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conservation genetics

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https://www.readbyqxmd.com/read/28431248/spontaneous-chitin-accumulation-in-airways-and-age-related-fibrotic-lung-disease
#1
Steven J Van Dyken, Hong-Erh Liang, Ram P Naikawadi, Prescott G Woodruff, Paul J Wolters, David J Erle, Richard M Locksley
The environmentally widespread polysaccharide chitin is degraded and recycled by ubiquitous bacterial and fungal chitinases. Although vertebrates express active chitinases from evolutionarily conserved loci, their role in mammalian physiology is unclear. We show that distinct lung epithelial cells secrete acidic mammalian chitinase (AMCase), which is required for airway chitinase activity. AMCase-deficient mice exhibit premature morbidity and mortality, concomitant with accumulation of environmentally derived chitin polymers in the airways and expression of pro-fibrotic cytokines...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28431246/fatty-acids-regulate-germline-sex-determination-through-acs-4-dependent-myristoylation
#2
Hongyun Tang, Min Han
Fat metabolism has been linked to fertility and reproductive adaptation in animals and humans, and environmental sex determination potentially plays a role in the process. To investigate the impact of fatty acids (FA) on sex determination and reproductive development, we examined and observed an impact of FA synthesis and mobilization by lipolysis in somatic tissues on oocyte fate in Caenorhabditis elegans. The subsequent genetic analysis identified ACS-4, an acyl-CoA synthetase and its FA-CoA product, as key germline factors that mediate the role of FA in promoting oocyte fate through protein myristoylation...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28430826/geographic-origin-and-individual-assignment-of-shorea-platyclados-dipterocarpaceae-for-forensic-identification
#3
Chin Hong Ng, Soon Leong Lee, Lee Hong Tnah, Kevin Kit Siong Ng, Chai Ting Lee, Bibian Diway, Eyen Khoo
The development of timber tracking methods based on genetic markers can provide scientific evidence to verify the origin of timber products and fulfill the growing requirement for sustainable forestry practices. In this study, the origin of an important Dark Red Meranti wood, Shorea platyclados, was studied by using the combination of seven chloroplast DNA and 15 short tandem repeats (STRs) markers. A total of 27 natural populations of S. platyclados were sampled throughout Malaysia to establish population level and individual level identification databases...
2017: PloS One
https://www.readbyqxmd.com/read/28430023/harnessing-effector-triggered-immunity-for-durable-disease-resistance
#4
Meixiang Zhang, Gitta Coaker
Genetic control of plant diseases has traditionally included the deployment of single immune receptors with nucleotide-binding leucine-rich repeat (NLR) domain architecture. These NLRs recognize corresponding pathogen effector proteins inside plant cells, resulting in effector-triggered immunity (ETI). Although ETI triggers robust resistance, deployment of single NLRs can be rapidly overcome by pathogen populations within a single or a few growing seasons. In order to generate more durable disease resistance against devastating plant pathogens, a multi-tiered strategy that incorporates stacked NLRs combined with other sources of disease resistance is necessary...
April 21, 2017: Phytopathology
https://www.readbyqxmd.com/read/28429848/stuck-in-fragments-population-genetics-of-the-endangered-collared-brown-lemur-eulemur-collaris-in-the-malagasy-littoral-forest
#5
Stefania Bertoncini, Jacopo D'Ercole, Francesca Brisighelli, Jean-Baptiste Ramanamanjato, Cristian Capelli, Sergio Tofanelli, Giuseppe Donati
OBJECTIVES: The Endangered collared brown lemur (Eulemur collaris) is the largest primate living in the littoral forest of southeastern Madagascar, a top priority habitat for biodiversity conservation on the island. Because this lemur is a key seed-disperser, an evaluation of the structure and connectivity of the populations surviving in the forest fragments is urgently needed to guide conservation plans. MATERIALS AND METHODS: Genetic variability at autosomal microsatellites and mitochondrial DNA was investigated in a total of 49 collared brown lemurs sampled by non-invasive methods in three littoral forest fragments and in the nearby lowland humid forest...
April 21, 2017: American Journal of Physical Anthropology
https://www.readbyqxmd.com/read/28429742/crossing-lines-a-multidisciplinary-framework-for-assessing-connectivity-of-hammerhead-sharks-across-jurisdictional-boundaries
#6
A Chin, C A Simpfendorfer, W T White, G J Johnson, R B McAuley, M R Heupel
Conservation and management of migratory species can be complex and challenging. International agreements such as the Convention on Migratory Species (CMS) provide policy frameworks, but assessments and management can be hampered by lack of data and tractable mechanisms to integrate disparate datasets. An assessment of scalloped (Sphyrna lewini) and great (Sphyrna mokarran) hammerhead population structure and connectivity across northern Australia, Indonesia and Papua New Guinea (PNG) was conducted to inform management responses to CMS and Convention on International Trade in Endangered Species listings of these species...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429737/the-glutamate-cystine-xct-antiporter-antagonizes-glutamine-metabolism-and-reduces-nutrient-flexibility
#7
Chun-Shik Shin, Prashant Mishra, Jeramie D Watrous, Valerio Carelli, Marilena D'Aurelio, Mohit Jain, David C Chan
As noted by Warburg, many cancer cells depend on the consumption of glucose. We performed a genetic screen to identify factors responsible for glucose addiction and recovered the two subunits of the xCT antiporter (system xc(-)), which plays an antioxidant role by exporting glutamate for cystine. Disruption of the xCT antiporter greatly improves cell viability after glucose withdrawal, because conservation of glutamate enables cells to maintain mitochondrial respiration. In some breast cancer cells, xCT antiporter expression is upregulated through the antioxidant transcription factor Nrf2 and contributes to their requirement for glucose as a carbon source...
April 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28428870/gene-expression-profiling-during-the-embryo-to-larva-transition-in-the-giant-red-sea-urchin-mesocentrotus-franciscanus
#8
Juan Diego Gaitán-Espitia, Gretchen E Hofmann
In echinoderms, major morphological transitions during early development are attributed to different genetic interactions and changes in global expression patterns that shape the regulatory program for the specification of embryonic territories. In order more thoroughly to understand these biological and molecular processes, we examined the transcriptome structure and expression profiles during the embryo-to-larva transition of a keystone species, the giant red sea urchin Mesocentrotus franciscanus. Using a de novo assembly approach, we obtained 176,885 transcripts from which 60,439 (34%) had significant alignments to known proteins...
April 2017: Ecology and Evolution
https://www.readbyqxmd.com/read/28427716/xenopus-egg-extract-a-powerful-tool-to-study-genome-maintenance-mechanisms
#9
REVIEW
Wouter S Hoogenboom, Daisy Klein Douwel, Puck Knipscheer
DNA repair pathways are crucial to maintain the integrity of our genome and prevent genetic diseases such as cancer. There are many different types of DNA damage and specific DNA repair mechanisms have evolved to deal with these lesions. In addition to these repair pathways there is an extensive signaling network that regulates processes important for repair, such as cell cycle control and transcription. Despite extensive research, DNA damage repair and signaling are not fully understood. In vitro systems such as the Xenopus egg extract system, have played, and still play, an important role in deciphering the molecular details of these processes...
April 17, 2017: Developmental Biology
https://www.readbyqxmd.com/read/28427341/reactive-oxygen-species-mediate-tapetal-programmed-cell-death-in-tobacco-and-tomato
#10
Shi-Xia Yu, Qiang-Nan Feng, Hong-Tao Xie, Sha Li, Yan Zhang
BACKGROUND: Hybrid vigor is highly valued in the agricultural industry. Male sterility is an important trait for crop breeding. Pollen development is under strict control of both gametophytic and sporophytic factors, and defects in this process can result in male sterility. Both in the dicot Arabidopsis and in the moncot rice, proper timing of programmed cell death (PCD) in the tapetum ensures pollen development. Dynamic ROS levels have been reported to control tapetal PCD, and thus pollen development, in Arabidopsis and rice...
April 20, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28427283/break-induced-replication-in-eukaryotes-mechanisms-functions-and-consequences
#11
Cynthia J Sakofsky, Anna Malkova
Break-induced replication (BIR) is an important pathway specializing in repair of one-ended double-strand DNA breaks (DSBs). This type of DSB break typically arises at collapsed replication forks or at eroded telomeres. BIR initiates by invasion of a broken DNA end into a homologous template followed by initiation of DNA synthesis that can proceed for hundreds of kilobases. This synthesis is drastically different from S-phase replication in that instead of a replication fork, BIR proceeds via a migrating bubble and is associated with conservative inheritance of newly synthesized DNA...
April 21, 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28426822/genomics-of-a-revived-breed-case-study-of-the-belgian-campine-cattle
#12
Liesbeth François, Katrien Wijnrocx, Frédéric G Colinet, Nicolas Gengler, Bettine Hulsegge, Jack J Windig, Nadine Buys, Steven Janssens
Through centuries of both natural and artificial selection, a variety of local cattle populations arose with highly specific phenotypes. However, the intensification and expansion of scale in animal production systems led to the predominance of a few highly productive cattle breeds. The loss of local populations is often considered irreversible and with them specific qualities and rare variants could be lost as well. Over these last years, the interest in these local breeds has increased again leading to increasing efforts to conserve these breeds or even revive lost populations, e...
2017: PloS One
https://www.readbyqxmd.com/read/28426790/lethality-of-mice-bearing-a-knockout-of-the-ngly1-gene-is-partially-rescued-by-the-additional-deletion-of-the-engase-gene
#13
Haruhiko Fujihira, Yuki Masahara-Negishi, Masaru Tamura, Chengcheng Huang, Yoichiro Harada, Shigeharu Wakana, Daisuke Takakura, Nana Kawasaki, Naoyuki Taniguchi, Gen Kondoh, Tadashi Yamashita, Yoko Funakoshi, Tadashi Suzuki
The cytoplasmic peptide:N-glycanase (Ngly1 in mammals) is a de-N-glycosylating enzyme that is highly conserved among eukaryotes. It was recently reported that subjects harboring mutations in the NGLY1 gene exhibited severe systemic symptoms (NGLY1-deficiency). While the enzyme obviously has a critical role in mammals, its precise function remains unclear. In this study, we analyzed Ngly1-deficient mice and found that they are embryonic lethal in C57BL/6 background. Surprisingly, the additional deletion of the gene encoding endo-β-N-acetylglucosaminidase (Engase), which is another de-N-glycosylating enzyme but leaves a single GlcNAc at glycosylated Asn residues, resulted in the partial rescue of the lethality of the Ngly1-deficient mice...
April 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28424761/sequencing-of-blaimp-carrying-incn2-plasmids-and-comparative-genomics-of-incn2-plasmids-harboring-class-1-integrons
#14
Xiaoyuan Jiang, Zhe Yin, Xiuyun Yin, Haihong Fang, Qiang Sun, Yigang Tong, Yuanhong Xu, Defu Zhang, Jiao Feng, Weijun Chen, Yajun Song, Jinglin Wang, Shuiping Chen, Dongsheng Zhou
This work presents the complete nucleotide sequences of p0801-IMP from Klebsiella pneumoniae, p7121-IMP from K. oxytoca, and p17285-IMP from Citrobacter freundii, which are recovered from three different cases of nosocomial infection. These three plasmids represent the first fully sequenced blaIMP-carrying IncN2 plasmids. Further comparative genomics analysis of all the five integron-carrying IncN2 plasmids p0801-IMP, p7121-IMP, p17285-IMP, pJIE137, and p34983-59.134kb indicates that they possess conserved IncN2 backbones with limited genetic variations with respect to gene content and organization...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28424460/generation-of-heritable-germline-mutations-in-the-jewel-wasp-nasonia-vitripennis-using-crispr-cas9
#15
Ming Li, Lauren Yun Cook Au, Deema Douglah, Abigail Chong, Bradley J White, Patrick M Ferree, Omar S Akbari
The revolutionary RNA-guided endonuclease CRISPR/Cas9 system has proven to be a powerful tool for gene editing in a plethora of organisms. Here, utilizing this system we developed an efficient protocol for the generation of heritable germline mutations in the parasitoid jewel wasp, Nasonia vitripennis, a rising insect model organism for the study of evolution, development of axis pattern formation, venom production, haplo-diploid sex determination, and host-symbiont interactions. To establish CRISPR-directed gene editing in N...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28423965/historical-mitochondrial-diversity-in-african-leopards-panthera-pardus-revealed-by-archival-museum-specimens
#16
Corey Anco, Sergios-Orestis Kolokotronis, Philipp Henschel, Seth W Cunningham, George Amato, Evon Hekkala
Once found throughout Africa and Eurasia, the leopard (Panthera pardus) was recently uplisted from Near Threatened to Vulnerable by the International Union for the Conservation of Nature (IUCN). Historically, more than 50% of the leopard's global range occurred in continental Africa, yet sampling from this part of the species' distribution is only sparsely represented in prior studies examining patterns of genetic variation at the continental or global level. Broad sampling to determine baseline patterns of genetic variation throughout the leopard's historical distribution is important, as these measures are currently used by the IUCN to direct conservation priorities and management plans...
April 19, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28423046/genetic-structure-and-isolation-by-altitude-in-rice-landraces-of-yunnan-china-revealed-by-nucleotide-and-microsatellite-marker-polymorphisms
#17
Di Cui, Cuifeng Tang, Jinmei Li, Xinxiang A, Tengqiong Yu, Xiaoding Ma, Enlai Zhang, Yanjie Wang, Guilan Cao, Furong Xu, Luyuan Dai, Longzhi Han, Hee-Jong Koh
Rice landraces, a genetic reservoir for varietal improvement, are developed by farmers through artificial selection during the long-term domestication process. To efficiently conserve, manage, and use such germplasm resources, an understanding of the genetic structure and differentiation of local rice landraces is required. In this study, we analyzed 188 accessions of rice landraces collected from localities across an altitudinal gradient from 425 to 2, 274 m above sea level in Yunnan Province, China using ten target genes and 48 SSR markers...
2017: PloS One
https://www.readbyqxmd.com/read/28423033/can-soda-ash-dumping-grounds-provide-replacement-habitats-for-digger-wasps-hymenoptera-apoidea-spheciformes
#18
Lucyna Twerd, Maciej Krzyżyński, Barbara Waldon-Rudzionek, Piotr Olszewski
BACKGROUND: Published sources document a loss of biodiversity at an extreme rate, mainly because natural and semi-natural ecosystems are becoming fragmented and isolated, thus losing their biological functions. These changes significantly influence biological diversity, which is a complex phenomenon that changes over time. Contemporary ecologists must therefore draw attention to anthropogenic replacement habitats and increase their conservation status. In our studies we show the positive role of soda ash dumping grounds as an alternative habitat for digger wasps, especially the thermophilic species...
2017: PloS One
https://www.readbyqxmd.com/read/28422966/taming-the-late-quaternary-phylogeography-of-the-eurasiatic-wild-ass-through-ancient-and-modern-dna
#19
E Andrew Bennett, Sophie Champlot, Joris Peters, Benjamin S Arbuckle, Silvia Guimaraes, Mélanie Pruvost, Shirli Bar-David, Simon J M Davis, Mathieu Gautier, Petra Kaczensky, Ralph Kuehn, Marjan Mashkour, Arturo Morales-Muñiz, Erich Pucher, Jean-François Tournepiche, Hans-Peter Uerpmann, Adrian Bălăşescu, Mietje Germonpré, Can Y Gündem, Mahmoud-Reza Hemami, Pierre-Elie Moullé, Aliye Ötzan, Margarete Uerpmann, Chris Walzer, Thierry Grange, Eva-Maria Geigl
Taxonomic over-splitting of extinct or endangered taxa, due to an incomplete knowledge of both skeletal morphological variability and the geographical ranges of past populations, continues to confuse the link between isolated extant populations and their ancestors. This is particularly problematic with the genus Equus. To more reliably determine the evolution and phylogeographic history of the endangered Asiatic wild ass, we studied the genetic diversity and inter-relationships of both extinct and extant populations over the last 100,000 years, including samples throughout its previous range from Western Europe to Southwest and East Asia...
2017: PloS One
https://www.readbyqxmd.com/read/28422147/construction-of-a-high-density-linkage-map-and-fine-mapping-of-qtls-for-growth-and-gonad-related-traits-in-blunt-snout-bream
#20
Shi-Ming Wan, Hong Liu, Bo-Wen Zhao, Chun-Hong Nie, Wei-Min Wang, Ze-Xia Gao
High-density genetic maps based on SNPs are essential for fine mapping loci controlling specific traits for fish species. Using restriction-site associated DNA tag sequencing (RAD-Seq) technology, we identified 42,784 SNPs evenly distributed across the Megalobrama amblycephala genome. Based on 2 parents and 187 intra-specific hybridization progenies, a total of 14,648 high-confidence SNPs were assigned to 24 consensus linkage groups (LGs) of maternal and paternal map. The total length of the integrated map was 3,258...
April 19, 2017: Scientific Reports
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