The Purkinje cell degeneration 5J mutation is a single amino acid insertion that destabilizes Nna1 protein

In the mouse, Purkinje cell degeneration (pcd) is a recessive mutation characterized by degeneration of cerebellar Purkinje cells, retinal photoreceptors, olfactory bulb mitral neurons, and certain thalamic neurons, and is accompanied by defective spermatogenesis. Previous studies of pcd have led to the identification of Nna1 as the causal gene; however, how loss of Nna1 function results in neurodegeneration remains unresolved. One useful approach for establishing which functional domains of a protein underlie a recessive phenotype has been to determine the genetic basis of the various alleles at the locus of interest. Because none of the pcd alleles analyzed at the time of the identification of Nna1 provided insight into the molecular basis of Nna1 loss-of-function, we obtained a recent pcd remutation—pcd^5J, and after determining that its phenotype is comparable to existing pcd severe alleles, we sought its genetic basis by sequencing Nna1. In this article we report that pcd^5J results from the insertion of a single GAC triplet encoding an aspartic acid residue at position 775 of Nna1. Although this insertion does not affect Nna1 expression at the RNA level, Nna1^pcd-5J protein expression is markedly decreased. Pulse-chase experiments reveal that the aspartic acid insertion dramatically destabilizes Nna1^pcd-5J protein, accounting for the observation that pcd^5J is a severe allele. The presence of a readily detectable genetic mutation in pcd^5J confirms that Nna1 loss-of-function alone underlies the broad pcd phenotype and will facilitate further studies of how Nna1 loss-of-function produces neurodegeneration and defective spermatogenesis in pcd mice.     

Decolorisation, biodegradation and detoxification of benzidine based azo dye

The present study deals with the decolorisation, biodegradation and detoxification of Direct Black-38, a benzidine based azo dye, by a mixed microbial culture isolated from an aerobic bioreactor treating textile wastewater. The studies revealed a biotransformation of Direct Black-38 into benzidine and 4-aminobiphenyl followed by complete decolorisation and biodegradation of these toxic intermediates. From cytotoxicity studies, it was concluded that detoxification of the dye took place after degradation of the toxic intermediates by the culture.     

Biodegradation of tech-hexachlorocyclohexane in a upflow anaerobic sludge blanket (UASB) reactor

Biodegradability of technical grade hexachlorocyclohexane (tech-HCH) was studied in an upflow anaerobic sludge blanket reactor (UASB) under continuous mode of operation in concentration range of 100-200 mg/l and constant HRT of 48 h. At steady state operation more than 85% removal of tech-HCH (upto 175 mg/l concentration) and complete disappearance of beta-HCH was observed. Kinetic constants in terms of maximum specific tech-HCH utilization rate (k) and half saturation velocity constant (K(L)) were found to be 11.88 mg/g/day and 8.11 mg/g/day, respectively. The tech-HCH degrading seed preparation, UASB reactor startup and degradation in continuous mode of operation of the reactor is presented in this paper.     

Role of <Emphasis Type="Italic">Yersinia enterocolitica</Emphasis> heat-stable enterotoxin (Y-STa) on differential regulation of nuclear and cytosolic calcium signaling in rat intestinal epithelial cells

The heat-stable enterotoxin (Y-STa) produced by the pathogenic strains of Yersinia enterocolitica is a causative agent of secretory diarrhea. We have reported earlier that Y-STa-induced inositol trisphosphate-mediated cytosolic calcium rise occurs in rat intestinal epithelial cells. In the present communication, the involvement of a nuclear calcium store in the action mechanism of Y-STa in rat intestinal epithelial cells has been shown. Calcium imaging with time series confocal microscopy shows that Y-STa stimulates both the nuclear and cytosolic calcium levels in rat intestinal epithelial cells where a rise in nuclear calcium precedes the cytosolic events. Moreover, Y-STa stimulates both cytosolic and nuclear inositol trisphosphate (IP₃) levels in a time-dependent manner. Western blot and immunocytochemical analysis reveal a higher density of IP₃ receptor type II in the nuclear membrane compared to the cytosol, which may be the cause of an early rise of the nuclear calcium level. Therefore, it is suggested that Y-STa regulates the nuclear and cytosolic calcium signals in a distinct temporal manner in rat intestinal epithelial cells.     

Method for isolation of floating fetal RBCs from maternal circulation based on their inherent magnetic property

Isolation of floating fetal cells from maternal circulation has immense potential in diagnosing of various genetic alterations in the developing fetus. Currently, non-invasive fetal cell isolation methods include fluorescence/magnetic activated cell sorting that use antibodies specific to fetal cells. Apart from being complex and expensive the biggest challenge associated with these cell sorting methods is low concentration of fetal cells in maternal peripheral blood. In order to make the complete process much simpler and effective, we propose a novel method for isolation of floating fetal cells that uses a continuous flow of maternal blood for effectively harvesting a higher fetal cell volume compared to any other existing method. The isolation mechanism is based on the difference in the magnetic susceptibility of fetal hemoglobin (HbF-α₂γ₂) and maternal hemoglobin (HbA-α₂β₂). HbF has high oxygen saturation capacity (diamagnetic) compared to HbA (paramagnetic), and this difference in saturation is further enhanced by presence of 2,3-bisphosphoglycerate (2,3-BPG). When placed in magnetic field, these cells get separated based on the difference (p ≤ 0.001) in their magnetophoretic mobility. This separation method may also be used for detection of fetomaternal hemorrhages and also treatment of Rh incompatibility.     

Isolation and characterization of microcystin producing Microcystis from a Central Indian water bloom

Microcystis aeruginosa Kütz, a well-known microcystin (hepatotoxin) producing cyanobacterium was the dominant bloom-forming organism in a mesotrophic lake at Nagpur in Central India, which was isolated and characterized for morphospecies and microcystin content. Compact spherical colonies, formation of daughter colonies, and clathration of older colonies leading to release of solitary cells, were characteristics of laboratory grown M. aeruginosa. Its growth, monitored as increase in optical density (OD) measured at 678 nm (the wavelength selected using dilution curve technique), exhibited a maximum specific growth rate (μ_max) of 0.34 day⁻¹ which, was attained on the 5th day of the experiment with a doubling time of 3.25 days. Though the morphological characters of the M. aeruginosa under field conditions were not retained under laboratory conditions, the microcystin content and type of variants did match with bloom samples. Reverse phase high performance liquid chromatography (RP-HPLC) analyses revealed that the laboratory grown isolate of Microcystis produced microcystin-RR (732 μg g⁻¹ dry weight biomass) and demethylated microcystin-RR (165 μg g⁻¹ dry weight biomass) variants, which are reported to be less toxic when compared to microcystin-LR. LC/ESI/MS further confirmed the presence of these two variants. Geographical distribution of microcystin variants and their prevailing concentrations need to be considered during formulation of guideline values for drinking and recreational waters.     

Primate-specific evolution of noncoding element insertion into PLA2G4C and human preterm birth

Background

The use of biological annotation such as genes and pathways in the analysis of gene expression data has aided the identification of genes for follow-up studies and suggested functional information to uncharacterized genes. Several studies have applied similar methods to genome wide association studies and identified a number of disease related pathways. However, many questions remain on how to best approach this problem, such as whether there is a need to obtain a score to summarize association evidence at the gene level, and whether a pathway, dominated by just a few highly significant genes, is of interest.

Methods

We evaluated the performance of two pathway-based methods (Random Set, and Binomial approximation to the hypergeometric test) based on their applications to three data sets of Crohn's disease. We consider both the disease status as a phenotype as well as the residuals after conditioning on IL23R, a known Crohn's related gene, as a phenotype.

Results

Our results show that Random Set method has the most power to identify disease related pathways. We confirm previously reported disease related pathways and provide evidence for IL-2 Receptor Beta Chain in T cell Activation and IL-9 signaling as Crohn's disease associated pathways.

Conclusions

Our results highlight the need to apply powerful gene score methods prior to pathway enrichment tests, and that controlling for genes that attain genome wide significance enable further biological insight.     

State of the art: refinement of multiple sequence alignments

Background  

Accurate multiple sequence alignments of proteins are very important in computational biology today. Despite the numerous efforts made in this field, all alignment strategies have certain shortcomings resulting in alignments that are not always correct. Refinement of existing alignment can prove to be an intelligent choice considering the increasing importance of high quality alignments in large scale high-throughput analysis.