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Md Ashrafuzzaman, Zahidul Haque, Basharat Ali, Boby Mathew, Peng Yu, Frank Hochholdinger, Joao Braga de Abreu Neto, Max R McGillen, Hans-Jürgen Ensikat, William J Manning, Michael Frei
Monitoring of ozone damage to crops plays an increasingly important role for the food security of many developing countries. Ethylenediurea (EDU) could be a tool to assess ozone damage to vegetation on field scale, but its physiological mode of action remains unclear. This study investigated mechanisms underlying the ozone-protection effect of EDU in controlled chamber experiments. Ozone sensitive and tolerant rice genotypes were exposed to ozone (108 ppb, 7 h day-1 ) and control conditions. EDU alleviated ozone effects on plant morphology, foliar symptoms, lipid peroxidation and photosynthetic parameters in sensitive genotypes...
August 14, 2018: Plant, Cell & Environment
Marlies Vanden Bempt, Sofie Demeyer, Michaël Broux, Jolien De Bie, Simon Bornschein, Nicole Mentens, Roel Vandepoel, Ellen Geerdens, Enrico Radaelli, Beat C Bornhauser, Andreas E Kulozik, Jules P Meijerink, Jean-Pierre Bourquin, Charles E de Bock, Jan Cools
The NUP214-ABL1 fusion is a constitutively activated tyrosine kinase that is significantly associated with overexpression of the TLX1 and TLX3 transcription factors in T cell acute lymphoblastic leukemia (T-ALL). Here we show that NUP214-ABL1 cooperates with TLX1 in driving T-ALL development using a transgenic mouse model and human T-ALL cells. Using integrated ChIP-sequencing, ATAC-sequencing, and RNA-sequencing data, we demonstrate that TLX1 and STAT5, the downstream effector of NUP214-ABL1, co-bind poised enhancer regions, and cooperatively activate the expression of key proto-oncogenes such as MYC and BCL2...
August 13, 2018: Cancer Cell
Emilia Maria Cristina Mazza, Jolanda Brummelman, Giorgia Alvisi, Alessandra Roberto, Federica De Paoli, Veronica Zanon, Federico Colombo, Mario Roederer, Enrico Lugli
Multidimensional single-cell analysis requires approaches to visualize complex data in intuitive 2D graphs. In this regard, t-distributed stochastic neighboring embedding (tSNE) is the most popular algorithm for single-cell RNA sequencing and cytometry by time-of-flight (CyTOF), but its application to polychromatic flow cytometry, including the recently developed 30-parameter platform, is still under investigation. We identified differential distribution of background values between samples, generated by either background calculation or spreading error (SE), as a major source of variability in polychromatic flow cytometry data representation by tSNE, ultimately resulting in the identification of erroneous heterogeneity among cell populations...
August 14, 2018: Cytometry. Part A: the Journal of the International Society for Analytical Cytology
Yu Shi, Zuhua Chen, Juanjuan Gao, Si Wu, Haer Gao, Guoshuang Feng
Alternative mRNA splicing (AS) contributes greatly to expanding the diversity and function of the proteome. Increasing evidence has suggested that dysregulation of mRNA splicing may be associated with various types of cancer. In the present study, RNA sequencing data were used to investigate alterations to the global mRNA splicing landscape of cellular genes from 452 stomach adenocarcinoma (STAD) tissues available in The Cancer Genome Atlas. Seven types of AS events, including the profiles of exon skipping events, were analyzed using SpliceSeq software...
August 2, 2018: Oncology Reports
Qingzhuo Dong, Chengcheng Lv, Gejun Zhang, Zi Yu, Chuize Kong, Cheng Fu, Yu Zeng
RNA‑binding motif 3 (RBM3) is a cold‑shock protein that has been previously shown to attenuate cancer stem cell‑like features in prostate cancer (PCa) cells. However, the mechanism underlying RBM3 regulation in PCa cells is largely unknown. The present study investigated the impact of RBM3 expression on the whole transcriptome of PCa cells using high‑throughput RNA sequencing (RNA‑seq). Differentially expressed genes (DEGs) that were identified through RNA‑seq were applied to Gene Ontology (GO), pathway analysis, pathway‑action networks and protein‑protein interaction network analysis...
August 1, 2018: Oncology Reports
Lu Shi, Ruowen Xiao, Menghe Wang, Meiyin Zhang, Nuoqing Weng, Xinge Zhao, X F Steven Zheng, Huiyun Wang, Shijuan Mai
Deregulated microRNAs play an important role in the development and progression of various types of cancer. In our previous study, we observed that microRNA‑342‑3p (miR‑342‑3p) was one of the most markedly downregulated microRNAs in two nasopharyngeal carcinoma (NPC) cell lines compared to non‑neoplastic cells by using whole genome small RNA sequencing. In the present study, we confirmed that the expression of miR‑342‑3p was significantly reduced in NPC tissues compared with normal nasopharyngeal epithelial tissues...
August 10, 2018: Oncology Reports
Cun-Yi Zou, Ge-Fei Guan, Chen Zhu, Tian-Qi Liu, Qing Guo, Wen Cheng, An-Hua Wu
AIMS: Immune checkpoint blockade has made breakthroughs in immunotherapy for glioma. However, current immunotherapy has therapeutic benefits only in a subset of patients and accompanied by immune-related side effects. SLAMF8 is a costimulatory molecule that affects the activation of macrophages in inflammation. The study of SLAMF8 may provide new information for immunological research and treatment of glioma. METHODS: CGGA and TCGA cohorts of 946 patients with RNA sequencing data and full clinical information were analyzed using R language and GraphPad Prism 7...
August 13, 2018: CNS Neuroscience & Therapeutics
Kyu Jin Sa, Ik-Young Choi, Kyong-Cheul Park, Ju Kyong Lee
SSRs were successfully isolated from the Perilla crop in our current study, and used to analyze Perilla accessions from East Asia. Analyses of the clear genetic diversity and relationship for Perilla crop still remain insufficient. In this study, 40 new simple sequence repeat (SSR) primer sets were developed from RNA sequences using transcriptome analysis. These new SSR markers were applied to analyze the diversity, relationships, and population structure among 35 accessions of the two cultivated types of Perilla crop and their weedy types...
August 13, 2018: Genes & Genomics
Wentao Cai, Cong Li, Shuli Liu, Chenghao Zhou, Hongwei Yin, Jiuzhou Song, Qin Zhang, Shengli Zhang
Long non-coding RNAs (lncRNAs) have emerged as a novel class of regulatory molecules involved in various biological processes. However, their role in milk performance is unknown. Here, whole transcriptome RNA sequencing was used to generate the lncRNA transcriptome profiles in mammary tissue samples from 6 Chinese Holstein cows with 3 extremely high and 3 low milk protein percentage phenotypes. In this study, 6,450 lncRNA transcripts were identified through 5 stringent steps and filtration by coding potential...
2018: Frontiers in Genetics
Pavithra Sampath, Kadar Moideen, Uma Devi Ranganathan, Ramalingam Bethunaickan
Monocytes are critical defense components that play an important role in the primary innate immune response. The heterogeneous nature of monocytes and their ability to differentiate into either monocyte-derived macrophages or monocyte-derived dendritic cells allows them to serve as a bridge between the innate and adaptive immune responses. Current studies of monocytes based on immunofluorescence, single-cell RNA sequencing and whole mass spectrometry finger printing reveals different classification systems for monocyte subsets...
2018: Frontiers in Immunology
Jiao Wang, Jie Li, Qian Wang, Yanyan Kong, Fangfang Zhou, Qian Li, Weihao Li, Yangyang Sun, Yanli Wang, Yihui Guan, Minghong Wu, Tieqiao Wen
Microglia serve as the principal immune cells and play crucial roles in the central nervous system, responding to neuroinflammation via migration and the execution of phagocytosis. Dendritic cell-derived factor 1 (Dcf1) is known to play an important role in neural stem cell differentiation, glioma apoptosis, dendritic spine formation, and Alzheimer's disease (AD), nevertheless, the involvement of the Dcf1 gene in the brain immune response has not yet been reported. In the present paper, the RNA-sequencing and function enrichment analysis suggested that the majority of the down-regulated genes in Dcf1 -/- ( Dcf1 -KO) mice are immune-related...
2018: Frontiers in Molecular Neuroscience
Ayush T Raman, Amy E Pohodich, Ying-Wooi Wan, Hari Krishna Yalamanchili, William E Lowry, Huda Y Zoghbi, Zhandong Liu
Recent studies have suggested that genes longer than 100 kb are more likely to be misregulated in neurological diseases associated with synaptic dysfunction, such as autism and Rett syndrome. These length-dependent transcriptional changes are modest in MeCP2-mutant samples, but, given the low sensitivity of high-throughput transcriptome profiling technology, here we re-evaluate the statistical significance of these results. We find that the apparent length-dependent trends previously observed in MeCP2 microarray and RNA-sequencing datasets disappear after estimating baseline variability from randomized control samples...
August 13, 2018: Nature Communications
Qingqing Wang, Donald C Rio
Alternative pre-mRNA splicing (AS) greatly diversifies metazoan transcriptomes and proteomes and is crucial for gene regulation. Current computational analysis methods of AS from Illumina RNA-sequencing data rely on preannotated libraries of known spliced transcripts, which hinders AS analysis with poorly annotated genomes and can further mask unknown AS patterns. To address this critical bioinformatics problem, we developed a method called the junction usage model (JUM) that uses a bottom-up approach to identify, analyze, and quantitate global AS profiles without any prior transcriptome annotations...
August 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
Yumei Li, Chen Li, Shuxian Li, Qi Peng, Ni A An, Aibin He, Chuan-Yun Li
Nucleosomal modifications have been implicated in fundamental epigenetic regulation, but the roles of nucleosome occupancy in shaping changes through evolution remain to be addressed. Here we present high-resolution nucleosome occupancy profiles for multiple tissues derived from human, macaque, tree shrew, mouse, and pig. Genome-wide comparison reveals conserved nucleosome occupancy profiles across both different species and tissue types. Notably, we found significantly higher levels of nucleosome occupancy in exons than in introns, a pattern correlated with the different exon-intron GC content...
August 13, 2018: Proceedings of the National Academy of Sciences of the United States of America
Jeffrey Zuber, B Joseph Cabral, Iain McFadyen, David M Mauger, David H Mathews
RNA secondary structure prediction is often used to develop hypotheses about structure-function relationships for newly discovered RNA sequences, to identify unknown functional RNAs, and to design sequences. Secondary structure prediction methods typically use a thermodynamic model that estimates the free energy change of possible structures based on a set of nearest neighbor parameters. These parameters were derived from optical melting experiments of small model oligonucleotides. This work aims to better understand the precision of structure prediction...
August 13, 2018: RNA
Long Jin, Jian Ping Yu, Zai Jun Yang, Juha Merilä, Wen Bo Liao
Hibernation is an effective energy conservation strategy that has been widely adopted by animals to cope with unpredictable environmental conditions. The liver, in particular, plays an important role in adaptive metabolic adjustment during hibernation. Mammalian studies have revealed that many genes involved in metabolism are differentially expressed during the hibernation period. However, the differentiation in global gene expression between active and torpid states in amphibians remains largely unknown. We analyzed gene expression in the liver of active and torpid Asiatic toads ( Bufo gargarizans ) using RNA-sequencing...
August 10, 2018: International Journal of Molecular Sciences
Hyosun Hong, Han-Ha Chai, Kyoungwoo Nam, Dajeong Lim, Kyung-Tai Lee, Yoon Jung Do, Chang-Yeon Cho, Jin-Wu Nam
Yeonsan Ogye is a rare Korean domestic chicken breed whose entire body, including feathers and skin, has a unique black coloring. Although some protein-coding genes related to this unique feature have been examined, non-coding elements have not been widely investigated. Thus, we evaluated coding and non-coding transcriptome expression and identified long non-coding RNAs functionally linked to protein-coding genes in Ogye. High-throughput RNA sequencing and DNA methylation sequencing were performed to profile the expression of 14,264 Ogye protein-coding and 6900 long non-coding RNA (lncRNA) genes and detect DNA methylation in 20 different tissues of an individual Ogye...
August 10, 2018: International Journal of Molecular Sciences
Veronica L Massey, Liya Qin, Joaquin Cabezas, Juan Caballeria, Pau Sancho-Bru, Ramon Bataller, Fulton Crews
BACKGROUND: Toll like receptor 7 (TLR7) is an endosomal TLR that is activated by ssRNA, including endogenous microRNAs (e.g. let-7b). Increased hepatic expression of TLRs, microRNAs, and inflammatory mediators are linked to ethanol exposure and to alcoholic liver disease (ALD). ALD invovles chronic hepatic inflammation that can progress to alcoholic hepatitis (AH), a particularly severe form of ALD. This study aimed to investigate TLR7 expression in patients with different liver disease phenotypes and in mouse liver following alcohol exposure...
August 13, 2018: Alcoholism, Clinical and Experimental Research
Sijie Lin, Kuancan Liu, Yongchun Zhang, Ming Jiang, Rong Lu, Christopher J Folts, Xia Gao, Mark D Noble, Tingting Zhao, Zhongren Zhou, Xiaopeng Lan, Jianwen Que
Drug repurposing with a better understanding of the underlying mechanism has provided new avenues to find treatment for malignancies. Esophageal adenocarcinoma (EAC) is a rapidly increasing cancer with a dismal 5-year survival rate of <15%. Lack of efficient treatment options contributes to the high mortality rate of EAC. To find new therapy against EAC we performed unbiased drug screening of an FDA-approved drug library and identified that the cardiac glycosides including Ouabain, Digoxin and Digitoxin efficiently inhibit the proliferation of EAC cell lines (OE33 and OE19) both in vitro and in vivo...
August 10, 2018: Cellular Signalling
Jialu Zhao, Xu Liu, Chunyue Huo, Tian Zhao, Haihong Ye
MK-801, a non-competitive NMDA receptor antagonist, disturbs NMDA receptor function in rodents and induces psychological and behavioral changes similar to schizophrenia (SCZ). However, the effects of MK-801 treatment on gene expression are largely unknown. Here we performed RNA-sequencing on the prefrontal cortex of MK-801-exposed male mice in order to analyze gene expression and co-expression patterns related to SCZ and to identify mechanisms that underlie the molecular etiology of this disorder. Transcriptome analysis revealed that the differentially expressed genes were more often associated with biological processes that included postsynaptic transmission, immune system process, response to external stimulus and hemostasis...
August 10, 2018: Neuroscience
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