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https://www.readbyqxmd.com/read/29150651/comprehensive-functional-enrichment-analysis-of-male-infertility
#1
Seyed Morteza Razavi, Marjan Sabbaghian, Mahdi Jalili, Adeleh Divsalar, Olaf Wolkenhauer, Ali Salehzadeh-Yazdi
Spermatogenesis is a multifactorial process that forms differentiated sperm cells in a complex microenvironment. This process involves the genome, epigenome, transcriptome, and proteome to ensure the stability of the spermatogonia and supporting cells. The identification of signaling pathways linked to infertility has been hampered by the inherent complexity and multifactorial aspects of spermatogenesis. Systems biology is a promising approach to unveil underlying signaling pathways and genes and identify putative biomarkers...
November 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29150511/sulfolobus-acidocaldarius-uptakes-pentoses-via-a-cut2-type-abc-transporter-and-metabolizes-them-through-the-aldolase-independent-weimberg-pathway
#2
Michaela Wagner, Lu Shen, Andreas Albersmeier, Nienke van der Kolk, Sujin Kim, Jaeho Cha, Christopher Bräsen, Jörn Kalinowski, Bettina Siebers, Sonja-Verena Albers
Sulfolobus spp. possess a great metabolic versatility and grow heterotrophically on various carbon sources such as different sugars and peptides. Known sugar transporters in Archaea predominantly belong to ABC transport systems. Although several ABC transporters for sugar uptake have been characterized in the crenarchaeon Sulfolobus solfataricus, only one homologue of these transporters, the maltose/maltooligomer transporter, could be identified in the closely related Sulfolobus acidocaldarius Comparison of the transcriptome of S...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29150499/understanding-functional-roles-of-native-pentose-specific-transporters-for-activating-dormant-pentose-metabolism-in-yarrowia-lipolytica
#3
Seunghyun Ryu, Cong T Trinh
Pentoses including xylose and arabinose are the second-most prevalent sugars of lignocellulosic biomass that can be harnessed for biological conversion. Although Yarrowia lipolytica has emerged as a promising industrial microorganism for production of high-value chemicals and biofuels, its native pentose metabolism is poorly understood. Our previous study demonstrated that Y. lipolytica (ATCC MYA-2613) has endogenous enzymes for D-xylose assimilation, but inefficient xylitol dehydrogenase causes Y. lipolytica to assimilate xylose poorly...
November 17, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29149845/early-nutritional-programming-affects-liver-transcriptome-in-diploid-and-triploid-atlantic-salmon-salmo-salar
#4
L M Vera, C Metochis, J F Taylor, M Clarkson, K H Skjærven, H Migaud, D R Tocher
BACKGROUND: To ensure sustainability of aquaculture, plant-based ingredients are being used in feeds to replace marine-derived products. However, plants contain secondary metabolites which can affect food intake and nutrient utilisation of fish. The application of nutritional stimuli during early development can induce long-term changes in animal physiology. Recently, we successfully used this approach to improve the utilisation of plant-based diets in diploid and triploid Atlantic salmon...
November 17, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29149642/oxidative-stress-cell-cycle-arrest-dna-damage-and-apoptosis-in-adult-zebrafish-danio-rerio-induced-by-tris-1-3-dichloro-2-propyl-phosphate
#5
Hanyan Chen, Pingping Wang, Zhongkun Du, Guowei Wang, Shixiang Gao
Tris(1,3-dichloro-2-propyl)phosphate (TDCPP) is an additive flame retardant of high production volume, and frequently detected in biota and environment. However, knowledge on its potential risk and toxicological mechanism still remains limited. In this study, DNA damage, transcriptomic responses and biochemical changes in the liver of zebrafish (Danio rerio) induced by TDCPP were investigated. Zebrafish was exposed to 45.81μg/L (1/100 (96h-LC50)) and 229.05μg/L (1/20 (96h-LC50)) TDCPP for 7 d. The reactive oxygen species (ROS) and GSH contents, in addition to antioxidant enzyme activities in the liver changed significantly, and the mRNA levels of genes related to oxidative stress were alerted in a dose-dependent and/or sex-dependent manner after exposure to TDCPP...
November 10, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/29149221/dietary-protein-sources-differentially-affect-microbiota-mtor-activity-and-transcription-of-mtor-signaling-pathways-in-the-small-intestine
#6
Soumya K Kar, Alfons J M Jansman, Nirupama Benis, Javier Ramiro-Garcia, Dirkjan Schokker, Leo Kruijt, Ellen H Stolte, Johanna J Taverne-Thiele, Mari A Smits, Jerry M Wells
Dietary protein sources can have profound effects on host-microbe interactions in the gut that are critically important for immune resilience. However more knowledge is needed to assess the impact of different protein sources on gut and animal health. Thirty-six wildtype male C57BL/6J mice of 35 d age (n = 6/group; mean ± SEM body weight 21.9 ± 0.25 g) were randomly assigned to groups fed for four weeks with semi synthetic diets prepared with one of the following protein sources containing (300 g/kg as fed basis): soybean meal (SBM), casein, partially delactosed whey powder, spray dried plasma protein, wheat gluten meal and yellow meal worm...
2017: PloS One
https://www.readbyqxmd.com/read/29148541/integrated-genomic-analysis-identifies-deregulated-jak-stat-myc-biosynthesis-axis-in-aggressive-nk-cell-leukemia
#7
Liang Huang, Dan Liu, Na Wang, Shaoping Ling, Yuting Tang, Jun Wu, Lingtong Hao, Hui Luo, Xuelian Hu, Lingshuang Sheng, Lijun Zhu, Di Wang, Yi Luo, Zhen Shang, Min Xiao, Xia Mao, Kuangguo Zhou, Lihua Cao, Lili Dong, Xinchang Zheng, Pinpin Sui, Jianlin He, Shanlan Mo, Jin Yan, Qilin Ao, Lugui Qiu, Hongsheng Zhou, Qifa Liu, Hongyu Zhang, Jianyong Li, Jie Jin, Li Fu, Weili Zhao, Jieping Chen, Xin Du, Guoliang Qing, Hudan Liu, Xin Liu, Gang Huang, Ding Ma, Jianfeng Zhou, Qian-Fei Wang
Aggressive NK-cell leukemia (ANKL) is a rare form of NK cell neoplasm that is more prevalent among people from Asia and Central and South America. Patients usually die within days to months, even after receiving prompt therapeutic management. Here we performed the first comprehensive study of ANKL by integrating whole genome, transcriptome and targeted sequencing, cytokine array as well as functional assays. Mutations in the JAK-STAT pathway were identified in 48% (14/29) of ANKL patients, while the extracellular STAT3 stimulator IL10 was elevated by an average of 56-fold (P < 0...
November 17, 2017: Cell Research
https://www.readbyqxmd.com/read/29147886/peromyscus-leucopus-mouse-brain-transcriptome-response-to-powassan-virus-infection
#8
Luwanika Mlera, Kimberly Meade-White, Eric Dahlstrom, Rachel Baur, Kishore Kanakabandi, Kimmo Virtaneva, Stephen F Porcella, Marshall E Bloom
Powassan virus (POWV) is a tick-borne Flavivirus responsible for life-threatening encephalitis in North America and some regions of Russia. The ticks that have been reported to transmit the virus belong to the Ixodes species, and they feed on small-to-medium-sized mammals, such as Peromyscus leucopus mice, skunks, and woodchucks. We previously developed a P. leucopus mouse model of POWV infection, and the model is characterized by a lack of clinical signs of disease following intraperitoneal or intracranial inoculation...
November 16, 2017: Journal of Neurovirology
https://www.readbyqxmd.com/read/29147649/knockdown-of-sirt1-suppresses-bladder-cancer-cell-proliferation-and-migration-and-induces-cell-cycle-arrest-and-antioxidant-response-through-foxo3a-mediated-pathways
#9
Qingxuan Hu, Gang Wang, Jianping Peng, Guofeng Qian, Wei Jiang, Conghua Xie, Yu Xiao, Xinghuan Wang
Bladder cancer (BCa) is one of the most common tumors, but its underlying mechanism has not been fully clarified. Our transcriptome analysis suggested a close link of Sirtuins, Peroxisome Proliferator-Activated Receptor (PPAR), cell cycle regulation, reactive oxygen species (ROS) metabolism, and Forkhead Box Class O (FOXO) signaling pathway in BCa. SIRT1 is a key member of Sirtuins, playing important roles in aging and energy metabolism, which has been reported to be involved in various metabolic diseases and tumors...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29147625/a-transcriptomic-insight-into-the-impacts-of-mast-cells-in-lung-breast-and-colon-cancers
#10
Eun-A Ko, Kenton M Sanders, Tong Zhou
To date, the exact impact of mast cells in tumor microenvironment is still controversial because of inconsistency in observations regarding the relationship between mast cell infiltrates and cancer development and prognosis. The discrepancies in previous studies have motivated us to examine the roles of mast cells in cancer pathology from different perspectives. Here, we investigated the impact of mast cells on transcriptomic profiles in the tissue microenvironment. Mice carrying the W-sh mutation in c-kit (Kit(W-sh) ) are deficient in mast cell production and were used to assess the influence of mast cells on gene expression...
2017: Oncoimmunology
https://www.readbyqxmd.com/read/29147013/integrin-alpha-11-in-the-regulation-of-the-myofibroblast-phenotype-implications-for-fibrotic-diseases
#11
Ruchi Bansal, Shigeki Nakagawa, Saleh Yazdani, Joop van Baarlen, Anu Venkatesh, Anna P Koh, Won-Min Song, Nicolas Goossens, Hideo Watanabe, Mary B Beasley, Charles A Powell, Gert Storm, Naftali Kaminski, Harry van Goor, Scott L Friedman, Yujin Hoshida, Jai Prakash
Tissue fibrosis, characterized by excessive accumulation of aberrant extracellular matrix (ECM) produced by myofibroblasts, is a growing cause of mortality worldwide. Understanding the factors that induce myofibroblastic differentiation is paramount to prevent or reverse the fibrogenic process. Integrin-mediated interaction between the ECM and cytoskeleton promotes myofibroblast differentiation. In the present study, we explored the significance of integrin alpha 11 (ITGA11), the integrin alpha subunit that selectively binds to type I collagen during tissue fibrosis in the liver, lungs and kidneys...
November 17, 2017: Experimental & Molecular Medicine
https://www.readbyqxmd.com/read/29146946/de-novo-transcriptome-sequencing-of-meja-induced-taraxacum-koksaghyz-rodin-to-identify-genes-related-to-rubber-formation
#12
XinWen Cao, Jie Yan, JiLiang Lei, Jin Li, JianBo Zhu, HuiYan Zhang
Increase in the consumption of natural rubber (NR) has necessitated the identification of alternative sources of NR. The quality of NR produced by Taraxacum koksaghyz Rodin (TKS) is comparable to that from Hevea brasiliensis (H.brasiliensis), and therefore, TKS is being considered as an alternative source of NR. Here, we sequenced the TKS root transcriptome after wild TKS seedlings were treated with methyl jasmonate (MeJA) for 0, 6, and 24 h. The clean reads generated for each experimental line were assembled into 127,833 unigenes...
November 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29146547/a-gene-module-associated-with-dysregulated-tcr-signaling-pathways-in-cd4-t-cell-subsets-in-rheumatoid-arthritis
#13
Shuji Sumitomo, Yasuo Nagafuchi, Yumi Tsuchida, Haruka Tsuchiya, Mineto Ota, Kazuyoshi Ishigaki, Shinichiro Nakachi, Rika Kato, Keiichi Sakurai, Norio Hanata, Shoko Tateishi, Hiroko Kanda, Akari Suzuki, Yuta Kochi, Keishi Fujio, Kazuhiko Yamamoto
We analyzed the transcriptome of detailed CD4(+) T cell subsets including them after abatacept treatment, and examined the difference among CD4(+) T cell subsets and identified gene sets that are closely associated disease activity and abatacept treatment. Seven CD4(+) T cell subsets (naive, Th1, Th17, Th1/17, nonTh1/17, Tfh and Treg) were sorted from PBMCs taken from 10 RA patients and 10 healthy controls, and three RA patients donated samples before and 6 months after abatacept treatment. Paired-end RNA sequencing was performed using HiSeq 2500...
November 13, 2017: Journal of Autoimmunity
https://www.readbyqxmd.com/read/29146147/age-induced-and-photoinduced-changes-in-gene-expression-profiles-in-facial-skin-of-caucasian-females-across-6%C3%A2-decades-of-age
#14
Alexa B Kimball, Maria B Alora-Palli, Makio Tamura, Lisa A Mullins, Chieko Soh, Robert L Binder, Neil A Houston, Emily D Conley, Joyce Y Tung, Nikki E Annunziata, Charles C Bascom, Robert J Isfort, Bradley B Jarrold, Raghu Kainkaryam, Heather L Rocchetta, Dionne D Swift, Jay P Tiesman, Kazumi Toyama, Jun Xu, Xianghong Yan, Rosemarie Osborne
BACKGROUND: Intrinsic and extrinsic factors, including ultraviolet irradiation, lead to visible signs of skin aging. OBJECTIVE: We evaluated molecular changes occurring in photoexposed and photoprotected skin of white women 20 to 74 years of age, some of whom appeared substantially younger than their chronologic age. METHODS: Histologic and transcriptomics profiling were conducted on skin biopsy samples of photoexposed (face and dorsal forearm) or photoprotected (buttocks) body sites from 158 women...
November 14, 2017: Journal of the American Academy of Dermatology
https://www.readbyqxmd.com/read/29146145/adars-and-editing-the-role-of-a-to-i-rna-modification-in-cancer-progression
#15
REVIEW
Kajsa Fritzell, Lidi Xu, Jens Lagergren, Marie Öhman
Cancer arises when pathways that control cell functions such as proliferation and migration are dysregulated to such an extent that cells start to divide uncontrollably and eventually spread throughout the body, ultimately endangering the survival of an affected individual. It is well established that somatic mutations are important in cancer initiation and progression as well as in creation of tumor diversity. Now also modifications of the transcriptome are emerging as a significant force during the transition from normal cell to malignant tumor...
November 13, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29145825/assembling-large-genomes-analysis-of-the-stick-insect-clitarchus-hookeri-genome-reveals-a-high-repeat-content-and-sex-biased-genes-associated-with-reproduction
#16
Chen Wu, Victoria G Twort, Ross N Crowhurst, Richard D Newcomb, Thomas R Buckley
BACKGROUND: Stick insects (Phasmatodea) have a high incidence of parthenogenesis and other alternative reproductive strategies, yet the genetic basis of reproduction is poorly understood. Phasmatodea includes nearly 3000 species, yet only the genome of Timema cristinae has been published to date. Clitarchus hookeri is a geographical parthenogenetic stick insect distributed across New Zealand. Sexual reproduction dominates in northern habitats but is replaced by parthenogenesis in the south...
November 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29145444/inhibition-of-the-h3k9-methyltransferase-g9a-attenuates-oncogenicity-and-activates-the-hypoxia-signaling-pathway
#17
Jolene Caifeng Ho, Lissa Nurrul Abdullah, Qing You Pang, Sudhakar Jha, Edward Kai-Hua Chow, Henry Yang, Hiroyuki Kato, Lorenz Poellinger, Jun Ueda, Kian Leong Lee
Epigenetic mechanisms play important roles in the regulation of tumorigenesis, and hypoxia-induced epigenetic changes may be critical for the adaptation of cancer cells to the hypoxic microenvironment of solid tumors. Previously, we showed that loss-of-function of the hypoxia-regulated H3K9 methyltransferase G9A attenuates tumor growth. However, the mechanisms by which blockade of G9A leads to a tumor suppressive effect remain poorly understood. We show that G9A is highly expressed in breast cancer and is associated with poor patient prognosis, where it may function as a potent oncogenic driver...
2017: PloS One
https://www.readbyqxmd.com/read/29143776/gastric-cancer-cell-glycosylation-as-a-modulator-of-the-erbb2-oncogenic-receptor
#18
Henrique O Duarte, Meritxell Balmaña, Stefan Mereiter, Hugo Osório, Joana Gomes, Celso A Reis
Aberrant expression and hyperactivation of the human epidermal growth factor receptor 2 (ErbB2) constitute crucial molecular events underpinning gastric neoplastic transformation. Despite ErbB2 extracellular domain being a well-known target for glycosylation, its glycosylation profile and the molecular mechanisms through which it actively tunes tumorigenesis in gastric cancer (GC) cells remain elusive. We aimed at disclosing relevant ErbB2 glycan signatures and their functional impact on receptor's biology in GC cells...
October 28, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29143341/a-toxicogenomics-approach-to-screen-chlorinated-flame-retardants-tris-2-chloroethyl-phosphate-and-tris-2-chloroisopropyl-phosphate-for-potential-health-effects
#19
Boris V Krivoshiev, Gerrit T S Beemster, Katrien Sprangers, Ronny Blust, Steven J Husson
Tris(2-chloroethyl) phosphate (TCEP) is a pervasive flame retardant that has been identified as a chemical of concern given its health effects and therefore its use has since been tightly regulated. Tris(2-chloroisopropyl) phosphate (TCIPP), an analogue of TCEP, is believed to be its replacement. However, compared to TCEP, little is known of the toxicological impacts of TCIPP. We used RNA sequencing as unbiased and sensitive tool to identify and compare effects on a transcriptome level of TCEP and TCIPP in the human hepatocellular carcinoma cell line, HepG2...
November 16, 2017: Journal of Applied Toxicology: JAT
https://www.readbyqxmd.com/read/29143326/lncrna-rp11-670e13-6-regulates-cell-cycle-progression-in-uvb-damaged-human-dermal-fibroblasts
#20
Mengna Li, Li Li, Xiaofeng Zhang, Yan Yan, Baoxi Wang
Long noncoding RNAs (lncRNAs) have gained extensive attention in recent years, however, their effects on ultraviolet (UV) radiation-induced skin photodamage remain to be elucidated. In this study, we performed high-throughput RNA sequencing and comprehensive bioinformatics analyses to characterize the transcriptome profiles including lncRNAs and mRNAs in UVB-irradiated primary human dermal fibroblasts (HDFs) and to explore the roles of lncRNAs in photoaging. Quantitative reverse transcription-polymerase chain reaction amplification was performed to verify the differentially expressed genes...
November 16, 2017: Photochemistry and Photobiology
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