Identification of a potent small-molecule inhibitor of bacterial DNA repair that potentiates quinolone antibiotic activity in methicillin-resistant Staphylococcus aureus

The global emergence of antibiotic resistance is one of the most serious challenges facing modern medicine. There is an urgent need for validation of new drug targets and the development of small molecules with novel mechanisms of action. We therefore sought to inhibit bacterial DNA repair mediated by the AddAB/RecBCD protein complexes as a means to sensitize bacteria to DNA damage caused by the host immune system or quinolone antibiotics. A rational, hypothesis-driven compound optimization identified IMP-1700 as a cell-active, nanomolar potency compound. IMP-1700 sensitized multidrug-resistant Staphylococcus aureus to the fluoroquinolone antibiotic ciprofloxacin, where resistance results from a point mutation in the fluoroquinolone target, DNA gyrase. Cellular reporter assays indicated IMP-1700 inhibited the bacterial SOS-response to DNA damage, and compound-functionalized Sepharose successfully pulled-down the AddAB repair complex. This work provides validation of bacterial DNA repair as a novel therapeutic target and delivers IMP-1700 as a tool molecule and starting point for therapeutic development to address the pressing challenge of antibiotic resistance.     

Bioassay of kinship in Micronesia

Phenotype bioassay agrees with clan isonymy, anthropometrics, and migration in estimating the mean kinship within a Micronesian population, relative to large distances, as 0.05. Various calculations of occupancy for the Eastern Carolines from ethnohistory, kinship, and glottochronology average around 1,000 years. Estimates of isolation by distance are in agreement for different indicators of population structure. Problems of kinship bioassay are discussed.     

Comparison of growth rate and formation of otolith increments in age-0 red snapper

For wild red snapper Lutjanus campechanus , mean otolith increment deposition rate after marking with oxytetracycline dihydrate (OTC) was daily (0.97 increments day⁻¹) when growth rates were fast (0.63 mm fork length, L _F day⁻¹), but were not daily (0.82 increments day⁻¹) when somatic growth was slow (0.2 mm L _F day⁻¹). For reared larvae ( n =8), increment deposition rates were daily (0.99–1.03 increments day⁻¹), and growth rates ranged from 0.6 to 0.9 mm L _F day⁻¹. Growth rate affected increment deposition rate as a threshold function, i.e. when growth rate was <0.3 mm L _F day⁻¹, deposition was less than daily, but above this level increment deposition did not exceed a daily rate. As growth rates increased increment widths increased. Examination of a sub-sample ( n =8) of the otoliths from the slowest growing wild fish by scanning electron microscopy did not increase increment counts. Because L. campechanus are late spring-early summer spawners, young fish can expect maximum growth due to warm summer temperatures. Thus, daily ageing methods should be well suited to this species.     

Validation of indices for functional assessment of dentures

Aims: To validate an assessment of qualities of complete dentures that may relate to functional success. Subjects: A consecutive sample of 131 complete denture wearers took part in the study. Setting: a Greek department of prosthetic dentistry. Intervention : All participants and their dentures underwent clinical examination. Design: The Functional Assessment of Dentures (FAD) 10‐item criteria¹ describing clinical factors of denture quality was used. The rationale for selecting these particular criteria was to include a range of clinical factors to produce an overall assessment of complete dentures. The 10‐item scale was examined for Internal Consistency and Construct Validity providing a summated rating scale whose total score could be used as an index for the quality of dentures. Results: Both intra‐ and inter‐examiner agreement for all 10 dichotomous scale criteria were all good or very good; the intra‐examiner Kappa values were 0.72 to 0.91 and the inter‐ examiner values were 0.72 to 0.99. Statistical analysis revealed that a 7‐item summated rating scale could be constructed which has marginally better internal consistency (reliability) and Construct Validity with fewer questions. Conclusions: The FAD criteria¹ can be used to give good repeatability. The adjustments made to the original summation scale, if confirmed by new studies, would further increase the practical utility of a FAD index for general dentists. In due course with data from future studies, discrimination on weighting of items will be appropriate to relate the impact of denture quality on quality of life.     

Methods and method evaluation for mycotoxins

Mycotoxins are metabolites of molds frequently found on and in agricultural commodities, food and feeds. Owing to their demonstrated acute, sub-acute and, in some cases, chronic toxicity, an effort has been made, worldwide, to control human and animal exposure to these toxic chemicals. This effort depends upon the availability of validated analytical methods for their detection and quantitation. This paper outlines the methodology available, and the procedures used to validate, i.e. evaluate, these methods based on the use of interlaboratory collaborative studies and the application of the HORRAT.     

Impact of incorporating the 2C5 crystal structure into comparative models of cytochrome P450 2D6

Cytochrome P450 2D6 (CYP2D6) metabolizes approximately one third of the drugs in current clinical use. To gain insight into its structure and function, we have produced four different sets of comparative models of 2D6: one based on the structures of P450s from four different microorganisms (P450 terp, P450 eryF, P450 cam, and P450 BM3), another on the only mammalian P450 (2C5) structure available, and the other two based on alternative amino acid sequence alignments of 2D6 with all five of these structures. Principal component analysis suggests that inclusion of the 2C5 crystal structure has a profound effect on the modeling process, altering the general topology of the active site, and that the models produced differ significantly from all of the templates. The four models of 2D6 were also used in conjunction with molecular docking to produce complexes with the substrates codeine and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP); this identified Glu 216 [in the F-helix; substrate recognition site (SRS) 2] as a key determinant in the binding of the basic moiety of the substrate. Our studies suggest that both Asp 301 and Glu 216 are required for metabolism of basic substrates. Furthermore, they suggest that Asp 301 (I-helix, SRS-4), a residue thought from mutagenesis studies to bind directly to the basic moiety of substrates, may play a key role in positioning the B'-C loop (SRS-1) and that the loss of activity on mutating Asp 301 may therefore be the result of an indirect effect (movement of the B'-C loop) on replacing this residue.     

对“小鼠腹腔巨噬细胞吞噬作用的观察实验”的拓展探索

以"小鼠腹腔巨噬细胞吞噬作用的观察实验"为例,从发现疑问、确定拓展方向、设计拓展方案等方面拓展传统验证性实验项目,使其一般验证性实验具有了综合性和设计性的作用,让学生体会到在小实验中发现大问题的乐趣,进一步激发学生参与实验的积极性。     

The neglected tool in the Bayesian ecologist's shed: a case study testing informative priors' effect on model accuracy

Despite benefits for precision, ecologists rarely use informative priors. One reason that ecologists may prefer vague priors is the perception that informative priors reduce accuracy. To date, no ecological study has empirically evaluated data‐derived informative priors' effects on precision and accuracy. To determine the impacts of priors, we evaluated mortality models for tree species using data from a forest dynamics plot in Thailand. Half the models used vague priors, and the remaining half had informative priors. We found precision was greater when using informative priors, but effects on accuracy were more variable. In some cases, prior information improved accuracy, while in others, it was reduced. On average, models with informative priors were no more or less accurate than models without. Our analyses provide a detailed case study on the simultaneous effect of prior information on precision and accuracy and demonstrate that when priors are specified appropriately, they lead to greater precision without systematically reducing model accuracy.     

A validation study of Fitbit Charge 2™ compared with polysomnography in adults

We evaluated the performance of a consumer multi-sensory wristband (Fitbit Charge 2?), against polysomnography (PSG) in measuring sleep/wake state and sleep stage composition in healthy adults.

In-lab PSG and Fitbit Charge 2? data were obtained from a single overnight recording at the SRI Human Sleep Research Laboratory in 44 adults (19—61 years; 26 women; 25 Caucasian). Participants were screened to be free from mental and medical conditions. Presence of sleep disorders was evaluated with clinical PSG. PSG findings indicated periodic limb movement of sleep (PLMS, > 15/h) in nine participants, who were analyzed separately from the main group (n = 35). PSG and Fitbit Charge 2? sleep data were compared using paired t-tests, Bland–Altman plots, and epoch-by-epoch (EBE) analysis.

In the main group, Fitbit Charge 2? showed 0.96 sensitivity (accuracy to detect sleep), 0.61 specificity (accuracy to detect wake), 0.81 accuracy in detecting N1+N2 sleep (“light sleep”), 0.49 accuracy in detecting N3 sleep (“deep sleep”), and 0.74 accuracy in detecting rapid-eye-movement (REM) sleep. Fitbit Charge 2? significantly (p < 0.05) overestimated PSG TST by 9 min, N1+N2 sleep by 34 min, and underestimated PSG SOL by 4 min and N3 sleep by 24 min. PSG and Fitbit Charge 2? outcomes did not differ for WASO and time spent in REM sleep. No more than two participants fell outside the Bland–Altman agreement limits for all sleep measures. Fitbit Charge 2? correctly identified 82% of PSG-defined non-REM–REM sleep cycles across the night. Similar outcomes were found for the PLMS group.

Fitbit Charge 2? shows promise in detecting sleep-wake states and sleep stage composition relative to gold standard PSG, particularly in the estimation of REM sleep, but with limitations in N3 detection. Fitbit Charge 2? accuracy and reliability need to be further investigated in different settings (at-home, multiple nights) and in different populations in which sleep composition is known to vary (adolescents, elderly, patients with sleep disorders).