A robust measure of correlation between two genes on a microarray

Background  

The underlying goal of microarray experiments is to identify gene expression patterns across different experimental conditions. Genes that are contained in a particular pathway or that respond similarly to experimental conditions could be co-expressed and show similar patterns of expression on a microarray. Using any of a variety of clustering methods or gene network analyses we can partition genes of interest into groups, clusters, or modules based on measures of similarity. Typically, Pearson correlation is used to measure distance (or similarity) before implementing a clustering algorithm. Pearson correlation is quite susceptible to outliers, however, an unfortunate characteristic when dealing with microarray data (well known to be typically quite noisy.)     

Infectivity of different genotypes of human Blastocystis hominis isolates in chickens and rats

Most Blastocystis hominis isolates from humans are believed to be potentially zoonotic. This is because B. hominis isolates found in a variety of other host species have been found to have identical or relatively similar genotypes to those found in human isolates. However, the transmission of human B. hominis isolates to other animals has not been confirmed experimentally. In this study, the infectivity associated with several unique human Blastocystis genotypes (subtypes 2, 3, 4 and 7) was therefore investigated by infecting chickens and rats with two isolates of each subtype experimentally. The results showed that one isolate of subtype 4 and one isolate of subtype 7 was capable of infecting both chickens and rats, while two isolates of subtype 2, another isolate of subtype 4, and another isolate of subtype 7 could only infect chickens. Conversely, two isolates of subtype 3 failed to infect either of the animals. These results confirmed that several genotypes from human isolates could infect chickens and/or rats, indicating that chickens and rats are suitable experimental animal models for studying the zoonotic potential of human Blastocystis isolates.     

Diet composition,feed preferences and mouth morphology of early stage silver therapon (Leiopotherapon plumbeus,Kner 1864) larvae reared in outdoor tanks

This study examined the diet composition, feeding preferences, and mouth morphology of the silver therapon (Leiopotherapon plumbeus, Kner 1864) larvae under captive conditions. Larvae were reared in outdoor tanks (4 m³) with natural food grown 2 weeks prior to start of larval rearing. Food preference was measured by the Chesson's electivity index (α_i). Gut content analysis of larvae sampled between 5 and 25 days after hatching (DAH) showed the dominance in the diet by zooplankton, mainly copepod nauplii, cladocerans and insect larvae. Small fish larvae (5–9 DAH; 3.32–6.29 mm standard length) preferred cladocerans, ciliates and copepod nauplii; whereas older larvae (12–25 DAH; 5.45–19.26 mm standard length) preferred insect larvae over cladocerans and adult insects. The mouth gape size at 5 DAH was 359 μm and increased to 3.75 mm at 40 DAH when body size grew at an average rate of 0.59 mm d^?1. The standard length (SL) of L. plumbeus larvae was strongly associated with mouth size (r² = 0.98, P < 0.05), indicating a progressive increase of ingested prey size of the fish larvae. These results clarified the early life feeding ecology of this species, which is essential in developing effective hatchery techniques.     

A radioisotope-nondependent high-sensitivity method for measuring the activity of glioblastoma-related O-methylguanine DNA methyltransferase

O⁶-Methylguanine DNA methyltransferase (MGMT) cancels the anticancer effect of temozolomide (drug for glioblastoma), which introduces methylation to DNA. Therefore, developing an MGMT inhibitor is a promising strategy for the treatment of this cancer. For this purpose, a sensitive detection method that does not depend on the conventional radioisotope (RI) method was developed. This was realized by a fluorescence-based method that measured the amount of cleavable restriction sites demethylated by the action of MGMT; this method was enhanced by introducing a polymerase chain reaction (PCR) amplification step. As an assay of enzyme activity, 20-fold higher sensitivity (subnanomolar) was attained compared with our and others’ fluorescence-based approaches.     

Regulation of Hyaluronan (HA) Metabolism Mediated by HYBID (Hyaluronan-binding Protein Involved in HA Depolymerization,KIAA1199) and HA Synthases in Growth Factor-stimulated Fibroblasts

Regulation of hyaluronan (HA) synthesis and degradation is essential to maintenance of extracellular matrix homeostasis. We recently reported that HYBID (HYaluronan-Binding protein Involved in hyaluronan Depolymerization), also called KIAA1199, plays a key role in HA depolymerization in skin and arthritic synovial fibroblasts. However, regulation of HA metabolism mediated by HYBID and HA synthases (HASs) under stimulation with growth factors remains obscure. Here we report that TGF-β1, basic FGF, EGF, and PDGF-BB commonly enhance total amount of HA in skin fibroblasts through up-regulation of HAS expression, but molecular size of newly produced HA is dependent on HYBID expression levels. Stimulation of HAS1/2 expression and suppression of HYBID expression by TGF-β1 were abrogated by blockade of the MAPK and/or Smad signaling and the PI3K-Akt signaling, respectively. In normal human skin, expression of the TGF-β1 receptors correlated positively with HAS2 expression and inversely with HYBID expression. On the other hand, TGF-β1 up-regulated HAS1/2 expression but exerted only a slight suppressive effect on HYBID expression in synovial fibroblasts from the patients with osteoarthritis or rheumatoid arthritis, resulting in the production of lower molecular weight HA compared with normal skin and synovial fibroblasts. These data demonstrate that although TGF-β1, basic FGF, EGF, and PDGF-BB enhance HA production in skin fibroblasts, TGF-β1 most efficiently contributes to production of high molecular weight HA by HAS up-regulation and HYBID down-regulation and suggests that inefficient down-regulation of HYBID by TGF-β1 in arthritic synovial fibroblasts may be linked to accumulation of depolymerized HA in synovial fluids in arthritis patients.     

Synthesis of soluble aromatic multilayered tetra(m-phenylurea) and analysis of its helical conformation in various solvents

Aromatic N,N'-dimethylated urea exists in (cis, cis) form, both in the crystal and in solution, and this structure can be utilized to construct intramolecular aromatic multilayered oligomers. These structures show helical conformation with all-R or all-S axis chirality, when the benzene rings are connected at the meta positions. To investigate the dynamic conformational behavior of such aromatic multilayered ureas in various solvents, we synthesized tetra(m-phenylurea) 3 bearing two chiral N-2-(methoxyethoxyethoxy)propyl groups and six N-methoxyethoxyethyl groups. The high solubility of compound 3 enabled its analysis in various solvents, including water. The CD spectra of compound 3 showed broad electronic absorption with high temperature-dependency, owing to the induction of handedness, in acetonitrile, chloroform, and methanol. In water, the CD signals of compound 3 indicated the presence of similar helical structure, but temperature-dependency was not observed.     

Structure of fomitellan A, a mannofucogalactan from the fruiting bodies of Fomitella fraxinea

Chemical structure of fomitellan A, a polysaccharide with a mitogenic effect isolated from the fruiting bodies of Fomitella fraxinea, has been assigned as a mannofucogalactan with a repeating unit of penta-saccharide, which was composed of a (1→6)-linked d-galactopyranosyl backbone having a C-2 position substituted with disaccharide units of 3-O-d-mannopyranosyl-l-fucopyranosyl residue. The ¹H and ¹³C NMR signals of fomitellan A have been completely assigned by extensive NMR experiments.