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Biochemical Society Transactions

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https://www.readbyqxmd.com/read/29743277/small-gtpase-dependent-regulation-of-leukocyte-endothelial-interactions-in-inflammation
#1
REVIEW
Julia Y Chu, Barry McCormick, Sonja Vermeren
Inflammation is a complex biological response that serves to protect the body's tissues following harmful stimuli such as infection, irritation or injury and initiates tissue repair. At the start of an inflammatory response, pro-inflammatory mediators induce changes in the endothelial lining of the blood vessels and in leukocytes. This results in increased vascular permeability and increased expression of adhesion proteins, and promotes adhesion of leukocytes, especially neutrophils to the endothelium. Adhesion is a prerequisite for neutrophil extravasation and chemoattractant-stimulated recruitment to inflammatory sites, where neutrophils phagocytose and kill microbes, release inflammatory mediators and cross-talk with other immune cells to co-ordinate the immune response in preparation for tissue repair...
May 9, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29743276/non-coding-rna-in-cystic-fibrosis
#2
REVIEW
Arlene M A Glasgow, Chiara De Santi, Catherine M Greene
Non-coding RNAs (ncRNAs) are an abundant class of RNAs that include small ncRNAs, long non-coding RNAs (lncRNA) and pseudogenes. The human ncRNA atlas includes thousands of these specialised RNA molecules that are further subcategorised based on their size or function. Two of the more well-known and widely studied ncRNA species are microRNAs (miRNAs) and lncRNAs. These are regulatory RNAs and their altered expression has been implicated in the pathogenesis of a variety of human diseases. Failure to express a functional cystic fibrosis (CF) transmembrane receptor (CFTR) chloride ion channel in epithelial cells underpins CF...
May 9, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29743275/thermodynamic-constraints-for-identifying-elementary-flux-modes
#3
REVIEW
Sabine Peres, Stefan Schuster, Philippe Dague
Metabolic pathway analysis is a key method to study metabolism and the elementary flux modes (EFMs) is one major concept allowing one to analyze the network in terms of minimal pathways. Their practical use has been hampered by the combinatorial explosion of their number in large systems. The EFMs give the possible pathways at steady state, but the real pathways are limited by biological constraints. In this review, we display three different methods that integrate thermodynamic constraints in terms of Gibbs free energy in the EFMs computation...
May 9, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29743274/communicating-with-the-dead-lipids-lipid-mediators-and-extracellular-vesicles
#4
REVIEW
Andrew Devitt, Helen R Griffiths, Ivana Milic
Apoptosis is a key event in the control of inflammation. However, for this to be successful, dying cells must efficiently and effectively communicate their presence to phagocytes to ensure timely removal of dying cells. Here, we consider apoptotic cell-derived extracellular vesicles and the role of contained lipids and lipid mediators in ensuring effective control of inflammation. We discuss key outstanding issues in the study of cell death and cell communication, and introduce the concept of the ' active extracellular vesicle ' as a metabolically active and potentially changing intercellular communicator...
May 9, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29678956/local-actin-polymerization-during-endocytic-carrier-formation
#5
REVIEW
Claudia Hinze, Emmanuel Boucrot
Extracellular macromolecules, pathogens and cell surface proteins rely on endocytosis to enter cells. Key steps of endocytic carrier formation are cargo molecule selection, plasma membrane folding and detachment from the cell surface. While dedicated proteins mediate each step, the actin cytoskeleton contributes to all. However, its role can be indirect to the actual molecular events driving endocytosis. Here, we review our understanding of the molecular steps mediating local actin polymerization during the formation of endocytic carriers...
April 20, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29678955/studying-x-chromosome-inactivation-in-the-single-cell-genomic-era
#6
REVIEW
Andrew Keniry, Marnie E Blewitt
Single-cell genomics is set to revolutionise our understanding of how epigenetic silencing works; by studying specific epigenetic marks or chromatin conformations in single cells, it is possible to ask whether they cause transcriptional silencing or are instead a consequence of the silent state. Here, we review what single-cell genomics has revealed about X chromosome inactivation, perhaps the best characterised mammalian epigenetic process, highlighting the novel findings and important differences between mouse and human X inactivation uncovered through these studies...
April 20, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29678954/self-organization-entropy-and-allostery
#7
REVIEW
Alexandr P Kornev
Allostery is a fundamental regulatory mechanism in biology. Although generally accepted that it is a dynamics-driven process, the exact molecular mechanism of allosteric signal transmission is hotly debated. We argue that allostery is as a part of a bigger picture that also includes fractal-like properties of protein interior, hierarchical protein folding and entropy-driven molecular recognition. Although so far all these phenomena were studied separately, they stem from the same common root: self-organization of polypeptide chains and, thus, has to be studied collectively...
April 20, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29678953/metabolic-adjustment-to-high-altitude-hypoxia-from-genetic-signals-to-physiological-implications
#8
REVIEW
Andrew J Murray, Hugh E Montgomery, Martin Feelisch, Michael P W Grocott, Daniel S Martin
Ascent to high altitude is associated with physiological responses that counter the stress of hypobaric hypoxia by increasing oxygen delivery and by altering tissue oxygen utilisation via metabolic modulation. At the cellular level, the transcriptional response to hypoxia is mediated by the hypoxia-inducible factor (HIF) pathway and results in promotion of glycolytic capacity and suppression of oxidative metabolism. In Tibetan highlanders, gene variants encoding components of the HIF pathway have undergone selection and are associated with adaptive phenotypic changes, including suppression of erythropoiesis and increased blood lactate levels...
April 20, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29678952/subverting-the-mechanisms-of-cell-death-flavivirus-manipulation-of-host-cell-responses-to-infection
#9
REVIEW
Elisa Vicenzi, Isabel Pagani, Silvia Ghezzi, Sarah L Taylor, Timothy R Rudd, Marcelo A Lima, Mark A Skidmore, Edwin A Yates
Viruses exploit host metabolic and defence machinery for their own replication. The flaviviruses, which include Dengue (DENV), Yellow Fever (YFV), Japanese Encephalitis (JEV), West Nile (WNV) and Zika (ZIKV) viruses, infect a broad range of hosts, cells and tissues. Flaviviruses are largely transmitted by mosquito bites and humans are usually incidental, dead-end hosts, with the notable exceptions of YFV, DENV and ZIKV. Infection by flaviviruses elicits cellular responses including cell death via necrosis, pyroptosis (involving inflammation) or apoptosis (which avoids inflammation)...
April 20, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29666216/progress-towards-platform-chemical-production-using-clostridium-autoethanogenum
#10
REVIEW
Rupert O J Norman, Thomas Millat, Klaus Winzer, Nigel P Minton, Charlie Hodgman
Since 2013, there has been an explosion in the number of research articles published on Clostridium autoethanogenum , an acetogen capable of producing platform chemicals such as ethanol and 2,3-butanediol from greenhouse gases. However, no review focusing solely on C. autoethanogenum has appeared in the literature. This review outlines the research conducted into this organism in three broad categories (Enzymology, Genetics, and Systems Biology) and suggestions for future research are offered.
April 17, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29666215/control-of-pancreatic-%C3%AE-cell-bioenergetics
#11
REVIEW
Charles Affourtit, Ben Alberts, Jonathan Barlow, Jane E Carré, Anthony G Wynne
The canonical model of glucose-stimulated insulin secretion (GSIS) by pancreatic β-cells predicts a glucose-induced rise in the cytosolic ATP/ADP ratio. Such bioenergetic sensitivity to metabolic fuel is unusual as it implies that ATP flux is governed, to a significant extent, by ATP supply, while it is predominantly demand-driven in other cell types. Metabolic control is generally shared between different processes, but potential control of ATP consumption over β-cell bioenergetics has been largely ignored to date...
April 17, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29666214/metabolic-abnormalities-in-chronic-fatigue-syndrome-myalgic-encephalomyelitis-a-mini-review
#12
REVIEW
Cara Tomas, Julia Newton
Chronic fatigue syndrome (CFS), commonly known as myalgic encephalomyelitis (ME), is a debilitating disease of unknown etiology. CFS/ME is a heterogeneous disease associated with a myriad of symptoms but with severe, prolonged fatigue as the core symptom associated with the disease. There are currently no known biomarkers for the disease, largely due to the lack of knowledge surrounding the eitopathogenesis of CFS/ME. Numerous studies have been conducted in an attempt to identify potential biomarkers for the disease...
April 17, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29666213/escrt-mediated-sorting-and-intralumenal-vesicle-concatenation-in-plants
#13
REVIEW
Marisa S Otegui
The degradation of plasma membrane and other membrane-associated proteins require their sorting at endosomes for delivery to the vacuole. Through the endocytic pathway, ubiquitinated membrane proteins (cargo) are delivered to endosomes where the ESCRT (endosomal sorting complex required for transport) machinery sorts them into intralumenal vesicles for degradation. Plants contain both conserved and plant-specific ESCRT subunits. In this review, I discuss the role of characterized plant ESCRT components, the evolutionary diversification of the plant ESCRT machinery, and a recent study showing that endosomal intralumenal vesicles form in clusters of concatenated vesicle buds by temporally uncoupling membrane constriction from membrane fission...
April 17, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29626148/new-insights-into-the-interplay-between-the-translation-machinery-and-nonsense-mediated-mrna-decay-factors
#14
REVIEW
Etienne Raimondeau, Joshua C Bufton, Christiane Schaffitzel
Faulty mRNAs with a premature stop codon (PTC) are recognized and degraded by nonsense-mediated mRNA decay (NMD). Recognition of a nonsense mRNA depends on translation and on the presence of NMD-enhancing or the absence of NMD-inhibiting factors in the 3'-untranslated region. Our review summarizes our current understanding of the molecular function of the conserved NMD factors UPF3B and UPF1, and of the anti-NMD factor Poly(A)-binding protein, and their interactions with ribosomes translating PTC-containing mRNAs...
April 6, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29626147/nucleosome-level-3d-organization-of-the-genome
#15
REVIEW
Masae Ohno, David G Priest, Yuichi Taniguchi
Nucleosomes are the unitary structures of chromosome folding, and their arrangements are intimately coupled to the regulation of genome activities. Conventionally, structural analyses using electron microscopy and X-ray crystallography have been used to study such spatial nucleosome arrangements. In contrast, recent improvements in the resolution of sequencing-based methods allowed investigation of nucleosome arrangements separately at each genomic locus, enabling exploration of gene-dependent regulation mechanisms...
April 6, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29626146/exploring-the-combinatorial-space-of-complete-pathways-to-chemicals
#16
REVIEW
Lin Wang, Chiam Yu Ng, Satyakam Dash, Costas D Maranas
Computational pathway design tools often face the challenges of balancing the stoichiometry of co-metabolites and cofactors, and dealing with reaction rule utilization in a single workflow. To this end, we provide an overview of two complementary stoichiometry-based pathway design tools optStoic and novoStoic developed in our group to tackle these challenges. optStoic is designed to determine the stoichiometry of overall conversion first which optimizes a performance criterion (e.g. high carbon/energy efficiency) and ensures a comprehensive search of co-metabolites and cofactors...
April 6, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29588387/constraint-based-modeling-in-microbial-food-biotechnology
#17
REVIEW
Martin H Rau, Ahmad A Zeidan
Genome-scale metabolic network reconstruction offers a means to leverage the value of the exponentially growing genomics data and integrate it with other biological knowledge in a structured format. Constraint-based modeling (CBM) enables both the qualitative and quantitative analyses of the reconstructed networks. The rapid advancements in these areas can benefit both the industrial production of microbial food cultures and their application in food processing. CBM provides several avenues for improving our mechanistic understanding of physiology and genotype-phenotype relationships...
March 27, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29588386/probing-ubiquitin-and-sumo-conjugation-and-deconjugation
#18
REVIEW
Huib Ovaa, Alfred C O Vertegaal
Ubiquitin (Ub) and ubiquitin-like (Ubl) proteins including small Ubl modifier (SUMO) are small proteins which are covalently linked to target proteins to regulate their functions. In this review, we discuss the current state of the art and point out what we feel this field urgently needs in order to delineate the wiring of the system. We discuss what is needed to unravel the connections between different components of the conjugation machineries for ubiquitylation and SUMOylation, and to unravel the connections between the conjugation machineries and their substrates...
March 27, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29588385/non-vesicular-lipid-trafficking-at-the-endoplasmic-reticulum-mitochondria-interface
#19
REVIEW
Francesca Giordano
Mitochondria are highly dynamic organelles involved in various cellular processes such as energy production, regulation of calcium homeostasis, lipid trafficking, and apoptosis. To fulfill all these functions and preserve their morphology and dynamic behavior, mitochondria need to maintain a defined protein and lipid composition in both their membranes. The maintenance of mitochondrial membrane identity requires a selective and regulated transport of specific lipids from/to the endoplasmic reticulum (ER) and across the mitochondria outer and inner membranes...
March 27, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29540508/membrane-re-modelling-by-bar-domain-superfamily-proteins-via-molecular-and-non-molecular-factors
#20
REVIEW
Tamako Nishimura, Nobuhiro Morone, Shiro Suetsugu
Lipid membranes are structural components of cell surfaces and intracellular organelles. Alterations in lipid membrane shape are accompanied by numerous cellular functions, including endocytosis, intracellular transport, and cell migration. Proteins containing Bin-Amphiphysin-Rvs (BAR) domains (BAR proteins) are unique, because their structures correspond to the membrane curvature, that is, the shape of the lipid membrane. BAR proteins present at high concentration determine the shape of the membrane, because BAR domain oligomers function as scaffolds that mould the membrane...
March 14, 2018: Biochemical Society Transactions
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