Deorphanization of Malonyl CoA:ACP Transacylase Drug Target in Plasmodium falciparum (PfFabD) Using Bacterial Antagonists: A Piggyback' Approach for Antimalarial Drug Discovery

Quest for new drug targets in Plasmodium sp. has underscored malonyl CoA:ACP transacylase (PfFabD) of fatty acid biosynthetic pathway in apicoplast. In this study, a piggyback approach was employed for the receptor deorphanization using inhibitors of bacterial FabD enzymes. Due to the lack of crystal structure, theoretical model was constructed using the structural details of homologous enzymes. Sequence and structure analysis has localized the presence of two conserved pentapeptide motifs: GQGXG and GXSXG and five key invariant residues viz., Gln109, Ser193, Arg218, His305 and Gln354 characteristic of FabD enzyme. Active site mapping of PfFabD using substrate molecules has disclosed the spatial arrangement of key residues in the cavity. As structurally similar molecules exhibit similar biological activities, signature pharmacophore fingerprints of FabD antagonists were generated using 0D-3D descriptors for molecular similarity-based cluster analysis and to correlate with their binding profiles. It was observed that antagonists showing good geometrical fitness score were grouped in cluster-1, whereas those exhibiting high binding affinities in cluster-2. This study proves important to shed light on the active site environment to reveal the hotspot for binding with higher affinity and to narrow down the virtual screening process by searching for close neighbors of the active compounds.

Coalescent Method in Conjunction with Niche Modeling Reveals Cryptic Diversity among Centipedes in the Western Ghats of South India

Background: There has been growing interest in integrative taxonomy that uses data from multiple disciplines for species delimitation. Typically, in such studies, monophyly is taken as a proxy for taxonomic distinctiveness and these units are treated as potential species. However, monophyly could arise due to stochastic processes. Thus here, we have employed a recently developed tool based on coalescent approach to ascertain the taxonomic distinctiveness of various monophyletic units. Subsequently, the species status of these taxonomic units was further tested using corroborative evidence from morphology and ecology. This inter-disciplinary approach was implemented on endemic centipedes of the genus Digitipes (Attems 1930) from the Western Ghats (WG) biodiversity hotspot of India. The species of the genus Digitipes are morphologically conserved, despite their ancient late Cretaceous origin. Principal Findings: Our coalescent analysis based on mitochondrial dataset indicated the presence of nine putative species. The integrative approach, which includes nuclear, morphology, and climate datasets supported distinctiveness of eight putative species, of which three represent described species and five were new species. Among the five new species, three were morphologically cryptic species, emphasizing the effectiveness of this approach in discovering cryptic diversity in less explored areas of the tropics like the WG. In addition, species pairs showed variable divergence along the molecular, morphological and climate axes. Conclusions: A multidisciplinary approach illustrated here is successful in discovering cryptic diversity with an indication that the current estimates of invertebrate species richness for the WG might have been underestimated. Additionally, the importance of measuring multiple secondary properties of species while defining species boundaries was highlighted given variable divergence of each species pair across the disciplines.

Did southern Western Ghats of peninsular India serve as refugia for its endemic biota during the Cretaceous volcanism?

The Western Ghats (WG) of south India, a global biodiversity hotspot, has experienced complex geological history being part of Gondwana landmass and encountered extensive volcanic activity at the end of Cretaceous epoch. It also has a climatically and topographically heterogeneous landscape. Thus, the WG offer a unique setting to explore the influence of ecological and geological processes on the current diversity and distribution of its biota. To this end, three explicit biogeographical scenarios were hypothesized to evaluate the distribution and diversification of wet evergreen species of the WG - (1) southern WG was a refuge for the wet evergreen species during the Cretaceous volcanism, (2) phylogenetic breaks in the species phylogeny would correspond to geographic breaks (i.e., the Palghat gap) in the WG, and (3) species from each of the biogeographic subdivisions within the WG would form distinct clades. These hypotheses were tested on the centipede genus Digitipes from the WG which is known to be an ancient, endemic, and monophyletic group. The Digitipes molecular phylogeny was subjected to divergence date estimation using Bayesian approach, and ancestral areas were reconstructed using parsimony approach for each node in the phylogeny. Ancestral-area reconstruction suggested 13 independent dispersal events to explain the current distribution of the Digitipes species in the WG. Among these 13 dispersals, two dispersal events were at higher level in the Digitipes phylogeny and were from the southern WG to the central and northern WG independently in the Early Paleocene, after the Cretaceous Volcanism. The remaining 11 dispersal events explained the species' range expansions of which nine dispersals were from the southern WG to other biogeographic subdivisions in the Eocene-Miocene in the post-volcanic periods where species-level diversifications occurred. Taken together, these results suggest that southern WG might have served as a refuge for Digitipes species during Cretaceous volcanism.

Elastic thickness structure of the Andaman subduction zone: Implications for convergence of the Ninetyeast Ridge

We use the Bouguer coherence (Morlet isostatic response function) technique to compute the spatial variation of effective elastic thickness (T-e) of the Andaman subduction zone. The recovered T-e map resolves regional-scale features that correlate well with known surface structures of the subducting Indian plate and the overriding Burma plate. The major structure on the India plate, the Ninetyeast Ridge (NER), exhibits a weak mechanical strength, which is consistent with the expected signature of an oceanic ridge of hotspot origin. However, a markedly low strength (0< T-e <3 km) in that region, where the NER is close to the Andaman trench (north of 10 N), receives our main attention in this study. The subduction geometry derived from the Bouguer gravity forward modeling suggests that the NER has indented beneath the Andaman arc. We infer that the bending stresses of the viscous plate, which were reinforced within the subducting oceanic plate as a result of the partial subduction of the NER buoyant load, have reduced the lithospheric strength. The correlation, T-e < T-s (seismogenic thickness) reveals that the upper crust is actively deforming beneath the frontal arc Andaman region. The occurrence of normal-fault earthquakes in the frontal arc, low Te zone, is indicative of structural heterogeneities within the subducting plate. The fact that the NER along with its buoyant root is subducting under the Andaman region is inhibiting the subduction processes, as suggested by the changes in trench line, interrupted back-arc volcanism, variation in seismicity mechanism, slow subduction, etc. The low T-e and thinned crustal structure of the Andaman back-arc basin are attributed to a thermomechanically weakened lithosphere. The present study reveals that the ongoing back-arc spreading and strike-slip motion along the West Andaman Fault coupled with the ridge subduction exerts an important control on the frequency and magnitude of seismicity in the Andaman region. (C) 2013 Elsevier Ltd. All rights reserved.

Spatial variations of effective elastic thickness over the Ninetyeast Ridge and implications for its structure and tectonic evolution

We present new data on the strength of oceanic lithosphere along the Ninetyeast Ridge (NER) from two independent methods: spectral analysis (Bouguer coherence) using the fan wavelet transform technique, and spatial analysis (flexure inversion) with the convolution method. The two methods provide effective elastic thickness (T-e) patterns that broadly complement each other, and correlate well with known surface structures and regional-scale features. Furthermore, our study presents a new high resolution database on the Moho configuration, which obeys flexural isostasy, and exhibit regional correlations with the T-e variations. A continuous ridge structure with a much lower T-e value than that of normal oceanic lithosphere provides strong support for the hotspot theory. The derived T-e values vary over the northern (higher T-e similar to 10-20 km), central (anomalously low T-e similar to 0-5 km), and southern (low T-e similar to 5 km) segments of the NER. The lack of correlation of the T-e value with the progressive aging of the lithosphere implies differences in thermo-mechanical setting of the crust and underlying mantle in different parts of the NER, again indicating diversity in their evolution. The anomalously low T-e and deeper Moho (similar to 22 km) estimates of the central NER (between 0.5 degrees N and 17 degrees S) are attributed to the interaction of a hotspot with the Wharton spreading ridge that caused significant thermal rejuvenation and hence weakening of the lithosphere. The higher mechanical strength values in the northern NER (north of 0.5 degrees N) may support the idea of off-ridge emplacement and a relatively large plate motion at the time of volcanism. The low T-e and deeper Moho (similar to 22 km) estimates in the southern part (south of 17 degrees S) suggest that the lithosphere was weak and therefore younger at the time of volcanism, and this supports the idea that the southern NER was emplaced on the edge of the Indian plate. (C) 2013 Elsevier B.V. All rights reserved.

Phylogeny of the freshwater crabs of the Western Ghats (Brachyura, Gecarcinucidae)

The Western Ghats mountain range in India is a biodiversity hotspot for a variety of organisms including a large number of endemic freshwater crab species and genera of the family Gecarcinucidae. The phylogenetic relationships of these taxa, however, have remained poorly understood. Here, we present a phylogeny that includes 90% of peninsular Indian genera based on mitochondrial 16S rRNA and nuclear histone H3 gene sequences. The subfamily Gecarcinucinae was found to be paraphyletic with members of two other subfamilies, Liotelphusinae and Parathelphusinae, nesting within. We identify a well-supported clade consisting of north Indian species and one clade comprising mostly south Indian species that inhabit the southern sky islands' of the Western Ghats. Relationships of early diverging genera, however, were resolved with low support. This study also includes newly sampled material from an isolated mountain plateau in the northern part of the Western Ghats, representing a new species of Gubernatoriana, which we describe here as Gubernatoriana basalticola sp. n. The new species is immediately distinguished from its congeners and the related genera Ghatiana and Inglethelphusa by its carapace and cheliped morphology, which are unique among Indian freshwater crabs. This study highlights the urgent need for continued faunistic studies to assess the true diversity of gecarcinucid crabs on the Indian subcontinent, to fully understand the basal phylogenetic relationships within the freshwater crab family Gecarcinucidae, and to evaluate the conservation threat status and biogeography of the montane freshwater crabs of the Western Ghats.

India-Madagascar paleo-fit based on flexural isostasy of their rifted margins

The present study contributes new constraints on, and definitions of, the reconstructed plate margins of India and Madagascar based on flexural isostasy along the Western Continental Margin of India (WCMI) and the Eastern Continental Margin of Madagascar (ECMM). We have estimated the nature of isostasy and crustal geometry along the two margins, and have examined their possible conjugate structure. Here we utilize elastic thickness (Te) and Moho depth data as the primary basis for the correlation of these passive margins. We employ the flexure inversion technique that operates in spatial domain in order to estimate the spatial variation of effective elastic thickness. Gravity inversion and flexure inversion techniques are used to estimate the configuration of the Moho/Crust-Mantle Interface that reveals regional correlations with the elastic thickness variations. These results correlate well with the continental and oceanic segments of the Indian and African plates. The present study has found a linear zone of anomalously low-Te (1-5 km) along the WCMI (similar to 1680 km), which correlates well with the low-Te patterns obtained all along the ECMM. We suggest that the low-Te zones along the WCMI and ECMM represent paleo-rift inception points of lithosphere thermally and mechanically weakened by the combined effects of the Marion hotspot and lithospheric extension due to rifting. We have produced an India-Madagascar paleo-fit representing the initial phase of separation based on the Te estimates of the rifted conjugate margins, which is confirmed by a close-fit correlation of Moho geometry and bathymetry of the shelf margins. The matching of tectonic lineaments, lithologies and geochronological belts between India and Madagascar provide an additional support for the present plate reconstruction. (C) 2014 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

The 2014 M-w 6.1 Bay of Bengal, Indian Ocean, Earthquake: A Possible Association with the 85 degrees E Ridge

Oceanic intraplate earthquakes are known to occur either on active ridge-transform structures or by reactivation of their inactive counterparts, generally referred to as fossil ridges or transforms. The Indian Ocean, one of the most active oceanic intraplate regions, has generated large earthquakes associated with both these types of structures. The moderate earthquake that occurred on 21 May 2014 (M-w 6.1) in the northern Bay of Bengal followed an alternate mechanism, as it showed no clear association either with active or extinct ridge-transform structures. Its focal depth of >50 km is uncommon but not improbable, given the similar to 90 Ma age of the ocean floor with 12-km-thick overlying sediments. No tectonic features have been mapped in the near vicinity of its epicenter, the closest being the 85 degrees E ridge, located similar to 100 km to its west, hitherto regarded as seismically inactive. The few earthquakes that have occurred here in the past are clustered around its southern or northern limits, and a few are located midway, at around 10 degrees N. The 2014 earthquake, sourced close to the northern cluster, seems to be associated with a northwest-southeast-oriented fracture, located on the eastern flanks of the 85 degrees E ridge. If this causal association is possible, we believe that reactivation of fossil hotspot trails could be considered as another mechanism for oceanic intraplate seismicity.

Field Guide to Nonindigenous Marine Fishes of Florida

The purpose of this field guide is to provide information on nonindigenous (i.e., non-native) fishes that have been observed in Florida’s marine waters. Introductions of non-native marine fishes into Florida’s waters could be intentional or unintentional, and are likely from a variety of sources, including aquarium releases, escape from aquaculture, loss due to extreme weather events (e.g., flooding from hurricanes), and possibly transfer with ballast water or hull-fouling. Presently the lionfishes (Pterois volitans and P. miles) are the only non-native marine fish species known to be established along the coast of Florida. All other marine fishes in this guide (except the euryhaline species, see below) have infrequent occurrences, occur singly or in small groups, and have not yet become self-sustaining populations. Aquarium releases are one of the major pathways whereby nonindigenous fishes gain access to new environments (Ruiz et al. 1997; Fuller et al. 1999). Most of the nonindigenous marine fishes found in Florida’s waters are thought to be aquarium fishes that either were illegally released into the ocean or escaped captivity (e.g., during severe storm/flooding events). Indeed, south Florida is a hotspot for nonindigenous marine aquarium fishes (Semmens et al. 2004). Increased public awareness of the problems caused by released or escaped aquarium fishes may aid in stemming the frequency of releases. For example, HabitattitudeTM (www.habitattitude.net) is a national public awareness and partnership campaign that encourages aquarists and water gardeners to prevent the release of unwanted aquarium plants, fish and other animals. It prompts hobbyists to adopt alternative actions when dealing with these aquatic plants and animals. (PDF file contains 133 pages.)

SYSTEMATICS OF GROUNDWATER OLIGOCHAETES (ANNELIDA, CLITELLATA) IN KARSTIC AREAS OF THE CANTABRIAN REGION/ ERREGIO KANTAURIARREKO EREMU KARSTIKOETAN DAUDEN LURPEKO OLIGOKETO (ANNELIDA, CLITELLATA) URT

This thesis deals with the oligochaete taxa (Annelida, Clitellata) from several karst units in the Cantabrian region, northern Iberian Peninsula. Groundwater oligochaetes are still poorly known fauna and the area seems to be a promising hotspot for groundwater taxa. Metodology is based on both morphological and molecular analyses. More than 7,000 specimens were collected from five karst units and >60 taxa were identified. Stygobiont oligochaete fauna in the northern Iberian Peninsula is diverse and mostly endemic (range areas <300 km). Three new stygogiont oligochaete species are described: Gianius navarroi Rodriguez & Achurra, 2010, Isochaetides gianii Rodriguez & Achurra, 2010 and Troglodrilus jugeti Achurra et al., 2012; and another four new taxa will be described in the near future. Taxonomic remarks on Lophochaeta ignota Stolc, 1886 and Troglodrilus galarzai (Giani & Rodriguez, 1988) are provided. The controversial separation of L. ignota and Heterochaeta costata Claparède, 1863 from Tubifex Lamarck, 1816 is corroborated by mitochondrial molecular data. Following the DNA barcoding method, individuals of the stygoxene species Stylodrilus heringianus Claparède, 1862 from different geographic areas are shown to represent a single metapopulation. The first phylogenetic analysis of the subfamily Tubificinae based on molecular data is attemped, which although incompletely resolved, evidences for the first time a close relationship between a stygobiont oligochaete (Troglodrilus Juget et al. 2006) and an estuarine especies (Heterochaeta costata Claparéde, 1863). A marine ancestor is hypothesised for Troglodrilus. Finally, Ereñozar karst unit (Biscay) is suggested to be a hotspot for groundwater oligochaetes (11 stygobiont taxa, of which 4 are endemic to the karst unit) and several biodiversity indices (Species richness, Rarity, Vulnerability and Complementarity) are shown to be useful tools for conservation management of groundwater habitats in that karst area.

纳米光存储薄膜结构的光学性质

近场超分辨纳米薄膜结构可以突破衍射极限实现纳米尺寸信息存储,是下一代海量存储技术的重要方案之一,也是纳米光子学研究中的热点。纳米膜层结构基于激光作用下的非线性局域光学效应实现超分辨。分析了超分辨近场薄膜结构突破衍射极限的光学原理,对超分辨纳米薄膜结构的表面等离子体激发特性、非线性光学特性、近场光学特性和超透镜效应等重要光学性质的最新研究进展做了系统介绍。

Estudo do magmatismo máfico de complexos alcalinos do sudeste do Brasil

Nesta dissertação foram estudas rochas máficas dos complexos alcalinos de Morro de São João, Rio Bonito, Tanguá, Gericinó-Mendanha, Morro Redondo, Itatiaia e Passa Quatro. Essas rochas ocorrem na forma de diques e/ou sills. As amostras coletadas foram classificadas como lamprófiros, fonolitos, gabros e diabásios alcalinos. A análise geoquímica permitiu identificar um trend fortemente insaturado e um trend moderadamente alcalino para os complexos estudados. O primeiro é caracterizado por foiditos e fonolitos como membros parentais e mais evoluídos, respectivamente, enquanto o segundo tem basaltos alcalinos como membros parentais e traquitos como os mais evoluídos. Todas as amostras plotam no campo da série alcalina, sendo majoritariamente miaskíticas, sódicas ou potássicas. Adicionalmente, o estudo geoquímico indicou que os complexos alcalinos representam câmaras magmáticas distintas, onde diferentes processos evolutivos tiveram lugar. As modelagens apontaram dois processos de diferenciação distintos nos complexos estudados. Os complexos alcalinos de Morro de São João, Morro Redondo, Gericinó-Mendanha e Itatiaia estariam relacionados a processos de cristalização fracionada. Por outro lado, o Complexo Alcalino de Passa Quatro teria sido diferenciado por processos de cristalização fracionada com esvaziamento e posterior reabastecimento da câmara magmática (RTF). De um modo geral, esses modelos indicaram a presença de mais do que uma série magmática nos complexos estudados e a não cogeneticidade entre as séries agpaíticas e miaskíticas. A discriminação de fontes foi feita com base na análise dos elementos terras raras das amostras parentais de cada um dos complexos (gabro em Morro de São João e lamprófiro nos demais). No entanto, este procedimento não foi aplicado para o Complexo Alcalino de Morro Redondo, uma vez que todas as suas amostras apresentaram valores de MgO muito abaixo do típico para líquidos parentais. O líquido parental do Complexo Alcalino do Gericinó-Mendanha apresentou razões de La/Yb e La/Nb, maior e menor que a unidade, respectivamente, típicas de derivação a partir fontes férteis. Os líquidos parentais dos outros complexos alcalinos tiveram suas razões La/Yb e La/Nb maiores que a unidade, típicas de derivação a partir de fontes enriquecidas. Os modelos desenvolvidos revelaram que os líquidos parentais de cada um dos complexos estudados estariam relacionados a fontes lherzolíticas com granada residual. Além disso, a fusão parcial destas fontes teria ocorrido num intervalo de 1 a 7% dentro da zona da granada. Finalmente, as modelagens petrogenéticas elaboradas permitiram a proposição de um cenário geodinâmico, envolvendo a descompressão adiabática do manto litosférico e sublitosférico anomalamente aquecidos. As características geoquímicas dos líquidos parentais parecem ter sido controladas essencialmente pela mistura desses dois tipos de fontes.

Conservação de morcegos no estado do Rio de Janeiro: como e onde já foram amostrados e que locais merecem atenção

A demarcação de Unidades de Conservação é uma forma supostamente eficaz para a conservação da biodiversidade. A Mata Atlântica é caracterizada por apresentar uma elevada biodiversidade e altos níveis de ameaça. O estado do Rio de Janeiro encontra-se totalmente inserido nesse bioma e seus remanescentes florestais são considerados um hotspot dentro de outro hotspot. O Rio de Janeiro pode ser considerado um dos estados melhor amostrados, porém ainda existem lacunas de conhecimentos geográficos sobre a ocorrência de morcegos. Esta tese foi desenvolvida em três capítulos com o objetivo de contribuir com conservação de morcegos no estado do Rio de Janeiro, focando em como e onde eles já foram amostrados e que locais ainda carecem de atenção. Para este estudo foram utilizados dados referentes a buscas bibliográficas e dados de amostragens do Laboratório de Diversidade de Morcegos da Universidade Federal Rural do Rio de Janeiro. No primeiro capítulo pode-se observar que as localidades com mais de 30 espécies de morcegos são resultado de grande esforço de captura e amostragens usando diversas metodologias. Para uma melhor amostragem da riqueza local, devem-se armar redes não somente em trilhas e próximas a árvores em frutificação, mas também sobre corpos de água. Fazer busca em refúgios diurnos também é aconselhável. Devem ser realizadas amostragens durante a noite toda e variar a fase do ciclo lunar, não restringindo a apenas uma ou partes das fases do ciclo lunar. No segundo capítulo observou-se que 43% das Unidades de Conservação aqui estudadas apresentam 20 ou mais espécies. Localidades que apresentam de 20 a 40 espécies de morcegos na Mata Atlântica podem ser consideradas bem amostradas. Isso demonstra que mais da metade das Unidades de Conservação não podem ser consideradas bem inventariadas. Muitos projetos de pesquisas dão prioridade para a localidade estudada ser uma Unidade de Conservação, porém existem poucos trabalhos de longa duração. No Rio de Janeiro ainda existem diversas Unidades de Conservação não amostradas, principalmente aquelas de difícil acesso e em altitudes elevadas. No terceiro capítulo foi possível observar que há uma maior proporção de espécies que apresentam distribuição geográfica restrita. Esse padrão constitui uma informação importante em termos de conservação, visto que indiretamente poderia indicar uma menor capacidade de dispersão desses animais em médias e grandes distâncias. Entretanto existem lacunas de conhecimento em decorrência da falta de amostragem em algumas regiões, sendo imperativos maiores esforços de captura. Importantes municípios para a conservação e/ou preservação de morcegos como Varre-Sai, Cambuci, Miracema, Carmo, Cantagalo, Valença, Barra do Piraí e Piraí não estão sob proteção legal, mesmo constituindo possíveis corredores entre Unidades de Conservação ou mesmo fragmentos importantes que ainda detém espécies que não estão representadas em Unidades de Conservação já estabelecidas. É imperativo que mais estudos e esforços de conservação sejam direcionados para essas áreas

Statistical analyses to support guidelines for marine avian sampling: Final report. [Digital Supplements A-G attached]

Interest in development of offshore renewable energy facilities has led to a need for high-quality, statistically robust information on marine wildlife distributions. A practical approach is described to estimate the amount of sampling effort required to have sufficient statistical power to identify species specific “hotspots” and “coldspots” of marine bird abundance and occurrence in an offshore environment divided into discrete spatial units (e.g., lease blocks), where “hotspots” and “coldspots” are defined relative to a reference (e.g., regional) mean abundance and/or occurrence probability for each species of interest. For example, a location with average abundance or occurrence that is three times larger the mean (3x effect size) could be defined as a “hotspot,” and a location that is three times smaller than the mean (1/3x effect size) as a “coldspot.” The choice of the effect size used to define hot and coldspots will generally depend on a combination of ecological and regulatory considerations. A method is also developed for testing the statistical significance of possible hotspots and coldspots. Both methods are illustrated with historical seabird survey data from the USGS Avian Compendium Database.

Molecular systematics and historical biogeography of the Black-browed Barbet species complex (Megalaima oorti)

Although Southeast Asia is a global biodiversity hotspot, the tempo and mode of avian diversification there has not been well studied. We investigated the history of the diversification of an endemic Asian tropical bird, the Black-browed Barbet Megalaima