Background In this comparative study we evaluate the performance of four software tools: DNAstar-... more Background In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. Results In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (...
Background In this comparative study we evaluate the performance of four software tools: DNAstar-... more Background In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. Results In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (...
Background The impact of human activities on the environmental resistome has been documented in m... more Background The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities. Results The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile gene...
A highly fluoroquinolone-resistant isolate of Aeromonas species was isolated from a wastewater tr... more A highly fluoroquinolone-resistant isolate of Aeromonas species was isolated from a wastewater treatment plant and found to possess multiple resistance mechanisms, including mutations in gyrA and parC, efflux pumps, and plasmid-mediated quinolone resistance (PMQR) genes. Complete sequencing of the IncU-type plasmid, pAC3, present in the strain revealed a circular plasmid DNA 15,872 bp long containing two PMQR genes [qnrS2 and aac(6')-Ib-cr]. A mobile insertion cassette element containing the qnrS2 gene and a typical miniature inverted-repeat transposable element (MITE) structure was identified in the plasmid. The present study revealed that this MITE sequence appears in other Aeromonas species plasmids and chromosomes. Plasmid pAC3 was introduced into Escherichia coli, and its PMQR genes were expressed, resulting in the acquisition of resistance. Proteome analysis of the recipient E. coli strain harboring the plasmid revealed that aac(6')-Ib-cr expression was constitutive an...
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2013
A novel bacterial strain designated CJ70T was isolated from tidal flat sediment in Korea. A polyp... more A novel bacterial strain designated CJ70T was isolated from tidal flat sediment in Korea. A polyphasic approach was used to identify this strain taxonomically. The isolate was Gram-stain-negative, strictly aerobic, yellow-pigmented, rod-shaped and non-motile. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CJ70T was related most closely to Stakelama pacifica JLT832T with 95.7 % similarity and formed an independent phyletic line from recognized species of the genus Sphingomonas , comprising a clade with Stakelama pacifica , which is the only recognized species of the genus Stakelama . The predominant cellular fatty acids of strain CJ70T were C18 : 1ω7c (60.0 %), C16 : 0 (21.2 %) and C14 : 0 2-OH (5.8 %). The major isoprenoid quinone was ubiquinone-10. The G+C content of the genomic DNA was 61.4 mol%. The results obtained from this study suggested that strain CJ70T represents a novel species of the genus Stakelama , for which the name Stakelama sediminis sp. n...
International journal of systematic and evolutionary microbiology, 2013
A novel bacterial strain designated CJ70(T) was isolated from tidal flat sediment in Korea. A pol... more A novel bacterial strain designated CJ70(T) was isolated from tidal flat sediment in Korea. A polyphasic approach was used to identify this strain taxonomically. The isolate was Gram-stain-negative, strictly aerobic, yellow-pigmented, rod-shaped and non-motile. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CJ70(T) was related most closely to Stakelama pacifica JLT832(T) with 95.7 % similarity and formed an independent phyletic line from recognized species of the genus Sphingomonas, comprising a clade with Stakelama pacifica, which is the only recognized species of the genus Stakelama. The predominant cellular fatty acids of strain CJ70(T) were C(18 : 1)ω7c (60.0 %), C(16 : 0) (21.2 %) and C(14 : 0) 2-OH (5.8 %). The major isoprenoid quinone was ubiquinone-10. The G+C content of the genomic DNA was 61.4 mol%. The results obtained from this study suggested that strain CJ70(T) represents a novel species of the genus Stakelama, for which the name Stakelama sed...
Background In this comparative study we evaluate the performance of four software tools: DNAstar-... more Background In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. Results In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (...
Background In this comparative study we evaluate the performance of four software tools: DNAstar-... more Background In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. Results In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (...
Background The impact of human activities on the environmental resistome has been documented in m... more Background The impact of human activities on the environmental resistome has been documented in many studies, but there remains the controversial question of whether the increased antibiotic resistance observed in anthropogenically impacted environments is just a result of contamination by resistant fecal microbes or is mediated by indigenous environmental organisms. Here, to determine exactly how anthropogenic influences shape the environmental resistome, we resolved the microbiome, resistome, and mobilome of the planktonic microbial communities along a single river, the Han, which spans a gradient of human activities. Results The bloom of antibiotic resistance genes (ARGs) was evident in the downstream regions and distinct successional dynamics of the river resistome occurred across the spatial continuum. We identified a number of widespread ARG sequences shared between the river, human gut, and pathogenic bacteria. These human-related ARGs were largely associated with mobile gene...
A highly fluoroquinolone-resistant isolate of Aeromonas species was isolated from a wastewater tr... more A highly fluoroquinolone-resistant isolate of Aeromonas species was isolated from a wastewater treatment plant and found to possess multiple resistance mechanisms, including mutations in gyrA and parC, efflux pumps, and plasmid-mediated quinolone resistance (PMQR) genes. Complete sequencing of the IncU-type plasmid, pAC3, present in the strain revealed a circular plasmid DNA 15,872 bp long containing two PMQR genes [qnrS2 and aac(6')-Ib-cr]. A mobile insertion cassette element containing the qnrS2 gene and a typical miniature inverted-repeat transposable element (MITE) structure was identified in the plasmid. The present study revealed that this MITE sequence appears in other Aeromonas species plasmids and chromosomes. Plasmid pAC3 was introduced into Escherichia coli, and its PMQR genes were expressed, resulting in the acquisition of resistance. Proteome analysis of the recipient E. coli strain harboring the plasmid revealed that aac(6')-Ib-cr expression was constitutive an...
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2013
A novel bacterial strain designated CJ70T was isolated from tidal flat sediment in Korea. A polyp... more A novel bacterial strain designated CJ70T was isolated from tidal flat sediment in Korea. A polyphasic approach was used to identify this strain taxonomically. The isolate was Gram-stain-negative, strictly aerobic, yellow-pigmented, rod-shaped and non-motile. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CJ70T was related most closely to Stakelama pacifica JLT832T with 95.7 % similarity and formed an independent phyletic line from recognized species of the genus Sphingomonas , comprising a clade with Stakelama pacifica , which is the only recognized species of the genus Stakelama . The predominant cellular fatty acids of strain CJ70T were C18 : 1ω7c (60.0 %), C16 : 0 (21.2 %) and C14 : 0 2-OH (5.8 %). The major isoprenoid quinone was ubiquinone-10. The G+C content of the genomic DNA was 61.4 mol%. The results obtained from this study suggested that strain CJ70T represents a novel species of the genus Stakelama , for which the name Stakelama sediminis sp. n...
International journal of systematic and evolutionary microbiology, 2013
A novel bacterial strain designated CJ70(T) was isolated from tidal flat sediment in Korea. A pol... more A novel bacterial strain designated CJ70(T) was isolated from tidal flat sediment in Korea. A polyphasic approach was used to identify this strain taxonomically. The isolate was Gram-stain-negative, strictly aerobic, yellow-pigmented, rod-shaped and non-motile. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain CJ70(T) was related most closely to Stakelama pacifica JLT832(T) with 95.7 % similarity and formed an independent phyletic line from recognized species of the genus Sphingomonas, comprising a clade with Stakelama pacifica, which is the only recognized species of the genus Stakelama. The predominant cellular fatty acids of strain CJ70(T) were C(18 : 1)ω7c (60.0 %), C(16 : 0) (21.2 %) and C(14 : 0) 2-OH (5.8 %). The major isoprenoid quinone was ubiquinone-10. The G+C content of the genomic DNA was 61.4 mol%. The results obtained from this study suggested that strain CJ70(T) represents a novel species of the genus Stakelama, for which the name Stakelama sed...
Uploads
Papers by Cung Nawl Thawng