Interaction of human and bacterial AlkB proteins with DNA as probed through chemical cross-linking studies

The Escherichia coli AlkB protein was recently found to repair cytotoxic DNA lesions 1-methyladenine and 3-methylcytosine by using a novel iron-catalyzed oxidative demethylation mechanism. Three human homologs, ABH1, ABH2 and ABH3, have been identified, and two of them, ABH2 and ABH3, were shown to have similar repair activities to E.coli AlkB. However, ABH1 did not show any repair activity. It was suggested that ABH3 prefers single-stranded DNA and RNA substrates, whereas AlkB and ABH2 can repair damage in both single- and double-stranded DNA. We employed a chemical cross-linking approach to probe the structure and substrate preferences of AlkB and its three human homologs. The putative active site iron ligands in these proteins were mutated to cysteine residues. These mutant proteins were used to cross-link to different DNA probes bearing thiol-tethered bases. Disulfide-linked protein–DNA complexes can be trapped and analyzed by SDS–PAGE. Our results show that ABH2 and ABH3 have structural and functional similarities to E.coli AlkB. ABH3 shows preference for the single-stranded DNA probe. ABH1 failed to cross-link to the probes tested. This protein, unlike other AlkB proteins, does not seem to interact with DNA in its E.coli expressed form.     

Quantification bias caused by plasmid DNA conformation in quantitative real-time PCR assay

Quantitative real-time PCR (qPCR) is the gold standard for the quantification of specific nucleic acid sequences. However, a serious concern has been revealed in a recent report: supercoiled plasmid standards cause significant over-estimation in qPCR quantification. In this study, we investigated the effect of plasmid DNA conformation on the quantification of DNA and the efficiency of qPCR. Our results suggest that plasmid DNA conformation has significant impact on the accuracy of absolute quantification by qPCR. DNA standard curves shifted significantly among plasmid standards with different DNA conformations. Moreover, the choice of DNA measurement method and plasmid DNA conformation may also contribute to the measurement error of DNA standard curves. Due to the multiple effects of plasmid DNA conformation on the accuracy of qPCR, efforts should be made to assure the highest consistency of plasmid standards for qPCR. Thus, we suggest that the conformation, preparation, quantification, purification, handling, and storage of standard plasmid DNA should be described and defined in the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) to assure the reproducibility and accuracy of qPCR absolute quantification.     

Intraspecific karyotypic polymorphism is highly concordant with allozyme variation in Lysimachia mauritiana (Primulaceae: Myrsinoideae) in Taiwan: implications for the colonization history and dispersal patterns of coastal plants

Background and Aims

Investigating intraspecific karyotypic and genetic variations jointly can provide unique insights into how historical, ecological and cytogenetic factors influence microevolution. A coastal herb, Lysimachia mauritiana, exhibits extensive karyotypic polymorphism and displays a complex cytogeographic pattern across the Ryukyus. To explore whether a similar degree of chromosomal variation exists south of the Ryukyus, and in an attempt to ascertain the mechanisms that may have generated the patterns, comprehensive sampling was conducted in Taiwan.

Methods

Karyotypes were analysed at mitotic metaphase for 550 individuals from 42 populations throughout Taiwan Proper and its adjacent islands. In addition, genetic variation was estimated using 12 allozymes (21 loci) of 314 individuals sampled from 12 localities.

Key Results

Four chromosome numbers and eight cytotypes, including four endemic cytotypes, were detected. Cytotype distributions were highly structured geographically, with single cytotypes present in most populations and four major cytotypes dominating the north, east and south of Taiwan and the Penghu Archipelago. Allozyme variation was very low and F-statistics indicated an extremely high level of population differentiation, implying limited gene flow among populations. Cluster analysis of allozyme variation uncovered four geographic groups, each corresponding perfectly to the four dominant cytotypes. The geographic structure of cytotype distribution and allozyme variation probably resulted from severe genetic drift triggered by genetic bottlenecks, suggesting that Taiwanese populations were likely to be derived from four independent founder events. In the few localities with multiple cytotypes, cytogeographic patterns and inferences of chromosomal evolution revealed a trend of northward dispersal, consistent with the course of the Kuroshio Current that has been influential in shaping the coastal biota of the region.

Conclusions

The data elucidate the patterns of colonization and the effects of the Kuroshio Current on the distribution of L. mauritiana in Taiwan. These inferences are highly relevant to other coastal plant species in the region and will stimulate further studies.     

The implication of probiotics in the prevention of dental caries

The current oral health crisis, whose causes are varied and complex, necessitates timely oral evaluation and early detection and treatment of oral health problems. Dramatic changes in eating habits and lifestyles are associated with the recent decline in oral health. Probiotics are “good” bacteria that support digestion and a healthy immune system and offer various health benefits to the host. Traditionally, probiotics have been used to improve gut health; the most common uses have historically been as a treatment or prevention of gastrointestinal infections and disease. During the last decade, studies have additionally suggested the intake of probiotics for oral health purposes. Probiotic use provides an effective strategy to combat oral disease, including the development of dental caries and periodontal infection. The aim of this review is to describe the beneficial roles of probiotic bacteria in the oral cavity and the potential mechanisms by which these bacteria exert their effects on oral health.

     

Assessing the Intraoperative Accuracy of Pedicle Screw Placement by Using a Bone-Mounted Miniature Robot System through Secondary Registration

IntroductionPedicle screws are commonly employed to restore spinal stability and correct deformities. The Renaissance robotic system was developed to improve the accuracy of pedicle screw placement.PurposeIn this study, we developed an intraoperative classification system for evaluating the accuracy of pedicle screw placements through secondary registration. Furthermore, we evaluated the benefits of using the Renaissance robotic system in pedicle screw placement and postoperative evaluations. Finally, we examined the factors affecting the accuracy of pedicle screw implantation.ResultsThrough use of the Renaissance robotic system, the accuracy of Kirschner-wire (K-wire) placements deviating <3 mm from the planned trajectory was determined to be 98.74%. According to our classification system, the robot-guided pedicle screw implantation attained an accuracy of 94.00% before repositioning and 98.74% after repositioning. However, the malposition rate before repositioning was 5.99%; among these placements, 4.73% were immediately repositioned using the robot system and 1.26% were manually repositioned after a failed robot repositioning attempt. Most K-wire entry points deviated caudally and laterally.ConclusionThe Renaissance robotic system offers high accuracy in pedicle screw placement. Secondary registration improves the accuracy through increasing the precision of the positioning; moreover, intraoperative evaluation enables immediate repositioning. Furthermore, the K-wire tends to deviate caudally and laterally from the entry point because of skiving, which is characteristic of robot-assisted pedicle screw placement.     

An assessment of the toxicity of metals to Pseudomonas aeruginosa PU21 (Rip64)

The toxicity of Co(II), Mn(II), Cd(II), and Zn(II) for Pseudomonas aeruginosa PU21, a Hg(II)-hyperresistant strain containing the mercury resistance mer operon, was determined. The metal tolerance of PU21 was strongly influenced by environmental conditions (e.g., existing metal, medium composition). Dose-response analysis on chronic and acute toxicity (e.g., EC(20), median effective dose EC(50), and slope factor B) of divalent cobalt, manganese, cadmium, and zinc cations in LB medium amended with citric acid phosphate buffered saline (CAPBS) suggested a toxicity series of Co > Mn approximately Zn > Cd for EC(50). In contrast, excluding the likely precipitate of Zn(II), the toxicity ranking in phosphate-buffered saline (PBS)-amended LB medium was Co > Cd > Mn. The metal toxicity in PBS, irrespective of metals, was greater than that in CAPBS. This might be attributed to the presence of citric acid in CAPBS as a chelating ligand donating electrons to hold free metals (e.g., Cd(2+), Zn(2+) tetrahedral ML(4) complex). The toxicity assessment established viable operation ranges (ca. 相似文献   

Microfluidic synthesis of microfibers for magnetic-responsive controlled drug release and cell culture

This study demonstrated the fabrication of alginate microfibers using a modular microfluidic system for magnetic-responsive controlled drug release and cell culture. A novel two-dimensional fluid-focusing technique with multi-inlets and junctions was used to spatiotemporally control the continuous laminar flow of alginate solutions. The diameter of the manufactured microfibers, which ranged from 211 μm to 364 μm, could be well controlled by changing the flow rate of the continuous phase. While the model drug, diclofenac, was encapsulated into microfibers, the drug release profile exhibited the characteristic of a proper and steady release. Furthermore, the diclofenac release kinetics from the magnetic iron oxide-loaded microfibers could be controlled externally, allowing for a rapid drug release by applying a magnetic force. In addition, the successful culture of glioblastoma multiforme cells in the microfibers demonstrated a good structural integrity and environment to grow cells that could be applied in drug screening for targeting cancer cells. The proposed microfluidic system has the advantages of ease of fabrication, simplicity, and a fast and low-cost process that is capable of generating functional microfibers with the potential for biomedical applications, such as drug controlled release and cell culture.