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https://www.readbyqxmd.com/read/28917952/identification-of-potential-allosteric-communication-pathways-between-functional-sites-of-the-bacterial-ribosome-by-graph-and-elastic-network-models
#1
Pelin Guzel, Ozge Kurkcuoglu
BACKGROUND: Accumulated evidence indicates that bacterial ribosome employs allostery throughout its structure for protein synthesis. The nature of the allosteric communication between remote functional sites remains unclear, but the contact topology and dynamics of residues may play role in transmission of a perturbation to distant sites. METHODS/RESULTS: We employ two computationally efficient approaches - graph and elastic network modeling to gain insights about the allosteric communication in ribosome...
September 13, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28917914/structure-enzymatic-transformation-anticancer-activity-of-fucoidan-and-sulphated-fucooligosaccharides-from-sargassum-horneri
#2
Artem S Silchenko, Anton B Rasin, Mikhail I Kusaykin, Anatoly I Kalinovsky, Zhang Miansong, Liu Changheng, Olesya Malyarenko, Anastasiya O Zueva, Tatyana N Zvyagintseva, Svetlana P Ermakova
Structure and anticancer activity of fucoidan from Sargassum horneri and from products of its enzymatic transformation were investigated. A gene that encodes fucoidanase ffa1 in the marine bacteria F. algae was identified, cloned and the protein (FFA1) was produced in Escherichia coli. The mass of the gene product FFA1 is 111kDa. Sequence analysis has revealed that fucoidanase FFA1 belongs to the GH107 (CAZy) family. Recombinant fucoidanase FFA1 was used to produce fucooligosaccharides. Structure of 5 sulphated oligosaccharides with polymerization degree 4-10 was established by NMR-spectroscopy...
November 1, 2017: Carbohydrate Polymers
https://www.readbyqxmd.com/read/28917834/hexameric-assembly-of-membrane-fusion-protein-yknx-of-the-sporulation-delaying-efflux-pump-from-bacillus-amyloliquefaciens
#3
Yongbin Xu, Inseong Jo, Lulu Wang, Jinli Chen, Shengdi Fan, Yuesheng Dong, Chun-Shan Quan, Nam-Chul Ha
Membrane fusion proteins (MFPs) play an essential role in the action of the drug efflux pumps and protein secretion systems in bacteria. The sporulation delaying protein (SDP) efflux pump YknWXYZ has been identified in diverse Bacillus species. The MFP YknX requires the ATP-binding cassette (ABC) transporter YknYZ and the Yip1 family protein YknW to form a functional complex. To date, the crystal structure, molecular function and mechanism of action of YknX remain unknown. In this study, to characterize the structural and biochemical roles of YknX in the functional assembly of YknWXYZ from B...
September 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28917788/glass-polytetrafluoroethylene-glass-based-sandwich-microdevice-for-continuous-flow-polymerase-chain-reaction-and-its-application-for-fast-identification-of-foodborne-pathogens
#4
Kieu The Loan Trinh, Nae Yoon Lee
A uniquely fabricated microdevice with a glass-polytetrafluoroethylene (PTFE)-glass (GPG) sandwich configuration was developed for the fast identification of foodborne pathogens by using continuous-flow polymerase chain reaction (PCR) followed by on-site fluorescence detection of PCR products. A PTFE tube was simply folded into a serpentine configuration and sandwiched between two glass slides to maintain a 2D planar structure. By using a PTFE tube, the microchannel has the advantage of seamlessness without the need for photolithography methods, and is less expensive and less time-consuming to fabricate than alternative devices...
January 1, 2018: Talanta
https://www.readbyqxmd.com/read/28917104/bacteria-and-archaea-communities-in-full-scale-thermophilic-and-mesophilic-anaerobic-digesters-treating-food-wastewater-key-process-parameters-and-microbial-indicators-of-process-instability
#5
Joonyeob Lee, Seung Gu Shin, Gyuseong Han, Taewoan Koo, Seokhwan Hwang
In this study, four different mesophilic and thermophilic full-scale anaerobic digesters treating food wastewater (FWW) were monitored for 1-2years in order to investigate: 1) microbial communities underpinning anaerobic digestion of FWW, 2) significant factors shaping microbial community structures, and 3) potential microbial indicators of process instability. Twenty-seven bacterial genera were identified as abundant bacteria underpinning the anaerobic digestion of FWW. Methanosaeta harundinacea, M. concilii, Methanoculleus bourgensis, M...
September 5, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28917060/lipids-and-ions-traverse-the-membrane-by-the-same-physical-pathway-in-the-nhtmem16-scramblase
#6
Tao Jiang, Kuai Yu, H Criss Hartzell, Emad Tajkhorshid
From bacteria to mammals, different phospholipid species are segregated between the inner and outer leaflets of the plasma membrane by ATP-dependent lipid transporters. Disruption of this asymmetry by ATP-independent phospholipid scrambling is important in cellular signaling, but its mechanism remains incompletely understood. Using MD simulations coupled with experimental assays, we show that the surface hydrophilic transmembrane cavity exposed to the lipid bilayer on the fungal scramblase nhTMEM16 serves as the pathway for both lipid translocation and ion conduction across the membrane...
September 16, 2017: ELife
https://www.readbyqxmd.com/read/28916990/transformation-of-anaerobic-granules-into-aerobic-granules-and-the-succession-of-bacterial-community
#7
Haohao Sun, Ping Yu, Qiaoling Li, Hongqiang Ren, Bo Liu, Lin Ye, Xu-Xiang Zhang
In this study, we demonstrated that anaerobic granular sludge could be successfully transformed into aerobic granular sludge in a continuous up-flow reactor in 45 days. An aerobic microbial community successfully developed in the granules and high organic matter and nitrogen removal performance was achieved. Under an ammonia nitrogen loading rate of 0.8 kg N/(m(3) day), ammonia nitrogen and the total nitrogen removal efficiency of the reactor reached up to 100 and 93%, respectively. An obvious bacterial community shift in granular sludge was observed during the transformation process...
September 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28916375/bacterial-community-in-ancient-permafrost-alluvium-at-the-mammoth-mountain-eastern-siberia
#8
Anatoli Brouchkov, Marsel Kabilov, Svetlana Filippova, Olga Baturina, Victor Rogov, Valery Galchenko, Andrey Mulyukin, Oksana Fursova, Gennady Pogorelko
Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa...
September 12, 2017: Gene
https://www.readbyqxmd.com/read/28916095/review-novel-sensing-strategies-for-bacterial-detection-based-on-active-and-passive-methods-driven-by-external-field
#9
REVIEW
Shiho Tokonami, Takuya Iida
For sustainable human life, biosensing systems for contaminants or disease-causing bacteria are crucial for food security, environmental improvement, and disease prevention. With an aim of enhancing the sensitivity and detection speed, many researchers have developed efficient detection methods for target bacteria. In this review, we discuss recent topics related to active and passive bacterial detection methods, including (1) optical approaches with unique functional nano- and micro-structures, and (2) electrical approaches involving mechanical modulation and electrochemical reactions...
October 2, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28915390/navy-and-black-bean-supplementation-primes-the-colonic-mucosal-microenvironment-to-improve-gut-health
#10
Jennifer M Monk, Dion Lepp, Wenqing Wu, K Peter Pauls, Lindsay E Robinson, Krista A Power
Common beans (Phaseolus vulgaris L.) are enriched in non-digestible fermentable carbohydrates and phenolic compounds that can modulate the colonic microenvironment (microbiota and host epithelial barrier) to improve gut health. In a comprehensive assessment of the impact of two commonly consumed bean varieties (differing in levels and types of phenolic compounds) within the colonic microenvironment, C57Bl/6 mice were fed diets supplemented with 20% cooked navy bean (NB) or black bean (BB) flours or an isocaloric basal diet control (BD) for 3 weeks...
August 10, 2017: Journal of Nutritional Biochemistry
https://www.readbyqxmd.com/read/28915035/photoelectrochemistry-of-photosystem-ii-in-vitro-vs-in-vivo
#11
Jenny Z Zhang, Paolo Bombelli, Katarzyna P Sokol, Andrea Fantuzzi, A William Rutherford, Christopher J Howe, Erwin Reisner
Factors governing the photoelectrochemical output of photosynthetic microorganisms are poorly understood, which can lead to energy losses through inefficient electron transfer (ET) processes. Here, we systematically compare the photoe-lectrochemistry of photosystem II (PSII) protein-films to cyano-bacteria biofilms to derive: (i) the losses in light-to-charge con-version efficiencies, (ii) gains in photocatalytic longevity, and (iii) insights into the ET mechanism at the biofilm interface. This study was enabled by the use of hierarchically structured elec-trodes, which could be tailored for high/stable loadings of PSII core complexes and Synechocystis sp...
September 15, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28914678/update-topical-antimicrobial-agents-for-chronic-wounds
#12
R Gary Sibbald, James A Elliott, Luvneed Verma, Alisa Brandon, Reneeka Persaud, Elizabeth A Ayello
GENERAL PURPOSE: To provide information on the use of topical antimicrobial agents for the treatment of chronic wounds. TARGET AUDIENCE: This continuing education activity is intended for physicians, physician assistants, nurse practitioners, and nurses with an interest in skin and wound care. LEARNING OBJECTIVES/OUTCOMES: After participating in this educational activity, the participant should be better able to:1. Examine features of wounds and wound healing as well as the purpose of specific antimicrobial agents...
October 2017: Advances in Skin & Wound Care
https://www.readbyqxmd.com/read/28914591/mucosa-associated-microbiota-dysbiosis-in-colitis-associated-cancer
#13
Mathias L Richard, Giuseppina Liguori, Bruno Lamas, Giovanni Brandi, Gregory da Costa, Thomas W Hoffmann, Massimo Pierluigi Di Simone, Carlo Calabrese, Gilberto Poggioli, Philippe Langella, Massimo Campieri, Harry Sokol
Gut microbiota dysbiosis has been associated with inflammatory bowel diseases (IBD). In colorectal cancer, the gut microbiota has also been recognized as potentially involved in aggravating or favoring the tumor development. However, very little is known on the structure and role of the microbiota in colitis associated cancer (CAC), an important complication of IBD in human. Here we analyzed the bacterial and fungal composition of the mucosa associated microbiota of patients suffering CAC, sporadic cancer (SC) and of healthy subjects (HS) by barcode sequences analysis on the following cohort: 7 CAC patients, 10 SC patients and 10 HS using 16S (MiSeq) and ITS2 (pyrosequencing) sequencing, for bacteria and fungi respectively...
September 15, 2017: Gut Microbes
https://www.readbyqxmd.com/read/28913898/structural-basis-for-binding-and-transfer-of-heme-in-bacterial-heme-acquisition-systems
#14
Youichi Naoe, Nozomi Nakamura, Md Mahfuzur Rahman, Takehiko Tosha, Satoru Nagatoishi, Kouhei Tsumoto, Yoshitsugu Shiro, Hiroshi Sugimoto
Periplasmic heme-binding proteins (PBPs) in Gram-negative bacteria are components of the heme acquisition system. These proteins shuttle heme across the periplasmic space from outer membrane receptors to ATP-binding cassette (ABC) heme importers located in the inner-membrane. In the present study, we characterized the structures of PBPs found in the pathogen Burkholderia cenocepacia (BhuT) and in the thermophile Roseiflexus sp. RS-1 (RhuT) in the heme-free and heme-bound forms. The conserved motif, in which a well-conserved Tyr interacts with the nearby Arg coordinates on heme iron, was observed in both PBPs...
September 14, 2017: Proteins
https://www.readbyqxmd.com/read/28912729/multiplicity-of-mathematical-modeling-strategies-to-search-for-molecular-and-cellular-insights-into-bacteria-lung-infection
#15
REVIEW
Martina Cantone, Guido Santos, Pia Wentker, Xin Lai, Julio Vera
Even today two bacterial lung infections, namely pneumonia and tuberculosis, are among the 10 most frequent causes of death worldwide. These infections still lack effective treatments in many developing countries and in immunocompromised populations like infants, elderly people and transplanted patients. The interaction between bacteria and the host is a complex system of interlinked intercellular and the intracellular processes, enriched in regulatory structures like positive and negative feedback loops. Severe pathological condition can emerge when the immune system of the host fails to neutralize the infection...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28912448/a-general-reaction-mechanism-for-carbapenem-hydrolysis-by-mononuclear-and-binuclear-metallo-%C3%AE-lactamases
#16
María-Natalia Lisa, Antonela R Palacios, Mahesh Aitha, Mariano M González, Diego M Moreno, Michael W Crowder, Robert A Bonomo, James Spencer, David L Tierney, Leticia I Llarrull, Alejandro J Vila
Carbapenem-resistant Enterobacteriaceae threaten human health, since carbapenems are last resort drugs for infections by such organisms. Metallo-β-lactamases (MβLs) are the main mechanism of resistance against carbapenems. Clinically approved inhibitors of MBLs are currently unavailable as design has been limited by the incomplete knowledge of their mechanism. Here, we report a biochemical and biophysical study of carbapenem hydrolysis by the B1 enzymes NDM-1 and BcII in the bi-Zn(II) form, the mono-Zn(II) B2 Sfh-I and the mono-Zn(II) B3 GOB-18...
September 14, 2017: Nature Communications
https://www.readbyqxmd.com/read/28912268/structural-and-functional-diversity-in-listeria-cell-wall-teichoic-acids
#17
Yang Shen, Samy Boulos, Eric Sumrall, Benjamin Gerber, Alicia Julian-Rodero, Marcel R Eugster, Lars Fieseler, Laura Nyström, Marc-Olivier Ebert, Martin J Loessner
Wall teichoic acids (WTAs) are the most abundant glycopolymers found on the cell wall of many Gram-positive bacteria, whose diverse surface structures play key roles in multiple biological processes. Despite recent technological advances in glycan analysis, structural elucidation of WTAs remains challenging due to their complex nature. Here, we employed a combination of UPLC-MS/MS and NMR to determine the structural complexity of WTAs from Listeria species. We unveiled more than 10 different types of WTA polymers that vary in their linkage and repeating units...
September 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28911652/microbiological-histological-and-biochemical-evidence-for-the-adverse-effects-of-food-azo-dyes-on-rats
#18
Khaled Elbanna, Osama Mohamed Sarhan, Manal Khider, Mohamed Elmogy, Hussein Hasan Abulreesh, Mohamed Rabie Shaaban
In this study, 120 lactic acid bacterial strains from different fermented dairy products as well as 10 bacterial intestinal isolates were evaluated for in vitro and in vivo degradation of various food azo dyes. Of these isolates, lactic acid bacteria (LAB) strains 13 and 100 and the intestinal isolates Ent2 and Eco5 exhibited 96-98% degradation of the tested food azo dyes within 5-6 hours. High performance liquid chromatography mass spectra of sunset yellow (E110) and carmoisine (E122) anaerobic degradation products by the intestinal isolates showed that they were structurally related to toxic aromatic amines...
July 2017: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/28911112/integrative-and-conjugative-elements-and-their-hosts-composition-distribution-and-organization
#19
Jean Cury, Marie Touchon, Eduardo P C Rocha
Conjugation of single-stranded DNA drives horizontal gene transfer between bacteria and was widely studied in conjugative plasmids. The organization and function of integrative and conjugative elements (ICE), even if they are more abundant, was only studied in a few model systems. Comparative genomics of ICE has been precluded by the difficulty in finding and delimiting these elements. Here, we present the results of a method that circumvents these problems by requiring only the identification of the conjugation genes and the species' pan-genome...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28910352/deep-learning-approach-to-bacterial-colony-classification
#20
Bartosz Zieliński, Anna Plichta, Krzysztof Misztal, Przemysław Spurek, Monika Brzychczy-Włoch, Dorota Ochońska
In microbiology it is diagnostically useful to recognize various genera and species of bacteria. It can be achieved using computer-aided methods, which make the recognition processes more automatic and thus significantly reduce the time necessary for the classification. Moreover, in case of diagnostic uncertainty (the misleading similarity in shape or structure of bacterial cells), such methods can minimize the risk of incorrect recognition. In this article, we apply the state of the art method for texture analysis to classify genera and species of bacteria...
2017: PloS One
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