keyword
MENU ▼
Read by QxMD icon Read
search

System biology integrative biology

keyword
https://www.readbyqxmd.com/read/28938616/identification-of-potential-cancer-related-pseudogenes-in-lung-adenocarcinoma-based-on-cerna-hypothesis
#1
Yunzhen Wei, Zhiqiang Chang, Cheng Wu, Yinling Zhu, Kun Li, Yan Xu
Pseudogenes are initially regarded as non-functional genomic fossils resulted from inactivating gene mutations during evolution. Far from being silent, pseudogenes are proved to regulate the expression of protein-coding genes through function as microRNA sponge in vivo. The aim of our study was to propose an integrative systems biology approach to identify disease pseudogenes base on competitive endogenous RNA (ceRNA) hypothesis. Here, we applied our method to lung adenocarcinoma (LUAD) RNASeq data from TCGA and identified 33 candidate pseudogenes...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28937978/a-new-discrete-dynamic-model-of-aba-induced-stomatal-closure-predicts-key-feedback-loops
#2
Réka Albert, Biswa R Acharya, Byeong Wook Jeon, Jorge G T Zañudo, Mengmeng Zhu, Karim Osman, Sarah M Assmann
Stomata, microscopic pores in leaf surfaces through which water loss and carbon dioxide uptake occur, are closed in response to drought by the phytohormone abscisic acid (ABA). This process is vital for drought tolerance and has been the topic of extensive experimental investigation in the last decades. Although a core signaling chain has been elucidated consisting of ABA binding to receptors, which alleviates negative regulation by protein phosphatases 2C (PP2Cs) of the protein kinase OPEN STOMATA 1 (OST1) and ultimately results in activation of anion channels, osmotic water loss, and stomatal closure, over 70 additional components have been identified, yet their relationships with each other and the core components are poorly elucidated...
September 22, 2017: PLoS Biology
https://www.readbyqxmd.com/read/28936624/dermal-epidermal-separation-methods-research-implications
#3
REVIEW
Ying Zou, Howard I Maibach
Dermal-epidermal separation is an important basic investigation technique for pharmacology, toxicology and biology. To choose the optimal method for a given research need, we reviewed studies on epidermal separation. PubMed, Embase, and Web of Science were utilized. Different separation systems have been compared, including chemical, enzyme, heat and mechanical separation; each has advantages and disadvantages. Heat is simple but causes thermal damage. Chemical reagents are effective but disturb cellular electrolyte equilibrium...
September 21, 2017: Archives of Dermatological Research
https://www.readbyqxmd.com/read/28935855/establishing-multiple-omics-baselines-for-three-southeast-asian-populations-in-the-singapore-integrative-omics-study
#4
Woei-Yuh Saw, Erwin Tantoso, Husna Begum, Lihan Zhou, Ruiyang Zou, Cheng He, Sze Ling Chan, Linda Wei-Lin Tan, Lai-Ping Wong, Wenting Xu, Don Kyin Nwe Moong, Yenly Lim, Bowen Li, Nisha Esakimuthu Pillai, Trevor A Peterson, Tomasz Bielawny, Peter J Meikle, Piyushkumar A Mundra, Wei-Yen Lim, Ma Luo, Kee-Seng Chia, Rick Twee-Hee Ong, Liam R Brunham, Chiea-Chuen Khor, Heng Phon Too, Richie Soong, Markus R Wenk, Peter Little, Yik-Ying Teo
The Singapore Integrative Omics Study provides valuable insights on establishing population reference measurement in 364 Chinese, Malay, and Indian individuals. These measurements include > 2.5 millions genetic variants, 21,649 transcripts expression, 282 lipid species quantification, and 284 clinical, lifestyle, and dietary variables. This concept paper introduces the depth of the data resource, and investigates the extent of ethnic variation at these omics and non-omics biomarkers. It is evident that there are specific biomarkers in each of these platforms to differentiate between the ethnicities, and intra-population analyses suggest that Chinese and Indians are the most biologically homogeneous and heterogeneous, respectively, of the three groups...
September 21, 2017: Nature Communications
https://www.readbyqxmd.com/read/28935166/mitochondrial-nanotunnels
#5
REVIEW
Amy E Vincent, Doug M Turnbull, Veronica Eisner, György Hajnóczky, Martin Picard
Insight into the regulation of complex physiological systems emerges from understanding how biological units communicate with each other. Recent findings show that mitochondria communicate at a distance with each other via nanotunnels, thin double-membrane protrusions that connect the matrices of non-adjacent mitochondria. Emerging evidence suggest that mitochondrial nanotunnels are generated by immobilized mitochondria and transport proteins. This review integrates data from the evolutionarily conserved structure and function of intercellular projections in bacteria with recent developments in mitochondrial imaging that permit nanotunnel visualization in eukaryotes...
September 18, 2017: Trends in Cell Biology
https://www.readbyqxmd.com/read/28934726/application-of-adverse-outcome-pathways-to-u-s-epa-s-endocrine-disruptor-screening-program
#6
REVIEW
Patience Browne, Pamela D Noyes, Warren M Casey, David J Dix
BACKGROUND: The U.S. EPA's Endocrine Disruptor Screening Program (EDSP) screens and tests environmental chemicals for potential effects in estrogen, androgen, and thyroid hormone pathways, and it is one of the only regulatory programs designed around chemical mode of action. OBJECTIVES: This review describes the EDSP's use of adverse outcome pathway (AOP) and toxicity pathway frameworks to organize and integrate diverse biological data for evaluating the endocrine activity of chemicals...
September 1, 2017: Environmental Health Perspectives
https://www.readbyqxmd.com/read/28933415/integrative-systems-biology-investigation-of-fabry-disease
#7
Marco Fernandes, Holger Husi
Fabry disease (FD) is a rare X-linked recessive genetic disorder caused by a deficient activity of the lysosomal enzyme alpha-galactosidase A (GLA) and is characterised by intra-lysosomal accumulation of globotriaosylceramide (Gb3). We performed a meta-analysis of peer-reviewed publications including high-throughput omics technologies including naïve patients and those undergoing enzyme replacement therapy (ERT). This study describes FD on a systems level using a systems biology approach, in which molecular data sourced from multi-omics studies is extracted from the literature and integrated as a whole in order to reveal the biochemical processes and molecular pathways potentially affected by the dysregulation of differentially expressed molecules...
November 15, 2016: Diseases (Basel)
https://www.readbyqxmd.com/read/28933072/-metabolomics-research-of-medicinal-plants
#8
Li-Xin Duan, Yun-Tao Dai, Chao Sun, Shi-Lin Chen
Metabolomics is the comprehensively study of chemical processes involving small molecule metabolites. It is an important part of systems biology, and is widely applied in complex traditional Chinese medicine(TCM)system. Metabolites biosynthesized by medicinal plants are the effective basis for TCM. Metabolomics studies of medicinal plants will usher in a new period of vigorous development with the implementation of Herb Genome Program and the development of TCM synthetic biology. This manuscript introduces the recent research progresses of metabolomics technology and the main research contents of metabolomics studies for medicinal plants, including identification and quality evaluation for medicinal plants, cultivars breeding, stress resistance, metabolic pathways, metabolic network, metabolic engineering and synthetic biology researches...
November 2016: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/28932698/quantitative-magnetic-resonance-mr-neurography-for-evaluation-of-peripheral-nerves-and-plexus-injuries
#9
REVIEW
Teodoro Martín Noguerol, Rafael Barousse, Mariano Socolovsky, Antonio Luna
Traumatic conditions of peripheral nerves and plexus have been classically evaluated by morphological imaging techniques and electrophysiological tests. New magnetic resonance imaging (MRI) studies based on 3D fat-suppressed techniques are providing high accuracy for peripheral nerve injury evaluation from a qualitative point of view. However, these techniques do not provide quantitative information. Diffusion weighted imaging (DWI) and diffusion tensor imaging (DTI) are functional MRI techniques that are able to evaluate and quantify the movement of water molecules within different biological structures...
August 2017: Quantitative Imaging in Medicine and Surgery
https://www.readbyqxmd.com/read/28932622/high-throughput-nuclear-delivery-and-rapid-expression-of-dna-via-mechanical-and-electrical-cell-membrane-disruption
#10
Xiaoyun Ding, Martin Stewart, Armon Sharei, James C Weaver, Robert S Langer, Klavs F Jensen
Nuclear transfection of DNA into mammalian cells is challenging yet critical for many biological and medical studies. Here, by combining cell squeezing and electric-field-driven transport in a device that integrates microfluidic channels with constrictions and microelectrodes, we demonstrate nuclear delivery of plasmid DNA within 1 hour after treatment, the most rapid DNA expression in a high-throughput setting (up to millions of cells per minute per device). Passing cells at high speed through microfluidic constrictions smaller than the cell diameter mechanically disrupts the cell membrane, allowing a subsequent electric field to further disrupt the nuclear envelope and drive DNA molecules into the cytoplasm and nucleus...
2017: Nature biomedical engineering
https://www.readbyqxmd.com/read/28932181/invasive-intraneural-interfaces-foreign-body-reaction-issues
#11
REVIEW
Fiorenza Lotti, Federico Ranieri, Gianluca Vadalà, Loredana Zollo, Giovanni Di Pino
Intraneural interfaces are stimulation/registration devices designed to couple the peripheral nervous system (PNS) with the environment. Over the last years, their use has increased in a wide range of applications, such as the control of a new generation of neural-interfaced prostheses. At present, the success of this technology is limited by an electrical impedance increase, due to an inflammatory response called foreign body reaction (FBR), which leads to the formation of a fibrotic tissue around the interface, eventually causing an inefficient transduction of the electrical signal...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28931422/pibas-fedsparql-a-web-based-platform-for-integration-and-exploration-of-bioinformatics-datasets
#12
Marija Djokic-Petrovic, Vladimir Cvjetkovic, Jeremy Yang, Marko Zivanovic, David J Wild
BACKGROUND: There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources...
September 20, 2017: Journal of Biomedical Semantics
https://www.readbyqxmd.com/read/28930989/demonstration-of-a-hyperlens-integrated-microscope-and-super-resolution-imaging
#13
Dasol Lee, Minkyung Kim, Sunae So, Inki Kim, Gwanho Yoon, Kyunghoon Kim, Junsuk Rho
The use of super-resolution imaging to overcome the diffraction limit of conventional microscopy has attracted the interest of researchers in biology and nanotechnology. Although near-field scanning microscopy and superlenses have improved the resolution in the near-field region, far-field imaging in real-time remains a significant challenge. Recently, the hyperlens, which magnifies and converts evanescent waves into propagating waves, has emerged as a novel approach to far-field imaging. Here, we report the fabrication of a spherical hyperlens composed of alternating silver (Ag) and titanium oxide (TiO2) thin layers...
September 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28929969/cellnetvis-a-web-tool-for-visualization-of-biological-networks-using-force-directed-layout-constrained-by-cellular-components
#14
Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P Telles, Gabriela Vaz Meirelles, Rosane Minghim
BACKGROUND: The advent of "omics" science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28928672/micrornas-clustered-within-the-14q32-locus-are-associated-with-endothelial-damage-and-microparticle-secretion-in-bicuspid-aortic-valve-disease
#15
Neus Martínez-Micaelo, Raúl Beltrán-Debón, Gerard Aragonés, Marta Faiges, Josep M Alegret
Background: We previously described that PECAM(+) circulating endothelial microparticles (EMPs) are elevated in bicuspid aortic valve (BAV) disease as a manifestation of endothelial damage. In this study, we hypothesized that this endothelial damage, is functionally related to the secretion of a specific pattern of EMP-associated miRNAs. Methods: We used a bioinformatics approach to correlate the PECAM(+) EMP levels with the miRNA expression profile in plasma in healthy individuals and BAV patients (n = 36)...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28923279/needs-and-opportunities-in-bio-design-automation-four-areas-for-focus
#16
REVIEW
Evan Appleton, Douglas Densmore, Curtis Madsen, Nicholas Roehner
Bio-design automation (BDA) is an emerging field focused on computer-aided design, engineering principles, and automated manufacturing of biological systems. Here we discuss some outstanding challenges for bio-design that can be addressed by developing new tools for combinatorial engineering, equipment interfacing, next-generation sequencing, and workflow integration. These four areas, while not an exhaustive list of those that need to be addressed, could yield advances in bio-design, laboratory automation, and biometrology...
September 15, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28923156/functional-constructivism-in-search-of-formal-descriptors
#17
Irina Trofimova
The Functional Constructivism (FC) paradigm is an alternative to behaviorism and considers behavior as being generated every time anew, based on an individual's capacities, environmental resources and demands. Walter Freeman's work provided us with evidence supporting the FC principles. In this paper we make parallels between gradual construction processes leading to the formation of individual behavior and habits, and evolutionary processes leading to the establishment of biological systems. Referencing evolutionary theory, several formal descriptors of such processes are proposed...
October 2017: Nonlinear Dynamics, Psychology, and Life Sciences
https://www.readbyqxmd.com/read/28922391/impedance-biosensor-for-real-time-monitoring-and-prediction-of-thrombotic-individual-profile-in-flowing-blood
#18
Denise De Zanet, Monica Battiston, Elisabetta Lombardi, Ruben Specogna, Francesco Trevisan, Luigi De Marco, Antonio Affanni, Mario Mazzucato
A new biosensor for the real-time analysis of thrombus formation is reported. The fast and accurate monitoring of the individual thrombotic risk represents a challenge in cardiovascular diagnostics and in treatment of hemostatic diseases. Thrombus volume, as representative index of the related thrombotic status, is usually estimated with confocal microscope at the end of each in vitro experiment, without providing a useful behavioral information of the biological sample such as platelets adhesion and aggregation in flowing blood...
2017: PloS One
https://www.readbyqxmd.com/read/28922353/synthesizing-developmental-trajectories
#19
Paul Villoutreix, Joakim Andén, Bomyi Lim, Hang Lu, Ioannis G Kevrekidis, Amit Singer, Stanislav Y Shvartsman
Dynamical processes in biology are studied using an ever-increasing number of techniques, each of which brings out unique features of the system. One of the current challenges is to develop systematic approaches for fusing heterogeneous datasets into an integrated view of multivariable dynamics. We demonstrate that heterogeneous data fusion can be successfully implemented within a semi-supervised learning framework that exploits the intrinsic geometry of high-dimensional datasets. We illustrate our approach using a dataset from studies of pattern formation in Drosophila...
September 18, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28921376/legal-issues-in-governing-genetic-biobanks-the-italian-framework-as-a-case-study-for-the-implications-for-citizen-s-health-through-public-private-initiatives
#20
Cinzia Piciocchi, Rossana Ducato, Lucia Martinelli, Silvia Perra, Marta Tomasi, Carla Zuddas, Deborah Mascalzoni
This paper outlines some of the challenges faced by regulation of genetic biobanking, using case studies coming from the Italian legal system. The governance of genetic resources in the context of genetic biobanks in Italy is discussed, as an example of the stratification of different inputs and rules: EU law, national law, orders made by authorities and soft law, which need to be integrated with ethical principles, technological strategies and solutions. After providing an overview of the Italian legal regulation of genetic data processing, it considers the fate of genetic material and IP rights in the event of a biobank's insolvency...
September 18, 2017: Journal of Community Genetics
keyword
keyword
10317
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"