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System biology integrative biology

Dimosthenis A Sarigiannis, Spyros P Karakitsios, Evangelos Handakas, Konstantina Simou, Ermioni Solomou, Alberto Gotti
The current study aims at a comprehensive risk characterization of bisphenol A (BPA) supported by an integrated exposure modelling framework that comprises far field and near field exposure modelling coupled to a dynamic lifetime PBTK model. Exposure analysis was done on European data of BPA food residues and human biomonitoring (HBM). The latter were further assimilated through an advanced exposure reconstruction modelling framework to estimate the corresponding external and internal systemic dose of BPA and its metabolites...
October 18, 2016: Food and Chemical Toxicology
Olivier Taboureau, Karine Audouze
During the past decades, many epidemiological, toxicological and biological studies have been performed to assess the role of environmental chemicals as potential toxicants for diverse human disorders. However, the relationships between diseases based on chemical exposure have been rarely studied by computational biology. We developed a human environmental disease network (EDN) to explore and suggest novel disease-disease and chemical-disease relationships. The presented scored EDN model is built upon the integration on systems biology and chemical toxicology using chemical contaminants information and their disease relationships from the reported TDDB database...
October 21, 2016: ALTEX
Kristin Bösch, Lamprinos Frantzeskakis, Miroslav Vraneš, Jörg Kämper, Kerstin Schipper, Vera Göhre
Gene deletion plays an important role in the analysis of gene function. One of the most efficient methods to disrupt genes in a targeted manner is the replacement of the entire gene with a selectable marker via homologous recombination. During homologous recombination, exchange of DNA takes place between sequences with high similarity. Therefore, linear genomic sequences flanking a target gene can be used to specifically direct a selectable marker to the desired integration site. Blunt ends of the deletion construct activate the cell's DNA repair systems and thereby promote integration of the construct either via homologous recombination or by non-homologous-end-joining...
September 30, 2016: Journal of Visualized Experiments: JoVE
Yang Liu, Saad M Khan, Juexin Wang, Mats Rynge, Yuanxun Zhang, Shuai Zeng, Shiyuan Chen, Joao V Maldonado Dos Santos, Babu Valliyodan, Prasad P Calyam, Nirav Merchant, Henry T Nguyen, Dong Xu, Trupti Joshi
BACKGROUND: With the advances in next-generation sequencing (NGS) technology and significant reductions in sequencing costs, it is now possible to sequence large collections of germplasm in crops for detecting genome-scale genetic variations and to apply the knowledge towards improvements in traits. To efficiently facilitate large-scale NGS resequencing data analysis of genomic variations, we have developed "PGen", an integrated and optimized workflow using the Extreme Science and Engineering Discovery Environment (XSEDE) high-performance computing (HPC) virtual system, iPlant cloud data storage resources and Pegasus workflow management system (Pegasus-WMS)...
October 6, 2016: BMC Bioinformatics
Alex R Hardisty, Finn Bacall, Niall Beard, Maria-Paula Balcázar-Vargas, Bachir Balech, Zoltán Barcza, Sarah J Bourlat, Renato De Giovanni, Yde de Jong, Francesca De Leo, Laura Dobor, Giacinto Donvito, Donal Fellows, Antonio Fernandez Guerra, Nuno Ferreira, Yuliya Fetyukova, Bruno Fosso, Jonathan Giddy, Carole Goble, Anton Güntsch, Robert Haines, Vera Hernández Ernst, Hannes Hettling, Dóra Hidy, Ferenc Horváth, Dóra Ittzés, Péter Ittzés, Andrew Jones, Renzo Kottmann, Robert Kulawik, Sonja Leidenberger, Päivi Lyytikäinen-Saarenmaa, Cherian Mathew, Norman Morrison, Aleksandra Nenadic, Abraham Nieva de la Hidalga, Matthias Obst, Gerard Oostermeijer, Elisabeth Paymal, Graziano Pesole, Salvatore Pinto, Axel Poigné, Francisco Quevedo Fernandez, Monica Santamaria, Hannu Saarenmaa, Gergely Sipos, Karl-Heinz Sylla, Marko Tähtinen, Saverio Vicario, Rutger Aldo Vos, Alan R Williams, Pelin Yilmaz
BACKGROUND: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science...
October 20, 2016: BMC Ecology
Masayuki Sano, Minoru Iijima, Manami Ohtaka, Mahito Nakanishi
Tissue-specific control of gene expression is an invaluable tool for studying various biological processes and medical applications. Efficient regulatory systems have been utilized to control transgene expression in various types of DNA viral or integrating viral vectors. However, existing regulatory systems are difficult to transfer into negative-strand RNA virus vector platforms because of significant differences in their transcriptional machineries. In this study, we developed a novel strategy for regulating transgene expression mediated by a cytoplasmic RNA vector based on a replication-defective and persistent Sendai virus (SeVdp)...
2016: PloS One
Nicole R Bush, Richard D Lane, Katie A McLaughlin
Early-life adversities (ELA) are associated with subsequent pervasive alterations across a wide range of neurobiological systems and psychosocial factors that contribute to accelerated onset of health problems and diseases. In this article, we provide an integrated perspective on recent developments in research on ELA, based on the articles published in this Special Issue of Psychosomatic Medicine. We focus on the following: 1) the distinction between specific versus general aspects of ELA with regard to the nature of exposure (e...
October 19, 2016: Psychosomatic Medicine
Alessandro Consolaro, Esi M Morgan, Gabriella Giancane, Silvia Rosina, Stefano Lanni, Angelo Ravelli
Information technology in paediatric rheumatology has seen several exciting developments in recent years. The new multidimensional questionnaires for juvenile idiopathic arthritis, juvenile dermatomyositis, and juvenile autoinflammatory diseases integrate all major parent- and child-reported outcomes (PCROs) used in these diseases into a single tool, and provide an effective guide to manage, document change in health, assess effectiveness of therapeutic interventions, and verify the parent and child satisfaction with illness outcome...
September 2016: Clinical and Experimental Rheumatology
Katherine R Amato
Research examining the gut microbiota is currently exploding, and results are providing new perspectives on human biology. Factors such as host diet and physiology influence the composition and function of the gut microbiota, which in turn affects human nutrition, health, and behavior via interactions with metabolism, the immune system, and the brain. These findings represent an exciting new twist on familiar topics, and as a result, gut microbiome research is likely to provide insight into unresolved biological mechanisms driving human health...
October 20, 2016: American Journal of Human Biology: the Official Journal of the Human Biology Council
Markus Seeger, Angelos Karlas, Dominik Soliman, Jaroslav Pelisek, Vasilis Ntziachristos
Carotid artery atherosclerosis is a main cause of stroke. Understanding atherosclerosis biology is critical in the development of targeted prevention and treatment strategies. Consequently, there is demand for advanced tools investigating atheroma pathology. We consider hybrid optoacoustic and multiphoton microscopy for the integrated and complementary interrogation of plaque tissue constituents and their mutual interactions. Herein, we visualize human carotid plaque using a hybrid multimodal imaging system that combines optical resolution optoacoustic (photoacoustic) microscopy, second and third harmonic generation microscopy, and two-photon excitation fluorescence microscopy...
September 2016: Photoacoustics
Marcelo E Fuentes, Renato A Quinones
Facultative marine filamentous fungi have recently emerged as a functional component in coastal marine systems. However, little is known about their ecological role and functions in biogeochemical cycles. Penicillium decumbens, S. strictum, and F. fujikuroi were isolated from the coastal upwelling zone off south-central Chile. Their carbon profiles were characterized using Biolog FF MicroPlates. These species used a wide range of carbon sources, mainly carbohydrates, but also amino acids, suggesting the use of metabolic routes that include glycolysis/gluconeogenesis...
October 19, 2016: Mycologia
(no author information available yet)
Purpose: Radiology represents a highly relevant part of undergraduate medical education from preclinical studies to subinternship training. It is therefore important to establish a content base for teaching radiology in German Medical Faculties. Materials and Methods: The German Society of Radiology (DRG) developed a model curriculum for radiological teaching at German medical universities, which is presented in this article. There is also a European model curriculum for undergraduate teaching (U-level curriculum of the European Society of Radiology)...
November 2016: RöFo: Fortschritte Auf Dem Gebiete der Röntgenstrahlen und der Nuklearmedizin
Predrag Jevtić, Ana Milunović-Jevtić, Matthew R Dilsaver, Jesse C Gatlin, Daniel L Levy
Striking size variations are prominent throughout biology, at the organismal, cellular, and subcellular levels. Important fundamental questions concern organelle size regulation and how organelle size is regulated relative to cell size, also known as scaling. Uncovering mechanisms of organelle size regulation will inform the functional significance of size as well as the implications of misregulated size, for instance in the case of nuclear enlargement in cancer. Xenopus egg and embryo extracts are powerful cell-free systems that have been utilized extensively for mechanistic and functional studies of various organelles and subcellular structures...
2016: International Journal of Developmental Biology
Vincenzo Sannino, Arun M Kolinjivadi, Giorgio Baldi, Vincenzo Costanzo
The correct duplication of genetic information is essential to maintain genome stability, which is lost in cancer cells. Replication fork integrity is ensured by a number of DNA metabolism proteins that assist replication of chromatin regions difficult to replicate due to their intrinsic DNA sequence composition, coordinate repair of DNA molecules resulting from aberrant replication events or protect replication forks in the presence of lesions impairing their progression. Some DNA metabolism genes involved in DNA repair are essential in higher eukaryotes even in unchallenged conditions, suggesting the existence of biological processes requiring these specialized functions in organisms with complex genomes...
2016: International Journal of Developmental Biology
Kirti M Yenkie, WenZhao Wu, Ryan L Clark, Brian F Pfleger, Thatcher W Root, Christos T Maravelias
Microbial conversion of renewable feedstocks to high-value chemicals is an attractive alternative to current petrochemical processes because it offers the potential to reduce net CO2 emissions and integrate with bioremediation objectives. Microbes have been genetically engineered to produce a growing number of high-value chemicals in sufficient titer, rate, and yield from renewable feedstocks. However, high-yield bioconversion is only one aspect of an economically viable process. Separation of biologically synthesized chemicals from process streams is a major challenge that can contribute to >70% of the total production costs...
October 15, 2016: Biotechnology Advances
Lindsey J Anstine, Chris Bobba, Samir Ghadiali, Joy Lincoln
Risk factors of heart valve disease are well defined and prolonged exposure throughout life leads to degeneration and dysfunction in up to 33% of the population. While aortic valve replacement remains the most common need for cardiovascular surgery particularly in those aged over 65, the underlying mechanisms of progressive deterioration are unknown. In other cardiovascular systems, a decline in endothelial cell integrity and function play a major role in promoting pathological changes, and while similar mechanisms have been speculated in the valves, studies to support this are lacking...
October 15, 2016: Journal of Molecular and Cellular Cardiology
Cui Hongzhou, Guo Shuping, Wang Wenju, Li Li, Wei Lulu, Deng Linjun, Li Jingmin, Ren Xiaoli, Bai Li
In recent years, molecular biology has proven to be a great asset in our understanding of mechanisms in genodermatoses. However, bench to bedside translation research lags far behind. Advances in lab-on-a-chip technologies enabled programmable, reconfigurable, and scalable manipulation of a variety of laboratory procedures. Sample preparation, microfluidic reactions, and continuous monitoring systems can be integrated on a small chip. These advantages have attracted attention in various fields of clinical application including diagnosis of inherited skin diseases...
September 13, 2016: Journal of Dermatological Science
Susana Vacas, Vincent Degos, Mervyn Maze
BACKGROUND: Sleep is integral to biologic function, and sleep disruption can result in both physiological and psychologic dysfunction including cognitive decline. Surgery activates the innate immune system, inducing neuroinflammatory changes that interfere with cognition. Because surgical patients with sleep disorders have an increased likelihood of exhibiting postoperative delirium, an acute form of cognitive decline, we investigated the contribution of perioperative sleep fragmentation (SF) to the neuroinflammatory and cognitive responses of surgery...
October 11, 2016: Anesthesia and Analgesia
Jhih-Rong Lin, Ying Cai, Quanwei Zhang, Wen Zhang, Ruben Nogales, Zhengdong Zhang
Schizophrenia is a severe mental disorder with a large genetic component. Recent genome-wide association studies (GWAS) have identified many schizophrenia-associated common variants. For most of the reported associations, however, the underlying biological mechanisms are not clear. The critical first step for their elucidation is to identify the most likely disease genes as the source of the association signals. Here, we describe a general computational framework of post-GWAS analysis for complex disease gene prioritization...
October 17, 2016: Genetics
Riccardo Sarzani
Atrial natriuretic peptide (ANP) and B-type natriuretic peptide (BNP) are the cardiac natriuretic peptides (NP), true "cardiometabolic" hormones well known for their renal, endocrine and cardiovascular activities leading to reduced sodium reabsorption and arterial blood pressure. These effects are mainly mediated by the second messenger cGMP that also stimulates lipolysis, mitochondriogenesis and a thermogenic program with potency similar to catecholamines. Two distinct NP receptors modulate the final response to cardiac NP: the cGMP-signaling receptor NPRA and the clearance receptor NPRC...
September 2016: Journal of Hypertension
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