ISER: selection of differentially expressed genes from DNA array data by non-linear data transformations and local fitting

SUMMARY: This report describes an algorithm (intensity-dependent selection of expression ratios or ISER) developed to analyse DNA array data by optimizing the selection of genes with the most significant variations in expression amongst two RNA samples. The algorithm is designed for use when little or no replication of array hybridizations is available.     

How essential are nonessential genes?

Gene essentiality in bacteria has been identified in silico, focusing on gene persistence, or experimentally, focusing on the growth of knockouts in rich media. Comparing 55 genomes of Firmicutes and Gamma-proteobacteria to identify the genes which, while persistent among genomes, do not lead to a lethal phenotype when inactivated, we show that the characteristics of persistence, conservation, expression, and location are shared between persistent nonessential (PNE) genes and experimentally essential genes. PNE genes show an overrepresentation of genes related to maintenance and stress response. This outlines the limits of current experimental techniques to define gene essentiality and highlights the essential role of genes implicated in maintenance which, although dispensable for growth, are not dispensable from an evolutionary point of view. Firmicutes and Gamma-proteobacteria are mostly differing in the construction of the cell envelope, DNA replication and proofreading, and RNA degradation. In addition to suggesting functions for persistent genes that had until now resisted identification, we show that these genes have many characters in common with experimentally identified essential genes. They should then be regarded as truly essential genes.     

Evaluating concentration estimation errors in ELISA microarray experiments

Background  

Enzyme-linked immunosorbent assay (ELISA) is a standard immunoassay to estimate a protein's concentration in a sample. Deploying ELISA in a microarray format permits simultaneous estimation of the concentrations of numerous proteins in a small sample. These estimates, however, are uncertain due to processing error and biological variability. Evaluating estimation error is critical to interpreting biological significance and improving the ELISA microarray process. Estimation error evaluation must be automated to realize a reliable high-throughput ELISA microarray system.     

Effects of hydrochlorothiazide and propranolol treatment on chylomicron metabolism in hypertensive objects

Modifications in chylomicron metabolism caused by antihypertensive drugs were investigated in hypertensive subjects because previous studies had indicated that diuretics and beta-blockers modify the plasma lipid concentrations through mechanisms that were not fully understood. A triglyceride-rich emulsion resembling lymph chylomicrons, labeled with (3H) triolein and (14C) cholesteryl oleate, was infused intravenously into mildly hypertensive patients after 8 weeks on placebo and subsequently on hydrochlorothiazide (n = 10) or propranolol (n = 8). The residence time of both radioactivities in plasma was utilized for the simultaneous calculation of the particle remnant removal rate and of the lipoprotein lipase activity expressed as a delipidation index = 1 - [(3H) triolein residence time/(14C) cholesteryl oleate residence time]. Treatment with hydrochlorothiazide diminished the delipidation rate value whereas propranolol mildly increased the removal rate of the remnant particle. These alterations of the chylomicron kinetics were not accompanied by changes in plasma triglycerides, glucose, and insulin concentration as measured in the fasting state. The impairment of the lipoprotein lipase activity by thiazides and the faster removal rate of the whole particle by propranolol could explain the reason why in previous clinical studies the simultaneous use of these drugs does not aggravate the hyperlipidemia known to be induced by thiazides alone.     

Comparative morphology of eggs and nymphs of Triatoma vandae Carcavallo, Jurberg, Rocha, Galvão, Noireau & Lent, 2002 and Triatoma williami Galvão, Souza & Lima, 1965

Eggs and all nymphs of these species were studied employing light microscopy (LM) and scanning electron microscopy (SEM). The major differences observed by LM in the eggs were related to the presence and the distribution of pores on the surface of their chorion. Morphological differences among three nymphal stages (1st, 3rd, and 5th) development of each species were observed. The differential characteristics are chromatic and in the shape of connexival spots. The ultrastructure of the ventral region of the head and the IX, X, and XI abdominal segments (anal tube) of the both species were described demonstrating morphological differences that can be used for diagnosis of the species.     

Low viscosity hydrogel of guar gum: preparation and physicochemical characterization

Guar gum was cross-linked with glutaraldehyde and characterized by GPC, rheology, WADX, SEM and TGA. This guar gum is a galactomannan polysaccharide, that contains small amount of arabinose, glucose and uronic acid, besides galactose and mannose. The polymer has high molar mass, with Mw, Mn and Mv values of 2.0x10(6), 1.2x10(6) and 1.9x10(6)g/mol, respectively. The reticulation follows a slow process and lead to a viscosity increase of 40 times compared with the original gum solution. The final viscosity was similar to that of Hylan G-F 20, a hyaluronate derivative, commercially used in viscosupplementation treatment. The gel contains 95.6% of water and the amount of residual glutaraldehyde is much lower than the LD-50. Porous structure was detected by SEM and thermal stability was improved by the cross-linking. The low viscosity, the small amount of remained glutaraldehyde, and the thermal stability indicates that the guar hydrogel has potential to be applied as biomaterial with specific rheological requirements.     

Floral venation patterns in Siphocampylus (Campanulaceae)

Siphocampylus is a neotropical genus that comprises 221 species distributed from Costa Rica to Argentina and in the Greater Antilles. Twenty-eight species have been reported from Brazil, mainly occupying mountainous terrain. The floral venation patterns and the origin of the hypanthium in eight Brazilian species, including three varieties, are described. Eleven ovarian vascular bundles depart from the siphonostele or receptacular stele: five of these bundles result from sepalar and staminal adnation and are alternate to five petalar bundles; the remaining bundle is central carpellary. The staminal bundles diverge from the sepalar bundles at the sinus, while the carpellary bundles form a cross, resulting in four ventral bundles; two of these feed the ovules; the other two feed the style. Apparently, the dorsal carpellary bundles diverge at the same site and then ramify profusely. The venation pattern observed is unprecedented in Siphocampylus and is quite different from other reports on genera of Campanulaceae. Further, these findings suggest that the origin of the hypanthium is appendicular, increasing knowledge of venation in this group, thus providing data for phylogenetic considerations.