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https://www.readbyqxmd.com/read/28938616/identification-of-potential-cancer-related-pseudogenes-in-lung-adenocarcinoma-based-on-cerna-hypothesis
#1
Yunzhen Wei, Zhiqiang Chang, Cheng Wu, Yinling Zhu, Kun Li, Yan Xu
Pseudogenes are initially regarded as non-functional genomic fossils resulted from inactivating gene mutations during evolution. Far from being silent, pseudogenes are proved to regulate the expression of protein-coding genes through function as microRNA sponge in vivo. The aim of our study was to propose an integrative systems biology approach to identify disease pseudogenes base on competitive endogenous RNA (ceRNA) hypothesis. Here, we applied our method to lung adenocarcinoma (LUAD) RNASeq data from TCGA and identified 33 candidate pseudogenes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938536/integrating-omics-data-and-protein-interaction-networks-to-prioritize-driver-genes-in-cancer
#2
Tiejun Zhang, Di Zhang
Although numerous approaches have been proposed to discern driver from passenger, identification of driver genes remains a critical challenge in the cancer genomics field. Driver genes with low mutated frequency tend to be filtered in cancer research. In addition, the accumulation of different omics data necessitates the development of algorithmic frameworks for nominating putative driver genes. In this study, we presented a novel framework to identify driver genes through integrating multi-omics data such as somatic mutation, gene expression, and copy number alterations...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938250/listening-effort-how-the-cognitive-consequences-of-acoustic-challenge-are-reflected-in-brain-and-behavior
#3
Jonathan E Peelle
Everyday conversation frequently includes challenges to the clarity of the acoustic speech signal, including hearing impairment, background noise, and foreign accents. Although an obvious problem is the increased risk of making word identification errors, extracting meaning from a degraded acoustic signal is also cognitively demanding, which contributes to increased listening effort. The concepts of cognitive demand and listening effort are critical in understanding the challenges listeners face in comprehension, which are not fully predicted by audiometric measures...
September 21, 2017: Ear and Hearing
https://www.readbyqxmd.com/read/28937978/a-new-discrete-dynamic-model-of-aba-induced-stomatal-closure-predicts-key-feedback-loops
#4
Réka Albert, Biswa R Acharya, Byeong Wook Jeon, Jorge G T Zañudo, Mengmeng Zhu, Karim Osman, Sarah M Assmann
Stomata, microscopic pores in leaf surfaces through which water loss and carbon dioxide uptake occur, are closed in response to drought by the phytohormone abscisic acid (ABA). This process is vital for drought tolerance and has been the topic of extensive experimental investigation in the last decades. Although a core signaling chain has been elucidated consisting of ABA binding to receptors, which alleviates negative regulation by protein phosphatases 2C (PP2Cs) of the protein kinase OPEN STOMATA 1 (OST1) and ultimately results in activation of anion channels, osmotic water loss, and stomatal closure, over 70 additional components have been identified, yet their relationships with each other and the core components are poorly elucidated...
September 22, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28936833/-mechanism-of-salvianolate-injection-combined-with-aspirin-in-treatment-of-stable-angina-pectoris-based-on-biomolecules-network
#5
Yuan Li, Lian-Xin Wang, Yan-Ming Xie
Biomolecular network analysis was used to predict the mechanism of Salvianolate injection combined with aspirin for the treatment of stable angina pectoris(SAP). Related genes of Salvianolate injection, aspirin and SAP were obtained from Genecards, STITCH and DisGeNET databases. Agilent literature search software was used to construct biomolecular network; modules were identified by AP, MCODE and MCL methods. DAVID software was used for identification of related KEGG pathways. Results showed that Salvianolate injection and aspirin had a coverage rate of 45...
December 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28934488/de-novo-pathway-based-biomarker-identification
#6
Nicolas Alcaraz, Markus List, Richa Batra, Fabio Vandin, Henrik J Ditzel, Jan Baumbach
Gene expression profiles have been extensively discussed as an aid to guide the therapy by predicting disease outcome for the patients suffering from complex diseases, such as cancer. However, prediction models built upon single-gene (SG) features show poor stability and performance on independent datasets. Attempts to mitigate these drawbacks have led to the development of network-based approaches that integrate pathway information to produce meta-gene (MG) features. Also, MG approaches have only dealt with the two-class problem of good versus poor outcome prediction...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28933595/phosphoproteome-based-kinase-activity-profiling-reveals-the-critical-role-of-map2k2-and-plk1-in-neuronal-autophagy
#7
Lei-Lei Chen, Yong-Bo Wang, Ju-Xian Song, Wan-Kun Deng, Jia-Hong Lu, Li-Li Ma, Chuan-Bin Yang, Min Li, Yu Xue
Recent studies have demonstrated that dysregulation of macroautophagy/autophagy may play a central role in the pathogenesis of neurodegenerative disorders, and the induction of autophagy protects against the toxic insults of aggregate-prone proteins by enhancing their clearance. Thus, autophagy has become a promising therapeutic target against neurodegenerative diseases. In this study, quantitative phosphoproteomic profiling together with a computational analysis was performed to delineate the phosphorylation signalling networks regulated by 2 natural neuroprotective autophagy enhancers, corynoxine (Cory) and corynoxine B (Cory B)...
September 21, 2017: Autophagy
https://www.readbyqxmd.com/read/28933255/organizational-hierarchy-and-structural-diversity-of-microvascular-pericytes-in-adult-mouse-cortex
#8
Roger I Grant, David A Hartmann, Robert G Underly, Andrée-Anne Berthiaume, Narayan R Bhat, Andy Y Shih
Smooth muscle cells and pericytes, together called mural cells, coordinate many distinct vascular functions. Canonically, smooth muscle cells are ring-shaped and cover arterioles with circumferential processes, whereas pericytes extend thin processes that run longitudinally along capillaries. In between these canonical mural cell types are cells with features of both smooth muscle cells and pericytes. Recent studies suggest that these transitional cells are critical for controlling blood flow to the capillary bed during health and disease, but there remains confusion on how to identify them and where they are located in the brain microvasculature...
January 1, 2017: Journal of Cerebral Blood Flow and Metabolism
https://www.readbyqxmd.com/read/28933072/-metabolomics-research-of-medicinal-plants
#9
Li-Xin Duan, Yun-Tao Dai, Chao Sun, Shi-Lin Chen
Metabolomics is the comprehensively study of chemical processes involving small molecule metabolites. It is an important part of systems biology, and is widely applied in complex traditional Chinese medicine(TCM)system. Metabolites biosynthesized by medicinal plants are the effective basis for TCM. Metabolomics studies of medicinal plants will usher in a new period of vigorous development with the implementation of Herb Genome Program and the development of TCM synthetic biology. This manuscript introduces the recent research progresses of metabolomics technology and the main research contents of metabolomics studies for medicinal plants, including identification and quality evaluation for medicinal plants, cultivars breeding, stress resistance, metabolic pathways, metabolic network, metabolic engineering and synthetic biology researches...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28931525/ectopic-ilt3-controls-bcr-dependent-activation-of-akt-in-b-cell-chronic-lymphocytic-leukemia
#10
Vanessa Zurli, Giuliana Wimmer, Francesca Cattaneo, Veronica Candi, Emanuele Cencini, Alessandro Gozzetti, Donatella Raspadori, Giuseppe Campoccia, Francesca Sanseviero, Monica Bocchia, Cosima Tatiana Baldari, Anna Kabanova
The high proportion of long-term non-progressors among chronic lymphocytic leukemia (CLL) patients suggests the existence of a regulatory network which restrains the proliferation of tumor B cells. The identification of molecular determinants composing such network is hence fundamental for our understanding of CLL pathogenesis. Based on our previous finding establishing a deficiency in the signaling adaptor p66Shc in CLL cells, we undertook to identify unique phenotypic traits caused by this defect. Here we show that a lack of p66Shc shapes the transcriptional profile of CLL cells and leads to an upregulation of the surface receptor ILT3, the immunoglobulin-like transcript 3 which is normally found on myeloid cells...
September 20, 2017: Blood
https://www.readbyqxmd.com/read/28931375/identification-of-fasciclin-like-arabinogalactan-proteins-in-textile-hemp-cannabis-sativa-l-in-silico-analyses-and-gene-expression-patterns-in-different-tissues
#11
Gea Guerriero, Lauralie Mangeot-Peter, Sylvain Legay, Marc Behr, Stanley Lutts, Khawar Sohail Siddiqui, Jean-Francois Hausman
BACKGROUND: The fasciclin-like arabinogalactan proteins (FLAs) belong to the arabinogalactan protein (AGP) superfamily and are known to play different physiological roles in plants. This class of proteins was shown to participate in plant growth, development, defense against abiotic stresses and, notably, cell wall biosynthesis. Although some studies are available on the characterization of FLA genes from different species, both woody and herbaceous, no detailed information is available on the FLA family of textile hemp (Cannabis sativa L...
September 20, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28931372/transcriptional-profile-of-breast-muscle-in-heat-stressed-layers-is-similar-to-that-of-broiler-chickens-at-control-temperature
#12
Imran Zahoor, Dirk-Jan de Koning, Paul M Hocking
BACKGROUND: In recent years, the commercial importance of changes in muscle function of broiler chickens and of the corresponding effects on meat quality has increased. Furthermore, broilers are more sensitive to heat stress during transport and at high ambient temperatures than smaller egg-laying chickens. We hypothesised that heat stress would amplify muscle damage and expression of genes that are involved in such changes and, thus, lead to the identification of pathways and networks associated with broiler muscle and meat quality traits...
September 20, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28929670/-herbgenomics
#13
Shi-Lin Chen, Jing-Yuan Song
Traditional Chinese medicine (TCM) has contributad greatly to improving human health. However, the biological characteristics and molecular mechanisms of TCM in the treatment of human diseases remain largely unknown. Genomics plays an important role in modern medicine and biology. Here, we introduce genomics and other related omics to the study of herbs to propose a new discipline, Herbgenomics, that aims to uncover the genetic information and regulatory networks of herbs and to clarify their molecular mechanisms in the prevention and treatment of human diseases...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28928808/identification-of-novel-methylated-targets-in-colorectal-cancer-by-microarray-analysis-and-construction-of-co-expression-network
#14
Dongsheng Li, Jialin Guo, Song Wang, Liangchen Zhu, Zugang Shen
The present study was conducted to investigate novel methylated targets in colorectal cancer (CRC). The mRNA expression profiles of GSE32323 in 17 cancer and non-cancerous tissues from CRC patients, as well as expression profiles of 5 CRC cell lines prior and subsequent to 5-aza-2'-deoxycytidine (5-aza-dC) treatment, were obtained from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in 5 CRC cell lines prior and subsequent to 5-aza-dC treatment were combined with the CRC-specific gene expression profiling array data...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28928474/using-experimental-evolution-to-identify-druggable-targets-that-could-inhibit-the-evolution-of-antimicrobial-resistance
#15
Heer H Mehta, Amy G Prater, Yousif Shamoo
With multi-drug and pan-drug-resistant bacteria becoming increasingly common in hospitals, antibiotic resistance has threatened to return us to a pre-antibiotic era that would completely undermine modern medicine. There is an urgent need to develop new antibiotics and strategies to combat resistance that are substantially different from earlier drug discovery efforts. One such strategy that would complement current and future antibiotics would be a class of co-drugs that target the evolution of resistance and thereby extend the efficacy of specific classes of antibiotics...
September 20, 2017: Journal of Antibiotics
https://www.readbyqxmd.com/read/28928460/molecular-dissection-of-transcriptional-reprogramming-of-steviol-glycosides-synthesis-in-leaf-tissue-during-developmental-phase-transitions-in-stevia-rebaudiana-bert
#16
Gopal Singh, Gagandeep Singh, Pradeep Singh, Rajni Parmar, Navgeet Paul, Radhika Vashist, Mohit Kumar Swarnkar, Ashok Kumar, Sanatsujat Singh, Anil Kumar Singh, Sanjay Kumar, Ram Kumar Sharma
Stevia is a natural source of commercially important steviol glycosides (SGs), which share biosynthesis route with gibberellic acids (GAs) through plastidal MEP and cytosolic MVA pathways. Ontogeny-dependent deviation in SGs biosynthesis is one of the key factor for global cultivation of Stevia, has not been studied at transcriptional level. To dissect underlying molecular mechanism, we followed a global transcriptome sequencing approach and generated more than 100 million reads. Annotation of 41,262 de novo assembled transcripts identified all the genes required for SGs and GAs biosynthesis...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28928409/modelling-sequences-and-temporal-networks-with-dynamic-community-structures
#17
Tiago P Peixoto, Martin Rosvall
In evolving complex systems such as air traffic and social organisations, collective effects emerge from their many components' dynamic interactions. While the dynamic interactions can be represented by temporal networks with nodes and links that change over time, they remain highly complex. It is therefore often necessary to use methods that extract the temporal networks' large-scale dynamic community structure. However, such methods are subject to overfitting or suffer from effects of arbitrary, a priori-imposed timescales, which should instead be extracted from data...
September 19, 2017: Nature Communications
https://www.readbyqxmd.com/read/28928185/comparative-effectiveness-of-injectable-penicillin-versus-a-combination-of-penicillin-and-gentamicin-in-children-with-pneumonia-characterised-by-indrawing-in-kenya-protocol-for-an-observational-study
#18
Lucas Malla, Rafael Perera-Salazar, Emily McFadden, Mike English
INTRODUCTION: WHO treatment guidelines are widely recommended for guiding treatment for millions of children with pneumonia every year across multiple low-income and middle-income countries. Guidelines are based on synthesis of available evidence that provides moderate certainty in evidence of effects for forms of pneumonia that can result in hospitalisation. However, trials have included fewer children from Africa than other settings, and it is suggested that African children with pneumonia have higher mortality...
September 18, 2017: BMJ Open
https://www.readbyqxmd.com/read/28928112/influenzanet-citizens-among-10-countries-collaborating-to-monitor-influenza-in-europe
#19
Carl E Koppeschaar, Vittoria Colizza, Caroline Guerrisi, Clément Turbelin, Jim Duggan, W John Edmunds, Charlotte Kjelsø, Ricardo Mexia, Yamir Moreno, Sandro Meloni, Daniela Paolotti, Daniela Perrotta, Edward van Straten, Ana O Franco
BACKGROUND: The wide availability of the Internet and the growth of digital communication technologies have become an important tool for epidemiological studies and health surveillance. Influenzanet is a participatory surveillance system monitoring the incidence of influenza-like illness (ILI) in Europe since 2003. It is based on data provided by volunteers who self-report their symptoms via the Internet throughout the influenza season and currently involves 10 countries. OBJECTIVE: In this paper, we describe the Influenzanet system and provide an overview of results from several analyses that have been performed with the collected data, which include participant representativeness analyses, data validation (comparing ILI incidence rates between Influenzanet and sentinel medical practice networks), identification of ILI risk factors, and influenza vaccine effectiveness (VE) studies previously published...
September 19, 2017: JMIR Public Health and Surveillance
https://www.readbyqxmd.com/read/28927989/identification-of-susceptible-genes-for-complex-chronic-diseases-based-on-disease-risk-functional-snps-and-interaction-networks
#20
Wan Li, Lina Zhu, Hao Huang, Yuehan He, Junjie Lv, Weimin Li, Lina Chen, Weiming He
Complex chronic diseases are caused by the effects of genetic and environmental factors. Single nucleotide polymorphisms (SNPs), one common type of genetic variations, played vital roles in diseases. We hypothesized that disease risk functional SNPs in coding regions and protein interaction network modules were more likely to contribute to the identification of disease susceptible genes for complex chronic diseases. This could help to further reveal the pathogenesis of complex chronic diseases. Disease risk SNPs were first recognized from public SNP data for coronary heart disease (CHD), hypertension (HT) and type 2 diabetes (T2D)...
September 16, 2017: Journal of Biomedical Informatics
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