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Journal of Biochemistry

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https://www.readbyqxmd.com/read/28443981/mapping-the-dengue-scientific-landscape-worldwide-a-bibliometric-and-network-analysis
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
https://www.readbyqxmd.com/read/28375743/engineering-and-in-vivo-applications-of-riboswitches
#13
Zachary F Hallberg, Yichi Su, Rebekah Z Kitto, Ming C Hammond
Riboswitches are common gene regulatory units mostly found in bacteria that are capable of altering gene expression in response to a small molecule. These structured RNA elements consist of two modular subunits: an aptamer domain that binds with high specificity and affinity to a target ligand and an expression platform that transduces ligand binding to a gene expression output. Significant progress has been made in engineering novel aptamer domains for new small molecule inducers of gene expression. Modified expression platforms have also been optimized to function when fused with both natural and synthetic aptamer domains...
March 30, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28375742/how-%C3%AE-helical-motifs-form-functionally-diverse-lipid-binding-compartments
#14
Lucy Malinina, Dinshaw J Patel, Rhoderick E Brown
Lipids are produced site-specifically in cells and then distributed nonrandomly among membranes via vesicular and nonvesicular trafficking mechanisms. The latter involves soluble amphitropic proteins extracting specific lipids from source membranes to function as molecular solubilizers that envelope their insoluble cargo before transporting to destination sites. Lipid-binding and lipid transfer structural motifs range from multi-β-strand barrels, to β-sheet cups and baskets covered by α-helical lids, to multi-α-helical bundles and layers...
March 30, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28375741/isocitrate-dehydrogenase-mutation-and-r-2-hydroxyglutarate-from-basic-discovery-to-therapeutics-development
#15
Lenny Dang, Shin-San Michael Su
The identification of heterozygous mutations in the metabolic enzyme isocitrate dehydrogenase (IDH) in subsets of cancers, including secondary glioblastoma, acute myeloid leukemia, intrahepatic cholangiocarcinoma, and chondrosarcomas, led to intense discovery efforts to delineate the mutations' involvement in carcinogenesis and to develop therapeutics, which we review here. The three IDH isoforms nicotinamide adenine dinucleotide phosphate-dependent IDH1 and IDH2, and nicotinamide adenine dinucleotide-dependent IDH3) contribute to regulating the circuitry of central metabolism...
April 3, 2017: Annual Review of Biochemistry
https://www.readbyqxmd.com/read/28375733/single-molecule-analysis-of-bacterial-dna-repair-and-mutagenesis
#16
Stephan Uphoff, David J Sherratt
Ubiquitous conserved processes that repair DNA damage are essential for the maintenance and propagation of genomes over generations. Then again, inaccuracies in DNA transactions and failures to remove mutagenic lesions cause heritable genome changes. Building on decades of research using genetics and biochemistry, unprecedented quantitative insight into DNA repair mechanisms has come from the new-found ability to measure single proteins in vitro and inside individual living cells. This has brought together biologists, chemists, engineers, physicists, and mathematicians to solve longstanding questions about the way in which repair enzymes search for DNA lesions and form protein complexes that act in DNA repair pathways...
March 24, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28351545/corrigendum-to-specific-changes-in-the-proteomic-pattern-produced-by-the-brca1-ser1841asn-missense-mutation-international-journal-of-biochemistry-and-cell-biology-2007-220-226
#17
Telma Crugliano, Barbara Quaresima, Marco Gaspari, Maria Concetta Faniello, Francesco Romeo, Francesco Baudi, Giovanni Cuda, Francesco Costanzo, Salvatore Venuta
No abstract text is available yet for this article.
March 25, 2017: International Journal of Biochemistry & Cell Biology
https://www.readbyqxmd.com/read/28301769/reconstructing-ancient-proteins-to-understand-the-causes-of-structure-and-function
#18
Georg K A Hochberg, Joseph W Thornton
A central goal in biochemistry is to explain the causes of protein sequence, structure, and function. Mainstream approaches rationalize sequence and structure by how they determine function and compare related proteins to find mechanisms underlying their functional differences. Although productive, both strategies suffer from intrinsic limitations that have left important aspects of many proteins unexplained. These limits can be overcome by reconstructing ancient proteins, experimentally characterizing their properties, and retracing their evolution through time...
March 15, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28301754/bioanalytical-measurements-enabled-by-surface-enhanced-raman-scattering-sers-probes
#19
Lauren E Jamieson, Steven M Asiala, Kirsten Gracie, Karen Faulds, Duncan Graham
Since its discovery in 1974, surface-enhanced Raman scattering (SERS) has gained momentum as an important tool in analytical chemistry. SERS is used widely for analysis of biological samples, ranging from in vitro cell culture models, ex vivo tissue and blood samples, and direct in vivo application. New insights have been gained into biochemistry, with an emphasis on biomolecule detection, from small molecules such as glucose and amino acids to larger biomolecules such as DNA, proteins, and lipids. These measurements have increased our understanding of biological systems, and significantly, they have improved diagnostic capabilities...
February 23, 2017: Annual Review of Analytical Chemistry
https://www.readbyqxmd.com/read/28301747/single-cell-transcriptional-analysis
#20
Angela R Wu, Jianbin Wang, Aaron M Streets, Yanyi Huang
Despite being a relatively recent technological development, single-cell transcriptional analysis through high-throughput sequencing has already been used in hundreds of fruitful studies to make exciting new biological discoveries that would otherwise be challenging or even impossible. Consequently, this has fueled a virtuous cycle of even greater interest in the field and compelled development of further improved technical methodologies and approaches. Thanks to the combined efforts of the research community, including the fields of biochemistry and molecular biology, technology and instrumentation, data science, computational biology, and bioinformatics, the single-cell RNA-sequencing field is advancing at a pace that is both astounding and unprecedented...
March 16, 2017: Annual Review of Analytical Chemistry
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