What Can the Kinetics of Amyloid Fibril Formation Tell about Off-pathway Aggregation?

Some of the most prevalent neurodegenerative diseases are characterized by the accumulation of amyloid fibrils in organs and tissues. Although the pathogenic role of these fibrils has not been completely established, increasing evidence suggests off-pathway aggregation as a source of toxic/detoxicating deposits that still remains to be targeted. The present work is a step toward the development of off-pathway modulators using the same amyloid-specific dyes as those conventionally employed to screen amyloid inhibitors. We identified a series of kinetic signatures revealing the quantitative importance of off-pathway aggregation relative to amyloid fibrillization; these include non-linear semilog plots of amyloid progress curves, highly variable end point signals, and half-life coordinates weakly influenced by concentration. Molecules that attenuate/intensify the magnitude of these signals are considered promising off-pathway inhibitors/promoters. An illustrative example shows that amyloid deposits of lysozyme are only the tip of an iceberg hiding a crowd of insoluble aggregates. Thoroughly validated using advanced microscopy techniques and complementary measurements of dynamic light scattering, CD, and soluble protein depletion, the new analytical tools are compatible with the high-throughput methods currently employed in drug discovery.     

Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations

The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter, analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin. We investigated biogeographical variation in highly recombining genes to determine the extent of clustering between genomes from geographically distinct Campylobacter populations. Whole‐genome sequences from 294 Campylobacter isolates from North America and the UK were analysed. Isolates from within the same country shared more recently recombined DNA than isolates from different countries. Using 15 UK/American closely matched pairs of isolates that shared ancestors, we identify regions that have frequently and recently recombined to test their correlation with geographical origin. The seven genes that demonstrated the greatest clustering by geography were used in an attribution model to infer geographical origin which was tested using a further 383 UK clinical isolates to detect signatures of recent foreign travel. Patient records indicated that in 46 cases, travel abroad had occurred <2 weeks prior to sampling, and genomic analysis identified that 34 (74%) of these isolates were of a non‐UK origin. Identification of biogeographical markers in Campylobacter genomes will contribute to improved source attribution of clinical Campylobacter infection and inform intervention strategies to reduce campylobacteriosis.     

Comparative genomic assessment of Multi-Locus Sequence Typing: rapid accumulation of genomic heterogeneity among clonal isolates of <Emphasis Type="Italic">Campylobacter jejuni</Emphasis>

Background  

Multi-Locus Sequence Typing (MLST) has emerged as a leading molecular typing method owing to its high ability to discriminate among bacterial isolates, the relative ease with which data acquisition and analysis can be standardized, and the high portability of the resulting sequence data. While MLST has been successfully applied to the study of the population structure for a number of different bacterial species, it has also provided compelling evidence for high rates of recombination in some species. We have analyzed a set of Campylobacter jejuni strains using MLST and Comparative Genomic Hybridization (CGH) on a full-genome microarray in order to determine whether recombination and high levels of genomic mosaicism adversely affect the inference of strain relationships based on the analysis of a restricted number of genetic loci.     

Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions

Background  

The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq.     

Resultados de la endarterectomía carotídea en pacientes ancianos

Introduction

Forty-five per cent of stoke patients have a surgically accessible stenosis. The objective of our study is to describe the response to carotid endarterectomy (EA) in patients of advanced age compared to younger ones.

Material and method

Retrospective evaluation of the clinical history of all patients who underwent an endarterectomy in a tertiary hospital between January 1995 and December 2006. The patients were grouped into those 75 years or older and those less than this age. The incidence of peri-operative complications in the first month after surgery, and the long-term mortality was evaluated using a survival analysis.

Results

Data were collected on 147 EA in 134 patients of 75 years or more, and on 201 EA in 177 patients less than 75 years-old. The incidence of peri-operative complications was similar in both groups, with a mortality of 2% in the older age group and a stroke incidence of 2.6% (half transient ischaemic accidents). The older patients had a mean follow-up of 4.1 years, with a survival of 86% at one year and 54% at 5 years and with the main cause of death being heart disease.

Conclusions

Carotid EA is a safe and effective technique for the treatment of extracranial carotid stenosis in the elderly, having the same peri-operative morbidity and mortality as younger ones. Age must not affect our therapeutic attitude, although an exhaustive cardiology study must be made in the elderly prior to the operation.     

Scalable PGAS collective operations in NUMA clusters

The increasing number of cores per processor is turning manycore-based systems in pervasive. This involves dealing with multiple levels of memory in non uniform memory access (NUMA) systems and processor cores hierarchies, accessible via complex interconnects in order to dispatch the increasing amount of data required by the processing elements. The key for efficient and scalable provision of data is the use of collective communication operations that minimize the impact of bottlenecks. Leveraging one sided communications becomes more important in these systems, to avoid unnecessary synchronization between pairs of processes in collective operations implemented in terms of two sided point to point functions. This work proposes a series of algorithms that provide a good performance and scalability in collective operations, based on the use of hierarchical trees, overlapping one-sided communications, message pipelining and the available NUMA binding features. An implementation has been developed for Unified Parallel C, a Partitioned Global Address Space language, which presents a shared memory view across the nodes for programmability, while keeping private memory regions for performance. The performance evaluation of the proposed implementation, conducted on five representative systems (JuRoPA, JUDGE, Finis Terrae, SVG and Superdome), has shown generally good performance and scalability, even outperforming MPI in some cases, which confirms the suitability of the developed algorithms for manycore architectures.     

Effect of somatostatin on small intestine enzyme activities in rat and chick

The influence of somatostatin injection on intestinal disaccharidase and alkaline phosphatase activity in rat and chick was investigated. Disaccharidase and alkaline phosphatase activities of rat and chick homogenates were not modified. In rat the activities of mucosal brush-border maltase and sucrase were significantly increased. In chick brush-border a significant increase of duodenal mucosal activity and duodenal and jejunal sucrase activity is observed.     

Changes in enzymatic activity of small intestine and kidney of rats by a methionine deficient diet

The effect of methionine dietary deficiency on food intake, weight gain, liver and kidney weight, feed conversion rate, protein efficiency ratio, maltase and leucineaminopeptidase (LAPase) activities of the intestinal mucosa as well as renal LAPase activity was studied. Three groups of female Wistar rats, weighing between 40-60 g, were fed for 25 days on either Diet A (casein supplemented with 0.6% DL-methionine), Diet B (amino acid mixture simulating casein also supplemented with 0.6% methionine) or Diet C (amino acid mixture with 0.67% methionine deficiency with respect to Diet A). The results show no significant differences in either growth or enzymatic activity between the rats fed on Diet A and those on Diet B. The animals fed on Diet C show an increase in intestinal (P less than 0.01, vs Diet B) and renal (P less than 0.005, vs Diet A) LAPase activity, although intestinal maltase activity remained unchanged. Food intake, weight gain, organ weight and nutritional parameters obtained in rats fed on Diet C showed no statistically significant changes, with the exception of kidney weight which decreased (P less than 0.005) when compared to those fed on Diet B.