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Journal of Biochemistry

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https://www.readbyqxmd.com/read/28560354/citation-analysis-of-scientific-categories
#1
Gregory S Patience, Christian A Patience, Bruno Blais, Francois Bertrand
Databases catalogue the corpus of research literature into scientific categories and report classes of bibliometric data such as the number of citations to articles, the number of authors, journals, funding agencies, institutes, references, etc. The number of articles and citations in a category are gauges of productivity and scientific impact but a quantitative basis to compare researchers between categories is limited. Here, we compile a list of bibliometric indicators for 236 science categories and citation rates of the 500 most cited articles of each category...
May 2017: Heliyon
https://www.readbyqxmd.com/read/28548882/finding-conducting-and-nurturing-science-a-virologist-s-memoir
#2
Anna Marie Ann Skalka Skalka
My laboratory investigations have been driven by an abiding interest in understanding the consequences of genetic rearrangement in evolution and disease, and in using viruses to elucidate fundamental mechanisms in biology. Starting with bacteriophages and moving to the retroviruses, my use of the tools of genetics, molecular biology, biochemistry, and biophysics has spanned more than half a century-from the time when DNA structure was just discovered to the present day of big data and epigenetics. Both riding and contributing to the successive waves of technology, my laboratory has elucidated fundamental mechanisms in DNA replication, repair, and recombination...
May 26, 2017: Annual Review of Virology
https://www.readbyqxmd.com/read/28498721/mechanisms-of-deubiquitinase-specificity-and-regulation
#3
Tycho E T Mevissen, David Komander
Protein ubiquitination is one of the most powerful posttranslational modifications of proteins, as it regulates a plethora of cellular processes in distinct manners. Simple monoubiquitination events coexist with more complex forms of polyubiquitination, the latter featuring many different chain architectures. Ubiquitin can be subjected to further posttranslational modifications (e.g., phosphorylation and acetylation) and can also be part of mixed polymers with ubiquitin-like modifiers such as SUMO (small ubiquitinrelated modifier) or NEDD8 (neural precursor cell expressed, developmentally downregulated 8)...
May 12, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28498720/protein-misfolding-amyloid-formation-and-human-disease-a-summary-of-progress-over-the-last-decade
#4
Fabrizio Chiti, Christopher M Dobson
Peptides and proteins have been found to possess an inherent tendency to convert from their native functional states into intractable amyloid aggregates. This phenomenon is associated with a range of increasingly common human disorders, including Alzheimer and Parkinson diseases, type II diabetes, and a number of systemic amyloidoses. In this review, we describe this field of science with particular reference to the advances that have been made over the last decade in our understanding of its fundamental nature and consequences...
May 12, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28495032/meat-science-from-1976-a-history-of-the-journal
#5
REVIEW
D A Ledward, D L Hopkins
The journal Meat Science was first published in 1976/77 and it initially comprised 4 issues per year. The first issue contained 4 papers and the first volume (4 issues) contained 27 articles, a mixture of papers and research notes. Its growth/popularity increased, and it has continued to thrive and in 2016 of the 1010 papers processed 292 were accepted. Over 90% of the papers published in the first volume were concerned with muscle biochemistry/meat properties. During the last years of the 20th century, meat products and their properties became a far larger proportion of the submissions as did those concerned with nutrition and safety...
May 3, 2017: Meat Science
https://www.readbyqxmd.com/read/28489421/mechanisms-and-functions-of-spatial-protein-quality-control
#6
Emily Mitchell Sontag, Rahul S Samant, Judith Frydman
A healthy proteome is essential for cell survival. Protein misfolding is linked to a rapidly expanding list of human diseases, ranging from neurodegenerative diseases to aging and cancer. Many of these diseases are characterized by the accumulation of misfolded proteins in intra- and extracellular inclusions, such as amyloid plaques. The clear link between protein misfolding and disease highlights the need to better understand the elaborate machinery that manages proteome homeostasis, or proteostasis, in the cell...
May 10, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28471691/the-evolution-of-organellar-coat-complexes-and-organization-of-the-eukaryotic-cell
#7
Michael P Rout, Mark C Field
Eukaryotic cells possess a remarkably diverse range of organelles that provide compartmentalization for distinct cellular functions and are likely responsible for the remarkable success of these organisms. The origins and subsequent elaboration of these compartments represent a key aspect in the transition between prokaryotic and eukaryotic cellular forms. The protein machinery required to build, maintain, and define many membranebound compartments is encoded by several paralog families, including small GTPases, coiled-bundle proteins, and proteins with β-propeller and α-solenoid secondary structures...
May 3, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28460188/proteasomal-and-autophagy-degradation-systems
#8
Ivan Dikic
Autophagy and the ubiquitin-proteasome system are the two major quality control pathways responsible for cellular homeostasis. As such, they provide protection against age-associated changes and a plethora of human diseases. Ubiquitination is utilized as a degradation signal by both systems, albeit in different ways, to mark cargoes for proteasomal and lysosomal degradation. Both systems intersect and communicate at multiple points to coordinate their actions in proteostasis and organelle homeostasis. This review summarizes molecular details of how proteasome and autophagy pathways are functionally interconnected in cells and indicates common principles and nodes of communication that can be therapeutically exploited...
May 1, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28443981/mapping-the-dengue-scientific-landscape-worldwide-a-bibliometric-and-network-analysis
#9
Fabio Batista Mota, Bruna de Paula Fonseca E Fonseca, Andréia Cristina Galina, Roseli Monteiro da Silva
BACKGROUND: Despite the current global trend of reduction in the morbidity and mortality of neglected diseases, dengue's incidence has increased and occurrence areas have expanded. Dengue also persists as a scientific and technological challenge since there is no effective treatment, vaccine, vector control or public health intervention. Combining bibliometrics and social network analysis methods can support the mapping of dengue research and development (R&D) activities worldwide. OBJECTIVES: The aim of this paper is to map the scientific scenario related to dengue research worldwide...
May 2017: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/28441058/protein-misfolding-diseases
#10
F Ulrich Hartl
The majority of protein molecules must fold into defined three-dimensional structures to acquire functional activity. However, protein chains can adopt a multitude of conformational states, and their biologically active conformation is often only marginally stable. Metastable proteins tend to populate misfolded species that are prone to forming toxic aggregates, including soluble oligomers and fibrillar amyloid deposits, which are linked with neurodegeneration in Alzheimer and Parkinson disease, and many other pathologies...
April 24, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28441057/oxidative-stress
#11
Helmut Sies, Carsten Berndt, Dean P Jones
Oxidative stress is two sided: Whereas excessive oxidant challenge causes damage to biomolecules, maintenance of a physiological level of oxidant challenge, termed oxidative eustress, is essential for governing life processes through redox signaling. Recent interest has focused on the intricate ways by which redox signaling integrates these converse properties. Redox balance is maintained by prevention, interception, and repair, and concomitantly the regulatory potential of molecular thiol-driven master switches such as Nrf2/Keap1 or NF-κB/IκB is used for system-wide oxidative stress response...
April 24, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28439041/cues-from-the-membrane-bacterial-glycerophospholipids
#12
Zachary D Dalebroux
In this issue of Journal of Bacteriology, Rowlett et al. unveil new Escherichia coli circuitry linking membrane glycerophospholipid (GPL) homeostasis to bacterial stress response and adaptation mechanisms. Glycerophospholipids comprise critical components of the dual-membrane envelope of Gram-negative bacteria and participate in many processes. The new evidence suggests that in some instances distinct E. coli GPL molecules function for distinct biochemistry, and bacteria sense perturbations in membrane GPL concentrations to coordinate survival strategies...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28426242/cellular-electron-cryotomography-toward-structural-biology-in-situ
#13
Catherine M Oikonomou, Grant J Jensen
Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ...
April 19, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28426241/extracellular-heme-uptake-and-the-challenge-of-bacterial-cell-membranes
#14
Weiliang Huang, Angela Wilks
Iron is essential for the survival of most bacteria but presents a significant challenge given its limited bioavailability. Furthermore, the toxicity of iron combined with the need to maintain physiological iron levels within a narrow concentration range requires sophisticated systems to sense, regulate, and transport iron. Most bacteria have evolved mechanisms to chelate and transport ferric iron (Fe(3+)) via siderophore receptor systems, and pathogenic bacteria have further lowered this barrier by employing mechanisms to utilize the host's hemoproteins...
April 19, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28425189/the-global-ethics-corner-foundations-beliefs-and-the-teaching-of-biomedical-and-scientific-ethics-around-the-world
#15
Henry Jakubowski, Jianping Xie, Arup Kumar Mitra, Ravindra Ghooi, Saman Hosseinkhani, Mohsen Alipour, Behnam Hajipour, George Obiero
The profound advances in the biomolecular sciences over the last decades have enabled similar advances in biomedicine. These advances have increasingly challenged our abilities to deploy them in an equitable and ethically acceptable manner. As such, it has become necessary and important to teach biomedical and scientific ethics to our students who will become the researchers, medical professionals, and global citizens of the future. As advances in the biosciences and medicine are made, developed, and used across the globe, our survival on an endangered planet requires global dialog and consensual action...
April 19, 2017: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/28399656/teaching-old-dyes-new-tricks-biological-probes-built-from-fluoresceins-and-rhodamines
#16
Luke D Lavis
Small-molecule fluorophores, such as fluorescein and rhodamine derivatives, are critical tools in modern biochemical and biological research. The field of chemical dyes is old; colored molecules were first discovered in the 1800s, and the fluorescein and rhodamine scaffolds have been known for over a century. Nevertheless, there has been a renaissance in using these dyes to create tools for biochemistry and biology. The application of modern chemistry, biochemistry, molecular genetics, and optical physics to these old structures enables and drives the development of novel, sophisticated fluorescent dyes...
April 7, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28399655/cyclic-gmp-amp-as-an-endogenous-second-messenger-in-innate-immune-signaling-by-cytosolic-dna
#17
Kazuki Kato, Hiroki Omura, Ryuichiro Ishitani, Osamu Nureki
The innate immune system functions as the first line of defense against invading bacteria and viruses. In this context, the cGAS/STING [cyclic guanosine monophosphate (GMP)-adenosine monophosphate (AMP) synthase/ STING] signaling axis perceives the nonself DNA associated with bacterial and viral infections, as well as the leakage of self DNA by cellular dysfunction and stresses, to elicit the host's immune responses. In this pathway, the noncanonical cyclic dinucleotide 2',3'-cyclicGMP-AMP(2',3'-cGAMP) functions as a second messenger for signal transduction: 2',3'-cGAMP is produced by the enzyme cGAS upon its recognition of double-stranded DNA, and then the 2',3'-cGAMP is recognized by the receptor STING to induce the phosphorylation of downstream factors, including TBK1 (TANK binding kinase 1) and IRF3 (interferon regulatory factor 3)...
April 7, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28378846/forearm-to-fingertip-skin-temperature-gradients-in-the-thermoneutral-zone-were-significantly-related-to-resting-metabolic-rate-potential-implications-for-nutrition-research
#18
K Pathak, E K Calton, M J Soares, Y Zhao, A P James, K Keane, P Newsholme
BACKGROUND: Resting metabolic rate (RMR) should be measured in the thermoneutral zone (TNZ). Forearm to fingertip skin temperature gradients (FFG) could serve as an objective measure of this pre-condition. SUBJECTS/METHODS: Eighty-six adult Australians were studied at 25 °C in a temperature-controlled chamber. Measurements of overnight fasted RMR, respiratory quotient (RQ) and FFG were complemented by clinical biochemistry. McAuley's Index of insulin sensitivity (McA_ISI) and presence of metabolic syndrome was determined...
April 5, 2017: European Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28375745/electric-fields-and-enzyme-catalysis
#19
Stephen D Fried, Steven G Boxer
What happens inside an enzyme's active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists' attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme's active site...
March 24, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28375744/ubiquitin-ligases-structure-function-and-regulation
#20
Ning Zheng, Nitzan Shabek
Ubiquitin E3 ligases control every aspect of eukaryotic biology by promoting protein ubiquitination and degradation. At the end of a three-enzyme cascade, ubiquitin ligases mediate the transfer of ubiquitin from an E2 ubiquitinconjugating enzyme to specific substrate proteins. Early investigations of E3s of the RING (really interesting new gene) and HECT (homologous to the E6AP carboxyl terminus) types shed light on their enzymatic activities, general architectures, and substrate degron-binding modes. Recent studies have provided deeper mechanistic insights into their catalysis, activation, and regulation...
March 27, 2017: Annual Review of Biochemistry
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