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https://www.readbyqxmd.com/read/27923054/fused-regression-for-multi-source-gene-regulatory-network-inference
#1
Kari Y Lam, Zachary M Westrick, Christian L Müller, Lionel Christiaen, Richard Bonneau
Understanding gene regulatory networks is critical to understanding cellular differentiation and response to external stimuli. Methods for global network inference have been developed and applied to a variety of species. Most approaches consider the problem of network inference independently in each species, despite evidence that gene regulation can be conserved even in distantly related species. Further, network inference is often confined to single data-types (single platforms) and single cell types. We introduce a method for multi-source network inference that allows simultaneous estimation of gene regulatory networks in multiple species or biological processes through the introduction of priors based on known gene relationships such as orthology incorporated using fused regression...
December 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27922023/systematic-site-directed-mutagenesis-of-the-helicobacter-pylori-cagl-protein-of-the-cag-type-iv-secretion-system-identifies-novel-functional-domains
#2
Tobias Bönig, Patrick Olbermann, Simon H Bats, Wolfgang Fischer, Christine Josenhans
The Cag Type IV secretion system, which contributes to inflammation and cancerogenesis during chronic infection, is one of the major virulence factors of the bacterial gastric pathogen Helicobacter pylori. We have generated and characterized a series of non-marked site-directed chromosomal mutants in H. pylori to define domains of unknown function of the essential tip protein CagL of the Cag secretion system. Characterizing the CagL mutants, we determined that their function to activate cells and transport the effector CagA was reduced to different extents...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920211/outer-membrane-proteins-bb0405-and-bb0406-are-immunogenic-but-only-bb0405-is-required-for-borrelia-burgdorferi-infection
#3
Binu Shrestha, Melisha R Kenedy, Darrin R Akins
We recently identified the Borrelia burgdorferi outer membrane protein (OMP) BB0406 and found that the gene encoding this OMP was co-transcribed with the gene encoding the OMP BB0405. Interestingly, BB0405 and BB0406 share 59% similarity and are grouped into the same B. burgdorferi paralogous gene family. Given their overall similarity, it is plausible that both OMPs have similar or overlapping functions in this pathogenic spirochete. BB0405 has recently been shown to be required for mammalian infection despite the observations that BB0405 is poorly immunogenic and not recognized during mouse or human infection...
December 5, 2016: Infection and Immunity
https://www.readbyqxmd.com/read/27919758/the-chemokinome-superfamily-in-channel-catfish-i-cxc-subfamily-and-their-involvement-in-disease-defense-and-hypoxia-responses
#4
Qiang Fu, Qifan Zeng, Yun Li, Yujia Yang, Chao Li, Shikai Liu, Tao Zhou, Ning Li, Jun Yao, Chen Jiang, Daoji Li, Zhanjiang Liu
Chemokines are a superfamily of structurally related chemotactic cytokines exerting significant roles in regulating cell migration and activation. They are defined by the presence of four conserved cysteine residues and are divided into four subfamilies depending on the arrangement of the first two conserved cysteines residues: CXC, CC, C and CX3C. In this study, a complete set of 17 CXC chemokine ligand (CXCL) genes was systematically identified and characterized from channel catfish genome through data mining of existing genomic resources...
December 2, 2016: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/27918943/expression-of-metallothionein-in-the-liver-and-kidneys-of-the-red-deer-cervus-elaphus-l-from-an-industrial-metal-smelting-area-of-poland
#5
Maciej Durkalec, Rafał Kolenda, Tomasz Owczarek, Józef Szkoda, Agnieszka Nawrocka, Jędrzej Grzegrzółka, Piotr Dzięgiel, Piotr Socha, Roman Kołacz, Peter Schierack, Jan Żmudzki, Andrzej Posyniak
The metallothionein 1 (MT1) coding sequence of red deer was identified and compared to orthologous sequences from other mammals. Over 90% identity was observed between red deer MT1 amino acid sequence and MT1 sequences of other ruminants. Liver and kidney samples of red deer were collected from the industrial zinc smelting site of Miasteczko Slaskie and from the Masuria Lake District serving as a pollution-free control site. The concentrations of cadmium (Cd), lead (Pb), copper (Cu) and zinc (Zn) were analyzed by the atomic absorption spectrometry technique (AAS)...
December 2, 2016: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/27918582/investigating-conservation-of-the-cell-cycle-regulated-transcriptional-program-in-the-fungal-pathogen-cryptococcus-neoformans
#6
Christina M Kelliher, Adam R Leman, Crystal S Sierra, Steven B Haase
The pathogenic yeast Cryptococcus neoformans causes fungal meningitis in immune-compromised patients. Cell proliferation in the budding yeast form is required for C. neoformans to infect human hosts, and virulence factors such as capsule formation and melanin production are affected by cell-cycle perturbation. Thus, understanding cell-cycle regulation is critical for a full understanding of virulence factors for disease. Our group and others have demonstrated that a large fraction of genes in Saccharomyces cerevisiae is expressed periodically during the cell cycle, and that proper regulation of this transcriptional program is important for proper cell division...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27918468/transcriptome-analysis-of-the-tadpole-shrimp-triops-longicaudatus-by-illumina-paired-end-sequencing-assembly-annotation-and-marker-discovery
#7
Jiyeon Seong, Se Won Kang, Bharat Bhusan Patnaik, So Young Park, Hee Ju Hwang, Jong Min Chung, Dae Kwon Song, Mi Young Noh, Seung-Hwan Park, Gwang Joo Jeon, Hong Sik Kong, Soonok Kim, Ui Wook Hwang, Hong Seog Park, Yeon Soo Han, Yong Seok Lee
The tadpole shrimp (Triops longicaudatus) is an aquatic crustacean that helps control pest populations. It inhabits freshwater ponds and pools and has been described as a living fossil. T. longicaudatus was officially declared an endangered species South Korea in 2005; however, through subsequent protection and conservation management, it was removed from the endangered species list in 2012. The limited number of available genetic resources on T. longicaudatus makes it difficult to obtain valuable genetic information for marker-aided selection programs...
December 2, 2016: Genes
https://www.readbyqxmd.com/read/27918306/targeting-integrin-%C3%AE-5%C3%AE-1-ameliorates-severe-airway-hyperresponsiveness-in-experimental-asthma
#8
Aparna Sundaram, Chun Chen, Amin Khalifeh-Soltani, Amha Atakilit, Xin Ren, Wenli Qiu, Hyunil Jo, William DeGrado, Xiaozhu Huang, Dean Sheppard
Treatment options are limited for severe asthma, and the need for additional therapies remains great. Previously, we demonstrated that integrin αvβ6-deficient mice are protected from airway hyperresponsiveness, due in part to increased expression of the murine ortholog of human chymase. Here, we determined that chymase protects against cytokine-enhanced bronchoconstriction by cleaving fibronectin to impair tension transmission in airway smooth muscle (ASM). Additionally, we identified a pathway that can be therapeutically targeted to mitigate the effects of airway hyperresponsiveness...
December 5, 2016: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/27917941/comparative-phylogenomic-analysis-provides-insights-into-tcp-gene-functions-in-sorghum
#9
Aleena Francis, Namrata Dhaka, Mohit Bakshi, Ki-Hong Jung, Manoj K Sharma, Rita Sharma
Sorghum is a highly efficient C4 crop with potential to mitigate challenges associated with food, feed and fuel. TCP proteins are of particular interest for crop improvement programs due to their well-demonstrated roles in crop domestication and shaping plant architecture thereby, affecting agronomic traits. We identified 20 TCP genes from Sorghum. Except SbTCP8, all are either intronless or contain introns in the untranslated regions. Comparative phylogenetic analysis of Arabidopsis, rice, Brachypodium and Sorghum TCP proteins revealed two distinct classes categorized into ten sub-clades...
December 5, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27917435/analysis-of-the-ionic-interaction-between-the-hydrophobin-roda-and-two-cutinases-of-aspergillus-nidulans-obtained-via-an-aspergillus-oryzae-expression-system
#10
Takumi Tanaka, Mayumi Nakayama, Toru Takahashi, Kei Nanatani, Youhei Yamagata, Keietsu Abe
Hydrophobins are amphipathic secretory proteins with eight conserved cysteine residues and are ubiquitous among filamentous fungi. In the fungus Aspergillus oryzae, the hydrophobin RolA and the polyesterase CutL1 are co-expressed when the sole available carbon source is the biodegradable polyester polybutylene succinate-co-adipate (PBSA). RolA promotes the degradation of PBSA by attaching to the particle surface, changing its structure and interacting with CutL1 to concentrate CutL1 on the PBSA surface. We previously reported that positively charged residues in RolA and negatively charged residues in CutL1 are cooperatively involved in the ionic interaction between RolA and CutL1...
December 5, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27917290/functional-analysis-of-alternative-splicing-of-the-flowering-locus-t-orthologous-gene-in-chrysanthemum-morifolium
#11
Yachao Mao, Jing Sun, Peipei Cao, Rong Zhang, Qike Fu, Sumei Chen, Fadi Chen, Jiafu Jiang
As the junction of floral development pathways, the FLOWERING LOCUS T (FT) protein called 'florigen' plays an important role in the process of plant flowering through signal integration. We isolated four transcripts encoding different isoforms of a FT orthologous gene CmFTL1, from Chrysanthemum morifolium cultivar 'Jimba'. Sequence alignments suggested that the four transcripts are related to the intron 1. Expression analysis showed that four alternative splicing (AS) forms of CmFTL1 varied depending on the developmental stage of the flower...
2016: Horticulture Research
https://www.readbyqxmd.com/read/27917166/temporal-metagenomic-and-metabolomic-characterization-of-fresh-perennial-ryegrass-degradation-by-rumen-bacteria
#12
Olga L Mayorga, Alison H Kingston-Smith, Eun J Kim, Gordon G Allison, Toby J Wilkinson, Matthew J Hegarty, Michael K Theodorou, Charles J Newbold, Sharon A Huws
Understanding the relationship between ingested plant material and the attached microbiome is essential for developing methodologies to improve ruminant nutrient use efficiency. We have previously shown that perennial ryegrass (PRG) rumen bacterial colonization events follow a primary (up to 4 h) and secondary (after 4 h) pattern based on the differences in diversity of the attached bacteria. In this study, we investigated temporal niche specialization of primary and secondary populations of attached rumen microbiota using metagenomic shotgun sequencing as well as monitoring changes in the plant chemistry using mid-infrared spectroscopy (FT-IR)...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27916924/divergent-expression-patterns-in-two-vernicia-species-revealed-the-potential-role-of-the-hub-gene-vmap2-erf036-in-resistance-to-fusarium-oxysporum-in-vernicia-montana
#13
Qiyan Zhang, Ming Gao, Liwen Wu, Yangdong Wang, Yicun Chen
Tung oil tree (Vernicia fordii) is a promising industrial oil crop; however, this tree is highly susceptible to Fusarium wilt disease. Conversely, Vernicia montana is resistant to the pathogen. The APETALA2/ethylene-responsive element binding factor (AP2/ERF) transcription factor superfamily has been reported to play a significant role in resistance to Fusarium oxysporum. In this study, comprehensive analysis identified 75 and 81 putative Vf/VmAP2/ERF transcription factor-encoding genes in V. fordii and V. montana, respectively, which were divided into AP2, ERF, related to ABI3 and VP1 (RAV) and Soloist families...
December 1, 2016: Genes
https://www.readbyqxmd.com/read/27915410/the-properties-and-potential-metabolic-role-of-glucokinase-in-halotolerant-obligate-methanotroph-methylomicrobium-alcaliphilum-20z
#14
Ildar I Mustakhimov, Olga N Rozova, Natalia P Solntseva, Valentina N Khmelenina, Alexander S Reshetnikov, Yuri A Trotsenko
Aerobic bacteria utilizing methane as the carbon and energy source do not use sugars as growth substrates but possess the gene coding for glucokinase (Glk), an enzyme converting glucose into glucose 6-phosphate. Here we demonstrate the functionality and properties of Glk from an obligate methanotroph Methylomicrobium alcaliphilum 20Z. The recombinant Glk obtained by heterologous expression in Escherichia coli was found to be close in biochemical properties to other prokaryotic Glks. The homodimeric enzyme (2 × 35 kDa) catalyzed ATP-dependent phosphorylation of glucose and glucosamine with nearly equal activity, being inhibited by ADP (K i = 2...
December 3, 2016: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/27914199/filamin-a-synaptic-organizer-in-drosophila-determines-glutamate-receptor-composition-and-membrane-growth
#15
GaYoung Lee, Thomas L Schwarz
Filamin is a scaffolding protein that functions in many cells as an actin-crosslinker. FLN90, an isoform of the Drosophila ortholog Filamin/cheerio that lacks the actin-binding domain, is here shown to govern the growth of postsynaptic membrane folds and the composition of glutamate receptor clusters at the larval neuromuscular junction. Genetic and biochemical analyses revealed that FLN90 is present surrounding synaptic boutons. FLN90 is required in the muscle for localization of the kinase dPak and, downstream of dPak, for localization of the GTPase Ral and the exocyst complex to this region...
December 3, 2016: ELife
https://www.readbyqxmd.com/read/27913623/chac2-an-enzyme-for-slow-turnover-of-cytosolic-glutathione
#16
Amandeep Kaur, Ruchi Gautam, Ritika Srivastava, Avinash Chandel, Akhilesh Kumar, Subramanian Karthikeyan, Anand Kumar Bachhawat
Glutathione degradation plays an important role in glutathione and redox homeostasis and thus it is imperative to understand the enzymes and the mechanisms involved in glutathione degradation in detail. We describe here ChaC2, a member of the ChaC family of γ-glutamylcyclotransferases, as an enzyme that degrades glutathione in the cytosol of mammalian cells. ChaC2 is distinct from the previously described ChaC1, to which ChaC2 shows about 50% sequence identity. Human and mouse ChaC2 proteins, purified in vitro, show 10-20 fold lower catalytic efficiency than ChaC1, although they showed comparable Km values (Km of 3...
December 2, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27913622/a-venom-serpin-splicing-isoform-of-the-endoparasitoid-wasp-pteromalus-puparum-suppresses-host-prophenoloxidase-cascade-by-forming-complexes-with-host-hemolymph-proteinases
#17
Zhichao Yan, Qi Fang, Yang Liu, Shan Xiao, Lei Yang, Fei Wang, Chunju An, John H Werren, Gongyin Ye
To ensure successful parasitism, parasitoid wasps inject venom along with their eggs into their hosts. The venom serves to suppress host immune responses, including melanization. Venom from Pteromalus puparum, a pupal endoparasitoid, inhibits melanization of host hemolymph in vitro in a dose-dependent manner. Using assay guided fractionation, a serpin splicing isoform with phenoloxidase (PO) inhibitory activity was identified as P. puparum serpin-1, venom isoform (PpS1V). This serpin gene has 16 predicted splicing isoforms that differ only in the C-terminal region...
December 2, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/27913309/sequence-determinants-of-the-caenhorhabditis-elegansdopamine-transporter-dictating-in-vivoaxonal-export-and-synaptic-localization
#18
Sarah B Robinson, J Andrew Hardaway, Shannon L Hardie, Jane Wright, Ryan M Glynn, Daniel P Bermingham, Qiao Han, Sarah M Sturgeon, Phyllis Freeman, Randy D Blakely
The monoamine neurotransmitter dopamine (DA) acts across phylogeny to modulate both simple and complex behaviors. The presynaptic DA transporter (DAT) is a major determinant of DA signaling capacity in ensuring efficient extracellular DA clearance. In humans, DAT is also a major target for prescribed and abused psychostimulants. Multiple structural determinants of DAT function and regulation have been defined, though largely these findings have arisen from heterologous expression or ex vivo cell culture studies...
November 29, 2016: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/27913140/comparative-analysis-of-tcdd-induced-ahr-mediated-gene-expression-in-human-mouse-and-rat-primary-b-cells
#19
Natalia Kovalova, Rance Nault, Robert Crawford, Timothy R Zacharewski, Norbert E Kaminski
2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) is a persistent environmental pollutant that activates the aryl hydrocarbon receptor (AhR) resulting in altered gene expression. In vivo, in vitro, and ex vivo studies have demonstrated that B cells are directly impaired by TCDD, and are a sensitive target as evidenced by suppression of antibody responses. The window of sensitivity to TCDD-induced suppression of IgM secretion among mouse, rat and human B cells is similar. Specifically, TCDD must be present within the initial 12h post B cell stimulation, indicating that TCDD disrupts early signaling network(s) necessary for B lymphocyte activation and differentiation...
November 29, 2016: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/27911958/advantages-of-an-improved-rhesus-macaque-genome-for-evolutionary-analyses
#20
Julien S Gradnigo, Abhishek Majumdar, Robert B Norgren, Etsuko N Moriyama
The rhesus macaque (Macaca mulatta) is widely used in molecular evolutionary analyses, particularly to identify genes under adaptive or unique evolution in the human lineage. For such studies, it is necessary to align nucleotide sequences of homologous protein-coding genes among multiple species. The validity of these analyses is dependent on high quality genomic data. However, for most mammalian species (other than humans and mice), only draft genomes are available. There has been concern that some results obtained from evolutionary analyses using draft genomes may not be correct...
2016: PloS One
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