Assessing the genetic diversity of rice originating from Bangladesh, Assam and West Bengal

Acknowledgements This work was funded by BBSRC research project BB/J00336/1. FS and a part of the proportion of the cost of the Illumina genotyping was funded by a Beachell-Borlag International Fellowship. The authors would like to acknowledge the help of Dr MK Sarmah in collecting seed samples of the landraces and improved cultivars from Assam used in this study and Dr. Ma. Elizabeth B. Naredo and Ms. Sheila Mae Q. Mercado for handling of IRGC accessions and preparation of DNAs for genotyping. All rice seeds used here were obtained with MTA agreements and seed and dry leaves imported into the UK under import licence IMP⁄SOIL⁄18⁄2009 issued by Science and Advice for Scottish Agriculture.Peer reviewedPublisher PD

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]

<p>Abstract</p> <p>Background</p> <p>Pigeonpea [<it>Cajanus cajan </it>(L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping.</p> <p>Results</p> <p>In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped <it>in silico </it>identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population.</p> <p>Conclusion</p> <p>We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus <it>Cajanus</it>. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.</p

Risk factors for orofacial clefts in India:A case-control study

BACKGROUND: Orofacial clefts (OFC) are linked with several genetic and environmental factors. The aim of this study was to explore the association of potential risk factors with OFCs in India. METHODS: This was a hospital-based, matched case-control (1:4 ratio; matching done for parity) study conducted in Hyderabad, Bengaluru, and Delhi-National Capital Region. Cases (nonsyndromic clefts) were recruited from treatment centers, while controls (live births) were recruited from maternity centers. Information on exposures was collected during personal interviews. Exposures of interest included folic acid supplementation during the peri-conceptional period, consanguineous marriage, exposure to drugs, infections during pregnancy, family history of OFC, and dietary factors. RESULTS: A total of 785 participants were included in the study: 157 cases and 628 controls. A family history of cleft lip/palate (adjusted odds ratio [AOR], 15.48; 95% confidence interval [CI], 4.36-54.96; p value = 0.001), exclusive vegetarianism (AOR, 4.47; 95% CI, 1.83-10.98; p value = 0.001), and delayed first conception (AOR, 2.55, 95% CI, 1.25-5.21, p = 0.01) were found to be strongly associated with higher risk of OFCs. Supplementation with folic acid during first 3 months of pregnancy was not found to be protective against OFCs (AOR, 1.24; 95% CI, 0.59-2.58; p value = 0.56). CONCLUSION: Our study confirmed the importance of family history as a risk factor for OFC. Our study did not show an association with folic acid supplementation but was underpowered to detect small effects. Our finding of higher risk among vegetarians requires replication. Birth Defects Research 109:1284-1291, 2017. © 2017 The Authors. Birth Defects Research Published by Wiley Periodicals, Inc

Supporting dataset

<p>Positive and negative phosphorylation site sequence data corresponding to four kinases PKA, PKC, MAPK and CK2 divided into training and test dataset. </p

A composite method based on formal grammar and DNA structural features in detecting human polymerase II promoter region.

An important step in understanding gene regulation is to identify the promoter regions where the transcription factor binding takes place. Predicting a promoter region de novo has been a theoretical goal for many researchers for a long time. There exists a number of in silico methods to predict the promoter region de novo but most of these methods are still suffering from various shortcomings, a major one being the selection of appropriate features of promoter region distinguishing them from non-promoters. In this communication, we have proposed a new composite method that predicts promoter sequences based on the interrelationship between structural profiles of DNA and primary sequence elements of the promoter regions. We have shown that a Context Free Grammar (CFG) can formalize the relationships between different primary sequence features and by utilizing the CFG, we demonstrate that an efficient parser can be constructed for extracting these relationships from DNA sequences to distinguish the true promoter sequences from non-promoter sequences. Along with CFG, we have extracted the structural features of the promoter region to improve upon the efficiency of our prediction system. Extensive experiments performed on different datasets reveals that our method is effective in predicting promoter sequences on a genome-wide scale and performs satisfactorily as compared to other promoter prediction techniques

The prevalence of behavioral disorders among children under parental care and out of parental care: A comparative study in India

Background: Children may suffer from a wide range of behavioral problems, but children living under conditions of perpetual stress and trauma and experiencing breakdown of family structures are tremendously affected. This study was adopted to identify the prevalence of behavioral disorders among children under parental care and out of parental care. Methods: A cross-sectional comparative descriptive study was conducted among 300 children of age 6-12 years from a pediatric outpatient department of a selected hospital and 300 children from selected orphanages in Kolkata to compare the prevalence of behavioral disorders in children under parental care and out of parental care using Strengths and Difficulties Questionnaire (SDQ). Results: Total difficulty was more prevalent in children out of parental care (220 children) than in children under parental care (128 children). Conduct problem was the most prevalent behavioral disorder among all the subscales of SDQ with 48.70% and 84.30% of children, respectively. This was followed by peer problem (44.60% and 48.30%), emotional problem (33.70% and 55.60%), and hyperactivity problem (26.70% and 32.30%), respectively. There was significant difference in total difficulty, all subscales, externalizing score, internalizing score, and impact score between the two groups. Regression analysis showed significant relationship of selected variables such as the child’s favorite hobbies and number of close friends the child has using total difficulty score in both the groups. Significant correlation was found among subscales in both the groups. Conclusion: Family-based care and improvised institutional care should be emphasized to reduce the burden of behavioral problem in children. Keywords: Behavioral, Comparative, Parental care, Prevalence, Strengths and difficulties questionnair

A Grammar Inference Approach for Predicting Kinase Specific Phosphorylation Sites

<div><p>Kinase mediated phosphorylation site detection is the key mechanism of post translational mechanism that plays an important role in regulating various cellular processes and phenotypes. Many diseases, like cancer are related with the signaling defects which are associated with protein phosphorylation. Characterizing the protein kinases and their substrates enhances our ability to understand the mechanism of protein phosphorylation and extends our knowledge of signaling network; thereby helping us to treat such diseases. Experimental methods for predicting phosphorylation sites are labour intensive and expensive. Also, manifold increase of protein sequences in the databanks over the years necessitates the improvement of high speed and accurate computational methods for predicting phosphorylation sites in protein sequences. Till date, a number of computational methods have been proposed by various researchers in predicting phosphorylation sites, but there remains much scope of improvement. In this communication, we present a simple and novel method based on Grammatical Inference (GI) approach to automate the prediction of kinase specific phosphorylation sites. In this regard, we have used a popular GI algorithm Alergia to infer Deterministic Stochastic Finite State Automata (DSFA) which equally represents the regular grammar corresponding to the phosphorylation sites. Extensive experiments on several datasets generated by us reveal that, our inferred grammar successfully predicts phosphorylation sites in a kinase specific manner. It performs significantly better when compared with the other existing phosphorylation site prediction methods. We have also compared our inferred DSFA with two other GI inference algorithms. The DSFA generated by our method performs superior which indicates that our method is robust and has a potential for predicting the phosphorylation sites in a kinase specific manner.</p></div

ROC curve by varying threshold values for PHSDB dataset for the four kinases PKA, PKC, MAPK and CK2.

<p>ROC curve by varying threshold values for PHSDB dataset for the four kinases PKA, PKC, MAPK and CK2.</p

Structural pattern of eight different features for the nonpromoter sequences taken from EMBL and EID database.

<p>The sequences used here are predicted as true promoters by grammars. The structural profiles are plotted with average value of window size 3 nt.</p

Production rules of grammar G1 generation the promoter region of a human DNA sequence.

<p>Production rules of grammar G1 generation the promoter region of a human DNA sequence.</p