Mismatch repair genes of eukaryotes

Mismatches that arise during replication or genetic recombination or owing to damage to DNA by chemical agents are recognized by mismatch repair systems. The pathway has been characterized in detail in Escherichia coli. Several homologues of the genes encoding the proteins of this pathway have been identified in the yeast Saccharomyces cerevisiae and in human cells. Mutations in the human genes hMSH2, hMLH1, hPMS1 and hPMS2 have been linked to hereditary nonpolyposis colon cancer (HNPCC) and to some sporadic tumours. Mismatch repair also plays an antirecombinogenic role and is implicated in speciation.

Remote detection and distinction of ants using nest-site specific LISS-derived Normalised Difference Vegetation Index

This study in Western Ghats, India, investigates the relation between nesting sites of ants and a single remotely sensed variable: the Normalised Difference Vegetation Index (NDVI). We carried out sampling in 60 plots each measuring 30 x 30 m and recorded nest sites of 13 ant species. We found that NDVI values at the nesting sites varied considerably between individual species and also between the six functional groups the ants belong to. The functional groups Cryptic Species, Tropical Climate Specialists and Specialist Predators were present in regions with high NDVI whereas Hot Climate Specialists and Opportunists were found in sites with low NDVI. As expected we found that low NDVI values were associated with scrub jungles and high NDVI values with evergreen forests. Interestingly, we found that Pachycondyla rufipes, an ant species found only in deciduous and evergreen forests, established nests only in sites with low NDVI (range = 0.015 - 0.1779). Our results show that these low NDVI values in deciduous and evergreen forests correspond to canopy gaps in otherwise closed deciduous and evergreen forests. Subsequent fieldwork confirmed the observed high prevalence of P. rufipes in these NDVI-constrained areas. We discuss the value of using NDVI for the remote detection and distinction of ant nest sites.

Testing concordance in species boundaries using acoustic, morphological, and molecular data in the field cricket genus Itaropsis (Orthoptera: Grylloidea, Gryllidae: Gryllinae)

In most taxa, species boundaries are inferred based on differences in morphology or DNA sequences revealed by taxonomic or phylogenetic analyses. In crickets, acoustic mating signals or calling songs have species-specific structures and provide a third data set to infer species boundaries. We examined the concordance in species boundaries obtained using acoustic, morphological, and molecular data sets in the field cricket genus Itaropsis. This genus is currently described by only one valid species, Itaropsis tenella, with a broad distribution in western peninsular India and Sri Lanka. Calling songs of males sampled from four sites in peninsular India exhibited significant differences in a number of call features, suggesting the existence of multiple species. Cluster analysis of the acoustic data, molecular phylogenetic analyses, and phylogenetic analyses combining all data sets suggested the existence of three clades. Whatever the differences in calling signals, no full congruence was obtained between all the data sets, even though the resultant lineages were largely concordant with the acoustic clusters. The genus Itaropsis could thus be represented by three morphologically cryptic incipient species in peninsular India; their distributions are congruent with usual patterns of endemism in the Western Ghats, India. Song evolution is analysed through the divergence in syllable period, syllable and call duration, and dominant frequency.

Anomalous low-temperature magnetic and magnetotransport properties in Ru-deficient SrRuO3

SrRuO3 is a well-known itinerant ferromagnet with many intriguing characteristics. The Ru deficiency in this system is believed to play a pivotal role in influencing many of its magnetic and transport properties. The present study involves the magnetic and transport properties of the Ru-deficient SrRu0.93O3 sample to gain more insight into the unusual low-temperature behavior. The ac susceptibility study reveals a sharp ferromagnetic transition at 150 K followed by a hump at T-h similar to 50 K, which has anomalous frequency dependence. Besides, the T-h shifts to lower temperatures with an increase in the superposed dc-biasing field and adheres to H-2 dependence, in accordance with the Gabay and Toulouse line for the Heisenberg spin glass systems. We also observe a pronounced memory effect toward the low-temperature side, signifying the characteristic of glassy behavior. The temperature-dependent magnetoresistance indicates the signature of an additional ordering toward the low-temperature side. All of the interesting findings combined unveil the existence of low-temperature cryptic magnetic phase in SrRu0.93O3. (C) 2012 American Institute of Physics. doi:10.1063/1.3673427]

Thermo-physical and structural studies of sodium zinc borovanadate glasses in the region of high concentration of modifier oxides

This paper reports investigation of Na2O and ZnO modified borovanadate glasses in the highly modified regime of compositions. These glasses have been prepared by microwave route. Ultraviolet (UV) and visible, infrared (IR), Magic Angle Spinning Nuclear Magnetic Resonance (MAS NMR) and Electron Paramagnetic Resonance (EPR) spectroscopies have been used to characterize the speciation in the glasses. Together with the variation of properties such as molar volume and glass transition temperatures, spectroscopic data indicate that at high levels of modification, ZnO tends to behave like network former. It is proposed that the observed variation of all the properties can be reasonably well understood with a structural model. The model considers that the modification and speciation in glasses are strongly determined by the hierarchy of group electronegativities. Further, it is proposed that the width of the transitions of glasses obtained under same condition reflects the fragility of the glasses. An empirical expression has been suggested to quantify fragility on the basis of width of the transition regions. (C) 2012 Elsevier Ltd. All rights reserved.

Peraluminous sapphirine-cordierite pods in Mg-rich orthopyroxene granulite from southern India: Implications for lower crustal processes

Sapphirine-cordierite intergrowths occur as pods within garnet-absent, high-Mg orthopyroxene-granulite xenoliths in the Kambam valley, Madurai Block, southern India. Whereas the cores of the pods are composed of sapphirine (X-Mg = 0.871-0.897) - cordierite (X-Mg = 0.892-0.931) intergrowth along with rutile, zircon and monazite, the rims are characterized by cordierite, apatite, plagioclase, K-feldspar, quartz and minor calcite. The surrounding matrix comprises orthopyroxene (maximum Al2O3 4.1 wt.%, X-Mg 0.848-0.850), plagioclase, biotite and quartz, similar to the assemblage in the surrounding charnockites. Sapphirine in the Kambam rocks is characterized by high Al contents with an end-member composition in the range of 7:9:3 and 3:5:1. The occurrence of peraluminous sapphirine in association with cordierite and in the absence of phases such as sillimanite and garnet is distinct from ultrahigh-temperature assemblages in other localities within the Madurai Block. The peraluminous composition of the pods suggests that these domains could represent cryptic pathways through which aluminous melts migrated. The reaction of such peraluminous melts with Mg-rich orthopyroxene in the host granulite at temperatures of 1025 degrees C and pressures around 8 kbar as computed from phase equilibria modeling followed by an isobaric cooling is inferred to have generated the sapphirine-cordierite pods. The unusual high-Mg orthopyroxene granulite suggests interaction of supracrustal rocks with mafic magmas, which probably acted as the heat source for the partial melting of lower crust and UHT metamorphism.

Reproductive queue without overt conflict in the primitively eusocial wasp Ropalidia marginata

Colonies of the primitively eusocial wasp Ropalidia marginata consist of a single egg layer (queen) and a number of non-egg-laying workers. Although the queen is a docile individual, not at the top of the behavioral dominance hierarchy of the colony, she maintains complete reproductive monopoly. If the queen is lost or removed, one and only one of the workers potential queen (PQ)] becomes hyperaggressive and will become the next queen of the colony. The PQ is almost never challenged because she first becomes hyperaggressive and then gradually loses her aggression, develops her ovaries, and starts laying eggs. Although we are unable to identify the PQ when the queen is present, she appears to be a ``cryptic heir designate.'' Here, we show that there is not just one heir designate but a long reproductive queue and that PQs take over the role of egg-laying, successively, without overt conflict, as the queen or previous PQs are removed. The dominance rank of an individual is not a significant predictor of its position in the succession hierarchy. The age of an individual is a significant predictor, but it is not a perfect predictor because PQs often bypass older individuals to become successors. We suggest that such a predesignated reproductive queue that is implemented without overt conflict is adaptive in the tropics, where conspecific usurpers from outside the colony, which can take advantage of the anarchy prevailing in a queenless colony and invade it, are likely to be present throughout the year.

Antibodies against the extracellular domain of human Notch1 receptor reveal the critical role of epidermal-growth-factor-like repeats 25-26 in ligand binding and receptor activation

The Notch signalling pathway is implicated in a wide variety of cellular processes throughout metazoan development. Although the downstream mechanism of Notch signalling has been extensively studied, the details of its ligand-mediated receptor activation are not clearly understood. Although the role of Notch ELRs EGF (epidermal growth factor)-like-repeats] 11-12 in ligand binding is known, recent studies have suggested interactions within different ELRs of the Notch receptor whose significance remains to be understood. Here, we report critical inter-domain interactions between human Notch1 ELRs 21-30 and the ELRs 11-15 that are modulated by calcium. Surface plasmon resonance analysis revealed that the interaction between ELRs 21-30 and ELRs 11-15 is similar to 10-fold stronger than that between ELRs 11-15 and the ligands. Although there was no interaction between Notch 1 ELRs 21-30 and the ligands in vitro, addition of pre-clustered Jagged1Fc resulted in the dissociation of the preformed complex between ELRs 21-30 and 11-15, suggesting that inter-domain interactions compete for ligand binding. Furthermore, the antibodies against ELRs 21-30 inhibited ligand binding to the full-length Notch1 and subsequent receptor activation, with the antibodies against ELRs 25-26 being the most effective. These results suggest that the ELRs 25-26 represent a cryptic ligand-binding site which becomes exposed only upon the presence of the ligand. Thus, using specific antibodies against various domains of the Notch1 receptor, we demonstrate that, although ELRs 11-12 are the principal ligand-binding site, the ELRs 25-26 serve as a secondary binding site and play an important role in receptor activation.

Revision of the scolopendrid centipede digitipes Attems, 1930, from India (Chilopoda: Scolopendromorpha): reconciling molecular and morphological estimates of species diversity

Recent work on molecular phylogenetics of Scolopendridae from the Western Ghats, Peninsular India, has suggested the presence of six cryptic species of the otostigmine Digitipes Attems, 1930, together with three species described in previous taxonomic work by Jangi and Dass (1984). Digitipes is the correct generic attribution for a monophyletic group of Indian species, these being united with three species from tropical Africa (including the type) that share a distomedial process on the ultimate leg femur of males that is otherwise unknown in Otostigminae. Second maxillary characters previously used in the diagnosis of Digitipes are dismissed because Indian species do not possess the putatively diagnostic character states. Two new species from the Western Ghats that correspond to groupings identified based on monophyly, sequence divergence and coalescent analysis using molecular data are diagnosed based on distinct morphological characters. They are D. jangii and D. periyarensis n. spp. Three species named by Jangi and Dass (Digitipes barnabasi, D. coonoorensis and D. indicus) are revised based on new collections; D. indicus is a junior subjective synonym of Arthrorhabdus jonesii Verhoeff, 1938, the combination becoming Digitipes jonesii (Verhoeff, 1938) n. comb. The presence of Arthrorhabdus in India is accordingly refuted. Three putative species delimited by molecular and ecological data remain cryptic from the perspective of diagnostic morphological characters and are presently retained in D. barnabasi, D. jangii and D. jonesii. A molecularly-delimited species that resolved as sister group to a well-supported clade of Indian Digitipes is identified as Otostigmus ruficeps Pocock, 1890, originally described from a single specimen and revised herein. One Indian species originally assigned to Digitipes, D. gravelyi, deviates from confidently-assigned Digitipes with respect to several characters and is reassigned to Otostigmus, as O. gravelyi (Jangi and Dass, 1984) n. comb.

Evaluation of census techniques to estimate the density of slender Loris (Loris lydekkerianus) in Southern India

Reliable estimates of species density are fundamental to planning conservation strategies for any species; further, it is equally crucial to identify the most appropriate technique to estimate animal density. Nocturnal, small-sized animal species are notoriously difficult to census accurately and this issue critically affects their conservation status, We carried out a field study in southern India to estimate the density of slender loris, a small-sized nocturnal primate using line and strip transects. Actual counts of study individuals yielded a density estimate of 1.61 ha(-1); density estimate from line transects was 1.08 ha(-1); and density estimates varied from 1.06 ha(-1) to 0.59 ha(-1) in different fixed-width strip transects. We conclude that line and strip transects may typically underestimate densities of cryptic, nocturnal primates.

Memory effect in SrRu(1-x)O3 (0.01 < x < 0.07)

SrRuO3 is widely known to be an itinerant ferromagnet with a T-C similar to 160 K. It is well known that glassy materials exhibit time dependent phenomena such as memory effect due to their generic slow dynamics. However, for the first time, we have observed memory effect in SrRu(1-x)O3 (0.01cryptic interactions arises in the low temperature. Our effort on neutron diffraction study has been able to trace the cause of such hidden magnetic interaction responsible for bringing glassiness in a ferromagnet.

Hydrolysis of aromatic beta-glucosides by non-pathogenic bacteria confers a chemical weapon against predators

Bacteria present in natural environments such as soil have evolved multiple strategies to escape predation. We report that natural isolates of Enterobacteriaceae that actively hydrolyze plant-derived aromatic beta-glucosides such as salicin, arbutin and esculin, are able to avoid predation by the bacteriovorous amoeba Dictyostelium discoideum and nematodes of multiple genera belonging to the family Rhabditidae. This advantage can be observed under laboratory culture conditions as well as in the soil environment. The aglycone moiety released by the hydrolysis of beta-glucosides is toxic to predators and acts via the dopaminergic receptor Dop-1 in the case of Caenorhabditis elegans. While soil isolates of nematodes belonging to the family Rhabditidae are repelled by the aglycone, laboratory strains and natural isolates of Caenorhabditis sp. are attracted to the compound, mediated by receptors that are independent of Dop-1, leading to their death. The b-glucosides-positive (Bgl(+)) bacteria that are otherwise non-pathogenic can obtain additional nutrients from the dead predators, thereby switching their role from prey to predator. This study also offers an evolutionary explanation for the retention by bacteria of `cryptic' or `silent' genetic systems such as the bgl operon.

Examining the Effectiveness of Discriminant Function Analysis and Cluster Analysis in Species Identification of Male Field Crickets Based on Their Calling Songs

Traditional taxonomy based on morphology has often failed in accurate species identification owing to the occurrence of cryptic species, which are reproductively isolated but morphologically identical. Molecular data have thus been used to complement morphology in species identification. The sexual advertisement calls in several groups of acoustically communicating animals are species-specific and can thus complement molecular data as non-invasive tools for identification. Several statistical tools and automated identifier algorithms have been used to investigate the efficiency of acoustic signals in species identification. Despite a plethora of such methods, there is a general lack of knowledge regarding the appropriate usage of these methods in specific taxa. In this study, we investigated the performance of two commonly used statistical methods, discriminant function analysis (DFA) and cluster analysis, in identification and classification based on acoustic signals of field cricket species belonging to the subfamily Gryllinae. Using a comparative approach we evaluated the optimal number of species and calling song characteristics for both the methods that lead to most accurate classification and identification. The accuracy of classification using DFA was high and was not affected by the number of taxa used. However, a constraint in using discriminant function analysis is the need for a priori classification of songs. Accuracy of classification using cluster analysis, which does not require a priori knowledge, was maximum for 6-7 taxa and decreased significantly when more than ten taxa were analysed together. We also investigated the efficacy of two novel derived acoustic features in improving the accuracy of identification. Our results show that DFA is a reliable statistical tool for species identification using acoustic signals. Our results also show that cluster analysis of acoustic signals in crickets works effectively for species classification and identification.

Evolution of social behaviour in the primitively eusocial wasp Ropalidia marginata: do we need to look beyond kin selection?

Ropalidia marginata is a primitively eusocial wasp widely distributed in peninsular India. Although solitary females found a small proportion of nests, the vast majority of new nests are founded by small groups of females. In suchmultiple foundress nests, a single dominant female functions as the queen and lays eggs, while the rest function as sterile workers and care for the queen's brood. Previous attempts to understand the evolution of social behaviour and altruism in this species have employed inclusive fitness theory (kin selection) as a guiding framework. Although inclusive fitness theory is quite successful in explaining the high propensity of the wasps to found nests in groups, several features of their social organization suggest that forces other than kin selection may also have played a significant role in the evolution of this species. These features include lowering of genetic relatedness owing to polyandry and serial polygyny, nest foundation by unrelated individuals, acceptance of young non-nest-mates, a combination of well-developed nest-mate recognition and lack of intra-colony kin recognition, a combination of meek and docile queens and a decentralized self-organized work force, long reproductive queues with cryptic heir designates and conflict-free queen succession, all resulting in extreme intra-colony cooperation and inter-colony conflict.

Report of the 2005 Workshop on Ocean Ecodynamics Comparison in the Subarctic Pacific

I. Scientific Issues Posed by OECOS II. Participant Contributions to the OECOS Workshop A. ASPECTS OF PHYTOPLANKTON ECOLOGY IN THE SUBARCTIC PACIFIC Microbial community compositions by Karen E. Selph Subarctic Pacific lower trophic interactions: Production-based grazing rates and grazing-corrected production rates by Nicholas Welschmeyer Phytoplankton bloom dynamics and their physiological status in the western subarctic Pacific by Ken Furuya Temporal and spatial variability of phytoplankton biomass and productivity in the northwestern Pacific by Sei-ichi Saitoh, Suguru Okamoto, Hiroki Takemura and Kosei Sasaoka The use of molecular indicators of phytoplankton iron limitation by Deana Erdner B. IRON CONCENTRATION AND CHEMICAL SPECIATION Iron measurements during OECOS by Zanna Chase and Jay Cullen 25 The measurement of iron, nutrients and other chemical components in the northwestern North Pacific Ocean by Kenshi Kuma The measurement of iron, nutrients and other chemical components in the northwestern North Pacific Ocean by Kenshi Kuma C. PHYSICAL OCEANOGRAPHY, FINE-SCALE DISTRIBUTION PATTERNS AND AUTONOMOUS DRIFTERS The use of drifters in Lagrangian experiments: Positives, negatives and what can really be measured by Peter Strutton The interaction between plankton distribution patterns and vertical and horizontal physical processes in the eastern subarctic North Pacific by Timothy J. Cowles D. MICROZOOPLANKTON Microzooplankton processes in oceanic waters of the eastern subarctic Pacific: Project OECOS by Suzanne Strom Functional role of microzooplankton in the pelagic marine ecosystem during phytoplankton blooms in the western subarctic Pacific by Takashi Ota and Akiyoshi Shinada E. MESOZOOPLANKTON Vertical zonation of mesozooplankton, and its variability in response to food availability, density stratification, and turbulence by David L. Mackas and Moira Galbraith Marine ecosystem characteristics and seasonal abundance of dominant calanoid copepods in the Oyashio region by Atsushi Yamaguchi, Tsutomu Ikeda and Naonobu Shiga OECOS: Proposed mesozooplankton research in the Oyashio region, western subarctic Pacific by Tsutomu Ikeda Some background on Neocalanus feeding by Michael Dagg Size and growth of interzonally migrating copepods by Charles B. Miller Growth of large interzonal migrating copepods by Toru Kobari F. MODELING Ecosystem and population dynamics modeling by Harold P. Batchelder III. Reports from Workshop Breakout Groups A. PHYSICAL AND CHEMICAL ASPECTS WITH EMPHASIS ON IRON AND IRON SPECIATION B. PHYTOPLANKTON/MICROZOOPLANKTON STUDIES C. MESOZOOPLANKTON STUDIES IV. Issues arising during the workshop A. PHYTOPLANKTON STOCK VARIATIONS IN HNLC SYSTEMS AND TROPHIC CASCADES IN THE NANO AND MICRO REGIMES B. DIFFERENCES BETWEEN EAST AND WEST IN SITE SELECTION FOR OECOS TIME SERIES C. TIMING OF OECOS EXPEDITIONS D. CHARACTERIZATION OF PHYSICAL OCEANOGRAPHY V. Concluding Remarks VI. References (109 page document)