Community structures of total bacterial DNA, cultivable bacteria and prototrophs in bulk soil and rhizospheres

Aims: It has been hypothesized that root exudates can be a nutritional factor influencing the bacterial community structure as well as the occurrence of prototrophs and auxotrophs in rhizospheres. The present study was performed to examine the community structures of total bacterial DNA, cultivable bacteria and prototrophs in 3 soil samples with different levels of abundance of root exudates. Methodology and results: Denaturing gradient gel electrophoresis (DGGE) was performed to examine the community structures of total bacterial DNA, cultivable bacteria and prototrophs in 3 soil samples including bulk soil, rhizosphere of a single plant species and rhizosphere of multiple plant species. For clustering analysis, a dendrogram generated from the DGGE patterns revealed the different bacterial community structures in these soil samples. Both rhizospheres claded together, separating from bulk soil. The DGGE patterns of cultivable bacteria showed particular fingerprints corresponding to kinds of media and soil samples. Nutrient agar (NA) medium, isolation medium for prototroph (IMP) and IMP supplemented with soil extracts were used for bacterial cultivations. Prototrophs were isolated and examined by random amplified polymorphic DNA (RAPD) and 16S rRNA gene sequence analysis. The genetic diversity of prototrophs in 3 soil samples was similar (approximately 5% to 10% similarities) and most of them (13 of 28 strains) were members of Pseudomonas with 97% to 100% identities. Conclusion, significance, and impact of study: The present study provides a strong evidence of the influence of root exudates and plant species on bacterial community structures.

Modulation of mitochondrial membrane integrity and ROS formation by high temperature in Saccharomyces cerevisiae

Background Yeast strains are exposed to numerous environmental stresses during industrial alcoholic fermentation. High temperature accumulated acetic acid, enhanced the growth inhibition and decreased ethanol production. Results In this study the influence of high temperature on the cellular and mitochondrial membrane integrity of Saccharomyces cerevisiae as well as reactive oxygen species (ROS) formation was investigated to understand the mechanisms of the high temperature fermentation process. However, increasing the temperature to 42°C resulted in a clear decrease in the cytoplasmic and mitochondrial membrane potential and an increase in intracellular ROS formation. It was also determined that the different thermostability between YZ1 and YF31 strains had a clear correlation with the yeast's intracellular trehalose content of the cell. Finally, random amplified polymorphic DNA (RAPD) was used to explore the genome differences between the YZ1 and YF31 strains. Conclusions Thus, the stability of the mitochondrial membrane and subsequently, the clearance ROS ability could be important factors for the viability of S. cerevisiae at high temperatures.

Random amplified polymeric DNA fingerprinting of antler by high performance capillary electrophoresis / 中国药学杂志

OBJECTIVE: To establish a high performance capillary electrophoresis-random amplified polymorphic DNA (HPCE-RAPD) fingerprinting method of antler.

Analysis on genetic relationship of plants in Curculigo Gaertn. from China by RAPD / 中草药

Objective: The genetic relationship of plants in Curculigo Gaertn. was analyzed in molecular level. Methods: Thirty individuls of seven species in Curculigo Gaertn. were employed to be analyzed by the approach of random amplified polymorphic DNA (RAPD). The parameters were calculated by Popgene Version 1.31 and the relationship was constructed based on UPGMA method. Results: Eleven primers screened out from 40 primers were used for RAPD amplification. A total of 157 bands were generated, of which 145 bands were polymorphism bands. The result showed that there was a high genetic diversity among the seven species in Curculigo Gaertn. At species level: percentage of polymorphic loci PPB was 92.36%, effective number of alleles Ne was 1.493 7, Nei's gene diversity H was 0.300 1, and Shannon's information index Hsp was 0.457 7; Within species levels: PPB was 5.09%, Ne was 1.036 6, Nei's gene diversity H was 0.020 4, and Shannon's information index Hpop was 0.029 8. The Nei's coefficient of genetic differentiation was 0.931 3, which was consistent with the Shannon's coefficient of genetic differentiation (0.934 9). Most of the genetic variation existed among populations. The gene flow was 0.036 9, which indicated that it was less among the populations and the degree of genetic differentiation was higher. Nei's genetic identity (I) was changed from 0.520 8 to 0.823 7. By clustering analysis, the classified result of RAPD marker was almost same with the traditional modal character. Conclusion: The genetic diversity of the seven species in Curculigo Gaertn. is high. The genetic difference among populations is higher than that within the species.

Molecular Typing of Urinary Isolates of Candida tropicalis by Pulsed-Field Gel Electrophoresis (PFGE) and Random Amplified Polymorphic DNA (RAPD) Analysis / 감염

BACKGROUND: Despite the recognized increase of frequency of candiduria due to Candida tropicalis, little was known of its molecular epidemiology. We applied PFGE and RAPD assay for urinary C. tropicalis isolates and evaluated the utilities of PFGE and RAPD for the epidemiological typing of C. tropicalis isolates. METHODS: A total of urinary 57 isolates of C. tropicalis from 40 patients at two hospitals was analyzed. PFGE analysis were performed by electrophoretic karyotyping (EK) and restriction endonuclease analysis of genomic DNA (REAG) using two restriction enzymes (BssHII and SfiI). For RAPD, a total of 31 primers (30 random 10-mer primers and M13 primer) were used. RESULTS: EK and RAPD analysis showed the same or similar patterns among the isolates. REAG with BssHII separated 57 isolates into 28 distinct types. Six patterns were generated by REAG with using SfiI. By combining the two REAG, a total of 31 different DNA types were identified among 57 isolates from 40 patients. Three strain types were common to 23 isolates from 12 patients of a University Hospital, which suggested possible nosocomial transmission. In 19 patients with serial urinary isolates, the sequential strains from each patient exhibited the same REAG pattern. CONCLUSION: These suggest that REAG with BssHII and SfiI is useful for the investigation of molecular epidemiology of C. tropicalis isolates. In addition, some clusters of C. tropicalis isolates with the same DNA type suggest that nosocomial transmission may occur.

The Random Amplified Polymorphic DNA Identification of 9 Taenia saginata Isolates from Four Provinces / 中国寄生虫学与寄生虫病杂志

Objective To make molecular identification for 9 isolates of Taenia saginata from 4 provinces.Methods Genomic DNA was extracted from the segments of adult tapeworms collected from Taoyuan of Taiwan(TW1),Duyun of Guizhou(DY1,DY2),Congjiang of Guizhou(CJ1,CJ2,CJ3,CJ4),Dali of Yunnan(DL1) and Wushi of Xinjiang(XJ1) respectively.PCRs were carried out with 13 random primers.A phylogenetic tree of different geographical strains was constructed.Results 331 DNA fragments were amplified.The number of DNA fragments amplified by single primer was between 3 and 28.The average number of amplified DNA fragments by the 13 primers was 14.15.The average number of fragments from the 9 isolates of T.saginata was 14.08.Phylogenetic tree revealed that there were two branches in the tree,DY1,DY2,DL1 and TW1 occupied one branch,while CJ1,CJ2,CJ3,CJ4 and XJ1 occupied the other one.Conclusions By the RAPD analysis,the isolates DY1,DY2,DL1 and TW1 belong to Taenia saginata asiatica,and the isolates CJ1,CJ2,CJ3,CJ4 and XJ1 belong to T.saginata saginata.

Identification of Schisandra chinensis(Turcz.) Baill.(Beiwuwei) and Schisandra sphenanthera Rehd. Et Wils.(Nanwuwei) by Random Amplified Polymorphic DNA / 中药新药与临床药理

Objective: To establish a new method for the identification of Schisandra chinensis(Turcz.) Baill. (Beiwuwei) and Schisandra sphenanthera Rehd. Et Wils. (Nanwuwei). Methods: Random amplified polymorphic DNA method was applied to screen random primers. Results:Screening from 80 primers,only S429, which can be used to identify Schisandra chinensis(Turcz.) Baill.(Beiwuwei) and Schisandra sphenanthera Rehd. Et Wils. (Nanwuwei) accurately and is of good reproducibility. Conclusion: S429 can be used to identify Schisandra chinensis(Turcz.) Baill. (Beiwuwei) and Schisandra sphenanthera Rehd. Et Wils. (Nanwuwei) accurately.