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https://www.readbyqxmd.com/read/28738077/consequences-of-severe-habitat-fragmentation-on-density-genetics-and-spatial-capture-recapture-analysis-of-a-small-bear-population
#1
Sean M Murphy, Ben C Augustine, Wade A Ulrey, Joseph M Guthrie, Brian K Scheick, J Walter McCown, John J Cox
Loss and fragmentation of natural habitats caused by human land uses have subdivided several formerly contiguous large carnivore populations into multiple small and often isolated subpopulations, which can reduce genetic variation and lead to precipitous population declines. Substantial habitat loss and fragmentation from urban development and agriculture expansion relegated the Highlands-Glades subpopulation (HGS) of Florida, USA, black bears (Ursus americanus floridanus) to prolonged isolation; increasing human land development is projected to cause ≥ 50% loss of remaining natural habitats occupied by the HGS in coming decades...
2017: PloS One
https://www.readbyqxmd.com/read/28738066/expansion-by-whole-genome-duplication-and-evolution-of-the-sox-gene-family-in-teleost-fish
#2
Emilien Voldoire, Frédéric Brunet, Magali Naville, Jean-Nicolas Volff, Delphine Galiana
It is now recognized that several rounds of whole genome duplication (WGD) have occurred during the evolution of vertebrates, but the link between WGDs and phenotypic diversification remains unsolved. We have investigated in this study the impact of the teleost-specific WGD on the evolution of the sox gene family in teleostean fishes. The sox gene family, which encodes for transcription factors, has essential role in morphology, physiology and behavior of vertebrates and teleosts, the current largest group of vertebrates...
2017: PloS One
https://www.readbyqxmd.com/read/28737009/non-additive-stabilization-by-halogenated-amino-acids-reveals-protein-plasticity-on-a-sub-angstrom-scale
#3
Azade S Hosseini, Christopher J Pace, Adam A Esposito, Jianmin Gao
It has been a long-standing goal to understand the structure-stability relationship of proteins, as optimal stability is essential for protein function and highly desirable for protein therapeutics. Halogenation has emerged as a minimally invasive strategy to probe the physical characteristics of proteins in solution, as well as enhance the structural stabilities of proteins for therapeutic applications. Although advances in synthetic chemistry and genetic code expansion have allowed for the rapid synthesis of proteins with diverse chemical sequences, much remains to be learned regarding the impact of these mutations on their structural integrity...
July 24, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28736585/late-onset-asymptomatic-pancreatic-neuroendocrine-tumor-a-case-report-on-the-phenotypic-expansion-for-men1
#4
Charu Kaiwar, Sarah K Macklin, Jennifer M Gass, Jessica Jackson, Eric W Klee, Stephanie L Hines, John A Stauffer, Paldeep S Atwal
BACKGROUND: Multiple endocrine neoplasia type 1 (MEN1) is a hereditary cancer syndrome associated with several endocrine as well as non-endocrine tumors and is caused by mutations in the MEN1 gene. Primary hyperparathyroidism affects the majority of MEN1 individuals by age 50 years. Additionally, MEN1 mutations trigger familial isolated hyperparathyroidism. We describe a seemingly unaffected 76-year-old female who presented to our Genetics Clinic with a family history of primary hyperparathyroidism and the identification of a pathogenic MEN1 variant...
2017: Hereditary Cancer in Clinical Practice
https://www.readbyqxmd.com/read/28735389/the-fundamental-role-of-reactive-oxygen-species-in-plant-stress-response
#5
Michael Liebthal, Karl-Josef Dietz
Chemical, physical, and biotic factors continuously vary in the natural environment. Such parameters are considered as stressors if the magnitude of their change exceeds the current acclimation norm of the plant. Activation of genetic programs allows for conditional expansion of the acclimation norm and depends on specific sensing mechanisms, intracellular communication, and regulation. The redox and reactive oxygen species (ROS) network plays a fundamental role in directing the acclimation response. These highly reactive compounds like H2O2 are generated and scavenged under normal conditions and participate in realizing a basal acclimation level...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28734067/range-instability-leads-to-cytonuclear-discordance-in-a-morphologically-cryptic-ground-squirrel-species-complex
#6
Mark A Phuong, Ke Bi, Craig Moritz
The processes responsible for cytonuclear discordance frequently remain unclear. Here, we employed an exon capture dataset and demographic methods to test hypotheses generated by species distribution models to examine how contrasting histories of range stability vs. fluctuation have caused cytonuclear concordance and discordance in ground squirrel lineages from the Otospermophilus beecheyi species complex. Previous studies in O. beecheyi revealed three morphologically cryptic and highly divergent mitochondrial DNA lineages (named the Northern, Central, and Southern lineages based on geography) with only the Northern lineage exhibiting concordant divergence for nuclear genes...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28734050/estimating-synchronous-demographic-changes-across-populations-using-habc-and-its-application-for-a-herpetological-community-from-northeastern-brazil
#7
Marcelo Gehara, Adrian Antonio Garda, Fernanda P Werneck, Eliana F Oliveira, Emanuel Masiero da Fonseca, Felipe Camurugi, Felipe M de Magalhães, Flávia Mol Lanna, Jack W Sites, Ricardo Marques, Ricardo Silveira-Filho, Vinícius A São Pedro, Guarino R Colli, Gabriel C Costa, Frank T Burbrink
Many studies propose that Quaternary climatic cycles contracted and /or expanded the ranges of species and biomes. Strong expansion-contraction dynamics of biomes presume concerted demographic changes of associated fauna. The analysis of temporal concordance of demographic changes can be used to test the influence of Quaternary climate on diversification processes. Hierarchical approximate Bayesian computation (hABC) is a powerful and flexible approach that models genetic data from multiple species, and can be used to estimate the temporal concordance of demographic processes...
July 22, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28733345/genes-of-cellular-components-of-morphogenesis-in-porcine-oocytes-before-and-after-ivm
#8
Joanna Budna, Artur Bryja, Piotr Celichowski, Rotem Kahan, Wiesława Kranc, Sylwia Ciesiółka, Marta Rybska, Sylwia Borys, Michal Jeseta, Dorota Bukowska, Paweł Antosik, Klaus Peter Brüssow, Małgorzata Bruska, Michał Nowicki, Maciej Zabel, Bartosz Kempisty
Proper oocyte maturation in mammals produces an oocyte capable of monospermic fertilization and embryo preimplantation. The cumulus-oocyte complexes (COCs), surrounding an oocyte, play a significant role in oocyte maturation. During this process, when the COCs undergo cumulus expansion wherein tightly compact cumulus cells (CCs) form a dispersed structure, permanent biochemical and molecular modifications occur in the maturing oocytes, indicating the gene expression between immature and mature oocytes differs significantly...
July 21, 2017: Reproduction: the Official Journal of the Society for the Study of Fertility
https://www.readbyqxmd.com/read/28732789/effect-of-ceftiofur-and-enrofloxacin-on-e-coli-sub-population-in-pig-gastrointestinal-tract
#9
Dachuan Lin, Kaichao Chen, Miaomiao Xie, Lianwei Ye, Edward Wai-Chi Chan, Sheng Chen
BACKGROUND: Antibiotic resistant sub-population of the gut microbiome in both human and animals may be enriched during antimicrobial treatment. METHODS: This study investigated how the size and antibiotic susceptibility profiles of antibiotic resistant sub-population organisms in the animal gastrointestinal tract changed upon exposure to different levels of ceftiofur and enrofloxacin by plating fecal samples collected from piglets before and after antibiotic treatment onto MacConkey agar containing 0...
July 18, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28729869/genetic-patterns-of-myrceugenia-correifolia-a-rare-species-of-fog-dependent-forests-of-mediterranean-chile-is-it-a-climatic-relict
#10
Fernanda Pérez, Luis F Hinojosa, Gioconda Peralta, Paz Montenegro, Carla Irarrázabal, Michel Cossio
Rare species frequently occur in areas with microclimatic conditions that are atypical for their regions, but that were more common in the past, and that probably have operated as climatic refugia for a long time. Myrceugenia correifolia is a rare arboreal species that grows in deep canyons and hilltops of the Coast Range of north-central Chile between 30° and 35°S. In the northern edge of its distribution M. correifolia grows in small patches of fog-dependent forest surrounding by xeric vegetation. These forest formations are thought to be remnants of an ancient and continuous rainforest that according to some authors became fragmented during aridization of the Neogene (Neogene relict) and to others during warm-dry cycles of the Pleistocene (glacial relicts)...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28729824/mouse-models-of-c9orf72-hexanucleotide-repeat-expansion-in-amyotrophic-lateral-sclerosis-frontotemporal-dementia
#11
REVIEW
Ranjan Batra, Chris W Lee
The presence of hexanucleotide repeat expansion (HRE) in the first intron of the human C9orf72 gene is the most common genetic cause underlying both familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Studies aimed at elucidating the pathogenic mechanisms associated of C9orf72 FTD and ALS (C9FTD/ALS) have focused on the hypothesis of RNA and protein toxic gain-of-function models, including formation of nuclear RNA foci containing GGGGCC (G4C2) HRE, inclusions containing dipeptide repeat proteins through a non-canonical repeat associated non-ATG (RAN) translation mechanism, and on loss-of-function of the C9orf72 protein...
2017: Frontiers in Cellular Neuroscience
https://www.readbyqxmd.com/read/28729708/new-mycobacterium-tuberculosis-beijing-clonal-complexes-in-china-revealed-by-phylogenetic-and-bayesian-population-structure-analyses-of-24-loci-miru-vntrs
#12
Chao Zheng, Yann Reynaud, Changsong Zhao, Thierry Zozio, Song Li, Dongxia Luo, Qun Sun, Nalin Rastogi
Beijing lineage of Mycobacterium tuberculosis constitutes the most predominant lineage in East Asia. Beijing epidemiology, evolutionary history, genetics are studied in details for years revealing probable origin from China followed by worldwide expansion, partially linked to higher mutation rate, hypervirulence, drug-resistance, and association with cases of mixed infections. Considering huge amount of data available for 24-loci Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats, we performed detailed phylogenetic and Bayesian population structure analyses of Beijing lineage strains in mainland China and Taiwan using available 24-loci MIRU-VNTR data extracted from publications or the SITVIT2 database (n = 1490)...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729659/identification-of-a-hybrid-myocardial-zone-in-the-mammalian-heart-after-birth
#13
Xueying Tian, Yan Li, Lingjuan He, Hui Zhang, Xiuzhen Huang, Qiaozhen Liu, Wenjuan Pu, Libo Zhang, Yi Li, Huan Zhao, Zhifu Wang, Jianhong Zhu, Yu Nie, Shengshou Hu, David Sedmera, Tao P Zhong, Ying Yu, Li Zhang, Yan Yan, Zengyong Qiao, Qing-Dong Wang, Sean M Wu, William T Pu, Robert H Anderson, Bin Zhou
Noncompaction cardiomyopathy is characterized by the presence of extensive trabeculations, which could lead to heart failure and malignant arrhythmias. How trabeculations resolve to form compact myocardium is poorly understood. Elucidation of this process is critical to understanding the pathophysiology of noncompaction disease. Here we use genetic lineage tracing to mark the Nppa(+) or Hey2(+) cardiomyocytes as trabecular and compact components of the ventricular wall. We find that Nppa(+) and Hey2(+) cardiomyocytes, respectively, from the endocardial and epicardial zones of the ventricular wall postnatally...
July 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28727934/phylogenomics-reveals-a-complex-evolutionary-history-of-lobed-leaf-white-oaks-in-western-north-america
#14
John D McVay, Duncan Hauser, Andrew L Hipp, Paul Manos
Quercus (oak) species hybridize in complex patterns that have yet to be fully explored with phylogenomic data. Analyses to date have recovered reasonable divergent patterns, suggesting that the impact of introgression may not always be obvious in inferred oak phylogenies. We explore this phenomenon using RADseq data for 136 samples representing 54 oak species by conducting phylogenetic analyses designed to distinguish signals of lineage diversification and hybridization, focusing on the lobed-leaf species Quercus gambelii, Q...
July 20, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28726130/transmission-network-characteristics-based-on-env-and-gag-sequences-from-msm-during-acute-hiv-1-infection-in-beijing-china
#15
Zhimin Zhang, Lili Dai, Yan Jiang, Kaidi Feng, Lifeng Liu, Wei Xia, Fengjiao Yu, Jun Yao, Wenge Xing, Lijun Sun, Tong Zhang, Hao Wu, Bin Su, Maofeng Qiu
Molecular epidemiology can be used to identify human immunodeficiency virus (HIV) transmission clusters, usually using pol sequence for analysis. In the present study, we explored appropriate parameters to construct a simple network using HIV env and gag sequences instead of pol sequences for constructing a phylogenetic tree and a genetic transmission subnetwork, which were used to identify individuals with many potential transmission links and to explore the evolutionary dynamics of the virus among men who have sex with men (MSM) in Beijing...
July 19, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28725414/snps-across-time-and-space-population-genomic-signatures-of-founder-events-and-epizootics-in-the-house-finch-haemorhous-mexicanus
#16
Allison J Shultz, Allan J Baker, Geoffrey E Hill, Paul M Nolan, Scott V Edwards
Identifying genomic signatures of natural selection can be challenging against a background of demographic changes such as bottlenecks and population expansions. Here, we disentangle the effects of demography from selection in the House Finch (Haemorhous mexicanus) using samples collected before and after a pathogen-induced selection event. Using ddRADseq, we genotyped over 18,000 SNPs across the genome in native pre-epizootic western US birds, introduced birds from Hawaii and the eastern United States, post-epizootic eastern birds, and western birds sampled across a similar time span...
October 2016: Ecology and Evolution
https://www.readbyqxmd.com/read/28722653/directing-visceral-white-adipocyte-precursors-to-a-thermogenic-adipocyte-fate-improves-insulin-sensitivity-in-obese-mice
#17
Chelsea Hepler, Mengle Shao, Jonathan Y Xia, Alexandra L Ghaben, Mackenzie J Pearson, Lavanya Vishvanath, Ankit X Sharma, Thomas S Morley, William L Holland, Rana K Gupta
Visceral adiposity confers significant risk for developing metabolic disease in obesity whereas preferential expansion of subcutaneous white adipose tissue (WAT) appears protective. Unlike subcutaneous WAT, visceral WAT is resistant to adopting a protective thermogenic phenotype characterized by the accumulation of Ucp1(+) beige/BRITE adipocytes (termed "browning"). In this study, we investigated the physiological consequences of browning murine visceral WAT by selective genetic ablation of Zfp423, a transcriptional suppressor of the adipocyte thermogenic program...
July 19, 2017: ELife
https://www.readbyqxmd.com/read/28720156/fmr1-cgg-repeat-expansion-mutation-detection-and-linked-haplotype-analysis-for-reliable-and-accurate-preimplantation-genetic-diagnosis-of-fragile-x-syndrome
#18
Indhu-Shree Rajan-Babu, Mulias Lian, Felicia S H Cheah, Min Chen, Arnold S C Tan, Ethiraj B Prasath, Seong Feei Loh, Samuel S Chong
Fragile X mental retardation 1 (FMR1) full-mutation expansion causes fragile X syndrome. Trans-generational fragile X syndrome transmission can be avoided by preimplantation genetic diagnosis (PGD). We describe a robust PGD strategy that can be applied to virtually any couple at risk of transmitting fragile X syndrome. This novel strategy utilises whole-genome amplification, followed by triplet-primed polymerase chain reaction (TP-PCR) for robust detection of expanded FMR1 alleles, in parallel with linked multi-marker haplotype analysis of 13 highly polymorphic microsatellite markers located within 1 Mb of the FMR1 CGG repeat, and the AMELX/Y dimorphism for gender identification...
July 19, 2017: Expert Reviews in Molecular Medicine
https://www.readbyqxmd.com/read/28720120/interrogating-the-unsequenceable-genomic-trinucleotide-repeat-disorders-by-long-read-sequencing
#19
Qian Liu, Peng Zhang, Depeng Wang, Weihong Gu, Kai Wang
Microsatellite expansion, such as trinucleotide repeat expansion (TRE), is known to cause a number of genetic diseases. Sanger sequencing and next-generation short-read sequencing are unable to interrogate TRE reliably. We developed a novel algorithm called RepeatHMM to estimate repeat counts from long-read sequencing data. Evaluation on simulation data, real amplicon sequencing data on two repeat expansion disorders, and whole-genome sequencing data generated by PacBio and Oxford Nanopore technologies showed superior performance over competing approaches...
July 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28719574/ancient-european-dog-genomes-reveal-continuity-since-the-early-neolithic
#20
Laura R Botigué, Shiya Song, Amelie Scheu, Shyamalika Gopalan, Amanda L Pendleton, Matthew Oetjens, Angela M Taravella, Timo Seregély, Andrea Zeeb-Lanz, Rose-Marie Arbogast, Dean Bobo, Kevin Daly, Martina Unterländer, Joachim Burger, Jeffrey M Kidd, Krishna R Veeramah
Europe has played a major role in dog evolution, harbouring the oldest uncontested Palaeolithic remains and having been the centre of modern dog breed creation. Here we sequence the genomes of an Early and End Neolithic dog from Germany, including a sample associated with an early European farming community. Both dogs demonstrate continuity with each other and predominantly share ancestry with modern European dogs, contradicting a previously suggested Late Neolithic population replacement. We find no genetic evidence to support the recent hypothesis proposing dual origins of dog domestication...
July 18, 2017: Nature Communications
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