Identification of host cellular requirements for positive strand RNA viruses: Hepatitis C virus and hepatitis E virus

Investigation of the host cellular requirements of two positive strand RNA viruses, by microarray, phospho-proteome array and by siRNA screening identified differential expression of host genes during hepatitis C virus viral entry. Also my studies suggest that NS4B regulates a newly identified oncogenic pathway. For hepatitis E virus, I looked for the cellular effects conferred by the capsid protein ORF2, and the results showed that ORF2 induced activation of CHOP did not lead to apoptosis which might be due to the up regulation of anti-apoptotic chaperones like Hsp72

Population Structure of Denison’s barb, Puntius denisonii (Pisces: Cyprinidae): A Species Complex Endemic to the Western Ghats of India

Genetic and morphologic variation, haplotype relationships, and structuring of populations within Puntius denisonii and its close related species Puntius chalakkudiensis have been tested using molecular and biometric data, to infer phylogeographic patterns. Sequences of mitochondrial DNA ATPase 8 and 6 genes, and morphometric data, were used to find population structuring. Specimens were collected from 7 locations in the southern region of Western Ghats, a global biodiversity hotspot in India. Biometric analysis revealed apparent heterogeneity in the morphology and color pattern between the species at juvenile and adult stages, and among different geographically separated populations of these species. High values for mean pair wise distances and a high proportion of the total variance attributed to differences between the geographically isolated populations with AMOVA, indicated clear population structuring within these species. Extremely high values for Pair wise FST and significantly lower Nm values observed among the populations studied, suggested little or no effective gene flow among them. Constructed phylogenies further confirmed a high degree of population structuring within the species, showing local endemism with population specific haplotypes forming a species complex. The present study thus estimates the validity of subpopulations within P. denisonii and P. chalakkudiensis; clarifies the relationships of populations of P. denisonii with that of P. chalakkudiensis, and also indicates the presence of four different independent evolutionary lineages forming cryptic species within P. denisonii. The study further emphasizes the need for a conservation policy to be developed for each population of both species, separately based on MUs (Management Units)

Population genetic structure of indigenous ornamental teleosts, Puntius denisonii and Puntius chalakkudiensis from the Western Ghats, India

Our riverine system, especially the torrential streams and rivers originating in the Western Ghats are known to have variety of ornamental fishes. Except for traditional taxonomic description we have little information on these species, their ecology, biology, life habits, life history and population structure. There is large scale depletion of habitats due to anthropogenic factors which affect the ecosystems of these streams. At the same time, a growing trade in ornamental fish resulting in the exploitation of the resources from the wild stock threatening their existence. On account of this, Government of Kerala State has promulgated a ban on the capture from wild of one of the species Puntius denisonii (Day) during its peek breeding season. The importance of learning more about the species such as P. denisonii and its associated species has motivated me to take-up the present study, the subject of this thesis entitled “Population genetic structure of indigenous ornamental teleosts, Puntius denisonii and Puntius chalakkudiensis from the Western Ghats, India.” My study has brought out some important findings on P. denisonii species complex which I am sure will help towards developing management strategies for conservation and well being of the species

Genetic identity of Tormalabaricus(Jerdon)(Teleostei : Cyprinidae) as revealed by RAPD markers

Tor malabaricus (Jerdon) is a mahseer species endemic to the Western Ghats. Since its original description, taxonomic position of the species has been extremely confusing. In the present study, Random Amplified polymorphic DNA (RAPD) markers were used to determine the taxonomic status of T.malabaricus collected from Balamore River, Tamil Nadu, India, by comparing its RAPD profile with that of Tor khudreee.15 random oligodecamers were used to amplify DNA from Tor malabaricus and Tor khudree (n=30 each) collected from two geographically isolated localities and a total of 119 amphicons were detected

Improving the coordination in the humanitarian supply chain: exploring the role of options contract

The uncertainty associated with the location, severity and timing of disaster makes it difficult for the humanitarian organization (HO) to predict demand for the aid material and thereby making the relief material procurement even more challenging. This research explores whether options contract can be used as a mechanism to aid the HO in making procurement of relief material less challenging by addressing two main issues: inventory risk for buyers and over-production risk for suppliers. Furthermore, a contracting mechanism is designed to achieve coordination between the HO and aid material suppliers in the humanitarian supply chain through optimal pricing. The options contract is modelled as a stylized version of the newsvendor problem that allows the HO to adjust their order quantity after placing the initial order at the beginning of the planning horizon. This flexibility helps to mitigate the risk of both overstocking and understocking for the HO as well as the risk of overproduction for the supplier. Our results indicate that the optimal values for decision parameters are not “point estimates” but a range of prices, which can facilitate negotiation between the two parties for appropriate selection of contract parameters under an options contract. The results imply that options contract can aid in the decentralized approach of fixing the prices between the HO and the supplier, which in turn would help in achieving systemic coordination

Pathological manifestations of the acanthocephalan parasite, Tenuiproboscis sp. in the mangrove red snapper (Lutjanus argentimaculatus) (Forsskål, 1775), a candidate species for aquaculture from Southern India

The study describes the pathological manifestations of the acanthocephalan, Tenuiproboscis sp. in the mangrove red snapper, Lutjanus argentimaculatus, a highly valued food fish along the southwest coast of India. The fish collected from Calicut, Cochin and Kannur harboured the acanthocephalan parasite, Tenuiproboscis sp. with up to 100% prevalence. Heavy infections with the parasites were observed in the posterior region of the intestine, almost blocking the lumen. At the site of parasite attachment, the surface of the intestine appeared thickened and the mucosal epithelium showed compression and abrasion

Hepatitis E Virus ORF2 Protein Activates the Pro-Apoptotic Gene CHOP and Anti-Apoptotic Heat Shock Proteins

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Mitochondrial DNA (Cytochrome c oxidase I) sequencing of Indian marine mussels

Two species of marine mussels, the green mussel Perna viridis (Linnaeus, 1758) and the brown mussel Perna indica (Kuriakose and Nair, 1976) are found along the Indian coast. It had been suggested that P. indica, which occurs only along the Indian coast, is a synonym of the globally distributed Perna perna. Along the south-west coast of India, where both P. viridis and P. indica co-exist, a third type referred to as parrot mussel, which has shell shape of brown mussel and color of green mussel (suspected to be their hybrid/morphotype) also occurs. The present investigation is a preliminary attempt for resolving the taxonomic ambiguity among Indian marine mussel species using the mitochondrial cytochrome oxidase I (COI) gene. P. indica revealed 95% sequence similarity to P. perna. The sequence divergence between P. indica and parrot mussel was negligibly low (< 2%). Green mussel P. viridis showed 20.87% of sequence divergence with brown mussel P. indica as well as with the parrot mussel

Phenotypic and genetic characterization of Dunaliella (Chlorophyta) from Indian salinas and their diversity

Background: The genus Dunaliella (Class – Chlorophyceae) is widely studied for its tolerance to extreme habitat conditions, physiological aspects and many biotechnological applications, such as a source of carotenoids and many other bioactive compounds. Biochemical and molecular characterization is very much essential to fully explore the properties and possibilities of the new isolates of Dunaliella. In India, hyper saline lakes and salt pans were reported to bloom with Dunaliella spp. However, except for the economically important D. salina, other species are rarely characterized taxonomically from India. Present study was conducted to describe Dunaliella strains from Indian salinas using a combined morphological, physiological and molecular approach with an aim to have a better understanding on the taxonomy and diversity of this genus from India. Results: Comparative phenotypic and genetic studies revealed high level of diversity within the Indian Dunaliella isolates. Species level identification using morphological characteristics clearly delineated two strains of D. salina with considerable β-carotene content (>20 pg/cell). The variation in 18S rRNA gene size, amplified with MA1-MA2 primers, ranged between ~1800 and ~2650 base pairs, and together with the phylogeny based on ITS gene sequence provided a pattern, forming five different groups within Indian Dunaliella isolates. Superficial congruency was observed between ITS and rbcL gene phylogenetic trees with consistent formation of major clades separating Indian isolates into two distinct clusters, one with D. salina and allied strains, and another one with D. viridis and allied strains. Further in both the trees, few isolates showed high level of genetic divergence than reported previously for Dunaliella spp. This indicates the scope of more numbers of clearly defined/unidentified species/subspecies within Indian Dunaliella isolates. Conclusion: Present work illustrates Indian Dunaliella strains phenotypically and genetically, and confirms the presence of not less than five different species (or sub-species) in Indian saline waters, including D. salina and D. viridis. The study emphasizes the need for a combined morphological, physiological and molecular approach in the taxonomic studies of Dunaliella