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https://www.readbyqxmd.com/read/28938749/the-testicular-transcriptome-associated-with-spermatogonia-differentiation-initiated-by-gonadotrophin-stimulation-in-the-juvenile-rhesus-monkey-macaca-mulatta
#1
Suresh Ramaswamy, William H Walker, Paula Aliberti, Rahil Sethi, Gary R Marshall, Alyxzandria Smith, Seyedmehdi Nourashrafeddin, Alicia Belgorosky, Uma R Chandran, Mark P Hedger, Tony M Plant
STUDY QUESTION: What is the genetic landscape within the testis of the juvenile rhesus monkey (Macaca mulatta) that underlies the decision of undifferentiated spermatogonia to commit to a pathway of differentiation when puberty is induced prematurely by exogenous LH and FSH stimulation? SUMMARY ANSWER: Forty-eight hours of gonadotrophin stimulation of the juvenile monkey testis resulted in the appearance of differentiating B spermatogonia and the emergence of 1362 up-regulated and 225 down-regulated testicular mRNAs encoding a complex network of proteins ranging from enzymes regulating Leydig cell steroidogenesis to membrane receptors, and from juxtacrine and paracrine factors to transcriptional factors governing spermatogonial stem cell fate...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28938722/novel-transcriptome-resources-for-three-scleractinian-coral-species-from-the-indo-pacific
#2
Carly D Kenkel, Line K Bay
Transcriptomic resources for coral species can provide insight into coral evolutionary history and stress-response physiology. Goniopora columna, Galaxea astreata, and Galaxea acrhelia are scleractinian corals of the Indo-Pacific, representing a diversity of morphologies and life-history traits. G. columna and G. astreata are common and cosmopolitan, while G. acrhelia is largely restricted to the coral triangle and Great Barrier Reef. Reference transcriptomes for these species were assembled from replicate colony fragments exposed to elevated (31°C) and ambient (27°C) temperatures...
September 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28938650/genomic-variants-link-to-hepatitis-c-racial-disparities
#3
Matthew M Yeh, Sarag Boukhar, Benjamin Roberts, Nairanjana Dasgupta, Sayed S Daoud
Chronic liver diseases are one of the major public health issues in United States, and there are substantial racial disparities in liver cancer-related mortality. We previously identified racially distinct alterations in the expression of transcripts and proteins of hepatitis C (HCV)-induced hepatocellular carcinoma (HCC) between Caucasian (CA) and African American (AA) subgroups. Here, we performed a comparative genome-wide analysis of normal vs. HCV+ (cirrhotic state), and normal adjacent tissues (HCCN) vs...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938607/hgfl-mediated-ron-signaling-supports-breast-cancer-stem-cell-phenotypes-via-activation-of-non-canonical-%C3%AE-catenin-signaling
#4
Sasha J Ruiz-Torres, Nancy M Benight, Rebekah A Karns, Elyse E Lower, Jun-Lin Guan, Susan E Waltz
Breast cancer stem cells (BCSCs), which drive tumor progression, recurrence, and metastasis, are considered a major challenge for breast cancer treatments, thus the discovery of novel pathways regulating BCSC maintenance remains essential to develop new strategies to effectively target this population and combat disease mortality. The HGFL-RON signaling is overexpressed in human breast cancers and is associated with increased breast cancer progression, metastasis, and poor prognosis. Here, we report that overexpression of RON/MST1R and HGFL/MST1 in cell lines and primary tumors increases BCSC self-renewal, numbers, and tumorigenic potential after syngeneic transplantation...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938587/transcriptomic-profiles-of-human-foreskin-fibroblast-cells-in-response-to-orf-virus
#5
Daxiang Chen, Mingjian Long, Bin Xiao, Yufeng Xiong, Huiqin Chen, Yu Chen, Zhenzhan Kuang, Ming Li, Yingsong Wu, Daniel L Rock, Daoyuan Gong, Yong Wang, Haijian He, Fang Liu, Shuhong Luo, Wenbo Hao
Orf virus has been utilized as a safe and efficient viral vector against not only diverse infectious diseases, but also against tumors. However, the nature of the genes triggered by the vector in human cells is poorly characterized. Using RNA sequencing technology, we compared specific changes in the transcriptomic profiles in human foreskin fibroblast cells following infection by the orf virus. The results indicated that orf virus upregulates or downregulates expression of a variety of genes, including genes involved in antiviral immune response, apoptosis, cell cycle and a series of signaling pathways, such as the IFN and p53-signaling pathways...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938541/differential-expression-of-circulating-biomarkers-of-tumor-phenotype-and-outcomes-in-previously-treated-non-small-cell-lung-cancer-patients-receiving-erlotinib-vs-cytotoxic-chemotherapy
#6
Mary Jo Fidler, Casey Frankenberger, Richard Seto, Gabriela C Lobato, Cristina L Fhied, Selina Sayidine, Sanjib Basu, Mark Pool, Reem Karmali, Marta Batus, Wen-Rong Lie, David Hayes, Jehangir Mistry, Philip Bonomi, Jeffrey A Borgia
BACKGROUND: The objective of this study was to identify serum biomarkers capable of predicting clinical outcomes in previously-treated NSCLC patients with wild-type for EGFR activating mutations or insufficient tissue for mutation status determination. METHODS: Sixty-six Luminex immunoassays representative of biological themes that emerged from a re-analysis of transcriptome data from the Cancer Genome Atlas (TCGA) were evaluate against pretreatment serum specimens from previously-treated advanced NSCLC patients received either cytotoxic chemotherapy (n=32) or erlotinib (n=79)...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938490/expression-of-contactin-4-is-associated-with-malignant-behavior-in-pheochromocytomas-and-paragangliomas
#7
Lucie Evenepoel, Francien H van Nederveen, Lindsey Oudijk, Thomas G Papathomas, David F Restuccia, Eric J T Belt, Wouter W de Herder, Richard A Feelders, Gaston J H Franssen, Marc Hamoir, Dominique Maiter, Aurel Perren, Henri J L M Timmers, Susanne van Eeden, Laurent Vroonen, Selda Aydin, Mercedes Robledo, Miikka Vikkula, Ronald R de Krijger, Winand N M Dinjens, Alexandre Persu, Esther Korpershoek
Context: Pheochromocytomas and paragangliomas (PPGL) are rare neuroendocrine, usually benign tumors. Currently, the only reliable criterion of malignancy is the presence of metastases. Objective: The aim was to identify genes associated with malignancy in PPGL. Design: Transcriptomic profiling was performed on 40 benign and 11 malignant PPGL. Genes showing a significantly different expression between benign and malignant PPGL with a ratio ≥ 4 were confirmed, and subsequently tested in an independent series by qRT-PCR...
August 17, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28938455/bile-acid-alterations-are-associated-with-insulin-resistance-but-not-with-nash-in-obese-subjects
#8
Vanessa Legry, Sven Francque, Joel T Haas, An Verrijken, Sandrine Caron, Oscar Chávez-Talavera, Emmanuelle Vallez, Luisa Vonghia, Eveline Dirinck, Ann Verhaegen, Mostafa Kouach, Sophie Lestavel, Philippe Lefebvre, Luc Van Gaal, Anne Tailleux, Réjane Paumelle, Bart Staels
Context: Bile acids (BA) are signalling molecules controlling energy homeostasis which can be both toxic and protective for the liver. BA alterations have been reported in obesity, insulin resistance (IR) and non-alcoholic steatohepatitis (NASH). However whether BA alterations contribute to NASH independently of the metabolic status is unclear. Objective: To assess BA alterations associated with NASH independently of BMI and IR. Design & Setting: Patients visiting the obesity clinic of the Antwerp University Hospital (a tertiary referral facility) were recruited from 2006 to 2014...
August 4, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28938404/the-transcriptome-of-estrogen-independent-mammary-growth-in-female-mice-reveals-that-not-all-mammary-glands-are-created-equally
#9
Grace E Berryhill, Danielle G Lemay, Josephine F Trott, Lucila Aimo, Adam L Lock, Russell C Hovey
Allometric growth of ducts in the mammary glands (MG) is widely-held to be estrogen (E)-dependent. We previously discovered that the dietary fatty acid trans-10, cis-12 conjugated linoleic acid (CLA) stimulates E-independent allometric growth and TEB formation in ovariectomized mice. Given the similar phenotype induced by E and CLA, we investigated the shared and/or divergent mechanisms underlying these changes. We confirmed MG growth induced by CLA is temporally distinct from that elicited by E, then used RNA-Sequencing to compare the transcriptome of the MG during similar proliferative and morphological states...
July 27, 2017: Endocrinology
https://www.readbyqxmd.com/read/28938089/drug-discovery-and-chemical-biology-of-cancer-epigenetics
#10
REVIEW
Scott Ribich, Darren Harvey, Robert A Copeland
Comprehensive whole-exome sequencing, DNA copy-number determination, and transcriptomic analyses of diverse cancers have greatly expanded our understanding of the biology of many tumor types. In addition to mutations in the common cell-of-origin specific driver mutations, these studies have also revealed a large number of loss-of-function and gain-of-function mutations in chromatin-modifying proteins (CMPs). This has revealed that epigenetic dysregulation is a common feature of most pediatric and adult cancers...
September 21, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28937943/multiomics-analysis-of-tumor-microenvironment-reveals-gata2-and-mirna-124-3p-as-potential-novel-biomarkers-in-ovarian-cancer
#11
Esra Gov, Medi Kori, Kazim Yalcin Arga
Ovarian cancer is a common and, yet, one of the most deadly human cancers due to its insidious onset and the current lack of robust early diagnostic tests. Tumors are complex tissues comprised of not only malignant cells but also genetically stable stromal cells. Understanding the molecular mechanisms behind epithelial-stromal crosstalk in ovarian cancer is a great challenge in particular. In the present study, we performed comparative analyses of transcriptome data from laser microdissected epithelial, stromal, and ovarian tumor tissues, and identified common and tissue-specific reporter biomolecules-genes, receptors, membrane proteins, transcription factors (TFs), microRNAs (miRNAs), and metabolites-by integration of transcriptome data with genome-scale biomolecular networks...
September 22, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28936660/isolation-of-arabidopsis-pollen-sperm-cells-and-vegetative-nuclei-by-fluorescence-activated-cell-sorting-facs
#12
Mário R Santos, Cláudia Bispo, Jörg D Becker
Efficient methods to isolate highly purified Arabidopsis thaliana pollen and the subcellular components of the male gametophyte (the vegetative nucleus and two sperm cells) have enabled genome-scale studies revealing a highly dynamic reprogramming of the transcriptome and epigenome during pollen development. Here, we describe the isolation of uninucleate microspores, mature pollen, as well as sperm cells and vegetative nuclei by Fluorescence-Activated Cell Sorting.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28936220/de-novo-assembly-of-the-camellia-nitidissima-transcriptome-reveals-key-genes-of-flower-pigment-biosynthesis
#13
Xingwen Zhou, Jiyuan Li, Yulin Zhu, Sui Ni, Jinling Chen, Xiaojuan Feng, Yunfeng Zhang, Shuangquan Li, Hongguang Zhu, Yuanguang Wen
The golden camellia, Camellia nitidissima Chi., is a well-known ornamental plant that is known as "the queen of camellias" because of its golden yellow flowers. The principal pigments in the flowers are carotenoids and flavonol glycosides. Understanding the biosynthesis of the golden color and its regulation is important in camellia breeding. To obtain a comprehensive understanding of flower development in C. nitidissima, a number of cDNA libraries were independently constructed during flower development. Using the Illumina Hiseq2500 platform, approximately 71...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28936215/omics-approaches-for-understanding-grapevine-berry-development-regulatory-networks-associated-with-endogenous-processes-and-environmental-responses
#14
REVIEW
Alejandra Serrano, Carmen Espinoza, Grace Armijo, Claudio Inostroza-Blancheteau, Evelyn Poblete, Carlos Meyer-Regueiro, Anibal Arce, Francisca Parada, Claudia Santibáñez, Patricio Arce-Johnson
Grapevine fruit development is a dynamic process that can be divided into three stages: formation (I), lag (II), and ripening (III), in which physiological and biochemical changes occur, leading to cell differentiation and accumulation of different solutes. These stages can be positively or negatively affected by multiple environmental factors. During the last decade, efforts have been made to understand berry development from a global perspective. Special attention has been paid to transcriptional and metabolic networks associated with the control of grape berry development, and how external factors affect the ripening process...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28936204/modulatory-influence-of-segmented-filamentous-bacteria-on-transcriptomic-response-of-gnotobiotic-mice-exposed-to-tcdd
#15
Robert D Stedtfeld, Benli Chai, Robert B Crawford, Tiffany M Stedtfeld, Maggie R Williams, Shao Xiangwen, Tomomi Kuwahara, James R Cole, Norbert E Kaminski, James M Tiedje, Syed A Hashsham
Environmental toxicants such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), an aryl hydrocarbon receptor (AhR), are known to induce host toxicity and structural shifts in the gut microbiota. Key bacterial populations with similar or opposing functional responses to AhR ligand exposure may potentially help regulate expression of genes associated with immune dysfunction. To examine this question and the mechanisms for AhR ligand-induced bacterial shifts, C57BL/6 gnotobiotic mice were colonized with and without segmented filamentous bacteria (SFB) - an immune activator...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28936162/rna-sequencing-analysis-reveals-a-regulatory-role-for-transcription-factor-fezf2-in-the-mature-motor-cortex
#16
Alison J Clare, Hollie E Wicky, Ruth M Empson, Stephanie M Hughes
Forebrain embryonic zinc finger (Fezf2) encodes a transcription factor essential for the specification of layer 5 projection neurons (PNs) in the developing cerebral cortex. As with many developmental transcription factors, Fezf2 continues to be expressed into adulthood, suggesting it remains crucial to the maintenance of neuronal phenotypes. Despite the continued expression, a function has yet to be explored for Fezf2 in the PNs of the developed cortex. Here, we investigated the role of Fezf2 in mature neurons, using lentiviral-mediated delivery of a shRNA to conditionally knockdown the expression of Fezf2 in the mouse primary motor cortex (M1)...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28935979/intergrative-metabolomic-and-transcriptomic-analyses-unveil-nutrient-remobilization-events-in-leaf-senescence-of-tobacco
#17
Wei Li, Hailiang Zhang, Xiaoxu Li, Fengxia Zhang, Cheng Liu, Yongmei Du, Xiaoming Gao, Zenglin Zhang, Xiaobing Zhang, Zhihui Hou, Hui Zhou, Xiaofei Sheng, Guodong Wang, Yongfeng Guo
Leaf senescence in plants is a coordinated process that involves remobilization of nutrients from senescing leaves to sink tissues. The molecular events associated with nutrient remobilization are however not well understood. In this study the tobacco system with a source-sink relationship between different leaf positions was used in analyzing the spatiotemporal changes of 76 metabolites from leaves at 3 different stalk positions and 8 developmental stages. The metabolomic data was then compared with RNA-seq data from the same samples to analyze the activities of the metabolic pathways that are important for nutrient remobilization...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935950/transcriptome-analyses-suggest-a-novel-hypothesis-for-whitefly-adaptation-to-tobacco
#18
Wen-Qiang Xia, Xin-Ru Wang, Yan Liang, Shu-Sheng Liu, Xiao-Wei Wang
The adaptation of herbivorous insects to various host plants facilitates the spread and outbreak of many important invasive pests, however, the molecular mechanisms that underneath this process are poorly understood. In the past three decades, two species of the whitefly Bemisia tabaci complex, Middle East-Asia Minor 1 and Mediterranean, have invaded many countries. Their rapid and widespread invasions are partially due to their ability to infest a wide range of host plants. In this study, we determined the transcriptome and phenotypic changes of one Mediterranean whitefly population during its adaptation to tobacco, an unsuitable host plant...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935875/differential-gene-expression-and-snp-association-between-fast-and-slow-growing-turbot-scophthalmus-maximus
#19
Diego Robledo, Juan A Rubiolo, Santiago Cabaleiro, Paulino Martínez, Carmen Bouza
Growth is among the most important traits for animal breeding. Understanding the mechanisms underlying growth differences between individuals can contribute to improving growth rates through more efficient breeding schemes. Here, we report a transcriptomic study in muscle and brain of fast- and slow-growing turbot (Scophthalmus maximus), a relevant flatfish in European and Asian aquaculture. Gene expression and allelic association between the two groups were explored. Up-regulation of the anaerobic glycolytic pathway in the muscle of fast-growing fish was observed, indicating a higher metabolic rate of white muscle...
September 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28935855/establishing-multiple-omics-baselines-for-three-southeast-asian-populations-in-the-singapore-integrative-omics-study
#20
Woei-Yuh Saw, Erwin Tantoso, Husna Begum, Lihan Zhou, Ruiyang Zou, Cheng He, Sze Ling Chan, Linda Wei-Lin Tan, Lai-Ping Wong, Wenting Xu, Don Kyin Nwe Moong, Yenly Lim, Bowen Li, Nisha Esakimuthu Pillai, Trevor A Peterson, Tomasz Bielawny, Peter J Meikle, Piyushkumar A Mundra, Wei-Yen Lim, Ma Luo, Kee-Seng Chia, Rick Twee-Hee Ong, Liam R Brunham, Chiea-Chuen Khor, Heng Phon Too, Richie Soong, Markus R Wenk, Peter Little, Yik-Ying Teo
The Singapore Integrative Omics Study provides valuable insights on establishing population reference measurement in 364 Chinese, Malay, and Indian individuals. These measurements include > 2.5 millions genetic variants, 21,649 transcripts expression, 282 lipid species quantification, and 284 clinical, lifestyle, and dietary variables. This concept paper introduces the depth of the data resource, and investigates the extent of ethnic variation at these omics and non-omics biomarkers. It is evident that there are specific biomarkers in each of these platforms to differentiate between the ethnicities, and intra-population analyses suggest that Chinese and Indians are the most biologically homogeneous and heterogeneous, respectively, of the three groups...
September 21, 2017: Nature Communications
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