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https://www.readbyqxmd.com/read/28630801/characterization-of-the-transcriptome-and-est-ssr-development-in-boea-clarkeana-a-desiccation-tolerant-plant-endemic-to-china
#1
Ying Wang, Kun Liu, De Bi, Shoubiao Zhou, Jianwen Shao
BACKGROUND: Desiccation-tolerant (DT) plants can recover full metabolic competence upon rehydration after losing most of their cellular water (>95%) for extended periods of time. Functional genomic approaches such as transcriptome sequencing can help us understand how DT plants survive and respond to dehydration, which has great significance for plant biology and improving the drought tolerance of crops. Boea clarkeana Hemsl. (Gesneriaceae) is a DT dicotyledonous herb. Its genomic sequences characteristics remain unknown...
2017: PeerJ
https://www.readbyqxmd.com/read/28627725/proteomic-analysis-of-host-cell-protein-dynamics-in-the-supernatant-of-fc-fusion-protein-producing-cho-dg44-and-dukx-b11-cell-lines-in-batch-and-fed-batch-cultures
#2
Jin Hyoung Park, Jong Hwa Jin, In Jung Ji, Hyun Joo An, Jong Won Kim, Gyun Min Lee
Chinese hamster ovary (CHO) cells are the most widely used host cell lines for the commercial production of therapeutic proteins including Fc-fusion proteins. During the culture of recombinant CHO (rCHO) cells, host cell proteins (HCPs), secreted from viable cells and released from dead cells, accumulate extracellularly, potentially impairing product quality. In this study, the HCPs that accumulated extracellularly in batch and fed-batch cultures of Fc-fusion protein-producing rCHO cell lines (DG-Fc and DUKX-Fc) were identified and quantified using nanoflow liquid chromatography-tandem mass spectrometry (LC-MS/MS), followed by gene ontology and functional analysis...
June 19, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28624811/altered-erythropoiesis-and-decreased-number-of-erythrocytes-in-children-with-neuroblastoma
#3
Fabio Morandi, Sebastiano Barco, Sara Stigliani, Michela Croce, Luca Persico, Corrado Lagazio, Francesca Scuderi, Maria Luisa Belli, Mariapina Montera, Giuliana Cangemi, Sarah Pozzi, Valentina Rigo, Paola Scaruffi, Loredana Amoroso, Giovanni Erminio, Vito Pistoia, Silvano Ferrini, Maria Valeria Corrias
Neuroblastoma (NB) is a pediatric tumor presenting at diagnosis either as localized or metastatic disease, which mainly involves the bone marrow (BM). The physical occupancy of BM space by metastatic NB cells has been held responsible for impairment of BM function. Here, we investigated whether localized or metastatic NB may alter hematopoietic lineages' maturation and release of mature cells in the periphery, through gene expression profiling, analysis of BM smears, cell blood count and flow cytometry analysis...
May 30, 2017: Oncotarget
https://www.readbyqxmd.com/read/28622634/type-of-gonadotropin-used-during-controlled-ovarian-stimulation-induces-differential-gene-expression-in-human-cumulus-cells-a-randomized-study
#4
María Cruz, Antonio Requena, David Agudo, Juan Antonio García-Velasco
BACKGROUND: The cumulus-oocyte complex plays a central role in the regulation of folliculogenesis where it is important for the maturation, reprogramming, and fertilization of oocytes. Consequently, cumulus cell gene expression profiling is being explored as a promising method for assessing oocyte competence in the near future. Through DNA microarray technology, we analyzed the potential differences in the gene expression profiles of cumulus cells from preovulatory follicles after controlled ovarian stimulation using different types of gonadotropins...
June 8, 2017: European Journal of Obstetrics, Gynecology, and Reproductive Biology
https://www.readbyqxmd.com/read/28621239/a-microrna-signature-associated-with-pathological-complete-response-to-novel-neoadjuvant-therapy-regimen-in-triple-negative-breast-cancer
#5
Raúl García-Vazquez, Erika Ruiz-García, Abelardo Meneses García, Horacio Astudillo-de la Vega, Fernando Lara-Medina, Alberto Alvarado-Miranda, Héctor Maldonado-Martínez, Juan A González-Barrios, Alma D Campos-Parra, Sergio Rodríguez Cuevas, Laurence A Marchat, César López-Camarillo
Neoadjuvant chemotherapy aims to improve the outcome of breast cancer patients, but only few would benefit from this treatment. Pathological complete response has been proposed as a surrogate marker for the prediction of long-term clinical benefits; however, 50%-85% patients have an unfavorable pathological complete response to chemotherapy. MicroRNAs are known biomarkers of breast cancer progression; nevertheless, their potential to identify patients with pathological complete response remains poorly understood...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28620206/analysis-of-m%C3%A3-ller-glia-specific-genes-and-their-histone-modification-using-hes1-promoter-driven-egfp-expressing-mouse
#6
Kazuko Ueno, Toshiro Iwagawa, Genki Ochiai, Hideto Koso, Hiromitsu Nakauchi, Masao Nagasaki, Yutaka Suzuki, Sumiko Watanabe
Retinal neurons and Müller glia are generated from a common population of multipotent retinal progenitor cells. We purposed to identify Müller glia-specific molecular signatures during retinal development. Using transgenic mice carrying the Hes1 promoter (pHes1) followed by EGFP, we purified EGFP-positive Müller glia and other EGFP-negative retinal cells from developing retinas and subjected them to RNA sequencing analysis. Gene expression pattern of EGFP-positive cell was similar to genes expressed in retinal progenitors, and they were downregulated in other cell lineages...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28614366/de-novo-transcriptomic-analysis-and-development-of-est-ssrs-for-sorbus-pohuashanensis-hance-hedl
#7
Congcong Liu, Ying Dou, Xuelian Guan, Qiang Fu, Ze Zhang, Zenghui Hu, Jian Zheng, Yizeng Lu, Wei Li
Sorbus pohuashanensis is a native tree species of northern China that is used for a variety of ecological purposes. The species is often grown as an ornamental landscape tree because of its beautiful form, silver flowers in early summer, attractive pinnate leaves in summer, and red leaves and fruits in autumn. However, development and further utilization of the species are hindered by the lack of comprehensive genetic information, which impedes research into its genetics and molecular biology. Recent advances in de novo transcriptome sequencing (RNA-seq) technology have provided an effective means to obtain genomic information from non-model species...
2017: PloS One
https://www.readbyqxmd.com/read/28611792/structural-and-functional-insights-into-wrky3-and-wrky4-transcription-factors-to-unravel-the-wrky-dna-w-box-complex-interaction-in-tomato-solanum-lycopersicum-l-a-computational-approach
#8
Mohd Aamir, Vinay K Singh, Mukesh Meena, Ram S Upadhyay, Vijai K Gupta, Surendra Singh
The WRKY transcription factors (TFs), play crucial role in plant defense response against various abiotic and biotic stresses. The role of WRKY3 and WRKY4 genes in plant defense response against necrotrophic pathogens is well-reported. However, their functional annotation in tomato is largely unknown. In the present work, we have characterized the structural and functional attributes of the two identified tomato WRKY transcription factors, WRKY3 (SlWRKY3), and WRKY4 (SlWRKY4) using computational approaches...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28595953/inhalation-of-a-racemic-mixture-r-s-linalool-by-rats-experiencing-restraint-stress-alters-neuropeptide-and-mhc-class-i-gene-expression-in-the-hypothalamus
#9
Kazushi Yoshida, Naoto Yamamoto, Satoshi Fujiwara, Asuka Kamei, Keiko Abe, Akio Nakamura
Some odorants have physiological and psychological effects on organisms. However, little is known about the effects of inhaling them, particularly on the central nervous system. Using DNA microarray analysis, we obtained gene expression profiles of the hypothalamus from restraint stressed rats exposed to racemic (R,S)-linalool. Hierarchical clustering across all probe sets showed that this inhalation of (R,S)-linalool influenced the expression levels of a wide range of genes in the hypothalamus. A comparison of transcription levels revealed that the inhalation of (R,S)-linalool restored the expression of 560 stress-induced probe sets to a normal status...
June 6, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28585144/weighted-gene-co-expression-network-analysis-of-gene-modules-for-the-prognosis-of-esophageal-cancer
#10
Cong Zhang, Qian Sun
Esophageal cancer is a common malignant tumor, whose pathogenesis and prognosis factors are not fully understood. This study aimed to discover the gene clusters that have similar functions and can be used to predict the prognosis of esophageal cancer. The matched microarray and RNA sequencing data of 185 patients with esophageal cancer were downloaded from The Cancer Genome Atlas (TCGA), and gene co-expression networks were built without distinguishing between squamous carcinoma and adenocarcinoma. The result showed that 12 modules were associated with one or more survival data such as recurrence status, recurrence time, vital status or vital time...
June 2017: Journal of Huazhong University of Science and Technology. Medical Sciences
https://www.readbyqxmd.com/read/28582664/interactions-between-water-activity-and-temperature-on-the-aspergillus-flavus-transcriptome-and-aflatoxin-b1-production
#11
Angel Medina, Matthew K Gilbert, Brian M Mack, Gregory R OBrian, Alicia Rodríguez, Deepak Bhatnagar, Gary Payne, Naresh Magan
Effects of Aspergillus flavus colonization of maize kernels under different water activities (aw; 0.99 and 0.91) and temperatures (30, 37°C) on (a) aflatoxin B1 (AFB1) production and (b) the transcriptome using RNAseq were examined. There was no significant difference (p=0.05) in AFB1 production at 30 and 37°C and 0.99 aw. However, there was a significant (p=0.05) increase in AFB1 at 0.91 aw at 37°C when compared with 30°C/0.99 aw. Environmental stress effects using gene ontology enrichment analysis of the RNA-seq results for increasing temperature at 0...
May 26, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28578698/dictyexpress-a-web-based-platform-for-sequence-data-management-and-analytics-in-dictyostelium-and-beyond
#12
Miha Stajdohar, Rafael D Rosengarten, Janez Kokosar, Luka Jeran, Domen Blenkus, Gad Shaulsky, Blaz Zupan
BACKGROUND: Dictyostelium discoideum, a soil-dwelling social amoeba, is a model for the study of numerous biological processes. Research in the field has benefited mightily from the adoption of next-generation sequencing for genomics and transcriptomics. Dictyostelium biologists now face the widespread challenges of analyzing and exploring high dimensional data sets to generate hypotheses and discovering novel insights. RESULTS: We present dictyExpress (2.0), a web application designed for exploratory analysis of gene expression data, as well as data from related experiments such as Chromatin Immunoprecipitation sequencing (ChIP-Seq)...
June 2, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28578413/dna-methylation-in-schizophrenia-in-different-patient-derived-cell-types
#13
Alejandra M Vitale, Nicholas A Matigian, Alexandre S Cristino, Katia Nones, Sugandha Ravishankar, Bernadette Bellette, Yongjun Fan, Stephen A Wood, Ernst Wolvetang, Alan Mackay-Sim
DNA methylation of gene promoter regions represses transcription and is a mechanism via which environmental risk factors could affect cells during development in individuals at risk for schizophrenia. We investigated DNA methylation in patient-derived cells that might shed light on early development in schizophrenia. Induced pluripotent stem cells may reflect a "ground state" upon which developmental and environmental influences would be minimal. Olfactory neurosphere-derived cells are an adult-derived neuro-ectodermal stem cell modified by developmental and environmental influences...
January 23, 2017: NPJ Schizophrenia
https://www.readbyqxmd.com/read/28574782/rna-based-ovarian-cancer-research-from-a-gene-to-systems-biomedicine-perspective
#14
Esra Gov, Medi Kori, Kazim Yalcin Arga
Ovarian cancer remains the leading cause of death from a gynecologic malignancy, and treatment of this disease is harder than any other type of female reproductive cancer. Improvements in the diagnosis and development of novel and effective treatment strategies for complex pathophysiologies, such as ovarian cancer, require a better understanding of disease emergence and mechanisms of progression through systems medicine approaches. RNA-level analyses generate new information that can help in understanding the mechanisms behind disease pathogenesis, to identify new biomarkers and therapeutic targets and in new drug discovery...
August 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28574720/-bone-development-is-an-ontology-group-upregulated-in-porcine-oocytes-before-in-vitro-maturation-a-microarray-approach
#15
Joanna Budna, Artur Bryja, Piotr Celichowski, Wiesława Kranc, Sylwia Ciesiółka, Sylwia Borys, Marta Rybska, Agata Kolecka-Bednarczyk, Michal Jeseta, Dorota Bukowska, Paweł Antosik, Klaus P Brüssow, Małgorzata Bruska, Michał Nowicki, Maciej Zabel, Bartosz Kempisty
Mammalian cumulus-oocyte complexes (COCs) reach full developmental capability during folliculogenesis and oogenesis. It is well recognized that only gametes achieving MII stage after in vivo or in vitro maturation (IVM) are successfully fertilized by a single spermatozoon. Although the process of oocyte nuclear and/or cytoplasmic maturation in pigs is well determined, there exist many differences that promote these processes in vivo and in vitro. Therefore, this study aimed to investigate the differences in RNA expression profiles between porcine oocytes before and after IVM using microarray and real-time quantitative polymerase chain reaction (RT-qPCR) assays...
June 2, 2017: DNA and Cell Biology
https://www.readbyqxmd.com/read/28570707/de-novo-characterization-of-the-pine-aphid-cinara-pinitabulaeformis-zhang-et-zhang-transcriptome-and-analysis-of-genes-relevant-to-pesticides
#16
Songqing Wu, Zhicheng Huang, Carballar-Lejarazú Rebeca, Xiaoli Zhu, Yajie Guo, Qiannan Lin, Xia Hu, Rong Wang, Guanghong Liang, Xiong Guan, Feiping Zhang
The pine aphid Cinara pinitabulaeformis Zhang et Zhang is the main pine pest in China, it causes pine needles to produce dense dew (honeydew) which can lead to sooty mold (black filamentous saprophytic ascomycetes). Although common chemical and physical strategies are used to prevent the disease caused by C. pinitabulaeformis Zhang et Zhang, new strategies based on biological and/or genetic approaches are promising to control and eradicate the disease. However, there is no information about genomics, proteomics or transcriptomics to allow the design of new control strategies for this pine aphid...
2017: PloS One
https://www.readbyqxmd.com/read/28560252/dna-methylation-in-schizophrenia-in-different-patient-derived-cell-types
#17
Alejandra M Vitale, Nicholas A Matigian, Alexandre S Cristino, Katia Nones, Sugandha Ravishankar, Bernadette Bellette, Yongjun Fan, Stephen A Wood, Ernst Wolvetang, Alan Mackay-Sim
DNA methylation of gene promoter regions represses transcription and is a mechanism via which environmental risk factors could affect cells during development in individuals at risk for schizophrenia. We investigated DNA methylation in patient-derived cells that might shed light on early development in schizophrenia. Induced pluripotent stem cells may reflect a "ground state" upon which developmental and environmental influences would be minimal. Olfactory neurosphere-derived cells are an adult-derived neuro-ectodermal stem cell modified by developmental and environmental influences...
2017: NPJ Schizophrenia
https://www.readbyqxmd.com/read/28559911/comparative-analysis-of-transcriptomes-in-rhizophoraceae-provides-insights-into-the-origin-and-adaptive-evolution-of-mangrove-plants-in-intertidal-environments
#18
Wuxia Guo, Haidan Wu, Zhang Zhang, Chao Yang, Ling Hu, Xianggang Shi, Shuguang Jian, Suhua Shi, Yelin Huang
Mangroves are woody plants that grow at the interface between land and sea in tropical and subtropical latitudes, where they exist in conditions of high salinity, extreme tides, strong winds, high temperatures, and muddy, anaerobic soils. Rhizophoraceae is a key mangrove family, with highly developed morphological and physiological adaptations to extreme conditions. It is an ideal system for the study of the origin and adaptive evolution of mangrove plants. In this study, we characterized and comprehensively compared the transcriptomes of four mangrove species, from all four mangrove genera, as well as their closest terrestrial relative in Rhizophoraceae, using RNA-Seq...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28552634/itraq-based-quantitative-proteomic-analysis-reveals-bai-hu-tang-enhances-phagocytosis-and-cross-presentation-against-lps-fever-in-rabbit
#19
Shidong Zhang, Dongsheng Wang, Shuwei Dong, Zhiqiang Yang, Zuoting Yan
ETHNOPHARMACOLOGICAL RELEVANCE: Bai-Hu-Tang (BHT), a classical anti-febrile Chinese formula comprising of liquorice, anemarrhena rhizome, gypsum and rice, has been traditionally used to anti-febrile treatment and promote the production of body fluid to relieve thirst. In this paper, we aim to explore anti-febrile mechanism of BHT at protein level through analyzing alteration of differentially expressed proteins (DEPs) both lipopolysaccharide (LPS) fever syndrome and that was treated with BHT in rabbits...
May 24, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28545501/pregnancy-induced-gene-expression-changes-in-vivo-among-women-with-rheumatoid-arthritis-a-pilot-study
#20
Dana E Goin, Mette Kiel Smed, Lior Pachter, Elizabeth Purdom, J Lee Nelson, Hanne Kjærgaard, Jørn Olsen, Merete Lund Hetland, Vibeke Zoffmann, Bent Ottesen, Damini Jawaheer
BACKGROUND: Little is known about gene expression changes induced by pregnancy in women with rheumatoid arthritis (RA) and healthy women because the few studies previously conducted did not have pre-pregnancy samples available as baseline. We have established a cohort of women with RA and healthy women followed prospectively from a pre-pregnancy baseline. In this study, we tested the hypothesis that pregnancy-induced changes in gene expression among women with RA who improve during pregnancy (pregDASimproved) overlap substantially with changes observed among healthy women and differ from changes observed among women with RA who worsen during pregnancy (pregDASworse)...
May 25, 2017: Arthritis Research & Therapy
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