The glutamate switch of bacteriophage T7 DNA helicase: role in coupling nucleotide triphosphate (NTP) and DNA binding to NTP hydrolysis

The DNA helicase encoded by gene 4 of bacteriophage T7 forms a hexameric ring in the presence of dTTP, allowing it to bind DNA in its central core. The oligomerization also creates nucleotide-binding sites located at the interfaces of the subunits. DNA binding stimulates the hydrolysis of dTTP but the mechanism for this two-step control is not clear. We have identified a glutamate switch, analogous to the glutamate switch found in AAA+ enzymes that couples dTTP hydrolysis to DNA binding. A crystal structure of T7 helicase shows that a glutamate residue (Glu-343), located at the subunit interface, is positioned to catalyze a nucleophilic attack on the γ-phosphate of a bound nucleoside 5'-triphosphate. However, in the absence of a nucleotide, Glu-343 changes orientation, interacting with Arg-493 on the adjacent subunit. This interaction interrupts the interaction of Arg-493 with Asn-468 of the central β-hairpin, which in turn disrupts DNA binding. When Glu-343 is replaced with glutamine the altered helicase, unlike the wild-type helicase, binds DNA in the presence of dTDP. When both Arg-493 and Asn-468 are replaced with alanine, dTTP hydrolysis is no longer stimulated in the presence of DNA. Taken together, these results suggest that the orientation of Glu-343 plays a key role in coupling nucleotide hydrolysis to the binding of DNA.     

Whole plant response of Pongamia pinnata to drought stress tolerance revealed by morpho-physiological,biochemical and transcriptome analysis

Molecular Biology Reports - Pongamia is considered an important biofuel species worldwide. Drought stress in the early growth stages of Pongamia influences negatively on the germination and...     

Predicting breast cancer using an expression values weighted clinical classifier

Background

Clinical data, such as patient history, laboratory analysis, ultrasound parameters-which are the basis of day-to-day clinical decision support-are often used to guide the clinical management of cancer in the presence of microarray data. Several data fusion techniques are available to integrate genomics or proteomics data, but only a few studies have created a single prediction model using both gene expression and clinical data. These studies often remain inconclusive regarding an obtained improvement in prediction performance. To improve clinical management, these data should be fully exploited. This requires efficient algorithms to integrate these data sets and design a final classifier.LS-SVM classifiers and generalized eigenvalue/singular value decompositions are successfully used in many bioinformatics applications for prediction tasks. While bringing up the benefits of these two techniques, we propose a machine learning approach, a weighted LS-SVM classifier to integrate two data sources: microarray and clinical parameters.

Results

We compared and evaluated the proposed methods on five breast cancer case studies. Compared to LS-SVM classifier on individual data sets, generalized eigenvalue decomposition (GEVD) and kernel GEVD, the proposed weighted LS-SVM classifier offers good prediction performance, in terms of test area under ROC Curve (AUC), on all breast cancer case studies.

Conclusions

Thus a clinical classifier weighted with microarray data set results in significantly improved diagnosis, prognosis and prediction responses to therapy. The proposed model has been shown as a promising mathematical framework in both data fusion and non-linear classification problems.     

Constraint on di-nucleotides by codon usage bias in bacterial genomes

It has been reported earlier that the relative di-nucleotide frequency (RDF) in different parts of a genome is similar while the frequency is variable among different genomes. So RDF is termed as genome signature in bacteria. It is not known if the constancy in RDF is governed by genome wide mutational bias or by selection. Here we did comparative analysis of RDF between the inter-genic and the coding sequences in seventeen bacterial genomes, whose gene expression data was available. The constraint on di-nucleotides was found to be higher in the coding sequences than that in the inter-genic regions and the constraint at the 2nd codon position was more than that in the 3rd position within a genome. Further analysis revealed that the constraint on di-nucleotides at the 2nd codon position is greater in the high expression genes (HEG) than that in the whole genomes as well as in the low expression genes (LEG). We analyzed RDF at the 2nd and the 3rd codon positions in simulated coding sequences that were computationally generated by keeping the codon usage bias (CUB) according to genome G+C composition and the sequence of amino acids unaltered. In the simulated coding sequences, the constraint observed was significantly low and no significant difference was observed between the HEG and the LEG in terms of di-nucleotide constraint. This indicated that the greater constraint on di-nucleotides in the HEG was due to the stronger selection on CUB in these genes in comparison to the LEG within a genome. Further, we did comparative analyses of the RDF in the HEG rpoB and rpoC of 199 bacteria, which revealed a common pattern of constraints on di-nucleotides at the 2nd codon position across these bacteria. To validate the role of CUB on di-nucleotide constraint, we analyzed RDF at the 2nd and the 3rd codon positions in simulated rpoB/rpoC sequences. The analysis revealed that selection on CUB is an important attribute for the constraint on di-nucleotides at these positions in bacterial genomes. We believe that this study has come with major findings of the role of CUB on di-nucleotide constraint in bacterial genomes.     

Variability of nutrients and phytoplankton biomass in a shallow brackish water ecosystem (Chilika Lagoon, India)

Seasonal and spatial variations in water quality parameters, such as nutrients [NH₄ ⁺–N, NO₂⁻–N, NO₃⁻–N, PO₄³⁻–P, total nitrogen (TN) and total phosphorus (TP)], Secchi disc depth, salinity, dissolved oxygen, chlorophyll a, primary productivity and phytoplankton standing stock, were studied in Chilika Lagoon (from 27 sampling locations) during 2001–2003 to assess the present ecological status. The study was undertaken after a major hydrological intervention in September 2000, which connected the lagoon body and the Bay of Bengal via a manmade opening (new mouth). Current and old data on water quality were also compared to establish the changes that had occurred after the hydrological intervention. Multivariate techniques and gridding methods were used to investigate the spatial and seasonal variability of the data and to characterize the trophic evolution of the basin. Results of principal component analysis (PCA) indicated that the 27 stations can be classified into five groups based on similarities in the temporal variation of nutrients, chlorophyll a concentration, salinity, and other physicochemical parameters. The tributaries and the exchange of lagoon water with the Bay of Bengal most probably determine the water quality and the dynamics of the ecosystem. Hydrodynamics of the lagoon, weed coverage, input of urban sewage through tributaries and agricultural runoff are probably the key factors controlling the trophic conditions of the lagoon. An increase in salinity and total phosphorus was noted after the new mouth was opened, while the total suspended sediment load, the water column depth, and nitrogenous nutrients decreased. The new mouth opening also brought changes in the phytoplankton species composition.     

Multiple factors interact to produce responses resembling spectrum of human disease in Campylobacter jejuni infected C57BL/6 IL-10-/- mice

Background  

Campylobacter jejuni infection produces a spectrum of clinical presentations in humans - including asymptomatic carriage, watery diarrhea, and bloody diarrhea - and has been epidemiologically associated with subsequent autoimmune neuropathies. This microorganism is genetically variable and possesses genetic mechanisms that may contribute to variability in nature. However, relationships between genetic variation in the pathogen and variation in disease manifestation in the host are not understood. We took a comparative experimental approach to explore differences among different C. jejuni strains and studied the effect of diet on disease manifestation in an interleukin-10 deficient mouse model.     

Human bancroftian filariasis: immunological markers of morbidity and infection

Induction of host cytokines plays a critical role in infection as well as disease in human filariasis. Measurements of such molecules in plasma could be used as windows of markers both for understanding the pathogenesis of the disease and for identifying markers of morbidity. Eight inflammatory and non-inflammatory host molecules in circulation were quantified in 207 subjects in filariasis endemic area of Orissa, India. IL-6, IL-8, IL-10, TNF-alpha, TNFR-I, TNFR-II, LBP and sICAM-1 were quantified by immunoassays and were analyzed by multivariate exploratory data analysis methods followed by multivariate analysis of variance. Raised levels of IL-6 and IL-8 emerged as markers of acute as well as chronic disease, while increased TNF-alpha was a feature found only in acute filariasis. Decreased sICAM-1 was a feature found only in asymptomatic subjects with filarial infection. There was a dichotomy in plasma levels of two TNF receptors between infected subjects and patients with filarial disease. Since plasma levels of these cytokines are often determined by host genetics, studies on cytokine genetic polymorphisms could offer new insights into the relationship between infection and disease in human lymphatic filariasis.     

Higher tRNA diversity in thermophilic bacteria: A possible adaptation to growth at high temperature

We have done a comparative study of tRNA diversity and total tRNA genes among different strains of bacteria with respect to the optimum growth temperature of the cells. Our observation suggests that higher tRNA diversity usually occurs in thermophiles in comparison to non-thermophiles. Among psychrophiles total tRNA was observed to be more than two-fold higher than in the non-psychrophiles. Though tRNA diversity and total tRNA have recently been shown to be affected by an organism's genomic GC% and growth rate, this work is the first report on growth temperature affecting these features in bacteria. This work extends the list of molecular features undergoing adaptation due to growth temperature and supports the view that growth temperature acts as a selecting factor at the molecular level during evolution.     

Contrasting intra-annual inorganic carbon dynamics and air–water CO2 exchange in Dhamra and Mahanadi Estuaries of northern Bay of Bengal,India

Limnology - Surface water partial pressure of carbon dioxide [pCO2 (water)], total alkalinity (TA), dissolved inorganic carbon (DIC), and air–water CO2 flux were measured in two estuaries of...