Simple synthesis of 32P-labelled inositol hexakisphosphates for study of phosphate transformations

In many soils inositol hexakisphosphate in its various forms is as abundant as inorganic phosphate. The organismal and geochemical processes that exchange phosphate between inositol hexakisphosphate and other pools of soil phosphate are poorly defined, as are the organisms and enzymes involved. We rationalized that simple enzymic synthesis of inositol hexakisphosphate labeled with 32P would greatly enable study of transformation of soil inositol phosphates when combined with robust HPLC separations of different inositol phosphates

Seepage forces, important factors in the formation of horizontal hydraulic fractures and bedding-parallel fibrous veins ('beef' and 'cone-in-cone')

International audienceBedding-parallel fibrous veins ('beef' and 'cone-in-cone') are common to a number of sedimentary basins, especially those containing black shale. The type locality is SW England. The commonest mineral in the fibres is calcite. The fibres indicate vertical opening, against the force of gravity. In the past, this has been attributed to fluid overpressure. However, a simple analysis, based on Von Terzaghi's concepts, leads to the conclusion that, for the fractures to be horizontal, either the rock must be anisotropic, or it must be subject to horizontal compression. By means of a more complete analysis, supported by physical models, we show that horizontal fractures are to be expected, even if the rock is isotropic and there are no tectonic stresses. Upward fluid flow, in response to an overpressure gradient, imparts seepage forces to all elements of the solid framework. The seepage forces counteract the weight of the rock, and even surpass it, generating a tensile effective stress. The process may lead, either to tensile hydraulic fracturing, or to dilatant shear failure. We suggest that these two failure modes, and the availability of suitable solutes, explain the frequent occurrence of 'beef' and 'cone-in-cone' respectively

A finite strain fibre-reinforced viscoelasto-viscoplastic model of plant cell wall growth

A finite strain fibre-reinforced viscoelasto-viscoplastic model implemented in a finite element (FE) analysis is presented to study the expansive growth of plant cell walls. Three components of the deformation of growing cell wall, i.e. elasticity, viscoelasticity and viscoplasticity-like growth, are modelled within a consistent framework aiming to present an integrative growth model. The two aspects of growth—turgor-driven creep and new material deposition—and the interplay between them are considered by presenting a yield function, flow rule and hardening law. A fibre-reinforcement formulation is used to account for the role of cellulose microfibrils in the anisotropic growth. Mechanisms in in vivo growth are taken into account to represent the corresponding biologycontrolled behaviour of a cell wall. A viscoelastic formulation is proposed to capture the viscoelastic response in the cell wall. The proposed constitutive model provides a unique framework for modelling both the in vivo growth of cell wall dominated by viscoplasticity-like behaviour and in vitro deformation dominated by elastic or viscoelastic responses. A numerical scheme is devised, and FE case studies are reported and compared with experimental data

Reasons for and consequences of missed appointments in general practice in the UK: questionnaire survey and prospective review of medical records

Background Missed appointments are a common occurrence in primary care in the UK, yet little is known about the reasons for them, or the consequences of missing an appointment. This paper aims to determine the reasons for missed appointments and whether patients who miss an appointment subsequently consult their general practitioner (GP). Secondary aims are to compare psychological morbidity, and the previous appointments with GPs between subjects and a comparison group. Methods Postal questionnaire survey and prospective medical notes review of adult patients missing an appointment and the comparison group who attended appointments over a three week period in seven general practices in West Yorkshire. Results Of the 386 who missed appointments 122 (32%) responded. Of the 386 in the comparison group 223 (58%) responded, resulting in 23 case-control matched pairs with complete data collection. Over 40% of individuals who missed an appointment and participated said that they forgot the appointment and a quarter said that they tried very hard to cancel the appointment or that it was at an inconvenient time. A fifth reported family commitments or being too ill to attend. Over 90% of the patients who missed an appointment subsequently consulted within three months and of these nearly 60% consulted for the stated problem that was going to be presented in the missed consultation. The odds of missing an appointment decreased with increasing age and were greater among those who had missed at least one appointment in the previous 12 months. However, estimates for comparisons between those who missed appointments and the comparison group were imprecise due to the low response rate. Conclusion Patients who miss appointments tend to cite practice factors and their own forgetfulness as the main reasons for doing so, and most attend within three months of a missed appointment. This study highlights a number of implications for future research. More work needs to be done to engage people who miss appointments into research in a meaningful way

Ability of SP12 mutant of S. typhi to effectively induce antibody responses to the mucosal antigen enterotoxigenic E. coli heat labile toxin B subunit after oral delivery to humans

We have evaluated an oral vaccine based on an Salmonella enteric serovar typhi (S. typhi) Ty2 derivative TSB7 harboring deletion mutations in ssaV (SPI-2) and aroC together with a chromosomally integrated copy of eltB encoding the B subunit of enterotoxigenic Escherichia coli heat labile toxin (LT-B) in volunteers. Two oral doses of 108 or 109 CFU were administered to two groups of volunteers and both doses were well tolerated, with no vaccinemia, and only transient stool shedding. Immune responses to LT-B and S. typhi lipopolysaccharide were demonstrated in 67 and 97% of subjects, respectively, without evidence of anti-carrier immunity preventing boosting of LT-B responses in many cases. Further development of this salmonella-based (spi-VEC) system for oral delivery of heterologous antigens appears warranted

Evaluation of single and double-locus real-time PCR assays for methicillin-resistant Staphylococcus aureus (MRSA) surveillance

<p>Abstract</p> <p>Background</p> <p>Methicillin-resistant <it>Staphylococcus aureus </it>(MRSA) is a human pathogen, representing an infection control challenge. Conventional MRSA screening takes up to three days, therefore development of rapid detection is essential. Real time-PCR (rt-PCR) is the fastest method fulfilling this task. All currently published or commercially available rt-PCR MRSA assays relay on single or double-locus detection. Double-locus assays are based on simultaneous detection of <it>mecA </it>gene and a <it>S. aureus</it>-specific gene. Such assays cannot be applied on clinical samples, which often contain both coagulase-negative staphylococci (CoNS) and <it>S. aureus</it>, either of which can carry <it>mecA</it>. Single-locus assays are based on detection of the staphylococcal cassette chromosome <it>mec </it>(SCC<it>mec</it>) element and the <it>S. aureus</it>-specific <it>orfX </it>gene, assuming that it is equivalent to <it>mecA </it>detection.</p> <p>Findings</p> <p>Parallel evaluation of several published single and double-locus rt-PCR MRSA assays of 150 pure culture strains, followed by analysis of 460 swab-derived clinical samples which included standard identification, susceptibility testing, followed by PCR detection of staphylococcal suspected isolates and in-PCR mixed bacterial populations analysis indicated the following findings.</p> <p>Pure cultures analysis indicated that one of the single-locus assay had very high prevalence of false positives (Positive predictive value = 77.8%) and was excluded from further analysis. Analysis of 460 swab-derived samples indicated that the second single-locus assay misidentified 16 out of 219 MRSA's and 13 out of 90 methicillin-sensitive <it>S</it>. <it>aureus</it>'s (MSSA) were misidentified as MRSA's. The double-locus detection assay misidentified 55 out of 90 MSSA's. 46 MSSA containing samples were misidentified as MRSA and 9 as other than <it>S. aureus </it>ending with low positive predicted value (<85%) and very low specificity (<62%).</p> <p>Conclusion</p> <p>The results indicate that high prevalence of false-positive and false-negative reactions occurs in such assays.</p

Evaluation of machine-learning methods for ligand-based virtual screening

Machine-learning methods can be used for virtual screening by analysing the structural characteristics of molecules of known (in)activity, and we here discuss the use of kernel discrimination and naive Bayesian classifier (NBC) methods for this purpose. We report a kernel method that allows the processing of molecules represented by binary, integer and real-valued descriptors, and show that it is little different in screening performance from a previously described kernel that had been developed specifically for the analysis of binary fingerprint representations of molecular structure. We then evaluate the performance of an NBC when the training-set contains only a very few active molecules. In such cases, a simpler approach based on group fusion would appear to provide superior screening performance, especially when structurally heterogeneous datasets are to be processed

Immunolocalization of cell wall polymers in grapevine (Vitis vinifera) internodes under nitrogen, phosphorus or sulfur deficiency

Abstract The impact on cell wall (CW) of the deficiency in nitrogen (–N), phosphorus (–P) or sulphur (–S), known to impair essential metabolic pathways, was investigated in the economically important fruit species Vitis vinifera L. Using cuttings as an experimental model a reduction in total internode number and altered xylem shape was observed. Under –N an increased internode length was also seen. CW composition, visualised after staining with calcofluor white, Toluidine blue and ruthenium red, showed decreased cellulose in all stresses and increased pectin content in recently formed internodes under –N compared to the control. Using CW-epitope specific monoclonal antibodies (mAbs), lower amounts of extensins incorporated in the wall were also observed under –N and –P conditions. Conversely, increased pectins with a low degree of methyl-esterification and richer in long linear 1,5-arabinan rhamnogalacturonan-I (RG-I) side chains were observed under –N and –P in mature internodes which, in the former condition, were able to form dimeric association through calcium ions. –N was the only condition in which 1,5-arabinan branched RG- content was not altered, as –P and –S older internodes showed, respectively, lower and higher amounts of this polymer. Higher xyloglucan content in older internodes was also observed under –N. The results suggest that impairments of specific CW components led to changes in the deposition of other polymers to promote stiffening of the CW. The unchanged extensin amount observed under –S may contribute to attenuating the effects on the CW integrity caused by this stress. Our work showed that, in organized V. vinifera tissues, modifications in a given CW component can be compensated by synthesis of different polymers and/or alternative linking between polymers. The results also pinpoint different strategies at the CW level to overcome mineral stress depending on how essential they are to cell growth and plant development