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conservation genetics

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https://www.readbyqxmd.com/read/28211534/in-vitro-differentiation-of-fertile-sperm-from-cryopreserved-spermatogonia-of-the-endangered-endemic-cyprinid-honmoroko-gnathopogon-caerulescens
#1
Shogo Higaki, Manami Shimada, Kazuaki Kawamoto, Takaaki Todo, Toshihiro Kawasaki, Ikuo Tooyama, Yasuhiro Fujioka, Noriyoshi Sakai, Tatsuyuki Takada
Many endemic fish species are threatened with extinction. Conservation strategies and the restoration of endemic fish after extinction must therefore be investigated. Although sperm cryopreservation is indispensable for the conservation of endangered fishes, the limited number of mature fish and limited availability (volume and period) of sperm from small endemic fish hinders the optimization and practical use of this material. In this report, we demonstrate the in vitro differentiation of fertile sperm from cryopreserved spermatogonia of juveniles of the endangered small cyprinid honmoroko (Gnathopogon caerulescens), which is endemic to Lake Biwa in Japan...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211527/depth-specific-fluctuations-of-gene-expression-and-protein-abundance-modulate-the-photophysiology-in-the-seagrass-posidonia-oceanica
#2
Gabriele Procaccini, Miriam Ruocco, Lázaro Marín-Guirao, Emanuela Dattolo, Christophe Brunet, Daniela D'Esposito, Chiara Lauritano, Silvia Mazzuca, Ilia Anna Serra, Letizia Bernardo, Amalia Piro, Sven Beer, Mats Björk, Martin Gullström, Pimchanok Buapet, Lina M Rasmusson, Paulo Felisberto, Sylvie Gobert, John W Runcie, João Silva, Irene Olivé, Monya M Costa, Isabel Barrote, Rui Santos
Here we present the results of a multiple organizational level analysis conceived to identify acclimative/adaptive strategies exhibited by the seagrass Posidonia oceanica to the daily fluctuations in the light environment, at contrasting depths. We assessed changes in photophysiological parameters, leaf respiration, pigments, and protein and mRNA expression levels. The results show that the diel oscillations of P. oceanica photophysiological and respiratory responses were related to transcripts and proteins expression of the genes involved in those processes and that there was a response asynchrony between shallow and deep plants probably caused by the strong differences in the light environment...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211522/structure-and-polymorphisms-of-the-major-histocompatibility-complex-in-the-oriental-stork-ciconia-boyciana
#3
Hiroki Tsuji, Yukio Taniguchi, Shintaro Ishizuka, Hirokazu Matsuda, Takahisa Yamada, Kazuaki Naito, Hiroaki Iwaisaki
The major histocompatibility complex (MHC) is highly polymorphic and plays a central role in the vertebrate immune system. Despite its functional consistency, the MHC genomic structure differs substantially among organisms. In birds, the MHCs of Galliformes and the Japanese crested ibis (Pelecaniformes) are well-characterized, but information about other avian MHCs remains scarce. The Oriental stork (Ciconia boyciana, order Ciconiiformes) is a large endangered migrant. The current Japanese population of this bird originates from a few founders; thus, understanding the genetic diversity among them is critical for effective population management...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28207953/sgs1-a-neomorphic-nac52-allele-impairing-ptgs-through-sgs3-down-regulation
#4
Nicolas Butel, Ivan Le Masson, Nathalie Bouteiller, Hervé Vaucheret, Taline Elmayan
Post-transcriptional gene silencing (PTGS) is a defense mechanism that targets invading nucleic acids from endogenous (transposons) or exogenous (pathogens, transgenes) origins. Genetic screens based on the reactivation of silenced transgenes have long been used to identify cellular PTGS components and regulators. Here we show that the first isolated PTGS-deficient mutant, sgs1, is impaired in the transcription factor NAC52. This mutant exhibits striking similarities with a mutant impaired in the H3K4me3 demethylase JMJ14 isolated from the same genetic screen...
February 16, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28207173/sensitivity-analysis-of-effective-population-size-to-demographic-parameters-in-house-sparrow-populations
#5
Marlene Waege Stubberud, Ane Marlene Myhre, Håkon Holand, Thomas Kvalnes, Thor Harald Ringsby, Bernt-Erik Saether, Henrik Jensen
The ratio between the effective and the census population size, Ne/N, is an important measure of the long-term viability and sustainability of a population. Understanding which demographic processes that affect Ne/N most will improve our understanding of how genetic drift and the probability of fixation of alleles is affected by demography. This knowledge may also be of vital importance in management of endangered populations and species. Here, we use data from 13 natural populations of house sparrow (Passer domesticus) in Norway to calculate the demographic parameters that determine Ne/N...
February 16, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28205536/genomic-structure-and-insertion-sites-of-helicobacter-pylori-prophages-from-various-geographical-origins
#6
Filipa F Vale, Alexandra Nunes, Mónica Oleastro, João P Gomes, Daniel A Sampaio, Raquel Rocha, Jorge M B Vítor, Lars Engstrand, Ben Pascoe, Elvire Berthenet, Samuel K Sheppard, Matthew D Hitchings, Francis Mégraud, Jamuna Vadivelu, Philippe Lehours
Helicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6-33.0 Kbp, consisting of 27-39 open reading frames...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28202815/covariation-in-levels-of-nucleotide-diversity-in-homologous-regions-of-the-avian-genome-long-after-completion-of-lineage-sorting
#7
Ludovic Dutoit, Nagarjun Vijay, Carina F Mugal, Christen M Bossu, Reto Burri, Jochen Wolf, Hans Ellegren
Closely related species may show similar levels of genetic diversity in homologous regions of the genome owing to shared ancestral variation still segregating in the extant species. However, after completion of lineage sorting, such covariation is not necessarily expected. On the other hand, if the processes that govern genetic diversity are conserved, diversity may potentially covary even among distantly related species. We mapped regions of conserved synteny between the genomes of two divergent bird species-collared flycatcher and hooded crow-and identified more than 600 Mb of homologous regions (66% of the genome)...
February 22, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28199447/population-structure-and-genetic-diversity-of-the-giant-anteater-myrmecophaga-tridactyla-myrmecophagidae-pilosa-in-brazil
#8
Camila L Clozato, Flávia R Miranda, Paula Lara-Ruiz, Rosane G Collevatti, Fabrício R Santos
The giant anteater (Myrmecophaga tridactyla, Pilosa, Linnaeus 1758) belongs to the mammalian order Pilosa and presents a large distribution along South America, occupying a great variety of habitats. It is listed in the IUCN Red List of threatened species as Vulnerable. Despite threatened, there is a lack of studies regarding its genetic variability. The aim of this study was to examine the genetic diversity and patterns of genetic structure within remaining populations. We analyzed 77 individuals from seven different populations distributed in four biomes across Brazil: Cerrado, Pantanal, Atlantic Forest and Amazon Forest...
February 13, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/28199404/loss-of-genes-related-to-nucleotide-excision-repair-ner-and-implications-for-reductive-genome-evolution-in-symbionts-of-deep-sea-vesicomyid-clams
#9
Shigeru Shimamura, Takashi Kaneko, Genki Ozawa, Mamiko Nishino Matsumoto, Takeru Koshiishi, Yoshihiro Takaki, Chiaki Kato, Ken Takai, Takao Yoshida, Katsunori Fujikura, James P Barry, Tadashi Maruyama
Intracellular thioautotrophic symbionts of deep-sea vesicomyid clams lack some DNA repair genes and are thought to be undergoing reductive genome evolution (RGE). In this study, we addressed two questions, 1) how these symbionts lost their DNA repair genes and 2) how such losses affect RGE. For the first question, we examined genes associated with nucleotide excision repair (NER; uvrA, uvrB, uvrC, uvrD, uvrD paralog [uvrDp] and mfd) in 12 symbionts of vesicomyid clams belonging to two clades (5 clade I and 7 clade II symbionts)...
2017: PloS One
https://www.readbyqxmd.com/read/28199145/characterization-and-virulence-potential-of-serogroup-o113-shiga-toxin-producing-escherichia-coli-strains-isolated-from-beef-and-cattle-in-the-united-states
#10
Peter Feng, Sabine Delannoy, David W Lacher, Joseph M Bosilevac, Patrick Fach
Shiga toxin-producing Escherichia coli (STEC) of serotype O113:H21 have caused severe diseases but are unusual in that they do not produce the intimin protein required for adherence to intestinal epithelial cells. Strains of serogroup O113 are one of the most common STEC found in ground beef and beef products in the United States, but their virulence potential is unknown. We used a microarray to characterize 65 O113 strains isolated in the United States from ground beef, beef trim, cattle feces, and fresh spinach...
February 15, 2017: Journal of Food Protection
https://www.readbyqxmd.com/read/28198511/rapid-communication-genetic-diversity-and-differentiation-in-natural-populations-of-arapaima-gigas-from-lower-amazon-revealed-by-microsatellites
#11
P F Fazzi-Gomes, N Melo, G Palheta, S Guerreiro, M Amador, A K Ribeiro-Dos-Santos, S Santos, I Hamoy
Genetic variability is one of the important criteria for species conservation decisions. This study aimed to analyze the genetic diversity and the population differentiation of two natural populations of Arapaima gigas, a species with a long history of being commercially exploited. We collected 87 samples of A. gigas from Grande Curuai Lake and Paru Lake, located in the Lower Amazon region of Amazônia, Brazil, and genotyped these samples using a multiplex panel of microsatellite markers. Our results showed that the populations of A...
February 8, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28198391/mcm5-a-new-actor-in-the-link-between-dna-replication-and-meier-gorlin-syndrome
#12
Annalisa Vetro, Salvatore Savasta, Annalisa Russo Raucci, Cristina Cerqua, Geppo Sartori, Ivan Limongelli, Antonella Forlino, Silvia Maruelli, Paola Perucca, Debora Vergani, Giuliano Mazzini, Andrea Mattevi, Lucia Anna Stivala, Leonardo Salviati, Orsetta Zuffardi
Meier-Gorlin syndrome (MGORS) is a rare disorder characterized by primordial dwarfism, microtia, and patellar aplasia/hypoplasia. Recessive mutations in ORC1, ORC4, ORC6, CDT1, CDC6, and CDC45, encoding members of the pre-replication (pre-RC) and pre-initiation (pre-IC) complexes, and heterozygous mutations in GMNN, a regulator of cell-cycle progression and DNA replication, have already been associated with this condition. We performed whole-exome sequencing (WES) in a patient with a clinical diagnosis of MGORS and identified biallelic variants in MCM5...
February 15, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28196534/comparative-genomics-reveals-high-biological-diversity-and-specific-adaptations-in-the-industrially-and-medically-important-fungal-genus-aspergillus
#13
Ronald P de Vries, Robert Riley, Ad Wiebenga, Guillermo Aguilar-Osorio, Sotiris Amillis, Cristiane Akemi Uchima, Gregor Anderluh, Mojtaba Asadollahi, Marion Askin, Kerrie Barry, Evy Battaglia, Özgür Bayram, Tiziano Benocci, Susanna A Braus-Stromeyer, Camila Caldana, David Cánovas, Gustavo C Cerqueira, Fusheng Chen, Wanping Chen, Cindy Choi, Alicia Clum, Renato Augusto Corrêa Dos Santos, André Ricardo de Lima Damásio, George Diallinas, Tamás Emri, Erzsébet Fekete, Michel Flipphi, Susanne Freyberg, Antonia Gallo, Christos Gournas, Rob Habgood, Matthieu Hainaut, María Laura Harispe, Bernard Henrissat, Kristiina S Hildén, Ryan Hope, Abeer Hossain, Eugenia Karabika, Levente Karaffa, Zsolt Karányi, Nada Kraševec, Alan Kuo, Harald Kusch, Kurt LaButti, Ellen L Lagendijk, Alla Lapidus, Anthony Levasseur, Erika Lindquist, Anna Lipzen, Antonio F Logrieco, Andrew MacCabe, Miia R Mäkelä, Iran Malavazi, Petter Melin, Vera Meyer, Natalia Mielnichuk, Márton Miskei, Ákos P Molnár, Giuseppina Mulé, Chew Yee Ngan, Margarita Orejas, Erzsébet Orosz, Jean Paul Ouedraogo, Karin M Overkamp, Hee-Soo Park, Giancarlo Perrone, Francois Piumi, Peter J Punt, Arthur F J Ram, Ana Ramón, Stefan Rauscher, Eric Record, Diego Mauricio Riaño-Pachón, Vincent Robert, Julian Röhrig, Roberto Ruller, Asaf Salamov, Nadhira S Salih, Rob A Samson, Erzsébet Sándor, Manuel Sanguinetti, Tabea Schütze, Kristina Sepčić, Ekaterina Shelest, Gavin Sherlock, Vicky Sophianopoulou, Fabio M Squina, Hui Sun, Antonia Susca, Richard B Todd, Adrian Tsang, Shiela E Unkles, Nathalie van de Wiele, Diana van Rossen-Uffink, Juliana Velasco de Castro Oliveira, Tammi C Vesth, Jaap Visser, Jae-Hyuk Yu, Miaomiao Zhou, Mikael R Andersen, David B Archer, Scott E Baker, Isabelle Benoit, Axel A Brakhage, Gerhard H Braus, Reinhard Fischer, Jens C Frisvad, Gustavo H Goldman, Jos Houbraken, Berl Oakley, István Pócsi, Claudio Scazzocchio, Bernhard Seiboth, Patricia A vanKuyk, Jennifer Wortman, Paul S Dyer, Igor V Grigoriev
BACKGROUND: The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS: We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera...
February 14, 2017: Genome Biology
https://www.readbyqxmd.com/read/28196485/rapid-evolution-of-genetic-and-phenotypic-divergence-in-atlantic-salmon-following-the-colonisation-of-two-new-branches-of-a-watercourse
#14
Arne Johan Jensen, Lars Petter Hansen, Bjørn Ove Johnsen, Sten Karlsson
BACKGROUND: Selection acts strongly on individuals that colonise a habitat and have phenotypic traits that deviate from the local optima. Our objective was to investigate the evolutionary rates in Atlantic salmon (Salmo salar) in a river system (the Vefsna watershed in Norway), fewer than 15 generations after colonisation of two new branches of the watercourse for spawning, which were made available by construction of fish ladders in 1889. METHODS: Differences in age and size were analysed using scale samples collected by anglers...
February 14, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28196402/pimelic-acid-the-first-precursor-of-the-bacillus-subtilis-biotin-synthesis-pathway-exists-as-the-free-acid-and-is-assembled-by-fatty-acid-synthesis
#15
Miglena Manandhar, John E Cronan
Biotin synthetic pathways are readily separated into two stages, synthesis of the seven carbon α, ω-dicarboxylic acid pimelate moiety and assembly of the fused heterocyclic rings. The biotin pathway genes responsible for pimelate moiety synthesis vary widely among bacteria whereas the ring synthesis genes are highly conserved. Bacillus subtilis seems to have redundant genes, bioI and bioW, for generation of the pimelate intermediate. Largely consistent with previous genetic studies we found that deletion of bioW caused a biotin auxotrophic phenotype whereas deletion of bioI did not...
February 14, 2017: Molecular Microbiology
https://www.readbyqxmd.com/read/28195213/spatial-assessment-of-wolf-dog-hybridization-in-a-single-breeding-period
#16
C Pacheco, J V López-Bao, E J García, F J Lema, L Llaneza, V Palacios, R Godinho
Understanding the dynamics of wolf-dog hybridization and delineating evidence-based conservation strategies requires information on the spatial extent of wolf-dog hybridization in real-time, which remains largely unknown. We collected 332 wolf-like scats over ca. 5,000km(2) in the NW Iberian Peninsula to evaluate wolf-dog hybridization at population level in a single breeding/pup-rearing season. Mitochondrial DNA (MtDNA) and 18 ancestry informative markers were used for species and individual identification, and to detect wolf-dog hybrids...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28194146/modulation-of-replicative-lifespan-in-cryptococcus-neoformans-implications-for-virulence
#17
Tejas Bouklas, Neena Jain, Bettina C Fries
The fungal pathogen, Cryptococcus neoformans, has been shown to undergo replicative aging. Old cells are characterized by advanced generational age and phenotypic changes that appear to mediate enhanced resistance to host and antifungal-based killing. As a consequence of this age-associated resilience, old cells accumulate during chronic infection. Based on these findings, we hypothesized that shifting the generational age of a pathogenic yeast population would alter its vulnerability to the host and affect its virulence...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28193840/co-chaperone-hsp70-hsp90-organizing-protein-hop-is-required-for-transposon-silencing-and-pirna-biogenesis
#18
Joseph A Karam, Rasesh Y Parikh, Dhananjaya Nayak, David Rosenkranz, Vamsi K Gangaraju
piRNAs are 26-30nt germ-line specific small non-coding RNAs that have evolutionarily conserved function in mobile genetic element (transposons) silencing and maintenance of genome integrity. Drosophila Hsp70/90 Organizing Protein Homolog (Hop), a co-chaperone, interacts with piRNA binding protein Piwi and mediates silencing of phenotypic variations. However, it is not known if Hop has a direct role in piRNA biogenesis and transposon silencing. Here, we show that knockdown of Hop in the germ-line nurse cells (GLKD) of Drosophila ovaries leads to activation of transposons...
February 13, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28193728/mobile-introns-shape-the-genetic-diversity-of-their-host-genes
#19
Jelena Repar, Tobias Warnecke
Self-splicing introns populate several highly conserved protein-coding genes in fungal and plant mitochondria. In fungi, many of these introns have retained their ability to spread to intron-free target sites, often assisted by intron-encoded endonucleases that initiate the homing process. Here, leveraging population genomic data from Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Lachancea kluyveri, we expose non-random patterns of genetic diversity in exons that border self-splicing introns. In particular, we show that, in all three species, the density of single nucleotide polymorphisms increases as one approaches a mobile intron...
February 13, 2017: Genetics
https://www.readbyqxmd.com/read/28193573/structure-and-function-of-hwe-hiska2-family-sensor-histidine-kinases
#20
REVIEW
Julien Herrou, Sean Crosson, Aretha Fiebig
Sensor histidine kinases regulate adaptive cellular responses to changes in the chemical or physical state of the environment. HWE/HisKA2-family kinases comprise a subset of histidine kinases that is defined by unique sequence motifs in both the catalytic and non-catalytic regions. Recent crystal structures have defined conserved intramolecular interactions that inform models of kinase regulation that are unique to the HWE/HisKA2 superfamily. Emerging genetic, biochemical and genomic data indicate that, unlike typical histidine kinases, HWE/HisKA2 kinases do not generally signal via classical DNA-binding response regulators...
February 10, 2017: Current Opinion in Microbiology
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