High Molecular Weight Typing with MALDI-TOF MS - A Novel Method for Rapid Typing of Clostridium difficile

Clostridium difficile strains were typed by a newly developed MALDI-TOF method, high molecular weight typing, and compared to PCR ribotyping. Among 500 isolates representing 59 PCR ribotypes a total of 35 high molecular weight types could be resolved. Although less discriminatory than PCR ribotyping, the method is extremely fast and simple, and supports for cost-effective screening of isolates during outbreak situations.     

Repeated Sampling to Determine the Precision of Estimating Nematode Population Densities

The first phase of this study involved repeated samplings of five fields using composite samples of 10, 20, 40, and 80 soil cores, to determine the precision of nematode assays. The second phase focused on randomly selecting two and four 2-ha subunits (data on Meloidogyne spp.) of 24 fields ranging from 6 to 40 ha and computing the precision of estimated means for these numbers ofsubunits versus the general field mean (based on all 2-ha subunits). Average numbers of nematodes from most samples containing Meloidogyne spp., Heterodera glycines, Helicotylenchus dihystera, Scutellonema brachyurum, and (or) Hoplolaimus galeatus were within 50% of the overall means. Coefficient of variation (CV) values were generally lower for 40 cores than for 10, 20, and 80 cores per sample. When data for all nematodes and fields were combined, this value was lowest for 40 and 80 cores. The CV values were higher for Meloidogyne spp. than for H. glycines. Means of two samplings increased the probability of obtaining numbers nearer the mean for that field than numbers from a single composite sample. For the second phase, population estimates of Meloidogyne spp. based on four 2-ha subunits generally were closer to field means than were those for two subunits. Sampling precision with these subunits diminished greatly in large fields with variable soils and (or) mixed cropping histories. Either two or four subunits gave population estimates within 3-20% of the field mean in most instances. The mean man hours required for sampling ca. 2-ha parcels of 4-20-ha fields was 0.54 hours.     

DSMM: a Database of Simulated Molecular Motions

We describe a Database of Simulated Molecular Motions (DSMM). This database is designed to serve as a single searchable site for locating movies and animations from simulations of biomolecules. DSMM is accessible via a webserver at: http://projects.villa-bosch.de/mcm/database/dsmm.     

Simulated Sampling Strategies for Nematodes Distributed According to a Negative Binomial Model

A FORTRAN computer program was developed to simulate nematode soil sampling strategies consisting of various numbers of samples per field, with each sample consisting of various numbers of soil cores. The program assumes that the nematode species involved fit a negative binomial distribution. Required input data are estimates of the mean and k values, the number of samples per field and cores per sample in the strategy to be investigated, and the number of times the simulation is to be replicated. Output consists of simulated values of the relative deviation from the mean and standard error to mean ratio, both averaged over all replications. The program was used to compare 150 simulated sampling strategies for Meloidogyne incognita, involving all combinations of two mean values (2.0 and 10.0 la.rvae/10 cm³ soil), three k values (1.35, 0.544, and 0.294), five different numbers of samples per field (1, 2, 4. 10, 20), and five different numbers of cores per sample (1, 2, 4, 10, 20). Simulations resulting from different mean values were similar, but best results were obtained with higher k values and 20 cores per sample. Relatively few 20-core samples were needed to obtain average deviations from the mean of 20-25%.     

Molecular Characterization of Photomixotrophic Tobacco Cells Resistant to Protoporphyrinogen Oxidase-Inhibiting Herbicides

Peroxidizing herbicides inhibit protoporphyrinogen oxidase (Protox), the last enzyme of the common branch of the chlorophyll- and heme-synthesis pathways. There are two isoenzymes of Protox, one of which is located in the plastid and the other in the mitochondria. Sequence analysis of the cloned Protox cDNAs showed that the deduced amino acid sequences of plastidial and mitochondrial Protox in wild-type cells and in herbicide-resistant YZI-1S cells are the same. The level of plastidial Protox mRNA was the same in both wild-type and YZI-1S cells, whereas the level of mitochondrial Protox mRNA YZI-1S cells was up to 10 times the level of wild-type cells. Wild-type cells were observed by fluorescence microscopy to emit strong autofluorescence from chlorophyll. Only a weak fluorescence signal was observed from chlorophyll in YZI-1S cells grown in the Protox inhibitor N-(4-chloro-2-fluoro-5-propagyloxy)-phenyl-3,4,5,6-tetrahydrophthalimide. Staining with DiOC6 showed no visible difference in the number or strength of fluorescence between wild-type and YZI-1S mitochondria. Electron micrography of YZI-1S cells showed that, in contrast to wild-type cells, the chloroplasts of YZI-1S cells grown in the presence of N-(4-chloro-2-fluoro-5-propagyloxy)-phenyl-3,4,5,6-tetrahydrophthalimide exhibited no grana stacking. These results suggest that the herbicide resistance of YZI-1S cells is due to the overproduction of mitochondrial Protox.     

Molecular Dynamics Simulation of Collective Motions in Binary Liquids

Collective dynamic properties of different kind of binary liquid mixtures have been investigated by molecular dynamics simulation. The study includes both the longitudinal and the transverse current spectra in simple liquid alloys, 1:1 molten salts and liquid binary mixtures of neutral particles with an ionic-like structure. These systems were chosen as representative of binary liquids with different static structures in order to analyse the effects of structural ordering on the mechanisms of dynamic collective properties. The effect of the mass asymmetry between the two species in the mixture has been also discussed from the results for two different mass ratios for each kind of structure. Two length scales have been considered. On the one hand, the hydrodynamic scale (low wave numbers), where the modes for the partial currents of the two species are characterised by very close frequencies. On the other hand, the molecular scale (higher wave numbers), where the characteristic frequencies for the two species show noticeable differences. Vibrational concentration current modes (optic modes) have been found in neutral mixtures though their influence is rather weak, being the collective dynamic properties of this kind of systems dominated by the mass current modes (acoustic modes). On the contrary, in mixtures of charged particles such as molten salts the contribution of the concentration (charge) currents to the collective dynamics is important and optic modes can be characterised by a well-defined frequency for a wide range of wave numbers. It has been observed that heavy particles have a more relevant role on the mass current correlations whereas light particles play a dominant role on the concentration current correlations. The overall results for the three kinds of liquid mixtures analysed in this paper show that both the longitudinal and transverse current spectra are little dependent on the static structure of the system whereas marked differences are revealed when the particles in the system are either neutral or carry an electric charge.     

Molecular Dynamics Simulation of Protein Folding with Supersecondary Structure Constraints

We integrate molecular dynamics simulation methods with a newly developed supersecondary structure prediction method and compute the structure of a protein molecule, crambin. The computed structure is similar to the crystal structure with an rms error of 3.94 Å.     

Rapid detection of multidrug-resistant Mycobacterium tuberculosis using the malachite green decolourisation assay

Early detection of drug resistance in Mycobacterium tuberculosis isolates allows for earlier and more effective treatment of patients. The aim of this study was to investigate the performance of the malachite green decolourisation assay (MGDA) in detecting isoniazid (INH) and rifampicin (RIF) resistance in M. tuberculosis clinical isolates. Fifty M. tuberculosis isolates, including 19 multidrug-resistant, eight INH-resistant and 23 INH and RIF-susceptible samples, were tested. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and agreement of the assay for INH were 92.5%, 91.3%, 92.5%, 91.3% and 92%, respectively. Similarly, the sensitivity, specificity, PPV, NPV and agreement of the assay for RIF were 94.7%, 100%, 100%, 96.8% and 98%, respectively. There was a major discrepancy in the tests of two isolates, as they were sensitive to INH by the MGDA test, but resistant by the reference method. There was a minor discrepancy in the tests of two additional isolates, as they were sensitive to INH by the reference method, but resistant by the MGDA test. The drug susceptibility test results were obtained within eight-nine days. In conclusion, the MGDA test is a reliable and accurate method for the rapid detection of INH and RIF resistance compared with the reference method and the MGDA test additionally requires less time to obtain results.     

Protein Design by Sampling an Undirected Graphical Model of Residue Constraints

This paper develops an approach for designing protein variants by sampling sequences that satisfy residue constraints encoded in an undirected probabilistic graphical model. Due to evolutionary pressures on proteins to maintain structure and function, the sequence record of a protein family contains valuable information regarding position-specific residue conservation and coupling (or covariation) constraints. Representing these constraints with a graphical model provides two key benefits for protein design: a probabilistic semantics enabling evaluation of possible sequences for consistency with the constraints, and an explicit factorization of residue dependence and independence supporting efficient exploration of the constrained sequence space. We leverage these benefits in developing two complementary MCMC algorithms for protein design: constrained shuffling mixes wild-type sequences positionwise and evaluates graphical model likelihood, while component sampling directly generates sequences by sampling clique values and propagating to other cliques. We apply our methods to design WW domains. We demonstrate that likelihood under a model of wild-type WWs is highly predictive of foldedness of new WWs. We then show both theoretical and rapid empirical convergence of our algorithms in generating high-likelihood, diverse new sequences. We further show that these sequences capture the original sequence constraints, yielding a model as predictive of foldedness as the original one.     

Systematic Review and Consensus Guidelines for Environmental Sampling of Burkholderia pseudomallei

Background

Burkholderia pseudomallei, a Tier 1 Select Agent and the cause of melioidosis, is a Gram-negative bacillus present in the environment in many tropical countries. Defining the global pattern of B. pseudomallei distribution underpins efforts to prevent infection, and is dependent upon robust environmental sampling methodology. Our objective was to review the literature on the detection of environmental B. pseudomallei, update the risk map for melioidosis, and propose international consensus guidelines for soil sampling.

Methods/Principal Findings

An international working party (Detection of Environmental Burkholderia pseudomallei Working Party (DEBWorP)) was formed during the VIth World Melioidosis Congress in 2010. PubMed (January 1912 to December 2011) was searched using the following MeSH terms: pseudomallei or melioidosis. Bibliographies were hand-searched for secondary references. The reported geographical distribution of B. pseudomallei in the environment was mapped and categorized as definite, probable, or possible. The methodology used for detecting environmental B. pseudomallei was extracted and collated. We found that global coverage was patchy, with a lack of studies in many areas where melioidosis is suspected to occur. The sampling strategies and bacterial identification methods used were highly variable, and not all were robust. We developed consensus guidelines with the goals of reducing the probability of false-negative results, and the provision of affordable and ‘low-tech’ methodology that is applicable in both developed and developing countries.

Conclusions/Significance

The proposed consensus guidelines provide the basis for the development of an accurate and comprehensive global map of environmental B. pseudomallei.     

Molecular Basis of Sulfonamide and Trimethoprim Resistance in Fish-Pathogenic Aeromonas Isolates

Sulfonamide-trimethoprim-resistant Aeromonas salmonicida and motile Aeromonas spp. from diseased fish of the GERM-Vet study carried the sul1 gene together with mostly cassette-borne trimethoprim resistance genes, including the novel gene dfrA28. The seven dfrA and dfrB genes identified were located mostly in class 1 integrons which commonly harbored other gene cassettes.     

Molecular and Enzymatic Characterization of Three Phosphoinositide-Specific Phospholipase C Isoforms from Potato

Many cellular responses to stimulation of cell-surface receptors by extracellular signals are transmitted across the plasma membrane by hydrolysis of phosphatidylinositol-4,5-bisphosphate (PIP₂), which is cleaved into diacylglycerol and inositol-1,4,5-tris-phosphate by phosphoinositide-specific phospholipase C (PI-PLC). We present structural, biochemical, and RNA expression data for three distinct PI-PLC isoforms, StPLC1, StPLC2, and StPLC3, which were cloned from a guard cell-enriched tissue preparation of potato (Solanum tuberosum) leaves. All three enzymes contain the catalytic X and Y domains, as well as C₂-like domains also present in all PI-PLCs. Analysis of the reaction products obtained from PIP₂ hydrolysis unequivocally identified these enzymes as genuine PI-PLC isoforms. Recombinant StPLCs showed an optimal PIP₂-hydrolyzing activity at 10 μm Ca²⁺ and were inhibited by Al³⁺ in equimolar amounts. In contrast to PI-PLC activity in plant plasma membranes, however, recombinant enzymes could not be activated by Mg²⁺. All three stplc genes are expressed in various tissues of potato, including leaves, flowers, tubers, and roots, and are affected by drought stress in a gene-specific manner.     

CRY2 Is Associated with Rapid Cycling in Bipolar Disorder Patients

Background

Bipolar disorder patients often display abnormalities in circadian rhythm, and they are sensitive to irregular diurnal rhythms. CRY2 participates in the core clock that generates circadian rhythms. CRY2 mRNA expression in blood mononuclear cells was recently shown to display a marked diurnal variation and to respond to total sleep deprivation in healthy human volunteers. It was also shown that bipolar patients in a depressive state had lower CRY2 mRNA levels, nonresponsive to total sleep deprivation, compared to healthy controls, and that CRY2 gene variation was associated with winter depression in both Swedish and Finnish cohorts.

Principal Findings

Four CRY2 SNPs spanning from intron 2 to downstream 3′UTR were analyzed for association to bipolar disorder type 1 (n = 497), bipolar disorder type 2 (n = 60) and bipolar disorder with the feature rapid cycling (n = 155) versus blood donors (n = 1044) in Sweden. Also, the rapid cycling cases were compared with bipolar disorder cases without rapid cycling (n = 422). The haplotype GGAC was underrepresented among rapid cycling cases versus controls and versus bipolar disorder cases without rapid cycling (OR = 0.7, P = 0.006−0.02), whereas overrepresentation among rapid cycling cases was seen for AAAC (OR = 1.3−1.4, P = 0.03−0.04) and AGGA (OR = 1.5, P = 0.05). The risk and protective CRY2 haplotypes and their effect sizes were similar to those recently suggested to be associated with winter depression in Swedes.

Conclusions

We propose that the circadian gene CRY2 is associated with rapid cycling in bipolar disorder. This is the first time a clock gene is implicated in rapid cycling, and one of few findings showing a molecular discrimination between rapid cycling and other forms of bipolar disorder.     

Rapid Induction of Ferritin in Laboratory Animals Prior to Its Isolation

Oral ingestion, by guinea pigs, of concentrated solutions of soluble hydroxy-iron(III) polymers rapidly induces a 7-fold increase of liver ferritin. Young guinea pigs imbibing 0.1 M iron for 2 weeks produced a significantly greater amount of ferritin than animals injected with an iron-dextran complex at 1.0 mmole Fe/kg body weight. Conventional methods for the isolation of tissue ferritin are more efficient and provide higher yields from such iron-replete animals. Dose/response curves are presented for the mouse to illustrate the kinetics of liver iron assimilation at various levels of oral iron supplementation.