Elucidating the status of malaria in Andaman and Nicobar Islands post-millennium 2000.

Malaria is a major vector-borne disease in the Indian sub-continent and has been pestering Andaman and Nicobar islands (ANI's) as well since British colonial times. A retrospective data mining technique has been adhered to assess the status of malaria for nineteen years from 2000 to 2019 in ANI's. The altered environment due to 2004 tsunami had increased malaria incidence significantly during (2005-2010). The Nicobar district recorded high incidence of malaria while the least in the north and middle Andaman district. Comparative high incidence of malaria was documented due to Plasmodium falciparum than Plasmodium vivax in the Nicobar district between 2005 and 2009. The declining trend of malaria-positive cases in ANI's was observed post 2010, articulating various initiatives taken by the local Andaman and Nicobar administration to curb this vector-borne disease. The initiatives were like (1) large-scale release of larvivorous fish, Gambusia affinis in the transient water pools, (2) outdoor application of DDT, (3) indoor application of Pyrethrum, (4) malaria awareness drive that led to the curbing of the proliferation not only the malaria vector but also other potential mosquito vector species as well, and (5) implementation of revised drug policy.

A baseline study of meso and microplastic predominance in pristine beach sediment of the Indian tropical island ecosystem.

The global presence and prevalence of microplastic have moved microplastic from an emerging pollutant to a persistent contaminant. Microplastic prevails in almost all spheres of the environment viz. terrestrial, marine and atmosphere the globe abundantly. The prevalence and toxic effects on marine organisms have been studied around the world but the studies are limited to the coastal regime of the Andaman and Nicobar Islands (ANI). This study aims to record microplastic prevalence on the tourist beaches of Port Blair, ANI. Three coastal stations namely Cove beach, Quarry beach and Wandoor beach were examined in detail in this regard. Microplastics in the form of lines, fragments, pellets, foams and fibres were found at the sampled sites. Wandoor beach recorded the highest microplastic particles ranging from 105-475 particles kg-1 of sediment with the mean value of 249.82 ± 105.78 particles kg-1. Quarry beach near the municipal waste dumpsite showed the lowest of 72.5-222.5 particles kg-1 with a mean value of 135.625 ± 62.83 particles kg-1. The polymeric forms found were High-density polyethylene (HDPE), polystyrene (PS), polypropylene (PP) and polyethylene terephthalate (PET). This study revealed microplastic input from municipal dump waste near the beach. Fourier Transform Infrared spectroscopy (FTIR) revealed the presence of a new type of polymer namely plasta zinc in the beach sediment, which possibly could be a nanoplastic. Its presence reveals the biological enzymatic degradation of microplastic occurring in the marine environment. Further investigations are required to determine the factors influencing the prevalence of microplastic, its toxic effects on marine habitat and microplastic degradation mechanisms in the marine habitat.

Assessing the source of oil deposited in the surface sediment of Mormugao Port, Goa - A case study of MV Qing incident.

In June 2016, a cruise vessel was grounded in the Mormugao Port, resulting in unnoticed oil spill. The surface water and sediment samples were collected from the vicinity of the ship, and also an oil sample from the ship (OIL). These samples were subject to petroleum biomarker such as pentacyclic triterpenes (hopanes) and compound specific carbon isotopic (δ13C) analyses to assess the source of hydrocarbon pollution in the Mormugao Port. While no clear trend was observed in water samples, the bottom surface sediments did show an identical pattern of hopanes with the oil. The chemometric analyses of hopane Diagnostic Ratios (DRs) and δ13C ratios confirmed the ship oil as the source of oil pollution in sediments. Whereas the water is comparatively more dynamic than the sediment, the physical processes arising out of winds, waves, tides and currents might have dispersed the oil away from the grounded ship.

Modern rain-isotope data from Indian island and the mainland on the daily scale for the summer monsoon season.

The atmospheric stable isotopes in rainwater are measured as the ratio of heavy to the lighter (e.g., 18O/16O). This data article describes two datasets of daily rain isotopic variations during the Indian Summer Monsoon (ISM) season. Firstly, an island site (namely Port Blair) dataset for four years (2012-2015) and another dataset of Indian mainland sites (namely Nagpur, Tezpur, and Kolkata) for the year 2015. Port Blair is strategically situated in the Bay of Bengal (BoB), which is known to be a significant moisture source to ISM rainfall over the Indian landmass. On the other hand, sites in the mainland are receivers of the BoB moisture. This dataset includes 1030 isotopic analyses made on daily water samples as well as rainfall amount (24 hours) during ISM. The data is related to "Isotopic investigation of the moisture transport processes over the Bay of Bengal" [1].

New Records and Range Extensions of Some Marine Sponges (Porifera: Demospongiae and Homoscleromorpha) from the Andaman Islands, India; Part of the Indo-Burma Biodiversity Hotspot.

Vibha V. Ubare and P. M. Mohan (2018) The present study reports seven new records of marine sponges from the Andaman Islands, India. Among them, six species are from the Class Demospongiae and one is from the Class Homoscleromorpha. These seven species were earlier recorded from Australian and South-east Asian regions and islands in the Indian Ocean. The current study documents the range extension of these sponges and highlights the importance of filling the gaps in distributional patterns (Wallacean shortfall). Out of the seven species, four species are reported here, from the Indian waters, for the first time.

Antimicrobial Activity and Phylogenetic Analysis of Streptomyces Parvulus Dosmb-D105 Isolated from the Mangrove Sediments of Andaman Islands.

Actinomycetes, especially species of Streptomyces are prolific producers of pharmacologically significant compounds accounting for about 70% of the naturally derived antibiotics that are presently in clinical use. In this study, we used five solvents to extract the secondary metabolites from marine Streptomyces parvulus DOSMB-D105, which was isolated from the mangrove sediments of the South Andaman Islands. Among them, ethyl acetate crude extract showed maximum activity against 11 pathogenic bacteria and six fungi. Presence of bioactive compounds in the ethyl acetate extract was determined using GC-MS and the compounds detected in the ethyl acetate extract were matched with the National Institute of Standards and Technology (NIST) library. Totally eight compounds were identified and the prevalent compounds were 2 steroids, 2 alkaloids, 2 plasticizers, 1 phenolic and 1 alkane. Present study revealed that S. parvulus DOSMB-D105 is a promising species for the isolation of valuable bioactive compounds to combat pathogenic microbes.

Atmospheric controls on the precipitation isotopes over the Andaman Islands, Bay of Bengal.

Isotopic analysis of precipitation over the Andaman Island, Bay of Bengal was carried out for the year 2012 and 2013 in order to study the atmospheric controls on rainwater isotopic variations. The oxygen and hydrogen isotopic compositions are typical of the tropical marine sites but show significant variations depending on the ocean-atmosphere conditions; maximum depletion was observed during the tropical cyclones. The isotopic composition of rainwater seems to be controlled by the dynamical nature of the moisture rather than the individual rain events. Precipitation isotopes undergo systematic depletions in response to the organized convection occurring over a large area and are modulated by the integrated effect of convective activities. Precipitation isotopes appear to be linked with the monsoon intraseasonal variability in addition to synoptic scale fluctuations. During the early to mid monsoon the amount effect arose primarily due to rain re-evaporation but in the later phase it was driven by moisture convergence rather than evaporation. Amount effect had distinct characteristics in these two years, which appeared to be modulated by the intraseasonal variability of monsoon. It is shown that the variable nature of amount effect limits our ability to reconstruct the past-monsoon rainfall variability on annual to sub-annual time scale.

A New Species of Genus Plakortis Schulze 1880 (Porifera: Homoscleromorpha) from Badabalu, Andaman and Nicobar Islands, India.

Vibha V. Ubare and PM. Mohan (2016) Recently revealed Class: Homoscleromorpha play a significant role in sponge systematics. The smaller size, cryptic habits and unresolved species complex are greater obstacles for the taxonomic identification of this class. Out of < 100 species, only 6 species have been described from the Indian region. Till date, only one species of the genus Plakortis, that is, P. simplex has been described from this region. The present study provides a detailed description of new species of the genus Plakortis, Schulze 1880. P. badabaluensis sp. nov. is characterized by the two size classes of diods (one is thick and the other is thin), triods and smooth microrhabds; with well differentiated ectosome, presence of subectosomal lacunae and confused choanosome. The identification of this new species has increased the number of plakinid species from one to two in the Andaman and Nicobar Islands, India. Further detailed studies are required to explore this type of cryptic species in this region.

Rhizophoramucronatavar.alokii - a new variety of mangrove species from the Andaman and Nicobar Islands, India (Rhizophoraceae).

Rhizophoramucronatavar.alokii (Rhizophoraceae), a new variety of Rhizophora from the Andaman and Nicobar Islands, India, is described and illustrated. The new variety is remarkable in having four stamens, laterally folded leaves, a short peduncle, thick leathery petals, and a four-sided ovary with a sessile style. A key for the species of Rhizophora of the Andaman and Nicobar Islands is also provided.

Eigenvalue equation and core-mode cutoff of weakly guiding tapered fiber as three layer optical waveguide and used as biochemical sensor.

The core-mode cutoff plays a major role in evanescent field absorption based sensors. A method has been proposed to calculate the core-mode cutoff by solving the eigenvalue equations of a weakly guiding three layer optical waveguide graphically. The variation of normalized waveguide parameter (V) is also calculated with different wavelengths at core-mode cutoff. At the first step, theoretical analysis of tapered fiber parameters has been performed for core-mode cutoff. The taper angle of an adiabatic tapered fiber is also analyzed using the length-scale criterion. Secondly, single-mode tapered fiber has been developed to make a precision sensor element suitable for chemical detection. Finally, the sensor element has been used to detect absorption peak of ethylenediamine. Results are presented in which an absorption peak at 1540 nm is observed.

Residual structure and dynamics in DMSO-d6 denatured dynein light chain protein.

Structural and motional features in the denatured state of a protein dictate the early folding events starting from that state and these features vary depending upon the nature of the denaturant used. Here, we have attempted to decipher the early events in the folding of Dynein Light Chain protein (DLC8), starting from DMSO-d6 denatured state. Multinuclear NMR experiments were used to obtain the full spectral assignment. The HSQC spectrum shows the presence of two sets of peaks for the residues Met 1, Ser 2, Arg 4, Ala 11, Met 17, Thr 26, Lys 44, Tyr 50, Asn 51, Trp 54, His 55, Val 58, Gly 59, Ser 64, Tyr 65, His 68, Phe 86, Lys 87 indicating the presence of slow conformational transition in the heterogeneous ensemble. Analysis of residual structural propensities with secondary (13)C chemical shifts, (3)J(H(N)(-)H(α)) coupling constants and (1)H-(1)H NOE revealed the presence of local preferences which encompass both native and non-native like structures. The spectral density calculations, as obtained from measured R(1), R(2) and (1)H-(15)N steady state NOE values provide insights into the backbone dynamics on the milli to picosecond timescale. The segment Ser 14 - His 55 exhibits slow motions on the milli- to microsecond timescale arising from conformational exchange. The presence of native like structural preference, as well as conformational exchange classifies the above segment as the nucleation site of folding. Based on the observations, we propose here, the probable hierarchy of folding of DLC8 on dilution of denaturant: the two helices are formed first followed by the formation of ß2 and ß5.

Hierarchy of local structural and dynamics perturbations due to subdenaturing urea in the native state ensemble of DLC8 dimer.

Local structural and dynamic modulations due to small environmental perturbations reflect the adaptability of the protein to different interactors. We have investigated here the preferential local perturbations in Dynein light chain protein (DLC8), a cargo adapter, by sub-denaturing urea concentrations. Equilibrium unfolding experiments by optical spectroscopic methods indicated a two state like unfolding of DLC8 dimer, with the transition mid-point occurring around 8.6M urea. NMR studies identified the ß3 and ß4 strands, N-, C- terminal regions, loops connecting ß1 to α1, α1 to α2 and ß3 to ß4 as the soft targets of urea perturbation and thus indicated potential unfolding initiation sites. Native-state hydrogen exchange studies suggested the unfolding to traverse from the edges towards the centre of the secondary structural elements. At 6M urea the whole protein chain acts like a cooperative unit. These observations are expected to have important implications for the protein's multiple functions.

Structure-function-folding relationships and native energy landscape of dynein light chain protein: nuclear magnetic resonance insights.

The detailed characterization of the structure, dynamics and folding process of a protein is crucial for understanding the biological functions it performs. Modern biophysical and nuclear magnetic resonance (NMR) techniques have provided a way to obtain accurate structural and thermodynamic information on various species populated on the energy landscape of a given protein. In this context, we review here the structure-function-folding relationship of an important protein, namely, dynein light chain protein (DLC8). DLC8, the smallest subunit of the dynein motor complex, acts as a cargo adaptor. The protein exists as a dimer under physiological conditions and dissociates into a pure monomer below pH 4. Cargo binding occurs at the dimer interface. Dimer stability and relay of perturbations through the dimer interface are anticipated to be playing crucial roles in the variety of functions the protein performs. NMR investigations have provided great insights into these aspects of DLC8 in recent years.

NMR investigations on residue level unfolding thermodynamics in DLC8 dimer by temperature dependent native state hydrogen exchange.

Understanding protein stability at residue level detail in the native state ensemble of a protein is crucial to understanding its biological function. At the same time, deriving thermodynamic parameters using conventional spectroscopic and calorimetric techniques remains a major challenge for some proteins due to protein aggregation and irreversibility of denaturation at higher temperature values. In this regard, we describe here the NMR investigations on the conformational stabilities and related thermodynamic parameters such as local unfolding enthalpies, heat capacities and transition midpoints in DLC8 dimer, by using temperature dependent native state hydrogen exchange; this protein aggregates at high (>65 degrees C) temperatures. The stability (free energy) of the native state was found to vary substantially with temperature at every residue. Significant differences were found in the thermodynamic parameters at individual residue sites indicating that the local environments in the protein structure would respond differently to external perturbations; this reflects on plasticity differences in different regions of the protein. Further, comparison of this data with similar data obtained from GdnHCl dependent native state hydrogen exchange indicated many similarities at residue level, suggesting that local unfolding transitions may be similar in both the cases. This has implications for the folding/unfolding mechanisms of the protein.

Residue-wise conformational stability of DLC8 dimer from native-state hydrogen exchange.

Dynein light chain (DLC8) is the smallest subunit of the dynein motor complex, which is known to act as a cargo adaptor in intracellular trafficking. The protein exists as a pure dimer at physiological pH and a completely folded monomer below pH 4. Here, we have determined the energy landscape of the dimeric protein using a combination of optical techniques and native-state hydrogen exchange of amide groups, the former giving the global features and the latter yielding the residue level details. The data indicated the presence of intermediates along the equilibrium unfolding transition. The hydrogen exchange data suggested that the molecule has differential stability in its various segments. We deduce from the free energy data that the antiparallel beta-sheets (beta4 and beta5) that form the hydrophobic core of the protein and the alpha2 helix, all of which are highly protected with regard to hydrogen exchange, contribute significantly to the initial step of the protein folding mechanism. Denaturant-dependent hydrogen exchange indicated further that some amides exchange via local fluctuations, whereas there are others which exchange via global unfolding events. Implications of these to cargo adaptability of the dimer are discussed.

Hierarchy in guanidine unfolding of DLC8 dimer: regulatory functional implications.

Folding-unfolding caused by environmental changes play crucial regulatory roles in protein functions. To gain an insight into these for DLC8, a cargo adaptor in dynein motor complex, we investigated here the unfolding of homodimeric DLC8 by GdnHCl, a standard unfolding agent. Fluorescence spectroscopy revealed a three-state unfolding transition with midpoints at 1.5 and 4.0 M GdnHCl. The HSQC spectrum at 1.5 M GdnHCl displayed peaks belonging to a folded monomer. NMR chemical shift perturbations, line broadening effects and (15)N relaxation measurements at low GdnHCl concentrations identified a hierarchy in the unfolding process, with the dimer interface--the cargo binding site--being the most susceptible followed by the helices in the interior. Similar observations were made earlier for small pH perturbations and thus the early unfolding events appear to be intrinsic to the protein. These, by virtue of their location, influence target binding efficacies and thus have important regulatory implications.

pH dependent unfolding characteristics of DLC8 dimer: Residue level details from NMR.

Environment dependence of folding and unfolding of a protein is central to its function. In the same vein, knowledge of pH dependence of stability and folding/unfolding is crucial for many biophysical equilibrium and kinetic studies designed to understand protein folding mechanisms. In the present study we investigated the guanidine induced unfolding transition of dynein light chain protein (DLC8), a cargo adaptor of the dynein complex in the pH range 7-10. It is observed that while the protein remains a dimer in the entire pH range, its stability is somewhat reduced at alkaline pH. Global unfolding features monitored using fluorescence spectroscopy revealed that the unfolding transition of DLC8 at pH 7 is best described by a three-state model, whereas, that at pH 10 is best described by a two-state model. Chemical shift perturbations due to pH change provided insights into the corresponding residue level structural perturbations in the DLC8 dimer. Likewise, backbone (15)N relaxation measurements threw light on the corresponding motional changes in the dimeric protein. These observations have been rationalized on the basis of expected changes with increasing pH in the protonation states of the titratable residues on the structure of the protein. These, in turn provide an explanation for the change from three-state to two-state guanidine induced unfolding transition as the pH is increased from 7 to 10. All these results exemplify and highlight the role of environment vis-à-vis the sequence and structure of a given protein in dictating its folding/unfolding characteristics.

NMR characterization of structural and dynamics perturbations due to a single point mutation in Drosophila DLC8 dimer: functional implications.

Dynein light chain protein (DLC8), the smallest subunit of the dynein motor complex, acts as a cargo adaptor. The protein exists as a dimer under physiological conditions, and cargo binding occurs at the dimer interface. Dimer stability and relay of perturbations through the dimer interface can thus be anticipated to play crucial roles in the variety of functions the protein performs. Recent investigations point out that DLC8 also gets phosphorylated at Ser 88, which is located at the extreme C-terminal end. In this background, we investigate here by NMR the effects of a small perturbation by way of a single point mutation, S88A, on the structure, dynamics, and cargo binding efficacy of the DLC8 dimer. We observe that the perturbation travels far away along the sequence from the site of the mutation. This relay has been explained at the atomic level by looking into the packing of the side chains in the crystal structure of the protein. It follows that the interface is highly adaptable, which may account for the versatility of the dimer's cargo binding ability. Binding studies with a peptide indicate that the mutation compromises binding efficacy. These observations show how remote residues that may not be directly bound to a target can still affect the affinity of the protein to the target. Furthermore, the S88A mutational perturbations seen here in Drosophila DLC8 are dramatically different from those of the same mutation in human DLC8 (also known as DLC1) ( Song, C. , et al., ( 2008) J. Biol. Chem, 283, 4004- 4013. ) which differs from Drosophila DLC8 at only five locations. All of these observations put together highlight the sensitivity of dynein light chain protein to small perturbations, and this would have great functional implications.

NMR comparison of the native energy landscapes of DLC8 dimer and monomer.

Characterization of the low energy excited states on the energy landscape of a protein is one of the exciting and challenging problems in structural biology today. In this context, we present here residue level NMR description of the low energy excited states representing locally different alternative conformations in the dynein light chain protein, in its dimeric as well as monomeric forms. Important differences have been observed between the two cases and these are not necessarily restricted to the dimer interface. Simulations indicate that the low energy excited states are within a free energy of 2-3 kcal/mol above the native state. In both the monomer and the dimer the energy landscape is very sensitive to small pH perturbations. Nearly 25% of the residues (total of residues at pH 3.0 and 3.5 for the monomer, and at pH 7.0 and 6.0 for the dimer) access alternative conformations. The observations have been rationalized on the basis of protonation-deprotonation equilibria in the side chains; histidines in the case of the dimer and aspartates/glutamates in the case of the monomer. The possible relationship of the observed ruggedness of the native energy landscape with the protein structure, and its implications to protein adaptability and unfolding have been discussed.

Differential native state ruggedness of the two Ca2+-binding domains in a Ca2+ sensor protein.

Characterization of near-native excited states of a protein provides insights into various biological functions such as co-operativity, protein-ligand, and protein-protein interactions. In the present study, we investigated the ruggedness of the native state of EhCaBP using nonlinear temperature dependence of backbone amide-proton chemical shifts. EhCaBP is a two-domain EF-hand calcium sensor protein consisting of two EF-hands in each domain and binds four Ca2+ ions. It has been observed that approximately 30% of the residues in the protein access alternative conformations. Theoretical modeling suggested that these low-energy excited states are within 2-3 kcal/mol from the native state. Further, it is interesting to note that the residues accessing alternative conformations are more dominated in the C-terminal domain compared with its N-terminal counterpart suggesting that the former is more rugged in its native state. These distinct characteristics of N- and C-terminal domains of a calcium sensor protein belonging to the super family of calmodulin would have implications for domain dependent Ca2+ signaling pathways.