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https://www.readbyqxmd.com/read/28821810/extracting-intercellular-signaling-network-of-cancer-tissues-using-ligand-receptor-expression-patterns-from-whole-tumor-and-single-cell-transcriptomes
#1
Joseph X Zhou, Roberto Taramelli, Edoardo Pedrini, Theo Knijnenburg, Sui Huang
Many behaviors of cancer, such as progression, metastasis and drug resistance etc., cannot be fully understood by genetic mutations or intracellular signaling alone. Instead, they are emergent properties of the cell community which forms a tumor. Studies of tumor heterogeneity reveal that many cancer behaviors critically depend on intercellular communication between cancer cells themselves and between cancer-stromal cells by secreted signaling molecules (ligands) and their cognate receptors. We analyzed public cancer transcriptome database for changes in cell-cell interactions as the characteristic of malignancy...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821716/transcriptome-analysis-reveals-long-intergenic-non-coding-rnas-involved-in-skeletal-muscle-growth-and-development-in-pig
#2
Cheng Zou, Jingxuan Li, Wenzhe Luo, Long Li, An Hu, Yuhua Fu, Ye Hou, Changchun Li
Long intergenic non-coding RNAs (lincRNAs) play essential roles in numerous biological processes and are widely studied. The skeletal muscle is an important tissue that plays an essential role in individual movement ability. However, lincRNAs in pig skeletal muscles are largely undiscovered and their biological functions remain elusive. In this study, we assembled transcriptomes using RNA-seq data published in previous studies of our laboratory group and identified 323 lincRNAs in porcine leg muscle. We found that these lincRNAs have shorter transcript length, fewer exons and lower expression level than protein-coding genes...
August 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28821665/molecular-and-functional-properties-of-regional-astrocytes-in-the-adult-brain
#3
Lydie Morel, Ming Sum R Chiang, Haruki Higashimori, Temitope Shoneye, Lakshmanan K Iyer, Julia Yelick, Albert Tai, Yongjie Yang
The molecular signature and functional properties of astroglial subtypes in the adult central nervous system (CNS) remain largely undefined. By employing translational ribosome affinity purification (TRAP) followed by RNA-seq, we profiled astroglial ribosome-associated (presumably translating) mRNAs in major cortical and subcortical brain regions (cortex, hippocampus, caudate putamen, nucleus accumbens, thalamus, and hypothalamus) of BAC aldh1l1-TRAP mice (both sexes). We found that the expression of astroglial translating mRNAs closely follows the dorsoventral axis especially from cortex/hippocampus to thalamus/hypothalamus posteriorly...
August 7, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28820494/immune-response-patterns-and-next-generation-sequencing-diagnostics-for-the-detection-of-mycoses-in-patients-with-septic-shock-results-of-a-combined-clinical-and-experimental-investigation
#4
Sebastian O Decker, Annette Sigl, Christian Grumaz, Philip Stevens, Yevhen Vainshtein, Stefan Zimmermann, Markus A Weigand, Stefan Hofer, Kai Sohn, Thorsten Brenner
Fungi are of increasing importance in sepsis. However, culture-based diagnostic procedures are associated with relevant weaknesses. Therefore, culture- and next-generation sequencing (NGS)-based fungal findings as well as corresponding plasma levels of β-d-glucan, interferon gamma (INF-γ), tumor necrosis factor alpha (TNF-α), interleukin (IL)-2, -4, -6, -10, -17A, and mid-regional proadrenomedullin (MR-proADM) were evaluated in 50 septic patients at six consecutive time points within 28 days after sepsis onset...
August 18, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28819439/development-and-validation-of-a-serum-biomarker-panel-for-the-detection-of-esophageal-squamous-cell-carcinoma-through-rna-transcriptome-sequencing
#5
Shan Xing, Xin Zheng, Li-Qiang Wei, Shi-Jian Song, Dan Liu, Ning Xue, Xiao-Min Liu, Mian-Tao Wu, Qian Zhong, Chu-Mei Huang, Mu-Sheng Zeng, Wan-Li Liu
Serum tumor markers for the diagnosis of esophageal squamous cell carcinoma (ESCC) have low sensitivity. This study aims to identify new serum markers for ESCC diagnosis from RNA sequencing (RNA-seq) data. RNA-seq was performed using six pairs of ESCC and matched normal tissues. The candidates for ESCC were screened from the differentially expressed genes. The candidates were analyzed by ELISA from the serum of a test group and a validation group. Real-time PCR, Western blotting and immunohistochemistry were used to detect the expression of the candidates in tumor cell lines and tumor tissues...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/28819177/comparative-transcriptome-analysis-of-se-initial-dedifferentiation-in-cotton-of-different-se-capability
#6
Aiping Cao, Yinying Zheng, Yu Yu, Xuwen Wang, Dongnan Shao, Jie Sun, Baiming Cui
Somatic embryogenesis (SE) is a critical transition from vegetative to embryogenic growth in higher plants; however, few studies have investigated the mechanism that regulates SE initial differentiation. Most cotton varieties have not undergone regeneration by SE, so only a few varieties can be used in genetic engineering. Here, two varieties of cotton with different SE capabilities (HD, higher differentiation and LD, lower differentiation) were analyzed by high throughout RNA-Seq at the pre-induction stage (0h) and two induction stages (3h and 3d) under callus-induction medium (CIM)...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819115/genome-wide-identification-and-expression-profiling-of-long-non-coding-rnas-in-auditory-and-vestibular-systems
#7
Kathy Ushakov, Tal Koffler-Brill, Aviv Rom, Kobi Perl, Igor Ulitsky, Karen B Avraham
Mammalian genomes encode multiple layers of regulation, including a class of RNA molecules known as long non-coding RNAs (lncRNAs). These are >200 nucleotides in length and similar to mRNAs, they are capped, polyadenylated, and spliced. In contrast to mRNAs, lncRNAs are less abundant and have higher tissue specificity, and have been linked to development, epigenetic processes, and disease. However, little is known about lncRNA function in the auditory and vestibular systems, or how they play a role in deafness and vestibular dysfunction...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28819105/a-novel-method-for-genome-wide-profiling-of-dynamic-host-pathogen-interactions-using-3-end-enriched-rna-seq
#8
Jie Li, Liangliang He, Yun Zhang, Chunyi Xue, Yongchang Cao
Marek's disease is a contagious lymphoproliferative disease of chickens and typical model of viral oncogenesis. Mapping changes or different states over the course of infection for both host and pathogen would provide important insights into dynamic host-pathogen interactions. Here we introduced 3' end enriched RNA-seq as a novel method to study host-pathogen interactions in chicken embryo fibroblasts cells challenged with Marek's disease virus. The method allowed accurate profiling of gene expression and alternative polyadenylation sites for host and pathogen simultaneously...
August 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28818938/comprehensive-single-cell-transcriptional-profiling-of-a-multicellular-organism
#9
Junyue Cao, Jonathan S Packer, Vijay Ramani, Darren A Cusanovich, Chau Huynh, Riza Daza, Xiaojie Qiu, Choli Lee, Scott N Furlan, Frank J Steemers, Andrew Adey, Robert H Waterston, Cole Trapnell, Jay Shendure
To resolve cellular heterogeneity, we developed a combinatorial indexing strategy to profile the transcriptomes of single cells or nuclei, termed sci-RNA-seq (single-cell combinatorial indexing RNA sequencing). We applied sci-RNA-seq to profile nearly 50,000 cells from the nematode Caenorhabditis elegans at the L2 larval stage, which provided >50-fold "shotgun" cellular coverage of its somatic cell composition. From these data, we defined consensus expression profiles for 27 cell types and recovered rare neuronal cell types corresponding to as few as one or two cells in the L2 worm...
August 18, 2017: Science
https://www.readbyqxmd.com/read/28818871/sexual-dimorphism-of-the-pulmonary-transcriptome-in-neonatal-hyperoxic-lung-injury-identification-of-angiogenesis-as-a-key-pathway
#10
Cristian Coarfa, Yuhao Zhang, Suman Maity, Dimuthu Perera, Weiwu Jiang, Lihua Wang, Xanthi Couroucli, Bhagavatula Moorthy, Krithika Lingappan
Bronchopulmonary dysplasia (BPD) is characterized by impaired alveolar secondary septation and vascular growth. Exposure to high concentrations of oxygen (hyperoxia) contributes to the development of BPD. Male sex is considered an independent risk factor for the development of BPD. The reasons underlying sexually dimorphic outcomes in premature neonates are not known. We hypothesized that sex-specific modulation of biological processes in the lung under hyperoxic conditions, contributes to sex-based differences...
August 17, 2017: American Journal of Physiology. Lung Cellular and Molecular Physiology
https://www.readbyqxmd.com/read/28818508/the-role-of-the-il-8-signaling-pathway-in-the-infiltration-of-granulocytes-into-the-livers-of-patients-with-alcoholic-hepatitis
#11
S W French, A S Mendoza, N Afifiyan, B Tillman, E Vitocruz, B A French
BACKGROUND AND AIM: IL-8 (C-X-L motif chemokine ligase 8) and CXCR2 (C-X-C-motif chemokine receptor 2) are up regulated in alcoholic hepatitis (AH) liver biopsies. One of the consequences is the attraction and chemotactic neutrophilic infiltrate seen at the AH stage of alcoholic liver disease. MATERIALS AND METHODS: Human formalin-fixed, paraffin-embedded (FFPE) liver biopsies from patients who have AH were studied by (2.1) RNA sequencing, (2.2) PCR and (2.3) semi quantitation of specific proteins in biopsy sections using immunohistochemical measurements of antibody fluorescent intensity with morphometric technology...
August 14, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28818039/the-impact-of-rna-sequence-library-construction-protocols-on-transcriptomic-profiling-of-leukemia
#12
Ashwini Kumar, Matti Kankainen, Alun Parsons, Olli Kallioniemi, Pirkko Mattila, Caroline A Heckman
BACKGROUND: RNA sequencing (RNA-seq) has become an indispensable tool to identify disease associated transcriptional profiles and determine the molecular underpinnings of diseases. However, the broad adaptation of the methodology into the clinic is still hampered by inconsistent results from different RNA-seq protocols and involves further evaluation of its analytical reliability using patient samples. Here, we applied two commonly used RNA-seq library preparation protocols to samples from acute leukemia patients to understand how poly-A-tailed mRNA selection (PA) and ribo-depletion (RD) based RNA-seq library preparation protocols affect gene fusion detection, variant calling, and gene expression profiling...
August 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28818037/association-of-coral-algal-symbionts-with-a-diverse-viral-community-responsive-to-heat-shock
#13
Jan D Brüwer, Shobhit Agrawal, Yi Jin Liew, Manuel Aranda, Christian R Voolstra
BACKGROUND: Stony corals provide the structural foundation of coral reef ecosystems and are termed holobionts given they engage in symbioses, in particular with photosynthetic dinoflagellates of the genus Symbiodinium. Besides Symbiodinium, corals also engage with bacteria affecting metabolism, immunity, and resilience of the coral holobiont, but the role of associated viruses is largely unknown. In this regard, the increase of studies using RNA sequencing (RNA-Seq) to assess gene expression provides an opportunity to elucidate viral signatures encompassed within the data via careful delineation of sequence reads and their source of origin...
August 17, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28817735/association-of-gene-expression-with-biomass-content-and-composition-in-sugarcane
#14
Nam V Hoang, Agnelo Furtado, Angela J O'Keeffe, Frederik C Botha, Robert J Henry
About 64% of the total aboveground biomass in sugarcane production is from the culm, of which ~90% is present in fiber and sugars. Understanding the transcriptome in the sugarcane culm, and the transcripts that are associated with the accumulation of the sugar and fiber components would facilitate the modification of biomass composition for enhanced biofuel and biomaterial production. The Sugarcane Iso-Seq Transcriptome (SUGIT) database was used as a reference for RNA-Seq analysis of variation in gene expression between young and mature tissues, and between 10 genotypes with varying fiber content...
2017: PloS One
https://www.readbyqxmd.com/read/28817612/expression-and-functional-implications-of-the-renal-apelinergic-system-in-rodents
#15
Anne-Marie O'Carroll, Sabrine Salih, Philip R Griffiths, Aarifah Bijabhai, Mark A Knepper, Stephen J Lolait
Apelin binds to the G protein-coupled apelin receptor (APJ; gene name aplnr) to modulate diverse physiological systems including cardiovascular function, and hydromineral and metabolic balance. Recently a second endogenous ligand for APJ, named apela, has been discovered. We confirm that apela activates signal transduction pathways (ERK activation) in cells expressing the cloned rat APJ. Previous studies suggest that exogenous apela is diuretic, attributable wholly or in part to an action on renal APJ. Thus far the cellular distribution of apela in the kidney has not been reported...
2017: PloS One
https://www.readbyqxmd.com/read/28817234/osmium-mediated-4su-to-c-transformation-as-key-to-study-rna-dynamics-by-sequencing-tuc-seq
#16
Christian Riml, Thomas Amort, Dietmar Rieder, Catherina Gasser, Alexandra Lusser, Ronald Micura
To understand the functional roles of RNA in the cell, it is essential to elucidate the dynamics of their production, processing and decay. A recent method for assessing mRNA dynamics is metabolic labeling with 4-thiouridine (4sU), followed by thio-selective attachment of affinity tags. Detection of labeled transcripts by affinity purification and hybridization to microarrays or by deep sequencing then reveals RNA expression levels. Here, we present a novel sequencing method that eliminates affinity purification and allows for direct assessment of 4sU labeled RNA...
August 17, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28814802/relationship-between-necrotic-patterns-in-glioblastoma-and-patient-survival-fractal-dimension-and-lacunarity-analyses-using-magnetic-resonance-imaging
#17
Shuai Liu, Yinyan Wang, Kaibin Xu, Zheng Wang, Xing Fan, Chuanbao Zhang, Shaowu Li, Xiaoguang Qiu, Tao Jiang
Necrosis is a hallmark feature of glioblastoma (GBM). This study investigated the prognostic role of necrotic patterns in GBM using fractal dimension (FD) and lacunarity analyses of magnetic resonance imaging (MRI) data and evaluated the role of lacunarity in the biological processes leading to necrosis. We retrospectively reviewed clinical and MRI data of 95 patients with GBM. FD and lacunarity of the necrosis on MRI were calculated by fractal analysis and subjected to survival analysis. We also performed gene ontology analysis in 32 patients with available RNA-seq data...
August 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28814645/zygotic-genome-activation-occurs-shortly-after-fertilization-in-maize
#18
Junyi Chen, Nicholas Strieder, Nadia G Krohn, Philippe Cyprys, Stefanie Sprunck, Julia C Engelmann, Thomas Dresselhaus
The formation of a zygote via the fusion of an egg and sperm cell and its subsequent asymmetric division (ACD) herald the start of the plant's life cycle. Zygotic genome activation (ZGA) is thought to occur gradually, with the initial steps of zygote and embryo development being primarily maternally controlled, and subsequent steps being governed by the zygotic genome. Here, using maize (Zea mays) as a model plant system, we determined the timing of zygote development and generated RNA-Seq transcriptome profiles of gametes, zygotes, and apical and basal daughter cells...
August 16, 2017: Plant Cell
https://www.readbyqxmd.com/read/28814335/comparative-transcriptome-analysis-of-second-and-third-generation-merozoites-of-eimeria-necatrix
#19
Shijie Su, Zhaofeng Hou, Dandan Liu, Chuanli Jia, Lele Wang, Jinjun Xu, Jianping Tao
BACKGROUND: Eimeria is a common genus of apicomplexan parasites that infect diverse vertebrates, most notably poultry, causing serious disease and economic losses. Eimeria species have complex life-cycles consisting of three developmental stages. However, the molecular basis of the Eimeria reproductive mode switch remains an enigma. METHODS: Total RNA extracted from second- (MZ-2) and third-generation merozoites (MZ-3) of Eimeria necatrix was subjected to transcriptome analysis using RNA sequencing (RNA-seq) followed by qRT-PCR validation...
August 16, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/28814283/comparative-studies-on-tolerance-of-rice-genotypes-differing-in-their-tolerance-to-moderate-salt-stress
#20
Qian Li, An Yang, Wen-Hao Zhang
BACKGROUND: Moderate salt stress, which often occurs in most saline agriculture land, suppresses crop growth and reduces crop yield. Rice, as an important food crop, is sensitive to salt stress and rice genotypes differ in their tolerance to salt stress. Despite extensive studies on salt tolerance of rice, a few studies have specifically investigated the mechanism by which rice plants respond and tolerate to moderate salt stress. Two rice genotypes differing in their tolerance to saline-alkaline stress, Dongdao-4 and Jigeng-88, were used to explore physiological and molecular mechanisms underlying tolerance to moderate salt stress...
August 17, 2017: BMC Plant Biology
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