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https://www.readbyqxmd.com/read/29156765/network-directed-cis-mediator-analysis-of-normal-prostate-tissue-expression-profiles-reveals-downstream-regulatory-associations-of-prostate-cancer-susceptibility-loci
#1
Nicholas B Larson, Shannon K McDonnell, Zach Fogarty, Melissa C Larson, John Cheville, Shaun Riska, Saurabh Baheti, Alexandra M Weber, Asha A Nair, Liang Wang, Daniel O'Brien, Jaime Davila, Daniel J Schaid, Stephen N Thibodeau
Large-scale genome-wide association studies have identified multiple single-nucleotide polymorphisms associated with risk of prostate cancer. Many of these genetic variants are presumed to be regulatory in nature; however, follow-up expression quantitative trait loci (eQTL) association studies have to-date been restricted largely to cis-acting associations due to study limitations. While trans-eQTL scans suffer from high testing dimensionality, recent evidence indicates most trans-eQTL associations are mediated by cis-regulated genes, such as transcription factors...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156709/using-molecular-functional-networks-to-manifest-connections-between-obesity-and-obesity-related-diseases
#2
Jialiang Yang, Jing Qiu, Kejing Wang, Lijuan Zhu, Jingjing Fan, Deyin Zheng, Xiaodi Meng, Jiasheng Yang, Lihong Peng, Yu Fu, Dahan Zhang, Shouneng Peng, Haiyun Huang, Yi Zhang
Obesity is a primary risk factor for many diseases such as certain cancers. In this study, we have developed three algorithms including a random-walk based method OBNet, a shortest-path based method OBsp and a direct-overlap method OBoverlap, to reveal obesity-disease connections at protein-interaction subnetworks corresponding to thousands of biological functions and pathways. Through literature mining, we also curated an obesity-associated disease list, by which we compared the methods. As a result, OBNet outperforms other two methods...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156521/micrornas-as-novel-biomarkers-for-colorectal-cancer-new-outlooks
#3
REVIEW
Naghmeh Shirafkan, Behzad Mansoori, Ali Mohammadi, Navid Shomali, Mehri Ghasbi, Behzad Baradaran
Colorectal cancer is one of the most prevalent cancers with high mortality in the world. MicroRNAs are a class of small non-coding RNAs that regulate gene expression through targeting mRNAs. MicroRNAs involve in many biological and pathological processes such as cell growth, differentiation, apoptosis. etc. Dysregulation of miRNAs expression patterns have been reported in many tumors including Colorectal Cancer. Various studies indicate that miRNAs can be utilized as diagnostic and prognostic biomarkers for evaluation of tumor initiation, development, invasion, metastasis and response to chemotherapeutic drugs...
November 14, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29156375/downregulation-of-the-protein-synthesis-machinery-is-a-major-regulatory-event-during-early-adipogenic-differentiation-of-human-adipose-derived-stromal-cells
#4
Bruna H Marcon, Fabíola B Holetz, Guillermo Eastman, Ana Carolina Origa-Alves, Mariana Andrea Amorós, Alessandra Melo de Aguiar, Carmen K Rebelatto, Paulo R S Brofman, Jose Sotelo-Silveira, Bruno Dallagiovanna
Commitment of adult stem cells involves the activation of specific gene networks regulated from transcription to protein synthesis. Here, we used ribosome profiling to identify mRNAs regulated at the translational level, through both differential association to polysomes and modulation of their translational rates. We observed that translational regulation during the differentiation of human adipose-derived stromal cells (hASCs, also known as adipose-derived mesenchymal stem cells), a subset of which are stem cells, to adipocytes was a major regulatory event...
November 1, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/29156196/familial-myelodysplastic-syndrome-acute-myeloid-leukemia
#5
REVIEW
Jane E Churpek
A growing number of inherited genetic loci that contribute to myelodysplastic syndrome/acute myeloid leukemia (MDS/AML) development in both children as well as adults are rapidly being identified. In recognition of the clinical impact of this emerging field, the World Health Organization, National Comprehensive Cancer Network, and European LeukemiaNet have all added consideration of inherited predisposition to MDS/AML classification and management. Study of these disorders is providing unique insight into the biology of both sporadic and familial MDS/AML...
December 2017: Best Practice & Research. Clinical Haematology
https://www.readbyqxmd.com/read/29155944/molecular-interaction-search-tool-mist-an-integrated-resource-for-mining-gene-and-protein-interaction-data
#6
Yanhui Hu, Arunachalam Vinayagam, Ankita Nand, Aram Comjean, Verena Chung, Tong Hao, Stephanie E Mohr, Norbert Perrimon
Model organism and human databases are rich with information about genetic and physical interactions. These data can be used to interpret and guide the analysis of results from new studies and develop new hypotheses. Here, we report the development of the Molecular Interaction Search Tool (MIST; http://fgrtools.hms.harvard.edu/MIST/). The MIST database integrates biological interaction data from yeast, nematode, fly, zebrafish, frog, rat and mouse model systems, as well as human. For individual or short gene lists, the MIST user interface can be used to identify interacting partners based on protein-protein and genetic interaction (GI) data from the species of interest as well as inferred interactions, known as interologs, and to view a corresponding network...
November 16, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29155820/mass-spectrometry-based-quantification-of-the-cellular-response-to-ultraviolet-radiation-in-hela-cells
#7
Hong Xu, Xuanyi Chen, Nanjiao Ying, Meixia Wang, Xiaoli Xu, Rongyi Shi, Yuejin Hua
Ultraviolet (UV) irradiation is a common form of DNA damage that can cause pyrimidine dimers between DNA, which can cause gene mutations, even double-strand breaks and threaten genome stability. If DNA repair systems default their roles at this stage, the organism can be damaged and result in disease, especially cancer. To better understand the cellular response to this form of damage, we applied highly sensitive mass spectrometry to perform comparative proteomics of phosphorylation in HeLa cells. A total of 4367 phosphorylation sites in 2100 proteins were identified, many of which had not been reported previously...
2017: PloS One
https://www.readbyqxmd.com/read/29155710/dna-nanotubes-as-a-versatile-tool-to-study-semiflexible-polymers
#8
Jörg Schnauß, Martin Glaser, Jessica S Lorenz, Carsten Schuldt, Christin Möser, Martin Sajfutdinow, Tina Händler, Josef A Käs, David M Smith
Mechanical properties of complex, polymer-based soft matter, such as cells or biopolymer networks, can be understood in neither the classical frame of flexible polymers nor of rigid rods. Underlying filaments remain outstretched due to their non-vanishing backbone stiffness, which is quantified via the persistence length (lp), but they are also subject to strong thermal fluctuations. Their finite bending stiffness leads to unique, non-trivial collective mechanics of bulk networks, enabling the formation of stable scaffolds at low volume fractions while providing large mesh sizes...
October 25, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155653/enhancing-laboratory-response-network-capacity-in-south-korea
#9
J Todd Parker, Ann-Christian Juren, Luis Lowe, Scott Santibañez, Gi-Eun Rhie, Toby L Merlin
Laboratory Response Network (LRN) laboratories help protect populations from biological and chemical public health threats. We examined the role of LRN biological laboratories in enhancing capacity to detect and respond to public health infectious disease emergencies in South Korea. The model for responding to infectious disease emergencies leverages standardized laboratory testing procedures, a repository of standardized testing reagents, laboratory testing cooperation among hospital sentinel laboratories and reference laboratories, and maintenance of a trained workforce through traditional and on-demand training...
October 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29155562/quantification-of-nanomaterial-nanomedicine-trafficking-in-vivo
#10
Liming Wang, Liang Yan, Jing Liu, Chunying Chen, Yuliang Zhao
Absorption, distribution, metabolism and excretion (ADME) of nanomaterials (NMs) or nanomedicines (NMs), are fundamental biological processes that dominate their nanomedical functions or nanotoxicities. Mostly, NMs exist in biological systems as a form of nanoparticles (NPs). However, to determine the composition, spatial distribution, and states of existence of NMs/NPs in vivo, upon entry into the body, as well as to monitor the dynamic changes of these information over time remain a challenge for the current analytical methodology due to their limited efficiently in characterizing interactions between these complex(nano)-complex(bio) systems...
November 20, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29155333/ima-identifying-disease-related-genes-using-mesh-terms-and-association-rules
#11
Jeongwoo Kim, Changbae Bang, Hyeonseo Hwang, Doyoung Kim, Chihyun Park, Sanghyun Park
Genes play an important role in several diseases. Hence, in biology, identifying relationships between diseases and genes is important for the analysis of diseases, because mutated or dysregulated genes play an important role in pathogenesis. Here, we propose a method to identify disease-related genes using MeSH terms and association rules. We identified genes by analyzing the MeSH terms and extracted information on gene-gene interactions based on association rules. By integrating the extracted interactions, we constructed gene-gene networks and identified disease-related genes...
November 15, 2017: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29154777/an-attempt-to-understand-glioma-stem-cell-biology-through-centrality-analysis-of-a-protein-interaction-network
#12
Mrinmay Kumar Mallik
No abstract text is available yet for this article.
November 14, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/29154475/identification-and-analysis-of-a-key-long-non-coding-rnas-lncrnas-associated-module-reveal-functional-lncrnas-in-cardiac-hypertrophy
#13
Jian Zhang, Chenchen Feng, Chao Song, Bo Ai, Xuefeng Bai, Yuejuan Liu, Xuecang Li, Jianmei Zhao, Shengshu Shi, Xin Chen, Xiaojie Su, Chunquan Li
Cardiac hypertrophy (CH) is a common disease that originates from long-term heart pressure overload and finally leads to heart failure. Recently, long non-coding RNAs (lncRNAs) have attracted attention because they have broad and crucial functions in regulating complex biological processes. Some studies had found that lncRNAs play vital roles in complex cardiovascular diseases. However, the function and mechanism of lncRNAs in CH have not been elucidated. In our study, to investigate the potential roles of lncRNAs in CH, the Cardiac Hypertrophy-associated LncRNAs-Protein coding genes Network (CHLPN) was constructed by integrating gene microarray re-annotation and subpathway enrichment analyses...
November 20, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29154163/upstairs-downstairs-spatial-regulation-of-hippo-signalling
#14
REVIEW
Alexander Fulford, Nicolas Tapon, Paulo S Ribeiro
Cellular signalling lies at the heart of every decision involved in the development and homeostasis of multicellular organisms. The Hippo pathway was discovered nearly two decades ago through seminal work in Drosophila and rapidly emerged as a crucial signalling network implicated in developmental and oncogenic growth, tissue regeneration and stem cell biology. Here, we review recent advances in the field relating to the upstream regulation of Hippo signalling and the intracellular tug-of-war that tightly controls its main target, the transcriptional co-activator Yorkie/YAP...
November 16, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/29154065/does-nurses-role-health-or-symptoms-influence-their-personal-use-of-ingestible-complementary-and-alternative-medicines
#15
Sofia Dimitrelis, Lin Perry, Robyn Gallagher, Christine Duffield, David Sibbritt, Rachel Nicholls, Xiaoyue Xu
OBJECTIVES: To investigate the influence of work-related characteristics, health, health behaviours and symptoms on ingestible biologically-based Complementary and Alternative Medicine (CAM) use within the Australian nursing and midwifery workforce. BACKGROUND: CAM use is widespread worldwide, but there is little research into nurses' and midwives' personal use of ingestible CAM in Australia. METHODS: An online survey in 2014-15 used validated instruments and items to examine use of ingestible biologically-based CAM (herbs, foods and vitamins, minerals, amino acids, enzymes and other supplements), and the health and work-related characteristics of 5041 nurses and midwives recruited through the New South Wales Nurses and Midwives Association and professional networks...
December 2017: Complementary Therapies in Medicine
https://www.readbyqxmd.com/read/29153892/penalized-estimation-of-sparse-concentration-matrices-based-on-prior-knowledge-with-applications-to-placenta-elemental-data
#16
Jai Woo Lee, Tracy Punshon, Erika L Moen, Margaret R Karagas, Jiang Gui
Identifying patterns of association or dependency among high-dimensional biological datasets with sparse precision matrices remains a challenge. In this paper, we introduce a weighted sparse Gaussian graphical model that can incorporate prior knowledge to infer the structure of the network of trace element concentrations, including essential elements as well as toxic metals and metaloids measured in the human placentas. We present the weighted L1 penalized regularization procedure for estimating the sparse precision matrix in the setting of Gaussian graphical models...
November 4, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29153862/tumor-necrosis-factor-alpha-in-sleep-regulation
#17
REVIEW
Matthew D Rockstrom, Liangyu Chen, Ping Taishi, Joseph T Nguyen, Cody M Gibbons, Sigrid C Veasey, James M Krueger
This review details tumor necrosis factor alpha (TNF) biology and its role in sleep, and describes how TNF medications influence sleep/wake activity. Substantial evidence from healthy young animals indicates acute enhancement or inhibition of endogenous brain TNF respectively promotes and inhibits sleep. In contrast, the role of TNF in sleep in most human studies involves pathological conditions associated with chronic elevations of systemic TNF and disrupted sleep. Normalization of TNF levels in such patients improves sleep...
November 16, 2017: Sleep Medicine Reviews
https://www.readbyqxmd.com/read/29153315/what-are-the-keys-to-a-longer-happier-life-answers-from-five-decades-of-health-psychology-research
#18
Blair T Johnson, Rebecca L Acabchuk
RATIONALE: It has long been known that factors of the mind and of interpersonal relationships influence health, but it is only in the last 50 years that an independent scientific field of health psychology appeared, dedicated to understanding psychological and behavioral processes in health, illness, and healthcare. OBJECTIVE AND METHOD: This article (a) reviews important research that answers the question of how human beings can have longer, happier lives; and (b) highlights trends in health psychology featuring articles in Social Science & Medicine as well as other related literature...
November 4, 2017: Social Science & Medicine
https://www.readbyqxmd.com/read/29152808/observational-safety-study-of-specific-outcomes-after-trivalent-cell-culture-seasonal-influenza-vaccination-optaflu-%C3%A2-among-adults-in-thin-database-of-electronic-uk-primary-healthcare-records
#19
Gillian C Hall, Paul T G Davies, M Yousuf Karim, Mendel D M Haag, Caroline O'Leary
PURPOSE: To investigate the safety of trivalent seasonal influenza vaccine (TIVc) (Optaflu(®) ), the first cell culture seasonal trivalent influenza vaccine available in Europe. METHODS: Codes and unstructured text in adult electronic healthcare records (The Health Improvement Network) were searched for a TIVc brand name or batch number and possible outcomes within a 3 month pre- to 6 month post-TIVc exposure study period (2012-2015). The outcomes were severe allergic reactions, Bell's palsy, convulsions, demyelination, paresthesia, noninfectious encephalitis, neuritis (optic and brachial), vasculitis, inflammatory bowel disease, and thrombocytopenia...
November 20, 2017: Pharmacoepidemiology and Drug Safety
https://www.readbyqxmd.com/read/29152692/left-frontoparietal-network-activity-is-modulated-by-drug-stimuli-in-cocaine-addiction
#20
Víctor Costumero, Patricia Rosell-Negre, Juan Carlos Bustamante, Paola Fuentes-Claramonte, Juan José Llopis, Cesar Ávila, Alfonso Barrós-Loscertales
Cocaine addicts present reduced activity in the left frontoparietal network, a brain network associated with cognitive control, during the processing of non-drug reward related stimuli (Costumero et al., Addiction Biology 22:479-489, 2015). However, the involvement of this network in drug-related stimuli processing remains unclear. Here, fifteen cocaine-dependent men and fifteen healthy matched controls viewed cocaine-related, erotic, aversive, and neutral pictures during an fMRI session. Group independent component analysis was then performed to investigate how functional networks were modulated by the different emotional images...
November 20, 2017: Brain Imaging and Behavior
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