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https://www.readbyqxmd.com/read/29777414/altered-gut-microbiota-associated-with-intestinal-disease-in-grass-carp-ctenopharyngodon-idellus
#1
Ngoc Tuan Tran, Jing Zhang, Fan Xiong, Gui-Tang Wang, Wen-Xiang Li, Shan-Gong Wu
Gut microbiota plays a crucial importance in their host. Disturbance of the microbial structure and function is known to be associated with inflammatory intestinal disorders. Enteritis is a significant cause of high mortality in fish species, including grass carp (Ctenopharyngodon idellus). Study regarding the association between microbial alternations and enteritis in grass carp is still absent. In this study, changes in the gut microbiota of grass carp suffering from enteritis were investigated using NGS-based 16S rRNA sequencing...
May 18, 2018: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/29763307/genetic-code-expansion-in-rhodobacter-sphaeroides-to-incorporate-non-canonical-amino-acids-into-photosynthetic-reaction-centers
#2
Jared Weaver, Steven G Boxer
Photosynthetic reaction centers (RCs) are the membrane proteins responsible for the initial charge separation steps central to photosynthesis. As a complex and spectroscopically complicated membrane protein, the RC (and other associated photosynthetic proteins) would benefit greatly from the insight offered by site-specifically encoded non-canonical amino acids in the form of probes and an increased chemical range in key amino acid analogues. Towards that goal, we developed a method to transfer amber codon suppression machinery developed for E...
May 15, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29758915/dissolved-organic-matter-release-in-overlying-water-and-bacterial-community-shifts-in-biofilm-during-the-decomposition-of-myriophyllum-verticillatum
#3
Lisha Zhang, Songhe Zhang, Xiaoyang Lv, Zheng Qiu, Ziqiu Zhang, Liying Yan
This study investigated the alterations in biomass, nutrients and dissolved organic matter concentration in overlying water and determined the bacterial 16S rRNA gene in biofilms attached to plant residual during the decomposition of Myriophyllum verticillatum. The 55-day decomposition experimental results show that plant decay process can be well described by the exponential model, with the average decomposition rate of 0.037d-1 . Total organic carbon, total nitrogen, and organic nitrogen concentrations increased significantly in overlying water during decomposition compared to control within 35d...
August 15, 2018: Science of the Total Environment
https://www.readbyqxmd.com/read/29750518/altered-microbiome-leads-to-significant-phenotypic-and-transcriptomic-differences-in-a-lipid-accumulating-chlorophyte
#4
Lubna Richter, Cresten B Mansfeldt, Michael M Kuan, Alexandra Cesare, Stephen T Menefee, Ruth E Richardson, Beth A Ahner
Given the challenges facing the economically favorable production of products from microalgae, understanding factors that might impact productivity rates including growth rates and accumulation of desired products, e.g., triacylglycerols (TAG) for biodiesel feedstock, remains critical. Although operational parameters such as media composition and reactor design can clearly effect growth rates, the role of microbe-microbe interactions is just beginning to be elucidated. In this study an oleaginous marine algae Chlorella spp...
May 11, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29732092/impact-of-the-lipid-bilayer-on-energy-transfer-kinetics-in-the-photosynthetic-protein-lh2
#5
John I Ogren, Ashley L Tong, Samuel C Gordon, Aurélia Chenu, Yue Lu, Robert E Blankenship, Jianshu Cao, Gabriela S Schlau-Cohen
Photosynthetic purple bacteria convert solar energy to chemical energy with near unity quantum efficiency. The light-harvesting process begins with absorption of solar energy by an antenna protein called Light-Harvesting Complex 2 (LH2). Energy is subsequently transferred within LH2 and then through a network of additional light-harvesting proteins to a central location, termed the reaction center, where charge separation occurs. The energy transfer dynamics of LH2 are highly sensitive to intermolecular distances and relative organizations...
March 28, 2018: Chemical Science
https://www.readbyqxmd.com/read/29708639/the-distribution-of-active-iron-cycling-bacteria-in-marine-and-freshwater-sediments-is-decoupled-from-geochemical-gradients
#6
Julia M Otte, Johannes Harter, Katja Laufer, Nia Blackwell, Daniel Straub, Andreas Kappler, Sara Kleindienst
Microaerophilic, phototrophic, and nitrate-reducing Fe(II)-oxidizers co-exist in coastal marine and littoral freshwater sediments. However, the in situ abundance, distribution, and diversity of metabolically active Fe(II)-oxidizers remained largely unexplored. Here, we characterized the microbial community composition at the oxic-anoxic interface of littoral freshwater (Lake Constance, Germany) and coastal marine sediments (Kalø Vig and Norsminde Fjord, Denmark) using DNA-/RNA-based next-generation 16S rRNA (gene) amplicon sequencing...
April 30, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29656686/lipopolysaccharide-from-rhodobacter-sphaeroides-tlr4-antagonist-attenuates-hypersensitivity-and-modulates-nociceptive-factors
#7
Agnieszka M Jurga, Ewelina Rojewska, Wioletta Makuch, Joanna Mika
CONTEXT: Accumulating evidence has demonstrated that Toll-like receptors (TLRs), especially TLR4 localized on microglia/macrophages, may play a significant role in nociception. OBJECTIVE: We examine the role of TLR4 in a neuropathic pain model. Using behavioural/biochemical methods, we examined the influence of TLR4 antagonist on levels of hypersensitivity and nociceptive factors whose contribution to neuropathy development has been confirmed. MATERIALS AND METHODS: Behavioural (von Frey's/cold plate) tests were performed with Wistar male rats after intrathecal administration of a TLR4 antagonist (LPS-RS ULTRAPURE (LPS-RSU), 20 μG: lipopolysaccharide from Rhodobacter sphaeroides, InvivoGen, San Diego, CA) 16 H and 1 h before chronic constriction injury (cci) to the sciatic nerve and then daily for 7 d...
December 2018: Pharmaceutical Biology
https://www.readbyqxmd.com/read/29642620/rhodobacter-sphaeroides-extract-lycogen%C3%A2-attenuates-testosterone-induced-benign-prostate-hyperplasia-in-rats
#8
Chiang-Ting Wang, Ya-Yun Wang, Wen-Sheng Liu, Chun-Ming Cheng, Kuo-Hsun Chiu, Li-Lian Liu, Xue-Zhu Liu, Zhi-Hong Wen, Ya-Huey Chen, Tsung-Ming Chen
Benign prostate hyperplasia (BPH) is one of the most common urological problems in mid-aged to elderly men. Risk factors of BPH include family history, obesity, type 2 diabetes, and high oxidative stress. The main medication classes for BPH management are alpha blockers and 5α-reductase inhibitors. However, these conventional medicines cause adverse effects. Lycogen™, extracted from Rhodobacter sphaeroides WL-APD911, is an anti-oxidant and anti-inflammatory compound. In this study, the effect of Lycogen™ was evaluated in rats with testosterone-induced benign prostate hyperplasia (BPH)...
April 10, 2018: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29626419/the-k-path-entrance-in-cytochrome-c-oxidase-is-defined-by-mutation-of-e101-and-controlled-by-an-adjacent-ligand-binding-domain
#9
Carrie Hiser, Jian Liu, Shelagh Ferguson-Miller
Three mutant forms of Rhodobacter sphaeroides cytochrome c oxidase (RsCcO) were created to test for multiple K-path entry sites (E101W), the existence of an "upper ligand site" (M350 W), and the nature and binding specificity of the "lower ligand site" (P315W/E101A) in the region of a crystallographically-defined deoxycholate at the K-path entrance. The effects of inhibitory and stimulatory detergents (dodecyl maltoside and Tween20) on these mutants are presented, as well as competition with other ligands, including the potentially physiologically relevant ligands cholesterol and retinoic acid...
April 4, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29625982/the-protease-clpxp-and-the-pas-domain-protein-divl-regulate-ctra-and-gene-transfer-agent-production-in-rhodobacter-capsulatus
#10
A B Westbye, L Kater, C Wiesmann, H Ding, C K Yip, J T Beatty
Several members of the Rhodobacterales ( Alphaproteobacteria ) produce a conserved horizontal gene transfer vector, called gene transfer agent (GTA), that appears to have evolved from a bacteriophage. The model system to study GTA biology is the R. capsulatus GTA (RcGTA), a small, tailed bacteriophage-like particle produced by a subset of the cells in a culture. The response regulator CtrA is conserved in the Alphaproteobacteria and is an essential regulator of RcGTA production: it controls production and maturation of the RcGTA particle and RcGTA release from cells...
April 6, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29625547/endonuclease-activity-of-mutl-protein-of-the-rhodobacter-sphaeroides-mismatch-repair-system
#11
M V Monakhova, A I Penkina, A V Pavlova, A M Lyaschuk, V V Kucherenko, A V Alexeevski, V G Lunin, P Friedhoff, G Klug, T S Oretskaya, E A Kubareva
We have purified the MutL protein from Rhodobacter sphaeroides mismatch repair system (rsMutL) for the first time. rsMutL demonstrated endonuclease activity in vitro, as predicted by bioinformatics analysis. Based on the alignment of 1483 sequences of bacterial MutL homologs with presumed endonuclease activity, conserved functional motifs and amino acid residues in the rsMutL sequence were identified: five motifs comprising the catalytic site responsible for DNA cleavage were found in the C-terminal domain; seven conserved motifs involved in ATP binding and hydrolysis and specific to the GHKL family of ATPases were found in the N-terminal domain...
March 2018: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/29625088/dissecting-the-pattern-of-proton-release-from-partial-process-involved-in-ubihydroquinone-oxidation-in-the-q-cycle
#12
Charles A Wilson, Antony R Crofts
A key feature of the modified Q-cycle of the cytochrome bc1 and related complexes is a bifurcation of QH2 oxidation involving electron transfer to two different acceptor chains, each coupled to proton release. We have studied the kinetics of proton release in chromatophore vesicles from Rhodobacter sphaeroides, using the pH-sensitive dye neutral red to follow pH changes inside on activation of the photosynthetic chain, focusing on the bifurcated reaction, in which 4H+ are released on complete turnover of the Q-cycle (2H+ /ubiquinol (QH2 ) oxidized)...
April 3, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29613755/a-copper-relay-system-involving-two-periplasmic-chaperones-drives-cbb3-type-cytochrome-c-oxidase-biogenesis-in-rhodobacter-capsulatus
#13
Petru-Iulian Trasnea, Andreea Andrei, Dorian Marckmann, Marcel Utz, Bahia Khalfaoui-Hassani, Nur Selamoglu, Fevzi Daldal, Hans-Georg Koch
PccA and SenC are periplasmic copper chaperones required for the biogenesis of cbb3-type cytochrome c oxidase (cbb3-Cox) in Rhodobacter capsulatus at physiological Cu concentrations. However, both proteins are dispensable for cbb3-Cox assembly when external Cu concentration is high. PccA and SenC bind Cu using Met and His, and Cys and His residues as ligands, respectively, and both proteins form a complex during cbb3-Cox biogenesis. SenC also interacts directly with cbb3-Cox as shown by chemical crosslinking...
April 3, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29605571/structural-and-functional-analysis-of-erwinia-amylovora-srld-the-first-crystal-structure-of-a-sorbitol-6-phosphate-2-dehydrogenase
#14
Marco Salomone-Stagni, Joseph D Bartho, Eeshan Kalita, Martin Rejzek, Robert A Field, Dom Bellini, Martin A Walsh, Stefano Benini
Sorbitol-6-phosphate 2-dehydrogenases (S6PDH) catalyze the interconversion of d-sorbitol 6-phosphate to d-fructose 6-phosphate. In the plant pathogen Erwinia amylovora the S6PDH SrlD is used by the bacterium to utilize sorbitol, which is used for carbohydrate transport in the host plants belonging to the Amygdaloideae subfamily (e.g., apple, pear, and quince). We have determined the crystal structure of S6PDH SrlD at 1.84 Å resolution, which is the first structure of an EC 1.1.1.140 enzyme. Kinetic data show that SrlD is much faster at oxidizing d-sorbitol 6-phosphate than in reducing d-fructose 6-phosphate, however, equilibrium analysis revealed that only part of the d-sorbitol 6-phosphate present in the in vitro environment is converted into d-fructose 6-phosphate...
March 29, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29584941/vibronic-coherence-in-the-charge-separation-process-of-the-rhodobacter-sphaeroides-reaction-center
#15
Fei Ma, Elisabet Romero, Michael R Jones, Vladimir I Novoderezhkin, Rienk van Grondelle
Two-dimensional electronic spectroscopy was applied to a variant of the reaction center (RC) of purple bacterium Rhodobacter sphaeroides lacking the primary acceptor ubiquinone in order to understand the ultrafast separation and transfer of charge between the bacteriochlorin cofactors. For the first time characteristic 2D spectra were obtained for the participating excited and charge-transfer states, and the electron transfer cascade (including two different channels, the P* and B* channels) was fully mapped...
March 27, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29569108/rhodobacter-sp-rb3-an-aerobic-anoxygenic-phototroph-which-thrives-in-the-polyextreme-ecosystem-of-the-salar-de-huasco-in-the-chilean-altiplano
#16
Vilma Pérez, Cristina Dorador, Verónica Molina, Carolina Yáñez, Martha Hengst
The Salar de Huasco is an evaporitic basin located in the Chilean Altiplano, which presents extreme environmental conditions for life, i.e. high altitude (3800 m.a.s.l.), negative water balance, a wide salinity range, high daily temperature changes and the occurrence of the highest registered solar radiation on the planet (> 1200 W m-2 ). This ecosystem is considered as a natural laboratory to understand different adaptations of microorganisms to extreme conditions. Rhodobacter, an anoxygenic aerobic phototrophic bacterial genus, represents one of the most abundant groups reported based on taxonomic diversity surveys in this ecosystem...
March 22, 2018: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29555931/alarmin-hmgb1-induces-systemic-and-brain-inflammatory-exacerbation-in-post-stroke-infection-rat-model
#17
Il-Doo Kim, Hahnbie Lee, Seung-Woo Kim, Hye-Kyung Lee, Juli Choi, Pyung-Lim Han, Ja-Kyeong Lee
Post-stroke infection (PSI) is known to worsen functional outcomes of stroke patients and accounts to one-third of stroke-related deaths in hospital. In our previous reports, we demonstrated that massive release of high-mobility group box protein 1 (HMGB1), an endogenous danger signal molecule, is promoted by N-methyl-D-aspartic acid-induced acute damage in the postischemic brain, exacerbating neuronal damage by triggering delayed inflammatory processes. Moreover, augmentation of proinflammatory function of lipopolysaccharides (LPS) by HMGB1 via direct interaction has been reported...
March 19, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29555738/primary-processes-in-the-bacterial-reaction-center-probed-by-two-dimensional-electronic-spectroscopy
#18
Andrew Niedringhaus, Veronica R Policht, Riley Sechrist, Arkaprabha Konar, Philip D Laible, David F Bocian, Dewey Holten, Christine Kirmaier, Jennifer P Ogilvie
In the initial steps of photosynthesis, reaction centers convert solar energy to stable charge-separated states with near-unity quantum efficiency. The reaction center from purple bacteria remains an important model system for probing the structure-function relationship and understanding mechanisms of photosynthetic charge separation. Here we perform 2D electronic spectroscopy (2DES) on bacterial reaction centers (BRCs) from two mutants of the purple bacterium Rhodobacter capsulatus , spanning the Q y absorption bands of the BRC...
March 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29546752/cytochrome-aa-3-oxygen-reductase-utilizes-the-tunnel-observed-in-the-crystal-structures-to-deliver-o-2-for-catalysis
#19
Paween Mahinthichaichan, Robert B Gennis, Emad Tajkhorshid
Cytochrome aa3 is the terminal respiratory enzyme of all eukaryotes and many bacteria and archaea, reducing O2 to water and harnessing the free energy from the reaction to generate the transmembrane electrochemical potential. The diffusion of O2 to the heme-copper catalytic site, which is buried deep inside the enzyme, is the initiation step of the reaction chemistry. Our previous molecular dynamics (MD) study with cytochrome ba3 , a homologous enzyme of cytochrome aa3 in Thermus thermophilus, demonstrated that O2 diffuses from the lipid bilayer to its reduction site through a 25 Å long tunnel inferred by Xe binding sites detected by X-ray crystallography [Mahinthichaichan, P...
April 10, 2018: Biochemistry
https://www.readbyqxmd.com/read/29524035/in-vivo-assembly-of-a-truncated-h-subunit-mutant-of-the-rhodobacter-sphaeroides-photosynthetic-reaction-centre-and-direct-electron-transfer-from-the-q-a-quinone-to-an-electrode
#20
D Jun, H S Dhupar, A Mahmoudzadeh, F Duong, J D W Madden, J T Beatty
We address a challenge in the engineering of proteins to redirect electron transfer pathways, using the bacterial photosynthetic reaction centre (RC) pigment-protein complex. Direct electron transfer is shown to occur from the QA quinone of the Rhodobacter sphaeroides RC containing a truncated H protein and bound on the quinone side to a gold electrode. In previous reports of binding to the quinone side of the RC, electron transfer has relied on the use of a soluble mediator between the RC and an electrode, in part because the probability of QB quinone reduction is much greater than that of direct electron transfer through the large cytoplasmic domain of the H subunit, presenting a ~ 25 Å barrier...
March 9, 2018: Photosynthesis Research
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