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Wiley Interdisciplinary Reviews. Systems Biology and Medicine

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https://www.readbyqxmd.com/read/29334187/surveying-the-landscape-of-optogenetic-methods-for-detection-of-protein-protein-interactions
#1
REVIEW
Matthew D Wiens, Robert E Campbell
Mapping the protein-protein interaction (PPi) landscape is of critical importance to furthering our understanding how cells and organisms function. Optogenetic methods, that is, approaches that utilize genetically encoded fluorophores or fluorogenic enzyme reactions, uniquely enable the visualization of biochemical phenomena in live cells with high spatial and temporal accuracy. Applying optogenetic methods to the detection of PPis requires the engineering of protein-based systems in which an optical signal undergoes a substantial change when the two proteins of interest interact...
January 15, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29316320/human-microbiota-blood-group-antigens-and-disease
#2
REVIEW
D Rose Ewald, Susan C J Sumner
Far from being just "bugs in our guts," the microbiota interacts with the body in previously unimagined ways. Research into the genome and the microbiome has revealed that the human body and the microbiota have a long-established but only recently recognized symbiotic relationship; homeostatic balance between them regulates body function. That balance is fragile, easily disturbed, and plays a fundamental role in human health-our very survival depends on the healthy functioning of these microorganisms. Increasing rates of cardiovascular, autoimmune, and inflammatory diseases, as well as epidemics in obesity and diabetes in recent decades are believed to be explained, in part, by unintended effects on the microbiota from vaccinations, poor diets, environmental chemicals, indiscriminate antibiotic use, and "germophobia...
January 9, 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29195023/computational-modeling-of-single-cell-mechanics-and-cytoskeletal-mechanobiology
#3
REVIEW
Vijay Rajagopal, William R Holmes, Peter Vee Sin Lee
Cellular cytoskeletal mechanics plays a major role in many aspects of human health from organ development to wound healing, tissue homeostasis and cancer metastasis. We summarize the state-of-the-art techniques for mathematically modeling cellular stiffness and mechanics and the cytoskeletal components and factors that regulate them. We highlight key experiments that have assisted model parameterization and compare the advantages of different models that have been used to recapitulate these experiments. An overview of feed-forward mechanisms from signaling to cytoskeleton remodeling is provided, followed by a discussion of the rapidly growing niche of encapsulating feedback mechanisms from cytoskeletal and cell mechanics to signaling...
November 30, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29194997/piecing-together-cis-regulatory-networks-insights-from-epigenomics-studies-in-plants
#4
REVIEW
Shao-Shan Huang, Joseph Ecker
5-Methylcytosine, a chemical modification of DNA, is a covalent modification found in the genomes of both plants and animals. Epigenetic inheritance of phenotypes mediated by DNA methylation is well established in plants. Most of the known mechanisms of establishing, maintaining and modifying DNA methylation have been worked out in the reference plant Arabidopsis thaliana. Major functions of DNA methylation in plants include regulation of gene expression and silencing of transposable elements (TEs) and repetitive sequences, both of which have parallels in mammalian biology, involve interaction with the transcriptional machinery, and may have profound effects on the regulatory networks in the cell...
November 30, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29148257/multiscale-memory-and-bioelectric-error-correction-in-the-cytoplasm-cytoskeleton-membrane-system
#5
REVIEW
Chris Fields, Michael Levin
A fundamental aspect of life is the modification of anatomy, physiology, and behavior in the face of changing conditions. This is especially illustrated by the adaptive regulation of growth and form that underlies the ability of most organisms-from single cells to complex large metazoa-to develop, remodel, and regenerate to specific anatomical patterns. What is the relationship of the genome and other cellular components to the robust computations that underlie this remarkable pattern homeostasis? Here we examine the role of constraints defined at the cellular level, especially endogenous bioelectricity, in generating and propagating biological information...
November 17, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29083112/immunity-to-crispr-cas9-and-cas12a-therapeutics
#6
REVIEW
Wei Leong Chew
Genome-editing therapeutics are poised to treat human diseases. As we enter clinical trials with the most promising CRISPR-Cas9 and CRISPR-Cas12a (Cpf1) modalities, the risks associated with administering these foreign biomolecules into human patients become increasingly salient. Preclinical discovery with CRISPR-Cas9 and CRISPR-Cas12a systems and foundational gene therapy studies indicate that the host immune system can mount undesired responses against the administered proteins and nucleic acids, the gene-edited cells, and the host itself...
January 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28644920/genome-scale-metabolic-models-applied-to-human-health-and-disease
#7
REVIEW
Daniel J Cook, Jens Nielsen
Advances in genome sequencing, high throughput measurement of gene and protein expression levels, data accessibility, and computational power have allowed genome-scale metabolic models (GEMs) to become a useful tool for understanding metabolic alterations associated with many different diseases. Despite the proven utility of GEMs, researchers confront multiple challenges in the use of GEMs, their application to human health and disease, and their construction and simulation in an organ-specific and disease-specific manner...
November 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28608962/image-based-computational-fluid-dynamics-in-the-lung-virtual-reality-or-new-clinical-practice
#8
REVIEW
Kelly S Burrowes, Jan De Backer, Haribalan Kumar
The development and implementation of personalized medicine is paramount to improving the efficiency and efficacy of patient care. In the respiratory system, function is largely dictated by the choreographed movement of air and blood to the gas exchange surface. The passage of air begins in the upper airways, either via the mouth or nose, and terminates at the alveolar interface, while blood flows from the heart to the alveoli and back again. Computational fluid dynamics (CFD) is a well-established tool for predicting fluid flows and pressure distributions within complex systems...
November 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28544810/the-best-models-of-metabolism
#9
REVIEW
Eberhard O Voit
Biochemical systems are among of the oldest application areas of mathematical modeling. Spanning a time period of over one hundred years, the repertoire of options for structuring a model and for formulating reactions has been constantly growing, and yet, it is still unclear whether or to what degree some models are better than others and how the modeler is to choose among them. In fact, the variety of options has become overwhelming and difficult to maneuver for novices and experts alike. This review outlines the metabolic model design process and discusses the numerous choices for modeling frameworks and mathematical representations...
November 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28990735/metabolism-in-cancer-metastasis-bioenergetics-biosynthesis-and-beyond
#10
REVIEW
Shao Thing Teoh, Sophia Y Lunt
Metabolic changes accompany tumor progression and metastatic dissemination of cancer cells. Yet, until recently, metabolism has received little attention in the study of cancer metastasis. Cancer cells undergo significant metabolic rewiring as they acquire metastatic traits and adapt to survive in multiple environments with varying nutrient availability, oxygen concentrations, and extracellular signals. Therefore, to effectively treat metastatic cancer, it is important to understand the metabolic strategies adopted by cancer cells during the metastatic process...
October 9, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28960879/small-molecule-signaling-regulation-and-potential-applications-in-cellular-therapeutics
#11
REVIEW
Monica P McNerney, Mark P Styczynski
Small molecules have many important roles across the tree of life: they regulate processes from metabolism to transcription, they enable signaling within and between species, and they serve as the biochemical building blocks for cells. They also represent valuable phenotypic endpoints that are promising for use as biomarkers of disease states. In the context of engineering cell-based therapeutics, they hold particularly great promise for enabling finer control over the therapeutic cells and allowing them to be responsive to extracellular cues...
September 28, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28892308/targeting-epidermal-growth-factor-receptor-co-dependent-signaling-pathways-in-glioblastoma
#12
Feng Liu, Paul S Mischel
The epidermal growth factor receptor (EGFR) is a transmembrane receptor tyrosine kinase (RTK) that is critical for normal development and function. EGFR is also amplified or mutated in a variety of cancers including in nearly 60% of cases of the highly lethal brain cancer glioblastoma (GBM). EGFR amplification and mutation reprogram cellular metabolism and broadly alter gene transcription to drive tumor formation and progression, rendering EGFR as a compelling drug target. To date, brain tumor patients have yet to benefit from anti-EGFR therapy due in part to an inability to achieve sufficient intratumoral drug levels in the brain, cultivating adaptive mechanisms of resistance...
September 11, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28510289/genome-organization-during-the-cell-cycle-unity-in-division
#13
REVIEW
Rosela Golloshi, Jacob T Sanders, Rachel Patton McCord
During the cell cycle, the genome must undergo dramatic changes in structure, from a decondensed, yet highly organized interphase structure to a condensed, generic mitotic chromosome and then back again. For faithful cell division, the genome must be replicated and chromosomes and sister chromatids physically segregated from one another. Throughout these processes, there is feedback and tension between the information-storing role and the physical properties of chromosomes. With a combination of recent techniques in fluorescence microscopy, chromosome conformation capture (Hi-C), biophysical experiments, and computational modeling, we can now attribute mechanisms to many long-observed features of chromosome structure changes during cell division...
September 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28498625/biomechanics-of-the-human-uterus
#14
REVIEW
Kristin M Myers, David Elad
The appropriate biomechanical function of the uterus is required for the execution of human reproduction. These functions range from aiding the transport of the embryo to the implantation site, to remodeling its tissue walls to host the placenta, to protecting the fetus during gestation, to contracting forcefully for a safe parturition and postpartum, to remodeling back to its nonpregnant condition to renew the cycle of menstruation. To serve these remarkably diverse functions, the uterus is optimally geared with evolving and contractile muscle and tissue layers that are cued by chemical, hormonal, electrical, and mechanical signals...
September 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28488813/imaging-mass-spectrometry-for-metabolites-technical-progress-multimodal-imaging-and-biological-interactions
#15
REVIEW
Ying-Ning Ho, Lin-Jie Shu, Yu-Liang Yang
Imaging mass spectrometry (IMS) allows the study of the spatial distribution of small molecules in biological samples. IMS is able to identify and quantify chemicals in situ from whole tissue sections to single cells. Both vacuum mass spectrometry (MS) and ambient MS systems have advanced considerably over the last decade; however, some limitations are still hard to surmount. Sample pretreatment, matrix or solvent choices, and instrument improvement are the key factors that determine the successful application of IMS to different samples and analytes...
September 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28475297/systems-biology-of-cellular-membranes-a-convergence-with-biophysics
#16
REVIEW
Morgan Chabanon, Jeanne C Stachowiak, Padmini Rangamani
Systems biology and systems medicine have played an important role in the last two decades in shaping our understanding of biological processes. While systems biology is synonymous with network maps and '-omics' approaches, it is not often associated with mechanical processes. Here, we make the case for considering the mechanical and geometrical aspects of biological membranes as a key step in pushing the frontiers of systems biology of cellular membranes forward. We begin by introducing the basic components of cellular membranes, and highlight their dynamical aspects...
September 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28857478/metabolic-interactions-in-cancer-cellular-metabolism-at-the-interface-between-the-microenvironment-the-cancer-cell-phenotype-and-the-epigenetic-landscape
#17
REVIEW
Gianmarco Rinaldi, Matteo Rossi, Sarah-Maria Fendt
Metabolism is tied into complex interactions with cell intrinsic and extrinsic processes that go beyond the conversion of nutrients into energy and biomass. Indeed, metabolism is a central cellular hub that interconnects and influences the microenvironment, the cellular phenotype, cell signaling, and the (epi)genetic landscape. While these interactions evolved to support survival and function of normal cells, they are hijacked by cancer cells to enable cancer maintenance and progression. Thus, a mechanistic and functional understanding of complex metabolic interactions provides a basis for the discovery of novel metabolic vulnerabilities in cancer...
August 30, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28810056/crosstalk-between-transcription-and-metabolism-how-much-enzyme-is-enough-for-a-cell
#18
REVIEW
Stefano Donati, Timur Sander, Hannes Link
Cells employ various mechanisms for dynamic control of enzyme expression. An important mechanism is mutual feedback-or crosstalk-between transcription and metabolism. As recently suggested, enzyme levels are often much higher than absolutely needed to maintain metabolic flux. However, given the potential burden of high enzyme levels it seems likely that cells control enzyme expression to meet other cellular objectives. In this review, we discuss whether crosstalk between metabolism and transcription could inform cells about how much enzyme is optimal for various fitness aspects...
August 15, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28787545/stability-analysis-in-spatial-modeling-of-cell-signaling
#19
REVIEW
Michael C Getz, Jasmine A Nirody, Padmini Rangamani
Advances in high-resolution microscopy and other techniques have emphasized the spatio-temporal nature of information transfer through signal transduction pathways. The compartmentalization of signaling molecules and the existence of microdomains are now widely acknowledged as key features in biochemical signaling. To complement experimental observations of spatio-temporal dynamics, mathematical modeling has emerged as a powerful tool. Using modeling, one can not only recapitulate experimentally observed dynamics of signaling molecules, but also gain an understanding of the underlying mechanisms in order to generate experimentally testable predictions...
August 8, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28221004/systems-biology-of-oxygen-homeostasis
#20
REVIEW
Debangshu Samanta, Nanduri R Prabhakar, Gregg L Semenza
Metazoan species maintain oxygen homeostasis through the activity of hypoxia-inducible factors, which are transcriptional activators that regulate the expression of hundreds of genes to match O2 supply and demand. Here, we review the involvement of hypoxia-inducible factors in the molecular physiology and pathophysiology of cellular O2 sensing, O2 delivery, O2 utilization, and systemic O2 sensing. WIREs Syst Biol Med 2017, 9:e1382. doi: 10.1002/wsbm.1382 For further resources related to this article, please visit the WIREs website...
July 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
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