Sagar S. Patel

DNA sequence analysis by ORF FINDER & GENOMATIX tool: Bioinformatics analysis of some tree species of Leguminosae family

Bioinformatics is rapidly growing field of applied science, here we have done DNA sequence analyses of few legume tree species by bioinformatics tools. In this paper bioinformatics data of some leguminous trees have been explored and brought to one platform. Various analytical bioinformatics tools were used to generate the information for particular species or group of species. DNA sequence analyses have been done by ORF FINDER & GENOMATIX. The results were discussed in context with all available data generated through above methods for leguminous trees. We have done analysis of 23 legume species of Leguminosae family, and it is further classified in three subfamily, 1. Fabaceae (Papilionaceae) 2. Caesalpiniaceae 3. Mimosaeae and made a database which contains all legume species results, but here we have taken only two legume species in two tools to demonstrate our work. We have used DNA sequence from EMBL database.

Phylogenetic analysis of some leguminous trees using CLUSTALW2 bioinformatics tool

A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally for Protein. MSA has wide range of applications and to cite few of them such as phylogenetic analysis, protein pattern identification, protein domain identification, prediction of protein structure, structural similarity of amino acids and to get evolutionary similarity. ClustalW2 is a general purpose global multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. The output from ClustalW2 shows the best match for the selected sequences and lines up them in such a way that the identities, similarities and differences can be easily understood. Evolutionary relationships can be seen by creating Cladograms or Phylograms. Firstly, individual weights are assigned to each sequence in a partial alignment in order to down-weight near-duplicate sequences and up-weight the most divergent ones. Secondly, amino acid substitution matrices are varied at different alignment stages according to the divergence of the sequences to be aligned. Thirdly, residue-specific gap penalties and locally reduced gap penalties in hydrophilic regions encourage new gaps in potential loop regions rather than regular secondary structure. Fourthly, positions in early alignments where gaps have been opened receive locally reduced gap penalties to encourage the opening up of new gaps at these positions. In this paper, protein sequences of few legume species from UNIPROT database were taken and focused on MSA for protein sequences for these tree species of family Leguminosae, where ClustalW2 tool have used to generate biological data. The results are discussed with the help of Cladograms and Phylograms for selected tree species.

Homology Modelling of Conserved rbcL Amino Acid Sequences in Leguminosae Family

This study is focus on Homology modelling of few Leguminosae family species which are found in Gujarat state, INDIA. There are three subfamilies of Leguminosae family which are Fabaceae (Papilionaceae), Caesalpiniaceae and Mimosaceae. Multiple sequence alignment carried out of few species’ rbcL protein sequences in each subfamily and conserved amino acid considered for homology modelling. Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure. It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone; we found that there are few amino acids which are common with same base pairs in each sub-family even though they are from different genus. There is no Protein structure available of conserved amino acids in PDB database of our study so we did homology modelling of three rbcL protein sequences (one from each sub family) which are found conserved in Multiple sequence alignment and structure validation with Ramachandran Plot was carried out and CASTp server was used to find out active sites in predicted protein structure and finally function of each predicted protein reported after this homology modeling of few conserved rbcL amino acid sequences in Leguminosae family.

Evolutionary studies of some species belonging to leguminosae family based on rbcl gene

Although conifers are of immense ecological and economic value, bioengineering of their chloroplasts remains undeveloped. Understanding chloroplast genomic organization in conifers can facilitate their bioengineering. Members of the conifer II clade (or cupressophytes) are highly diverse in both morphologic features and chloroplast genomic organization. We compared six cupressophyte chloroplast genomes (cpDNAs) that represent four of the five cupressophyte families, including three genomes that are first reported here (Agathis dammara, Calocedrus formosana, and Nageia nagi). The six cupressophyte cpDNAs have lost a pair of large inverted repeats (IRs) and vary greatly in size, organization, and tRNA copies. We demonstrate that cupressophyte cpDNAs have evolved toward reduced size, largely due to shrunken intergenic spacers. In cupressophytes, cpDNA rearrangements are capable of extending intergenic spacers, and synonymous mutations are negatively associated with the size and frequency of rearrangements. The variable cpDNA sizes of cupressophytes may have been shaped by mutational burden and genomic rearrangements. Based on cpDNA organization, our analyses reveal that in gymnosperms, cpDNA rearrangements are phylogenetically informative, which supports the “gnepines” clade. As well, removal of a specific IR influences the minimal rearrangements required for the gnepines and cupressophyte clades, whereby Pinaceae favors removal of IRB but cupressophytes exclusion of IRA. This result strongly suggests that different IR copies have been lost from conifers I and II. Our data helps understand the structural complexity and evolution of cupressophyte cpDNAs.Acute myeloid leukemia (AML) is the second most common form of childhood leukemia and has the worst prognosis of all major childhood cancers. Improving the treatment outcome for patients with AML remains a major clinical challenge. The nucleoside analog, cytarabine (ara-C), has been the mainstay of AML chemotherapy for more than 40 years. However, wide inter-patient variation in treatment response, development of resistance, and severe toxicity remain as major hurdles to effective ara-C chemotherapy. Ara-C is a prodrug that requires activation to ara-CTP by multiple phosphorylation steps. Incorporation of ara-CTP in place of dCTP results in chain termination, thereby blocking DNA and RNA synthesis and causing leukemic cell death. Thus, cellular pathways involved in ara-CTP formation and metabolism as well as in ara-CTP mediated cell death are likely to be significant determinants of ara-C treatment response. Inter-patient variation in relevant pharmacokinetic (PK) and pharmacodynamic (PD) genes may impact the clinical response and toxicity among patients receiving ara-C. We have evaluated genes of importance in ara-C chemotherapy and have found that genetic variation in the ara-C pathway genes had similar prognostic relevance as the well-established factors listed above. We will share our results on ara-C pharmcogenomics and its impact on clinical outcome in AM. Overall our results indicate that understanding of genetic variation in key ara-C metabolic pathway genes might be clinically relevant by providing additional explanation of the variability in clinical response beyond known prognostic factors and might have the potential of being additional prognostic markers of clinical outcome.

De novo RNA seq assembly and annotation of important legume-Vicia sativa L. (SRR403901)

D (Dpp) is the homolog of vertebrate BMP-2 and BMP-4 and functionally interchangeable BMPs. The Bombyx mori (B. mori) and Bombyx mandarina (B. mandarina) Dpp genes share genetic homology with human BMPs and Drosophila Dpp, but few studies have been executed to examine the functions of B. mori and B. mandarina Dpp and its function is not well understood. To date, there was also no reported splicing form of Dpp in silkworm. In this study, we investigated Dpp expression using synthesized cDNA from midgut tissue of B. mandarina by RT-PCR. Interestingly, lower band was discovered with band of full-length Dppc DNA and it was identified as novel splicing form that a part (333 bp) of B. mandarina Dpp was deleted through DNA sequencing analysis. In addition, we found that the delated part in the variant was a portion of proprotein region compared to human BMP-2 and 7 candidate single nucleotide variants (SNVs) were able to affect formation of novel splicing form using variant calling analysis. To the best of our knowledge, this is the first approach to address the novel splicing form of Dpp in B. mandarina which have been not found in B. mori. These results suggest that discovered splicing form of B. mandarina was degenerated in evolution process toward more advanced and domesticated B. mori.Introduction Fusion genes, also known as chimeras, play important roles in tumorigenesis and cancer progression. Then, their role becomes crucial in the areas of biomarkers and therapeutic targets investigation. High-throughput sequencing technologies combined with sophisticated bioinformatics tools might facilitate the discovery of such aberrations. A significant number of bioinformatics algorithms have been developed to detect fusion genes. Detection strategies are quite variegated. In this review, we inspect the strategy of 18 fusion-finder algorithms to understand how these tools call chimeras. Materials and methods In this review, we considered 18 tools which, to the best of our knowledge, are the current state-of-the-art chimera detection tools. Results The considered tools can be classified according to their alignment strategies into four different macro-groups as follows: whole paired-end, paired-end + fragmentation, direct fragmentation and statistical read distribution. The first two techniques require pairedend reads because they exploit encompassing reads during the first alignment phase, while the last two can be applied on both the read formats. Conclusion There is still some work to be done in the area of chimeras detection, especially concerning the definition of common benchmarks and increased specificity.A are powerful reagents for biomedical research, diagnostics and therapeutics. The vast majority of antibody applications have focused on targeting features of the terrestrial proteome. Engineering antibodies to bind RNA directly offers a way to harness powerful technologies to study transcriptomes. We are developing phage display antibody libraries for engineering antibodies that recognize structured RNAs with high affinity and specificity. In one particular application, we are using the antibodies as chaperones for the crystallization and structure determination of RNAs.O meyeriana (O. meyeriana), a GG genome type (2n=24), accumulated plentiful excellent characteristics with respect to tolerance to shade, blast and bacterial blight. However, limited genomic or transcriptomic data of O. meyeriana are currently available. In this study, we present the first comprehensive characterization of the O. meyeriana transcriptome using RNA-seq. We obtained 185,323 contigs with an average length of 1,692 bp and an N50 of 2,391 bp. Through differential expression analysis, we found there were most tissue-specifically expressed genes in roots, and next to stems and leaves. By similarity search against protein databases, 146,450 had at least a significant alignment to existed gene models. Comparison with the Oryza sativa (O. sativa) genome revealed similar rate of alignment across different plant species, however 13% of the O. meyeriana contigs had not been detected as expressed in O. sativa. Furthermore, the enrichment of the plant-pathogen interaction pathway in O. meyeriana showed difference with O. sativa, including the similarity of these aligned candidate genes and the absence of candidate genes involved in the plant-pathogen interaction pathway. In addition, we identified 52 contigs as disease resistance protein which was not existed in O. sativa. Taken together, there are significant differences between O. meyeriana and O. sativa in disease resistance. This information provides a foundation for future investigations into the discovery of a huge amount of novel genes which will facilitate gene mining and provides a basis for comparative studies within the genus Oryza.H mobility group protein A1 (HMGA1) is a non-histone chromosomal protein also known as ‘architectural’ transcription factor that facilitates the assembly of ‘enhanceosome’. Expression of HMGA1 is elevated in a number of human malignancies, however, is practically absent in healthy adults. In the present study, we made an attempt to inhibit hmga1 expression in cancer by using anti-gene strategy. Two triplex forming oligonucleotides (TFOs), TFO-1 and TFO-2 were chosen to target the promoter region of HMGA1 at positions, -284 to -304 and -2800 to -2826 respectively. Stability of DNA triplexes were characterized using UV-Vis spectroscopy, Circular Dichroic spectroscopy, Isothermal titration and Differential scanning calorimetry and was confirmed by gel retardation assay using -32P [ATP]. Expression analysis of HMGA1 was evaluated in HeLa cells using MTT assay, Flow cytometry, Western blot and RT-PCR. Results reveal a higher binding affinity of TFO-1 to HMGA1 as compared to that of TFO-2 which correlates well with the greater efficacy of TFO-1, both in terms of HMGA1 expression and apoptosis. Further, the combination treatment of TFO-1 and adriamycin illustrates an additive effect on HMGA1 expression. Present results indicate that TFO-mediated inhibition of HMGA1 expression is a promising strategy for the development of novel anticancer therapeutics.L plays critical roles in plant development. Depending on the light conditions, plants flexibly elongate or shorten their hypocotyls and leaves. Plant hormones including auxins, gibberellins, and brassinosteroids (BRs) regulate these processes acting alone or in concert. To understand the molecular signature of gene expression under the control of both light and BRs, we performed an Affymetrix genome-wide transcriptome analysis using total RNAs prepared from the four genotypes of Arabidopsis seedlings, Ws-2 wild type, phyB-77, bri1-5, and phyB-77 bri1-5 double. Using the list of genes filtered through the criteria of p 1.5, we made three comparisons: phyB-77 vs. Ws-2; bri1-5vs.Ws-2; and phyB-77 bri1-5vs. Ws-2. Comparisons enabled us to find list of genes under epistatic interactions; bri1-5was epistatic to phyB-77. The genes were further validated through quantitative RT-PCR and transgenic analysis. When At5g53870 was over expressed in the bri1-5 mutant, the dwarf phenotype of bri1-5 was suppressed. Furthermore, we expressed two Peroxidases (PRX2 and PRX73) that were down regulated in phyB-77 but were up regulated in bri1-5 in the antisense orientation; both PRX2 RNAi and PRX73RNAi transgenic plants exhibited elongated hypocotyls and the expression of the target genes was greatly reduced. Our transcriptome analysis followed by qRT-PCR and transgenic expression identified the genes that are critical in light-dependent growth of Arabidopsis.C disease (CD) and ulcerative colitis (UC) are inflammatory bowel diseases (IBD) characterized by chronic and relapsing inflammation of the gastro-intestinal tract (GIT). They cause lifelong suffering, as well as considerable drainage of health care resources. Although their aetiology is still unclear there is a growing body of evidence for a significant microbial factor. Previous research in this area has focused on examining the microbiota composition in stool and in the GIT producing conflicting and inconclusive results. Here, we adapt a new approach and focus on the meta-transcriptome through RNA sequencing of colonic biopsies. Biopsies were collected from inflamed and non-inflamed colonic mucosa from 6 CD and 12 CD patients and sequenced using RNA-Seq using Illumina HiSeq at 15Gb/sample. Raw reads were quality filtered and trimmed using Trimmomatic before aligning to the human genome (hg20) with STAR. The SILVA database along with Bowtie2 was used for identifying and removing rRNA sequences. Remaining reads were aligned using Bowtie2 against a non-redundant gene catalogue constructed from multiple previously published meta-genomic studies of the human GIT. DESeq2 was subsequently used to analyse the count data and identify differentially expressed genes. This led to the finding of microbial genes which are significantly differentially expressed between inflamed and non-inflamed mucosa in bacterial species. Furthermore the count data from these samples show a clear distinction between bacterial gene expression of UC and CD. Thus, our analysis has revealed a clear difference in the gene expression of bacteria in the colon of IBD patients and demonstrated that novel approaches are required in order to understand complex multi-factorial diseases.Materials & Methods: This descriptive analytical study was performed on 100 adult patients (>18 years old) who were affected by cancer and referred to the hospital and the related private centers. The Convenience sampling was performed. Two standard DASS21questionnaires were given to the patients in order to evaluate the rate of their depression; anxiety and religious view standard questionnaire was given them in order to evaluate their religious beliefs. Obtained data were analyzed and investigated using Chi square test and correlation coefficient. Findings among 100 patients, 56 patients were female and 44 patients were male. 23% of the patients were older than 60 years old. 45% were uneducated, 7% elementary educated, 36% guidance school and high school and 12% were under graduated from university. 78% were married, 10% were single and 12% widow. DASS-21 questionnaire indicated rate of depression equal to 36% (24% slight and 12% mean) and rate of anxiety were shown equal to 42% in the under studied patients (14% slight, 18% mean and 10% severe). Also rate of depression, anxiety and religious beliefs of the under studied patients were measured separated from the variables of gender, age, education level and marital statue.R is a common strategy to treat cancer patients. In this case, a high dose (e.g. 80 Gy) of ionizing radiation is often delivered in fractions of 2-3 Gy. However, natural or induced solar radiation can cause deleterious effects to individuals exposed to it at certain conditions of time, dose and distance. The risk/benefit ratio of received ionizing or non-ionizing radiation could be estimated from the expression of key biomarkers involved in the radiation response. The identification and characterization of these biomarkers have been performed from MCF-7 breast cancer cells as well as from biopsies of patients with metastatic breast cancers. SSH and then microarrays has been performed to identify radio-modulated genes. Messenger RNA and total protein have been isolated to performed qPCR and Western blots, respectively. The signalling pathways of new key genes have been unravelled.At present, the exact mechanism and biological basis of aging is unknown. The antagonistic pleiotropy theory and competing model of senescence explain the aging occurrence of some physiological functions of human body from different angles. The single nucleotide polymorphisms (SNPs) of genome suggest the individual’s difference of aging process is associated with SNPs-related individual’s sensitivity to diseases. As the naturally occurring DNA damages and age-associated accumulation of DNA damage as well as decline in gene expression regulation indicate individual life expectancy, whereas the shortening mechanism of telomeric terminals of chromosomes and Hayflick limit of cell division determine human life span.

古吉拉特邦豆科家庭数据库(GLDB)：存在于印度古吉拉特邦的豆科植物生物信息学数据库

生物数据库在生物信息学中发挥着重要的作用，它们为科学家提供了集中访问各种生物数据的机会。目前，分子数据可用于对许多不同植物物种进行分类、进化和情缘关系分析。我们尝试为豆科家族物种生成初步的生物信息学数据，尽可能在一种平台上提供特定类型的信息。总之，我们做了一个包括在印度的古杰雷特州发现的豆科家族所有信息的数据库，包含每个物种的植物学信息和生物信息学信息，并在一个平台上进行分析。创建这种类型的数据库反映出生物信息学可以在植物数据库中发挥重要作用的当代的跨学科方法。开发生物信息学数据库并将所有这些相关信息放在社会特别是科学界一个广泛的平台上，使之得到进一步延伸。