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Journal of Molecular Microbiology and Biotechnology

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https://www.readbyqxmd.com/read/29258075/contribution-of-pcr-denaturing-gradient-gel-electrophoresis-combined-with-mixed-chromatogram-software-separation-for-complex-urinary-sample-analysis
#1
Iva Kotásková, Barbora Mališová, Hana Obručová, Veronika Holá, Tereza Peroutková, Filip Růžička, Tomáš Freiberger
Complex samples are a challenge for sequencing-based broad-range diagnostics. We analysed 19 urinary catheter, ureteral Double-J catheter, and urine samples using 3 methodological approaches. Out of the total 84 operational taxonomic units, 37, 61, and 88% were identified by culture, PCR-DGGE-SS (PCR denaturing gradient gel electrophoresis followed by Sanger sequencing), and PCR-DGGE-RM (PCR- DGGE combined with software chromatogram separation by RipSeq Mixed tool), respectively. The latter approach was shown to be an efficient tool to complement culture in complex sample assessment...
December 20, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29212086/comparative-analyses-of-transport-proteins-encoded-within-the-genomes-of-bdellovibrio-bacteriovorus-hd100-and-bdellovibrio-exovorus-jss
#2
Fereshteh Heidari Tajabadi, Arturo Medrano-Soto, Masoud Ahmadzadeh, Gholamreza Salehi Jouzani, Milton H Saier
Bdellovibrio, δ-proteobacteria, including B. bacteriovorus (Bba) and B. exovorus (Bex), are obligate predators of other Gram-negative bacteria. While Bba grows in the periplasm of the prey cell, Bex grows externally. We have analyzed and compared the transport proteins of these 2 organisms based on the current contents of the Transporter Classification Database (TCDB; www.tcdb.org). Bba has 103 transporters more than Bex, 50% more secondary carriers, and 3 times as many MFS carriers. Bba has far more metabolite transporters than Bex as expected from its larger genome, but there are 2 times more carbohydrate uptake and drug efflux systems, and 3 times more lipid transporters...
December 7, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29197868/the-dual-carboxymethyl-cellulase-and-gelatinase-activities-of-a-newly-isolated-protein-from-brevibacillus-agri-st15c10-confer-reciprocal-regulations-in-substrate-utilization
#3
Smarajit Maiti, Tanmoy Samanta, Sumit Sahoo, Sudipta Roy
A protein showing endoglucanase-peptidase activity was prepared from a newly isolated bacterium (ST15c10). We identified ST15c10 as Brevibacillus agri based on electron-microscopic images and its 16S-rDNA sequence (GenBank accession No. HM446043), which exhibits 98.9% sequence identity to B. agri (KZ17)/B. formosus (DSM-9885T)/B. brevis. The enzyme was purified to homogeneity and gave a single peak during high-performance liquid chromatography on a Seralose 6B-150 gel-matrix/C-18 column. MALDI-TOF mass-spectrometry and bioinformatics studies revealed significant similarity to M42-aminopeptidases/endoglucanases of the CelM family...
December 2, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29186720/archaeal-and-bacterial-community-structure-in-an-anaerobic-digestion-reactor-lagoon-type-used-for-biogas-production-at-a-pig-farm
#4
Liliana Pampillón-González, Nadia L Ortiz-Cornejo, Marco Luna-Guido, Luc Dendooven, Yendi E Navarro-Noya
Biogas production from animal waste is an economically viable way to reduce environmental pollution and produce valuable products, i.e., methane and a nutrient-rich organic waste product. An anaerobic digestion reactor for biogas production from pig waste was sampled at the entrance, middle (digestion chamber), and exit of a digester, while the bacterial and archaeal community structure was studied by 16S rRNA gene metagenomics. The number of bacterial operational taxonomic units (OTU)-97% was 3-7 times larger than that of archaeal ones...
November 30, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29183031/novel-pcr-assays-for-the-detection-of-biological-agents-responsible-for-wheat-rust-diseases-puccinia-triticina-and-puccinia-striiformis-f-sp-tritici
#5
Adam Kuzdraliński, Anna Kot, Hubert Szczerba, Agnieszka Ostrowska, Michał Nowak, Marta Muszyńska, Michał Lechowski, Paweł Muzyka
The species Puccinia triticina (Pt) and Puccinia striiformis f. sp. tritici (Pst) are devastating cereal pathogens that cause leaf and stripe rust diseases. We developed PCR assays for the species-specific detection of Pt and Pst, 2 biological agents that cause wheat rust disease. For each pathogen, we validated 3 primer sets that target the second largest subunits of the RNA polymerase II (rpb2) and β-tubulin 1 (tub1) genes. The specificities of the primers were verified using naturally infected plant materials with visual symptoms of disease...
November 29, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29166641/agrowastes-as-feedstock-for-the-production-of-endo-%C3%AE-xylanase-from-cohnella-sp-strain-ar92
#6
José H Pisa, Adriana P Manfredi, Nora I Perotti, Héctor G Romero, Javier D Breccia, María Alejandra Martínez
Members of Cohnella sp. isolated from a variety of environments have been shown to be glycoside hydrolase producers. Nevertheless, most evaluations of members of this genus are limited to their taxonomic description. The strain AR92, previously identified as belonging to the genus Cohnella, formed a well-supported cluster with C. thailandensis and C. formosensis (>80% bootstrap confidence). Its growth and xylanase production were approached by using a mineral-based medium containing alkali-pretreated sugarcane bagasse as the main carbon source, which was assayed as a convenient source to produce biocatalysts potentially fitting its degradation...
November 23, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29166640/lactic-acid-bacteria-from-andean-grain-amaranth-a-source-of-vitamins-and-functional-value-enzymes
#7
Silvana L Carrizo, Cecilia E Montes de Oca, María Elvira Hébert, Lucila Saavedra, Graciela Vignolo, Jean Guy LeBlanc, Graciela Celestina Rollán
Amaranth is a rediscovered pseudocereal with high nutritional properties. Lactic acid fermentation can increase the functional and nutritional value of foods. The aims of this study were to isolate and evaluate the functionality of lactic acid bacteria (LAB) from amaranth. LAB strains (n = 29) isolated from amaranth sourdough and grains included Lactobacillus (L.) plantarum (n = 8), L. rhamnosus (n = 6), Enterococcus (E.) mundtii (n = 4), E. hermanniensis (n = 3), E. durans (n = 1), Enterococcus sp. (n = 1), Leuconostoc (Lc...
November 23, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29161696/the-protein-expression-level-of-a-heterogeneous-gene-inserted-in-lipi-1-of-the-listeria-ivanovii-genome-relies-on-its-insertion-orientation
#8
Sijing Liu, Mingjuan Jiang, Lin Su, Tian Tang, Xiang Zhang, Yongyu Li, Qikang Pu, Chenyan Ren, Chuan Wang
Due to its capability to multiply in either phagocytic or nonphagocytic cells, and to subsequently elicit a robust cellular immune response, Listeria ivanovii (LI) is thought to be feasible for developing bacteria-based live attenuated vaccines. We previously generated several recombinant LI strains expressing Mycobacterium tuberculosis antigens. Since the expression level of heterogeneous protein was sometimes very low, we attempted to elucidate the principle of heterogeneous protein expression in such recombinant LI strains...
November 22, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29145176/the-membrane-attack-complex-perforin-superfamily
#9
Gabriel Moreno-Hagelsieb, Bennett Vitug, Arturo Medrano-Soto, Milton H Saier
The membrane attack complex/perforin (MACPF) superfamily consists of a diverse group of proteins involved in bacterial pathogenesis and sporulation as well as eukaryotic immunity, embryonic development, neural migration and fruiting body formation. The present work shows that the evolutionary relationships between the members of the superfamily, previously suggested by comparison of their tertiary structures, can also be supported by analyses of their primary structures. The superfamily includes the MACPF family (TC 1...
November 17, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29055951/cell-wall-treated-lactococcus-lactis-increases-the-plasmid-transfer-efficiency-of-internal-ribosome-entry-site-incorporated-lactococcal-bicistronic-vector-into-df1-cells
#10
Nurulfiza Mat Isa, Nur Elina Abdul Mutalib, Noorjahan Banu Alitheen, Adelene Ai-Lian Song, Raha Abdul Rahim
This study demonstrates that cell wall treatment of Lactococcus lactis harbouring the internal ribosome entry site-incorporated lactococcal bicistronic vector pNZ:VIG mediated the delivery of genes into an eukaryotic cell line, DF1 cells, through bactofection. Bactofection analysis showed that the pNZ:VIG plasmid in L. lactis can be transferred into DF1 cells and that both the VP2 and gfp genes cloned in the plasmid can be transcribed and translated. The protein band relative to the Mr of VP2 protein (49 kDa) was successfully detected via Western blot analysis, while green fluorescence was successfully detected using a fluorescence microscope...
October 21, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28903115/erap1-and-pde8a-are-downregulated-in-cattle-protected-against-bovine-tuberculosis
#11
Federico Carlos Blanco, Marcelo Abel Soria, Laura Inés Klepp, Fabiana Bigi
Bovine tuberculosis (bTB) is a zoonotic disease caused by Mycobacterium bovis that is responsible for significant economic losses worldwide. In spite of its relevance, the limited knowledge about the host immune responses that provide effective protection against the disease has long hampered the development of an effective vaccine. The identification of host proteins with an expression that correlates with protection against bTB would contribute to the understanding of the cattle defence mechanisms against M...
September 14, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28889121/structure-function-analysis-of-the-periplasmic-escherichia-coli-cyclophilin-ppia-in-relation-to-biofilm-formation
#12
Aggeliki Skagia, Eleni Vezyri, Konstantinos Grados, Anastasia Venieraki, Michael Karpusas, Panagiotis Katinakis, Maria Dimou
The presence of peptidyl-prolyl cis/trans isomerases (PPIases, EC: 5.2.1.8) in all domains of life indicates their biological importance. Cyclophilin PpiA, present in the periplasm of gram-negative bacteria, possesses PPIase activity but its physiological functions are still not clearly defined. Here, we demonstrate that the ΔppiA deletion strain from Escherichia coli exhibits an increased ability for biofilm formation and enhanced swimming motility compared to the wild-type strain. To identify structural features of PpiA which are necessary for the negative modulation of biofilm formation, we constructed a series of mutant PpiA proteins using a combination of error-prone and site-directed mutagenesis approaches...
September 9, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28858877/rare-human-codons-and-hcmv-translational-regulation
#13
Darja Kanduc
Restriction of protein synthesis characterizes human cytomegalovirus (HCMV) latency in the human host. In analyzing the molecular factors that hinder HCMV expression, the present study shows that HCMV genes frequently use 6 rare codons, i.e., GCG (Ala), CCG (Pro), CGT (Arg), CGC (Arg), TCG (Ser), and ACG (Thr). In some instances, the rare host codons are clustered along viral nucleotide sequences and represent the majority in sequences encoding short alanine and proline repeats. Given the positive correlation between codon usage, tRNA content, and protein production, the results support the hypothesis that HCMV usage of rare human codons might hinder HCMV protein synthesis, in this way leading to HCMV latency...
September 1, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28858869/overexpression-of-a-laccase-with-dye-decolorization-activity-from-bacillus-sp-induced-in-escherichia-coli
#14
Haipeng Guo, Bingsong Zheng, Dean Jiang, Wensheng Qin
Laccases from bacteria have been widely studied in the past 2 decades due to the higher growth rate of bacteria and their excellent thermal and alkaline pH stability. In this study, a novel laccase gene was cloned from Bacillus sp., analyzed, and functionally expressed in Escherichia coli. The laccase was highly induced in the E. coli expression system with a maximum intracellular activity of 16 U mg-1 protein. The optimal temperature and pH of the purified laccase were 40°C and 4.6, respectively, when ABTS (2,2'-azino-bis[3-ethylbenzothiazoline-6-sulfonate]) was used as the substrate...
September 1, 2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28850952/influence-of-nanolc-column-and-gradient-length-as-well-as-ms-ms-frequency-and-sample-complexity-on-shotgun-protein-identification-of-marine-bacteria
#15
Lars Wöhlbrand, Ralf Rabus, Bernd Blasius, Christoph Feenders
Protein identification by shotgun proteomics, i.e., nano-liquid chromatography (nanoLC) peptide separation online coupled to electrospray ionization (ESI) mass spectrometry (MS)/MS, is the most widely used gel-free approach in proteome research. While the mass spectrometer accounts for mass accuracy and MS/MS frequency, the nanoLC setup and gradient time influence the number of peptides available for MS analysis, which ultimately determine the number of proteins identifiable. Here, we report on the influence of (i) analytical column length (15, 25, or 50 cm) coupled to (ii) the applied gradient length (120, 240, 360, 480, or 600 min), as well as (iii) MS/MS frequency on peptide/protein identification by shotgun proteomics of (iv) 2 marine bacteria...
2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28848197/heterologous-expression-of-spinosyn-biosynthetic-gene-cluster-in-streptomyces-species-is-dependent-on-the-expression-of-rhamnose-biosynthesis-genes
#16
Chen Zhao, Ying Huang, Chao Guo, Bolei Yang, Yan Zhang, Zhou Lan, Xiong Guan, Yuan Song, Xiaolin Zhang
Spinosyns are a group of macrolide insecticides produced by Saccharopolyspora spinosa. Although S. spinosa can be used for industrial-scale production of spinosyns, this might suffer from several limitations, mainly related to its long growth cycle, low fermentation biomass, and inefficient utilization of starch. It is crucial to generate a robust strain for further spinosyn production and the development of spinosyn derivatives. A BAC vector, containing the whole biosynthetic gene cluster for spinosyn (74 kb) and the elements required for conjugal transfer and site-specific integration, was introduced into different Streptomyces hosts in order to obtain heterologous spinosyn-producing strains...
2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28772274/a-review-of-conventional-pcr-assays-for-the-detection-of-selected-phytopathogens-of-wheat
#17
Adam Kuzdraliński, Anna Kot, Hubert Szczerba, Michał Nowak, Marta Muszyńska
Infection of phyllosphere (stems, leaves, husks, and grains) by pathogenic fungi reduces the wheat yield and grain quality. Detection of the main wheat pathogenic fungi provides information about species composition and allows effective and targeted plant treatment. Since conventional procedures for the detection of these organisms are unreliable and time consuming, diagnostic DNA-based methods are required. Nucleic acid amplification technologies are independent of the morphological and biochemical characteristics of fungi...
2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28772273/antitumor-effect-of-a-dna-vaccine-harboring-prostate-cancer-specific-antigen-with-il-12-as-an-intramolecular-adjuvant
#18
Yu Yang, Zhiqiang Shao, Jiangping Gao
To improve the lower immune intensity of DNA vaccines, we developed a DNA vaccine based on prostate cancer-specific antigen (PSA), which has been suggested as a potential target for prostate cancer therapy, and enhanced the DNA vaccine potency using interleukin-12 (IL-12) as an intramolecular adjuvant. A series of DNA plasmids encoding human PSA, IL-12, and their conjugates was constructed and injected into female mice intramuscularly, followed by an electric pulse. The humoral and cellular immune responses after immunization were detected by ELISA and ELISPOT, respectively...
2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28605732/progress-in-bacillus-subtilis-spore-surface-display-technology-towards-environment-vaccine-development-and-biocatalysis
#19
Huayou Chen, Jawad Ullah, Jinru Jia
Spore surface display is the most desirable with enhanced effects, low cost, less time consuming and the most promising technology for environmental, medical, and industrial development. Spores have various applications in industry due to their ability to survive in harsh industrial processes including heat resistance, alkaline tolerance, chemical tolerance, easy recovery, and reusability. Yeast and bacteria, including gram-positive and -negative, are the most frequently used organisms for the display of various proteins (eukaryotic and prokaryotic), but unlike spores, they can rupture easily due to nutritive properties, susceptibility to heat, pH, and chemicals...
2017: Journal of Molecular Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28595177/genomics-perspectives-on-metabolism-survival-strategies-and-biotechnological-applications-of-brettanomyces-bruxellensis-lamap2480
#20
Liliana Godoy, Evelyn Silva-Moreno, Wladimir Mardones, Darwin Guzman, Francisco A Cubillos, Angélica Ganga
Wine production is an important commercial issue for the liquor industry. The global production was estimated at 275.7 million hectoliters in 2015. The loss of wine production due to Brettanomyces bruxellensis contamination is currently a problem. This yeast causes a "horse sweat" flavor in wine, which is an undesired organoleptic attribute. To date, 6 B. bruxellensis annotated genome sequences are available (LAMAP2480, AWRI1499, AWRI1608, AWRI1613, ST05.12/22, and CBS2499), and whole genome comparisons between strains are limited...
2017: Journal of Molecular Microbiology and Biotechnology
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