journal
MENU ▼
Read by QxMD icon Read
search

BMC Genomics

journal
https://www.readbyqxmd.com/read/29347977/expansion-of-cytochrome-p450-and-cathepsin-genes-in-the-generalist-herbivore-brown-marmorated-stink-bug
#1
Raman Bansal, Andy Michel
BACKGROUND: The brown marmorated stink bug (Halyomorpha halys) is an invasive pest in North America which causes severe economic losses on tree fruits, ornamentals, vegetables, and field crops. The H. halys is an extreme generalist and this feeding behaviour may have been a major contributor behind its establishment and successful adaptation in invasive habitats of North America. To develop an understanding into the mechanism of H. halys' generalist herbivory, here we specifically focused on genes putatively facilitating its adaptation on diverse host plants...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29347914/in-depth-proteomic-analysis-of-boar-spermatozoa-through-shotgun-and-gel-based-methods
#2
Jean M Feugang, Shengfa F Liao, Scott T Willard, Peter L Ryan
BACKGROUND: Mature spermatozoa contain numerous epididymal and seminal plasma proteins, which full identification through high-throughput technologies may allow for a better understanding of the sperm biology. Therefore, we conducted a global proteomic analysis of boar spermatozoa through shotgun and gel-based methodologies. RESULTS: The total proteins were extracted from mature spermatozoa and subjecsted to proteome analyses. Functional analyses of gene ontology representations and pathway enrichments were conducted on the shotgun dataset, followed by immunology and gene expression validations...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29347912/genome-wide-analysis-of-the-potato-hsp20-gene-family-identification-genomic-organization-and-expression-profiles-in-response-to-heat-stress
#3
Peng Zhao, Dongdong Wang, Ruoqiu Wang, Nana Kong, Chao Zhang, Chenghui Yang, Wentao Wu, Haoli Ma, Qin Chen
BACKGROUND: Heat shock proteins (Hsps) are essential components in plant tolerance mechanism under various abiotic stresses. Hsp20 is the major family of heat shock proteins, but little of Hsp20 family is known in potato (Solanum tuberosum), which is an important vegetable crop that is thermosensitive. RESULTS: To reveal the mechanisms of potato Hsp20s coping with abiotic stresses, analyses of the potato Hsp20 gene family were conducted using bioinformatics-based methods...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29347911/micrornas-associated-with-early-neural-crest-development-in-xenopus-laevis
#4
Nicole J Ward, Darrell Green, Janet Higgins, Tamas Dalmay, Andrea Münsterberg, Simon Moxon, Grant N Wheeler
BACKGROUND: The neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos. NC cells arise within the dorsal neural tube where they undergo an epithelial to mesenchymal transition in order to migrate and differentiate throughout the developing embryo. The derivative cell types give rise to multiple tissues, including the craniofacial skeleton, peripheral nervous system and skin pigment cells. Several well-studied gene regulatory networks underpin NC development, which when disrupted can lead to various neurocristopathies such as craniofrontonasal dysplasia, DiGeorge syndrome and some forms of cancer...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29343235/comparison-of-three-assembly-strategies-for-a-heterozygous-seedless-grapevine-genome-assembly
#5
Sagar Patel, Zhixiu Lu, Xiaozhu Jin, Padmapriya Swaminathan, Erliang Zeng, Anne Y Fennell
BACKGROUND: De novo heterozygous assembly is an ongoing challenge requiring improved assembly approaches. In this study, three strategies were used to develop de novo Vitis vinifera 'Sultanina' genome assemblies for comparison with the inbred V. vinifera (PN40024 12X.v2) reference genome and a published Sultanina ALLPATHS-LG assembly (AP). The strategies were: 1) a default PLATANUS assembly (PLAT_d) for direct comparison with AP assembly, 2) an iterative merging strategy using METASSEMBLER to combine PLAT_d and AP assemblies (MERGE) and 3) PLATANUS parameter modifications plus GapCloser (PLAT*_GC)...
January 17, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29343217/ceratocystis-cacaofunesta-genome-analysis-reveals-a-large-expansion-of-extracellular-phosphatidylinositol-specific-phospholipase-c-genes-pi-plc
#6
Eddy Patricia Lopez Molano, Odalys García Cabrera, Juliana Jose, Leandro Costa do Nascimento, Marcelo Falsarella Carazzolle, Paulo José Pereira Lima Teixeira, Javier Correa Alvarez, Ricardo Augusto Tiburcio, Paulo Massanari Tokimatu Filho, Gustavo Machado Alvares de Lima, Rafael Victório Carvalho Guido, Thamy Lívia Ribeiro Corrêa, Adriana Franco Paes Leme, Piotr Mieczkowski, Gonçalo Amarante Guimarães Pereira
BACKGROUND: The Ceratocystis genus harbors a large number of phytopathogenic fungi that cause xylem parenchyma degradation and vascular destruction on a broad range of economically important plants. Ceratocystis cacaofunesta is a necrotrophic fungus responsible for lethal wilt disease in cacao. The aim of this work is to analyze the genome of C. cacaofunesta through a comparative approach with genomes of other Sordariomycetes in order to better understand the molecular basis of pathogenicity in the Ceratocystis genus...
January 17, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29338766/identification-of-differentially-expressed-genes-and-pathways-for-intramuscular-fat-metabolism-between-breast-and-thigh-tissues-of-chickens
#7
Huanxian Cui, Maiqing Zheng, Guiping Zhao, Ranran Liu, Jie Wen
BACKGROUND: Intramuscular fat (IMF) is one of the important factors influencing meat quality, however, for chickens, the molecular regulatory mechanisms underlying this trait have not yet been clear. In this study, a systematic identification of differentially expressed genes (DEGs) and molecular regulatory mechanism related to IMF metabolism between Beijing-you chicken breast and thigh at 42 and 90 days of age was performed. RESULTS: IMF contents, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, The results showed that both IMF contents in breast at 42 and 90 d were significantly lower (P < 0...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29338715/landscape-genomics-natural-selection-drives-the-evolution-of-mitogenome-in-penguins
#8
Barbara Ramos, Daniel González-Acuña, David E Loyola, Warren E Johnson, Patricia G Parker, Melanie Massaro, Gisele P M Dantas, Marcelo D Miranda, Juliana A Vianna
BACKGROUND: Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29338696/transcriptional-responses-of-escherichia-coli-during-recovery-from-inorganic-or-organic-mercury-exposure
#9
Stephen P LaVoie, Anne O Summers
BACKGROUND: The protean chemical properties of mercury have long made it attractive for diverse applications, but its toxicity requires great care in its use, disposal, and recycling. Mercury occurs in multiple chemical forms, and the molecular basis for the distinct toxicity of its various forms is only partly understood. Global transcriptomics applied over time can reveal how a cell recognizes a toxicant and what cellular subsystems it marshals to repair and recover from the damage...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29338691/morca-ubiquitous-access-to-life-science-web-services
#10
Sergio Diaz-Del-Pino, Oswaldo Trelles, Juan Falgueras
BACKGROUND: Technical advances in mobile devices such as smartphones and tablets have produced an extraordinary increase in their use around the world and have become part of our daily lives. The possibility of carrying these devices in a pocket, particularly mobile phones, has enabled ubiquitous access to Internet resources. Furthermore, in the life sciences world there has been a vast proliferation of data types and services that finish as Web Services. This suggests the need for research into mobile clients to deal with life sciences applications for effective usage and exploitation...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29338683/genomic-repeats-misassembly-and-reannotation-a-case-study-with-long-read-resequencing-of-porphyromonas-gingivalis-reference-strains
#11
Luis Acuña-Amador, Aline Primot, Edouard Cadieu, Alain Roulet, Frédérique Barloy-Hubler
BACKGROUND: Without knowledge of their genomic sequences, it is impossible to make functional models of the bacteria that make up human and animal microbiota. Unfortunately, the vast majority of publicly available genomes are only working drafts, an incompleteness that causes numerous problems and constitutes a major obstacle to genotypic and phenotypic interpretation. In this work, we began with an example from the class Bacteroidia in the phylum Bacteroidetes, which is preponderant among human orodigestive microbiota...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29338682/soybean-mads-box-gene-gmagl1-promotes-flowering-via-the-photoperiod-pathway
#12
Xuanrui Zeng, Hailun Liu, Hongyang Du, Sujing Wang, Wenming Yang, Yingjun Chi, Jiao Wang, Fang Huang, Deyue Yu
BACKGROUND: The MADS-box transcription factors are an ancient family of genes that regulate numerous physiological and biochemical processes in plants and facilitate the development of floral organs. However, the functions of most of these transcription factors in soybean remain unknown. RESULTS: In this work, a MADS-box gene, GmAGL1, was overexpressed in soybean. Phenotypic analysis showed that GmAGL1 overexpression not only resulted in early maturation but also promoted flowering and affected petal development...
January 16, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29334898/seq-seq-pan-building-a-computational-pan-genome-data-structure-on-whole-genome-alignment
#13
Christine Jandrasits, Piotr W Dabrowski, Stephan Fuchs, Bernhard Y Renard
BACKGROUND: The increasing application of next generation sequencing technologies has led to the availability of thousands of reference genomes, often providing multiple genomes for the same or closely related species. The current approach to represent a species or a population with a single reference sequence and a set of variations cannot represent their full diversity and introduces bias towards the chosen reference. There is a need for the representation of multiple sequences in a composite way that is compatible with existing data sources for annotation and suitable for established sequence analysis methods...
January 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29334897/the-genome-sequence-of-the-commercially-cultivated-mushroom-agrocybe-aegerita-reveals-a-conserved-repertoire-of-fruiting-related-genes-and-a-versatile-suite-of-biopolymer-degrading-enzymes
#14
Deepak K Gupta, Martin Rühl, Bagdevi Mishra, Vanessa Kleofas, Martin Hofrichter, Robert Herzog, Marek J Pecyna, Rahul Sharma, Harald Kellner, Florian Hennicke, Marco Thines
BACKGROUND: Agrocybe aegerita is an agaricomycete fungus with typical mushroom features, which is commercially cultivated for its culinary use. In nature, it is a saprotrophic or facultative pathogenic fungus causing a white-rot of hardwood in forests of warm and mild climate. The ease of cultivation and fructification on solidified media as well as its archetypal mushroom fruit body morphology render A. aegerita a well-suited model for investigating mushroom developmental biology. RESULTS: Here, the genome of the species is reported and analysed with respect to carbohydrate active genes and genes known to play a role during fruit body formation...
January 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29334896/global-analysis-of-prokaryotic-trna-derived-cyclodipeptide-biosynthesis
#15
Michael A Skinnider, Chad W Johnston, Nishanth J Merwin, Chris A Dejong, Nathan A Magarvey
BACKGROUND: Among naturally occurring small molecules, tRNA-derived cyclodipeptides are a class that have attracted attention for their diverse and desirable biological activities. However, no tools are available to link cyclodipeptide synthases identified within prokaryotic genome sequences to their chemical products. Consequently, it is unclear how many genetically encoded cyclodipeptides represent novel products, and which producing organisms should be targeted for discovery. RESULTS: We developed a pipeline for identification and classification of cyclodipeptide biosynthetic gene clusters and prediction of aminoacyl-tRNA substrates and complete chemical structures...
January 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29334895/challenges-imposed-by-minor-reference-alleles-on-the-identification-and-reporting-of-clinical-variants-from-exome-data
#16
Mahmoud Koko, Mohammed O E Abdallah, Mutaz Amin, Muntaser Ibrahim
BACKGROUND: The conventional variant calling of pathogenic alleles in exome and genome sequencing requires the presence of the non-pathogenic alleles as genome references. This hinders the correct identification of variants with minor and/or pathogenic reference alleles warranting additional approaches for variant calling. RESULTS: More than 26,000 Exome Aggregation Consortium (ExAC) variants have a minor reference allele including variants with known ClinVar disease alleles...
January 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29334893/high-sensitivity-hla-typing-by-saturated-tiling-capture-sequencing-stc-seq
#17
Yang Jiao, Ran Li, Chao Wu, Yibin Ding, Yanning Liu, Danmei Jia, Lifeng Wang, Xiang Xu, Jing Zhu, Min Zheng, Junling Jia
BACKGROUND: Highly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases. Additionally, it is routinely performed for identifying matched donors in transplantation medicine. Although many HLA typing approaches have been developed, the complexity, low-efficiency and high-cost of current HLA-typing assays limit their application in population-based high-throughput HLA typing for donors, which is required for creating large-scale databases for transplantation and precision medicine...
January 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29334892/the-genome-of-a-prasinoviruses-related-freshwater-virus-reveals-unusual-diversity-of-phycodnaviruses
#18
Hao Chen, Weijia Zhang, Xiefei Li, Yingjie Pan, Shuling Yan, Yongjie Wang
BACKGROUND: Phycodnaviruses are widespread algae-infecting large dsDNA viruses and presently contain six genera: Chlorovirus, Prasinovirus, Prymnesiovirus, Phaeovirus, Coccolithovirus and Raphidovirus. The members in Prasinovirus are identified as marine viruses due to their marine algal hosts, while prasinovirus freshwater relatives remain rarely reported. RESULTS: Here we present the complete genomic sequence of a novel phycodnavirus, Dishui Lake Phycodnavirus 1 (DSLPV1), which was assembled from Dishui Lake metagenomic datasets...
January 15, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29329522/a-game-improving-the-assembly-of-pooled-functional-metagenomics-sequence-data
#19
Matteo Chiara, Antonio Placido, Ernesto Picardi, Luigi Ruggiero Ceci, David Stephen Horner, Graziano Pesole
BACKGROUND: Expression screening of environmental DNA (eDNA) libraries is a popular approach for the identification and characterization of novel microbial enzymes with promising biotechnological properties. In such "functional metagenomics" experiments, inserts, selected on the basis of activity assays, are sequenced with high throughput sequencing technologies. Assembly is followed by gene prediction, annotation and identification of candidate genes that are subsequently evaluated for biotechnological applications...
January 12, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29329517/genome-wide-analyses-of-direct-target-genes-of-four-rice-nac-domain-transcription-factors-involved-in-drought-tolerance
#20
Pil Joong Chung, Harin Jung, Yang Do Choi, Ju-Kon Kim
BACKGROUND: Plant stress responses and mechanisms determining tolerance are controlled by diverse sets of genes. Transcription factors (TFs) have been implicated in conferring drought tolerance under drought stress conditions, and the identification of their target genes can elucidate molecular regulatory networks that orchestrate tolerance mechanisms. RESULTS: We generated transgenic rice plants overexpressing the 4 rice TFs, OsNAC5, 6, 9, and 10, under the control of the root-specific RCc3 promoter...
January 12, 2018: BMC Genomics
journal
journal
35180
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"