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Wiley Interdisciplinary Reviews. Systems Biology and Medicine

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https://www.readbyqxmd.com/read/28093886/regulatory-elements-in-molecular-networks
#1
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...
January 17, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28078793/insights-into-nuclear-dynamics-using-live-cell-imaging-approaches
#2
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...
January 12, 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
#3
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...
January 9, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28009109/computational-models-of-the-neural-control-of-breathing
#4
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...
December 23, 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28002649/toward-modeling-locomotion-using-electromyography-informed-3d-models-application-to-cerebral-palsy
#5
REVIEW
M Sartori, J W Fernandez, L Modenese, C P Carty, L A Barber, K Oberhofer, J Zhang, G G Handsfield, N S Stott, T F Besier, D Farina, D G Lloyd
This position paper proposes a modeling pipeline to develop clinically relevant neuromusculoskeletal models to understand and treat complex neurological disorders. Although applicable to a variety of neurological conditions, we provide direct pipeline applicative examples in the context of cerebral palsy (CP). This paper highlights technologies in: (1) patient-specific segmental rigid body models developed from magnetic resonance imaging for use in inverse kinematics and inverse dynamics pipelines; (2) efficient population-based approaches to derive skeletal models and muscle origins/insertions that are useful for population statistics and consistent creation of continuum models; (3) continuum muscle descriptions to account for complex muscle architecture including spatially varying material properties with muscle wrapping; (4) muscle and tendon properties specific to CP; and (5) neural-based electromyography-informed methods for muscle force prediction...
December 21, 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28001340/quantitative-approaches-for-investigating-the-spatial-context-of-gene-expression
#6
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...
December 21, 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27943646/cancer-and-inflammation
#7
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...
December 12, 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27911047/modified-mrna-as-a-therapeutic-tool-to-induce-cardiac-regeneration-in-ischemic-heart-disease
#8
REVIEW
Yoav Hadas, Michael G Katz, Charles R Bridges, Lior Zangi
Ischemic heart disease (IHD) is a leading cause of morbidity and mortality in developed countries. Current pharmacological and interventional therapies provide significant improvement in the life quality of patient; however, they are mostly symptom-oriented and not curative. A high disease and economic burden of IHD requires the search for new therapeutic strategies to significantly improve patients' prognosis and quality of life. One of the main challenges during IHD is the massive loss of cardiomyocytes that possess minimal regenerative capacity...
January 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27906527/behavioral-epigenetics
#9
REVIEW
David S Moore
Why do we grow up to have the traits we do? Most 20th century scientists answered this question by referring only to our genes and our environments. But recent discoveries in the emerging field of behavioral epigenetics have revealed factors at the interface between genes and environments that also play crucial roles in development. These factors affect how genes work; scientists now know that what matters as much as which genes you have (and what environments you encounter) is how your genes are affected by their contexts...
January 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27863122/modeling-signaling-and-cytoskeleton-dynamics-integrated-modeling-experimental-frameworks-in-cell-migration
#10
REVIEW
Meng Sun, Muhammad H Zaman
Cell migration is a complex and multistep process involved in homeostasis maintenance, morphogenesis, and disease development, such as cancer metastasis. Modeling cell migration and the relevant cytoskeleton dynamics have profound implications for studying fundamental development and disease diagnosis. This review focuses on some recent models of both cell migration and migration-related cytoskeleton dynamics, addressing issues such as the difference between amoeboid and mesenchymal migration modes, and between single-cell migration and collective cell migration...
January 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27863091/computational-approaches-for-the-identification-of-cancer-genes-and-pathways
#11
REVIEW
Christos M Dimitrakopoulos, Niko Beerenwinkel
High-throughput DNA sequencing techniques enable large-scale measurement of somatic mutations in tumors. Cancer genomics research aims at identifying all cancer-related genes and solid interpretation of their contribution to cancer initiation and development. However, this venture is characterized by various challenges, such as the high number of neutral passenger mutations and the complexity of the biological networks affected by driver mutations. Based on biological pathway and network information, sophisticated computational methods have been developed to facilitate the detection of cancer driver mutations and pathways...
January 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27612162/mathematical-modeling-of-the-female-reproductive-system-from-oocyte-to-delivery
#12
REVIEW
Alys R Clark, Jennifer A Kruger
From ovulation to delivery, and through the menstrual cycle, the female reproductive system undergoes many dynamic changes to provide an optimal environment for the embryo to implant, and to develop successfully. It is difficult ethically and practically to observe the system over the timescales involved in growth and development (often hours to days). Even in carefully monitored conditions clinicians and biologists can only see snapshots of the development process. Mathematical models are emerging as a key means to supplement our knowledge of the reproductive process, and to tease apart complexity in the reproductive system...
January 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27599643/network-dynamics-quantitative-analysis-of-complex-behavior-in-metabolism-organelles-and-cells-from-experiments-to-models-and-back
#13
REVIEW
Felix T Kurz, Jackelyn M Kembro, Ana G Flesia, Antonis A Armoundas, Sonia Cortassa, Miguel A Aon, David Lloyd
Advancing from two core traits of biological systems: multilevel network organization and nonlinearity, we review a host of novel and readily available techniques to explore and analyze their complex dynamic behavior within the framework of experimental-computational synergy. In the context of concrete biological examples, analytical methods such as wavelet, power spectra, and metabolomics-fluxomics analyses, are presented, discussed, and their strengths and limitations highlighted. Further shown is how time series from stationary and nonstationary biological variables and signals, such as membrane potential, high-throughput metabolomics, O2 and CO2 levels, bird locomotion, at the molecular, (sub)cellular, tissue, and whole organ and animal levels, can reveal important information on the properties of the underlying biological networks...
January 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27600060/in-silico-bone-mechanobiology-modeling-a-multifaceted-biological-system
#14
REVIEW
Mario Giorgi, Stefaan W Verbruggen, Damien Lacroix
Mechanobiology, the study of the influence of mechanical loads on biological processes through signaling to cells, is fundamental to the inherent ability of bone tissue to adapt its structure in response to mechanical stimulation. The immense contribution of computational modeling to the nascent field of bone mechanobiology is indisputable, having aided in the interpretation of experimental findings and identified new avenues of inquiry. Indeed, advances in computational modeling have spurred the development of this field, shedding new light on problems ranging from the mechanical response to loading by individual cells to tissue differentiation during events such as fracture healing...
November 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27599872/blood-type-biochemistry-and-human-disease
#15
REVIEW
D Rose Ewald, Susan C J Sumner
Associations between blood type and disease have been studied since the early 1900s when researchers determined that antibodies and antigens are inherited. In the 1950s, the chemical identification of the carbohydrate structure of surface antigens led to the understanding of biosynthetic pathways. The blood type is defined by oligosaccharide structures, which are specific to the antigens, thus, blood group antigens are secondary gene products, while the primary gene products are various glycosyltransferase enzymes that attach the sugar molecules to the oligosaccharide chain...
November 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27599755/data-sources-for-in-vivo-molecular-profiling-of-human-phenotypes
#16
REVIEW
Timothy Cardozo, Priyanka Gupta, Eric Ni, Lauren M Young, Doreen Tivon, Klara Felsovalyi
Molecular profiling of human diseases has been approached at the genetic (DNA), expression (RNA), and proteomic (protein) levels. An important goal of these efforts is to map observed molecular patterns to specific, mechanistic organic entities, such as loci in the genome, individual RNA molecules or defined proteins or protein assemblies. Importantly, such maps have been historically approached in the more intuitive context of a theoretical individual cell, but diseases are better described in reality using an in vivo framework, namely a library of several tissue-specific maps...
November 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27558763/modeling-the-second-stage-of-labor
#17
Xiani Yan, Jennifer A Kruger, Xinshan Li, Poul M F Nielsen, Martyn P Nash
Vaginal delivery is the primary cause of levator ani muscle injury, which is in turn the leading factor contributing to pelvic floor disorders including pelvic organ prolapse and urinary stress incontinence. Existing biomechanical models of childbirth have provided some understanding of pelvic floor function during delivery and have helped in the investigation of preventative strategies. The modeling frameworks for childbirth simulation are described with emphasis on (1) the recent advances in medical imaging quality and computational power; (2) improvements in the anatomical representation of the pelvic floor and fetal head; (3) more realistic boundary conditions for delivery; and (4) mechanical properties determined from experiments...
November 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27348217/systems-level-airway-models-of-bronchoconstriction
#18
REVIEW
Graham M Donovan
Understanding lung and airway behavior presents a number of challenges, both experimental and theoretical, but the potential rewards are great in terms of both potential treatments for disease and interesting biophysical phenomena. This presents an opportunity for modeling to contribute to greater understanding, and here, we focus on modeling efforts that work toward understanding the behavior of airways in vivo, with an emphasis on asthma. We look particularly at those models that address not just isolated airways but many of the important ways in which airways are coupled both with each other and with other structures...
September 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27341681/engineering-of-synthetic-gene-circuits-for-re-balancing-physiological-processes-in-chronic-diseases
#19
REVIEW
Lina Schukur, Martin Fussenegger
Synthetic biology is a promising multidisciplinary field that brings together experts in scientific disciplines from cell biology to engineering with the goal of constructing elements that do not occur in nature for use in various applications, such as the development of novel approaches to improving healthcare management. Current disease treatment strategies are typically based on the diagnosis of phenotypic changes, which are often the result of an accumulation of endogenous metabolic defects in the human body...
September 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/27341633/omics-based-approaches-to-understand-mechanosensitive-endothelial-biology-and-atherosclerosis
#20
REVIEW
Rachel D Simmons, Sandeep Kumar, Salim Raid Thabet, Sanjoli Sur, Hanjoong Jo
Atherosclerosis is a multifactorial disease that preferentially occurs in arterial regions exposed to d-flow can be used to indicate disturbed flow or disturbed blood flow. The mechanisms by which d-flow induces atherosclerosis involve changes in the transcriptome, methylome, proteome, and metabolome of multiple vascular cells, especially endothelial cells. Initially, we begin with the pathogenesis of atherosclerosis and the changes that occur at multiple levels owing to d-flow, especially in the endothelium...
September 2016: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
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