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Biochemical Society Transactions

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https://www.readbyqxmd.com/read/28939695/oxidative-stress-and-endoplasmic-reticulum-er-stress-in-the-development-of-neonatal-hypoxic-ischaemic-brain-injury
#1
REVIEW
Claire Thornton, Ana A Baburamani, Anton Kichev, Henrik Hagberg
Birth asphyxia in term neonates affects 1-2/1000 live births and results in the development of hypoxic-ischaemic encephalopathy with devastating life-long consequences. The majority of neuronal cell death occurs with a delay, providing the potential of a treatment window within which to act. Currently, treatment options are limited to therapeutic hypothermia which is not universally successful. To identify new interventions, we need to understand the molecular mechanisms underlying the injury. Here, we provide an overview of the contribution of both oxidative stress and endoplasmic reticulum stress in the development of neonatal brain injury and identify current preclinical therapeutic strategies...
September 22, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28939694/g-quadruplex-unwinding-helicases-and-their-function-in-vivo
#2
REVIEW
Markus Sauer, Katrin Paeschke
The concept that G-quadruplex (G4) structures can form within DNA or RNA in vitro has been long known and extensively discussed. In recent years, accumulating evidences imply that G-quadruplex structures form in vivo Initially, inefficient regulation of G-quadruplex structures was mainly associated with genome instability. However, due to the location of G-quadruplex motifs and their evolutionary conservation, different cellular functions of these structures have been postulated (e.g. in telomere maintenance, DNA replication, transcription, and translation)...
September 22, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28939693/mass-spectrometry-techniques-for-studying-the-ubiquitin-system
#3
REVIEW
Rachel E Heap, Megan S Gant, Frederic Lamoliatte, Julien Peltier, Matthias Trost
Post-translational control of proteins through covalent attachment of ubiquitin plays important roles in all eukaryotic cell functions. The ubiquitin system in humans consists of 2 E1, 35 E2 and >600 E3 ubiquitin ligases as well as hundreds of deubiquitylases, which reverse ubiquitin attachment. Moreover, there are hundreds of proteins with ubiquitin-binding domains that bind one of the eight possible polyubiquitin chains. Dysfunction of the ubiquitin system is associated with many diseases such as cancer, autoimmunity and neurodegeneration, demonstrating the importance of ubiquitylation...
September 22, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28939692/long-and-small-noncoding-rnas-during-oocyte-to-embryo-transition-in-mammals
#4
REVIEW
Petr Svoboda
Oocyte-to-embryo transition is a process during which an oocyte ovulates, is fertilized, and becomes a developing embryo. It involves the first major genome reprogramming event in life of an organism where gene expression, which gave rise to a differentiated oocyte, is remodeled in order to establish totipotency in blastomeres of an early embryo. This remodeling involves replacement of maternal RNAs with zygotic RNAs through maternal RNA degradation and zygotic genome activation. This review is focused on expression and function of long noncoding RNAs (lncRNAs) and small RNAs during oocyte-to-embryo transition in mammals...
September 22, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28900017/omega-3-fatty-acids-and-inflammatory-processes-from-molecules-to-man
#5
REVIEW
Philip C Calder
Inappropriate, excessive or uncontrolled inflammation contributes to a range of human diseases. Inflammation involves a multitude of cell types, chemical mediators and interactions. The present article will describe nutritional and metabolic aspects of omega-6 (n-6) and omega-3 (n-3) fatty acids and explain the roles of bioactive members of those fatty acid families in inflammatory processes. Eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) are n-3 fatty acids found in oily fish and fish oil supplements...
September 12, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28900016/geometries-of-vasculature-bifurcation-can-affect-the-level-of-trophic-damage-during-formation-of-a-brain-ischemic-lesion
#6
REVIEW
Yaroslav R Nartsissov
Ischemic lesion is a common cause of various diseases in humans. Brain tissue is especially sensitive to this type of damage. A common reason for the appearance of an ischemic area is a stop in blood flow in some branch of the vasculature system. Then, a decreasing concentration gradient results in a low mean level of oxygen in surrounding tissues. After that, the biochemical ischemic cascade spreads. In this review, we examine these well-known events from a new angle. It is stressed that there is essential evidence to predict the formation of an ischemic micro-area at the base of vascular bifurcation geometries...
September 12, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28900015/structure-and-function-of-pif1-helicase
#7
REVIEW
Alicia K Byrd, Kevin D Raney
Pif1 family helicases have multiple roles in the maintenance of nuclear and mitochondrial DNA in eukaryotes. Saccharomyces cerevisiae Pif1 is involved in replication through barriers to replication, such as G-quadruplexes and protein blocks, and reduces genetic instability at these sites. Another Pif1 family helicase in S. cerevisiae, Rrm3, assists in fork progression through replication fork barriers at the rDNA locus and tRNA genes. ScPif1 (Saccharomyces cerevisiae Pif1) also negatively regulates telomerase, facilitates Okazaki fragment processing, and acts with polymerase δ in break-induced repair...
September 12, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28900014/regulation-of-the-cell-cycle-and-centrosome-biology-by-deubiquitylases
#8
REVIEW
Sarah Darling, Andrew B Fielding, Dorota Sabat-Pośpiech, Ian A Prior, Judy M Coulson
Post-translational modification of proteins by ubiquitylation is increasingly recognised as a highly complex code that contributes to the regulation of diverse cellular processes. In humans, a family of almost 100 deubiquitylase enzymes (DUBs) are assigned to six subfamilies and many of these DUBs can remove ubiquitin from proteins to reverse signals. Roles for individual DUBs have been delineated within specific cellular processes, including many that are dysregulated in diseases, particularly cancer. As potentially druggable enzymes, disease-associated DUBs are of increasing interest as pharmaceutical targets...
September 12, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28842531/role-of-conformational-change-and-k-path-ligands-in-controlling-cytochrome-c-oxidase-activity
#9
REVIEW
Jian Liu, Carrie Hiser, Shelagh Ferguson-Miller
Given the central role of cytochrome c oxidase (CcO) in health and disease, it is an increasingly important question as to how the activity and efficiency of this key enzyme are regulated to respond to a variety of metabolic states. The present paper summarizes evidence for two modes of regulation of activity: first, by redox-induced conformational changes involving the K-proton uptake path; and secondly, by ligand binding to a conserved site immediately adjacent to the entrance of the K-path that leads to the active site...
August 24, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28842530/visualising-pattern-recognition-receptor-signalling
#10
REVIEW
Charlotte Macleod, Clare E Bryant
Signalling by pattern recognition receptors (PRRs) is critical for protecting the host against pathogens. Disruption of these signalling pathways has been implicated in many diseases ranging from infection susceptibility to cancer and autoimmune disease. Understanding how PRRs signal is of critical importance due to their potential as therapeutic targets to ameliorate symptoms of inflammatory diseases. The recent advances in microscopy, such as the discovery of fluorescent proteins and the breaking of the diffraction limit of light, offer a unique opportunity to visualise receptor signalling at a single protein level within living cells...
August 24, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28842529/structure-of-the-holliday-junction-applications-beyond-recombination
#11
REVIEW
P Shing Ho
The Holliday junction (HJ) is an essential element in recombination and related mechanisms. The structure of this four-stranded DNA assembly, which is now well-defined alone and in complex with proteins, has led to its applications in areas well outside of molecular recombination, including nanotechnology and biophysics. This minireview explores some interesting recent research on the HJ, as it has been adapted to design regular two- or three-dimensional lattices for crystal engineering, and more complex systems through DNA origami...
August 24, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28778985/mitochondrial-health-maintenance-in-axons
#12
REVIEW
Angelika B Harbauer
Neurons are post-mitotic cells that must function throughout the life of an organism. The high energetic requirements and Ca(2+) spikes of synaptic transmission place a burden on neuronal mitochondria. The removal of older mitochondria and the replenishment of the functional mitochondrial pool in axons with freshly synthesized components are therefore important parts of neuronal maintenance. Although the mechanism of mitochondrial protein import and dynamics is studied in great detail, the length of neurons poses additional challenges to those processes...
August 4, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28778984/consequences-of-rna-oxidation-on-protein-synthesis-rate-and-fidelity-implications-for-the-pathophysiology-of-neuropsychiatric-disorders
#13
REVIEW
Akihiko Nunomura, Hyoung-Gon Lee, Xiongwei Zhu, George Perry
Unlike DNA, oxidative damage to RNA has received little attention presumably due to the assumed transient nature of RNA. However, RNAs including mRNA can persist for several hours to days in certain tissues and are demonstrated to sustain greater oxidative damage than DNA. Because neuronal cells in the brain are continuously exposed to reactive oxygen species due to a high oxygen consumption rate, it is not surprising that neuronal RNA oxidation is observed as a common feature at an early stage in a series of neurodegenerative disorders...
August 4, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28754658/deciphering-the-regulation-of-metabolism-with-dynamic-optimization-an-overview-of-recent-advances
#14
REVIEW
Jan Ewald, Martin Bartl, Christoph Kaleta
Understanding optimality principles shaping the evolution of regulatory networks controlling metabolism is crucial for deriving a holistic picture of how metabolism is integrated into key cellular processes such as growth, adaptation and pathogenicity. While in the past the focus of research in pathway regulation was mainly based on stationary states, more recently dynamic optimization has proved to be an ideal tool to decipher regulatory strategies for metabolic pathways in response to environmental cues. In this short review, we summarize recent advances in the elucidation of optimal regulatory strategies and identification of optimal control points in metabolic pathways...
July 28, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28733489/interaction-of-misfolded-proteins-and-mitochondria-in-neurodegenerative-disorders
#15
REVIEW
Andrey Y Abramov, Alexey V Berezhnov, Evgeniya I Fedotova, Valery P Zinchenko, Ludmila P Dolgacheva
The number of the people affected by neurodegenerative disorders is growing dramatically due to the ageing of population. The major neurodegenerative diseases share some common pathological features including the involvement of mitochondria in the mechanism of pathology and misfolding and the accumulation of abnormally aggregated proteins. Neurotoxicity of aggregated β-amyloid, tau, α-synuclein and huntingtin is linked to the effects of these proteins on mitochondria. All these misfolded aggregates affect mitochondrial energy metabolism by inhibiting diverse mitochondrial complexes and limit ATP availability in neurones...
July 21, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28733488/identification-of-optimal-strategies-for-state-transition-of-complex-biological-networks
#16
REVIEW
Meichen Yuan, Weirong Hong, Pu Li
Complex biological networks typically contain numerous parameters, and determining feasible strategies for state transition by parameter perturbation is not a trivial task. In the present study, based on dynamical and structural analyses of the biological network, we optimized strategies for controlling variables in a two-node gene regulatory network and a T-cell large granular lymphocyte signaling network associated with blood cancer by using an efficient dynamic optimization method. Optimization revealed the critical value for each decision variable to steer the system from an undesired state into a desired attractor...
July 21, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28710289/nutritional-modulation-of-metabolic-inflammation
#17
REVIEW
Anna M Kirwan, Yvonne M Lenighan, Marcella E O'Reilly, Fiona C McGillicuddy, Helen M Roche
Metabolic inflammation is a very topical area of research, wherein aberrations in metabolic and inflammatory pathways probably contribute to atherosclerosis, insulin resistance (IR) and type 2 diabetes. Metabolic insults arising from obesity promote inflammation, which in turn impedes insulin signalling and reverse cholesterol transport (RCT). Key cells in the process are metabolically activated macrophages, which up-regulate both pro- and anti-inflammatory pathways in response to lipid spillover from adipocytes...
August 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28710288/post-transcriptional-control-of-gene-expression-following-stress-the-role-of-rna-binding-proteins
#18
REVIEW
Robert Harvey, Veronica Dezi, Mariavittoria Pizzinga, Anne E Willis
The ability of mammalian cells to modulate global protein synthesis in response to cellular stress is essential for cell survival. While control of protein synthesis is mediated by the regulation of eukaryotic initiation and elongation factors, RNA-binding proteins (RBPs) provide a crucial additional layer to post-transcriptional regulation. RBPs bind specific RNA through conserved RNA-binding domains and ensure that the information contained within the genome and transcribed in the form of RNA is exported to the cytoplasm, chemically modified, and translated prior to folding into a functional protein...
August 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28710287/rna-search-engines-empower-the-bacterial-intranet
#19
REVIEW
Tom Dendooven, Ben F Luisi
RNA acts not only as an information bearer in the biogenesis of proteins from genes, but also as a regulator that participates in the control of gene expression. In bacteria, small RNA molecules (sRNAs) play controlling roles in numerous processes and help to orchestrate complex regulatory networks. Such processes include cell growth and development, response to stress and metabolic change, transcription termination, cell-to-cell communication, and the launching of programmes for host invasion. All these processes require recognition of target messenger RNAs by the sRNAs...
August 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28710286/how-tetraspanins-shape-endothelial-and-leukocyte-nano-architecture-during-inflammation
#20
REVIEW
Jonas Franz, Marco Tarantola, Christoph Riethmüller
Tetraspanins are ubiquitous membrane proteins that induce local membrane curvature and hence co-ordinate cell-to-cell contacts. This review highlights their role in inflammation, which requires control of the nano-architecture of attachment sites between endothelial cells and leukocytes. The active role of endothelial cells in preparing for transmigration of leukocytes and determining the severity of an inflammation is often underscored. A clear hint to endothelial pre-activation is their ability to protrude clustered adhesion proteins upward prior to leukocyte contact...
August 15, 2017: Biochemical Society Transactions
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