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https://www.readbyqxmd.com/read/28231264/precision-engineering-for-prrsv-resistance-in-pigs-macrophages-from-genome-edited-pigs-lacking-cd163-srcr5-domain-are-fully-resistant-to-both-prrsv-genotypes-while-maintaining-biological-function
#1
Christine Burkard, Simon G Lillico, Elizabeth Reid, Ben Jackson, Alan J Mileham, Tahar Ait-Ali, C Bruce A Whitelaw, Alan L Archibald
Porcine Reproductive and Respiratory Syndrome (PRRS) is a panzootic infectious disease of pigs, causing major economic losses to the world-wide pig industry. PRRS manifests differently in pigs of all ages but primarily causes late-term abortions and stillbirths in sows and respiratory disease in piglets. The causative agent of the disease is the positive-strand RNA PRRS virus (PRRSV). PRRSV has a narrow host cell tropism, limited to cells of the monocyte/macrophage lineage. CD163 has been described as a fusion receptor for PRRSV, whereby the scavenger receptor cysteine-rich domain 5 (SRCR5) region was shown to be an interaction site for the virus in vitro...
February 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28229641/food-additives-sodium-benzoate-potassium-sorbate-azorubine-and-tartrazine-modify-the-expression-of-nf%C3%AE%C2%BAb-gadd45%C3%AE-and-mapk8-genes
#2
B Raposa, R Pónusz, G Gerencsér, F Budán, Z Gyöngyi, A Tibold, D Hegyi, I Kiss, Á Koller, T Varjas
It has been reported that some of the food additives may cause sensitization, inflammation of tissues, and potentially risk factors in the development of several chronic diseases. Thus, we hypothesized that expressions of common inflammatory molecules - known to be involved in the development of various inflammatory conditions and cancers - are affected by these food additives. We investigated the effects of commonly used food preservatives and artificial food colorants based on the expressions of NFκB, GADD45α, and MAPK8 (JNK1) from the tissues of liver...
September 2016: Physiol Int
https://www.readbyqxmd.com/read/28228125/rna-seq-of-life-stages-of-the-oomycete-phytophthora-infestans-reveals-dynamic-changes-in-metabolic-signal-transduction-and-pathogenesis-genes-and-a-major-role-for-calcium-signaling-in-development
#3
Audrey M V Ah-Fong, Kyoung Su Kim, Howard S Judelson
BACKGROUND: The oomycete Phytophthora infestans causes the devastating late blight diseases of potato and tomato. P. infestans uses spores for dissemination and infection, like many other filamentous eukaryotic plant pathogens. The expression of a subset of its genes during spore formation and germination were studied previously, but comprehensive genome-wide data have not been available. RESULTS: RNA-seq was used to profile hyphae, sporangia, sporangia undergoing zoosporogenesis, motile zoospores, and germinated cysts of P...
February 23, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28228067/epigenetic-characteristics-of-the-mitotic-chromosome-in-1d-and-3d
#4
Marlies E Oomen, Job Dekker
While chromatin characteristics in interphase are widely studied, characteristics of mitotic chromatin and their inheritance through mitosis are still poorly understood. During mitosis, chromatin undergoes dramatic changes: transcription stalls, chromatin-binding factors leave the chromatin, histone modifications change and chromatin becomes highly condensed. Many key insights into mitotic chromosome state and conformation have come from extensive microscopy studies over the last century. Over the last decade, the development of 3C-based techniques has enabled the study of higher order chromosome organization during mitosis in a genome-wide manner...
April 2017: Critical Reviews in Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28224655/rna-seq-analysis-of-transcriptional-change-in-the-freshwater-mussel-elliptio-complanata-after-environmentally-relevant-sodium-chloride-exposure
#5
Laura S Robertson, Heather S Galbraith, Deborah Iwanowicz, Carrie J Blakeslee, R Scott Cornman
To identify potential biomarkers of salt stress in a freshwater sentinel species, we examined transcriptional responses of the common mussel Elliptio complanata to controlled NaCl exposures. RNA-Seq of mantle tissue identified 481 transcripts differentially expressed in adult mussels exposed to 2 ppt NaCl (1.2 ppt chloride) for seven days, of which 290 had non-overlapping intervals. Differentially expressed gene categories included ion and transmembrane transport, oxidoreductase activity, maintenance of protein folding, and amino acid metabolism...
February 22, 2017: Environmental Toxicology and Chemistry
https://www.readbyqxmd.com/read/28224052/compacting-and-correcting-trinity-and-oases-rna-seq-de-novo-assemblies
#6
Cédric Cabau, Frédéric Escudié, Anis Djari, Yann Guiguen, Julien Bobe, Christophe Klopp
BACKGROUND: De novo transcriptome assembly of short reads is now a common step in expression analysis of organisms lacking a reference genome sequence. Several software packages are available to perform this task. Even if their results are of good quality it is still possible to improve them in several ways including redundancy reduction or error correction. Trinity and Oases are two commonly used de novo transcriptome assemblers. The contig sets they produce are of good quality. Still, their compaction (number of contigs needed to represent the transcriptome) and their quality (chimera and nucleotide error rates) can be improved...
2017: PeerJ
https://www.readbyqxmd.com/read/28223366/la-deletion-from-mouse-brain-alters-pre-trna-metabolism-and-accumulation-of-pre-5-8s-rrna-with-neuron-death-and-reactive-astrocytosis
#7
Nathan H Blewett, James R Iben, Sergei Gaidamakov, Richard J Maraia
Human La antigen (Sjögren's syndrome antigen B, SSB) is an abundant multifunctional RNA-binding protein. In the nucleoplasm, La binds to and protects from 3' exonucleases, the ends of precursor-tRNAs and other transcripts synthesized by RNA polymerase III, and facilitates their maturation, while a nucleolar isoform has been implicated in rRNA biogenesis by multiple independent lines of evidence. We showed earlier that conditional La knockout (La cKO) from mouse cortex neurons results in defective tRNA processing although pathway(s) involved in neuronal loss thereafter was unknown...
February 21, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28222054/ucp2-expression-is-increased-in-pancreas-from-brain-dead-donors-and-involved-in-cytokine-induced-%C3%AE-cells-apoptosis
#8
Leticia A Brondani, Tatiana H Rech, Gabriela Boelter, Andrea C Bauer, Cristiane B Leitão, Décio L Eizirik, Daisy Crispim
BACKGROUND: Systemic inflammation associated with brain death (BD) decreases islet yield and quality, negatively affecting outcomes of human islet transplantation. A recent study from our group showed an increased expression of uncoupling protein-2 (UCP2) in pancreas from rats with BD as compared with controls. UCP2 is located in the mitochondrial inner membrane and regulates production of reactive oxygen species and glucose-stimulated insulin secretion. It has been suggested that UCP2 also plays a role in β cell apoptosis, but these findings remain controversial...
March 2017: Transplantation
https://www.readbyqxmd.com/read/28220154/dna-display-of-folded-rna-libraries-enabling-rna-selex-without-reverse-transcription
#9
I S MacPherson, J S Temme, I J Krauss
A method for the physical attachment of folded RNA libraries to their encoding DNA is presented as a way to circumvent the reverse transcription step during systematic evolution of RNA ligands by exponential enrichment (RNA-SELEX). A DNA library is modified with one isodC base to stall T7 polymerase and a 5' "capture strand" which anneals to the nascent RNA transcript. This method is validated in a selection of RNA aptamers against human α-thrombin with dissociation constants in the low nanomolar range. This method will be useful in the discovery of RNA aptamers and ribozymes containing base modifications that make them resistant to accurate reverse transcription...
February 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28219892/an-infectious-disease-associated-il12b-polymorphism-regulates-il-12-23-p40-transcription-involving-poly-adp-ribose-polymerase-1
#10
Quanju Zhao, Qinglin Du, Fang Wei, Jianping Xie, Xiaojing Ma
IL-12 and IL-23 are important host defense factors produced by APCs against certain intracellular and extracellular pathogens. Their dysregulation has also been implicated in several autoimmune diseases. The nucleotide polymorphism in the promoter region of Il12b (rs41292470 consisting of the long or short allele) encoding the shared subunit of IL-12 and IL-23, p40, has been reported to associate with susceptibility to infectious diseases and autoimmune disorders. How these genetic variants impact Il12b expression at the molecular level was unclear...
February 20, 2017: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/28217959/anti-rnpc3-antibodies-as-a-marker-of-cancer-associated-scleroderma
#11
Ami A Shah, George Xu, Antony Rosen, Laura K Hummers, Fredrick M Wigley, Stephen J Elledge, Livia Casciola-Rosen
INTRODUCTION: Prior studies have demonstrated an increased risk of cancer-associated scleroderma in patients with RNA polymerase III (POL) autoantibodies and in patients negative for anti-centromere (CENP), anti-topoisomerase-1 (TOPO), and anti-POL antibodies (referred to as CENP/TOPO/POL (CTP)-Negative). In a recent study of 16 CTP-negative scleroderma patients with coincident cancer, we found that 25% had autoantibodies to RNPC3, a member of the minor spliceosome complex. In this investigation, we validated the relationship between anti-RNPC3 antibodies and cancer and examined the associated clinical phenotype in a large sample of scleroderma patients...
February 19, 2017: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/28213091/convergence-of-hepcidin-deficiency-systemic-iron-overloading-heme-accumulation-and-rev-erb%C3%AE-%C3%AE-activation-in-aryl-hydrocarbon-receptor-elicited-hepatotoxicity
#12
Kelly A Fader, Rance Nault, Mathew P Kirby, Gena Markous, Jason Matthews, Timothy R Zacharewski
Persistent aryl hydrocarbon receptor (AhR) agonists elicit dose-dependent hepatic lipid accumulation, oxidative stress, inflammation, and fibrosis in mice. Iron (Fe) promotes AhR-mediated oxidative stress by catalyzing reactive oxygen species (ROS) production. To further characterize the role of Fe in AhR-mediated hepatotoxicity, male C57BL/6 mice were orally gavaged with sesame oil vehicle or 0.01-30μg/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) every 4days for 28days. Duodenal epithelial and hepatic RNA-Seq data were integrated with hepatic AhR ChIP-Seq, capillary electrophoresis protein measurements, and clinical chemistry analyses...
February 14, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28212815/systematic-testing-of-enzyme-perturbation-sensitivities-via-graded-dcas9-modulation-in-saccharomyces-cerevisiae
#13
Matthew Deaner, Hal S Alper
Dissecting genotype-phenotype relationships in a high-throughput and scalable manner is still an unresolved problem facing metabolic engineers. While the RNA-guided nuclease Cas9 has been repurposed as a programmable transcription regulator, its application has typically been limited to binary on/off regulation and thus misses informative and potentially optimal intermediate levels of gene expression. In this work, we establish a rapid method for fine-tuned, graded expression of pathway enzymes via dCas9 regulation by varying sgRNA target location as the dominant parameter...
February 14, 2017: Metabolic Engineering
https://www.readbyqxmd.com/read/28212614/transcriptomic-profiling-provides-molecular-insights-into-hydrogen-peroxide-induced-adventitious-rooting-in-mung-bean-seedlings
#14
Shi-Weng Li, Yan Leng, Rui-Fang Shi
BACKGROUND: Hydrogen peroxide (H2O2) has been known to function as a signalling molecule involved in the modulation of various physiological processes in plants. H2O2 has been shown to act as a promoter during adventitious root formation in hypocotyl cuttings. In this study, RNA-Seq was performed to reveal the molecular mechanisms underlying H2O2-induced adventitious rooting. RESULTS: RNA-Seq data revealed that H2O2 treatment greatly increased the numbers of clean reads and expressed genes and abundance of gene expression relative to the water treatment...
February 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28212183/cxcl12-cxcr4-signaling-contributes-to-the-pathogenesis-of-opioid-tolerance-a-translational-study
#15
Chih-Peng Lin, Kai-Hsiang Kang, Huang-Ju Tu, Ming-Yueh Wu, Tzu-Hung Lin, Houng-Chi Liou, Wei-Zen Sun, Wen-Mei Fu
BACKGROUND: Long-term opioid therapy for chronic pain may lead to analgesic tolerance, especially when administered intrathecally, thus preventing adequate pain relief. Discovering drug targets to treat opioid tolerance using a mechanism-based approach targeting opioid-induced neuroinflammation provides new therapeutic opportunities. In this study, we provide translational evidence that CXCL12/CXCR4 signaling contributes to the pathogenesis of opioid tolerance. METHODS: The CXCL12 levels in the cerebrospinal fluid of opioid-tolerant patients were compared with those of opioid-naive subjects...
March 2017: Anesthesia and Analgesia
https://www.readbyqxmd.com/read/28211892/high-throughput-in-situ-cell-electroporation-microsystem-for-parallel-delivery-of-single-guide-rnas-into-mammalian-cells
#16
Shengtai Bian, Yicen Zhou, Yawei Hu, Jing Cheng, Xiaofang Chen, Youchun Xu, Peng Liu
Arrayed genetic screens mediated by the CRISPR/Cas9 technology with single guide RNA (sgRNA) libraries demand a high-throughput platform capable of transfecting diverse cell types at a high efficiency in a genome-wide scale for detection and analysis of sophisticated cellular phenotypes. Here we developed a high-throughput in situ cell electroporation (HiCEP) microsystem which leveraged the superhydrophobic feature of the microwell array to achieve individually controlled conditions in each microwell and coupled an interdigital electrode array chip with the microwells in a modular-based scheme for highly efficient delivery of exogenous molecules into cells...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210664/fibronectin-and-androgen-receptor-expression-data-in-prostate-cancer-obtained-from-a-rna-sequencing-bioinformatics-analysis
#17
Dibash K Das, Thahmina Ali, Konstantinos Krampis, Olorunseun O Ogunwobi
Prostate cancer is the second most commonly diagnosed male cancer in the world. The molecular mechanisms underlying its development and progression are still unclear. Here we show analysis of a prostate cancer RNA-sequencing dataset that was originally generated by Ren et al. [3] from the prostate tumor and adjacent normal tissues of 14 patients. The data presented here was analyzed using our RNA-sequencing bioinformatics analysis pipeline implemented on the bioinformatics web platform, Galaxy. The relative expression of fibronectin (FN1) and the androgen receptor (AR) were calculated in fragments per kilobase of transcript per million mapped reads, and represented in FPKM unit...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28209995/rna-seq-based-transcriptomic-and-metabolomic-analysis-reveal-stress-responses-and-programmed-cell-death-induced-by-acetic-acid-in-saccharomyces-cerevisiae
#18
Yachen Dong, Jingjin Hu, Linlin Fan, Qihe Chen
As a typical harmful inhibitor in cellulosic hydrolyzates, acetic acid not only hinders bioethanol production, but also induces cell death in Saccharomyces cerevisiae. Herein, we conducted both transcriptomic and metabolomic analyses to investigate the global responses under acetic acid stress at different stages. There were 295 up-regulated and 427 down-regulated genes identified at more than two time points during acetic acid treatment (150 mM, pH 3.0). These differentially expressed genes (DEGs) were mainly involved in intracellular homeostasis, central metabolic pathway, transcription regulation, protein folding and stabilization, ubiquitin-dependent protein catabolic process, vesicle-mediated transport, protein synthesis, MAPK signaling pathways, cell cycle, programmed cell death, etc...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28208259/ultrasensitive-electrochemical-detection-of-mirna-21-using-a-zinc-finger-protein-specific-to-dna-rna-hybrids
#19
Chiew San Fang, Kwang-Sun Kim, Byeongjun Yu, Sangyong Jon, Moon-Soo Kim, Haesik Yang
Both high sensitivity and high specificity are crucial for detection of miRNAs that have emerged as important clinical biomarkers. Just Another Zinc finger proteins (JAZ, ZNF346) bind preferably (but nonsequence-specifically) to DNA-RNA hybrids over single-stranded RNAs, single-stranded DNAs, and double-stranded DNAs. We present an ultrasensitive and highly specific electrochemical method for miRNA-21 detection based on the selective binding of JAZ to the DNA-RNA hybrid formed between a DNA capture probe and a target miRNA-21...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28205506/prospective-surveillance-of-antiviral-resistance-in-hospitalized-infants-less-than-12-months-of-age-with-a-h3n2-influenza-infection-and-treated-with-oseltamivir
#20
Barbara Rath, Xi Chen, Vera Spies, Susann Muehlhans, Patrick Obermeier, Franziska Tief, Lea Seeber, Katharina Karsch, Jeanette Milde, Heino Skopnik, Brunhilde Schweiger, Susanne C Duwe
BACKGROUND: Infants exhibit elevated influenza virus loads and prolonged viral shedding, which may increase the risk for resistance development, especially in cases of suboptimal exposure to antiviral therapy. METHODS: We performed a prospective surveillance of hospitalized infants undergoing oseltamivir therapy during the 2008-2009 and 2011-2012 influenza seasons at two paediatric hospitals in Germany. A total of 37 infants less than one year of age with laboratory confirmed influenza A(H3N2) infection received oseltamivir as per physician's order for 5 days (2008-2009 season: 2mg/kg BID; 2011-2012 season: 2...
February 16, 2017: Antiviral Therapy
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