Haseena Khan

Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach

BackgroundEukaryotic promoter prediction using computational analysis techniques is one of the most difficult jobs in computational genomics that is essential for constructing and understanding genetic regulatory networks. The increased availability of sequence data for various eukaryotic organisms in recent years has necessitated for better tools and techniques for the prediction and analysis of promoters in eukaryotic sequences. Many promoter prediction methods and tools have been developed to date but they have yet to provide acceptable predictive performance. One obvious criteria to improve on current methods is to devise a better system for selecting appropriate features of promoters that distinguish them from non-promoters. Secondly improved performance can be achieved by enhancing the predictive ability of the machine learning algorithms used.ResultsIn this paper, a novel approach is presented in which 128 4-mer motifs in conjunction with a non-linear machine-learning algorithm utilising a Support Vector Machine (SVM) are used to distinguish between promoter and non-promoter DNA sequences. By applying this approach to plant, Drosophila, human, mouse and rat sequences, the classification model has showed 7-fold cross-validation percentage accuracies of 83.81%, 94.82%, 91.25%, 90.77% and 82.35% respectively. The high sensitivity and specificity value of 0.86 and 0.90 for plant; 0.96 and 0.92 for Drosophila; 0.88 and 0.92 for human; 0.78 and 0.84 for mouse and 0.82 and 0.80 for rat demonstrate that this technique is less prone to false positive results and exhibits better performance than many other tools. Moreover, this model successfully identifies location of promoter using TATA weight matrix.ConclusionThe high sensitivity and specificity indicate that 4-mer frequencies in conjunction with supervised machine-learning methods can be beneficial in the identification of RNA pol II promoters comparative to other methods. This approach can be extended to identify promoters in sequences for other eukaryotic genomes.

Comparative genomics of two jute species and insight into fibre biogenesis

Jute (Corchorus sp.) is one of the most important sources of natural fibre, covering ∼80% of global bast fibre production1. Only Corchorus olitorius and Corchorus capsularis are commercially cultivated, though there are more than 100 Corchorus species2 in the Malvaceae family. Here we describe high-quality draft genomes of these two species and their comparisons at the functional genomics level to support tailor-designed breeding. The assemblies cover 91.6% and 82.2% of the estimated genome sizes for C. olitorius and C. capsularis, respectively. In total, 37,031 C. olitorius and 30,096 C. capsularis genes are identified, and most of the genes are validated by cDNA and RNA-seq data. Analyses of clustered gene families and gene collinearity show that jute underwent shared whole-genome duplication ∼18.66 million years (Myr) ago prior to speciation. RNA expression analysis from isolated fibre cells reveals the key regulatory and structural genes involved in fibre formation. This work expands our understanding of the molecular basis of fibre formation laying the foundation for the genetic improvement of jute.

Identification and characterization of jute LTR retrotransposons:: Their abundance, heterogeneity and transcriptional activity.

Long Terminal Repeat (LTR) retrotransposons constitute a significant part of eukaryotic genomes and play an important role in genome evolution especially in plants. Jute is an important fiber crop with a large genome of 1250 Mbps. This genome is still mostly unexplored. In this study we aimed at identifying and characterizing the LTR retrotransposons of jute with a view to understanding the jute genome better. In this study, the Reverse Transcriptase domain of Ty1-copia and Ty3-gypsy LTR retrotransposons of jute were amplified by degenerate primers and their expressions were examined by reverse transcription PCR. Copy numbers of reverse transcriptase (RT) genes of Ty1-copia and Ty3-gypsy elements were determined by dot blot analysis. Sequence analysis revealed higher heterogeneity among Ty1-copia retrotransposons than Ty3-gypsy and clustered each of them in three groups. Copy number of RT genes in Ty1-copia was found to be higher than that of Ty3-gypsy elements from dot blot hybridization. Cumulatively Ty1-copia and Ty3-gypsy may constitute around 19% of the jute genome where two groups of Ty1-copia were found to be transcriptionally active. Since the LTR retrotransposons constitute a large portion of jute genome, these findings imply the importance of these elements in the evolution of jute genome.

Mutation Analysis of the HBB Gene in Selected Bangladeshi β-Thalassemic Individuals: Presence of Rare Mutations

INTRODUCTION AND AIMS Bangladesh has a large number of thalassemic patients. However, no extensive analysis of the mutations in the HBB gene of thalassemic patients has been previously carried out. We have conducted a systematic research to reveal thalassemia mutations in the Bangladeshi population. In this preliminary analysis of 587 bp of the HBB gene in selected thalassemic individuals, some rare mutations in world perspective have been found to be significantly high in the Bangladeshi population, together with the common mutations for thalassemia. RESULTS A 587-bp segment of the HBB gene from 32 chromosomes of 16 beta-thalassemic individuals was analyzed for molecular characterization of the disease. Splice junction mutation IVS-I-5 was found to be the most common. The analysis also revealed some rare mutations HBB: c.-80T>C, HBB: c. 92G>C, HBB: c-92C>G, which are not prevalent in geographically adjacent populations. CONCLUSION This is a first of this kind of study in the Bangladeshi population. Although the small sample size makes it difficult to make any population genetics inference, this study can be regarded as the seminal research for a large-scale study to determine the complete mutation profile underlying thalassemia in the Bangladeshi population. The complete mutation profile will provide invaluable strategies (e.g., prenatal diagnosis and genetic counseling) for better management of thalassemia in the Bangladeshi population.

Xyloglucan endotransglycosylase/hydrolase genes from a susceptible and resistant jute species show opposite expression pattern following Macrophomina phaseolina infection

Two of the most widely and intensively cultivated jute species, Corchorus capsularis and Corchorus olitorius, suffer severely from a stem rot disease caused by the fungus Macrophomina phaseolina. Wild jute species, C. trilocularis, shows resistance to this pathogenic fungus. In this study, the technique of differential display was applied to identify genes which are differentially expressed, under both infected and un-infected conditions, between C. trilocularis and C. olitorius var O-72. Two xyloglucan endotransglycosylase/hydrolase (XTH) genes designated CoXTH1 (from Corchorus olitorius) and CtXTH1 (from C.trilocularis) were identified from each of the two species which show different expression patterns upon fungal infection. A steady rise in the expression of CtXTH1 in response to infection was observed by quantitative real time PCR whereas the expression of CoXTH1 was found to be downregulated. Full length sequences of these two genes were determined using primer based gene walking and RACE PCR. This study confirms the involvement of XTH in molecular interactions between M. phaseolina and jute. However, it remains to be explored whether XTH is an essential component of the signaling pathway involved in plant-fungal interaction.

An endophytic Basidiomycete, Grammothele lineata, isolated from Corchorus olitorius, produces paclitaxel that shows cytotoxicity

Grammothele lineata, an endophyte isolated in our laboratory from jute (Corchorus olitorius acc. 2015) was found to be a substantial paclitaxel producer. Taxol and its related compounds, produced by this endophyte were extracted by growing the fungus in simple nutrient media (potato dextrose broth, PDB). Taxol was identified and characterized by different analytical techniques (TLC, HPLC, FTIR, LC-ESI-MS/MS) following its extraction by ethyl acetate. In PDB media, this fungus was found to produce 382.2 μgL-1 of taxol which is about 7.6 x103 fold higher than the first reported endophytic fungi, Taxomyces andreanae. The extracted taxol exhibited cytotoxic activity in an in vitro culture of HeLa cancer cell line. The fungal extract also exhibited antifungal and antibacterial activities against different pathogenic strains. This is the first report of a jute endophytic fungus harboring the capacity to produce taxol and also the first reported taxol producing species that belongs to the Basidiomycota phylum, so far unknown to be a taxol producer. These findings suggest that the fungal endophyte, Grammothele lineata can be an excellent source of taxol and can also serve as a potential species for chemical and genetic engineering to enhance further the production of taxol.

High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute.

MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops.

Protein secondary structure prediction with high accuracy using Support Vector Machine

Mining bioinformatics data is an emerging area of research. Proteomics is one of the largest areas of focus in bioinformatics and data mining research. Protein structure prediction is one of the most crucial and decisive problem in all the areas of research. Protein secondary structure can be used for the determination of the tertiary structure via the fold recognition method. Hence, predicting the secondary structures from the proteinpsilas primary sequences has attracted the attention of many researchers. Experimental methods have proved to be complex and expensive. So to develop a simple and accurate method for structure prediction is of great importance. In this paper, a new method has been proposed based on the machine learning technique. The first step of this proposal is to find out frequent patterns of consecutive amino acids in a protein database. After this, a set of frequent words (feature set) is found. Then support vector machine (SVM) is used as a binary/tertiary classifier for the classification of protein secondary structure with these frequent words.

Modification of Monolignol Biosynthetic Pathway in Jute: Different Gene, Different Consequence.

Lignin, a cross-linked macromolecule of hydrophobic aromatic structure, provides additional rigidity to a plant cell wall. Although it is an integral part of the plant cell, presence of lignin considerably reduces the quality of the fiber of fiber-yielding plants. Decreasing lignin in such plants holds significant commercial and environmental potential. This study aimed at reducing the lignin content in jute-a fiber crop, by introducing hpRNA-based vectors for downregulation of two monolignoid biosynthetic genes- cinnamate 4-hydroxylase (C4H) and caffeic acid O-methyltransferase (COMT). Transgenic generations, analyzed through Southern, RT-PCR and northern assays showed downregulation of the selected genes. Transgenic lines exhibited reduced level of gene expression with ~ 16–25% reduction in acid insoluble lignin for the whole stem and ~13–14% reduction in fiber lignin content compared to the control lines. Among the two transgenic plant types one exhibited an increase in cellulose content and concomitant improvement of glucose release. Composition of the lignin building blocks was found to alter and this alteration resulted in a pattern, different from other plants where the same genes were manipulated. It is expected that successful COMT-hpRNA and C4H-hpRNA transgenesis in jute will have far-reaching commercial implications leading to product diversification and value addition.

A diverse community of jute (Corchorus spp.) endophytes reveals mutualistic host–microbe interactions

Endophytes are plant-associated microbes that live within plants as an integral part of the host metabolism and function. This study aimed to identify the molecular and physiological characteristics of both culturable and non-culturable endophytic bacteria and fungi present in different parts of the jute (Corchorus olitorius) plant. Using universal primers used to amplify hypervariable bacterial 16S rDNA and fungal internal transcribed spacer (ITS) regions of 18S rDNA, we identified five different culturable and 20 non-culturable endophytic bacteria as well as 14 different fungal endophytes from various parts of jute. Biochemical and physiological tests suggest that these microbes may bring a wide range of benefits to their hosts. For example, all five culturable endophytic bacteria were positive for auxin and catalase activity, which may lead to improved root elongation and stress resistance, respectively. These bacteria also have metal uptake, haemolytic and hydrolytic activities that could be useful in medical, environmental and industrial applications. The fungal endophytes were positive for lignin peroxidase, cellulase and xylanase activities, all of which may influence jute physiology. Another important finding was the antifungal activity of one of the fungi against a devastating pernicious fungus that affects hundreds of plant species.