scholarly journals Chitinases from Uncultured Marine Microorganisms

1999 ◽  
Vol 65 (6) ◽  
pp. 2553-2557 ◽  
Author(s):  
Matthew T. Cottrell ◽  
Jessica A. Moore ◽  
David L. Kirchman
Keyword(s):  
Coastal Waters ◽  
Bacterial Communities ◽  
Plaque Assay ◽  
Microtiter Plate ◽  
Culturable Bacteria ◽  
Marine Microorganisms ◽  
Microtiter Plate Assay ◽  
Genes Encoding ◽  
Chitinase Genes ◽  
Hydrolysis Of

ABSTRACT Our understanding of the degradation of organic matter will benefit from a greater appreciation for the genes encoding enzymes involved in the hydrolysis of biopolymers such as chitin, one of the most abundant polymers in nature. To isolate representative and abundant chitinase genes from uncultivated marine bacteria, we constructed libraries of genomic DNA isolated from coastal and estuarine waters. The libraries were screened for genes encoding proteins that hydrolyze a fluorogenic analogue of chitin, 4-methylumbelliferyl β-d-N,N′-diacetylchitobioside (MUF-diNAG). The abundance of clones capable of MUF-diNAG hydrolysis was higher in the library constructed with DNA from the estuary than in that constructed with DNA from coastal waters, although the abundance of positive clones was also dependent on the method used to screen the library. Plaque assays revealed nine MUF-diNAG-positive clones of 75,000 screened for the estuarine sample and two clones of 750,000 for the coastal sample. A microtiter plate assay revealed approximately 1 positive clone for every 500 clones screened in the coastal library. The number of clones detected with the plaque assay was consistent with estimates of the portion of culturable bacteria that degrade chitin. Our results suggest that culture-dependent methods do not greatly underestimate the portion of marine bacterial communities capable of chitin degradation.

scholarly journals Drug Targeting Mycobacterium tuberculosis Cell Wall Synthesis: Genetics of dTDP-Rhamnose Synthetic Enzymes and Development of a Microtiter Plate-Based Screen for Inhibitors of Conversion of dTDP-Glucose to dTDP-Rhamnose

2001 ◽  
Vol 45 (5) ◽  
pp. 1407-1416 ◽  
Author(s):  
Yufang Ma ◽  
Richard J. Stern ◽  
Michael S. Scherman ◽  
Varalakshmi D. Vissa ◽  
Wenxin Yan ◽  
...  
Keyword(s):  
Cell Wall ◽  
Mycobacterium Tuberculosis ◽  
Enzyme Assay ◽  
Enzyme Inhibitors ◽  
Microtiter Plate ◽  
Structural Motif ◽  
Chemical Library ◽  
Microtiter Plate Assay ◽  
Synthetic Enzymes ◽  
Genes Encoding

ABSTRACT An l-rhamnosyl residue plays an essential structural role in the cell wall of Mycobacterium tuberculosis. Therefore, the four enzymes (RmlA to RmlD) that form dTDP-rhamnose from dTTP and glucose-1-phosphate are important targets for the development of new tuberculosis therapeutics. M. tuberculosis genes encoding RmlA, RmlC, and RmlD have been identified and expressed inEscherichia coli. It is shown here that genes for only one isotype each of RmlA to RmlD are present in the M. tuberculosis genome. The gene for RmlB is Rv3464. Rv3264c was shown to encode ManB, not a second isotype of RmlA. Using recombinant RmlB, -C, and -D enzymes, a microtiter plate assay was developed to screen for inhibitors of the formation of dTDP-rhamnose. The three enzymes were incubated with dTDP-glucose and NADPH to form dTDP-rhamnose and NADP+ with a concomitant decrease in optical density at 340 nm (OD340). Inhibitor candidates were monitored for their ability to lower the rate of OD340change. To test the robustness and practicality of the assay, a chemical library of 8,000 compounds was screened. Eleven inhibitors active at 10 μM were identified; four of these showed activities against whole M. tuberculosis cells, with MICs from 128 to 16 μg/ml. A rhodanine structural motif was present in three of the enzyme inhibitors, and two of these showed activity against wholeM. tuberculosis cells. The enzyme assay was used to screen 60 Peruvian plant extracts known to inhibit the growth ofM. tuberculosis in culture; two extracts were active inhibitors in the enzyme assay at concentrations of less than 2 μg/ml.

scholarly journals Metaplasmidome-encoded functions of Siberian low-centered polygonal tundra soils

2021 ◽  
Author(s):  
Adrian Gorecki ◽  
Stine Holm ◽  
Mikolaj Dziurzynski ◽  
Matthias Winkel ◽  
Sizhong Yang ◽  
...  
Keyword(s):  
Active Layer ◽  
Bacterial Communities ◽  
Extraction Methods ◽  
Metal Resistance ◽  
Rapid Adaptation ◽  
Tundra Soils ◽  
Genetic Traits ◽  
Functional Potential ◽  
Stress Response Genes ◽  
Genes Encoding

AbstractPlasmids have the potential to transfer genetic traits within bacterial communities and thereby serve as a crucial tool for the rapid adaptation of bacteria in response to changing environmental conditions. Our knowledge of the environmental pool of plasmids (the metaplasmidome) and encoded functions is still limited due to a lack of sufficient extraction methods and tools for identifying and assembling plasmids from metagenomic datasets. Here, we present the first insights into the functional potential of the metaplasmidome of permafrost-affected active-layer soil—an environment with a relatively low biomass and seasonal freeze–thaw cycles that is strongly affected by global warming. The obtained results were compared with plasmid-derived sequences extracted from polar metagenomes. Metaplasmidomes from the Siberian active layer were enriched via cultivation, which resulted in a longer contig length as compared with plasmids that had been directly retrieved from the metagenomes of polar environments. The predicted hosts of plasmids belonged to Moraxellaceae, Pseudomonadaceae, Enterobacteriaceae, Pectobacteriaceae, Burkholderiaceae, and Firmicutes. Analysis of their genetic content revealed the presence of stress-response genes, including antibiotic and metal resistance determinants, as well as genes encoding protectants against the cold.

scholarly journals Drug Targeting Mycobacterium tuberculosis Cell Wall Synthesis: Development of a Microtiter Plate-Based Screen for UDP-Galactopyranose Mutase and Identification of an Inhibitor from a Uridine-Based Library

2003 ◽  
Vol 47 (1) ◽  
pp. 378-382 ◽  
Author(s):  
Michael S. Scherman ◽  
Katharine A. Winans ◽  
Richard J. Stern ◽  
Victoria Jones ◽  
Carolyn R. Bertozzi ◽  
...  
Keyword(s):  
Cell Wall ◽  
Mycobacterium Tuberculosis ◽  
Drug Targeting ◽  
Enzyme Inhibitor ◽  
Microtiter Plate ◽  
Biosynthetic Enzyme ◽  
Cell Wall Synthesis ◽  
Chemical Library ◽  
Microtiter Plate Assay ◽  
Plate Assay

ABSTRACT A microtiter plate assay for UDP-galactopyranose mutase, an essential cell wall biosynthetic enzyme of Mycobacterium tuberculosis, was developed. The assay is based on the release of tritiated formaldehyde from UDP-galactofuranose but not UDP-galactopyranose by periodate and was used to identify a uridine-based enzyme inhibitor from a chemical library.

scholarly journals Effect of S-PRG Eluate on Biofilm Formation and Enzyme Activity of Oral Bacteria

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Masahiro Yoneda ◽  
Nao Suzuki ◽  
Yosuke Masuo ◽  
Akie Fujimoto ◽  
Kosaku Iha ◽  
...  
Keyword(s):  
Biofilm Formation ◽  
Composite Resin ◽  
Fusobacterium Nucleatum ◽  
Microtiter Plate ◽  
Oral Bacteria ◽  
Gelatin Film ◽  
Glass Ionomer ◽  
Microtiter Plate Assay ◽  
Substrate Hydrolysis ◽  
Adherence Ability

Recently, the antibacterial activity of a composite resin containing prereacted glass ionomer (S-PRG) filler was revealed. We examined the effect of an S-PRG eluate on various biologic activities ofStreptococcus mutansandPorphyromonas gingivalis. Adherence ability ofS. mutanswas evaluated by microtiter plate assay; protease and gelatinase activities ofP. gingivaliswere examined by synthetic substrate hydrolysis and gelatin film spot assay, respectively. Coaggregation ofP. gingivaliswithFusobacterium nucleatumwas also examined. S-PRG eluate was found to suppress streptococcal adherence. S-PRG eluate inhibited the protease and gelatinase activities ofP. gingivalisand the coaggregation betweenP. gingivalisandF. nucleatum. These results indicate that S-PRG eluate suppresses streptococcal adherence and inhibits the protease and coaggregation activities ofP. gingivalis. These findings may prompt research into novel strategies for preventing caries and periodontitis.

Evaluation of the Role of Staphylococci in the Pathomechanism of Conjunctivitis

2021 ◽  
Author(s):  
Ewa Jasińska ◽  
Agnieszka Bogut ◽  
Agnieszka Magryś ◽  
Alina Olender
Keyword(s):  
Antibiotic Resistance ◽  
Epithelial Cells ◽  
Biofilm Formation ◽  
Methicillin Resistance ◽  
Microtiter Plate ◽  
Host Cells ◽  
Diffusion Method ◽  
Microtiter Plate Assay ◽  
Low Prevalence

Abstract Purpose: Determination of the association between ica genes and phenotypic biofilm formation in staphylococcal isolates involved in conjunctivitis, their antibiotic resistance as well as detection of selected virulence characteristics: adhesion to epithelial cells and in vitro cytotoxicity.Methods: The study included 26 Staphylococcus aureus (SA) and 26 Staphylococcus epidermidis (SE) isolates. The presence of icaAD genes and ica operon was determined by the PCR assay. Phenotypic biofilm formation was verified using the microtiter plate assay. Antibiotic resistance was performed using the disc diffusion method. Staphylococcal ability to attach to host cells was assessed by flow cytometry. Cytotoxicity on epithelial cells was evaluated by LDH assay.Results: The ica genes were detected in 26.9% of SE and in 42.3% of SA isolates. Only 15.3% of isolates (SE) were positive for both the icaAD and the ica operon. Phenotypically, 19.2% of SE isolates were strong biofilm producers, among which three were both icaAD- and ica operon-positive. 26.9% of SA isolates were strong biofilm producers. Methicillin resistance (MR) was detected in 34.6% of SE and 26.9% of SA isolates. 75% of MR isolates were multidrug resistant. SA isolates adhered to host cells more extensively than SE. SA isolates released higher level of LDH than SE.Conclusions: Adherence abilities were commonly observed in staphylococci associated with conjunctivitis. However, low prevalence of isolates positive for a complete and functional ica locus and low prevalence of strong biofilm producers was detected. SA adhered to a greater extent to eukaryotic cells than SE and were more cytotoxic.

Immobilized Enzyme-Based Microtiter Plate Assay for Glucose in Foods

1996 ◽  
Vol 44 (12) ◽  
pp. 3858-3863 ◽  
Author(s):  
Hiroyuki Ukeda ◽  
Yoshihiro Fujita ◽  
Miki Ohira ◽  
Masayoshi Sawamura
Keyword(s):  
Immobilized Enzyme ◽  
Microtiter Plate ◽  
Microtiter Plate Assay ◽  
Plate Assay

scholarly journals GC-MS Analysis and Antimicrobial Assessment of Syzygium cumini (L.) Skeels Seed Ethanol Extract

2021 ◽  
pp. 271-283
Author(s):  
S. Mabel Parimala ◽  
A. Antilin Salomi
Keyword(s):  
Bacterial Species ◽  
Ethanol Extract ◽  
Microtiter Plate ◽  
Salmonella Typhi ◽  
Fungal Species ◽  
Gas Chromatography Mass Spectrometry ◽  
Diffusion Method ◽  
Syzygium Cumini ◽  
Microtiter Plate Assay ◽  
Agar Well Diffusion Method

People use plants to treat infections, and this has led to search of antimicrobials from medicinal plants. In this work, we evaluated the ethanol extract of Syzygium cumini seeds for their antibacterial and antifungal activities. Extraction was performed by maceration method using ethanol. The antimicrobial efficacy of the extract was assessed by agar well diffusion method against ten bacterial species, Bacillus cereus, Bacillus subtilis, Enterococcus faecalis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella typhi, Serratia marcescens, Staphylococcus aureus and Streptococcus mutans, and five fungal species, Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, Candida albicans and Mucor sp. Minimum inhibitory concentrations (MICs) of the extract were determined by resazurin microtiter plate assay.  Phytochemicals in the extract was identified by gas chromatography mass spectrometry (GC-MS) information.  In agar well diffusion method, Gram-negative bacteria such as P. aeruginosa and S. marcescens, Gram-positive bacteria such as B. subtilis and E. faecalis and fungi A. fumigatus were more susceptible showing larger zones of inhibition.  In resazurin method, low MICs were recorded for bacteria, B. cereus (<7.8 µg) and P. aeruginosa (15.6 µg) and fungi, A. fumigatus (31.2 µg).  Fifteen compounds were identified by GC-MS profiling of the extract.  The antimicrobial activity of the extract can be rightly related to the secondary metabolites in the ethanol extract of Syzygium cumini seeds.

scholarly journals Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

2021 ◽  
Author(s):  
◽  
Joshua J Carter
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Quantitative Measurement ◽  
Target Gene ◽  
Microtiter Plate ◽  
Drug Susceptibility ◽  
Drug Susceptibility Testing ◽  
World Health ◽  
Genetic Determinants ◽  
Microtiter Plate Assay ◽  
Health Organization

AbstractThe World Health Organization goal of universal drug susceptibility testing for patients with tuberculosis is most likely to be achieved through molecular diagnostics; however, to date these have focused largely on first-line drugs, and always on predicting binary susceptibilities. Here, we used whole genome sequencing and a quantitative microtiter plate assay to relate genomic mutations to minimum inhibitory concentration in 15,211 Mycobacterium tuberculosis patient isolates from 27 countries across five continents.This work identifies 449 unique MIC-elevating genetic determinants across thirteen drugs, as well as 91 mutations resulting in hypersensitivity for eleven drugs. Our results provide a guide for further implementation of personalized medicine for the treatment of tuberculosis using genetics-based diagnostics and can serve as a training set for novel approaches to predict drug resistance.

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