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https://www.readbyqxmd.com/read/28729736/the-relationship-between-folding-and-activity-in-ureg-an-intrinsically-disordered-enzyme
#1
Marta Palombo, Alessio Bonucci, Emilien Etienne, Stefano Ciurli, Vladimir N Uversky, Bruno Guigliarelli, Valérie Belle, Elisabetta Mileo, Barbara Zambelli
A growing body of literature on intrinsically disordered proteins (IDPs) led scientists to rethink the structure-function paradigm of protein folding. Enzymes are often considered an exception to the rule of intrinsic disorder (ID), believed to require a unique structure for catalysis. However, recent studies revealed the presence of disorder in several functional native enzymes. In the present work, we address the importance of dynamics for catalysis, by investigating the relationship between folding and activity in Sporosarcina pasteurii UreG (SpUreG), a P-loop GTPase and the first discovered native ID enzyme, involved in the maturation of the nickel-containing urease...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28725170/helicobacter-pylori-infection-status-had-no-influence-on-upper-gastrointestinal-symptoms-a-cross-sectional-analysis-of-3-005-japanese-subjects-without-upper-gastrointestinal-lesions-undergoing-medical-health-checkups
#2
Tomomi Yoshioka, Eri Takeshita, Yasuhisa Sakata, Megumi Hara, Kayo Akutagawa, Natsuko Sakata, Hiroyoshi Endo, Takashi Ohyama, Keiji Matsunaga, Yuichiro Tanaka, Shinpei Shirai, Yoichiro Ito, Nanae Tsuruoka, Ryuichi Iwakiri, Motoyasu Kusano, Kazuma Fujimoto
BACKGROUND: This study aimed to evaluate the influence of Helicobacter pylori infection and its eradication on the upper gastrointestinal symptoms of relatively healthy Japanese subjects. METHODS: A total of 3,005 subjects (male/female: 1,549/1,456) undergoing medical health checkups were enrolled in the present study, at five hospitals in Saga, Japan, from January to December 2013. They had no significant findings following upper gastrointestinal endoscopy. All subjects completed a questionnaire that addressed a frequency scale for symptoms of gastroesophageal reflux disease...
2017: Esophagus: Official Journal of the Japan Esophageal Society
https://www.readbyqxmd.com/read/28717209/non-target-effects-on-soil-microbial-parameters-of-the-synthetic-pesticide-carbendazim-with-the-biopesticides-cantharidin-and-norcantharidin
#3
Hainan Shao, Yalin Zhang
Considering the fact that biopesticides are increasingly used to replace synthetic pesticides in pest control, it is necessary to assess their ecotoxicity and especially their non-target effects on soil microorganisms, which is largely unknown. In this study, the effects of the synthetic pesticide carbendazim and the biopesticides (cantharidin and norcantharidin) on soil microbial parameters in a silt loam soil were evaluated. By using commercial formulations at the recommended and higher rates, both cantharidin and norcantharidin induced adverse effects on soil invertase, phosphatase activities and fungal gene structure, but these changes were transient...
July 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28714845/bacillus-mangrovi-sp-nov-isolated-from-a-sediment-sample-from-a-mangrove-forest
#4
Vasundhera Gupta, Pradip Kumar Singh, Suresh Korpole, Naga Radha Srinivas Tanuku, Anil Kumar Pinnaka
A facultatively anaerobic, endospore forming, alkali-tolerant, Gram-stain-positive, motile, rod-shaped bacterium, designated strain AK61T, was isolated from a sediment sample collected from Coringa mangrove forest, India. Colonies were circular, 1.5 mm in diameter, shiny, smooth, yellowish and convex with entire margins after 48 h growth at 30 °C. Growth occurred at 15-42 °C, with 0-3 % (w/v) NaCl and at pH 6-9. AK61T was positive for amylase activity and negative for oxidase, catalase, aesculinase, caseinase, cellulase, DNase, gelatinase, lipase and urease activities...
July 17, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28710280/the-assembly-of-the-plant-urease-activation-complex-and-the-essential-role-of-the-urease-accessory-protein-g-ureg-in-delivery-of-nickel-to-urease
#5
Till Myrach, Anting Zhu, Claus-Peter Witte
Urease is a ubiquitous nickel metalloenzyme. In plants, its activation requires three urease accessory proteins (UAPs), UreD, UreF, and UreG. In bacteria, the UAPs interact with urease and facilitate activation, which involves the channeling of two nickel ions into the active site. So far this process has not been investigated in eukaryotes. Using affinity pull-downs of Strep-tagged UAPs from Arabidopsis and rice transiently expressed in planta, we demonstrate that a urease:UreD:UreF:UreG complex exists in plants and show its stepwise assembly...
July 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28709075/effects-of-chromium-iii-on-enzyme-activities-and-bacterial-communities-during-swine-manure-composting
#6
Yanan Yin, Jie Gu, Xiaojuan Wang, Wen Song, Kaiyu Zhang, Xin Zhang, Chunya Lu, Jiayao Liu
The present study investigated the effects of different concentrations of chromium (i.e., 200 and 700mgkg(-1) Cr corresponding to Cr200 and Cr700, respectively) on the microorganisms in swine manure compost. The results demonstrated that a high concentration of Cr(III) could inhibit the activity of key microbial enzymes (i.e., dehydrogenase, cellulase, and urease) in the early composting stages, with maximal inhibition rates of 54.9%, 32.8%, and 46.7% for cellulase, urease, and dehydrogenase, respectively. Furthermore, the bacterial abundances were determined by quantitative PCR and their compositions were evaluated by denaturing gradient gel electrophoresis...
July 1, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28702150/adding-ofloxacin-to-standard-triple-drug-regimens-increased-the-helicobacter-pylori-eradication-rate-data-from-randomized-clinical-trial
#7
Mahmoud Sadeghi-Hadad-Zavareh, Seyyedsaeid Mohammadi, Mahmoud Hajiahmadi, Mostafa Javanian, Masoomeh Habibian
BACKGROUND: The rate of Helicobacter pylori (H.pylori) eradication in dyspeptic patients using bismuth- based triple therapy is low due to bacterial that are resistant to antibiotics. The results of recent studies regarding levofloxacin have been encouraging, but the high cost of treatment prevents its routine administration. We, therefore, performed the present double-blind clinical trial to compare the efficiency of quadruple-drug regimen containing ofloxacin, clarithromycin, amoxicillin, and omeprazole and the same standard triple-therapy regimen minus ofloxacin in H...
2017: Caspian Journal of Internal Medicine
https://www.readbyqxmd.com/read/28700609/organic-farming-enhances-soil-microbial-abundance-and-activity-a-meta-analysis-and-meta-regression
#8
Martina Lori, Sarah Symnaczik, Paul Mäder, Gerlinde De Deyn, Andreas Gattinger
Population growth and climate change challenge our food and farming systems and provide arguments for an increased intensification of agriculture. A promising option is eco-functional intensification through organic farming, an approach based on using and enhancing internal natural resources and processes to secure and improve agricultural productivity, while minimizing negative environmental impacts. In this concept an active soil microbiota plays an important role for various soil based ecosystem services such as nutrient cycling, erosion control and pest and disease regulation...
2017: PloS One
https://www.readbyqxmd.com/read/28698866/analysis-of-gastric-body-microbiota-by-pyrosequencing-possible-role-of-bacteria-other-than-helicobacter-pylori-in-the-gastric-carcinogenesis
#9
Sung-Hwa Sohn, Nayoung Kim, Hyun Jin Jo, Jaeyeon Kim, Ji Hyun Park, Ryoung Hee Nam, Yeong-Jae Seok, Yeon-Ran Kim, Dong Ho Lee
BACKGROUND: Gastric microbiota along with Helicobacter pylori (HP) plays a key role in gastric disease. The aim of our study is to investigate the difference of human gastric microbiota between antrum and body according to disease (control vs. gastric cancer) and HP status. METHODS: Each antrum and body biopsy was collected from 12 subjects at Seoul National University Bundang Hospital. Gastric microbiota was analyzed by bar-coded 454 pyrosequencing of the 16S rRNA gene...
June 2017: Journal of Cancer Prevention
https://www.readbyqxmd.com/read/28693684/clostridium-tepidum-sp-nov-a-close-relative-of-clostridium-sporogenes-and-clostridium-botulinum-group-i
#10
Anatoly P Dobritsa, Kirthi K Kutumbaka, Kirsten Werner, Martin Wiedmann, Aaron Asmus, Mansour Samadpour
Obligately anaerobic, Gram-stain-positive, spore-forming bacteria indistinguishable by pulsed-field gel electrophoresis were isolated from non-dairy protein shakes in bloated bottles. One of the isolates, strain IEH 97212T, was selected for further study. The strain was closely related to Clostridium sporogenes and Clostridium botulinum Group 1 based on 16S rRNA gene sequence similarities. Phylogenetic analysis also showed that strain IEH 97212T and strain PE (=DSM 18688), a bacterium isolated from solfataric mud, had identical 16S rRNA gene sequences...
July 10, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28689111/two-dimensional-ytterbium-oxide-nanodisks-based-biosensor-for-selective-detection-of-urea
#11
Ahmed A Ibrahim, Rafiq Ahmad, Ahmad Umar, M S Al-Assiri, A E Al-Salami, Rajesh Kumar, S G Ansari, S Baskoutas
Herein, we demonstrate synthesis and application of two-dimensional (2D) rectangular ytterbium oxide (Yb2O3) nanodisks via a facile hydrothermal method. The structural, morphological, compositional, crystallinity, and phase properties of as-synthesized nanodisks were carried out using several analytical techniques that showed well defined 2D rectangular nanodisks/sheet like morphologies. The average thickness and edge length of the nanosheet structures were 20 ± 5nm and 600 ± 50nm, respectively. To develop urea biosensor, glassy carbon electrodes (GCE) were modified with Yb2O3 nanodisks, followed by urease immobilization and Nafion membrane covering (GCE/Yb2O3/Urease/Nafion)...
June 15, 2017: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/28688253/effects-of-apple-branch-biochar-on-soil-c-mineralization-and-nutrient-cycling-under-two-levels-of-n
#12
Shuailin Li, Chutao Liang, Zhouping Shangguan
The incorporation of biochar into soil has been proposed as a strategy for enhancing soil fertility and crop productivity. However, there is limited information regarding the responses of soil respiration and the C, N and P cycles to the addition of apple branch biochar at different rates to soil with different levels of N. A 108-day incubation experiment was conducted to investigate the effects of the rate of biochar addition (0, 1, 2 and 4% by mass) on soil respiration and nutrients and the activities of enzymes involved in C, N and P cycling under two levels of N...
July 5, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28680066/effects-of-long-term-cultivation-of-transgenic-bt-rice-kefeng-6-on-soil-microbial-functioning-and-c-cycling
#13
Lee Zhaolei, Bu Naishun, Cui Jun, Chen Xueping, Xiao Manqiu, Wang Feng, Song Zhiping, Fang Changming
Understanding how soil ecosystem responds to transgenic Bacillus thuringiensis (Bt) rice is necessary for environmental risk assessment. While the influences of short-term cultivation of Bt rice on soil properties have been reported previously, little is known about the long-term effects of Bt rice on soil ecosystems. In this study, soil samples were taken from a long-term rice cultivation site in Fujian Province, China, where transgenic Bt rice (Kefeng-6) and its non-Bt parent breed (Minghui-86) had been continuously cultivated for 8 years...
July 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28677839/nitrogen-release-from-urea-with-different-coatings-or-urease-inhibitor
#14
Odirley R Campos, Edson Marcio Mattiello, Reinaldo Bertola Cantarutti, Lenardus Vergutz
BACKGROUND: Coatings or urease inhibitors are designed to reduce losses of ammonia (NH3(g) ) from urea fertilizers. However, nitrogen (N) release and its effects on soil solution have not previously been evaluated under standardized conditions in soils. In this study, the urea fertilizers were incubated in chambers filled with sandy loam soil, adapted for the collection of NH3(g) and soil solution by centrifugation. RESULTS: In the fast-release N fertilizers, around 93 and 100% of urea-N applied were recovered within the first incubation hours...
July 5, 2017: Journal of the Science of Food and Agriculture
https://www.readbyqxmd.com/read/28675006/-construction-of-a-low-ph-sensing-system-in-streptococcus-mutans
#15
Kang Di, Li Yuqing, Zhou Xuedong
OBJECTIVE: To construct a low-pH-sensing system in Streptococcus mutans (S. mutans) and to visually detect the pH in situ. METHODS: Promoter of ureaseⅠ(PureⅠ) and green fluorescence protein (gfp) DNA fragments were amplified by polymerase chain reaction (PCR) from the genome of Streptococcus salivarius 57.I and S. mutans containing the gfp fragment. The two amplified DNA fragments were ligated together and further integrated into pDL278 to construct the recombinant plasmid pDL278-pureⅠ-gfp...
June 1, 2017: Hua Xi Kou Qiang Yi Xue za Zhi, Huaxi Kouqiang Yixue Zazhi, West China Journal of Stomatology
https://www.readbyqxmd.com/read/28672409/jack-bean-urease-inhibitors-and-antioxidant-activity-based-on-palmitic-acid-derived-1-acyl-3-arylthioureas-synthesis-kinetic-mechanism-and-molecular-docking-studies
#16
Aamer Saeed, Sajid Ur-Rehman, Pervaiz Ali Channar, Fayaz Ali Larik, Qamar Abbas, Mubashir Hassan, Hussain Raza, Sung-Yum Seo
A series of acylthioureas was synthesized and their inhibitory effects on the DPPH and jack bean urease were evaluated. The results showed that all of the synthesized compounds exhibited significant jack bean urease inhibitory activities. Especially, 1-(4-chlorophenyl)-3 palmitoylthiourea 5a bearing 4-chloro substituted phenyl ring exhibited the most potent tyrosinase inhibitory activity with an IC50 value 0.0170 μM compared to the IC50 value of 4.720 μM of thiourea used as standard. The inhibition mechanism analyzed by Lineweaver-Burk plots revealed that the type of inhibition of compound 5a on tyrosinase was noncompetitive...
July 3, 2017: Drug Research
https://www.readbyqxmd.com/read/28667775/a-one-step-immune-chromatographic-helicobacter-pylori-stool-antigen-test-for-children-was-quick-consistent-reliable-and-specific
#17
Nicolas Kalach, Pierre Gosset, Eric Dehecq, Anne Decoster, Anne-France Georgel, Claire Spyckerelle, Stephanos Papadopoulos, Christophe Dupont, Josette Raymond
AIM: This French study assessed a quick, non-invasive, immuno-chromatographic, Helicobacter pylori (H. pylori) stool antigen test for detecting infections in children. METHODS: We enrolled 158 children, with a median age of 8.5 years (range eight months to 17 years), with digestive symptoms suggesting upper gastrointestinal tract disease. Upper digestive endoscopy was performed with gastric biopsy-specimens for histology, a rapid urease test, culture test and quantitative real-time polymerase chain reaction...
July 1, 2017: Acta Paediatrica
https://www.readbyqxmd.com/read/28655347/helicobacter-pylori-caga-and-vaca-genes-in-dyspeptic-ghanaian-patients
#18
Timothy N Archampong, Richard H Asmah, Ebenezer K Aidoo, Edwin K Wiredu, Richard K Gyasi, David N Adjei, Sandra Beleza, Christopher D Bayliss, Karen Krogfelt
BACKGROUND: Helicobacter pylori infection is prevalent in Ghana. The development of gastro-duodenal disease is dependent on virulence of the infecting strain, host susceptibility and environmental factors. Helicobacter pylori cagA and vacA strains induce more inflammation, ulceration and oncogenesis. Here, for the first time we present data on H. pylori cagA and vacA genes and their association with gastro-duodenal disease in Ghana. A total of 159 patients with dyspepsia at Korle-Bu Teaching Hospital, Accra, were investigated for H...
June 27, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28647240/ammonia-and-greenhouse-gas-emissions-from-a-subtropical-wheat-field-under-different-nitrogen-fertilization-strategies
#19
Shuai Liu, Jim J Wang, Zhou Tian, Xudong Wang, Stephen Harrison
Minimizing soil ammonia (NH3) and nitrous oxide (N2O) emission factors (EFs) has significant implications in regional air quality and greenhouse gas (GHG) emissions besides nitrogen (N) nutrient loss. The aim of this study was to investigate the impacts of different N fertilizer treatments of conventional urea, polymer-coated urea, ammonia sulfate, urease inhibitor (NBPT, N-(n-butyl) thiophosphoric triamide)-treated urea, and nitrification inhibitor (DCD, dicyandiamide)-treated urea on emissions of NH3 and GHGs from subtropical wheat cultivation...
July 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/28647123/zinc-solubilizing-bacillus-spp-potential-candidates-for-biofortification-in-maize
#20
Muhammad Zahid Mumtaz, Maqshoof Ahmad, Moazzam Jamil, Tanveer Hussain
Bioaugmentation of Zn solubilizing rhizobacteria could be a sustainable intervention to increase bioavailability of Zn in soil which can be helpful in mitigation of yield loss and malnutrition of zinc. In present study, a number of pure rhizobacterial colonies were isolated from maize rhizosphere and screened for their ability to solubilize zinc oxide. These isolates were screened on the basis of zinc and phosphate solubilization, IAA production, protease production, catalase activity and starch hydrolysis...
September 2017: Microbiological Research
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