Permutation pattern discovery in biosequences.

Functionally related genes often appear in each other's neighborhood on the genome; however, the order of the genes may not be the same. These groups or clusters of genes may have an ancient evolutionary origin or may signify some other critical phenomenon and may also aid in function prediction of genes. Such gene clusters also aid toward solving the problem of local alignment of genes. Similarly, clusters of protein domains, albeit appearing in different orders in the protein sequence, suggest common functionality in spite of being nonhomologous. In the paper, we address the problem of automatically discovering clusters of entities, be they genes or domains: we formalize the abstract problem as a discovery problem called the (pi)pattern problem and give an algorithm that automatically discovers the clusters of patterns in multiple data sequences. We take a model-less approach and introduce a notation for maximal patterns that drastically reduces the number of valid cluster patterns, without any loss of information, We demonstrate the automatic pattern discovery tool on motifs on E. Coli protein sequences.     

Synthesis of thiazolidine-2,4-dione derivatives: anticancer,antimicrobial and DNA cleavage studies

In the search of efficient anticancer agents, here, new 5-(4-alkylbenzyledene)thiazolidine-2,4-dione derivatives (5a–g) have been successfully synthesized and characterized and are evaluated for anticancer and antimicrobial activities using DNA cleavage studies. In vitro studies on anticancer activity of compound 5d (NSC: 768619/1) was done against the full panel of 60 human tumor cell lines. The five-level dose activity results revealed that, the compound 5d was active against all the cell lines, it has shown potential activity against leukemia SR (GI₅₀: 2.04 μM), non-small cell lung cancer NCI-H522 (GI₅₀: 1.36 μM), colon cancer COLO 205 (GI₅₀: 1.64 μM), CNS cancer SF-539 (GI₅₀: 1.87 μM), melanoma SK-MEL-2 (GI₅₀: 1.64 μM), ovarian cancer OVCAR-3 (GI₅₀: 1.87 μM), renal cancer RXF 393 (GI₅₀: 1.15 μM), prostate cancer PC-3 (GI₅₀: 1.90 μM), and breast cancer MDA-MB-468(GI₅₀: 1.11 μM). DNA cleavage studies revealed that at 50 μg/mL concentration, partial DNA digestion was observed and when the concentration is increasing to threefold (150 μg/mL), complete linear DNA digestion and partial supercoiled DNA digestion was observed. Further antimicrobial studies indicate that all the synthesized compounds except compound 5a possess prominent activity against all the screened microbial species. This study throws a ray of light in the field of anticancer drugs.     

Species identification in seven small millet species using polymerase chain reaction-restriction fragment length polymorphism of trnS-psbC gene region.

The chloroplast trnS-psbC gene regions from total genomic DNA of 119 accessions from seven small millet species were amplified by polymerase chain reaction (PCR) and digested with eight restriction enzymes individually as well as in combinations of two enzymes to generate restriction fragment length polymorphism (PCR-RFLP). PCR-RFLP with individual enzymes revealed polymorphism between only some species. However, all the species could be distinguished by using a combination of two enzymes, specifically HaeIII and MspI. PCR-RFLP of 11 to 20 accessions with the same enzyme combination showed no intraspecific variation, which established that the differential banding patterns were species specific. In contrast, the same enzyme combination was not useful for differentiating different species of the genera Cajanus, Rhyncosia, Abies, Rhizophora, Ceriops, and Bruguiera, and it also revealed intraspecies variation in three species of Abies. The present study indicated that digestion of trnS-psbC with two four-base recognizing enzymes reveals more variation than with either enzyme alone and that it may be a method of choice for species identification in some genera.     

Real-time loop-mediated isothermal amplification assay for rapid and sensitive detection of anthrax spores in spiked soil and talcum powder

Loop-mediated isothermal amplification (LAMP) assay is a powerful and innovative gene amplification technique that specifically amplifies the target gene under isothermal conditions with a high degree of sensitivity, rapidity and specificity. The major advantage of the LAMP assay is monitoring of amplified products without the requirement of any sophisticated equipment. In the present study a real time LAMP assay was employed for rapid and real time detection of Bacillus anthracis spores spiked in 0.1 g of soil and talcum powder ranging from 2 to 10⁷ spores. DNA was isolated from spiked soil and talcum powder using PBS containing 1% Triton X-100, and heat treatment. Isolated DNA was used as template for LAMP and PCR. LAMP amplification was obtained in 60 min under isothermal condition at 63°C by employing a set of six primers targeting the pag gene of B. anthracis. The detection limit of LAMP assay in soil and talcum powder was found to be as low as 5 spores, compared to 10³ spores and 10⁴ spores by PCR in talcum powder and soil, respectively. The findings suggest that LAMP is a more rapid and sensitive assay than PCR for detecting anthrax spores, additionally the methodology to prepare DNA from spiked samples is simple, rapid and cost effective.     

Halophytes as a source of genes for abiotic stress tolerance

Agricultural productivity is majorly impacted due to various abiotic stresses, particularly salinity and drought. Halophytes serve as an excellent resource for identifying and developing new crop systems, as these grow very luxuriously in very high saline soils. Understanding salinity stress tolerance mechanisms in such plants is an important step towards generating crop varieties that can cope with environmental stresses. Use of modern tools of ‘omics’ analyses and small RNA sequencing has helped to gain insights into the complex plant stress responses. Salinity tolerance being a multigenic trait requires a combination of strategies and techniques to successfully develop improved crops varieties. Many transgenic crops are being developed through genetic transformation. Besides marker-assisted breeding/QTL approaches are also being used to improve abiotic stress tolerance. In this review, we focus on the recent developments in the utilization of halophytes as a source of genes for genetic improvement in abiotic stress tolerance of crops.     

Methylenetetrahydrofolate reductase mutations, a genetic cause for familial recurrent neural tube defects

Methylenetetrahydrofolate reductase (MTHFR) gene mutations have been implicated as risk factors for neural tube defects (NTDs). The best-characterized MTHFR genetic mutation 677C→T is associated with a 2-4 fold increased risk of NTD if patient is homozygous for this mutation. This risk factor is modulated by folate levels in the body. A second mutation in the MTHFR gene is an A→C transition at position 1298. The 1298A→C mutation is also a risk factor for NTD, but with a smaller relative risk than 677C→T mutation. Under conditions of low folate intake or high folate requirements, such as pregnancy, this mutation could become of clinical importance. We present a case report with MTHFR genetic mutation, who presented with recurrent familial pregnancy losses due to anencephaly/NTDs.     

Inhibitory effect of tannins from galls of Carpinus tschonoskii on the degranulation of RBL-2H3 Cells

In this study, the anti-allergy potency of thirteen tannins isolated from the galls on buds of Carpinus tschonoskii (including two tannin derivatives) was investigated. RBL-2H3 (rat basophilic leukemia) cells were incubated with these compounds, and the release of β-hexosaminidase and cytotoxicity were measured. Of the thirteen tannins, tetragalloylglucose (2), pentagalloylglucose (3), casuarictin (4), and casuarinin (9) were the most potent inhibitors, and all the tannins showed no cytotoxic effect after 24 h of incubation. The results obtained suggest that tannins from C. tschonoskii are capable of inhibiting allergic reactions and may be useful for the treatment or prevention of type I allergic diseases.     

Recombination gives a new insight in the effective population size and the history of the old world human populations

The information left by recombination in our genomes can be used to make inferences on our recent evolutionary history. Specifically, the number of past recombination events in a population sample is a function of its effective population size (Ne). We have applied a method, Identifying Recombination in Sequences (IRiS), to detect specific past recombination events in 30 Old World populations to infer their Ne. We have found that sub-Saharan African populations have an Ne that is approximately four times greater than those of non-African populations and that outside of Africa, South Asian populations had the largest Ne. We also observe that the patterns of recombinational diversity of these populations correlate with distance out of Africa if that distance is measured along a path crossing South Arabia. No such correlation is found through a Sinai route, suggesting that anatomically modern humans first left Africa through the Bab-el-Mandeb strait rather than through present Egypt.