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https://www.readbyqxmd.com/read/29793206/effects-on-the-hepatic-transcriptome-of-chicken-embryos-in-ovo-exposed-to-phenobarbital
#1
Jiahua Guo, Shohei Ito, Hoa Thanh Nguyen, Kimika Yamamoto, Hisato Iwata
This work aimed at evaluating the toxic effects of in ovo exposure to phenobarbital (PB) and unveiling the mode of action by transcriptome analysis in the embryonic liver of a model avian species, chicken (Gallus gallus). Embryos were initially treated with saline or 1 μg PB /g egg at Hamburger Hamilton Stage (HHS) 1 (1st day), followed by 20 days of incubation to HHS 46. At 21st day, chicks that pipped successfully were euthanized and dissected for assessing the PB caused effects on phenotypes and the liver transcriptome in both genders...
May 21, 2018: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/29793044/isolation-of-ferritin-and-its-interaction-with-bmnpv-in-the-silkworm-bombyx-mori
#2
Dong-Qiong Fei, Hai-Zhong Yu, Jia-Ping Xu, Shang-Zhi Zhang, Jie Wang, Bing Li, Li-Ang Yang, Pei Hu, Xin Xu, Kang Zhao, Toufeeq Shahzad
Ferritin is a ubiquitous iron storage protein that plays an important role in host defence against pathogen infections. In the present study, native ferritin was isolated from the hemolymph of Bombyx mori using native-polyacrylamide gel electrophoresis (native-PAGE) and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The results revealed that ferritin consisted of two subunits, designated as BmFerHCH and BmFerLCH. Previously integrated previous transcriptome and iTRAQ data showed that the two subunits were down-regulated in resistant silkworm strain BC9 and there was no obvious change in the expression levels of the subunits in susceptible silkworm strain P50 after BmNPV infection...
May 9, 2018: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/29792950/transcriptome-profile-analysis-reveals-the-ontogenesis-of-rooted-chichi-in-ginkgo-biloba-l
#3
Xiaojing Liu, Limin Sun, Qikui Wu, Xiaoyan Men, Linmei Yao, Shiyan Xing
The Ginkgo biloba L. chichi is a unique organ. To explore the molecular mechanisms underlying the ontogenesis of G. biloba chichi, we used RNA-seq to analyse the transcriptome profile of rooted chichi at two developmental stages (ch1 and ch2) and nearby tissues (ck), and each sample had three biological replicates. A total of 57.74 Gb of clean bases were generated in nine cDNA libraries. These bases were de novo assembled into 68,277 unigenes with average length of 844 bp, and 51.47% of the unigenes had a match in at least one public database...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792949/srnaome-and-transcriptome-analysis-provide-insight-into-chilling-response-of-cowpea-pods
#4
Jinhua Zuo, Yunxiang Wang, Benzhong Zhu, Yunbo Luo, Qing Wang, Lipu Gao
Cowpea is an important horticultural crop in tropical and subtropical areas of Asia, Africa, and Latin America, as well as parts of southern Europe and Central and South America. Chilling injury is a common physiological hazard of cowpea in cold chain logistics which reduce the cowpea pod's nutritional quality and product value. However, the molecular mechanism involved in chilling injury remains unclear in cowpea pods. RNA-Seq and sRNA-Seq technologies were employed to decipher the miRNAs and mRNAs expression profiles and their regulatory networks in cowpea pods involved in chilling stress...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792948/comparative-transcriptome-analysis-reveals-significant-differences-in-gene-expression-between-appressoria-and-hyphae-in-colletotrichum-gloeosporioides
#5
Meiyu Wang, Zongshan Zhou, Jianyuan Wu, Zhirui Ji, Junxiang Zhang
Fruit rot caused mainly by Colletotrichum gloeosporioides is a major cause of pre- and/or post-harvest diseases, which seriously constrains production, marketing, and export of fruits. To infect the host, this fungus evolves a specialized infection structure called the appressorium. Extensive past studies have characterized many appressorium-related genes in C. gloeosporioides, separately. However, a comprehensive understanding of the genes contributing to appressorium formation is far from complete. Here, global changes in gene expression were analyzed between appressoria and hyphae using RNA-Seq...
May 21, 2018: Gene
https://www.readbyqxmd.com/read/29792923/high-throughput-sequencing-identifies-chilling-responsive-genes-in-sweetpotato-ipomoea-batatas-lam-during-storage
#6
Zeyi Xie, Zhilin Zhou, Hongmin Li, Jingjing Yu, Jiaojiao Jiang, Zhonghou Tang, Daifu Ma, Baohong Zhang, Yonghua Han, Zongyun Li
Sweetpotato (Ipomoea batatas L.) is a globally important economic food crop. It belongs to Convolvulaceae family and origins in the tropics; however, sweetpotato is sensitive to cold stress during storage. In this study, we performed transcriptome sequencing to investigate the sweetpotato response to chilling stress during storage. A total of 110,110 unigenes were generated via high-throughput sequencing. Differentially expressed genes (DEGs) analysis showed that 18,681 genes were up-regulated and 21,983 genes were down-regulated in low temperature condition...
May 21, 2018: Genomics
https://www.readbyqxmd.com/read/29792918/translational-omics-future-potential-and-current-challenges-in-precision-medicine
#7
Arsalan Wafi, Reza Mirnezami
Rapid advances in computational science and biotechnology are paving the way for precision medicine - a vision in next-generation healthcare that promises to provide a care package uniquely tailored to each individual's molecular make-up. Until relatively recently, the focus has been firmly centred around the genome; however, over the past two decades there has been a surge in the study of molecular activity within other biological domains (proteome/transcriptome/metabolome) involved in health and pathogenesis...
May 21, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29792880/molecular-alterations-during-larval-development-of-haemonchus-contortus-in-vitro-are-under-tight-post-transcriptional-control
#8
Guangxu Ma, Tao Wang, Pasi K Korhonen, Ching-Seng Ang, Nicholas A Williamson, Neil D Young, Andreas J Stroehlein, Ross S Hall, Anson V Koehler, Andreas Hofmann, Robin B Gasser
In this study, we explored the molecular alterations in the developmental switch from the L3 to the exsheathed L3 (×L3) and to the L4 stage of Haemonchus contortus in vitro using an integrated transcriptomic, proteomic and bioinformatic approach. Totals of 9,754 mRNAs, 88 microRNAs (miRNAs) and 1,591 proteins were identified, and 6,686 miRNA-mRNA pairs inferred in all larval stages studied. Approximately 16% of transcripts in the combined transcriptome (representing all three larval stages) were expressed as proteins, and there were positive correlations (r = 0...
May 22, 2018: International Journal for Parasitology
https://www.readbyqxmd.com/read/29792173/impact-of-growth-ph-and-glucose-concentrations-on-the-cody-regulatory-network-in-streptococcus-salivarius
#9
Jianing Geng, Szu-Chuan Huang, Yueh-Ying Chen, Cheng-Hsun Chiu, Songnian Hu, Yi-Ywan M Chen
BACKGROUND: Streptococcus salivarius is an abundant isolate of the human oral microbiota. Since both pH and glucose availability fluctuate frequently in the oral cavity, the goal of this study was to investigate regulation by CodY, a conserved pleiotropic regulator of Gram positive bacteria, in response to these two signals. The chemostat culture system was employed to precisely control the growth parameters, and the transcriptomes of wild-type S. salivarius 57.I and its CodY-null derivative (ΔcodY) grown at pH 7 and 5...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29792171/embryonic-transcriptome-and-proteome-analyses-on-hepatic-lipid-metabolism-in-chickens-divergently-selected-for-abdominal-fat-content
#10
Wei Na, Yuan-Yuan Wu, Peng-Fei Gong, Chun-Yan Wu, Bo-Han Cheng, Yu-Xiang Wang, Ning Wang, Zhi-Qiang Du, Hui Li
BACKGROUND: In avian species, liver is the main site of de novo lipogenesis, and hepatic lipid metabolism relates closely to adipose fat deposition. Using our fat and lean chicken lines of striking differences in abdominal fat content, post-hatch lipid metabolism in both liver and adipose tissues has been studied extensively. However, whether molecular discrepancy for hepatic lipid metabolism exists in chicken embryos remains obscure. RESULTS: We performed transcriptome and proteome profiling on chicken livers at five embryonic stages (E7, E12, E14, E17 and E21) between the fat and lean chicken lines...
May 23, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29791965/searching-for-non-transposable-targets-of-planarian-nuclear-piwi-in-pluripotent-stem-cells-and-differentiated-cells
#11
Makoto Kashima, Kiyokazu Agata, Norito Shibata
Nuclear PIWIs together with their guide RNAs (piRNAs) epigenetically silence various genes including transposons in many organisms. In planarians, the nuclear piwi family gene, DjpiwiB is specifically transcribed in adult pluripotent stem cells (adult PSC, neoblast), but not in differentiated cells. However, the protein accumulates in the nuclei of both neoblasts and their descendant differentiated cells. Interestingly, PIWI(DjPiwiB)-piRNA complexes are indispensable for the repression of transposable genes at the onset of differentiation from neoblasts...
May 23, 2018: Development, Growth & Differentiation
https://www.readbyqxmd.com/read/29791872/gene-expression-in-cord-blood-links-genetic-risk-for-neurodevelopmental-disorders-with-maternal-psychological-distress-and-adverse-childhood-outcomes
#12
Michael S Breen, Aliza P Wingo, Nastassja Koen, Kirsten A Donald, Mark Nicol, Heather J Zar, Kerry J Ressler, Joseph D Buxbaum, Dan J Stein
Prenatal exposure to maternal stress and depression has been identified as a risk factor for adverse behavioral and neurodevelopmental outcomes in early childhood. However, the molecular mechanisms through which maternal psychopathology shapes offspring development remain poorly understood. We applied transcriptome-wide screens to 149 umbilical cord blood samples from neonates born to mothers with posttraumatic stress disorder (PTSD; n=20), depression (n=31) and PTSD with comorbid depression (n=13), compared to carefully matched trauma exposed controls (n=23) and healthy mothers (n=62)...
May 20, 2018: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/29791852/melanopsin-retinal-ganglion-cells-regulate-cone-photoreceptor-lamination-in-the-mouse-retina
#13
Adele R Tufford, Jessica R Onyak, Katelyn B Sondereker, Jasmine A Lucas, Aaron M Earley, Pierre Mattar, Samer Hattar, Tiffany M Schmidt, Jordan M Renna, Michel Cayouette
Newborn neurons follow molecular cues to reach their final destination, but whether early life experience influences lamination remains largely unexplored. As light is among the first stimuli to reach the developing nervous system via intrinsically photosensitive retinal ganglion cells (ipRGCs), we asked whether ipRGCs could affect lamination in the developing mouse retina. We show here that ablation of ipRGCs causes cone photoreceptors to mislocalize at different apicobasal positions in the retina. This effect is partly mediated by light-evoked activity in ipRGCs, as dark rearing or silencing of ipRGCs leads a subset of cones to mislocalize...
May 22, 2018: Cell Reports
https://www.readbyqxmd.com/read/29791134/identification-of-yth-domain-containing-proteins-as-the-readers-for-n1-methyladenosine-in-rna
#14
Xiaoxia Dai, Tianlu Wang, Gwendolyn Gonzalez, Yinsheng Wang
N1-methyladenosine (m1 A) is an important post-transcriptional modification in RNA; however, the exact biological role of m1 A remains to be determined. By employing a quantitative proteomics method, we identified multiple putative protein readers of m1 A in RNA, including several YTH domain family proteins. We showed that YTHDF1-3 and YTHDC1, but not YTHDC2, could bind directly to m1 A in RNA. We also found that Trp432 in YTHDF2, a conserved residue in the hydrophobic pocket of the YTH domain that is necessary for its binding to N6 -methyladenosine (m6 A), is required for its recognition of m1 A...
May 25, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29791078/molecular-subtype-classification-of-urothelial-carcinoma-in-lynch-syndrome
#15
Christina Therkildsen, Pontus Eriksson, Mattias Höglund, Mats Jönsson, Gottfrid Sjödahl, Mef Nilbert, Fredrik Liedberg
Lynch syndrome confers an increased risk for urothelial carcinoma (UC). Molecular subtypes may be relevant to prognosis and therapeutic possibilities, but have to date not been defined in Lynch syndrome-associated urothelial cancer. We aimed to provide a molecular description of Lynch syndrome-associated UC. Thus, Lynch syndrome-associated UC of the upper urinary tract and the urinary bladder were identified in the Danish hereditary non-polyposis colorectal cancer (HNPCC) register and were transcriptionally and immunohistochemically profiled and further related to data from 307 sporadic urothelial carcinomas...
May 23, 2018: Molecular Oncology
https://www.readbyqxmd.com/read/29790959/peripheral-blood-gene-expression-reveals-an-inflammatory-transcriptomic-signature-in-friedreich-s-ataxia-patients
#16
Daniel Nachun, Fuying Gao, Charles Isaacs, Cassandra Strawser, Zhongan Yang, Deepika Dokuru, Victoria Van Berlo, Renee Sears, Jennifer Farmer, Susan Perlman, David R Lynch, Giovanni Coppola
Transcriptional changes in Friedreich's ataxia (FRDA), a rare and debilitating recessive Mendelian neurodegenerative disorder, have been studied in affected but inaccessible tissues - such as dorsal root ganglia, sensory neurons, and cerebellum - in animal models or small patient series. However, transcriptional changes induced by FRDA in peripheral blood, a readily accessible tissue, have not been characterized in a large sample. We used differential expression, association with disability stage, network analysis, and enrichment analysis to characterize the peripheral blood transcriptome and identify genes that were differentially expressed in FRDA patients (n = 418) compared to both heterozygous expansion carriers (n = 228) and controls (n = 93, 739 individuals in total), or were associated with disease progression, resulting in a disease signature for FRDA...
May 22, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29790953/identifying-and-avoiding-off-target-effects-of-rnase-h-dependent-antisense-oligonucleotides-in-mice
#17
Peter H Hagedorn, Malene Pontoppidan, Tina S Bisgaard, Marco Berrera, Andreas Dieckmann, Martin Ebeling, Marianne R Møller, Heidi Hudlebusch, Marianne L Jensen, Henrik F Hansen, Troels Koch, Morten Lindow
Antisense oligonucleotides that are dependent on RNase H for cleavage and subsequent degradation of complementary RNA are being developed as therapeutics. Besides the intended RNA target, such oligonucleotides may also cause degradation of unintended RNA off-targets by binding to partially complementary target sites. Here, we characterized the global effects on the mouse liver transcriptome of four oligonucleotides designed as gapmers, two targeting Apob and two targeting Pcsk9, all in different regions on their respective intended targets...
May 22, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29790899/advances-in-the-systemic-treatment-of-melanoma-brain-metastases
#18
I C Glitza Oliva, G Schvartsman, H Tawbi
Of the solid tumor types that metastasize to the brain, melanoma has the highest propensity to form brain metastases. In addition, much remains unknown regarding the pathophysiology involved in melanoma cell extravasation through the blood-brain barrier, which enables interactions with the microenvironment, and melanoma cell transcriptomic responses to brain-specific cues. However, recent developments in targeted therapy and immunotherapy have generated considerable optimism regarding the treatment of metastatic melanoma...
May 22, 2018: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29790577/esophageal-igg4-levels-correlate-with-histopathologic-and-transcriptomic-features-in-eosinophilic-esophagitis
#19
Chen E Rosenberg, Melissa K Mingler, Julie M Caldwell, Margaret H Collins, Patricia C Fulkerson, David W Morris, Vincent A Mukkada, Philip E Putnam, Tetsuo Shoda, Ting Wen, Marc E Rothenberg
BACKGROUND: Recent data associate eosinophilic esophagitis (EoE) with IgG4 rather than IgE, but its significance and function have not been determined. Our aims were to measure esophageal IgG4 levels and to determine functional correlations as assessed by histologic and transcriptome analyses. METHODS: This case-control study included pediatric subjects with EoE (≥ 15 eosinophils/HPF) and non-EoE controls. Protein lysates were analyzed for IgA, IgM, and IgG1-IgG4 using the Luminex 100 system; IgE was quantified by ELISA...
May 23, 2018: Allergy
https://www.readbyqxmd.com/read/29790574/investigations-on-velvet-regulatory-mutants-confirm-the-role-of-host-tissue-acidification-and-secretion-of-proteins-in-the-pathogenesis-of-botrytis-cinerea
#20
Nathalie Müller, Michaela Leroch, Julia Schumacher, David Zimmer, Anne Könnel, Klaus Klug, Thomas Leisen, David Scheuring, Frederik Sommer, Timo Mühlhaus, Michael Schroda, Matthias Hahn
The Botrytis cinerea VELVET complex regulates light-dependent development and virulence. The goal of this study was to identify common virulence defects of several VELVET mutants and to reveal their molecular basis. Growth, differentiation, physiology, gene expression and infection of fungal strains were analyzed, and quantitative comparisons of in planta transcriptomes and secretomes were performed. VELVET mutants showed reduced release of citric acid, the major acid secreted by the wild-type, whereas no significant role for oxalic acid was observed...
May 23, 2018: New Phytologist
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