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https://www.readbyqxmd.com/read/28544881/mammalian-systems-biotechnology-reveals-global-cellular-adaptations-in-a-recombinant-cho-cell-line
#1
Faraaz Noor Khan Yusufi, Meiyappan Lakshmanan, Ying Swan Ho, Bernard Liat Wen Loo, Pramila Ariyaratne, Yuansheng Yang, Say Kong Ng, Tessa Rui Min Tan, Hock Chuan Yeo, Hsueh Lee Lim, Sze Wai Ng, Ai Ping Hiu, Chung Ping Chow, Corrine Wan, Shuwen Chen, Gavin Teo, Gao Song, Ju Xin Chin, Xiaoan Ruan, Ken Wing Kin Sung, Wei-Shou Hu, Miranda Gek Sim Yap, Muriel Bardor, Niranjan Nagarajan, Dong-Yup Lee
Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28544876/principles-of-systems-biology-no-17
#2
(no author information available yet)
This month: understanding spatial arrangements (Süel/Laue/Schweisguth/de Lorenzo), a giant virus sheds light on evolution (Koonin), synthetic systems (Comtet, Wang, Pósfai), and omics tools (Siuzdak, Kim).
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28542205/rots-an-r-package-for-reproducibility-optimized-statistical-testing
#3
Tomi Suomi, Fatemeh Seyednasrollah, Maria K Jaakkola, Thomas Faux, Laura L Elo
Differential expression analysis is one of the most common types of analyses performed on various biological data (e.g. RNA-seq or mass spectrometry proteomics). It is the process that detects features, such as genes or proteins, showing statistically significant differences between the sample groups under comparison. A major challenge in the analysis is the choice of an appropriate test statistic, as different statistics have been shown to perform well in different datasets. To this end, the reproducibility-optimized test statistic (ROTS) adjusts a modified t-statistic according to the inherent properties of the data and provides a ranking of the features based on their statistical evidence for differential expression between two groups...
May 25, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28541380/a-fully-bayesian-latent-variable-model-for-integrative-clustering-analysis-of-multi-type-omics-data
#4
Qianxing Mo, Ronglai Shen, Cui Guo, Marina Vannucci, Keith S Chan, Susan G Hilsenbeck
Identification of clinically relevant tumor subtypes and omics signatures is an important task in cancer translational research for precision medicine. Large-scale genomic profiling studies such as The Cancer Genome Atlas (TCGA) Research Network have generated vast amounts of genomic, transcriptomic, epigenomic, and proteomic data. While these studies have provided great resources for researchers to discover clinically relevant tumor subtypes and driver molecular alterations, there are few computationally efficient methods and tools for integrative clustering analysis of these multi-type omics data...
May 24, 2017: Biostatistics
https://www.readbyqxmd.com/read/28539364/integrative-proteomics-and-biochemical-analyses-define-ptc6p-as-the-saccharomyces-cerevisiae-pyruvate-dehydrogenase-phosphatase
#5
Xiao Guo, Natalie M Niemi, Joshua J Coon, Dave J Pagliarini
The pyruvate dehydrogenase complex (PDC) is the primary metabolic checkpoint connecting glycolysis and mitochondrial oxidative phosphorylation, and is important for maintaining cellular and organismal glucose homeostasis. Phosphorylation of the PDC E1 subunit was identified as a key inhibitory modification in bovine tissue approximately 50 years ago, and this regulatory process is now known to be conserved throughout evolution. Although Saccharomyces cerevisiae is a pervasive model organism for investigating cellular metabolism and its regulation by signaling processes, the phosphatase(s) responsible for activating the PDC in S...
May 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28539122/an-inference-method-from-multi-layered-structure-of-biomedical-data
#6
Myungjun Kim, Yonghyun Nam, Hyunjung Shin
BACKGROUND: Biological system is a multi-layered structure of omics with genome, epigenome, transcriptome, metabolome, proteome, etc., and can be further stretched to clinical/medical layers such as diseasome, drugs, and symptoms. One advantage of omics is that we can figure out an unknown component or its trait by inferring from known omics components. The component can be inferred by the ones in the same level of omics or the ones in different levels. METHODS: To implement the inference process, an algorithm that can be applied to the multi-layered complex system is required...
May 18, 2017: BMC Medical Informatics and Decision Making
https://www.readbyqxmd.com/read/28536942/lrrc25-plays-a-key-role-in-all-trans-retinoic-acid-induced-granulocytic-differentiation-as-a-novel-potential-leukocyte-differentiation-antigen
#7
Weili Liu, Ting Li, Pingzhang Wang, Wanchang Liu, Fujun Liu, Xiaoning Mo, Zhengyang Liu, Quansheng Song, Ping Lv, Guorui Ruan, Wenling Han
Leukocyte differentiation antigens (LDAs) play important roles in the immune system, by serving as surface markers and participating in multiple biological activities, such as recognizing pathogens, mediating membrane signals, interacting with other cells or systems, and regulating cell differentiation and activation. Data mining is a powerful tool used to identify novel LDAs from whole genome. LRRC25 (leucine rich repeat-containing 25) was predicted to have a role in the function of myeloid cells by a large-scale "omics" data analysis...
May 23, 2017: Protein & Cell
https://www.readbyqxmd.com/read/28533770/from-vineyard-soil-to-wine-fermentation-microbiome-approximations-to-explain-the-terroir-concept
#8
REVIEW
Ignacio Belda, Iratxe Zarraonaindia, Matthew Perisin, Antonio Palacios, Alberto Acedo
Wine originally emerged as a serendipitous mix of chemistry and biology, where microorganisms played a decisive role. From these ancient fermentations to the current monitored industrial processes, winegrowers and winemakers have been continuously changing their practices according to scientific knowledge and advances. A new enology direction is emerging and aiming to blend the complexity of spontaneous fermentations with industrial safety of monitored fermentations. In this context, wines with distinctive autochthonous peculiarities have a great acceptance among consumers, causing important economic returns...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28533479/the-landscape-of-dna-methylation-mediated-regulation-of-long-non-coding-rnas-in-breast-cancer
#9
Chunlong Zhang, Xinyu Wang, Xuecang Li, Ning Zhao, Yihan Wang, Xiaole Han, Ce Ci, Jian Zhang, Meng Li, Yan Zhang
Although systematic studies have identified a host of long non-coding RNAs (lncRNAs) which are involved in breast cancer, the knowledge about the methyla-tion-mediated dysregulation of those lncRNAs remains limited. Here, we integrated multi-omics data to analyze the methylated alteration of lncRNAs in breast invasive carcinoma (BRCA). We found that lncRNAs showed diverse methylation patterns on promoter regions in BRCA. LncRNAs were divided into two categories and four subcategories based on their promoter methylation patterns and expression levels be-tween tumor and normal samples...
May 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28532233/updates-on-sj%C3%A3-gren-s-syndrome-from-proteomics-to-protein-biomarkers
#10
Chiara Baldini, Antonella Cecchettini, Alessia Gallo, Stefano Bombardieri
Primary Sjögren's syndrome (pSS) is a complex heterogeneous autoimmune disorder, typically affecting exocrine glands. Recently, a great interest has arisen in searching for novel biomarkers able to improve the diagnostic work-up of the disease as well as the general assessment and the prognostic stratification of pSS patients. From this perspective, salivary proteomics has appeared as a promising tool considering that salivary proteins may closely reflect the underlying disease processes in the salivary glands...
May 23, 2017: Expert Review of Proteomics
https://www.readbyqxmd.com/read/28532215/matrix-mechanosensing-from-scaling-concepts-in-omics-data-to-mechanisms-in-the-nucleus-regeneration-and-cancer
#11
Dennis E Discher, Lucas Smith, Sangkyun Cho, Mark Colasurdo, Andrés J García, Sam Safran
Many of the most important molecules of life are polymers. In animals, the most abundant of the proteinaceous polymers are the collagens, which constitute the fibrous matrix outside cells and which can also self-assemble into gels. The physically measurable stiffness of gels, as well as tissues, increases with the amount of collagen, and cells seem to sense this stiffness. An understanding of this mechanosensing process in complex tissues, including fibrotic disease states with high collagen, is now utilizing 'omics data sets and is revealing polymer physics-type, nonlinear scaling relationships between concentrations of seemingly unrelated biopolymers...
May 22, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28531195/livestock-metabolomics-and-the-livestock-metabolome-a-systematic-review
#12
Seyed Ali Goldansaz, An Chi Guo, Tanvir Sajed, Michael A Steele, Graham S Plastow, David S Wishart
Metabolomics uses advanced analytical chemistry techniques to comprehensively measure large numbers of small molecule metabolites in cells, tissues and biofluids. The ability to rapidly detect and quantify hundreds or even thousands of metabolites within a single sample is helping scientists paint a far more complete picture of system-wide metabolism and biology. Metabolomics is also allowing researchers to focus on measuring the end-products of complex, hard-to-decipher genetic, epigenetic and environmental interactions...
2017: PloS One
https://www.readbyqxmd.com/read/28530140/associations-of-nasopharyngeal-metabolome-and-microbiome-with-severity-among-infants-with-bronchiolitis-a-multi-omic-analysis
#13
Christopher J Stewart, Jonathan M Mansbach, Matthew C Wong, Nadim J Ajami, Joseph F Petrosino, Carlos A Camargo, Kohei Hasegawa
RATIONALE: Bronchiolitis is the most common lower respiratory infection in infants; however, it remains unclear which infants with bronchiolitis will develop severe illness. In addition, while emerging evidence indicates associations of the upper-airway microbiome with bronchiolitis severity, little is known about the mechanisms linking airway microbes and host response to disease severity. OBJECTIVES: To determine the relations among the nasopharyngeal airway metabolome profiles, microbiome profiles, and severity in infants with bronchiolitis...
May 21, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28529704/towards-a-systems-approach-for-chronic-diseases-based-on-health-state-modeling
#14
Michael Rebhan
Rising pressure from chronic diseases means that we need to learn how to deal with challenges at a different level, including the use of systems approaches that better connect across fragments, such as disciplines, stakeholders, institutions, and technologies. By learning from progress in leading areas of health innovation (including oncology and AIDS), as well as complementary indications (Alzheimer's disease), I try to extract the most enabling innovation paradigms, and discuss their extension to additional areas of application within a systems approach...
2017: F1000Research
https://www.readbyqxmd.com/read/28528356/operating-room-fires-in-periocular-surgery
#15
Michael A Connor, Anne M Menke, Ivan Vrcek, John W Shore
AIM: A survey of ophthalmic plastic and reconstructive surgeons as well as seven-year data regarding claims made to the Ophthalmic Mutual Insurance Company (OMIC) is used to discuss operating room fires in periocular surgery. METHODS: A retrospective review of all closed claim operating room fires submitted to OMIC was performed. A survey soliciting personal experiences with operating room fires was distributed to all American Society of Oculoplastic and Reconstructive Surgeons...
May 20, 2017: International Ophthalmology
https://www.readbyqxmd.com/read/28528178/expanding-biological-activities-of-ts19-frag-ii-toxin-insights-into-il-17-production
#16
Felipe Augusto Cerni, Manuela Berto Pucca, Karina Furlani Zoccal, Fabiani Gai Frantz, Lucia Helena Faccioli, Eliane Candiani Arantes
Tityus serrulatus (Ts) venom is composed of a mixture of toxins presenting diverse biological functions. However, although this venom has been studied over the past three decades, omics analysis revealed that most of its toxins are not identified or their biological activities are unknown. Ts19 Frag-II is included is this group, which function is still uncertain. This study aimed to expand the biological activities of Ts19 Frag-II through in vivo investigation. Our results demonstrates that mice challenged with Ts19 Frag-II presented biochemical alterations, increasing serum levels of urea, ALT and β-globulin, besides decreasing γ-globulins...
May 17, 2017: Toxicon: Official Journal of the International Society on Toxinology
https://www.readbyqxmd.com/read/28527535/computing-in-biotechnology-omics-and-beyond
#17
EDITORIAL
Matthew Pavlovich
No abstract text is available yet for this article.
April 25, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28527522/precision-medicine-genomic-profiles-to-individualize-therapy
#18
REVIEW
Oscar E Streeter, Phillip J Beron, Prashant Natarajan Iyer
Precision medicine is the application of genotypic and Omics biomarkers to determine the most appropriate, outcome-driven therapy for individual patients. To determine the best choice of therapy, institutions use significant information technology-enabled data from imaging, electronic medical records, sensors in the clinic/hospitals, and wearable sensors to determine treatment response. With genomic profiling, targets to affect a disease course are continuing to be developed. As clonal mutational prevalence continues to be understood, information can be communicated to patients to inform them that resistance is common, requiring collection of more genetic mutations from patients with further biopsies or blood collection...
May 17, 2017: Otolaryngologic Clinics of North America
https://www.readbyqxmd.com/read/28527489/computing-in-biotechnology-omics-and-beyond
#19
EDITORIAL
Matthew Pavlovich
No abstract text is available yet for this article.
June 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/28525648/the-role-of-omics-in-the-application-of-adverse-outcome-pathways-for-chemical-risk-assessment
#20
Erica K Brockmeier, Geoff Hodges, Thomas H Hutchinson, Emma Butler, Markus Hecker, Knut Erik Tollefsen, Natalia Garcia-Reyero, Peter Kille, Dörthe Becker, Kevin Chipman, John Colbourne, Timothy W Collette, Andrew Cossins, Mark Cronin, Peter Graystock, Steve Gutsell, Dries Knapen, Ioanna Katsiadaki, Anke Lange, Stuart Marshall, Stewart F Owen, Edward J Perkins, Stewart Plaistow, Anthony Schroeder, Daisy Taylor, Mark Viant, Gerald Ankley, Francesco Falciani
In conjunction with the second International Environmental Omics Symposium (iEOS) conference, held at the University of Liverpool (UK) in September 2014, a workshop was held to bring together experts in toxicology and regulatory science from academia, government and industry. The purpose of the workshop was to review the specific roles that high-content omics datasets (e.g., transcriptomics, metabolomics, lipidomics, and proteomics) can hold within the adverse outcome pathway (AOP) framework for supporting ecological and human health risk assessments...
May 19, 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
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