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https://www.readbyqxmd.com/read/29792822/genetic-identity-in-genebanks-application-of-the-solcap-12k-snp-array-in-fingerprinting-and-diversity-analysis-in-the-global-in-trust-potato-collection
#1
David Ellis, Oswaldo Chavez, Joseph J Coombs, Julian V Soto, Rene Gomez, David S Douches, Ana Panta, Rocio Silvestre, Noelle Lynette Anglin
Breeders rely on genetic integrity of material from genebanks, however, mislabeling and errors in original data can occur. Paired samples of original material and their in vitro counterparts from 250 diverse potato landrace accessions from the International Potato Center (CIP), were fingerprinted using the Infinium 12K V2 Potato Array to confirm genetic identity and evaluate genetic diversity. Diploid, triploid, and tetraploid accessions were included representing seven cultivated potato taxa (Hawkes, 1990)...
May 24, 2018: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/29790980/contrasting-patterns-of-genomic-diversity-reveal-accelerated-genetic-drift-but-reduced-directional-selection-on-x-chromosome-in-wild-and-domestic-sheep-species
#2
Ze-Hui Chen, Min Zhang, Feng-Hua Lv, Xue Ren, Wen-Rong Li, Ming-Jun Liu, Kiwoong Nam, Michael W Bruford, Meng-Hua Li
Analyses of genomic diversity along the X chromosome and of its correlation with autosomal diversity can facilitate understanding of evolutionary forces in shaping sex-linked genomic architecture. Strong selective sweeps and accelerated genetic drift on the X-chromosome have been inferred in primates and other model species, but no such insight has yet been gained in domestic animals compared with their wild relatives. Here, we analyzed X-chromosome variability in a large ovine data set, including a BeadChip array for 943 ewes from the world's sheep populations and 110 whole genomes of wild and domestic sheep...
April 1, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29788330/the-evolution-of-gene-expression-underlying-vision-loss-in-cave-animals
#3
David B Stern, Keith A Crandall
Dissecting the evolutionary genetic processes underlying eye reduction and vision loss in obligate cave-dwelling organisms has been a long-standing challenge in evolutionary biology. Independent vision loss events in related subterranean organisms can provide critical insight into these processes as well as into the nature of convergent loss of complex traits. Advances in evolutionary developmental biology have illuminated the significant role of heritable gene expression variation in the evolution of new forms...
May 21, 2018: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29787744/repression-of-map3k1-expression-and-jnk-activity-by-canonical-wnt-signaling
#4
Qinghang Meng, Maureen Mongan, Jingjing Wang, Ying Xia
Morphogenesis is a complex and highly coordinated process orchestrated by temporal spatial activity of developmental pathways. How the different pathways interact to guide the developmental program remains an intriguing and open question. MAP3K1-JNK and Wnt are signaling pathways crucial for embryonic eyelid closure, an epithelial morphogenetic event conserved in mammals. Here we used a mouse model of eyelid development and genetic and biochemistry tools to investigate the relationships between the two pathways...
May 19, 2018: Developmental Biology
https://www.readbyqxmd.com/read/29786943/integrating-a-comprehensive-dna-barcode-reference-library-with-a-global-map-of-yews-taxus-l-for-forensic-identification
#5
Jie Liu, Richard I Milne, Michael Möller, Guang-Fu Zhu, Lin-Jiang Ye, Ya-Huang Luo, Jun-Bo Yang, Moses Cheloti Wambulwa, Chun-Neng Wang, De-Zhu Li, Lian-Ming Gao
Rapid and accurate identification of endangered species is a critical component of bio-surveillance and conservation management, and potentially policing illegal trades. However, this is often not possible using traditional taxonomy, especially where only small or pre-processed parts of plants are available. Reliable identification can be achieved via a comprehensive DNA barcode reference library, accompanied by precise distribution data. However, these require extensive sampling at spatial and taxonomic scales, which has rarely been achieved for cosmopolitan taxa...
May 22, 2018: Molecular Ecology Resources
https://www.readbyqxmd.com/read/29786924/reproductive-ecology-of-ocotea-catharinensis-an-endangered-tree-species
#6
Tiago Montagna, Juliano Zago da Silva, Tiago Georg Pickart, Maurício Sedrez Dos Reis
Ocotea catharinensis (Lauraceae) is an endangered tree species from the Brazilian Atlantic Rainforest. Currently, little is known about the reproductive ecology of this species. Aiming to propose conservation measures, we described aspects related to phenology, floral biology, pollination, seed dispersal, and mating system of O. catharinensis. We conducted phenological observations in 62 individuals for two years. In one reproductive event, we evaluated nectar production, stigmatic receptivity, and pollen viability...
May 22, 2018: Plant Biology
https://www.readbyqxmd.com/read/29786778/development-and-characterization-of-microsatellite-markers-for-endangered-species-stipa-pennata-poaceae-and-their-usefulness-in-intraspecific-delimitation
#7
Ewelina Klichowska, Monika Ślipiko, Marcin Nobis, Monika Szczecińska
Stipa pennata (Poaceae), has become a rare and endangered species in Central Europe due habitat loss and fragmentation. This species is characterized by high morphological variability, which has resulted in the description of numerous intraspecific taxa. The aim of present work is to develop microsatellite markers useful in population genetics studies as well as in intraspecific taxonomy of S. pennata s.l. We developed ten microsatellite markers using Illumina high-throughput. Polymorphism at each marker was evaluated using 4-15 individuals from four morphotypes of S...
May 21, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29786095/high-throughput-creation-and-functional-profiling-of-dna-sequence-variant-libraries-using-crispr-cas9-in-yeast
#8
Xiaoge Guo, Alejandro Chavez, Angela Tung, Yingleong Chan, Christian Kaas, Yi Yin, Ryan Cecchi, Santiago Lopez Garnier, Eric D Kelsic, Max Schubert, James E DiCarlo, James J Collins, George M Church
Construction and characterization of large genetic variant libraries is essential for understanding genome function, but remains challenging. Here, we introduce a Cas9-based approach for generating pools of mutants with defined genetic alterations (deletions, substitutions, and insertions) with an efficiency of 80-100% in yeast, along with methods for tracking their fitness en masse. We demonstrate the utility of our approach by characterizing the DNA helicase SGS1 with small tiling deletion mutants that span the length of the protein and a series of point mutations against highly conserved residues in the protein...
May 21, 2018: Nature Biotechnology
https://www.readbyqxmd.com/read/29784875/a-human-specific-truncated-%C3%AE-7-nicotinic-receptor-subunit-assembles-with-full-length-%C3%AE-7-and-forms-functional-receptors-with-different-stoichiometries
#9
Matías Lasala, Jeremías Corradi, Ariana Bruzzone, María Del Carmen Esandi, Cecilia Bouzat
The cholinergic α7 nicotinic receptor gene, CHRNA7, encodes a subunit that forms the homopentameric α7 receptor, involved in learning and memory. In humans, exons 5-10 in CHRNA7 are duplicated and fused to the FAM7A genetic element, giving rise to the hybrid gene CHRFAM7A. Its product, dupα7, is a truncated subunit lacking part of the N-terminal extracellular ligand-binding domain and is associated with neurological disorders, including schizophrenia, and immunomodulation.We combined dupα7 expression on mammalian cells with patch clamp recordings to understand its functional role...
May 21, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29784863/the-gpi-transamidase-complex-subunit-pbgpi16-of-plasmodium-berghei-is-important-for-inducing-experimental-cerebral-malaria
#10
Qingyang Liu, Yan Zhao, Li Zheng, Xiaotong Zhu, Liwang Cui, Yaming Cao
In animal models of experimental cerebral malaria (ECM), the glycosylphosphatidylinositols (GPIs) and GPI anchors are the major factors that induce nuclear factor kappa B (NF-κB) activation and proinflammatory responses, which contribute to malaria pathogenesis. GPIs and GPI anchors are transported to the cell surface via a process called GPI transamidation, which involves the GPI transamidase (GPI-T) complex. In this study, we showed that GPI16, one of the GPI-T subunits, is highly conserved among Plasmodium species...
May 21, 2018: Infection and Immunity
https://www.readbyqxmd.com/read/29783946/novel-flax-orbitide-derived-from-genetic-deletion
#11
Peta-Gaye Gillian Burnett, Lester Warren Young, Clara Marisa Olivia, Pramodkumar Dinkar Jadhav, Denis Paskal Okinyo-Owiti, Martin John Tarsisius Reaney
BACKGROUND: Flaxseed orbitides are homodetic plant cyclic peptides arising from ribosomal synthesis and post-translation modification (N to C cyclization), and lacking cysteine double bonds (Nat Prod Rep 30:108-160, 2013). Screening for orbitide composition was conducted on the flax core collection (FCC) grown at both Saskatoon, Saskatchewan and Morden, Manitoba over three growing seasons (2009-2011). Two flax (Linum usitatissimum L.) accessions 'Hollandia' (CN 98056) and 'Z 11637' (CN 98150) produce neither [1-9-NαC]-linusorb B2 (3) nor [1-9-NαC]-linusorb B3 (1)...
May 21, 2018: BMC Plant Biology
https://www.readbyqxmd.com/read/29781994/a-drosophila-in-vivo-injury-model-for-studying-neuroregeneration-in-the-peripheral-and-central-nervous-system
#12
Dan Li, Feng Li, Pavithran Guttipatti, Yuanquan Song
The regrowth capacity of damaged neurons governs neuroregeneration and functional recovery after nervous system trauma. Over the past few decades, various intrinsic and extrinsic inhibitory factors involved in the restriction of axon regeneration have been identified. However, simply removing these inhibitory cues is insufficient for successful regeneration, indicating the existence of additional regulatory machinery. Drosophila melanogaster, the fruit fly, shares evolutionarily conserved genes and signaling pathways with vertebrates, including humans...
May 5, 2018: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29781800/linkage-of-the-nit1c-gene-cluster-to-bacterial-cyanide-assimilation-as-a-nitrogen-source
#13
Lauren B Jones, Pallab Ghosh, Jung-Hyun Lee, Chia-Ni Chou, Daniel A Kunz
A genetic linkage between a conserved gene cluster (Nit1C) and the ability of bacteria to utilize cyanide as the sole nitrogen source was demonstrated for nine different bacterial species. These included three strains whose cyanide nutritional ability has formerly been documented (Pseudomonas fluorescens Pf11764, Pseudomonas putida BCN3 and Klebsiella pneumoniae BCN33), and six not previously known to have this ability [Burkholderia (Paraburkholderia) xenovorans LB400, Paraburkholderia phymatum STM815, Paraburkholderia phytofirmans PsJN, Cupriavidus (Ralstonia) eutropha H16, Gluconoacetobacter diazotrophicus PA1 5 and Methylobacterium extorquens AM1]...
May 21, 2018: Microbiology
https://www.readbyqxmd.com/read/29781169/effects-of-urbanization-on-the-population-structure-of-freshwater-turtles-across-the-united-states
#14
David R Bowne, Bradley J Cosentino, Laurel J Anderson, Christopher P Bloch, Sandra Cooke, Patrick W Crumrine, Jason Dallas, Alexandra Doran, Jerald J Dosch, Daniel L Druckenbrod, Richard D Durtsche, Danielle Garneau, Kristen S Genet, Todd S Fredericksen, Peter A Kish, Mary Beth Kolozsvary, Frank T Kuserk, Erin S Lindquist, Carol Mankiewicz, James G March, Timothy J Muir, K Greg Murray, Madeline N Santulli, Frank J Sicignano, Peter D Smallwood, Rebecca A Urban, Kathy Winnett-Murray, Craig R Zimmermann
Landscape-scale alterations that accompany urbanization may negatively affect the population structure of wildlife species such as freshwater turtles. Changes to nesting sites and higher mortality rates due to vehicular collisions and increased predator populations may particularly affect immature turtles and mature female turtles. We hypothesized that the proportions of adult female and immature turtles in a population will negatively correlate with landscape urbanization. As a collaborative effort of the Ecological Research as Education Network (EREN), we sampled freshwater turtle populations in 11 states across the central and eastern United States...
May 20, 2018: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/29780932/case-series-pyramidal-cataracts-intact-irides-and-nystagmus-from-three-novel-pax6-mutations
#15
Bharesh K Chauhan, Anagha Medsinge, Matthew P Baumgartner, Hannah L Scanga, Smaragda Kamakari, Eva Gajdosova, Carlos J Camacho, Ken K Nischal
Purpose: To investigate the association between novel PAX6 mutations to bilateral anterior pyramidal congenital cataracts (APyC), complete and intact irides, and nystagmus. Observations: This is a retrospective observational case series in a multi-center setting with genetic testing. Three female patients were diagnosed with bilateral APyC, intact irides and nystagmus. Genetic testing identified the three patients had novel missense mutations in PAX6 - c.128C > T; p...
June 2018: American Journal of Ophthalmology Case Reports
https://www.readbyqxmd.com/read/29780368/-salmonella-enterica-prophage-sequence-profiles-reflect-genome-diversity-and-can-be-used-for-high-discrimination-subtyping
#16
Walid Mottawea, Marc-Olivier Duceppe, Andrée A Dupras, Valentine Usongo, Julie Jeukens, Luca Freschi, Jean-Guillaume Emond-Rheault, Jeremie Hamel, Irena Kukavica-Ibrulj, Brian Boyle, Alexander Gill, Elton Burnett, Eelco Franz, Gitanjali Arya, Joel T Weadge, Samantha Gruenheid, Martin Wiedmann, Hongsheng Huang, France Daigle, Sylvain Moineau, Sadjia Bekal, Roger C Levesque, Lawrence D Goodridge, Dele Ogunremi
Non-typhoidal Salmonella is a leading cause of foodborne illness worldwide. Prompt and accurate identification of the sources of Salmonella responsible for disease outbreaks is crucial to minimize infections and eliminate ongoing sources of contamination. Current subtyping tools including single nucleotide polymorphism (SNP) typing may be inadequate, in some instances, to provide the required discrimination among epidemiologically unrelated Salmonella strains. Prophage genes represent the majority of the accessory genes in bacteria genomes and have potential to be used as high discrimination markers in Salmonella ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29779253/community-based-native-seed-production-for-restoration-in-brazil-the-role-of-science-and-policy
#17
Isabel B Schmidt, Danilo I de Urzedo, Fatima C M Piña-Rodrigues, Daniel L M Vieira, Gustavo M de Rezende, Alexandre B Sampaio, Rodrigo G P Junqueira
Large-scale restoration programs in the tropics require large volumes of high quality, genetically diverse and locally adapted seeds from large number of species. However, scarcity of native seeds is a critical restriction to achieve restoration targets. In this paper, we analyze three successful community-based networks that supply native seeds and seedlings for Brazilian Amazon and Cerrado restoration projects. In addition, we propose directions to promote local participation, legal, technical and commercialization issues for upscaling the market of native seeds for restoration with high quality and social justice...
May 20, 2018: Plant Biology
https://www.readbyqxmd.com/read/29779236/arabidopsis-inositol-phosphate-kinases-ipk1-and-itpk1-constitute-a-metabolic-pathway-in-maintaining-phosphate-homeostasis
#18
Hui-Fen Kuo, Yu-Ying Hsu, Wei-Chi Lin, Kai-Yu Chen, Teun Munnik, Charles A Brearley, Tzyy-Jen Chiou
Emerging studies have implicated a close link between inositol phosphate (InsP) metabolism and cellular phosphate (Pi ) homeostasis in eukaryotes; however, whether a common InsP species is deployed as an evolutionarily conserved metabolic messenger to mediate Pi signaling remains unknown. Here, using genetics and InsP profiling combined with Pi starvation response (PSR) analysis in Arabidopsis thaliana, we showed that the kinase activity of inositol pentakisphosphate 2-kinase (IPK1), an enzyme required for phytate (inositol hexakisphosphates; InsP6 ) synthesis, is indispensable for maintaining Pi homeostasis under Pi -replete conditions, and inositol 1,3,4-trisphosphate 5/6-kinase 1 (ITPK1) plays an equivalent role...
May 19, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29779125/genetic-diversity-and-structure-of-a-rare-endemic-cactus-and-an-assessment-of-its-genetic-relationship-with-a-more-common-congener
#19
Niraj Rayamajhi, Jyotsna Sharma
Endemic, obligate outcrossing plant species with narrow geographic distributions and disjunct populations are prone to loss of genetic diversity. Simultaneously, delineating clear species boundaries is important for targeted conservation efforts. The rare and endemic cactus, Sclerocactus brevihamatus subsp. tobuschii (SBT), has a parapatric relationship with Sclerocactus brevihamatus subsp. brevihamatus (SBB) but genetic distance between the two taxa is unknown. We: (1) developed taxon-specific polymorphic microsatellites, (2) assessed genetic diversity within and among nine populations of SBT, and within one population of SBB, and (3) estimated the genetic relationship between the two subspecies...
May 19, 2018: Genetica
https://www.readbyqxmd.com/read/29778216/nitric-oxide-signalling-in-yeast
#20
Rika I Astuti, Ryo Nasuno, Hiroshi Takagi
Nitric oxide (NO) is a cellular signalling molecule widely conserved among organisms, including microorganisms such as bacteria, yeasts, and fungi, and higher eukaryotes such as plants and mammals. NO is mainly produced by the activities of NO synthase (NOS) or nitrite reductase (NIR). There are several NO detoxification systems, including NO dioxygenase (NOD) and S-nitrosoglutathione reductase (GSNOR). NO homeostasis, based on the balance between NO synthesis and degradation, is important for regulating its physiological functions, since an excess of NO causes nitrosative stress due to the high reactivity of NO and NO-derived compounds...
2018: Advances in Microbial Physiology
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