keyword
MENU ▼
Read by QxMD icon Read
search

System biology integrative biology

keyword
https://www.readbyqxmd.com/read/28531348/plant-derived-transcription-factors-for-orthologous-regulation-of-gene-expression-in-the-yeast-saccharomyces-cerevisiae
#1
Gita Naseri, Salma Balazadeh, Fabian Machens, Iman Kamranfar, Katrin Messerschmidt, Bernd Mueller-Roeber
Control of gene expression by transcription factors (TFs) is central in many synthetic biology projects where tailored expression of one or multiple genes is often needed. As TFs from evolutionary distant organisms are unlikely to affect gene expression in a host of choice, they represent excellent candidates for establishing orthogonal control systems. To establish orthogonal regulators for use in yeast (Saccharomyces cerevisiae), we chose TFs from the plant Arabidopsis thaliana. We established a library of 106 different combinations of chromosomally integrated TFs, activation domains (yeast GAL4 AD, herpes simplex virus VP64, and plant EDLL) and synthetic promoters harbouring cognate cis-regulatory motifs driving a yEGFP reporter...
May 22, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28531339/limtox-a-web-tool-for-applied-text-mining-of-adverse-event-and-toxicity-associations-of-compounds-drugs-and-genes
#2
Andres Cañada, Salvador Capella-Gutierrez, Obdulia Rabal, Julen Oyarzabal, Alfonso Valencia, Martin Krallinger
A considerable effort has been devoted to retrieve systematically information for genes and proteins as well as relationships between them. Despite the importance of chemical compounds and drugs as a central bio-entity in pharmacological and biological research, only a limited number of freely available chemical text-mining/search engine technologies are currently accessible. Here we present LimTox (Literature Mining for Toxicology), a web-based online biomedical search tool with special focus on adverse hepatobiliary reactions...
May 22, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28531139/dual-component-gelatinous-peptide-reactive-oligomer-formulations-as-conduit-material-and-luminal-filler-for-peripheral-nerve-regeneration
#3
Caroline Kohn-Polster, Divya Bhatnagar, Derek J Woloszyn, Matthew Richtmyer, Annett Starke, Alexandra H Springwald, Sandra Franz, Michaela Schulz-Siegmund, Hilton M Kaplan, Joachim Kohn, Michael C Hacker
Toward the next generation of nerve guidance conduits (NGCs), novel biomaterials and functionalization concepts are required to address clinical demands in peripheral nerve regeneration (PNR). As a biological polymer with bioactive motifs, gelatinous peptides are promising building blocks. In combination with an anhydride-containing oligomer, a dual-component hydrogel system (cGEL) was established. First, hollow cGEL tubes were fabricated by a continuous dosing and templating process. Conduits were characterized concerning their mechanical strength, in vitro and in vivo degradation and biocompatibility...
May 21, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28530715/nanofluidic-device-for-continuous-multiparameter-quality-assurance-of-biologics
#4
Sung Hee Ko, Divya Chandra, Wei Ouyang, Taehong Kwon, Pankaj Karande, Jongyoon Han
Process analytical technology (PAT) is critical for the manufacture of high-quality biologics as it enables continuous, real-time and on-line/at-line monitoring during biomanufacturing processes. The conventional analytical tools currently used have many restrictions to realizing the PAT of current and future biomanufacturing. Here we describe a nanofluidic device for the continuous monitoring of biologics' purity and bioactivity with high sensitivity, resolution and speed. Periodic and angled nanofilter arrays served as the molecular sieve structures to conduct a continuous size-based analysis of biologics...
May 22, 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/28530340/-can-post-traumatic-stress-disorder-be-prevented-with-glucocorticoids
#5
REVIEW
Hagit Cohen, Zeev Kaplan, Joseph Zohar
Glucocorticoids (GCs) play a major role in orchestrating the complex physiological and behavioral reactions essential for the maintenance of homeostasis. These compounds enable the organism to prepare for, respond to and cope with the acute demands of physical and emotional stressors. The appropriate GC release, commensurate with stressor severity, enables the body to properly contain stress responses so as to promote recovery by rapidly restoring homeostasis. Indeed, inadequate GC release following stress not only delays recovery by disrupting biological homeostasis in the short run but can also interfere with the processing or interpretation of stressful information that results in long-term disruptions in memory integration...
December 2016: Harefuah
https://www.readbyqxmd.com/read/28528284/biomarkers-in-epilepsy-a-modelling-perspective
#6
Sven C van Dijkman, Rob A Voskuyl, Elizabeth C de Lange
Biomarkers can be categorised from type 0 (genotype or phenotype), through 6 (clinical scales), each level representing a part of the processes involved in the biological system and drug treatment. This classification facilitates the identification and connection of information required to fully (mathematically) model a disease and its treatment using integrated information from biomarkers. Two recent reviews thoroughly discussed the current status and development of biomarkers for epilepsy, but a path towards the integration of such biomarkers for the personalisation of anti-epileptic drug treatment is lacking...
May 17, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28526435/the-bidirectional-gut-brain-microbiota-axis-as-a-potential-nexus-between-traumatic-brain-injury-inflammation-and-disease
#7
Mark H Sundman, Nan-Kuei Chen, Vignesh Subbian, Ying-Hui Chou
As head injuries and their sequelae have become an increasingly salient matter of public health, experts in the field have made great progress elucidating the biological processes occurring within the brain at the moment of injury and throughout the recovery thereafter. Given the extraordinary rate at which our collective knowledge of neurotrauma has grown, new insights may be revealed by examining the existing literature across disciplines with a new perspective. This article will aim to expand the scope of this rapidly evolving field of research beyond the confines of the central nervous system (CNS)...
May 16, 2017: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/28525642/dynamics-of-sequestration-based-gene-regulatory-cascades
#8
Tatenda Shopera, William R Henson, Tae Seok Moon
Gene regulatory cascades are ubiquitous in biology. Because regulatory cascades are integrated within complex networks, their quantitative analysis is challenging in native systems. Synthetic biologists have gained quantitative insights into the properties of regulatory cascades by building simple circuits, but sequestration-based regulatory cascades remain relatively unexplored. Particularly, it remains unclear how the cascade components collectively control the output dynamics. Here, we report the construction and quantitative analysis of the longest sequestration-based cascade in Escherichia coli...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28525563/omics-biomarkers-in-ophthalmology
#9
Susette Lauwen, Eiko K de Jong, Dirk J Lefeber, Anneke I den Hollander
"Omics" refers to high-throughput analyses of genes, proteins, or metabolites in a biological system, and is increasingly used for ophthalmic research. These system-based approaches can unravel disease-related processes and are valuable for biomarker discovery. Furthermore, potential therapeutic targets can be identified based on omics results, and targeted follow-up experiments can be designed to gain molecular understanding of the disease and to test new therapies. Here, we review the application of omics techniques in eye diseases, focusing on age-related macular degeneration (AMD), diabetic retinopathy (DR), retinal detachment (RD), myopia, glaucoma, Fuchs' corneal dystrophy (FCD), cataract, keratoconus, and dry eyes...
May 1, 2017: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/28524913/periodic-oscillation-of-ion-conduction-of-nanofluidic-diodes-using-a-chemical-oscillator
#10
Huacheng Zhang, Jue Hou, Ranwen Ou, Yaoxin Hu, Huanting Wang, Lei Jiang
Periodic ion-conduction oscillation of biological ion channels in a living system is essential for numerous life processes. Here we report an oscillatory nanofluidic system that can self-regulate its ion-conduction states under constant conditions. The oscillatory nanofluidic system is constructed by integrating a chemical oscillator into an artificial single nanochannel system. Oscillating chemical reactions of the pH oscillator carried out inside the nanochannel are used to switch the surface properties of the channel between highly and lowly charged states, thus realizing an autonomous, continuous and periodic oscillation of the ion conductance of the channel between high and low ion-conduction states...
May 19, 2017: Nanoscale
https://www.readbyqxmd.com/read/28524183/artificial-photosynthesis-closing-remarks
#11
Leif Hammarström
This paper derives from my closing remarks lecture at the 198(th) Faraday Discussion meeting on Artificial Photosynthesis, Kyoto, Japan, February 28-March 2. The meeting had sessions on biological approaches and fundamental processes, molecular catalysts, inorganic assembly catalysts, and integration of systems for demonstrating realistic devices. The field has had much progress since the previous Faraday Discussion on Artificial Photosynthesis in Edinburgh, UK, in 2011. This paper is a personal account of recent discussions and developments in the field, as reflected in and discussed during the meeting...
May 19, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28523275/online-detection-of-peroxidase-using-3d-printing-active-magnetic-mixing-and-spectra-analysis
#12
Shanshan Bai, Chengqi Gan, Gaozhe Cai, Lei Wang, Mingyong Chen, Qingan Han, Jianhan Lin
A new method for online detection of peroxidase (POD) using 3D printing, active magnetic mixing, fluidic control, and optical detection was developed and demonstrated in this study. The proposed POD detection system consisted of a 3D printing and active magnetic mixing based fluidic chip for online catalytic reaction, an optical detector with a fluidic flow cell for quantitative determination of the final catalysate, and a single-chip microcontroller based controller for automatic control of two rotating magnetic fields and four precise peristaltic pumps...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28523006/virtual-plant-tissue-building-blocks-for-next-generation-plant-growth-simulation
#13
Dirk De Vos, Abdiravuf Dzhurakhalov, Sean Stijven, Przemyslaw Klosiewicz, Gerrit T S Beemster, Jan Broeckhove
Motivation: Computational modeling of plant developmental processes is becoming increasingly important. Cellular resolution plant tissue simulators have been developed, yet they are typically describing physiological processes in an isolated way, strongly delimited in space and time. Results: With plant systems biology moving toward an integrative perspective on development we have built the Virtual Plant Tissue (VPTissue) package to couple functional modules or models in the same framework and across different frameworks...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28522411/halloysite-and-chitosan-oligosaccharide-nanocomposite-for-wound-healing
#14
Giuseppina Sandri, Carola Aguzzi, Silvia Rossi, Maria Cristina Bonferoni, Giovanna Bruni, Cinzia Boselli, Antonia Icaro Cornaglia, Federica Riva, Cesar Viseras, Carla Caramella, Franca Ferrari
Halloysite is a natural nanotubular clay mineral (HNTs, Halloysite Nano Tubes) chemically identical to kaolinite and, due to its good biocompatibility, is an attractive nanomaterial for a vast range of biological applications. Chitosan oligosaccharides are homo- or heterooligomers of N-acetylglucosamine and D-glucosamine, that accelerate wound healing by enhancing the functions of inflammatory and repairing cells. The aim of the work was the development of a nanocomposite based on HNTs and chitosan oligosaccharides, to be used as pour powder to enhance healing in the treatment of chronic wounds...
May 15, 2017: Acta Biomaterialia
https://www.readbyqxmd.com/read/28520765/an-integrative-analysis-of-tissue-specific-transcriptomic-and-metabolomic-responses-to-short-term-dietary-methionine-restriction-in-mice
#15
Sujoy Ghosh, Laura A Forney, Desiree Wanders, Kirsten P Stone, Thomas W Gettys
Dietary methionine restriction (MR) produces a coordinated series of transcriptional responses in peripheral tissues that limit fat accretion, remodel lipid metabolism in liver and adipose tissue, and improve overall insulin sensitivity. Hepatic sensing of reduced methionine leads to induction and release of fibroblast growth factor 21 (FGF21), which acts centrally to increase sympathetic tone and activate thermogenesis in adipose tissue. FGF21 also has direct effects in adipose to enhance glucose uptake and oxidation...
2017: PloS One
https://www.readbyqxmd.com/read/28515914/analysis-of-the-function-of-microrna-375-in-humans-using-bioinformatics
#16
Xiaohua Chen, Baoxia Li, Rongcheng Luo, Sina Cai, Cao Zhang, Xiaolong Cao
MicroRNA-375 (miR-375) is expressed at low levels in many types of solid tumor, particularly in gastrointestinal tumors. It is considered to be important in the development of cancer and certain diseases. Thus, more detailed knowledge is required on the particular functions of miR-375. miRs function by regulating target genes. Therefore, in the current study, miRWalk (which includes the data from 10 prediction software programs) was used to predict the target genes of miR-375. The genes, which were co-predicted using five different software programs were further analyzed using Database for Annotation, Visualization and Integrated Discovery online software [including gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis]...
May 2017: Biomedical Reports
https://www.readbyqxmd.com/read/28513415/the-fungal-cell-wall-structure-biosynthesis-and-function
#17
Neil A R Gow, Jean-Paul Latge, Carol A Munro
The molecular composition of the cell wall is critical for the biology and ecology of each fungal species. Fungal walls are composed of matrix components that are embedded and linked to scaffolds of fibrous load-bearing polysaccharides. Most of the major cell wall components of fungal pathogens are not represented in humans, other mammals, or plants, and therefore the immune systems of animals and plants have evolved to recognize many of the conserved elements of fungal walls. For similar reasons the enzymes that assemble fungal cell wall components are excellent targets for antifungal chemotherapies and fungicides...
May 2017: Microbiology Spectrum
https://www.readbyqxmd.com/read/28511544/structural-characterization-of-membrane-bound-human-immunodeficiency-virus-1-gag-matrix-with-neutron-reflectometry
#18
Rebecca Eells, Marilia Barros, Kerry M Scott, Ioannis Karageorgos, Frank Heinrich, Mathias Lösche
The structural characterization of peripheral membrane proteins represents a tremendous challenge in structural biology due to their transient interaction with the membrane and the potential multitude of protein conformations during this interaction. Neutron reflectometry is uniquely suited to address this problem because of its ability to structurally characterize biological model systems nondestructively and under biomimetic conditions that retain full protein functionality. Being sensitive to only the membrane-bound fraction of a water-soluble peripheral protein, neutron reflectometry obtains a low-resolution average structure of the protein-membrane complex that is further refined using integrative modeling strategies...
May 16, 2017: Biointerphases
https://www.readbyqxmd.com/read/28508360/genome-to-phenome-a-systems-biology-approach-to-ptsd-using-an-animal-model
#19
Nabarun Chakraborty, James Meyerhoff, Marti Jett, Rasha Hammamieh
Post-traumatic stress disorder (PTSD) is a debilitating illness that imposes significant emotional and financial burdens on military families. The understanding of PTSD etiology remains elusive; nonetheless, it is clear that PTSD is manifested by a cluster of symptoms including hyperarousal, reexperiencing of traumatic events, and avoidance of trauma reminders. With these characteristics in mind, several rodent models have been developed eliciting PTSD-like features. Animal models with social dimensions are of particular interest, since the social context plays a major role in the development and manifestation of PTSD...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28508359/evolving-relevance-of-neuroproteomics-in-alzheimer-s-disease
#20
Simone Lista, Henrik Zetterberg, Sid E O'Bryant, Kaj Blennow, Harald Hampel
Substantial progress in the understanding of the biology of Alzheimer's disease (AD) has been achieved over the past decades. The early detection and diagnosis of AD and other age-related neurodegenerative diseases, however, remain a challenging scientific frontier. Therefore, the comprehensive discovery (relating to all individual, converging or diverging biochemical disease mechanisms), development, validation, and qualification of standardized biological markers with diagnostic and prognostic functions with a precise performance profile regarding specificity, sensitivity, and positive and negative predictive value are warranted...
2017: Methods in Molecular Biology
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"