Granulometric analysis of spots in DNA microarray images

As the topological properties of each spot in DNA microarray images may vary from one another, we employed granulometries to understand the shape-size content contributed due to a significant intensity value within a spot. Analysis was performed on the microarray image that consisted of 240 spots by using concepts from mathematical morphology. In order to find out indices for each spot and to further classify them, we adopted morphological multiscale openings, which provided microarrays at multiple scales. Successive opened microarrays were subtracted to identify the protrusions that were smaller than the size of structuring element. Spot-wise details, in terms of probability of these observed protrusions,were computed by placing a regularly spaced grid on microarray such that each spot was centered in each grid. Based on the probability of size distribution functions of these protrusions isolated at each level, we estimated the mean size and texture index for each spot. With these characteristics, we classified the spots in a microarray image into bright and dull categories through pattern spectrum and shape-size complexity measures. These segregated spots can be compared with those of hybridization levels.     

Short-Term Consequences of Angiographically-Confirmed Coronary Stent Thrombosis

Objectives

To conduct a meta-analysis to quantify the real-world incidence of in-hospital or 30-day death or myocardial infarction (MI), and angiographically-confirmed ST-related treatment costs.

Background

The short-term clinical and economic consequences of coronary stent thrombosis (ST) are thought to be significant.

Methods

We searched MEDLINE, Embase and Scopus from January 2000-July 2012 to identify observational/registry studies that evaluated a cohort of ≥25 patients experiencing angiographically-confirmed thrombosis of a drug-eluting or bare-metal stent, required the use of dual-antiplatelet therapy for guideline-recommended durations, and reported incidences of in-hospital or 30-day death or MI and/or ST-related treatment costs. Incidences and costs from each study were pooled using random-effects meta-analysis.

Results

Twenty-three studies were included. Of the 13 studies reporting in-hospital outcomes, 12 (N=8,832 STs) reported mortality data, with the pooled incidence rate estimated to be 7.9%, 95%CI=5.4%-11.3%, I²=86%. Ten studies (N=1,294 STs) reported 30-day death, with a pooled incidence of 11.6%, 95%CI=8.8%-15.1%, I²=55%. Patients experiencing early ST (within 30-days of implant) had higher in-hospital and 30-day mortality than those experiencing very-late ST (interaction p<0.04 for both). Stent type had no significant effect on in-hospital or 30-day mortality. In the 5 studies (N=542 STs) and 3 studies (N=180 STs) reporting in-hospital and 30-day MI, respectively, the pooled incidence rates were 6.1%, 95%CI=2.1%-16.2%, I²=88% and 9.5%, 95%CI=3.8%-22.0%, I²=65%. One study reported costs associated with ST, estimating the median/patient cost of hospitalization to treat early ST at $11,134 (in 2000US$).

Conclusions

Regardless of stent type used, the short-term consequences of coronary ST appear significant.     

Influence of seed and root exudations on the rhizosphere effect inSorghum vulgare andCrotalaria juncea

The influence of seed and root exudations on the rhizosphere effect ofSorghum vulgare andCrotalaria juncea was examined. While the quantitative occurrence of certain morphological and physiological groups of bacteria on the seeds and rhizospheres of the two plant species differed, there were similarities in the occurrence of certain physiological and nutritional groups of bacteria on the seed as well as on the rhizosphere. The occurrence of some genera of fungi on the seeds and in the rhizosphere indicated the influence of both seeds and root exudations on the rhizosphere effect. Increase in root exudations of amino acids and sugars correlated with a concomitant increase in microbial activity in the rhizosphere on the 15th day of growth in both plant species but there was a delayed effect of the exuded chemicals on the rhizosphere microflora after 30 d of plant growth. Based on the Ph.D. thesis of the first author submitted to the University of Agricultural Sciences, Bangalore.     

Essential oil composition of aerial parts of Angelica glauca growing wild in North-West Himalaya (India)

Fresh aerial parts of Angelica glauca, growing wild in Kashmir valley in higher Himalaya (Jammu and Kashmir, India), collected at flowering stage from different locations, on hydro-distillation provided a refreshing light pale coloured essential oil with characteristic floral woody flavour. The oil was found to be a complex mixture of mono- and sesquiterpenes and 34 compounds accounting for nearly 97.4% of the oil were characterized with the help of capillary GC, GC-MS, and NMR. Major compounds of the oil were characterized as alpha-phellandrene (13.5%), trans-carveol (12.0%), beta-pinene (11.7%), thujene (7.5%), beta-caryophyllene oxide (7.2%), beta-caryophyllene (7.0%), gamma-terpinene (6.7%), nerolidol (6.5%), beta-bisabolene (5.2%) and germacrene D (4.5%). It is the first report to exploit the essential oil from Himalayan A. glauca herb collected at flowering stage.     

Selection of zinc fingers that bind single-stranded telomeric DNA in the G-quadruplex conformation

There is considerable interest in molecules that bind to telomeric DNA sequences and G-quadruplexes with specificity. Such molecules would be useful to test hypotheses for telomere length regulation, and may have therapeutic potential. The versatility and modular nature of the zinc finger motif makes it an ideal candidate for engineering G-quadruplex-binding proteins. Phage display technology has previously been widely used to screen libraries of zinc fingers for binding to novel duplex DNA sequences. In this study, a three-finger library has been screened for clones that bind to an oligonucleotide containing the human telomeric repeat sequence folded in the G-quadruplex conformation. The selected clones show a strong amino acid consensus, suggesting analogous modes of binding. Binding was found to be both sequence dependent and structure specific. This is the first example of an engineered protein that binds to G-quadruplex DNA, and represents a new type of binding interaction for a zinc finger protein.     

Characterization of phosphotyrosine containing proteins at the cholinergic synapse

Tyrosine phosphorylation has been associated with several aspects of the regulation of cholinergic synaptic function, including nicotinic acetylcholine receptor (AChR) desensitization as well as the synthesis and clustering of synaptic components. While some progress has been made in elucidating the molecular events initiating such signals, the downstream targets of these tyrosine kinase pathways have yet to be characterized. In this paper we have used molecular cloning techniques to identify proteins which are tyrosine phosphorylated at the cholinergic synapse. Phosphotyrosine containing proteins (PYCPs) were isolated from the electric organ of Torpedo californica by anti-phosphotyrosine immunoaffinity chromatography. Peptide sequencing and expression cloning then identified the isolated proteins. The proteins identified included heat shock protein 90, type III intermediate filament from Torpedo electric organ, alpha-fodrin, beta-tubulin, actin and rapsyn. These tyrosine phosphorylated proteins may play a role in the regulation of synaptic function by tyrosine kinases.     

S. pombe Pbh1p: an inhibitor of apoptosis domain containing protein is essential for chromosome segregation

Proteins containing the baculovirus inhibitor of apoptosis repeats (BIR domains) have been identified in a wide range of species. BIR domain containing proteins are thought to inhibit caspases and thereby cause inhibition of apoptosis. A BIR domain containing protein has been recently identified by the Schizosaccharomyces pombe genome sequencing project. However, caspase-like proteins have not been found in yeasts, suggesting that the BIR domain containing proteins might play a fundamental role in cell regulation, in addition to their well-characterized role in inhibition of apoptosis. In this study, we have characterized Pbh1p, an S. pombe BIR domain containing protein. Construction and analysis of a null mutant in pbh1+ revealed that pbh1+ is essential for cell viability. Moreover, cells devoid of Pbh1p are defective in chromosome condensation and chromosome segregation. Thus, proper chromosome segregation requires the function of Pbh1p. Over-production of Pbh1p led to abnormalities in mitosis and cytokinesis, suggesting that the levels of Pbh1p are important for regulation of mitosis and cytokinesis.     

Fatty acid production from amino acids and alpha-keto acids by Brevibacterium linens BL2

Low concentrations of branched-chain fatty acids, such as isobutyric and isovaleric acids, develop during the ripening of hard cheeses and contribute to the beneficial flavor profile. Catabolism of amino acids, such as branched-chain amino acids, by bacteria via aminotransferase reactions and alpha-keto acids is one mechanism to generate these flavorful compounds; however, metabolism of alpha-keto acids to flavor-associated compounds is controversial. The objective of this study was to determine the ability of Brevibacterium linens BL2 to produce fatty acids from amino acids and alpha-keto acids and determine the occurrence of the likely genes in the draft genome sequence. BL2 catabolized amino acids to fatty acids only under carbohydrate starvation conditions. The primary fatty acid end products from leucine were isovaleric acid, acetic acid, and propionic acid. In contrast, logarithmic-phase cells of BL2 produced fatty acids from alpha-keto acids only. BL2 also converted alpha-keto acids to branched-chain fatty acids after carbohydrate starvation was achieved. At least 100 genes are potentially involved in five different metabolic pathways. The genome of B. linens ATCC 9174 contained these genes for production and degradation of fatty acids. These data indicate that brevibacteria have the ability to produce fatty acids from amino and alpha-keto acids and that carbon metabolism is important in regulating this event.     

1,2-Diaryl-1-ethanone and pyrazolo [4,3-c] quinoline-4-one as novel selective cyclooxygenase-2 inhibitors

Novel 1,2-diaryl-1-ethanone 1 and pyrazolo [4,3-c] quinoline-4-one 2, with pharmacophores different from the known COX inhibitors were identified as selective COX-2 inhibitors. The communication briefly describes SAR of both the series.