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Wiley Interdisciplinary Reviews. Systems Biology and Medicine

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https://www.readbyqxmd.com/read/28544514/dynamic-enhancer-function-in-the-chromatin-context
#1
REVIEW
Ido Goldstein, Gordon L Hager
Enhancers serve as critical regulatory elements in higher eukaryotic cells. The characterization of enhancer function has evolved primarily from genome-wide methodologies, including chromatin immunoprecipitation (ChIP-seq), DNase-I hypersensitivity (DNase-seq), digital genomic footprinting (DGF), and the chromosome conformation capture techniques (3C, 4C, and Hi-C). These population-based assays average signals across millions of cells and lead to enhancer models characterized by static and sequential binding...
May 22, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28544810/the-best-models-of-metabolism
#2
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...
May 19, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28510289/genome-organization-during-the-cell-cycle-unity-in-division
#3
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...
May 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28498625/biomechanics-of-the-human-uterus
#4
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...
May 12, 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
#5
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...
May 10, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28488754/virtual-endovascular-treatment-of-intracranial-aneurysms-models-and-uncertainty
#6
REVIEW
Ali Sarrami-Foroushani, Toni Lassila, Alejandro F Frangi
Virtual endovascular treatment models (VETMs) have been developed with the view to aid interventional neuroradiologists and neurosurgeons to pre-operatively analyze the comparative efficacy and safety of endovascular treatments for intracranial aneurysms. Based on the current state of VETMs in aneurysm rupture risk stratification and in patient-specific prediction of treatment outcomes, we argue there is a need to go beyond personalized biomechanical flow modeling assuming deterministic parameters and error-free measurements...
May 10, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28475297/systems-biology-of-cellular-membranes-a-convergence-with-biophysics
#7
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...
May 5, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28207198/integrated-precision-medicine-the-role-of-electronic-health-records-in-delivering-personalized-treatment
#8
REVIEW
Amy Sitapati, Hyeoneui Kim, Barbara Berkovich, Rebecca Marmor, Siddharth Singh, Robert El-Kareh, Brian Clay, Lucila Ohno-Machado
Precision Medicine involves the delivery of a targeted, personalized treatment for a given patient. By harnessing the power of electronic health records (EHRs), we are increasingly able to practice precision medicine to improve patient outcomes. In this article, we introduce the scientific community at large to important building blocks for personalized treatment, such as terminology standards that are the foundation of the EHR and allow for exchange of health information across systems. We briefly review different types of clinical decision support (CDS) and present the current state of CDS, which is already improving the care patients receive with genetic profile-based tailored recommendations regarding diagnostic and treatment plans...
May 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28206708/physiological-metabolic-and-biotechnological-features-of-extremely-thermophilic-microorganisms
#9
REVIEW
James A Counts, Benjamin M Zeldes, Laura L Lee, Christopher T Straub, Michael W W Adams, Robert M Kelly
The current upper thermal limit for life as we know it is approximately 120°C. Microorganisms that grow optimally at temperatures of 75°C and above are usually referred to as 'extreme thermophiles' and include both bacteria and archaea. For over a century, there has been great scientific curiosity in the basic tenets that support life in thermal biotopes on earth and potentially on other solar bodies. Extreme thermophiles can be aerobes, anaerobes, autotrophs, heterotrophs, or chemolithotrophs, and are found in diverse environments including shallow marine fissures, deep sea hydrothermal vents, terrestrial hot springs-basically, anywhere there is hot water...
May 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28102563/multiscale-modeling-methods-in-biomechanics
#10
REVIEW
Pinaki Bhattacharya, Marco Viceconti
More and more frequently, computational biomechanics deals with problems where the portion of physical reality to be modeled spans over such a large range of spatial and temporal dimensions, that it is impossible to represent it as a single space-time continuum. We are forced to consider multiple space-time continua, each representing the phenomenon of interest at a characteristic space-time scale. Multiscale models describe a complex process across multiple scales, and account for how quantities transform as we move from one scale to another...
May 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28093886/regulatory-elements-in-molecular-networks
#11
REVIEW
Ashley S Doane, Olivier Elemento
Regulatory elements determine the connectivity of molecular networks and mediate a variety of regulatory processes ranging from DNA looping to transcriptional, posttranscriptional, and posttranslational regulation. This review highlights our current understanding of the different types of regulatory elements found in molecular networks with a focus on DNA regulatory elements. We highlight technical advances and current challenges for the mapping of regulatory elements at the genome-wide scale, and describe new computational methods to uncover these elements via reconstructing regulatory networks from large genomic datasets...
May 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28078793/insights-into-nuclear-dynamics-using-live-cell-imaging-approaches
#12
REVIEW
Rachel B Bigley, Alexander Y Payumo, Jeffrey M Alexander, Guo N Huang
The nucleus contains the genetic blueprint of the cell and myriad interactions within this subcellular structure are required for gene regulation. In the current scientific era, characterization of these gene regulatory networks through biochemical techniques coupled with systems-wide 'omic' approaches has become commonplace. However, these strategies are limited because they represent a mere snapshot of the cellular state. To obtain a holistic understanding of nuclear dynamics, relevant molecules must be studied in their native contexts in living systems...
March 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28067471/traditional-and-novel-tools-to-probe-the-mitochondrial-metabolism-in-health-and-disease
#13
REVIEW
Yanfei Zhang, José L Avalos
Mitochondrial metabolism links energy production to other essential cellular processes such as signaling, cellular differentiation, and apoptosis. In addition to producing adenosine triphosphate (ATP) as an energy source, mitochondria are responsible for the synthesis of a myriad of important metabolites and cofactors such as tetrahydrofolate, α-ketoacids, steroids, aminolevulinic acid, biotin, lipoic acid, acetyl-CoA, iron-sulfur clusters, heme, and ubiquinone. Furthermore, mitochondria and their metabolism have been implicated in aging and several human diseases, including inherited mitochondrial disorders, cardiac dysfunction, heart failure, neurodegenerative diseases, diabetes, and cancer...
March 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28009109/computational-models-of-the-neural-control-of-breathing
#14
REVIEW
Yaroslav I Molkov, Jonathan E Rubin, Ilya A Rybak, Jeffrey C Smith
The ongoing process of breathing underlies the gas exchange essential for mammalian life. Each respiratory cycle ensues from the activity of rhythmic neural circuits in the brainstem, shaped by various modulatory signals, including mechanoreceptor feedback sensitive to lung inflation and chemoreceptor feedback dependent on gas composition in blood and tissues. This paper reviews a variety of computational models designed to reproduce experimental findings related to the neural control of breathing and generate predictions for future experimental testing...
March 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28001340/quantitative-approaches-for-investigating-the-spatial-context-of-gene-expression
#15
REVIEW
Je H Lee
The spatial information associated with gene expression is important for elucidating the context-dependent transcriptional regulation during development. Recently, high-resolution sampling approaches, such as RNA tomography or single-cell RNA-seq combined with fluorescence in situ hybridization (FISH), have provided indirect ways to view global gene expression patterns in three dimensions. Now in situ sequencing technologies, such as fluorescent in situ sequencing (FISSEQ), are attempting to visualize the genetic signature directly in microscope images...
March 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27943646/cancer-and-inflammation
#16
REVIEW
Lance L Munn
The relationship between inflammation and cancer has been recognized since the 17(th) century,(1) and we now know much about the cells, cytokines and physiological processes that are central to both inflammation and cancer.(2-9) Chronic inflammation can induce certain cancers,(10-17) and solid tumors, in turn, can initiate and perpetuate local inflammatory processes that foster tumor growth and dissemination.(5) ,(18-20) Consequently, inflammatory pathways have been targeted in attempts to control cancer.(21-23) Inflammation is a central aspect of the innate immune system's response to tissue damage or infection, and also facilitates the recruitment of circulating cells and antibodies of the adaptive immune response to the tissue...
March 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28221004/systems-biology-of-oxygen-homeostasis
#17
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. For further resources related to this article, please visit the WIREs website.
February 21, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28221003/trends-in-high-throughput-and-functional-neuroimaging-in-caenorhabditis-elegans
#18
REVIEW
Yongmin Cho, Charles L Zhao, Hang Lu
The nervous system of Caenorhabditis elegans is an important model system for understanding the development and function of larger, more complex nervous systems. It is prized for its ease of handling, rapid life cycle, and stereotyped, well-cataloged development, with the development of all 302 neurons mapped all the way from zygote to adult. The combination of easy genetic manipulation and optical transparency of the worm allows for the direct imaging of its interior with fluorescent microscopy, without physically compromising the normal physiology of the animal itself...
February 21, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28211993/recent-lab-on-chip-developments-for-novel-drug-discovery
#19
REVIEW
Nauman Khalid, Isao Kobayashi, Mitsutoshi Nakajima
Microelectromechanical systems (MEMS) and micro total analysis systems (μTAS) revolutionized the biochemical and electronic industries, and this miniaturization process became a key driver for many markets. Now, it is a driving force for innovations in life sciences, diagnostics, analytical sciences, and chemistry, which are called 'lab-on-a-chip, (LOC)' devices. The use of these devices allows the development of fast, portable, and easy-to-use systems with a high level of functional integration for applications such as point-of-care diagnostics, forensics, the analysis of biomolecules, environmental or food analysis, and drug development...
February 17, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28198142/therapeutic-genome-engineering-via-crispr-cas-systems
#20
REVIEW
Ana M Moreno, Prashant Mali
Differences in genomes underlie most organismal diversity, and aberrations in genomes underlie many disease states. With the growing knowledge of the genetic and pathogenic basis of human disease, development of safe and efficient platforms for genome and epigenome engineering will transform our ability to therapeutically target human diseases and also potentially engineer disease resistance. In this regard, the recent advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) RNA-guided nuclease systems have transformed our ability to target nucleic acids...
February 15, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
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