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https://www.readbyqxmd.com/read/28087947/lichenized-fungi-and-the-evolution-of-symbiotic-organization
#1
Martin Grube, Mats Wedin
Lichen symbioses comprise a fascinating relationship between algae and fungi. The lichen symbiotic lifestyle evolved early in the evolution of ascomycetes and is also known from a few basidiomycetes. The ascomycete lineages have diversified in the lichenized stage to give rise to a tremendous variety of morphologies. Their thalli are often internally complex and stratified for optimized integration of algal and fungal metabolisms. Thalli are frequently colonized by specific nonlichenized fungi and occasionally also by other lichens...
December 2016: Microbiology Spectrum
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#2
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28079125/establishment-of-a-integrative-multi-omics-expression-database-ckddb-in-the-context-of-chronic-kidney-disease-ckd
#3
Marco Fernandes, Holger Husi
Complex human traits such as chronic kidney disease (CKD) are a major health and financial burden in modern societies. Currently, the description of the CKD onset and progression at the molecular level is still not fully understood. Meanwhile, the prolific use of high-throughput omic technologies in disease biomarker discovery studies yielded a vast amount of disjointed data that cannot be easily collated. Therefore, we aimed to develop a molecule-centric database featuring CKD-related experiments from available literature publications...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28078827/fam83-family-oncogenes-are-broadly-involved-in-human-cancers-an-integrative-multi-omics-approach
#4
Antoine M Snijders, Sun-Young Lee, Bo Hang, Wenshan Hao, Mina J Bissell, Jian-Hua Mao
The development of novel targeted therapies for cancer treatment requires identification of reliable targets. FAM83 ('family with sequence similarity 83') family members A, B, and D were shown recently to have oncogenic potential. However, the overall oncogenic abilities of FAM83 family genes remain largely unknown. Here, we used a systematic and integrative genomics approach to investigate oncogenic properties of the entire FAM83 family members. We assessed transcriptional expression patterns of eight FAM83 family genes (FAM83A-H) across tumor types, the relationship between their expression and changes in DNA copy number, and the association with patient survival...
October 26, 2016: Molecular Oncology
https://www.readbyqxmd.com/read/28078242/saffron-omics-the-challenges-of-integrating-omic-technologies
#5
REVIEW
Sameera Sastry Panchangam, Maryam Vahedi, Mohankumar Janardhan Megha, Anuj Kumar, Kaamini Raithatha, Raithatha Suravajhala, Pratap Reddy
Saffron is one of the highly exotic spices known for traditional values and antiquity. It is used for home décor besides serving as a colorant flavor and is widely known for medicinal value. Over the last few years, saffron has garnered a lot of interest due to its anti-cancer, anti-mutagenic, anti-oxidant and immunomodulatory properties. Integration of systems biology approaches with wide applications of saffron remains a growing challenge as new techniques and methods advance. Keeping in view of the dearth of a review summarizing the omics and systems biology of saffron, we bring an outline on advancements in integrating omic technologies, the medicinal plant has seen in recent times...
November 2016: Avicenna Journal of Phytomedicine
https://www.readbyqxmd.com/read/28077967/integrated-omics-analyses-reveal-the-details-of-metabolic-adaptation-of-clostridium-thermocellum-to-lignocellulose-derived-growth-inhibitors-released-during-the-deconstruction-of-switchgrass
#6
Suresh Poudel, Richard J Giannone, Miguel Rodriguez, Babu Raman, Madhavi Z Martin, Nancy L Engle, Jonathan R Mielenz, Intawat Nookaew, Steven D Brown, Timothy J Tschaplinski, David Ussery, Robert L Hettich
BACKGROUND: Clostridium thermocellum is capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe's growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand its metabolism on more complex, lignocellulosic substrates to identify relevant industrial bottlenecks that could undermine efficient biofuel production. To this end, we have examined a time course progression of C...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28075450/integrated-analysis-of-differentially-expressed-genes-and-pathways-in-triple%C3%A2-negative-breast-cancer
#7
Cancan Peng, Wenli Ma, Wei Xia, Wenling Zheng
Triple‑negative breast cancer (TNBC) is a heterogeneous disease characterized by an aggressive phenotype and reduced survival. The aim of the present study was to investigate the molecular mechanisms involved in the carcinogenesis of TNBC and to identify novel target molecules for therapy. The differentially expressed genes (DEGs) in TNBC and normal adjacent tissue were assessed by analyzing the GSE41970 microarray data using Qlucore Omics Explorer, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes...
January 4, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28069396/multi-level-evaluation-of-escherichia-coli-polyphosphate-related-mutants-using-global-transcriptomic-proteomic-and-phenomic-analyses
#8
Macarena Varas, Camilo Valdivieso, Cecilia Mauriaca, Javiera Ortíz-Severín, Alberto Paradela, Ignacio Poblete-Castro, Ricardo Cabrera, Francisco P Chávez
BACKGROUND: Polyphosphate (polyP) is a linear biopolymer found in all living cells. In bacteria, mutants lacking polyphosphate kinase 1 (PPK1), the enzyme responsible for synthesis of most polyP, have many structural and functional defects. However, little is known about the causes of these pleiotropic alterations. The link between ppk1 deletion and those numerous phenotypes observed can be the result of complex molecular interactions that can be elucidated via a systems biology approach...
January 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28065937/dynomics-to-identify-delays-and-co-expression-patterns-across-time-course-experiments
#9
Jasmin Straube, Bevan Emma Huang, Kim-Anh Lê Cao
Dynamic changes in biological systems can be captured by measuring molecular expression from different levels (e.g., genes and proteins) across time. Integration of such data aims to identify molecules that show similar expression changes over time; such molecules may be co-regulated and thus involved in similar biological processes. Combining data sources presents a systematic approach to study molecular behaviour. It can compensate for missing data in one source, and can reduce false positives when multiple sources highlight the same pathways...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28065881/an-integrated-transcriptomics-guided-genome-wide-promoter-analysis-and-next-generation-proteomics-approach-to-mine-factor-s-regulating-cellular-differentiation
#10
Kamal Mandal, Samuel L Bader, Pankaj Kumar, Dipankar Malakar, David S Campbell, Bhola Shankar Pradhan, Rajesh K Sarkar, Neerja Wadhwa, Souvik Sensharma, Vaibhav Jain, Robert L Moritz, Subeer S Majumdar
Differential next-generation-omics approaches aid in the visualization of biological processes and pave the way for divulging important events and/or interactions leading to a functional output at cellular or systems level. To this end, we undertook an integrated Nextgen transcriptomics and proteomics approach to divulge differential gene expression of infant and pubertal rat Sertoli cells (Sc).Unlike, pubertal Sc, infant Sc are immature and fail to support spermatogenesis. We found exclusive association of 14 and 19 transcription factor binding sites to infantile and pubertal states of Sc, respectively, using differential transcriptomics-guided genome-wide computational analysis of relevant promoters employing 220 Positional Weight Matrices from the TRANSFAC database...
January 8, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28049741/integrating-omics-and-alternative-splicing-reveals-insights-into-grape-response-to-high-temperature
#11
Jianfu Jiang, Xinna Liu, Guotian Liu, Chonghuai Liu, Shaohua Li, Lijun Wang
Heat stress is one of the primary abiotic stresses that limit crop production. Grape is a cultivated fruit with high economic value throughout the world, with its growth and development often influenced by high temperature. Alternative splicing (AS) is a widespread phenomenon increasing transcriptome and proteome diversity. We conducted high temperature treatments (35oC, 40oC and 45oC) on grapevines (Vitis vinifera), and assessed transcriptomic (especially AS) and proteomic changes in leaves. We found that nearly 70% of the genes were alternatively spliced under high temperature...
January 3, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28042536/central-nodes-in-protein-interaction-networks-drive-critical-functions-in-transforming-growth-factor-beta-1-stimulated-kidney-cells
#12
Reyhaneh Rabieian, Maryam Abedi, Yousof Gheisari
OBJECTIVE: Despite the huge efforts, chronic kidney disease (CKD) remains as an unsolved problem in medicine. Many studies have shown a central role for transforming growth factor beta-1 (TGFβ-1) and its downstream signaling cascades in the pathogenesis of CKD. In this study, we have reanalyzed a microarray dataset to recognize critical signaling pathways controlled by TGFβ-1. MATERIALS AND METHODS: This study is a bioinformatics reanalysis for a microarray data...
2017: Cell Journal
https://www.readbyqxmd.com/read/28039431/data-integration-in-physiology-using-bayes-rule-and-minimum-bayes-factors-deubiquitylating-enzymes-in-the-renal-collecting-duct
#13
Zhe Xue, Jia-Xu Chen, Yue Zhao, Barbara Medvar, Mark A Knepper
A major challenge in physiology is to exploit the many large-scale datasets available from "-omic" studies in order to seek answers to key physiological questions. In previous studies, Bayes' Theorem has been used for this purpose. This approach requires a means to map continuously distributed experimental data to probabilities (likelihood values) in order to derive posterior probabilities from the combination of prior probabilities and new data. Here, we introduce the use of Minimum Bayes' Factors for this purpose and illustrate the approach by addressing a physiological question, "Which deubiquitylating enzymes (DUBs) encoded by mammalian genomes are most likely to regulate plasma membrane transport processes in renal cortical collecting duct principal cells?" To do this, we have created a comprehensive online database of 110 DUBs present in the mammalian genome (https://hpcwebapps...
December 30, 2016: Physiological Genomics
https://www.readbyqxmd.com/read/28038993/inflammaging-and-omics-in-human-longevity
#14
REVIEW
Daniela Monti, Rita Ostan, Vincenzo Borelli, Gastone Castellani, Claudio Franceschi
Inflammaging is a recent theory of aging originally proposed in 2000 where data and conceptualizations regarding the aging of the immune system (immunosenescence) and the evolution of immune responses from invertebrates to mammals converged. This theory has received an increasing number of citations and experimental confirmations. Here we present an updated version of inflammaging focused on omic data - particularly on glycomics - collected on centenarians, supercentenarians and their offspring. Accordingly, we arrived to the following conclusions: i) inflammaging has a structure where specific combinations of pro- and anti-inflammatory mediators are involved; ii) inflammaging is systemic and more complex than we previously thought, as many organs, tissues and cell types participate in producing pro- and anti-inflammatory stimuli conceptualized as "molecular garbage"; iii) inflammaging is dynamic, can be propagated locally to neighboring cells and systemically from organ to organ by circulating products and microvesicles, and amplified by chronic age-related diseases constituting a "local fire" which in turn produces additional inflammatory stimuli and molecular garbage; iv) an integrated Systems Medicine approach is urgently needed to let emerge a robust and highly informative set/combination of omic markers able to better grasp the complex molecular core of inflammaging in elderly and centenarians...
December 27, 2016: Mechanisms of Ageing and Development
https://www.readbyqxmd.com/read/28032857/heme-oxygenase-1-in-the-forefront-of-a-multi-molecular-network-that-governs-cell-cell-contacts-and-filopodia-induced-zippering-in-prostate-cancer
#15
Alejandra V Paez, Carla Pallavicini, Federico Schuster, Maria Pia Valacco, Jimena Giudice, Emiliano G Ortiz, Nicolás Anselmino, Estefania Labanca, Maria Binaghi, Marcelo Salierno, Marcelo A Martí, Javier H Cotignola, Anna Woloszynska-Read, Luciana Bruno, Valeria Levi, Nora Navone, Elba S Vazquez, Geraldine Gueron
Prostate cancer (PCa) cells display abnormal expression of cytoskeletal proteins resulting in an augmented capacity to resist chemotherapy and colonize distant organs. We have previously shown that heme oxygenase 1 (HO-1) is implicated in cell morphology regulation in PCa. Here, through a multi 'omics' approach we define the HO-1 interactome in PCa, identifying HO-1 molecular partners associated with the integrity of the cellular cytoskeleton. The bioinformatics screening for these cytoskeletal-related partners reveal that they are highly misregulated in prostate adenocarcinoma compared with normal prostate tissue...
December 29, 2016: Cell Death & Disease
https://www.readbyqxmd.com/read/28032247/a-systemic-identification-approach-for-primary-transcription-start-site-of-arabidopsis-mirnas-from-multidimensional-omics-data
#16
Qi You, Hengyu Yan, Yue Liu, Xin Yi, Kang Zhang, Wenying Xu, Zhen Su
The 22-nucleotide non-coding microRNAs (miRNAs) are mostly transcribed by RNA polymerase II and are similar to protein-coding genes. Unlike the clear process from stem-loop precursors to mature miRNAs, the primary transcriptional regulation of miRNA, especially in plants, still needs to be further clarified, including the original transcription start site, functional cis-elements and primary transcript structures. Due to several well-characterized transcription signals in the promoter region, we proposed a systemic approach integrating multidimensional "omics" (including genomics, transcriptomics, and epigenomics) data to improve the genome-wide identification of primary miRNA transcripts...
December 28, 2016: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28031971/bluepen-biomarkers-llc-integrated-biomarker-solutions
#17
EDITORIAL
Ian A Blair, Clementina Mesaros, Patrick Lilley, Matthew Nunez
BluePen Biomarkers provides a unique comprehensive multi-omics biomarker discovery and validation platform. We can quantify, integrate and analyze genomics, proteomics, metabolomics and lipidomics biomarkers, alongside clinical data, demographics and other phenotypic data. A unique bio-inspired signal processing analytic approach is used that has the proven ability to identify biomarkers in a wide variety of diseases. The resulting biomarkers can be used for diagnosis, prognosis, mechanistic studies and predicting treatment response, in contexts from core research through clinical trials...
June 2016: Future Science OA
https://www.readbyqxmd.com/read/28028815/metabolic-systems-biology-a-brief-primer
#18
REVIEW
Lindsay M Edwards
In the early to mid 20(th) Century, reductionism as a concept in biology was challenged by key thinkers, including Ludwig Von Bertalanffy. He proposed that living organisms were specific examples of complex systems and, as such, they should display characteristics including hierarchical organisation and emergent behaviour. Yet the true study of complete biological systems (for example, metabolism) was not possible until technological advances that occurred 60 years later. Technology now exists that permits the measurement of complete levels of the biological hierarchy, for example the genome and transcriptome...
December 28, 2016: Journal of Physiology
https://www.readbyqxmd.com/read/28027405/george-tseng-debashish-ghosh-xianghon-jasmine-zhou-eds-integrating-omics-data-new-york-cambridge-university-press
#19
Jonathan A L Gelfond
No abstract text is available yet for this article.
December 2016: Biometrics
https://www.readbyqxmd.com/read/28019039/integration-of-gene-expression-and-methylation-to-unravel-biological-networks-in-glioblastoma-patients
#20
Francesco Gadaleta, Kyrylo Bessonov, Kristel Van Steen
The vast amount of heterogeneous omics data, encompassing a broad range of biomolecular information, requires novel methods of analysis, including those that integrate the available levels of information. In this work, we describe Regression2Net, a computational approach that is able to integrate gene expression and genomic or methylation data in two steps. First, penalized regressions are used to build Expression-Expression (EEnet) and Expression-Genomic or Expression-Methylation (EMnet) networks. Second, network theory is used to highlight important communities of genes...
December 26, 2016: Genetic Epidemiology
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