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https://www.readbyqxmd.com/read/29663582/the-skin-microbiome-of-wound-scars-and-unaffected-skin-in-patients-with-moderate-to-severe-burns-in-the-subacute-phase
#1
Su-Hsun Liu, Yhu-Chering Huang, Leslie Y Chen, Shu-Chuan Yu, Hsiao-Yun Yu, Shiow-Shuh Chuang
Although studies on skin microbiome of acute and chronic wounds abound, evidence on newly-built microbial communities of subacute wounds remains scant. To characterize the skin microbiome of recently-healed (scarred) burn wounds in relation to unaffected skin surfaces, we collected weekly swabs from patients with moderate to severe burns in the 3rd postburn month for 4 weeks in 2015. We performed skin type (moist, dry, and oily)-matched comparisons within six burn patients (43 pairs of swabs) and with 13 skin-healthy, control patients (22 pairs of samples) using 16S ribosomal RNA (rRNA) gene sequencing results...
April 17, 2018: Wound Repair and Regeneration
https://www.readbyqxmd.com/read/29661800/chorionic-somatomammotropin-impacts-early-fetal-growth-and-placental-gene-expression
#2
Kimberly M Jeckel, Alexander C Boyarko, Gerrit Bouma, Quinton Winger, Russ V Anthony
Several developmental windows, including placentation, must be negotiated to establish and maintain pregnancy. Impaired placental function can lead to pre-eclampsia and/or intrauterine growth restriction (IUGR), resulting in increased infant mortality and morbidity. It has been hypothesized that chorionic somatomammotropin (CSH), plays a significant role in fetal development, potentially by modifying maternal and fetal metabolism. Recently, using lentiviral-mediated in vivo RNA interference in sheep, we demonstrated significant reductions in near-term (135 days of gestation; dGA) fetal and placental size, and altered fetal liver gene expression, resulting from CSH deficiency...
April 16, 2018: Journal of Endocrinology
https://www.readbyqxmd.com/read/29661230/a-comparison-of-methods-used-to-unveil-the-genetic-and-metabolic-pool-in-the-built-environment
#3
Cinta Gomez-Silvan, Marcus H Y Leung, Katherine A Grue, Randeep Kaur, Xinzhao Tong, Patrick K H Lee, Gary L Andersen
BACKGROUND: A majority of indoor residential microbes originate from humans, pets, and outdoor air and are not adapted to the built environment (BE). Consequently, a large portion of the microbes identified by DNA-based methods are either dead or metabolically inactive. Although many exceptions have been noted, the ribosomal RNA fraction of the sample is more likely to represent either viable or metabolically active cells. We examined methodological variations in sample processing using a defined, mock BE microbial community to better understand the scope of technique-based vs...
April 16, 2018: Microbiome
https://www.readbyqxmd.com/read/29660433/slit2-robo2-signaling-modulates-the-fibrogenic-activity-and-migration-of-hepatic-stellate-cells
#4
Zhiping Zeng, Yujing Wu, Yirong Cao, Ziying Yuan, Yuanqing Zhang, David Y Zhang, Daisuke Hasegawa, Scott L Friedman, Jinsheng Guo
BACKGROUND & AIM: Slit/Robo signaling was originally identified as a repulsive guidance cue in regulating axon branching and neuronal migration. Hepatic stellate cells (HSCs) are the key fibrogenic cells in the liver, which are migratory when activated, and express neural crest markers. The aim of the present study was to investigate the functional significance of Slit/Robo signaling in liver fibrogenesis and in HSCs. KEY FINDINGS: By transcriptomic analysis it was found that axon guidance signaling pathways were significantly upregulated in both diethylnitrosamine (DEN) and thioacetamide (TAA)-induced experimental liver fibrosis...
April 13, 2018: Life Sciences
https://www.readbyqxmd.com/read/29660200/odd-skipped-related-1-inhibits-lung-cancer-proliferation-and-invasion-by-reducing-wnt-signaling-through-the-suppression-of-sox9-and-%C3%AE-catenin
#5
Yuan Wang, Lei Lei, Yi-Wen Zheng, Li Zhang, Zhi-Han Li, Hao-Yue Shen, Gui-Yang Jiang, Xiu-Peng Zhang, En-Hua Wang, Hong-Tao Xu
The odd-skipped related 1 (OSR1) gene encodes a zinc-finger transcription factor. The expression and significance of OSR1 in human tumors remains unclear. We found that OSR1 was downregulated in lung cancers, and its expression correlated with poor differentiation. Overexpression of OSR1 by OSR1 gene transfection into H1299 cells (H1299-OSR1) inhibited the proliferation and invasion of lung cancer cells. Knockdown of OSR1 with small interfering (si)RNA against OSR1 in A549 cells (A549-siOSR1) enhanced the proliferation and invasion of lung cancer cells...
April 16, 2018: Cancer Science
https://www.readbyqxmd.com/read/29659518/examining-the-genetic-background-of-porcine-muscle-growth-and-development-based-on-transcriptome-and-mirnaome-data
#6
Katarzyna Ropka-Molik, Klaudia Pawlina-Tyszko, Kacper Żukowski, Katarzyna Piórkowska, Grzegorz Żak, Artur Gurgul, Natalia Derebecka, Joanna Wesoły
Recently, selection in pigs has been focused on improving the lean meat content in carcasses; this focus has been most evident in breeds constituting a paternal component in breeding. Such sire-breeds are used to improve the meat quantity of cross-breed pig lines. However, even in one breed, a significant variation in the meatiness level can be observed. In the present study, the comprehensive analysis of genes and microRNA expression profiles in porcine muscle tissue was applied to identify the genetic background of meat content...
April 16, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29656754/malignant-cells-from-pleural-fluids-in-malignant-mesothelioma-patients-reveal-novel-mutations
#7
Sophie Sneddon, Ian Dick, Y C Gary Lee, A W Bill Musk, Ann-Marie Patch, John V Pearson, Nicola Waddell, Richard J N Allcock, Robert A Holt, Bruce W S Robinson, Jenette Creaney
OBJECTIVES: Malignant mesothelioma (MM) is an asbestos related tumour affecting cells of serosal cavities. More than 70% of MM patients develop pleural effusions which contain tumour cells, representing a readily accessible source of malignant cells for genetic analysis. Although common somatic mutations and losses have been identified in solid MM tumours, the characterization of tumour cells within pleural effusions could provide novel insights but is little studied. MATERIALS AND METHODS: DNA and RNA were extracted from cells from short term cultures of 27 human MM pleural effusion samples...
May 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29651979/rnases-and-helicases-in-gram-positive-bacteria
#8
Sylvain Durand, Ciaran Condon
RNases are key enzymes involved in RNA maturation and degradation. Although they play a crucial role in all domains of life, bacteria, archaea, and eukaryotes have evolved with their own sets of RNases and proteins modulating their activities. In bacteria, these enzymes allow modulation of gene expression to adapt to rapidly changing environments. Today, >20 RNases have been identified in both Escherichia coli and Bacillus subtilis , the paradigms of the Gram-negative and Gram-positive bacteria, respectively...
April 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29651726/biosorption-of-strontium-ions-from-simulated-high-level-liquid-waste-by-living-saccharomyces-cerevisiae
#9
Liang Qiu, Jundong Feng, Yaodong Dai, Shuquan Chang
In this study, the Saccharomyces cerevisiae (S. cerevisiae) was modified by γ-ray. The RNA-seq results reflect that the high γ-ray energies could change some gene fragments, such as deletion, recombination, and mutation. The biosorption of strontium ions (Sr2+ ) to different types of S. cerevisiae (S. cerevisiae (K-0), modified S. cerevisiae (Y-7), and non-living S. cerevisiae (H-K)) from the simulated high-level liquid waste (S-HLLW) was assessed at different experimental conditions. The sorption experimental results show that, under an appropriate condition, γ-ray radiation can enhance its biosorption capacity slightly of Sr2+ to S...
April 12, 2018: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/29650350/loss-of-dorsomedial-hypothalamic-glp-1-signaling-reduces-bat-thermogenesis-and-increases-adiposity
#10
Shin J Lee, Graciela Sanchez-Watts, Jean-Philippe Krieger, Angelica Pignalosa, Puck N Norell, Alyssa Cortella, Klaus G Pettersen, Dubravka Vrdoljak, Matthew R Hayes, Scott Kanoski, Wolfgang Langhans, Alan G Watts
OBJECTIVE: Glucagon-like peptide-1 (GLP-1) neurons in the hindbrain densely innervate the dorsomedial hypothalamus (DMH), a nucleus strongly implicated in body weight regulation and the sympathetic control of brown adipose tissue (BAT) thermogenesis. Therefore, DMH GLP-1 receptors (GLP-1R) are well placed to regulate energy balance by controlling sympathetic outflow and BAT function. METHODS: We investigate this possibility in adult male rats by using direct administration of GLP-1 (0...
March 21, 2018: Molecular Metabolism
https://www.readbyqxmd.com/read/29648602/factors-associated-with-prolonged-viral-shedding-in-patients-with-avian-influenza-a-h7n9-virus-infection
#11
Yeming Wang, Qiang Guo, Zheng Yan, Daming Zhou, Wei Zhang, Shujun Zhou, Yu-Ping Li, Jing Yuan, Timothy M Uyeki, Xinghua Shen, Wenjuan Wu, Hui Zhao, Yun-Fu Wu, Jia Shang, Zhengguang He, Yi Yang, Hongsheng Zhao, Yongqing Hong, Zehua Zhang, Min Wu, Tiemin Wei, Xilong Deng, Yijun Deng, Li-Hua Cai, Weihua Lu, Hongmei Shu, Lin Zhang, Hong Luo, Y Ing Zhou, Heng Weng, Keyi Song, Li Yao, Mingguang Jiang, Boliang Zhao, Ruibin Chi, Boqi Guo, Lin Fu, Long Yu, Haiyan Min, Pu Chen, Shuifang Chen, Liang Hong, Wei Mao, Xiaoping Huang, Lijun Gu, Hui Li, Chen Wang, Bin Cao
Background: Data are limited on the impact of neuraminidase inhibitor (NAI) treatment on avian influenza A(H7N9) virus RNA shedding. Methods: In this multicenter, retrospective study, data were collected from adults hospitalized with A(H7N9) infection during 2013-2017 in China. We compared clinical features and A(H7N9) shedding among patients with different NAI doses and combination therapies and evaluated factors associated with A(H7N9) shedding, using Cox proportional hazards regression...
April 10, 2018: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/29648573/a-comprehensive-web-tool-for-toehold-switch-design
#12
Andrew Ching-Yuet To, David Ho Ting Chu, Angela Ruoning Wang, Frances Cheuk-Yau Li, Alan Wai-On Chiu, Daisy Yuwei Gao, Chung Hang Jonathan Choi, Siu-Kai Kong, Ting-Fung Chan, King-Ming Chan, Kevin Y Yip
Background: Toehold switches are a class of RNAs with a hairpin loop that can be unfolded upon binding a trigger RNA, thereby exposing a ribosome binding site (RBS) and permitting translation of the reporter protein. They have been shown very useful in detecting a variety of targets including RNAs from Zika and Ebola viruses. The base complementation between the toehold switch and the trigger RNA also makes it sensitive to sequence variations. Design of toehold switches involves a series of considerations related to their sequence properties, structures and specificities...
April 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29643334/performance-of-the-trioplex-real-time-rt-pcr-assay-for-detection-of-zika-dengue-and-chikungunya-viruses
#13
Gilberto A Santiago, Jesús Vázquez, Sean Courtney, Katia Y Matías, Lauren E Andersen, Candimar Colón, Angela E Butler, Rebecca Roulo, John Bowzard, Julie M Villanueva, Jorge L Muñoz-Jordan
The emergence and spread of Zika virus (ZIKV) presented a challenge to the diagnosis of ZIKV infections in areas with transmission of dengue (DENV) and chikungunya (CHIKV) viruses. To facilitate detection of ZIKV infections, and differentiate these infections from DENV and CHIKV, we developed the Trioplex real-time RT-PCR assay (Trioplex assay). Here, we describe the optimization of multiplex and singleplex formats of the assay for a variety of chemistries and instruments to facilitate global standardization and implementation...
April 11, 2018: Nature Communications
https://www.readbyqxmd.com/read/29630117/urg4-silencing-suppresses-cell-proliferation-in-nasopharyngeal-carcinoma-through-induction-of-apoptosis
#14
X-Y Luo, B Yan, C-F Cai, A-M Chen, M Zhou
OBJECTIVE: To investigate the expression and function of up-regulator of gene-4 (URG4) in nasopharyngeal carcinoma (NPC). PATIENTS AND METHODS: Fresh NPC tumor tissue samples with paired adjacent normal nasopharyngeal tissues samples of 9 NPC patients were collected from NPC curative resection surgery. NPC cell lines (CNE1, CNE2 and HONE1) were cultured. Lentivirus-mediated URG4-specific short hairpin RNA (shRNA) stable transfection was done. The effect of URG4 on CNE4 and HONE1 cells viability was determined via 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT)...
March 2018: European Review for Medical and Pharmacological Sciences
https://www.readbyqxmd.com/read/29628369/rna-sequencing-of-stentor-cell-fragments-reveals-transcriptional-changes-during-cellular-regeneration
#15
Henning Onsbring, Mahwash Jamy, Thijs J G Ettema
While ciliates of the genus Stentor are known for their ability to regenerate when their cells are damaged or even fragmented, the physical and molecular mechanisms underlying this process are poorly understood. To identify genes involved in the regenerative capability of Stentor cells, RNA sequencing of individual Stentor polymorphus cell fragments was performed. After splitting a cell over the anterior-posterior axis, the posterior fragment has to regenerate the oral apparatus, while the anterior part needs to regenerate the hold fast...
March 29, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29626929/structure-and-functions-of-the-mediator-complex
#16
REVIEW
E V Putlyaev, A N Ibragimov, L A Lebedeva, P G Georgiev, Y V Shidlovskii
Mediator is a key factor in the regulation of expression of RNA polymerase II-transcribed genes. Recent studies have shown that Mediator acts as a coordinator of transcription activation and participates in maintaining chromatin architecture in the cell nucleus. In this review, we present current concepts on the structure and functions of Mediator.
April 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29626310/ga-3-application-in-grapes-vitis-vinifera-l-modulates-different-sets-of-genes-at-cluster-emergence-full-bloom-and-berry-stage-as-revealed-by-rna-sequence-based-transcriptome-analysis
#17
Anuradha Upadhyay, Smita Maske, Satisha Jogaiah, Narendra Y Kadoo, Vidya S Gupta
In grapes (Vitis vinifera L.), exogenous gibberellic acid (GA3 ) is applied at different stages of bunch development to achieve desirable bunch shape and berry size in seedless grapes used for table purpose. RNA sequence-based transcriptome analysis was used to understand the mechanism of GA3 action at cluster emergence, full bloom, and berry stage in table grape variety Thompson Seedless. At cluster emergence, rachis samples were collected at 6 and 24 h after application of GA3 , whereas flower clusters and berry samples were collected at 6, 24, and 48 h after application at full bloom and 3-4 mm berry stages...
April 6, 2018: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/29625468/the-role-of-wnt-%C3%AE-catenin-signaling-and-k-cadherin-in-the-regulation-of-intraocular-pressure
#18
Hannah C Webber, Jaclyn Y Bermudez, J Cameron Millar, Weiming Mao, Abbot F Clark
Purpose: Wnt/β-catenin signaling in the trabecular meshwork (TM) is required for maintaining normal intraocular pressure (IOP), although the mechanism(s) behind this are unknown. We hypothesize that Wnt/β-catenin signaling regulates IOP via β-catenin's effects on cadherin junctions. Methods: Nonglaucomatous primary human TM (NTM) cells were treated with or without 100 ng/ml Wnt3a, 1 μg/ml sFRP1, or both for 4 to 48 hours. Cells were immunostained for β-catenin, total cadherins, or cadherin isoforms...
March 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29619825/proteogenomics-of-malignant-melanoma-cell-lines-the-effect-of-stringency-of-exome-data-filtering-on-variant-peptide-identification-in-shotgun-proteomics
#19
Anna A Lobas, Mikhail A Pyatnitskiy, Alexey L Chernobrovkin, Irina Y Ilina, Dmitry S Karpov, Elizaveta M Solovyeva, Ksenia G Kuznetsova, Mark V Ivanov, Elena Y Lyssuk, Anna A Kliuchnikova, Olga E Voronko, Sergey S Larin, Roman A Zubarev, Mikhail V Gorshkov, Sergei A Moshkovskii
Identification of genetically encoded variants at the proteome level is an important problem in cancer proteogenomics. Generation of customized protein databases from DNA or RNA sequencing data is a crucial stage of the identification workflow. Genomic data filtering applied at this stage may significantly modify variant search results, yet its effect is generally left out of the scope of proteogenomic studies. In this work, we focused on this impact using data of exome sequencing and LC-MS/MS analyses of six replicates for eight melanoma cell lines processed by a proteogenomics workflow...
April 5, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29618939/-syk-expression-level-distinguishes-control-from-brca1-mutated-lymphocytes
#20
Tamar Zahavi, Amir Sonnenblick, Yael Shimshon, Luna Kadouri, Tamar Peretz, Asher Y Salmon, Mali Salmon-Divon
Background: About 5%-10% of breast cancer and 10%-15% of ovarian cancer are hereditary. BRCA1 and BRCA2 are the most common germline mutations found in both inherited breast and ovarian cancers. Once these mutations are identified and classified, a course of action to reduce the risk of developing either ovarian or breast cancer - including surveillance and surgery - is carried out. Purpose: The purpose of the current research is to characterize the gene expression differences between healthy cells harboring a mutation in BRCA1 /2 genes and normal cells...
2018: Cancer Management and Research
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