DNA numerical encoding schemes for exon prediction: a recent history.

Bioinformatics in the present day has been firmly established as a regulator in genomics. In recent times, applications of Signal processing in exon prediction have gained a lot of attention. The exons carry protein information. Proteins are composed of connected constituents known as amino acids that characterize the specific function. Conversion of the nucleotide character string into a numerical sequence is the gateway before analyzing it through signal processing methods. This numeric encoding is the mathematical descriptor of nucleotides and is based on some statistical properties of the structure of nucleic acids. Since the type of encoding extremely affects the exon detection accuracy, this paper is devised for the review of existing encoding (mapping) schemes. The comparative analysis is formulated to emphasize the importance of the genetic code setting of amino acids considered for application related to computational elucidation for exon detection. This work covers much helpful information for future applications.

Detection of exon location in eukaryotic DNA using a fuzzy adaptive Gabor wavelet transform.

The existing model-independent methods for the detection of exons in DNA could not prove to be ideal as commonly employed fixed window length strategy produces spectral leakage causing signal noise The Modified-Gabor-wavelet-transform exploits a multiscale strategy to deal with the issue to some extent. Yet, no rule regarding the occurrence of small and large exons has been specified. To overcome this randomness, scaling-factor of GWT has been adapted based on a fuzzy rule. Due to the nucleotides' genetic code and fuzzy behaviors in DNA configuration, this work could adopt the fuzzy approach. Two fuzzy membership functions (large and small) take care of the variation in the coding regions. The fuzzy-based learning parameter adaptively tunes the scale factor for fast and precise prediction of exons. The proposed approach has an immense plus point of being capable of isolating detailed sub-regions in each exon efficiently proving its efficacy comparing with existing techniques.

Hereditary disease prediction in eukaryotic DNA: an adaptive signal processing approach.

Hereditary disease prediction in eukaryotic DNA using signal processing approaches is an incredible work in bioinformatics. Researchers of various fields are trying to put forth a noninvasive approach to forecast the disease-related genes. As diseased genes are more random than the healthy ones, in this work, a comparison of the diseased gene is made against the healthy ones. An adaptive signal processing method like functional link artificial neural network-based Levenberg-Marquardt filter has been proposed in this regard. For parameter upgradation, the algorithm is modified using particle swarm optimization. Here, disease genes are discriminated from healthy ones based on the magnitude of mean square error (MSE), which is calculated through the adaptive filter. The performance of the algorithm is inspected by computing some evaluation parameters. Since accuracy is the prime concern, authors in this work have taken an attempt to improve the accuracy level compared to the existing methods. Taking the reference gene as healthy, the overall process is accomplished by categorizing the diseased and healthy targets with MSE value at a threshold of 0.012. The proposed technique predicts the test gene sets successfully.

An integrated approach for identification of exon locations using recursive Gauss Newton tuned adaptive Kaiser window.

Identification of exon location in a DNA sequence has been considered as the most demanding and challenging research topic in the field of Bioinformatics. This work proposes a robust approach combining the Trigonometric mapping with Adaptive tuned Kaiser Windowing approach for locating the protein coding regions (EXONS) in a genetic sequence. For better convergence as well as improved accurateness, the side lobe height control parameter (ß) of Kaiser Window in the proposed algorithm is made adaptive to track the changing dynamics of the genetic sequence. This yields better tracking potential of the anticipated Adaptive Kaiser algorithm as it uses the recursive Gauss Newton tuning which in turn utilizes the covariance of the error signal to tune the ß factor which has been shown through numerous simulation results under a variety of practical test conditions. A detailed comparative analysis with the existing mapping schemes, windowing techniques, and other signal processing methods like SVD, AN, DFT, STDFT, WT, and ST has also been included in the paper to focus on the strength and efficiency of the proposed approach. Moreover, some critical performance parameters have been computed using the proposed approach to investigate the effectiveness and robustness of the algorithm. In addition to this, the proposed approach has also been successfully applied on a number of benchmark gene sets like Musmusculus, Homosapiens, and C. elegans, etc., where the proposed approach revealed efficient prediction of exon location in contrast to the other existing mapping methods.

Isolation, culture, characterization, and osteogenic differentiation of canine endometrial mesenchymal stem cell.

AIM: In this study, the canine endometrium tissue is characterized for its stem cell properties such as adherence to tissue culture plate (plasticity), short population doubling time, serial clonal passaging, long-term culturing properties, stem cell marker expression, and multilineage differentiation potential. MATERIALS AND METHODS: The present work describes a novel isolation protocol for obtaining mesenchymal stem cells from the uterine endometrium and is compared with cells derived from umbilical cord matrix as a positive control. These cells are clonogenic, can undergo several population doublings in vitro, and can be differentiated to the osteocytes in mature mesenchymal tissues when grown in osteogenic differentiation media as detected by Alizarin Red-S staining. RESULTS: It is reported for the first time that the cells derived from the canine endometrium (e-multipotent stem cells [MSCs]) were able to differentiate into a heterologous cell type: Osteocytes, thus demonstrating the presence of MSCs. Thus, the endometrium may be told as a potential source of MSCs which can be used for various therapeutic purposes. CONCLUSION: The endometrium can be used as a potential source of MSCs, which can be used for various therapeutic purposes.

Antimicrobial activity of metal based nanoparticles against microbes associated with diseases in aquaculture.

The emergence of diseases and mortalities in aquaculture and development of antibiotics resistance in aquatic microbes, has renewed a great interest towards alternative methods of prevention and control of diseases. Nanoparticles have enormous potential in controlling human and animal pathogens and have scope of application in aquaculture. The present investigation was carried out to find out suitable nanoparticles having antimicrobial effect against aquatic microbes. Different commercial as well as laboratory synthesized metal and metal oxide nanoparticles were screened for their antimicrobial activities against a wide range of bacterial and fungal agents including certain freshwater cyanobacteria. Among different nanoparticles, synthesized copper oxide (CuO), zinc oxide (ZnO), silver (Ag) and silver doped titanium dioxide (Ag-TiO2) showed broad spectrum antibacterial activity. On the contrary, nanoparticles like Zn and ZnO showed antifungal activity against fungi like Penicillium and Mucor species. Since CuO, ZnO and Ag nanoparticles showed higher antimicrobial activity, they may be explored for aquaculture use.

Correlation of phase values with CT Hounsfield and R2* values in calcified neurocysticercosis.

PURPOSE: To correlate phase and R2* derived from susceptibility-weighted magnetic resonance imaging (MRI) with computed tomography-Hounsfield (CT-HU) values in calcified neurocysticercosis and to evaluate phase imaging in the assessment of calcified neurocysticercosis. MATERIALS AND METHODS: Thirty-five patients with 52 calcified lesions underwent both CT and MRI. Phase and R2* were calculated from multi-echo 3D-T2-star-weighted-angiography data. MRI and CT data were coregistered using mutual information. Spearman's correlation was performed between quantitative phase and CT-HU and R2* values. The Mann-Whitney U-test was used to see differences between CT-HU and R2* values from corresponding positive and negative phase regions. RESULTS: The median values of CT-HU and R2* from regions with positive and negative phase were found to be 142.10 (range: 41.89-491.75) and 68.5/sec (range: 20-110/sec) and 137.30 (range: 30.83-458.88) and 69/sec (range: 0-110/sec), respectively. There was a significant correlation of positive phase values with corresponding CT-HU and R2* values. In addition, there was a significant correlation of R2* and CT-HU with negative phase values. CONCLUSION: We conclude that there is a significant correlation between negative and positive phase with CT-HU and R2* values, suggesting that the CT hyperdense lesion may have both calcium and other minerals, which can be differentiated using phase imaging. Conventional MRI should include phase imaging to detect calcified neurocysticercosis.

Precancerous and non-cancer disease endpoints of chronic arsenic exposure: the level of chromosomal damage and XRCC3 T241M polymorphism.

Genetic variants are expected to play an important role in arsenic susceptibility. Our previous study revealed deficient DNA repair capacity to be a susceptibility factor for arsenicism. T241M polymorphism in XRCC3 (a homologous recombination repair pathway gene) is widely studied for its association with several cancers. We have investigated the association of XRCC3 T241M polymorphism with arsenic-induced precancerous and non-cancer disease outcomes. The present study evaluated the association of T241M polymorphism with arsenic-induced skin lesions, peripheral neuropathy (neurodegenerative changes), conjunctivitis and other ocular diseases. A case-control study was conducted in West Bengal, India, involving 206 cases with arsenic-induced skin lesions and 215 controls without arsenic-induced skin lesions having similar arsenic exposure. XRCC3 T241M polymorphism was determined using conventional PCR-sequencing method. Chromosomal aberration assay, arsenic-induced neuropathy and ocular diseases were also evaluated. The data revealed that presence of at least one Met allele (Met/Met or Thr/Met) was protective towards development of arsenic-induced skin lesions [OR=0.45, 95% CI: 0.30-0.67], peripheral neuropathy [OR=0.49; 95%CI: 0.30-0.82] and conjunctivitis [OR=0.60; 95%CI: 0.40-0.92]. A significant correlation was also observed between protective genotype and decreased frequency of chromosomal aberrations. Thus the results indicate the protective role of Met allele against the arsenic-induced skin lesions, chromosomal instability, peripheral neuropathy and conjunctivitis.

Logistics and supply management system of drugs at different levels in Darbhanga District of Bihar.

OBJECTIVES: To understand the logistics and supply management system of drugs at different levels within the district health care delivery system of Dharbanga in Bihar. METHOD: This was a cross-sectional study in 3 Primary Health Centres (PHCs), 3 Additional Primary Health Centres (APHCs) and 6 Subcentres (SCs) during September-December 2008. The study subjects were Civil Surgeon, Pharmacists, Medical Officers, ANMs. Data was collected using qualitative and quantitative techniques from different stakeholders. RESULT: The health centers were severely understaffed and drug stores are managed by unqualified/untrained pharmacists. Drug list available was not fully matching with the need/requirement of the population. The vital and essential drugs required for various health centers were of short supply or unavailable in medical stores. MOs were unaware of budget allocation/allotment for their centers. Demand estimation of the drug items were not done scientifically hence quantity of drugs supplied was not in consonance with community needs. The existing guidelines were not followed as a result drugs like Zinc, Misoprostol and Magsulf were not available at the PHCs or APHCs. The storage and transportation facilities of drugs were found to be poor. Community members were not satisfied with the availability of drugs. CONCLUSION: The logistic and supply system of drugs in Darbhanga district is very weak, hence the needs of the catering population related to medicines was not fully met.

Analysis of T-cell proliferation and cytokine secretion in the individuals exposed to arsenic.

Over six million people in nine districts of West Bengal, India are exposed to very high levels of arsenic primarily through their drinking water. More than 300,000 people showed arsenic-induced skin lesions in these districts. This is regarded as the greatest arsenic calamity in the world. Chronic arsenicosis causes varied dermatological signs ranging from pigmentation changes, hyperkeratosis to non-melanocytic cancer of skin, and also malignancies in different internal organs. Higher incidences of opportunistic infections are found in the arsenic-exposed individuals, indicating that their immune systems may be impaired somehow. We have thus investigated the effect of arsenic on T-cell proliferation and cytokine secretion in 20 individuals with arsenic-induced skin lesions and compared the results with 18 arsenic-unexposed individuals. A marked dose-dependent suppression of Concanavalin A (Con A) induced T-cell proliferation was observed in the arsenic-exposed individuals compared with the unexposed (P < 0.001) individuals. This correlated with a significant decrease in the levels of secreted cytokines by the T cells (TNF-alpha, IFN-gamma, IL2, IL10, IL5, and IL4) in the exposed individuals (P < 0.001). Thus it can be inferred that arsenic exposure can cause immunosuppression in humans.

Eradicating polio: it's feasibility in near future?

Continuous wild poliovirus transmission despite 12 years of intensive surveillance has raised serious questions about the feasibility of polio eradication programme with current strategy in near future. At present most of the cases are confined to four endemic countries, which are causing sporadic outbreaks in non-endemic areas. India has experienced a significant increase in number of cases reported in 2006 compared to previous year. Outbreaks originated in western UP which was due to the accumulation of susceptibles between the last outbreak in 2002 and early 2006. Substantial improvement has been observed in strategies of polio eradication but still there are gaps in the programme implementation which needs immediate attention so that goal of polio eradication can be achieved at the earliest opportunity. Even though there are many issues but there are also many factors, which favour polio eradication. These factors include new tool in form of m OPV, natural immunity due to recent outbreak, limiting international spread of polio, new researches to guide programme in right direction, political commitments from endemic countries, etc. 2008 presents the best opportunity ever to interrupt wild polio virus transmission which will lead to global eradication of Polio. Since global eradication is within sight, it is scientifically possible to eradicate the disease in near future.

Preponderance of GC-rich sites in silver-stained nucleolus organizing regions of Rita rita (Hamilton) and Mystus gulio (Hamilton) (Bagridae, Pisces), as revealed by chromomycin A3-staining technique and scanning electron microscopic studies.

The karyotypes of two species of catfish, Rita rita (Hamilton) (2n = 54; 14m + 34sm + 6st; NF = 102) and Mystus gulio (Hamilton) (2n = 58; 30m + 12sm + 2st + 14t, NF = 100) were studied through Giemsa-, silver- and chromomycin A(3)-staining techniques. The silver-stained karyotypes in both sexes of R. rita and M. gulio revealed that the nucleolus organizing regions were located terminally at the shorter arms (Tp) of one pair of submetacentric chromosomes, placed at positions Nos. 2 and 1, respectively, which was confirmed by scanning electron microscopy. Staining with a GC-specific fluorochrome, chromomycin A(3), produced bright fluorescence in the Ag-positive nucleolus organizer regions, suggesting thereby that nucleolus organizing regions actually included GC-rich sites of active r-RNA genes in metaphase chromosomes of these two bagrids. Further such studies are needed due to the extreme paucity of data on fish.

Preponderance of GC-rich sites in silver-stained nucleolus organizing regions of Rita rita (Hamilton) and Mystus gulio (Hamilton) (Bagridae, Pisces), as revealed by chromomycin A3-staining technique and scanning electron microscopic studies

The karyotypes of two species of catfish, Rita rita (Hamilton) (2n = 54; 14m + 34sm + 6st; NF = 102) and Mystus gulio (Hamilton) (2n = 58; 30m + 12sm + 2st + 14t, NF = 100) were studied through Giemsa-, silver- and chromomycin A(3)-staining techniques. The silver-stained karyotypes in both sexes of R. rita and M. gulio revealed that the nucleolus organizing regions were located terminally at the shorter arms (Tp) of one pair of submetacentric chromosomes, placed at positions Nos. 2 and 1, respectively, which was confirmed by scanning electron microscopy. Staining with a GC-specific fluorochrome, chromomycin A(3), produced bright fluorescence in the Ag-positive nucleolus organizer regions, suggesting thereby that nucleolus organizing regions actually included GC-rich sites of active r-RNA genes in metaphase chromosomes of these two bagrids. Further such studies are needed due to the extreme paucity of data on fish.