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https://www.readbyqxmd.com/read/29331675/module-analysis-captures-pancancer-genetically-and-epigenetically-deregulated-cancer-driver-genes-for-smoking-and-antiviral-response
#1
Magali Champion, Kevin Brennan, Tom Croonenborghs, Andrew J Gentles, Nathalie Pochet, Olivier Gevaert
The availability of increasing volumes of multi-omics profiles across many cancers promises to improve our understanding of the regulatory mechanisms underlying cancer. The main challenge is to integrate these multiple levels of omics profiles and especially to analyze them across many cancers. Here we present AMARETTO, an algorithm that addresses both challenges in three steps. First, AMARETTO identifies potential cancer driver genes through integration of copy number, DNA methylation and gene expression data...
December 1, 2017: EBioMedicine
https://www.readbyqxmd.com/read/29329368/discovering-personalized-driver-mutation-profiles-of-single-samples-in-cancer-by-network-control-strategy
#2
Wei-Feng Guo, Shao-Wu Zhang, Li-Li Liu, Fei Liu, Qian-Qian Shi, Lei Zhang, Ying Tang, Tao Zeng, Luonan Chen
Motivation: It is a challenging task to discover personalized driver genes that provide crucial information on disease risk and drug sensitivity for individual patients. However, few methods have been proposed to identify the personalized-sample driver genes from the cancer omics data due to the lack of samples for each individual. To circumvent this problem, here we present a novel single-sample controller strategy (SCS) to identify personalized driver mutation profiles from network controllability perspective...
January 10, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29328914/rewiring-of-the-fruit-metabolome-in-tomato-breeding
#3
Guangtao Zhu, Shouchuang Wang, Zejun Huang, Shuaibin Zhang, Qinggang Liao, Chunzhi Zhang, Tao Lin, Mao Qin, Meng Peng, Chenkun Yang, Xue Cao, Xu Han, Xiaoxuan Wang, Esther van der Knaap, Zhonghua Zhang, Xia Cui, Harry Klee, Alisdair R Fernie, Jie Luo, Sanwen Huang
Humans heavily rely on dozens of domesticated plant species that have been further improved through intensive breeding. To evaluate how breeding changed the tomato fruit metabolome, we have generated and analyzed a dataset encompassing genomes, transcriptomes, and metabolomes from hundreds of tomato genotypes. The combined results illustrate how breeding globally altered fruit metabolite content. Selection for alleles of genes associated with larger fruits altered metabolite profiles as a consequence of linkage with nearby genes...
January 11, 2018: Cell
https://www.readbyqxmd.com/read/29328543/the-sarda-sheep-host-fecal-proteome
#4
Antonio Palomba, Alessandro Tanca, Maria Filippa Addis, Daniela Pagnozzi, Sergio Uzzau
We recently reported the first characterization of the sheep fecal microbiota, obtained by using a multi-meta-omic approach. Here, the mass spectra generated by single-run LC/high-resolution MS in the context of that study were reanalyzed using a host-specific database, in order to gain insights for the first time into the host fecal proteome of healthy Sarda sheep. On the whole, 5349 non-redundant tryptic peptide sequences were identified, belonging to 1046 different proteins. The "core" fecal proteome (common to all animals) comprised 431 proteins, mainly related to biological processes as immune response and proteolysis...
January 12, 2018: Proteomics
https://www.readbyqxmd.com/read/29327330/microbiome-analysis-and-omics-studies-of-microbial-denitrification-processes-in-wastewater-treatment-recent-advances
#5
REVIEW
Lili Miao, Zhipei Liu
Nitrogen pollution is an increasingly severe worldwide problem because of drainage of nitrogen-containing wastewater and intensive application of nitrogen-containing fertilizers. Denitrification, a key process in nitrogen cycles, is commonly employed for nitrogen removal in engineered wastewater treatment systems. Biological denitrification is performed by denitrifying microbes (bacteria) that use nitrate as terminal electron acceptor. Better understanding the functions of diverse microbial populations in denitrification-based wastewater treatment systems, and the interactions of these populations with operating environments, is essential for improving both treatment performance and system stability...
January 9, 2018: Science China. Life Sciences
https://www.readbyqxmd.com/read/29326176/combinatorial-omics-analysis-reveals-perturbed-lysosomal-homeostasis-in-collagen-vii-deficient-keratinocytes
#6
Kerstin Thriene, Björn Andreas Grüning, Olivier Bornert, Anika Erxleben, Juna Leppert, Ioannis Athanasiou, Ekkehard Weber, Dimitra Kiritsi, Alexander Nyström, Thomas Reinheckel, Rolf Backofen, Cristina Has, Leena Bruckner-Tuderman, Joern Dengjel
The extracellular matrix protein collagen VII is part of the microenvironment of stratified epithelia and critical in organismal homeostasis. Mutations in the encoding gene COL7A1 lead to the skin disorder dystrophic epidermolysis bullosa (DEB), are linked to skin fragility and progressive inflammation-driven fibrosis that facilitates aggressive skin cancer. So far, these changes have been linked to mesenchymal alterations, the epithelial consequences of collagen VII loss remaining under-addressed. As epithelial dysfunction is a principal initiator of fibrosis, we performed a comprehensive transcriptome and proteome profiling of primary human keratinocytes to generate global and detailed images of dysregulated epidermal molecular pathways linked to loss of collagen VII...
January 11, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29325450/symptom-science-omics-supports-common-biological-underpinnings-across-symptoms
#7
Maura K McCall, Ansley Grimes Stanfill, Elizabeth Skrovanek, Jessica Renee Pforr, Susan W Wesmiller, Yvette P Conley
For precision health care to be successful, an in-depth understanding of the biological mechanisms for symptom development and severity is essential. Omics-based research approaches facilitate identification of the biological underpinnings of symptoms. We reviewed literature for omics-based approaches and exemplar symptoms (sleep disruption, cognitive impairment, fatigue, gastrointestinal [GI] distress, and pain) to identify genes associated with the symptom or symptoms across disease processes. The review yielded 27 genes associated with more than one symptom...
January 1, 2018: Biological Research for Nursing
https://www.readbyqxmd.com/read/29325019/deep-molecular-phenotypes-link-complex-disorders-and-physiological-insult-to-cpg-methylation
#8
Shaza B Zaghlool, Dennis O Mook-Kanamori, Sara Kader, Nisha Stephan, Anna Halama, Rudolf Engelke, Hina Sarwath, Eman K Al-Dous, Yasmin A Mohamoud, Werner Roemisch-Margl, Jerzy Adamski, Gabi Kastenmüller, Nele Friedrich, Alessia Visconti, Pei-Chien Tsai, Tim Spector, Jordana Bell, Mario Falchi, Annika Wahl, Melanie Waldenberger, Annette Peters, Christian Gieger, Maija Pezer, Gordan Lauc, Johannes Graumann, Joel A Malek, Karsten Suhre
Epigenetic regulation of cellular function provides a mechanism for rapid organismal adaptation to changes in health, lifestyle, and environment. Associations of cytosine-guanine di-nucleotide (CpG) methylation with clinical endpoints that overlap with metabolic phenotypes suggest a regulatory role for these CpG sites in the body's response to disease or environmental stress. We previously identified 20 CpG sites in an epigenome-wide association study (EWAS) with metabolomics that were also associated in recent EWASs with diabetes-, obesity-, and smoking-related endpoints...
January 8, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29324394/effects-of-ocean-acidification-on-copepods
#9
REVIEW
Minghua Wang, Chang-Bum Jeong, Young Hwan Lee, Jae-Seong Lee
Ocean acidification (OA) leads to significant changes in seawater carbon chemistry, broadly affects marine organisms, and considered as a global threat to the fitness of marine ecosystems. Due to the crucial role of copepods in marine food webs of transferring energy from primary producers to higher trophic levels, numerous studies have been conducted to examine the impacts of OA on biological traits of copepods such as growth and reproduction. Under OA stress, the copepods demonstrated species-specific and stage-dependent responses...
January 5, 2018: Aquatic Toxicology
https://www.readbyqxmd.com/read/29324045/neuroparasitology-of-parasite-insect-associations
#10
David P Hughes, Frederic Libersat
Insect behavior can be manipulated by parasites, and in many cases, such manipulation involves the central and peripheral nervous system. Neuroparasitology is an emerging branch of biology that deals with parasites that can control the nervous system of their host. The diversity of parasites that can manipulate insect behavior ranges from viruses to macroscopic worms and also includes other insects that have evolved to become parasites (notably, parasitic wasps). It is remarkable that the precise manipulation observed does not require direct entry into the insect brain and can even occur when the parasite is outside the body...
January 7, 2018: Annual Review of Entomology
https://www.readbyqxmd.com/read/29323249/probabilistic-data-integration-identifies-reliable-gametocyte-specific-proteins-and-transcripts-in-malaria-parasites
#11
Lisette Meerstein-Kessel, Robin van der Lee, Will Stone, Kjerstin Lanke, David A Baker, Pietro Alano, Francesco Silvestrini, Chris J Janse, Shahid M Khan, Marga van de Vegte-Bolmer, Wouter Graumans, Rianne Siebelink-Stoter, Taco W A Kooij, Matthias Marti, Chris Drakeley, Joseph J Campo, Teunis J P van Dam, Robert Sauerwein, Teun Bousema, Martijn A Huynen
Plasmodium gametocytes are the sexual forms of the malaria parasite essential for transmission to mosquitoes. To better understand how gametocytes differ from asexual blood-stage parasites, we performed a systematic analysis of available 'omics data for P. falciparum and other Plasmodium species. 18 transcriptomic and proteomic data sets were evaluated for the presence of curated "gold standards" of 41 gametocyte-specific versus 46 non-gametocyte genes and integrated using Bayesian probabilities, resulting in gametocyte-specificity scores for all P...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322918/a-linear-programming-computational-framework-integrates-phosphor-proteomics-and-prior-knowledge-to-predict-drug-efficacy
#12
Zhiwei Ji, Bing Wang, Ke Yan, Ligang Dong, Guanmin Meng, Lei Shi
BACKGROUND: In recent years, the integration of 'omics' technologies, high performance computation, and mathematical modeling of biological processes marks that the systems biology has started to fundamentally impact the way of approaching drug discovery. The LINCS public data warehouse provides detailed information about cell responses with various genetic and environmental stressors. It can be greatly helpful in developing new drugs and therapeutics, as well as improving the situations of lacking effective drugs, drug resistance and relapse in cancer therapies, etc...
December 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29320604/reconstruction-of-molecular-network-evolution-from-cross-sectional-omics-data
#13
Mehran Aflakparast, Mathisca C M de Gunst, Wessel N van Wieringen
Cross-sectional studies may shed light on the evolution of a disease like cancer through the comparison of patient traits among disease stages. This problem is especially challenging when a gene-gene interaction network needs to be reconstructed from omics data, and, in addition, the patients of each stage need not form a homogeneous group. Here, the problem is operationalized as the estimation of stage-wise mixtures of Gaussian graphical models (GGMs) from high-dimensional data. These mixtures are fitted by a (fused) ridge penalized EM algorithm...
January 10, 2018: Biometrical Journal. Biometrische Zeitschrift
https://www.readbyqxmd.com/read/29319603/population-neuroscience-dementia-epidemiology-serving-precision-medicine-and-population-health
#14
Mary Ganguli, Emiliano Albanese, Sudha Seshadri, David A Bennett, Constantine Lyketsos, Walter A Kukull, Ingmar Skoog, Hugh C Hendrie
Over recent decades, epidemiology has made significant contributions to our understanding of dementia, translating scientific discoveries into population health. Here, we propose reframing dementia epidemiology as "population neuroscience," blending techniques and models from contemporary neuroscience with those of epidemiology and biostatistics. On the basis of emerging evidence and newer paradigms and methods, population neuroscience will minimize the bias typical of traditional clinical research, identify the relatively homogenous subgroups that comprise the general population, and investigate broader and denser phenotypes of dementia and cognitive impairment...
January 9, 2018: Alzheimer Disease and Associated Disorders
https://www.readbyqxmd.com/read/29318371/proteomics-and-transcriptomics-in-atrial-fibrillation
#15
REVIEW
Marc Sühling, Carmen Wolke, Christian Scharf, Uwe Lendeckel
Atrial fibrillation (AF) is the most common tachyarrhythmia. AF, due to substantial remodeling processes initiated in the atria, is a typically self-sustaining and progressive disease. Atrial remodeling has been intensively investigated at the molecular level in recent decades. Although the application of "omics" technologies has already significantly contributed to our current understanding of the pathophysiology of AF, the complexity of the latter and the large heterogeneity of AF patients remained a major limitation...
January 9, 2018: Herzschrittmachertherapie & Elektrophysiologie
https://www.readbyqxmd.com/read/29317621/integrated-omics-dissection-of-proteome-dynamics-during-cardiac-remodeling
#16
Edward Lau, Quan Cao, Maggie P Y Lam, Jie Wang, Dominic C M Ng, Brian J Bleakley, Jessica M Lee, David A Liem, Ding Wang, Henning Hermjakob, Peipei Ping
Transcript abundance and protein abundance show modest correlation in many biological models, but how this impacts disease signature discovery in omics experiments is rarely explored. Here we report an integrated omics approach, incorporating measurements of transcript abundance, protein abundance, and protein turnover to map the landscape of proteome remodeling in a mouse model of pathological cardiac hypertrophy. Analyzing the hypertrophy signatures that are reproducibly discovered from each omics data type across six genetic strains of mice, we find that the integration of transcript abundance, protein abundance, and protein turnover data leads to 75% gain in discovered disease gene candidates...
January 9, 2018: Nature Communications
https://www.readbyqxmd.com/read/29317511/exploration-of-the-germline-genome-of-the-ciliate-chilodonella-uncinata-through-single-cell-omics-transcriptomics-and-genomics
#17
Xyrus X Maurer-Alcalá, Rob Knight, Laura A Katz
Separate germline and somatic genomes are found in numerous lineages across the eukaryotic tree of life, often separated into distinct tissues (e.g., in plants, animals, and fungi) or distinct nuclei sharing a common cytoplasm (e.g., in ciliates and some foraminifera). In ciliates, germline-limited (i.e., micronuclear-specific) DNA is eliminated during the development of a new somatic (i.e., macronuclear) genome in a process that is tightly linked to large-scale genome rearrangements, such as deletions and reordering of protein-coding sequences...
January 9, 2018: MBio
https://www.readbyqxmd.com/read/29317475/omics-assisted-n-terminal-proteoform-and-protein-expression-profiling-upon-methionine-aminopeptidase-1-metap1-deletion
#18
Veronique Jonckheere, Daria Fijałkowska, Petra Van Damme
Excision of the N-terminal initiator methionine (iMet) residue from nascent peptide chains is an essential and omnipresent protein modification carried out by methionine aminopeptidases (MetAPs) that accounts for a major source of N-terminal proteoform diversity. While MetAP2 is known to be implicated in processes such as angiogenesis and proliferation in mammals, the physiological role of MetAP1 is much less clear. In this report we studied the omics-wide effects of human MetAP1 deletion and general MetAP inhibition...
January 9, 2018: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/29317273/mitochondrial-network-responses-in-oxidative-physiology-and-disease
#19
REVIEW
Young-Mi Go, Jolyn Fernandes, Xin Hu, Karan Uppal, Dean P Jones
Mitochondrial activities are linked directly or indirectly to all cellular functions in aerobic eukaryotes. Omics methods enable new approaches to study functional organization of mitochondria and their adaptive and maladaptive network responses to bioenergetic fuels, physiologic demands, environmental challenges and aging. In this review, we consider mitochondria collectively within a multicellular organism as a macroscale "mitochondriome", functioning to organize bioenergetics and metabolism as an organism utilizes environmental resources and protects against environmental threats...
January 6, 2018: Free Radical Biology & Medicine
https://www.readbyqxmd.com/read/29316700/sea-anemones-quiet-achievers-in-the-field-of-peptide-toxins
#20
REVIEW
Peter J Prentis, Ana Pavasovic, Raymond S Norton
Sea anemones have been understudied as a source of peptide and protein toxins, with relatively few examined as a source of new pharmacological tools or therapeutic leads. This is surprising given the success of some anemone peptides that have been tested, such as the potassium channel blocker from Stichodactyla helianthus known as ShK. An analogue of this peptide, ShK-186, which is now known as dalazatide, has successfully completed Phase 1 clinical trials and is about to enter Phase 2 trials for the treatment of autoimmune diseases...
January 8, 2018: Toxins
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