. Here, we use DNA polymorphism data and genome-wide variation in recombination rate to jointly infer the strength and timing of selection, as well as the baseline level of gene flow under various demographic scenarios. We model how divergent selection leads to a genome-wide negative correlation between recombination rate and genetic differentiation among populations...
June 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28631370/microbial-manganese-iii-reduction-fueled-by-anaerobic-acetate-oxidation
#10
Nadia Szeinbaum, Hui Lin, Jay A Brandes, Martial Taillefert, Jennifer B Glass, Thomas J DiChristina
Soluble manganese in the intermediate +III oxidation state (Mn(3+) ) is a newly identified oxidant in anoxic environments, whereas acetate is a naturally abundant substrate that fuels microbial activity. Microbial populations coupling anaerobic acetate oxidation to Mn(3+) reduction, however, have yet to be identified. We isolated a Shewanella strain capable of oxidizing acetate anaerobically with Mn(3+) as the electron acceptor, and confirmed this phenotype in other strains,. This metabolic connection between acetate and soluble Mn(3+) represents a new biogeochemical link between carbon and manganese cycles...
June 19, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/28630393/sample-size-re-estimation-without-un-blinding-for-time-to-event-outcomes-in-oncology-clinical-trials
#11
Huang Lihong, Bai Jianling, Yu Hao, Chen Feng
Sample size re-estimation is essential in oncology studies. However, the use of blinded sample size reassessment for survival data has been rarely reported. Based on the density function of the exponential distribution, an expectation-maximization (EM) algorithm of the hazard ratio was derived, and several simulation studies were used to verify its applications. The method had obvious variation in the hazard ratio estimates and overestimation for the relatively small hazard ratios. Our studies showed that the stability of the EM estimation results directly correlated with the sample size, the convergence of the EM algorithm was impacted by the initial values, and a balanced design produced the best estimates...
June 20, 2017: Journal of Biomedical Research
https://www.readbyqxmd.com/read/28630130/how-a-genetically-stable-extremophile-evolves-modes-of-genome-diversification-in-the-archaeon-sulfolobus-acidocaldarius
#12
Dominic Mao, Dennis W Grogan
In order to analyze in molecular terms how Sulfolobus genomes diverge, damage-induced mutations and natural polymorphisms (PMs) were identified in laboratory constructs and wild-type isolates, respectively, of Sulfolobus acidocaldarius Among wild-type isolates drawn from one local population, pairwise nucleotide divergence averaged 4 x 10(-6), which is about 0.15% of the corresponding divergence reported for Sulfolobus islandicus The most variable features of wild-type S. acidocaldarius genomes were homopolymer (mononucleotide) tracts and longer tandem repeats, consistent with the spontaneous mutations that occur under laboratory conditions...
June 19, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28629758/implications-of-the-gut-microbiota-in-vulnerability-to-the-social-avoidance-effects-of-chronic-social-defeat-in-male-mice
#13
Joanna Kasia Szyszkowicz, Alex Wong, Hymie Anisman, Zul Merali, Marie-Claude Audet
Appreciable evidence suggests that perturbations within the gut microbiome and the immune system may play a key role in the pathogenesis of depression stemming from earlier stressful experiences. In the present investigation we examined whether microbial changes in cecum contents were associated with social avoidance behaviors, a feature of depression, and pro-inflammatory variations among socially stressed mice. Male C57BL/6 mice experienced social defeat or a control condition once a day for 10 consecutive days...
June 16, 2017: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/28627970/genome-wide-codon-usage-profiling-of-ocular-infective-chlamydia-trachomatis-serovars-and-drug-target-identification
#14
Anupriya Sadhasivam, Umashankar Vetrivel
Chlamydia trachomatis (C.t) is a gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B & C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC...
June 19, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28626457/characterization-of-novel-integrons-in1085-and-in1086-and-the-surrounding-genes-in-plasmids-from-enterobacteriaceae-and-the-role-for-attcaada16-structural-features-during-atti1-%C3%A3-attc-integration
#15
Dongguo Wang, Wei Hou, Jiayu Chen, Linjun Yang, Zhihui Liu, Zhe Yin, Jiao Feng, Dongsheng Zhou
Novel class 1 integrons In1085 and In1086, containing the class D β-lactamase -encoding gene blaOXA, were identified in clinical enterobacterial strains. In this study, we aimed to characterize the genetic contexts of In1085 and In1086, with the goal of identifying putative mechanisms of integron mobilization. Four plasmids, approximately 5.3, 5.3, 5.7, and 6.6 kb, from 71 clinical Enterobacteriaceae strains were found to contain class 1 integrons (In37, In62, In1085, and In1086, respectively). Two of these plasmids, pEco336 and pNsa292, containing In1085 and In1086, respectively, were further characterized by antibiotic susceptibility testing, conjugation experiments, PCR, sequencing, and gene mapping...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28625360/hypoxia-primed-placental-mesenchymal-stem-cells-for-wound-healing
#16
Suja Ann Mathew, Bhawna Chandravanshi, Ramesh Bhonde
AIMS: To investigate how Placental Mesenchymal Stem Cells (P-MSCs) would adapt themselves and survive under hypoxic conditions which are prevalent in most injury sites. MAIN METHODS: P-MSCs were isolated from term placenta and characterised under normoxia and hypoxia (2-2.5% O2). Cells were examined for morphology and surface marker variations by flow cytometry analysis. Glucose stimulated insulin secretion was assayed by Insulin ELISA Kit. Gene expression levels were estimated using Real Time PCR for hypoxia inducible factor1 alpha, Insulin (INS), Glucose transporters (GLUT-1, GLUT-2 and GLUT-3), Adhesion Proteins- Integrins, Fibronectin1 (FN1), E-Cadherin (CDH1), and N-Cadherin (CDH2) and angiogenesis marker VEGFA...
June 15, 2017: Life Sciences
https://www.readbyqxmd.com/read/28623316/revealing-protein-networks-and-gene-drug-connectivity-in-cancer-from-direct-information
#17
Xian-Li Jiang, Emmanuel Martinez-Ledesma, Faruck Morcos
The connection between genetic variation and drug response has long been explored to facilitate the optimization and personalization of cancer therapy. Crucial to the identification of drug response related genetic features is the ability to separate indirect correlations from direct correlations across abundant datasets with large number of variables. Here we analyzed proteomic and pharmacogenomic data in cancer tissues and cell lines using a global statistical model connecting protein pairs, genes and anti-cancer drugs...
June 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28622924/functional-associations-between-support-use-and-forelimb-shape-in-strepsirrhines-and-their-relevance-to-inferring-locomotor-behavior-in-early-primates
#18
Anne-Claire Fabre, Judit Marigó, Michael C Granatosky, Daniel Schmitt
The evolution of primates is intimately linked to their initial invasion of an arboreal environment. However, moving and foraging in this milieu creates significant mechanical challenges related to the presence of substrates differing in their size and orientation. It is widely assumed that primates are behaviorally and anatomically adapted to movement on specific substrates, but few explicit tests of this relationship in an evolutionary context have been conducted. Without direct tests of form-function relationships in living primates it is impossible to reliably infer behavior in fossil taxa...
July 2017: Journal of Human Evolution
https://www.readbyqxmd.com/read/28621366/cation-distribution-a-key-to-ascertain-the-magnetic-interactions-in-a-cobalt-substituted-mg-mn-nanoferrite-matrix
#19
Gagan Kumar, R K Kotnala, Jyoti Shah, Vijay Kumar, Arun Kumar, Pooja Dhiman, M Singh
The effect of Co(2+) substitution into nanocrystalline Mg-Mn ferrite synthesized by a solution combustion technique has been studied. The cation distribution has been inferred from X-ray diffraction, the magnetization technique, and Mössbauer spectroscopy. The X-ray analysis and cation distribution data have been used to investigate the detailed structural parameters such as hopping lengths, ionic radii of tetrahedral and octahedral sites, oxygen positional parameter, site bond as well as edge lengths, bond lengths, and bond angles...
June 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28620985/development-of-a-patient-and-institutional-based-model-for-estimation-of-operative-times-for-robot-assisted-radical-cystectomy-results-from-the-international-robotic-cystectomy-consortium
#20
Ahmed A Hussein, Paul R May, Youssef E Ahmed, Matthias Saar, Carl J Wijburg, Lee Richstone, Andrew Wagner, Timothy Wilson, Bertram Yuh, Joan Palou Redorta, Prokar Dasgupta, Omar Kawa, Mohammad Shamim Khan, Mani Menon, James O Peabody, Abolfazl Hosseini, Franco Gaboardi, Giovannalberto Pini, Francis Schanne, Alexandre Mottrie, Koon-Ho Rha, Ashok Hemal, Michael Stockle, John Kelly, Wei Shen Tan, Thomas J Maatman, Vassilis Poulakis, Jihad Kaouk, Abdullah Erdem Canda, Mevlana Derya Balbay, Peter Wiklund, Khurshid A Guru
OBJECTIVES: To design a methodology to predict operative times for robot-assisted radical cystectomy (RARC) based on variation in institutional, patient and disease characteristic to help in operating room scheduling and quality control. METHODS: The model included preoperative variables and therefore can be used for prediction of surgical times: institutional volume, age, gender, BMI, ASA Score, history of prior surgery and radiation, clinical stage, neoadjuvant chemotherapy, type, technique of diversion and the extent of lymph node dissection...
June 16, 2017: BJU International
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