Pseudomonas aeruginosa ( P. aeruginosa ) is an opportunistic Gram-negative bacterium that causes ... more Pseudomonas aeruginosa ( P. aeruginosa ) is an opportunistic Gram-negative bacterium that causes severe infection in immune-weakened individuals, especially patients with cystic fibrosis, burn wounds, cancer, or chronic obstructive pulmonary disease (COPD). Treating P. aeruginosa infection with conventional antibiotics is difficult due to its intrinsic multidrug resistance.
A list of complete genomes of Pseudomonas aeruginosa employed in the present study. Table S2. Ann... more A list of complete genomes of Pseudomonas aeruginosa employed in the present study. Table S2. Annotations of ORFs in Prophage 2 predicted in P. aeruginosa ATCC 27853. Table S3. Table S3 Differentially expressed genes in P. aeruginosa ATCC 2853 and PAO1 revealed by DESeq of the RNA-seq data (see supplemented excel file). Table S4 Top 50 ranked genes with numbers of non-synonymous variants between Pseudomonas aeruginosa ATCC 2853 and PAO1 with function description. Table S5 RNA-seq statistics and coverage after quality filtering for PAO1 and ATCC 27853. Fig. S1. Location of prophage B3 in four P. aeruginosa genomes: ATCC 27853, P. aeruginosa NCGM2.S1, P. aeruginosa VRFPA04 and P. aeruginosa Carb01_63. Fig. S2 Distribution of nucleotide change numbers in the genomes of P. aeruginosa ATCC 27853 and PAO1. (ZIP 718Â kb)
Anaerobic expression of the gadE-mdtEF multidrug efflux operon is primarily regulated by the two-... more Anaerobic expression of the gadE-mdtEF multidrug efflux operon is primarily regulated by the two-component system ArcBA through antagonizing the H-NS mediated repression
Bacteria adapt to the constantly changing environments largely by transcriptional regulation thro... more Bacteria adapt to the constantly changing environments largely by transcriptional regulation through the activities of various transcription factors (TFs). However, techniques that monitor the in situ TF-promoter interactions in living bacteria are lacking. Herein, we developed a whole-cell TF-promoter binding assay based on the intermolecular Förster resonance energy transfer (FRET) between a fluorescent unnatural amino acid CouA which is genetically encoded into defined sites in TFs and the live cell fluorescent nucleic acid stain SYTO 9. We show that this new FRET pair monitors the intricate TF-promoter interactions elicited by various types of signal transduction systems with specificity and sensitivity. Furthermore, the assay is applicable to identify novel modulators of the regulatory systems of interest and monitor TF activities in bacteria colonized in C. elegans. In conclusion, we established a tractable and sensitive TF-promoter binding assay in living bacteria which not o...
A water soluble polyhydroxy derivative of 1,4\|diazine has been isolated from Panax pseudoginseng... more A water soluble polyhydroxy derivative of 1,4\|diazine has been isolated from Panax pseudoginseng var notoginseng for the first time.Its structure was determined as 2\|(1′,2′,3′,4′\|tetrahydroxybutyl) 6 (2″,3″,4″\|trihydroxybutyl) pyrazine by MS,NMR, 1H\| 1H?COSY, 1H\| 13 C?COSY,HMBC etc.,it was also confirmed by chemical synthesis.
International Biodeterioration & Biodegradation, 2021
Abstract The ancient Angkorian sandstone monuments in Cambodia are well known for biodeterioratio... more Abstract The ancient Angkorian sandstone monuments in Cambodia are well known for biodeterioration of the sandstone under tropic climate. This study examined ammonia oxidizing bacteria (AOB and Comammox) and archaea (AOA) in stone-dwelling microbiome from three important Angkor monuments, namely Angor Wat, Bayon of Angkor Thom, and Preah Vihear, by DNA-based metagenomics analysis, RNA-based functional gene reverse-transcriptional (RT)-qPCR quantification, and N-15 isotope analysis. Our metagenomics datasets on these three monuments reveal a rich microbiome and abundant microbial nitrogen transforming reactions of ammonia oxidation and nitrite oxidation, Comammox and dissimilatory nitrate reduction to ammonium (DNRA), and these results support an internal recycling mechanism between ammonia/ammonium and nitrate by AOA, AOB, Comammox and DNRA on the stone monuments to support the microbial community. Though a wide range of AOB and AOA lineages together with Comammox were retrieved from these metagenomes as the potential ammonia-oxidizers, only AOA and Comammox were most abundant, likely to contribute to the biochemical processes of ammonia oxidation. The RNA-based qPCR quantification of the functional gene amoA in this study showed that AOA were the more active ammonia oxidizers over AOB in the microbiome of these Angkor sandstone monuments. In addition, a rich population of nitrite/nitrate producing AOA and Comammox drove the sequestration of CO2 onto the stone and this process was in turn supported by DNRA to provide the substrate ammonia/ammonium for a further cyclic reaction to take place continuously between ammonia/ammonium and nitrate. This model is further supported by the high enrichment of stable isotope 15N signature of NO3− in sandstone surface biofilms. The findings of this study are insightful for elucidation of nitrate accumulation by an internal N cycling mechanism proposed, and are important for understanding the sustainable microbial community and protection management of stone cultural heritage.
We report for the first time that antimicrobial Ag+ targets the glycolytic pathway through inhibi... more We report for the first time that antimicrobial Ag+ targets the glycolytic pathway through inhibiting the key enzyme of GAPDH.
Abstract Food preservatives are important for the storage of foods, and natural polyphenols with ... more Abstract Food preservatives are important for the storage of foods, and natural polyphenols with antioxidant and antibacterial effects are often effective as food preservatives. In this study, we systemically investigated the phenolic composition, antioxidant and antibacterial effects of 28 pigmented edible bean coat extracts. Most of these bean coat extracts had a relatively high level of total phenolic content, mainly flavonoids and proanthocyanidins, and they also exhibited much higher antioxidant effect than most common fruits, vegetables and cereal grains. In addition, most of them showed antibacterial effects, mainly against gram-positive bacteria, higher than the effect of phenol. Correlation analysis and principal component analysis indicated that flavonoids and proanthocyanidins were mostly responsible for the antioxidant and antibacterial effects of these bean coat extracts. Therefore, the pigmented bean coats rich in polyphenols with antioxidant and antibacterial effects are potential candidates as food preservatives.
Infections caused by carbapenem-resistant Pseudomonas aeruginosa are life-threatening due to its ... more Infections caused by carbapenem-resistant Pseudomonas aeruginosa are life-threatening due to its synergistic resistance mechanisms resulting in the ineffectiveness of the used antimicrobials. This study aimed to characterize P. aeruginosa isolates for antimicrobial susceptibility, biofilm formation virulence genes, and molecular mechanisms responsible for resistance against various antimicrobials. Out of 700 samples, 91 isolates were confirmed as P. aeruginosa which were further classified into 19 non-multidrug-resistant (non-MDR), 7 multidrug-resistant (MDR), 19 extensively drug-resistant (XDR), and 8 pan drug-resistant (PDR) pulsotypes based on standard Kirby Bauer disc diffusion test and pulse field gel electrophoresis. In M9 minimal media, strong biofilms were formed by the XDR and PDR pulsotypes as compared to the non-MDR pulsotypes. The virulence genes, responsible for the worsening of wounds including LasB, plcH, toxA, and exoU, were detected among all MDR, XDR, and PDR pulsotypes. Carbapenemase activity was phenotypically detected in 45% pulsotypes and the responsible genes were found as blaGES (100%), blaVIM (58%), blaIMP (4%), and blaNDM (4%). Real-time polymerase chain reaction showed the concomitant use of multiple mechanisms such as oprD under-expression, enhanced efflux pump activity, and ampC overexpression in the resistant isolates. Polymyxin is found as the only class left with more than 80% susceptibility among the isolates which is an alarming situation suggesting appropriate measures to be taken including alternative therapies. KEY POINTS: • Multidrug-resistant P. aeruginosa isolates formed stronger biofilms in minimal media. • Only polymyxin antimicrobial was found effective against MDR P. aeruginosa isolates. • Under-expression of oprD and overexpression of ampC were found in resistant isolates.
Three-dimensional (3D) microfibrillar network represents an important structural design for vario... more Three-dimensional (3D) microfibrillar network represents an important structural design for various natural tissues and synthetic aerogels. Despite extensive efforts, achieving high mechanical properties for synthetic 3D microfibrillar networks remains challenging. Here, we report ultrastrong polymeric aerogels involving self-assembled 3D networks of aramid nanofiber composites. The interactions between the nanoscale constituents lead to assembled networks with high nodal connectivity and strong crosslinking between fibrils. As revealed by theoretical simulations of 3D networks, these features at fibrillar joints may lead to an enhancement of macroscopic mechanical properties by orders of magnitude even with a constant level of solid content. Indeed, the polymeric aerogels achieved both high specific tensile modulus of ~625.3 MPa cm3 g−1 and fracture energy of ~4700 J m−2, which are advantageous for diverse structural applications. Furthermore, their simple processing techniques all...
The Class 1 type I CRISPR–Cas systems represent the most abundant and diverse CRISPR systems in n... more The Class 1 type I CRISPR–Cas systems represent the most abundant and diverse CRISPR systems in nature. However, their applications for generic genome editing have been hindered due to difficulties of introducing the class-specific, multi-component effectors (Cascade) in heterologous hosts for functioning. Here we established a transferrable Cascade system that enables stable integration and expression of a highly active type I-F Cascade in heterologous bacterial hosts for various genetic exploitations. Using the genetically recalcitrant Pseudomonas species as a paradigm, we show that the transferred Cascade displayed substantially higher DNA interference activity and greater editing capacity than both the integrative and plasmid-borne Cas9 systems, and enabled deletion of large fragments such as the 21-kb integrated cassette with efficiency and simplicity. An advanced I-F-λred system was further developed to enable editing in genotypes with poor homologous recombination capacity, c...
Pseudomonas aeruginosa ( P. aeruginosa ) is an opportunistic Gram-negative bacterium that causes ... more Pseudomonas aeruginosa ( P. aeruginosa ) is an opportunistic Gram-negative bacterium that causes severe infection in immune-weakened individuals, especially patients with cystic fibrosis, burn wounds, cancer, or chronic obstructive pulmonary disease (COPD). Treating P. aeruginosa infection with conventional antibiotics is difficult due to its intrinsic multidrug resistance.
A list of complete genomes of Pseudomonas aeruginosa employed in the present study. Table S2. Ann... more A list of complete genomes of Pseudomonas aeruginosa employed in the present study. Table S2. Annotations of ORFs in Prophage 2 predicted in P. aeruginosa ATCC 27853. Table S3. Table S3 Differentially expressed genes in P. aeruginosa ATCC 2853 and PAO1 revealed by DESeq of the RNA-seq data (see supplemented excel file). Table S4 Top 50 ranked genes with numbers of non-synonymous variants between Pseudomonas aeruginosa ATCC 2853 and PAO1 with function description. Table S5 RNA-seq statistics and coverage after quality filtering for PAO1 and ATCC 27853. Fig. S1. Location of prophage B3 in four P. aeruginosa genomes: ATCC 27853, P. aeruginosa NCGM2.S1, P. aeruginosa VRFPA04 and P. aeruginosa Carb01_63. Fig. S2 Distribution of nucleotide change numbers in the genomes of P. aeruginosa ATCC 27853 and PAO1. (ZIP 718Â kb)
Anaerobic expression of the gadE-mdtEF multidrug efflux operon is primarily regulated by the two-... more Anaerobic expression of the gadE-mdtEF multidrug efflux operon is primarily regulated by the two-component system ArcBA through antagonizing the H-NS mediated repression
Bacteria adapt to the constantly changing environments largely by transcriptional regulation thro... more Bacteria adapt to the constantly changing environments largely by transcriptional regulation through the activities of various transcription factors (TFs). However, techniques that monitor the in situ TF-promoter interactions in living bacteria are lacking. Herein, we developed a whole-cell TF-promoter binding assay based on the intermolecular Förster resonance energy transfer (FRET) between a fluorescent unnatural amino acid CouA which is genetically encoded into defined sites in TFs and the live cell fluorescent nucleic acid stain SYTO 9. We show that this new FRET pair monitors the intricate TF-promoter interactions elicited by various types of signal transduction systems with specificity and sensitivity. Furthermore, the assay is applicable to identify novel modulators of the regulatory systems of interest and monitor TF activities in bacteria colonized in C. elegans. In conclusion, we established a tractable and sensitive TF-promoter binding assay in living bacteria which not o...
A water soluble polyhydroxy derivative of 1,4\|diazine has been isolated from Panax pseudoginseng... more A water soluble polyhydroxy derivative of 1,4\|diazine has been isolated from Panax pseudoginseng var notoginseng for the first time.Its structure was determined as 2\|(1′,2′,3′,4′\|tetrahydroxybutyl) 6 (2″,3″,4″\|trihydroxybutyl) pyrazine by MS,NMR, 1H\| 1H?COSY, 1H\| 13 C?COSY,HMBC etc.,it was also confirmed by chemical synthesis.
International Biodeterioration & Biodegradation, 2021
Abstract The ancient Angkorian sandstone monuments in Cambodia are well known for biodeterioratio... more Abstract The ancient Angkorian sandstone monuments in Cambodia are well known for biodeterioration of the sandstone under tropic climate. This study examined ammonia oxidizing bacteria (AOB and Comammox) and archaea (AOA) in stone-dwelling microbiome from three important Angkor monuments, namely Angor Wat, Bayon of Angkor Thom, and Preah Vihear, by DNA-based metagenomics analysis, RNA-based functional gene reverse-transcriptional (RT)-qPCR quantification, and N-15 isotope analysis. Our metagenomics datasets on these three monuments reveal a rich microbiome and abundant microbial nitrogen transforming reactions of ammonia oxidation and nitrite oxidation, Comammox and dissimilatory nitrate reduction to ammonium (DNRA), and these results support an internal recycling mechanism between ammonia/ammonium and nitrate by AOA, AOB, Comammox and DNRA on the stone monuments to support the microbial community. Though a wide range of AOB and AOA lineages together with Comammox were retrieved from these metagenomes as the potential ammonia-oxidizers, only AOA and Comammox were most abundant, likely to contribute to the biochemical processes of ammonia oxidation. The RNA-based qPCR quantification of the functional gene amoA in this study showed that AOA were the more active ammonia oxidizers over AOB in the microbiome of these Angkor sandstone monuments. In addition, a rich population of nitrite/nitrate producing AOA and Comammox drove the sequestration of CO2 onto the stone and this process was in turn supported by DNRA to provide the substrate ammonia/ammonium for a further cyclic reaction to take place continuously between ammonia/ammonium and nitrate. This model is further supported by the high enrichment of stable isotope 15N signature of NO3− in sandstone surface biofilms. The findings of this study are insightful for elucidation of nitrate accumulation by an internal N cycling mechanism proposed, and are important for understanding the sustainable microbial community and protection management of stone cultural heritage.
We report for the first time that antimicrobial Ag+ targets the glycolytic pathway through inhibi... more We report for the first time that antimicrobial Ag+ targets the glycolytic pathway through inhibiting the key enzyme of GAPDH.
Abstract Food preservatives are important for the storage of foods, and natural polyphenols with ... more Abstract Food preservatives are important for the storage of foods, and natural polyphenols with antioxidant and antibacterial effects are often effective as food preservatives. In this study, we systemically investigated the phenolic composition, antioxidant and antibacterial effects of 28 pigmented edible bean coat extracts. Most of these bean coat extracts had a relatively high level of total phenolic content, mainly flavonoids and proanthocyanidins, and they also exhibited much higher antioxidant effect than most common fruits, vegetables and cereal grains. In addition, most of them showed antibacterial effects, mainly against gram-positive bacteria, higher than the effect of phenol. Correlation analysis and principal component analysis indicated that flavonoids and proanthocyanidins were mostly responsible for the antioxidant and antibacterial effects of these bean coat extracts. Therefore, the pigmented bean coats rich in polyphenols with antioxidant and antibacterial effects are potential candidates as food preservatives.
Infections caused by carbapenem-resistant Pseudomonas aeruginosa are life-threatening due to its ... more Infections caused by carbapenem-resistant Pseudomonas aeruginosa are life-threatening due to its synergistic resistance mechanisms resulting in the ineffectiveness of the used antimicrobials. This study aimed to characterize P. aeruginosa isolates for antimicrobial susceptibility, biofilm formation virulence genes, and molecular mechanisms responsible for resistance against various antimicrobials. Out of 700 samples, 91 isolates were confirmed as P. aeruginosa which were further classified into 19 non-multidrug-resistant (non-MDR), 7 multidrug-resistant (MDR), 19 extensively drug-resistant (XDR), and 8 pan drug-resistant (PDR) pulsotypes based on standard Kirby Bauer disc diffusion test and pulse field gel electrophoresis. In M9 minimal media, strong biofilms were formed by the XDR and PDR pulsotypes as compared to the non-MDR pulsotypes. The virulence genes, responsible for the worsening of wounds including LasB, plcH, toxA, and exoU, were detected among all MDR, XDR, and PDR pulsotypes. Carbapenemase activity was phenotypically detected in 45% pulsotypes and the responsible genes were found as blaGES (100%), blaVIM (58%), blaIMP (4%), and blaNDM (4%). Real-time polymerase chain reaction showed the concomitant use of multiple mechanisms such as oprD under-expression, enhanced efflux pump activity, and ampC overexpression in the resistant isolates. Polymyxin is found as the only class left with more than 80% susceptibility among the isolates which is an alarming situation suggesting appropriate measures to be taken including alternative therapies. KEY POINTS: • Multidrug-resistant P. aeruginosa isolates formed stronger biofilms in minimal media. • Only polymyxin antimicrobial was found effective against MDR P. aeruginosa isolates. • Under-expression of oprD and overexpression of ampC were found in resistant isolates.
Three-dimensional (3D) microfibrillar network represents an important structural design for vario... more Three-dimensional (3D) microfibrillar network represents an important structural design for various natural tissues and synthetic aerogels. Despite extensive efforts, achieving high mechanical properties for synthetic 3D microfibrillar networks remains challenging. Here, we report ultrastrong polymeric aerogels involving self-assembled 3D networks of aramid nanofiber composites. The interactions between the nanoscale constituents lead to assembled networks with high nodal connectivity and strong crosslinking between fibrils. As revealed by theoretical simulations of 3D networks, these features at fibrillar joints may lead to an enhancement of macroscopic mechanical properties by orders of magnitude even with a constant level of solid content. Indeed, the polymeric aerogels achieved both high specific tensile modulus of ~625.3 MPa cm3 g−1 and fracture energy of ~4700 J m−2, which are advantageous for diverse structural applications. Furthermore, their simple processing techniques all...
The Class 1 type I CRISPR–Cas systems represent the most abundant and diverse CRISPR systems in n... more The Class 1 type I CRISPR–Cas systems represent the most abundant and diverse CRISPR systems in nature. However, their applications for generic genome editing have been hindered due to difficulties of introducing the class-specific, multi-component effectors (Cascade) in heterologous hosts for functioning. Here we established a transferrable Cascade system that enables stable integration and expression of a highly active type I-F Cascade in heterologous bacterial hosts for various genetic exploitations. Using the genetically recalcitrant Pseudomonas species as a paradigm, we show that the transferred Cascade displayed substantially higher DNA interference activity and greater editing capacity than both the integrative and plasmid-borne Cas9 systems, and enabled deletion of large fragments such as the 21-kb integrated cassette with efficiency and simplicity. An advanced I-F-λred system was further developed to enable editing in genotypes with poor homologous recombination capacity, c...
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