Uncoupling of proopiomelanocortin (POMC) fragments is related to self-injury

Proopiomelanocortin (POMC) contains several interesting, behaviorally active peptides. Release patterns of these fragments have been related to bizarre episodes of self-injurious behavior (SIB) among autistic individuals. Moreover, elevation in beta-endorphin (betaE) but not ACTH levels was associated with a positive response to an acutely administered, centrally acting opioid blocker among autistic individuals exhibiting SIB. In the present study, POMC fragments were measured in 12 self-injurious patients before and after long term (3 month) treatment with an opiate blocker naltrexone (NTX). POMC fragments were sampled from blood collected at the beginning of the baseline and placebo-controlled treatment phases of the study. Results indicated that the co-release (coupling) of POMC fragments were stable over time and the profile of POMC fragments in plasma predicted the effectiveness of a CNS acting drug in autistic subjects who self-injure.     

The Wavelet-Based Cluster Analysis for Temporal Gene Expression Data

A variety of high-throughput methods have made it possible to generate detailed temporal expression data for a single gene or large numbers of genes. Common methods for analysis of these large data sets can be problematic. One challenge is the comparison of temporal expression data obtained from different growth conditions where the patterns of expression may be shifted in time. We propose the use of wavelet analysis to transform the data obtained under different growth conditions to permit comparison of expression patterns from experiments that have time shifts or delays. We demonstrate this approach using detailed temporal data for a single bacterial gene obtained under 72 different growth conditions. This general strategy can be applied in the analysis of data sets of thousands of genes under different conditions.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]     

Validity of Antibodies in Lymphocyte Supernatant in Diagnosing Tuberculosis in Severely Malnourished Children Presenting with Pneumonia

BackgroundThe diagnosis of tuberculosis (TB) in young children can be challenging, especially in severely malnourished children. There is a critical need for improved diagnostics for children. Thus, we sought to evaluate the performance of a technique that measures antibodies in lymphocyte supernatant (ALS) for the diagnosis of TB in severely malnourished children presenting with suspected pneumonia.MethodsChildren less than 5 years with severe acute malnutrition and radiological features of pneumonia admitted to the Dhaka Hospital of International Centre for Diarrhoeal Disease Research, Bangladesh, were enrolled consecutively following informed written consent. In addition to clinical and radiological assessment, samples taken for TB diagnosis included gastric lavage fluid and induced sputum for microbiological confirmation. ALS was measured from venous blood, and results were evaluated in children classified as “confirmed”, “non-confirmed TB” or “not TB”.ResultsAmong 224 children who had ALS analysis, 12 (5.4%) children had microbiologically “confirmed TB”, a further 41 (18%) had clinically diagnosed “non-confirmed TB” and the remaining 168 (75%) were considered not to have TB. ALS was positive in 89 (40%) and negative in 85 (39%) of children, with a large number (47 or 21%) reported as “borderline”. These proportions were similar between the three diagnostic groups. The sensitivity and specificity of ALS when comparing “Confirmed TB” to “Not TB” was only 67% (95% CI: 31–91%) and 51% (95% CI: 42–60%), respectively.

Conclusions and Significance

Our data suggest that ALS is not sufficiently accurate to improve the diagnosis of TB in children with severe malnutrition.     

ArchAlign: coordinate-free chromatin alignment reveals novel architectures

To facilitate identification and characterization of genomic functional elements, we have developed a chromatin architecture alignment algorithm (ArchAlign). ArchAlign identifies shared chromatin structural patterns from high-resolution chromatin structural datasets derived from next-generation sequencing or tiled microarray approaches for user defined regions of interest. We validated ArchAlign using well characterized functional elements, and used it to explore the chromatin structural architecture at CTCF binding sites in the human genome. ArchAlign is freely available at http://www.acsu.buffalo.edu/~mjbuck/ArchAlign.html.     

Mechanism of poliovirus inactivation by cell-free filtrates of marine bacteria

The mechanism of enterovirus inactivation by marine bacteria was investigated using poliovirus type 1 as a model virus and with strains of Pseudomonas and Vibrio isolated from the marine environment. Treatment of virus with cell-free filtrates from late log phase bacterial cultures produced alterations in the viral capsid as shown by a reduction in efficiency of adsorption to host cells, increased sensitivity to ribonuclease, and by the release of ribonucleic acid from the treated virions. Filtration of 14C-labelled, treated virus through 25-nm filters revealed that the majority of the isotope (85-96%) passed the filters, indicating extensive capsid disruption. However, the most rapid and pronounced change observed during virus inactivation was the loss of infectivity, suggesting that enzymatic degradation is not the first event in the poliovirus inactivation process by marine bacteria.     

Phosphorylated l-caldesmon is involved in disassembly of actin stress fibers and postmitotic spreading

The function of the ubiquitous actin-binding protein, caldesmon (l-CaD) in mammalian non-muscle cells remains elusive. During mitosis, l-CaD becomes markedly phosphorylated at Ser497 and Ser527 (in the rat sequence), therefore, it has been suggested that l-CaD is involved in cytokinesis by inhibiting the actomyosin interaction until it is phosphorylated, although direct in vivo evidence is still missing. In the present study, we used F-actin staining and specific antibodies against these two phosphorylation sites of l-CaD to simultaneously monitor actin assembly and l-CaD phosphorylation. Our observations demonstrated that the level of l-CaD phosphorylation undergoes dynamic changes during the cell cycle. The spatial and temporal distributions of phospho-CaD do not correlate with cytokinesis per se, but rather, with the level of actin bundles in a reciprocal manner. The highest l-CaD phosphorylation level coincides with the disassembly of actin cytoskeleton during mitotic cell rounding. Ser-to-Ala mutations at these two positions prevent stress fibers from disassembly upon migratory stimulation. In addition, phospho-CaD appears to colocalize with nascent focal adhesion complexes during postmitotic spreading. These findings suggest that l-CaD phosphorylation plays an important role not only in cytoskeleton remodeling during cell shape changes, but also in cell spreading and migration.     

P51-T Optimizing Heat Lysis for High-Throughput Sequencing of Various Plasmid Libraries

Heat lysis is a very reliable method for high-throughput labs to decrease costs and increase throughput with little sacrifice in quality of sequence data compared to typically used two-plate or magnetic-bead DNA purification methods. Laboratories employing this procedure on high-copy plasmids, using a sequencing reaction with a 1/8^th Big Dye (Applied Biosystems) dilution, have reported generating data with 85% of all wells having read lengths of at least 600 bases with quality value (QV) 20 or above.¹We have adopted this procedure in our laboratory and optimized it for sequencing from various in-house cDNA and genomic shotgun libraries cloned into high-copy plasmids, as well as for libraries constructed outside of our sequencing center. To fully develop the procedure, we utilized a number of culture plates, testing different plate volumes, well shapes, and growth times. Also, we tested various volumes of resuspension buffer in order to generate the highest sequencing success rates and read lengths. To further cut costs, we optimized the sequencing reactions by testing various dilutions of Big Dye and template amounts.Based upon over 55,000 reads, we have been able to consistently generate sequencing results with average success rates of 90–95% and read lengths of over 700 bases with QV 20 or above. Our past protocol employed a standard two-plate DNA preparation method with a 1/16^th Big Dye dilution in the sequencing reaction. In contrast, we now use the optimized heat lysis protocol combined with a 1/32^nd Big Dye dilution. These changes have increased throughput and produced the high-quality sequencing results stated above, yet reduced our consumables cost by over 55%.