A method for clustering of miRNA sequences using fragmented programming.

Clustering of miRNA sequences is an important problem in molecular genetics associated cellular biology. Thousands of such sequences are known today through advancement in sophisticated molecular tools, sequencing techniques, computational resources and rule based mathematical models. Analysis of such large-scale miRNA sequences for inferring patterns towards deducing cellular function is a great challenge in modern molecular biology. Therefore, it is of interest to develop mathematical models specific for miRNA sequences. The process is to group (cluster) such miRNA sequences using well-defined known features. We describe a method for clustering of miRNA sequences using fragmented programming. Subsequently, we illustrated the utility of the model using a dendrogram (a tree diagram) for publically known A.thaliana miRNA nucleotide sequences towards the inference of observed conserved patterns.

miR-1322 Binding Sites in Paralogous and Orthologous Genes.

We searched for 2,563 microRNA (miRNA) binding sites in 17,494 mRNA sequences of human genes. miR-1322 has more than 2,000 binding sites in 1,058 genes with ΔG/ΔG m ratio of 85% and more. miR-1322 has 1,889 binding sites in CDSs, 215 binding sites in 5' UTRs, and 160 binding sites in 3' UTRs. From two to 28 binding sites have arranged localization with the start position through three nucleotides of each following binding site. The nucleotide sequences of these sites in CDSs encode oligopeptides with the same and/or different amino acid sequences. We found that 33% of the target genes encoded transcription factors. miR-1322 has arranged binding sites in the CDSs of orthologous MAMLD1, MAML2, and MAML3 genes. These sites encode a polyglutamine oligopeptide ranging from six to 47 amino acids in length. The properties of miR-1322 binding sites in orthologous and paralogous target genes are discussed.

Binding sites of miR-1273 family on the mRNA of target genes.

This study examined binding sites of 2,578 miRNAs in the mRNAs of 12,175 human genes using the MirTarget program. It found that the miRNAs of miR-1273 family have between 33 and 1,074 mRNA target genes, with a free hybridization energy of 90% or more of its maximum value. The miR-1273 family consists of miR-1273a, miR-1273c, miR-1273d, miR-1273e, miR-1273f, miR-1273g-3p, miR-1273g-5p, miR-1273h-3p, and miR-1273h-5p. Unique miRNAs (miR-1273e, miR-1273f, and miR-1273g-3p) have more than 400 target genes. We established 99 mRNA nucleotide sequences that contain arranged binding sites for the miR-1273 family. High conservation of each miRNA binding site in the mRNA of the target genes was found. The arranged binding sites of the miR-1273 family are located in the 5'UTR, CDS, or 3'UTR of many mRNAs. Five repeating sites containing some of the miR-1273 family's binding sites were found in the 3'UTR of several target genes. The oligonucleotide sequences of miR-1273 binding sites located in CDSs code for homologous amino acid sequences in the proteins of target genes. The biological role of unique miRNAs was also discussed.

miRAFinder and GeneAFinder scripts: large-scale searching for miRNA and related information in indexed literature abstracts.

UNLABELLED: In recent times, information on miRNAs and their binding sites is gaining momentum. Therefore, there is interest in the development of tools extracting miRNA related information from known literature. Hence, we describe GeneAFinder and miRAFinder scripts (open source) developed using python programming for the semi-automatic extraction and arrangement of updated information on miRNAs, genes and additional data from published article abstracts in PubMed. The scripts are suitable for custom modification as per requirement. AVAILABILITY: miRAFinder and GeneAFinder scripts are free and available for download at http://sites.google.com /site/malaheenee/software.

MiR-3960 binding sites with mRNA of human genes.

The importance of miRNA in cellular regulation is gaining momentum. Therefore, it is of interest to study miRNA in human genes. Hence, the humanmRNA sequences (12,175) were searched for miRNA binding sites and 2,563predicted sites were found. We observed that the miR-3960 has more than 1000mRNA binding sites with high affinity (with ΔG/ΔGm values greater than or equal to 90%) for 375genes. The miR-3960 has 565 binding sites in the 5'UTRs and 515 sites in theCDS of mRNAs. Nucleotide sequences of the binding sites in CDS encode for polyalanine orpolyproline. It is observed that miR-3960 has binding sites in 73 mRNAs of target genesencoded transcription factors. Thus, we document predictedproperties (polysites, sites in CDS) of uncharacterized miR-3960 binding sites. The studying of the miRNA properties is important for creation of diagnostic methods of cancer.

TmiRUSite and TmiROSite scripts: searching for mRNA fragments with miRNA binding sites with encoded amino acid residues.

UNLABELLED: microRNAs are small RNA molecules that inhibit the translation of target genes. microRNA binding sites are located in the untranslated regions as well as in the coding domains. We describe TmiRUSite and TmiROSite scripts developed using python as tools for the extraction of nucleotide sequences for miRNA binding sites with their encoded amino acid residue sequences. The scripts allow for retrieving a set of additional sequences at left and at right from the binding site. The scripts presents all received data in table formats that are easy to analyse further. The predicted data finds utility in molecular and evolutionary biology studies. They find use in studying miRNA binding sites in animals and plants. AVAILABILITY: TmiRUSite and TmiROSite scripts are available for free from authors upon request and at https: //sites.google.com/site/malaheenee/downloads for download.

The properties of binding sites of miR-619-5p, miR-5095, miR-5096, and miR-5585-3p in the mRNAs of human genes.

The binding of 2,578 human miRNAs with the mRNAs of 12,175 human genes was studied. It was established that miR-619-5p, miR-5095, miR-5096, and miR-5585-3p bind with high affinity to the mRNAs of the 1215, 832, 725, and 655 genes, respectively. These unique miRNAs have binding sites in the coding sequences and untranslated regions of mRNAs. The mRNAs of many genes have multiple miR-619-5p, miR-5095, miR-5096, and miR-5585-3p binding sites. Groups of mRNAs in which the ordering of the miR-619-5p, miR-5095, miR-5096, and miR-5585-3p binding sites differ were established. The possible functional and evolutional properties of unique miRNAs are discussed.

miRNA and tropism of human parvovirus B19.

Parvovirus B19 has an extreme tropism for human erythroid progenitors. Here we propose the hypothesis explaining the tropism of human parvovirus B19. Our speculations are based on experimental results related to the capsid proteins VP1 and VP2. These proteins were not detectable in nonpermissive cells in course of these experiments, although the corresponding mRNAs were synthesized. Our interpretation of these results is an inhibition of translation in nonpermissive cells by human miRNAs. We bring support to our hypothesis and propose detailed experimental procedure to test it.

Physiological change in camel milk composition (Camelus dromedarius) 1. Effect of lactation stage.

The change in the composition of camel milk in four dromedaries was studied by including the common measured parameters: protein, total fat, lactose, main minerals (calcium, phosphorus, and iron), and vitamin C. The fat matter varied from 4.34% to 7.81% with a slight decrease all along the lactation and a minimal value at the 14th week corresponding to the lactation peak. Those variations were less important for protein content (from 2.58% to 3.64%), but the minimal value was observed at the 14th week also. The lactose varied slightly around its mean of 3.46%. The vitamin C concentration varied from 48 to 256 mg/l with a tendency of increasing all along the lactation. Calcium and phosphorus concentrations were quite parallel and their ratio Ca/P was constant. The minimal values (1.43 g/l for calcium and 1.16 g/l for phosphorus) were observed at the beginning of the lactation. The iron concentrations varied around the mean of 1.73 mg/l.

Using profiles based on nucleotide hydrophobicity to define essential regions for splicing.

The splice-site sequences of U2-type introns are highly degenerate, so many different sequences can function as U2-type splice sites. Using our new profiles based on hydrophobicity properties we pointed out specific properties for regions surrounding splice sites. We built a set T of flanking regions of genes with 1-3 introns from 21st and 22nd chromosomes extracted from GenBank to define positions having conserved properties, namely hydrophobicity, that are potentially essential for recognition by spliceosome. GT-AG introns exist in U2 and U12-types. Therefore, intron type cannot be simply determined by the dinucleotide termini. We attempted to distinguish U2 and U12-types introns with help of hydrophobicity profiles on sets of spice sites for U2 or U12-type introns extracted from SpliceRack database. The positions given by our method, which may be important for recognition by spliceosome, were compared to the nucleotide consensus provided by a classical method, Pictogram. We showed that there is a similarity of hydrophobicity profiles inside intron types. On one hand, GT-AG and GC-AG introns belonging to U2-type have resembling hydrophobicity profiles as well as AT-AC and GT-AG introns belonging to U12-type. On the other hand, hydrophobicity profiles of U2 and U12-types GT-AG introns are completely different. We suggest that hydrophobicity profiles facilitate definition of intron type, distinguishing U2 and U12 intron types and can be used to build programs to search splice site and to evaluate their strength. Therefore, our study proves that hydrophobicity profiles are informative method providing insights into mechanisms of splice sites recognition.