PDB-2-PB: a curated online protein block sequence database

This article describes the development of a curated online protein block sequence database, PDB-2-PB. The protein block sequences for protein structures with complete backbone coordinates have been encoded using the encoding procedure of de Brevern, Etchebest & Hazout [Proteins(2000),41, 271–287]. In the current release of the PDB-2-PB database (version 1.0), the protein entries from a recent release of the World Wide Protein Data Bank (wwPDB), which has 74 297 solved PDB entries as of 7 July 2011, have been used as a primary source. The PDB-2-PB database stores the protein block sequences for all the chains present in a protein structure. PDB-2-PB version 1.0 has the curated protein block sequences for 103 252 PDB chain entries (93 547 X-ray, 7033 NMR and 2672 other experimental chain entries). From the PDB-2-PB database, users can extract the curated protein block sequence and its corresponding amino acid sequence, which is extracted from the PDB ATOM records. Users can download these sequences either by using the PDB code or by using various parameters listed in the database. The PDB-2-PB database is freely available at http://bioinfo.bdu.ac.in/~pb/.

In vitro anti-inflammatory and anti-cancer activities of Cuscuta reflexa Roxb

AIM OF THE STUDY

To determine anti-inflammatory and anti-cancer activities of Cuscuta reflexa in cell lines (in vitro).

MATERIALS AND METHODS

Anti-inflammatory activity of the water extract was analysed in vitro using lipopolysaccharide (LPS) induced inflammatory reactions in murine macrophage cell line RAW264.7. The expression of COX-2 and TNF-α genes involved in inflammation was analysed by SQ RT-PCR. EMSA was conducted to analyse the influence of the extract on NF-κB signalling. Anti-cancer activity was analysed on Hep3B cells by MTT assay, DAPI staining, annexin V staining and SQ-RT PCR analysis of BAX, Bcl-2, p53 and survivin.

RESULTS

The extract down regulated LPS induced over expression of TNF-α and COX-2 in RAW264.7 cells; blocked NF-κB binding to its motifs and induced apoptosis in Hep3B cells as evidenced from MTT, DAPI staining and annexin V staining assays. The extract up regulated pro-apoptotic factors BAX and p53, and down regulated anti-apoptotic factors Bcl-2 and survivin.

CONCLUSIONS

The study showed that Cuscuta reflexa inhibits LPS induced inflammatory responses in RAW264.7 cells through interplay of TNF-α, COX-2 and NF-κB signalling. It induced apoptosis in Hep3B cells through the up regulation of p53, BAX and down regulation of Bcl-2 and survivin.

Efficacy of low dose atorvastatin in diabetic dyslipidaemia

Coronary heart disease (CHD), the commonest cause of morbidity and mortality in patients with type 2 diabetes, requires multipronged approach for management, including especially treating dyslipidaemia with statins. We conducted this study to demonstrate that low dose (10 mg) atorvastatin is effective in reducing LDL cholesterol (LDL-C) to the target levels in patients from Indian subcontinent. Eighty-one subjects with type 2 diabetes mellitus and dyslipidaemia (LDL-C >100 mg/dl in those without coronary artery disease, n=77; LDL-C >70 mg/dl in those with coronary artery disease, n=4) were included. All patients were initiated on 10 mg atorvastatin daily. Serum lipid profile was repeated after 3 months. The mean body mass index among men and women were 25.0 +/- 4 and 26.7 +/- 3.6 kg/m2 respectively. Pretreatment mean HbA(1c) was 7.9 +/- 1.8 % and total cholesterol, triglycerides and HDL cholestrol (HDL-C) and LDL-C was 214 +/- 27 mg/dl, 164 +/- 63 mg/dl, 46 +/- 6 mg/dl and 135 +/- 24 mg/dl respectively. After three months of treatment the mean decrease was 62 +/- 31 mg/dl in total cholesterol (p < 0.001), 31 +/- 57 mg/dl in triglycerides (p < 0.001), 51 +/- 27 mg/dl in LDL-C (p < 0.001) and 4 +/- 8 mg/dl in HDL-C (p < 0.001). The LDL-C level was reduced by 37.6% in these patients, from 135 +/- 24 mg/dl to 84 = 27 mg/dl (p < 0.001) with 10 mg of atorvastatin daily. It was possible to achieve target LDL-C of less than 100 mg/dl in 75.5% (n=58) in subjects without CHD (n=77) and less than 70 mg/dl in 75% (n=3) of those patients with CHD (n=4). The present study showed that in patients with type 2 diabetes mellitus, 10 mg of atorvastatin daily was safe, well tolerated, and effective in reducing LDL-C to target levels.

The effect of factors such as handedness, sex and age on body temperature measured by an infrared ‘tympanic’ thermometer

BACKGROUND

The effectiveness of IRET has been called into question. However, there are a number of factors that might affect ear temperature measurement. Some of these are the focus of this study.

METHOD

366 asymptomatic subjects (0.75 to 53 years old) volunteered to take part in this ethically approved study. The data were analysed in respect to handedness, sex and age.

RESULTS

Two-way ANOVAs showed significant interactions between age group and sex (first ear measured, p = 0.017; second p = 0.298), and between handedness and sex (first ear measured, p = 0.011; second p = 0.040) in relation to their ear temperature. Ear temperatures of males tended to be lower than females, however this only found significance in the 'Early Puberty' age group (p < 0.001).

DISCUSSION

Significant differences in ear temperature were seen for handedness, sex and age.

CONCLUSION

We have shown that handedness, sex and age might be contributory factors to ear temperature differences in the population.

Preventive effect of ethanol extract of Phyllanthus rheedii Wight. on D-galactosamine induced hepatic damage in Wistar rats

AIM OF THE STUDY

Phyllanthus rheedii Wight. (Euphorbiaceae) has been used by Muthuvan tribes of Kerala for curing liver diseases. The present study was conducted to assess the hepatoprotective activity of this plant. The ethanol extract of Phyllanthus rheedii was pharmacologically analysed for its preventive effect in d-galactosamine (d-GalN) induced liver damage in rats.

MATERIAL AND METHODS

The levels of hepatotoxicity in various groups were quantified by different parameters of liver damage viz. serum levels of ALT, AST, LDH, GGT, ALP and total bilirubin. The effect of extract on the expression levels of pro-inflammatory cytokines like TNF-alpha, and TGF-beta were analysed by RT-PCR. Histological changes in the liver were evaluated by hematoxylin and eosin staining of paraffin processed liver sections. The antioxidant and choleretic activity of the extract were also analysed.

RESULTS

Comparison of serum values of control and extract treated groups have revealed that the d-GalN induced alterations in the serum and liver markers were normalized in extract treatment groups showing hepatoprotective activity of the extract. The extract also prevented the toxin induced histological changes in liver. The mRNA levels of TGF-beta and TNF-alpha in the liver were up regulated by the hepatotoxin. The extract treatment has normalized this change, giving light to the probable mechanism of action of the extract. It has showed marked antioxidant and choleretic activity. Preliminary phytochemical screening has revealed the presence of tannins, flavanoids and phenolics as major components.

CONCLUSIONS

This study concluded the ethanol extract of P. rheedii could be a promissory candidate for drug development and validated the tribal claim.

A mild and efficient synthesis of chloroesters by the cleavage of cyclic and acyclic ethers using Bi(NO3)3·5H2O as a catalyst under solvent-free conditions

A facile, efficient synthesis of chloroesters is described. The reaction of cyclic and acyclic ethers with acid chlorides in the presence of catalytic amounts of Bi(NO3)3·5H2O under solvent-free conditions yielded the corresponding chloroesters. Also, the catalyst can be recovered conveniently and reused efficiently for at least six times.Key words: Bismuth(III) nitrate pentahydrate, cyclic and acyclic ethers, chloroesters.

Hepatoprotection of Phyllanthus maderaspatensis against experimentally induced liver injury in rats

The hexane extract of Phyllanthus maderaspatensis (200 and 100 mg/kg) showed significant hepatoprotection on carbon tetrachloride and thioacetamide induced liver damage in rats. The protective effect was evident from serum biochemical parameters and histopathological analysis. Rats treated with P. maderaspatensis remarkably prevented the elevation of serum AST, ALT and LDH and liver lipid peroxides in CCl(4) and thioacetamide treated rats. Hepatic glutathione levels significantly increased by the treatment with the extracts. Histopathological changes induced by CCl(4) and thioacetamide were also significantly reduced by the extract treatment. The activity of hexane extracts of P. maderaspatensis was comparable to that of silymarin, the reference hepatoprotective drug.

Antiangiogenic effect of Lygodium flexuosum against N-nitrosodiethylamine-induced hepatotoxicity in rats

The antiangiogenic effect of Lygodium flexuosum extract was evaluated in Wistar rats intoxicated with N-nitrosodiethylamine (NDEA) in preventive and curative models. In preventive groups, NDEA was administered for 20 weeks. Daily doses of L. flexuosumn-hexane extract (200mg/kg) started 1 week before the onset of NDEA intoxication and continued for 20 weeks. In curative animals, NDEA was administered for 20 weeks followed by treatment with the n-hexane extract of L. flexuosum for 28 days. Rats intoxicated with NDEA had elevated levels of serum gamma-GT, AST, ALT, LDH levels and hepatic MDA and decreased levels of hepatic GSH. When treated with L. flexuosum extract had normal levels of gamma-GT, AST, ALT, LDH levels, hepatic MDA and GSH. NDEA administered rat liver showed an overexpressed levels of angiopoietins 1 (Ang-1) and 2 (Ang-2) and its receptor Tie-2 mRNA. L. flexuosum extract treatment significantly (p<or=0.05) reduced the levels of Ang-1 and Ang-2 and Tie-2 in rat livers evidenced by RT-PCR. Immunohistochemical analysis showed that vascular endothelial growth factor (VEGF) was overexpressed and localized around periportal area of liver sections intoxicated with NDEA and its overexpression was effectively reduced by the treatment with L. flexuosum extract. Histopathological observations also substantiated NDEA-induced hepatotoxicity and the effect was significantly (p<or=0.05) reduced by L. flexuosum extract treatment. Thus, L. flexuosum extract at a dose of 200mg/kg effectively reversed the hepatotoxicity induced by N-nitrosodiethylamine in both experimental models.

Bacterial meningitis - complication from a dialysis catheter

Various infective complications associated with dialysis catheter infection have been reported in the literature previously. We report a case of a hemodialysis patient presented with confusion and dysarthria secondary to Staphylococcus aureus septicemia and meningitis originating from a tunneled catheter used for providing dialysis. Blood cultures from the periphery, central venous catheter and culture of the line tip grew methicillin-sensitive Staphylococcus aureus. Lumbar puncture after CT brain confirmed Staphylococcus aureus. He was treated with high dose of an appropriate parenteral antibiotic and also removal of the infected line. In spite of optimal treatment, he died 15 days following his admission. The ideal option will be to use a definitive access like a fistula or AV graft, but in practice a significant proportion of hemodialysis patients is dialyzed with temporary or tunneled catheters all over the world, and infection poses a serious threat to dialysis patients resulting in significant mortality and morbidity. In patients with dialysis catheter-related sepsis, removal of the infected catheters and appropriate antibiotic treatment will prevent serious metastatic complications. Planning definitive access well ahead in chronic kidney disease patients and minimizing the use of temporary access is the only way forward.