MicroRNA–mRNA interaction network using TSK-type recurrent neural fuzzy network

MicroRNAs are short non-coding RNAs that can regulate gene expression during various crucial cell processes such as differentiation, proliferation and apoptosis. Changes in expression profiles of miRNA play an important role in the development of many cancers, including CRC. Therefore, the identification of cancer related miRNAs and their target genes are important for cancer biology research. In this paper, we applied TSK-type recurrent neural fuzzy network (TRNFN) to infer miRNA–mRNA association network from paired miRNA, mRNA expression profiles of CRC patients. We demonstrated that the method we proposed achieved good performance in recovering known experimentally verified miRNA–mRNA associations. Moreover, our approach proved successful in identifying 17 validated cancer miRNAs which are directly involved in the CRC related pathways. Targeting such miRNAs may help not only to prevent the recurrence of disease but also to control the growth of advanced metastatic tumors. Our regulatory modules provide valuable insights into the pathogenesis of cancer

PSWT Based Linear Predictive Coding and Development of a Parallel Multiple Subsequence Structure for DWT Computation

During 1990's the Wavelet Transform emerged as an important signal processing tool with potential applications in time-frequency analysis and non-stationary signal processing.Wavelets have gained popularity in broad range of disciplines like signal/image compression, medical diagnostics, boundary value problems, geophysical signal processing, statistical signal processing,pattern recognition,underwater acoustics etc.In 1993, G. Evangelista introduced the Pitch- synchronous Wavelet Transform, which is particularly suited for pseudo-periodic signal processing.The work presented in this thesis mainly concentrates on two interrelated topics in signal processing,viz. the Wavelet Transform based signal compression and the computation of Discrete Wavelet Transform. A new compression scheme is described in which the Pitch-Synchronous Wavelet Transform technique is combined with the popular linear Predictive Coding method for pseudo-periodic signal processing. Subsequently,A novel Parallel Multiple Subsequence structure is presented for the efficient computation of Wavelet Transform. Case studies also presented to highlight the potential applications.

Structural Characterization and Non-linear Optical Properties of Metal Complexes of Some Donor-Acceptor Substituted N-salicylidene-N' -aroylhydrazine Ligands

The present work deals with the complexation of Schiff bases of aroylhydrazines with various transition metal ions. The hydrazone systems selected for study have long 7I:-delocalized chain in the ligand molecule itself, which get intensified due to metal-to-ligand or ligand-to-metal charge transfer excitations upon coordination. Complexation with metal ions like copper, nickel, cobalt, manganese, iron, zinc and cadmium are tried. Various spectral techniques are employed for characterization. The structures of some complexes have been well established by single crystal X-ray diffraction studies. The nonIinaer optical studies of the ligands and complexes synthesized have been studied by hyper-Rayleigh scattering technique.The work is presented in seven chapters and the last one deals with summary and conclusion. One of the hydrazone system selected for study proved that it could give rise to polymeric metal complexes. Some of the copper, nickel, zinc and cadmium complexes showed non-linear optical activity. The NLO studies of manganese and iron showed negative result, may be due to the inversion centre of symmetry within the molecular lattice.

Penaeus monodon larvae can be protected from Vibrio harveyi infection by pre-emptive treatment of a rearing system with antagonistic or non-antagonistic bacterial probiotics

This study shows that the disease resistance and survival rate of Penaeus monodon in a larval rearing systems can be enhanced by supplementing with antagonistic or non-antagonistic probiotics. The antagonistic mode of action of Pseudomonas MCCB 102 and MCCB 103 against vibrios was demonstrated in larval mesocosm with cultures having su⁄cient concentration of antagonistic compounds in their culture supernatant. Investigations on the antagonistic properties of Bacillus MCCB 101, Pseudomonas MCCB 102 and MCCB 103 and Arthrobacter MCCB 104 against Vibrio harveyi MCCB111under in vitro conditions revealed that Pseudomonas MCCB 102 and MCCB 103 were inhibitory to the pathogen.These inhibitory propertieswere further con¢rmed in the larval rearing systems of P. monodon. All these four probionts signi¢cantly improved larval survival in long-term treatments as well as when challengedwith a pathogenic strain ofV. harveyiMCCB111. We could demonstrate that Pseudomonas MCCB 102 andMCCB103 accorded disease resistance and a higher survival rate in P. monodon larval rearing systems throughactive antagonism of vibrios,whereas Bacillus MCCB 101 and Arthrobacter MCCB 104 functioned as probiotics through immunostimulatory and digestive enzyme-supporting modes of action.

Fast Fractal Coding Method for the Detection of Microcalcification in Mammograms

The presence of microcalcifications in mammograms can be considered as an early indication of breast cancer. A fastfractal block coding method to model the mammograms fordetecting the presence of microcalcifications is presented in this paper. The conventional fractal image coding method takes enormous amount of time during the fractal block encoding.procedure. In the proposed method, the image is divided intoshade and non shade blocks based on the dynamic range, andonly non shade blocks are encoded using the fractal encodingtechnique. Since the number of image blocks is considerablyreduced in the matching domain search pool, a saving of97.996% of the encoding time is obtained as compared to theconventional fractal coding method, for modeling mammograms.The above developed mammograms are used for detectingmicrocalcifications and a diagnostic efficiency of 85.7% isobtained for the 28 mammograms used.

Differential induction, isolation, physicochemical and molecular characterization of temperate phages of environmental Vibrio cholerae as evidence of phage mediated Horizontal Gene Transfer

The resurgence of the enteric pathogen Vibrio cholerae, the causative organism of epidemic cholera, remains a major health problem in many developing countries like India. The southern Indian state of Kerala is endemic to cholera. The outbreaks of cholera follow a seasonal pattern in regions of endemicity. Marine aquaculture settings and mangrove environments of Kerala serve as reservoirs for V. cholerae. The non-O1/non-O139 environmental isolates of V. cholerae with incomplete ‘virulence casette’ are to be dealt with caution as they constitute a major reservoir of diverse virulence genes in the marine environment and play a crucial role in pathogenicity and horizontal gene transfer. The genes coding cholera toxin are borne on, and can be infectiously transmitted by CTXΦ, a filamentous lysogenic vibriophages. Temperate phages can provide crucial virulence and fitness factors affecting cell metabolism, bacterial adhesion, colonization, immunity, antibiotic resistance and serum resistance. The present study was an attempt to screen the marine environments like aquafarms and mangroves of coastal areas of Alappuzha and Cochin, Kerala for the presence of lysogenic V. cholerae, to study their pathogenicity and also gene transfer potential. Phenotypic and molecular methods were used for identification of isolates as V. cholerae. The thirty one isolates which were Gram negative, oxidase positive, fermentative, with or without gas production on MOF media and which showed yellow coloured colonies on TCBS (Thiosulfate Citrate Bile salt Sucrose) agar were segregated as vibrios. Twenty two environmental V. cholerae strains of both O1 and non- O1/non-O139 serogroups on induction with mitomycin C showed the presence of lysogenic phages. They produced characteristic turbid plaques in double agar overlay assay using the indicator strain V. cholerae El Tor MAK 757. PCR based molecular typing with primers targeting specific conserved sequences in the bacterial genome, demonstrated genetic diversity among these lysogen containing non-O1 V. cholerae . Polymerase chain reaction was also employed as a rapid screening method to verify the presence of 9 virulence genes namely, ctxA, ctxB, ace, hlyA, toxR, zot,tcpA, ninT and nanH, using gene specific primers. The presence of tcpA gene in ALPVC3 was alarming, as it indicates the possibility of an epidemic by accepting the cholera. Differential induction studies used ΦALPVC3, ΦALPVC11, ΦALPVC12 and ΦEKM14, underlining the possibility of prophage induction in natural ecosystems, due to abiotic factors like antibiotics, pollutants, temperature and UV. The efficiency of induction of prophages varied considerably in response to the different induction agents. The growth curve of lysogenic V. cholerae used in the study drastically varied in the presence of strong prophage inducers like antibiotics and UV. Bacterial cell lysis was directly proportional to increase in phage number due to induction. Morphological characterization of vibriophages by Transmission Electron Microscopy revealed hexagonal heads for all the four phages. Vibriophage ΦALPVC3 exhibited isometric and contractile tails characteristic of family Myoviridae, while phages ΦALPVC11 and ΦALPVC12 demonstrated the typical hexagonal head and non-contractile tail of family Siphoviridae. ΦEKM14, the podophage was distinguished by short non-contractile tail and icosahedral head. This work demonstrated that environmental parameters can influence the viability and cell adsorption rates of V. cholerae phages. Adsorption studies showed 100% adsorption of ΦALPVC3 ΦALPVC11, ΦALPVC12 and ΦEKM14 after 25, 30, 40 and 35 minutes respectively. Exposure to high temperatures ranging from 50ºC to 100ºC drastically reduced phage viability. The optimum concentration of NaCl required for survival of vibriophages except ΦEKM14 was 0.5 M and that for ΦEKM14 was 1M NaCl. Survival of phage particles was maximum at pH 7-8. V. cholerae is assumed to have existed long before their human host and so the pathogenic clones may have evolved from aquatic forms which later colonized the human intestine by progressive acquisition of genes. This is supported by the fact that the vast majority of V. cholerae strains are still part of the natural aquatic environment. CTXΦ has played a critical role in the evolution of the pathogenicity of V. cholerae as it can transmit the ctxAB gene. The unusual transformation of V. cholerae strains associated with epidemics and the emergence of V. cholera O139 demonstrates the evolutionary success of the organism in attaining greater fitness. Genetic changes in pathogenic V. cholerae constitute a natural process for developing immunity within an endemically infected population. The alternative hosts and lysogenic environmental V. cholerae strains may potentially act as cofactors in promoting cholera phage ‘‘blooms’’ within aquatic environments, thereby influencing transmission of phage sensitive, pathogenic V. cholerae strains by aquatic vehicles. Differential induction of the phages is a clear indication of the impact of environmental pollution and global changes on phage induction. The development of molecular biology techniques offered an accessible gateway for investigating the molecular events leading to genetic diversity in the marine environment. Using nucleic acids as targets, the methods of fingerprinting like ERIC PCR and BOX PCR, revealed that the marine environment harbours potentially pathogenic group of bacteria with genetic diversity. The distribution of virulence associated genes in the environmental isolates of V. cholerae provides tangible material for further investigation. Nucleotide and protein sequence analysis alongwith protein structure prediction aids in better understanding of the variation inalleles of same gene in different ecological niche and its impact on the protein structure for attaining greater fitness of pathogens. The evidences of the co-evolution of virulence genes in toxigenic V. cholerae O1 from different lineages of environmental non-O1 strains is alarming. Transduction studies would indicate that the phenomenon of acquisition of these virulence genes by lateral gene transfer, although rare, is not quite uncommon amongst non-O1/non-O139 V. cholerae and it has a key role in diversification. All these considerations justify the need for an integrated approach towards the development of an effective surveillance system to monitor evolution of V. cholerae strains with epidemic potential. Results presented in this study, if considered together with the mechanism proposed as above, would strongly suggest that the bacteriophage also intervenes as a variable in shaping the cholera bacterium, which cannot be ignored and hinting at imminent future epidemics.