Isolation and Identification of Polycyclic Aromatic Hydrocarbon–Degrading Bacteria from Crude Oil Exploration Bore Well Sludge

Two bacterial strains capable of degrading polycyclic aromatic hydrocarbons were isolated from the crude oil exploration bore well sludge and identified by 16s rRNA gene sequencing as Pseudomonas stutzeri and Bacillus subtilis. The bacterial strains Pseudomonas stutzeri and Bacillus subtilis were able to degrade 95.1% and 99.4% of naphthalene (100 mg L^?1) and 99.5% and 94.6% of anthracene (50 mg L^?1), respectively, as a sole carbon and energy source in the liquid phase within a period of 6 days. The specific growth rate was determined for both the species and found to be 0.169 and 0.124 day^?1.     

Isolation and Characterization of Two β-d-Glucosidases from Bifidobacterium breve 203

Two β-d-glucosidases were purified to homogeneity from Bifidobacterium breve 203: one ( β-d-glucosidase I; molecular weight, 96,000) showed reactivity toward p-nitrophenyl (p-NP) β-d-fucoside, 74% of that to p-NP β-d-glucoside, and the other ( β-dglucosidase II; molecular weight, 450,000) did not. They also differed in their thermal and pH stabilities. Laminaribiose, cellobiose and gentiobiose were hydrolyzed by β-d-glucosidase I, with 53%, 34% and 3% of the reactivity in the case of p-NP β-d-glucoside, and by β-dglucosidase II, with 53%, 6% and 107% of the reactivity. The reaction of β-dglucosidase I with p-NP β-dfucoside was enhanced by the addition of glucose and other monosaccharides to the reaction mixture, whereas that with p-NP β-dglucoside was not affected. The activity of β-dglucosidase II with p-NP β-dglucoside was inhibited by glucose.     

Isolation and Characterization of β-1,4- Endoxylanase from Trichoderma pseudokonigi

13-1,4-endoxylanase from Triehoderma pseudokonigi Rifai has been purified by anion-exchange chromatography on DEAE-Sephadex A50, DEAE-Sepharose CL-6B and mono Q. The endoxylanase was shown to be homogeneous by Native-PAGE and SDS-PAGE. This endoxylanase is a single-peptide chain protein with a molecular weight estimated as 66 kD. The endoxylanase was purified by 10-fold with a specific activity of 15.87 U·mg－1 Optimum endoxylanase activity was obtained when the enzyme was incubated at pH 4.5, 55 ℃ with a Km of 20 mg/mL and Vmax of 3.3 μmol·min－1·mg－1. Hg2 + and Cu2 + have a strong inhibition while Fe2 + and Mn2 + have a increasing effect on the enzymatic reaction rate.     

Isolation and Characterization of a Δ5-Desaturase from Oblongichytrium sp.

We isolated a cDNA clone with homology to known desaturase genes from Oblongichytrium sp., recently classified as a new genus of thraustochytrids (Labyrinthulomycetes), and found that it encoded Δ5-desaturase by its heterologous expression in yeast. The enzyme had higher activity toward 20:4n-3 than 20:3n-6, indicating that this Δ5-desaturase can be used in the production of n-3 polyunsaturated fatty acids in transgenic organisms.     

Phylogenetic and Molecular Characterization of H9N2 Influenza Isolates from Chickens in Northern China from 2007–2009

The repeated transmission to pigs and humans, and the long-term endemicity in terrestrial poultry of H9N2 viruses in China lend urgency to the study of their ecology and pathogenicity. In the present paper, we reported an H9N2 virus sublineage isolated from chickens in northern China from 2007 to 2009 has high lethality for mice. Phylogenetic analysis of the full genome indicated that six representative H9N2 isolates shared high homology to each other, and they clustered in the same sublineage with other H9N2 viruses isolated recently in northern China. The isolates were double-reassortant viruses containing M genes similar to A/Quail/Hong Kong/G1/97 (H9N2) and the other seven gene segments from A/Chicken/Shanghai/F/98 (H9N2). These six isolates were capable of replicating in the lungs of infected chickens without producing observable clinical signs of disease or death. However, they were highly lethal to mice with mortality rates as high as 100% (14/14) without prior adaptation. The affected mice exhibited severe respiratory syndromes and diffuse lung injury. The H9N2 viruses could be detected in multiple organs of the infected mice, including hearts, livers, spleens, lungs and kidneys. Our findings demonstrated that H9N2 viruses isolated from the chickens in northern China have established a stable sublineage with enhanced pathogenicity to mice, suggesting that urgent attention will need to be paid to the transmission of H9N2 viruses from chickens to mammals.     

Isolation and Characterization of Novel β-Cyanoalanine Synthase and Cysteine Synthase Genes from Cassava

Cassava is an important staple food crop, feeding 600 million people worldwide, which produce cyanogenic glycosides. Cyanogenic glycosides in cassava are known to act as a deterrent for herbivores as well as serve as a mobile source of reduced nitrogen. Cassava is also equipped with a cyanide detoxification pathway, mediated by β-cyanoalanine synthase (β-CAS) which converts cyanide into asparagine. β-CAS, belonging to the Bsas family of enzymes, is multi functional and shares sequence homology with cysteine synthase (CS). Using rapid amplification of cDNA end-polymerase chain reaction (RACE-PCR), two cDNA sequences were isolated from cassava. The two clones named MANes;BsasA (accession no. EU350583) and MANes;BsasB (accession no. HQ257219), showed high homology to known β-CAS enzymes (80% and 75% amino acid similarity to Arabidopsis and 76% and 82% similarity to spinach, respectively). The kinetic properties of the two clones were characterized in a Escherichia coli NK3 mutant strain which lacks activity for any of the Bsas proteins. Kinetic studies showed that MANes;BsasB is a β-CAS with a CAS/CS activity ratio of 72 while MANes;BsasA is a CS showing bifunctional capabilities and with a CAS/CS activity ratio of 11. The isolation of cassava β-CAS and CS genes reported here paves the way for their utilization in genetically enhancing the cyanide detoxification potential of cassava and/or increase of the essential amino acid cysteine, which has been found to be low in nutritionally compromised individuals.     

Screening and Characterization of Several 2,2-Dicholoropropionic Acid–Degrading Bacteria Isolated from Marine Sediment of Danga Bay and East Coast of Singapore Island

Industries and agriculture activities extensively utilize halogenated compounds. These compounds were found to be toxic and pollute the environment. Thus, many studies have been done on microbial degradation of these chemicals. In this study, an attempt was made to isolate bacterial strains EK1–EK5 from marine sediments collected at Danga Bay and east coast of Singapore island. The 16S rRNA analysis suggested that the isolated bacteria had more than 96% sequence identity to the sequence in the database; therefore, they were designated as Bacillus sp., Rhodococcus sp., Lysinibacillus sp., Microbacterium sp., and Aminobacter sp. The results of molecular analysis were supported by biochemical and microscopic examinations. Bacterial isolates were able to grow slowly in minimal medium containing only 2,2-dichloropropionate as the sole carbon source. The cellular doubling times were 39.60 ± 0.1, 36.60 ± 0.2, 30.71 ± 0.1, 41.23 ± 0.1, and 36.70 ± 0.3 h for EK1, EK2, EK3, EK4, and EK5, respectively. In the future, it will be important to further investigate the presence of the dehalogenase gene in their genomic DNA for further characterization.     

Isolation and Characterization of a Novel Endo-β-galactofuranosidase from Bacillus sp.

A soil bacterium capable of growing on a polysaccharide containing β(1→6)galactofuranoside residues derived from the acidic polysaccharide of Fusarium sp. as a carbon source has been isolated. From various bacteriological characteristics, the organism was identified as a Bacillus sp. The bacterium produced β- galactofuranosidase inductively in the culture media. The most effective inducer for the β-galactofuranosidase production was a polysaccharide containing β(1→5) or β(1→6)-linked galactofuranoside residues, but gum arabic, gum guar, gum ghati, arabinogalactam, araban, and pectic acid did not induce the enzyme. The enzyme had three different molecular weight forms. The low molecular-weight form was purified by a combination of Toyopearl HW-55 and DEAE-Toyopearl 650S column chromatographies, and preparative polyacrylamide gel electrophoresis. The molecular weight of the enzyme was estimated to be 67,000 by SDS–polyacrylamide gel electrophoresis. The enzyme was most active at pH 6 and 37°C, and was stable between pH 4 to 8 at 5°C. The action of the enzyme was inhibited by the addition of Cd²⁺, Co²⁺, Hg²⁺, Zn²⁺, iodoacetic acid, and EDT A. The purified enzyme cleaved β(1→5) and β(1→6)-linked galactofuranosyl chains. Based upon the mode of liberation of galactofuranosyl residues from pyridylamino β(1→6)-linked galactofuranoside oligomers, the enzyme can be classified as an endo-β-galactofuranosidase that randomly hydrolyzes the linkage.     

Purification and Characterization of Konjac Glucomannan Degrading Enzyme from Anaerobic Human Intestinal Bacterium,Clostridium butyricum–Clostvidium beijerinckii Group

Konjac glucomannan degrading enzyme was purified to homogeneity from the culture broth of an anaerobic human intestinal bacterium, Clostridium butyricum–Clostridium beijerinckii group. The enzyme was composed of a single polypeptide chain with a molecular weight of 50,000?53,000. The enzyme was an endo-β-mannanase that acted specifically on the polysaccharides such as konjac glucomannan and coffee mannan, producing exclusively their smaller oligosaccharides and the monosaccharides. The optimal pH of the enzyme for the hydrolysis of konjac glucomannan was around 7–8 and the enzyme was stable in rather alkaline pH range of 8–10. The enzyme reaction was activated by the addition of CaCl₂ and dithiothreitol. It was suggested that the enzyme might contribute to the decomposition of konjac glucomannan in human digestive tract.     

Biosurfactant-Mediated Biodegradation of Polycyclic Aromatic Hydrocarbons—Naphthalene

The present study is aimed at the naphthalene degradation with and without biosurfactant produced from Pseudomonas aeruginosa isolated from oil-contaminated soil. The present study was carried out to isolate the bacterial strains for the naphthalene degradation and also for biosurfactant production. The isolated strains were screened for their ability to degrade the naphthalene by the methods of optimum growth rate test and for the production of biosurfactants by cetyltrimethylammonium bromide, blood agar medium, and thin-layer chromatography. The present study also focused on the effect of biosurfactant for the degradation of naphthalene by isolate-1. Two bacterial strains were isolated and screened, one for biodegradation and another for biosurfactant production. The second organism was identified as Pseudomonas aeruginosa by 16S rRNA analysis. The purified biosurfactant reduces the surface tension of water and also forms stable emulsification with hexadecane and kerosene. The end product of naphthalene degradation was estimated as salicylic acid equivalent by spectrophotometric method. The results demonstrated that Pseudomonas aeruginosa has the potential to produce biosurfactant, which enhances the biodegradation of naphthalene. The study reflects the potential use of biosurfactants for an effective bioremediation in the management of contaminated soils.     

Isolation and Characterization of Photosystem Ⅱ of Porphyra yezoensis Ueda

The thylakoid membranes were isolated and purified from gametophyte of Porphyra yezoensis Ueda (P. yezoensis) by sucrose density gradient ultracentrifugation. After P. yezoensis gametophyte thylakoid membranes were solubilized with SDS, the photosystem Ⅱ (PSⅡ) particles were isolated and purified. The activity of PSⅡ     

Isolation and Characterization of Oligosaccharides from the Hydrolyzate of Larch Wood Glucomannan with Endo-β-d-Mannanase

The glucomannan isolated from larch holocellulose was hydrolyzed by a purified endo-d-β-mannanase. The products were fractionated by gel filtration on a Polyacrylamide gel in water and partition chromatography on ion exchange resins in 80% ethanol. The following oligosaccharides were isolated and identified: (a) 4-O-β-d-Manp-d-Man, (b) 4-O-β-d-Glcp-d-Man, (c) 4-O-β-d-Glcp-d-Glc, (d) O-β-d-Manp-(1 →4)-O-β-d-Manp-(1 →4)-d-Man, (e) O-β-dGlcp-(l →4)-O-β-d-Manp-(l →4)-d-Man, (f) O-β-d-Manp-(l →4)-Oβ-d-Glcp-(l →4)-d-Man, (g) O-β-d-Manp-(l →4)-O-[α-d-Galp-(l →6)]-d-Man, (h) O-β-d-Manp-(l →4)-O-β-d-Manp-(l →4)-O-β-d-Manp-(l →4)-d-Man, and (i) O-β-d-Glcp-(1 →4)-O-β-d-Manp-(1 →4)-O-β-d-Manp-(1 →4)-d-Man.     

Characterization of the putative tryptophan synthase β-subunit from Mycobacterium tuberculosis

The increasing emergence of drug-resistant tuberculosis （TB） poses a serious threat to the control of this disease. It is in urgent need to develop new TB drugs. Tryptophan biosynthetic pathway plays an important role in the growth and replication of Mycobacterium tuberculosis （Mtb）. The β-subunit of tryptophan synthase （TrpB） catalyzes the last step of the tryptophan biosynthetic pathway, and it might be a potential target for TB drug design. In this study, we overexpressed, purified, and characterized the putative TrpB-encoding gene Rv1612 in Mtb H37Rv. Results showed that Mtb His-TrpB optimal enzymatic activity is at pH 7.8 with 0.15 M Na^＋ or 0.18 M Mg^2＋ at 37℃. Structure analysis indicated that Mtb TrpB exhibited a typical β/α barrel structure. The amino acid residues believed to interact with the enzyme cofactor pyridoxal-5＇-phosphate were predicted by homology modeling and structure alignment. The role of these residues in catalytic activity of the Mtb His-TrpB was confirmed by site-directed mutagenesis. These results provided reassuring structural information for drug design based on TrpB.     

Characterization of Fosfomycin Resistant Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates from Human and Pig in Taiwan

To investigate the efficacy of fosfomycin against extended-spectrum β-lactamases (ESBL) producing Escherichia coli in Taiwan and the resistance mechanisms and characterization of human and pig isolates, we analyzed 145 ESBL-producing isolates collected from two hospitals (n = 123) and five farms (n = 22) in Taiwan from February to May, 2013. Antimicrobial susceptibilities were determined. Clonal relatedness was determined by PFGE and multi-locus sequence typing. ESBLs, ampC, and fosfomycin resistant genes were detected by PCR, and their flanking regions were determined by PCR mapping and sequencing. The fosfomycin resistant mechanisms, including modification of the antibiotic target (MurA), functionless transporters (GlpT and UhpT) and their regulating genes such as uhpA, cyaA, and ptsI, and antibiotic inactivation by enzymes (FosA and FosC), were examined. The size and replicon type of plasmids carrying fosfomycin resistant genes were analyzed. Our results revealed the susceptibility rates of fosfomycin were 94% for human ESBL-producing E. coli isolates and 77% for pig isolates. The PFGE analysis revealed 79 pulsotypes. No pulsotype was found existing in both human and pig isolates. Three pulsotypes were distributed among isolates from two hospitals. ISEcp1 carrying bla_{CTX-M-group 9} was the predominant transposable elements of the ESBL genes. Among the thirteen fosfomycin resistant isolates, functionless transporters were identified in 9 isolates. Three isolates contained novel amino acid substitutions (Asn67Ile, Phe151Ser and Trp164Ser, Val146Ala and His159Tyr, respectively) in MurA (the target of fosfomycin). Four isolates had fosfomycin modified enzyme (fosA3) in their plasmids. The fosA3 gene was harboured in an IncN-type plasmid (101 kbp) in the three pig isolates and an IncB/O-type plasmid (113 kbp) in the human isolate. In conclusion, we identified that 6% and 23% of the ESBL-producing E. coli from human and pigs were resistant to fosfomycin, respectively, in Taiwan. No clonal spread was found between human and pig isolates. Functionless transporters were the major cause of fosfomycin resistance, and the fosA3-transferring plasmid between isolates warrants further monitoring.     

A Comparative Study on Biosurfactant Activity of Crude Oil–Degrading Bacteria and Its Correlation to Total Petroleum Hydrocarbon Degradation

In this study, 11 bacteria isolated from Tapis crude oil–contaminated sites were identified by using biochemical tests and 16S rDNA gene sequencing. Their abilities to biodegrade Tapis crude oil was determined by gas chromatography before they were further screened for biosurfactant activity by employing qualitative (blood agar hemolysis, microplate assay, drop-collapse test), semiquantitative (emulsification formation), and quantitative (surface tension measurement) methods. Four isolates, namely, Acinetobacter baumanii UKMP-12T, Pseudomonas aeruginosa UKMP-14T, Rhodococcus sp. UKMP-5T, and Rhodococcus sp. UKMP-7T, exhibited high percentages in total petroleum hydrocarbon (TPH) degradation. A strong correlation between the emulsification index (E ₂₄) and surface tension measurement (r _s = +.866) as shown by Spearman rank correlation analysis suggested that these two methods were more reliable to predict biosurfactant activity. The TPH removal was also positively correlated to the ability of bacterial isolates to reduce the surface tension of growth medium, as revealed by Pearson correlation test (r_p = +.886). In conclusion, not all the biosurfactant detection protocols employed were effective. Nevertheless, the measurement of surface tension and E ₂₄ determination provided a rather rapid, easy, reproducible, and accurate result in identifying bacteria with biosurfactant-producing ability.     

In-Depth Molecular Characterization of Mycobacterium tuberculosis from New Delhi – Predominance of Drug Resistant Isolates of the ‘Modern’ (TbD1?) Type

Background

India has the highest estimated burden of tuberculosis in the world, accounting for 21% of all tuberculosis cases world-wide. However, due to lack of systematic analysis using multiple markers the available information on the genomic diversity of Mycobacterium tuberculosis in India is limited.

Methodology/Principal Findings

Thus, 65 M. tuberculosis isolates from New Delhi, India were analyzed by spoligotyping, MIRU-VNTR, large deletion PCR typing and single nucleotide polymorphism analysis (SNP). The Central Asian (CAS) 1 _DELHI sub-lineage was the most prevalent sub-lineage comprising 46.2% (n = 30) of all isolates, with shared-type (ST) 26 being the most dominant genotype comprising 24.6% (n = 16) of all isolates. Other sub-lineages observed were: East-African Indian (EAI)-5 (9.2%, n = 6), EAI6_BGD1 (6.2%, n = 4), EAI3_IND, CAS and T1 with 6.2% each (n = 4 each), Beijing (4.6%, n = 3), CAS2 (3.1%, n = 2), and X1 and X2 with 1 isolate each. Genotyping results from five isolates (7.7%) did not match any existing spoligopatterns, and one isolate, ST124, belonged to an undefined lineage. Twenty-six percent of the isolates belonged to the TbD1+ PGG1 genogroup. SNP analysis of the pncA gene revealed a CAS-lineage specific silent mutation, S65S, which was observed for all CAS-lineage isolates (except two ST26 isolates) and in 1 orphan. Mutations in the pncA gene, conferring resistance to pyrazinamide, were observed in 15.4% of all isolates. Collectively, mutations in the rpoB gene, the katG gene and in both rpoB and katG genes, conferring resistance to rifampicin and isoniazid, respectively, were more frequent in CAS1_DELHI isolates compared to non-CAS_DELHI isolates (OR: 3.1, CI95% [1.11, 8.70], P = 0.045). The increased frequency of drug-resistance could not be linked to the patients'' history of previous anti-tuberculosis treatment (OR: 1.156, CI95% [0.40, 3.36], P = 0.79). Fifty-six percent of all new tuberculosis patients had mutations in either the katG gene or the rpoB gene, or in both katG and rpoB genes.

Conclusion

CAS1_DELHI isolates circulating in New Delhi, India have a high frequency of mutations in the rpoB and katG genes. A silent mutation (S65S) in the pncA gene can be used as a putative genetic marker for CAS-lineage isolates.     

Isolation and Characterization of New Virulent Actinophage Φr5

A new virulent phage, Φr5, was isolated from soil on Streptomyces ribosidificus SF733. Electron microscopic observation showed that this phage belongs to group B of Bradley′s morphological classification. The molecular weight of Φr5 DNA was about 29 × 10⁶. Φr5 DNA showed resistance to many restriction enzymes. Φr5 required Ca^{+ +} for plaque formation and grew at 28°C on S. ribosidificus SF733, S. chartreusis SF1623, S.flavus, S. flavovirens, S. sulfonofaciens SF2103, S. sulfonofaciens SF2138 and S. sulfonofaciens SF2144. The restriction-modification of Φr5 by the strains susceptible to this phage was examined.     

Characterization of protein–polysaccharides of articular cartilage from mature and immature pigs

Protein-polysaccharides of femoral articular cartilage from pigs of ages 9 months and 5 weeks were compared after extraction at pH6.8 with iso-osmotic sodium acetate followed by 0.63m-calcium acetate. The cartilage from the younger animals had a higher moisture content and contained considerably larger amounts of protein-polysaccharide, but less than half as much collagen/g. dry weight, than cartilage from the older pigs. There was notably less keratan sulphate in the fractions from the less mature animals. After gel filtration on 6% agarose, elution profiles of the calcium acetate extracts were similar to those of the sodium acetate extracts of the same tissue. Chemical analyses, however, showed that in both age-groups the extraction procedure had achieved a sequential solubilization of protein-polysaccharides in that the initial extracts contained a higher proportion of keratan sulphate than those that were extracted subsequently. Both extracts from the older animals contained up to 25% of a relatively small protein-polysaccharide that was retarded on 6% agarose and that had a lower protein content and less keratan sulphate than the larger protein-polysaccharides. In contrast, in extracts from the less mature cartilage only about 5% of the protein-polysaccharides were small enough to be retarded by 6% agarose, suggesting that the small components may not be precursors of the larger. The average length of chondroitin sulphate chains, as calculated from the analytical data, was the same in the smaller protein-polysaccharides as in the larger.