Anti-apoptotic effects of arachidonic acid and prostaglandin E2 in pancreatic beta-cells.

BACKGROUND/AIMS: The polyunsaturated fatty acid arachidonic acid (AA) has been implicated in beta-cell defence mechanisms and prostaglandin (PG) products of cyclooxygenase (COX) 2 action confer resistance to alloxan-induced apoptosis in insulin-secreting RIN cells. We have now investigated the anti-apoptotic effects of AA and its metabolite, PGE(2), in the MIN6 mouse insulin-secreting beta-cell line and mouse islets. METHODS: Apoptosis was determined in MIN6 beta-cell and mouse islet extracts by measurement of capase-3 activity, and COX2 mRNA levels were quantified by real-time RT-PCR. RESULTS: Exposure of MIN6 cells to AA (3.1-12.5 microM) caused concentration-dependent reductions in apoptosis, and similar results were obtained when endogenous AA levels were elevated in cytosolic phospholipase A(2)-overexpressing MIN6 cells. 25mM glucose caused both a significant up-regulation of MIN6 cell COX2 mRNA levels and a decrease in apoptosis. Inhibition of MIN6 cell COX2 activity with a selective inhibitor, NS-398 (10-100 microM), increased apoptosis and exogenous PGE(2) (0.2-5 microM) reduced NS-398-induced apoptosis in a concentration-dependent manner. The protective effects of AA and PGE(2) were also observed in primary mouse islets. CONCLUSION: These data show that AA and its COX2-generated metabolite, PGE(2), can protect beta-cells from apoptosis.     

Sclerosperma fossils from the late Oligocene of Chilga,north-western Ethiopia

The palm family, Arecaceae, is notoriously depauperate in Africa today, and its evolutionary, paleobiogeographic, and extinction history there are not well documented by fossils. In this article we report the pollen of two new extinct species of the small genus, Sclerosperma (Arecoideae), from a late Oligocene (27–28 Ma) stratum exposed along the Guang River in Chilga Wereda of north-western Ethiopia. The pollen are triporate, and the two taxa can be distinguished from each other and from modern species using a combination of light and scanning electron microscopy, which reveals variations in the finer details of their reticulate to perforate exine sculpture. We also report a palm leaf fragment from a stratum higher in the same section that is in the Arecoideae subfamily, and most likely belongs to Sclerosperma. The implications of these discoveries for the evolutionary history of this clade of African arecoid palms is that their diversification was well underway by the middle to late Oligocene, and they were much more widespread in Africa at that time than they are now, limited to West and Central Africa. Sclerosperma exhibits ecological conservatism, as today it occurs primarily in swamps and flooded forests, and the sedimentology of the Guang River deposits at Chilga indicate a heterogeneous landscape with a high water table. The matrix containing the fossil pollen is lignite, which itself indicates standing water, and a variety of plant macrofossils from higher in the section have been interpreted as representing moist tropical forest or seasonally inundated forest communities.     

Reduced genetic diversity and low effective size in peripheral northern European catfish Silurus glanis populations

Using 10 polymorphic microsatellites and 1251 individual samples (some dating back to the early 1980s), genetic structure and effective population size in all native and introduced Swedish populations of the European wels catfish or Silurus glanis were studied. Levels of genetic variability and phylogeographic relationships were compared with data from a previous study of populations in other parts of Europe. The genetically distinct Swedish populations displayed comparably low levels of genetic variability and according to one-sample estimates based on linkage disequilibrium and sib ship-reconstruction, current local effective population sizes were lower than minimum levels recommended for short-term genetic conservation. In line with a previous suggestion of postglacial colonisation from a single refugium, all Swedish populations were assembled on a common branch in a star-shaped dendrogram together with other European populations. Two distinct subpopulations were detected in upper and lower habitats of River Emån, indicating that even minor dispersal barriers may restrict gene flow for wels in running waters. Genetic assignment of specimens encountered in the brackish Baltic Sea and in lakes where the species does not occur naturally indicated presence of long-distance sea dispersal and confirmed unauthorised translocations, respectively.     

Hsp70 regulates the doxorubicin-mediated heart failure in Hsp70-transgenic mice

The aim of this study was to investigate the potential protective effect of the Hsp70 protein in the cardiac dysfunction induced by doxorubicin (DOX) and the mechanisms of its action. For this purpose, we used both wild-type mice (F1/F1) and Hsp70-transgenic mice (Tg/Tg) overexpressing human HSP70. Both types were subjected to chronic DOX administration (3 mg/kg intraperitoneally every week for 10 weeks, with an interval from weeks 4 to 6). Primary cell cultures isolated from embryos of these mice were also studied. During DOX administration, the mortality rate as well as weight reduction were lower in Tg/Tg compared to F1/F1 mice (P < 0.05). In vivo cardiac function assessment by transthoracic echocardiography showed that the reduction in left ventricular systolic function observed after DOX administration was lower in Tg/Tg mice (P < 0.05). The study in primary embryonic cell lines showed that the apoptosis after incubation with DOX was reduced in cells overexpressing Hsp70 (Tg/Tg), while the apoptotic pathway that was activated by DOX administration involved activated protein factors such as p53, Bax, caspase-9, caspase-3, and PARP-1. In myocardial protein extracts from identical mice with DOX-induced heart failure, the particular activated apoptotic pathway was confirmed, while the presence of Hsp70 appeared to inhibit the apoptotic pathway upstream of the p53 activation. Our results, in this DOX-induced heart failure model, indicate that Hsp70 overexpression in Tg/Tg transgenic mice provides protection from myocardial damage via an Hsp70-block in p53 activation, thus reducing the subsequent apoptotic mechanism.     

Use of an electronic nose system for diagnoses of urinary tract infections

The use of volatile production patterns produced by bacterial contaminants in urine samples were examined using electronic nose technology. In two experiments 25 and 45 samples from patients were analysed for specific bacterial contaminants using agar culture techniques and the major UTI bacterial species identified. These samples were also analysed by incubation in a volatile generation test tube system for 4-5 h. The volatile production patterns were then analysed using an electronic nose system with 14 conducting polymer sensors. In the first experiment analysis of the data using a neural network (NN) enabled identification of all but one of the samples correctly when compared to the culture information. Four groups could be distinguished, i.e. normal urine, Escherichia coli infected, Proteus spp. and Staphylococcus spp. In the second experiment it was again possible to use NN systems to examine the volatile production patterns and identify 18 of 19 unknown UTI cases. Only one normal patient sample was mis-identified as an E. coli infected sample. Discriminant function analysis also differentiated between normal urine samples, that infected with E. coli and with Staphylococcus spp. This study has shown the potential for early detection of microbial contaminants in urine samples using electronic nose technology for the first time. These findings will have implications for the development of rapid systems for use in clinical practice.     

Coupling SIMD and SIMT Architectures to Boost Performance of a Phylogeny-aware Alignment Kernel

ABSTRACT: BACKGROUND: Aligning short DNA reads to a reference sequence alignment is a prerequisite fordetecting their biological origin and analyzing them in a phylogenetic context. With thePaPaRa tool we introduced a dedicated dynamic programming algorithm forsimultaneously aligning short reads to reference alignments and correspondingevolutionary reference trees. The algorithm aligns short reads to phylogenetic profiles thatcorrespond to the branches of such a reference tree. The algorithm needs to perform animmense number of pairwise alignments. Therefore, we explore vector intrinsics andGPUs to accelerate the PaPaRa alignment kernel. RESULTS: We optimized and parallelized PaPaRa on CPUs and GPUs. Via SSE 4.1 SIMD (SingleInstruction, Multiple Data) intrinsics for x86 SIMD architectures and multi-threading, weobtained a 9-fold acceleration on a single core as well as linear speedups with respect tothe number of cores. The peak CPU performance amounts to 18.1 GCUPS (Giga CellUpdates per Second) using all four physical cores on an Intel i7 2600 CPU running at 3.4GHz. The average CPU performance (averaged over all test runs) is 12.33 GCUPS. Wealso used OpenCL to execute PaPaRa on a GPU SIMT (Single Instruction, MultipleThreads) architecture. A NVIDIA GeForce 560 GPU delivered peak and averageperformance of 22.1 and 18.4 GCUPS respectively. Finally, we combined the SIMD andSIMT implementations into a hybrid CPU-GPU system that achieved an accumulatedpeak performance of 33.8 GCUPS. CONCLUSIONS: This accelerated version of PaPaRa (available at www.exelixis-lab.org/software.html)provides a significant performance improvement that allows for analyzing larger datasetsin less time. We observe that state-of-the-art SIMD and SIMT architectures delivercomparable performance for this dynamic programming kernel when the "competingprogrammer approach" is deployed. Finally, we show that overall performance can besubstantially increased by designing a hybrid CPU-GPU system with appropriate loaddistribution mechanisms.     

Immunodeficiency and autoimmunity: lessons from systemic lupus erythematosus

Recent evidence suggests that systemic autoimmunity and immunodeficiency are not separate entities, but rather are interconnected processes. Immunodeficiency results from distinct defects of the immune response and primarily presents as infections but also frequently with autoimmune features. Systemic autoimmunity is the combined effect of multiple genetic variations and infectious and immunoregulatory factors that result in dominant autoimmune manifestations, in addition to frequent and opportunistic infections. The overlap in disease manifestations and symptoms suggests that immunodeficiency should be considered in the presence of autoimmunity, and vice versa. In this review, we present the shared or similar aspects of immunodeficiency and autoimmunity using systemic lupus erythematosus as a paradigm and discuss the implications for clinical care.     

Stepwise binding of tylosin and erythromycin to Escherichia coli ribosomes, characterized by kinetic and footprinting analysis

Erythromycin and tylosin are 14- and 16-membered lactone ring macrolides, respectively. The current work shows by means of kinetic and chemical footprinting analysis that both antibiotics bind to Escherichia coli ribosomes in a two-step process. The first step established rapidly, involves a low-affinity binding site placed at the entrance of the exit tunnel in the large ribosomal subunit, where macrolides bind primarily through their hydrophobic portions. Subsequently, slow conformational changes mediated by the antibiotic hydrophilic portion push the drugs deeper into the tunnel, in a high-affinity site. Compared with erythromycin, tylosin shifts to the high-affinity site more rapidly, due to the interaction of the mycinose sugar of the drug with the loop of H35 in domain II of 23 S rRNA. Consistently, mutations of nucleosides U2609 and U754 implicated in the high-affinity site reduce the shift of tylosin to this site and destabilize, respectively, the final drug-ribosome complex. The weak interaction between tylosin and the ribosome is Mg2+ independent, unlike the tight binding. In contrast, both interactions between erythromycin and the ribosome are reduced by increasing concentrations of Mg2+ ions. Polyamines attenuate erythromycin affinity for the ribosome at both sequential steps of binding. In contrast, polyamines facilitate the initial binding of tylosin, but exert a detrimental, more pronounced, effect on the drug accommodation at its final position. Our results emphasize the role of the particular interactions that side chains of tylosin and erythromycin establish with 23 S rRNA, which govern the exact binding process of each drug and its response to the ionic environment.