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BMC Genomics | Page 2

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https://read.qxmd.com/read/31477016/dynamics-of-transcriptome-changes-during-subcutaneous-preadipocyte-differentiation-in-ducks
#21
Zheng Wang, Zhong-Tao Yin, Fan Zhang, Xiao-Qin Li, Si-Rui Chen, Ning Yang, Tom E Porter, Zhuocheng Hou
BACKGROUND: Pekin duck is an important animal model for its ability for fat synthesis and deposition. However, transcriptional dynamic regulation of adipose differentiation driven by complex signal cascades remains largely unexplored in this model. This study aimed to explore adipogenic transcriptional dynamics before (proliferation) and after (differentiation) initial preadipocyte differentiation in ducks. RESULTS: Exogenous oleic acid alone successfully induced duck subcutaneous preadipocyte differentiation...
September 2, 2019: BMC Genomics
https://read.qxmd.com/read/31477015/exploration-of-tissue-specific-gene-expression-patterns-underlying-timing-of-breeding-in-contrasting-temperature-environments-in-a-song-bird
#22
Veronika N Laine, Irene Verhagen, A Christa Mateman, Agata Pijl, Tony D Williams, Phillip Gienapp, Kees van Oers, Marcel E Visser
BACKGROUND: Seasonal timing of breeding is a life history trait with major fitness consequences but the genetic basis of the physiological mechanism underlying it, and how gene expression is affected by date and temperature, is not well known. In order to study this, we measured patterns of gene expression over different time points in three different tissues of the hypothalamic-pituitary-gonadal-liver axis, and investigated specifically how temperature affects this axis during breeding...
September 2, 2019: BMC Genomics
https://read.qxmd.com/read/31477011/genomic-content-of-chemosensory-genes-correlates-with-host-range-in-wood-boring-beetles-dendroctonus-ponderosae-agrilus-planipennis-and-anoplophora-glabripennis
#23
Martin N Andersson, Christopher I Keeling, Robert F Mitchell
BACKGROUND: Olfaction and gustation underlie behaviors that are crucial for insect fitness, such as host and mate selection. The detection of semiochemicals is mediated via proteins from large and rapidly evolving chemosensory gene families; however, the links between a species' ecology and the diversification of these genes remain poorly understood. Hence, we annotated the chemosensory genes from genomes of select wood-boring coleopterans, and compared the gene repertoires from stenophagous species with those from polyphagous species...
September 2, 2019: BMC Genomics
https://read.qxmd.com/read/31477010/bioinformatics-and-dna-extraction-strategies-to-reliably-detect-genetic-variants-from-ffpe-breast-tissue-samples
#24
Aditya Vijay Bhagwate, Yuanhang Liu, Stacey J Winham, Samantha J McDonough, Melody L Stallings-Mann, Ethan P Heinzen, Jaime I Davila, Robert A Vierkant, Tanya L Hoskin, Marlene Frost, Jodi M Carter, Derek C Radisky, Julie M Cunningham, Amy C Degnim, Chen Wang
BACKGROUND: Archived formalin fixed paraffin embedded (FFPE) samples are valuable clinical resources to examine clinically relevant morphology features and also to study genetic changes. However, DNA quality and quantity of FFPE samples are often sub-optimal, and resulting NGS-based genetics variant detections are prone to false positives. Evaluations of wet-lab and bioinformatics approaches are needed to optimize variant detection from FFPE samples. RESULTS: As a pilot study, we designed within-subject triplicate samples of DNA derived from paired FFPE and fresh frozen breast tissues to highlight FFPE-specific artifacts...
September 2, 2019: BMC Genomics
https://read.qxmd.com/read/31477008/mitochondrial-genomic-variation-drives-differential-nuclear-gene-expression-in-discrete-regions-of-drosophila-gene-and-protein-interaction-networks
#25
Jim A Mossman, Leann M Biancani, David M Rand
BACKGROUND: Mitochondria perform many key roles in their eukaryotic hosts, from integrating signaling pathways through to modulating whole organism phenotypes. The > 1 billion years of nuclear and mitochondrial gene co-evolution has necessitated coordinated expression of gene products from both genomes that maintain mitochondrial, and more generally, eukaryotic cellular function. How mitochondrial DNA (mtDNA) variation modifies host fitness has proved a challenging question but has profound implications for evolutionary and medical genetics...
September 2, 2019: BMC Genomics
https://read.qxmd.com/read/31477007/salmotifdb-a-tool-for-analyzing-putative-transcription-factor-binding-sites-in-salmonid-genomes
#26
Teshome Dagne Mulugeta, Torfinn Nome, Thu-Hien To, Manu Kumar Gundappa, Daniel J Macqueen, Dag Inge Våge, Simen Rød Sandve, Torgeir R Hvidsten
BACKGROUND: Recently developed genome resources in Salmonid fish provides tools for studying the genomics underlying a wide range of properties including life history trait variation in the wild, economically important traits in aquaculture and the evolutionary consequences of whole genome duplications. Although genome assemblies now exist for a number of salmonid species, the lack of regulatory annotations are holding back our mechanistic understanding of how genetic variation in non-coding regulatory regions affect gene expression and the downstream phenotypic effects...
September 2, 2019: BMC Genomics
https://read.qxmd.com/read/31472675/transcriptome-profiling-reveals-candidate-flavonol-related-genes-of-tetrastigma-hemsleyanum-under-cold-stress
#27
Xin Peng, Hao Wu, Hongjiang Chen, Yujiong Zhang, Dan Qiu, Zhongyi Zhang
BACKGROUND: Tetrastigma hemsleyanum Diels et Gilg is a valuable medicinal herb, whose main bioactive constituents are flavonoids. Chilling sensitivity is the dominant environmental factor limiting growth and development of the plants. But the mechanisms of cold sensitivity in this plant are still unclear. Also, not enough information on genes involved in flavonoid biosynthesis in T. hemsleyanum is available to understand the mechanisms of its physiological and pharmaceutical effects. RESULTS: The electrolyte leakage, POD activity, soluble protein, and MDA content showed a linear sustained increase under cold stress...
August 31, 2019: BMC Genomics
https://read.qxmd.com/read/31470809/minor-intron-splicing-revisited-identification-of-new-minor-intron-containing-genes-and-tissue-dependent-retention-and-alternative-splicing-of-minor-introns
#28
Anouk M Olthof, Katery C Hyatt, Rahul N Kanadia
BACKGROUND: Mutations in minor spliceosome components such as U12 snRNA (cerebellar ataxia) and U4atac snRNA (microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1)) result in tissue-specific symptoms. Given that the minor spliceosome is ubiquitously expressed, we hypothesized that these restricted phenotypes might be caused by the tissue-specific regulation of the minor spliceosome targets, i.e. minor intron-containing genes (MIGs). The current model of inefficient splicing is thought to apply to the regulation of the ~ 500 MIGs identified in the U12DB...
August 30, 2019: BMC Genomics
https://read.qxmd.com/read/31470795/the-komodo-dragon-varanus-komodoensis-genome-and-identification-of-innate-immunity-genes-and-clusters
#29
Monique L van Hoek, M Dennis Prickett, Robert E Settlage, Lin Kang, Pawel Michalak, Kent A Vliet, Barney M Bishop
BACKGROUND: We report the sequencing, assembly and analysis of the genome of the Komodo dragon (Varanus komodoensis), the largest extant lizard, with a focus on antimicrobial host-defense peptides. The Komodo dragon diet includes carrion, and a complex milieu of bacteria, including potentially pathogenic strains, has been detected in the saliva of wild dragons. They appear to be unaffected, suggesting that dragons have robust defenses against infection. While little information is available regarding the molecular biology of reptile immunity, it is believed that innate immunity, which employs antimicrobial host-defense peptides including defensins and cathelicidins, plays a more prominent role in reptile immunity than it does in mammals...
August 30, 2019: BMC Genomics
https://read.qxmd.com/read/31470794/sigprofilermatrixgenerator-a-tool-for-visualizing-and-exploring-patterns-of-small-mutational-events
#30
Erik N Bergstrom, Mi Ni Huang, Uma Mahto, Mark Barnes, Michael R Stratton, Steven G Rozen, Ludmil B Alexandrov
BACKGROUND: Cancer genomes are peppered with somatic mutations imprinted by different mutational processes. The mutational pattern of a cancer genome can be used to identify and understand the etiology of the underlying mutational processes. A plethora of prior research has focused on examining mutational signatures and mutational patterns from single base substitutions and their immediate sequencing context. We recently demonstrated that further classification of small mutational events (including substitutions, insertions, deletions, and doublet substitutions) can be used to provide a deeper understanding of the mutational processes that have molded a cancer genome...
August 30, 2019: BMC Genomics
https://read.qxmd.com/read/31464595/comparative-transcriptome-and-coexpression-network-analysis-of-carpel-quantitative-variation-in-paeonia-rockii
#31
Na Liu, Fangyun Cheng, Yuan Zhong, Xin Guo
BACKGROUND: Quantitative variation of floral organs in plants is caused by an extremely complex process of transcriptional regulation. Despite progress in model plants, the molecular mechanisms of quantitative variation remain unknown in woody flower plants. The Paeonia rockii originated in China is a precious woody plant with ornamental, medicinal and oil properties. There is a wide variation in the number of carpel in P. rockii, but the molecular mechanism of the variation has rarely been studied...
August 29, 2019: BMC Genomics
https://read.qxmd.com/read/31464583/combining-next-generation-sequencing-and-single-molecule-sequencing-to-explore-brown-plant-hopper-responses-to-contrasting-genotypes-of-japonica-rice
#32
Jing Zhang, Wei Guan, Chaomei Huang, Yinxia Hu, Yu Chen, Jianping Guo, Cong Zhou, Rongzhi Chen, Bo Du, Lili Zhu, Danax Huanhan, Guangcun He
BACKGROUND: The brown plant hopper (BPH), Nilaparvata lugens, is one of the major pest of rice (Oryza sativa). Plant defenses against insect herbivores have been extensively studied, but our understanding of insect responses to host plants' resistance mechanisms is still limited. The purpose of this study is to characterize transcripts of BPH and reveal the responses of BPH insects to resistant rice at transcription level by using the advanced molecular techniques, the next-generation sequencing (NGS) and the single-molecule, real-time (SMRT) sequencing...
August 29, 2019: BMC Genomics
https://read.qxmd.com/read/31462233/itraq-based-quantitative-proteomic-and-physiological-analysis-of-the-response-to-n-deficiency-and-the-compensation-effect-in-rice
#33
Qiangqiang Xiong, Lei Zhong, Tianhua Shen, Chaohao Cao, Haohua He, Xiaorong Chen
BACKGROUND: The crop growth compensation effect is a naturally biological phenomenon, and nitrogen (N) is essential for crop growth and development, especially for yield formation. Little is known about the molecular mechanism of N deficiency and N compensation in rice. Thus, the N-sensitive stage of rice was selected to study N deficiency at the tillering stage and N compensation at the young panicle differentiation stage. In this study, a proteome analysis was performed to analyze leaf differentially expressed proteins (DEPs), and to investigate the leaf physiological characteristics and yield under N deficiency and after N compensation...
August 28, 2019: BMC Genomics
https://read.qxmd.com/read/31462226/differential-transcriptome-dynamics-during-the-onset-of-conceptus-elongation-and-between-female-and-male-porcine-embryos
#34
Shuqin Zeng, Jochen Bick, David Kradolfer, Johannes Knubben, Veronika L Flöter, Stefan Bauersachs, Susanne E Ulbrich
BACKGROUND: Porcine embryos undergo rapid differentiation and expansion between Days 8 and 12 before attaching to the maternal uterine epithelial surface after Day 13. It is known that maternal recognition of pregnancy and successful implantation are driven by mutual interactions between the elongated conceptus and the maternal endometrium. While most of the genes involved in regulation of embryo development are located on autosomal chromosomes, gene expression on sex chromosomes is modulating development through sex-specific transcription...
August 28, 2019: BMC Genomics
https://read.qxmd.com/read/31462217/natural-allelic-variations-of-saccharomyces-cerevisiae-impact-stuck-fermentation-due-to-the-combined-effect-of-ethanol-and-temperature-a-qtl-mapping-study
#35
Philippe Marullo, Pascal Durrens, Emilien Peltier, Margaux Bernard, Chantal Mansour, Denis Dubourdieu
BACKGROUND: Fermentation completion is a major prerequisite in many industrial processes involving the bakery yeast Saccharomyces cerevisiae. Stuck fermentations can be due to the combination of many environmental stresses. Among them, high temperature and ethanol content are particularly deleterious especially in bioethanol and red wine production. Although the genetic causes of temperature and/or ethanol tolerance were widely investigated in laboratory conditions, few studies investigated natural genetic variations related to stuck fermentations in high gravity matrixes...
August 28, 2019: BMC Genomics
https://read.qxmd.com/read/31455240/evidence-for-a-non-canonical-jak-stat-signaling-pathway-in-the-synthesis-of-the-brain-s-major-ion-channels-and-neurotransmitter-receptors
#36
Kathryn M Hixson, Meaghan Cogswell, Amy R Brooks-Kayal, Shelley J Russek
BACKGROUND: Brain-derived neurotrophic factor (BDNF) is a major signaling molecule that the brain uses to control a vast network of intracellular cascades fundamental to properties of learning and memory, and cognition. While much is known about BDNF signaling in the healthy nervous system where it controls the mitogen activated protein kinase (MAPK) and cyclic-AMP pathways, less is known about its role in multiple brain disorders where it contributes to the dysregulated neuroplasticity seen in epilepsy and traumatic brain injury (TBI)...
August 28, 2019: BMC Genomics
https://read.qxmd.com/read/31455224/rna-seq-of-eight-different-poplar-clones-reveals-conserved-up-regulation-of-gene-expression-in-response-to-insect-herbivory
#37
Niels A Müller, Birgit Kersten, Matthias Fladung, Hilke Schroeder
BACKGROUND: Herbivorous insects can have a profound impact on plant growth performance. In some years, canopy damage in poplar plantations exceeds 50% of the total leaf surface, thereby possibly compromising carbon fixation and biomass yield. To assess the transcriptional response of elite poplar clones to insect feeding and to test whether this response varies between different genotypes, we performed an RNA-sequencing experiment. We deeply sequenced the transcriptomes of eight elite clones belonging to three poplar species (Populus trichocarpa, P...
August 28, 2019: BMC Genomics
https://read.qxmd.com/read/31455222/comparative-transcription-analysis-of-photosensitive-and-non-photosensitive-eggplants-to-identify-genes-involved-in-dark-regulated-anthocyanin-synthesis
#38
Yongjun He, Hang Chen, Lu Zhou, Yang Liu, Huoying Chen
BACKGROUND: Light is a key environmental factor in regulation of anthocyanin biosynthesis. Through a large number of bagging screenings, we obtained non-photosensitive eggplants that still have decent amount of anthocyanin synthesized after bagging. In the present study, transcriptome was made to explore the molecular mechanism of dark-regulated anthocyanin synthesis in non-photosensitive eggplant. RESULTS: The transcriptome of the pericarp at 0 h, 0.5 h, 4 h, and 8 h after bag removal were sequenced and analyzed...
August 28, 2019: BMC Genomics
https://read.qxmd.com/read/31455241/proteomic-informed-by-transcriptomic-for-salivary-glands-components-of-the-camel-tick-hyalomma-dromedarii
#39
Chaima Bensaoud, Hajer Aounallah, Juliana Mozer Sciani, Fernanda Faria, Ana Marisa Chudzinski-Tavassi, Ali Bouattour, Youmna M'ghirbi
BACKGROUND: The hard tick Hyalomma dromedarii is one of the most injurious ectoparasites affecting camels and apparently best adapted to deserts. As long-term blood feeders, ticks are threatened by host defense system compounds that can cause them to be rejected and, ultimately, to die. However, their saliva contains a cocktail of bioactive molecules that enables them to succeed in taking their blood meal. A recent sialotranscriptomic study uncovered the complexity of the salivary composition of the tick H...
August 27, 2019: BMC Genomics
https://read.qxmd.com/read/31455220/single-cell-explorer-collaboration-driven-tools-to-leverage-large-scale-single-cell-rna-seq-data
#40
Di Feng, Charles E Whitehurst, Dechao Shan, Jon D Hill, Yong G Yue
BACKGROUND: Single cell transcriptome sequencing has become an increasingly valuable technology for dissecting complex biology at a resolution impossible with bulk sequencing. However, the gap between the technical expertise required to effectively work with the resultant high dimensional data and the biological expertise required to interpret the results in their biological context remains incompletely addressed by the currently available tools. RESULTS: Single Cell Explorer is a Python-based web server application we developed to enable computational and experimental scientists to iteratively and collaboratively annotate cell expression phenotypes within a user-friendly and visually appealing platform...
August 27, 2019: BMC Genomics
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