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Search Results: 1 - 10 of 3095 matches for " clone library "
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Comparison of the Bacterial Microbiota in a Bale of Collected Cardboard Determined by 454 Pyrosequencing and Clone Library  [PDF]
Valérie Lalande, Simon Barnabé, Jean-Charles C?té
Advances in Microbiology (AiM) , 2014, DOI: 10.4236/aim.2014.412082
Abstract: Biofouling, the accumulation of microorganisms, is a major problem in paper mills processing paper and cardboard. This leads to the production of lower quality recycled products. Several studies have focused on the microbial content in the paper mill and the final products. Our aim was to determine the microbial biota in a bale of collected cardboard prior to entering the paper mill. Total genomic DNA was isolated and analyzed using two different methods for comparison purposes: 454 pyrosequencing and clone library. A total of 3268 V6-V8 454 pyrosequencing reads and 322 cloned V6-V8 16S rRNA nucleotide sequences were obtained. Both methods showed the presence of three major bacterial genera: Bacillus, Solibacillus and Paenibacillus, all members of the spore-forming phylum Firmicutes. Pyrosequencing, however, revealed a richer and more diverse bacterial community than clone library. It showed the presence of additional minor Firmicute genera and of a small number of Proteobacteria. The sorting at the recycling plant, the storing, and the processing at the paper mill, the end uses, will all contribute to the bacterial microbiota present in a bale of collected cardboard as revealed here.
Identification of the bacterial community responsible for traditional fermentation during sour cassava starch, cacha?a and minas cheese production using culture-independent 16s rRNA gene sequence analysis
Lacerda, Inayara C. A.;Gomes, Fátima C. O.;Borelli, Beatriz M.;Faria Jr, César L. L.;Franco, Gloria R.;Mour?o, Marina M.;Morais, Paula B.;Rosa, Carlos A.;
Brazilian Journal of Microbiology , 2011, DOI: 10.1590/S1517-83822011000200029
Abstract: we used a cultivation-independent, clone library-based 16s rrna gene sequence analysis to identify bacterial communities present during traditional fermentation in sour cassava starch, cacha?a and cheese production in brazil. partial 16s rrna gene clone sequences from sour cassava starch samples collected on day five of the fermentation process indicated that leuconostoc citreum was the most prevalent species, representing 47.6% of the clones. after 27 days of fermentation, clones (genbank accession numbers gq999786 and gq999788) related to unculturable bacteria were the most prevalent, representing 43.8% of the clones from the bacterial community analyzed. the clone represented by the sequence gq999786 was the most prevalent at the end of the fermentation period. the majority of clones obtained from cacha?a samples during the fermentation of sugar cane juice were from the genus lactobacillus. lactobacillus nagelli was the most prevalent at the beginning of the fermentation process, representing 76.9% of the clones analyzed. after 21 days, lactobacillus harbinensis was the most prevalent species, representing 75% of the total clones. at the end of the fermentation period, lactobacillus buchneri was the most prevalent species, representing 57.9% of the total clones. in the minas cheese samples, lactococcus lactis was the most prevalent species after seven days of ripening. after 60 days of ripening, streptococcus salivarius was the most prevalent species. our data show that these three fermentation processes are conducted by a succession of bacterial species, of which lactic acid bacteria are the most prevalent.
Long-Term Exclusion of Grazing Increases Soil Microbial Biomass but Not Diversity in a Temperate Grassland  [PDF]
Xiaoqi Zhou, Chengrong Chen, Yanfen Wang
Open Journal of Soil Science (OJSS) , 2012, DOI: 10.4236/ojss.2012.24043

Restoration of grassland such as exclusion of grazing has been considered to increase aboveground plant diversity and soil fertility. However, knowledge on the effect of long-term exclusion of grazing on soil bacterial community structure and diversity is not well understood. The two sites were selected in the Inner Mongolian grassland, i.e., one fenced off since 1979 (UG79) and the other continually grazed by sheep (FG) all along. Soil microbial biomass was measured using fumigation method and bacterial community structure and diversity were assessed using methods of Denaturing Gradient Gel Electrophoresis (DGGE) and clone library. Results showed that the UG79 soil had significantly higher microbial biomass carbon and nitrogen compared with the FG soil. There was a clear separation in soil bacterial community structure, but not in bacterial diversity between the two sites. Moreover, 55 clones from the UG79 soil and 56 clones from the FG soil were selected and sequenced. Phylogenetic analysis of all clone sequences indicated that bacterial communities were dominated by the groups of Actinomycetes, Proteobacteria and Bacteroidetes, but there were no significant differences in bacterial diversity between the two sites, consistent with the results obtained from DGGE. The results highlighted that although long-term exclusion of grazing increased soil microbial biomass, but it did not harbor higher bacterial diversity compared with freely grazed site.

Diversity of Microflora in Colonic Mucus from Severe Ulcerative Colitis Patients Analyzed by Terminal Restriction Fragment Length Polymorphism and Clone Libraries of Bacterial 16S rRNA Gene Sequences  [PDF]
I-Nung Huang, Yuri Sato, Mitsuo Sakamoto, Moriya Ohkuma, Shinobu Ohnuma, Takeshi Naitoh, Chikashi Shibata, Akira Horii, Junko Nishimura, Haruki Kitazawa, Tadao Saito
Advances in Microbiology (AiM) , 2014, DOI: 10.4236/aim.2014.413095
Abstract: Although the gut microflora is thought to be an essential factor in the development of ulcerative colitis (UC), the entire gut microflora occurring in UC remains unknown. Most studies use feces to represent the microflora distribution; however, here we analyzed the bacterial diversity in colonic mucus from UC patients receiving colectomy surgery and control patients. The diversity of microflora was investigated using a combination of terminal restriction fragment length polymorphism (T-RFLP) and clone library analyses of the 16S rRNA gene sequences. In the T-RFLP analysis, the number of terminal restriction fragments (T-RFs) decreased significantly in UC patients when compared to control samples. Also in the clone library analysis, the number of operational taxonomic units (OTU) and the Shannon diversity index were reduced significantly in UC patients. These molecular analyses reveal an overall dysbiosis in UC patients. No specific pathogen was found, and a strong negative correlation in relative abundance of bacterial populations was observed between the phyla Bacteroidetes and Firmicutes in the UC patients. This is the first report showing a significant correlation between these two phyla, which may be important characteristics in the pathogenesis of UC.
Isolation and mapping of bacterial artificial chromosome (BAC) clone containing telomere-associated sequence
Xueqian Gong,Shouyi Chen,Jiming Gong,Feng Liu
Science China Life Sciences , 1998, DOI: 10.1007/BF02882903
Abstract: Using single primer (TTTAGGG)3 or (CCCTAAA)3CCC corresponding to rice telomeric repeat sequences, two fragments were amplified from rice genomic DNA and named Tas1 and Tas2. These two fragments did not show polymorphism between the mapping parents. Tasl was found to hybridize to rice telomeric regions byin situ hybridization (FISH). Then a rice bacterial artificial chromosome (BAC) library was constructed and Tasl was used to screen it. One positive clone was identified. A single copy sequence of this BAC clone was mapped at the end of the 6th chromosome of rice.
Isolation and mapping of bacterial artificial chromosome (BAC) clone containing telomere-associated sequence

GONG XueqianCHEN Shouyi GONG Jiming LIU Feng,

中国科学C辑(英文版) , 1998,
Abstract: Using single primer (TTTAGGG)\-3 or (CCCTAAA)\-3CCC corresponding to rice telomeric repeat sequences, two fragments were amplified from rice genomic DNA and named Tas1 and Tas2. These two fragments did not show polymorphism between the mapping parents. Tas1 was found to hybridize to rice telomeric regions by in situ hybridization (FISH). Then a rice bacterial artificial chromosome (BAC) library was constructed and Tas1 was used to screen it. One positive clone was identified. A single copy sequence of this BAC clone was mapped at the end of the 6th chromosome of rice.
Start-up of the anammox process from the conventional activated sludge in a hybrid bioreactor
Xiumei Duan,Jiti Zhou,Sen Qiao,Xin Yin,Tian Tian,Fangdi Xu,
Xiumei Duan
,Jiti Zhou,Sen Qiao,Xin Yin,Tian Tian,Fangdi Xu

环境科学学报(英文版) , 2012,
Abstract: The anaerobic ammonium oxidation (anammox) process was successfully started up from conventional activated sludge using a hybrid bioreactor within 2 months. The average removal efficiencies of ammonia and nitrite were both over 80%, and the maximum total nitrogen removal rate of 1.85 kg N/(m3.day) was obtained on day 362 with the initial sludge concentration of 0.7 g mixed liquor suspended solids (MLSS)/L. Scanning electron microscope (SEM) observation of the granular sludge in the hybrid reactor clearly showed a high degree of compactness and cell sphericity, and the cell size was quite uniform. Transmission electron microscope photos showed that cells were round or oval, the cellular diameter was 0.6--1.0 μupm, and the percentage of the anammoxosome compartment was 51%--85% of the whole cell volume. Fluorescence in situ hybridization analysis (FISH) indicated that anammox bacteria became the dominant population in the community (accounting for more than 51% of total bacteria on day 250). Seven planctomycete 16S rRNA gene sequences were present in the 16S rRNA gene clone library generated from the biomass and affiliated to Candidatus Kuenenia stuttgartiensis and Candidatus Brocadia sp., a new anammox species. In addition, the average effluent suspended solid (MLSS) concentrations of outlets I (above the non-woven carrier) and II (below the non-woven carrier) were 0.0009 and 0.0035 g/L, respectively. This showed that the non-woven carrier could catch the biomass effectively, which increased biomass and improved the nitrogen removal rate in the reactor.
Characterization of the airborne bacteria community at different distances from the rotating brushes in a wastewater treatment plant by 16S rRNA gene clone libraries
Yunping Han,Lin Li,Junxin Liu,
Yunping Han
,Lin Li,Junxin Liu

环境科学学报(英文版) , 2013,
Abstract: Biological risks of bioaerosols emitted from wastewater treatment processes have attracted wide attention in the recent years. However, the culture-based analysis method has been mostly adopted for detecting the bacterial community in bioaerosols, which may result in the underestimation of total microorganism concentration as not all microorganisms are cultivable. In this study, oligonucleotide fingerprinting of 16S rRNA genes was applied to reveal the composition and structure of the bacterial community in bioaerosols from an Orbal oxidation ditch in a Beijing wastewater treatment plant (WWTP). Bioaerosols were collected at different distances from the aerosol source, rotating brushes, and the sampling height was 1.5 m which is the common respiratory height of a human being. The bacterial communities of bioaerosols were diverse, and the lowest bacterial diversity was found at the sampling site just after the rotating brush rotating brush. A large proportion of bacteria in bioaerosols were affiliated with Proteobacteria and Bacteroidetes. Numerous bacteria present in the bioaerosols also emerged in water, indicating that the bacterial community in the bioaerosols was related to that of the aerosols' sources. The forced aeration of rotating brushes brought about observably distinct bacterial communities between sampling sites situated before and after the rotating brush. Isolation sources of closest relatives in bioaerosols clone libraries were associated with the aqueous environment in the WWTP. Common potential pathogens in bioaerosols as well as those not reported in previous research were also analyzed in this study. Measures should be adopted to reduce the emission of bioaerosols and prevent their exposure to workers.
Molecular Analysis of Bacterial Community DNA in Sludge Undergoing Autothermal Thermophilic Aerobic Digestion (ATAD): Pitfalls and Improved Methodology to Enhance Diversity Recovery
Anna V. Piterina,John Bartlett,J. Tony Pembroke
Diversity , 2010, DOI: 10.3390/d2040505
Abstract: Molecular analysis of the bacterial community structure associated with sludge processed by autothermal thermophilic aerobic digestion (ATAD), was performed using a number of extraction and amplification procedures which differed in yield, integrity, ability to amplify extracted templates and specificity in recovering species present. Interference to PCR and qPCR amplification was observed due to chelation, nuclease activity and the presence of thermolabile components derived from the ATAD sludge. Addition of selected adjuvant restored the ability to amplify community DNA, derived from the thermophilic sludge, via a number of primer sets of ecological importance and various DNA polymerases. Resolution of community profiles by molecular techniques was also influenced by the ATAD sludge extraction procedure as demonstrated by PCR-DGGE profiling and comparison of taxonomic affiliations of the most predominant members within 16S rRNA gene libraries constructed from ATAD DNA extracted by different methods. Several modifications have been shown to be necessary to optimize the molecular analysis of the ATAD thermal niche which may have general applicability to diversity recovery from similar environments.
Identification of Transcribed Sequences (ESTs) in the Trypanosoma cruzi Genome Project
Brand?o, Adeílton;Urmenyi, Turan;Rondinelli, Edson;Gonzalez, Antonio;Miranda, Antonio B de;Degrave, Wim;
Memórias do Instituto Oswaldo Cruz , 1997, DOI: 10.1590/S0074-02761997000600024
Abstract: random single pass sequencing of cdna fragments, also known as generation of expressed sequence tags (ests), has been highly successful in the study of the gene content of higher organisms, and forms an integral part of most genome projects, with the objective to identify new genes and targets for disease control and prevention and to generate mapping probes. in the trypanosoma cruzi genome project, est sequencing has also been a starting point, and here we report data on the first 797 sequences obtained, partly from a cl brener epimastigote non-normalized library, partly on a normalized library. only around 30% of the sequences obtained showed similarity with genbank and dbest databases, half of which with sequences already reported for t. cruzi.
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