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Genetic diversity

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https://www.readbyqxmd.com/read/28635966/testing-models-of-refugial-isolation-colonization-and-population-connectivity-in-two-species-of-montane-salamanders
#1
S M Rovito, S D Schoville
Pleistocene glaciations have profoundly affected patterns of genetic diversity within many species. Temperate alpine organisms likely experienced dramatic range shifts, given that much of their habitat was glaciated during this time. While the effects of glaciations are relatively well understood, the spatial locations of refugia and processes that gave rise to current patterns of diversity are less well known. We use a microsatellite data set to test hypotheses of population connectivity and refugial isolation in the web-toed salamanders (Hydromantes) of the Sierra Nevada...
June 21, 2017: Heredity
https://www.readbyqxmd.com/read/28635965/identification-genealogical-structure-and-population-genetics-of-s-alleles-in-malus-sieversii-the-wild-ancestor-of-domesticated-apple
#2
X Ma, Z Cai, W Liu, S Ge, L Tang
The self-incompatibility (SI) gene that is specifically expressed in pistils encodes the SI-associated ribonuclease (S-RNase), functioning as the female-specificity determinant of a gametophytic SI system. Despite extensive surveys in Malus domestica, the S-alleles have not been fully investigated for Malus sieversii, the primary wild ancestor of the domesticated apple. Here we screened the M. sieversii S-alleles via PCR amplification and sequencing, and identified 14 distinct alleles in this species. By contrast, nearly 40 are present in its close wild relative, Malus sylvestris...
June 21, 2017: Heredity
https://www.readbyqxmd.com/read/28635663/assessing-genetic-diversity-and-population-differentiation-of-colored-calla-lily-zantedeschia-hybrid-for-an-efficient-breeding-program
#3
Zunzheng Wei, Huali Zhang, Yi Wang, Youli Li, Min Xiong, Xian Wang, Di Zhou
Plastome-genome incompatibility (PGI) is prevalent in several plants including the Zantedeschia species, a worldwide commercial flower crop native to South Africa. Generally, hybrids suffering from PGI appear less vigorous and more susceptible than normal plants. Previous reports revealed that the PGI level in interspecific hybrids is correlated with the relatedness of the parental species in the genus Zantedeschia. To provide a basis for utilizing and improving resources in breeding programs, a total of 117 accessions of colored calla lily (Zantedeschia hybrid), collected from New Zealand, the Netherlands and the United States, were genotyped using 31 transferable expressed sequence tags-simple sequence repeats (EST-SSR) markers from the white calla lily (Zantedeschia aethiopica)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28634597/molecular-characterization-of-salmonella-from-human-and-animal-origins-in-uganda
#4
Atek Atwiine Kagirita, Andrew Baguma, Tonny Jimmy Owalla, Joel Bazira, Samuel Majalija
Sporadic Salmonella outbreaks with varying clinical presentations have been on the rise in various parts of Uganda. The sources of outbreaks and factors underlying the different clinical manifestation are curtailed by paucity of information on Salmonella genotypes and the associated virulence genes. This study reports molecular diversity of Salmonella enterica and their genetic virulence profiles among human and animal isolates. Characterization was done using Kauffman-White classification scheme and virulence genes analysis using multiplex PCR...
2017: International Journal of Bacteriology
https://www.readbyqxmd.com/read/28634552/inherited-paediatric-motor-neuron-disorders-beyond-spinal-muscular-atrophy
#5
REVIEW
Hooi Ling Teoh, Kate Carey, Hugo Sampaio, David Mowat, Tony Roscioli, Michelle Farrar
Paediatric motor neuron diseases encompass a group of neurodegenerative diseases characterised by the onset of muscle weakness and atrophy before the age of 18 years, attributable to motor neuron loss across various neuronal networks in the brain and spinal cord. While the genetic underpinnings are diverse, advances in next generation sequencing have transformed diagnostic paradigms. This has reinforced the clinical phenotyping and molecular genetic expertise required to navigate the complexities of such diagnoses...
2017: Neural Plasticity
https://www.readbyqxmd.com/read/28634160/high-throughput-characterization-of-cascade-type-i-e-crispr-guide-efficacy-reveals-unexpected-pam-diversity-and-target-sequence-preferences
#6
Becky Xu Hua Fu, Michael Wainberg, Anshul Kundaje, Andrew Z Fire
Interactions between Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs and CRISPR-associated (Cas) proteins form an RNA-guided adaptive immune system in prokaryotes. The adaptive immune system utilizes segments of the genetic material of invasive foreign elements in the CRISPR locus. The loci are transcribed and processed to produce small CRISPR RNAs (crRNAs), with degradation of invading genetic material directed by a combination of complementarity between RNA and DNA and in some cases recognition of adjacent motifs called PAMs (Protospacer Adjacent Motifs)...
June 20, 2017: Genetics
https://www.readbyqxmd.com/read/28634105/genetic-diversity-in-the-c-terminus-of-merozoite-surface-protein-1-among-plasmodium-knowlesi-isolates-from-selangor-and-sabah-borneo-malaysia
#7
Nan Jiun Yap, Xiang Ting Goh, Anson V Koehler, Timothy William, Tsin Wen Yeo, Indra Vythilingam, Robin B Gasser, Yvonne A L Lim
Plasmodium knowlesi, a malaria parasite of macaques, has emerged as an important parasite of humans. Despite the significance of P. knowlesi malaria in parts of Southeast Asia, very little is known about the genetic variation in this parasite. Our aim here was to explore sequence variation in a molecule called the 42kDa merozoite surface protein-1 (MSP-1), which is found on the surface of blood stages of Plasmodium spp. and plays a key role in erythrocyte invasion. Several studies of P. falciparum have reported that the C-terminus (a 42kDa fragment) of merozoite surface protein-1 (MSP-142; consisting of MSP-119 and MSP-133) is a potential candidate for a malaria vaccine...
June 17, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28633662/orthored-a-rapid-and-accurate-orthology-prediction-tool-with-low-computational-requirement
#8
Kai Battenberg, Ernest K Lee, Joanna C Chiu, Alison M Berry, Daniel Potter
BACKGROUND: Identifying orthologous genes is an initial step required for phylogenetics, and it is also a common strategy employed in functional genetics to find candidates for functionally equivalent genes across multiple species. At the same time, in silico orthology prediction tools often require large computational resources only available on computing clusters. Here we present OrthoReD, an open-source orthology prediction tool with accuracy comparable to published tools that requires only a desktop computer...
June 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28633633/utilization-and-farmers-knowledge-on-pigeonpea-diversity-in-benin-west-africa
#9
Mathieu Anatole Tele Ayenan, Agyemang Danquah, Léonard Essehou Ahoton, Kwadwo Ofori
BACKGROUND: Understanding factors driving farmers' uses of crop genetic resources is a key component not only to design appropriate conservation strategies but also to promote sustainable production. However, in Benin, limited information is available on farmers' knowledge related to pigeonpea uses and conservation. This study aimed at i) identifying and investigating the different uses of pigeonpea in relation with socio-cultural factors, namely age, gender, ethnic group and respondents' residence, ii) assessing pigeonpea varieties richness at household level and iii) evaluating the extent and distribution of pigeonpea varieties...
June 20, 2017: Journal of Ethnobiology and Ethnomedicine
https://www.readbyqxmd.com/read/28633563/mammalian-synthetic-biology-engineering-biological-systems
#10
Joshua B Black, Pablo Perez-Pinera, Charles A Gersbach
The programming of new functions into mammalian cells has tremendous application in research and medicine. Continued improvements in the capacity to sequence and synthesize DNA have rapidly increased our understanding of mechanisms of gene function and regulation on a genome-wide scale and have expanded the set of genetic components available for programming cell biology. The invention of new research tools, including targetable DNA-binding systems such as CRISPR/Cas9 and sensor-actuator devices that can recognize and respond to diverse chemical, mechanical, and optical inputs, has enabled precise control of complex cellular behaviors at unprecedented spatial and temporal resolution...
June 21, 2017: Annual Review of Biomedical Engineering
https://www.readbyqxmd.com/read/28633403/structured-populations-of-sulfolobus-acidocaldarius-with-susceptibility-to-mobile-genetic-elements
#11
Rika E Anderson, Angela Kouris, Christopher H Seward, Kate M Campbell, Rachel J Whitaker
The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28633358/phylogeography-of-herbarium-specimens-of-asexually-propagated-paper-mulberry-broussonetia-papyrifera-l-l-h%C3%A3-r-ex-vent-moraceae-reveals-genetic-diversity-across-the-pacific
#12
Claudia Payacan, Ximena Moncada, Gloria Rojas, Andrew Clarke, Kuo-Fang Chung, Robin Allaby, Daniela Seelenfreund, Andrea Seelenfreund
Background and Aims: Paper mulberry or Broussonetia papyrifera (L.) L'Hér. ex Vent. (Moraceae) is a dioecious species native to continental South-east Asia and East Asia, including Taiwan, that was introduced to the Pacific by pre-historic voyagers and transported intentionally and propagated asexually across the full range of Austronesian expansion from Taiwan to East Polynesia. The aim of this study was to gain insight into the dispersal of paper mulberry into Oceania through the genetic analysis of herbaria samples which represent a more complete coverage of the historical geographical range of the species in the Pacific before later introductions and local extinctions occurred...
June 14, 2017: Annals of Botany
https://www.readbyqxmd.com/read/28632759/analysis-of-intra-host-genetic-diversity-of-prunus-necrotic-ringspot-virus-pnrsv-using-amplicon-next-generation-sequencing
#13
Wycliff M Kinoti, Fiona E Constable, Narelle Nancarrow, Kim M Plummer, Brendan Rodoni
PCR amplicon next generation sequencing (NGS) analysis offers a broadly applicable and targeted approach to detect populations of both high- or low-frequency virus variants in one or more plant samples. In this study, amplicon NGS was used to explore the diversity of the tripartite genome virus, Prunus necrotic ringspot virus (PNRSV) from 53 PNRSV-infected trees using amplicons from conserved gene regions of each of PNRSV RNA1, RNA2 and RNA3. Sequencing of the amplicons from 53 PNRSV-infected trees revealed differing levels of polymorphism across the three different components of the PNRSV genome with a total number of 5040, 2083 and 5486 sequence variants observed for RNA1, RNA2 and RNA3 respectively...
2017: PloS One
https://www.readbyqxmd.com/read/28632342/variation-in-gene-regulation-underlying-annual-and-perennial-flowering-in-arabideae-species
#14
Jannice Friedman
The diversity of life history strategies within the angiosperms illustrates the evolutionary flexibility of reproductive characteristics. The number of times an individual reproduces is a key life history trait, and transitions from iteroparous perennials to semelparous annuals have occurred frequently in the flowering plants. Despite the frequency of this evolutionary transition, and the importance of annuality versus perenniality to both agriculture and ecology, understanding the molecular and genetic mechanisms involved in perennial flowering is in their infancy...
July 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28632152/isolation-and-characterization-of-microsatellite-loci-for-cotesia-plutellae-hymenoptera-braconidae
#15
Tiansheng Liu, Fushi Ke, Shijun You, Wenbin Chen, Weiyi He, Minsheng You
Fourteen polymorphic microsatellite loci were isolated in this transcriptome-based data analysis for Cotesia plutellae, which is an important larval parasitoid of the worldwide pest Plutella xylostella. A subsequent test was performed for a wild C. plutellae population (N = 32) from Fuzhou, Fujian, southeastern China, to verify the effectiveness of the 14 microsatellite loci in future studies on C. plutellae genetic diversity. The observed number of alleles ranged from two to six. The expected and observed heterozygosity ranged from 0...
June 20, 2017: Insects
https://www.readbyqxmd.com/read/28631859/determining-the-drivers-of-population-structure-in-a-highly-urbanized-landscape-to-inform-conservation-planning
#16
Henri A Thomassen, Ryan J Harrigan, Kathleen Semple Delaney, Seth P D Riley, Laurel E K Serieys, Katherine Pease, Robert K Wayne, Thomas B Smith
Understanding the environmental contributors to population structure is of paramount importance for conservation in urbanized environments. We used spatially-explicit models to determine genetic population structure under current and future environmental conditions across a highly fragmented, human-dominated environment in Southern California to assess the effects of natural ecological variation and urbanization. We focused on seven common species with diverse habitat requirements, home range sizes, and dispersal abilities...
June 20, 2017: Conservation Biology: the Journal of the Society for Conservation Biology
https://www.readbyqxmd.com/read/28631610/a-large-gene-family-in-fission-yeast-encodes-spore-killers-that-subvert-mendel-s-law
#17
Wen Hu, Zhao-Di Jiang, Fang Suo, Jin-Xin Zheng, Wan-Zhong He, Li-Lin Du
Spore killers in fungi are selfish genetic elements that distort Mendelian segregation in their favor. It remains unclear how many species harbor them and how diverse their mechanisms are. Here, we discover two spore killers from a natural isolate of the fission yeast Schizosaccharomyces pombe. Both killers belong to the previously uncharacterized wtf gene family with 25 members in the reference genome. These two killers act in strain-background-independent and genome-location-independent manners to perturb the maturation of spores not inheriting them...
June 20, 2017: ELife
https://www.readbyqxmd.com/read/28631436/characterization-of-a-novel-p110%C3%AE-specific-inhibitor-bl140-that-overcomes-mdv3100-resistance-in-castration-resistant-prostate-cancer-cells
#18
Chenchen He, Shaofeng Duan, Liang Dong, Yifen Wang, Qingting Hu, Chunjing Liu, Marcus L Forrest, Jeffrey M Holzbeierlein, Suxia Han, Benyi Li
BACKGROUND: Our previous studies demonstrated that the class IA PI3K/p110β is critical in castration-resistant progression of prostate cancer (CRPC) and that targeting prostate cancer with nanomicelle-loaded p110β-specific inhibitor TGX221 blocked xenograft tumor growth in nude mice, confirming the feasibility of p110β-targeted therapy for CRPCs. To improve TGX221's aqueous solubility, in this study, we characterized four recently synthesized TGX221 analogs. METHODS: TGX221 analog efficacy were examined in multiple prostate cancer cell lines with the SRB cell growth assay, Western blot assay for AKT phosphorylation and cell cycle protein levels...
June 20, 2017: Prostate
https://www.readbyqxmd.com/read/28631344/evaluation-of-the-genetic-structure-of-sika-deer-cervus-nippon-in-japan-s-kanto-and-tanzawa-mountain-areas-based-on-microsatellite-markers
#19
Sayaka Konishi, Shoko Hata, Sayumi Matsuda, Kazushi Arai, Yasushi Mizoguchi
The browsing habits of sika deer (Cervus nippon) in Japan have caused serious ecological problems. Appropriate management of sika deer populations requires understanding the different genetic structures of local populations. In the present study, we used 10 microsatellite polymorphisms to explore the genetic structures of sika deer populations (162 individuals) living in the Kanto region. The expected heterozygosity of the Tanzawa mountain range population (Group I) was lower than that of the populations in the Kanto mountain areas (Group II)...
June 19, 2017: Animal Science Journal, Nihon Chikusan Gakkaihō
https://www.readbyqxmd.com/read/28631340/insights-into-the-genomic-plasticity-of-pseudomonas-putida-kf715-a-strain-with-unique-biphenyl-utilizing-activity-and-genome-instability-properties
#20
Hikaru Suenaga, Hidehiko Fujihara, Nobutada Kimura, Jun Hirose, Takahito Watanabe, Taiki Futagami, Masatoshi Goto, Jun Shimodaira, Kensuke Furukawa
Pseudomonas putida KF715 exhibits unique properties in both catabolic activity and genome plasticity. Our previous studies revealed that the DNA region containing biphenyl and salycilate metabolism gene clusters (termed the bph-sal element) was frequently deleted and transferred by conjugation to closely related P. putida strains. In this study, we first determined the complete nucleotide sequence of the KF715 genome. Next, to determine the underlying cause of genome plasticity in KF715, we compared the KF715 genome with the genomes of one KF715 defective mutant, two transconjugants, and several P...
June 19, 2017: Environmental Microbiology Reports
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