Synthetic DNA probes for detection of genes for enterotoxins A, B, C, D, E and for TSST-1 in staphylococcal strains

B. JAULHAC, M. BES, N. BORNSTEIN, Y. PIÉMONTY. BRUN AND J. FLEURETTE. 1992. A dot blot hybridization technique with oligonucleotide probes was developed for the specific detection of the TSST-1 gene and the staphylococcal enterotoxin (SE) genes A, B, C, D and E. For each toxin gene a probe sequence was chosen from the previously determined sequence. A total of 145 staphylococcal strains (133 Staphylococcus aureus and 12 coagulase-negative staphylococci (CNS)) were studied by this genotypic method and by two phenotypic assays (gel immunodiffusion and ELISA). An excellent correlation (96%) was observed between the genotypic and phenotypic assays. DNA from two CNS strains hybridized with a probe without detection of the corresponding toxin (SEB for one strain and SEC for the other strain). One Staph. aureus strain was shown to be an SEC producer, but was not detected by the corresponding probe. Gene probe and immunological assays seem to be complementary methods for studies of staphylococcal strains producing (or potentially producing) TSST-1 or enterotoxins.     

Synthetic DNA probes for detection of genes for enterotoxins A, B, C, D, E and for TSST-1 in staphylococcal strains.

A dot blot hybridization technique with oligonucleotide probes was developed for the specific detection of the TSST-1 gene and the staphylococcal enterotoxin (SE) genes A, B, C, D and E. For each toxin gene a probe sequence was chosen from the previously determined sequence. A total of 145 staphylococcal strains (133 Staphylococcus aureus and 12 coagulase-negative staphylococci (CNS) were studied by this genotypic method and by two phenotypic assays (gel immunodiffusion and ELISA). An excellent correlation (96%) was observed between the genotypic and phenotypic assays. DNA from two CNS strains hybridized with a probe without detection of the corresponding toxin (SEB for one strain and SEC for the other strain). One Staph. aureus strain was shown to be an SEC producer, but was not detected by the corresponding probe. Gene probe and immunological assays seem to be complementary methods for studies of staphylococcal strains producing (or potentially producing) TSST-1 or enterotoxins.     

Evidence for the occurrence of, and possible physiological role for, cyanobacterial calmodulin

Phosphate uptake by the blue-green alga Oscillatoria limnetica Lemmerman is stimulated by micromolar concentrations of Ca²⁺. The calmodulin antagonists 4-(3-[2(trifluoromethyl)phenylthiazin-10-yl]propyl)-1-piperazine ethanol-HCl and its monofluoro-analog inhibit orthophosphate uptake of Oscillatoria limnetica by over 97% implying involvement of calmodulin in this process. A calmodulin-like protein was quantitated in cell-free extracts from O. limnetica by radioimmunoassay.     

Apparatus for fixing, staining, and rinsing of tissue cultures for fluorescent-antibody testing

A staining tray and tray-housing container have been developed to facilitate fluorescent-antibody staining of tissue cultures on cover slips, which allows fixing, staining, and rinsing with a minimum of handling. Breakage and loss of cells were negligible.     

Chemiluminescent method for determination of tetracycline, chlortetracycline, minocycline, doxycycline, and demeclocycline

A chemiluminescent method is described for the determination of tetracycline, chlortetracycline, minocycline, doxycycline, and demeclocycline. The method is based on the photon counting technique and the spline functions approximation. The simple formula S = b + Ax(2) is proposed for the observed dependency of the integrated number of countings S on the concentration x of a given antibiotic. The correlation between S and the half-life of a drug in the human body is proved.     

Methods for analysis of unbalanced,longitudinal, growth data

We describe an approach to analysis of growth that does not depend on assumptions about the underlying functional growth pattern and that allows for multiple observations arising from individual-specific, irregularly spaced data. We produce estimated growth curves for predefined subject groups by using LOWESS, a nonparametric smoothing algorithm. We describe how statistical significance of curve features may be evaluated by using the “jackknife,” a sample re-use method; this technique can be used to assess differences between subject groups. We then obtain residuals at each data point by reference to the estimated curve. Consistency of residuals is evaluated as a characteristic of individual subjects, and in the presence of individual consistency, relative size-for-age is then scored by the average residual for each individual. This allows study of relationships between relative size and other individual characteristics such as birth order, dominance rank, or age of maturation. Finally, we indicate flexibility of these methods and alternatives, propose uses related to other questions about growth, and suggest potential applications to variables other than body size. Appendices demonstrate application of the LOWESS and jackknife algorithms to the problem of testing sex differences in growth. © 1992 Wiley-Liss, Inc.     

Antiparasitic drugs for paediatrics: systematic review, formulations, pharmacokinetics, safety, efficacy and implications for control

Drug development for paediatric applications entails a number of challenges, such as the wide age spectrum covered - from birth to adolescence - and developmental changes in physiology during biological maturation that influence the efficacy and toxicity of drugs. Safe and efficacious antiparasitic drugs for children are of pivotal importance given the large proportion of burden attributable to parasitic diseases in this age group, and growing efforts to administer, as widely as possible, antiparasitic drugs to at-risk populations, such as infants and school-aged children, often without prior diagnosis. The purpose of this review is to investigate whether antiparasitic drugs have been adequately studied for use in paediatrics. We approached this issue through a systematic review using PubMed and the Cochrane Central Register of Trials covering a period of 10 years and 8 months until the end of August 2010 to identify trials that investigated efficacy, safety and pharmacokinetic (PK) parameters of antiparasitic drugs for paediatrics. Overall, 269 clinical drug trials and 17 PK studies met our inclusion criteria. Antimalarial drugs were the most commonly studied medicines (82·6%). Most trials were carried out in Africa and children aged 2-11 years were the age group most often investigated. Additionally, we critically examined available drug formulations for anthelminthics and identified a number of shortcomings that are discussed. Finally, we shed new light on current proposals to expand 'preventive chemotherapy' to preschool-aged children and emphasise that new research, including risk-benefit analyses, are needed before such a strategy can be adopted more widely.     

A Genomic Resource for the Development,Improvement, and Exploitation of Sorghum for Bioenergy

With high productivity and stress tolerance, numerous grass genera of the Andropogoneae have emerged as candidates for bioenergy production. To optimize these candidates, research examining the genetic architecture of yield, carbon partitioning, and composition is required to advance breeding objectives. Significant progress has been made developing genetic and genomic resources for Andropogoneae, and advances in comparative and computational genomics have enabled research examining the genetic basis of photosynthesis, carbon partitioning, composition, and sink strength. To provide a pivotal resource aimed at developing a comparative understanding of key bioenergy traits in the Andropogoneae, we have established and characterized an association panel of 390 racially, geographically, and phenotypically diverse Sorghum bicolor accessions with 232,303 genetic markers. Sorghum bicolor was selected because of its genomic simplicity, phenotypic diversity, significant genomic tools, and its agricultural productivity and resilience. We have demonstrated the value of sorghum as a functional model for candidate gene discovery for bioenergy Andropogoneae by performing genome-wide association analysis for two contrasting phenotypes representing key components of structural and non-structural carbohydrates. We identified potential genes, including a cellulase enzyme and a vacuolar transporter, associated with increased non-structural carbohydrates that could lead to bioenergy sorghum improvement. Although our analysis identified genes with potentially clear functions, other candidates did not have assigned functions, suggesting novel molecular mechanisms for carbon partitioning traits. These results, combined with our characterization of phenotypic and genetic diversity and the public accessibility of each accession and genomic data, demonstrate the value of this resource and provide a foundation for future improvement of sorghum and related grasses for bioenergy production.     

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips

Mass spectrometry (MS)-based proteomics measures peptides derived from proteins by proteolytic cleavage. Before performing the analysis by matrix-assisted laser desorption/ionization-tandem mass spectrometry (MALDI-MS/MS), nanoelectrospray-MS/MS (NanoES-MS/MS) or liquid chromatography-MS/MS (LC-MS/MS), the peptide mixtures need to be cleaned, concentrated and often selectively enriched or pre-fractionated, for which we employ simple, self-made and extremely economical stop-and-go-extraction tips (StageTips). StageTips are ordinary pipette tips containing very small disks made of beads with reversed phase, cation-exchange or anion-exchange surfaces embedded in a Teflon mesh. The fixed nature of the beads allows flexible combination of disks with different surfaces to obtain multi-functional tips. Disks containing different surface functionalities and loose beads such as titania and zirconia for phosphopeptide enrichment can be combined. Incorporation into an automated workflow has also been demonstrated. Desalting and concentration takes approximately 5 min while fractionation or enrichment takes approximately 30 min.     

Nanoemulsion for Solubilization,Stabilization, and In Vitro Release of Pterostilbene for Oral Delivery

Pterostilbene, being extracted from many plants, has significant biological activities in preventing cancer, diabetes, and cardiovascular diseases so as to have great potential applications in pharmaceutical fields. But the poor solubility and stability of pterostilbene strictly restrained its applications. As a good protection and oral delivery system, an optimal nanoemulsion for pterostilbene was developed by using low-energy emulsification method. Systematic pseudo-ternary phase diagrams have been studied in optimization of nanoemulsion formulations. The prepared pterostilbene nanoemulsion was characterized by transmission electron microscope, Fourier transform Raman spectrum, and laser droplet size analyzer. Nanoemulsion droplets are circular with smooth margin, and the mean size is 55.8 ± 10.5 nm. The results illustrated that the nanoemulsion as oral delivery system dramatically improved the stability and solubility of pterostilbene, and in vitro release of pterostilbene was significantly improved (96.5% in pH 3.6 buffer; 13.2% in pH 7.4 buffer) in comparison to the pterostilbene suspension (lower than 21.4% in pH 3.6 buffer; 2.6% in pH 7.4 buffer).KEY WORDS: 3,5-dimethoxyl-4′-hydroxystilbene, nanoemulsion, pseudo-ternary phase diagram, pterostilbene, release study     

Disturbance, coexistence, history, and competition for space

A simple model to elucidate the effect of disturbance on a large number of competitors that compete for space and exhibit a competitive hierarchy is developed. Conditions are derived that determine presence of species, and diversity is calculated as a function of percentage cover. The model is compared to data from coral reefs collected by J. W. Porter (1974, Science 186, 543–545). Using parameter values in the model that allow a fit to Porter's data, the response of an individual species to changes in disturbance becomes quite complex, depending on the position (odd or even) of the species in the competitive hierarchy. For these same parameter values, the system is interactive: the existence of a particular species may effect the presence of another. Different parameter values would lead to a noninteractive system.     

Computational methods for prediction of T-cell epitopes--a framework for modelling, testing, and applications

Computational models complement laboratory experimentation for efficient identification of MHC-binding peptides and T-cell epitopes. Methods for prediction of MHC-binding peptides include binding motifs, quantitative matrices, artificial neural networks, hidden Markov models, and molecular modelling. Models derived by these methods have been successfully used for prediction of T-cell epitopes in cancer, autoimmunity, infectious disease, and allergy. For maximum benefit, the use of computer models must be treated as experiments analogous to standard laboratory procedures and performed according to strict standards. This requires careful selection of data for model building, and adequate testing and validation. A range of web-based databases and MHC-binding prediction programs are available. Although some available prediction programs for particular MHC alleles have reasonable accuracy, there is no guarantee that all models produce good quality predictions. In this article, we present and discuss a framework for modelling, testing, and applications of computational methods used in predictions of T-cell epitopes.