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BMC Genomics

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https://www.readbyqxmd.com/read/28335741/high-throughput-sequencing-of-pituitary-and-hypothalamic-microrna-transcriptome-associated-with-high-rate-of-egg-production
#1
Nan Wu, Qing Zhu, Binlong Chen, Jian Gao, Zhongxian Xu, Diyan Li
BACKGROUND: MicroRNAs exist widely in viruses, plants and animals. As endogenous small non-coding RNAs, miRNAs regulate a variety of biological processes. Tissue miRNA expression studies have discovered numerous functions for miRNAs in various tissues of chicken, but the regulation of miRNAs in chicken pituitary and hypothalamic development related to high and low egg-laying performance has remained unclear. RESULTS: In this study, using high-throughput sequencing technology, we sequenced two tissues (pituitary and hypothalamus) in 3 high- and 3 low-rate egg production Luhua chickens at the age of 300 days...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335738/genome-wide-expression-profiling-establishes-novel-modulatory-roles-of-vitamin-c-in-thp-1-human-monocytic-cell-line
#2
Sakshi Dhingra Batra, Malobi Nandi, Kriti Sikri, Jaya Sivaswami Tyagi
BACKGROUND: Vitamin C (vit C) is an essential dietary nutrient, which is a potent antioxidant, a free radical scavenger and functions as a cofactor in many enzymatic reactions. Vit C is also considered to enhance the immune effector function of macrophages, which are regarded to be the first line of defence in response to any pathogen. The THP-1 cell line is widely used for studying macrophage functions and for analyzing host cell-pathogen interactions. RESULTS: We performed a genome-wide temporal gene expression and functional enrichment analysis of THP-1 cells treated with 100 μM of vit C, a physiologically relevant concentration of the vitamin...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335735/population-diversity-of-the-genetically-determined-ttr-expression-in-human-tissues-and-its-implications-in-ttr-amyloidosis
#3
Andrea Iorio, Flavio De Angelis, Marco Di Girolamo, Marco Luigetti, Luca G Pradotto, Anna Mazzeo, Sabrina Frusconi, Filomena My, Dario Manfellotto, Maria Fuciarelli, Renato Polimanti
BACKGROUND: Transthyretin (TTR) amyloidosis is a hereditary disease with a complex genotype-phenotype correlation. We conducted a literature survey to define the clinical landscape of TTR amyloidosis across populations worldwide. Then, we investigated whether the genetically determined TTR expression differs among human populations, contributing to the differences observed in patients. Polygenic scores for genetically determined TTR expression in 14 clinically relevant tissues were constructed using data from the GTEx (Genotype-Tissue Expression) project and tested in the samples from the 1,000 Genomes Project...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335732/lung-function-associated-gene-integrator-complex-subunit-12-regulates-protein-synthesis-pathways
#4
Alexander K Kheirallah, Cornelia H de Moor, Alen Faiz, Ian Sayers, Ian P Hall
BACKGROUND: Genetic studies of human lung function and Chronic Obstructive Pulmonary Disease have identified a highly significant and reproducible signal on 4q24. It remains unclear which of the two candidate genes within this locus may regulate lung function: GSTCD, a gene with unknown function, and/or INTS12, a member of the Integrator Complex which is currently thought to mediate 3'end processing of small nuclear RNAs. RESULTS: We found that, in lung tissue, 4q24 polymorphisms associated with lung function correlate with INTS12 but not neighbouring GSTCD expression...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335731/highly-diverse-population-of-picornaviridae-and-other-members-of-the-picornavirales-in-cameroonian-fruit-bats
#5
Claude Kwe Yinda, Roland Zell, Ward Deboutte, Mark Zeller, Nádia Conceição-Neto, Elisabeth Heylen, Piet Maes, Nick J Knowles, Stephen Mbigha Ghogomu, Marc Van Ranst, Jelle Matthijnssens
BACKGROUND: The order Picornavirales represents a diverse group of positive-stranded RNA viruses with small non-enveloped icosahedral virions. Recently, bats have been identified as an important reservoir of several highly pathogenic human viruses. Since many members of the Picornaviridae family cause a wide range of diseases in humans and animals, this study aimed to characterize members of the order Picornavirales in fruit bat populations located in the Southwest region of Cameroon...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335728/allelic-incompatibility-can-explain-female-biased-sex-ratios-in-dioecious-plants
#6
Pascal Pucholt, Henrik R Hallingbäck, Sofia Berlin
BACKGROUND: Biased sex ratios are common among dioecious plant species despite the theoretical prediction of selective advantage of even sex ratios. Albeit the high prevalence of deviations from even sex ratios, the genetic causes to sex biases are rarely known outside of a few model species. Here we present a mechanism underlying the female biased sex ratio in the dioecious willow species Salix viminalis. RESULTS: We compared the segregation pattern of genome-wide single nucleotide polymorphism markers in two contrasting bi-parental pedigree populations, the S3 with even sex ratio and the S5 with a female biased sex ratio...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335726/analysis-of-hepatic-transcript-profile-and-plasma-lipid-profile-in-early-lactating-dairy-cows-fed-grape-seed-and-grape-marc-meal-extract
#7
Denise K Gessner, Anne Winkler, Christian Koch, Georg Dusel, Gerhard Liebisch, Robert Ringseis, Klaus Eder
BACKGROUND: It was recently reported that dairy cows fed a polyphenol-rich grape seed and grape marc meal extract (GSGME) during the transition period had an increased milk yield, but the underlying reasons remained unclear. As polyphenols exert a broad spectrum of metabolic effects, we hypothesized that feeding of GSGME influences metabolic pathways in the liver which could account for the positive effects of GSGME in dairy cows. In order to identify these pathways, we performed genome-wide transcript profiling in the liver and lipid profiling in plasma of dairy cows fed GSGME during the transition period at 1 week postpartum...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335723/erratum-to-unity-in-defence-honeybee-workers-exhibit-conserved-molecular-responses-to-diverse-pathogens
#8
Vincent Doublet, Yvonne Poeschl, Andreas Gogol-Döring, Cédric Alaux, Desiderato Annoscia, Christian Aurori, Seth M Barribeau, Oscar C Bedoya-Reina, Mark J F Brown, James C Bull, Michelle L Flenniken, David A Galbraith, Elke Genersch, Sebastian Gisder, Ivo Grosse, Holly L Holt, Dan Hultmark, H Michael G Lattorff, Yves Le Conte, Fabio Manfredini, Dino P McMahon, Robin F A Moritz, Francesco Nazzi, Elina L Niño, Katja Nowick, Ronald P van Rij, Robert J Paxton, Christina M Grozinger
No abstract text is available yet for this article.
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28335720/widespread-promoter-methylation-of-synaptic-plasticity-genes-in-long-term-potentiation-in-the-adult-brain-in-vivo
#9
Jesper L V Maag, Dominik C Kaczorowski, Debabrata Panja, Timothy J Peters, Clive R Bramham, Karin Wibrand, Marcel E Dinger
BACKGROUND: DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not been explored. RESULTS: To investigate the occurrence of DNA methylation changes in LTP, we undertook the first detailed study to describe the methylation status of all known LTP-associated genes during LTP induction in the dentate gyrus of live rats...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28330454/uncovering-snp-and-indel-variations-of-tetraploid-cottons-by-slaf-seq
#10
Chao Shen, Xin Jin, De Zhu, Zhongxu Lin
BACKGROUND: Cotton (Gossypium spp.), as the world's most utilized textile fibre source, is an important, economically valuable crop worldwide. Understanding the genomic variation of tetraploid cotton species is important for exploitation of the excellent characteristics of wild cotton and for improving the diversity of cotton in breeding. However, the discovery of DNA polymorphisms in tetraploid cotton genomes has lagged behind other important crops. RESULTS: A total of 111,795,823 reads, 467,735 specific length amplified fragment (SLAF) tags and 139,176 high-quality DNA polymorphisms were identified using specific length amplified fragment sequencing (SLAF-seq), including 132,880 SNPs and 6,296 InDels between the reference genome (TM-1) and the five tetraploid cotton species...
March 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28330463/global-transcriptome-analysis-of-huperzia-serrata-and-identification-of-critical-genes-involved-in-the-biosynthesis-of-huperzine-a
#11
Mengquan Yang, Wenjing You, Shiwen Wu, Zhen Fan, Baofu Xu, Mulan Zhu, Xuan Li, Youli Xiao
BACKGROUND: Huperzia serrata (H. serrata) is an economically important traditional Chinese herb with the notably medicinal value. As a representative member of the Lycopodiaceae family, the H. serrata produces various types of effectively bioactive lycopodium alkaloids, especially the huperzine A (HupA) which is a promising drug for Alzheimer's disease. Despite their medicinal importance, the public genomic and transcriptomic resources are very limited and the biosynthesis of HupA is largely unknown...
March 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28330456/genome-wide-expression-profiling-in-leaves-and-roots-of-date-palm-phoenix-dactylifera-l-exposed-to-salinity
#12
Mahmoud W Yaish, Himanshu V Patankar, Dekoum V M Assaha, Yun Zheng, Rashid Al-Yahyai, Ramanjulu Sunkar
BACKGROUND: Date palm, as one of the most important fruit crops in North African and West Asian countries including Oman, is facing serious growth problems due to salinity, arising from persistent use of saline water for irrigation. Although date palm is a relatively salt-tolerant plant species, its adaptive mechanisms to salt stress are largely unknown. RESULTS: In order to get an insight into molecular mechanisms of salt tolerance, RNA was profiled in leaves and roots of date palm seedlings subjected to NaCl for 10 days...
March 22, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28327106/truke-a-web-tool-to-check-for-and-handle-excel-misidentified-gene-symbols
#13
Izaskun Mallona, Miguel A Peinado
BACKGROUND: Genomic datasets accompanying scientific publications show a surprisingly high rate of gene name corruption. This error is generated when files and tables are imported into Microsoft Excel and certain gene symbols are automatically converted into dates. RESULTS: We have developed Truke, a fexible Web tool to detect, tag and fix, if possible, such misconversions. Aside, Truke is language and regional locale-aware, providing file format customization (decimal symbol, field sepator, etc...
March 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28327095/interferon-signaling-in-ascites-associated-macrophages-is-linked-to-a-favorable-clinical-outcome-in-a-subgroup-of-ovarian-carcinoma-patients
#14
Till Adhikary, Annika Wortmann, Florian Finkernagel, Sonja Lieber, Andrea Nist, Thorsten Stiewe, Uwe Wagner, Sabine Müller-Brüsselbach, Silke Reinartz, Rolf Müller
BACKGROUND: Although tumor-associated macrophages (TAMs) are essential for cancer progression, connections between different clinical outcomes and transcriptional networks have not been reported. We have addressed this issue by analyzing global expression patterns of TAMs isolated from the ascites of ovarian cancer patients. RESULTS: TAMs isolated from different ovarian cancer patients can be stratified by coexpression or principal component analysis into subgroups with specific biological features and associated with distinct clinical outcomes...
March 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28327084/a-transcriptome-multi-tissue-analysis-identifies-biological-pathways-and-genes-associated-with-variations-in-feed-efficiency-of-growing-pigs
#15
Florence Gondret, Annie Vincent, Magalie Houée-Bigot, Anne Siegel, Sandrine Lagarrigue, David Causeur, Hélène Gilbert, Isabelle Louveau
BACKGROUND: Animal's efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI). RESULTS: Pigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age...
March 21, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28320322/exploring-the-nature-of-prediagnostic-blood-transcriptome-markers-of-chronic-lymphocytic-leukemia-by-assessing-their-overlap-with-the-transcriptome-at-the-clinical-stage
#16
Jelle Vlaanderen, Max Leenders, Marc Chadeau-Hyam, Lützen Portengen, Soterios A Kyrtopoulos, Ingvar A Bergdahl, Ann-Sofie Johansson, Dennie D G A J Hebels, Theo M C M de Kok, Paolo Vineis, Roel C H Vermeulen
BACKGROUND: We recently identified 700 genes whose expression levels were predictive of chronic lymphocytic leukemia (CLL) in a genome-wide gene expression analysis of prediagnostic blood from future cases and matched controls. We hypothesized that a large fraction of these markers were likely related to early disease manifestations. Here we aim to gain a better understanding of the natural history of the identified markers by comparing results from our prediagnostic analysis, the only prediagnostic analysis to date, to results obtained from a meta-analysis of a series of publically available transcriptomics profiles obtained in incident CLL cases and controls...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28320315/comparative-transcriptome-analyses-of-flower-development-in-four-species-of-achimenes-gesneriaceae
#17
Wade R Roberts, Eric H Roalson
BACKGROUND: Flowers have an amazingly diverse display of colors and shapes, and these characteristics often vary significantly among closely related species. The evolution of diverse floral form can be thought of as an adaptive response to pollination and reproduction, but it can also be seen through the lens of morphological and developmental constraints. To explore these interactions, we use RNA-seq across species and development to investigate gene expression and sequence evolution as they relate to the evolution of the diverse flowers in a group of Neotropical plants native to Mexico-magic flowers (Achimenes, Gesneriaceae)...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28320314/quorum-sensing-of-streptococcus-mutans-is-activated-by-aggregatibacter-actinomycetemcomitans-and-by-the-periodontal-microbiome
#18
Szymon P Szafrański, Zhi-Luo Deng, Jürgen Tomasch, Michael Jarek, Sabin Bhuju, Manfred Rohde, Helena Sztajer, Irene Wagner-Döbler
BACKGROUND: The oral cavity is inhabited by complex microbial communities forming biofilms that can cause caries and periodontitis. Cell-cell communication might play an important role in modulating the physiologies of individual species, but evidence so far is limited. RESULTS: Here we demonstrate that a pathogen of the oral cavity, Aggregatibacter actinomycetemcomitans (A. act.), triggers expression of the quorum sensing (QS) regulon of Streptococcus mutans, a well-studied model organism for cariogenic streptococci, in dual-species biofilms grown on artificial saliva...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28320307/perturbation-of-microbiota-in-one-day-old-broiler-chickens-with-antibiotic-for-24-hours-negatively-affects-intestinal-immune-development
#19
Dirkjan Schokker, Alfons J M Jansman, Gosse Veninga, Naomi de Bruin, Stephanie A Vastenhouw, Freddy M de Bree, Alex Bossers, Johanna M J Rebel, Mari A Smits
BACKGROUND: Gut microbial colonization and development of immune competence are intertwined and are influenced by early-life nutritional, environmental, and management factors. Perturbation of the gut microbiome at young age affects the crosstalk between intestinal bacteria and host cells of the intestinal mucosa. RESULTS: We investigated the effect of a perturbation of the normal early life microbial colonization of the jejunum in 1-day old chickens. Perturbation was induced by administering 0...
March 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28302071/sex-differences-in-the-molecular-signature-of-the-developing-mouse-hippocampus
#20
Joseph L Bundy, Cynthia Vied, Richard S Nowakowski
BACKGROUND: A variety of neurological disorders, including Alzheimer's disease, Parkinson's disease, major depressive disorder, dyslexia and autism, are differentially prevalent between females and males. To better understand the possible molecular basis for the sex-biased nature of neurological disorders, we used a developmental series of female and male mice at 1, 2, and 4 months of age to assess both mRNA and protein in the hippocampus with RNA-sequencing and mass-spectrometry, respectively...
March 16, 2017: BMC Genomics
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