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https://www.readbyqxmd.com/read/29240926/exocet-exonuclease-in-vitro-assembly-combined-with-recet-recombination-for-highly-efficient-direct-dna-cloning-from-complex-genomes
#1
Hailong Wang, Zhen Li, Ruonan Jia, Jia Yin, Aiying Li, Liqiu Xia, Yulong Yin, Rolf Müller, Jun Fu, A Francis Stewart, Youming Zhang
The exponentially increasing volumes of DNA sequence data highlight the need for new DNA cloning methods to explore the new information. Here, we describe 'ExoCET' (Exonuclease Combined with RecET recombination) to directly clone any chosen region from bacterial and mammalian genomes with nucleotide precision into operational plasmids. ExoCET combines in vitro exonuclease and annealing with the remarkable capacity of full length RecET homologous recombination (HR) to retrieve specified regions from genomic DNA preparations...
December 12, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29240876/machine-learning-for-classifying-tuberculosis-drug-resistance-from-dna-sequencing-data
#2
Yang Yang, Katherine E Niehaus, Timothy M Walker, Zamin Iqbal, A Sarah Walker, Daniel J Wilson, Tim E Peto, Derrick W Crook, E Grace Smith, Tingting Zhu, David A Clifton
Motivation: Correct and rapid determination of Mycobacterium tuberculosis (MTB) resistance against available tuberculosis (TB) drugs is essential for the control and management of TB. Conventional molecular diagnostic test assumes that the presence of any well-studied single nucleotide polymorphisms is sufficient to cause resistance, which yields low sensitivity for resistance classification. Methods: Given the availability of DNA sequencing data from MTB, we developed machine learning models for a cohort of 1839 UK bacterial isolates to classify MTB resistance against eight anti-TB drugs (isoniazid, rifampicin, ethambutol, pyrazinamide, ciprofloxacin, moxifloxacin, ofloxacin, streptomycin) and to classify multi-drug resistance...
December 12, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29240697/cymantrenyl-nucleobases-synthesis-anticancer-antitrypanosomal-and-antimicrobial-activity-studies
#3
Artur Jabłoński, Karolina Matczak, Aneta Koceva-Chyła, Kamil Durka, Dietmar Steverding, Katarzyna Jakubiec-Krześniak, Jolanta Solecka, Damian Trzybiński, Krzysztof Woźniak, Vanesa Andreu, Gracia Mendoza, Manuel Arruebo, Krzysztof Kochel, Barbara Krawczyk, Dominik Szczukocki, Konrad Kowalski
The synthesis of four cymantrene-5-fluorouracil derivatives (1-4) and two cymantrene-adenine derivatives (5 and 6) is reported. All of the compounds were characterized by spectroscopic methods and the crystal structure of two derivatives (1 and 6), together with the previously described cymantrene-adenine compound C was determined by X-ray crystallography. While the compounds 1 and 6 crystallized in the triclinic P-1 space group, compound C crystallized in the monoclinic P2₁/m space group. The newly synthesized compounds 1-6 were tested together with the two previously described cymantrene derivatives B and C for their in vitro antiproliferative activity against seven cancer cell lines (MCF-7, MCF-7/DX, MDA-MB-231, SKOV-3, A549, HepG2m and U-87-MG), five bacterial strains Staphylococcus aureus (methicillin-sensitive, methicillin-resistant and vancomycin-intermediate strains), Staphylococcus epidermidis, and Escherichia coli, including clinical isolates of S...
December 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29240520/draft-whole-genome-sequence-analyses-on-pseudomonas-syringae-pv-actinidiae-hr-negative-strains-detected-from-kiwifruit-bleeding-sap-samples
#4
Enrico Biondi, Alan Zamorano, Ernesto Vega, Stefano Ardizzi, Davide Sitta, Roberto De Salvador, Reinaldo Campos-Vargas, Claudio Meneses, Set Pérez, Assunta Bertaccini, Nicola Fiore
Kiwifruit bleeding sap samples, collected in Italian and Chilean orchards from symptomatic and asymptomatic plants, were evaluated for the presence of Pseudomonas syringae pv. actinidiae, the causal agent of bacterial canker. The saps were sampled during the spring of both hemispheres, before the bud sprouting, during the optimal time window for the collection of an adequate volume of sample for the early detection of the pathogen, preliminarily by molecular assays, and then, through its direct isolation and identification...
December 14, 2017: Phytopathology
https://www.readbyqxmd.com/read/29239792/francisella-tularensis-and-other-bacteria-in-hares-and-ticks-in-north-rhine-westphalia-germany
#5
Herbert Tomaso, Peter Otto, Martin Peters, Jochen Süss, Axel Karger, Heinz Schamoni, Eric Zuchantke, Helmut Hotzel
Tularemia is a zoonotic disease caused by the bacterium Francisella tularensis. The disease can be transmitted to humans through contact with infected animals such as the European brown hare (Lepus europaeus) and ticks as vectors. The aim of this study was to isolate F. tularensis from ticks and hares in North Rhine-Westphalia using cysteine heart agar to determine their genetic relatedness and to identify other bacteria that grow on this medium. 848 European brown hares and 1556 questing ticks (all Ixodes ricinus) from forests were tested using cultivation and MALDI-TOF mass spectrometry or partial 16S rRNA gene sequencing...
November 21, 2017: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/29239717/niveispirillum-lacus-sp-nov-isolated-from-cyanobacterial-aggregates-in-a-eutrophic-lake
#6
Haiyuan Cai, Henglin Cui, Yonghui Zeng, Yanan Wang, Helong Jiang
A bacterial strain, 1-14T, was isolated from cyanobacterial aggregates in a eutrophic lake, Taihu Lake, China. Cells were observed to be slightly curved, rod-shaped, aerobic and Gram-stain-negative. Optimal growth occurred at pH 7.0 (range: 5.0-9.0), 28 °C (range: 20-32 °C) and 0 % (w/v) NaCl (range: 0-1.0 %) in R2A broth. No growth is observed at 37 °C. The cells were found to be positive for oxidase and catalase activities. The major respiratory quinone was ubiquinone Q-10. The major fatty acids (>10 %) were identified as C18 : 1ω6c/C18 : 1ω7c, C16 : 0 3-OH and C18 : 1 2-OH...
December 14, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29239716/pseudomonas-fluvialis-sp-nov-a-novel-member-of-the-genus-pseudomonas-isolated-from-the-river-ganges-india
#7
Sarabjeet Kour Sudan, Deepika Pal, Bhawana Bisht, Narender Kumar, Vasvi Chaudhry, Prabhu Patil, Girish Sahni, Shanmugam Mayilraj, Srinivasan Krishnamurthi
A bacterial strain, designated ASS-1T, was isolated and identified from a sediment sample of the river Ganges, Allahabad, India. The strain was Gram-stain-negative, formed straw-yellow pigmented colonies, was strictly aerobic, motile with a single polar flagellum, and positive for oxidase and catalase. The major fatty acids were C16 : 1ω7c/ 16 : 1 C16 : 1ω6c, C18 : 1ω7c and C16 : 0. Sequence analysis based on the 16S rRNA gene revealed that strain ASS-1T showed high similarity to Pseudomonas guguanensis CC-G9AT (98...
December 14, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29238751/tree-leaf-bacterial-community-structure-and-diversity-differ-along-a-gradient-of-urban-intensity
#8
Isabelle Laforest-Lapointe, Christian Messier, Steven W Kembel
Tree leaf-associated microbiota have been studied in natural ecosystems but less so in urban settings, where anthropogenic pressures on trees could impact microbial communities and modify their interaction with their hosts. Additionally, trees act as vectors spreading bacterial cells in the air in urban environments due to the density of microbial cells on aerial plant surfaces. Characterizing tree leaf bacterial communities along an urban gradient is thus key to understand the impact of anthropogenic pressures on urban tree-bacterium interactions and on the overall urban microbiome...
November 2017: MSystems
https://www.readbyqxmd.com/read/29238278/role-of-metcalfa-pruinosa-as-a-vector-for-pseudomonas-syringae-pv-actinidiae
#9
Irene Donati, Sofia Mauri, Giampaolo Buriani, Antonio Cellini, Francesco Spinelli
After 20 years of steady increase, kiwifruit industry faced a severe arrest due to the pandemic spread of the bacterial canker, caused by Pseudomonas syringae pv. actinidiae (Psa). The bacterium penetrates the host plant primarily via natural openings or wounds, and its spread is mainly mediated by atmospheric events and cultural activities. Since the role of sucking insects as vectors of bacterial pathogens is widely documented, we investigated the ability of Metcalfa pruinosa Say (1830), one of the most common kiwifruit pests, to transmit Psa to healthy plants in laboratory conditions...
December 2017: Plant Pathology Journal
https://www.readbyqxmd.com/read/29237787/point-counterpoint-piperacillin-tazobactam-should-be-used-to-treat-infections-with-esbl-positive-organisms
#10
Audrey Schuetz, Sergio Reyes Salcedo, Pranita D Tamma
Beta-lactam/beta-lactamase inhibitor combinations (BLBLIs) are among the most controversial classes of antibiotic agents available for the treatment of infections caused by extended-spectrum beta-lactamase (ESBL)-producing Gram-negative bacteria (ESBL-GNR). Piperacillin-tazobactam (PTZ) is one of the most frequently utilized antibiotic agents for empiric gram-negative bacterial coverage and remains active against a large proportion of ESBL-GNR. Furthermore, good antimicrobial stewardship practices encourage the use of carbapenem-sparing treatment regimens for infections due to ESBL-GNR...
December 13, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/29237453/human-microglia-and-astrocytes-constitutively-express-the-neurokinin-1-receptor-and-functionally-respond-to-substance-p
#11
Amanda R Burmeister, M Brittany Johnson, Vinita S Chauhan, Megan J Moerdyk-Schauwecker, Ada D Young, Ian D Cooley, Alejandra N Martinez, Geeta Ramesh, Mario T Philipp, Ian Marriott
BACKGROUND: The tachykinin substance P (SP) is recognized to exacerbate inflammation at peripheral sites via its target receptor, neurokinin 1 receptor (NK-1R), expressed by leukocytes. More recently, SP/NK-1R interactions have been associated with severe neuroinflammation and neuronal damage. We have previously demonstrated that NK-1R antagonists can limit neuroinflammatory damage in a mouse model of bacterial meningitis. Furthermore, we have since shown that these agents can attenuate bacteria-induced neuronal and glial inflammatory mediator production in nonhuman primate (NHP) brain explants and isolated neuronal cells, and following in vivo infection...
December 13, 2017: Journal of Neuroinflammation
https://www.readbyqxmd.com/read/29237086/enterobacteriaceae-producing-oxa-48-like-carbapenemases-in-poland-2013-january-2017
#12
R Izdebski, A Baraniak, D Zabicka, M Machulska, P Urbanowicz, J Fiett, E Literacka, K Bojarska, A Kozinska, B Zieniuk, W Hryniewicz, M Gniadkowski
Objectives: To analyse OXA-48 (OXA-48/181)-type carbapenemase-producing Enterobacteriaceae reported in Poland from 2013 until January 2017. Methods: Bacterial isolates were typed by PFGE and MLST. Genes coding for OXA-48/181 types and other β-lactamases were amplified and sequenced. Mobile elements with blaOXA-48/181-like genes were PCR mapped. blaOXA-48/181-carrying plasmids were characterized by nuclease S1-hybridization profiling, transfer assays and PCR-based replicon typing, while the chromosomal location of the genes was confirmed by the I-CeuI analysis...
December 9, 2017: Journal of Antimicrobial Chemotherapy
https://www.readbyqxmd.com/read/29236862/ecology-and-biotechnological-potential-of-bacterial-community-from-three-marine-sponges-of-the-coast-of-rio-de-janeiro-brazil
#13
Fábio V DE Araújo, Marcelle C M Netto, Gustavo P Azevedo, Marcelly M A Jayme, Monica C Nunes-Carvalho, Mariana M Silva, Flávia L DO Carmo
Marine sponges has been a large reservoir of microbial diversity, with the presence of many species specific populations as well as producing biologically active compounds, which has attracted great biotechnological interest. In order to verify the influence of the environment in the composition of the bacterial community present in marine sponges and biotechnological potential of bacteria isolated from these organisms, three species of sponges and the waters surrounding them were collected in different beaches of Rio de Janeiro, Brazil...
December 11, 2017: Anais da Academia Brasileira de Ciências
https://www.readbyqxmd.com/read/29236588/topical-glycyrrhizin-is-therapeutic-for-pseudomonas-aeruginosa-keratitis
#14
Sandamali A Ekanayaka, Sharon A McClellan, Ronald P Barrett, Linda D Hazlett
PURPOSE: Glycyrrhizin (GLY), an inhibitor of high-mobility group box 1 (HMGB1) protects prophylactically against Pseudomonas aeruginosa keratitis. However, the therapeutic potential of GLY to enhance an antibiotic has not been tested and is our purpose. METHODS: C57BL/6 mice (B6) were infected with a clinical isolate (KEI 1025) of P. aeruginosa and treated topically at 6 h postinfection (p.i.) with GLY or phosphate-buffered saline (PBS). Clinical scores, photography with a slit lamp, enzyme-linked immunosorbent assay, myeloperoxidase assay, bacterial plate counts, histopathology, reactive oxygen/nitrogen species (ROS/RNS) assays, and in vitro macrophage (Mφ) stimulation assays were used to assess effects of GLY treatment...
December 13, 2017: Journal of Ocular Pharmacology and Therapeutics
https://www.readbyqxmd.com/read/29236553/progesterone-suppresses-the-lipopolysaccharide-induced-pro-inflammatory-response-in-primary-mononuclear-cells-isolated-from-human-placental-blood
#15
E Preciado-Martínez, G García-Ruíz, P Flores-Espinosa, L Bermejo-Martínez, A Espejel-Nuñez, G Estrada-Gutiérrez, G Razo-Aguilera, M Granados-Cepeda, A C Helguera-Repetto, C Irles, V Zaga-Clavellina
Progesterone is an essential hormone that induces deep immune adaptations favoring pregnancy maintenance. We aimed at evaluating the effects of progesterone on the synthesis of pro- and anti-inflammatory cytokines by mononuclear cells isolated from human placental blood stimulated with lipopolysaccharide, emulating an infection-inflammation environment. Mononuclear cells isolated form human placental blood were obtained from nine women undergoing elective cesarean delivery at term (not in labor), isolated by density gradient sedimentation, cultured and co-stimulated with lipopolysaccharide (500 ng/ml) from Escherichia coli in the presence or not of progesterone (0...
December 13, 2017: Immunological Investigations
https://www.readbyqxmd.com/read/29236233/thauera-sinica-sp-nov-a-phenol-derivative-degrading-bacterium-isolated-from-activated-sludge
#16
Nenghu Qiao, Lijun Xi, Jingjing Zhang, Dejian Liu, Baosheng Ge, Jianguo Liu
A bacterial strain, K11T, capable of degrading phenol derivatives was isolated from activated sludge of a sewage treatment plant in China. This strain, which can degrade more than ten phenol derivatives, was identified as a Gram-stain negative, rod-shaped, asporogenous, facultative anaerobic bacterium with a polar flagellum. The strain was found to grow in tryptic soy broth in the presence of 0-2.5% (w/v) NaCl (optimum 0-1%), at 4-43 °C (optimum 30-35 °C) and pH 4.5-10.5 (optimum 7.5-8). Comparative analysis of nearly full-length 16S rRNA gene sequences showed that this strain belongs to the genus Thauera...
December 13, 2017: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/29235981/paenibacillus-limicola-sp-nov-isolated-from-tidal-flat-sediment
#17
Shamsun Nahar, Chang-Jun Cha
An aerobic, Gram-staining-variable, rod-shaped, endospore-forming and motile bacterial strain, designated CJ6T, was isolated from a tidal flat on Ganghwa Island, South Korea. The isolate was characterized based on a polyphasic taxonomy approach. Strain CJ6T grew optimally on R2A agar media at 30 °C and pH 7. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CJ6T belonged to the genus Paenibacillus, displaying the highest sequence similarity to Paenibacillus vulneris CCUG 53270T (97...
December 13, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29235979/aminipila-butyrica-gen-nov-sp-nov-a-strictly-anaerobic-arginine-decomposing-bacterium-isolated-from-a-methanogenic-reactor-of-cattle-waste
#18
Atsuko Ueki, Kazushi Goto, Nobuo Kaku, Katsuji Ueki
A strictly anaerobic bacterial strain (FH042T) was isolated from a methanogenic reactor treating waste from cattle farms. Cells were stained Gram-positive, straight to gently curved rods with polar flagella. The strain was asaccharolytic. The strain fermented amino acids (l-arginine, l-lysine and l-serine) as growth substrates and produced acetate and butyrate. The optimum temperature for growth was 30 °C and the optimum pH was 6.1-6.8. Oxidase, catalase and nitrate-reducing activities were negative. Hydrogen sulfide was produced...
December 13, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/29235725/low-temperature-chemotaxis-halotaxis-and-chemohalotaxis-by-the-psychrophilic-marine-bacterium-colwellia-psychrerythraea-34h
#19
G M Showalter, J W Deming
A variety of ecologically important processes are driven by bacterial motility and taxis, yet these basic bacterial behaviors remain understudied in cold habitats. Here we present a series of experiments designed to test the chemotactic ability of the model marine psychrophilic bacterium Colwellia psychrerythraea 34H, when grown at optimal temperature and salinity (8°C, 35 ppt) or its original isolation conditions (-1°C, 35 ppt), towards serine and mannose at temperatures from -8 to 27°C (above its upper growth temperature of 18°C), and at salinities of 15, 35 and 55 ppt (at 8 and -1°C)...
December 13, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/29235706/a-conserved-tad-pilus-promotes-vibrio-vulnificus-oyster-colonization
#20
Meng Pu, Patrick Duriez, Mattan Arazi, Dean A Rowe-Magnus
Vibrio vulnificus has the highest death rate (>35%) and per-case economic burden ($3.3 million) of any foodborne pathogen in the US. Infections occur via open wounds or following ingestion of contaminated seafood, most infamously oysters. We isolated a 1000th generation descendant, designated NT, that exhibited increased biofilm and aggregate formation relative to its parent. We identified two significant causal changes underlying these NT phenotypes. First, the entire 24-kb capsular polysaccharide biosynthesis locus, which is essential for virulence but inhibits biofilm formation, had been purged from the genome...
December 13, 2017: Environmental Microbiology
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