Unearthing new ccr genes and SCC elements in staphylococci through genome mining.

The SCCmec typing is crucial for investigating methicillin-resistant S. aureus, relying primarily on the combination of ccr and mec gene complexes. To date, 19 ccr genes and 10 ccr gene complexes have been identified, forming 15 SCCmec types. With the vast release of bacterial genome sequences, mining the database for novel ccr gene complexes and SCC/SCCmec elements could enhance MRSA epidemiological studies. In this study, we identified 12 novel ccr genes (6 ccrA, 3 ccrB and 3 ccrC) through mining of the NCBI database, which forming 12 novel ccr gene complexes and 10 novel SCC elements. Overexpression of five groups of novel Ccr recombinases (CcrA9B3, CcrA10B1, CcrC3, CcrC4, and CcrC5) in a mutant MRSA strain lacking the ccr gene and extrachromosomal circular intermediate (ciSCC) production significantly promoted ciSCC production, demonstrating their biological activity. This discovery provides an opportunity to advance MRSA epidemiological research and develop database-based bacterial typing methods.

Novel cassette chromosome recombinases CcrA8B9 catalyse the excision and integration of the staphylococcal cassette chromosome mec element.

OBJECTIVES: A defining feature of MRSA is the SCCmec element. The excision and integration of SCCmec elements are catalysed by Ccr recombinases. Currently, seven ccrA, eight ccrB and two ccrC allotypes have been described. However, there have been no recent reports of a novel Ccr recombinase and thus this area should be explored. METHODS: According to the proposed criteria of the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements (IWG-SCC) committee, novel ccr genes were explored by searching the genome of our laboratory staphylococcal strains, which were isolated from bovine mastitis in Northwest China. The biological activity of the novel Ccr recombinases to excise and integrate SCCmec elements was determined. The distribution of the novel ccr genes in staphylococci was conducted by querying the NCBI nr/nt database. RESULTS: We report a set of novel Ccr recombinases CcrA8B9, which share nucleotide identities of 46.6%-50.2% and 47.4%-52.8% with the ccrA and ccrB alleles, respectively. We used PCR to show that CcrA8B9 can excise and integrate the SCCmec element. Furthermore, using NCBI BLAST we showed that the ccrA8B9 genes exist in other staphylococcal strains. Unlike the common ccr genes, ccrA8B9 is located outside the SCCmec/SCC element. CONCLUSIONS: The novel Ccr recombinases CcrA8B9 can help excise and integrate SCCmec/SCC from the genome and provide a new way to facilitate the transmission of SCCmec/SCC elements among staphylococci.

Conductive polymer sorbent for extraction and determination of resveratrol and polydatin in Polygonum cuspidatum root samples.

INTRODUCTION: The quantitative analysis of trace resveratrol and polydatin in plant tissues is suitable for elucidation of the compounds' mechanisms of action. OBJECTIVES: The main objective of this work was to develop a feasible and effective sample pretreatment method to measure the concentrations of resveratrol and polydatin in complex samples. METHODOLOGY: A polymer sorbent, poly(2-mercaptobenzimidazole), was electrochemically prepared and utilized for selective extraction, while resveratrol and polydatin were used as target analytes. The sorbent was characterized by cyclic voltammetry, scanning electron microscopy and Fourier transform infrared spectroscopy. After extraction and elution, the analytes were analyzed by a Thermo U3000 HPLC system. Several affecting parameters, including the volume of elution solution, sample pH value, sample flow rate and sample volume, were evaluated and optimized. RESULTS: The proposed method showed good linearity with low limits of detection (from 0.5 to 0.8 ng·mL-1 ) and ideal accuracy with spiked recoveries from 81.30% to 99.16%. A good enrichment factor (more than 200-fold) together with good sensitivity was obtained with this method. Analysis of resveratrol and polydatin in Polygonum cuspidatum samples by this method is efficient. CONCLUSION: The method developed in this work exhibits several significant merits, including easy operation and high extraction efficiency, indicating that electrochemically prepared polymer sorbent is useful for sample pretreatment and analysis of traditional Chinese medicine samples.

Item-Weighted Likelihood Method for Measuring Growth in Longitudinal Study With Tests Composed of Both Dichotomous and Polytomous Items.

In this paper, a new item-weighted scheme is proposed to assess examinees' growth in longitudinal analysis. A multidimensional Rasch model for measuring learning and change (MRMLC) and its polytomous extension is used to fit the longitudinal item response data. In fact, the new item-weighted likelihood estimation method is not only suitable for complex longitudinal IRT models, but also it can be used to estimate the unidimensional IRT models. For example, the combination of the two-parameter logistic (2PL) model and the partial credit model (PCM, Masters, 1982) with a varying number of categories. Two simulation studies are carried out to further illustrate the advantages of the item-weighted likelihood estimation method compared to the traditional Maximum a Posteriori (MAP) estimation method, Maximum likelihood estimation method (MLE), Warm's (1989) weighted likelihood estimation (WLE) method, and type-weighted maximum likelihood estimation (TWLE) method. Simulation results indicate that the improved item-weighted likelihood estimation method better recover examinees' true ability level for both complex longitudinal IRT models and unidimensional IRT models compared to the existing likelihood estimation (MLE, WLE and TWLE) methods and MAP estimation method, with smaller bias, root-mean-square errors, and root-mean-square difference especially at the low-and high-ability levels.