Mutational diversity in mutY deficient Helicobacter pylori and its effect on adaptation to the gastric environment.

Helicobacter pylori, a pathogenic bacterium that colonizes in the human stomach, harbors DNA repair genes to counter the gastric environment during chronic infection. In addition, H. pylori adapts to the host environment by undergoing antigenic phase variation caused by genomic mutations. The emergence of mutations in nucleotide sequences is one of the major factors underlying drug resistance and genetic diversity in bacteria. However, it is not clear how DNA repair genes contribute to driving the genetic change of H. pylori during chronic infection. To elucidate the physiological roles of DNA repair genes, we generated DNA repair-deficient strains of H. pylori (ΔuvrA, ΔuvrB, ΔruvA, Δnth, ΔmutY, ΔmutS, and Δung). We performed susceptibility testing to rifampicin in vitro and found that ΔmutY exhibited the highest mutation frequency among the mutants. The number of bacteria colonizing the stomach was significantly lower with ΔmutY strain compared with wild-type strains in a Mongolian gerbil model of H. pylori infection. Furthermore, we performed a genomic sequence analysis of the strains isolated from the Mongolian gerbil stomachs eight weeks after infection. We found that the isolated ΔmutY strains exhibited a high frequency of spontaneous G:C to T:A mutations. However, the frequency of phase variations in the ΔmutY strain was almost similar to the wild-type strain. These results suggest that MutY may play a role in modes of gastric environmental adaptation distinct from phase variation.

[Research progress on chemical constituents from Artemisiae Argyi Folium and their pharmacological activities and quality control].

Artemisiae Argyi Folium is a traditional medicine commonly used in traditional Chinese medicine(TCM). It contains volatile oil, flavones, phenylpropanoids, terpenes and other chemical constituents. It has the functions of antibacterial, antiviral, hemostasis, anti-tumor, liver protection, analgesic, anti-inflammatory, anti-oxidation, relieving cough and asthma and other pharmacological activities. At present, many useful researches on the quality of moxa floss and Artemisiae Argyi Folium have been carried out on the contents of volatile oil, flavones, phenylpropanoids, the storage time of Artemisiae Argyi Folium, the processing of moxa, the genuineness of Artemisiae Argyi Folium, and their heat release properties in combustion. This paper summarized the literature on the chemical composition, pharmacological activities and quality control of Artemisiae Argyi Folium and provided the basis for the further development and utilization of Artemisiae Argyi Folium.

[Quality evaluation method of Lepidium meyenii using UPLC-UV-Q-TOF-MS].

In order to evaluate the quality of different varieties of Maca(Lepidium meyenii), the main chemical components in Maca were investigated and a method for simultaneous determination of the main chemical components in Maca was established. UPLC-UV-Q-TOF-MS technology and reference materials were used to identify the structures of 19 main components in Maca. Seven compounds with UV absorption and high contents were selected to establish a simultaneous concentration determination method. The method was employed with a Waters Acquity I-Class~(TM) liquid chromatographic system coupled with a PDA detector and a Waters Acquity Cortecs C_(18)~+ column(2.1 mm×100 mm, 1.6 µm), and acetonitrile-0.2% phosphoric acid water was used as mobile phase(0.45 mL·min~(-1)). The detection wavelength was 195 nm and the column temperature was maintained at 40 ℃. There was efficient separation of seven compounds, p-hydroxybenzylglucosinolate, benzylglucosinolate, N-benzyl-9Z,12Z,15Z-octadecatrienamid, N-benzyl-9Z,12Z-octadecadienamide, N-(3-methoxybenzyl)-hexadecanamide, N-benzyl-hexadecanamide, and N-benzyl-9Z-octadecenamide. The stan-dard calibration curves were good(R~2>0.999). The precision, stability and repeatability were also good. The linearity ranges were 0.197-4.980 µg·mL~(-1) to 193.67-796.8 µg·mL~(-1), and the average recovery rate was 96.71%-103.9%. The average concentration of glucosinolates and macamides in Maca were 1.20% and 0.20%, respectively. Among four kinds of Maca grown in China, the concentration of glucosinolates in yellow Maca and black Maca were relatively high(1.55%), followed by white Maca(0.93%), and purple Maca(0.76%). The concentration of macamides in yellow, purple and white Maca was similar(0.23%-0.29%), however black Maca had significantly lower concentration(0.15%). Peru Maca tested in this study had the lowest concentration of these compounds. This qua-lity evaluation method was fast, accurate, and comprehensively reflects the concentration of the main chemical components in Maca, which provides a useful reference for the quality control and evaluation of Maca.

Bulk phosphorous deposition at four typical land use sites in Southwest China.

Whilst ongoing increases in the deposition of atmospheric nitrogen (N) in China have attracted a lot of attention, to date there has been little research on phosphorus (P) deposition. In this study, we quantified inorganic P (PO43-), dissolved organic P (DOP) and total P (TP) in bulk deposition at four sites in the Sichuan Basin, Southwest China. Chengdu (CD), Shifang (SF), Yanting (YT), and Gongga (GG). They represent the land use categories urban, suburban, agricultural and forest, respectively, during 2008-2018 at CD and YT, 2015-2018 at SF, and 2007-2014 at GG. Annual average TP concentrations (deposition rates) were 0.07 (0.61), 0.49 (3.22), 0.17 (1.07) and 0.01 (0.20) mg L-1 (kg ha-1 yr-1), at CD, SF, YT and GG, respectively. The TP concentrations at YT and GG showed significant increasing trends over the years, with very little change at CD and a decline at SF because of the implementation of environmental control measures. Average PO43- to DOP ratios were 0.65, 0.95, 0.82 and 0.81 at CD, SF, YT and GG, respectively, indicating that DOP accounts for a higher proportion at the urban site, and dominated by combustion sources. Bulk P deposition showed higher deposition rates in summer and lower in winter. These results highlight the importance of long term monitoring in detecting spatial and temporal changing trends of the chemical composition, so as to implement effective policies to eliminate air pollution, especially for Southwest China, where there is limited research on atmospheric P deposition.

The Effect of Allograft Inflammatory Factor-1 on Inflammation, Oxidative Stress, and Autophagy via miR-34a/ATG4B Pathway in Diabetic Kidney Disease.

Increasing evidence suggests that disorders of inflammation, oxidative stress, and autophagy contribute to the pathogenesis of diabetic kidney disease (DKD). This study attempted to clarify the effect of allograft inflammatory factor-1 (AIF-1), miR-34a, and ATG4B on inflammation, oxidative stress, and autophagy in DKD both in vitro and in vivo experiments. In vivo, it was found that the levels of AIF-1, miR-34a, oxidative stress, and inflammatory factors were significantly increased in blood and urine samples of DKD patients and mouse models and correlated with the level of urinary protein. In vitro, it was also found that the expressions of AIF-1, miR-34a, ROS, and inflammatory factors were increased, while ATG4B and other autophagy related proteins were decreased in human renal glomerular endothelial cells (HRGECs) cultured with high concentration glucose medium (30 mmol/L). When AIF-1 gene was overexpressed, the levels of miR-34a, ROS, and inflammatory factors were significantly upregulated, and autophagy-related proteins such as ATG4B were downregulated, while downregulation of AIF-1 gene had the opposite effect. In addition, miR-34a inhibited the expression of ATG4B and autophagy-related proteins and increased the levels of ROS and inflammation. Furthermore, the result of luciferase reporter assay suggested that ATG4B was the target gene of miR-34a. When ATG4B gene was overexpressed, the level of autophagy was upregulated, and inflammatory factors were downregulated. Conversely, when ATG4B gene was inhibited, the level of autophagy was downregulated, and inflammatory factors were upregulated. Then, autophagy inducers inhibited the levels of inflammation and ROS, whereas autophagy inhibitors had the opposite function in HRGECs induced by glucose (30 mmol/L). In conclusion, the above data suggested that AIF-1 regulated the levels of inflammation, oxidative stress, and autophagy in HRGECs via miR-34a/ATG4B pathway to contribute to the pathogenesis of diabetic kidney disease.

A bacterial small RNA regulates the adaptation of Helicobacter pylori to the host environment.

Long-term infection of the stomach with Helicobacter pylori can cause gastric cancer. However, the mechanisms by which the bacteria adapt to the stomach environment are poorly understood. Here, we show that a small non-coding RNA of H. pylori (HPnc4160, also known as IsoB or NikS) regulates the pathogen's adaptation to the host environment as well as bacterial oncoprotein production. In a rodent model of H. pylori infection, the genomes of bacteria isolated from the stomach possess an increased number of T-repeats upstream of the HPnc4160-coding region, and this leads to reduced HPnc4160 expression. We use RNA-seq and iTRAQ analyses to identify eight targets of HPnc4160, including genes encoding outer membrane proteins and oncoprotein CagA. Mutant strains with HPnc4160 deficiency display increased colonization ability of the mouse stomach, in comparison with the wild-type strain. Furthermore, HPnc4160 expression is lower in clinical isolates from gastric cancer patients than in isolates derived from non-cancer patients, while the expression of HPnc4160's targets is higher in the isolates from gastric cancer patients. Therefore, the small RNA HPnc4160 regulates H. pylori adaptation to the host environment and, potentially, gastric carcinogenesis.

Genome-wide Analysis of Four Enterobacter cloacae complex type strains: Insights into Virulence and Niche Adaptation.

Enterobacter cloacae complex (Ecc) species are widely distributed opportunistic pathogens mainly associated with humans and plants. In this study, the genomes of clinical isolates including E. hormaechei, E. kobei, and E. ludwigii and non-clinical isolate including E. nimipressuralis were analysed in combination with the genome of E. asburiae by using the reference strain E. cloacae subsp. cloacae ATCC 13047; the Ecc strains were tested on artificial sputum media (ASM), which mimics the host, to evaluate T6SS genes as a case study. All five Ecc strains were sequenced in our lab. Comparative genome analysis of the Ecc strains revealed that genes associated with the survival of Ecc strains, including genes of metal-requiring proteins, defence-associated genes and genes associated with general physiology, were highly conserved in the genomes. However, the genes involved in virulence and drug resistance, specifically those involved in bacterial secretion, host determination and colonization of different strains, were present in different genomic regions. For example, T6SS accessory and core components, T4SS, and multidrug resistance genes/efflux system genes seemed vital for the survival of Ecc strains in various environmental niches, such as humans and plants. Moreover, the ASM host-mimicking growth medium revealed significantly high expression of T6SS genes, including PrpC, which is a regulatory gene of the T6SS, in all tested Ecc strains compared to the control medium. The variations in T6SS gene expression in ASM vs. control showed that the ASM system represents a simple, reproducible and economical alternative to animal models for studies such as those aimed at understanding the divergence of Ecc populations. In summary, genome sequencing of clinical and environmental Ecc genomes will assist in understanding the epidemiology of Ecc strains, including the isolation, virulence characteristics, prevention and treatment of infectious disease caused by these broad-host-range niche-associated species.

Genome re-seqeunce and analysis of Burkholderia glumae strain AU6208 and evidence of toxoflavin: A potential bacterial toxin.

Burkholderia glumae, the primary causative agent of bacterial panicle blight in rice, has been reported as an opportunistic pathogen in patients with chronic infections. This study aimed to re-sequence the clinical isolate B. glumae strain AU6208 and comparatively analyze its genome using B. glumae strain BGR1 from rice plant as the reference. Re-sequencing results revealed that the genome of strain AU6208 comprised 96 contigs corresponding to a 6.1 Mbp genome of the strain AU6208, with 5322 coding sequences and 68.2 % GC content; this is much larger compared to the genome previously sequenced by us and described by Seo et al (2015), which was reported to be 4.1 Mbp comprising >1200 contigs, 4361 coding sequences, and 67.31 % GC content. Moreover, this updated genome shares >80 % identity to the 7.2 Mbp genome of BGR1, which encodes 6491 coding sequences and has 68.3 % GC content. Further computational analysis revealed that the strain AU6208 encodes several bacteriocin biosynthesis genes, antibiotic, as well as virulent genes such as toxoflavin genes, which included 425 specialty genes and 12 toxoflavin genes. Upon further characterization, 12 toxoflavins (ToxA, B, C, D, E, F, G, H, I, J, TofI, and TofR) were found in AU6208 with 70-100 % sequence, family, and domain similarity with that of BGR1. Upon comparison with BGR1, the structural characterizations of selected toxoflavin genes (ToxB, ToxC, ToxG, H, and TofI) revealed variations in 2D and 3D structures such as differences in α-helix, ß-sheets, loops, physiological properties of proteins, RMSD values, etc. These variations may play significant role in different mode of action in different hosts thereby indicating that in addition to their respective hosts, toxoflavins could also contribute to exploit other hosts across the kingdom. In addition to understanding the epidemiology of strain AU6208, this updated genomics data will also unfold the pathogenicity of bacteria in diversity of various hosts and anti-virulence.

New descriptors of amino acids and their application to peptide QSAR study.

A new set of descriptors was derived from a matrix of three structural variables of the natural amino acid, including van der Waal's volume, net charge index and hydrophobic parameter of side residues. They were selected from many properties of amino acid residues, which have been validated being the key factors to influence the interaction between peptides and its protein receptor. They were then applied to structure characterization and QSAR analysis on bitter tasting di-peptide, agiotensin-converting enzyme inhibitor and bactericidal peptides by using multiple linear regression (MLR) method. The leave one out cross validation values (Q(2)) were 0.921, 0.943 and 0.773. The multiple correlation coefficients (R(2)) were 0.948, 0.970 and 0.926, the root mean square (RMS) error for estimated error were 0.165, 0.154 and 0.41, respectively for bitter tasting di-peptide, angiotensin-converting enzyme inhibitor and bactericidal peptides. Test sets of peptides were used to validate the quantitative model, and it was shown that all these QSAR models had good predictability for outside samples. The results showed that, in comparison with the conventional descriptors, the new set of descriptors is a useful structure characterization method for peptide QSAR analysis, which has multiple advantages, such as definite physical and chemical meaning, easy to get, and good structural characterization ability.

Genetic Diversity and Functional Analysis of Sigma Factors in Enterobacter cloacae Complex Resourced From Various Niche.

Sigma factors are bacterial transcription factors that bind the core RNA polymerase and direct transcription initiation at a specific promoter site. These specialized sigma factors bind the promoters of genes appropriate to the environmental conditions and selectively increase the transcription of those genes. Here, we attempt to identify sigma factors in 5 genomes belonging to the Enterobacter cloacae complex (Ecc), a group of gram-negative bacteria that are important nosocomial pathogens. This process includes the identification of orthologous sequences, conserved motifs, domains, families, phylogenetic profiles, and protein-protein associations of these components. Based on the reference genome, genome-wide comparison revealed that the genomes of Enterobacter asburiae JCM6051, Enterobacter nimipressuralis CIP 104980, Enterobacter hormaechei ATCC49162, Enterobacter kobei JCM 8580, and Enterobacter ludwigii EN-119 encode 10 sigma factors that exist in the reference strain Enterobacter cloacae subsp cloacae ATCC13047. Moreover, the sequence similarity, protein domains and families of the sigma factors, protein-protein association, and phylogenetic profile indicate that the sigma factor proteins of these 5 strains may have evolutionary relatedness and functional characteristics important to their various environmental niches. Interestingly, the absence of RpoS in E kobei, which contributes to bacterial survival under environmental stress conditions, indicates that RpoS might have been independently acquired and may play different roles relating to pathogenicity, host range determination, and/or niche adaptation. Future work such as RNA sequencing will be directed towards investigating the roles that these sigma factors play in the biology of the Ecc.

Comparative Genome Analysis of 2 Mycobacterium Tuberculosis Strains from Pakistan: Insights Globally Into Drug Resistance, Virulence, and Niche Adaptation.

Multidrug-resistant Mycobacterium tuberculosis is a global threat particularly in developing countries like Pakistan. In this study, we identified 2 M tuberculosis strains, mnpk and swlpk, by 16S RNA genes, sequenced their draft genome, and compared the 2 genomes with reference strain H37Rv and gene expression analysis of selected virulent genes. Phylogenetic analysis of M tuberculosis strains, mnpk and swlpk, using 16S RNA genes revealed that the strains are closely related with reference strain H37Rv. The draft genome sequence of mnpk and swlpk contains 4305 and 4295 protein-coding genes, respectively, having 99.9% with high collinearity when compared with H37Rv. Although some important drug-resistant genes such as fabG, faDE24, and iniA were missing, genome mining also revealed key drug-resistant genes such as katG, inhA, rpoA, rpoB, and rpoC against first-line isoniazid and rifampicin drug. The strain mnpk and swlpk encodes 257 putative and 86 verified virulent genes including type 7 secretion system (T7SS) key genes. The variation in the expression profile of selected T7SS genes, particularly low expression level of EspK, raised concern that the mechanism of virulence of mnpk and swlpk might be different from H37Rv strains as espK is associated with ATPase EccC1a and EccC1b which showed high expression level. Briefly, this study shows that the strains mnpk and swlpk are linked with H37Rv having 99% similarity in genomes, but the absence of drug-resistant genes and variation in key genes' expression profile espK, EccE1, PPE41, and espC provide a rationale for the future investigation of M tuberculosis mnpk and swlpk pathogenesis via RNA sequencing, single-nucleotide polymorphisms, as well as gene manipulation.

Systematic identification of Celastrol-binding proteins reveals that Shoc2 is inhibited by Celastrol.

Colorectal cancer (CRC) is the third most commonly diagnosed cancer. Celastrol exhibits anti-tumor activities in a variety of cancers. However, the effect of Celastrol on human CRC and the underlying mechanisms still need to be elucidated. The present study aimed to use in vitro and in vivo methods to clarify the anti-tumor effect of Celastrol and use protein microarrays to explore its mechanisms. We demonstrated that Celastrol effectively inhibited SW480 CRC cell proliferation. Two weeks of Celastrol gavage significantly inhibited the growth of xenografts in nude mice. A total of 69 candidate proteins were identified in the protein microarray experiment, including the most highly enriched protein Shoc2, which is a scaffold protein that modulates cell motility and metastasis through the ERK pathway. Celastrol significantly inhibited ERK1/2 phosphorylation in cell lines and xenograft tumors. Down-regulation of Shoc2 expression using Shoc2 siRNA also inhibited ERK1/2 phosphorylation. Furthermore, down-regulation of Shoc2 expression also significantly inhibited proliferation, colony formation, and migration functions of tumor cells. In addition, the LD0 of Celastrol by gavage is equal or more than 80 mg/kg in C57 male mice. In summary, we unraveled the anti-CRC function of Celastrol and confirmed for the first time that it inhibited the ERK1/2 pathway through binding to Shoc2.

Interferon alpha antagonizes the anti-hepatoma activity of the oncolytic virus M1 by stimulating anti-viral immunity.

Alpha virus M1 is an oncolytic virus that targets zinc-finger antiviral protein (ZAP)-defective cancer cells, and may be useful for treatment of hepatocellular carcinoma (HCC). Most of HCC patients have hepatitis and need long-term antiviral medication. Thus, it is necessary to clarify whether anti-virus medicines influence oncolytic effect of M1. We examined the effect of drugs used to treat hepatitis B/C on M1-mediated oncolysis in vitro and in vivo. Interferon (IFN)-α induces expression of antiviral IFN-stimulated genes (ISGs) in HCC cells with moderate sensitivity to M1 virus. This leads to reduced replication of M1, and blocking of M1-mediated apoptosis. The antagonistic effect of IFN-α is positively related with the expressive level of ISGs. We also examined a population of 147 HCC patients. A total of 107 patients (73%) had low ZAP expression in liver tissues relative to adjacent tissues. Among these 107 patients, 77% were positive for hepatitis B and 2% were positive for hepatitis C. A combination of M1 virus and IFN should be avoided in those patients with HBV or HCV infection, of who ZAP expression is low but ISGs expression is moderate. In conclusion, this study provides a basis for anti-viral regimens for HCC patients with hepatitis B or C who are given oncolytic virus M1.

Effects of effluent recirculation in vertical-flow constructed wetland on treatment efficiency of livestock wastewater.

Enhancing the treatment efficiency of livestock wastewater by effluent recirculation is investigated in a pilot-scale vertical-flow constructed wetland. The wetland system is composed of downflow and upflow stages, on which narrow-leaf Phragmites communis and common reed Phragmites typhia are planted, respectively; each stage has a dimension of 4 m(2) (2 m x 2 m). Wastewater from the facultative pond is fed into the system intermittently at a flow rate of 0.4 m(3)/d. Recirculation rates of 0, 25%, 50%0, 100% and 150% are adopted to evaluate the effect of the recirculation rate on pollutants removal. This shows that with effluent recirculation the average removal efficiencies of NH4-N, BOD5 and SS obviously increase to 61.7%, 81.3%, and 77.1%, respectively, in comparison with the values of 35.6%o, 50.2%, and 49.3% without effluent recirculation. But the improvement of TP removal is slight, only from 42.3% to 48.9%. The variations of NH4-N, DO and oxidation-reduction potential (ORP) of inflow and outflow reveal that the adoption of effluent recirculation is beneficial to the formation of oxide environment in wetland. The exponential relationships with excellent correlation coefficients (R(2) > 0.93) are found between the removal rates of NH4-N and BOD5 and the recirculation rates. With recirculation the pH value of the outflow decreases as the alkalinity is consumed by the gradually enhanced nitrification process. When recirculation rate is kept constant at 100%, the ambient temperature appears to affect NH4-N removal, but does not have significant influence on BOD5 removal.

Toward the quantitative prediction of T-cell epitopes: QSAR studies on peptides having affinity with the class I MHC molecular HLA-A*0201.

It would be useful for vaccine development to develop a method of rapidly identifying peptide epitopes. In this paper, the empirical three-dimensional quantitative structure-affinity relationship (3D-QSAR) methods were used to study the relationship between the three dimensional structural parameters (the isotropic surface area, ISA, and the electronic charge index, ECI) of the HLA-A*0201 binding peptide and the HLA-A*0201/peptide binding affinities. A set of 102 peptides having affinity with the class I MHC HLA-A*0201 molecule was used as training set. A test set of 40 peptides was used to determine the predictive value of the models. The 3D-QSAR models yielded a q2 = 0.5724 and a high rpred2 = 0.6955. The standard regression coefficients indicated that the hydrophobic interactions played an important role in peptide-MHC molecule binding and predicted the specific amino acid residue essential at a certain position of the peptide. The approach tested in the current paper is highly complementary to many of the methods described in references and possesses good predictability. It is a rapid and convenient method to detect high affinity peptide epitopes.

Copper as an antimicrobial agent against opportunistic pathogenic and multidrug resistant Enterobacter bacteria.

Infections by Enterobacter species are common and are multidrug resistant. The use of bactericidal surface materials such as copper has lately gained attention as an effective antimicrobial agent due to its deadly effects on bacteria, yeast, and viruses. The aim of the current study was to assess the antibacterial activity of copper surfaces against Enterobacter species. The antibacterial activity of copper surfaces was tested by overlying 5×10(6) CFU/ml suspensions of representative Enterobacter strains and comparing bacterial survival counts on copper surfaces at room temperature. Iron, stainless steel, and polyvinylchloride (PVC) were used as controls. The mechanisms responsible for bacterial killing on copper surfaces were investigated by a mutagenicity assay of the D-cycloserin (cyclA gene), single cell gel electrophoresis, a staining technique, and inductively coupled plasma mass spectroscopy. Copper yielded a significant decrease in the viable bacterial counts at 2 h exposure and a highly significant decrease at 4 h. Loss of cell integrity and a significantly higher influx of copper into bacterial cells exposed to copper surfaces, as compared to those exposed to the controls, were documented. There was no increase in mutation rate and DNA damage indicating that copper contributes to bacterial killing by adversely affecting cellular structure without directly targeting the genomic DNA. These findings suggest that copper's antibacterial activity against Enterobacter species could be utilized in health care facilities and in food processing plants to reduce the bioburden, which would increase protection for susceptible members of the community.

Copper as an antibacterial agent for human pathogenic multidrug resistant Burkholderia cepacia complex bacteria.

The Burkholderia cepacia complex (Bcc) consists of 17 closely related multidrug resistant bacterial species that are difficult to eradicate. Copper has recently gained attention as an antimicrobial agent because of its inhibitory effects on bacteria, yeast, and viruses. The objective of this study was to evaluate the antibacterial activity of copper surfaces and copper powder against members of the B. cepacia complex. The antibacterial activity of different copper surfaces was evaluated by incubating them with Bcc strain suspensions (5×10(7)cfu/ml). The bacterial survival counts were calculated and the data for various copper surfaces were compared to the data for stainless steel and polyvinylchloride, which were used as control surfaces. The antibacterial activity of copper powder was determined with the diffusimetrical technique and the zone of inhibition was evaluated with paper disks. A single cell gel electrophoresis assay, staining assays, and inductively coupled plasma mass spectroscopy were performed to determine the mechanism responsible for the bactericidal activity. The results showed a significant decrease in the viable bacterial count after exposure to copper surfaces. Moreover, the copper powder produced a large zone of inhibition and there was a significantly higher influx of copper ions into the bacterial cells that were exposed to copper surfaces compared to the controls. The present study demonstrates that metallic copper has an antibacterial effect against Bcc bacteria and that copper adversely affects the bacterial cellular structure, thus resulting in cell death. These findings suggest that copper could be utilized in health care facilities to reduce the bioburden of Bcc species, which may protect susceptible members of the community from bacterial infection.

Quantitative sequence-kinetics relationship in antigen-antibody interaction kinetics based on a set of descriptors [corrected].

The interaction between recombinant Fab57P and the coat protein of tobacco mosaic virus was studied using quantitative structure-activity relationship (QSAR) method. The development of quantitative multivariate model has shown to be a promising approach for unraveling protein-protein interactions by designed mutations in peptide sequence. This approach makes it possible to stereo-chemically determine which residue properties contribute most to the interaction. A set of side-chain descriptors was proposed and applied in structural characterization of three positions (positions 142, 145 and 146) in the peptide antigen. Quantitative sequence-kinetics relationship (QSKR) models describing the dissociation rates (log k(d) ) were developed successfully using orthogonal signal correction-partial least squares method. The results showed that peptides will have high log k(d) values when the amino acids in position 142 and 145 have high net charge index, and when residue 145 has high hydrophobicity and residue 146 has low hydrophobicity.

Estimation of affinity of HLA-A*0201 restricted CTL epitope based on the SCORE function.

A set of 70 peptides with affinity for the class I MHC HLA-A*0201 molecule was subjected to quantitative analyses of structure-affinity relationship based on the SCORE function with good results (r(2)=0.6982, q(2)=0.6188, RMS=0.280). Then the 'leave-one-out' cross-validation (LOO-CV) and an outer test set including 18 outer samples were used to validate the QSAR model, and the results show that the QSAR model has good predictability for outside samples. Statistical analysis showed that the hydrophobic and hydrogen bond interaction played a significant role in peptide-MHC molecule binding. The study also provided useful information for structure modification of CTL epitope, and laid theoretical base for molecular design of therapeutic vaccine.