Comparative evaluation of microarray analysis software

A wide variety of software tools are available to analyze microarray data. To identify the optimum software for any project, it is essential to define specific and essential criteria on which to evaluate the advantages of the key features. In this review we describe the results of our comparison of several software tools. We then conclude with a discussion of the subset of tools that are most commonly used and describe the features that would constitute the “ideal microarray analysis software suite.”     

Mutation of Gluconobacter oxydans and Bacillus megaterium in a two-step process of l-ascorbic acid manufacture by ion beam

AIM: To increase the transformation rate of l-sorbose to 2-keto-l-gulonic (2-KLG) acid in a two-step process of l-ascrobic acid manufacture by ion beam. METHODS AND RESULTS: Gluconobacter oxydans (GO29) and Bacillus megaterium (BM80) were used in the present study. Ion implantation was carried out with the heavy ion implantation facility at the institute of Plasma Physics in China. 2-KLG in whole culture broth was determined by iodometry. Mutants were screened by single-colony isolation and 2-KLG accumulation in broth. GO29 and BM80 were implanted by either hydrogen ions (H(+)) or nitrogen ions (N(+)) with various doses, respectively. The average transformation rate of GM112-302 bred by ion beam in Gram-molecule was increased from 79.3 to 94.5% after eight passages in shaking flasks. Furthermore, in 180-ton fermentors in Jiangsu Jiangshan Pharmaceutical Co. Ltd, the transformation rate was stable at 92.0%, indicating a producer could get 0.99 kg of gulonic acid from 1.0 kg of sorbose. CONCLUSION: Ion beam as a new mutation source had potential advantages in breeding. Comparing with original mixture GO29 and BM80, GM112-302 is more efficient in accumulating 2-KLG, especially at the later phase. SIGNIFICANCE AND IMPACT OF THE STUDY: GM112-302 bred by ion beam implantation dramatically increased the transformation rate by 19.2%, which greatly increased efficiency and reduced the cost of l-ascorbic acid manufacture in a two-step process.     

Probing the binding of scutellarin to human serum albumin by circular dichroism, fluorescence spectroscopy, FTIR, and molecular modeling method

The binding of scutellarin with human serum albumin (HSA) was investigated at four temperatures, 296, 303, 310, and 318 K, by fluorescence, circular dichroism (CD), Fourier transform infrared spectroscopy (FT-IR), and molecular modeling study at pH 7.40. The binding parameters were determined by Scatchard's procedure, which are approximately consistent with the results of Stern-Volmer equation. The thermodynamic parameters were calculated according to the dependence of enthalpy change on the temperature as follows: DeltaH degrees is a small negative value (-8.55 kJ/mol), whereas DeltaS degrees is a positive value (65.15 J/mol K). Quenching of the fluorescence HSA in the presence of scutellarin was observed. Data obtained by fluorescence spectroscopy and CD experiment, FT-IR experiment, and molecular modeling method suggested that scutellarin can strongly bind to the HSA and the primary binding site of scutellarin is located in site I of HSA. It is considered that scutellarin binds to site I (subdomain II) mainly by a hydrophobic interaction and there are hydrogen bond interactions between the scutellarin and the residues Arg222 and Arg257.     

Alpha-actinin-4-mediated FSGS: an inherited kidney disease caused by an aggregated and rapidly degraded cytoskeletal protein

Focal segmental glomerulosclerosis (FSGS) is a common pattern of renal injury, seen as both a primary disorder and as a consequence of underlying insults such as diabetes, HIV infection, and hypertension. Point mutations in the alpha-actinin-4 gene ACTN4 cause an autosomal dominant form of human FSGS. We characterized the biological effect of these mutations by biochemical assays, cell-based studies, and the development of a new mouse model. We found that a fraction of the mutant protein forms large aggregates with a high sedimentation coefficient. Localization of mutant alpha-actinin-4 in transfected and injected cells, as well as in situ glomeruli, showed aggregates of the mutant protein. Video microscopy showed the mutant alpha-actinin-4 to be markedly less dynamic than the wild-type protein. We developed a "knockin" mouse model by replacing Actn4 with a copy of the gene bearing an FSGS-associated point mutation. We used cells from these mice to show increased degradation of mutant alpha-actinin-4, mediated, at least in part, by the ubiquitin-proteasome pathway. We correlate these findings with studies of alpha-actinin-4 expression in human samples. "Knockin" mice with a disease-associated Actn4 mutation develop a phenotype similar to that observed in humans. Comparison of the phenotype in wild-type, heterozygous, and homozygous Actn4 "knockin" and "knockout" mice, together with our in vitro data, suggests that the phenotypes in mice and humans involve both gain-of-function and loss-of-function mechanisms.     

TGF-beta1 induces alveolar epithelial to mesenchymal transition in vitro

The aim of this study was to investigate whether transforming growth factor-beta1 (TGF-beta1) could induce alveolar epithelial to mesenchymal transition (EMT) in vitro. Alveolar epithelial cells (AECs) from SD rats were isolated by elastase cell dispersion and IgG panning. Expression of alpha-smooth muscle actin (alpha-SMA) was assayed using Western blotting and immunostaining analysis. Morphological changes, the markers of epithelial cell (E-cadherin), and stress fiber by actin reorganization were detected by an indirect immunostaining. The contents of collagen I were determined by spectrophotometry. The levels of endogenous TGF-beta1 were measured with ELISA. Incubation of AECs with TGF-beta1 (0.1 approximately 10 ng/mL) induced abundant expression of alpha-SMA protein, and alpha-SMA expression in AECs reached a plateau when TGF-beta1 was > 3 ng/mL. Furthermore, we found that TGF-beta1 (3 ng/mL) exposure of AECs induced an authentic EMT characterized by abundant expression of alpha-smooth muscle actin, transformation of myofibroblastic morphology, increased formation of stress fiber by actin reorganization, and loss of epithelial marker E-cadherin. Meanwhile, significant increase in the levels of collagen I from 32.0 +/- 6.6 mg/g in control to 98 +/- 10.8 mg/g in TGF-beta1-treated group was found over a 72 h incubation period. Moreover, following stimulated by TGF-beta1 (3 ng/mL), a marked and time-dependent increase in endogenous TGF-beta1 released from AECs was observed. At time points 72 h, TGF-beta1 release mounted to 3451 pg/ml, which was much enough to induce EMT in vitro. These results demonstrated that AECs, under stimulation of TGF-beta1, underwent a conversion process into myofibroblasts in vitro.     

Molecular and cellular events at the site of myocardial infarction: from the perspective of rebuilding myocardial tissue

The potential for bone marrow-derived progenitor cells (BMDPC) to regenerate myocardial tissue following infarction depends on homing, migration, nourishment, and spatially appropriate growth of BMDPC. Requisite to these objectives is the expression of adhesion molecules (ICAM-1) and chemoattractant cytokines (MCP-1), matrix metalloproteinase (MMP) activity, a neovasculature, and fibrillar collagen scaffolding. We found that enhanced ICAM-l and MCP-1, as well as MMP activity on day 3 and 7 postMI, are present to facilitate the homing, chemotaxis, and migration of circulating cells into the infarct site. The vascular network formed at the infarct site contains a ratio of conduit to exchange vessels that is greater than that for control tissue and therefore its ability to nourish BMDPC for their growth appears to be tenuous. These findings, together with the dense formation of a fibrillar collagen scar beyond week 2, suggest the optimal time to rebuild myocardium from BMDPC resides within 2 week postMI.     

alpha-Amylase immobilized on bulk acoustic-wave sensor by UV-curing coating

A new method for immobilization of alpha-amylase by UV-curing coating is proposed in this paper. The immobilization procedure of UV-curing coating on piezoelectric quartz crystal is simple and convenient, and causes less loss of enzymatic activity. The activity of the immobilized alpha-amylase is monitored by a technique based on bulk acoustic-wave (BAW) sensor. The frequency shift of BAW sensor can reflect the degree of hydrolysis of starch by the immobilized alpha-amylase. It is appropriate for the immobilized alpha-amylase to hydrolyze the soluble starch under pH 7.0 condition, which is similar to that of the free alpha-amylase. Kinetic parameters (the Michaelis constant, K(m), and the maximum initial rate V(max)) of the enzymatic hydrolysis of starch by the immobilized alpha-amylase are estimated by using a linear method of Lineweaver-Burk plot. K(m)=12.7mgml(-1) and V(max)=15.9Hzmin(-1). And the experimental results show that the immobilized alpha-amylase entrapped by the UV-curing coating retains adequate enzymatic activity and can be reused more than 50 times under certain experimental conditions.     

Gene admixture in the silk road region of China: evidence from mtDNA and melanocortin 1 receptor polymorphism

Mitochondrial DNA control region segment I sequences and melanocortin 1 receptor (MC1R) gene polymorphism were examined in ethnic populations in the silk road region of China. Both the frequencies of the MC1R variants and the results of mtDNA data in this region presented intermediate values between those of Europe and East and Southeast Asia, which suggested extensive gene admixture in this area and was in general agreement with previous studies. Phylogenetic analysis of the ethnic populations in the Silk Road region that based on mtDNA data didn't show expected cluster pattern according to their ethnogenesis. We suspect that a high migration rate in female among these closely related populations and other three demographic events might account for it.