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https://www.readbyqxmd.com/read/29161754/the-sorghum-bicolor-reference-genome-improved-assembly-gene-annotations-a-transcriptome-atlas-and-signatures-of-genome-organization
#1
Ryan F McCormick, Sandra K Truong, Avinash Sreedasyam, Jerry Jenkins, Shengqiang Shu, David Sims, Megan Kennedy, Mojgan Amirebrahimi, Brock D Weers, Brian McKinley, Ashley Mattison, Daryl T Morishige, Jane Grimwood, Jeremy Schmutz, John E Mullet
Sorghum bicolor is a drought tolerant C4 grass used for production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (~800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34,211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp...
November 21, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29161425/linnorm-improved-statistical-analysis-for-single-cell-rna-seq-expression-data
#2
Shun H Yip, Panwen Wang, Jean-Pierre A Kocher, Pak Chung Sham, Junwen Wang
No abstract text is available yet for this article.
November 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29161413/nrf2-regulates-endothelial-glycolysis-and-proliferation-with-mir-93-and-mediates-the-effects-of-oxidized-phospholipids-on-endothelial-activation
#3
Suvi M Kuosmanen, Emilia Kansanen, Minna U Kaikkonen, Virve Sihvola, Kati Pulkkinen, Henna-Kaisa Jyrkkänen, Pauli Tuoresmäki, Juha Hartikainen, Mikko Hippeläinen, Hannu Kokki, Pasi Tavi, Sami Heikkinen, Anna-Liisa Levonen
Phospholipids, such as 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphocholine (PAPC), are the major components of cell membranes. Their exposure to reactive oxygen species creates oxidized phospholipids, which predispose to the development of chronic inflammatory diseases and metabolic disorders through endothelial activation and dysfunction. Although the effects of oxidized PAPC (oxPAPC) on endothelial cells have been previously studied, the underlying molecular mechanisms evoking biological responses remain largely unknown...
November 17, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29159068/transcriptome-analysis-of-the-chinese-giant-salamander-andrias-davidianus-using-rna-sequencing
#4
Yong Huang, Jian Li Xiong, Xiao Chan Gao, Xi Hong Sun
The Chinese giant salamander (Andrias davidianus) is an economically important animal on academic value. However, the genomic information of this species has been less studied. In our study, the transcripts of A. davidianus were obtained by RNA-seq to conduct a transcriptomic analysis. In total 132,912 unigenes were generated with an average length of 690 bp and N50 of 1263 bp by de novo assembly using Trinity software. Using a sequence similarity search against the nine public databases (CDD, KOG, NR, NT, PFAM, Swiss-prot, TrEMBL, GO and KEGG databases), a total of 24,049, 18,406, 36,711, 15,858, 20,500, 27,515, 36,705, 28,879 and 10,958 unigenes were annotated in databases, respectively...
December 2017: Genomics Data
https://www.readbyqxmd.com/read/29158625/comparative-genomic-hybridization-and-transcriptome-sequencing-reveal-that-two-genes-osi_14279-loc_os03g62620-and-osi_10794-loc_os03g14950-regulate-the-mutation-in-the-%C3%AE-rl-rice-mutant
#5
Xulong Wang, Fanhua Wang, Huiqiong Chen, Xiaoyu Liang, Yingmei Huang, Jicai Yi
We previously established the genetic locus of the rolled-leaf mutant, γ-rl, to chromosome 3. In this study, we performed a comparative genomic hybridization (CGH) analysis to identify the genes responsible for the γ-rl mutant phenotype. This was combined with RNA transcriptome sequencing (RNA-seq) to analyze differences in the mRNA expression in seeds 12 h after germination. Using the reference genome of the "indica type" rice from GenBank, we created a chip with 386,000 high density DNA probes designed to target chromosome 3...
October 2017: Physiology and Molecular Biology of Plants: An International Journal of Functional Plant Biology
https://www.readbyqxmd.com/read/29158595/genome-wide-identification-of-long-non-coding-rna-genes-and-their-association-with-insecticide-resistance-and-metamorphosis-in-diamondback-moth-plutella-xylostella
#6
Feiling Liu, Dianhao Guo, Zhuting Yuan, Chen Chen, Huamei Xiao
Long non-coding RNA (lncRNA) is a class of noncoding RNA >200 bp in length that has essential roles in regulating a variety of biological processes. Here, we constructed a computational pipeline to identify lncRNA genes in the diamondback moth (Plutella xylostella), a major insect pest of cruciferous vegetables. In total, 3,324 lncRNAs corresponding to 2,475 loci were identified from 13 RNA-Seq datasets, including samples from parasitized, insecticide-resistant strains and different developmental stages...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158586/insights-into-gene-expression-profiles-induced-by-socs3-depletion-in-keratinocytes
#7
Archana Bajpai, Takashi Ishii, Kosuke Miyauchi, Vipul Gupta, Yuka Nishio-Masaike, Yuki Shimizu-Yoshida, Masato Kubo, Hiroaki Kitano
Specific deletion of suppressor of cytokine signaling 3 (Socs3) in keratinocytes can cause severe skin inflammation with infiltration of immune cells. The molecular mechanisms and key regulatory pathways involved in these processes remain elusive. To investigate the role of Socs3 in keratinocytes, we generated and analyzed global RNA-Seq profiles from Socs3 conditional knockout (cKO) mice of two different ages (2 and 10 weeks). Over 400 genes were significantly regulated at both time points. Samples from 2-week-old mice exhibited down-regulation of genes involved in keratin-related functions and up-regulation of genes involved in lipid metabolism...
November 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29158441/shep-regulates-drosophila-neuronal-remodeling-by-controlling-transcription-of-its-chromatin-targets
#8
Dahong Chen, Ryan K Dale, Elissa P Lei
Neuronal remodeling is critical to form the mature nervous system and can lead to neuropsychiatric diseases when disrupted. Global gene expression changes in neurons during remodeling as well as the factors that regulate these changes remain poorly defined. To elucidate this process, we performed RNA-seq on isolated Drosophila larval and pupal neurons and found up-regulated synaptic signaling and down-regulated gene expression regulators as a result of normal neuronal metamorphosis. We further tested the role of alan shepard (shep), which encodes an evolutionarily conserved RNA-binding protein required for proper neuronal remodeling...
November 20, 2017: Development
https://www.readbyqxmd.com/read/29158334/global-transcriptome-sequencing-reveals-molecular-profiles-of-summer-diapause-induction-stage-of-onion-maggot-delia-antiqua-diptera-anthomyiidae
#9
Shuang Ren, You-Jin Hao, Bin Chen, You-Ping Yin
The onion maggot, Delia antiqua, is a worldwide subterranean pest and can enter diapause during summer and winter seasons. The molecular regulation of the ontogenesis transition remains largely unknown. Here we used high-throughput RNA-Seq to identify candidate genes and processes linked to summer diapause induction by comparing the transcriptome differences between the most sensitive larval developmental stage of summer-diapause (SD) and non-diapause (ND). Nine pair-wise comparisons were performed and significantly differentially regulated transcripts were identified...
November 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29158074/a-novel-feature-selection-for-rna-seq-analysis
#10
Henry Han
RNA-seq data are challenging existing omics data analytics for its volume and complexity. Although quite a few computational models were proposed from different standing points to conduct differential expression (D.E.) analysis, almost all these methods do not provide a rigorous feature selection for high-dimensional RNA-seq count data. Instead, most or even all genes are invited into differential calls no matter they have real contributions to data variations or not. Thus, it would inevitably affect the robustness of D...
November 5, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29157442/a-deep-learning-based-multi-model-ensemble-method-for-cancer-prediction
#11
Yawen Xiao, Jun Wu, Zongli Lin, Xiaodong Zhao
BACKGROUND AND OBJECTIVE: Cancer is a complex worldwide health problem associated with high mortality. With the rapid development of the high-throughput sequencing technology and the application of various machine learning methods that have emerged in recent years, progress in cancer prediction has been increasingly made based on gene expression, providing insight into effective and accurate treatment decision making. Thus, developing machine learning methods, which can successfully distinguish cancer patients from healthy persons, is of great current interest...
January 2018: Computer Methods and Programs in Biomedicine
https://www.readbyqxmd.com/read/29157215/integration-of-rna-seq-data-with-heterogeneous-microarray-data-for-breast-cancer-profiling
#12
Daniel Castillo, Juan Manuel Gálvez, Luis Javier Herrera, Belén San Román, Fernando Rojas, Ignacio Rojas
BACKGROUND: Nowadays, many public repositories containing large microarray gene expression datasets are available. However, the problem lies in the fact that microarray technology are less powerful and accurate than more recent Next Generation Sequencing technologies, such as RNA-Seq. In any case, information from microarrays is truthful and robust, thus it can be exploited through the integration of microarray data with RNA-Seq data. Additionally, information extraction and acquisition of large number of samples in RNA-Seq still entails very high costs in terms of time and computational resources...
November 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/29157094/tead4-promotes-colorectal-tumorigenesis-via-transcriptionally-targeting-yap1
#13
Jia-Yin Tang, Chen-Yang Yu, Yu-Jie Bao, Lu Chen, Jinxian Chen, Sheng-Li Yang, Hao-Yan Chen, Jie Hong, Jing-Yuan Fang
TEAD4 (TEA domain family member 4) was recently revealed as an oncogenic character in tumorigenesis. However, its role remains unclear in colorectal tumorigenesis. Here, we firstly found that the expression level of TEAD4 was significantly elevated in clinical samples of colorectal adenomas (CRA) and correlated with the size and histological type of CRA. Moreover, patients with higher TEAD4 expression in normal colon mucosa are more prone to be recurrent after polypectomy. TEAD4 knockdown significantly inhibited colorectal cell proliferation in vitro and suppressed tumor growth in vivo...
November 20, 2017: Cell Cycle
https://www.readbyqxmd.com/read/29156803/tet1-inhibits-cell-proliferation-by-inducing-rassf5-expression
#14
Bo-Tai Li, Chao Yu, Ying Xu, Sheng-Bing Liu, Heng-Yu Fan, Wei-Wei Pan
Tet methylcytosine dioxygenases (TETs) catalyze the oxidative reactions of 5-methylcytosine to 5-hydroxymethylcytosine (5hmC). However, TET1 roles in ovarian cancer cell growth are unknown. Here, we show that ectopic expression of TET1 increased 5hmC levels, and inhibited proliferation and colony formation in ovarian cancer cell lines. Furthermore, in vitro and in vivo functional studies demonstrated that TET1 overexpression is necessary for the suppression of ovarian cancer growth, whereas depletion of TET1 expression had the opposite effect...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156765/network-directed-cis-mediator-analysis-of-normal-prostate-tissue-expression-profiles-reveals-downstream-regulatory-associations-of-prostate-cancer-susceptibility-loci
#15
Nicholas B Larson, Shannon K McDonnell, Zach Fogarty, Melissa C Larson, John Cheville, Shaun Riska, Saurabh Baheti, Alexandra M Weber, Asha A Nair, Liang Wang, Daniel O'Brien, Jaime Davila, Daniel J Schaid, Stephen N Thibodeau
Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis-acting associations due to study limitations. While trans-eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans-eQTL associations are mediated by cis-regulated genes, such as transcription factors...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156759/smoking-and-gender-modify-the-effect-of-twist-on-patient-survival-in-head-and-neck-squamous-carcinoma
#16
Yun Zhu, Wenjuan Zhang, Ping Wang
Purpose: TWIST is a critical factor for predicting prognosis in several human cancers. Here, we study the prognostic significance of TWIST1 and TWIST2 in Head and Neck squamous cell carcinoma (HNSCC) as well as interactions of TWISTs with both gender and smoking in patient survival. Methods: upper quartile normalized RNA-seq V2 RSEM values of TWIST1 and TWIST2 expressions were retrieved from a TCGA HNSCC dataset. Kaplan-Meier survival curves were used to assess the associations of TWIST1 and TWIST2 with patient survival, and multivariate Cox proportional hazards regression models were used to estimate the hazards ratios (HRs) and their 95% confidence intervals (CIs)...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156693/cdk3-target-of-mir-4469-suppresses-breast-cancer-metastasis-via-inhibiting-wnt-%C3%AE-catenin-pathway
#17
Ting Cao, Tian Xiao, Guanqun Huang, Yafei Xu, Joe Jiang Zhu, Kaixin Wang, Wencai Ye, Hong Guan, Jinsong He, Duo Zheng
Cyclin-dependent kinase 3 (CDK3), a member of CDK family, is involved in G0/G1 and G1/S cell cycle transitions. Although several researchers discovered that CDK3 related to cell growth in some kinds of cancer, the functions of CDK3 during tumor development remains unclear. Here, we first found that the expression of CDK3 was higher in primary tumors of non-metastatic breast cancer compared with those in metastatic breast cancer. Overexpression of CDK3 suppressed cell migration and invasion of breast cancer cells, and decreased the metastasis in nude mice...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29155997/immune-activation-and-benefit-from-avelumab-in-ebv-positive-gastric-cancer
#18
Anshuman Panda, Janice M Mehnert, Kim M Hirshfield, Greg Riedlinger, Sherri Damare, Tracie Saunders, Michael Kane, Levi Sokol, Mark N Stein, Elizabeth Poplin, Lorna Rodriguez-Rodriguez, Ann W Silk, Joseph Aisner, Nancy Chan, Jyoti Malhotra, Melissa Frankel, Howard L Kaufman, Siraj Ali, Jeffrey S Ross, Eileen P White, Gyan Bhanot, Shridar Ganesan
Response to immune checkpoint therapy can be associated with a high mutation burden, but other mechanisms are also likely to be important. We identified a patient with metastatic gastric cancer with meaningful clinical benefit from treatment with the anti-programmed death-ligand 1 (PD-L1) antibody avelumab. This tumor showed no evidence of high mutation burden or mismatch repair defect but was strongly positive for presence of Epstein-Barr virus (EBV) encoded RNA. Analysis of The Cancer Genome Atlas gastric cancer data (25 EBV+, 80 microsatellite-instable [MSI], 310 microsatellite-stable [MSS]) showed that EBV-positive tumors were MSS...
November 15, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29155830/molecular-characterization-of-tsetse-s-proboscis-and-its-response-to-trypanosoma-congolense-infection
#19
Erick O Awuoche, Brian L Weiss, Aurélien Vigneron, Paul O Mireji, Emre Aksoy, Benson Nyambega, Geoffrey M Attardo, Yineng Wu, Michelle O'Neill, Grace Murilla, Serap Aksoy
Tsetse flies (Glossina spp.) transmit parasitic African trypanosomes (Trypanosoma spp.), including Trypanosoma congolense, which causes animal African trypanosomiasis (AAT). AAT detrimentally affects agricultural activities in sub-Saharan Africa and has negative impacts on the livelihood and nutrient availability for the affected communities. After tsetse ingests an infectious blood meal, T. congolense sequentially colonizes the fly's gut and proboscis (PB) organs before being transmitted to new mammalian hosts during subsequent feedings...
November 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/29154927/integrative-transcriptome-and-proteome-analyses-define-marked-differences-between-neospora-caninum-isolates-throughout-the-tachyzoite-lytic-cycle
#20
P Horcajo, D Xia, N Randle, E Collantes-Fernández, J Wastling, L M Ortega-Mora, J Regidor-Cerrillo
Neospora caninum is one of the main causes of transmissible abortion in cattle. Intraspecific variations in virulence have been widely shown among N. caninum isolates. However, the molecular basis governing such variability have not been elucidated to date. In this study label free LC-MS/MS was used to investigate proteome differences between the high virulence isolate Nc-Spain7 and the low virulence isolate Nc-Spain1H throughout the tachyzoite lytic cycle. The results showed greater differences in the abundance of proteins at invasion and egress with 77 and 62 proteins, respectively...
November 14, 2017: Journal of Proteomics
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