Longitudinal qPCR Study of the Dynamics of L. crispatus,L. iners,A. vaginae, (Sialidase Positive) G. vaginalis,and P. bivia in the Vagina

Background

To obtain more detailed understanding of the causes of disturbance of the vaginal microflora (VMF), a longitudinal study was carried out for 17 women during two menstrual cycles.

Methods

Vaginal swabs were obtained daily from 17 non-pregnant, menarchal volunteers. For each woman, Gram stains were scored, the quantitative changes of 5 key vaginal species, i.e. Atopobium vaginae, Lactobacillus crispatus, L. iners, (sialidase positive) Gardnerella vaginalis and Prevotella bivia were quantified with qPCR and hydrogen-peroxide production was assessed on TMB+ agar.

Results

Women could be divided in 9 subjects with predominantly normal VMF (grades Ia, Ib and Iab, group N) and 8 with predominantly disturbed VMF (grades I-like, II, III and IV, group D).VMF was variable between women, but overall stable for most of the women. Menses were the strongest disturbing factor of the VMF. L. crispatus was present at log7–9 cells/ml in grade Ia, Iab and II VMF, but concentrations declined 100-fold during menses. L. crispatus below log7 cells/ml corresponded with poor H₂O₂-production. L. iners was present at log 10 cells/ml in grade Ib, II and III VMF. Sialidase negative G. vaginalis strains (average log5 cells/ml) were detected in grade I, I-like and IV VMF. In grade II VMF, predominantly a mixture of both sialidase negative and positive G. vaginalis strains (average log9 cells/ml) were present, and predominantly sialidase positive strains in grade III VMF. The presence of A. vaginae (average log9 cells/ml) coincided with grade II and III VMF. P. bivia (log4–8 cells/ml) was mostly present in grade III vaginal microflora. L. iners, G. vaginalis, A. vaginae and P. bivia all increased around menses for group N women, and as such L. iners was considered a member of disturbed VMF.

Conclusions

This qPCR-based study confirms largely the results of previous culture-based, microscopy-based and pyrosequencing-based studies.     

An optimizing start-up strategy for a bio-methanator

This paper presents an optimizing start-up strategy for a bio-methanator. The goal of the control strategy is to maximize the outflow rate of methane in anaerobic digestion processes, which can be described by a two-population model. The methodology relies on a thorough analysis of the system dynamics and involves the solution of two optimization problems: steady-state optimization for determining the optimal operating point and transient optimization. The latter is a classical optimal control problem, which can be solved using the maximum principle of Pontryagin. The proposed control law is of the bang–bang type. The process is driven from an initial state to a small neighborhood of the optimal steady state by switching the manipulated variable (dilution rate) from the minimum to the maximum value at a certain time instant. Then the dilution rate is set to the optimal value and the system settles down in the optimal steady state. This control law ensures the convergence of the system to the optimal steady state and substantially increases its stability region. The region of attraction of the steady state corresponding to maximum production of methane is considerably enlarged. In some cases, which are related to the possibility of selecting the minimum dilution rate below a certain level, the stability region of the optimal steady state equals the interior of the state space. Aside its efficiency, which is evaluated not only in terms of biogas production but also from the perspective of treatment of the organic load, the strategy is also characterized by simplicity, being thus appropriate for implementation in real-life systems. Another important advantage is its generality: this technique may be applied to any anaerobic digestion process, for which the acidogenesis and methanogenesis are, respectively, characterized by Monod and Haldane kinetics.     

Predicting the effect of a point mutation on a protein fold: the villin and advillin headpieces and their Pro62Ala mutants

Homology modeling of unknown proteins is based on the assumption that highly similar sequences are likely to share the same fold. However, this does not provide any information on the stability of a given fold, which is ultimately determined by the subtle interplay of enthalpic and entropic contributions. Herein it is shown that ab initio atomistic simulations can be used to predict the effect of point mutations on the stability of a protein fold. The calculations indicate that the fold stabilities of two proteins of similar sequence and identical fold, the villin and advillin C-terminal headpiece fragments, are different and that the same P62A point mutation has a dramatic effect on the fold of villin but a minor one on that of advillin. These predictions were subsequently validated by NMR and CD experiments.     

Transformation by bovine papillomavirus type 1 E6 requires paxillin

Papillomavirus E6 proteins are adapters that change the function of cellular regulatory proteins. The bovine papillomavirus type 1 E6 (BE6) binds to LXXLL peptide sequences termed LD motifs (consensus sequence LDXLLXXL) on the cellular protein paxillin that is a substrate of Src and focal adhesion kinases. Anchorage-independent transformation induced by BE6 required both paxillin and BE6-binding LD motifs on paxillin but was independent of the major tyrosine phosphorylation sites of paxillin. The essential role of paxillin in transformation by BE6 highlights the role of paxillin in the transduction of cellular signals that result in anchorage-independent cell proliferation.     

Poor reporting of scientific leadership information in clinical trial registers

Background

In September 2004, the International Committee of Medical Journal Editors (ICMJE) issued a Statement requiring that all clinical trials be registered at inception in a public register in order to be considered for publication. The World Health Organization (WHO) and ICMJE have identified 20 items that should be provided before a trial is considered registered, including contact information. Identifying those scientifically responsible for trial conduct increases accountability. The objective is to examine the proportion of registered clinical trials providing valid scientific leadership information.

Methodology/Principal Findings

We reviewed clinical trial entries listing Canadian investigators in the two largest international and public trial registers, the International Standard Randomized Controlled Trial Number (ISRCTN) register, and ClinicalTrials.gov. The main outcome measures were the proportion of clinical trials reporting valid contact information for the trials'' Principal Investigator (PI)/Co-ordinating Investigator/Study Chair/Site PI, and trial e-mail contact address, stratified by funding source, recruiting status, and register. A total of 1388 entries (142 from ISRCTN and 1246 from ClinicalTrials.gov) comprised our sample. We found non-compliance with mandatory registration requirements regarding scientific leadership and trial contact information. Non-industry and partial industry funded trials were significantly more likely to identify the individual responsible for scientific leadership (OR = 259, 95% CI: 95–701) and to provide a contact e-mail address (OR = 9.6, 95% CI: 6.6–14) than were solely industry funded trials.

Conclusions/Significance

Despite the requirements set by WHO and ICMJE, data on scientific leadership and contact e-mail addresses are frequently omitted from clinical trials registered in the two leading public clinical trial registers. To promote accountability and transparency in clinical trials research, public clinical trials registers should ensure adequate monitoring of trial registration to ensure completion of mandatory contact information fields identifying scientific leadership     

Accumulation of metal-binding peptides in fission yeast requires hmt2+

The fission yeast Schizosaccharomyces pombe detoxifies cadmium by synthesizing phytochelatins, peptides of the structure (gamma-GluCys)nGly, which bind cadmium and mediate its sequestration into the vacuole. The fission yeast protein HMT2, a mitochondrial enzyme that can oxidize sulphide, appears to be essential for tolerance to multiple forms of stress, including exposure to cadmium. We found that the hmt2- mutant is unable to accumulate normal levels of phytochelatins in response to cadmium, although the cells possess a phytochelatin synthase that is active in vitro. Radioactive pulse-chase experiments demonstrated that the defect lies in two steps: the synthesis of phytochelations and the upregulation of glutathione production. Phytochelatins, once formed, are stable. hmt2- cells accumulate high levels of sulphide and, when exposed to cadmium, display bright fluorescent bodies consistent with cadmium sulphide. We propose that the precipitation of free cadmium blocks phytochelatin synthesis in vivo, by preventing upregulation of glutathione production and formation of the cadmium-glutathione thiolate required as a substrate by phytochelatin synthase. Thus, although sulphide is required for phytochelatin-mediated metal tolerance, aberrantly high sulphide levels can inhibit this pathway. Precise regulation of sulphur metabolism, mediated in part by HMT2, is essential for metal tolerance in fission yeast.     

Nuclear Medicine: Bone Pain and Radionuclide Therapy

The Council on Scientific Affairs of the California Medical Association presents the following epitomes of progress in nuclear medicine. Each item, in the judgment of a panel of knowledgeable physicians, has recently become reasonably firmly established, both as to scientific fact and clinical importance. The items are presented in simple epitome, and an authoritative reference, both to the item itself and to the subject as a whole, is generally given for those who may be unfamiliar with a particular item. The purpose is to assist busy practitioners, students, researchers, and scholars to stay abreast of progress in medicine, whether in their own field of special interest or another.The epitomes included here were selected by the Advisory Panel to the Section on Nuclear Medicine of the California Medical Association, and the summaries were prepared under the direction of Dr Lyons and the panel.     

A dynamical interpretation of strong observability and detectability concepts for nonlinear systems with unknown inputs: application to biochemical processes

Determination of the observability/detectability properties of a nonlinear system is fundamental to assess the possibility of constructing observers and the properties that can be assigned to them, as e.g., the assignability of the convergence rate. For linear systems this task can be solved by well-known techniques, for the case without perturbations as much as for the perturbed case. However, for nonlinear systems this study is usually a very hard task, in particular, when unknown inputs and/or perturbations are present. In this paper a general method to study these properties will be described, and its capabilities and feasibility will be assessed by means of a few case studies related to the culture of phytoplankton in the chemostat.