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Purpose: To analyze the hesitancy and motivational factors related to coronavirus disease 2019 (COVID-19) vaccination among patients visiting for eye care., Methods: A telephonic survey was conducted using validated questionnaires consisting of 36 questions in five sections from July 1 to July 31, 2021. Patients visiting six tertiary centers and one secondary center of our eye hospitals were interviewed over their phones, and their responses were entered onto the Google forms. The responses were recorded as demographics, health status, awareness about vaccination, factors contributing to hesitancy or acceptance to vaccinate, and general perception about the vaccine., Results: A total of 5033 patients were surveyed. The mean age was 49.0 ± 14.2 years. A total of 563 (11.2%) patients gave a history of symptoms or were tested positive for COVID-19; 2225 (44.2%) patients were already COVID-19 vaccinated. Around 2883 (56%) patients were aware of getting infection despite vaccination, and 4092 (81.3%) perceived vaccination should be compulsory. The main reason for vaccination hesitancy was the fear of side effects (n = 487, 17.3%). The fear of getting infected was the most common reason for vaccination (n = 911, 40.9%). Factors associated with a lower proportion of vaccinated individuals included younger age (P < 0.001), female gender (P < 0.001), lower education (P < 0.001), lower income (P < 0.001), and rural residence (P = 0.33)., Conclusion: Creating awareness about the minor side effects and reassurance can allay an individual's fears. The fear associated with the rapid spread of infection and associated mortality needs to be utilized to increase vaccination acceptance. A targeted approach toward groups with poor uptake of vaccination is necessary., Competing Interests: None

Aim: The aim of this present study was to investigate the antifungal mechanism of sertraline against Candida auris (C. auris) and its effect on biofilm formation., Methods and Results: Sertraline, a repurposing drug with a history of human use for the treatment of depression was screened against three different isolates of C. auris, and was found to possess efficient antifungal activity. The antifungal activity of sertraline was further confirmed by killing kinetics assay and post-antifungal effect (PAFE). Sertraline inhibited C. auris yeast to hyphae conversion and further the inhibition of biofilm formation showed 71% inhibition upon treatment. Cell damage caused due to C. auris after treatment with sertraline was observed using SEM and cell membrane damage was ascertained using flow cytometry by Propidium Iodide (PI) uptake assay. The results of sorbitol protection assay and ergosterol effect assay suggested that sertraline did not affect the cell wall and did not act by binding to membrane ergosterol. The mechanism of action of sertraline against C. auris was understood through in silico docking studies that revealed the binding nature of sertraline to the sterol 14 alpha demethylase which is involved in ergosterol biosynthesis. Ergosterol that was quantified from treated cells showed a 5·5-fold decrease in ergosterol production., Conclusion: Sertraline displayed promising antifungal activity against C. auris involved in candidiasis infection and the mechanism of action was predicted., Significance and Impact of This Study: The results of this study can encourage for the development of new antifungal agents and can be promising antifungal agent against C. auris infection., (© 2019 The Society for Applied Microbiology.)

The importance of the polo-like kinase 1 (PLK1) gene is increasing substantially both as a biomarker and as a target for highly specific cancer therapy. This is due to its involvement in multiple points of cell progression and carcinogenesis. PLK1 inhibitors' efficacy in treating human cancers has been limited due to the lack of a specific targeting strategy. Here, we describe a method of targeted downregulation of PLK1 in cancer cells and the concomitant rapid detection of surface lipidomic perturbations using desorption electrospray ionization mass spectrometry (DESI MS). The efficient delivery of siRNA targeting PLK1 gene selectively to the cancer cells is achieved by targeting overexpressed cell surface epithelial cell adhesion molecule (EpCAM) by the EpDT3 aptamer. The chimeric aptamer (EpDT3-siPLK1) showed the knockdown of PLK1 gene expression and PLK1 protein levels by quantitative PCR and western blotting, respectively. The abundant surface lipids, phosphatidylcholines (PCs), such as PC(32:1) (m/z 754.6), PC(34:1) (m/z 782.6), and PC(36:2) (m/z 808.6), were highly expressed in MCF-7 and WERI-RB1 cancer cells compared to normal MIO-M1 cells and they were observed using DESI MS. These overexpressed cell surface lipids in the cancer cells were downregulated upon the treatment of EpDT3-siPLK1 chimera indicating a novel role of PLK1 to regulate surface lipid expression in addition to the efficient selective cancer targeting ability. Our results indicate that DESI MS has a potential ability to rapidly monitor aptamer-mediated cancer therapy and accelerate the drug discovery process. Graphical abstract Binding of aptamer chimera to the cells and changes in lipid profile.

Background: Functionalized gold nanoparticles are emerging as a promising nanocarrier for target specific delivery of the therapeutic molecules in a cancer cell, as a result it targeted selectively to the cancer cell and minimized the off-target effect. The functionalized nanomaterial (bio conjugate) brings novel functional properties, for example, the high payload of anticancer, antioxidant molecules and selective targeting of the cancer molecular markers. The current study reported the synthesis of multifunctional bioconjugate (GNPs-Pep-A) to target the cancer cell., Methods: The GNPs-Pep-A conjugate was prepared by functionalization of GNPs with peptide-A (Pro-His-Cys-Lys-Arg-Met; Pep-A) using thioctic acid as a linker molecule. The GNPs-Pep-A was characterized and functional efficacy was tested using Retinoblastoma (RB) cancer model in vitro., Results: The GNPs-Pep-A target the reactive oxygen species (ROS) in RB, Y79, cancer cell more effectively, and bring down the ROS up to 70 % relative to control (untreated cells) in vitro. On the other hand, Pep-A and GNPs showed 40 and 9 % reductions in ROS, respectively, compared to control. The effectiveness of bioconjugate indicates the synergistic effect, due to the coexistence of both organic (Pep-A) and inorganic phase (GNPs) in novel GNPs-Pep-A functional material. In addition to this, it modulates the mRNA expression of antioxidant genes glutathione peroxidase (GPX), superoxide dismutase (SOD) and catalase (CAT) by two-threefolds as observed., Conclusions: The effects of GNPs-Pep-A on ROS reduction and regulation of antioxidant genes confirmed that Vitis vinifera L . polyphenol-coated GNPs synergistically improve the radical scavenging properties and enhanced the apoptosis of cancer cell.

Rationale: Various disease conditions, particularly tumours, can be understood easily by studying changes in the lipid profile of cells. While lipid profiles of tissues have been recorded by desorption electrospray ionization mass spectrometric (DESI-MS) imaging, there is paucity in standardized protocols for sample preparation involving cell cultures to generate reliable results. In this study, we report a method for the direct analysis of lipids from cultured cells by incorporating them onto Whatman 42 filter paper as a substrate for reliable DESI-MS analysis., Methods: The WERI-RB1 cell line was spotted on commonly used substrates for DESI-MS analysis, such as glass slides, Teflon coated glass slides, thin layer chromatography (TLC) plates, and Whatman 42 filter paper. A comparison of mass spectrometric images with two different lipids was made to understand the behaviour of different surfaces when the same sample was spotted on them. Relative intensities of different lipid peaks in the WERI-RB1 cell line were compared and relative lipid abundances were also compared across two different human retinoblastoma cell lines; WERI-RB1 and Y79., Results: The study demonstrates that good lipid signals can be obtained by DESI-MS when the cells are spotted on Whatman 42 filter paper. Tandem mass spectrometry was performed to identify the lipids as glycerophosphocholines (PC). Better lipid images from assembly of cells were obtained with distinct boundary when they were spotted on Whatman 42 filter paper than other surfaces., Conclusions: We demonstrate the use of a simple substrate for reliable DESI-MS analysis of cultured cells. This method has the potential to understand various interactions of cells with other external agents. The current method would help in the application of DESI-MS for biology in general and medical sciences in particular., (Copyright © 2015 John Wiley & Sons, Ltd.)

Emerging data indicate that gut-derived endotoxin (metabolic endotoxemia) may contribute to low-grade systemic inflammation in insulin-resistant states. Specific gut bacteria seem to serve as lipopolysaccharide (LPS) sources and several reports claim a role for increased intestinal permeability in the genesis of metabolic disorders. Therefore, we investigated the serum levels of LPS and zonulin (ZO-1, a marker of gut permeability) along with systemic levels of tumor necrosis factor-α (TNF-α) and Interleukin-6 (IL-6) in patients with type 2 diabetes mellitus (T2DM) compared to control subjects. Study subjects were recruited from the Chennai Urban Rural Epidemiology Study [CURES], Chennai, India. Study group (n = 45 each) comprised of a) subjects with normal glucose tolerance (NGT) and (b) patients with T2DM. LPS, ZO-1, TNF-α, and IL-6 levels were measured by ELISA. Serum levels of LPS [p < 0.05], LPS activity [p < 0.001], ZO-1 [p < 0.001], TNFα [p < 0.001], and IL-6 [p < 0.001] were significantly increased in patients with T2DM compared to control subjects. Pearson correlation analysis revealed that LPS activity was significantly and positively correlated with ZO-1, fasting plasma glucose, 2 h post glucose, HbA1c, serum triglycerides, TNF-α, IL-6, and negatively correlated with HDL cholesterol. Regression analysis showed that increased LPS levels were significantly associated with type 2 diabetes [odds ratio (OR) 13.43, 95 % CI 1.998-18.9; p = 0.003]. In Asian Indians who are considered highly insulin resistant, the circulatory LPS levels, LPS activity, and ZO-1 were significantly increased in patients with type 2 diabetes and showed positive correlation with inflammatory markers and poor glycemic/lipid control.

Background and Objectives: The clinical presentation of thyroglossal cyst and its variation from adult thyroglossal cyst has not been well studied. This study is to determine if the clinical presentation of thyroglossal duct cysts (TGDC) varies between children and adults and whether this affects the optimal management of individual cases., Design and Setting: Retrospective study of all cases operated on for TGDC from February 2008 to November 2011 in a tertiary care teaching hospital., Subjects and Methods: The gender, age, clinical presentation, radiologic imaging, surgical management, post operative complications, and recurrence rates between the children ( 18 years) were compared., Results: Of the 46 patients, 30 were adults and 16 pediatric; 46.5% of the adults and 74% of the children were females (P=.11). The mean (SD) age in adults was 40.5 (16.0) years, while in children the mean (SD) age was 9.0 (1.4) years, suggesting a bimodal presentation. Hypothyroidism was present in 6.7% of the adults and 56.3% of pediatric cases (P=.0004). Twenty percent of the adults had either an infected TGDC or fistulae, but none of the children had either infection (P=.0001). In both adults and children the duration of disease was significantly shorter in females. In the pediatric group, males had a larger compared to females (P=.006). The most common location of TGDC was the infrahyoid region. The Sistrunk procedure resulted in cure with no recurrences and complications in all., Conclusion: TGDC is commoner in adults with no sex predilection. Children have a shorter duration of disease. Male children present with larger cysts. Hypothyroidism is more common in pediatric TGDC. Infected TGDC and fistulae are uncommon in children. The Sistrunk procedure is adequate for both groups.

Context: No single factor can predict the occurrence of post total thyroidectomy (TT) hypocalcemia., Aims: This study was conducted to look at various factors usually implicated in post TT clinically significant hypocalcemia (CSH) and to develop a scoring system using a combination of these factors to predict CSH., Settings and Design: Prospective study, tertiary care center., Materials and Methods: 145 patients, who underwent total thyroidectomy for benign goiters and early carcinoma thyroid ( < T2/N0/M0), were included. Age of the patient, presence, or absence of hyperthyroidism, pre-operative levels of serum calcium and 25 OH vitamin D, post-operative iPTH at 8 hours and calcium at 12 hours, intra-operative parathyroid preservation status, and nodule size were studied. CSH prediction score (0 to 8) was designed based on these 8 factors., Statistical Analysis: SPSS 13 software was used. For comparison between groups' independent samples T-test and Chi-square test was used. Statistical significance was set at P<0.05. A logistic regression analysis model was built to assess the significant predictors., Results: There were 22 males and 123 females. 64.82% had euthyroid multinodular goiters, 24.82% had toxic MNG, and 10.34% had an early carcinoma of thyroid. 30.34% developed CSH. CSH was observed in patients with low pre-operative calcium (P=0.008), low 25 OH vitamin D (P=0.001), low post-operative iPTH at 8 hours (P=0.001), low serum calcium at 12 hours after surgery (P=0.001) and lesser number of parathyroid identification at surgery (P=0.001). Patient age (P=0.2) and nodule size (P - 0.17) was not significant. Hypocalcemia risk score of > 3 had 91% sensitivity, 84% specificity with a PPV of 71% and NPV of 95%, whereas score of ≥ 4 had 100% specificity and PPV in predicting CSH., Conclusions: CSH after TT is multi-factorial, and a combination of factors (Hypocalcemia prediction score > 3) can be used to predict it so as to discharge patients within 24 hours after surgery.

Morbidity after thyroidectomy is related to injuries to the parathyroids, recurrent laryngeal (RLN) and external branch of superior laryngeal nerves (EBSLN). Mostly these are due to variations in the surgical anatomy. In this study we analyse the surgical anatomy of the laryngeal nerves in Indian patients undergoing thyroidectomy. Materials and Methods. Retrospective study (February 2008 to February 2010). Patients undergoing surgery for benign goitres, T1, T2 thyroid cancers without lymph node involvement were included. Data on EBSLN types, RLN course and its relation to the TZ & LOB were recorded. Results. 404 thyroid surgeries (180 total & 224 hemithyroidectomy) were performed. Data related to 584 EBSLN and RLN were included (324 right sided & 260 left sided). EBSLN patterns were Type 1 in 71.4%, Type IIA in 12.3%, and Type IIB in 7.36%. The nerve was not seen in 4.3% cases. RLN had one branch in 69.34%, two branches in 29.11% and three branches in 1.36%. 25% of the RLN was superficial to the inferior thyroid artery, 65% deep to it and 8.2% between the branches. TZ was Grade 1 in 65.2%, Grade II in 25.1% and Grade III in 9.5%. 31.16% of the RLN passes through the LOB. Conclusions. A thorough knowledge of the laryngeal nerves and anatomical variations is necessary for safe thyroid surgery.

Primary hyperparathyroidism (PHPT) has become an asymptomatic disease in the Western world with the introduction of routine calcium screening. However, the same phenomenon is not observed in India. We have now systematically reviewed the status of PHPT in India. While there is a paucity of literature on PHPT from India when compared to Western countries, some information can be gleaned upon. Most patients present with symptomatic disease whereas very few are screen-detected cases (bone disease 77%, renal disease 36%, and 5.6% asymptomatic). Mean calcium, parathyroid hormone (PTH), and alkaline phosphate levels are high while Vitamin D levels are low. The average parathyroid gland weight is large and the majority being parathyroid adenomas (89.1%). Hungry bone syndrome (HBS) is common in the postoperative period. The disease-related mortality rate is 7.4%, recurrence 4.16%, and persistent disease 2.17%. We suggest that dedicated efforts are needed to pick up asymptomatic disease in India by methods like incorporating calcium estimation in the routine health check-up programs.

Background: Pigeonpea (Cajanus cajan (L.) Millsp) is one of the major grain legume crops of the tropics and subtropics, but biotic stresses [Fusarium wilt (FW), sterility mosaic disease (SMD), etc.] are serious challenges for sustainable crop production. Modern genomic tools such as molecular markers and candidate genes associated with resistance to these stresses offer the possibility of facilitating pigeonpea breeding for improving biotic stress resistance. Availability of limited genomic resources, however, is a serious bottleneck to undertake molecular breeding in pigeonpea to develop superior genotypes with enhanced resistance to above mentioned biotic stresses. With an objective of enhancing genomic resources in pigeonpea, this study reports generation and analysis of comprehensive resource of FW- and SMD- responsive expressed sequence tags (ESTs)., Results: A total of 16 cDNA libraries were constructed from four pigeonpea genotypes that are resistant and susceptible to FW ('ICPL 20102' and 'ICP 2376') and SMD ('ICP 7035' and 'TTB 7') and a total of 9,888 (9,468 high quality) ESTs were generated and deposited in dbEST of GenBank under accession numbers GR463974 to GR473857 and GR958228 to GR958231. Clustering and assembly analyses of these ESTs resulted into 4,557 unique sequences (unigenes) including 697 contigs and 3,860 singletons. BLASTN analysis of 4,557 unigenes showed a significant identity with ESTs of different legumes (23.2-60.3%), rice (28.3%), Arabidopsis (33.7%) and poplar (35.4%). As expected, pigeonpea ESTs are more closely related to soybean (60.3%) and cowpea ESTs (43.6%) than other plant ESTs. Similarly, BLASTX similarity results showed that only 1,603 (35.1%) out of 4,557 total unigenes correspond to known proteins in the UniProt database (or= 5 sequences detected 102 single nucleotide polymorphisms (SNPs) in 37 contigs. As an example, a set of 10 contigs were used for confirming in silico predicted SNPs in a set of four genotypes using wet lab experiments. Occurrence of SNPs were confirmed for all the 6 contigs for which scorable and sequenceable amplicons were generated. PCR amplicons were not obtained in case of 4 contigs. Recognition sites for restriction enzymes were identified for 102 SNPs in 37 contigs that indicates possibility of assaying SNPs in 37 genes using cleaved amplified polymorphic sequences (CAPS) assay., Conclusion: The pigeonpea EST dataset generated here provides a transcriptomic resource for gene discovery and development of functional markers associated with biotic stress resistance. Sequence analyses of this dataset have showed conservation of a considerable number of pigeonpea transcripts across legume and model plant species analysed as well as some putative pigeonpea specific genes. Validation of identified biotic stress responsive genes should provide candidate genes for allele mining as well as candidate markers for molecular breeding.

The sequencing and detailed comparative functional analysis of genomes of a number of select botanical models open new doors into comparative genomics among the angiosperms, with potential benefits for improvement of many orphan crops that feed large populations. In this study, a set of simple sequence repeat (SSR) markers was developed by mining the expressed sequence tag (EST) database of sorghum. Among the SSR-containing sequences, only those sharing considerable homology with rice genomic sequences across the lengths of the 12 rice chromosomes were selected. Thus, 600 SSR-containing sorghum EST sequences (50 homologous sequences on each of the 12 rice chromosomes) were selected, with the intention of providing coverage for corresponding homologous regions of the sorghum genome. Primer pairs were designed and polymorphism detection ability was assessed using parental pairs of two existing sorghum mapping populations. About 28% of these new markers detected polymorphism in this 4-entry panel. A subset of 55 polymorphic EST-derived SSR markers were mapped onto the existing skeleton map of a recombinant inbred population derived from cross N13 x E 36-1, which is segregating for Striga resistance and the stay-green component of terminal drought tolerance. These new EST-derived SSR markers mapped across all 10 sorghum linkage groups, mostly to regions expected based on prior knowledge of rice-sorghum synteny. The ESTs from which these markers were derived were then mapped in silico onto the aligned sorghum genome sequence, and 88% of the best hits corresponded to linkage-based positions. This study demonstrates the utility of comparative genomic information in targeted development of markers to fill gaps in linkage maps of related crop species for which sufficient genomic tools are not available.

Background: There is a need for software scripts and modules for format parsing, data manipulation, statistical analysis and annotation especially for tasks related to marker identification from sequence data and sequence diversity analysis., Results: Here we present several new Perl scripts and a module for sequence data diversity analysis. To enable the use of these software with other public domain tools, we also make available PISE (Pasteur Institute Software Environment) wrappers for these Perl scripts and module. This enables the user to generate pipelines for automated analysis, since PISE is a web interface generator for bioinformatics programmes., Conclusion: A new set of modules and scripts for diversity statistic calculation, format parsing and data manipulation are available with PISE wrappers that enable pipelining of these scripts with commonly used contig assembly and sequence feature prediction software, to answer specific sequence diversity related questions.

Background: Pigeonpea is a nutritious tropical legume with several desirable characteristics but has been relatively neglected in terms of research. More efficient improvement can be achieved in this crop through molecular breeding but adequate molecular markers are lacking and no linkage map has been developed so far. Microsatellites remain the markers of choice due to their high polymorphism and their transferability from closely related genera. The overall objective of this study was to develop microsatellite markers from an enriched library of pigeonpea as well as testing the transferability of soybean microsatellites in pigeonpea., Results: Primers were designed for 113 pigeonpea genomic SSRs, 73 of which amplified interpretable bands. Thirty-five of the primers revealed polymorphism among 24 pigeonpea breeding lines. The number of alleles detected ranged from 2 to 6 with a total of 110 alleles and an average of 3.1 alleles per locus. GT/CA and GAA class of repeats were the most abundant di-nucleotide and tri-nucleotide repeats respectively. Additionally, 220 soybean primers were tested in pigeonpea, 39 of which amplified interpretable bands., Conclusion: Despite the observed morphological diversity, there is little genetic diversity within cultivated pigeonpea as revealed by the developed microsatellites. Although some of the tested soybean microsatellites may be transferable to pigeonpea, lack of useful polymorphism may hinder their full use. A robust set of markers will still have to be developed for pigeonpea genome if molecular breeding is to be achieved.

Background: Pearl millet [Pennisetum glaucum (L.) R. Br.] is a staple food and fodder crop of marginal agricultural lands of sub-Saharan Africa and the Indian subcontinent. It is also a summer forage crop in the southern USA, Australia and Latin America, and is the preferred mulch in Brazilian no-till soybean production systems. Use of molecular marker technology for pearl millet genetic improvement has been limited. Progress is hampered by insufficient numbers of PCR-compatible co-dominant markers that can be used readily in applied breeding programmes. Therefore, we sought to develop additional SSR markers for the pearl millet research community., Results: A set of new pearl millet SSR markers were developed using available sequence information from 3520 expressed sequence tags (ESTs). After clustering, unigene sequences (2175 singlets and 317 contigs) were searched for the presence of SSRs. We detected 164 sequences containing SSRs (at least 14 bases in length), with a density of one per 1.75 kb of EST sequence. Di-nucleotide repeats were the most abundant followed by tri-nucleotide repeats. Ninety primer pairs were designed and tested for their ability to detect polymorphism across a panel of 11 pairs of pearl millet mapping population parental lines. Clear amplification products were obtained for 58 primer pairs. Of these, 15 were monomorphic across the panel. A subset of 21 polymorphic EST-SSRs and 6 recently developed genomic SSR markers were mapped using existing mapping populations. Linkage map positions of these EST-SSR were compared by homology search with mapped rice genomic sequences on the basis of pearl millet-rice synteny. Most new EST-SSR markers mapped to distal regions of linkage groups, often to previous gaps in these linkage maps. These new EST-SSRs are now are used by ICRISAT in pearl millet diversity assessment and marker-aided breeding programs., Conclusion: This study has demonstrated the potential of EST-derived SSR primer pairs in pearl millet. As reported for other crops, EST-derived SSRs provide a cost-saving marker development option in pearl millet. Resources developed in this study have added a sizeable number of useful SSRs to the existing repertoire of circa 100 genomic SSRs that were previously available to pearl millet researchers.

Structure, is a widely used software tool to investigate population genetic structure with multi-locus genotyping data. The software uses an iterative algorithm to group individuals into "K" clusters, representing possibly K genetically distinct subpopulations. The serial implementation of this programme is processor-intensive even with small datasets. We describe an implementation of the program within a parallel framework. Speedup was achieved by running different replicates and values of K on each node of the cluster. A web-based user-oriented GUI has been implemented in PHP, through which the user can specify input parameters for the programme. The number of processors to be used can be specified in the background command. A web-based visualization tool "Visualstruct", written in PHP (HTML and Java script embedded), allows for the graphical display of population clusters output from Structure, where each individual may be visualized as a line segment with K colors defining its possible genomic composition with respect to the K genetic sub-populations. The advantage over available programs is in the increased number of individuals that can be visualized. The analyses of real datasets indicate a speedup of up to four, when comparing the speed of execution on clusters of eight processors with the speed of execution on one desktop. The software package is freely available to interested users upon request.

The availability of complete, annotated genomic sequence information in model organisms is a rich resource that can be extended to understudied orphan crops through comparative genomic approaches. We report here a software tool (cisprimertool) for the identification of conserved intron scanning regions using expressed sequence tag alignments to a completely sequenced model crop genome. The method used is based on earlier studies reporting the assessment of conserved intron scanning primers (called CISP) within relatively conserved exons located near exon-intron boundaries from onion, banana, sorghum and pearl millet alignments with rice. The tool is freely available to academic users at http://www.icrisat.org/gt-bt/CISPTool.htm., (© 2007 ICRISAT.)

The large amounts of EST sequence data available from a single species of an organism as well as for several species within a genus provide an easy source of identification of intra- and interspecies single nucleotide polymorphisms (SNPs). In the case of model organisms, the data available are numerous, given the degree of redundancy in the deposited EST data. There are several available bioinformatics tools that can be used to mine this data; however, using them requires a certain level of expertise: the tools have to be used sequentially with accompanying format conversion and steps like clustering and assembly of sequences become time-intensive jobs even for moderately sized datasets. We report here a pipeline of open source software extended to run on multiple CPU architectures that can be used to mine large EST datasets for SNPs and identify restriction sites for assaying the SNPs so that cost-effective CAPS assays can be developed for SNP genotyping in genetics and breeding applications. At the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), the pipeline has been implemented to run on a Paracel high-performance system consisting of four dual AMD Opteron processors running Linux with MPICH. The pipeline can be accessed through user-friendly web interfaces at http://hpc.icrisat.cgiar.org/PBSWeb and is available on request for academic use. We have validated the developed pipeline by mining chickpea ESTs for interspecies SNPs, development of CAPS assays for SNP genotyping, and confirmation of restriction digestion pattern at the sequence level.

Background: With the advances in DNA sequencer-based technologies, it has become possible to automate several steps of the genotyping process leading to increased throughput. To efficiently handle the large amounts of genotypic data generated and help with quality control, there is a strong need for a software system that can help with the tracking of samples and capture and management of data at different steps of the process. Such systems, while serving to manage the workflow precisely, also encourage good laboratory practice by standardizing protocols, recording and annotating data from every step of the workflow., Results: A laboratory information management system (LIMS) has been designed and implemented at the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) that meets the requirements of a moderately high throughput molecular genotyping facility. The application is designed as modules and is simple to learn and use. The application leads the user through each step of the process from starting an experiment to the storing of output data from the genotype detection step with auto-binning of alleles; thus ensuring that every DNA sample is handled in an identical manner and all the necessary data are captured. The application keeps track of DNA samples and generated data. Data entry into the system is through the use of forms for file uploads. The LIMS provides functions to trace back to the electrophoresis gel files or sample source for any genotypic data and for repeating experiments. The LIMS is being presently used for the capture of high throughput SSR (simple-sequence repeat) genotyping data from the legume (chickpea, groundnut and pigeonpea) and cereal (sorghum and millets) crops of importance in the semi-arid tropics., Conclusion: A laboratory information management system is available that has been found useful in the management of microsatellite genotype data in a moderately high throughput genotyping laboratory. The application with source code is freely available for academic users and can be downloaded from http://www.icrisat.org/gt-bt/lims/lims.asp.

Simple sequence repeats (SSRs) or microsatellites are an important class of molecular markers for genome analysis and plant breeding applications. In this paper, the SSR distributions within ESTs from the legumes soybean (Glycine max, representing 135.86 Mb), medicago (Medicago truncatula, 121.1 Mb) and lotus (Lotus japonicus, 45.4 Mb) have been studied relative to the distributions in cereals such as sorghum (Sorghum bicolor, 98.9 Mb), rice (Oryza sativa, 143.9 Mb) and maize (Zea mays, 183.7 Mb). The relative abundance, density, composition and putative annotations of di-, tri-, tetra- and penta-nucleotide repeats have been compared and SSR containing ESTs (SSR-ESTs) have been clustered to give a non-redundant set of EST-SSRs, available in a database. Further, a subset of such candidate EST-SSRs from sorghum have been tested for their ability to detect polymorphism between Striga-susceptible, stay-green drought tolerant mapping population parent 'E 36-1' and its Striga-resistant, non-stay-green counterpart 'N13'. Primer sets for 64% of the EST-SSRs tested produced a clear and specific PCR product band and 34% of these detected scorable polymorphism between the N13 and E 36-1 parental lines. Over half of these markers have been genotyped on 94 RILs from the (N13 x E 36-1)-based mapping population, with 42 markers mapping onto the ten sorghum linkage groups. This establishes the value of this database as a resource of molecular markers for practical applications in cereal and legume genetics and breeding. The primer pairs for non-redundant EST-SSRs have been designed and are freely available through the database (http://intranet.icrisat.org/gt1/ssr/ssrdatabase.html).

Background: Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag. Molecular genetic diversity analysis may help predict which accessions are most likely to produce fertile progeny when crossed with chickpea cultivars. While, trait-markers may provide an effective tool for breaking linkage drag. Although SSR markers are the assay of choice for marker-assisted selection of specific traits in conventional breeding populations, they may not provide reliable estimates of interspecific diversity, and may lose selective power in backcross programs based on interspecific introgressions. Thus, we have pursued the development of gene-based markers to resolve these problems and to provide candidate gene markers for QTL mapping of important agronomic traits., Results: An EST library was constructed after subtractive suppressive hybridization (SSH) of root tissue from two very closely related chickpea genotypes (Cicer arietinum). A total of 106 EST-based markers were designed from 477 sequences with functional annotations and these were tested on C. arietinum. Forty-four EST markers were polymorphic when screened across nine Cicer species (including the cultigen). Parsimony and PCoA analysis of the resultant EST-marker dataset indicated that most accessions cluster in accordance with the previously defined classification of primary (C. arietinum, C. echinospermum and C. reticulatum), secondary (C. pinnatifidum, C. bijugum and C. judaicum), and tertiary (C. yamashitae, C. chrossanicum and C. cuneatum) gene-pools. A large proportion of EST alleles (45%) were only present in one or two of the accessions tested whilst the others were represented in up to twelve of the accessions tested., Conclusion: Gene-based markers have proven to be effective tools for diversity analysis in Cicer and EST diversity analysis may be useful in identifying promising candidates for interspecific hybridization programs. The EST markers generated in this study have detected high levels of polymorphism amongst both common and rare alleles. This suggests that they would be useful for allele-mining of germplasm collections for identification of candidate accessions in the search for new sources of resistance to pests / diseases, and tolerance to abiotic stresses.

Purpose: Caffeine (1,3,7-trimethyl xanthine), a dietary component, has been shown to have widely varying effects on DNA damage induced by UV and ionizing radiation, depending upon pre- or post-irradiation administration and its concentration. Caffeine administered post-UV irradiation is known to inhibit enzymatic repair of DNA lesions, leading to potentiation of damage, whereas its presence before or during irradiation elicits protection in a wide range of test systems: bacteria, cultured human cells, plant seeds and mouse. The purpose of this study is to test whether caffeine present during gamma-irradiation of plasmid DNA, a system devoid of replication and repair, could elicit protection by scavenging free radicals., Materials and Methods: Plasmid pBR322 DNA was exposed to gamma-radiation in the presence or absence of caffeine at a dose-rate of 1.20 Gy min(-1) and damage measured as single-strand breaks. To understand the mechanisms of the observed protection, especially under oxic conditions, reaction of caffeine with superoxide radical (O(2)(-)), hydrogen peroxide (H(2)O(2)) and the deoxyribose peroxyl radical (ROO(*)) were studied., Results: Irradiation of pBR322 was observed to induce a dose-dependent increase in single-strand breaks. Caffeine itself did not induce strand breaks but reduced radiation-induced strand breaks at micromolar to millimolar concentrations. Caffeine has been shown to react with the radiation-derived oxidants. The reaction rate constants observed were 7.5x10(1) M(-1) s(-1) with O(2)(-) 1.05x10(8) M(-1) s(-1) with ROO(*) and 8.8x10(1) M(-1) s(-1) with H(2)O(2)., Conclusions: Caffeine effectively protects DNA against ionizing radiation in a system devoid of repair and replication machinery. Thus, DNA protection shown by caffeine is possibly due to the scavenging of radiation-derived primary as well as secondary reactive oxygen species, and this physicochemical protective pathway possibly pre-empts any subsequent inhibitory effect of caffeine on the enzymatic repair of DNA.

Purpose: Following the demonstration that caffeine effectively competes with oxygen for electrons and also scavenges hydroxyl radicals and singlet oxygen, the differential modification of oxygen-dependent and independent effects of gamma-radiation by caffeine in membranes was examined, using rat liver mitochondria as a model system., Materials and Methods: Mitochondria were isolated from the livers of Wistar rats and exposed to gamma-radiation in the dose range of 45-600 Gy (dose rate 15 Gy/min) in the presence or absence of caffeine. To examine the 'oxygen effect', post-irradiation incubation was carried out in the presence of oxygen or nitrogen in buffers saturated with the respective gases. Membrane damage was examined as lipid peroxidation (assessed as formation of thiobarbituric acid-reactive substances (TBARS), lipid hydroperoxides (LOOH) and conjugated dienes (CD), protein oxidation, depletion of protein thiols, superoxide dismutase or glutathione., Results: Lipid peroxidation increased as a function of radiation dose, from 45 to 600 Gv. Post-irradiation incubation of mitochondria under nitrogen decreased the response, while incubation under oxygen saturation enhanced it significantly. The presence of caffeine during radiation exposure inhibited lipid peroxidation significantly as a function of concentration, in the range of 5 microM to 4 mM. The inhibition was highest with 4 mM of caffeine. Under oxic conditions, inhibition at 1 mM was significantly more than under anoxia. Anoxia was either ineffective or marginally increased peroxidation in the presence of caffeine. A similar observation was obtained when membrane damage was assessed as protein oxidation. Radiation-induced depletion of protein thiols was greatly enhanced by oxygen saturation and this was completely prevented by caffeine. This compound also protected against the radiation-induced loss of the antioxidant glutathione and the enzyme superoxide dismutase., Conclusions: The results suggest that caffeine effectively protected membranes against the oxic component of damage but may not do so for the anoxic component.

Proton magnetic resonance Spectroscopy (PMRS) has been used to study the differences between immortalized fibroblasts and fibrosarcoma cells of different grade. One and two dimensional purged correlation spectroscopy (PCOSY) have been used to assess intact viable fibroblast and fibrosarcoma cells, and differences in the triglyceride, cellular metabolite, and cell surface fucosylation patterns between the three cell lines have been observed. The clinical implication of this study is the potential use of PMRS as an adjunct to conventional histopathology.