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Genetic diversity

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https://www.readbyqxmd.com/read/28728396/characterization-and-functional-inferences-of-a-genome-wide-dna-methylation-profile-in-the-loin-longissimus-dorsi-muscle-of-swine
#1
Woonsu Kim, Hyesun Park, Kang-Seok Seo, Seongwon Seo
Objective: DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin (longissimus dorsi) muscle (LDM) of swine. Methods: A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates)...
May 14, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28728378/phenotypic-diversity-major-genes-and-production-potential-of-local-chickens-and-guinea-fowl-in-tamale-northern-ghana
#2
Michael Mensah Brown, Benjamin Alenyorege, Gabriel Ayum Teye, Regina Roessler
Objective: Our study provides information on phenotypes of local chickens and guinea fowl and their body measures as well as on major genes in local chickens in northern Ghana. Methods: Qualitative and morphometric traits were recorded on 788 local chickens and 394 guinea fowl in urban households in Tamale, Ghana. Results: The results showed considerable variation of color traits and numerous major genes in local chickens, while color variations and related genotypes in guinea fowl were limited...
June 26, 2017: Asian-Australasian Journal of Animal Sciences
https://www.readbyqxmd.com/read/28728056/sequence-based-diversity-of-23-autosomal-str-loci-in-koreans-investigated-using-an-in-house-massively-parallel-sequencing-panel
#3
Eun Hye Kim, Hwan Young Lee, So Yeun Kwon, Eun Young Lee, Woo Ick Yang, Kyoung-Jin Shin
As DNA databases continue to grow and international cooperation increases, forensic STR loci have expanded to increase the discriminatory power and inter-database compatibility. Current capillary electrophoresis (CE) and/or massively parallel sequencing (MPS)-based commercial STR analysis systems reflect such changing trends of expanding STR loci. Due to the general gains of larger multiplexing and the detection of sequence variation, the application of MPS technology to STR analysis has further improved discrimination and is expected to aid in mixture interpretation by increasing the effective number of alleles...
July 9, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28727971/congenital-extrahepatic-portosystemic-shunt-abernethy-malformation-type-ib-with-associated-hepatocellular-carcinoma-case-report-and-literature-review
#4
Mark Benedict, Manuel Rodriguez-Davalos, Sukru Emre, Zenta Walther, Raffaella Morotti
Abernethy malformation, also termed congenital portosystemic shunt and congenital absence of portal vein is the result of malformation of the splanchnic venous system. Congenital portosystemic shunts are divided into extra- and intrahepatic shunts. Two shunts have been defined: Type I is characterized by the complete diversion of portal blood into the vena cava with an associated congenital absence of the portal vein. Type II is defined by an intact but diverted portal vein through a side-to-side, extrahepatic connection to the vena cava...
July 2017: Pediatric and Developmental Pathology
https://www.readbyqxmd.com/read/28727806/genocore-a-simple-and-fast-algorithm-for-core-subset-selection-from-large-genotype-datasets
#5
Seongmun Jeong, Jae-Yoon Kim, Soon-Chun Jeong, Sung-Taeg Kang, Jung-Kyung Moon, Namshin Kim
Selecting core subsets from plant genotype datasets is important for enhancing cost-effectiveness and to shorten the time required for analyses of genome-wide association studies (GWAS), and genomics-assisted breeding of crop species, etc. Recently, a large number of genetic markers (>100,000 single nucleotide polymorphisms) have been identified from high-density single nucleotide polymorphism (SNP) arrays and next-generation sequencing (NGS) data. However, there is no software available for picking out the efficient and consistent core subset from such a huge dataset...
2017: PloS One
https://www.readbyqxmd.com/read/28727785/novel-crispr-cas9-gene-drive-constructs-reveal-insights-into-mechanisms-of-resistance-allele-formation-and-drive-efficiency-in-genetically-diverse-populations
#6
Jackson Champer, Riona Reeves, Suh Yeon Oh, Chen Liu, Jingxian Liu, Andrew G Clark, Philipp W Messer
A functioning gene drive system could fundamentally change our strategies for the control of vector-borne diseases by facilitating rapid dissemination of transgenes that prevent pathogen transmission or reduce vector capacity. CRISPR/Cas9 gene drive promises such a mechanism, which works by converting cells that are heterozygous for the drive construct into homozygotes, thereby enabling super-Mendelian inheritance. Although CRISPR gene drive activity has already been demonstrated, a key obstacle for current systems is their propensity to generate resistance alleles, which cannot be converted to drive alleles...
July 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28727518/therapeutic-and-prognostic-implications-of-braf-v600e-in-pediatric-low-grade-gliomas
#7
Alvaro Lassaletta, Michal Zapotocky, Matthew Mistry, Vijay Ramaswamy, Marion Honnorat, Rahul Krishnatry, Ana Guerreiro Stucklin, Nataliya Zhukova, Anthony Arnoldo, Scott Ryall, Catriona Ling, Tara McKeown, Jim Loukides, Ofelia Cruz, Carmen de Torres, Cheng-Ying Ho, Roger J Packer, Ruth Tatevossian, Ibrahim Qaddoumi, Julie H Harreld, James D Dalton, Jean Mulcahy-Levy, Nicholas Foreman, Matthias A Karajannis, Shiyang Wang, Matija Snuderl, Amulya Nageswara Rao, Caterina Giannini, Mark Kieran, Keith L Ligon, Maria Luisa Garre, Paolo Nozza, Samantha Mascelli, Alessandro Raso, Sabine Mueller, Theodore Nicolaides, Karen Silva, Romain Perbet, Alexandre Vasiljevic, Cécile Faure Conter, Didier Frappaz, Sarah Leary, Courtney Crane, Aden Chan, Ho-Keung Ng, Zhi-Feng Shi, Ying Mao, Elizabeth Finch, David Eisenstat, Bev Wilson, Anne Sophie Carret, Peter Hauser, David Sumerauer, Lenka Krskova, Valerie Larouche, Adam Fleming, Shayna Zelcer, Nada Jabado, James T Rutka, Peter Dirks, Michael D Taylor, Shiyi Chen, Ute Bartels, Annie Huang, David W Ellison, Eric Bouffet, Cynthia Hawkins, Uri Tabori
Purpose BRAF V600E is a potentially highly targetable mutation detected in a subset of pediatric low-grade gliomas (PLGGs). Its biologic and clinical effect within this diverse group of tumors remains unknown. Patients and Methods A combined clinical and genetic institutional study of patients with PLGGs with long-term follow-up was performed (N = 510). Clinical and treatment data of patients with BRAF V600E mutated PLGG (n = 99) were compared with a large international independent cohort of patients with BRAF V600E mutated-PLGG (n = 180)...
July 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28727105/analysis-of-the-gut-bacterial-communities-in-beef-cattle-and-their-association-with-feed-intake-growth-and-efficiency
#8
P R Myer, H C Freetly, J E Wells, T P L Smith, L A Kuehn
The impetus behind the global food security challenge is direct, with the necessity to feed almost 10 billion people by 2050. Developing a food-secure world, where people have access to a safe and sustainable food supply, is the principal goal of this challenge. To achieve this end, beef production enterprises must develop methods to produce more pounds of animal protein with less. Selection for feed-efficient beef cattle using genetic improvement technologies has helped to understand and improve the stayability and longevity of such traits within the herd...
July 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28727001/analysis-of-genetic-diversity-of-chinese-dairy-goats-via-microsatellite-markers
#9
G Z Wang, S S Chen, T L Chao, Z B Ji, L Hou, Z J Qin, J M Wang
In this study, 15 polymorphic microsatellite markers were used to analyze the genetic structure and phylogenetic relationships of 6 dairy goat breeds in China, including 4 native developed breeds and 2 introduced breeds. The results showed that a total of 172 alleles were detected in 347 samples of the dairy goat breeds included in this study. The mean number of effective alleles per locus was 4.92. Except for BMS0812, all of the remaining microsatellite loci were highly polymorphic (polymorphism information content [PIC] > 0...
May 2017: Journal of Animal Science
https://www.readbyqxmd.com/read/28726721/identification-and-validation-of-new-alleles-of-falsiflora-and-compound-inflorescence-genes-controlling-the-number-of-branches-in-tomato-inflorescence
#10
Huan Zheng, Saneyuki Kawabata
The architecture of inflorescences shows extensive diversity in both branching frequency and flower number, which eventually, determines agricultural productivity. In this study, F₂ (second filial) populations derived from a cross between Solanum lycopersicum 10AS111A (highly-branched inflorescence) and the S. pimpinellifolium PI124039 (inflorescence having a single branch) were used to decipher the genetic control of branch number (BN) of inflorescence in plants bearing small-sized tomato fruits. The segregation ratio of single- and moderately-branched types to the highly-branched type was significantly different from 3:1 but not different from 15:1 at p < 0...
July 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28726664/expanded-phenotype-of-tmem67-gene-mutation-case-report
#11
T Tkemaladze, G Melikishvili, V Kherkheulidze, A Melikishvili, T Davitaia
Human ciliopathies are a class of multi-organ genetic disorders caused by defects of proteins expressed at the primary cilium, an organelle present on the cell surface of almost all cell types. Thus far, dozens of causative genes for ciliopathies have been identified and many of them are known to cause allelic disease. Of particular interest is the TMEM67 gene, encoding the transmembrane protein meckelin. The involvement of the mutant TMEM67 gene is known to be associated with a broad range of clinical presentations, namely Joubert syndrome 6 (JBTS6), nephronophthisis 11 (NPHP11), Bardet-Biedel syndrome (BBS), COACH syndrome, and lethal Meckel syndrome type 3 (MKS3)...
June 2017: Georgian Medical News
https://www.readbyqxmd.com/read/28726641/a-plant-fungal-type-phosphoenolpyruvate-carboxykinase-located-in-the-parasite-mitochondrion-ensures-glucose-independent-survival-of-toxoplasma-gondii
#12
Richard Nitzsche, Özlem Günay-Esiyok, Maximilian Tischer, Vyacheslav Zagoriy, Nishith Gupta
Toxoplasma gondii is considered as one of the most successful intracellular pathogens, because it can reproduce in varied nutritional milieus, encountered in diverse host-cell types of essentially any warm-blooded organism. Our earlier work has demonstrated that the acute (tachyzoite) stage of T. gondii depends on cooperativity of glucose and glutamine catabolism to meet biosynthetic demands. Either of these two nutrients can sustain the parasite survival; however, what determines the metabolic plasticity has not been resolved yet...
July 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28726639/mitochondrial-calcium-uniporter-in-drosophila-transfers-calcium-between-the-endoplasmic-reticulum-and-mitochondria-in-oxidative-stress-induced-cell-death
#13
Sekyu Choi, Xianglan Quan, Sunhoe Bang, Heesuk Yoo, Jiyoung Kim, Jiwon Park, Kyu-Sang Park, Jongkyeong Chung
Mitochondrial calcium plays critical roles in diverse cellular processes ranging from energy metabolism to cell death. Previous studies have demonstrated that mitochondrial calcium uptake is mainly mediated by the mitochondrial calcium uniporter (MCU) complex. However, the roles of the MCU complex in calcium transport, signaling, and dysregulation by oxidative stress still remain unclear. Here, we confirmed that Drosophila MCU contains evolutionarily conserved structures and requires essential MCU regulator (EMRE) for its calcium channel activities...
July 18, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28726087/population-specific-analysis-of-yakut-exomes
#14
A S Zlobin, S Sh Sharapov, V P Guryev, M R Bevova, Y A Tsepilov, T M Sivtseva, U A Boyarskih, E A Sokolova, Y S Aulchenko, M L Filipenko, V L Osakovsky
We studied the genetic diversity of the Yakut population using exome sequencing. We performed comparative analysis of the Yakut population and the populations that are included in the "1000 Genomes" project and we identified the alleles specific to the Yakut population. We showed, that the Yakuts population is a separate cluster between Europeans and East Asians.
May 2017: Doklady. Biochemistry and Biophysics
https://www.readbyqxmd.com/read/28726068/cardiac-complications-of-congenital-disorders-of-glycosylation-cdg-a-systematic-review-of-the-literature
#15
REVIEW
D Marques-da-Silva, R Francisco, D Webster, V Dos Reis Ferreira, J Jaeken, T Pulinilkunnil
Congenital disorders of glycosylation (CDG) are inborn errors of metabolism due to protein and lipid hypoglycosylation. This rapidly growing family of genetic diseases comprises 103 CDG types, with a broad phenotypic diversity ranging from mild to severe poly-organ -system dysfunction. This literature review summarizes cardiac involvement, reported in 20% of CDG. CDG with cardiac involvement were divided according to the associated type of glycosylation: N-glycosylation, O-glycosylation, dolichol synthesis, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, COG complex, V-ATPase complex, and other glycosylation pathways...
July 19, 2017: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/28725990/molecular-characterization-of-the-indigenous-stingless-bees-tetragonula-spp-complex-using-issr-marker-from-southern-peninsular-india
#16
P P Nayak, J Prakash
India is a country bestowed enormously with stingless bees, but genetic information about them is extremely minimal. This study focused to tap the geographic allocation, genetic variability, and differentiation among Tetragonula species complexes from natural and semi-urban habitats. Genetic analyses were assessed among 36 contrasting genotypes utilizing 20 ISSR primers. The dual combination exquisitely and productively amplified 245 DNA fragments at the loci, of which 240 bands were polymorphic (97.95%). Low to moderate level of genetic differentiation was detected from different estimators (Ht 0...
July 19, 2017: Neotropical Entomology
https://www.readbyqxmd.com/read/28725948/genomics-and-epigenomics-in-rheumatic-diseases-what-do-they-provide-in-terms-of-diagnosis-and-disease-management
#17
Patricia Castro-Santos, Roberto Díaz-Peña
Most rheumatic diseases are complex or multifactorial entities with pathogeneses that interact with both multiple genetic factors and a high number of diverse environmental factors. Knowledge of the human genome sequence and its diversity among populations has provided a crucial step forward in our understanding of genetic diseases, identifying many genetic loci or genes associated with diverse phenotypes. In general, susceptibility to autoimmunity is associated with multiple risk factors, but the mechanism of the environmental component influence is poorly understood...
July 20, 2017: Clinical Rheumatology
https://www.readbyqxmd.com/read/28725873/genetic-characterization-of-human-immunodeficiency-virus-type-1-transmission-in-the-middle-east-and-north-africa
#18
Malik Sallam, Gülşen Özkaya Şahin, Mikael Ingman, Anders Widell, Joakim Esbjörnsson, Patrik Medstrand
BACKGROUND: The HIV-1 spread in the Middle East and North Africa (MENA) has not been previously characterised using the phylogenetic approach. The aim of the current study was to investigate the genetic diversity and domestic transmission of HIV-1 in the MENA. METHODS: A total of 2036 HIV-1 sequences available in Genbank and collected in the MENA during 1988-2016 were used together with 715 HIV-1 reference sequences that were retrieved from Genbank based on genetic similarity with the MENA sequences...
July 2017: Heliyon
https://www.readbyqxmd.com/read/28725664/morphotypes-and-pigment-profiles-of-halophilic-bacteria-practical-data-useful-for-novelty-taxonomic-categorization-and-for-describing-novel-species-or-new-taxa
#19
Bhagwan N Rekadwad, Chandrahasya N Khobragade
Halophilic bacteria were isolated from oil spill samples collected from West-coast of Goa. Bacteria were isolated from oil studded soil, salt marsh and offshore samples (A, A7, CSM, CB and CM) collected along the West coastline in Goa (India) i.e. Arambol beach, Calanguate beach, Candolim beach and Colva beach on Zobell Marine agar, R2A agar, Mannitol salt agar and Blood agar at temperature 22 to 24 °C. Isolates showed growth in the presence of hydrocarbons (1% phenanthrene and 2% bitumen). Diverse profiles of pigments were observed on different nutrient medium...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28725416/contrasting-patterns-of-selection-between-mhc-i-and-ii-across-populations-of-humboldt-and-magellanic-penguins
#20
Nicole Sallaberry-Pincheira, Daniel González-Acuña, Pamela Padilla, Gisele P M Dantas, Guillermo Luna-Jorquera, Esteban Frere, Armando Valdés-Velásquez, Juliana A Vianna
The evolutionary and adaptive potential of populations or species facing an emerging infectious disease depends on their genetic diversity in genes, such as the major histocompatibility complex (MHC). In birds, MHC class I deals predominantly with intracellular infections (e.g., viruses) and MHC class II with extracellular infections (e.g., bacteria). Therefore, patterns of MHC I and II diversity may differ between species and across populations of species depending on the relative effect of local and global environmental selective pressures, genetic drift, and gene flow...
October 2016: Ecology and Evolution
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