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Wiley Interdisciplinary Reviews. Systems Biology and Medicine

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https://www.readbyqxmd.com/read/28221004/systems-biology-of-oxygen-homeostasis
#1
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
#2
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
#3
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/28207198/integrated-precision-medicine-the-role-of-electronic-health-records-in-delivering-personalized-treatment
#4
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...
February 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28206708/physiological-metabolic-and-biotechnological-features-of-extremely-thermophilic-microorganisms
#5
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...
February 16, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28198142/therapeutic-genome-engineering-via-crispr-cas-systems
#6
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
https://www.readbyqxmd.com/read/28186392/understanding-the-mtor-signaling-pathway-via-mathematical-modeling
#7
REVIEW
Nurgazy Sulaimanov, Martin Klose, Hauke Busch, Melanie Boerries
The mechanistic target of rapamycin (mTOR) is a central regulatory pathway that integrates a variety of environmental cues to control cellular growth and homeostasis by intricate molecular feedbacks. In spite of extensive knowledge about its components, the molecular understanding of how these function together in space and time remains poor and there is a need for Systems Biology approaches to perform systematic analyses. In this work, we review the recent progress how the combined efforts of mathematical models and quantitative experiments shed new light on our understanding of the mTOR signaling pathway...
February 10, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28102563/multiscale-modeling-methods-in-biomechanics
#8
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...
January 19, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/28093886/regulatory-elements-in-molecular-networks
#9
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
#10
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
#11
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
#12
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
#13
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/27911047/modified-mrna-as-a-therapeutic-tool-to-induce-cardiac-regeneration-in-ischemic-heart-disease
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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/28002649/toward-modeling-locomotion-using-electromyography-informed-3d-models-application-to-cerebral-palsy
#20
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
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