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Promoter characterization

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https://www.readbyqxmd.com/read/28088687/whole-genome-dna-methylation-profiling-identifies-epigenetic-signatures-of-uterine-carcinosarcoma
#1
Jing Li, Xiaoyun Xing, Daofeng Li, Bo Zhang, David G Mutch, Ian S Hagemann, Ting Wang
Uterine carcinosarcoma (UCS) is a form of endometrial cancer simultaneously exhibiting carcinomatous and sarcomatous elements, but the underlying molecular and epigenetic basis of this disease is poorly understood. We generated complete DNA methylomes for both the carcinomatous and the sarcomatous components of three UCS samples separated by laser capture microdissection and compared DNA methylomes of UCS with those of normal endometrium as well as methylomes derived from endometrioid carcinoma, serous endometrial carcinoma, and endometrial stromal sarcoma...
January 12, 2017: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/28088650/assessing-the-identity-and-expression-level-of-the-cytochrome-p450-20a1-cyp20a1-gene-in-the-bpa-bde-47-and-waf-exposed-copepods-tigriopus-japonicus-and-paracyclopina-nana
#2
Jeonghoon Han, Duck-Hyun Kim, Jung Soo Seo, Il-Chan Kim, David R Nelson, Jayesh Puthumana, Jae-Seong Lee
CYP20A1 is a member of the cytochrome P450 (CYP) superfamily, identified as an orphan P450 without any assigned biological function; hence, its continued status as an "orphan" gene. In order to address this shortcoming in our understanding of this superfamily, we sought to characterize the CYP20A1 gene in the copepods Tigriopus japonicus (Tj-CYP20A1) and Paracyclopina nana (Pn-CYP20A1) at their mRNA transcriptional level. We assessed the response of this gene's expression in various developmental stages and in response to treatment with bisphenol A (BPA), 2, 2', 4, 4'-tetrabromodiphenyl ether (BDE-47), and water accommodated fractions (WAFs) of crude oil...
January 11, 2017: Comparative Biochemistry and Physiology. Toxicology & Pharmacology: CBP
https://www.readbyqxmd.com/read/28088458/non-thermal-atmospheric-pressure-plasma-functionalized-dental-implant-for-enhancement-of-bacterial-resistance-and-osseointegration
#3
Jung-Hwan Lee, Won-Seok Jeong, Seog-Jin Seo, Hae-Won Kim, Kyoung-Nam Kim, Eun-Ha Choi, Kwang-Mahn Kim
OBJECTIVE: Even though roughened titanium (Ti) and Ti alloys have been clinically used as dental implant, they encourage bacterial adhesion, leading to failure of the initial stability. Here, the non-thermal atmospheric pressure plasma jet (NTAPPJ) functionalized Ti and Ti alloy were investigated to promote cellular activities but inhibit the initial attachment of the adherent pioneer bacterium, Streptococcus sanguinis, without topographical changes. METHODS: After the produced radicals from NTAPPJ were characterized, bacterial adhesion to specimens was assessed by PrestoBlue assay and live-dead staining with or without the NTAPPJ functionalizing...
January 11, 2017: Dental Materials: Official Publication of the Academy of Dental Materials
https://www.readbyqxmd.com/read/28088321/surgeon-pathologist-and-hospital-level-variation-in-suboptimal-lymph-node-examination-after-colectomy-compartmentalizing-quality-improvement-strategies
#4
Adan Z Becerra, Christopher T Aquina, Mariana Berho, Francis P Boscoe, Maria J Schymura, Katia Noyes, John R Monson, Fergal J Fleming
BACKGROUND: The goals of this study were to characterize the variation in suboptimal lymph node examination for patients with colon cancer across individual surgeons, pathologists, and hospitals and to examine if this variation affects 5-year, disease-specific survival. METHODS: A retrospective cohort study was conducted by merging the New York State Cancer Registry with the Statewide Planning & Research Cooperative System, Medicaid, and Medicare claims to identify resections for stages I-III colon cancer from 2004-2011...
January 11, 2017: Surgery
https://www.readbyqxmd.com/read/28088234/stability-based-validation-of-dietary-patterns-obtained-by-cluster-analysis
#5
Nicolas Sauvageot, Anna Schritz, Sonia Leite, Ala'a Alkerwi, Saverio Stranges, Faiez Zannad, Sylvie Streel, Axelle Hoge, Anne-Françoise Donneau, Adelin Albert, Michèle Guillaume
BACKGROUND: Cluster analysis is a data-driven method used to create clusters of individuals sharing similar dietary habits. However, this method requires specific choices from the user which have an influence on the results. Therefore, there is a need of an objective methodology helping researchers in their decisions during cluster analysis. The objective of this study was to use such a methodology based on stability of clustering solutions to select the most appropriate clustering method and number of clusters for describing dietary patterns in the NESCAV study (Nutrition, Environment and Cardiovascular Health), a large population-based cross-sectional study in the Greater Region (N = 2298)...
January 14, 2017: Nutrition Journal
https://www.readbyqxmd.com/read/28088228/the-loss-of-function-mutations-and-down-regulated-expression-of-asb3-gene-promote-the-growth-and-metastasis-of-colorectal-cancer-cells
#6
Wu-Ying Du, Zhen-Hai Lu, Wen Ye, Xiang Fu, Yi Zhou, Chun-Mei Kuang, Jiang-Xue Wu, Zhi-Zhong Pan, Shuai Chen, Ran-Yi Liu, Wen-Lin Huang
BACKGROUND: Ankyrin repeat and SOCS box protein 3 (ASB3) is a member of ASB family and contains ankyrin repeat sequence and SOCS box domain. Previous studies indicated that it mediates the ubiquitination and degradation of tumor necrosis factor receptor 2 and is likely involved in inflammatory responses. However, its effects on oncogenesis are unclear. This study aimed to investigate the effects of ASB3 on the growth and metastasis of colorectal cancer (CRC). METHODS: We used next-generation sequencing or Sanger sequencing to detect ASB3 mutations in CRC specimens or cell lines, and used real-time quantitative polymerase chain reaction, Western blotting, and immunohistochemical or immunofluorescence assay to determine gene expression...
January 14, 2017: Chinese Journal of Cancer
https://www.readbyqxmd.com/read/28088132/expression-and-secretion-of-cyan-fluorescent-protein-cfp-in-b-subtilis-using-the-chitinase-promoter-from-bacillus-pumilus-sg2
#7
Abbas Shali, Garshasb Rigi, Majid Pornour, Gholamreza Ahmadian
Background: Improved cyan fluorescent protein (ICFP) is a monochromic, green fluorescent protein (GFP) derivative produced by Aequorea macrodactyla in a process similar to GFP. This protein has strong absorption spectra at wavelengths 426-446 nm. ICFP can be used in cell, organelle or intracellular protein labeling, investigating the protein-protein interactions as well as assessing the promoter activities. Methods: In our previous study, the promoters of two chitinases (ChiS and ChiL) from Bacillus pumilus SG2 were assessed in B...
15, 2017: Iranian Biomedical Journal
https://www.readbyqxmd.com/read/28087674/yeast-as-a-tool-to-express-sugar-acid-transporters-with-biotechnological-interest
#8
David Ribas, Joana Sá-Pessoa, Isabel Soares-Silva, Sandra Paiva, Yvonne Nygård, Laura Ruohonen, Merja Penttilä, Margarida Casal
Sugar acids can be used as platform chemicals to generate primary building blocks of industrially relevant products. Microbial production of these organic compounds at high yields requires the engineering of the enzymatic machinery and the presence of plasma membrane transporters able to export them outside the cells. In this study several yeast carboxylic acid transporters belonging to the Jen family were screened for the transport of biotechnologically relevant sugar acids, namely gluconic, saccharic, mucic, xylaric and xylonic acid, and functionally characterized in Saccharomyces cerevisiae We show that Jen permeases are capable of transporting most of these sugar acids, although with different specificities...
January 12, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28087651/frontline-science-multiple-cathepsins-promote-inflammasome-independent-particle-induced-cell-death-during-nlrp3-dependent-il-1%C3%AE-activation
#9
Gregory M Orlowski, Shruti Sharma, Jeff D Colbert, Matthew Bogyo, Stephanie A Robertson, Hiroshi Kataoka, Francis K Chan, Kenneth L Rock
Sterile particles cause several chronic, inflammatory diseases, characterized by repeating cycles of particle phagocytosis and inflammatory cell death. Recent studies have proposed that these processes are driven by the NLRP3 inflammasome, a platform activated by phagocytosed particles, which controls both caspase-1-dependent cell death (pyroptosis) and mature IL-1β secretion. After phagocytosis, particles can disrupt lysosomes, and inhibitor studies have suggested that the resulting release of a lysosomal protease-cathepsin B-into the cytosol somehow activates NLRP3...
January 13, 2017: Journal of Leukocyte Biology
https://www.readbyqxmd.com/read/28087610/long-non-coding-rna-exchange-during-the-oocyte-to-embryo-transition-in-mice
#10
Rosa Karlic, Sravya Ganesh, Vedran Franke, Eliska Svobodova, Jana Urbanova, Yutaka Suzuki, Fugaku Aoki, Kristian Vlahovicek, Petr Svoboda
The oocyte-to-embryo transition (OET) transforms a differentiated gamete into pluripotent blastomeres. The accompanying maternal-zygotic RNA exchange involves remodeling of the long non-coding RNA (lncRNA) pool. Here, we used next generation sequencing and de novo transcript assembly to define the core population of 1,600 lncRNAs expressed during the OET (lncRNAs). Relative to mRNAs, OET lncRNAs were less expressed and had shorter transcripts, mainly due to fewer exons and shorter 5' terminal exons. Approximately half of OET lncRNA promoters originated in retrotransposons suggesting their recent emergence...
January 13, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28087537/effects-of-lactobacillus-plantarum-oll2712-culture-conditions-on-the-anti-inflammatory-activity-for-murine-immune-cells-and-obese-and-type-2-diabetic-mice
#11
T Toshimitsu, S Ozaki, J Mochizuki, K Furuichi, Y Asami
: Studies on the health-promoting effects of lactic acid bacteria (LAB) are numerous, but few provide examples of the relationship between LAB function and culture conditions. We verified the effect of differences in culture conditions on Lactobacillus plantarum OLL2712 (OLL2712) functionality; this strain exhibits anti-inflammatory activity and preventive effects against metabolic disorders. We measured IL-10 and IL-12 production in murine immune cells treated with OLL2712 cells prepared under various culture conditions...
January 13, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28086949/nek2-promotes-aerobic-glycolysis-in-multiple-myeloma-through-regulating-splicing-of-pyruvate-kinase
#12
Zhimin Gu, Jiliang Xia, Hongwei Xu, Ivana Frech, Guido Tricot, Fenghuang Zhan
BACKGROUND: Aerobic glycolysis, a hallmark of cancer, is characterized by increased metabolism of glucose and production of lactate in normaxia. Recently, pyruvate kinase M2 (PKM2) has been identified as a key player for regulating aerobic glycolysis and promoting tumor cell proliferation and survival. METHODS: Tandem affinity purification followed up by mass spectrometry (TAP-MS) and co-immunoprecipitation (Co-IP) were used to study the interaction between NIMA (never in mitosis gene A)-related kinase 2 (NEK2) and heterogeneous nuclear ribonucleoproteins (hnRNP) A1/2...
January 13, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28081487/comparative-genome-wide-phylogenetic-and-expression-analysis-of-sbp-genes-from-potato-solanum-tuberosum
#13
Musa Kavas, Aslıhan Kurt Kızıldoğan, Büşra Abanoz
Flowering time is a very important phase in transition to reproductive stage of life in higher plants. SQUAMOSA promoter-binding protein (SBP) gene family encodes plant-specific transcription factors that are involved in regulation of several developmental processes, especially flowering. Although SBP-box genes have been identified in different plants, there have been no study indicating the regulatory effect of SBP box in potato flowering. Here, we report for the first time the identification and characterization of SBP-box transcription factors as well as determination of expression level of SBP-box genes in Solanum tuberosum L...
January 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28081140/bnlate-a-cys2-his2-type-zinc-finger-protein-enhances-silique-shattering-resistance-by-negatively-regulating-lignin-accumulation-in-the-silique-walls-of-brassica-napus
#14
Zhangsheng Tao, Yi Huang, Lida Zhang, Xinfa Wang, Guihua Liu, Hanzhong Wang
Silique shattering resistance is one of the most important agricultural traits in oil crop breeding. Seed shedding from siliques prior to and during harvest causes devastating losses in oilseed yield. Lignin biosynthesis in the silique walls is thought to affect silique-shattering resistance in oil crops. Here, we identified and characterized B. napus LATE FLOWERING (BnLATE), which encodes a Cys2/His2-type zinc-finger protein. Heterologous expression of BnLATE under the double enhanced CaMV 35S promoter (D35S) in wild-type Arabidopsis plants resulted in a marked decrease in lignification in the replum, valve layer (carpel) and dehiscence zone...
2017: PloS One
https://www.readbyqxmd.com/read/28079980/induction-of-mesenchymal-stem-cell-differentiation-in-the-absence-of-soluble-inducer-for-cutaneous-wound-regeneration-by-a-chitin-nanofibers-based-hydrogel
#15
Kangquan Shou, Yao Huang, Baiwen Qi, Xiang Hu, Zhanjun Ma, Ang Lu, Chao Jian, Lina Zhang, Aixi Yu
Transplantation of bone marrow mesenchymal stem cells (BMSCs) has been considered as a promising strategy for wound healing. However, poor viability of engrafted BMSCs and limited capabilities of differentiation into the desired cell types in wounds often hinder their application. Few studies report the induction of BMSCs differentiation into the skin regeneration related cell types using natural biopolymer, e.g., chitin and its derivative. Here we utilized a chitin nanofibers(CNFs) hydrogel as a directive cue to induce BMSCs differentiation for enhancing cutaneous wound regeneration in the absence of cell-differentiating factors...
January 12, 2017: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/28079892/hif-2%C3%AE-and-oct4-have-synergistic-effects-on-survival-and-myocardial-repair-of-very-small-embryonic-like-mesenchymal-stem-cells-in-infarcted-hearts
#16
Shaoheng Zhang, Lan Zhao, Jiahong Wang, Nannan Chen, Jian Yan, Xin Pan
Poor cell survival and limited functional benefits have restricted mesenchymal stem cell (MSC) efficacy for treating myocardial infarction (MI), suggesting that a better understanding of stem cell biology is needed. The transcription factor HIF-2α is an essential regulator of the transcriptional response to hypoxia, which can interact with embryonic stem cells (ESCs) transcription factor Oct4 and modulate its signaling. Here, we obtained very small embryonic-like mesenchymal stem cells (vselMSCs) from MI patients, which possessed the very small embryonic-like stem cells' (VSELs) morphology as well as ESCs' pluripotency...
January 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28079645/the-role-of-patient-navigators-in-building-a-medical-home-for-multiply-diagnosed-hiv-positive-homeless-populations
#17
Mariana Sarango, Alexander de Groot, Melissa Hirschi, Chukwuemeka Anthony Umeh, Serena Rajabiun
CONTEXT: People living with human immunodeficiency virus (HIV) (PLWH) who are most at risk for falling out of HIV primary care and detectable viral loads include homeless and unstably housed individuals and those codiagnosed with behavioral health disorders. The patient-centered medical home (PCMH) is a model that promotes provision of comprehensive, patient-centered, accessible, coordinated, and quality care for patients. This initiative provided patient navigation to HIV-positive homeless and unstably housed individuals codiagnosed with a mental health or substance use disorder as a means to create an adapted PCMH to meet the specific needs of this population...
January 11, 2017: Journal of Public Health Management and Practice: JPHMP
https://www.readbyqxmd.com/read/28078646/mucosal-healing-in-ulcerative-colitis-a-comprehensive-review
#18
REVIEW
Pedro Boal Carvalho, José Cotter
Ulcerative colitis (UC) is a chronic inflammatory bowel disease characterized by periods of remission and periods of relapse. Patients often present with symptoms such as rectal bleeding, diarrhea and weight loss, and may require hospitalization and even colectomy. Long-term complications of UC include decreased quality of life and productivity and an increased risk of colorectal cancer. Mucosal healing (MH) has gained progressive importance in the management of UC patients. In this article, we review the endoscopic findings that define both mucosal injury and MH, and the strengths and limitations of the scoring systems currently available in clinical practice...
January 11, 2017: Drugs
https://www.readbyqxmd.com/read/28078586/study-of-the-cd95-mediated-non-apoptotic-signaling-pathway-pi3k
#19
Amélie Fouqué, Patrick Legembre
CD95 is a plasma membrane receptor that belongs to the TNF receptor family (Itoh and Nagata, J Biol Chem 268(15):10932-10937, 1993; Trauth et al., Science 245(4915):301-305, 1989). Accumulating evidence indicate that this so-called death receptor can also trigger non-apoptotic signaling pathways promoting inflammation and oncogenesis (Barnhart et al., Embo J 23(15):3175-3185, 2004; Chen et al., Nature 465(7297):492-496, 2010; Legembre et al., Cell Cycle 3(10):1235-1239, 2004; Legembre et al., EMBO Rep 5(11):1084-1089, 2004; Malleter et al...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28078509/psg9-promotes-angiogenesis-by-stimulating-vegfa-production-and-is-associated-with-poor-prognosis-in-hepatocellular-carcinoma
#20
Weiqi Rong, Lei Yang, Liyuan Yin, Yanning Gao, Ting Xiao, Shujun Cheng
Hepatocellular carcinoma (HCC) is a common malignant solid tumor characterized by rich vascularization. Pregnancy-specific glycoprotein 9 (PSG9) is a member of the carcinoembryonic antigen (CEA)/PSG family and is produced at high levels during pregnancy. We previously identified PSG9 as an HCC-related protein. However, the expression of PSG9 and its regulation during HCC carcinogenesis remain poorly explored. In the present study, we first found that the levels of PSG9 protein were significantly increased in the plasma of HCC patients...
January 4, 2017: Science China. Life Sciences
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