CanGeneBase (CGB) ‐ a database on cancer related genes

The advent of genomic and proteomic technologies in this post-genomic era has urged the researchers to develop novel research strategies against cancer by targeting the human genes that would greatly facilitate to identify more promising treatment and to develop accurate early diagnosis for cancer. To harness the power of cancer genetic information towards better treatment we have developed a cancer gene database called CanGeneBase (CGB). It is a comprehensive data collection of cancer-related genes with the intention of helping the researchers to stay on a single platform to gain exclusive information on the genes of their interest. According to the Cancer Gene Data Curation Project, about 4,700 genes have been identified as being related to cancer. The present CanGeneBase covers about 12 different types of cancer which includes 190 unique gene entries. Each entry encompasses about 33 useful parameters to provide detailed information about specific gene. CanGeneBase is made in such a way that it can be easily accessed by either gene symbol or by the type of cancer.

Availability

The database is freely available at http://122.165.25.137/bioinfo/cancerdb/     

Ghrelin is dispensable for embryonic pancreatic islet development and differentiation

Ghrelin is a peptide hormone that has been implicated in the regulation of food intake and energy homeostasis. Ghrelin is predominantly produced in the stomach, but is also expressed in many other tissues where its functions are not well characterized. In the rodent and human pancreas, ghrelin levels peak at late gestation and gradually decline postnatally. Several studies have suggested that ghrelin regulates beta cell function during embryonic development and in the adult. In addition, in a number of mouse models, ghrelin cells appear to replace insulin- and glucagon-producing cells in the islet. In this analysis, we investigated whether the absence or overexpression of ghrelin influenced the development and differentiation of the pancreatic islet during embryonic development. These studies revealed that ghrelin is dispensable for normal pancreas development during gestation. Conversely, we demonstrated that elevated ghrelin in the Nkx2.2 null islets is not responsible for the absence of insulin- and glucagon-producing cells. Finally, we have also determined that in the absence of insulin, ghrelin cells form in their normal numbers and ghrelin is expressed at wild type levels.     

Anion-regulated binding selectivity of Cr(III) in collagen

We present a mechanism for the selectivity of covalent/electrostatic binding of the Cr(III) ion to collagen, mediated by the kosmotropicity of the anions. Although a change in the long-range ordered structure of collagen is observed after covalent binding (Cr(III)-OOC) in the presence of SO₄²⁻ at pH 4.5, the ν_sym(COO⁻) band remains intense, suggesting a relatively lower propensity for the Cr(III) to bind covalently instead of electrostatically through Cr(H₂O)₆³⁺. Replacing SO₄²⁻ with Cl⁻ reduces the kosmotropic effect which further favors the electrostatic binding of Cr(III) to collagen. Our findings allow a greater understanding of mechanism-specific metal binding in the collagen molecule. We also report for the first time, surface-enhanced Raman spectroscopy to analyze binding mechanisms in collagen, suggesting a novel way to study chemical modifications in collagen-based biomaterials.     

Cholesterol assimilation and biotransformation by Lactobacillus helveticus

Lactobacillus helveticus, grown at 37°C in MRS medium supplemented with 3 mM cholesterol, assimilated all the cholesterol in 42 h having 68 U mg⁻¹ of intracellular cholesterol oxidase activity. The strain transformed 1 g cholesterol to 0.05 g of androsta-1, 4-diene-3, 17-dione and 0.04 g of androst-4-ene-3, 17 dione within 48 h at 37°C with extracellular cholesterol oxidase activity at 12 U mg⁻¹ and intracellular oxidase at 0.5 U mg⁻¹.     

Strategies to evade false positives in the in situ analysis of peptide antibiotics in SDS-PAGE gels

In situ activity assay is one of the promising techniques for the characterization of peptide antibiotics. This assay was carried out for the peptide purified from a new bacterial isolate Paenibacillus alvei and commercial peptide antibiotic polymixin E. Towards this, the routine and new protocols were tried. Interestingly, the unexpected result of these experiments - the "switch over activity" has led us to have further investigations. Here, we have addressed the potential problem in the methodology of in situ assay and demonstrated a fool proof protocol to evade the false positive results.     

Potential role of aromatase over estrogen receptor gene polymorphisms in migraine susceptibility: a case control study from North India

Background

The present study was undertaken to find out the role of estrogen pathway related gene polymorphisms in susceptibility to migraine in Northern Indian population. Aromatase, CYP19A1 (rs10046 and rs4646); estrogen receptors, ESR1 (rs2234693, rs1801132, rs2228480 and rs9340799) and ESR2 (rs1271572 and rs1256049) polymorphisms were selected for the present study.

Methodology/Principal Findings

The patients were recruited in two cohorts – primary (207) and replicative (127) along with 200 healthy controls and genotyped for various polymorphisms. Logistic regression analysis was applied for statistical analyses. The results were validated in the replicative cohort and pooled by meta analysis using Fisher''s and Mantel-Haenszel test. Furthermore, Benjamini – Hochberg false discovery rate test was used to correct for multiple comparisons. CYP19A1 rs10046 and CYP19A1 rs4646 polymorphisms were found to confer risk and protective effect, respectively. Out of four ESR1 polymorphisms, only rs2234693 variant allele was significantly associated in migraine with aura. No significant associations were observed for ESR2 polymorphisms. Significant haplotypes were identified for CYP19A1 and ESR1 polymorphisms. Gene- gene interactions of genotypes as well as haplotypes were observed for CYP19A1- ESR1 showing both risk and protective combinations.

Conclusion

We strongly suggest CYP19A1 polymorphisms to be the major contributing factors in migraine susceptibility instead of genetic variants of estrogen receptors.     

A study on dosimetric properties of electronic portal imaging device and its use as a quality assurance tool in Volumetric Modulated Arc Therapy

Aim

In this study, the dosimetric properties of the electronic portal imaging device were examined and the quality assurance testing of Volumetric Modulated Arc Therapy was performed.

Background

RapidArc involves the variable dose rate, leaf speed and the gantry rotation. The imager was studied for the effects like dose, dose rate, field size, leaf speed and sag during gantry rotation.

Materials and methods

A Varian RapidArc machine equipped with 120 multileaf collimator and amorphous silicon detector was used for the study. The characteristics that are variable in RapidArc treatment were studied for the portal imager. The accuracy of a dynamic multileaf collimator position at different gantry angles and during gantry rotation was examined using the picket fence test. The control of the dose rate and gantry speed was verified using a test field irradiating seven strips of the same dose with different dose rate and gantry speeds. The control over leaf speed during arc was verified by irradiating four strips of different leaf speeds with the same dose in each strip. To verify the results, the RapidArc test procedure was compared with the X-Omat film and verified for a period of 6 weeks using EPID.

Results

The effect of gantry rotation on leaf accuracy was minimal. The dose in segments showed good agreement with mean deviation of 0.8% for dose rate control and 1.09% for leaf speed control over different gantry speeds.

Conclusion

The results provided a precise control of gantry speed, dose rate and leaf speeds during RapidArc delivery and were consistent over 6 weeks.     

Bacterial antagonists and hexanal-induced systemic resistance of mango fruits against Lasiodiplodia theobromae causing stem-end rot

Induction of defense-related enzymes, such as phenylalanine ammonia lyase (PAL), peroxidase (PO), polyphenol oxidase (PPO), superoxide dismutase (SOD) and catalase (CAT) due to bacterial antagonists viz., Pseudomonas fluorescens (Pf1) and Bacillus subtilis (EPCO16) and plant-derived lipoxygenase volatile compound hexanal, were studied in mango fruits against Lasiodiplodia theobromae causing stem-end rot disease. The results showed increased induction of all the defense-related enzymes in mango fruits 3–5 days after dipping treatment with combination of bacterial antagonists and hexanal when compared to untreated control treatment and treatment with fungicide carbendazim in storage condition. The increased activity was observed up to 3 days after treatment and thereafter declined. Further, increased expression of specific isoforms of PO, PPO, SOD and CAT were also observed in the treatment effect of P. fluorescens (0.5%)?+?hexanal (0.02%) treated fruits against L. theobromae. From the results obtained, it is inferred that due to the enhancement of defense-related enzymes via the phenylpropanoid pathway and due to secretion of secondary metabolites that would play significant role in hindering the pathogen quiescence and further invasion in mango fruits and thereby prevent the fruit rot.