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Quantification of miRNAs and Their Networks in the light of Integral Value Transformations
Get PDFMicroRNAs (miRNAs) which are on average only 21-25 nucleotides long are key post-transcriptional regulators of gene expression in metazoans and plants. A proper quantitative understanding of miRNAs is required to comprehend their structures, functions, evolutions etc. In this paper, the nucleotide strings of miRNAs of three organisms namely Homo sapiens (hsa), Macaca mulatta (mml) and Pan troglodytes (ptr) have been quantified and classified based on some characterizing features. A network has been built up among the miRNAs for these three organisms through a class of discrete transformations namely Integral Value Transformations (IVTs), proposed by Sk. S. Hassan et al [1, 2]. Through this study we have been able to nullify or justify one given nucleotide string as a miRNA. This study will help us to recognize a given nucleotide string as a probable miRNA, without the requirement of any conventional biological experiment. This method can be amalgamated with the existing analysis pipelines, for small RNA sequencing data (designed for finding novel miRNA). This method would provide more confidence and would make the current analysis pipeline more efficient in predicting the probable candidates of miRNA for biological validation and filter out the improbable candidates
Speciation & the origin of communities
No full textPatterns of biodiversity predicted by the neutral theory rely on a simple phenomenological model of speciation. To further investigate the effect of speciation on neutral biodiversity, we define the metacommunity as a system of populations exchanging migrants and use this framework to study allopatric & parapatric speciation. We find that with realistic mutation rates, our metacommunity model driven by neutral processes cannot support more than a few species. Adding natural selection in the population genetics of speciation increases the number of species in the metacommunity but the level of diversity found in Barro Colorado Island is difficult to reach
Insilico based designing of short peptide and ligands for calcineurin receptor
No full textCalcineurin is a target protein for Cyclosporin A (CsA) an immunosuppressive drug which prevents transplant rejection. CsA has complex structure of 11 amino acids, a cyclic structure with uncommon amino acids, and can’t be chemically synthesized. CsA can be synthesized commercially by using fermentation. One report shows chemical synthesis of CsA with partial success (Jason and Diver, 2002). In view of this it is proposed to model a peptide and ligand as an alternate for CsA with the same function and can be chemically synthesized. The target for Cyclosporin is Cyclophilin which forms a ternary complex with calcineurin (CN). An in silico study concludes that all four peptides (1 wild + 3 mutant) were found to bind in the catalytic site of calcineurin. Out of this, mutant3 shows better binding than the rest of the peptides with CN. Two experimental ligand molecules were selected using a virtual screening technique. Further, molecular properties and drug likeliness followed by ADMETox prediction were studied. The designed biomolecule will have great commercial value in pharmaceutical and clinical fields, and could serve as an alternative for natural Cyclosporin A obtained from biological resources. Chemosynthesis of the designed molecule will be economically feasible, and could be produced in adequate amount
Structures at the Atomic Level of Cobalt, Zinc and Lead Niobates (with an Appendix: Atomic structure of cobalt niobate crystal)
No full textThe author has found in recent years that bond lengths are exact sums of the radii of adjacent atoms and or ions, where the ions have Golden ratio based radii. This work was prompted by the exciting observation last year of the Golden ratio in the magnetic properties of cobalt niobate. It is shown here that in cobalt and zinc niobates, cobalt, zinc and oxygen ions have Golden ratio based ionic radii, whereas in lead niobate, all atoms have covalent radii. Also, the angles at the single bond oxygen anion and atom are close to 1080, as in a pentagon
SED-ML Script Language
Get PDFThe Simulation Experiment Description Markup Language (SED-ML) is a XML format describing simulation experiments, so that they can be easily exchanged independent of software tools that created them. This document describes the SED-ML Script, a Python based shorthand that makes it easy to create / edit SED-ML documents
OntoCAT - an integrated programming toolkit for common ontology application tasks
Get PDFOntoCAT provides high level abstraction for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies
Topological Characterization of Protein-Protein Interaction Networks in Human and Mouse
Get PDFThe elucidation of the cell's large-scale organization is a primary challenge for post-genomic biology, and understanding the structure and topological properties of protein-protein interaction networks offers an important starting point for such studies. We compare the protein-protein interaction network of the human and mouse, aiming to uncover the network's generic large-scale properties and the impact of the protein's function and cellular localization on the network topology. We show that both human and mouse protein-protein interaction supports a scale-free, topology with hierarchical modularity, indicating that these features represent a robust and generic property of the protein interactions network. We also find strong correlations between the network's structure and the functional role and sub cellular localization of its protein constituents, concluding that most functional and/or localization classes appear as relatively segregated sub networks of the full protein interaction network
CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0
No full textThe CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or HiSeq sequencing platforms or of combinations of Sanger and Roche/454 sequence data. The pipeline output consists of results and summary files generated during the different pipeline steps. Annotated sequence files are generated that are compatible with common genome browser tools and can be submitted to the GenBank repository at NCBI. This protocol is available in CloVR beta versions 0.5 and 0.6
Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for Composition Improvements
Get PDFAmino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions. Conventional “wet chemistry” analytical methods are time-consuming and costly. As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry. Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument performance and advancement in the field of grain analysis. 

Novel results are presented for amino acid calibrations for US soybean accessions relevant to the food and agricultural industry.

Human Cancer Cells Express Slug-based Epithelial-Mesenchymal Transition Gene Signature Obtained in Vivo
Get PDFThe biological mechanisms underlying cancer cell motility and invasiveness remain unclear, although it has been hypothesized that they involve some type of epithelial-mesenchymal transition (EMT). Here we show that human cancer cells express in vivo a precise multi-cancer invasion-associated gene expression signature characterized by the prominent presence of collagen COL11A1 and thrombospondin THBS2. The signature is present in the expression of all solid tumor datasets that we analyzed and includes numerous EMT markers, among them the transcription factor Slug, fibronectin, and α SMA. Using xenograft models of human cancer cells in immunocompromised mice and profiling the harvested tumors separately with species specific probes, we found that human, but not mouse, cells express most of the genes of the signature and Slug is the only upregulated EMT-inducing transcription factor. Taken together with the presence of the signature in many publicly available datasets, our results suggest that this Slug based EMT signature is produced by the cancer cells themselves in multiple cancer types, including even nonepithelial cancers such as neuroblastoma. Furthermore, we found that the presence of the signature in human xenografted cells was associated with a downregulation of adipocyte markers in the mouse tissue adjacent to the invasive tumor, suggesting contextual microenvironmental interactions when the cancer cells encounter adipocytes, as previously reported. The known and consistent gene composition of this cancer EMT signature, particularly when combined with simultaneous analysis of the adjacent microenvironment, provides unique opportunities for shedding light on the underlying mechanisms of cancer invasiveness as well as identifying potential diagnostic markers and targets for metastasis-inhibiting therapeutics