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https://www.readbyqxmd.com/read/27926995/frozen-but-no-accident-why-the-20-standard-amino-acids-were-selected
#1
REVIEW
Andrew J Doig
The 20 standard amino acids encoded by the Genetic Code were adopted during the RNA World, around 4 billion years ago. This amino acid set could be regarded as a frozen accident, implying that other possible structures could equally well have been chosen to use in proteins. Amino acids were not primarily selected for their ability to support catalysis, since the RNA World already had highly effective cofactors to perform reactions, such as oxidation, reduction and transfer of small molecules. Rather, they were selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets...
December 7, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27926991/human-mitochondrial-nucleases
#2
REVIEW
Francesco Bruni, Robert N Lightowlers, Zofia M Chrzanowska-Lightowlers
Mitochondria are cytosolic organelles that have many essential roles including ATP production via oxidative phosphorylation, apoptosis, iron-sulphur cluster biogenesis, heme and steroid synthesis, calcium homeostasis and regulation of cellular redox state. One of the unique features of these organelles is the presence of an extra-chromosomal mitochondrial genome (mtDNA), together with all the machinery required to replicate and transcribe mtDNA. The accurate maintenance of mitochondrial gene expression is essential for correct organellar metabolism, and is in part dependent on the levels of mtDNA and mt-RNA, which are regulated by balancing synthesis against degradation...
December 7, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27926916/elevated-temperature-and-allelopathy-impact-coral-recruitment
#3
Raphael Ritson-Williams, Cliff Ross, Valerie J Paul
As climate change continues to alter seawater temperature and chemistry on a global scale, coral reefs show multiple signs of degradation. One natural process that could facilitate the recovery of reef ecosystems is coral recruitment, which can be influenced by the benthic organisms in a local habitat. We experimentally tested both a global stressor (increased seawater temperature) and a local stressor (exposure to microcolin A, a natural product from a common marine benthic cyanobacterium) to determine how these stressors impacted coral larval sublethal stress, survival and settlement...
2016: PloS One
https://www.readbyqxmd.com/read/27926882/effect-of-reduced-humic-acid-on-the-transport-of-ferrihydrite-nanoparticles-under-anoxic-conditions
#4
Peng Liao, Wenlu Li, Dengjun Wang, Yi Jiang, Chao Pan, John D Fortner, Songhu Yuan
Humic acid (HA) occurs ubiquitously in the subsurface environments and is well-known to play a critical role in the fate and transport of ferrihydrite nanoparticles (NPs) and NPs-associated contaminants. Under anoxic conditions, HA can readily be reduced by microorganisms or geochemical reducing species, and the mechanisms and kinetics of ferrihydrite reduction by reduced HA (HAred) are well-documented; however, the role of these redox reactions on the transport of ferrihydrite NPs is largely underestimated...
December 1, 2016: Water Research
https://www.readbyqxmd.com/read/27926866/inflammation-induced-oxidative-stress-mediates-gene-fusion-formation-in-prostate-cancer
#5
Ram S Mani, Mohammad A Amin, Xiangyi Li, Shanker Kalyana-Sundaram, Brendan A Veeneman, Lei Wang, Aparna Ghosh, Adam Aslam, Susmita G Ramanand, Bradley J Rabquer, Wataru Kimura, Maxwell Tran, Xuhong Cao, Sameek Roychowdhury, Saravana M Dhanasekaran, Nallasivam Palanisamy, Hesham A Sadek, Payal Kapur, Alisa E Koch, Arul M Chinnaiyan
Approximately 50% of prostate cancers are associated with gene fusions of the androgen-regulated gene TMPRSS2 to the oncogenic erythroblast transformation-specific (ETS) transcription factor ERG. The three-dimensional proximity of TMPRSS2 and ERG genes, in combination with DNA breaks, facilitates the formation of TMPRSS2-ERG gene fusions. However, the origins of DNA breaks that underlie gene fusion formation in prostate cancers are far from clear. We demonstrate a role for inflammation-induced oxidative stress in the formation of DNA breaks leading to recurrent TMPRSS2-ERG gene fusions...
December 6, 2016: Cell Reports
https://www.readbyqxmd.com/read/27926818/disruption-of-miaa-provides-insights-into-the-regulation-of-phenazine-biosynthesis-under-suboptimal-growth-conditions-in-pseudomonas-chlororaphis-30-84
#6
Jun Myoung Yu, Donping Wang, Leland S Pierson, Elizabeth A Pierson
Many products of secondary metabolism are activated by quorum sensing (QS), yet even at cell densities sufficient for QS, their production may be repressed under suboptimal growth conditions via mechanisms that still require elucidation. For many beneficial plant-associated bacteria, secondary metabolites such as phenazines are important for their competitive survival and plant-protective activities. Previous work established that phenazine biosynthesis in Pseudomonas chlororaphis 30-84 is regulated by the PhzR/PhzI QS system, which in turn is regulated by transcriptional regulator Pip, two-component system RpeA/RpeB, and stationary-phase/stress sigma factor RpoS...
December 7, 2016: Microbiology
https://www.readbyqxmd.com/read/27926536/a-minimal-titration-model-of-the-mammalian-dynamical-heat-shock-response
#7
Aude Sivéry, Emmanuel Courtade, Quentin Thommen
Environmental stress, such as oxidative or heat stress, induces the activation of the heat shock response (HSR) and leads to an increase in the heat shock proteins (HSPs) level. These HSPs act as molecular chaperones to maintain cellular proteostasis. Controlled by highly intricate regulatory mechanisms, having stress-induced activation and feedback regulations with multiple partners, the HSR is still incompletely understood. In this context, we propose a minimal molecular model for the gene regulatory network of the HSR that reproduces quantitatively different heat shock experiments both on heat shock factor 1 (HSF1) and HSPs activities...
December 7, 2016: Physical Biology
https://www.readbyqxmd.com/read/27926530/the-association-between-serum-uric-acid-and-glaucoma-severity-in-primary-angle-closure-glaucoma-a-retrospective-case-control-study
#8
Shengjie Li, Mingxi Shao, Binghua Tang, Aiping Zhang, Wenjun Cao, Xinghuai Sun
Uric acid (UA) is a major antioxidant molecule and has been hypothesized to have a protective effect on the central nervous system against oxidative damage. We prospectively investigated the serum concentration of UA in primary angle closure glaucoma (PACG), and explored the association between serum concentration of UA and the severity of PACG. Using a retrospective case-control study design, 886 PACG subjects and 994 control subjects who attended the Eye & ENT Hospital of Fudan University, were eligible for this study...
December 1, 2016: Oncotarget
https://www.readbyqxmd.com/read/27926461/long-chain-polyunsaturated-fatty-acids-regulation-of-ppars-signaling-relationship-to-tissue-development-and-aging
#9
REVIEW
Francisca Echeverría, Macarena Ortiz, Rodrigo Valenzuela, Luis A Videla
Peroxisome proliferator-activated receptors (PPARs) are nuclear receptors that function as ligand-dependent transcription factors that can be activated by different types of fatty acids (FAs). Three isoforms of PPARs have been identify, namely, PPARα, PPARβ/δ, and PPARγ, which are able to bind long-chain polyunsaturated FAs (LCPUFAs), n-3 LCPUFAs being bound with greater affinity to achieve activation. FA binding induces a conformational change of the nuclear receptors, triggering the transcription of specific genes including those encoding for various metabolic and cellular processes such as FA β-oxidation and adipogenesis, thus representing key mediators of lipid homeostasis...
November 2016: Prostaglandins, Leukotrienes, and Essential Fatty Acids
https://www.readbyqxmd.com/read/27926429/biologically-produced-methane-as-a-renewable-energy-source
#10
D E Holmes, J A Smith
Methanogens are a unique group of strictly anaerobic archaea that are more metabolically diverse than previously thought. Traditionally, it was thought that methanogens could only generate methane by coupling the oxidation of products formed by fermentative bacteria with the reduction of CO2. However, it has recently been observed that many methanogens can also use electrons extruded from metal-respiring bacteria, biocathodes, or insoluble electron shuttles as energy sources. Methanogens are found in both human-made and natural environments and are responsible for the production of ∼71% of the global atmospheric methane...
2016: Advances in Applied Microbiology
https://www.readbyqxmd.com/read/27925795/oxidants-at-the-surface-of-mars-a-review-in-light-of-recent-exploration-results
#11
J Lasne, A Noblet, C Szopa, R Navarro-González, M Cabane, O Poch, F Stalport, P François, S K Atreya, P Coll
In 1976, the Viking landers carried out the most comprehensive search for organics and microbial life in the martian regolith. Their results indicate that Mars' surface is lifeless and, surprisingly, depleted in organics at part-per-billion levels. Several biology experiments on the Viking landers gave controversial results that have since been explained by the presence of oxidizing agents on the surface of Mars. These oxidants may degrade abiotic or biological organics, resulting in their nondetection in the regolith...
December 7, 2016: Astrobiology
https://www.readbyqxmd.com/read/27925724/interface-structure-band-alignment-and-built-in-potentials-at-lafeo_-3-n-srtio_-3-heterojunctions
#12
Ryan Comes, Scott Chambers
Interface structure at polar-nonpolar interfaces has been shown to be a key factor in controlling emergent behavior in oxide heterostructures, including the LaFeO_{3}/n-SrTiO_{3} system. We demonstrate via high-energy-resolution x-ray photoemission that epitaxial LaFeO_{3}/n-SrTiO_{3}(001) heterojunctions engineered to have opposite interface polarities exhibit very similar band offsets and potential gradients within the LaFeO_{3} films. However, differences in the potential gradient within the SrTiO_{3} layer depending on polarity may promote hole diffusion into LaFeO_{3} for applications in photocatalysis...
November 25, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27925687/dna-base-excision-repair-proteins-ape-1-and-xrcc-1-are-overexpressed-in-oral-tongue-squamous-cell-carcinoma
#13
Thalita Santana, Melka Coêlho Sá, Edilmar de Moura Santos, Hébel Cavalcanti Galvão, Ricardo D Coletta, Roseana de Almeida Freitas
BACKGROUND: DNA repair systems play a critical role in protecting the human genome from damage caused by carcinogens. Modifications in DNA repair genes may be responsible for tumor development and resistance of malignant cells to chemotherapeutic agents. The major pathway for oxidative DNA damage repair is the base excision repair pathway. This study aimed to assess the immunoexpression of DNA repair proteins APE-1 and XRCC-1 and its association with clinical, histological and survival parameters in oral tongue squamous cell carcinoma in order to investigate a possible role for those proteins in tumor behavior...
December 7, 2016: Journal of Oral Pathology & Medicine
https://www.readbyqxmd.com/read/27925633/shock-wave-enhances-angiogenesis-through-vegfr2-activation-and-recycling
#14
Tien-Hung Huang, Cheuk-Kwan Sun, Yi-Ling Chen, Ching-Jen Wang, Tsung-Cheng Yin, Mel S Lee, Hon-Kan Yip
Although low-energy shock wave (SW) is adopted to treat ischemic diseases because of its pro-angiogenic properties, the underlying mechanism remains unclear. This study aimed at testing whether SW-induced angiogenesis may be through endothelial vascular endothelial growth factor receptor 2 (VEGFR2) signaling and trafficking. Phosphorylation of VEGFR2-Akt-eNOS axis and production of nitric oxide (NO) were determined in human umbilical vein endothelial cells (HUVECs) treated with SW. Carotid artery in ob/ob mice was treated with SW before evaluation with sprouting assay...
December 6, 2016: Molecular Medicine
https://www.readbyqxmd.com/read/27925632/sepsis-induces-telomere-shortening-a-potential-mechanism-responsible-for-delayed-pathophysiological-events-in-sepsis-survivors
#15
Naara Mendes Oliveira, Ester C S Rios, Thais Martins de Lima, Vanessa Jacob Victorino, Hermes Barbeiro, Fabiano Pinheiro da Silva, Csaba Szabo, Francisco Garcia Soriano
Sepsis survivors suffer from additional morbidities, including higher disk of readmissions, nervous system disturbances and cognitive dysfunction, and increased mortality, even several years after the initial episode of sepsis. In many ways, the phenotype of sepsis survivors resembles the phenotype associated with accelerated aging. Since telomere shortening is a hallmark of aging, we investigated whether sepsis also leads to telomere shortening. Male balb/c mice were divided into two groups: the control group received 100 μl of normal saline intraperitoneally; the sepsis group received 15 mg/kg of bacterial lipopolysaccharide i...
December 5, 2016: Molecular Medicine
https://www.readbyqxmd.com/read/27925508/%C3%AE-cyclodextrin-carbon-nanotube-enhanced-sensor-for-ciprofloxacin-detection
#16
Jorge M P J Garrido, Manuel Melle-Franco, Karol Strutyński, Fernanda Borges, Christopher M A Brett, E Manuela P J Garrido
A simple and expedite electrochemical methodology was developed for the determination of ciprofloxacin, based on a glassy carbon (GC) electrode modified by a combination of multi-walled carbon nanotubes (MWCNT) with β-cyclodextrin (β-CD) incorporated in a polyaniline film. The combined use of β-CD and MWCNT in the electrochemical sensor leads to a significant signal improvement. The β-CD/MWCNT modified GC electrode exhibited efficient electrocatalytic behavior in the oxidation of ciprofloxacin with relatively high sensitivity, stability and lifetime...
December 7, 2016: Journal of Environmental Science and Health. Part A, Toxic/hazardous Substances & Environmental Engineering
https://www.readbyqxmd.com/read/27925493/the-effect-of-freeze-drying-on-the-nutrient-polyphenol-and-oxidant-levels-of-breast-milk
#17
Mariela Valentina Cortez, Elio Andrés Soria
OBJECTIVES: Human milk banks need to extend the suitability of milk for breastfeeding, and for this technological advances are required. Our aim was to establish the capacity of freeze-drying to conserve milk properties without further oxidative deterioration. METHODS: One hundred sixteen healthy women participated from the city of Cordoba (Argentina). Proteins, glucose, triglycerides, polyphenols, and markers (nitrites, superoxide anion, hydroperoxides, lipoperoxides, and γ-glutamyl transpeptidase) were measured in their fresh milk...
December 2016: Breastfeeding Medicine: the Official Journal of the Academy of Breastfeeding Medicine
https://www.readbyqxmd.com/read/27925461/in-it-for-the-long-haul-the-cytocompatibility-of-aged-graphene-oxide-and-its-degradation-products
#18
Brian D Holt, Anne M Arnold, Stefanie A Sydlik
Synthetic biomaterials are poised to transform medicine; however, current synthetic options have yet to ideally recapitulate the desirable properties of native tissue. Thus, the development of new synthetic biomaterials remains an active challenge. Due to its excellent properties, including electrical conductivity, water dispersibility, and capacity for functionalization, graphene oxide (GO) holds potential for myriads of applications, including biological devices. While many studies have evaluated the compatibility of freshly prepared GO, understanding the compatibility of GO as it ages in an aqueous environment is crucial for its safe implementation in long-term biological applications...
December 2016: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/27925439/surface-faceting-and-reconstruction-of-ceria-nanoparticles
#19
Chengwu Yang, Xiaojuan Yu, Stefan Heißler, Alexei Nefedov, Sara Colussi, Jordi Llorca, Alessandro Trovarelli, Yuemin Wang, Christof Wöll
The surface atomic arrangement of metal oxides determines their physical and chemical properties, and the ability to control and optimize structural parameters is of crucial importance for many applications, in particular in heterogeneous catalysis and photocatalysis. Whereas the structures of macroscopic single crystals can be determined with established methods, for nanoparticles (NPs), this is a challenging task. Herein, we describe the use of CO as a probe molecule to determine the structure of the surfaces exposed by rod-shaped ceria NPs...
December 7, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/27925431/diabetes-mellitus-superoxide-dismutase-and-peroxisome-proliferator-activated-receptor-gamma-polymorphisms-modify-the-outcome-of-end-stage-renal-disease-patients-of-han-chinese-origin
#20
Chia-Ter Chao, Jenq-Wen Huang, Chih-Kang Chiang, Yen-Ching Chen, Cheng-Chung Fang, Fu-Chang Hu, Chen-Chih Chang, Chung-Jen Yen
BACKGROUND: Increased oxidative stress significantly modifies the outcome of patients with diabetes mellitus (DM) and end-stage renal disease (ESRD), and is counteracted by anti-oxidative capacity. However, whether anti-oxidant single nucleotide polymorphisms (SNPs) influence the outcome of ESRD individuals with or without DM has not been tested before. METHODS: We prospectively enrolled multi-center ESRD patients of Han Chinese origin betwen 2002 and 2003, recording their anti-oxidant (superoxide dismutase [SOD2], glutathione peroxidase [GPX1]) and peroxisome proliferator activated receptor-γ (PPAR-γ) genotyping results, and stratified based on DM...
December 7, 2016: Nephrology
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