A method for predicting linear and conformational B-cell epitopes in an antigen from its primary sequence

B-cell is an essential component of the immune system that plays a vital role in providing the immune response against any pathogenic infection by producing antibodies. Existing methods either predict linear or conformational B-cell epitopes in an antigen. In this study, a single method was developed for predicting both types (linear/conformational) of B-cell epitopes. The dataset used in this study contains 3875 B-cell epitopes and 3996 non-B-cell epitopes, where B-cell epitopes consist of both linear and conformational B-cell epitopes. Our primary analysis indicates that certain residues (like Asp, Glu, Lys, and Asn) are more prominent in B-cell epitopes. We developed machine-learning based methods using different types of sequence composition and achieved the highest AUROC of 0.80 using dipeptide composition. In addition, models were developed on selected features, but no further improvement was observed. Our similarity-based method implemented using BLAST shows a high probability of correct prediction with poor sensitivity. Finally, we developed a hybrid model that combines alignment-free (dipeptide based random forest model) and alignment-based (BLAST-based similarity) models. Our hybrid model attained a maximum AUROC of 0.83 with an MCC of 0.49 on the independent dataset. Our hybrid model performs better than existing methods on an independent dataset used in this study. All models were trained and tested on 80 % of the data using a cross-validation technique, and the final model was evaluated on 20 % of the data, called an independent or validation dataset. A webserver and standalone package named "CLBTope" has been developed for predicting, designing, and scanning B-cell epitopes in an antigen sequence available at (https://webs.iiitd.edu.in/raghava/clbtope/).

Brain Hemisphere Dissimilarity, a Self-Supervised Learning Approach for alpha-synucleinopathies prediction with FDG PET

Idiopathic Rem sleep Behavior Disorder (iRBD) is a significant biomarker for the development of alpha-synucleinopathies, such as Parkinson's disease (PD) or Dementia with Lewy bodies (DLB). Methods to identify patterns in iRBD patients can help in the prediction of the future conversion to these diseases during the long prodromal phase when symptoms are non-specific. These methods are essential for disease management and clinical trial recruitment. Brain PET scans with 18F-FDG PET radiotracers have recently shown promise, however, the scarcity of longitudinal data and PD/DLB conversion information makes the use of representation learning approaches such as deep convolutional networks not feasible if trained in a supervised manner. In this work, we propose a self-supervised learning strategy to learn features by comparing the brain hemispheres of iRBD non-convertor subjects, which allows for pre-training a convolutional network on a small data regimen. We introduce a loss function called hemisphere dissimilarity loss (HDL), which extends the Barlow Twins loss, that promotes the creation of invariant and non-redundant features for brain hemispheres of the same subject, and the opposite for hemispheres of different subjects. This loss enables the pre-training of a network without any information about the disease, which is then used to generate full brain feature vectors that are fine-tuned to two downstream tasks: follow-up conversion, and the type of conversion (PD or DLB) using baseline 18F-FDG PET. In our results, we find that the HDL outperforms the variational autoencoder with different forms of inputs.

ViralVacDB: A manually curated repository of viral vaccines

Over the years, numerous vaccines have been developed against viral infections; however, a complete database that provides comprehensive information on viral vaccines has been lacking. In this review, along with our freely accessible database ViralVacDB, we provide details of the viral vaccines, their type, routes of administration and approving agencies. This repository systematically covers additional information such as disease name, adjuvant, manufacturer, clinical status, age and dosage against 422 viral vaccines, including 145 approved vaccines and 277 in clinical trials. We anticipate that this database will be highly beneficial to researchers and others working in pharmaceuticals and immuno-informatics.

Vascular risk factors affect different brain regions in people with Alzheimer’s disease

Introduction

Vascular risk factors including hypertension, diabetes and dyslipidaemia promote diverse pathological mechanisms in the brain leading to cerebral hypoperfusion and ultimately cognitive decline in people. Medial temporal, medial frontal and anterior cingulate atrophy has been closely associated with diabetes and medial temporal lobe atrophy is associated with hypertension in people with Alzheimer’s disease (AD).

Objectives

To assess if hypertension, diabetes and dyslipidaemia have differential effects on different brain locations using brain imaging in people with AD.

Methods

The current study is based on [¹⁸F] fluorodeoxyglucose- positron emission tomography (FDG-PET) data of 970 participants from two large Phase III multi-centre clinical trials of a novel tau aggregation inhibitor drug Leuco-Methylthioninium (LMTX)meeting research criteria for mild to moderate AD. Vascular risk factor data including hypertension, diabetes and dyslipidaemia were collected and quantification of FDG PET hypo-metabolism was done by calculating Standardized Uptake Value Ratio(SUVR).

Results

Hypertension, diabetes and dyslipidaemia were found to have differential effects on brain locations in people with AD. When people with hypertension, diabetes and dyslipidaemia were compared to those without, mean SUVR was increased significantly in both left and right parietal and occipital lobes and decreased in left and right anterior cingulate gyri in hypertensives. SUVR was significantly higher in both left and right temporal lobes in diabetics andlower in both left and right anterior cingulate gyri in people with dyslipidaemia.

Conclusions

Vascular risk factors including hypertension, diabetes and dyslipidaemia have differential effects on different brain regions, measured using SUVR analysis of FDG-PET.

Disclosure

The FDG-PET data was taken from participants of two large phase III clinical trials sponsored by TauRx Therapeutics (Singapore). TauRx Therapeutics has contributed towards my studentship during my PhD but the data related to drug used in the clinical tria

Genomic Surveillance of COVID-19 Variants With Language Models and Machine Learning

The global efforts to control COVID-19 are threatened by the rapid emergence of novel SARS-CoV-2 variants that may display undesirable characteristics such as immune escape, increased transmissibility or pathogenicity. Early prediction for emergence of new strains with these features is critical for pandemic preparedness. We present Strainflow, a supervised and causally predictive model using unsupervised latent space features of SARS-CoV-2 genome sequences. Strainflow was trained and validated on 0.9 million sequences for the period December, 2019 to June, 2021 and the frozen model was prospectively validated from July, 2021 to December, 2021. Strainflow captured the rise in cases 2 months ahead of the Delta and Omicron surges in most countries including the prediction of a surge in India as early as beginning of November, 2021. Entropy analysis of Strainflow unsupervised embeddings clearly reveals the explore-exploit cycles in genomic feature-space, thus adding interpretability to the deep learning based model. We also conducted codon-level analysis of our model for interpretability and biological validity of our unsupervised features. Strainflow application is openly available as an interactive web-application for prospective genomic surveillance of COVID-19 across the globe.

Bronco T (Shirisadi kasaya), a polyherbal formulation prevents LPS induced septicemia in rats

OBJECTIVE

Here, Bronco T (BT), a polyherbal formulation developed in 1984 for treating asthma, has been repurposed against septicemia-induced ALI.

MATERIALS AND METHODS

Lipopolysaccharides (3 mg/kg BW) were injected intraperitoneally before 24 hours of surgery to assess the cardiorespiratory parameters, blood PaO2/FiO2 and MPO, pulmonary water content and histological changes in the lungs. The pentoxifylline (PTX) (25 mg/kg BW) was used as the positive control and given one hour before LPS. BT was given 3 hours (orally at different doses of 3, 1.5 and 0.75 g/kg BW) before LPS.

RESULTS

The LPS treated group showed significant bradypnea, hypotension and bradycardia, through elongated peaks (RR) and (MAP) respectively and finally death after 95 minutes of LPS injection. The PTX and BT (3 g/kg BW) pretreatment significantly prevented these changes (dose-dependent in the BT group). The survival in these groups was maintained up to 190 min after LPS. The Pentoxifylline showed a better response (75%) than Bronco T (72%). In both the treatments, a significant decrease in pulmonary water content and minimal neutrophil infiltration and intact alveoli-capillary membrane was seen in the transverse section (T.S) of the lungs.

CONCLUSIONS

Significant improvement was noted in survival time with lesser tissue damage and improved pulmonary function was observed by pre-treating with Bronco T in LPS induced septicemia.

Comparison of Morphologic Findings in Patients with Dextrocardia with Situs Solitus vs Situs Inversus: a Retrospective Study

BACKGROUND

Studies on dextrocardia have been limited by low numbers. Hence, it is very difficult to find the most common diagnosis in patients with dextrocardia, who are seeking medical attention in tertiary care center.

AIMS AND OBJECTIVE

To identify the most common diagnostic pattern in patients with dextrocardia with different situs.

METHODS

It is a retrospective study with records dating back to up to last 21 years from a major tertiary care center in south India. All the patients with diagnosis of dextrocardia (defined as right-sided baso-apical axis of heart) will be included in the study. Segmental analysis will be done as defined previously.

RESULTS

There were total of n = 378 patients with dextrocardia, 43.3% were females and median age was 1 year while mean age was 7 years. Situs solitus was present in 43.1%, Situs inversus in 38.1%, and Situs ambiguus in 18.8%. In patients with situs solitus and dextrocardia, the most common diagnosis was congenitally corrected TGA ± PS/PA followed by Double outlet Right ventricle ± PS/PA; whereas in patients with Situs inversus and dextrocardia, the most common diagnosis was Double outlet Right ventricle ± PS/PA followed by normal hearts and Left to right shunts.

CONCLUSION

In patients with dextrocardia who are seeking medical advice in a tertiary care center, they are more likely to have situs solitus followed by situs inversus. In situs solitus atrio-ventricular discordance with right ventricular outflow obstruction is the most common lesion suggesting L-looping is the most predominant mechanism. In patients with situs inversus, DORV with RVOTO is the most common lesion.

Iliac crest apophyseal insufficiency avulsion fractures

Iliac crest apophyseal avulsion fractures are rare injuries caused mainly through forceful contraction of attached muscles during high level sporting activities. We present the first case of a spontaneous iliac crest apophyseal avulsion insufficiency fracture in a patient with severe atopic eczema on oral steroids and review the relevant literature.

Recent advancements and new perspectives in animal models for Neurocysticercosis immunopathogenesis

Neurocysticercosis (NCC), one of the most common parasitic diseases of the central nervous system, is caused by Taenia solium. This parasite involves two hosts, intermediate hosts (pig and human) and a definitive host (human) and has various stages in its complex life cycle (eggs, oncosphere, cysticerci and adult tapeworm). Hence, developing an animal model for T. solium that mimics its natural course of infection is quite challenging. We have reviewed here the animal models frequently used to study immunopathogenesis of cysticercosis and also discussed their usefulness for NCC studies. We found that researchers have used mice, rats, guinea pigs, dogs, cats and pigs as models for this disease with varying degrees of success. Mice and rats models have been utilized extensively for immunopathogenesis studies due to their relative ease of handling and abundance of commercially available reagents to study these small animal models. These models have provided some very exciting results for in-depth understanding of the disease. Of late, the experimentally/naturally infected swine model is turning out to be the best animal model as the disease progression closely resembles human infection in pigs. However, handling large experimental animals has its own challenges and limitations.

Effect of oxygen partial pressure in deposition ambient on the properties of RF magnetron sputter deposited Gd2O3 thin films

Gadolinium oxide is an excellent optical material that offers high transmission in a wide wavelength range of 200-1600 nm and exhibits a high bulk refractive index of ∼1.80 at 550 nm. In the present study, a set of Gd₂O₃ thin films has been deposited on fused silica substrates by RF sputtering of a Gd₂O₃ target under various O₂ to Ar flow ratios. The samples have been characterized by grazing incidence x-ray diffraction (GIXRD) to study the long range structural behavior, by GIXR to study density and surface roughness of the films, by atomic force microscopy measurements to study morphological properties, by Rutherford backscattering measurements for compositional studies, and by transmission spectrophotometry and spectroscopic ellipsometry techniques to study their optical properties. It has been observed that the films deposited with 10% oxygen partial pressure have low density, high surface roughness, and high void content, which results in a low value of refractive index of this film, and film quality improves as oxygen partial pressure is further increased. Extended x-ray absorption fine structure measurement with synchrotron radiation has also been employed to extract local structural information around Gd sites, which has in turn been used to explain some of the observed macroscopic properties of the films.

EXAFS studies on Gd-doped ZrO2 thin films deposited by RF magnetron sputtering

ZrO₂ thin films with 0%, 7%, 9%, 11%, and 13% Gd doping have been prepared by RF magnetron sputtering and have been characterized by grazing incidence x-ray diffraction, spectroscopic ellipsometry, and optical transmission measurements to probe their structural and optical properties. Extended x-ray absorption fine structure (EXAFS) measurements have also been carried out on the samples at the Zr K- and Gd L₃-edges. It has been observed that Gd goes to Zr sites up to 9%-11% doping concentration, and for Gd doping concentrations beyond 11%, Gd precipitates out as a separate Gd₂O₃ phase. The local structure information surrounding the Zr and Gd sites obtained from the analysis of the EXAFS studies have also been used to explain the macroscopic optical properties of the samples.

Severe non-infective systemic inflammatory response syndrome, shock, and end-organ dysfunction after zoledronic acid administration in a child

INTRODUCTION

Zoledronic acid is an intravenous bisphosphonate used to increase bone mineral density and reduce the risk of fractures. Its safety profile compares well with pamidronate in pediatric patients. We describe an acute, severe, life-threatening, inflammatory reaction in a child.

METHODS

A 7-year-old boy with complex medical problems and chronic ventilator requirements was admitted to the pediatric intensive care unit (due to ventilator needs) for zoledronic acid infusion and subsequent monitoring. His history was significant for osteoporosis secondary to immobilization with multiple fractures since 2 years of age, hypoxic-ischemic encephalopathy, quadriplegic cerebral palsy, seizure disorder, ventilator dependence, and pulmonary hypertension. He had previously been treated with four cycles of pamidronate without adverse events. He received 0.013 mg/kg of zoledronic acid infused over 30 minutes. Beginning 3 hours after completion of the infusion, he developed progressive tachycardia, fever, hypotension requiring vasopressor infusion, and increasing oxygen requirements. Laboratory studies revealed leukopenia, thrombocytopenia, elevated C-reactive protein, abnormal coagulation profile, metabolic acidosis, and negative cultures. The following day, he developed moderate acute respiratory distress syndrome and pulmonary hemorrhage requiring higher ventilatory settings, and subsequently diarrhea and abdominal distension. Initial clinical resolution was noted from the third day onward, and he was discharged on the sixth day after zoledronate administration.

RESULTS

Our pediatric patient demonstrated an acute, severe, life-threatening reaction to zoledronic acid requiring intensive cardiorespiratory support without an underlying pre-existing inflammatory disorder.

CONCLUSION

Our case highlights the importance of careful monitoring of children following zoledronic acid therapy. We recommend inpatient observation after an initial infusion of zoledronic acid in medically complex children. Children and their parents should be thoroughly counseled on the potential risks of bisphosphonate treatment, which can sometimes be severe and life threatening.

Codominant Role of Interferon-γ- and Interleukin-17-Producing T Cells During Rejection in Full Facial Transplant Recipients

Facial transplantation is a life-changing procedure for patients with severe composite facial defects. However, skin is the most immunogenic of all transplants, and better understanding of the immunological processes after facial transplantation is of paramount importance. Here, we describe six patients who underwent full facial transplantation at our institution, with a mean follow-up of 2.7 years. Seum, peripheral blood mononuclear cells, and skin biopsy specimens were collected prospectively, and a detailed characterization of their immune response (51 time points) was performed, defining 47 immune cell subsets, 24 serum cytokines, anti-HLA antibodies, and donor alloreactivity on each sample, producing 4269 data points. In a nonrejecting state, patients had a predominant T helper 2 cell phenotype in the blood. All patients developed at least one episode of acute cellular rejection, which was characterized by increases in interferon-γ/interleukin-17-producing cells in peripheral blood and in the allograft's skin. Serum monocyte chemotactic protein-1 level was significantly increased during rejection compared with prerejection time points. None of the patients developed de novo donor-specific antibodies, despite a fourfold expansion in T follicular helper cells at 1 year posttransplantation. In sum, facial transplantation is frequently complicated by a codominant interferon-γ/interleukin-17-mediated acute cellular rejection process. Despite that, medium-term outcomes are promising with no evidence of de novo donor-specific antibody development.

Expression and purification of recombinant H5HA1 protein of H5N1 avian influenza virus in E. coli and its application in indirect ELISA

The PCR amplified HA1 fragment of H5N1 (H5HA1) avian influenza virus (AIV) hemagglutinin gene was cloned into pET28a (+) expression vector and expressed in Rosetta Blue (DE3) pLysS cells. The recombinant H5HA1 (rH5HA1) protein purified by passive gel elution after SDS-PAGE of the inclusion bodies reacted specifically with H5N1 serum in Western blot analysis. A subtype specific indirect enzyme linked immunosorbent assay (iELISA) using the rH5HA1 protein as the coating antigen was developed for detecting antibodies to H5 subtype of AIV. The assay had 89.04% sensitivity and 95.95% specificity when compared with haemagglutination inhibition test. The Kappa value of 0.842 indicated a perfect agreement between the tests. The iELISA developed can be used for serosurveillance of avian influenza in chickens.

Non-destructive evaluation of teeth restored with different composite resins using synchrotron based micro-imaging

BACKGROUND

Application of high resolution synchrotron micro-imaging in microdefects studies of restored dental samples.

OBJECTIVE

The purpose of this study was to identify and compare the defects in restorations done by two different resin systems on teeth samples using synchrotron based micro-imaging techniques namely Phase Contrast Imaging (PCI) and micro-computed tomography (MCT). With this aim acquired image quality was also compared with routinely used RVG (Radiovisiograph).

METHODS

Crowns of human teeth samples were fractured mechanically involving only enamel and dentin, without exposure of pulp chamber and were divided into two groups depending on the restorative composite materials used. Group A samples were restored using a submicron Hybrid composite material and Group B samples were restored using a Nano-Hybrid restorative composite material. Synchrotron based PCI and MCT was performed with the aim of visualization of tooth structure, composite resin and their interface.

RESULTS

The quantitative and qualitative comparison of phase contrast and absorption contrast images along with MCT on the restored teeth samples shows comparatively large number of voids in Group A samples.

CONCLUSIONS

Quality assessment of dental restorations using synchrotron based micro-imaging suggests Nano-Hybrid resin restorations (Group B) are better than Group A.

Plan to Have No Unplanned: A Collaborative, Hospital-Based Quality-Improvement Project to Reduce the Rate of Unplanned Extubations in the Pediatric ICU

BACKGROUND

Although under-reported and understudied, unplanned extubations carry a significant risk of patient harm and even death. They are an important yardstick of quality control of care of intubated patients in the ICU. A unit-based risk assessment and multidisciplinary approach is required to decrease the incidence of unplanned extubations.

METHODS

As part of a quality-improvement initiative of Children's Hospital at Montefiore, all planned and unplanned extubations in a multidisciplinary 20-bed pediatric ICU were evaluated over a 12-month period (January to December 2010). At the end of 6 months, an interim analysis was performed, and high-risk patient groups and patient care factors were identified. These factors were targeted in the second phase of the project.

RESULTS

Over this period, there were a total of 267 extubations, of which 231 (87%) were planned extubations and 36 (13%) were unplanned. A patient care policy targeting the risk factors was instituted, along with extensive nursing and other personnel education in the second phase. As a result of this intervention, the unplanned extubation rate in the pediatric ICU decreased from 3.55 to 2.59/100 intubation days. All subjects who had an unplanned extubation during nursing procedures or transport required re-intubation, whereas none of the unplanned extubations during ventilator weaning required re-intubation.

CONCLUSIONS

A targeted approach based on unit-specific risk factors is most effective in quality-improvement projects. A specific policy for sedation and weaning can be very helpful in managing intubated patients and preventing unintended harm.

Effect of intermaxillary tooth-size discrepancy on accuracy of prediction equations for mixed dentition space analysis

AIM

Correlation-statistical methods are widely used for prediction of size of unerupted permanent canines and premolars in mixed dentition space analysis. The present study was planned to evaluate the effect of selecting dental study casts with no intermaxillary tooth-size discrepancy on the accuracy of predicting mesiodistal widths (MDWS) of permanent canines and premolars.

STUDY DESIGN

Bolton ratios were calculated for all the screened study dental casts fulfilling the inclusion criteria. Subjects were divided into two groups. Group A: all subjects with no intermaxillary tooth-size discrepancy within ±2 SD (Standard deviation) of the mean values. Group B: increased percentage of subjects with intermaxillary tooth-size discrepancy beyond ±2 SD (Standard deviation) of the mean values.

STATISTICS

Linear regression equations were established for both maxilla and mandible in both the groups, with different tooth combinations as independent variables. Validation of best possible regression equations was done on an independent set of 40 subjects. The actual and predicted values of MDWS of permanent canines and premolars were compared by paired samples t test in both groups, for both arches.

RESULTS

The accuracy of equations derived from group A was higher than those derived from group B. The difference between actual and predicted values was statistically insignificant in group A and statistically significant in group B.

CONCLUSION

The results confirm the accuracy of simple linear regression equations derived from a sample of children with no intermaxillary tooth-size discrepancy.

Assessment of water quality index of bore well water samples from some selected locations of South Gujarat, India

The present study calculates the water quality index (WQI) of some selected sites from South Gujarat (India) and assesses the impact of industries, agriculture and human activities. Chemical parameters were monitored for the calculation of WQI of some selected bore well samples. The results revealed that the WQI of the some bore well samples exceeded acceptable levels due to the dumping of wastes from municipal, industrial and domestic sources and agricultural runoff as well. Inverse Distance Weighting (IDW) was implemented for interpolation of each water quality parameter (pH, EC, alkalinity, total hardness, chloride, nitrate and sulphate) for the entire sampled area. The bore water is unsuitable for drinking and if the present state of affairs continues for long, it may soon become an ecologically dead bore.

Structural and photoluminescence study of Mn2+-activated CaYAl3 O7 blue phosphors

The structural and photoluminescence properties of CaYAl3 O7 phosphor material doped with varying concentration of Mn(2+) have been studied. The phosphor material was synthesized by the combustion method at 500 °C and was characterized using X-ray diffraction, Fourier transform infrared spectroscopy and photoluminescence spectroscopy (PL). X-ray diffraction showed that the crystallites have average sizes in the range of ~58-70 nm. Corresponding Fourier transform infrared spectroscopy investigations confirm the phase formation and the presence of aluminate group (Al-O bands) in CaYAl3 O7 :Mn(2+) phosphor. Under the excitation at 356 nm wavelength, the PL spectra show the occurrence of two emission peaks obtained in the blue region at 389 nm and 412 nm, which is attributed to the 4 T1(G) → 6A1 transition of Mn(2+) ion. Upon increasing Mn(2+) concentration, the relative PL intensity shows an initial decrement followed by an increase displaying the effect of concentration quenching. Overall the results suggest the possibility of using this material in white lighting devices and plasma display panels.

Differential functional connectivity within an emotion regulation neural network among individuals resilient and susceptible to the depressogenic effects of early life stress

BACKGROUND

Early life stress (ELS) is a significant risk factor for depression. The effects of ELS exposure on neural network organization have not been differentiated from the effect of depression. Furthermore, many individuals exposed to ELS do not develop depression, yet the network organization patterns differentiating resiliency versus susceptibility to the depressogenic effects of ELS are not clear.

METHOD

Women aged 18-44 years with either a history of ELS and no history of depression (n = 7), a history of ELS and current or past depression (n = 19), or a history of neither ELS nor depression (n = 12) underwent a resting-state 3-T functional magnetic resonance imaging (fMRI) scan. An emotion regulation brain network consisting of 21 nodes was described using graph analyses and compared between groups.

RESULTS

Group differences in network topology involved decreased global connectivity and hub-like properties for the right ventrolateral prefrontal cortex (vlPFC) and decreased local network connectivity for the dorsal anterior cingulate cortex (dACC) among resilient individuals. Decreased local connectivity and increased hub-like properties of the left amygdala, decreased hub-like properties of the dACC and decreased local connectivity of the left vlPFC were observed among susceptible individuals. Regression analyses suggested that the severity of ELS (measured by self-report) correlated negatively with global connectivity and hub-like qualities for the left dorsolateral PFC (dlPFC).

CONCLUSIONS

These preliminary results suggest functional neural connectivity patterns specific to ELS exposure and resiliency versus susceptibility to the depressogenic effects of ELS exposure.

Autopsy findings in fatal dengue haemorrhagic fever - 06 Cases

BACKGROUND

During recent outbreak of dengue fever in Delhi, there has been a significant increase in dengue-associated admission in hospitals. To better understand the pathology of dengue haemorrhagic fever, we conducted autopsies of dengue infections deaths within our hospital.

METHOD

This was an autopsy study of dengue-associated deaths at a large tertiary care hospital.

RESULTS

From Sep 2009 to Dec 2010, a total of 1032 patients with serological evidence of dengue infection were admitted to our hospital. There were twelve deaths and autopsies were conducted in six. Adult respiratory distress syndrome, bleeding diathesis, hypotension, hepatic failure and acute renal failure were the common causes of death despite early hospitalization, intravenous fluid, and blood-product support.

CONCLUSION

Dengue is associated with severe disease, and deaths do occur despite current supportive management. Early predictors of disease severity and better clinical interventions are needed.

Tolerance to MHC class II disparate allografts through genetic modification of bone marrow

Induction of molecular chimerism through genetic modification of bone marrow is a powerful tool for the induction of tolerance. Here we demonstrate for the first time that expression of an allogeneic MHC class II gene in autologous bone marrow cells, resulting in a state of molecular chimerism, induces tolerance to MHC class II mismatched skin grafts, a stringent test of transplant tolerance. Reconstitution of recipients with syngeneic bone marrow transduced with retrovirus encoding H-2I-A^b (I-A^b) resulted the long-term expression of the retroviral gene product on the surface of MHC class II-expressing bone marrow derived cell types. Mechanistically, tolerance was maintained by the presence of regulatory T cells, which prevented proliferation and cytokine production by alloreactive host T cells. Thus, the introduction of MHC class II genes into bone marrow derived cells through genetic engineering results in tolerance. These results have the potential to extend the clinical applicability of molecular chimerism for tolerance induction.

Regulation of GPCR-mediated smooth muscle contraction: implications for asthma and pulmonary hypertension

Contractile G-protein-coupled receptors (GPCRs) have emerged as key regulators of smooth muscle contraction, both under healthy and diseased conditions. This brief review will discuss some key topics and novel insights regarding GPCR-mediated airway and vascular smooth muscle contraction as discussed at the 7th International Young Investigators' Symposium on Smooth Muscle (2011, Winnipeg, Manitoba, Canada) and will in particular focus on processes driving Ca(2+)-mobilization and -sensitization.

First Report of Pepper mottle virus Infecting Tomato in Hawaii

In August 2011, tomato (Solanum lycopersicum L.) fruit from a University of Hawaii field trial displayed mottling symptoms similar to that caused by Tomato spotted wilt virus (TSWV) or other tospoviruses. The foliage from affected plants, however, appeared symptomless. Fruit and leaf tissue from affected plants were negative for TSWV analyzed by double antibody sandwich (DAS)-ELISA and/or TSWV ImmunoStrips (Agdia, Elkhart, IN) when performed following the manufacturer's instructions. Total RNA from a symptomatic and an asymptomatic plant was isolated using an RNeasy Plant Mini Kit (Qiagen, Valencia, CA) and reverse transcribed using Invitrogen SuperScript III reverse transcriptase (Life Technologies, Grand Island, NY) and primer 900 (5'- CACTCCCTATTATCCAGG(T)₁₆-3') following the enzyme manufacturer's instructions. The cDNA was then used as template in a universal potyvirus PCR assay using primers 900 and Sprimer, which amplify sequences encoding the partial inclusion body protein (NIb), coat protein, and 3' untranslated region of potyviruses (1). A ~1,700-bp product was amplified from the cDNA of the symptomatic plant but not the asymptomatic plant. This product was cloned using pGEM-T Easy (Promega, Madison, WI) and three clones were sequenced at the University of Hawaii's Advanced Studies in Genomics, Proteomics, and Bioinformatics laboratory. The 1,747-bp consensus sequence of the three clones was deposited in GenBank (Accession No. JQ429788) and, following primer sequence trimming, found to be 97% identical to positions 7,934 through 9,640 of Pepper mottle virus (PepMoV; family Potyviridae, genus Potyvirus) accessions from Korea (isolate '217' from tomato; EU586126) and California (isolate 'C' from pepper; M96425). To determine the incidence of PepMoV in the field trial, all 292 plants representing 14 tomato cultivars were assayed for the virus 17 weeks after planting using a PepMoV-specific DAS-ELISA (Agdia) following the manufacturer's directions. Plants were considered positive if their mean absorbance at 405 nm was greater than the mean absorbance + 3 standard deviations + 10% of the negative control samples. The virus incidence ranged from 4.8 to 47.6% for the different varieties, with an overall incidence of 19.9%. Although plant growth was not noticeably impaired by PepMoV infection, the majority of fruit from infected plants was unsaleable, making PepMoV a considerable threat to tomato production in Hawaii. PepMoV has been reported to naturally infect tomato in Guatemala (3) and South Korea (2). To our knowledge, this is the first report of this virus in Hawaii and the first report of this virus naturally infecting tomato in the United States. References: (1) J. Chen et al. Arch. Virol. 146:757, 2001. (2) M.-K. Kim et al. Plant Pathol. J. 24:152, 2008. (3) J. Th. J. Verhoeven et al. Plant Dis. 86:186, 2002.

The kinetic dose limit in room-temperature time-resolved macromolecular crystallography

Protein X-ray structures are determined with ionizing radiation that damages the protein at high X-ray doses. As a result, diffraction patterns deteriorate with the increased absorbed dose. Several strategies such as sample freezing or scavenging of X-ray-generated free radicals are currently employed to minimize this damage. However, little is known about how the absorbed X-ray dose affects time-resolved Laue data collected at physiological temperatures where the protein is fully functional in the crystal, and how the kinetic analysis of such data depends on the absorbed dose. Here, direct evidence for the impact of radiation damage on the function of a protein is presented using time-resolved macromolecular crystallography. The effect of radiation damage on the kinetic analysis of time-resolved X-ray data is also explored.

Iodine deficiency disorder control programme impact in pregnant women and status of universal salt iodization

BACKGROUND

Several studies pertaining to current status of Iodine Deficiency Disorder Control Programme in India have revealed goiter prevalence in the range of 1.5-44.5%, mean urinary iodine excretion level ranging from 92.5-160 mcg/L and iodized salt coverage ranging from 37-62.3%. Most of these studies were based on school children. However, very few studies have focused on pregnant women. This population is very sensitive to marginalized iodine deficiency throughout their gestational period.

METHODS

This 40 cluster cross sectional study was done in Raipur district. Iodine content of salt was estimated by using "Rapid Salt Testing Kits" along with observing salt storage practices, at household and in shops. Pregnant women were interviewed by using semi structured comprehensive questionnaire, which was based on knowledge attitude, and practices about salt use pattern and awareness about IDDCP, UIE level were also estimated.

RESULTS

Prevalence of goiter was 0.17%. Many (41.12%) pregnant women had <15ppm iodine content in the salt sample and 51.58% of women had subnormal iodine uptake. Wrong salt storage practice was observed in 36.3% of households.

CONCLUSIONS

There were lacunae in Iodine deficiency control program in Chhattisgarh. Implementation and monitoring of program was weak. Thus for monitoring purpose IDD Cell & IDD Laboratory should be established at district level. This will lead to periodic assessment of Iodine Deficiency Disorders, by monitoring of Iodine intake and all other preventive, promotive as well as curative measures in the state.

Progress in antimicrobial activities of chitin, chitosan and its oligosaccharides: a systematic study needs for food applications

In recent years, active biomolecules such as chitosan and its derivatives are undergoing a significant and very fast development in food application area. Due to recent outbreaks of contaminations associated with food products, there have been growing concerns regarding the negative environmental impact of packaging materials of antimicrobial biofilms, which have been studied. Chitosan has a great potential for a wide range of applications due to its biodegradability, biocompatibility, antimicrobial activity, nontoxicity and versatile chemical and physical properties. It can be formed into fibers, films, gels, sponges, beads or nanoparticles. Chitosan films have been used as a packaging material for the quality preservation of a variety of foods. Chitosan has high antimicrobial activities against a wide variety of pathogenic and spoilage microorganisms, including fungi, and Gram-positive and Gram-negative bacteria. A tremendous effort has been made over the past decade to develop and test films with antimicrobial properties to improve food safety and shelf-life. This review highlights the preparation, mechanism, antimicrobial activity, optimization of biocide properties of chitosan films and applications including biocatalysts for the improvement of quality and shelf-life of foods.