Methylenetetrahydrofolate reductase CpG islands: Epigenotyping

Background Determination of the differential DNA methylation patterns of methylenetetrahydrofolate reductase (MTHFR) that are associated with differential MTHFR activity is important to understand the pathogenesis of ischemic stroke. However, to date, no data are available on the differential DNA methylation profiles of Kelantanese Malays. Therefore, we developed a rapid and efficient serial pyrosequencing assay to determine differential DNA methylation profiles of MTHFR, which help to further our understanding of the pathogenesis of ischemic stroke. The developed assay also served as the validation platform for our previous computational epigenetic research on MTHFR. Methods Polymerase chain reaction primers were designed and validated to specifically amplify the cytosine that is followed by guanine residues (CpGs) A and B regions. Prior epigenotyping on 110 Kelantanese Malays, the serial pyrosequencing assays for the CpGs A and B regions were validated using five validation controls. The mean values of the DNA methylation profiles of CpGs A and B were calculated. Results The mean DNA methylation levels for CpGs A and B were 0.984 ± 0.582 and 2.456 ± 1.406, respectively. The CpGs 8 and 20 showed the highest (5.581 ± 4.497) and the lowest (0.414 ± 2.814) levels of DNA methylation at a single-base resolution. Conclusion We have successfully developed and validated a pyrosequencing assay that is fast and can yield high-quality pyrograms for DNA methylation analysis and is therefore applicable to high throughput study. Using this newly developed pyrosequencing assay, the MTHFR DNA methylation profiles of 110 Kelantanese Malays were successfully determined. It also validated our computational epigenetic research on MTHFR.

Crustal Deformation and Seismic History Associated with the 2004 Indian Ocean Earthquake: A Perspective from the Andaman–Nicobar Islands

The Indian Ocean earthquake of 26 December 2004 led to significant ground deformation in the Andaman and Nicobar region, accounting for ~800 km of the rupture. Part of this article deals with coseismic changes along these islands, observable from coastal morphology, biological indicators, and Global Positioning System (GPS) data. Our studies indicate that the islands south of 10° N latitude coseismically subsided by 1–1.5 m, both on their eastern and western margins, whereas those to the north showed a mixed response. The western margin of the Middle Andaman emerged by >1 m, and the eastern margin submerged by the same amount. In the North Andaman, both western and eastern margins emerged by >1 m. We also assess the pattern of long-term deformation (uplift/subsidence) and attempt to reconstruct earthquake/tsunami history, with the available data. Geological evidence for past submergence includes dead mangrove vegetation dating to 740 ± 100 yr B.P., near Port Blair and peat layers at 2–4 m and 10–15 m depths observed in core samples from nearby locations. Preliminary paleoseismological/tsunami evidence from the Andaman and Nicobar region and from the east coast of India, suggest at least one predecessor for the 2004 earthquake 900–1000 years ago. The history of earthquakes, although incomplete at this stage, seems to imply that the 2004-type earthquakes are infrequent and follow variable intervals

Under-representation of intrinsic terminators across bacterial genomic islands: Rho as a principal regulator of xenogenic DNA expression

Two transcription termination mechanisms - intrinsic and Rho-dependent - have evolved in bacteria. The Rho factor occurs in most bacterial lineages, and has been hypothesized to play a global regulatory role. Genome-wide studies using microarray, 2D-gel electrophoresis and ChIP-chip provided evidence that Rho serves to silence transcription from horizontally acquired genes and prophages in Escherichia coli K-12, implicating the factor to be a part of the ``cellular immune mechanism'' protecting against deleterious phages and aberrant gene expression from acquired xenogenic DNA. We have investigated this model by adopting an alternate in silico approach and have extended the study to other species. Our analysis shows that several genomic islands across diverse phyla have under-representation of intrinsic terminators, similar to that experimentally observed in E. coli K-12. This implies that Rho-dependent termination is the predominant process operational in these islands and that silencing of foreign DNA is a conserved function of Rho. From the present analysis, it is evident that horizontally acquired islands have lost intrinsic terminators to facilitate Rho-dependent termination. These results underscore the importance of Rho as a conserved, genome-wide sentinel that regulates potentially toxic xenogenic DNA. (C) 2012 Elsevier B.V. All rights reserved.

Shola habitats on sky islands: status of research on montane forests and grasslands in southern India

The Shola habitat on the high elevation sky islands of the Western Ghats in southern India is a unique habitat. Although this habitat hosts a disproportionately high level of endemism and is threatened by anthropogenic modifications, it has received little research attention. We compiled publications of research conducted in this habitat from scientific databases and the grey literature to examine trends in publication. For a quantitative summary, all publications were classified according to the taxa of research and the broad topic of research. We identified 279 publications from 1964 and found an almost threefold increase in the number of publications and diversity of research topics studied over the last decade. Studies on flora, birds and mammals have been numerous (62% of the studies examined), but certain taxa like fish (1%) have been ignored. Most studies (65%) are descriptive, focusing on diversity, distribution trends and management suggestions, while surprisingly few have concentrated on climate change, ecological restoration and invasive species, all major threats to this landscape. We have identified some key gaps in research and conservation focus that future studies could address. We also suggest that initiatives like edited volumes and special journal sections, along with the use of creative commons licensed data-sharing portals, can be used to usher unpublished work into the public domain.

Ages and relative sizes of pre-2004 tsunamis in the Bay of Bengal inferred from geologic evidence in the Andaman and Nicobar Islands

Geologic evidence along the northern part of the 2004 Aceh-Andaman rupture suggests that this region generated as many as five tsunamis in the prior 2000years. We identify this evidence by drawing analogy with geologic records of land-level change and the tsunami in 2004 from the Andaman and Nicobar Islands (A&N). These analogs include subsided mangrove swamps, uplifted coral terraces, liquefaction, and organic soils coated by sand and coral rubble. The pre-2004 evidence varies in potency, and materials dated provide limiting ages on inferred tsunamis. The earliest tsunamis occurred between the second and sixth centuries A.D., evidenced by coral debris of the southern Car Nicobar Island. A subsequent tsunami, probably in the range A.D. 770-1040, is inferred from deposits both in A&N and on the Indian subcontinent. It is the strongest candidate for a 2004-caliber earthquake in the past 2000years. A&N also contain tsunami deposits from A.D. 1250 to 1450 that probably match those previously reported from Sumatra and Thailand, and which likely date to the 1390s or 1450s if correlated with well-dated coral uplift offshore Sumatra. Thus, age data from A&N suggest that within the uncertainties in estimating relative sizes of paleo-earthquakes and tsunamis, the 1000year interval can be divided in half by the earthquake or earthquakes of A.D. 1250-1450 of magnitude >8.0 and consequent tsunamis. Unlike the transoceanic tsunamis generated by full or partial rupture of the subduction interface, the A&N geology further provides evidence for the smaller-sized historical tsunamis of 1762 and 1881, which may have been damaging locally.

Flying between Sky Islands: The Effect of Naturally Fragmented Habitat on Butterfly Population Structure

High elevation montane areas are called ``sky islands'' when they occur as a series of high mountains separated by lowland valleys. Different climatic conditions at high elevations makes sky islands a specialized type of habitat, rendering them naturally fragmented compared to more continuous habitat at lower elevations. Species in sky islands face unsuitable climate in the intervening valleys when moving from one montane area to another. The high elevation shola-grassland mosaic in the Western Ghats of southern India form one such sky island complex. The fragmented patches make this area ideal to study the effect of the spatial orientation of suitable habitat patches on population genetic structure of species found in these areas. Past studies have suggested that sky islands tend to have genetically structured populations, possibly due to reduced gene flow between montane areas. To test this hypothesis, we adopted the comparative approach. Using Amplified Fragment Length Polymorphisms, we compared population genetic structures of two closely related, similar sized butterfly species: Heteropsis oculus, a high elevation shola-grassland specialist restricted to the southern Western Ghats, and Mycalesis patnia, found more continuously distributed in lower elevations. In all analyses, as per expectation the sky island specialist H. oculus exhibited a greater degree of population genetic structure than M. patnia, implying a difference in geneflow. This difference in geneflow in turn appears to be due to the natural fragmentation of the sky island complexes. Detailed analysis of a subset of H. oculus samples from one sky island complex (the Anamalais) showed a surprising genetic break. A possible reason for this break could be unsuitable conditions of higher temperature and lower rainfall in the intervening valley region. Thus, sky island species are not only restricted by lack of habitat continuity between montane areas, but also by the nature of the intervening habitat.

Slow Slip Acceleration beneath Andaman Islands Triggered by the 11 April 2012 Indian Ocean Earthquakes

The M-w 8.6 and 8.2 strike-slip earthquakes that struck the northeast Indian Ocean on 11 April 2012 resulted in coseismic deformation both at near and distant sites. The slip distribution, deduced using seismic-wave analysis for the orthogonal faults that ruptured during these earthquakes, is sufficient to predict the coseismic displacements at the Global Positioning System (GPS) sites, such as NTUS, PALK, and CUSV, but fall short at four continuous sites in the Andaman Islands region. Slip modeling, for times prior to the events, suggests that the lower portion of the thrust fault beneath the Andaman Islands has been slipping at least at the rate of 40 cm/yr, in response to the 2004 Sumatra-Andaman coseismic stress change. Modeling of GPS displacements suggests that the en echelon and orthogonal fault ruptures of the 2012 intraplate oceanic earthquakes could have possibly accelerated the ongoing slow slip, along the lower portion of the thrust fault beneath the islands with a month-long slip of 4-10 cm. The misfit to the coseismic GPS displacements along the Andaman Islands could be improved with a better source model, assuming that no local process contributed to this anomaly.

Interactome analyses of Salmonella pathogenicity islands reveal SicA indispensable for virulence

Background: Serovars of Salmonella enterica, namely Typhi and Typhimurium, reportedly, are the bacterial pathogens causing systemic infections like gastroenteritis and typhoid fever. To elucidate the role and importance in such infection, the proteins of the Type III secretion system of Salmonella pathogenicity islands and two component signal transduction systems, have been mainly focused. However, the most indispensable of these virulent ones and their hierarchical role has not yet been studied extensively. Results: We have adopted a theoretical approach to build an interactome comprising the proteins from the Salmonella pathogeneicity islands (SPI) and two component signal transduction systems. This interactome was then analyzed by using network parameters like centrality and k-core measures. An initial step to capture the fingerprint of the core network resulted in a set of proteins which are involved in the process of invasion and colonization, thereby becoming more important in the process of infection. These proteins pertained to the Inv, Org, Prg, Sip, Spa, Ssa and Sse operons along with chaperone protein SicA. Amongst them, SicA was figured out to be the most indispensable protein from different network parametric analyses. Subsequently, the gene expression levels of all these theoretically identified important proteins were confirmed by microarray data analysis. Finally, we have proposed a hierarchy of the proteins involved in the total infection process. This theoretical approach is the first of its kind to figure out potential virulence determinants encoded by SPI for therapeutic targets for enteric infection. Conclusions: A set of responsible virulent proteins was identified and the expression level of their genes was validated by using independent, published microarray data. The result was a targeted set of proteins that could serve as sensitive predictors and form the foundation for a series of trials in the wet-lab setting. Understanding these regulatory and virulent proteins would provide insight into conditions which are encountered by this intracellular enteric pathogen during the course of infection. This would further contribute in identifying novel targets for antimicrobial agents. (C) 2014 Elsevier Ltd. All rights reserved.

Factors affecting distribution of fish within a tidally drained mangrove forest in the Andaman and Nicobar Islands, India

Mangrove forests in meso-tidal areas are completely drained during low tides, forming only temporary habitats for fish. We hypothesised that in such temporary habitats, where stranding risks are high, distance from tidal creeks that provided access to inundated areas during receding tides would be the primary determinant of fish distribution. Factors such as depth, root density and shade were hypothesised to have secondary effects. We tested these hypotheses in a tidally drained mangrove patch in the Andaman Islands, India. Using stake nets, we measured fish abundance and species richness relative to distance from creeks, root density/m(2), shade, water depth and size (total length) of fish. We also predicted that larger fish (including potential predators) would be closer to creeks, as they faced a greater chance of mortality if stranded. Thus we conducted tethering trials to examine if predation would be greater close to the creeks. Generalised linear mixed effects models showed that fish abundance was negatively influenced by increasing creek distance interacting with fish size and positively influenced by depth. Quantile regression analysis showed that species richness was limited by increasing creek distance. Proportion of predation was greatest close to the creeks (0-25 m) and declined with increasing distance. Abundance was also low very close to the creeks, suggesting that close to the creeks predation pressure may be an important determinant of fish abundance. The overall pattern however indicates that access to permanently inundated areas, may be an important determinant of fish distribution in tidally drained mangrove forests.

A new genus and species of arboreal toad with phytotelmonous larvae, from the Andaman Islands, India (Lissamphibia, Anura, Bufonidae)

A new bufonid amphibian, belonging to a new monotypic genus, is described from the Andaman Islands, in the Bay of Bengal, Republic of India, based on unique external morphological and skeletal characters which are compared with those of known Oriental and other relevant bufonid genera. Blythophryne gen. n. is distinguished from other bufonid genera by its small adult size (mean SVL 24.02 mm), the presence of six presacral vertebrae, an absence of coccygeal expansions, presence of an elongated pair of parotoid glands, expanded discs at digit tips and phytotelmonous tadpoles that lack oral denticles. The taxonomic and phylogenetic position of the new taxon (that we named as Blythophryne beryet gen. et sp. n.) was ascertained by comparing its 12S and 16S partial genes with those of Oriental and other relevant bufonid lineages. Resulting molecular phylogeny supports the erection of a novel monotypic genus for this lineage from the Andaman Islands of India.

Population Recovery of Nicobar Long-Tailed Macaque Macaca fascicularis umbrosus following a Tsunami in the Nicobar Islands, India

Natural disasters pose a threat to isolated populations of species with restricted distributions, especially those inhabiting islands. The Nicobar long tailed macaque. Macaca fascicularis umbrosus, is one such species found in the three southernmost islands (viz. Great Nicobar, Little Nicobar and Katchal) of the Andaman and Nicobar archipelago, India. These islands were hit by a massive tsunami (Indian Ocean tsunami, 26 December 2004) after a 9.2 magnitude earthquake. Earlier studies Umapathy et al. 2003; Sivakumar, 2004] reported a sharp decline in the population of M. f. umbrosus after thetsunami. We studied the distribution and population status of M. f. umbrosus on thethree Nicobar Islands and compared our results with those of the previous studies. We carried out trail surveys on existing paths and trails on three islands to get encounter rate as measure of abundance. We also checked the degree of inundation due to tsunami by using Normalized Difference Water Index (NDWI) on landsat imageries of the study area before and after tsunami. Theencounter rate of groups per kilometre of M. f. umbrosus in Great Nicobar, Little Nicobar and Katchal was 0.30, 0.35 and 0.48 respectively with the mean group size of 39 in Great Nicobar and 43 in Katchal following the tsunami. This was higher than that reported in the two earlier studies conducted before and after the tsunami. Post tsunami, there was a significant change in the proportion of adult males, adult females and immatures, but mean group size did not differ as compared to pre tsunami. The results show that population has recovered from a drastic decline caused by tsunami, but it cannot be ascertained whether it has reached stability because of the altered group structure. This study demonstrates the effect of natural disasters on island occurring species.