Structural requirements for efficient prion protein conversion: Cofactors may promote a conversion-competent structure for PrPC

To understand why cross-species infection of prion disease often results in inefficient transmission and reduced protein conversion, most research has focused on defining the effect of variations in PrP primary structures, including sequence compatibility of substrate and seed. By contrast, little research has been aimed at investigating structural differences between different variants of PrP^C and secondary structural requirements for efficient conversion. This is despite a clear role for molecular chaperones in formation of prions in non-mammalian systems, indicating the importance of secondary/tertiary structure during the conversion process. Recent data from our laboratory on the cellular location of disease-specific prion cofactors supports the critical role of specific secondary structural motifs and the stability of these motifs in determining the efficiency of disease-specific prion protein conversion. In this paper we summarize our recent results and build on the hypothesis previously suggested by Wuthrich and colleagues, that stability of certain regions of the prion protein is crucial for protein conversion to abnormal isoforms in vivo. It is suggested that one role for molecular cofactors in the conversion process is to stabilize PrP^C structure in a form that is amenable for conversion to PrP^Sc.Key words: cofactor, structure, cell-free conversion assay, fibrillization, stability, loop region     

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability

Background  

Large discrepancies in signature composition and outcome concordance have been observed between different microarray breast cancer expression profiling studies. This is often ascribed to differences in array platform as well as biological variability. We conjecture that other reasons for the observed discrepancies are the measurement error associated with each feature and the choice of preprocessing method. Microarray data are known to be subject to technical variation and the confidence intervals around individual point estimates of expression levels can be wide. Furthermore, the estimated expression values also vary depending on the selected preprocessing scheme. In microarray breast cancer classification studies, however, these two forms of feature variability are almost always ignored and hence their exact role is unclear.     

Comparative Genomic Characterization of Francisella tularensis Strains Belonging to Low and High Virulence Subspecies

Tularemia is a geographically widespread, severely debilitating, and occasionally lethal disease in humans. It is caused by infection by a gram-negative bacterium, Francisella tularensis. In order to better understand its potency as an etiological agent as well as its potential as a biological weapon, we have completed draft assemblies and report the first complete genomic characterization of five strains belonging to the following different Francisella subspecies (subsp.): the F. tularensis subsp. tularensis FSC033, F. tularensis subsp. holarctica FSC257 and FSC022, and F. tularensis subsp. novicida GA99-3548 and GA99-3549 strains. Here, we report the sequencing of these strains and comparative genomic analysis with recently available public Francisella sequences, including the rare F. tularensis subsp. mediasiatica FSC147 strain isolate from the Central Asian Region. We report evidence for the occurrence of large-scale rearrangement events in strains of the holarctica subspecies, supporting previous proposals that further phylogenetic subdivisions of the Type B clade are likely. We also find a significant enrichment of disrupted or absent ORFs proximal to predicted breakpoints in the FSC022 strain, including a genetic component of the Type I restriction-modification defense system. Many of the pseudogenes identified are also disrupted in the closely related rarely human pathogenic F. tularensis subsp. mediasiatica FSC147 strain, including modulator of drug activity B (mdaB) (FTT0961), which encodes a known NADPH quinone reductase involved in oxidative stress resistance. We have also identified genes exhibiting sequence similarity to effectors of the Type III (T3SS) and components of the Type IV secretion systems (T4SS). One of the genes, msrA2 (FTT1797c), is disrupted in F. tularensis subsp. mediasiatica and has recently been shown to mediate bacterial pathogen survival in host organisms. Our findings suggest that in addition to the duplication of the Francisella Pathogenicity Island, and acquisition of individual loci, adaptation by gene loss in the more recently emerged tularensis, holarctica, and mediasiatica subspecies occurred and was distinct from evolutionary events that differentiated these subspecies, and the novicida subspecies, from a common ancestor. Our findings are applicable to future studies focused on variations in Francisella subspecies pathogenesis, and of broader interest to studies of genomic pathoadaptation in bacteria.     

Identification of Francisella tularensis in natural water samples by PCR

Abstract Francisella tularensis , the causative agent of the epizootic disease tularemia in mammals, can be isolated from mud and water. To study the spread and persistence of Francisella tularensis in water, different strategies for pre-treatment of natural water samples prior to identification of the bacterium by polymerase chain reaction (PCR) were evaluated. A method for handling of samples taken from natural waters was developed. Applied on natural water samples amended with F. tularensis , the method rendered identification by PCR reproducible and it resulted in an amplified Francisella -specific product in all samples from natural waters tested. In addition, by employing primers targeting conserved regions of the 16S rDNA the presence of bacteria was demonstrated in all samples investigated. The results presented will, in combination with other techniques that allow identification, improve studies on the epizootiology and epidemiology of the genus Francisella .     

Maps of the Sri Lanka malaria situation preceding the tsunami and key aspects to be considered in the emergency phase and beyond

In Vietnam, a large proportion of all malaria cases and deaths occurs in the central mountainous and forested part of the country. Indeed, forest malaria, despite intensive control activities, is still a major problem which raises several questions about its dynamics. A large-scale malaria morbidity survey to measure malaria endemicity and identify important risk factors was carried out in 43 villages situated in a forested area of Ninh Thuan province, south central Vietnam. Four thousand three hundred and six randomly selected individuals, aged 10–60 years, participated in the survey. Rag Lays (86%), traditionally living in the forest and practising "slash and burn" cultivation represented the most common ethnic group. The overall parasite rate was 13.3% (range [0–42.3] while Plasmodium falciparum seroprevalence was 25.5% (range [2.1–75.6]). Mapping of these two variables showed a patchy distribution, suggesting that risk factors other than remoteness and forest proximity modulated the human-vector interactions. This was confirmed by the results of the multivariate-adjusted analysis, showing that forest work was a significant risk factor for malaria infection, further increased by staying in the forest overnight (OR= 2.86; 95%CI [1.62; 5.07]). Rag Lays had a higher risk of malaria infection, which inversely related to education level and socio-economic status. Women were less at risk than men (OR = 0.71; 95%CI [0.59; 0.86]), a possible consequence of different behaviour. This study confirms that malaria endemicity is still relatively high in this area and that the dynamics of transmission is constantly modulated by the behaviour of both humans and vectors. A well-targeted intervention reducing the "vector/forest worker" interaction, based on long-lasting insecticidal material, could be appropriate in this environment.     

An ITS region phylogeny of Siderastrea (Cnidaria: Anthozoa): is S. glynni endangered or introduced?

The genus Siderastrea contains only five extant species, including Siderastrea glynni, which is one of the few recognized species of endangered stony coral. Cloned sequences of the internal transcribed spacer (ITS) region had low levels of intragenomic nucleotide diversity, and few alignment ambiguities, which allowed for the first species-level phylogenetic analysis of the genus. Results indicated an unexpected deep divergence between the Western-Pacific and Atlantic species. ITS region sequences indicated that S. glynni is not derived from S. savignyana, as previously thought. Instead, S. glynni shared identical sequence types with S. siderea in the Caribbean. Given a range of previously published evolutionary rates for the ITS region, it is unlikely that S. glynni represents the remnants of a population that was divided by the closure of the Central American Seaway (approximately 3–3.8 MYA). It is more likely that S. glynni originated by a breach of the Isthmus (approximately 2 MYA), or a contemporary introduction by ship.     

Reproduction of northern spotted owls: The role of local weather and regional climate

We examined associations between annual reproduction and climate for 6 populations of individually marked northern spotted owls (Strix occidentalis caurina) in Washington and Oregon. We used an information-theoretical approach and mixed models to evaluate statistical models representing a priori hypotheses about the effects of weather and climate on reproduction. Reproduction was higher for adult than subadult owls and declined as the proportion of spotted owl territories with barred owl (Strix varia) detections increased. Similar to other spotted owl studies, we found that reproduction was negatively associated with cold, wet winters and nesting seasons at 3 of 6 study areas. In addition, we identified new relationships between reproduction, annual precipitation, storms, and regional climate cycles. For 3 of 6 areas, we found a quadratic relation between precipitation (rain and snow) and reproduction, with the number of young fledged per pair per year declining as precipitation in the previous year deviated from average levels. A meta-analysis conducted across all 6 areas indicated that reproduction at the regional level had a quadratic association with total winter snowfall in the preceding winter and was positively related to temperatures during the previous summer and fall. The amount of annual variation in reproduction accounted for by weather and climate varied widely across the 6 areas (4–79%), whereas variation in weather and climate across owl territories accounted for little of the spatial variation in reproduction (0–4%). Our results suggest that across the range of the species climate factors affecting prey abundance may have a greater effect on reproduction than direct effects of weather on nestlings. © 2011 The Wildlife Society.