Roles of DJ41_1407 and DJ41_1408 in Acinetobacter baumannii ATCC19606 Virulence and Antibiotic Response

Acinetobacter baumannii is a major cause of nosocomial infections, and its highly adaptive nature and broad range of antibiotic resistance enable it to persist in hospital environments. A. baumannii often employs two-component systems (TCSs) to regulate adaptive responses and virulence-related traits. This study describes a previously uncharacterized TCS in the A. baumannii ATCC19606 strain, consisting of a transcriptional sensor, DJ41_1407, and its regulator, DJ41_1408, located adjacent to GacA of the GacSA TCS. Markerless mutagenesis was performed to construct DJ41_1407 and DJ41_1408 single and double mutants. DJ41_1408 was found to upregulate 49 genes and downregulate 43 genes, most of which were associated with carbon metabolism and other metabolic pathways, such as benzoate degradation. MEME analysis revealed a putative binding box for DJ41_1408, 5'TGTAAATRATTAYCAWTWAT3'. Colony size, motility, biofilm-forming ability, virulence, and antibiotic resistance of DJ41_1407 and DJ41_1408 single and double mutant strains were assessed against wild type. DJ41_1407 was found to enhance motility, while DJ41_1408 was found to upregulate biofilm-forming ability, and may also modulate antibiotic response. Both DJ41_1407 and DJ41_1408 suppressed virulence, based on results from a G. mellonella infection assay. These results showcase a novel A. baumannii TCS involved in metabolism, with effects on motility, biofilm-forming ability, virulence, and antibiotic response.

Gene Expression of Ethanol and Acetate Metabolic Pathways in the Acinetobacter baumannii EmaSR Regulon

BACKGROUND

Previous studies have confirmed the involvement of EmaSR (ethanol metabolism a sensor/regulator) in the regulation of Acinetobacter baumannii ATCC 19606 ethanol and acetate metabolism. RNA-seq analysis further revealed that DJ41_568-571, DJ41_2796, DJ41_3218, and DJ41_3568 regulatory gene clusters potentially participate in ethanol and acetate metabolism under the control of EmaSR.

METHODS

This study fused the EmaSR regulon promoter segments with reporter genes and used fluorescence expression levels to determine whether EmaSR influences regulon expression in ethanol or acetate salt environments. The enzymatic function and kinetics of significantly regulated regulons were also studied.

RESULTS

The EmaSR regulons P2796 and P3218 exhibited > 2-fold increase in fluorescence expression in wild type compared to mutant strains in both ethanol and acetate environments, and PemaR demonstrated a comparable trend. Moreover, increases in DJ41_2796 concentration enhanced the conversion of acetate and succinyl-CoA into acetyl-CoA and succinate, suggesting that DJ41_2796 possesses acetate: succinyl-CoA transferase (ASCT) activity. The kcat/KM values for DJ41_2796 with potassium acetate, sodium acetate, and succinyl-CoA were 0.2131, 0.4547, and 20.4623 mM-1s-1, respectively.

CONCLUSIONS

In A. baumannii, EmaSR controls genes involved in ethanol and acetate metabolism, and the EmaSR regulon DJ41_2796 was found to possess ASCT activity.

[CT perfusion combined with energy spectrum imaging to evaluate the short-term efficacy of bronchial arterial chemoembolization for lung cancer]

Objective: To evaluate the clinical value of dynamic volumetric CT perfusion combined with energy spectrum imaging in bronchial arterial chemoembolization (BACE) in patients with lung cancer. Methods: The data of 31 patients with lung cancer confirmed by pathology and treated with BACE in Lishui Central Hospital from January 2018 to February 2022 were retrospectively collected, including 23 men and 8 women, aged 31-84 (67) years. All patients received perfusion scans of lesion sites within 1 week before surgery and 1 month after surgery. We collected and compared the changes in preoperative and postoperative perfusion parameters such as blood flow (BF), blood volume (BV), mean through time (MTT), permeability surface (PS) and energy spectrum parameters including arterial phase CT value (CTA), venous phase CT value (CTV), arterial phase iodine concentration (ICA), venous phase of iodine concentration (ICV), arterial standardization iodine concentration (NICA), and intravenous standardized iodine concentration (NICV) to confirm the significance of these parameters in evaluating the short-term efficacy of BACE in the treatment of advanced lung cancer. Data normality was tested using the Kolmogorov-Smirnov test and normally distributed measurement data are expressed here as mean ± standard deviation; the independent-samples t-test was used for comparisons between two groups. The measurement data that were not normally distributed are expressed as median (interquartile interval) [M (Q₁, Q₃)], and the comparison between the two groups used the Kruskal-Wallis test. Count data are expressed as cases (%), and comparisons between groups used the χ² test. Results: The objective response rate (ORR) and disease control rate (DCR) at 1 month after BACE were 54.8% (17/31) and 96.8% (30/31), respectively. CT perfusion parameters and energy spectrum parameters of patients before and after BACE treatment were compared. The results showed that BF, BV, MTT, ICA, ICV and NICV were significantly decreased after BACE treatment compared with before treatment, and the differences were statistically significant[58.06 (40.47,87.22) vs.23.57(10.92, 36.24) ml·min^-1·100g^-1,3.33(2.86,6.09) vs.2.12(1.96,3.61)ml/100g,2.70(2.19,3.88) vs.1.53 (1.12,2.25)s, 3.51 (3.11,4.14)vs.1.74 (1.26,2.50)mg/ml,2.00 (1.30,2.45) vs.1.32(0.92,1.76)mg/ml,0.51(0.42,0.57) vs.0.33(0.23,0.39)](all P<0.05). At the same time, compared with the non-remission group, the study results showed that the difference of parameters in remission group before and after BACE was more obvious, including ΔBF, ΔBV, ΔMTT, ΔPS, ΔCTA, ΔCTV, ΔICA, ΔICV, ΔNICA, ΔNICV were significantly increased, and the difference was statistically significant [36.82(32.38, 45.34) vs.9.50(-1.43, 12.34) ml·min^-1·100g^-1,4.46(2.52, 5.79) vs.0.22(-0.76, 4.09) ml/100g,4.22(2.25, 6.77) vs.0.43(-2.53, 1.88) s,10.07 (2.89, 13.13) vs.-2.01(-6.77, 4.28) ml·min^-1·100g^-1,14.22(11.88, 20.57) vs.4.18(-5.25, 6.37) HU, 34.6(14.88, 43.15) vs.11.60(0.26, 25.05) HU,0.95(0.54, 1.47) vs.0.11(0.20, 0.59) mg/ml,1.57(1.10, 2.38) vs. 0.26(-0.21, 0.63) mg/ml,0.05(0.03, 0.08) vs.-0.02(-0.04, 0.01),0.18(0.13, 0.21)vs. 0.11(-0.06, 0.16)](all P<0.05). Conclusions: CT perfusion combined with spectral imaging could effectively evaluate the changes in tumor vascular perfusion in patients with advanced lung cancer before and after BACE treatment, which has important value in judging the short-term efficacy after treatment.

[Construction of prediction model combined dual-energy CT quantitative parameters and conventional CT features for assessing the Ki-67 expression levels in invasive breast cancer]

Objective: To develop a model combined with dual-energy CT quantitative parameters and conventional CT features for evaluating the expression level of Ki-67 in invasive breast cancer. Methods: A total of 191 patients with histologically confirmed invasive breast cancer in Lishui Central Hospital from March 2019 to December 2020, were retrospectively enrolled, all of them were females, aged from 25 to 77 (53.2±11.3) years. All patients underwent preoperative non-contrast chest and contrast-enhanced Dual energy CT scans, and the normalized iodine concentration (NIC) of lesions on arterial and venous phase, spectral curve slope (λ_HU), and normalized effective atomic number (nZ_eff) were measured and calculated, and their conventional CT characteristics were assessed. According to the results of immunohistochemistry (IHC), the patients were divided into Ki-67 high expression group (n=129 patients) and low expression group (n=62 patients) level. The differences in clinical data, conventional CT characteristics and dual-energy CT quantitative parameters between the two groups were analyzed. The receiver operating characteristic curve (ROC) curve was conducted to assess the efficacy of each individual model and joint model in evaluating Ki-67 expression levels, and the area under the curve (AUC), sensitivity, specificity, and accuracy were calculated, respectively. Results: In the analysis of CT features, the longest diameter, shape and enhancement pattern of the tumor were significantly difference between the two groups (all P<0.05). The NIC, nZ_eff on the arterial phase and NIC, nZ_eff and λ_HU [M(Q₁,Q₃)] on the venous phase were higher in the high Ki-67 expression group compared to the low expression group [0.13 (0.12, 0.16) vs 0.11 (0.08, 0.14), 0.71 (0.70, 0.75) vs 0.70 (0.67, 0.72), 0.40 (0.32, 0.48) vs 0.23 (0.17, 0.32), 3.10 (2.58, 3.63) vs 2.86 (2.19, 3.48), 0.88 (0.85, 0.92) vs 0.85 (0.84, 0.86), all P<0.05]. The logistic regression model, which integrated significant conventional CT features and dual-energy CT quantitative parameters, demonstrated the highest diagnostic performance for assessing Ki-67 expression levels, with an AUC of 0.924, sensitivity of 88.37%, specificity of 83.87%, and accuracy of 86.91%; the AUC of the dual-energy CT parameter model was 0.908, sensitivity of 82.17%, specificity of 88.71%, and accuracy of 84.29%. Though the diagnostic efficacy was no significant difference (P=0.238), both models showed superior to the conventional CT feature model (all P<0.001). Conclusion: A dual-energy CT quantitative parameter combined with a conventional CT feature model was successfully constructed, which has a good evaluation performance on the expression level of Ki-67 in invasive breast cancer.

Role of Iron-Containing Alcohol Dehydrogenases in Acinetobacter baumannii ATCC 19606 Stress Resistance and Virulence

Most bacteria possess alcohol dehydrogenase (ADH) genes (Adh genes) to mitigate alcohol toxicity, but these genes have functions beyond alcohol degradation. Previous research has shown that ADH can modulate quorum sensing in Acinetobacter baumannii, a rising opportunistic pathogen. However, the number and nature of Adh genes in A. baumannii have not yet been fully characterized. We identified seven alcohol dehydrogenases (NAD⁺-ADHs) from A. baumannii ATCC 19606, and examined the roles of three iron-containing ADHs, ADH3, ADH4, and ADH6. Marker-less mutation was used to generate Adh3, Adh4, and Adh6 single, double, and triple mutants. Disrupted Adh4 mutants failed to grow in ethanol-, 1-butanol-, or 1-propanol-containing mediums, and recombinant ADH4 exhibited strongest activity against ethanol. Stress resistance assays with inorganic and organic hydroperoxides showed that Adh3 and Adh6 were key to oxidative stress resistance. Virulence assays performed on the Galleria mellonella model organism revealed that Adh4 mutants had comparable virulence to wild-type, while Adh3 and Adh6 mutants had reduced virulence. The results suggest that ADH4 is primarily involved in alcohol metabolism, while ADH3 and ADH6 are key to stress resistance and virulence. Further investigation into the roles of other ADHs in A. baumannii is warranted.

Regulation of tert-Butyl Hydroperoxide Resistance by Chromosomal OhrR in A. baumannii ATCC 19606

In this study, we show that Acinetobacter baumannii ATCC 19606 harbors two sets of ohrR-ohr genes, respectively encoded in chromosomal DNA and a pMAC plasmid. We found no significant difference in organic hydroperoxide (OHP) resistance between strains with or without pMAC. However, a disk diffusion assay conducted by exposing wild-type, ∆ohrR-C, C represented gene on chromosome, or ∆ohr-C single mutants, or ∆ohrR-C∆ohr-C double mutants to tert-butyl hydroperoxide (tBHP) found that the ohrR-p-ohr-p genes, p represented genes on pMAC plasmid, may be able to complement the function of their chromosomal counterparts. Interestingly, ∆ohr-C single mutants generated in A. baumannii ATCC 17978, which does not harbor pMAC, demonstrated delayed exponential growth and loss of viability following exposure to 135 μg of tBHP. In a survival assay conducted with Galleria mellonella larvae, these mutants demonstrated almost complete loss of virulence. Via an electrophoretic mobility shift assay (EMSA), we found that OhrR-C was able to bind to the promoter regions of both chromosomal and pMAC ohr-p genes, but with varying affinity. A gain-of-function assay conducted in Escherichia coli showed that OhrR-C was not only capable of suppressing transformed ohr-C genes but may also repress endogenous enzymes. Taken together, our findings suggest that chromosomal ohrR-C-ohr-C genes act as the major system in protecting A. baumannii ATCC 19606 from OHP stresses, but the ohrR-p-ohr-p genes on pMAC can provide a supplementary protective effect, and the interaction between these genes may affect other aspects of bacterial viability, such as growth and virulence.

Reactivity of human antisera to codon optimized SARS-CoV2 viral proteins expressed in Escherichia coli

Objective

The coronavirus disease 2019 (COVID-19) pandemic caused by the SARS-CoV2 virus continues to pose a serious threat to public health worldwide. The development of rapid diagnostic kits can assist the Tzu Chi Foundation in supporting global volunteers working to provide relief during the current pandemic.

Materials and Methods

In this study, nucleotide sequences derived from publicly available viral genome data for several domains of the SARS-CoV2 spike and nucleocapsid (N) proteins were chemically synthesized, with codon optimization for Escherichia coli protein expression. No actual viral particles were involved in these experiments. The synthesized sequences were cloned into an E. coli expression system based on pQE80L, and expressed viral proteins were subsequently purified using Ni-affinity chromatography. Western blotting was conducted using human antiviral sera to assess the response of codon-modified viral proteins to COVID-19 patient sera.

Results

N protein was expressed in amounts large enough to support large-scale production. The N-terminal domain, receptor-binding domain (RBD), Region 3, and the S2 domain were expressed in small but sufficient amounts for experiments. Immunoblotting results showed that anti-N IgG and anti-N IgM antibodies were detected in most patient sera, but only 60% of samples reacted with the recombinant RBD and S2 domain expressed by E. coli.

Conclusion

The results indicated that codon-optimized SARS-CoV2 viral proteins can be expressed in E. coli and purified for rapid antibody detection kit preparation, with the codon-optimized N protein, RBD, and S2 protein demonstrating the most potential.

The Role of Apoptotic Factors in Assessing Progression of Periodontal Disease

Background

The mechanisms responsible for periodontal disease progression remain unclear. However, recent studies suggest that apoptosis may be one mechanism underlying the pathophysiology of periodontal disease progression. This pilot study is the 3 month follow-up of our published baseline study on the presence of apoptotic factors in serum, saliva, and gingival crevicular fluid (GCF) and their association with periodontal disease severity and activity.

Methods

GCF samples were obtained from 37 adult patients with chronic periodontitis (CP) and 7 healthy controls. Clinical measurements, including probing depth (PD), clinical attachment level (CAL), and radiographs, were used to evaluate data by sites and to classify patients into healthy, mild, and moderate/severe CP groups. Enzyme-linked immunosorbent assays were used to measure apoptosis or DNA fragmentation levels in GCF. Western immunoblotting was used to detect several apoptotic proteins, Fas, FasL, sFasL, and caspase-3 expression and its cleavage products in GCF.

Results

At the patient level clinical and apoptotic measurements change minimally over time. At the site level, DNA fragmentation levels increase with increasing PDs at 3 months and baseline. Apoptotic protein expression exhibits increasing trends with increasing PDs at baseline and 3 months. FasL and Active FasL show a high specificity and PPV; low sensitivity and NPV. Caspase-3 products (ProCas35K and Active Cas) show a high PPV with moderate to high specificity; low sensitivity and NPV. ProCas70K shows a high PPV with moderate to high sensitivity; low specificity and NPV.

Conclusion

Factors associated with apoptosis show minimal changes in expression in periodontitis groups in comparison to a healthy group over a short time interval (3 months). However, at the site level, apoptotic factors (DNA fragmentation and apoptotic proteins) exhibit significant increases or increasing trends with increasing PDs at any time point examined (baseline or 3 months). Several of these apoptotic factors also exhibit a high sensitivity and high positive predictive value. Thus, apoptotic molecules may be helpful biomarkers of disease status at any point in time.

Detoxification of Indole by an Indole-Induced Flavoprotein Oxygenase from Acinetobacter baumannii

Indole, a derivative of the amino acid tryptophan, is a toxic signaling molecule, which can inhibit bacterial growth. To overcome indole-induced toxicity, many bacteria have developed enzymatic defense systems to convert indole to non-toxic, water-insoluble indigo. We previously demonstrated that, like other aromatic compound-degrading bacteria, Acinetobacter baumannii can also convert indole to indigo. However, no work has been published investigating this mechanism. Here, we have shown that the growth of wild-type A. baumannii is severely inhibited in the presence of 3.5 mM indole. However, at lower concentrations, growth is stable, implying that the bacteria may be utilizing a survival mechanism to oxidize indole. To this end, we have identified a flavoprotein oxygenase encoded by the iifC gene of A. baumannii. Further, our results suggest that expressing this recombinant oxygenase protein in Escherichia coli can drive indole oxidation to indigo in vitro. Genome analysis shows that the iif operon is exclusively present in the genomes of A. baumannii and Pseudomonas syringae pv. actinidiae. Quantitative PCR and Western blot analysis also indicate that the iif operon is activated by indole through the AraC-like transcriptional regulator IifR. Taken together, these data suggest that this species of bacteria utilizes a novel indole-detoxification mechanism that is modulated by IifC, a protein that appears to be, at least to some extent, regulated by IifR.

Transcriptional regulation of the iac locus from Acinetobacter baumannii by the phytohormone indole-3-acetic acid

The iac locus is involved in indole-3-acetic acid (IAA) catabolism in Acinetobacter baumannii. Nine structural genes of iac are transcribed in the same direction, whereas iacR, which encodes a MarR-type transcriptional regulator, is transcribed in the opposite direction. The IacA protein, which is encoded by the second structural gene of the iac locus, is expressed in an IAA-dependent manner. Here, we characterized gene expression from this locus in wild type A. baumannii and in an iacR mutant; this revealed that the iacH promoter is negatively regulated by IacR. The transcriptional site of iacH was determined by using 5' rapid amplification of cDNA ends; one IacR-binding site was identified between positions -35 and +28 of the iacH promoter. Sequence analysis and an electrophoretic mobility shift assay indicated that recombinant IacR binds specifically to a sequence with dyad symmetry in the iacR-iacH overlapping promoters in the absence of IAA. In addition, a two-plasmid expression system in Escherichia coli showed that IAA probably serves as a ligand that binds to IacR and releases it from the iacH promoter, thereby allowing RNA polymerase to transcribe iac. Thus, iac is expressed in order to promote IAA degradation, whereas free IacR is required for iac repression. We conclude that IacR serves as a key regulator of IAA degradation in A. baumannii in the rhizosphere. These results provide new insights into the possible role of A. baumannii in the environment.

Systematic profiling of indole-3-acetic acid biosynthesis in bacteria using LC-MS/MS

Indole-3-acetic acid (IAA) is produced from tryptophan through five synthesis pathways. A comprehensive method for the quantification of IAA and biosynthesis-related intermediates in a culture medium was developed. Sample preparation was simple with protein precipitation. The analytes were separated on a superficially porous C18 silica column and detected by electrospray ionization-tandem mass spectrometry in the positive ion multiple reaction monitoring mode. The limit of detection was 0.05 μM, and the lower limits of quantification ranged from 0.05 to 2 μM. The intra-day and inter-day precision and accuracy were less than 13.96%. Ion suppression was observed, and the deuterated internal standards were used to compensate for the matrix effect. The method was applied to analyze changes in tryptophan catabolism in a culture medium of Pseudomonas putida. The proposed method is robust and suitable for the systematic profiling of IAA biosynthesis in culture supernatant.

Phosphoproteomic analysis reveals the effects of PilF phosphorylation on type IV pilus and biofilm formation in Thermus thermophilus HB27

Thermus thermophilus HB27 is an extremely thermophilic eubacteria with a high frequency of natural competence. This organism is therefore often used as a thermophilic model to investigate the molecular basis of type IV pili-mediated functions, such as the uptake of free DNA, adhesion, twitching motility, and biofilm formation, in hot environments. In this study, the phosphoproteome of T. thermophilus HB27 was analyzed via a shotgun approach and high-accuracy mass spectrometry. Ninety-three unique phosphopeptides, including 67 in vivo phosphorylated sites on 53 phosphoproteins, were identified. The distribution of Ser/Thr/Tyr phosphorylation sites was 57%/36%/7%. The phosphoproteins were mostly involved in central metabolic pathways and protein/cell envelope biosynthesis. According to this analysis, the ATPase motor PilF, a type IV pili-related component, was first found to be phosphorylated on Thr-368 and Ser-372. Through the point mutation of PilF, mimic phosphorylated mutants T368D and S372E resulted in nonpiliated and nontwitching phenotypes, whereas nonphosphorylated mutants T368V and S372A displayed piliation and twitching motility. In addition, mimic phosphorylated mutants showed elevated biofilm-forming abilities with a higher initial attachment rate, caused by increasing exopolysaccharide production. In summary, the phosphorylation of PilF might regulate the pili and biofilm formation associated with exopolysaccharide production.

A novel exopolysaccharide from the biofilm of Thermus aquaticus YT-1 induces the immune response through Toll-like receptor 2

Bacterial polysaccharides are known to induce the immune response in macrophages. Here we isolated a novel extracellular polysaccharide from the biofilm of Thermus aquaticus YT-1 and evaluated its structure and immunomodulatory effects. The size of this polysaccharide, TA-1, was deduced by size-exclusion chromatography as 500 kDa. GC-MS, high performance anion-exchange chromatography with pulsed amperometric detection, electrospray ionization-MS/MS, and NMR revealed the novel structure of TA-1. The polysaccharide is composed of tetrasaccharide-repeating units of galactofuranose, galactopyranose, and N-acetylgalactosamine (1:1:2) and lacked acidic sugars. TA-1 stimulated macrophage cells to produce the cytokines TNF-α and IL-6. Screening of Toll-like receptors and antibody-blocking experiments indicated that the natural receptor of TA-1 in its immunoactivity is TLR2. Recognition of TA-1 by TLR2 was confirmed by TA-1 induction of IL-6 production in peritoneal macrophages from wild-type mice but not from TLR2(-/-) mice. TA-1, as a TLR2 agonist, could possibly be used as an adjuvant and could enhance cytokine release, which increases the immune response. Furthermore, TA-1 induced cytokine release is dependent on MyD88/TIRAP.

Analysis of community structure of a microbial consortium capable of degrading benzo(a)pyrene by DGGE

A microbial consortium was obtained by enrichment culture of sea water samples collected from Botan oil port in Xiamen, China, using the persistent high concentration of a mixture of polycyclic aromatic hydrocarbons enrichment strategy. Denaturing gradient gel electrophoresis (DGGE) was used to investigate the bacterial composition and community dynamic changes based on PCR amplification of 16S rRNA genes during batch culture enrichment. Using the spray-plate method, three bacteria, designated as BL01, BL02 and BL03, which corresponded to the dominant bands in the DGGE profiles, were isolated from the consortium. Sequence analysis showed that BL01, BL02 and BL03 were phylogenetically close to Ochrobactrum sp., Stenotrophomonas maltophilia and Pseudomonas fluorescens, respectively. The degradation of benzo(a)pyrene (BaP), a model high-molecular-weight polycyclic aromatic hydrocarbon (HMW PAH) compound was investigated using individual isolates, a mixture of the three isolates, and the microbial consortium (BL) originally isolated from the oil port sea water. Results showed that the order of degradative ability was BL>the mixture of the three isolates>individual isolates. BL degraded 44.07% of the 10 ppm BaP after 14 days incubation, which showed the highest capability for HMW PAH compound degradation.Our results revealed that this high selective pressure strategy was feasible and effective in enriching the HMW PAH-degraders from the original sea water samples.

Bacterial and archaeal assemblages in sediments of a large shallow freshwater lake, Lake Taihu, as revealed by denaturing gradient gel electrophoresis

AIMS

To explore the association of microbial community structure with the development of eutrophication in a large shallow freshwater lake, Lake Taihu.

METHODS AND RESULTS

The bacterial and archaeal assemblages in sediments of different lake areas were analysed using denaturing gradient gel electrophoresis (DGGE) of amplified 16S rDNA fragments. The bacterial DGGE profiles showed that eutrophied sites, grass-bottom areas and relatively clean sites with a eutrophic (albeit dredged) site are three respective clusters. Fifty-one dominant bacterial DGGE bands were detected and 92 corresponding clones were sequenced, most of which were affiliated with bacterial phylotypes commonly found in freshwater ecosystems. Actinobacteria were detected in the centre of the lake and not at eutrophied sites whereas the opposite was found with respect to Verrucomicrobiales. Twenty-five dominant archaeal DGGE bands were detected and 31 corresponding clones were sequenced, most of which were affiliated with freshwater archaeal phylotypes.

CONCLUSIONS

The bacterial community structures in the sediments of different areas with similar water quality and situation tend to be similar in Taihu Lake.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study may expand our knowledge on the relationship between the overall microbial assemblages and the development of eutrophication in the shallow freshwater lake.

Characterization and application of a rolling-circle-type plasmid from Cupriavidus taiwanensis

Two small cryptic plasmids, pTJ86-1 and pTJ86-2, identified in Cupriavidus taiwanensis strain TJ86, were detected and characterized. Complete sequencing of pTJ86-1 and pTJ86-2 revealed these plasmids to be 2221 and 2229bp in length with a GC content of 61.7% and 61.6%, respectively. Both plasmids harbored four open reading frames (ORF1, 2, 3 and 4). Only the predicted ORF1 gene product of both plasmids (436 amino acids) was homologous to Rep proteins previously identified on plasmids replicated using a rolling-circle replication (RCR). A double-stranded origin (DSO) of replication, highly conserved in the group III (cluster III) RCR plasmids, was identified and located immediately upstream of this putative Rep gene. In addition, both plasmids contained a putative single-stranded origin of replication (SSO) exhibiting similarity to the ssoA-type. Detection of single-stranded plasmid DNA by Southern analysis and S1 nuclease digestion confirmed that the cryptic plasmid replicated via an RCR mechanism. A potential shuttle vector, pS4-tet(R), was constructed by ligation of pTJ86-1 to the cloning vector pBluescript II SK(+) along with the insertion of a tetracycline-resistance (tet(R)) gene. It was successfully used for the transformation of genera Burkholderia and Cupriavidus.

Characterization of a rolling-circle replication plasmid from Thermus aquaticus NTU103

The thermophilic bacterium Thermus aquaticus NTU103 harbors a 1,965-bp plasmid, pTA103. Sequencing analysis revealed that pTA103 contains two open reading frames. One of the open reading frames (orf2) shares no significant homology with protein in the data bank. The other one has 50% similarity and 34% identity with RepA-like protein of pRm1132f, which is a rolling-circle replication (RCR) plasmid isolated from Sinorhizobium meliloti. S1 nuclease analysis demonstrated that pTA103 contains a single-stranded intermediate, confirming that pTA103 replicates via RCR mechanism. Sequence data also revealed putative double-stranded origin and single-stranded origin sites, indicating the importance of these cis elements in pTA103 replication.

Functional analysis of fengycin synthetase FenD

Fengycin is a cyclic lipopeptidic antibiotic produced nonribosomally by Bacillus subtilis. A fengycin synthetase mutant of B. subtilis F29-3 was generated with Tn917lux, which contains a transposon inserted in a 7716-bp gene, fenD. The mutation can be genetically complemented by transforming a plasmid carrying a wild-type fenD, confirming the participation of the gene in fengycin synthesis. Sequencing and biochemical analysis reveal that this gene encodes an enzyme that includes two amino acid-activating modules, FenD1 and FenD2, which activate l-Tyr and l-Thr, the third and the fourth amino acids in fengycin, respectively.

Pseudoxanthomonas kaohsiungensis, sp. nov., a novel bacterium isolated from oil-polluted site produces extracellular surface activity

During screening for biosurfactant-producing bacteria, a strain designated J36T was isolated from oil-polluted site near Kaohsiung city located in southern Taiwan. Cells of this organism were gram-negative rods motile by means of a single polar flagellum. Strain J36T grew well in complex media under optimum conditions of 35 degrees C and pH 7. The extracellular products of the strain expressed emulsification activity. During cultivation on olive oil as the sole carbon and energy source, the culture supernatant of strain J36T reduced surface tension of the medium from 68 to 32.6 dyne/cm. The 16S rRNA gene sequence analysis indicates that strain J36T is a member of Xanthomonas group within the gamma-Proteobacteria. The organism belongs to the genus Pseudoxanthomonas and represents a novel species within this genus according to phylogenetic analysis of 16S rDNA sequences, DNA-DNA similarity data, whole-cell protein analysis, physiological and biochemical characteristics, as well as fatty acid compositions. The predominant cellular fatty acids of strain J36T were 15:0 iso (about 26%), 17:1 iso omega9c (about 25%), and 15:0 anteiso (about 10%). Its DNA base ratio was 60.1 mol% G+C. We propose to classify strain J36T (= BCRC 17375T = LMG 22530T) as Pseudoxanthomonas kaohsiungensis sp. nov.

Rubrobacter taiwanensis sp. nov., a novel thermophilic, radiation-resistant species isolated from hot springs

Two novel bacteria, with an optimum growth temperature of approximately 60 degrees C, were isolated from Lu-shan hot springs in the central region of Taiwan. These isolates were aerobic, thermophilic, halotolerant, pink-pigmented, heterotrophic and resistant to gamma-radiation. Both pleomorphic, short, rod-shaped cells and coccoid cells were observed. Strains LS-286 (= ATCC BAA-452 = BCRC 17198) and LS-293T (= ATCC BAA-406T = BCRC 17173T) represented a novel species of the genus Rubrobacter, according to a phylogenetic analysis of the 16S rRNA gene, DNA-DNA hybridization, biochemical features and fatty acid composition. The name Rubrobacter taiwanensis sp. nov. is proposed for this novel species, with LS-293T as the type strain.

Influence of interleukin-2 on Ca2+ handling in rat ventricular myocytes

In the present study, we examined the effect of interleukin-2 (IL-2) on cardiomyocyte Ca(2+) handling. The effects of steady-state and transient changes in stimulation frequency on the intracellular Ca(2+) transient were investigated in isolated ventricular myocytes by spectrofluorometry. In the steady state (0.2 Hz) IL-2 (200 U/ml) decreased the amplitude of Ca(2+) transients induced by electrical stimulation and caffeine. At 1.25 mM extracellular Ca(2+) concentration ([Ca(2+)](o)), when the stimulation frequency increased from 0.2 to 1.0 Hz, diastolic Ca(2+) level and peak intracellular Ca(2+) concentration ([Ca(2+)](i)), as well as the amplitude of the transient, increased. The positive frequency relationships of the peak and amplitude of [Ca(2+)](i) transients were blunted in the IL-2-treated myocytes. The effect of IL-2 on the electrically induced [Ca(2+)](i) transient was not normalized by increasing [Ca(2+)](o) to 2.5 mM. IL-2 inhibited the frequency relationship of caffeine-induced Ca(2+) release. Blockade of sarcoplasmic reticulum (SR) Ca(2+)-ATPase with thapsigargin resulted in a significant reduction of the amplitude-frequency relationship of the transient similar to that induced by IL-2. The restitutions were not different between control and IL-2 groups at 1.25 mM [Ca(2+)](o), which was slowed in IL-2-treated myocytes when [Ca(2+)](o) was increased to 2.5 mM. There was no difference in the recirculation fraction (RF) between control and IL-2-treated myocytes at both 1.25 and 2.5 mM [Ca(2+)](o). The effects of IL-2 on frequency relationship, restitution, and RF may be due to depressed SR functions and an increased Na(+)-Ca(2+) exchange activity, but not to any change in L-type Ca(2+) channels.

Pseudoxanthomonas taiwanensis sp. nov., a novel thermophilic, N2O-producing species isolated from hot springs

Two novel thermophilic bacterial strains, with an optimum growth temperature of between 50 and 60 degrees C, were isolated from the Chi-ban Hot Springs in eastern Taiwan. Strains CB-225 and CB-226(T) were aerobic, thermophilic, non-sporulating, yellow-pigmented heterotrophic organisms. These strains exhibited an unusual denitrification reaction, reducing nitrite, but not nitrate, with the production of N2O only. On the basis of a phylogenetic analysis of 16S rDNA sequences, DNA-DNA similarity data, morphological, physiological and biochemical characteristics, and fatty acid compositions, it was found that the novel strains belonged to the genus Pseudoxanthomonas and represented a novel species within this genus, for which the name Pseudoxanthomonas taiwanensis is proposed; the type strain is CB-226(T) (= ATCC BAA-404(T) = CCRC 17172(T)). P. taiwanensis differs from the only member of the genus Pseudoxanthomonas, the mesophilic species Pseudoxanthomonas broegbernensis, in that it exhibits a higher growth temperature and different morphological characteristics, such as the absence of polar flagella.

Meiothermus taiwanensis sp. nov., a novel filamentous, thermophilic species isolated in Taiwan

Two novel filamentous bacterial isolates, strains WR-30T and WR-220, with an optimum growth temperature of approximately 55-60 degrees C were isolated from Wu-rai hot springs in the northern part of Taiwan. These isolates were aerobic, thermophilic, non-sporulating, red-pigmented and heterotrophic and formed extremely long, filamentous trichomes from cells of different lengths. Phylogenetic analysis of 16S rDNA, DNA-DNA hybridization, morphological and biochemical features and fatty acid composition revealed that the isolates represent a novel species of the genus Meiothermus. The name Meiothermus taiwanensis sp. nov. is proposed for this novel species. The type strain of M. taiwanensis is strain WR-30T (= ATCC BAA-399T = CCRC 17170T = DSM 14542T); strain WR-220 (= ATCC BAA400 = CCRC 17171 = DSM 14543) is a reference strain.

Amino acids activated by fengycin synthetase FenE

Fengycin is a lipopeptidic antibiotic produced nonribosomally by Bacillus subtilis F29-3. Synthesis of this antibiotic requires five fengycin synthetases encoded by fenC, fenD, fenE, fenA, and fenB. In this study, we analyze the functions of the enzyme encoded by fenE, which contains two amino acid activation modules, FenE1 and FenE2. ATP-PP(i) exchange assay revealed that FenE1 activates l-Glu and FenE2 activates l-Ala, l-Val, and l-2-aminobutyric acid, indicating that FenE activates the fifth and the sixth amino acids in fengycin. Furthermore, l-Val is a better substrate than l-Ala for FenE2 in vitro, explaining why B. subtilis F29-3 normally produces twice as much of fengycin B than fengycin A, which contains d-Val and d-Ala at the sixth amino acid position, respectively. Results presented herein suggest that fengycin synthetase genes and amino acids in fengycin are colinear.

Molecular cloning and characterization of fengycin synthetase gene fenB from Bacillus subtilis

A fengycin synthetase gene, fenB, has been cloned and sequenced. The protein (FenB) encoded by this gene has a predicted molecular mass of 143.6 kDa. This protein was overexpressed in Escherichia coli and was purified to near homogeneity by affinity chromatography. Experimental results indicated that the recombinant FenB has a substrate specificity toward isoleucine with an optimum temperature of 25 degrees C, an optimum pH of 4.5, a Km value of 922 microM, and a turnover number of 236 s(-1). FenB also consists of a thioesterase domain, suggesting that this protein may be involved in the activation of the last amino acid of fengycin.

Ocular and dermal irritation studies of some quaternary ammonium compounds

The primary ocular and dermal irritations of four quaternary ammonium compounds, namely cetylpyridinium chloride (CPC), stearylphenylethyldimethylammonium tosylate (SPDAT), dimethyldistearylammonium bisulfate (DDABS) and tri(N-butyl)benzylammonium 4-hydroxynapththalene-1-sulfonate (TBAHNS), were studied. Both CPC and SPDAT were extremely or severely irritating to the eyes of the test animals, whereas DDABS and TBAHNS were mildly or minimally irritating. Both CPC and SPDAT were also severely or extremely irritating to the skin of the test animals, while DDABS and TBAHNS were non-irritating. These quaternary ammonium compounds have little similarity in chemical structure and possess different solubilities. CPC is very soluble in both lipid and water; SPDAT is very soluble in lipid but only slightly soluble in water; and DDABS and TBAHNS are poorly soluble in either lipid or water. The irritancy of these compounds is likely to be related to their solubility, in addition to the cationic characteristics. It appears that not all quaternary ammonium compounds in this study are irritants. Those that are not soluble are not expected to be absorbed in eye/skin tissues and thus irritation reactions will not take place. The use of in vitro alternatives should be considered when assessing the ocular and dermal irritancy potential of water- and lipid-soluble quaternary ammonium compounds.

Mutagenicity studies on two triphenylmethane dyes, bromophenol blue and tetrabromophenol blue

Bromophenol blue and tetrabromophenol blue are two triphenylmethane dyes. Triphenylmethane derivatives and their structurally related compounds, such as fluoresceins and xathenes, are widely used as industrial dyes for foods, drugs, cosmetics, textiles, printing inks or laboratory indicators. Since a number of these types of dyes have been reported to be genotoxic, safety concerns on these two dyes of interest have been raised. Consequently, a battery of genetic toxicology assays, including the Ames Salmonella/microsome assay, L5178Y TK+/- mouse lymphoma assay, mouse micronucleus test and mitotic recombination assay with yeast Saccharomyces cerevisiae strain D5, has been performed on each of the two dyes. The results of the evaluations indicate that both bromophenol blue and tetrabromophenol blue were not active and can be considered non-genotoxic for the three genetic endpoints assessed (gene mutation, chromosome aberrations and primary DNA damage). Genetic activities in some structurally related compounds of these dyes have been reported but may be attributed to the presence of mutagenic impurities rather than the compound itself.

Acute inhalation toxicity of cetylpyridinium chloride

Cetylpyridinium chloride (CPC) is a quaternary ammonium salt and cationic surfactant. It has been used as a biocide in personal hygiene products and a charge control additive in some reprographic toners. CPC is orally toxic to rats, mice and rabbits and can cause severe eye irritation. Acute inhalation toxicity studies of CPC and other quaternary ammonium salts have not, however, been reported. Groups of five rats per sex were exposed to aerosols containing 0 (control), 0.05, 0.07, 0.13 and 0.29 mg CPC/litre for 4 hr and observed for toxicity and ocular effects for 14 days thereafter. All animals were subjected to autopsy and the eyes were examined microscopically. The LC50 (sexes combined) of CPC was 0.09 mg/litre with upper and lower 95% confidence limits of 0.13 and 0.07 mg/litre, respectively. Clinical signs of toxicity included weight loss, nasal discharge, chromodacryorrhoea, respiratory difficulty and eye irritation, and all these non-lethal effects were reversible. Acute inflammation of the cornea, iris and/or aqueous humour were found in one, seven and four of 10 rats exposed to 0.07, 0.13 and 0.29 mg CPC/litre, respectively. Corneal epithelial hyalinization, without evidence of ongoing inflammation, was found in three additional rats among the 10 exposed to 0.29 mg CPC/litre.

Structure-activity relationship studies on the mutagenicity of some azo dyes in the Salmonella/microsome assay

Analogs of Direct Black 19 and Direct Black 38 were synthesized and tested in the Salmonella/microsome assay. Those dyes which gave positive responses in strains TA98 and TA1538 would be expected to be metabolized to p-phenylenediamine by the liver microsomal enzymes (S9). Pure p-phenylenediamine is non-mutagenic in this assay but becomes mutagenic after it is oxidized. Thus the positive response of our synthetic azo compounds are most likely due to the formation of oxidized p-phenylenediamine. Modification of the moieties that can be metabolized to p-phenylenediamine by sulfonation, carboxylation or copper complexation eliminated the mutagenic responses.

Mutagenicity studies on FD&C red No.3

FD&C Red No.3 (erythrosine) has been used as a dye in foods, drugs and cosmetics since its approval by the US Department of Agriculture in 1907. In 1977 the Certified Color Manufacturers' Association (CCMA) initiated studies on FD&C Red No.3 including chronic toxicity and carcinogenicity studies in rats and mice. Data from the CCMA chronic studies revealed an increased incidence of thyroid follicular cell hyperplasia and adenomas in male rats that received 4% FD&C Red No.3 in the diet (2464 mg/kg/day) during life-time (30 months) following in utero exposure. In this report, results of published studies on the mutagenicity of FD&C Red No.3 are critically reviewed. Additional mutagenicity tests including Ames Salmonella/microsome assay, L5178Y TK+/- mouse lymphoma assay, mouse micronucleus test and mitotic recombination assay with yeast Saccharomyces cerevisiae strain D5 are described. These test results together with the literature review indicate that FD&C Red No.3 can be considered non-mutagenic across several genetic endpoints including gene mutation, chromosome aberrations, primary DNA damage and cell transformation. The results of the genotoxicity assessment generally exclude FD&C Red No.3 as a genotoxic initiator and suggest that some other mechanism is responsible for the increase in tumors.

[Use of a polyvalent intravenous immunoglobulin or specific cytomegalovirus hyperimmunoglobulin for modification of cytomegalovirus infections and prevention of interstitial pneumonias following bone marrow transplantation]

The effects of prophylactic, polyvalent intravenous immune globulin on cytomegalovirus infection and interstitial pneumonia in allogenic marrow transplants were evaluated in an ongoing, randomized controlled trial. Thirty-eight patients were given weekly doses (20 cc/kg) of polyvalent intravenous immune globulin before and after transplantation, and 37 patients were controls. Both symptomatic cytomegalovirus infection (17 of 37 or 46% vs. 8 of 38 or 21%, p = 0.04) and interstitial pneumonia (17 of 37 or 46% vs. 7 of 38 or 18%, p = 0.02) occurred less frequently in the recipients of polyvalent intravenous immune globulin. In separate kinetic studies, a 5 cc/kg dose of a cytomegalovirus-specific hyperimmune globulin produced cytomegalovirus antibody titers in patients equivalent to those achieved after the 20 cc/kg dose of polyvalent intravenous immune globulin. All immune globulin preparations were well-tolerated. These preliminary results suggest that intravenous immune globulin can modify the severity of cytomegalovirus infection and prevent interstitial pneumonia in marrow transplants. Additional trials are now needed to define the minimal effective dose of intravenous immune globulin and to compare the effectiveness of different intravenous immune globulin formulations.

Association of hepatitis B surface (HBs) antigenemia and membranous nephropathy in children in Taiwan

Fourteen out of 63 children with primary glomerular disease had membranous nephropathy (MN) that was not associated with systemic lupus erythematosus. Hepatitis B surface antigen (HBsAg) was detected in the sera of all 13 patients tested, but was found in only 6.25% of their parents, in 28.57% of their siblings, and in 18.8% of the children with other types of primary glomerular disease. These findings strongly suggest that MN in children in Taiwan is closely related to hepatitis B virus (HBV) infection, and that, in most, if not all, instances it is due to horizontal infection rather than vertical transmission. However, the antigen antibody system involved remains to be identified. In this study, 4 out of 12 cases also showed abnormal elevation of SGOT and SGPT. Liver biopsies obtained from 9 patients demonstrated chronic persistent hepatitis in 3 cases, focal necrosis in 2, and minimal change or normal histology in 4. Although both the liver and kidney diseases appeared to be relatively benign during a limited period of observation, the long-term influence of the diseases and their final outcomes remain to be clarified. With the strong association of HBs antigenemia and MN in children, and the high incidence of HBsAg-positive chronic hepatitis in MN, an investigation of liver function and HBsAg carriage in patients with MN and a study of renal function in HBsAg carriers are highly recommended.

Urinary fibronectin: potential as a biomarker in prostatic cancer

The levels of fibronectin in urine from patients with prostatic cancer, from patients with benign urologic disease, and from healthy control individuals were determined by the use of a gelatin affinity chromatography procedure. The assay does not seem to give false positive results, inasmuch as evaluation of 16 patients with benign urologic disease showed urinary fibronectin levels in the same range as those found in healthy controls. For a single determination, the levels in 42 per cent of prostatic cancer patients were elevated above control levels; when prostatic cancer patients were evaluated sequentially, the determination of urinary fibronectin levels over three sampling times approached a 100 per cent correlation with presence of disease. Inasmuch as levels of urinary fibronectin episodically elevate in patients with prostatic carcinoma, the differential frequency and magnitude of urinary fibronectin elevations may be useful markers to assess tumor aggressiveness and to monitor the impact of a therapeutic modality.