Immunoinformatics Approach to T-cell Epitopes in Human Immunodeficiency Virus

Human immunodeficiency virus (HIV) is major human disease which belongs to lentivirus (retrovirus). It is a major cause of acquired immunodeficiency syndrome (AIDS), a condition in humans in which progressive failure of the immune system allows life threatening opportunistic infections and cancers to thrive. A number of ways for transmission of HIV form human to another human through the blood, semen, vaginal fluid, pre-ejaculate or breast milk has been proved. An urgent need arises to establish antigen based immunodiagnostic for earlier monitoring of HIV and development of vaccines. In the present study, we have identified two major proteins i.e. ENV and NEF for identification of T-cell epitopes. We used two well established immunoinformatics tools Propred and Propred1 for identification. We identified a novel T-cell epitope for major histocompatibility complex class I and II with highest binding affinity. These finding provide a new insight for development of antigen based diagnostic kit and peptide based vaccine designing for controlling of AIDS

Evaluation of errors in a clinical laboratory: a one-year experience

Background: Efficient laboratory service is the cornerstone of modern health care systems. Scientific innovations have contributed to substantial improvements in the field of laboratory science, but errors still prevail. These errors are classified as preanalytical, analytical and postanalytical, depending upon the time of presentation. Methods: The data for 67,438 routine venous blood specimens were scrutinized, and errors were documented over the period of 1 year in the clinical biochemistry laboratory of Govind Ballabh Pant Hospital in Delhi, India. Results: Preanalytical errors were most common, with a frequency of 77.1% followed by postanalytical 15% and analytical 7.9%, respectively. Conclusions: Our study illustrates the importance of proper venipuncture procedures, analytical expertise and correct transcription of numerical data for precise and accurate reporting of results to clinicians. There is an urgent need for close inter-departmental cooperation to meet the goal of ensuring patient well being. Clin Chem Lab Med 2010;48:63–6.Peer Reviewe

Changes in elemental composition of scales of Channa punctatus on treatment with mercury

In the present study different regions in the scales of Channa punctatus were investigated for elemental composition to see the impact of mercury on them. Five sublethal concentrations of mercury were used after calculating the LC50 value which is 1.21mg/L in 96 hours. When focal and lepidontal regions of scales were seen under electron probe analysis (JEOL 8600M), they were composed of four major elements and these are: calcium (Ca); iron (Fe); aluminium (Al); and phosphorus (P). The percent composition of calcium was recorded to be maximum, followed by phosphorus, aluminium and iron. The percent composition of each element upon exposure to mercury was compared to corresponding control and the deviations were observed. When fish was exposed to different sublethal concentrations of mercury for 15d and 30d, an increase was observed in percentage composition of aluminium and phosphorus, whereas reverse trend was noticed for calcium and iron

A Randomized Placebo-controlled Trial of Iron Supplementation in Breastfed Young Infants Initiated on Complementary Feeding: Effect on Haematological Status

To combat iron deficiency manifesting around six months of age, iron-fortified complementary feeding has been recommended. In developing countries, in view of the poor bioavailability of iron from predominantly cereal-based diets and the high cost of fortification, medicinal iron supplementation is an alternative intervention. This double-blind randomized placebo-controlled trial was conducted from April 1999 to March 2000 in the Out-patient Department of a tertiary hospital in New Delhi, India, to evaluate the haematological effects of medicinal iron supplementation to breastfed young infants initiated on complementary feeding. One hundred healthy non-low birth-weight, predominantly breastfed infants aged 4-6 months were randomized into two groups to receive either iron (2 mg/kg/day) (IS group; n=49) or placebo drops (P group; n=51) beginning with the initiation of home-based non-fortified complementary feeding. Haematological parameters and anthropometry of mothers and infants were measured at baseline and repeated for infants after four and eight weeks of recruitment. Seventy-one subjects (35 in the IS group and the 36 in P group) came for the first follow-up, and of these, 43 (19 in the IS group and 24 in the P group) reported for the second visit. The adjusted (for maternal and baseline infant ferritin) serum ferritin levels were significantly higher in the IS group at both the follow-ups (p=0.006). The adjusted (for maternal ferritin and baseline infant ferritin) change in haemoglobin was significantly higher only at the second follow-up (0.7 g/dL; 95% confidence interval [CI] 0.3-1.0 g/dL). The adjusted rise in haemoglobin was higher in initially anaemic infants (at second follow-up by 1 g/dL; 95% CI 0.5-1.6 g/dL). Medicinal iron supplementation, at the time of initiating complementary feeding, to breastfed young infants resulted in an elevation of serum ferritin and haemoglobin. The response was higher in initially anaemic infants. From a programmatic perspective, evidence needs to be generated on the relative merits of selective (anaemic) versus general supplementation and daily versus weekly supplementation

Stress-induced changes in CARF expression determine growth arrest, apoptosis, or malignant transformation in cultured human cells: Molecular evidence and its application

Background: CARF (Collaborator of ARF)/CDKN2AIP is an essential protein, first cloned as a binding partner of ARF. It was subsequently shown to interact with p53, HDM2 proteins and regulate growth arrest and apoptosis by its multimodal mechanism of action. Over-expression of CARF caused senescence like growth arrest of cells, its knock-down triggered apoptosis. Intriguingly, malignantly transformed cells showed high level of CARF expression. Based on these findings, we hypothesized that level of CARF expression may be a key determinant of cell proliferation fates; where an increase in its levels causes growth arrest/senescence, but beyond a threshold it activates carcinogenesis. Methods: We utilized in vitro cell culture models using retrovirus-driven expression of CARF to achieve over-expression and super-expression of CARF. Analysis of CARF levels was undertaken by biochemical and imaging protocols. Cells exposed to a variety of stresses including physiological, environmental, oxidative, radiation and chemotherapeutics was examined for CARF expression and corresponding cell proliferation fates. Results: Induction of Senescence was seen in cells over-expressing CARF. On the other hand, cells compromised for CARF showed apoptosis, and the ones with super-expression of CARF exhibited malignant transformation. CARF expression analysis in these experimental models endorsed the concept of cell-fate determining role of CARF. Conclusions: We present molecular evidence of the bridging role of CARF in stress-aging-cancer phenotypes and its application in pharmaceuticals and nutraceuticals as a diagnostic and prognostic marker for stress and cancer treatments

Preliminary study of p53 and c-erbB-2 expression in gallbladder cancer in Indian patients manuscript id: 8962091628764582

BACKGROUND: The inactivation of the tumour suppressor gene and activation of the proto-oncogene are the key steps in the development of the human cancer. The p53 and c-erbB-2 are the best examples of it. In the present study, our aim was to determine the role of these genes in the carcinogenesis of gallbladder by immunohistochemistry. METHODS: In all 78 consecutive patients of gall bladder diseases were studied for p53 and c-erbB-2 expression immunohistochemically and their expression was correlated with the age, grades and stages of the disease and presence of stone. An informed consent was obtained in each case. Chi square and z test were applied to see the association of p53 and c-erbB-2 over expression with other clinicopathological factors. RESULTS: Eight (20%) patients of gall bladder cancer were positive for p53 expression and 10 (25%) patients for c-erbB-2. The p53 positivity increased with increasing grade while cerbB-2 positivity decreased with increasing grade of gall bladder cancer. Mean age in cerbB-2 positive cases were lesser as compared to negative cases while p53 did not show such association with age. CONCLUSION: Only one case of gall bladder cancer co-expressed the p53 and c-erbB-2, thereby suggesting that p53 and c-erbB-2 may have independent role in carcinogenesis of gall bladder cancer. c-erbB-2 over expression in adenoma and younger age group indicates its role as an early event in carcinogenesis of gallbladder. However study of larger sample is required to further validate the results

TOPS++FATCAT: Fast flexible structural alignment using constraints derived from TOPS+ Strings Model

<p>Abstract</p> <p>Background</p> <p>Protein structure analysis and comparison are major challenges in structural bioinformatics. Despite the existence of many tools and algorithms, very few of them have managed to capture the intuitive understanding of protein structures developed in structural biology, especially in the context of rapid database searches. Such intuitions could help speed up similarity searches and make it easier to understand the results of such analyses.</p> <p>Results</p> <p>We developed a TOPS++FATCAT algorithm that uses an intuitive description of the proteins' structures as captured in the popular TOPS diagrams to limit the search space of the aligned fragment pairs (AFPs) in the flexible alignment of protein structures performed by the FATCAT algorithm. The TOPS++FATCAT algorithm is faster than FATCAT by more than an order of magnitude with a minimal cost in classification and alignment accuracy. For beta-rich proteins its accuracy is better than FATCAT, because the TOPS+ strings models contains important information of the parallel and anti-parallel hydrogen-bond patterns between the beta-strand SSEs (Secondary Structural Elements). We show that the TOPS++FATCAT errors, rare as they are, can be clearly linked to oversimplifications of the TOPS diagrams and can be corrected by the development of more precise secondary structure element definitions.</p> <p>Software Availability</p> <p>The benchmark analysis results and the compressed archive of the TOPS++FATCAT program for Linux platform can be downloaded from the following web site: <url>http://fatcat.burnham.org/TOPS/</url></p> <p>Conclusion</p> <p>TOPS++FATCAT provides FATCAT accuracy and insights into protein structural changes at a speed comparable to sequence alignments, opening up a possibility of interactive protein structure similarity searches.</p