scholarly journals Further Analysis of Burkholderia pseudomallei MF2 and Identification of Putative Dehalogenase Gene by PCR

2020 ◽  
Vol 20 (2) ◽  
pp. 386
Author(s):  
Mohamed Faraj Edbeib ◽  
Roswanira Abdul Wahab ◽  
Fahrul Zaman Huyop ◽  
Hasan Murat Aksoy ◽  
Yilmaz Kaya
Keyword(s):  
Microscopic Observation ◽  
Chloride Ion ◽  
Pcr Primers ◽  
Sole Source ◽  
Biochemical Tests ◽  
Group I ◽  
Bacterium Strain ◽  
Rdna Analysis ◽  
Dehalogenase Gene ◽  
Pcr Primer

Halogenated organic compounds are extensively and widely used as pesticides, herbicides, and antibiotics that contribute to the pollution. This research was aimed to further analyze and characterize a bacterium that has the ability to utilize 2,2-dichloropropionic acid (2,2-DCP) as a model to study dehalogenase enzyme production.  Microscopic observation, biochemical tests and PCR technique were carried out in order to characterize the isolated bacterium. Strain MF2 showed its ability to grow on 10 mM 2,2-DCP liquid minimal medium with doubling time of 13 h with maximum chloride ion released of 19.8 molCl–/mL. The 16S rDNA analysis suggested that strain MF2 belongs to the genus Burkholderia. This was supported by the microscopic observation and biochemical tests. Dehalogenase gene was observed when using only primers dehIfor1 and dehIrev2 derived from group I deh PCR primer sequences, whereas no amplification using dhlB-314-forward and dhlB-637-reverse (group II dehalogenase) and haloacetate dehalogenase (H2-1157-forward and H2-1662-reverse) PCR primer sequences. The results suggested that, possibly, dehalogenase from MF2 was related to group I deh. In conclusion, strain MF2 showed the ability to utilize 2,2-DCP as sole source of carbon and energy. Further analysis revealed the MF2 strain consisted of dehalogenase gene that could be used for degradation of man-made halogenated compounds present in the environment. Using existing dehalogenase PCR primers, it was possible to amplify the dehalogenase genes sequence.

scholarly journals The relation of the pleural thickening in tuberculosis pleurisy with the activity of adenosine deaminase

2005 ◽  
Vol 63 (2) ◽  
Author(s):  
B. Uskul ◽  
H. Turker ◽  
C. Ulman ◽  
M. Ertugrul ◽  
A. Selvi ◽  
...  
Keyword(s):  
Pleural Effusion ◽  
Adenosine Deaminase ◽  
Pleural Fluid ◽  
Clinical Findings ◽  
X Rays ◽  
Biochemical Tests ◽  
Pleural Thickening ◽  
Group I ◽  
Immunological Mechanisms ◽  
Tuberculosis Pleurisy

Selvi, A. Kant, S. Arslan, M. Ozgel. Background: Residual pleural thickening (RPT) still occurs in most patients with tuberculosis pleurisy despite advances in the treatment of tuberculosis. The aim of this study was to evaluate the significance of RPT in tuberculosis pleurisy with the patients clinical findings, biochemical and microbiological properties of pleural effusion and with the total adenosine deaminase (ADA) and isoenzymes levels. Methods: 121 tuberculosis pleurisy patients were evaluated retrospectively. According to posteroanterior chest x-rays, the 63 (52%) cases with the thickness 2 mm or more in lower lateral hemithorax were grouped as I and the 58 (48%) cases without pleural thickness were grouped as II. The amount of pleural effusion was classified into small, medium or massive according to their chest x-rays. In both groups; sex, age, symptoms score, bacteriological and biochemical tests and ADA levels were recorded. Results: 81 (67%) male and 40 (33%) female, overall 121 patients were enrolled into the study. RPT was found higher in males (p=0.014) and the increase ran parallel with the amount of cigarette smoking (p=0.014). RPT was found to be lower in small effusions (p=0.001). The group with RPT, the serum albumin was found lower (p=0.002), pleural fluid total protein (p=0.047) and the ratio of pleural fluid protein to serum protein (p=0.002) were found higher. In group I, total ADA: 69.5±38.9 IU/L and ADA2: 41.3±31.6 IU/L were higher than the cases without RPT (p=0.032, p=0.017, respectively). Conclusions: We suggest that the immunological mechanisms are effective in the development of pleural thickening.

scholarly journals New PCR Primer Pairs Specific for Cryptococcus neoformans Serotype A or B Prepared on the Basis of Random Amplified Polymorphic DNA Fingerprint Pattern Analyses

1999 ◽  
Vol 37 (2) ◽  
pp. 315-320 ◽  
Author(s):  
Francisco Hideo Aoki ◽  
Tamae Imai ◽  
Reiko Tanaka ◽  
Yuzuru Mikami ◽  
Hideaki Taguchi ◽  
...  
Keyword(s):  
Cryptococcus Neoformans ◽  
Dna Sequences ◽  
Random Amplified Polymorphic Dna ◽  
Pcr Primers ◽  
Dna Fingerprint ◽  
Serotype A ◽  
Specific Pcr ◽  
Fingerprint Pattern ◽  
Serotype B ◽  
Pcr Primer

Thirty-three strains of Cryptococcus neoformans were isolated from clinical specimens, including specimens from AIDS patients in Brazil, and were classified into two serotypes; we detected 31 and 2 strains of serotypes A and B, respectively. Random amplified polymorphic DNA (RAPD) fingerprint pattern analyses of these strains of serotypes A and B showed that the patterns were similar for strains of each serotype when three 10-mer primers were used as the RAPD primers. Comparative studies of the fingerprint patterns of the study isolates with those of the reference strains also showed that the RAPD patterns for strains of each serotype were related and that most of the fingerprint bands existed commonly for all strains of each serotype tested. The common RAPD bands (an approximately 700-bp band for serotype A and an approximately 450-bp band for serotype B) were extracted and the DNA sequences were determined. Using this information, we prepared two and one PCR primer pairs which were expected to be specific for C. neoformans serotypes A and B, respectively. Use of each PCR primer combination thus prepared for serotype A or B was 100% successful in identifying the respectiveC. neoformans serotypes, including the 33 clinical isolates tested in the present study. Among these combinations, one for serotype A was found to amplify DNA from C. neoformans serotype B as well as serotype A. Serotype B-specific PCR primer pairs amplified DNA from not only serotype B strains but also from serotype C strains. The usefulness of other serotype-specific PCR primers for clinical C. neoformans isolates is discussed.

Terrabacter terrae sp. nov., a novel actinomycete isolated from soil in Spain

2005 ◽  
Vol 55 (6) ◽  
pp. 2491-2495 ◽  
Author(s):  
Marta Montero-Barrientos ◽  
Raúl Rivas ◽  
Encarna Velázquez ◽  
Enrique Monte ◽  
Manuel G. Roig
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Bacterium Strain

A Gram-positive, aerobic, long-rod-shaped, non-spore-forming bacterium (strain PPLBT) was isolated from soil mixed with Iberian pig hair. This actinomycete showed keratinase activity in vitro when chicken feathers were added to the culture medium. Strain PPLBT was oxidase-negative and catalase-positive and produced lipase and esterase lipase. This actinomycete grew at 40 °C on nutrient agar and in the same medium containing 5 % (w/v) NaCl. Growth was observed with many different carbohydrates as the sole carbon source. On the basis of 16S rRNA gene sequence similarity, strain PPLBT was shown to belong to the genus Terrabacter of the family Intrasporangiaceae. Strain PPLBT showed 98·8 % 16S rRNA gene sequence similarity to Terrabacter tumescens. Chemotaxonomic data, such as the main ubiquinone (MK-8), the main polar lipids (phosphatidylethanolamine, diphosphatidylglycerol and phosphatidylinositol) and the main fatty acids (i-C15 : 0, ai-C15 : 0, i-C16 : 0 and ai-C17 : 0) supported the affiliation of strain PPLBT to the genus Terrabacter. The G+C content of the DNA was 71 mol%. The results of DNA–DNA hybridization (36·6 % relatedness between Terrabacter tumescens and strain PPLBT) and physiological and biochemical tests suggested that strain PPLBT belongs to a novel species of the genus Terrabacter, for which the name Terrabacter terrae sp. nov. is proposed. The type strain is PPLBT (=CECT 3379T=LMG 22921T).

scholarly journals Kinneretia asaccharophila gen. nov., sp. nov., isolated from a freshwater lake, a member of the Rubrivivax branch of the family Comamonadaceae

2010 ◽  
Vol 60 (4) ◽  
pp. 809-814 ◽  
Author(s):  
Margarita Gomila ◽  
Jarone Pinhassi ◽  
Enevold Falsen ◽  
Edward R. B. Moore ◽  
Jorge Lalucat
Keyword(s):  
New Genus ◽  
Cellular Fatty Acid ◽  
Fatty Acid Analysis ◽  
Strictly Aerobic ◽  
Negative Bacterium ◽  
New Genus And Species ◽  
Biochemical Tests ◽  
The Family ◽  
Bacterium Strain ◽  
Physiological And Biochemical

A strictly aerobic, Gram-negative bacterium, strain KIN192T, isolated from fresh water from Lake Kinneret, Israel, was examined using a polyphasic approach to characterize and clarify its phylogenetic and taxonomic position. Sequences of the 16S rRNA and gyrB genes and ITS1 revealed close relationships to species of the genera Pelomonas, Mitsuaria and Roseateles, in the Rubrivivax branch of the family Comamonadaceae of the Betaproteobacteria. Physiological and biochemical tests, cellular fatty acid analysis and DNA–DNA hybridizations indicated that this strain should be assigned to a new genus and species in the Rubrivivax phylogenetic branch, for which the name Kinneretia asaccharophila gen. nov., sp. nov., is proposed. The type strain of Kinneretia asaccharophila is strain KIN192T (=CCUG 53117T =CECT 7319T).

scholarly journals Group-Specific Monitoring of Phenol Hydroxylase Genes for a Functional Assessment of Phenol-Stimulated Trichloroethylene Bioremediation

2001 ◽  
Vol 67 (10) ◽  
pp. 4671-4677 ◽  
Author(s):  
Hiroyuki Futamata ◽  
Shigeaki Harayama ◽  
Kazuya Watanabe
Keyword(s):  
Enrichment Culture ◽  
Pcr Primers ◽  
Amino Acid Residues ◽  
Phylogenetic Groups ◽  
Contaminated Aquifer ◽  
Consensus Sequences ◽  
Specific Pcr ◽  
Group I ◽  
Degrading Bacteria ◽  
Contrast Group

ABSTRACT The sequences of the largest subunit of bacterial multicomponent phenol hydroxylases (LmPHs) were compared. It was found that LmPHs formed three phylogenetic groups, I, II, and III, corresponding to three previously reported kinetic groups, low-K s (the half-saturation constant in Haldane's equation for trichloroethylene [TCE]), moderate-K s , and high-K s groups. Consensus sequences and specific amino acid residues for each group of LmPH were found, which facilitated the design of universal and group-specific PCR primers. PCR-mediated approaches using these primers were applied to analyze phenol/TCE-degrading populations in TCE-contaminated aquifer soil. It was found that the aquifer soil harbored diverse genotypes of LmPH, and the group-specific primers successfully amplified LmPH fragments affiliated with each of the three groups. Analyses of phenol-degrading bacteria isolated from the aquifer soil confirmed the correlation between genotype and phenotype. Competitive PCR assays were used to quantify LmPHs belonging to each group during the enrichment of phenol/TCE-degrading bacteria from the aquifer soil. We found that an enrichment culture established by batch phenol feeding expressed low TCE-degrading activity at a TCE concentration relevant to the contaminated aquifer (e.g., 0.5 mg liter−1); group II and III LmPHs were predominant in this batch enrichment. In contrast, group I LmPHs overgrew an enrichment culture when phenol was fed continuously. This enrichment expressed unexpectedly high TCE-degrading activity that was comparable to the activity expressed by a pure culture of Methylosinus trichosporium OB3b. These results demonstrate the utility of the group-specific monitoring of LmPH genes in phenol-stimulated TCE bioremediation. It is also suggested that phenol biostimulation could become a powerful TCE bioremediation strategy when bacteria possessing group I LmPHs are selectively stimulated.

Actinoplanes couchii sp. nov.

2007 ◽  
Vol 57 (4) ◽  
pp. 721-724 ◽  
Author(s):  
Peter Kämpfer ◽  
Birgit Huber ◽  
Kathrin Thummes ◽  
Iris Grün-Wollny ◽  
Hans-Jürgen Busse
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Gene Sequence ◽  
Sequence Similarity ◽  
16S Rrna Gene Sequence ◽  
Rrna Gene ◽  
Rrna Gene Sequence ◽  
Biochemical Tests ◽  
Closely Related Species ◽  
Bacterium Strain

A Gram-positive bacterium, strain GW8-1761T, was isolated from soil close to the Marmore waterfalls, Terni, Italy. 16S rRNA gene sequence similarity studies showed that strain GW8-1761T belonged to the genus Actinoplanes, being most closely related to Actinoplanes italicus JCM 3165T (98.9 %), A. rectilineatus IFO 13941T (98.5 %), A. palleronii JCM 7626T (97.8 %), A. utahensis IFO 13244T (97.6 %) and A. cyaneus DSM 46137T (97.6 %). Strain GW8-1761T could be distinguished from any other Actinoplanes species with validly published names by 16S rRNA gene sequence similarity values of less than 97.5 %. Chemotaxonomic data [major menaquinone MK-9(H4); major polar lipids diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol, with phosphatidylcholine and aminoglycolipids absent; major fatty acids C15 : 0, C16 : 0, C16 : 0 iso, C17 : 1 ω8c and summed feature 3 (C16 : 1 ω7c and/or C15 : 0 iso 2-OH)] supported the affiliation of strain GW8-1761T to the genus Actinoplanes. The results of DNA–DNA hybridizations and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain GW8-1761T from the most closely related species. Strain GW8-1761T therefore merits species status, and we propose the name Actinoplanes couchii sp. nov., with the type strain GW8-1761T (=DSM 45050T=CIP 109316T).

scholarly journals Comparing the Dehalogenase Gene Pool in Cultivated α-Halocarboxylic Acid-Degrading Bacteria with the Environmental Metagene Pool

2003 ◽  
Vol 69 (8) ◽  
pp. 4375-4382 ◽  
Author(s):  
Julian R. Marchesi ◽  
Andrew J. Weightman
Keyword(s):  
Activated Sludge ◽  
Gene Pool ◽  
Minor Component ◽  
Degenerate Pcr ◽  
Group I ◽  
Degrading Bacteria ◽  
Culture Independent ◽  
Pure Cultures ◽  
A Minor ◽  
Dehalogenase Gene

ABSTRACT Culture-dependent and culture-independent approaches were used to determine the relationship between the dehalogenase gene pool in bacteria enriched and isolated on 2,2-dichloropropionic acid (22DCPA) and the environmental metagene pool (the collective gene pool of both the culturable and uncultured microbes) from which they were isolated. The dehalogenases in the pure-cultures isolates, which were able to degrade 22DCPA, were similar to previously described group I and II dehalogenases. Significantly, the majority of the dehalogenases isolated from activated sludge by degenerate PCR with primers specific for α-halocarboxylic acid dehalogenases were not closely related to the dehalogenases in any isolate. Furthermore, the dehalogenases found in the pure cultures predominated in the enrichments but were a minor component of the community used to inoculate the batch cultures. Phylogenetic analysis of the dehalogenase sequences isolated by degenerate PCR showed that the diversity of the group II deh gene was greater than that of the group I deh gene. Direct plating of the activated sludge onto minimal media supplemented with 22DCPA resulted in biomass and DNA from which dehalogenases were amplified. Analysis of the sequences revealed that they were much more closely related to the sequences found in the community used to start the enrichments. However, no pure cultures were obtained with this isolation method, and thus no pure cultures were available for identification. In this study we examined the link between genes found in pure cultures with the metagene pool from which they were isolated. The results show that there is a large bias introduced by culturing, not just in the bacteria isolated but also the degradative genes that they contain. Moreover, our findings serve as a caveat for studies involving the culturing of pure cultures of bacteria and conclusions which are drawn from analysis of these organisms.

Methylobacterium oxalidis sp. nov., isolated from leaves of Oxalis corniculata

2012 ◽  
Vol 62 (Pt_7) ◽  
pp. 1647-1652 ◽  
Author(s):  
Akio Tani ◽  
Nurettin Sahin ◽  
Kazuhide Kimbara
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Type Species ◽  
Methylotrophic Bacterium ◽  
Rrna Gene ◽  
Biochemical Tests ◽  
Content Type ◽  
Link Type ◽  
Bacterium Strain ◽  
Sequence Similarities

A pink-pigmented, facultatively methylotrophic bacterium, strain 35aT, was isolated from the leaves of Oxalis corniculata. Cells of strain 35aT were Gram-reaction-negative, motile, non-spore-forming rods. The highest 16S rRNA gene pairwise sequence similarities for strain 35aT were found with the strains of Methylobacterium iners 5317S-33T (96.7 %), ‘Methylobacterium soli’ YIM 48816 (96.6 %) and Methylobacterium jeotgali S2R03-9T (96.3 %). 16S rRNA gene sequence similarities with the type strains of all other recognized species of the genus Methylobacterium were below 96 %. Major cellular fatty acids were C18 : 1ω7c, C18 : 0 and C16 : 0. The results of DNA–DNA hybridization experiments, analysis of cpn60 gene sequences, fatty acid profiles, whole-cell MALDI-TOF/MS spectral pattern analysis, and physiological and biochemical tests allowed genotypic and phenotypic differentiation of strain 35aT from its nearest phylogenetic neighbours. Strain 35aT is therefore considered to represent a novel species within the genus Methylobacterium , for which the name Methylobacterium oxalidis sp. nov. is proposed. The type strain is 35aT ( = DSM 24028T = NBRC 107715T).

scholarly journals Rhodococcus opacus expresses the xsc gene to utilize taurine as a carbon source or as a nitrogen source but not as a sulfur source

Microbiology ◽  
2004 ◽  
Vol 150 (6) ◽  
pp. 1859-1867 ◽  
Author(s):  
Karin Denger ◽  
Jürgen Ruff ◽  
David Schleheck ◽  
Alasdair M. Cook
Keyword(s):  
Gene Cluster ◽  
Gene Clusters ◽  
Pcr Primers ◽  
Sole Source ◽  
Amino Acid Sequences ◽  
Rhodococcus Opacus ◽  
Sulfur Source ◽  
Gram Positive Bacteria ◽  
Sulfoacetaldehyde Acetyltransferase ◽  
Different Levels

The Gram-positive bacteria Rhodococcus opacus ISO-5 and Rhodococcus sp. RHA1 utilized taurine (2-aminoethanesulfonate) as the sole source of carbon or of nitrogen or of sulfur for growth. Different gene clusters and enzymes were active under these different metabolic situations. Under carbon- or nitrogen-limited conditions three enzymes were induced, though to different levels: taurine-pyruvate aminotransferase (Tpa), alanine dehydrogenase (Ald) and sulfoacetaldehyde acetyltransferase (Xsc). The specific activities of these enzymes in R. opacus ISO-5 were sufficient to explain the growth rates under the different conditions. These three enzymes were purified and characterized, and the nature of each reaction was confirmed. Analyses of the genome of Rhodococcus sp. RHA1 revealed a gene cluster, tauR-ald-tpa, putatively encoding regulation and oxidation of taurine, located 20 kbp from the xsc gene and separate from two candidate phosphotransacetylase (pta) genes, as well as many candidate ABC transporters (tauBC). PCR primers allowed the amplification and sequencing of the tauR-ald-tpa gene cluster and the xsc gene in R. opacus ISO-5. The N-terminal sequences of the three tested proteins matched the derived amino acid sequences of the corresponding genes. The sequences of the four genes found in each Rhodococcus strain shared high degrees of identity (>95 % identical positions). RT-PCR studies proved transcription of the xsc gene when taurine was the source of carbon or of nitrogen. Under sulfur-limited conditions no xsc mRNA was generated and no Xsc was detected. Taurine dioxygenase (TauD), the enzyme catalysing the anticipated desulfonative reaction when taurine sulfur is assimilated, was presumed to be present because oxygen-dependent taurine disappearance was demonstrated with taurine-grown cells only. A putative tauD gene (with three other candidates) was detected in strain ISO-5. Regulation of the different forms of metabolism of taurine remains to be elucidated.

scholarly journals Ameliorative Effect of Methanol Extract of Hymenocardia acida Leaves on Gentamicin-Induced Renal Toxicity in Rats

2018 ◽  
pp. 1-9
Author(s):  
Nweje-Anyalowu Paul Chukwuemeka ◽  
Idakwoji Precious Adejoh ◽  
Iserhienrhien Lucky Osafanme ◽  
Anosike Joy Chizoba
Keyword(s):  
Methanol Extract ◽  
Histopathological Examination ◽  
Elevated Serum ◽  
Chloride Ion ◽  
Chloride Ions ◽  
Potassium Ion ◽  
Albino Rats ◽  
Histopathological Analysis ◽  
Serum Urea ◽  
Group I

Aim: This study evaluated the nephroprotective effect of methanol extract of Hymenocardia acida leaves in rat model of gentamicin induced renal damage. Materials and Methods: Twenty- four (24) Wistar albino rats of either sex weighing 150- 200g were divided into 4 groups of 6 animals each; Group I served as the control and received normal saline, Group II- IV received gentamicin (40 mg/kg, i.p), Groups III and IV also received 200 and 400 mg/kg body wt., p.o methanol extract of Hymenocardia acida leaves respectively for 15 days. Body weight measurement, serum urea, creatinine, electrolytes analyses and histopathological examination of kidney were carried out. Results: Gentamicin treatment caused nephrotoxicity as evidenced by marked elevation in Serum urea, creatinine, decreased sodium and chloride ions, elevated serum level of potassium ion and pathological signs such as congestion, focal areas of inflammation, tubular necrosis, and glomerular atrophy. Administration of the extract at doses of 200 and 400 mg/kg/ body wt significantly (p< 0.05) decreased Creatinine and urea levels, significantly (p< 0.05) increased sodium and chloride ion and significantly (p< 0.05)  decreased potassium ion level when compared to the gentamicin- alone- treated group. Histopathological analysis also revealed a gradual reversal of the pathological features caused by gentamicin toxicity. Conclusion: It was concluded that the extract possesses nephroprotective potential.

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