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Cells, Volume 2, Issue 4 (December 2013), Pages 635-767

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Review

Open AccessReview Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering
Cells 2013, 2(4), 635-688; doi:10.3390/cells2040635
Received: 16 April 2013 / Revised: 12 September 2013 / Accepted: 19 September 2013 / Published: 11 October 2013
Cited by 2 | PDF Full-text (3105 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism
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Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. Full article
(This article belongs to the Special Issue Feature Papers 2013)
Open AccessReview Pharmacological Profiles of Oligomerized μ-Opioid Receptors
Cells 2013, 2(4), 689-714; doi:10.3390/cells2040689
Received: 21 August 2013 / Revised: 30 September 2013 / Accepted: 9 October 2013 / Published: 11 October 2013
Cited by 3 | PDF Full-text (261 KB) | HTML Full-text | XML Full-text
Abstract
Opioids are widely prescribed pain relievers with multiple side effects and potential complications. They produce analgesia via G-protein-protein coupled receptors: μ-, δ-, κ-opioid and opioid receptor-like 1 receptors. Bivalent ligands targeted to the oligomerized opioid receptors might be the key to developing analgesics
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Opioids are widely prescribed pain relievers with multiple side effects and potential complications. They produce analgesia via G-protein-protein coupled receptors: μ-, δ-, κ-opioid and opioid receptor-like 1 receptors. Bivalent ligands targeted to the oligomerized opioid receptors might be the key to developing analgesics without undesired side effects and obtaining effective treatment for opioid addicts. In this review we will update the biological effects of μ-opioids on homo- or hetero-oligomerized μ-opioid receptor and discuss potential mechanisms through which bivalent ligands exert beneficial effects, including adenylate cyclase regulation and receptor-mediated signaling pathways. Full article
(This article belongs to the Special Issue Oligomerization & Trafficking of Opioid Receptors)
Open AccessReview Actin in Action: Imaging Approaches to Study Cytoskeleton Structure and Function
Cells 2013, 2(4), 715-731; doi:10.3390/cells2040715
Received: 1 September 2013 / Revised: 6 November 2013 / Accepted: 8 November 2013 / Published: 14 November 2013
Cited by 2 | PDF Full-text (1266 KB) | HTML Full-text | XML Full-text
Abstract
The cytoskeleton plays several fundamental roles in the cell, including organizing the spatial arrangement of subcellular organelles, regulating cell dynamics and motility, providing a platform for interaction with neighboring cells, and ultimately defining overall cell shape. Fluorescence imaging has proved to be vital
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The cytoskeleton plays several fundamental roles in the cell, including organizing the spatial arrangement of subcellular organelles, regulating cell dynamics and motility, providing a platform for interaction with neighboring cells, and ultimately defining overall cell shape. Fluorescence imaging has proved to be vital in furthering our understanding of the cytoskeleton, and is now a mainstay technique used widely by cell biologists. In this review we provide an introduction to various imaging modalities used to study focal adhesions and the actin cytoskeleton, and using specific examples we highlight a number of recent studies in animal cells that have advanced our knowledge of cytoskeletal behavior. Full article
(This article belongs to the Special Issue Imaging in Cell Biology and Development)
Open AccessReview Ubiquitination Regulates the Morphogenesis and Function of Sperm Organelles
Cells 2013, 2(4), 732-750; doi:10.3390/cells2040732
Received: 7 October 2013 / Revised: 12 November 2013 / Accepted: 29 November 2013 / Published: 5 December 2013
Cited by 6 | PDF Full-text (506 KB) | HTML Full-text | XML Full-text
Abstract
It is now understood that protein ubiquitination has diverse cellular functions in eukaryotes. The molecular mechanism and physiological significance of ubiquitin-mediated processes have been extensively studied in yeast, Drosophila and mammalian somatic cells. Moreover, an increasing number of studies have emphasized the importance
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It is now understood that protein ubiquitination has diverse cellular functions in eukaryotes. The molecular mechanism and physiological significance of ubiquitin-mediated processes have been extensively studied in yeast, Drosophila and mammalian somatic cells. Moreover, an increasing number of studies have emphasized the importance of ubiquitination in spermatogenesis and fertilization. The dysfunction of various ubiquitin systems results in impaired sperm development with abnormal organelle morphology and function, which in turn is highly associated with male infertility. This review will focus on the emerging roles of ubiquitination in biogenesis, function and stability of sperm organelles in mammals. Full article
(This article belongs to the Special Issue Protein Ubiquitination)
Open AccessReview How Do Gangliosides Regulate RTKs Signaling?
Cells 2013, 2(4), 751-767; doi:10.3390/cells2040751
Received: 29 October 2013 / Revised: 19 November 2013 / Accepted: 27 November 2013 / Published: 6 December 2013
Cited by 8 | PDF Full-text (488 KB) | HTML Full-text | XML Full-text
Abstract
Gangliosides, the glycosphingolipids carrying one or several sialic acid residues, are located on the outer leaflet of the plasma membrane in glycolipid-enriched microdomains, where they interact with molecules of signal transduction pathways including receptors tyrosine kinases (RTKs). The role of gangliosides in the
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Gangliosides, the glycosphingolipids carrying one or several sialic acid residues, are located on the outer leaflet of the plasma membrane in glycolipid-enriched microdomains, where they interact with molecules of signal transduction pathways including receptors tyrosine kinases (RTKs). The role of gangliosides in the regulation of signal transduction has been reported in many cases and in a large number of cell types. In this review, we summarize the current knowledge on the biosynthesis of gangliosides and the mechanism by which they regulate RTKs signaling. Full article
(This article belongs to the Special Issue Receptor Tyrosine Kinases)
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