keyword
MENU ▼
Read by QxMD icon Read
search

functional annotation

keyword
https://www.readbyqxmd.com/read/29352453/measuring-surgical-safety-during-minimally-invasive-surgical-procedures-a-validation-study
#1
Mathijs D Blikkendaal, Sara R C Driessen, Sharon P Rodrigues, Johann P T Rhemrev, Maddy J G H Smeets, Jenny Dankelman, John J van den Dobbelsteen, Frank Willem Jansen
BACKGROUND: During the implementation of new interventions (i.e., surgical devices and technologies) in the operating room, surgical safety might be compromised. Current safety measures are insufficient in detecting safety hazards during this process. The aim of the study was to observe whether surgical teams are capable of measuring surgical safety, especially with regard to the introduction of new interventions. METHODS: A Surgical Safety Questionnaire was developed that had to be filled out directly postoperative by three surgical team members...
January 19, 2018: Surgical Endoscopy
https://www.readbyqxmd.com/read/29352105/an-ornithine-%C3%AF-aminotransferase-required-for-growth-in-the-absence-of-exogenous-proline-in-the-archaeon-thermococcus-kodakarensis
#2
Ren-Chao Zheng, Shin-Ichi Hachisuka, Hiroya Tomita, Tadayuki Imanaka, Yu-Guo Zheng, Makoto Nishiyama, Haruyuki Atomi
Aminotransferases are pyridoxal 5'-phosphate-dependent enzymes that catalyze reversible transamination reactions between amino acids and α-keto acids, and are important for the cellular metabolism of nitrogen. Many bacterial and eukaryotic ω-aminotransferases that use L-ornithine (Orn), L-lysine (Lys) or γ-aminobutyrate (GABA) have been identified and characterized, but the corresponding enzymes from archaea are unknown. Here we examined the activity and function of TK2101, a gene annotated as GABA aminotransferase, from the hyperthermophilic archaeon Thermococcus kodakarensis We overexpressed the TK2101 gene in T...
January 19, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29351798/comparative-salivary-proteomics-analysis-of-children-with-and-without-dental-caries-using-the-itraq-mrm-approach
#3
Kun Wang, Yufei Wang, Xiuqing Wang, Qian Ren, Sili Han, Longjiang Ding, Zhongcheng Li, Xuedong Zhou, Wei Li, Linglin Zhang
BACKGROUND: Dental caries is a major worldwide oral disease afflicting a large proportion of children. As an important host factor of caries susceptibility, saliva plays a significant role in the occurrence and development of caries. The aim of the present study was to characterize the healthy and cariogenic salivary proteome and determine the changes in salivary protein expression of children with varying degrees of active caries, also to establish salivary proteome profiles with a potential therapeutic use against dental caries...
January 19, 2018: Journal of Translational Medicine
https://www.readbyqxmd.com/read/29351734/eogd-the-euplotes-octocarinatus-genome-database
#4
Ruan-Lin Wang, Wei Miao, Wei Wang, Jie Xiong, Ai-Hua Liang
BACKGROUND: Euplotes, a ciliated protozoan, is a useful unicellular model organism. Studies on Euplotes have provided excellent insights into various basic biological principles. We have recently sequenced the macronuclear genome of the common freshwater species Euplotes octocarinatus to provide novel insights into Euplotes genetics and molecular biology. RESULTS: In this study, we present the E. octocarinatus Genome Database (EOGD), a functional annotation and analysis platform for the global study of the Euplotes genome...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29351633/evolutionary-genetics-of-cytoplasmic-incompatibility-genes-cifa-and-cifb-in-prophage-wo-of-wolbachia
#5
Amelia R I Lindsey, Danny W Rice, Sarah R Bordenstein, Andrew W Brooks, Seth R Bordenstein, Irene L G Newton
The bacterial endosymbiont Wolbachia manipulates arthropod reproduction to facilitate its maternal spread through host populations. The most common manipulation is cytoplasmic incompatibility (CI): Wolbachia-infected males produce modified sperm that cause embryonic mortality, unless rescued by embryos harboring the same Wolbachia. The genes underlying CI, cifA and cifB, were recently identified in the eukaryotic association module of Wolbachia's prophage WO. Here, we use transcriptomic and genomic approaches to address three important evolutionary facets of the cif genes...
January 17, 2018: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29351317/hafts-are-novel-lncrna-transcripts-from-aflatoxin-exposure
#6
B Alex Merrick, Justin S Chang, Dhiral P Phadke, Meredith A Bostrom, Ruchir R Shah, Xinguo Wang, Oksana Gordon, Garron M Wright
The transcriptome can reveal insights into precancer biology. We recently conducted RNA-Seq analysis on liver RNA from male rats exposed to the carcinogen, aflatoxin B1 (AFB1), for 90 days prior to liver tumor onset. Among >1,000 differentially expressed transcripts, several novel, unannotated Cufflinks-assembled transcripts, or HAfTs (Hepatic Aflatoxin Transcripts) were found. We hypothesized PCR-cloning and RACE (rapid amplification of cDNA ends) could further HAfT identification. Sanger data was obtained for 6 transcripts by PCR and 16 transcripts by 5'- and 3'-RACE...
2018: PloS One
https://www.readbyqxmd.com/read/29351296/hybrid-genome-assembly-and-annotation-of-paenibacillus-pasadenensis-strain-r16-reveals-insights-on-endophytic-life-style-and-antifungal-activity
#7
Alessandro Passera, Luca Marcolungo, Paola Casati, Milena Brasca, Fabio Quaglino, Chiara Cantaloni, Massimo Delledonne
Bacteria of the Paenibacillus genus are becoming important in many fields of science, including agriculture, for their positive effects on the health of plants. However, there are little information available on this genus compared to other bacteria (such as Bacillus or Pseudomonas), especially when considering genomic information. Sequencing the genomes of plant-beneficial bacteria is a crucial step to identify the genetic elements underlying the adaptation to life inside a plant host and, in particular, which of these features determine the differences between a helpful microorganism and a pathogenic one...
2018: PloS One
https://www.readbyqxmd.com/read/29348878/identification-of-cancer-prognosis-associated-functional-modules-using-differential-co-expression-networks
#8
Wenshuai Yu, Shengjie Zhao, Yongcui Wang, Brian Nlong Zhao, Weiling Zhao, Xiaobo Zhou
The rapid accumulation of cancer-related data owing to high-throughput technologies has provided unprecedented choices to understand the progression of cancer and discover functional networks in multiple cancers. Establishment of co-expression networks will help us to discover the systemic properties of carcinogenesis features and regulatory mechanisms of multiple cancers. Here, we proposed a computational workflow to identify differentially co-expressed gene modules across 8 cancer types by using combined gene differential expression analysis methods and a higher-order generalized singular value decomposition...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348872/gene-expression-profiling-reveals-u1-snrna-regulates-cancer-gene-expression
#9
Zhi Cheng, Yu Sun, Xiaoran Niu, Yingchun Shang, Jishou Ruan, Ze Chen, Shan Gao, Tao Zhang
U1 small nuclear RNA (U1 snRNA), as one of the most abundant ncRNAs in human cells, plays an important role in splicing of pre-mRNAs. Compared to previous studies which have focused on the primary function of U1 snRNA and the neurodegenerative diseases caused by abnormalities of U1 snRNA, this study is to investigate how U1 snRNA over-expression affects the expression of mammal genes on a genome-wide scale. By comparing the gene expression profiles of U1 snRNA over-expressed cells with those of their controls using microarray experiments, 916 genes or loci were identified significantly Differentially Expressed (DE)...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348434/identification-of-genetic-elements-in-metabolism-by-high-throughput-mouse-phenotyping
#10
Jan Rozman, Birgit Rathkolb, Manuela A Oestereicher, Christine Schütt, Aakash Chavan Ravindranath, Stefanie Leuchtenberger, Sapna Sharma, Martin Kistler, Monja Willershäuser, Robert Brommage, Terrence F Meehan, Jeremy Mason, Hamed Haselimashhadi, Tertius Hough, Ann-Marie Mallon, Sara Wells, Luis Santos, Christopher J Lelliott, Jacqueline K White, Tania Sorg, Marie-France Champy, Lynette R Bower, Corey L Reynolds, Ann M Flenniken, Stephen A Murray, Lauryl M J Nutter, Karen L Svenson, David West, Glauco P Tocchini-Valentini, Arthur L Beaudet, Fatima Bosch, Robert B Braun, Michael S Dobbie, Xiang Gao, Yann Herault, Ala Moshiri, Bret A Moore, K C Kent Lloyd, Colin McKerlie, Hiroshi Masuya, Nobuhiko Tanaka, Paul Flicek, Helen E Parkinson, Radislav Sedlacek, Je Kyung Seong, Chi-Kuang Leo Wang, Mark Moore, Steve D Brown, Matthias H Tschöp, Wolfgang Wurst, Martin Klingenspor, Eckhard Wolf, Johannes Beckers, Fausto Machicao, Andreas Peter, Harald Staiger, Hans-Ulrich Häring, Harald Grallert, Monica Campillos, Holger Maier, Helmut Fuchs, Valerie Gailus-Durner, Thomas Werner, Martin Hrabe de Angelis
Metabolic diseases are a worldwide problem but the underlying genetic factors and their relevance to metabolic disease remain incompletely understood. Genome-wide research is needed to characterize so-far unannotated mammalian metabolic genes. Here, we generate and analyze metabolic phenotypic data of 2016 knockout mouse strains under the aegis of the International Mouse Phenotyping Consortium (IMPC) and find 974 gene knockouts with strong metabolic phenotypes. 429 of those had no previous link to metabolism and 51 genes remain functionally completely unannotated...
January 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29348067/physiological-response-and-transcription-profiling-analysis-reveals-the-role-of-h2s-in-alleviating-excess-nitrate-stress-tolerance-in-tomato-roots
#11
Zhaolai Guo, Yuanlin Liang, Jinping Yan, En Yang, Kunzhi Li, Huini Xu
Soil secondary salinization caused by excess nitrate addition is one of the major obstacles in greenhouse vegetable production. Excess nitrate inhibited the growth of tomato plants, while application of 100 μM H2S donor NaHS efficiently increased the plant height, fresh and dry weight of shoot and root, root length, endogenous H2S contents and L-cysteine desulfhydrases activities. NaHS altered the oxidative status of nitrate-stressed plants as inferred by changes in reactive oxygen species (ROS) accumulation and lipid peroxidation accompanied by regulation of the activities of superoxide dismutase (SOD), peroxidase (POD), catalase (CAT), ascorbate peroxidase (APX)...
January 11, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29347977/expansion-of-cytochrome-p450-and-cathepsin-genes-in-the-generalist-herbivore-brown-marmorated-stink-bug
#12
Raman Bansal, Andy Michel
BACKGROUND: The brown marmorated stink bug (Halyomorpha halys) is an invasive pest in North America which causes severe economic losses on tree fruits, ornamentals, vegetables, and field crops. The H. halys is an extreme generalist and this feeding behaviour may have been a major contributor behind its establishment and successful adaptation in invasive habitats of North America. To develop an understanding into the mechanism of H. halys' generalist herbivory, here we specifically focused on genes putatively facilitating its adaptation on diverse host plants...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29347945/microrna-transcriptome-analysis-of-porcine-vital-organ-responses-to-immunosuppressive-porcine-cytomegalovirus-infection
#13
Xiao Liu, Haoche Wei, Shan Liao, Jianheng Ye, Ling Zhu, Zhiwen Xu
BACKGROUND: Porcine cytomegalovirus (PCMV) is an immunosuppressive virus that mainly inhibits T-lymphocyte and macrophage immune functions; it has significantly damaged the farming industry. Although recent studies have shown that miRNAs play important roles in immune responses, the regulatory mechanisms of miRNAs during immunosuppressive virus infection remain unclear. METHODS: In this study, porcine small-RNA transcriptomes of PCMV-infected and uninfected vital organs were first characterised by high-throughput sequencing...
January 18, 2018: Virology Journal
https://www.readbyqxmd.com/read/29347914/in-depth-proteomic-analysis-of-boar-spermatozoa-through-shotgun-and-gel-based-methods
#14
Jean M Feugang, Shengfa F Liao, Scott T Willard, Peter L Ryan
BACKGROUND: Mature spermatozoa contain numerous epididymal and seminal plasma proteins, which full identification through high-throughput technologies may allow for a better understanding of the sperm biology. Therefore, we conducted a global proteomic analysis of boar spermatozoa through shotgun and gel-based methodologies. RESULTS: The total proteins were extracted from mature spermatozoa and subjecsted to proteome analyses. Functional analyses of gene ontology representations and pathway enrichments were conducted on the shotgun dataset, followed by immunology and gene expression validations...
January 18, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29346437/tissue-specific-transcriptome-analyses-provide-new-insights-into-gpcr-signalling-in-adult-schistosoma-mansoni
#15
REVIEW
Steffen Hahnel, Nic Wheeler, Zhigang Lu, Arporn Wangwiwatsin, Paul McVeigh, Aaron Maule, Matthew Berriman, Timothy Day, Paula Ribeiro, Christoph G Grevelding
Schistosomes are blood-dwelling trematodes with global impact on human and animal health. Because medical treatment is currently based on a single drug, praziquantel, there is urgent need for the development of alternative control strategies. The Schistosoma mansoni genome project provides a platform to study and connect the genetic repertoire of schistosomes to specific biological functions essential for successful parasitism. G protein-coupled receptors (GPCRs) form the largest superfamily of transmembrane receptors throughout the Eumetazoan phyla, including platyhelminths...
January 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29345323/vernalization-can-regulate-flowering-time-through-microrna-mechanism-in-brassica-rapa
#16
Feiyi Huang, Xiaoting Wu, Xilin Hou, Shuaixu Shao, Tongkun Liu
Vernalization is an important process that regulates the floral transition in plants. MiRNAs are endogenous non-coding sRNA molecules that function in plant growth and development. Despite that miRNAs related to flowering have previously been characterized, miRNAs roles in response to vernalization in Pak-choi (Brassica rapa ssp. chinensis) has never been studied. Here, two sRNA libraries from Brassica rapa leaves (vernalized and non-vernalized plants) were constructed and sequenced. 208 known and 535 novel miRNAs were obtained, of which 20 known and 66 new miRNAs were significantly differentially expressed and considered as vernalization-related miRNAs...
January 18, 2018: Physiologia Plantarum
https://www.readbyqxmd.com/read/29345285/the-epitranscriptome-m6a-writer-mettl3-promotes-chemo-and-radioresistance-in-pancreatic-cancer-cells
#17
Kosuke Taketo, Masamitsu Konno, Ayumu Asai, Jun Koseki, Masayasu Toratani, Taroh Satoh, Yuichiro Doki, Masaki Mori, Hideshi Ishii, Kazuhiko Ogawa
N6-methyladenosine (m6A) is the most abundant epitranscriptome modification in mammalian mRNA. Recent years have seen substantial progress in m6A epitranscriptomics, indicating its crucial roles in the initiation and progression of cancer through regulation of RNA stabilities, mRNA splicing, microRNA processing and mRNA translation. However, by what means m6A is dynamically regulated or written by enzymatic components represented by methyltransferase-like 3 (METTL3) and how m6A is significant for each of the numerous genes remain unclear...
February 2018: International Journal of Oncology
https://www.readbyqxmd.com/read/29344304/atherosclerosis-is-exacerbated-by-chitinase-3-like-1-in-amyloid-precursor-protein-transgenic-mice
#18
Yu Yeon Jung, Ki Cheon Kim, Mi Hee Park, Youngsik Seo, Heonyong Park, Min Hee Park, Jun Chang, Dae Youn Hwang, Sang Bae Han, Sanghyeon Kim, Dong Ju Son, Jin Tae Hong
Although the important role of amyloid precursor protein (APP) in vascular diseases associated with Alzheimer's disease (AD) has been demonstrated, the underlying molecular mechanisms and physiological consequences are unclear. We aimed to evaluate vascular inflammation and atherosclerosis in Swedish mutant of human APP transgenic (APPsw-Tg) and ApoE-/-/APPsw-Tg mice. We also aimed to explore the mechanisms underlying any changes observed in these mice compared with non-Tg controls. Methods: The transgenic and non-Tg mouse strains were subjected to partial ligation of the left carotid artery to induce atherosclerotic changes, which were measured using histological approaches, immunohistochemistry, quantitative polymerase chain reaction, and gene expression microarrays...
2018: Theranostics
https://www.readbyqxmd.com/read/29344166/identification-and-functional-analysis-of-risk-related-micrornas-for-the-prognosis-of-patients-with-bladder-urothelial-carcinoma
#19
Ji Gao, Hongyan Li, Lei Liu, Lide Song, Yanting Lv, Yuping Han
The aim of the present study was to investigate risk-related microRNAs (miRs) for bladder urothelial carcinoma (BUC) prognosis. Clinical and microRNA expression data downloaded from the Cancer Genome Atlas were utilized for survival analysis. Risk factor estimation was performed using Cox's proportional regression analysis. A microRNA-regulated target gene network was constructed and presented using Cytoscape. In addition, the Database for Annotation, Visualization and Integrated Discovery was used for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes pathway enrichment, followed by protein-protein interaction (PPI) network analysis...
December 2017: Oncology Letters
https://www.readbyqxmd.com/read/29344146/integrated-microrna-mrna-analyses-of-distinct-expression-profiles-in-follicular-thyroid-tumors
#20
Jiadong Chi, Xiangqian Zheng, Ming Gao, Jingzhu Zhao, Dapeng Li, Jiansen Li, Li Dong, Xianhui Ruan
MicroRNAs (miRNAs/miRs) are small non-coding RNAs identified in plants, animals and certain viruses; they function in RNA silencing and post-transcriptional regulation of gene expression. miRNAs also serve an important role in the pathogenesis, diagnosis and treatment of tumors. However, few studies have investigated the role of miRNAs in thyroid tumors. In the present study, the expression of miRNA and mRNA was compared between follicular thyroid carcinoma (FTC) and follicular thyroid adenoma (FA) samples, and then miRNA-mRNA regulatory network analysis was performed...
December 2017: Oncology Letters
keyword
keyword
117644
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"