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BMC Genomics

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https://www.readbyqxmd.com/read/29792182/boostme-accurately-predicts-dna-methylation-values-in-whole-genome-bisulfite-sequencing-of-multiple-human-tissues
#1
Luli S Zou, Michael R Erdos, D Leland Taylor, Peter S Chines, Arushi Varshney, Stephen C J Parker, Francis S Collins, John P Didion
BACKGROUND: Bisulfite sequencing is widely employed to study the role of DNA methylation in disease; however, the data suffer from biases due to coverage depth variability. Imputation of methylation values at low-coverage sites may mitigate these biases while also identifying important genomic features associated with predictive power. RESULTS: Here we describe BoostMe, a method for imputing low-quality DNA methylation estimates within whole-genome bisulfite sequencing (WGBS) data...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792177/investigation-of-the-thermophilic-mechanism-in-the-genus-porphyrobacter-by-comparative-genomic-analysis
#2
Lin Xu, Yue-Hong Wu, Peng Zhou, Hong Cheng, Qian Liu, Xue-Wei Xu
BACKGROUND: Type strains of the genus Porphyrobacter belonging to the family Erythrobacteraceae and the class Alphaproteobacteria have been isolated from various environments, such as swimming pools, lake water and hot springs. P. cryptus DSM 12079T and P. tepidarius DSM 10594T out of all Erythrobacteraceae type strains, are two type strains that have been isolated from geothermal environments. Next-generation sequencing (NGS) technology offers a convenient approach for detecting situational types based on protein sequence differences between thermophiles and mesophiles; amino acid substitutions can lead to protein structural changes, improving the thermal stabilities of proteins...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792173/impact-of-growth-ph-and-glucose-concentrations-on-the-cody-regulatory-network-in-streptococcus-salivarius
#3
Jianing Geng, Szu-Chuan Huang, Yueh-Ying Chen, Cheng-Hsun Chiu, Songnian Hu, Yi-Ywan M Chen
BACKGROUND: Streptococcus salivarius is an abundant isolate of the human oral microbiota. Since both pH and glucose availability fluctuate frequently in the oral cavity, the goal of this study was to investigate regulation by CodY, a conserved pleiotropic regulator of Gram positive bacteria, in response to these two signals. The chemostat culture system was employed to precisely control the growth parameters, and the transcriptomes of wild-type S. salivarius 57.I and its CodY-null derivative (ΔcodY) grown at pH 7 and 5...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792171/embryonic-transcriptome-and-proteome-analyses-on-hepatic-lipid-metabolism-in-chickens-divergently-selected-for-abdominal-fat-content
#4
Wei Na, Yuan-Yuan Wu, Peng-Fei Gong, Chun-Yan Wu, Bo-Han Cheng, Yu-Xiang Wang, Ning Wang, Zhi-Qiang Du, Hui Li
BACKGROUND: In avian species, liver is the main site of de novo lipogenesis, and hepatic lipid metabolism relates closely to adipose fat deposition. Using our fat and lean chicken lines of striking differences in abdominal fat content, post-hatch lipid metabolism in both liver and adipose tissues has been studied extensively. However, whether molecular discrepancy for hepatic lipid metabolism exists in chicken embryos remains obscure. RESULTS: We performed transcriptome and proteome profiling on chicken livers at five embryonic stages (E7, E12, E14, E17 and E21) between the fat and lean chicken lines...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792165/molecular-characterization-and-differential-expression-suggested-diverse-functions-of-p-type-ii-ca-2-atpases-in-triticum-aestivum-l
#5
Mehak Taneja, Santosh Kumar Upadhyay
BACKGROUND: Plant P-type II Ca2+ ATPases are formed by two distinct groups of proteins (ACAs and ECAs) that perform pumping of Ca2+ outside the cytoplasm during homeostasis, and play vital functions during development and stress management. In the present study, we have performed identification and characterisation of P-type II Ca 2+ ATPase gene family in an important crop plant Triticum aestivum. RESULTS: Herein, a total of 33 TaACA and 9 TaECA proteins were identified from the various chromosomes and sub-genomes of Triticum aestivum...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792162/overlapping-but-distinct-topology-for-zebrafish-v2r-like-olfactory-receptors-reminiscent-of-odorant-receptor-spatial-expression-zones
#6
Gaurav Ahuja, Vera Reichel, Daniel Kowatschew, Adnan S Syed, Aswani Kumar Kotagiri, Yuichiro Oka, Franco Weth, Sigrun I Korsching
BACKGROUND: The sense of smell is unrivaled in terms of molecular complexity of its input channels. Even zebrafish, a model vertebrate system in many research fields including olfaction, possesses several hundred different olfactory receptor genes, organized in four different gene families. For one of these families, the initially discovered odorant receptors proper, segregation of expression into distinct spatial subdomains within a common sensory surface has been observed both in teleost fish and in mammals...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792159/on-the-possibility-of-death-of-new-genes-evidence-from-the-deletion-of-de-novo-micrornas
#7
Guang-An Lu, Yixin Zhao, Zhongqi Liufu, Chung-I Wu
BACKGROUND: New genes are constantly formed, sometimes from non-genic sequences, creating what is referred to as de novo genes. Since the total number of genes remains relatively steady, gene deaths likely balance out new births. In metazoan genomes, microRNAs (miRs) genes, small and non-coding, account for the bulk of functional de novo genes and are particularly suited to the investigation of gene death. RESULTS: In this study, we discover a Drosophila-specific de novo miRNA (mir-977) that may be facing impending death...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792157/long-term-health-and-germline-transmission-in-transgenic-cattle-following-transposon-mediated-gene-transfer
#8
Soo-Young Yum, Song-Jeon Lee, Sin-Gi Park, In-Gang Shin, Sang-Eun Hahn, Woo-Jae Choi, Hee-Soo Kim, Hyeong-Jong Kim, Seong-Hun Bae, Je-Hyeong Lee, Joo-Yeong Moon, Woo-Sung Lee, Ji-Hyun Lee, Choong-Il Lee, Seong-Jin Kim, Goo Jang
BACKGROUND: Transposon-mediated, non-viral gene delivery is a powerful tool for generating stable cell lines and transgenic animals. However, as multi-copy insertion is the preferred integration pattern, there is the potential for uncontrolled changes in endogenous gene expression and detrimental effects in cells or animals. Our group has previously reported on the generation of several transgenic cattle by using microinjection of the Sleeping Beauty (SB) and PiggyBac (PB) transposons and seeks to explore the long-term effects of this technology on cattle...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788925/de-novo-transcriptome-assembly-of-the-eight-major-organs-of-sacha-inchi-plukenetia-volubilis-and-the-identification-of-genes-involved-in-%C3%AE-linolenic-acid-metabolism
#9
Xiao-Di Hu, Bang-Zhen Pan, Qiantang Fu, Longjian Niu, Mao-Sheng Chen, Zeng-Fu Xu
BACKGROUND: Sacha Inchi (Plukenetia volubilis L.), which belongs to the Euphorbiaceae, has been considered a new potential oil crop because of its high content of polyunsaturated fatty acids in its seed oil. The seed oil especially contains high amounts of α-linolenic acid (ALA), which is useful for the prevention of various diseases. However, little is known about the genetic information and genome sequence of Sacha Inchi, which has largely hindered functional genomics and molecular breeding studies...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788921/signatures-of-host-specialization-and-a-recent-transposable-element-burst-in-the-dynamic-one-speed-genome-of-the-fungal-barley-powdery-mildew-pathogen
#10
Lamprinos Frantzeskakis, Barbara Kracher, Stefan Kusch, Makoto Yoshikawa-Maekawa, Saskia Bauer, Carsten Pedersen, Pietro D Spanu, Takaki Maekawa, Paul Schulze-Lefert, Ralph Panstruga
BACKGROUND: Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). RESULTS: The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs)...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788916/in-silico-exploration-of-red-sea-bacillus-genomes-for-natural-product-biosynthetic-gene-clusters
#11
Ghofran Othoum, Salim Bougouffa, Rozaimi Razali, Ameerah Bokhari, Soha Alamoudi, André Antunes, Xin Gao, Robert Hoehndorf, Stefan T Arold, Takashi Gojobori, Heribert Hirt, Ivan Mijakovic, Vladimir B Bajic, Feras F Lafi, Magbubah Essack
BACKGROUND: The increasing spectrum of multidrug-resistant bacteria is a major global public health concern, necessitating discovery of novel antimicrobial agents. Here, members of the genus Bacillus are investigated as a potentially attractive source of novel antibiotics due to their broad spectrum of antimicrobial activities. We specifically focus on a computational analysis of the distinctive biosynthetic potential of Bacillus paralicheniformis strains isolated from the Red Sea, an ecosystem exposed to adverse, highly saline and hot conditions...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29788909/whole-genome-analysis-reveals-the-diversity-and-evolutionary-relationships-between-necrotic-enteritis-causing-strains-of-clostridium-perfringens
#12
Jake A Lacey, Theodore R Allnutt, Ben Vezina, Thi Thu Hao Van, Thomas Stent, Xiaoyan Han, Julian I Rood, Ben Wade, Anthony L Keyburn, Torsten Seemann, Honglei Chen, Volker Haring, Priscilla A Johanesen, Dena Lyras, Robert J Moore
BACKGROUND: Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783952/differences-between-fast-and-slow-muscles-in-scallops-revealed-through-proteomics-and-transcriptomics
#13
Xiujun Sun, Zhihong Liu, Biao Wu, Liqing Zhou, Qi Wang, Wei Wu, Aiguo Yang
BACKGROUND: Scallops possess striated and catch adductor muscles, which have different structure and contractile properties. The striated muscle contracts very quickly for swimming, whereas the smooth catch muscle can keep the shells closed for long periods with little expenditure of energy. In this study, we performed proteomic and transcriptomic analyses of differences between the striated (fast) and catch (slow) adductor muscles in Yesso scallop Patinopecten yessoensis. RESULTS: Transcriptomic analysis reveals 1316 upregulated and 8239 downregulated genes in slow compared to fast adductor muscle...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783941/a-transposable-element-annotation-pipeline-and-expression-analysis-reveal-potentially-active-elements-in-the-microalga-tisochrysis-lutea
#14
Jérémy Berthelier, Nathalie Casse, Nicolas Daccord, Véronique Jamilloux, Bruno Saint-Jean, Grégory Carrier
BACKGROUND: Transposable elements (TEs) are mobile DNA sequences known as drivers of genome evolution. Their impacts have been widely studied in animals, plants and insects, but little is known about them in microalgae. In a previous study, we compared the genetic polymorphisms between strains of the haptophyte microalga Tisochrysis lutea and suggested the involvement of active autonomous TEs in their genome evolution. RESULTS: To identify potentially autonomous TEs, we designed a pipeline named PiRATE (Pipeline to Retrieve and Annotate Transposable Elements, download: https://doi...
May 22, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783951/the-transcriptomic-and-proteomic-responses-of-daphnia-pulex-to-changes-in-temperature-and-food-supply-comprise-environment-specific-and-clone-specific-elements
#15
Dörthe Becker, Yann Reydelet, Jacqueline A Lopez, Craig Jackson, John K Colbourne, Susan Hawat, Michael Hippler, Bettina Zeis, Rüdiger J Paul
BACKGROUND: Regulatory adjustments to acute and chronic temperature changes are highly important for aquatic ectotherms because temperature affects their metabolic rate as well as the already low oxygen concentration in water, which can upset their energy balance. This also applies to severe changes in food supply. Thus, we studied on a molecular level (transcriptomics and/or proteomics) the immediate responses to heat stress and starvation and the acclimation to different temperatures in two clonal isolates of the model microcrustacean Daphnia pulex from more or less stressful environments, which showed a higher (clone M) or lower (clone G) tolerance to heat and starvation...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783949/gene-copy-number-variation-in-natural-populations-of-plasmodium-falciparum-in-eastern-africa
#16
Joan Simam, Martin Rono, Joyce Ngoi, Mary Nyonda, Sachel Mok, Kevin Marsh, Zbynek Bozdech, Margaret Mackinnon
BACKGROUND: Gene copy number variants (CNVs), which consist of deletions and amplifications of single or sets of contiguous genes, contribute to the great diversity in the Plasmodium falciparum genome. In vitro studies in the laboratory have revealed their important role in parasite fitness phenotypes such as red cell invasion, transmissibility and cytoadherence. Studies of natural parasite populations indicate that CNVs are also common in the field and thus may facilitate adaptation of the parasite to its local environment...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783948/expansion-of-the-sos-regulon-of-vibrio-cholerae-through-extensive-transcriptome-analysis-and-experimental-validation
#17
Evelyne Krin, Sebastian Aguilar Pierlé, Odile Sismeiro, Bernd Jagla, Marie-Agnès Dillies, Hugo Varet, Oihane Irazoki, Susana Campoy, Zoé Rouy, Stéphane Cruveiller, Claudine Médigue, Jean-Yves Coppée, Didier Mazel
BACKGROUND: The SOS response is an almost ubiquitous response of cells to genotoxic stresses. The full complement of genes in the SOS regulon for Vibrio species has only been addressed through bioinformatic analyses predicting LexA binding box consensus and in vitro validation. Here, we perform whole transcriptome sequencing from Vibrio cholerae treated with mitomycin C as an SOS inducer to characterize the SOS regulon and other pathways affected by this treatment. RESULTS: Comprehensive transcriptional profiling allowed us to define the full landscape of promoters and transcripts active in V...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783944/estimates-of-genomic-heritability-and-genome-wide-association-study-for-fatty-acids-profile-in-santa-in%C3%A3%C2%AAs-sheep
#18
G A Rovadoscki, S F N Pertile, A B Alvarenga, A S M Cesar, F Pértille, J Petrini, V Franzo, W V B Soares, G Morota, M L Spangler, L F B Pinto, G G P Carvalho, D P D Lanna, L L Coutinho, G B Mourão
BACKGROUND: Despite the health concerns and nutritional importance of fatty acids, there is a relative paucity of studies in the literature that report genetic or genomic parameters, especially in the case of sheep populations. To investigate the genetic architecture of fatty acid composition of sheep, we conducted genome-wide association studies (GWAS) and estimated genomic heritabilities for fatty acid profile in Longissimus dorsi muscle of 216 male sheep. RESULTS: Genomic heritability estimates for fatty acid content ranged from 0...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783940/small-rna-based-prediction-of-hybrid-performance-in-maize
#19
Felix Seifert, Alexander Thiemann, Tobias A Schrag, Dominika Rybka, Albrecht E Melchinger, Matthias Frisch, Stefan Scholten
BACKGROUND: Small RNA (sRNA) sequences are known to have a broad impact on gene regulation by various mechanisms. Their performance for the prediction of hybrid traits has not yet been analyzed. Our objective was to analyze the relation of parental sRNA expression with the performance of their hybrids, to develop a sRNA-based prediction approach, and to compare it to more common SNP and mRNA transcript based predictions using a factorial mating scheme of a maize hybrid breeding program...
May 21, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29783939/a-genome-wide-association-study-reveals-novel-genomic-regions-and-positional-candidate-genes-for-fat-deposition-in-broiler-chickens
#20
Gabriel Costa Monteiro Moreira, Clarissa Boschiero, Aline Silva Mello Cesar, James M Reecy, Thaís Fernanda Godoy, Priscila Anchieta Trevisoli, Maurício E Cantão, Mônica Corrêa Ledur, Adriana Mércia Guaratini Ibelli, Jane de Oliveira Peixoto, Ana Silvia Alves Meira Tavares Moura, Dorian Garrick, Luiz Lehmann Coutinho
BACKGROUND: Excess fat content in chickens has a negative impact on poultry production. The discovery of QTL associated with fat deposition in the carcass allows the identification of positional candidate genes (PCGs) that might regulate fat deposition and be useful for selection against excess fat content in chicken's carcass. This study aimed to estimate genomic heritability coefficients and to identify QTLs and PCGs for abdominal fat (ABF) and skin (SKIN) traits in a broiler chicken population, originated from the White Plymouth Rock and White Cornish breeds...
May 21, 2018: BMC Genomics
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