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Sample records for cryptic conserved conformationally

  1. DNA barcoding applied to ex situ tropical amphibian conservation programme reveals cryptic diversity in captive populations.

    PubMed

    Crawford, Andrew J; Cruz, Catalina; Griffith, Edgardo; Ross, Heidi; Ibáñez, Roberto; Lips, Karen R; Driskell, Amy C; Bermingham, Eldredge; Crump, Paul

    2013-11-01

    Amphibians constitute a diverse yet still incompletely characterized clade of vertebrates, in which new species are still being discovered and described at a high rate. Amphibians are also increasingly endangered, due in part to disease-driven threats of extinctions. As an emergency response, conservationists have begun ex situ assurance colonies for priority species. The abundance of cryptic amphibian diversity, however, may cause problems for ex situ conservation. In this study we used a DNA barcoding approach to survey mitochondrial DNA (mtDNA) variation in captive populations of 10 species of Neotropical amphibians maintained in an ex situ assurance programme at El Valle Amphibian Conservation Center (EVACC) in the Republic of Panama. We combined these mtDNA sequences with genetic data from presumably conspecific wild populations sampled from across Panama, and applied genetic distance-based and character-based analyses to identify cryptic lineages. We found that three of ten species harboured substantial cryptic genetic diversity within EVACC, and an additional three species harboured cryptic diversity among wild populations, but not in captivity. Ex situ conservation efforts focused on amphibians are therefore vulnerable to an incomplete taxonomy leading to misidentification among cryptic species. DNA barcoding may therefore provide a simple, standardized protocol to identify cryptic diversity readily applicable to any amphibian community. © 2012 John Wiley & Sons Ltd.

  2. Evolutionary Conserved Positions Define Protein Conformational Diversity

    PubMed Central

    Saldaño, Tadeo E.; Monzon, Alexander M.; Parisi, Gustavo; Fernandez-Alberti, Sebastian

    2016-01-01

    Conformational diversity of the native state plays a central role in modulating protein function. The selection paradigm sustains that different ligands shift the conformational equilibrium through their binding to highest-affinity conformers. Intramolecular vibrational dynamics associated to each conformation should guarantee conformational transitions, which due to its importance, could possibly be associated with evolutionary conserved traits. Normal mode analysis, based on a coarse-grained model of the protein, can provide the required information to explore these features. Herein, we present a novel procedure to identify key positions sustaining the conformational diversity associated to ligand binding. The method is applied to an adequate refined dataset of 188 paired protein structures in their bound and unbound forms. Firstly, normal modes most involved in the conformational change are selected according to their corresponding overlap with structural distortions introduced by ligand binding. The subspace defined by these modes is used to analyze the effect of simulated point mutations on preserving the conformational diversity of the protein. We find a negative correlation between the effects of mutations on these normal mode subspaces associated to ligand-binding and position-specific evolutionary conservations obtained from multiple sequence-structure alignments. Positions whose mutations are found to alter the most these subspaces are defined as key positions, that is, dynamically important residues that mediate the ligand-binding conformational change. These positions are shown to be evolutionary conserved, mostly buried aliphatic residues localized in regular structural regions of the protein like β-sheets and α-helix. PMID:27008419

  3. Interview-based sighting histories can inform regional conservation prioritization for highly threatened cryptic species

    PubMed Central

    Turvey, Samuel T; Trung, Cao Tien; Quyet, Vo Dai; Nhu, Hoang Van; Thoai, Do Van; Tuan, Vo Cong Anh; Hoa, Dang Thi; Kacha, Kouvang; Sysomphone, Thongsay; Wallate, Sousakhone; Hai, Chau Thi Thanh; Thanh, Nguyen Van; Wilkinson, Nicholas M

    2015-01-01

    The use of robust ecological data to make evidence-based management decisions is frequently prevented by limited data quantity or quality, and local ecological knowledge (LEK) is increasingly seen as an important source of information for conservation. However, there has been little assessment of LEK's usefulness for informing prioritization and management of landscapes for threatened species, or assessing comparative species status across landscapes. A large-scale interview survey in the Annamite Mountains (Vietnam and Lao PDR) compiled the first systematic LEK data set for saola Pseudoryx nghetinhensis, one of the world's rarest mammals, and eight other ungulates. Saola conservation is hindered by uncertainty over continued presence across much of its proposed distribution. We analysed comparative LEK-based last-sighting data across three landscapes to determine whether regional sighting histories support previous suggestions of landscape importance for saola conservation (Hue-Quang Nam: top-priority Vietnamese landscape; Pu Mat: lower priority Vietnamese landscape; Viengthong: high-priority Lao landscape) and whether they constitute an effective spatial prioritization tool for cryptic species management. Wild pig and red muntjac may be the only Annamite ungulates with stable populations; the regional status of all other species appears to be worse. Saola have declined more severely and/or are significantly rarer than most other ungulates and have been seen by relatively few respondents. Saola were also frequently considered locally rarest or declining, and never as species that had not declined. In contrast to other species, there are no regional differences in saola sighting histories, with continued persistence in all landscapes challenging suggestions that regional status differs greatly. Remnant populations persist in Vietnam despite heavy hunting, but even remote landscapes in Lao may be under intense pressure. Synthesis and applications. Our local

  4. Conservation Genetics of the Philippine Tarsier: Cryptic Genetic Variation Restructures Conservation Priorities for an Island Archipelago Primate

    PubMed Central

    Brown, Rafe M.; Weghorst, Jennifer A.; Olson, Karen V.; Duya, Mariano R. M.; Barley, Anthony J.; Duya, Melizar V.; Shekelle, Myron; Neri-Arboleda, Irene; Esselstyn, Jacob A.; Dominy, Nathaniel J.; Ong, Perry S.; Moritz, Gillian L.; Luczon, Adrian; Diesmos, Mae Lowe L.; Diesmos, Arvin C.; Siler, Cameron D.

    2014-01-01

    Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier. PMID:25136854

  5. Conservation genetics of the Philippine tarsier: cryptic genetic variation restructures conservation priorities for an island archipelago primate.

    PubMed

    Brown, Rafe M; Weghorst, Jennifer A; Olson, Karen V; Duya, Mariano R M; Barley, Anthony J; Duya, Melizar V; Shekelle, Myron; Neri-Arboleda, Irene; Esselstyn, Jacob A; Dominy, Nathaniel J; Ong, Perry S; Moritz, Gillian L; Luczon, Adrian; Diesmos, Mae Lowe L; Diesmos, Arvin C; Siler, Cameron D

    2014-01-01

    Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier.

  6. Cryptic bumblebee species: consequences for conservation and the trade in greenhouse pollinators.

    PubMed

    Williams, Paul H; An, Jiandong; Brown, Mark J F; Carolan, James C; Goulson, Dave; Huang, Jiaxing; Ito, Masao

    2012-01-01

    Commercial greenhouse growers in both Japan and China are increasingly using reared orange-tailed bumblebees known previously as Bombus hypocrita Pérez as pollinators. Phylogenetic analysis of the DNA (COI) barcodes with Bayesian methods shows that this "species" is a long-standing confusion of two cryptic species. We find that the orange-tailed bumblebees in North China are actually part of the widespread Russian (otherwise white-tailed) B. patagiatus Nylander (as B. patagiatus ganjsuensis Skorikov, n. comb.), whereas the orange-tailed bees in Japan are true B. hypocrita. This situation has been further complicated because two other cryptic species from North China that were previously confused with the Russian B. patagiatus are now recognised as separate: B. lantschouensis Vogt n. stat. and B. minshanensis Bischoff n. stat.. As demand for pollination services by greenhouse growers inevitably increases, these bees are more likely to be transported between countries. In order to conserve genetic resources of pollinator species for their option value for future food security, we advocate preventing trade and movement of B. patagiatus from China into Japan and of B. hypocrita from Japan into China.

  7. Cryptic diversity in Indo-Australian rainbowfishes revealed by DNA barcoding: implications for conservation in a biodiversity hotspot candidate.

    PubMed

    Kadarusman; Hubert, Nicolas; Hadiaty, Renny Kurnia; Sudarto; Paradis, Emmanuel; Pouyaud, Laurent

    2012-01-01

    The rainbowfishes of the family Melanotaeniidae represent one of the largest radiations of freshwater fishes from the Indo-Australian archipelago. A total of 75 nominal species have been described, among which several have become very popular among tropical fish hobbyists because of their tendency to form large schools of colourful individuals. Facing habitat loss and competition or predation by introduced species, this group has become a priority in the conservation of ornamental fishes in Indonesia. In this context, several expeditions have been conducted between 2007 and 2010 in Indonesian Papua with the aim to initiate a large-scale survey of the genetic resources in this group. We assessed the diversity of the Papua rainbowfishes with DNA barcoding. We sequenced the mitochondrial COI gene for 350 specimens belonging to 53 nominal species throughout the Indo-Australian archipelago. Unexpected levels of cryptic diversity and endemism were detected since additional cryptic lineages were detected in several watersheds from the Vogelkop and the Lengguru massif. DNA barcoding supports the presence of nearly 30 evolutionary lineages among the 15 nominal species sampled in the Vogelkop and all these lineages are endemic to a single lake or watershed. This result highlights that the diversity of the family has been largely underestimated and urges for the identification of conservation priorities in Papua.

  8. Conservation of the conformation of the porphyrin macrocycle in hemoproteins.

    PubMed Central

    Jentzen, W; Ma, J G; Shelnutt, J A

    1998-01-01

    The out-of-plane distortions of porphyrins in hemoproteins are characterized by displacements along the lowest-frequency out-of-plane normal coordinates of the D4h-symmetric macrocycle. X-ray crystal structures are analyzed using a computational procedure developed for determining these orthogonal displacements. The x-ray crystal structures of the heme groups are described within experimental error, using the set composed of only the lowest frequency normal coordinate of each out-of-plane symmetry type. That is, the distortion is accurately simulated by a linear combination of these orthonormal deformations, which include saddling (B2u), ruffling (B1u), doming (A2u), waving (Eg), and propellering (A1u). For example, orthonormal structural decomposition of the hemes in deoxymyoglobins reveals a predominantly dom heme deformation combined with a smaller wav(y) deformation. Generally, the heme conformation is remarkably similar for proteins from different species. For cytochromes c, the conformation is conserved as long as the amino acids between the cysteine linkages to the heme are homologous. Differences occur if this short segment varies in the number or type of residues, suggesting that this small segment causes the nonplanar distortion. Some noncovalently linked hemes like those in the peroxidases also have highly conserved characteristic distortions. Conservation occurs even for some proteins with a large natural variation in the amino acid sequence. PMID:9533688

  9. Detecting cryptic speciation in the widespread and morphologically conservative carpet chameleon (Furcifer lateralis) of Madagascar.

    PubMed

    Florio, A M; Ingram, C M; Rakotondravony, H A; Louis, E E; Raxworthy, C J

    2012-07-01

    Species delimitation within recently evolved groups can be challenging because species may be difficult to distinguish morphologically. Following the General Lineage Concept, we apply a multiple evidence approach to assess species limits within the carpet chameleon Furcifer lateralis, which is endemic to Madagascar and exported in large numbers for the pet trade. Cryptic speciation within F. lateralis was considered likely because this species (1) has a vast distribution, (2) occupies exceptionally diverse habitats and (3) exhibits subtle regional differences in morphology. Phylogenetic trees reconstructed using nuclear and mitochondrial genes recovered three well-supported clades corresponding with geography. Morphological results based on canonical variates analysis show that these clades exhibit subtle differences in head casque morphology. Ecological niche modelling results found that these phylogenetic groups also occupy unique environmental space and exhibit patterns of regional endemism typical of other endemic reptiles. Combined, our findings provide diverse yet consistent evidence for the existence of three species. Consequently, we elevate the subspecies F. lateralis major to species rank and name a new species distributed in northern and western Madagascar. Initial ecological divergence, associated with speciation of F. lateralis in humid eastern habitat, fits the Ecographic Constraint model for species diversification in Madagascar. By contrast, the second speciation event provides some support for the Riverine Barrier model, with the Mangoky River possibly causing initial isolation between species. These findings thus support two contrasting models of speciation within closely related species and demonstrate the utility of applying a combined-evidence approach for detecting cryptic speciation.

  10. Cryptic invasion of Northern Leopard Frogs (Rana pipiens) across phylogeographic boundaries and a dilemma for conservation of a declining amphibian

    USGS Publications Warehouse

    O'Donnell, Ryan P.; Drost, Charles A.; Mock, Karen E.

    2017-01-01

    Anthropogenic introduction of species is a major contributor to loss of biodiversity. Translocations within the range of a species are less frequently recognized, but have the potential for negative effects as well. Genetic mixing may lead to loss of local adaptations or further decline through outbreeding depression. These cryptic invasions may be quite difficult to recognize, but genetic tools can be used to recognize and monitor such intraspecific introductions. Conversely, translocations within species can be an important conservation tool to reduce inbreeding depression and replace lost genetic diversity. Thus, cryptic invasions can be either an aid or a hindrance to conservation efforts. We tested for the presence of non-native genotypes and assessed the extent and nature of introgression in populations of Northern Leopard Frog (Rana pipiens) in the southwestern US, where populations have declined to a few remnant populations. The most abundant and diverse complex of populations in the region contained a mitochondrial haplotype that was not native to the western US, probably resulting from the introduction of released pets, laboratory animals, or release during fish stocking. These non-native haplotypes were well integrated into a large complex of ponds and lakes, contributing to high genetic diversity in this area. Logistically, the geographic extent of non-native genetic influence within this population precludes eliminating or controlling the non-native component of this population. We recommend assessing the progress and fate of the introgression over time—along with population fitness parameters—to determine whether this introduction is beneficial or detrimental to population persistence. Meanwhile, translocations from nearby locations with similar environmental conditions have the best prospects for avoiding problems with outbreeding depression in other declining populations and will also most effectively preserve regional genetic diversity.

  11. The role of integrative taxonomy in the conservation management of cryptic species: the taxonomic status of endangered earless dragons (Agamidae: Tympanocryptis) in the grasslands of Queensland, Australia.

    PubMed

    Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

    2014-01-01

    Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered 'species' of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available.

  12. The Role of Integrative Taxonomy in the Conservation Management of Cryptic Species: The Taxonomic Status of Endangered Earless Dragons (Agamidae: Tympanocryptis) in the Grasslands of Queensland, Australia

    PubMed Central

    Melville, Jane; Smith, Katie; Hobson, Rod; Hunjan, Sumitha; Shoo, Luke

    2014-01-01

    Molecular phylogenetics is increasingly highlighting the prevalence of cryptic species, where morphologically similar organisms have long independent evolutionary histories. When such cryptic species are known to be declining in numbers and are at risk of extinction due to a range of threatening processes, the disjunction between molecular systematics research and conservation policy becomes a significant problem. We investigate the taxonomic status of Tympanocryptis populations in Queensland, which have previously been assigned to T. tetraporophora, using three species delimitation approaches. The taxonomic uncertainties in this species-group are of particular importance in the Darling Downs Earless Dragon (T. cf. tetraporophora), which is ranked as an endangered ‘species’ of high priority for conservation by the Queensland Department of Environment and Heritage Protection. We undertook a morphological study, integrated with a comprehensive genetic study and species delimitation analyses, to investigate the species status of populations in the region. Phylogenetic analyses of two gene regions (mtDNA: ND2; nuclear: RAG1) revealed high levels of genetic divergence between populations, indicating isolation over long evolutionary time frames, and strongly supporting two independent evolutionary lineages in southeastern Queensland, from the Darling Downs, and a third in the Gulf Region of northern Queensland. Of the three species delimitation protocols used, we found integrative taxonomy the most applicable to this cryptic species complex. Our study demonstrates the utility of integrative taxonomy as a species delimitation approach in cryptic complexes of species with conservation significance, where limited numbers of specimens are available. PMID:25076129

  13. Conformal field theories with infinitely many conservation laws

    NASA Astrophysics Data System (ADS)

    Todorov, Ivan

    2013-02-01

    Globally conformal invariant quantum field theories in a D-dimensional space-time (D even) have rational correlation functions and admit an infinite number of conserved (symmetric traceless) tensor currents. In a theory of a scalar field of dimension D-2 they were demonstrated to be generated by bilocal normal products of free massless scalar fields with an O(N), U(N), or Sp(2N) (global) gauge symmetry [B. Bakalov, N. M. Nikolov, K.-H. Rehren, and I. Todorov, "Unitary positive energy representations of scalar bilocal fields," Commun. Math. Phys. 271, 223-246 (2007), 10.1007/s00220-006-0182-2; e-print arXiv:math-ph/0604069v3; B. Bakalov, N. M. Nikolov, K.-H. Rehren, and I. Todorov, "Infinite dimensional Lie algebras in 4D conformal quantum field theory," J. Phys. A Math Theor. 41, 194002 (2008), 10.1088/1751-8113/41/19/194002; e-print arXiv:0711.0627v2 [hep-th

  14. A cryptic taxon of Galápagos tortoise in conservation peril

    PubMed Central

    Russello, Michael A; Glaberman, Scott; Gibbs, James P; Marquez, Cruz; Powell, Jeffrey R; Caccone, Adalgisa

    2005-01-01

    As once boldly stated, ‘bad taxonomy can kill’, highlighting the critical importance of accurate taxonomy for the conservation of endangered taxa. The concept continues to evolve almost 15 years later largely because most legal protections aimed at preserving biological diversity are based on formal taxonomic designations. In this paper we report unrecognized genetic divisions within the giant tortoises of the Galápagos. We found three distinct lineages among populations formerly considered a single taxon on the most populous and accessible island of Santa Cruz; their diagnosability, degree of genetic divergence and phylogenetic placement merit the recognition of at least one new taxon. These results demonstrate the fundamental importance of continuing taxonomic investigations to recognize biological diversity and designate units of conservation, even within long-studied organisms such as Galápagos tortoises, whose evolutionary heritage and contribution to human intellectual history warrant them special attention. PMID:17148189

  15. A cryptic taxon of Galápagos tortoise in conservation peril.

    PubMed

    Russello, Michael A; Glaberman, Scott; Gibbs, James P; Marquez, Cruz; Powell, Jeffrey R; Caccone, Adalgisa

    2005-09-22

    As once boldly stated, 'bad taxonomy can kill', highlighting the critical importance of accurate taxonomy for the conservation of endangered taxa. The concept continues to evolve almost 15 years later largely because most legal protections aimed at preserving biological diversity are based on formal taxonomic designations. In this paper we report unrecognized genetic divisions within the giant tortoises of the Galápagos. We found three distinct lineages among populations formerly considered a single taxon on the most populous and accessible island of Santa Cruz; their diagnosability, degree of genetic divergence and phylogenetic placement merit the recognition of at least one new taxon. These results demonstrate the fundamental importance of continuing taxonomic investigations to recognize biological diversity and designate units of conservation, even within long-studied organisms such as Galápagos tortoises, whose evolutionary heritage and contribution to human intellectual history warrant them special attention.

  16. De Sitter Transitivity, Conformal Transformations and Conservation Laws

    NASA Astrophysics Data System (ADS)

    Pereira, J. G.; Sampson, A. C.; Savi, L. L.

    2014-02-01

    Minkowski spacetime is transitive under ordinary translations, a transformation that do not have matrix representations. The de Sitter spacetime, on the other hand, is transitive under a combination of translations and proper conformal transformations, which do have a matrix representation. Such matrix, however, is not by itself a de Sitter generator: it gives rise to a conformal re-scaling of the metric, a transformation not belonging to the de Sitter group, and in general not associated with diffeomorphisms in spacetime. When dealing with variational principles and Noether's theorem in de Sitter spacetime, it is necessary to regularize the transformations in order to eliminate the conformal re-scaling of the metric.

  17. Targeting N-glycan cryptic sugar moieties for broad-spectrum virus neutralization: progress in identifying conserved molecular targets in viruses of distinct phylogenetic origins.

    PubMed

    Wang, Denong; Tang, Jin; Tang, Jiulai; Wang, Lai-Xi

    2015-03-12

    Identifying molecular targets for eliciting broadly virus-neutralizing antibodies is one of the key steps toward development of vaccines against emerging viral pathogens. Owing to genomic and somatic diversities among viral species, identifying protein targets for broad-spectrum virus neutralization is highly challenging even for the same virus, such as HIV-1. However, viruses rely on host glycosylation machineries to synthesize and express glycans and, thereby, may display common carbohydrate moieties. Thus, exploring glycan-binding profiles of broad-spectrum virus-neutralizing agents may provide key information to uncover the carbohydrate-based virus-neutralizing epitopes. In this study, we characterized two broadly HIV-neutralizing agents, human monoclonal antibody 2G12 and Galanthus nivalis lectin (GNA), for their viral targeting activities. Although these agents were known to be specific for oligomannosyl antigens, they differ strikingly in virus-binding activities. The former is HIV-1 specific; the latter is broadly reactive and is able to neutralize viruses of distinct phylogenetic origins, such as HIV-1, severe acute respiratory syndrome coronavirus (SARS-CoV), and human cytomegalovirus (HCMV). In carbohydrate microarray analyses, we explored the molecular basis underlying the striking differences in the spectrum of anti-virus activities of the two probes. Unlike 2G12, which is strictly specific for the high-density Man9GlcNAc2Asn (Man9)-clusters, GNA recognizes a number of N-glycan cryptic sugar moieties. These include not only the known oligomannosyl antigens but also previously unrecognized tri-antennary or multi-valent GlcNAc-terminating N-glycan epitopes (Tri/m-Gn). These findings highlight the potential of N-glycan cryptic sugar moieties as conserved targets for broad-spectrum virus neutralization and suggest the GNA-model of glycan-binding warrants focused investigation.

  18. Structure of the C. elegans ZYG-1 cryptic polo box suggests a conserved mechanism for centriolar docking of Plk4 kinases.

    PubMed

    Shimanovskaya, Ekaterina; Viscardi, Valeria; Lesigang, Johannes; Lettman, Molly M; Qiao, Renping; Svergun, Dmitri I; Round, Adam; Oegema, Karen; Dong, Gang

    2014-08-05

    Plk4 family kinases control centriole assembly. Plk4s target mother centrioles through an interaction between their cryptic polo box (CPB) and acidic regions in the centriolar receptors SPD-2/Cep192 and/or Asterless/Cep152. Here, we report a crystal structure for the CPB of C. elegans ZYG-1, which forms a Z-shaped dimer containing an intermolecular β sheet with an extended basic surface patch. Biochemical and in vivo analysis revealed that electrostatic interactions dock the ZYG-1 CPB basic patch onto the SPD-2-derived acidic region to promote ZYG-1 targeting and new centriole assembly. Analysis of a different crystal form of the Drosophila Plk4 (DmPlk4) CPB suggests that it also forms a Z-shaped dimer. Comparison of the ZYG-1 and DmPlk4 CPBs revealed structural changes in the ZYG-1 CPB that confer selectivity for binding SPD-2 over Asterless-derived acidic regions. Overall, our findings suggest a conserved mechanism for centriolar docking of Plk4 homologs that initiate daughter centriole assembly.

  19. Quorum sensing-controlled Evr regulates a conserved cryptic pigment biosynthetic cluster and a novel phenomycin-like locus in the plant pathogen, Pectobacterium carotovorum.

    PubMed

    Williamson, Neil R; Commander, Paul M B; Salmond, George P C

    2010-07-01

    Pectobacterium carotovorum SCRI193 is a phytopathogenic Gram-negative bacterium. In this study, we have identified a novel cryptic pigment biosynthetic locus in P. carotovorum SCRI193 which we have called the Pectobacterium orange pigment (pop) cluster. The pop cluster is flanked by two tRNA genes and contains genes that encode non-ribosomal peptide synthases and polyketide synthase and produces a negatively charged polar orange pigment. Orange pigment production is activated when an adjacent transcriptional activator sharing sequence similarity with the Erwinia virulence regulator (Evr) is overexpressed. Evr was shown to positively activate its own transcription and that of the pigment biosynthetic genes and an unlinked locus encoding a phenomycin homologue. In addition, the expression of Evr and orange pigment production was shown to be regulated by N-(3-oxohexanoyl)-HSL (OHHL) quorum sensing and have a virulence phenotype in potato. Finally, by comparative genomics and Southern blotting we demonstrate that this pigment biosynthetic cluster is present in multiple P. carotovorum spp., Pectobacterium brasiliensis 1692 and a truncated version of the cluster is present in Pectobacterium atrosepticum. The conserved nature of this cluster in P. carotovorum and P. brasiliensis suggests that the pop cluster has an important function in these broad-host-range soft rotting bacteria, which is no longer required in the narrow-host-range P. atrosepticum SCRI1043.

  20. Contribution of a conserved asparagine to the conformational stability of ribonucleases Sa, Ba, and T1.

    PubMed

    Hebert, E J; Giletto, A; Sevcik, J; Urbanikova, L; Wilson, K S; Dauter, Z; Pace, C N

    1998-11-17

    The contribution of hydrogen bonding by peptide groups to the conformational stability of globular proteins was studied. One of the conserved residues in the microbial ribonuclease (RNase) family is an asparagine at position 39 in RNase Sa, 44 in RNase T1, and 58 in RNase Ba (barnase). The amide group of this asparagine is buried and forms two similar intramolecular hydrogen bonds with a neighboring peptide group to anchor a loop on the surface of all three proteins. Thus, it is a good model for the hydrogen bonding of peptide groups. When the conserved asparagine is replaced with alanine, the decrease in the stability of the mutant proteins is 2.2 (Sa), 1.8 (T1), and 2.7 (Ba) kcal/mol. When the conserved asparagine is replaced by aspartate, the stability of the mutant proteins decreases by 1.5 and 1.8 kcal/mol for RNases Sa and T1, respectively, but increases by 0.5 kcal/mol for RNase Ba. When the conserved asparagine was replaced by serine, the stability of the mutant proteins was decreased by 2.3 and 1.7 kcal/mol for RNases Sa and T1, respectively. The structure of the Asn 39 --> Ser mutant of RNase Sa was determined at 1.7 A resolution. There is a significant conformational change near the site of the mutation: (1) the side chain of Ser 39 is oriented differently than that of Asn 39 and forms hydrogen bonds with two conserved water molecules; (2) the peptide bond of Ser 42 changes conformation in the mutant so that the side chain forms three new intramolecular hydrogen bonds with the backbone to replace three hydrogen bonds to water molecules present in the wild-type structure; and (3) the loss of the anchoring hydrogen bonds makes the surface loop more flexible in the mutant than it is in wild-type RNase Sa. The results show that burial and hydrogen bonding of the conserved asparagine make a large contribution to microbial RNase stability and emphasize the importance of structural information in interpreting stability studies of mutant proteins.

  1. Conservative handling of arbitrary non-conformal interfaces using an efficient supermesh

    NASA Astrophysics Data System (ADS)

    Aguerre, Horacio J.; Márquez Damián, Santiago; Gimenez, Juan M.; Nigro, Norberto M.

    2017-04-01

    This work presents a new and efficient strategy to handle non-conformal interfaces with the aim of assuring the conservation of fluxes in Finite Volume problems. A conservative interpolation is developed for general transport equations. Due to the arbitrary connectivity between the interfaces, the interpolations require flux-based weights defining a complex numerical stencil. In this context, a new method is proposed to simplify the coupling at the interface based on the construction of a simplified supermesh. Here, a supermesh is not completely defined, instead, the interface faces are logically duplicated (or multiplied) to generate a one-to-one connectivity between them. The simplified supermesh named pseudo-supermesh eliminates the interpolations and assures the conservation of fluxes based on the trivial connectivity. The area and the geometrical centroid of the new faces are redefined according to the overlapped sector of the original faces using the local supermeshing approach. Since the arbitrary polygons resulting from the face intersections are not generated and introduced into the mesh, computational cost and implementation efforts are saved. The proposed method is tested focusing on the conservation of fluxes and on the accuracy, showing conservation to machine precision and second order convergence as expected. In order to be able to solve large problems, the methodology is designed and implemented to be run in parallel architectures showing an excellent efficiency.

  2. Anthropogenic impacts drive niche and conservation metrics of a cryptic rattlesnake on the Colorado Plateau of western North America

    PubMed Central

    Douglas, M. R.; Davis, M. A.; Amarello, M.; Smith, J. J.; Schuett, G. W.; Herrmann, H.-W.; Holycross, A. T.; Douglas, M. E.

    2016-01-01

    Ecosystems transition quickly in the Anthropocene, whereas biodiversity adapts more slowly. Here we simulated a shifting woodland ecosystem on the Colorado Plateau of western North America by using as its proxy over space and time the fundamental niche of the Arizona black rattlesnake (Crotalus cerberus). We found an expansive (= end-of-Pleistocene) range that contracted sharply (= present), but is blocked topographically by Grand Canyon/Colorado River as it shifts predictably northwestward under moderate climate change (= 2080). Vulnerability to contemporary wildfire was quantified from available records, with forested area reduced more than 27% over 13 years. Both ‘ecosystem metrics' underscore how climate and wildfire are rapidly converting the Plateau ecosystem into novel habitat. To gauge potential effects on C. cerberus, we derived a series of relevant ‘conservation metrics' (i.e. genetic variability, dispersal capacity, effective population size) by sequencing 118 individuals across 846 bp of mitochondrial (mt)DNA-ATPase8/6. We identified five significantly different clades (net sequence divergence = 2.2%) isolated by drainage/topography, with low dispersal (FST = 0.82) and small sizes (2Nef = 5.2). Our compiled metrics (i.e. small-populations, topographic-isolation, low-dispersal versus conserved-niche, vulnerable-ecosystem, dispersal barriers) underscore the susceptibility of this woodland specialist to a climate and wildfire tandem. We offer adaptive management scenarios that may counterbalance these metrics and avoid the extirpation of this and other highly specialized, relictual woodland clades. PMID:27152218

  3. Autoinhibition of SNARE complex assembly by a conformational switch represents a conserved feature of syntaxins

    PubMed Central

    MacDonald, Chris; Munson, Mary; Bryant, Nia J.

    2017-01-01

    Regulation and specificity of membrane trafficking are required to maintain organelle integrity while performing essential cellular transport. Membrane fusion events in all eukaryotic cells are facilitated by the formation of specific SNARE (soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor) complexes between proteins on opposing lipid bilayers. Although regulation of SNARE complex assembly is not well understood, it is clear that two conserved protein families, the Sx (syntaxin) and the SM (Sec1p/Munc18) proteins, are central to this process. Sxs are a subfamily of SNARE proteins; in addition to the coiled-coil SNARE motif, Sxs possess an N-terminal, autonomously folded, triple-helical (Habc) domain. For some Sxs, it has been demonstrated that this Habc domain exerts an autoinhibitory effect on SNARE complex assembly by making intramolecular contacts with the SNARE motif. SM proteins regulate membrane fusion through interactions with their cognate Sxs. One hypothesis for SM protein function is that they facilitate a switch of the Sx from a closed to an open conformation, thus lifting the inhibitory action of the Habc domain and freeing the SNARE motif to participate in SNARE complexes. However, whether these regulatory mechanisms are conserved throughout the Sx/SM protein families remains contentious as it is not clear whether the closed conformation represents a universal feature of Sxs. PMID:20074061

  4. Autoinhibition of SNARE complex assembly by a conformational switch represents a conserved feature of syntaxins.

    PubMed

    MacDonald, Chris; Munson, Mary; Bryant, Nia J

    2010-02-01

    Regulation and specificity of membrane trafficking are required to maintain organelle integrity while performing essential cellular transport. Membrane fusion events in all eukaryotic cells are facilitated by the formation of specific SNARE (soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor) complexes between proteins on opposing lipid bilayers. Although regulation of SNARE complex assembly is not well understood, it is clear that two conserved protein families, the Sx (syntaxin) and the SM (Sec1p/Munc18) proteins, are central to this process. Sxs are a subfamily of SNARE proteins; in addition to the coiled-coil SNARE motif, Sxs possess an N-terminal, autonomously folded, triple-helical (Habc) domain. For some Sxs, it has been demonstrated that this Habc domain exerts an autoinhibitory effect on SNARE complex assembly by making intramolecular contacts with the SNARE motif. SM proteins regulate membrane fusion through interactions with their cognate Sxs. One hypothesis for SM protein function is that they facilitate a switch of the Sx from a closed to an open conformation, thus lifting the inhibitory action of the Habc domain and freeing the SNARE motif to participate in SNARE complexes. However, whether these regulatory mechanisms are conserved throughout the Sx/SM protein families remains contentious as it is not clear whether the closed conformation represents a universal feature of Sxs.

  5. A Highly Conserved gp120 Inner Domain Residue Modulates Env Conformation and Trimer Stability

    PubMed Central

    Ding, Shilei; Tolbert, William D.; Prévost, Jérémie; Pacheco, Beatriz; Coutu, Mathieu; Debbeche, Olfa; Xiang, Shi-Hua

    2016-01-01

    ABSTRACT Previous studies have shown that highly conserved residues in the inner domain of gp120 are required for HIV-1 envelope glycoprotein (Env) transitions to the CD4-bound conformation (A. Finzi, S. H. Xiang, B. Pacheco, L. Wang, J. Haight, et al., Mol Cell 37:656–667, 2010, http://dx.doi.org/10.1016/j.molcel.2010.02.012; A. Desormeaux, M. Coutu, H. Medjahed, B. Pacheco, A. Herschhorn, et al., J Virol 87:2549–2562, 2013, http://dx.doi.org/10.1128/JVI.03104-12). Moreover, W69, a highly conserved residue located at the interface between layer 1 and layer 2 of the inner domain, was recently shown to be important for efficient Env recognition by CD4-induced (CD4i) antibodies capable of potent antibody-dependent cellular cytotoxicity (W. D. Tolbert, N. Gohain, M. Veillette, J. P. Chapleau, C. Orlandi, et al., 2016, Structure 24:697–709, http://dx.doi.org/10.1016/j.str.2016.03.005; S. Ding, M. Veillette, M. Coutu, J. Prevost, L. Scharf, et al., 2016, J Virol 90:2127–2134, http://dx.doi.org/10.1128/JVI.02779-15). We evaluated the contribution of the hydrophobicity of W69 to conformational changes of Env by replacing it with a series of residues with aliphatic or aromatic side chains of decreasing chain length. We have found that the hydrophobicity of residue 69 is important for Env processing, CD4 binding, and its transition to the CD4-bound conformation. The most deleterious effect was observed when W69 was replaced with alanine or glycine residues. However, the functions lost due to W69 mutations could be progressively restored with amino acids of increasing aliphatic chain length and fully recovered with residues bearing an aromatic ring. Interestingly, poor CD4 binding of W69A could be fully restored by introducing a compensatory mutation within layer 2 (S115W). Structural studies of HIV-1 gp120 coree W69A/S115W mutant bound to the CD4 peptide mimetic M48U1 and Fab of anti-cluster A antibody N60-i3 revealed no perturbations to the overall structure of the

  6. Cryptic invasions: A review.

    PubMed

    Morais, Pedro; Reichard, Martin

    2017-06-22

    Cryptic invasions are defined as the introduction and spread of non-native lineages within the species' native range (intra-specific cryptic invasion) or the invasion of non-native species that goes unnoticed due to misidentification as a native or another invasive species (inter-specific cryptic invasion). While population-specific attributes are acknowledged to play a critical role in the success and impact of biological invasions in general, our knowledge of the causes and consequences of cryptic invasions is largely neglected. Cryptic invasions are inherently difficult to recognize and, despite being likely widespread, often go undetected. In this review, we analyse the sources, mechanisms, and consequences of cryptic invasions. Using a bibliometric survey, we first quantify the relative proportion of study questions, taxa, and geographic regions. We then highlight the value of comparative information from archived specimens in uncovering the occurrence and timing of cryptic invasions. We examine the mechanisms of cryptic invasions and emphasise the role of anthropogenic environmental changes on the arrival of cryptic invaders. We then discuss the role of interspecific biological interactions in the success of cryptic invasions and the role of hybridization between native and non-native lineages in cryptic invasions. We examine the competitive advantage of some invasive lineages in key physiological, ecological or sexually-selected traits. We argue that cryptic invasions, often undetected, may trigger subsequent rapid range expansions. We suggest that cryptic invasions are much more common than currently acknowledged. We highlight the role of coevolved associations (host-parasite, mutualism, herbivory), inherently population-specific, in the impacts of cryptic invasions on local communities. Finally, we outline a framework to manage intraspecific cryptic invasions. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Conserved conformational changes in the ATPase cycle of human Hsp90.

    PubMed

    Richter, Klaus; Soroka, Joanna; Skalniak, Lukasz; Leskovar, Adriane; Hessling, Martin; Reinstein, Jochen; Buchner, Johannes

    2008-06-27

    The dimeric molecular chaperone Hsp90 is required for the activation and stabilization of hundreds of substrate proteins, many of which participate in signal transduction pathways. The activation process depends on the hydrolysis of ATP by Hsp90. Hsp90 consists of a C-terminal dimerization domain, a middle domain, which may interact with substrate protein, and an N-terminal ATP-binding domain. A complex cycle of conformational changes has been proposed for the ATPase cycle of yeast Hsp90, where a critical step during the reaction requires the transient N-terminal dimerization of the two protomers. The ATPase cycle of human Hsp90 is less well understood, and significant differences have been proposed regarding key mechanistic aspects. ATP hydrolysis by human Hsp90alpha and Hsp90beta is 10-fold slower than that of yeast Hsp90. Despite these differences, our experiments suggest that the underlying enzymatic mechanisms are highly similar. In both cases, a concerted conformational rearrangement involving the N-terminal domains of both subunits is controlling the rate of ATP turnover, and N-terminal cross-talk determines the rate-limiting steps. Furthermore, similar to yeast Hsp90, the slow ATP hydrolysis by human Hsp90s can be stimulated up to over 100-fold by the addition of the co-chaperone Aha1 from either human or yeast origin. Together, our results show that the basic principles of the Hsp90 ATPase reaction are conserved between yeast and humans, including the dimerization of the N-terminal domains and its regulation by the repositioning of the ATP lid from its original position to a catalytically competent one.

  8. Identifying cryptic diversity with predictive phylogeography.

    PubMed

    Espíndola, Anahí; Ruffley, Megan; Smith, Megan L; Carstens, Bryan C; Tank, David C; Sullivan, Jack

    2016-10-26

    Identifying units of biological diversity is a major goal of organismal biology. An increasing literature has focused on the importance of cryptic diversity, defined as the presence of deeply diverged lineages within a single species. While most discoveries of cryptic lineages proceed on a taxon-by-taxon basis, rapid assessments of biodiversity are needed to inform conservation policy and decision-making. Here, we introduce a predictive framework for phylogeography that allows rapidly identifying cryptic diversity. Our approach proceeds by collecting environmental, taxonomic and genetic data from codistributed taxa with known phylogeographic histories. We define these taxa as a reference set, and categorize them as either harbouring or lacking cryptic diversity. We then build a random forest classifier that allows us to predict which other taxa endemic to the same biome are likely to contain cryptic diversity. We apply this framework to data from two sets of disjunct ecosystems known to harbour taxa with cryptic diversity: the mesic temperate forests of the Pacific Northwest of North America and the arid lands of Southwestern North America. The predictive approach presented here is accurate, with prediction accuracies placed between 65% and 98.79% depending of the ecosystem. This seems to indicate that our method can be successfully used to address ecosystem-level questions about cryptic diversity. Further, our application for the prediction of the cryptic/non-cryptic nature of unknown species is easily applicable and provides results that agree with recent discoveries from those systems. Our results demonstrate that the transition of phylogeography from a descriptive to a predictive discipline is possible and effective. © 2016 The Author(s).

  9. Conformational changes in the archaerhodopsin-3 proton pump: detection of conserved strongly hydrogen bonded water networks.

    PubMed

    Clair, Erica C Saint; Ogren, John I; Mamaev, Sergey; Kralj, Joel M; Rothschild, Kenneth J

    2012-01-01

    Archaerhodopsin-3 (AR3) is a light-driven proton pump from Halorubrum sodomense, but little is known about its photocycle. Recent interest has focused on AR3 because of its ability to serve both as a high-performance, genetically-targetable optical silencer of neuronal activity and as a membrane voltage sensor. We examined light-activated structural changes of the protein, retinal chromophore, and internal water molecules during the photocycle of AR3. Low-temperature and rapid-scan time-resolved FTIR-difference spectroscopy revealed that conformational changes during formation of the K, M, and N photocycle intermediates are similar, although not identical, to bacteriorhodopsin (BR). Positive/negative bands in the region above 3,600 cm( - 1), which have previously been assigned to structural changes of weakly hydrogen bonded internal water molecules, were substantially different between AR3 and BR. This included the absence of positive bands recently associated with a chain of proton transporting water molecules in the cytoplasmic channel and a weakly hydrogen bonded water (W401), which is part of a hydrogen-bonded pentagonal cluster located near the retinal Schiff base. However, many of the broad IR continuum absorption changes below 3,000 cm( - 1) assigned to networks of water molecules involved in proton transport through cytoplasmic and extracellular portions in BR were very similar in AR3. This work and subsequent studies comparing BR and AR3 structural changes will help identify conserved elements in BR-like proton pumps as well as bioengineer AR3 to optimize neural silencing and voltage sensing.

  10. Multiple conformations are a conserved and regulatory feature of the RB1 5′ UTR

    PubMed Central

    Kutchko, Katrina M.; Sanders, Wes; Ziehr, Ben; Phillips, Gabriela; Solem, Amanda; Halvorsen, Matthew; Weeks, Kevin M.; Moorman, Nathaniel

    2015-01-01

    Folding to a well-defined conformation is essential for the function of structured ribonucleic acids (RNAs) like the ribosome and tRNA. Structured elements in the untranslated regions (UTRs) of specific messenger RNAs (mRNAs) are known to control expression. The importance of unstructured regions adopting multiple conformations, however, is still poorly understood. High-resolution SHAPE-directed Boltzmann suboptimal sampling of the Homo sapiens Retinoblastoma 1 (RB1) 5′ UTR yields three distinct conformations compatible with the experimental data. Private single nucleotide variants (SNVs) identified in two patients with retinoblastoma each collapse the structural ensemble to a single but distinct well-defined conformation. The RB1 5′ UTRs from Bos taurus (cow) and Trichechus manatus latirostris (manatee) are divergent in sequence from H. sapiens (human) yet maintain structural compatibility with high-probability base pairs. SHAPE chemical probing of the cow and manatee RB1 5′ UTRs reveals that they also adopt multiple conformations. Luciferase reporter assays reveal that 5′ UTR mutations alter RB1 expression. In a traditional model of disease, causative SNVs disrupt a key structural element in the RNA. For the subset of patients with heritable retinoblastoma-associated SNVs in the RB1 5′ UTR, the absence of multiple structures is likely causative of the cancer. Our data therefore suggest that selective pressure will favor multiple conformations in eukaryotic UTRs to regulate expression. PMID:25999316

  11. Conserved leucine residue in the head region of morbillivirus fusion protein regulates the large conformational change during fusion activity.

    PubMed

    Plattet, Philippe; Langedijk, Johannes P M; Zipperle, Ljerka; Vandevelde, Marc; Orvell, Claes; Zurbriggen, Andreas

    2009-09-29

    Paramyxovirus cell entry is controlled by the concerted action of two viral envelope glycoproteins, the fusion (F) and the receptor-binding (H) proteins, which together with a cell surface receptor mediate plasma membrane fusion activity. The paramyxovirus F protein belongs to class I viral fusion proteins which typically contain two heptad repeat regions (HR). Particular to paramyxovirus F proteins is a long intervening sequence (IS) located between both HR domains. To investigate the role of the IS domain in regulating fusogenicity, we mutated in the canine distemper virus (CDV) F protein IS domain a highly conserved leucine residue (L372) previously reported to cause a hyperfusogenic phenotype. Beside one F mutant, which elicited significant defects in processing, transport competence, and fusogenicity, all remaining mutants were characterized by enhanced fusion activity despite normal or slightly impaired processing and cell surface targeting. Using anti-CDV-F monoclonal antibodies, modified conformational F states were detected in F mutants compared to the parental protein. Despite these structural differences, coimmunoprecipitation assays did not reveal any drastic modulation in F/H avidity of interaction. However, we found that F mutants had significantly enhanced fusogenicity at low temperature only, suggesting that they folded into conformations requiring less energy to activate fusion. Together, these data provide strong biochemical and functional evidence that the conserved leucine 372 at the base of the HRA coiled-coil of F(wt) controls the stabilization of the prefusogenic state, restraining the conformational switch and thereby preventing extensive cell-cell fusion activity.

  12. Conformational behavior of flavin adenine dinucleotide: conserved stereochemistry in bound and free states.

    PubMed

    Kuppuraj, Gopi; Kruise, Dennis; Yura, Kei

    2014-11-26

    Metabolic enzymes utilize the cofactor flavin adenine dinucleotide (FAD) to catalyze essential biochemical reactions. Because these enzymes have been implicated in disease pathways, it will be necessary to target them via FAD-based structural analogues that can either activate/inhibit the enzymatic activity. To achieve this, it is important to explore the conformational space of FAD in the enzyme-bound and free states. Herein, we analyze X-ray crystallographic data of the enzyme-bound FAD conformations and sample conformations of the molecule in explicit water by molecular dynamics (MD) simulations. Enzyme-bound FAD conformations segregate into five distinct groups based on dihedral angle principal component analysis (PCA). A notable feature in the bound FADs is that the adenine base and isoalloxazine ring are oppositely oriented relative to the pyrophosphate axis characterized by near trans hypothetical dihedral angle "δV" values. Not surprisingly, MD simulations in water show final compact but not perfectly stacked ring structures in FAD. Simulation data did not reveal noticeable changes in overall conformational dynamics of the dinucleotide in reduced and oxidized forms and in the presence and/or absence of ions. During unfolding-folding dynamics, the riboflavin moiety is more flexible than the adenosine monophosphate group in the molecule. Conversely, the isoalloxazine ring is more stable than the variable adenine base. The pyrophosphate group depicts an unusually highly organized fluctuation illustrated by its dihedral angle distribution. Conformations sampled from enzymes and MD are quantified. The extent to which the protein shifts the distribution from the unbound state is discussed in terms of prevalent FAD shapes and dihedral angle population.

  13. The beta-glucoside genes of Klebsiella aerogenes: conservation and divergence in relation to the cryptic bgl genes of Escherichia coli.

    PubMed

    Raghunand, Tirumalai R; Mahadevan, S

    2003-06-27

    The ability to metabolize aromatic beta-glucosides such as salicin and arbutin varies among members of the Enterobacteriaceae. The ability of Escherichia coli to degrade salicin and arbutin appears to be cryptic, subject to activation of the bgl genes, whereas many members of the Klebsiella genus can metabolize these sugars. We have examined the genetic basis for beta-glucoside utilization in Klebsiella aerogenes. The Klebsiella equivalents of bglG, bglB and bglR have been cloned using the genome sequence database of Klebsiella pneumoniae. Nucleotide sequencing shows that the K. aerogenes bgl genes show substantial similarities to the E. coli counterparts. The K. aerogenes bgl genes in multiple copies can also complement E. coli mutants deficient in bglG encoding the antiterminator and bglB encoding the phospho-beta-glucosidase, suggesting that they are functional homologues. The regulatory region bglR of K. aerogenes shows a high degree of similarity of the sequences involved in BglG-mediated regulation. Interestingly, the regions corresponding to the negative elements present in the E. coli regulatory region show substantial divergence in K. aerogenes. The possible evolutionary implications of the results are discussed.

  14. Range-wide molecular analysis of the western pond turtle (Emys marmorata): cryptic variation, isolation by distance, and their conservation implications.

    PubMed

    Spinks, Phillip Q; Shaffer, H Bradley

    2005-06-01

    We analysed phylogeography and population genetic variation across the range of the western pond turtle (Emys marmorata) using rapidly evolving mitochondrial and nuclear DNA sequence data. Nuclear DNA sequences from two unlinked introns displayed extremely low levels of variation, but phylogenetic analyses based on mtDNA recovered four well-supported and geographically coherent clades. These included a large Northern clade composed of populations from Washington south to San Luis Obispo County, California, west of the Coast Ranges; a San Joaquin Valley clade from the southern Great Central Valley; a geographically restricted Santa Barbara clade from a limited region in Santa Barbara and Ventura counties; and a Southern clade that occurs south of the Tehachapi Mountains and west of the Transverse Range south to Baja California, Mexico. An analysis of molecular variance (amova) based on regional hydrographic units revealed that populations from the Sacramento Valley north to Washington were virtually invariant, with no evidence of population substructure among northern river drainage basins. In other areas, E. marmorata contains considerable unrecognized variation, particularly in central and southern California and in northern Baja California, Mexico. Our northern clade is congruent with the distribution of the subspecies Emys marmorata marmorata (Washington-central California). However, no clade is congruent with the distribution of the southern subspecies Emys marmorata pallida from central California-Baja. Thus, recognition of the current subspecies split is not warranted, based on the available genetic evidence. Our amova and phylogenetic results, in conjunction with a growing comparative database for other codistributed aquatic taxa, confirm the occurrence of genetic breaks across the Tehachapi Mountains and Transverse Range bounding the southern end of the Great Central Valley, and point to southern California as a rich source of cryptic genetic variation.

  15. Quantitative analysis of cryptic splicing associated with TDP-43 depletion.

    PubMed

    Humphrey, Jack; Emmett, Warren; Fratta, Pietro; Isaacs, Adrian M; Plagnol, Vincent

    2017-05-26

    Reliable exon recognition is key to the splicing of pre-mRNAs into mature mRNAs. TDP-43 is an RNA-binding protein whose nuclear loss and cytoplasmic aggregation are a hallmark pathology in amyotrophic lateral sclerosis and frontotemporal dementia (ALS/FTD). TDP-43 depletion causes the aberrant inclusion of cryptic exons into a range of transcripts, but their extent, relevance to disease pathogenesis and whether they are caused by other RNA-binding proteins implicated in ALS/FTD are unknown. We developed an analysis pipeline to discover and quantify cryptic exon inclusion and applied it to publicly available human and murine RNA-sequencing data. We detected widespread cryptic splicing in TDP-43 depletion datasets but almost none in another ALS/FTD-linked protein FUS. Sequence motif and iCLIP analysis of cryptic exons demonstrated that they are bound by TDP-43. Unlike the cryptic exons seen in hnRNP C depletion, those repressed by TDP-43 cannot be linked to transposable elements. Cryptic exons are poorly conserved and inclusion overwhelmingly leads to nonsense-mediated decay of the host transcript, with reduced transcript levels observed in differential expression analysis. RNA-protein interaction data on 73 different RNA-binding proteins showed that, in addition to TDP-43, 7 specifically bind TDP-43 linked cryptic exons. This suggests that TDP-43 competes with other splicing factors for binding to cryptic exons and can repress cryptic exon inclusion. Our quantitative analysis pipeline confirms the presence of cryptic exons during the depletion of TDP-43 but not FUS providing new insight into to RNA-processing dysfunction as a cause or consequence in ALS/FTD.

  16. A Conformal, Fully-Conservative Approach for Predicting Blast Effects on Ground Vehicles

    DTIC Science & Technology

    2014-04-01

    Fluid-Structure Interaction (FSI) simulations ◦ Conservative load transfer between Loci/ BLAST and LS - DYNA ◦ Robust deformation of CFD mesh in response...impulse pendulum results UNCLASSIFIED UNCLASSIFIED  Loci/ BLAST - LS - DYNA two-way coupling validated using DRDC Plate experiment ◦ DRDC plate deflections...compared to results of Williams et al (7th International LS - DYNA Users Conference, 2002) for TACOM Impulse Loading model (Westline, 1972)  TARDEC

  17. The structure of Zika virus NS5 reveals a conserved domain conformation.

    PubMed

    Wang, Boxiao; Tan, Xiao-Feng; Thurmond, Stephanie; Zhang, Zhi-Min; Lin, Asher; Hai, Rong; Song, Jikui

    2017-03-27

    The recent outbreak of Zika virus (ZIKV) has imposed a serious threat to public health. Here we report the crystal structure of the ZIKV NS5 protein in complex with S-adenosyl-L-homocysteine, in which the tandem methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains stack into one of the two alternative conformations of flavivirus NS5 proteins. The activity of this NS5 protein is verified through a de novo RdRp assay on a subgenomic ZIKV RNA template. Importantly, our structural analysis leads to the identification of a potential drug-binding site of ZIKV NS5, which might facilitate the development of novel antivirals for ZIKV.

  18. The structure of Zika virus NS5 reveals a conserved domain conformation

    DOE PAGES

    Wang, Boxiao; Tan, Xiao -Feng; Thurmond, Stephanie; ...

    2017-03-27

    The recent outbreak of Zika virus (ZIKV) has imposed a serious threat to public health. Here we report the crystal structure of the ZIKV NS5 protein in complex with S-adenosyl-L-homocysteine, in which the tandem methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains stack into one of the two alternative conformations of flavivirus NS5 proteins. In conclusion, the activity of this NS5 protein is verified through a de novo RdRp assay on a subgenomic ZIKV RNA template. Importantly, our structural analysis leads to the identification of a potential drug-binding site of ZIKV NS5, which might facilitate the development of novel antiviralsmore » for ZIKV.« less

  19. The structure of Zika virus NS5 reveals a conserved domain conformation

    PubMed Central

    Wang, Boxiao; Tan, Xiao-Feng; Thurmond, Stephanie; Zhang, Zhi-Min; Lin, Asher; Hai, Rong; Song, Jikui

    2017-01-01

    The recent outbreak of Zika virus (ZIKV) has imposed a serious threat to public health. Here we report the crystal structure of the ZIKV NS5 protein in complex with S-adenosyl-L-homocysteine, in which the tandem methyltransferase (MTase) and RNA-dependent RNA polymerase (RdRp) domains stack into one of the two alternative conformations of flavivirus NS5 proteins. The activity of this NS5 protein is verified through a de novo RdRp assay on a subgenomic ZIKV RNA template. Importantly, our structural analysis leads to the identification of a potential drug-binding site of ZIKV NS5, which might facilitate the development of novel antivirals for ZIKV. PMID:28345600

  20. Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics

    SciTech Connect

    Borbulevych, Oleg Y.; Piepenbrink, Kurt H.; Baker, Brian M.

    2012-03-16

    Molecular mimicry between foreign and self Ags is a mechanism of TCR cross-reactivity and is thought to contribute to the development of autoimmunity. The {alpha}{beta} TCR A6 recognizes the foreign Ag Tax from the human T cell leukemia virus-1 when presented by the class I MHC HLA-A2. In a possible link with the autoimmune disease human T cell leukemia virus-1-associated myelopathy/tropical spastic paraparesis, A6 also recognizes a self peptide from the neuronal protein HuD in the context of HLA-A2. We found in our study that the complexes of the HuD and Tax epitopes with HLA-A2 are close but imperfect structural mimics and that in contrast with other recent structures of TCRs with self Ags, A6 engages the HuD Ag with the same traditional binding mode used to engage Tax. Although peptide and MHC conformational changes are needed for recognition of HuD but not Tax and the difference of a single hydroxyl triggers an altered TCR loop conformation, TCR affinity toward HuD is still within the range believed to result in negative selection. Probing further, we found that the HuD-HLA-A2 complex is only weakly stable. Overall, these findings help clarify how molecular mimicry can drive self/nonself cross-reactivity and illustrate how low peptide-MHC stability can permit the survival of T cells expressing self-reactive TCRs that nonetheless bind with a traditional binding mode.

  1. Probing the conformation of a conserved glutamic acid within the Cl(-) pathway of a CLC H(+)/Cl(-) exchanger.

    PubMed

    Vien, Malvin; Basilio, Daniel; Leisle, Lilia; Accardi, Alessio

    2017-04-03

    The CLC proteins form a broad family of anion-selective transport proteins that includes both channels and exchangers. Despite extensive structural, functional, and computational studies, the transport mechanism of the CLC exchangers remains poorly understood. Several transport models have been proposed but have failed to capture all the key features of these transporters. Multiple CLC crystal structures have suggested that a conserved glutamic acid, Gluex, can adopt three conformations and that the interconversion of its side chain between these states underlies H(+)/Cl(-) exchange. One of these states, in which Gluex occupies the central binding site (Scen) while Cl(-) ions fill the internal and external sites (Sint and Sext), has only been observed in one homologue, the eukaryotic cmCLC. The existence of such a state in other CLCs has not been demonstrated. In this study, we find that during transport, the prototypical prokaryotic CLC exchanger, CLC-ec1, adopts a conformation with functional characteristics that match those predicted for a cmCLC-like state, with Gluex trapped in Scen between two Cl(-) ions. Transport by CLC-ec1 is reduced when [Cl(-)] is symmetrically increased on both sides of the membrane and mutations that disrupt the hydrogen bonds stabilizing Gluex in Scen destabilize this trapped state. Furthermore, inhibition of transport by high [Cl(-)] is abolished in the E148A mutant, in which the Gluex side chain is removed. Collectively, our results suggest that, during the CLC transport cycle, Gluex can occupy Scen as well as the Sext position in which it has been captured crystallographically and that hydrogen bonds with the side chains of residues that coordinate ion binding to Scen play a role in determining the equilibrium between these two conformations.

  2. Conserved tertiary couplings stabilize elements in the PDZ fold, leading to characteristic patterns of domain conformational flexibility.

    PubMed

    Ho, Bosco K; Agard, David A

    2010-03-01

    Single-domain allostery has been postulated to occur through intramolecular pathways of signaling within a protein structure. We had previously investigated these pathways by introducing a local thermal perturbation and analyzed the anisotropic propagation of structural changes throughout the protein. Here, we develop an improved approach, the Rotamerically Induced Perturbation (RIP), that identifies strong couplings between residues by analyzing the pathways of heat-flow resulting from thermal excitation of rotameric rotations at individual residues. To explore the nature of these couplings, we calculate the complete coupling maps of 5 different PDZ domains. Although the PDZ domain is a well conserved structural fold that serves as a scaffold in many protein-protein complexes, different PDZ domains display unique patterns of conformational flexibility in response to ligand binding: some show a significant shift in a set of alpha-helices, while others do not. Analysis of the coupling maps suggests a simple relationship between the computed couplings and observed conformational flexibility. In domains where the alpha-helices are rigid, we find couplings of the alpha-helices to the body of the protein, whereas in domains having ligand-responsive alpha-helices, no couplings are found. This leads to a model where the alpha-helices are intrinsically dynamic but can be damped if sidechains interact at key tertiary contacts. These tertiary contacts correlate to high covariation contacts as identified by the statistical coupling analysis method. As these dynamic modules are exploited by various allosteric mechanisms, these tertiary contacts have been conserved by evolution.

  3. On the conservation of the slow conformational dynamics within the amino acid kinase family: NAGK the paradigm.

    PubMed

    Marcos, Enrique; Crehuet, Ramon; Bahar, Ivet

    2010-04-08

    N-acetyl-L-glutamate kinase (NAGK) is the structural paradigm for examining the catalytic mechanisms and dynamics of amino acid kinase family members. Given that the slow conformational dynamics of the NAGK (at the microseconds time scale or slower) may be rate-limiting, it is of importance to assess the mechanisms of the most cooperative modes of motion intrinsically accessible to this enzyme. Here, we present the results from normal mode analysis using an elastic network model representation, which shows that the conformational mechanisms for substrate binding by NAGK strongly correlate with the intrinsic dynamics of the enzyme in the unbound form. We further analyzed the potential mechanisms of allosteric signalling within NAGK using a Markov model for network communication. Comparative analysis of the dynamics of family members strongly suggests that the low-frequency modes of motion and the associated intramolecular couplings that establish signal transduction are highly conserved among family members, in support of the paradigm sequence-->structure-->dynamics-->function.

  4. Drug design from the cryptic inhibitor envelope.

    PubMed

    Lee, Chul-Jin; Liang, Xiaofei; Wu, Qinglin; Najeeb, Javaria; Zhao, Jinshi; Gopalaswamy, Ramesh; Titecat, Marie; Sebbane, Florent; Lemaitre, Nadine; Toone, Eric J; Zhou, Pei

    2016-02-25

    Conformational dynamics plays an important role in enzyme catalysis, allosteric regulation of protein functions and assembly of macromolecular complexes. Despite these well-established roles, such information has yet to be exploited for drug design. Here we show by nuclear magnetic resonance spectroscopy that inhibitors of LpxC--an essential enzyme of the lipid A biosynthetic pathway in Gram-negative bacteria and a validated novel antibiotic target--access alternative, minor population states in solution in addition to the ligand conformation observed in crystal structures. These conformations collectively delineate an inhibitor envelope that is invisible to crystallography, but is dynamically accessible by small molecules in solution. Drug design exploiting such a hidden inhibitor envelope has led to the development of potent antibiotics with inhibition constants in the single-digit picomolar range. The principle of the cryptic inhibitor envelope approach may be broadly applicable to other lead optimization campaigns to yield improved therapeutics.

  5. Drug design from the cryptic inhibitor envelope

    PubMed Central

    Lee, Chul-Jin; Liang, Xiaofei; Wu, Qinglin; Najeeb, Javaria; Zhao, Jinshi; Gopalaswamy, Ramesh; Titecat, Marie; Sebbane, Florent; Lemaitre, Nadine; Toone, Eric J.; Zhou, Pei

    2016-01-01

    Conformational dynamics plays an important role in enzyme catalysis, allosteric regulation of protein functions and assembly of macromolecular complexes. Despite these well-established roles, such information has yet to be exploited for drug design. Here we show by nuclear magnetic resonance spectroscopy that inhibitors of LpxC—an essential enzyme of the lipid A biosynthetic pathway in Gram-negative bacteria and a validated novel antibiotic target—access alternative, minor population states in solution in addition to the ligand conformation observed in crystal structures. These conformations collectively delineate an inhibitor envelope that is invisible to crystallography, but is dynamically accessible by small molecules in solution. Drug design exploiting such a hidden inhibitor envelope has led to the development of potent antibiotics with inhibition constants in the single-digit picomolar range. The principle of the cryptic inhibitor envelope approach may be broadly applicable to other lead optimization campaigns to yield improved therapeutics. PMID:26912110

  6. Sal k 4, a new allergen of Salsola kali, is profilin: a predictive value of conserved conformational regions in cross-reactivity with other plant-derived profilins.

    PubMed

    Assarehzadegan, Mohammad Ali; Amini, Akram; Sankian, Mojtaba; Tehrani, Mohsen; Jabbari, Farahzad; Varasteh, Abdolreza

    2010-01-01

    The aim of this study was to investigate a new allergen of Salsola kali, Sal k 4, and to investigate the predictive value of the conserved conformational regions in cross-reactivity with other plant-derived profilins. The Sal k 4-coding sequence was cloned, expressed, and purified by one-step Ni2+ affinity chromatography to recover high-purity target protein. We assessed cross-reactivity and predicted conserved conformational regions among rSal k 4 and other plant-derived profilins. Immunodetection and inhibition assays using 30 individual sera from S. kali allergic patients indicated that purified rSal k 4 might be the same as that in the crude extract. The results of inhibition assays among rSal k 4 and other plant-derived profilins were in accordance with the homology of the predicted conserved conformational regions. Amino acid sequence homology analysis showed that a high degree of IgE cross-reactivity among plant-derived profilins might depend on the predicted conserved conformational regions.

  7. ‘Naked’ and Hydrated Conformers of the Conserved Core Pentasaccharide of N-linked Glycoproteins and Its Building Blocks

    PubMed Central

    2013-01-01

    N-glycosylation of eukaryotic proteins is widespread and vital to survival. The pentasaccharide unit −Man3GlcNAc2– lies at the protein-junction core of all oligosaccharides attached to asparagine side chains during this process. Although its absolute conservation implies an indispensable role, associated perhaps with its structure, its unbiased conformation and the potential modulating role of solvation are unknown; both have now been explored through a combination of synthesis, laser spectroscopy, and computation. The proximal −GlcNAc-GlcNAc– unit acts as a rigid rod, while the central, and unusual, −Man-β-1,4-GlcNAc– linkage is more flexible and is modulated by the distal Man-α-1,3– and Man-α-1,6– branching units. Solvation stiffens the ‘rod’ but leaves the distal residues flexible, through a β-Man pivot, ensuring anchored projection from the protein shell while allowing flexible interaction of the distal portion of N-glycosylation with bulk water and biomolecular assemblies. PMID:24127839

  8. 'Naked' and hydrated conformers of the conserved core pentasaccharide of N-linked glycoproteins and its building blocks.

    PubMed

    Barry, Conor S; Cocinero, Emilio J; Carçabal, Pierre; Gamblin, David P; Stanca-Kaposta, E Cristina; Remmert, Sarah M; Fernández-Alonso, María C; Rudić, Svemir; Simons, John P; Davis, Benjamin G

    2013-11-13

    N-glycosylation of eukaryotic proteins is widespread and vital to survival. The pentasaccharide unit -Man3GlcNAc2- lies at the protein-junction core of all oligosaccharides attached to asparagine side chains during this process. Although its absolute conservation implies an indispensable role, associated perhaps with its structure, its unbiased conformation and the potential modulating role of solvation are unknown; both have now been explored through a combination of synthesis, laser spectroscopy, and computation. The proximal -GlcNAc-GlcNAc- unit acts as a rigid rod, while the central, and unusual, -Man-β-1,4-GlcNAc- linkage is more flexible and is modulated by the distal Man-α-1,3- and Man-α-1,6- branching units. Solvation stiffens the 'rod' but leaves the distal residues flexible, through a β-Man pivot, ensuring anchored projection from the protein shell while allowing flexible interaction of the distal portion of N-glycosylation with bulk water and biomolecular assemblies.

  9. Cryptic exposure to arsenic.

    PubMed

    Rossy, Kathleen M; Janusz, Christopher A; Schwartz, Robert A

    2005-01-01

    Arsenic is an odorless, colorless and tasteless element long linked with effects on the skin and viscera. Exposure to it may be cryptic. Although human intake can occur from four forms, elemental, inorganic (trivalent and pentavalent arsenic) and organic arsenic, the trivalent inorganic arsenicals constitute the major human hazard. Arsenic usually reaches the skin from occupational, therapeutic, or environmental exposure, although it still may be employed as a poison. Occupations involving new technologies are not exempt from arsenic exposure. Its acute and chronic effects are noteworthy. Treatment options exist for arsenic-induced pathology, but prevention of toxicity remains the main focus. Vitamin and mineral supplementation may play a role in the treatment of arsenic toxicity.

  10. Conservation.

    ERIC Educational Resources Information Center

    National Audubon Society, New York, NY.

    This set of teaching aids consists of seven Audubon Nature Bulletins, providing the teacher and student with informational reading on various topics in conservation. The bulletins have these titles: Plants as Makers of Soil, Water Pollution Control, The Ground Water Table, Conservation--To Keep This Earth Habitable, Our Threatened Air Supply,…

  11. Conservation.

    ERIC Educational Resources Information Center

    National Audubon Society, New York, NY.

    This set of teaching aids consists of seven Audubon Nature Bulletins, providing the teacher and student with informational reading on various topics in conservation. The bulletins have these titles: Plants as Makers of Soil, Water Pollution Control, The Ground Water Table, Conservation--To Keep This Earth Habitable, Our Threatened Air Supply,…

  12. The conserved disulfide bond of human tear lipocalin modulates conformation and lipid binding in a ligand selective manner

    PubMed Central

    Gasymov, Oktay K.; Abduragimov, Adil R.; Glasgow, Ben J.

    2011-01-01

    The primary aim of this study is the elucidation of the mechanism of disulfide induced alteration of ligand binding in human tear lipocalin (TL). Disulfide bonds may act as dynamic scaffolds to regulate conformational changes that alter protein function including receptor-ligand interactions. A single disulfide bond, (Cys61-Cys153), exists in TL that is highly conserved in the lipocalin superfamily. Circular dichroism and fluorescence spectroscopies were applied to investigate the mechanism by which disulfide bond removal effects protein stability, dynamics and ligand binding properties. Although the secondary structure is not altered by disulfide elimination, TL shows decreased stability against urea denaturation. Free energy change (ΔG0) decreases from 4.9± 0.2 to 2.1± 0.3 kcal/mol with removal of the disulfide bond. Furthermore, ligand binding properties of TL without the disulfide vary according to the type of ligand. The binding of a bulky ligand, NBD-cholesterol, has a decreased time constant (from 11.8± 0.2 to 3.3 s). In contrast, the NBD-labeled phospholipid shows a moderate decrease in the time constant for binding, from 33.2± 0.2 to 22.2± 0.4 s. FRET experiments indicate that the hairpin CD is directly involved in modulation of both ligand binding and flexibility of TL. In TL complexed with palmitc acid (PA-TL), the distance between the residues 62 of strand D and 81 of loop EF is decreased by disulfide bond reduction. Consequently, removal of the disulfide bond boosts flexibility of the protein to reach a CD-EF loop distance (24.3 Å, between residues 62 and 81), which is not accessible for the protein with an intact disulfide bond (26.2 Å). The results suggest that enhanced flexibility of the protein promotes a faster accommodation of the ligand inside the cavity and energetically favorable ligand-protein complex. PMID:21466861

  13. Cryptic biodiversity in a changing world.

    PubMed

    Beheregaray, Luciano B; Caccone, Adalgisa

    2007-01-01

    DNA studies are revealing the extent of hidden, or cryptic, biodiversity. Two new studies challenge paradigms about cryptic biodiversity and highlight the importance of adding a historical and biogeographic dimension to biodiversity research.

  14. Cryptic Terrain on Mars

    NASA Technical Reports Server (NTRS)

    2007-01-01

    [figure removed for brevity, see original site] Figure 1

    There is an enigmatic region near the south pole of Mars known as the 'cryptic' terrain. It stays cold in the spring, even as its albedo darkens and the sun rises in the sky.

    This region is covered by a layer of translucent seasonal carbon dioxide ice that warms and evaporates from below. As carbon dioxide gas escapes from below the slab of seasonal ice it scours dust from the surface. The gas vents to the surface, where the dust is carried downwind by the prevailing wind.

    The channels carved by the escaping gas are often radially organized and are known informally as 'spiders' (figure 1).

    Observation Geometry Image PSP_003179_0945 was taken by the High Resolution Imaging Science Experiment (HiRISE) camera onboard the Mars Reconnaissance Orbiter spacecraft on 01-Apr-2007. The complete image is centered at -85.4 degrees latitude, 104.0 degrees East longitude. The range to the target site was 245.9 km (153.7 miles). At this distance the image scale is 49.2 cm/pixel (with 2 x 2 binning) so objects 148 cm across are resolved. The image shown here has been map-projected to 50 cm/pixel . The image was taken at a local Mars time of 06:19 PM and the scene is illuminated from the west with a solar incidence angle of 78 degrees, thus the sun was about 12 degrees above the horizon. At a solar longitude of 210.8 degrees, the season on Mars is Northern Autumn.

  15. Cryptic Terrain on Mars

    NASA Technical Reports Server (NTRS)

    2007-01-01

    [figure removed for brevity, see original site] Figure 1

    There is an enigmatic region near the south pole of Mars known as the 'cryptic' terrain. It stays cold in the spring, even as its albedo darkens and the sun rises in the sky.

    This region is covered by a layer of translucent seasonal carbon dioxide ice that warms and evaporates from below. As carbon dioxide gas escapes from below the slab of seasonal ice it scours dust from the surface. The gas vents to the surface, where the dust is carried downwind by the prevailing wind.

    The channels carved by the escaping gas are often radially organized and are known informally as 'spiders' (figure 1).

    Observation Geometry Image PSP_003179_0945 was taken by the High Resolution Imaging Science Experiment (HiRISE) camera onboard the Mars Reconnaissance Orbiter spacecraft on 01-Apr-2007. The complete image is centered at -85.4 degrees latitude, 104.0 degrees East longitude. The range to the target site was 245.9 km (153.7 miles). At this distance the image scale is 49.2 cm/pixel (with 2 x 2 binning) so objects 148 cm across are resolved. The image shown here has been map-projected to 50 cm/pixel . The image was taken at a local Mars time of 06:19 PM and the scene is illuminated from the west with a solar incidence angle of 78 degrees, thus the sun was about 12 degrees above the horizon. At a solar longitude of 210.8 degrees, the season on Mars is Northern Autumn.

  16. Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.

    PubMed

    Liu, Jian; Qin, Ling; Ferguson-Miller, Shelagh

    2011-01-25

    Crystal structures in both oxidized and reduced forms are reported for two bacterial cytochrome c oxidase mutants that define the D and K proton paths, showing conformational change in response to reduction and the loss of strategic waters that can account for inhibition of proton transfer. In the oxidized state both mutants of the Rhodobacter sphaeroides enzyme, D132A and K362M, show overall structures similar to wild type, indicating no long-range effects of mutation. In the reduced state, the mutants show an altered conformation similar to that seen in reduced wild type, confirming this reproducible, reversible response to reduction. In the strongly inhibited D132A mutant, positions of residues and waters in the D pathway are unaffected except in the entry region close to the mutation, where a chloride ion replaces the missing carboxyl and a 2-Å shift in N207 results in loss of its associated water. In K362M, the methionine occupies the same position as the original lysine, but K362- and T359-associated waters in the wild-type structure are missing, likely accounting for the severe inhibition. Spectra of oxidized frozen crystals taken during X-ray radiation show metal center reduction, but indicate development of a strained configuration that only relaxes to a native form upon annealing. Resistance of the frozen crystal to structural change clarifies why the oxidized conformation is observable and supports the conclusion that the reduced conformation has functional significance. A mechanism is described that explains the conformational change and the incomplete response of the D-path mutant.

  17. Molecular characterization of a novel cryptic virus infecting pigeonpea plants

    PubMed Central

    Kumar, Surender; Subbarao, Burra L.; Kumari, Reenu

    2017-01-01

    A new member of the genus Deltapartitivirus was identified containing three dsRNAs with an estimated size of 1.71, 1.49 and 1.43 kb. The dsRNAs were extracted from symptomless pigeonpea [Cajanus cajan (L.) Millspaugh] plants cv. Erra Kandulu. This new virus with 4.64 kb genome was tentatively named Arhar cryptic virus-1 (ArCV-1). The genomic RNAs were amplified and characterized by sequence independent single primer amplification. The dsRNAs shared a highly conserved 16 nt 5’ non-coding region (5’-GATAATGATCCAAGGA-3’). The largest dsRNA (dsRNA-1) was identified as the viral RNA dependent RNA polymerase (replicase), predicted to encode a putative 55.34 kDa protein (P1). The two other smaller dsRNAs (dsRNA-2 and dsRNA-3) predicted to encode for putative capsid proteins of 38.50kDa (P2) and 38.51kDa (P3), respectively. Phylogenetic analysis indicated that ArCV-1 formed a clade together with Fragaria chiloensis cryptic virus, Rosa multiflora cryptic virus and Rose cryptic virus-1, indicating that ArCV-1 could be a new member of the genus Deltapartitivirus. ArCV-1 3Dpol structure revealed several interesting features. The 3Dpol in its full-length shares structural similarities with members of the family Caliciviridaeand family Picornaviridae. In addition, fourth dsRNA molecule (dsRNA-2A), not related to ArCV-1 genome, was found in the same plant tissue. The dsRNA-2A (1.6 kb) encodes a protein (P4), with a predicted size of 44.5 kDa. P4 shares similarity with coat protein genes of several cryptic viruses, in particular the bipartite cryptic viruses including Raphanus sativus cryptic virus-3. This is the first report of occurrence of a cryptic virus in pigeonpea plants. PMID:28771507

  18. The structures of RNase A complexed with 3'-CMP and d(CpA): active site conformation and conserved water molecules.

    PubMed Central

    Zegers, I.; Maes, D.; Dao-Thi, M. H.; Poortmans, F.; Palmer, R.; Wyns, L.

    1994-01-01

    The interactions of RNase A with cytidine 3'-monophosphate (3'-CMP) and deoxycytidyl-3',5'-deoxyadenosine (d(CpA)) were analyzed by X-ray crystallography. The 3'-CMP complex and the native structure were determined from trigonal crystals, and the d(CpA) complex from monoclinic crystals. The differences between the overall structures are concentrated in loop regions and are relatively small. The protein-inhibitor contacts are interpreted in terms of the catalytic mechanism. The general base His 12 interacts with the 2' oxygen, as does the electrostatic catalyst Lys 41. The general acid His 119 has 2 conformations (A and B) in the native structure and is found in, respectively, the A and the B conformation in the d(CpA) and the 3'-CMP complex. From the present structures and from a comparison with RNase T1, we propose that His 119 is active in the A conformation. The structure of the d(CpA) complex permits a detailed analysis of the downstream binding site, which includes His 119 and Asn 71. The comparison of the present RNase A structures with an inhibitor complex of RNase T1 shows that there are important similarities in the active sites of these 2 enzymes, despite the absence of any sequence homology. The water molecules were analyzed in order to identify conserved water sites. Seventeen water sites were found to be conserved in RNase A structures from 5 different space groups. It is proposed that 7 of those water molecules play a role in the binding of the N-terminal helix to the rest of the protein and in the stabilization of the active site. PMID:7756988

  19. High levels of cryptic species diversity uncovered in Amazonian frogs

    PubMed Central

    Funk, W. Chris; Caminer, Marcel; Ron, Santiago R.

    2012-01-01

    One of the greatest challenges for biodiversity conservation is the poor understanding of species diversity. Molecular methods have dramatically improved our ability to uncover cryptic species, but the magnitude of cryptic diversity remains unknown, particularly in diverse tropical regions such as the Amazon Basin. Uncovering cryptic diversity in amphibians is particularly pressing because amphibians are going extinct globally at an alarming rate. Here, we use an integrative analysis of two independent Amazonian frog clades, Engystomops toadlets and Hypsiboas treefrogs, to test whether species richness is underestimated and, if so, by how much. We sampled intensively in six countries with a focus in Ecuador (Engystomops: 252 individuals from 36 localities; Hypsiboas: 208 individuals from 65 localities) and combined mitochondrial DNA, nuclear DNA, morphological, and bioacoustic data to detect cryptic species. We found that in both clades, species richness was severely underestimated, with more undescribed species than described species. In Engystomops, the two currently recognized species are actually five to seven species (a 150–250% increase in species richness); in Hypsiboas, two recognized species represent six to nine species (a 200–350% increase). Our results suggest that Amazonian frog biodiversity is much more severely underestimated than previously thought. PMID:22130600

  20. When to stop managing or surveying cryptic threatened species

    PubMed Central

    Chadès, Iadine; McDonald-Madden, Eve; McCarthy, Michael A.; Wintle, Brendan; Linkie, Matthew; Possingham, Hugh P.

    2008-01-01

    Threatened species become increasingly difficult to detect as their populations decline. Managers of such cryptic threatened species face several dilemmas: if they are not sure the species is present, should they continue to manage for that species or invest the limited resources in surveying? We find optimal solutions to this problem using a Partially Observable Markov Decision Process and rules of thumb derived from an analytical approximation. We discover that managing a protected area for a cryptic threatened species can be optimal even if we are not sure the species is present. The more threatened and valuable the species is, relative to the costs of management, the more likely we are to manage this species without determining its continued persistence by using surveys. If a species remains unseen, our belief in the persistence of the species declines to a point where the optimal strategy is to shift resources from saving the species to surveying for it. Finally, when surveys lead to a sufficiently low belief that the species is extant, we surrender resources to other conservation actions. We illustrate our findings with a case study using parameters based on the critically endangered Sumatran tiger (Panthera tigris sumatrae), and we generate rules of thumb on how to allocate conservation effort for any cryptic species. Using Partially Observable Markov Decision Processes in conservation science, we determine the conditions under which it is better to abandon management for that species because our belief that it continues to exist is too low. PMID:18779594

  1. When to stop managing or surveying cryptic threatened species.

    PubMed

    Chadès, Iadine; McDonald-Madden, Eve; McCarthy, Michael A; Wintle, Brendan; Linkie, Matthew; Possingham, Hugh P

    2008-09-16

    Threatened species become increasingly difficult to detect as their populations decline. Managers of such cryptic threatened species face several dilemmas: if they are not sure the species is present, should they continue to manage for that species or invest the limited resources in surveying? We find optimal solutions to this problem using a Partially Observable Markov Decision Process and rules of thumb derived from an analytical approximation. We discover that managing a protected area for a cryptic threatened species can be optimal even if we are not sure the species is present. The more threatened and valuable the species is, relative to the costs of management, the more likely we are to manage this species without determining its continued persistence by using surveys. If a species remains unseen, our belief in the persistence of the species declines to a point where the optimal strategy is to shift resources from saving the species to surveying for it. Finally, when surveys lead to a sufficiently low belief that the species is extant, we surrender resources to other conservation actions. We illustrate our findings with a case study using parameters based on the critically endangered Sumatran tiger (Panthera tigris sumatrae), and we generate rules of thumb on how to allocate conservation effort for any cryptic species. Using Partially Observable Markov Decision Processes in conservation science, we determine the conditions under which it is better to abandon management for that species because our belief that it continues to exist is too low.

  2. The conformational stability and biophysical properties of the eukaryotic thioredoxins of Pisum sativum are not family-conserved.

    PubMed

    Aguado-Llera, David; Martínez-Gómez, Ana Isabel; Prieto, Jesús; Marenchino, Marco; Traverso, José Angel; Gómez, Javier; Chueca, Ana; Neira, José L

    2011-02-22

    Thioredoxins (TRXs) are ubiquitous proteins involved in redox processes. About forty genes encode TRX or TRX-related proteins in plants, grouped in different families according to their subcellular localization. For instance, the h-type TRXs are located in cytoplasm or mitochondria, whereas f-type TRXs have a plastidial origin, although both types of proteins have an eukaryotic origin as opposed to other TRXs. Herein, we study the conformational and the biophysical features of TRXh1, TRXh2 and TRXf from Pisum sativum. The modelled structures of the three proteins show the well-known TRX fold. While sharing similar pH-denaturations features, the chemical and thermal stabilities are different, being PsTRXh1 (Pisum sativum thioredoxin h1) the most stable isoform; moreover, the three proteins follow a three-state denaturation model, during the chemical-denaturations. These differences in the thermal- and chemical-denaturations result from changes, in a broad sense, of the several ASAs (accessible surface areas) of the proteins. Thus, although a strong relationship can be found between the primary amino acid sequence and the structure among TRXs, that between the residue sequence and the conformational stability and biophysical properties is not. We discuss how these differences in the biophysical properties of TRXs determine their unique functions in pea, and we show how residues involved in the biophysical features described (pH-titrations, dimerizations and chemical-denaturations) belong to regions involved in interaction with other proteins. Our results suggest that the sequence demands of protein-protein function are relatively rigid, with different protein-binding pockets (some in common) for each of the three proteins, but the demands of structure and conformational stability per se (as long as there is a maintained core), are less so.

  3. The Conformational Stability and Biophysical Properties of the Eukaryotic Thioredoxins of Pisum Sativum Are Not Family-Conserved

    PubMed Central

    Aguado-Llera, David; Martínez-Gómez, Ana Isabel; Prieto, Jesús; Marenchino, Marco; Traverso, José Angel; Gómez, Javier; Chueca, Ana; Neira, José L.

    2011-01-01

    Thioredoxins (TRXs) are ubiquitous proteins involved in redox processes. About forty genes encode TRX or TRX-related proteins in plants, grouped in different families according to their subcellular localization. For instance, the h-type TRXs are located in cytoplasm or mitochondria, whereas f-type TRXs have a plastidial origin, although both types of proteins have an eukaryotic origin as opposed to other TRXs. Herein, we study the conformational and the biophysical features of TRXh1, TRXh2 and TRXf from Pisum sativum. The modelled structures of the three proteins show the well-known TRX fold. While sharing similar pH-denaturations features, the chemical and thermal stabilities are different, being PsTRXh1 (Pisum sativum thioredoxin h1) the most stable isoform; moreover, the three proteins follow a three-state denaturation model, during the chemical-denaturations. These differences in the thermal- and chemical-denaturations result from changes, in a broad sense, of the several ASAs (accessible surface areas) of the proteins. Thus, although a strong relationship can be found between the primary amino acid sequence and the structure among TRXs, that between the residue sequence and the conformational stability and biophysical properties is not. We discuss how these differences in the biophysical properties of TRXs determine their unique functions in pea, and we show how residues involved in the biophysical features described (pH-titrations, dimerizations and chemical-denaturations) belong to regions involved in interaction with other proteins. Our results suggest that the sequence demands of protein-protein function are relatively rigid, with different protein-binding pockets (some in common) for each of the three proteins, but the demands of structure and conformational stability per se (as long as there is a maintained core), are less so. PMID:21364950

  4. The role of a conserved proline residue in mediating conformational changes associated with voltage gating of Cx32 gap junctions.

    PubMed Central

    Ri, Y; Ballesteros, J A; Abrams, C K; Oh, S; Verselis, V K; Weinstein, H; Bargiello, T A

    1999-01-01

    We have explored the role of a proline residue located at position 87 in the second transmembrane segment (TM2) of gap junctions in the mechanism of voltage-dependent gating of connexin32 (Cx32). Substitution of this proline (denoted Cx32P87) with residues G, A, or V affects channel function in a progressive manner consistent with the expectation that a proline kink (PK) motif exists in the second transmembrane segment (TM2) of this connexin. Mutations of the preceding threonine residue T86 to S, A, C, V, N, or L shift the conductance-voltage relation of wild-type Cx32, such that the mutated channels close at smaller transjunctional voltages. The observed shift in voltage dependence is consistent with a reduction in the open probability of the mutant hemichannels at a transjunctional voltage (Vj) of 0 mV. In both cases in which kinetics were examined, the time constants for reaching steady state were faster for T86N and T86A than for wild type at comparable voltages, suggesting that the T86 mutations cause the energetic destabilization of the open state relative to the other states of the channel protein. The structural underpinnings of the observed effects were explored with Monte Carlo simulations. The conformational space of TM2 helices was found to differ for the T86A, V, N, and L mutants, which produce a less bent helix ( approximately 20 degrees bend angle) compared to the wild type, which has a approximately 37 degrees bend angle. The greater bend angle of the wild-type helix reflects the propensity of the T86 residue to hydrogen bond with the backbone carbonyl of amino acid residue I82. The relative differences in propensity for hydrogen bonding of the mutants relative to the wild-type threonine residue in the constructs we studied (T86A, V, N, L, S, and C) correlate with the shift in the conductance-voltage relation observed for T86 mutations. The data are consistent with a structural model in which the open conformation of the Cx32 channel corresponds to

  5. TDP-43 repression of nonconserved cryptic exons is compromised in ALS-FTD.

    PubMed

    Ling, Jonathan P; Pletnikova, Olga; Troncoso, Juan C; Wong, Philip C

    2015-08-07

    Cytoplasmic aggregation of TDP-43, accompanied by its nuclear clearance, is a key common pathological hallmark of amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). However, a limited understanding of this RNA-binding protein (RBP) impedes the clarification of pathogenic mechanisms underlying TDP-43 proteinopathy. In contrast to RBPs that regulate splicing of conserved exons, we found that TDP-43 repressed the splicing of nonconserved cryptic exons, maintaining intron integrity. When TDP-43 was depleted from mouse embryonic stem cells, these cryptic exons were spliced into messenger RNAs, often disrupting their translation and promoting nonsense-mediated decay. Moreover, enforced repression of cryptic exons prevented cell death in TDP-43-deficient cells. Furthermore, repression of cryptic exons was impaired in ALS-FTD cases, suggesting that this splicing defect could potentially underlie TDP-43 proteinopathy.

  6. Mutational and Structural Analysis of Conserved Residues in Ribose-5-Phosphate Isomerase B from Leishmania donovani: Role in Substrate Recognition and Conformational Stability

    PubMed Central

    Kaur, Preet Kamal; Tripathi, Neha; Desale, Jayesh; Neelagiri, Soumya; Yadav, Shailendra; Bharatam, Prasad V.; Singh, Sushma

    2016-01-01

    Ribose-5-phosphate isomerase B from Leishmania donovani (LdRpiB) is one of the potential drug targets against visceral leishmaniasis. In the present study, we have targeted several conserved amino acids for mutational analysis (i.e. Cys69, His11, His102, His138, Asp45, Tyr46, Pro47 and Glu149) to gain crucial insights into their role in substrate binding, catalysis and conformational stability of the enzyme. All the eight LdRpiB variants were cloned, sequenced, expressed and purified. C69S, H102N, D45N and E149A mutants exhibited complete loss of enzyme activity indicating that they are indispensable for the enzyme activity. Kinetic parameters were altered in case of H138N, H11N and P47A variants; however Y46F exhibited similar kinetic behaviour as wild type. All the mutants except H138N exhibited altered protein structure as determined by CD and fluorescence spectral analysis. This data was supported by the atomic level details of the conformational changes and substrate binding using molecular dynamic simulations. LdRpiB also exhibited activity with D-form of various aldose substrates in the order of D-ribose > D-talose > D-allose > D-arabinose. Our study provides insights for better understanding of substrate enzyme interactions which can rationalize the process of drug design against parasite RpiB. PMID:26953696

  7. Cryptic eco-evolutionary dynamics.

    PubMed

    Kinnison, Michael T; Hairston, Nelson G; Hendry, Andrew P

    2015-12-01

    Natural systems harbor complex interactions that are fundamental parts of ecology and evolution. These interactions challenge our inclinations and training to seek the simplest explanations of patterns in nature. Not least is the likelihood that some complex processes might be missed when their patterns look similar to predictions for simpler mechanisms. Along these lines, theory and empirical evidence increasingly suggest that environmental, ecological, phenotypic, and genetic processes can be tightly intertwined, resulting in complex and sometimes surprising eco-evolutionary dynamics. The goal of this review is to temper inclinations to unquestioningly seek the simplest explanations in ecology and evolution, by recognizing that some eco-evolutionary outcomes may appear very similar to purely ecological, purely evolutionary, or even null expectations, and thus be cryptic. We provide theoretical and empirical evidence for observational biases and mechanisms that might operate among the various links in eco-evolutionary feedbacks to produce cryptic patterns. Recognition that cryptic dynamics can be associated with outcomes like stability, resilience, recovery, or coexistence in a dynamically changing world provides added impetus for finding ways to study them. © 2015 New York Academy of Sciences.

  8. Conservation of the Conformation and Positive Charges of Hepatitis C Virus E2 Envelope Glycoprotein Hypervariable Region 1 Points to a Role in Cell Attachment

    PubMed Central

    Penin, François; Combet, Christophe; Germanidis, Georgios; Frainais, Pierre-Olivier; Deléage, Gilbert; Pawlotsky, Jean-Michel

    2001-01-01

    Chronic hepatitis C virus (HCV) infection is a major cause of liver disease. The HCV polyprotein contains a hypervariable region (HVR1) located at the N terminus of the second envelope glycoprotein E2. The strong variability of this 27-amino-acid region is due to its apparent tolerance of amino acid substitutions together with strong selection pressures exerted by anti-HCV immune responses. No specific function has so far been attributed to HVR1. However, its presence at the surface of the viral particle suggests that it might be involved in viral entry. This would imply that HVR1 is not randomly variable. We sequenced 460 HVR1 clones isolated at various times from six HCV-infected patients receiving alpha interferon therapy (which exerts strong pressure towards quasispecies genetic evolution) and analyzed their amino acid sequences together with those of 1,382 nonredundant HVR1 sequences collected from the EMBL database. We found that (i) despite strong amino acid sequence variability related to strong pressures towards change, the chemicophysical properties and conformation of HVR1 were highly conserved, and (ii) HVR1 is a globally basic stretch, with the basic residues located at specific sequence positions. This conservation of positively charged residues indicates that HVR1 is involved in interactions with negatively charged molecules such as lipids, proteins, or glycosaminoglycans (GAGs). As with many other viruses, possible interaction with GAGs probably plays a role in host cell recognition and attachment. PMID:11356980

  9. Gauge natural formulation of conformal gravity

    SciTech Connect

    Campigotto, M.; Fatibene, L.

    2015-03-15

    We consider conformal gravity as a gauge natural theory. We study its conservation laws and superpotentials. We also consider the Mannheim and Kazanas spherically symmetric vacuum solution and discuss conserved quantities associated to conformal and diffeomorphism symmetries.

  10. A Highly Conserved Salt Bridge Stabilizes the Kinked Conformation of β2,3-Sheet Essential for Channel Function of P2X4 Receptors.

    PubMed

    Zhao, Wen-Shan; Sun, Meng-Yang; Sun, Liang-Fei; Liu, Yan; Yang, Yang; Huang, Li-Dong; Fan, Ying-Zhe; Cheng, Xiao-Yang; Cao, Peng; Hu, You-Min; Li, Lingyong; Tian, Yun; Wang, Rui; Yu, Ye

    2016-04-08

    Significant progress has been made in understanding the roles of crucial residues/motifs in the channel function of P2X receptors during the pre-structure era. The recent structural determination of P2X receptors allows us to reevaluate the role of those residues/motifs. Residues Arg-309 and Asp-85 (rat P2X4 numbering) are highly conserved throughout the P2X family and were involved in loss-of-function polymorphism in human P2X receptors. Previous studies proposed that they participated in direct ATP binding. However, the crystal structure of P2X demonstrated that those two residues form an intersubunit salt bridge located far away from the ATP-binding site. Therefore, it is necessary to reevaluate the role of this salt bridge in P2X receptors. Here, we suggest the crucial role of this structural element both in protein stability and in channel gating rather than direct ATP interaction and channel assembly. Combining mutagenesis, charge swap, and disulfide cross-linking, we revealed the stringent requirement of this salt bridge in normal P2X4 channel function. This salt bridge may contribute to stabilizing the bending conformation of the β2,3-sheet that is structurally coupled with this salt bridge and the α2-helix. Strongly kinked β2,3 is essential for domain-domain interactions between head domain, dorsal fin domain, right flipper domain, and loop β7,8 in P2X4 receptors. Disulfide cross-linking with directions opposing or along the bending angle of the β2,3-sheet toward the α2-helix led to loss-of-function and gain-of-function of P2X4 receptors, respectively. Further insertion of amino acids with bulky side chains into the linker between the β2,3-sheet or the conformational change of the α2-helix, interfering with the kinked conformation of β2,3, led to loss-of-function of P2X4 receptors. All these findings provided new insights in understanding the contribution of the salt bridge between Asp-85 and Arg-309 and its structurally coupled β2,3-sheet to the

  11. The great repression: chromatin and cryptic transcription.

    PubMed

    Hennig, Bianca P; Fischer, Tamás

    2013-01-01

    The eukaryotic chromatin structure is essential in correctly defining transcription units. Impairing this structure can activate cryptic promoters, and lead to the accumulation of aberrant RNA transcripts. Here we discuss critical pathways that are responsible for the repression of cryptic transcription and the maintenance of genome integrity.

  12. Transposable elements in disease-associated cryptic exons.

    PubMed

    Vorechovsky, Igor

    2010-02-01

    Transposable elements (TEs) make up a half of the human genome, but the extent of their contribution to cryptic exon activation that results in genetic disease is unknown. Here, a comprehensive survey of 78 mutation-induced cryptic exons previously identified in 51 disease genes revealed the presence of TEs in 40 cases (51%). Most TE-containing exons were derived from short interspersed nuclear elements (SINEs), with Alus and mammalian interspersed repeats (MIRs) covering >18 and >16% of the exonized sequences, respectively. The majority of SINE-derived cryptic exons had splice sites at the same positions of the Alu/MIR consensus as existing SINE exons and their inclusion in the mRNA was facilitated by phylogenetically conserved changes that improved both traditional and auxiliary splicing signals, thus marking intronic TEs amenable for pathogenic exonization. The overrepresentation of MIRs among TE exons is likely to result from their high average exon inclusion levels, which reflect their strong splice sites, a lack of splicing silencers and a high density of enhancers, particularly (G)AA(G) motifs. These elements were markedly depleted in antisense Alu exons, had the most prominent position on the exon-intron gradient scale and are proposed to promote exon definition through enhanced tertiary RNA interactions involving unpaired (di)adenosines. The identification of common mechanisms by which the most dynamic parts of the genome contribute both to new exon creation and genetic disease will facilitate detection of intronic mutations and the development of computational tools that predict TE hot-spots of cryptic exon activation.

  13. Pay Attention to the Overlooked Cryptic Diversity in Existing Barcoding Data: the Case of Mollusca with Character-Based DNA Barcoding.

    PubMed

    Zou, Shanmei; Li, Qi

    2016-06-01

    With the global biodiversity crisis, DNA barcoding aims for fast species identification and cryptic species diversity revelation. For more than 10 years, large amounts of DNA barcode data have been accumulating in publicly available databases, most of which were conducted by distance or tree-building methods that have often been argued, especially for cryptic species revelation. In this context, overlooked cryptic diversity may exist in the available barcoding data. The character-based DNA barcoding, however, has a good chance for detecting the overlooked cryptic diversity. In this study, marine mollusk was as the ideal case for detecting the overlooked potential cryptic species from existing cytochrome c oxidase I (COI) sequences with character-based DNA barcode. A total of 1081 COI sequences of mollusks, belonging to 176 species of 25 families of Gastropoda, Cephalopoda, and Lamellibranchia, were conducted by character analysis. As a whole, the character-based barcoding results were consistent with previous distance and tree-building analysis for species discrimination. More importantly, quite a number of species analyzed were divided into distinct clades with unique diagnostical characters. Based on the concept of cryptic species revelation of character-based barcoding, these species divided into separate taxonomic groups might be potential cryptic species. The detection of the overlooked potential cryptic diversity proves that the character-based barcoding mode possesses more advantages of revealing cryptic biodiversity. With the development of DNA barcoding, making the best use of barcoding data is worthy of our attention for species conservation.

  14. Silencing of cryptic prophages in Corynebacterium glutamicum.

    PubMed

    Pfeifer, Eugen; Hünnefeld, Max; Popa, Ovidiu; Polen, Tino; Kohlheyer, Dietrich; Baumgart, Meike; Frunzke, Julia

    2016-12-01

    DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  15. Silencing of cryptic prophages in Corynebacterium glutamicum

    PubMed Central

    Pfeifer, Eugen; Hünnefeld, Max; Popa, Ovidiu; Polen, Tino; Kohlheyer, Dietrich; Baumgart, Meike; Frunzke, Julia

    2016-01-01

    DNA of viral origin represents a ubiquitous element of bacterial genomes. Its integration into host regulatory circuits is a pivotal driver of microbial evolution but requires the stringent regulation of phage gene activity. In this study, we describe the nucleoid-associated protein CgpS, which represents an essential protein functioning as a xenogeneic silencer in the Gram-positive Corynebacterium glutamicum. CgpS is encoded by the cryptic prophage CGP3 of the C. glutamicum strain ATCC 13032 and was first identified by DNA affinity chromatography using an early phage promoter of CGP3. Genome-wide profiling of CgpS binding using chromatin affinity purification and sequencing (ChAP-Seq) revealed its association with AT-rich DNA elements, including the entire CGP3 prophage region (187 kbp), as well as several other elements acquired by horizontal gene transfer. Countersilencing of CgpS resulted in a significantly increased induction frequency of the CGP3 prophage. In contrast, a strain lacking the CGP3 prophage was not affected and displayed stable growth. In a bioinformatics approach, cgpS orthologs were identified primarily in actinobacterial genomes as well as several phage and prophage genomes. Sequence analysis of 618 orthologous proteins revealed a strong conservation of the secondary structure, supporting an ancient function of these xenogeneic silencers in phage-host interaction. PMID:27492287

  16. pH-induced conformational change of IscU at low pH correlates with protonation/deprotonation of two conserved histidine residues.

    PubMed

    Dai, Ziqi; Kim, Jin Hae; Tonelli, Marco; Ali, Ibrahim K; Markley, John L

    2014-08-19

    IscU, the scaffold protein for the major iron-sulfur cluster biosynthesis pathway in microorganisms and mitochondria (ISC pathway), plays important roles in the formation of [2Fe-2S] and [4Fe-4S] clusters and their delivery to acceptor apo-proteins. Our laboratory has shown that IscU populates two distinct, functionally relevant conformational states, a more structured state (S) and a more dynamic state (D), that differ by cis/trans isomerizations about two peptidyl-prolyl peptide bonds [Kim, J. H., Tonelli, M., and Markley, J. L. (2012) Proc. Natl. Acad. Sci. U.S.A., 109, 454-459. Dai Z., Tonelli, M., and Markley, J. L. (2012) Biochemistry, 51, 9595-9602. Cai, K., Frederick, R. O., Kim, J. H., Reinen, N. M., Tonelli, M., and Markley, J. L. (2013) J. Biol. Chem., 288, 28755-28770]. Here, we report our findings on the pH dependence of the D ⇄ S equilibrium for Escherichia coli IscU in which the D-state is stabilized at low and high pH values. We show that the lower limb of the pH dependence curve results from differences in the pKa values of two conserved histidine residues (His10 and His105) in the two states. The net proton affinity of His10 is about 50 times higher and that of His105 is 13 times higher in the D-state than in the S-state. The origin of the high limb of the D ⇄ S pH dependence remains to be determined. These results show that changes in proton inventory need to be taken into account in the steps in iron-sulfur cluster assembly and transfer that involve transitions of IscU between its S- and D-states.

  17. Cryptic vascular malformations involving the brainstem

    SciTech Connect

    Yeates, A.; Enzmann, D.

    1983-01-01

    Six patients with angiographically cryptic vascular malformations involving the brainstem were examined with computed tomography (CT). The clinical and CT findings of cryptic vascular malformations of the brainstem are described and distinguished from those of brainstem glioma and multiple sclerosis. Calcification within a brainstem lesion that displays relatively little mass effect and shows little contrast enhancement, particularly when associated with a long history of waxing and waning brainstem symptoms, should suggest a vascular malformation.

  18. Firefly luciferase gene contains a cryptic promoter

    PubMed Central

    Vopálenský, Václav; Mašek, Tomáš; Horváth, Ondřej; Vicenová, Blanka; Mokrejš, Martin; Pospíšek, Martin

    2008-01-01

    A firefly luciferase (FLuc) counts among the most popular reporters of present-day molecular and cellular biology. In this study, we report a cryptic promoter activity in the luc+ gene, which is the most frequently used version of the firefly luciferase. The FLuc coding region displays cryptic promoter activity both in mammalian and yeast cells. In human CCL13 and Huh7 cells, cryptic transcription from the luc+ gene is 10–16 times weaker in comparison to the strong immediate-early cytomegalovirus promoter. Additionally, we discuss a possible impact of the FLuc gene cryptic promoter on experimental results especially in some fields of the RNA-oriented research, for example, in analysis of translation initiation or analysis of miRNA/siRNA function. Specifically, we propose how this newly described cryptic promoter activity within the FLuc gene might contribute to the previous determination of the strength of the cryptic promoter found in the cDNA corresponding to the hepatitis C virus internal ribosome entry site. Our findings should appeal to the researchers to be more careful when designing firefly luciferase-based assays as well as open the possibility of performing some experiments with the hepatitis C virus internal ribosome entry site, which could not be considered until now. PMID:18697919

  19. Late radiation side effects, cosmetic outcomes and pain in breast cancer patients after breast-conserving surgery and three-dimensional conformal radiotherapy : Risk-modifying factors.

    PubMed

    Hille-Betz, Ursula; Vaske, Bernhard; Bremer, Michael; Soergel, Philipp; Kundu, Sudip; Klapdor, Rüdiger; Hillemanns, Peter; Henkenberens, Christoph

    2016-01-01

    The purpose of this work was to identify parameters influencing the risk of late radiation side effects, fair or poor cosmetic outcomes (COs) and pain in breast cancer patients after breast-conserving therapy (BCT) and three-dimensional conformal radiotherapy (3D-CRT). Between 2006 and 2013, 159 patients were treated at the Hannover Medical School. Physician-rated toxicity according to the LENT-SOMA criteria, CO and pain were assessed by multivariate analysis. LENT-SOMA grade 1-4 toxicity was observed as follows: fibrosis 10.7 %, telangiectasia 1.2 %, arm oedema 8.8 % and breast oedema 5.0 %. In addition, 15.1 % of patients reported moderate or severe breast pain, and 21.4 % complained about moderate or severe pain in the arm or shoulder. In multivariate analysis, axillary clearing (AC) was significantly associated with lymphoedema of the arm [odds ratio (OR) 4.37, p = 0.011, 95 % confidence interval (CI) 1.4-13.58]. Breast oedema was also highly associated with AC (OR 10.59, p = 0.004, 95 % CI 2.1-53.36), a ptosis grade 2/3 or pseudoptosis and a bra size ≥ cup C (OR 5.34, p = 0.029, 95 % CI 1.2-24.12). A ptosis grade 2/3 or pseudoptosis and a bra size ≥ cup C were the parameters significantly associated with an unfavourable CO (OR 3.19, p = 0.019, 95 % CI 1.2-8.4). Concerning chronic breast pain, we found a trend related to the prescribed radiation dose including boost (OR 1.077, p = 0.060, 95 % CI 0.997-1.164). Chronic shoulder or arm pain was statistically significantly associated with lymphoedema of the arm (OR 3.9, p = 0.027, 95 % CI 1.17-13.5). Chronic arm and breast oedema were significantly influenced by the extent of surgery (AC). Ptotic and large breasts were significantly associated with unfavourable COs and chronic breast oedema. Late toxicities exclusive breast pain were not associated with radiotherapy parameters.

  20. Wolbachia infections mimic cryptic speciation in two parasitic butterfly species, Phengaris teleius and P. nausithous (Lepidoptera: Lycaenidae).

    PubMed

    Ritter, Sylvia; Michalski, Stefan G; Settele, Josef; Wiemers, Martin; Fric, Zdenek F; Sielezniew, Marcin; Šašić, Martina; Rozier, Yves; Durka, Walter

    2013-01-01

    Deep mitochondrial divergence within species may result from cryptic speciation, from phylogeographic isolation or from endosymbiotic bacteria like Wolbachia that manipulate host reproduction. Phengaris butterflies are social parasites that spend most of their life in close relationship with ants. Previously, cryptic speciation has been hypothesised for two Phengaris species based on divergent mtDNA sequences. Since Phengaris species are highly endangered, the existence of cryptic species would have drastic consequences for conservation and management. We tested for cryptic speciation and alternative scenarios in P. teleius and P. nausithous based on a comprehensive sample across their Palaearctic ranges using COI gene sequences, nuclear microsatellites and tests for Wolbachia. In both species a deep mitochondrial split occurring 0.65-1.97 myrs ago was observed that did not correspond with microsatellite data but was concordant with Wolbachia infection. Haplotypes previously attributed to cryptic species were part of the Wolbachia-infected clades. In both species remaining phylogeographic structure was largely consistent between mitochondrial and nuclear genomes. In P. teleius several mitochondrial and nuclear groups were observed in East Asia while a single haplogroup and nuclear cluster prevailed across continental Eurasia. Neutrality tests suggested rapid demographic expansion into that area. In contrast, P. nausithous had several mitochondrial and nuclear groups in Europe, suggesting a complex phylogeographic history in the western part of the species range. We conclude that deep intraspecific divergences found in DNA barcode studies do not necessarily need to represent cryptic speciation but instead can be due to both infection by Wolbachia and phylogeographic structure.

  1. Cryptic Peptides from Collagen: A Critical Review.

    PubMed

    Banerjee, Pradipta; Shanthi, C

    2016-01-01

    Collagen, a predominant structural protein in extracellular matrix (ECM), is now considered to have probable roles in many biological activities and hence, in different forms have found application as nutraceutical or pharmaceutical therapy option. Many of the biological properties are believed to be due to small hidden peptide residues in the collagen molecules, which come into play after the biodegradation or biosorption of the parent molecule. These peptide regions are called cryptic peptides or by some, as cryptides. The proteolytic hydrolysis of the ECM protein releases the cryptic peptides with many novel biological activities not exhibited directly by the parental protein which include angiogenic, antimicrobial, mitogenic and chemotactic properties. The research for understanding the role of these cryptic peptide regions and making use of them in medical field is very active. Such an understanding could lead to the development of peptide supplements for many biomedical applications. The prolific research in this area is reviewed in this paper.

  2. Empirical evidence supporting frequent cryptic speciation in epiphyllous liverworts: a case study of the Cololejeunea lanciloba complex.

    PubMed

    Yu, Ying; Heinrichs, Jochen; Zhu, Rui-Liang; Schneider, Harald

    2013-01-01

    Cryptic species are frequently recovered in plant lineages, and considered an important cause for divergent of morphological disparity and species diversity. The identification of cryptic species has important implications for the assessment of conservation needs of species aggregates. The mechanisms and processes of the origin of cryptic species diversity are still poorly understand based on the lack of studies especially in context of environment factors. Here we explored evidence for cryptic species within the epiphyllous liverworts Cololejeunea lanciloba complex based on two loci, the plastid trnL-F region and the nuclear ribosomal ITS region. Several analytic approaches were employed to delimit species based on DNA sequence variation including phylogenetic reconstruction, statistical parsimony networks analysis and two recently introduced species delimitation criteria: Rosenberg's reciprocal monophyly and Rodrigo's randomly distinct. We found evidence for thirteen genetically distinct putative species, each consisting of more than one haplotype, rather than four morphologically-circumscribed species. The results implied that the highly conserved phenotypes are not congruent with the genetic differentiation, contributing to incorrect assessments of the biodiversity of epiphyllous liverworts. We hypothesize that evolution of cryptic species recovered may be caused by selection of traits critical to the survival in epiphyllous habitats combined with limited developmental options designed in the small body.

  3. Cryptic transposable phages of Pseudomonas aeruginosa

    SciTech Connect

    Krylov, V.N.; Mit`kina, L.N.; Pleteneva, E.A.; Aleshin, V.V.

    1995-11-01

    Frequencies of nucleotide sequences homologous to phage transposons (PT) of two species, D3112 and B3, were assessed in genomes of natural Pseudomonas aeruginosa strains by the dot-blot hybridization method. These strains were incapable of liberating viable phages on a lawn of the PA01 standard indicator strain of P. aeruginosa. It was shown that the homologies detected belong to two groups, high and intermediate, with respect to homology level. Homology patterns were classified as high when they provided signals comparable to those for hybridization in a positive control; patterns were classified as intermediate when the hybridization level was higher than the background level, but lower than in the positive control. Homologous PT sequences were designated as cryptic PT. Intact cryptic PT prophages were shown to exist in genomes of particular natural strains manifesting a higher level of hybridization. However, the growth of these phages was limited by the restriction system of strain PA01. It is possible to isolate strains maintaining the growth of some cryptic PT. These strains differed from P. aeruginosa with respect to the specificity of the restriction and modification system. Nevertheless, in most cases, the attempt to identify a novel host capable of maintaining growth of a cryptic PT failed. Natural strains often carry cryptic PT related to both known PT species, D3112 and B3. The frequency of cryptic PT is extremely high, reaching 30% in strains with a high level of homology only and up to 50% in all strains exhibiting homology. This high PT frequency is assumed to be associated with the considerable variation of P. aeruginosa. 15 refs., 1 fig., 2 tabs.

  4. Conformal Nets II: Conformal Blocks

    NASA Astrophysics Data System (ADS)

    Bartels, Arthur; Douglas, Christopher L.; Henriques, André

    2017-08-01

    Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

  5. Conformal Nets II: Conformal Blocks

    NASA Astrophysics Data System (ADS)

    Bartels, Arthur; Douglas, Christopher L.; Henriques, André

    2017-03-01

    Conformal nets provide a mathematical formalism for conformal field theory. Associated to a conformal net with finite index, we give a construction of the `bundle of conformal blocks', a representation of the mapping class groupoid of closed topological surfaces into the category of finite-dimensional projective Hilbert spaces. We also construct infinite-dimensional spaces of conformal blocks for topological surfaces with smooth boundary. We prove that the conformal blocks satisfy a factorization formula for gluing surfaces along circles, and an analogous formula for gluing surfaces along intervals. We use this interval factorization property to give a new proof of the modularity of the category of representations of a conformal net.

  6. Rounding up active cis-elements in the triple C corral: combining conservation, cleavage and conformation capture for the analysis of regulatory gene domains.

    PubMed

    McBride, David J; Kleinjan, Dirk A

    2004-11-01

    Identification and functional analysis of potential cis-regulatory elements is a laborious process that often depends on removing putative elements from their natural context to study their activity. While such methods provide valuable information about the isolated element, they disregard the potential role of an element's interaction(s) with other regulatory sequences and the three-dimensional structure of an active gene locus. Here, two novel methods are discussed--chromosome conformation capture (3C) and RNA-TRAP--that can be used to detect interactions between distal regulatory sites and which thus indicate the chromosomal conformation that is adopted by a gene locus in various states of transcriptional activity. Combined with comparative genomics and traditional DNase I hypersensitive site mapping, these methods form a powerful approach for the study of the mechanisms of long-range transcriptional regulation.

  7. Visualization of a substrate-induced productive conformation of the catalytic triad of the Neisseria meningitidis peptidoglycan O-acetylesterase reveals mechanistic conservation in SGNH esterase family members

    PubMed Central

    Williams, Allison H.; Veyrier, Frédéric J.; Bonis, Mathilde; Michaud, Yann; Raynal, Bertrand; Taha, Muhamed-Kheir; White, Stephen W.; Haouz, Ahmed; Boneca, Ivo G.

    2014-01-01

    Peptidoglycan O-acetylesterase (Ape1), which is required for host survival in Neisseria sp., belongs to the diverse SGNH hydrolase superfamily, which includes important viral and bacterial virulence factors. Here, multi-domain crystal structures of Ape1 with an SGNH catalytic domain and a newly identified putative peptidoglycan-detection module are reported. Enzyme catalysis was performed in Ape1 crystals and key catalytic intermediates along the SGNH esterase hydrolysis reaction pathway were visualized, revealing a substrate-induced productive conformation of the catalytic triad, a mechanistic detail that has not previously been observed. This substrate-induced productive conformation of the catalytic triad shifts the established dogma on these enzymes, generating valuable insight into the structure-based design of drugs targeting the SGNH esterase superfamily. PMID:25286847

  8. Antisense oligonucleotide binding to U5 snRNP induces a conformational change that exposes the conserved loop of U5 snRNA.

    PubMed Central

    Ast, G; Weiner, A M

    1997-01-01

    Conformational rearrangements of the spliceosomal small nuclear RNAs (U snRNAs) are essential for proper assembly of the active site prior to the first catalytic step of splicing. We have previously shown that conformational changes caused by binding of an antisense 2'-O-methyl RNA oligonucleotide (BU5Ae) to U5 snRNA nt 68-88 disrupted the U4/U5/U6 complex and induced formation of the U1/U4/U5 and U2/U6 complexes. Here we show that the conformational change induced by BU5Ae exposes the invariant loop of U5 that binds the 5'exon and also reorganizes internal loop 1 (IL1) and the top of stem 2. Interestingly, we have also previously found that the U1/U4/U5 complex induced by BU5Ae brings the invariant loop of U5 into close proximity with the 5'-end of U1. Taken together, these data suggest that U1 and U5 may both contribute to the ability of the U1/U4/U5 complex to bind the 5' splice site. PMID:9254712

  9. Activation and Characterization of a Cryptic Polycyclic Tetramate Macrolactam Biosynthetic Gene Cluster

    PubMed Central

    Luo, Yunzi; Huang, Hua; Liang, Jing; Wang, Meng; Lu, Lu; Shao, Zengyi; Cobb, Ryan E.; Zhao, Huimin

    2014-01-01

    Polycyclic tetramate macrolactams (PTMs) are a widely distributed class of natural products with important biological activities. However, many of them have not been characterized. Here we apply a plug and play synthetic biology strategy to activate a cryptic PTM biosynthetic gene cluster SGR810-815 from Streptomyces griseus and discover three potential PTMs. This gene cluster is highly conserved in phylogenetically diverse bacterial strains and contains an unusual hybrid polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS) which resembles iterative PKSs known in fungi. To further characterize this gene cluster, we use the same synthetic biology approach to create a series of gene deletion constructs and elucidate the biosynthetic steps for the formation of the polycyclic system. The strategy we employ bypasses the traditional laborious processes to elicit gene cluster expression and should be generally applicable to many other silent or cryptic gene clusters for discovery and characterization of new natural products. PMID:24305602

  10. Identifying biochemical phenotypic differences between cryptic species

    PubMed Central

    Liebeke, Manuel; Bruford, Michael W.; Donnelly, Robert K.; Ebbels, Timothy M. D.; Hao, Jie; Kille, Peter; Lahive, Elma; Madison, Rachael M.; Morgan, A. John; Pinto-Juma, Gabriela A.; Spurgeon, David J.; Svendsen, Claus; Bundy, Jacob G.

    2014-01-01

    Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus. There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as Nε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status. PMID:25252836

  11. Identifying biochemical phenotypic differences between cryptic species.

    PubMed

    Liebeke, Manuel; Bruford, Michael W; Donnelly, Robert K; Ebbels, Timothy M D; Hao, Jie; Kille, Peter; Lahive, Elma; Madison, Rachael M; Morgan, A John; Pinto-Juma, Gabriela A; Spurgeon, David J; Svendsen, Claus; Bundy, Jacob G

    2014-09-01

    Molecular genetic methods can distinguish divergent evolutionary lineages in what previously appeared to be single species, but it is not always clear what functional differences exist between such cryptic species. We used a metabolomic approach to profile biochemical phenotype (metabotype) differences between two putative cryptic species of the earthworm Lumbricus rubellus. There were no straightforward metabolite biomarkers of lineage, i.e. no metabolites that were always at higher concentration in one lineage. Multivariate methods, however, identified a small number of metabolites that together helped distinguish the lineages, including uncommon metabolites such as Nε-trimethyllysine, which is not usually found at high concentrations. This approach could be useful for characterizing functional trait differences, especially as it is applicable to essentially any species group, irrespective of its genome sequencing status. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  12. Location of Sites Within 'Cryptic Terrain'

    NASA Technical Reports Server (NTRS)

    2007-01-01

    A regional landscape near Mars' south pole is called 'cryptic terrain' because it once defied explanation, but new observations bolster and refine interpretations of how springtime outbursts of carbon-dioxide gas there sculpt intricate patterns and paint seasonal splotches. This map indicates locations of three sites that have been examined within the area of cryptic terrain, informally designated 'Manhattan,' 'Giza' and 'Ithaca.'

    The underlying map offers context of brightness measurements from the Thermal Emission Spectrometer instrument draped over a shaded relief map based on data from the Mars Orbiter Laser Altimeter instrument. Cool colors are areas with a low albedo (dark) and warm colors are areas which have high albedo (bright). Both of those instruments flew on NASA's Mars Global Surveyor orbiter.

  13. Cryptic function loss in animal populations.

    PubMed

    McConkey, Kim R; O'Farrill, Georgina

    2015-04-01

    The essential functional roles performed by animal species are lost when they become locally extinct, and ecosystems are critically threatened by this decline in functional diversity. Theory that links function, diversity, and ecosystem stability exists but fails to assess function loss that occurs in species with persistent populations. The entire functional role of a species, or a critical component of it, can be lost following large population declines (functional extinction), following population increase, or after behavioural adaptations to changes in the population, community, habitat, or climate. Here, we provide a framework that identifies the scenarios under which 'cryptic' function loss can occur in persistent populations. Cryptic function loss is potentially widespread and critically threatens ecosystem stability across the globe.

  14. Fetal hydrocephalus caused by cryptic intraventricular hemorrhage.

    PubMed

    Lategan, Belinda; Chodirker, Bernard N; Del Bigio, Marc R

    2010-03-01

    Cryptic intracerebral hemorrhage as an etiological factor in fetal hydrocephalus has been postulated but not described at autopsy. Four fetuses with overt hydrocephalus diagnosed by in utero ultrasound examination were examined at autopsy at 19-22 weeks gestation. Although a hemorrhagic etiology was not evident on ultrasound, hemosiderin-containing macrophages and associated reactive changes were found to obstruct the otherwise well-formed cerebral aqueduct in all four. Coagulopathy due to thrombocytopenia was implicated in one case. Anomalies involving other parts of the body were identified in two cases, although a direct link to the hydrocephalus was not obvious. The abnormality was isolated in one case. In three cases, possible sites of hemorrhage in the ventricles were identified. This abnormality represents a significant proportion of the fetuses examined for hydrocephalus in our referral center. We discuss the importance of careful autopsy examination in the diagnosis of cryptic intracerebral hemorrhage and the implications for counseling.

  15. Evolution of cryptic coloration in ectoparasites.

    PubMed

    Bush, Sarah E; Kim, Dukgun; Reed, Michelle; Clayton, Dale H

    2010-10-01

    Cryptic coloration is a classic example of evolution by natural selection. However, it has been studied almost exclusively in predator-prey systems, despite the fact that it may evolve in other groups, such as ectoparasites. The principle defense of hosts against ectoparasites is grooming behavior, which has a visual component. Host-imposed selection should lead to the evolution of background matching if it helps ectoparasites escape from grooming. Here we use sister taxa comparisons to show that avian feather lice (Phthiraptera: Ischnocera) have evolved coloration that matches the host's plumage, except in the case of head lice, which are protected from grooming. We also show covariation of parasite and host color within a single species of louse. Thus, cryptic coloration has evolved both within and between species of feather lice. Other examples of the evolution of crypsis presumably exist among the 70,000 known species of ectoparasites that collectively represent five animal phyla.

  16. Cryptic splice sites and split genes.

    PubMed

    Kapustin, Yuri; Chan, Elcie; Sarkar, Rupa; Wong, Frederick; Vorechovsky, Igor; Winston, Robert M; Tatusova, Tatiana; Dibb, Nick J

    2011-08-01

    We describe a new program called cryptic splice finder (CSF) that can reliably identify cryptic splice sites (css), so providing a useful tool to help investigate splicing mutations in genetic disease. We report that many css are not entirely dormant and are often already active at low levels in normal genes prior to their enhancement in genetic disease. We also report a fascinating correlation between the positions of css and introns, whereby css within the exons of one species frequently match the exact position of introns in equivalent genes from another species. These results strongly indicate that many introns were inserted into css during evolution and they also imply that the splicing information that lies outside some introns can be independently recognized by the splicing machinery and was in place prior to intron insertion. This indicates that non-intronic splicing information had a key role in shaping the split structure of eukaryote genes.

  17. Cryptic splice sites and split genes

    PubMed Central

    Kapustin, Yuri; Chan, Elcie; Sarkar, Rupa; Wong, Frederick; Vorechovsky, Igor; Winston, Robert M.; Tatusova, Tatiana; Dibb, Nick J.

    2011-01-01

    We describe a new program called cryptic splice finder (CSF) that can reliably identify cryptic splice sites (css), so providing a useful tool to help investigate splicing mutations in genetic disease. We report that many css are not entirely dormant and are often already active at low levels in normal genes prior to their enhancement in genetic disease. We also report a fascinating correlation between the positions of css and introns, whereby css within the exons of one species frequently match the exact position of introns in equivalent genes from another species. These results strongly indicate that many introns were inserted into css during evolution and they also imply that the splicing information that lies outside some introns can be independently recognized by the splicing machinery and was in place prior to intron insertion. This indicates that non-intronic splicing information had a key role in shaping the split structure of eukaryote genes. PMID:21470962

  18. Transportation Conformity

    EPA Pesticide Factsheets

    This section provides information on: current laws, regulations and guidance, policy and technical guidance, project-level conformity, general information, contacts and training, adequacy review of SIP submissions

  19. The predation costs of symmetrical cryptic coloration

    PubMed Central

    Cuthill, Innes C; Hiby, Elly; Lloyd, Emily

    2006-01-01

    In psychological studies of visual perception, symmetry is accepted as a potent cue in visual search for cryptic objects, yet its importance for non-human animals has been assumed rather than tested. Furthermore, while the salience of bilateral symmetry has been established in laboratory-based search tasks using human subjects, its role in more natural settings, closer to those for which such perceptual mechanisms evolved, has not, to our knowledge, been investigated previously. That said, the salience of symmetry in visual search has a plausible adaptive rationale, because biologically important objects, such as prey, predators or conspecifics, usually have a plane of symmetry that is not present in their surroundings. We tested the conspicuousness to avian predators of cryptic artificial, moth-like targets, with or without bilateral symmetry in background-matching coloration, against oak trees in the field. In two independent experiments, symmetrical targets were predated at a higher rate than otherwise identical asymmetrical targets. There was a small, but significant, fitness cost to symmetry in camouflage patterns. Given that birds are the most commonly invoked predators shaping the evolution of defensive coloration in insects, this raises the question of why bilateral asymmetry is not more common in cryptic insects. PMID:16720401

  20. DNA barcode reference library for Iberian butterflies enables a continental-scale preview of potential cryptic diversity.

    PubMed

    Dincă, Vlad; Montagud, Sergio; Talavera, Gerard; Hernández-Roldán, Juan; Munguira, Miguel L; García-Barros, Enrique; Hebert, Paul D N; Vila, Roger

    2015-07-24

    How common are cryptic species--those overlooked because of their morphological similarity? Despite its wide-ranging implications for biology and conservation, the answer remains open to debate. Butterflies constitute the best-studied invertebrates, playing a similar role as birds do in providing models for vertebrate biology. An accurate assessment of cryptic diversity in this emblematic group requires meticulous case-by-case assessments, but a preview to highlight cases of particular interest will help to direct future studies. We present a survey of mitochondrial genetic diversity for the butterfly fauna of the Iberian Peninsula with unprecedented resolution (3502 DNA barcodes for all 228 species), creating a reliable system for DNA-based identification and for the detection of overlooked diversity. After compiling available data for European butterflies (5782 sequences, 299 species), we applied the Generalized Mixed Yule-Coalescent model to explore potential cryptic diversity at a continental scale. The results indicate that 27.7% of these species include from two to four evolutionary significant units (ESUs), suggesting that cryptic biodiversity may be higher than expected for one of the best-studied invertebrate groups and regions. The ESUs represent important units for conservation, models for studies of evolutionary and speciation processes, and sentinels for future research to unveil hidden diversity.

  1. DNA barcode reference library for Iberian butterflies enables a continental-scale preview of potential cryptic diversity

    PubMed Central

    Dincă, Vlad; Montagud, Sergio; Talavera, Gerard; Hernández-Roldán, Juan; Munguira, Miguel L.; García-Barros, Enrique; Hebert, Paul D. N.; Vila, Roger

    2015-01-01

    How common are cryptic species - those overlooked because of their morphological similarity? Despite its wide-ranging implications for biology and conservation, the answer remains open to debate. Butterflies constitute the best-studied invertebrates, playing a similar role as birds do in providing models for vertebrate biology. An accurate assessment of cryptic diversity in this emblematic group requires meticulous case-by-case assessments, but a preview to highlight cases of particular interest will help to direct future studies. We present a survey of mitochondrial genetic diversity for the butterfly fauna of the Iberian Peninsula with unprecedented resolution (3502 DNA barcodes for all 228 species), creating a reliable system for DNA-based identification and for the detection of overlooked diversity. After compiling available data for European butterflies (5782 sequences, 299 species), we applied the Generalized Mixed Yule-Coalescent model to explore potential cryptic diversity at a continental scale. The results indicate that 27.7% of these species include from two to four evolutionary significant units (ESUs), suggesting that cryptic biodiversity may be higher than expected for one of the best-studied invertebrate groups and regions. The ESUs represent important units for conservation, models for studies of evolutionary and speciation processes, and sentinels for future research to unveil hidden diversity. PMID:26205828

  2. The Conformational Changes Induced by Ubiquinone Binding in the Na+-pumping NADH:Ubiquinone Oxidoreductase (Na+-NQR) Are Kinetically Controlled by Conserved Glycines 140 and 141 of the NqrB Subunit*

    PubMed Central

    Strickland, Madeleine; Juárez, Oscar; Neehaul, Yashvin; Cook, Darcie A.; Barquera, Blanca; Hellwig, Petra

    2014-01-01

    Na+-pumping NADH:ubiquinone oxidoreductase (Na+-NQR) is responsible for maintaining a sodium gradient across the inner bacterial membrane. This respiratory enzyme, which couples sodium pumping to the electron transfer between NADH and ubiquinone, is not present in eukaryotes and as such could be a target for antibiotics. In this paper it is shown that the site of ubiquinone reduction is conformationally coupled to the NqrB subunit, which also hosts the final cofactor in the electron transport chain, riboflavin. Previous work showed that mutations in conserved NqrB glycine residues 140 and 141 affect ubiquinone reduction and the proper functioning of the sodium pump. Surprisingly, these mutants did not affect the dissociation constant of ubiquinone or its analog HQNO (2-n-heptyl-4-hydroxyquinoline N-oxide) from Na+-NQR, which indicates that these residues do not participate directly in the ubiquinone binding site but probably control its accessibility. Indeed, redox-induced difference spectroscopy showed that these mutations prevented the conformational change involved in ubiquinone binding but did not modify the signals corresponding to bound ubiquinone. Moreover, data are presented that demonstrate the NqrA subunit is able to bind ubiquinone but with a low non-catalytically relevant affinity. It is also suggested that Na+-NQR contains a single catalytic ubiquinone binding site and a second site that can bind ubiquinone but is not active. PMID:25006248

  3. The conformational changes induced by ubiquinone binding in the Na+-pumping NADH:ubiquinone oxidoreductase (Na+-NQR) are kinetically controlled by conserved glycines 140 and 141 of the NqrB subunit.

    PubMed

    Strickland, Madeleine; Juárez, Oscar; Neehaul, Yashvin; Cook, Darcie A; Barquera, Blanca; Hellwig, Petra

    2014-08-22

    Na(+)-pumping NADH:ubiquinone oxidoreductase (Na(+)-NQR) is responsible for maintaining a sodium gradient across the inner bacterial membrane. This respiratory enzyme, which couples sodium pumping to the electron transfer between NADH and ubiquinone, is not present in eukaryotes and as such could be a target for antibiotics. In this paper it is shown that the site of ubiquinone reduction is conformationally coupled to the NqrB subunit, which also hosts the final cofactor in the electron transport chain, riboflavin. Previous work showed that mutations in conserved NqrB glycine residues 140 and 141 affect ubiquinone reduction and the proper functioning of the sodium pump. Surprisingly, these mutants did not affect the dissociation constant of ubiquinone or its analog HQNO (2-n-heptyl-4-hydroxyquinoline N-oxide) from Na(+)-NQR, which indicates that these residues do not participate directly in the ubiquinone binding site but probably control its accessibility. Indeed, redox-induced difference spectroscopy showed that these mutations prevented the conformational change involved in ubiquinone binding but did not modify the signals corresponding to bound ubiquinone. Moreover, data are presented that demonstrate the NqrA subunit is able to bind ubiquinone but with a low non-catalytically relevant affinity. It is also suggested that Na(+)-NQR contains a single catalytic ubiquinone binding site and a second site that can bind ubiquinone but is not active. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  4. Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America's open biomes.

    PubMed

    Gamble, Tony; Colli, Guarino R; Rodrigues, Miguel T; Werneck, Fernanda P; Simons, Andrew M

    2012-03-01

    The gecko genus Phyllopezus occurs across South America's open biomes: Cerrado, Seasonally Dry Tropical Forests (SDTF, including Caatinga), and Chaco. We generated a multi-gene dataset and estimated phylogenetic relationships among described Phyllopezus taxa and related species. We included exemplars from both described Phyllopezus pollicaris subspecies, P. p. pollicaris and P. p.przewalskii. Phylogenies from the concatenated data as well as species trees constructed from individual gene trees were largely congruent. All phylogeny reconstruction methods showed Bogertia lutzae as the sister species of Phyllopezus maranjonensis, rendering Phyllopezus paraphyletic. We synonymized the monotypic genus Bogertia with Phyllopezus to maintain a taxonomy that is isomorphic with phylogenetic history. We recovered multiple, deeply divergent, cryptic lineages within P. pollicaris. These cryptic lineages possessed mtDNA distances equivalent to distances among other gekkotan sister taxa. Described P. pollicaris subspecies are not reciprocally monophyletic and current subspecific taxonomy does not accurately reflect evolutionary relationships among cryptic lineages. We highlight the conservation significance of these results in light of the ongoing habitat loss in South America's open biomes. Copyright © 2011 Elsevier Inc. All rights reserved.

  5. Evidence of constrained phenotypic evolution in a cryptic species complex of agamid lizards.

    PubMed

    Smith, Katie L; Harmon, Luke J; Shoo, Luke P; Melville, Jane

    2011-04-01

    Lineages that exhibit little morphological change over time provide a unique opportunity to explore whether nonadaptive or adaptive processes explain the conservation of morphology over evolutionary time scales. We provide the most comprehensive evaluation to date of the evolutionary processes leading to morphological similarity among species in a cryptic species complex, incorporating two agamid lizard species (Diporiphora magna and D. bilineata). Phylogenetic analysis of mitochondrial (ND2) and nuclear (RAG-1) gene regions revealed the existence of eight deeply divergent clades. Analysis of morphological data confirmed the presence of cryptic species among these clades. Alternative evolutionary hypotheses for the morphological similarity of species were tested using a combination of phylogenetic, morphological, and ecological data. Likelihood model testing of morphological data suggested a history of constrained phenotypic evolution where lineages have a tendency to return to their medial state, whereas ecological data showed support for both Brownian motion and constrained evolution. Thus, there was an overriding signature of constrained evolution influencing morphological divergence between clades. Our study illustrates the utility of using a combination of phylogenetic, morphological, and ecological data to investigate evolutionary mechanisms maintaining cryptic species.

  6. Separation in flowering time contributes to the maintenance of sympatric cryptic plant lineages

    PubMed Central

    Michalski, Stefan G; Durka, Walter

    2015-01-01

    Sympatric cryptic lineages are a challenge for the understanding of species coexistence and lineage diversification as well as for management, conservation, and utilization of plant genetic resources. In higher plants studies providing insights into the mechanisms creating and maintaining sympatric cryptic lineages are rare. Here, using microsatellites and chloroplast sequence data, morphometric analyses, and phenological observations, we ask whether sympatrically coexisting lineages in the common wetland plant Juncus effusus are ecologically differentiated and reproductively isolated. Our results show two genetically highly differentiated, homoploid lineages within J. effusus that are morphologically cryptic and have similar preference for soil moisture content. However, flowering time differed significantly between the lineages contributing to reproductive isolation and the maintenance of these lineages. Furthermore, the later flowering lineage suffered less from predispersal seed predation by a Coleophora moth species. Still, we detected viable and reproducing hybrids between both lineages and the earlier flowering lineage and J. conglomeratus, a coexisting close relative. Flowering time differentiation between the lineages can be explained by neutral divergence alone and together with a lack of postzygotic isolation mechanisms; the sympatric coexistence of these lineages is most likely the result of an allopatric origin with secondary contact. PMID:26078854

  7. Conservation of biological diversity: all things considered

    Treesearch

    Jonathan Thompson; Martin Raphael; Randy Molina; Bruce Marcot; Deanna Olson

    2008-01-01

    Most ecosystems contain a few common species and many rare ones. By virtue of being rare, these species are often poorly understood and difficult to manage. Scientists at the PNW Research Station have recently published a landmark book that chronicles what is known and what they've recently learned about conserving cryptic biodiversity. For the past decade,...

  8. Conformal Infinity

    NASA Astrophysics Data System (ADS)

    Frauendiener, Jörg

    2004-12-01

    The notion of conformal infinity has a long history within the research in Einstein's theory of gravity. Today, "conformal infinity" is related to almost all other branches of research in general relativity, from quantisation procedures to abstract mathematical issues to numerical applications. This review article attempts to show how this concept gradually and inevitably evolved from physical issues, namely the need to understand gravitational radiation and isolated systems within the theory of gravitation, and how it lends itself very naturally to the solution of radiation problems in numerical relativity. The fundamental concept of null-infinity is introduced. Friedrich's regular conformal field equations are presented and various initial value problems for them are discussed. Finally, it is shown that the conformal field equations provide a very powerful method within numerical relativity to study global problems such as gravitational wave propagation and detection.

  9. General Conformity

    EPA Pesticide Factsheets

    The General Conformity requirements ensure that the actions taken by federal agencies in nonattainment and maintenance areas do not interfere with a state’s plans to meet national standards for air quality.

  10. Empirical Evidence Supporting Frequent Cryptic Speciation in Epiphyllous Liverworts: A Case Study of the Cololejeunea lanciloba Complex

    PubMed Central

    Yu, Ying; Heinrichs, Jochen; Zhu, Rui-Liang; Schneider, Harald

    2013-01-01

    Cryptic species are frequently recovered in plant lineages, and considered an important cause for divergent of morphological disparity and species diversity. The identification of cryptic species has important implications for the assessment of conservation needs of species aggregates. The mechanisms and processes of the origin of cryptic species diversity are still poorly understand based on the lack of studies especially in context of environment factors. Here we explored evidence for cryptic species within the epiphyllous liverworts Cololejeunea lanciloba complex based on two loci, the plastid trnL-F region and the nuclear ribosomal ITS region. Several analytic approaches were employed to delimit species based on DNA sequence variation including phylogenetic reconstruction, statistical parsimony networks analysis and two recently introduced species delimitation criteria: Rosenberg’s reciprocal monophyly and Rodrigo’s randomly distinct. We found evidence for thirteen genetically distinct putative species, each consisting of more than one haplotype, rather than four morphologically-circumscribed species. The results implied that the highly conserved phenotypes are not congruent with the genetic differentiation, contributing to incorrect assessments of the biodiversity of epiphyllous liverworts. We hypothesize that evolution of cryptic species recovered may be caused by selection of traits critical to the survival in epiphyllous habitats combined with limited developmental options designed in the small body. PMID:24367634

  11. An ancient icon reveals new mysteries: mummy DNA resurrects a cryptic species within the Nile crocodile.

    PubMed

    Hekkala, Evon; Shirley, Matthew H; Amato, George; Austin, James D; Charter, Suellen; Thorbjarnarson, John; Vliet, Kent A; Houck, Marlys L; Desalle, Rob; Blum, Michael J

    2011-10-01

    The Nile crocodile (Crocodylus niloticus) is an ancient icon of both cultural and scientific interest. The species is emblematic of the great civilizations of the Nile River valley and serves as a model for international wildlife conservation. Despite its familiarity, a centuries-long dispute over the taxonomic status of the Nile crocodile remains unresolved. This dispute not only confounds our understanding of the origins and biogeography of the 'true crocodiles' of the crown genus Crocodylus, but also complicates conservation and management of this commercially valuable species. We have taken a total evidence approach involving phylogenetic analysis of mitochondrial and nuclear markers, as well as karyotype analysis of chromosome number and structure, to assess the monophyletic status of the Nile crocodile. Samples were collected from throughout Africa, covering all major bioregions. We also utilized specimens from museum collections, including mummified crocodiles from the ancient Egyptian temples at Thebes and the Grottes de Samoun, to reconstruct the genetic profiles of extirpated populations. Our analyses reveal a cryptic evolutionary lineage within the Nile crocodile that elucidates the biogeographic history of the genus and clarifies long-standing arguments over the species' taxonomic identity and conservation status. An examination of crocodile mummy haplotypes indicates that the cryptic lineage corresponds to an earlier description of C. suchus and suggests that both African Crocodylus lineages historically inhabited the Nile River. Recent survey efforts indicate that C. suchus is declining or extirpated throughout much of its distribution. Without proper recognition of this cryptic species, current sustainable use-based management policies for the Nile crocodile may do more harm than good. © 2011 Blackwell Publishing Ltd.

  12. The N-terminus of the Montano virus nucleocapsid protein possesses broadly cross-reactive conformation-dependent epitopes conserved in rodent-borne hantaviruses.

    PubMed

    Saasa, Ngonda; Yoshida, Haruka; Shimizu, Kenta; Sánchez-Hernández, Cornelio; Romero-Almaraz, María de Lourdes; Koma, Takaaki; Sanada, Takahiro; Seto, Takahiro; Yoshii, Kentaro; Ramos, Celso; Yoshimatsu, Kumiko; Arikawa, Jiro; Takashima, Ikuo; Kariwa, Hiroaki

    2012-06-20

    The hantavirus nucleocapsid (N) protein is an important immunogen that stimulates a strong and cross-reactive immune response in humans and rodents. A large proportion of the response to N protein has been found to target its N-terminus. However, the exact nature of this bias towards the N-terminus is not yet fully understood. We characterized six monoclonal antibodies (mAbs) against the N protein of Montano virus (MTNV), a Mexican hantavirus. Five of these mAbs recognized eight American hantaviruses and six European and Asian hantaviruses, but not the Soricomorpha-borne Thottapalayam hantavirus. The N protein-reactive binding regions of the five mAbs were mapped to discontinuous epitopes within the N-terminal 13-51 amino acid residues, while a single serotype-specific mAb was mapped to residues 1-25 and 49-75. Our findings suggest that discontinuous epitopes at the N-terminus are conserved, at least in rodent-borne hantaviruses, and that they contribute considerably to N protein cross-reactivity.

  13. Familial cryptic translocation in Angelman syndrome

    SciTech Connect

    Weyerts, L.K.; Wiley, J.E.; Loud, K.M.

    1994-09-01

    The majority of patients with Angelman syndrome have been shown to have a cytogenetic or molecular deletion on the maternally derived chromosome 15. We report on a case of Angelman syndrome in which this deletion occurs as an unbalanced cryptic translocation involving chromosomes 14 and 15. The proband was diagnosed clinically as having Angelman syndrome. Multiple cytogenetic studies were done without detecting any deletion. When DNA probes (Oncor) specific for the Prader Willi/Angelman locus became available, the patient was restudied and found to be deleted for {open_quotes}region A{close_quotes} (D15S11) but not for {open_quotes}region B{close_quotes} (GABRB3). No other abnormality was detected. The proband`s mother was then studied. The chromosome 15 marker probe and D15S11 were detected on different chromosomes. Using alpha-satellite probes, a cryptic 14;15 translocation was uncovered. This balanced translocation was also found to be carried by the sister of the proband. This case, along with a case presented at the 1993 ASHG meeting, illustrates the need for using acrocentric probes when studying Angelman syndrome patients. The proband was studied using additional probes specific for this region and found to be deleted for SNRPN but not for D15S10. The breakpoint of the translocation in this patient delineates the smallest deletion of the Angelman syndrome region reported to date and therefore may represent the specific gene involved.

  14. Cryptic speciation in a model invertebrate chordate.

    PubMed

    Caputi, Luigi; Andreakis, Nikos; Mastrototaro, Francesco; Cirino, Paola; Vassillo, Mauro; Sordino, Paolo

    2007-05-29

    We applied independent species concepts to clarify the phylogeographic structure of the ascidian Ciona intestinalis, a powerful model system in chordate biology and for comparative genomic studies. Intensive research with this marine invertebrate is based on the assumption that natural populations globally belong to a single species. Therefore, understanding the true taxonomic classification may have implications for experimental design and data management. Phylogenies inferred from mitochondrial and nuclear DNA markers accredit the existence of two cryptic species: C. intestinalis sp. A, genetically homogeneous, distributed in the Mediterranean, northeast Atlantic, and Pacific, and C. intestinalis sp. B, geographically structured and encountered in the North Atlantic. Species-level divergence is further entailed by cross-breeding estimates. C. intestinalis A and B from allopatric populations cross-fertilize, but hybrids remain infertile because of defective gametogenesis. Although anatomy illustrates an overall interspecific similarity lacking in diagnostic features, we provide consistent tools for in-field and in-laboratory species discrimination. Finding of two cryptic taxa in C. intestinalis raises interest in a new tunicate genome as a gateway to studies in speciation and ecological adaptation of chordates.

  15. Shoot, shovel and shut up: cryptic poaching slows restoration of a large carnivore in Europe

    PubMed Central

    Liberg, Olof; Chapron, Guillaume; Wabakken, Petter; Pedersen, Hans Christian; Hobbs, N. Thompson; Sand, Håkan

    2012-01-01

    Poaching is a widespread and well-appreciated problem for the conservation of many threatened species. Because poaching is illegal, there is strong incentive for poachers to conceal their activities, and consequently, little data on the effects of poaching on population dynamics are available. Quantifying poaching mortality should be a required knowledge when developing conservation plans for endangered species but is hampered by methodological challenges. We show that rigorous estimates of the effects of poaching relative to other sources of mortality can be obtained with a hierarchical state–space model combined with multiple sources of data. Using the Scandinavian wolf (Canis lupus) population as an illustrative example, we show that poaching accounted for approximately half of total mortality and more than two-thirds of total poaching remained undetected by conventional methods, a source of mortality we term as ‘cryptic poaching’. Our simulations suggest that without poaching during the past decade, the population would have been almost four times as large in 2009. Such a severe impact of poaching on population recovery may be widespread among large carnivores. We believe that conservation strategies for large carnivores considering only observed data may not be adequate and should be revised by including and quantifying cryptic poaching. PMID:21849323

  16. Shoot, shovel and shut up: cryptic poaching slows restoration of a large carnivore in Europe.

    PubMed

    Liberg, Olof; Chapron, Guillaume; Wabakken, Petter; Pedersen, Hans Christian; Hobbs, N Thompson; Sand, Håkan

    2012-03-07

    Poaching is a widespread and well-appreciated problem for the conservation of many threatened species. Because poaching is illegal, there is strong incentive for poachers to conceal their activities, and consequently, little data on the effects of poaching on population dynamics are available. Quantifying poaching mortality should be a required knowledge when developing conservation plans for endangered species but is hampered by methodological challenges. We show that rigorous estimates of the effects of poaching relative to other sources of mortality can be obtained with a hierarchical state-space model combined with multiple sources of data. Using the Scandinavian wolf (Canis lupus) population as an illustrative example, we show that poaching accounted for approximately half of total mortality and more than two-thirds of total poaching remained undetected by conventional methods, a source of mortality we term as 'cryptic poaching'. Our simulations suggest that without poaching during the past decade, the population would have been almost four times as large in 2009. Such a severe impact of poaching on population recovery may be widespread among large carnivores. We believe that conservation strategies for large carnivores considering only observed data may not be adequate and should be revised by including and quantifying cryptic poaching.

  17. Intrinsic differences between authentic and cryptic 5′ splice sites

    PubMed Central

    Roca, Xavier; Sachidanandam, Ravi; Krainer, Adrian R.

    2003-01-01

    Cryptic splice sites are used only when use of a natural splice site is disrupted by mutation. To determine the features that distinguish authentic from cryptic 5′ splice sites (5′ss), we systematically analyzed a set of 76 cryptic 5′ss derived from 46 human genes. These cryptic 5′ss have a similar frequency distribution in exons and introns, and are usually located close to the authentic 5′ss. Statistical analysis of the strengths of the 5′ss using the Shapiro and Senapathy matrix revealed that authentic 5′ss have significantly higher score values than cryptic 5′ss, which in turn have higher values than the mutant ones. β-Globin provides an interesting exception to this rule, so we chose it for detailed experimental analysis in vitro. We found that the sequences of the β-globin authentic and cryptic 5′ss, but not their surrounding context, determine the correct 5′ss choice, although their respective scores do not reflect this functional difference. Our analysis provides a statistical basis to explain the competitive advantage of authentic over cryptic 5′ss in most cases, and should facilitate the development of tools to reliably predict the effect of disease-associated 5′ss-disrupting mutations at the mRNA level. PMID:14576320

  18. Cryptic Species in Putative Ancient Asexual Darwinulids (Crustacea, Ostracoda)

    PubMed Central

    Schön, Isa; Pinto, Ricardo L.; Halse, Stuart; Smith, Alison J.; Martens, Koen; Birky, C. William

    2012-01-01

    Background Fully asexually reproducing taxa lack outcrossing. Hence, the classic Biological Species Concept cannot be applied. Methodology/Principal Findings We used DNA sequences from the mitochondrial COI gene and the nuclear ITS2 region to check species boundaries according to the evolutionary genetic (EG) species concept in five morphospecies in the putative ancient asexual ostracod genera, Penthesilenula and Darwinula, from different continents. We applied two methods for detecting cryptic species, namely the K/θ method and the General Mixed Yule Coalescent model (GMYC). We could confirm the existence of species in all five darwinulid morphospecies and additional cryptic diversity in three morphospecies, namely in Penthesilenula brasiliensis, Darwinula stevensoni and in P. aotearoa. The number of cryptic species within one morphospecies varied between seven (P. brasiliensis), five to six (D. stevensoni) and two (P. aotearoa), respectively, depending on the method used. Cryptic species mainly followed continental distributions. We also found evidence for coexistence at the local scale for Brazilian cryptic species of P. brasiliensis and P. aotearoa. Our ITS2 data confirmed that species exist in darwinulids but detected far less EG species, namely two to three cryptic species in P. brasiliensis and no cryptic species at all in the other darwinulid morphospecies. Conclusions/Significance Our results clearly demonstrate that both species and cryptic diversity can be recognized in putative ancient asexual ostracods using the EG species concept, and that COI data are more suitable than ITS2 for this purpose. The discovery of up to eight cryptic species within a single morphospecies will significantly increase estimates of biodiversity in this asexual ostracod group. Which factors, other than long-term geographic isolation, are important for speciation processes in these ancient asexuals remains to be investigated. PMID:22802945

  19. Cryptic diversity in a fig wasp community-morphologically differentiated species are sympatric but cryptic species are parapatric.

    PubMed

    Darwell, C T; Cook, J M

    2017-02-01

    A key debate in ecology centres on the relative importance of niche and neutral processes in determining patterns of community assembly with particular focus on whether ecologically similar species with similar functional traits are able to coexist. Meanwhile, molecular studies are increasingly revealing morphologically indistinguishable cryptic species with presumably similar ecological roles. Determining the geographic distribution of such cryptic species provides opportunities to contrast predictions of niche vs. neutral models. Discovery of sympatric cryptic species increases alpha diversity and supports neutral models, while documentation of allopatric/parapatric cryptic species increases beta diversity and supports niche models. We tested these predictions using morphological and molecular data, coupled with environmental niche modelling analyses, of a fig wasp community along its 2700-km latitudinal range. Molecular methods increased previous species diversity estimates from eight to eleven species, revealing morphologically cryptic species in each of the four wasp genera studied. Congeneric species pairs that were differentiated by a key morphological functional trait (ovipositor length) coexisted sympatrically over large areas. In contrast, morphologically similar species, with similar ovipositor lengths, typically showed parapatric ranges with very little overlap. Despite parapatric ranges, environmental niche models of cryptic congeneric pairs indicate large regions of potential sympatry, suggesting that competitive processes are important in determining the distributions of ecologically similar species. Niche processes appear to structure this insect community, and cryptic diversity may typically contribute mostly to beta rather than alpha diversity.

  20. Evidence of female cryptic choice in crayfish.

    PubMed

    Aquiloni, Laura; Gherardi, Francesca

    2008-04-23

    To test whether male body size affects female reproductive investment in the polygamous crayfish Procambarus clarkii, we described mating behaviour of virgin females paired with either small or large males, and analysed the number, size and weight of both eggs and juveniles sired by either types of male. Along with confirming the overt selection by females of larger mates, we found that the size and weight of both the eggs and the juveniles were higher when sired by larger fathers. This suggests that P. clarkii females exert a form of cryptic choice for large males, seemingly adjusting the quantity of egg deutoplasm in function of the mate body size. The question of why females spend time and energy to brood low-fitness offspring is finally raised.

  1. Genome size differences in Hyalella cryptic species.

    PubMed

    Vergilino, Roland; Dionne, Kaven; Nozais, Christian; Dufresne, France; Belzile, Claude

    2012-02-01

    The Hyalella azteca (Saussure) complex includes numerous amphipod cryptic species in freshwater habitats in America as revealed by DNA barcoding surveys. Two ecomorphs (small and large) have evolved numerous times in this complex. Few phenotypic criteria have been found to differentiate between the numerous species of this complex. The present study aims to explore genome size differences between some species of the H. azteca complex co-occurring in a Canadian boreal lake using flow cytometry. Nuclear DNA content was estimated for 50 individuals belonging to six COI haplotypes corresponding to four provisional species of the H. azteca complex. Species from the large ecomorph had C-values significantly larger than species from the small ecomorph, whereas slight differences were found among species of the small ecomorph. These differences in genome sizes might be linked to ecological and physiological differences among species of the H. azteca complex.

  2. Conformational activation of ADAMTS13.

    PubMed

    South, Kieron; Luken, Brenda M; Crawley, James T B; Phillips, Rebecca; Thomas, Mari; Collins, Richard F; Deforche, Louis; Vanhoorelbeke, Karen; Lane, David A

    2014-12-30

    A disintegrin and metalloprotease with thrombospondin motifs 13 (ADAMTS13) is a metalloprotease that regulates von Willebrand factor (VWF) function. ADAMTS13-mediated proteolysis is determined by conformational changes in VWF, but also may depend on its own conformational activation. Kinetic analysis of WT ADAMTS13 revealed ∼ 2.5-fold reduced activity compared with ADAMTS13 lacking its C-terminal tail (MDTCS) or its CUB1-2 domains (WTΔCUB1-2), suggesting that the CUB domains naturally limit ADAMTS13 function. Consistent with this suggestion, WT ADAMTS13 activity was enhanced ∼ 2.5-fold by preincubation with either an anti-CUB mAb (20E9) or VWF D4CK (the natural binding partner for the CUB domains). Furthermore, the isolated CUB1-2 domains not only bound MDTCS, but also inhibited activity by up to 2.5-fold. Interestingly, a gain-of-function (GoF) ADAMTS13 spacer domain variant (R568K/F592Y/R660K/Y661F/Y665F) was ∼ 2.5-fold more active than WT ADAMTS13, but could not be further activated by 20E9 mAb or VWF D4CK and was unable to bind or to be inhibited by the CUB1-2 domains, suggesting that the inhibitory effects of the CUB domains involve an interaction with the spacer domain that is disrupted in GoF ADAMTS13. Electron microscopy demonstrated a "closed" conformation of WT ADAMTS13 and suggested a more "open" conformation for GoF ADAMTS13. The cryptic spacer domain epitope revealed by conformational unfolding also represents the core antigenic target for autoantibodies in thrombotic thrombocytopenic purpura. We propose that ADAMTS13 circulates in a closed conformation, which is maintained by a CUB-spacer domain binding interaction. ADAMTS13 becomes conformationally activated on demand through interaction of its C-terminal CUB domains with VWF, making it susceptible to immune recognition.

  3. Range of CD4-Bound Conformations of HIV-1 gp120, as Defined Using Conditional CD4-Induced Antibodies

    PubMed Central

    Kaplan, Gilad; Roitburd-Berman, Anna; Lewis, George K.

    2016-01-01

    ABSTRACT The HIV envelope binds cellular CD4 and undergoes a range of conformational changes that lead to membrane fusion and delivery of the viral nucleocapsid into the cellular cytoplasm. This binding to CD4 reveals cryptic and highly conserved epitopes, the molecular nature of which is still not fully understood. The atomic structures of CD4 complexed with gp120 core molecules (a form of gp120 in which the V1, V2, and V3 loops and N and C termini have been truncated) have indicated that a hallmark feature of the CD4-bound conformation is the bridging sheet minidomain. Variations in the orientation of the bridging sheet hairpins have been revealed when CD4-liganded gp120 was compared to CD4-unliganded trimeric envelope structures. Hence, there appears to be a number of conformational transitions possible in HIV-1 monomeric gp120 that are affected by CD4 binding. The spectrum of CD4-bound conformations has been interrogated in this study by using a well-characterized panel of conditional, CD4-induced (CD4i) monoclonal antibodies (MAbs) that bind HIV-1 gp120 and its mutations under various conditions. Two distinct CD4i epitopes of the outer domain were studied: the first comprises the bridging sheet, while the second contains elements of the V2 loop. Furthermore, we show that the unliganded extended monomeric core of gp120 (coree) assumes an intermediate CD4i conformation in solution that further undergoes detectable rearrangements upon association with CD4. These discoveries impact both accepted paradigms concerning gp120 structure and the field of HIV immunogen design. IMPORTANCE Elucidation of the conformational transitions that the HIV-1 envelope protein undergoes during the course of entry into CD4+ cells is fundamental to our understanding of HIV biology. The binding of CD4 triggers a range of gp120 structural rearrangements that could present targets for future drug design and development of preventive vaccines. Here we have systematically interrogated and

  4. Cryptic Species or Inadequate Taxonomy? Implementation of 2D Geometric Morphometrics Based on Integumental Organs as Landmarks for Delimitation and Description of Copepod Taxa.

    PubMed

    Karanovic, Tomislav; Djurakic, Marko; Eberhard, Stefan M

    2016-03-01

    Discovery of cryptic species using molecular tools has become common in many animal groups but it is rarely accompanied by morphological revision, creating ongoing problems in taxonomy and conservation. In copepods, cryptic species have been discovered in most groups where fast-evolving molecular markers were employed. In this study at Yeelirrie in Western Australia we investigate a subterranean species complex belonging to the harpacticoid genus Schizopera Sars, 1905, using both the barcoding mitochondrial COI gene and landmark-based two-dimensional geometric morphometrics. Integumental organs (sensilla and pores) are used as landmarks for the first time in any crustacean group. Complete congruence between DNA-based species delimitation and relative position of integumental organs in two independent morphological structures suggests the existence of three distinct evolutionary units. We describe two of them as new species, employing a condensed taxonomic format appropriate for cryptic species. We argue that many supposedly cryptic species might not be cryptic if researchers focus on analyzing morphological structures with multivariate tools that explicitly take into account geometry of the phenotype. A perceived supremacy of molecular methods in detecting cryptic species is in our view a consequence of disparity of investment and unexploited recent advancements in morphometrics among taxonomists. Our study shows that morphometric data alone could be used to find diagnostic morphological traits and gives hope to anyone studying small animals with a hard integument or shell, especially opening the door to assessing fossil diversity and rich museum collections. We expect that simultaneous use of molecular tools with geometry-oriented morphometrics may yield faster formal description of species. Decrypted species in this study are a good example for urgency of formal descriptions, as they display short-range endemism in small groundwater calcrete aquifers in a

  5. Scattering Via Conformal Higher Spin Exchanges

    NASA Astrophysics Data System (ADS)

    Tseytlin, A. A.

    We consider a model of massless scalars interacting (via bilinear conserved currents) with conformal higher spin fields in flat space. We compute the tree-level four-scalar scattering amplitude using a natural prescription for summation over an infinite set of conformal higher spin exchanges and find that it vanishes. Independently, we show that the vanishing of the scalar scattering amplitude is, in fact, implied by the global conformal higher spin symmetry of this model.

  6. Linker regions and flexibility around the metalloprotease domain account for conformational activation of ADAMTS13

    PubMed Central

    Deforche, L.; Roose, E.; Vandenbulcke, A.; Vandeputte, N.; Feys, H.B.; Springer, T.A.; Mi, L.Z.; Muia, J.; Sadler, J.E.; Soejima, K.; Rottensteiner, H.; Deckmyn, H.; De Meyer, S.F.; Vanhoorelbeke, K.

    2016-01-01

    Background Recently, conformational activation of ADAMTS13 was identified. This mechanism showed the evolution from a condensed and inhibited conformation, in which the proximal MDTCS and distal T2-CUB2 domains are in close contact with each other, to an activated structure due to ding with the von Willebrand factor (VWF). Objectives Identification of cryptic epitope/exosite exposure after conformational activation and of sites of flexibility in ADAMTS13. Methods The activating effect of 25 anti-T2-CUB2 antibodies was studied in the FRETS-VWF73 and the vortex assay. Cryptic epitope/exosite exposure was determined in ELISA and VWF binding assay. The molecular basis for flexibility was hypothesized through RADAR analysis, tested in ELISA using deletion variants and visualized using electron microscopy. Results Eleven activating anti-ADAMTS13 antibodies, directed against the T5-CUB2 domains, were identified in the FRETS-VWF73 assay. RADAR analysis identified three linker regions in the distal domains. Interestingly, identification of an antibody recognizing a cryptic epitope in the metalloprotease domain confirmed the contribution of these linker regions to conformational activation of the enzyme. The proof of flexibility around both the T2 and metalloprotease domains by electron microscopy furthermore supported this contribution. In addition, cryptic epitope exposure was identified in the distal domains, as activating anti-T2-CUB2 antibodies increased the binding to folded VWF up to ~3-fold. Conclusion Conformational activation of ADAMTS13 leads to cryptic epitope/exosite exposure in both proximal and distal domains, subsequently inducing increased activity. Furthermore, three linker regions in the distal domains are responsible for flexibility and enable the interaction between the proximal and the T8-CUB2 domains. PMID:26391536

  7. Tdp-43 cryptic exons are highly variable between cell types.

    PubMed

    Jeong, Yun Ha; Ling, Jonathan P; Lin, Sophie Z; Donde, Aneesh N; Braunstein, Kerstin E; Majounie, Elisa; Traynor, Bryan J; LaClair, Katherine D; Lloyd, Thomas E; Wong, Philip C

    2017-02-02

    TDP-43 proteinopathy is a prominent pathological feature that occurs in a number of human diseases including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and inclusion body myositis (IBM). Our recent finding that TDP-43 represses nonconserved cryptic exons led us to ask whether cell type-specific cryptic exons could exist to impact unique molecular pathways in brain or muscle. In the present work, we investigated TDP-43's function in various mouse tissues to model disease pathogenesis. We generated mice to conditionally delete TDP-43 in excitatory neurons or skeletal myocytes and identified the cell type-specific cryptic exons associated with TDP-43 loss of function. Comparative analysis of nonconserved cryptic exons in various mouse cell types revealed that only some cryptic exons were common amongst stem cells, neurons, and myocytes; the majority of these nonconserved cryptic exons were cell type-specific. Our results suggest that in human disease, TDP-43 loss of function may impair cell type-specific pathways.

  8. Crystal Structures of Beryllium Fluoride-Free and Beryllium Fluoride-Bound CheY in Complex with the Conserved C-Terminal Peptide of CheZ Reveal Dual Binding Modes Specific to CheY Conformation

    PubMed Central

    Guhaniyogi, Jayita; Robinson, Victoria L.; Stock, Ann M.

    2013-01-01

    Summary Chemotaxis, the environment-specific swimming behavior of a bacterial cell is controlled by flagellar rotation. The steady-state level of the phosphorylated or activated form of the response regulator CheY dictates the direction of flagellar rotation. CheY phosphorylation is regulated by a fine equilibrium of three phosphotransfer activities: phosphorylation by the kinase CheA, its auto-dephosphorylation and dephosphorylation by its phosphatase CheZ. Efficient dephosphorylation of CheY by CheZ requires two spatially distinct protein-protein contacts: tethering of the two proteins to each other and formation of an active site for dephosphorylation. The latter involves interaction of phosphorylated CheY with the small highly conserved C-terminal helix of CheZ (CheZC), an indispensable structural component of the functional CheZ protein. To understand how the CheZC helix, representing less than 1% of the full-length protein, ascertains molecular specificity of binding to CheY, we have determined crystal structures of CheY in complex with a synthetic peptide corresponding to 15 C-terminal residues of CheZ (CheZ200-214) at resolutions ranging from 2.0 Å to 2.3 Å. These structures provide a detailed view of the CheZC peptide interaction both in the presence and absence of the phosphoryl analog, BeF3−. Our studies reveal that two different modes of binding the CheZ200-214 peptide are dictated by the conformational state of CheY in the complex. Our structures suggest that the CheZC helix binds to a “meta-active” conformation of inactive CheY and it does so in an orientation that is distinct from the one in which it binds activated CheY. Our dual binding mode hypothesis provides implications for reverse information flow in CheY and extends previous observations on inherent resilience in CheY-like signaling domains. PMID:16674976

  9. Crystal Structures of Beryllium Fluoride-Free and Beryllium Fluoride-Bound CheY in Complex with the Conserved C-Terminal Peptide of CheZ Reveal Dual Binding Modes Specific to CheY Conformation

    SciTech Connect

    Guhaniyogi,J.; Robinson, V.; Stock, A.

    2006-01-01

    Chemotaxis, the environment-specific swimming behavior of a bacterial cell is controlled by flagellar rotation. The steady-state level of the phosphorylated or activated form of the response regulator CheY dictates the direction of flagellar rotation. CheY phosphorylation is regulated by a fine equilibrium of three phosphotransfer activities: phosphorylation by the kinase CheA, its auto-dephosphorylation and dephosphorylation by its phosphatase CheZ. Efficient dephosphorylation of CheY by CheZ requires two spatially distinct protein-protein contacts: tethering of the two proteins to each other and formation of an active site for dephosphorylation. The former involves interaction of phosphorylated CheY with the small highly conserved C-terminal helix of CheZ (CheZ{sub C}), an indispensable structural component of the functional CheZ protein. To understand how the CheZ{sub C} helix, representing less than 10% of the full-length protein, ascertains molecular specificity of binding to CheY, we have determined crystal structures of CheY in complex with a synthetic peptide corresponding to 15 C-terminal residues of CheZ (CheZ{sub 200-214}) at resolutions ranging from 2.0 Angstroms to 2.3 Angstroms. These structures provide a detailed view of the CheZC peptide interaction both in the presence and absence of the phosphoryl analog, BeF{sub 3}{sup -}. Our studies reveal that two different modes of binding the CheZ{sub 200-214} peptide are dictated by the conformational state of CheY in the complex. Our structures suggest that the CheZ{sub C} helix binds to a 'meta-active' conformation of inactive CheY and it does so in an orientation that is distinct from the one in which it binds activated CheY. Our dual binding mode hypothesis provides implications for reverse information flow in CheY and extends previous observations on inherent resilience in CheY-like signaling domains.

  10. River barriers and cryptic biodiversity in an evolutionary museum

    PubMed Central

    Voelker, G; Marks, B D; Kahindo, C; A'genonga, U; Bapeamoni, F; Duffie, L E; Huntley, J W; Mulotwa, E; Rosenbaum, S A; Light, J E

    2013-01-01

    The Riverine Barriers Hypothesis (RBH) posits that tropical rivers can be effective barriers to gene flow, based on observations that range boundaries often coincide with river barriers. Over the last 160 years, the RBH has received attention from various perspectives, with a particular focus on vertebrates in the Amazon Basin. To our knowledge, no molecular assessment of the RBH has been conducted on birds in the Afrotropics, despite its rich avifauna and many Afrotropical bird species being widely distributed across numerous watersheds and basins. Here, we provide the first genetic evidence that an Afrotropical river has served as a barrier for birds and for their lice, based on four understory bird species collected from sites north and south of the Congo River. Our results indicate near-contemporaneous, Pleistocene lineage diversification across the Congo River in these species. Our results further indicate differing levels of genetic variation in bird lice; the extent of this variation appears linked to the life-history of both the host and the louse. Extensive cryptic diversity likely is being harbored in Afrotropical forests, in both understory birds and their lice. Therefore, these forests may not be “museums” of old lineages. Rather, substantial evolutionary diversification may have occurred in Afrotropical forests throughout the Pleistocene, supporting the Pleistocene Forest Refuge Hypothesis. Strong genetic variation in birds and their lice within a small part of the Congo Basin forest indicates that we may have grossly underestimated diversity in the Afrotropics, making these forests home of substantial biodiversity in need of conservation. PMID:23532272

  11. Interim Cosmetic Results and Toxicity Using 3D Conformal External Beam Radiotherapy to Deliver Accelerated Partial Breast Irradiation in Patients With Early-Stage Breast Cancer Treated With Breast-Conserving Therapy

    SciTech Connect

    Vicini, Frank A. Chen, Peter; Wallace, Michelle; Mitchell, Christina; Hasan, Yasmin; Grills, Inga; Kestin, Larry; Schell, Scott; Goldstein, Neal S.; Kunzman, Jonathan; Gilbert, Sam; Martinez, Alvaro

    2007-11-15

    Purpose: We present our ongoing clinical experience utilizing three-dimensional (3D)-conformal radiation therapy (3D-CRT) to deliver accelerated partial breast irradiation (APBI) in patients with early-stage breast cancer treated with breast-conserving therapy. Methods and Materials: Ninety-one consecutive patients were treated with APBI using our previously reported 3D-CRT technique. The clinical target volume consisted of the lumpectomy cavity plus a 10- to 15 -mm margin. The prescribed dose was 34 or 38.5 Gy in 10 fractions given over 5 consecutive days. The median follow-up was 24 months. Twelve patients have been followed for {>=}4 years, 20 for {>=}3.5 years, 29 for >3.0 years, 33 for {>=}2.5 years, and 46 for {>=}2.0 years. Results: No local recurrences developed. Cosmetic results were rated as good/excellent in 100% of evaluable patients at {>=} 6 months (n = 47), 93% at 1 year (n = 43), 91% at 2 years (n = 21), and in 90% at {>=}3 years (n = 10). Erythema, hyperpigmentation, breast edema, breast pain, telangiectasias, fibrosis, and fat necrosis were evaluated at 6, 24, and 36 months after treatment. All factors stabilized by 3 years posttreatment with grade I or II rates of 0%, 0%, 0%, 0%, 9%, 18%, and 9%, respectively. Only 2 patients (3%) developed grade III toxicity (breast pain), which resolved with time. Conclusions: Delivery of APBI with 3D-CRT resulted in minimal chronic ({>=}6 months) toxicity to date with good/excellent cosmetic results. Additional follow-up is needed to assess the long-term efficacy of this form of APBI.

  12. Cryptic cuckoo eggs hide from competing cuckoos.

    PubMed

    Gloag, Ros; Keller, Laurie-Anne; Langmore, Naomi E

    2014-10-07

    Interspecific arms races between cuckoos and their hosts have produced remarkable examples of mimicry, with parasite eggs evolving to match host egg appearance and so evade removal by hosts. Certain bronze-cuckoo species, however, lay eggs that are cryptic rather than mimetic. These eggs are coated in a low luminance pigment that camouflages them within the dark interiors of hosts' nests. We investigated whether cuckoo egg crypsis is likely to have arisen from the same coevolutionary processes known to favour egg mimicry. We added high and low luminance-painted eggs to the nests of large-billed gerygones (Gerygone magnirostris), a host of the little bronze-cuckoo (Chalcites minutillus). Gerygones rarely rejected either egg type, and did not reject natural cuckoo eggs. Cuckoos, by contrast, regularly removed an egg from clutches before laying their own and were five times more likely to remove a high luminance model than its low luminance counterpart. Given that we found one-third of all parasitized nests were exploited by multiple cuckoos, our results suggest that competition between cuckoos has been the key selective agent for egg crypsis. In such intraspecific arms races, crypsis may be favoured over mimicry because it can reduce the risk of egg removal to levels below chance.

  13. Cryptic cuckoo eggs hide from competing cuckoos

    PubMed Central

    Gloag, Ros; Keller, Laurie-Anne; Langmore, Naomi E.

    2014-01-01

    Interspecific arms races between cuckoos and their hosts have produced remarkable examples of mimicry, with parasite eggs evolving to match host egg appearance and so evade removal by hosts. Certain bronze-cuckoo species, however, lay eggs that are cryptic rather than mimetic. These eggs are coated in a low luminance pigment that camouflages them within the dark interiors of hosts' nests. We investigated whether cuckoo egg crypsis is likely to have arisen from the same coevolutionary processes known to favour egg mimicry. We added high and low luminance-painted eggs to the nests of large-billed gerygones (Gerygone magnirostris), a host of the little bronze-cuckoo (Chalcites minutillus). Gerygones rarely rejected either egg type, and did not reject natural cuckoo eggs. Cuckoos, by contrast, regularly removed an egg from clutches before laying their own and were five times more likely to remove a high luminance model than its low luminance counterpart. Given that we found one-third of all parasitized nests were exploited by multiple cuckoos, our results suggest that competition between cuckoos has been the key selective agent for egg crypsis. In such intraspecific arms races, crypsis may be favoured over mimicry because it can reduce the risk of egg removal to levels below chance. PMID:25122227

  14. Cryptic Genetic Variation in Evolutionary Developmental Genetics.

    PubMed

    Paaby, Annalise B; Gibson, Greg

    2016-06-13

    Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes-processes that cannot be fully observed in continuously varying visible traits.

  15. Cryptic Genetic Variation in Evolutionary Developmental Genetics

    PubMed Central

    Paaby, Annalise B.; Gibson, Greg

    2016-01-01

    Evolutionary developmental genetics has traditionally been conducted by two groups: Molecular evolutionists who emphasize divergence between species or higher taxa, and quantitative geneticists who study variation within species. Neither approach really comes to grips with the complexities of evolutionary transitions, particularly in light of the realization from genome-wide association studies that most complex traits fit an infinitesimal architecture, being influenced by thousands of loci. This paper discusses robustness, plasticity and lability, phenomena that we argue potentiate major evolutionary changes and provide a bridge between the conceptual treatments of macro- and micro-evolution. We offer cryptic genetic variation and conditional neutrality as mechanisms by which standing genetic variation can lead to developmental system drift and, sheltered within canalized processes, may facilitate developmental transitions and the evolution of novelty. Synthesis of the two dominant perspectives will require recognition that adaptation, divergence, drift and stability all depend on similar underlying quantitative genetic processes—processes that cannot be fully observed in continuously varying visible traits. PMID:27304973

  16. Cryptic genetic variation in natural populations: a predictive framework.

    PubMed

    Ledón-Rettig, Cris C; Pfennig, David W; Chunco, Amanda J; Dworkin, Ian

    2014-11-01

    Understanding how populations respond to rapid environmental change is critical both for preserving biodiversity and for human health. An increasing number of studies have shown that genetic variation that has no discernable effect under common ecological conditions can become amplified under stressful or novel conditions, suggesting that environmental change per se can provide the raw materials for adaptation. Indeed, the release of such hidden, or "cryptic," genetic variants has been increasingly viewed as playing a general and important role in allowing populations to respond to rapid environmental change. However, additional studies have suggested that there is a balance between cryptic genetic variants that are potentially adaptive in future environments and genetic variants that are deleterious. In this article, we begin by discussing how population and environmental parameters-such as effective population size and the historical frequency and strength of selection under inducing conditions-influence relative amounts of cryptic genetic variation among populations and the overall phenotypic effects of such variation. The amount and distribution of cryptic genetic variation will, in turn, determine the likelihood that cryptic variants, once expressed, will be adaptive or maladaptive during environmental transitions. We then present specific approaches for measuring these parameters in natural populations. Finally, we discuss one natural system that will be conducive to testing whether populations that vary in these parameters harbor different amounts, or types, of cryptic genetic variation. Generally, teasing apart how population and environmental parameters influence the accumulation of cryptic genetic variation will help us to understand how populations endure and adapt (or fail to adapt) to natural environmental change and anthropogenic disturbance.

  17. Causes and methods to estimate cryptic sources of fishing mortality.

    PubMed

    Gilman, E; Suuronen, P; Hall, M; Kennelly, S

    2013-10-01

    Cryptic, not readily detectable, components of fishing mortality are not routinely accounted for in fisheries management because of a lack of adequate data, and for some components, a lack of accurate estimation methods. Cryptic fishing mortalities can cause adverse ecological effects, are a source of wastage, reduce the sustainability of fishery resources and, when unaccounted for, can cause errors in stock assessments and population models. Sources of cryptic fishing mortality are (1) pre-catch losses, where catch dies from the fishing operation but is not brought onboard when the gear is retrieved, (2) ghost-fishing mortality by fishing gear that was abandoned, lost or discarded, (3) post-release mortality of catch that is retrieved and then released alive but later dies as a result of stress and injury sustained from the fishing interaction, (4) collateral mortalities indirectly caused by various ecological effects of fishing and (5) losses due to synergistic effects of multiple interacting sources of stress and injury from fishing operations, or from cumulative stress and injury caused by repeated sub-lethal interactions with fishing operations. To fill a gap in international guidance on best practices, causes and methods for estimating each component of cryptic fishing mortality are described, and considerations for their effective application are identified. Research priorities to fill gaps in understanding the causes and estimating cryptic mortality are highlighted. © 2013 The Authors. Journal of Fish Biology © 2013 The Fisheries Society of the British Isles.

  18. A spider species complex revealed high cryptic diversity in South China caves.

    PubMed

    Zhang, Yuanyuan; Li, Shuqiang

    2014-10-01

    Cryptic species, which are an important component of biodiversity, have rarely been studied in South China karst. We investigated cryptic diversity in the cave species complex Telema cucurbitina, which has a narrow niche but widespread distribution among multiple caves. We sampled another 15 populations (caves) in addition to the population from the type locality. Phylogenetic results indicated that individuals from the same cave constituted well-supported clades. Species diversity within this species complex was assessed in a coalescent framework, first with a Bayesian extension of the general mixed Yule coalescent (bGMYC) model and a Bayesian species delimitation method (BPP). Both species delimitation methods identified each cave population as a separate species. We propose that each cave population within this species complex was a separate evolving lineage and therefore 16 OTUs were recovered based on our molecular data despite their high morphological similarities. We also propose that the unrecognized organism's diversity within South China caves might be extremely large considering our case. Furthermore, our work reveals that species discovery of cave organisms by morphological data has a high probability of underestimating hidden diversity. Our work also highlights the need for conservation strategies to protect this largely neglected diversity of cave organisms. Copyright © 2014 Elsevier Inc. All rights reserved.

  19. Identification and dynamics of a cryptic suture zone in tropical rainforest

    PubMed Central

    Moritz, C.; Hoskin, C.J.; MacKenzie, J.B.; Phillips, B.L.; Tonione, M.; Silva, N.; VanDerWal, J.; Williams, S.E.; Graham, C.H.

    2009-01-01

    Suture zones, shared regions of secondary contact between long-isolated lineages, are natural laboratories for studying divergence and speciation. For tropical rainforest, the existence of suture zones and their significance for speciation has been controversial. Using comparative phylogeographic evidence, we locate a morphologically cryptic suture zone in the Australian Wet Tropics rainforest. Fourteen out of 18 contacts involve morphologically cryptic phylogeographic lineages, with mtDNA sequence divergences ranging from 2 to 15 per cent. Contact zones are significantly clustered in a suture zone located between two major Quaternary refugia. Within this area, there is a trend for secondary contacts to occur in regions with low environmental suitability relative to both adjacent refugia and, by inference, the parental lineages. The extent and form of reproductive isolation among interacting lineages varies across species, ranging from random admixture to speciation, in one case via reinforcement. Comparative phylogeographic studies, combined with environmental analysis at a fine-scale and across varying climates, can generate new insights into suture zone formation and to diversification processes in species-rich tropical rainforests. As arenas for evolutionary experimentation, suture zones merit special attention for conservation. PMID:19203915

  20. Integrative taxonomy detects cryptic and overlooked fish species in a neotropical river basin.

    PubMed

    Gomes, Laís Carvalho; Pessali, Tiago Casarim; Sales, Naiara Guimarães; Pompeu, Paulo Santos; Carvalho, Daniel Cardoso

    2015-10-01

    The great freshwater fish diversity found in the neotropical region makes management and conservation actions challenging. Due to shortage of taxonomists and insufficient infrastructure to deal with such great biodiversity (i.e. taxonomic impediment), proposed remedies to accelerate species identification and descriptions include techniques that combine DNA-based identification and concise morphological description. The building of a DNA barcode reference database correlating meristic and genetic data was developed for 75 % of the Mucuri River basin's freshwater fish. We obtained a total of 141 DNA barcode sequences from 37 species belonging to 30 genera, 19 families, and 5 orders. Genetic distances within species, genera, and families were 0.74, 9.5, and 18.86 %, respectively. All species could be clearly identified by the DNA barcodes. Divergences between meristic morphological characteristics and DNA barcodes revealed two cryptic species among the Cyphocharax gilbert and Astyanax gr. bimaculatus specimens, and helped to identify two overlooked species within the Gymnotus and Astyanax taxa. Therefore, using a simplified model of neotropical biodiversity, we tested the efficiency of an integrative taxonomy approach for species discovery, identification of cryptic diversity, and accelerating biodiversity descriptions.

  1. DNA Barcoding Reveals Cryptic Diversity within Commercially Exploited Indo-Malay Carangidae (Teleosteii: Perciformes)

    PubMed Central

    Mat Jaafar, Tun Nurul Aimi; Taylor, Martin I.; Mohd Nor, Siti Azizah; de Bruyn, Mark; Carvalho, Gary R.

    2012-01-01

    that COI is an effective tool for species identification of Carangidae from the IMA. There were moderate levels of cryptic diversity among putative species within the central IMA. However, to explain the hypothesis of species richness in the IMA, it is necessary to sample the whole family across their broad geographic range. Such insights are helpful not only to document mechanisms driving diversification and recruitment in Carangidae, but also to provide a scientific framework for management strategies and conservation of commercially-important fisheries resources. PMID:23209586

  2. 18 CFR 153.21 - Conformity with requirements.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 1 2010-04-01 2010-04-01 false Conformity with requirements. 153.21 Section 153.21 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... Requirements § 153.21 Conformity with requirements. (a) General Rule. Applications under subparts B and C...

  3. 18 CFR 415.51 - Prior non-conforming structures.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Prior non-conforming structures. 415.51 Section 415.51 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION ADMINISTRATIVE MANUAL BASIN REGULATIONS-FLOOD PLAIN REGULATIONS Enforcement § 415.51 Prior non-conforming...

  4. 18 CFR 153.21 - Conformity with requirements.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 1 2011-04-01 2011-04-01 false Conformity with requirements. 153.21 Section 153.21 Conservation of Power and Water Resources FEDERAL ENERGY REGULATORY... Requirements § 153.21 Conformity with requirements. (a) General Rule. Applications under subparts B and C...

  5. 18 CFR 415.51 - Prior non-conforming structures.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 18 Conservation of Power and Water Resources 2 2012-04-01 2012-04-01 false Prior non-conforming structures. 415.51 Section 415.51 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION ADMINISTRATIVE MANUAL BASIN REGULATIONS-FLOOD PLAIN REGULATIONS Enforcement § 415.51 Prior non-conforming...

  6. 18 CFR 415.51 - Prior non-conforming structures.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 18 Conservation of Power and Water Resources 2 2013-04-01 2012-04-01 true Prior non-conforming structures. 415.51 Section 415.51 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION ADMINISTRATIVE MANUAL BASIN REGULATIONS-FLOOD PLAIN REGULATIONS Enforcement § 415.51 Prior non-conforming...

  7. Cryptic Methane Emissions from Upland Forest Ecosystems

    SciTech Connect

    Megonigal, Patrick; Pitz, Scott

    2016-04-19

    This exploratory research on Cryptic Methane Emissions from Upland Forest Ecosystems was motivated by evidence that upland ecosystems emit 36% as much methane to the atmosphere as global wetlands, yet we knew almost nothing about this source. The long-term objective was to refine Earth system models by quantifying methane emissions from upland forests, and elucidate the biogeochemical processes that govern upland methane emissions. The immediate objectives of the grant were to: (i) test the emerging paradigm that upland trees unexpectedly transpire methane, (ii) test the basic biogeochemical assumptions of an existing global model of upland methane emissions, and (iii) develop the suite of biogeochemical approaches that will be needed to advance research on upland methane emissions. We instrumented a temperate forest system in order to explore the processes that govern upland methane emissions. We demonstrated that methane is emitted from the stems of dominant tree species in temperate upland forests. Tree emissions occurred throughout the growing season, while soils adjacent to the trees consumed methane simultaneously, challenging the concept that forests are uniform sinks of methane. High frequency measurements revealed diurnal cycling in the rate of methane emissions, pointing to soils as the methane source and transpiration as the most likely pathway for methane transport. We propose the forests are smaller methane sinks than previously estimated due to stem emissions. Stem emissions may be particularly important in upland tropical forests characterized by high rainfall and transpiration, resolving differences between models and measurements. The methods we used can be effectively implemented in order to determine if the phenomenon is widespread.

  8. Five Cryptic Species in the Amazonian Catfish Centromochlus existimatus Identified Based on Biogeographic Predictions and Genetic Data

    PubMed Central

    Cooke, Georgina M.; Chao, Ning L.; Beheregaray, Luciano B.

    2012-01-01

    Accurately quantifying biodiversity is fundamental for both evolutionary theory and conservation strategies. DNA-based studies are exposing high cryptic diversity irrespective of taxonomic group or environmental setting, and increasing the ever-growing estimates of global biodiversity. This has severe implications for under-sampled and species-rich tropical regions, such as the Amazon Basin. We used biogeographic predictions derived from geomorphological history and contemporary hydrochemical and genetic data to examine cryptic diversity in the Amazonian driftwood catfish Centromochlus existimatus. Using both nuclear and mitochondrial DNA markers, five deeply divergent cryptic lineages are reported, for which at least three are sympatric in distribution. These lineages appear relatively old, with divergence times dating back to middle Miocene. Diversification events appear to be chronologically associated with the formation of the modern Amazon River system, and perhaps influenced by hydrochemical gradients between tributaries. The cause of apparent morphological stasis in the C. existimatus species complex is speculated within the context of hydrochemistry and non-visual mating cues and a full taxonomic revision is recommended. Our findings suggest that the diversity of Amazonian ichthyofauna is vastly underestimated and highlight the relevance of biogeographic predictions to guide sampling efforts in ecologically complex and under-studied ecosystems. PMID:23144977

  9. Erythrocyte nuclear size as a better diagnostic character than cell size in the identification of live cryptic polyploid species.

    PubMed

    Otero, Manuel A; Grenat, Pablo R; Valetti, Julian A; Salas, Nancy E; Martino, Adolfo L

    2013-01-01

    It is well documented in anurans the cryptic condition of many species complexes involving polyploids. In these complexes the character that clearly differentiates them is the number of chromosome complements. The blood cells of amphibians conserve their nucleus, and so the erythrocyte size is correlated with the DNA content. We analyzed two cryptic-polyploid complexes occurring in the center of Argentina: Odontophrynus cordobae (2n)/O. americanus (4n) and Pleurodema kriegi (4n)/P. cordobae (8n). Our aim was evaluate the efficiency in the utilization of nuclear area with respect to cellular area of the erythrocytes to define the limits values for the identification of cryptic-polyploid species. We studied 110 individuals of Pleurodema and 116 individuals of Odontoprhynus. For each individual, we measured the cellular and nuclear length (L) and width (A) of 40 erythrocytes (Area = L*A*π/4) and boundary values were calculated using distribution curves. In both complexes studied, the erythrometric parameters showed significant differences between related species. Moreover, in both complexes the nuclear area was more efficient for identifying the species (Pleurodema: 34.39 µm2 (probability = 99.96%) and Odontophrynus: 24.02 µm2 (99.075%)) than the cell area (Pleurodema: 273.08 µm2 (97.55%) y Odontophrynus: 197.69 µm2 (97.94%)). Greater efficiency found using nuclear area is novel and significant because most studies use only the cell area to differentiate polyploid complexes.

  10. Alpine scree plants benefit from cryptic coloration with limited cost.

    PubMed

    Niu, Yang; Sun, Hang

    2014-01-01

    Like animals, plants are attacked by enemies (herbivores) that forage using visual cues; however, the defensive coloration type known as cryptic coloration was rarely reported in plants. For most autotrophic plants, because photosynthesis relies on the presence of chlorophyll, a green leaf appearance is standard. However, if having leaves that are not green is more beneficial than costly, such coloration may evolve under certain conditions. Taking advantage of the leaf color dimorphism of Corydalis benecincta, we showed that the cryptically colored leaves confer a clear benefit without obvious cost in natural populations. Based on this study, we try to provide a framework on which to base a cost-benefit analysis to investigate the evolution of cryptic leaf coloration in plants.

  11. Cryptic asymmetry: unreliable signals mask asymmetric performance of crayfish weapons

    PubMed Central

    Angilletta, Michael J.; Wilson, Robbie S.

    2012-01-01

    Animals commonly use their limbs as signals and weapons during territorial aggression. Asymmetries of limb performance that do not relate to asymmetries of limb size (cryptic asymmetry) could substantially affect disputes, but this phenomenon has not been considered beyond primates. We investigated cryptic asymmetry in male crayfish (Cherax dispar), which commonly use unreliable signals of strength during aggression. Although the strength of a chela can vary by an order of magnitude for a given size, we found repeatable asymmetries of strength that were only weakly related to asymmetries of size. Size-adjusted strength of chelae and the asymmetry of strength between chelae were highly repeatable between environmental conditions, suggesting that asymmetries of strength stemmed from variation in capacity rather than motivation. Cryptic asymmetry adds another dimension of uncertainty during conflict between animals, which could influence the evolution of unreliable signals and morphological asymmetry. PMID:22417793

  12. Cryptic asymmetry: unreliable signals mask asymmetric performance of crayfish weapons.

    PubMed

    Angilletta, Michael J; Wilson, Robbie S

    2012-08-23

    Animals commonly use their limbs as signals and weapons during territorial aggression. Asymmetries of limb performance that do not relate to asymmetries of limb size (cryptic asymmetry) could substantially affect disputes, but this phenomenon has not been considered beyond primates. We investigated cryptic asymmetry in male crayfish (Cherax dispar), which commonly use unreliable signals of strength during aggression. Although the strength of a chela can vary by an order of magnitude for a given size, we found repeatable asymmetries of strength that were only weakly related to asymmetries of size. Size-adjusted strength of chelae and the asymmetry of strength between chelae were highly repeatable between environmental conditions, suggesting that asymmetries of strength stemmed from variation in capacity rather than motivation. Cryptic asymmetry adds another dimension of uncertainty during conflict between animals, which could influence the evolution of unreliable signals and morphological asymmetry.

  13. Gating by tryptophan 73 exposes a cryptic pocket at the protein-binding interface of the oncogenic eIF4E protein.

    PubMed

    Lama, Dilraj; Brown, Christopher J; Lane, David P; Verma, Chandra S

    2015-10-27

    Targeting protein-protein interacting sites for potential therapeutic applications is a challenge in the development of inhibitors, and this becomes more difficult when these interfaces are relatively planar, as in the eukaryotic translation initiation factor 4E (eIF4E) protein. eIF4E is an oncogene that is overexpressed in numerous forms of cancer, making it a prime target as a therapeutic molecule. We report here the presence of a cryptic pocket at the protein-binding interface of eIF4E, which opens transiently during molecular dynamics simulations of the protein in solvent water and is observed to be stable when solvent water is mixed with benzene molecules. This pocket can also be seen in the ensemble of structures available from the solution-state conformations of eIF4E. The accessibility of the pocket is gated by the side-chain transitions of an evolutionarily conserved tryptophan residue. It is found to be feasible for accommodating clusters of benzene molecules, which signify the plasticity and ligandability of the pocket. We also observe that the newly formed cavity provides a favorable binding environment for interaction of a well-recognized small molecule inhibitor of eIF4E. The occurrence of this transiently accessible cavity highlights the existence of a more pronounced binding groove in a region that has traditionally been considered to be planar. Together, the data suggest that an alternate binding cavity exists on eIF4E and could be exploited for the rational design and development of a new class of lead compounds against the protein.

  14. Analysis of Cryptic, Systemic Botrytis Infections in Symptomless Hosts

    PubMed Central

    Shaw, Michael W.; Emmanuel, Christy J.; Emilda, Deni; Terhem, Razak B.; Shafia, Aminath; Tsamaidi, Dimitra; Emblow, Mark; van Kan, Jan A. L.

    2016-01-01

    Botrytis species are generally considered to be aggressive, necrotrophic plant pathogens. By contrast to this general perception, however, Botrytis species could frequently be isolated from the interior of multiple tissues in apparently healthy hosts of many species. Infection frequencies reached 50% of samples or more, but were commonly less, and cryptic infections were rare or absent in some plant species. Prevalence varied substantially from year to year and from tissue to tissue, but some host species routinely had high prevalence. The same genotype was found to occur throughout a host, representing mycelial spread. Botrytis cinerea and Botrytis pseudocinerea are the species that most commonly occur as cryptic infections, but phylogenetically distant isolates of Botrytis were also detected, one of which does not correspond to previously described species. Sporulation and visible damage occurred only when infected tissues were stressed, or became mature or senescent. There was no evidence of cryptic infection having a deleterious effect on growth of the host, and prevalence was probably greater in plants grown in high light conditions. Isolates from cryptic infections were often capable of causing disease (to varying extents) when spore suspensions were inoculated onto their own host as well as on distinct host species, arguing against co-adaptation between cryptic isolates and their hosts. These data collectively suggest that several Botrytis species, including the most notorious pathogenic species, exist frequently in cryptic form to an extent that has thus far largely been neglected, and do not need to cause disease on healthy hosts in order to complete their life-cycles. PMID:27242829

  15. Misleading Contexts: The Construction of Ambiguity in the Cryptic Crossword Clue.

    ERIC Educational Resources Information Center

    Cleary, John

    1996-01-01

    This paper investigates the intentional creation of ambiguity by composers of cryptic crossword puzzles. Taking a research question of "what makes a cryptic clue more difficult to solve than a simple crossword clue," it compares a sample of cryptic and quick crosswords from "The Guardian" and attempts to isolate the linguistic…

  16. Toward Awakening Cryptic Secondary Metabolite Gene Clusters in Filamentous Fungi

    PubMed Central

    Lim, Fang Yun; Sanchez, James F.; Wang, Clay C.C.; Keller, Nancy P.

    2013-01-01

    Mining for novel natural compounds is of eminent importance owing to the continuous need for new pharmaceuticals. Filamentous fungi are historically known to harbor the genetic capacity for an arsenal of natural compounds, both beneficial and detrimental to humans. The majority of these metabolites are still cryptic or silent under standard laboratory culture conditions. Mining for these cryptic natural products can be an excellent source for identifying new compound classes. Capitalizing on the current knowledge on how secondary metabolite gene clusters are regulated has allowed the research community to unlock many hidden fungal treasures, as described in this chapter. PMID:23084945

  17. Toward Understanding the Conformal Gravity

    NASA Astrophysics Data System (ADS)

    Berezin, V. A.; Dokuchaev, V. I.; Eroshenko, Yu. N.

    2017-03-01

    We constructed the conformally invariant model for scalar particle creation induced by strong gravitational fields. Starting from the usual hydrodynamic description of the particle motion written in the Eulerian coordinates, we substituted the particle number conservation law (which enters the formalism) by the particle creation law, proportional to the square of the Weyl tensor, following the famous result by Ya. B. Zel'dovich and A. A. Starobinsky. Then, demanding the conformal invariance of the whole dynamical system, we have got both the Weyl-conformal gravity and the Einstein-Hilbert dilaton gravity action integral. Thus, we obtained something like the induced gravity suggested first by A. D. Sakharov. It is shown that the resulting system is self-consistent.

  18. Toward Understanding the Conformal Gravity

    NASA Astrophysics Data System (ADS)

    Berezin, V. A.; Dokuchaev, V. I.; Eroshenko, Yu. N.

    2017-03-01

    We constructed the conformally invariant model for scalar particle creation induced by strong gravitational fields. Starting from the usual hydrodynamic description of the particle motion written in the Eulerian coordinates, we substituted the particle number conservation law (which enters the formalism) by the particle creation law, proportional to the square of the Weyl tensor, following the famous result by Ya. B. Zel'dovich and A. A. Starobinsky. Then, demanding the conformal invariance of the whole dynamical system, we have got both the Weyl-conformal gravity and the Einstein-Hilbert dilaton gravity action integral. Thus, we obtained something like the induced gravity suggested first by A. D. Sakharov. It is shown that the resulting system is self-consistent.

  19. South Polar Cryptic Terrain in Early Spring

    NASA Technical Reports Server (NTRS)

    2007-01-01

    This image of the south polar region of Mars was taken by the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) at 1557 UTC (10:57 a.m. EST) on Feb. 10, 2007, near 77.55 degrees south latitude, 131.98 degrees east longitude. CRISM's image was taken in 544 colors covering 0.36-3.92 micrometers, and shows features as small as 30 meters (98 feet) across. The region covered is just over 9 kilometers (5.6 miles) wide at its narrowest point, and is one of several in which CRISM is monitoring the evaporation (or 'sublimation') of the seasonal frost cap.

    The Martian south polar seasonal cap consists of carbon dioxide ice and frost, whose sublimation in the Martian spring creates a variety of features unlike anything in Earth's circumpolar regions. Part of the cap known as the 'cryptic region' is so cold that it must be covered with carbon dioxide frost, but it is also unexpectedly low in brightness and exhibits a variety of unusual dark blotches. Many scientists believe that carbon dioxide gas trapped below the sublimating ice is released in bursts, which carry along dust that gradually darkens the ice. One idea is that geyser-like dust eruptions form the dark blotches, and that the blotches grow, coalesce, and eventually hide the frost under a thin layer of dust.

    This image was taken shortly after sunrise with the Sun only about five degrees above the horizon. The left version shows brightness of the surface at 1.3 micrometers. The right version shows strength of an absorption band due to carbon dioxide frost at 1.435 micrometers; brighter areas have a stronger absorption and more carbon dioxide frost. However, even the darkest areas still have frost. The correlation between brightness and carbon dioxide frost abundance is striking, supporting the idea that the frost is being darkened by dust. Frost in the upper right corner shows the expected dark blotches, whereas the frost over the rest of the image is more uniformly dark, hinting that another

  20. RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes

    PubMed Central

    Merelli, Ivan; Guffanti, Alessandro; Fabbri, Marco; Cocito, Andrea; Furia, Laura; Grazini, Ursula; Bonnal, Raoul J.; Milanesi, Luciano; McBlane, Fraser

    2010-01-01

    Recombination signal sequences (RSSs) flanking V, D and J gene segments are recognized and cut by the VDJ recombinase during development of B and T lymphocytes. All RSSs are composed of seven conserved nucleotides, followed by a spacer (containing either 12 ± 1 or 23 ± 1 poorly conserved nucleotides) and a conserved nonamer. Errors in V(D)J recombination, including cleavage of cryptic RSS outside the immunoglobulin and T cell receptor loci, are associated with oncogenic translocations observed in some lymphoid malignancies. We present in this paper the RSSsite web server, which is available from the address http://www.itb.cnr.it/rss. RSSsite consists of a web-accessible database, RSSdb, for the identification of pre-computed potential RSSs, and of the related search tool, DnaGrab, which allows the scoring of potential RSSs in user-supplied sequences. This latter algorithm makes use of probability models, which can be recasted to Bayesian network, taking into account correlations between groups of positions of a sequence, developed starting from specific reference sets of RSSs. In validation laboratory experiments, we selected 33 predicted cryptic RSSs (cRSSs) from 11 chromosomal regions outside the immunoglobulin and TCR loci for functional testing. PMID:20478831

  1. RSSsite: a reference database and prediction tool for the identification of cryptic Recombination Signal Sequences in human and murine genomes.

    PubMed

    Merelli, Ivan; Guffanti, Alessandro; Fabbri, Marco; Cocito, Andrea; Furia, Laura; Grazini, Ursula; Bonnal, Raoul J; Milanesi, Luciano; McBlane, Fraser

    2010-07-01

    Recombination signal sequences (RSSs) flanking V, D and J gene segments are recognized and cut by the VDJ recombinase during development of B and T lymphocytes. All RSSs are composed of seven conserved nucleotides, followed by a spacer (containing either 12 +/- 1 or 23 +/- 1 poorly conserved nucleotides) and a conserved nonamer. Errors in V(D)J recombination, including cleavage of cryptic RSS outside the immunoglobulin and T cell receptor loci, are associated with oncogenic translocations observed in some lymphoid malignancies. We present in this paper the RSSsite web server, which is available from the address http://www.itb.cnr.it/rss. RSSsite consists of a web-accessible database, RSSdb, for the identification of pre-computed potential RSSs, and of the related search tool, DnaGrab, which allows the scoring of potential RSSs in user-supplied sequences. This latter algorithm makes use of probability models, which can be recasted to Bayesian network, taking into account correlations between groups of positions of a sequence, developed starting from specific reference sets of RSSs. In validation laboratory experiments, we selected 33 predicted cryptic RSSs (cRSSs) from 11 chromosomal regions outside the immunoglobulin and TCR loci for functional testing.

  2. The complete nucleotide sequence and genome organization of Fig cryptic virus, a novel bipartite dsRNA virus infecting fig, widely distributed in the Mediterranean basin.

    PubMed

    Elbeaino, Toufic; Kubaa, Raied Abou; Digiaro, Michele; Minafra, Angelantonio; Martelli, Giovanni P

    2011-06-01

    Two double-stranded RNA (dsRNA) segments of a virus with a bipartite genome identified in fig (Ficus carica L.) and denoted Fig cryptic virus (FCV) were cloned and sequenced. Viral dsRNAs are 1696 bp (RNA-1) and 1415 bp (RNA-2) in size. RNA-1 contains a single ORF (1419 nt) potentially encoding a 54 kDa protein and comprising the conserved amino acid motifs of the RNA-dependent RNA polymerase (RdRp) domain of species of the genus Alphacryptovirus. Its full-length amino acid sequence has the highest identity with Raphanus sativus cryptic virus 2 (RsCV-2) (36%), Beet cryptic virus 3 (BCV-3) (36%) and Fragaria chiloensis cryptic virus (FCCV) (34%). RNA-2 has also a single ORF (1014 nt) coding for a polypeptide with a predicted molecular mass of 38 kDa, identified as the viral coat protein (CP). In a phylogenetic tree constructed with the amino acid sequences of the RdRp domain, FCV clusters in a clade comprising BCV-3 and a number of tentative species of the genus Alphacryptovirus. FCV is not mechanically transmissible. It was detected in fig orchards of six Mediterranean countries (Albania, Algeria, Italy, Lebanon, Syria and Tunisia) where it does not seem to induce a visible disease.

  3. The first nearly cryptic Scorpionfly (Mecoptera: Panorpidae) from North America

    USDA-ARS?s Scientific Manuscript database

    The first, nearly cryptic species of scorpionfly from the United States, Panorpa cryptica Bicha and Schiff, n. sp., is described from northern Georgia, southwestern North Carolina and northwestern South Carolina. This insect was initially differentiated from the very similar Panorpa nebulosa Westwoo...

  4. Stridulations Reveal Cryptic Speciation in Neotropical Sympatric Ants

    PubMed Central

    Ferreira, Ronara Souza; Poteaux, Chantal; Delabie, Jacques Hubert Charles; Fresneau, Dominique; Rybak, Fanny

    2010-01-01

    The taxonomic challenge posed by cryptic species underlines the importance of using multiple criteria in species delimitation. In the current paper we tested the use of acoustic analysis as a tool to assess the real diversity in a cryptic species complex of Neotropical ants. In order to understand the potential of acoustics and to improve consistency in the conclusions by comparing different approaches, phylogenetic relationships of all the morphs considered were assessed by the analysis of a fragment of the mitochondrial DNA cytochrome b. We observed that each of the cryptic morph studied presents a morphologically distinct stridulatory organ and that all sympatric morphs produce distinctive stridulations. This is the first evidence of such a degree of specialization in the acoustic organ and signals in ants, which suggests that stridulations may be among the cues used by these ants during inter-specific interactions. Mitochondrial DNA variation corroborated the acoustic differences observed, confirming acoustics as a helpful tool to determine cryptic species in this group of ants, and possibly in stridulating ants in general. Congruent morphological, acoustic and genetic results constitute sufficient evidence to propose each morph studied here as a valid new species, suggesting that P. apicalis is a complex of at least 6 to 9 species, even if they present different levels of divergence. Finally, our results highlight that ant stridulations may be much more informative than hitherto thought, as much for ant communication as for integrative taxonomists. PMID:21203529

  5. Geochemical evidence for cryptic sulfur cycling in salt marsh sediments

    NASA Astrophysics Data System (ADS)

    Mills, Jennifer V.; Antler, Gilad; Turchyn, Alexandra V.

    2016-11-01

    Cryptic sulfur cycling is an enigmatic process in which sulfate is reduced to some lower-valence state sulfur species and subsequently quantitatively reoxidized; the rate and microbial energetics of this process and how prevalent it may be in the environment remain controversial. Here we investigate sulfur cycling in salt marsh sediments from Norfolk, England where we observe high ferrous iron concentrations with no depletion of sulfate or change in the sulfur isotope ratio of that sulfate, but a 5‰ increase in the oxygen isotope ratio in sulfate, indicating that sulfate has been through a reductive cycle replacing its oxygen atoms. This cryptic sulfur cycle was replicated in laboratory incubations using 18O-enriched water, demonstrating that the field results do not solely result from mixing processes in the natural environment. Numerical modeling of the laboratory incubations scaled to represent the salt marsh sediments suggests that the uptake rate of sulfate during this cryptic sulfur cycling is similar to the uptake rate of sulfate during the fastest microbial sulfate reduction that has been measured in the natural environment. The difference is that during cryptic sulfur cycling, all of the sulfur is subsequently reoxidized to sulfate. We discuss mechanisms for this pathway of sulfur cycling including the possible link to the subsurface iron cycle.

  6. Cryptic introductions and the interpretation of island biodiversity.

    PubMed

    Avery, Julian D; Fonseca, Dina M; Campagne, Pascal; Lockwood, Julie L

    2013-04-01

    Species with cryptic origins (i.e. those that cannot be reliably classed as native or non-native) present a particular challenge to our understanding of the generation and maintenance of biodiversity. Such species may be especially common on islands given that some islands have had a relatively recent history of human settlement. It is likely that select island species considered native might have achieved their current distributions via direct or indirect human actions. As an example, we explore the origins of eastern bluebirds (Sialia sialis bermudensis) on the island of Bermuda. Considered native to the island and a distinct subspecies, this population has diverged in morphology relative to mainland North America. Using microsatellite markers and simulation of island colonization, we show that the Bermuda population of bluebirds is the likely result of a single colonization event that occurred during the 1600s, making this a cryptic invader. To our knowledge, this is one of the youngest examples of a terrestrial vertebrate cryptic invader. We suggest that the eastern bluebird is not an isolated case of cryptic invader on either Bermuda or elsewhere and that caution be exercised when studying present-day distributions of organisms.

  7. Conformation and conformational exchange of Olopatadine hydrochloride

    NASA Astrophysics Data System (ADS)

    Lei, Lian-di; Zhu, Chuan-jun; Yang, Chun-hui; Cui, Yu-xin

    2008-12-01

    Besides the assignments of the 13C and 1H shifts by 1D and 2D NMR, the experiment 1H spectra of Olopatadine hydrochloride were recorded at temperature range 228-338 K. The variable-temperature spectra revealed a dynamic NMR effect which is attributed to conformational interconversion of the drug. At low temperature, the solution was shown to contain two conformers and the ration of them was 1:1. A conformational process with a free energy of activation of 56.7 kJ mol -1, coalescence temperature 298 K, was interpreted as geminal 1H exchange. Using molecule simulation, conformational candidates for two conformers are proposed.

  8. Fibronectin forms the most extensible biological fibers displaying switchable force-exposed cryptic binding sites

    PubMed Central

    Klotzsch, Enrico; Smith, Michael L.; Kubow, Kristopher E.; Muntwyler, Simon; Little, William C.; Beyeler, Felix; Gourdon, Delphine; Nelson, Bradley J.; Vogel, Viola

    2009-01-01

    Rather than maximizing toughness, as needed for silk and muscle titin fibers to withstand external impact, the much softer extracellular matrix fibers made from fibronectin (Fn) can be stretched by cell generated forces and display extraordinary extensibility. We show that Fn fibers can be extended more than 8-fold (>700% strain) before 50% of the fibers break. The Young's modulus of single fibers, given by the highly nonlinear slope of the stress-strain curve, changes orders of magnitude, up to MPa. Although many other materials plastically deform before they rupture, evidence is provided that the reversible breakage of force-bearing backbone hydrogen bonds enables the large strain. When tension is released, the nano-sized Fn domains first contract in the crowded environment of fibers within seconds into random coil conformations (molten globule states), before the force-bearing hydrogen bond networks that stabilize the domain's secondary structures are reestablished within minutes (double exponential). The exposure of cryptic binding sites on Fn type III modules increases steeply upon stretching. Thus fiber extension steadily up-regulates fiber rigidity and cryptic epitope exposure, both of which are known to differentially alter cell behavior. Finally, since stress-strain relationships cannot directly be measured in native extracellular matrix (ECM), the stress-strain curves were correlated with stretch-induced alterations of intramolecular fluorescence resonance energy transfer (FRET) obtained from trace amounts of Fn probes (mechanical strain sensors) that can be incorporated into native ECM. Physiological implications of the extraordinary extensibility of Fn fibers and contraction kinetics are discussed. PMID:19826086

  9. Why do cryptic species tend not to co-occur? A case study on two cryptic pairs of butterflies.

    PubMed

    Vodă, Raluca; Dapporto, Leonardo; Dincă, Vlad; Vila, Roger

    2015-01-01

    As cryptic diversity is being discovered, mostly thanks to advances in molecular techniques, it is becoming evident that many of these taxa display parapatric distributions in mainland and that they rarely coexist on islands. Genetic landscapes, haplotype networks and ecological niche modeling analyses were performed for two pairs of non-sister cryptic butterfly species, Aricia agestis-A. cramera and Polyommatus icarus-P. celina (Lycaenidae), to specifically assess non-coexistence on western Mediterranean islands, and to test potential causes producing such chequered distribution patterns. We show that the morphologically and ecologically equivalent pairs of species do not coexist on any of the studied islands, although nearly all islands are colonized by one of them. According to our models, the cryptic pairs displayed marked climatic preferences and 'precipitation during the driest quarter' was recovered as the most important climatic determinant. However, neither dispersal capacity, nor climatic or ecological factors fully explain the observed distributions across particular sea straits, and the existence of species interactions resulting in mutual exclusion is suggested as a necessary hypothesis. Given that the studied species are habitat generalists, feeding on virtually unlimited resources, we propose that reproductive interference, together with climatic preferences, sustain density-dependent mechanisms like "founder takes all" and impede coexistence on islands. Chequered distributions among cryptic taxa, both sister and non-sister, are common in butterflies, suggesting that the phenomenon revealed here could be important in determining biodiversity patterns.

  10. Why Do Cryptic Species Tend Not to Co-Occur? A Case Study on Two Cryptic Pairs of Butterflies

    PubMed Central

    Vodă, Raluca; Dapporto, Leonardo; Dincă, Vlad; Vila, Roger

    2015-01-01

    As cryptic diversity is being discovered, mostly thanks to advances in molecular techniques, it is becoming evident that many of these taxa display parapatric distributions in mainland and that they rarely coexist on islands. Genetic landscapes, haplotype networks and ecological niche modeling analyses were performed for two pairs of non-sister cryptic butterfly species, Aricia agestis-A. cramera and Polyommatus icarus—P. celina (Lycaenidae), to specifically assess non-coexistence on western Mediterranean islands, and to test potential causes producing such chequered distribution patterns. We show that the morphologically and ecologically equivalent pairs of species do not coexist on any of the studied islands, although nearly all islands are colonized by one of them. According to our models, the cryptic pairs displayed marked climatic preferences and ‘precipitation during the driest quarter’ was recovered as the most important climatic determinant. However, neither dispersal capacity, nor climatic or ecological factors fully explain the observed distributions across particular sea straits, and the existence of species interactions resulting in mutual exclusion is suggested as a necessary hypothesis. Given that the studied species are habitat generalists, feeding on virtually unlimited resources, we propose that reproductive interference, together with climatic preferences, sustain density-dependent mechanisms like “founder takes all” and impede coexistence on islands. Chequered distributions among cryptic taxa, both sister and non-sister, are common in butterflies, suggesting that the phenomenon revealed here could be important in determining biodiversity patterns. PMID:25692577

  11. Steinberg conformal algebras

    NASA Astrophysics Data System (ADS)

    Mikhalev, A. V.; Pinchuk, I. A.

    2005-06-01

    The structure of Steinberg conformal algebras is studied; these are analogues of Steinberg groups (algebras, superalgebras).A Steinberg conformal algebra is defined as an abstract algebra by a system of generators and relations between the generators. It is proved that a Steinberg conformal algebra is the universal central extension of the corresponding conformal Lie algebra; the kernel of this extension is calculated.

  12. Conservation genetics and genomics of amphibians and reptiles.

    PubMed

    Shaffer, H Bradley; Gidiş, Müge; McCartney-Melstad, Evan; Neal, Kevin M; Oyamaguchi, Hilton M; Tellez, Marisa; Toffelmier, Erin M

    2015-01-01

    Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.

  13. Noether versus Killing symmetry of conformally flat Friedmann metric

    NASA Astrophysics Data System (ADS)

    Bokhari, Ashfaque H.; Kara, A. H.

    2007-12-01

    In a recent study Noether symmetries of some static spacetime metrics in comparison with Killing vectors of corresponding spacetimes were studied. It was shown that Noether symmetries provide additional conservation laws that are not given by Killing vectors. In an attempt to understand how Noether symmetries compare with conformal Killing vectors, we find the Noether symmetries of the flat Friedmann cosmological model. We show that the conformally transformed flat Friedman model admits additional conservation laws not given by the Killing or conformal Killing vectors. Inter alia, these additional conserved quantities provide a mechanism to twice reduce the geodesic equations via the associated Noether symmetries.

  14. Undiagnosed cryptic diversity in small, microendemic frogs (Leptolalax) from the Central Highlands of Vietnam.

    PubMed

    Rowley, Jodi J L; Tran, Dao T A; Frankham, Greta J; Dekker, Anthony H; Le, Duong T T; Nguyen, Truong Q; Dau, Vinh Q; Hoang, Huy D

    2015-01-01

    A major obstacle in prioritizing species or habitats for conservation is the degree of unrecognized diversity hidden within complexes of morphologically similar, "cryptic" species. Given that amphibians are one of the most threatened groups of organisms on the planet, our inability to diagnose their true diversity is likely to have significant conservation consequences. This is particularly true in areas undergoing rapid deforestation, such as Southeast Asia. The Southeast Asian genus Leptolalax is a group of small-bodied, morphologically conserved frogs that inhabit the forest-floor. We examined a particularly small-bodied and morphologically conserved subset, the Leptolalax applebyi group, using a combination of molecular, morphometric, and acoustic data to identify previously unknown diversity within. In order to predict the geographic distribution of the group, estimate the effects of habitat loss and assess the degree of habitat protection, we used our locality data to perform ecological niche modelling using MaxEnt. Molecular (mtDNA and nuDNA), acoustic and subtle morphometric differences revealed a significant underestimation of diversity in the L. applebyi group; at least two-thirds of the diversity may be unrecognised. Patterns of diversification and microendemism in the group appear driven by limited dispersal, likely due to their small body size, with several lineages restricted to watershed basins. The L. applebyi group is predicted to have historically occurred over a large area of the Central Highlands of Vietnam, a considerable portion of which has already been deforested. Less than a quarter of the remaining forest predicted to be suitable for the group falls within current protected areas. The predicted distribution of the L. applebyi group extends into unsurveyed watershed basins, each potentially containing unsampled diversity, some of which may have already been lost due to deforestation. Current estimates of amphibian diversity based on

  15. Cryptic Species Due to Hybridization: A Combined Approach to Describe a New Species (Carex: Cyperaceae)

    PubMed Central

    Escudero, Marcial

    2016-01-01

    Disappearance of diagnostic morphological characters due to hybridization is considered to be one of the causes of the complex taxonomy of the species-rich (ca. 2000 described species) genus Carex (Cyperaceae). Carex furva s.l. belongs to section Glareosae. It is an endemic species from the high mountains of the Iberian Peninsula (Spain and Portugal). Previous studies suggested the existence of two different, cryptic taxa within C. furva s.l. Intermediate morphologies found in the southern Iberian Peninsula precluded the description of a new taxa. We aimed to determine whether C. furva s.l. should be split into two different species based on the combination of morphological and molecular data. We sampled ten populations across its full range and performed a morphological study based on measurements on herbarium specimens and silica-dried inflorescences. Both morphological and phylogenetic data support the existence of two different species within C. furva s.l. Nevertheless, intermediate morphologies and sterile specimens were found in one of the southern populations (Sierra Nevada) of C. furva s.l., suggesting the presence of hybrid populations in areas where both supposed species coexist. Hybridization between these two putative species has blurred morphological and genetic limits among them in this hybrid zone. We have proved the utility of combining molecular and morphological data to discover a new cryptic species in a scenario of hybridization. We now recognize a new species, C. lucennoiberica, endemic to the Iberian Peninsula (Sierra Nevada, Central system and Cantabrian Mountains). On the other hand, C. furva s.s. is distributed only in Sierra Nevada, where it may be threatened by hybridization with C. lucennoiberica. The restricted distribution of both species and their specific habitat requirements are the main limiting factors for their conservation. PMID:27973589

  16. Cryptic extinction of a common Pacific lizard Emoia impar (Squamata, Scincidae) from the Hawaiian Islands.

    USGS Publications Warehouse

    Fisher, Robert; Ineich, Ivan

    2012-01-01

    Most documented declines of tropical reptiles are of dramatic or enigmatic species. Declines of widespread species tend to be cryptic. The early (1900s) decline and extinction of the common Pacific skink Emoia impar from the Hawaiian Islands is documented here through an assessment of literature, museum vouchers and recent fieldwork. This decline appears contemporaneous with the documented declines of invertebrates and birds across the Hawaiian Islands. A review of the plausible causal factors indicates that the spread of the introduced big-headed ant Pheidole megacephala is the most likely factor in this lizard decline. The introduction and spread of a similar skink Lampropholis delicata across the islands appears to temporally follow the decline of E. impar, although there is no evidence of competition between these species. It appears that L. delicata is spreading to occupy the niche vacated by the extirpated E. impar. Further confusion exists because the skink E. cyanura, which is very similar in appearance to E. impar, appears to have been introduced to one site within a hotel on Kaua'i and persisted as a population at that site for approximately 2 decades (1970s–1990s) but is now also extirpated. This study highlights the cryptic nature of this early species extinction as evidence that current biogeographical patterns of non-charismatic or enigmatic reptiles across the Pacific may be the historical result of early widespread invasion by ants. Conservation and restoration activities for reptiles in the tropical Pacific should consider this possibility and evaluate all evidence prior to any implementation.

  17. Cryptic Species Due to Hybridization: A Combined Approach to Describe a New Species (Carex: Cyperaceae).

    PubMed

    Maguilla, Enrique; Escudero, Marcial

    2016-01-01

    Disappearance of diagnostic morphological characters due to hybridization is considered to be one of the causes of the complex taxonomy of the species-rich (ca. 2000 described species) genus Carex (Cyperaceae). Carex furva s.l. belongs to section Glareosae. It is an endemic species from the high mountains of the Iberian Peninsula (Spain and Portugal). Previous studies suggested the existence of two different, cryptic taxa within C. furva s.l. Intermediate morphologies found in the southern Iberian Peninsula precluded the description of a new taxa. We aimed to determine whether C. furva s.l. should be split into two different species based on the combination of morphological and molecular data. We sampled ten populations across its full range and performed a morphological study based on measurements on herbarium specimens and silica-dried inflorescences. Both morphological and phylogenetic data support the existence of two different species within C. furva s.l. Nevertheless, intermediate morphologies and sterile specimens were found in one of the southern populations (Sierra Nevada) of C. furva s.l., suggesting the presence of hybrid populations in areas where both supposed species coexist. Hybridization between these two putative species has blurred morphological and genetic limits among them in this hybrid zone. We have proved the utility of combining molecular and morphological data to discover a new cryptic species in a scenario of hybridization. We now recognize a new species, C. lucennoiberica, endemic to the Iberian Peninsula (Sierra Nevada, Central system and Cantabrian Mountains). On the other hand, C. furva s.s. is distributed only in Sierra Nevada, where it may be threatened by hybridization with C. lucennoiberica. The restricted distribution of both species and their specific habitat requirements are the main limiting factors for their conservation.

  18. Locally differentiated cryptic pigmentation in the freshwater isopod Asellus aquaticus.

    PubMed

    Hargeby, A; Stoltz, J; Johansson, J

    2005-05-01

    A repeated pattern of background colour matching in animals is an indication that pigmentation may be cryptic. Here, we examine the relationship between pigmentation of the freshwater isopod Asellus aquaticus and background darkness in 29 lakes, wetlands and ponds in Southern Sweden. The results show that Asellus pigmentation was correlated with substrate darkness across all localities. In seven localities, in which two contrasting substrate types were noted, Asellus populations were differentiated with respect to pigmentation. These findings thus provide phenomenological support for cryptic pigmentation in Asellus. Pigmentation generally increased with body size, but the relationship between pigmentation and size differed among localities, possibly as a result of differences in correlational selection on pigmentation and size. Selection thus appears to have resulted in local differentiation over a small spatial scale, even within lakes and wetlands. This differentiation is a likely cause behind elevated phenotype variation noted in localities with two substrate types, suggesting that habitat heterogeneity promotes genetic diversity.

  19. Implicating Cryptic and Novel Anophelines as Malaria Vectors in Africa

    PubMed Central

    Stevenson, Jennifer C.; Norris, Douglas E.

    2016-01-01

    Entomological indices and bionomic descriptions of malaria vectors are essential to accurately describe and understand malaria transmission and for the design and evaluation of appropriate control interventions. In order to correctly assign spatio-temporal distributions, behaviors and responses to interventions to particular anopheline species, identification of mosquitoes must be accurately made. This paper reviews the current methods and their limitations in correctly identifying anopheline mosquitoes in sub-Saharan Africa, and highlights the importance of molecular methods to discriminate cryptic species and identify lesser known anophelines. The increasing number of reports of Plasmodium infections in assumed “minor”, non-vector, and cryptic and novel species is reviewed. Their importance in terms of evading current control and elimination strategies and therefore maintaining malaria transmission is emphasized. PMID:28025486

  20. Niche partitioning in a sympatric cryptic species complex.

    PubMed

    Scriven, Jessica J; Whitehorn, Penelope R; Goulson, Dave; Tinsley, Matthew C

    2016-03-01

    Competition theory states that multiple species should not be able to occupy the same niche indefinitely. Morphologically, similar species are expected to be ecologically alike and exhibit little niche differentiation, which makes it difficult to explain the co-occurrence of cryptic species. Here, we investigated interspecific niche differentiation within a complex of cryptic bumblebee species that co-occur extensively in the United Kingdom. We compared the interspecific variation along different niche dimensions, to determine how they partition a niche to avoid competitive exclusion. We studied the species B. cryptarum, B. lucorum, and B. magnus at a single location in the northwest of Scotland throughout the flight season. Using mitochondrial DNA for species identification, we investigated differences in phenology, response to weather variables and forage use. We also estimated niche region and niche overlap between different castes of the three species. Our results show varying levels of niche partitioning between the bumblebee species along three niche dimensions. The species had contrasting phenologies: The phenology of B. magnus was delayed relative to the other two species, while B. cryptarum had a relatively extended phenology, with workers and males more common than B. lucorum early and late in the season. We found divergent thermal specialisation: In contrast to B. cryptarum and B. magnus, B. lucorum worker activity was skewed toward warmer, sunnier conditions, leading to interspecific temporal variation. Furthermore, the three species differentially exploited the available forage plants: In particular, unlike the other two species, B. magnus fed predominantly on species of heather. The results suggest that ecological divergence in different niche dimensions and spatio-temporal heterogeneity in the environment may contribute to the persistence of cryptic species in sympatry. Furthermore, our study suggests that cryptic species provide distinct

  1. Cryptic individual scaling relationships and the evolution of morphological scaling.

    PubMed

    Dreyer, Austin P; Saleh Ziabari, Omid; Swanson, Eli M; Chawla, Akshita; Frankino, W Anthony; Shingleton, Alexander W

    2016-08-01

    Morphological scaling relationships between organ and body size-also known as allometries-describe the shape of a species, and the evolution of such scaling relationships is central to the generation of morphological diversity. Despite extensive modeling and empirical tests, however, the modes of selection that generate changes in scaling remain largely unknown. Here, we mathematically model the evolution of the group-level scaling as an emergent property of individual-level variation in the developmental mechanisms that regulate trait and body size. We show that these mechanisms generate a "cryptic individual scaling relationship" unique to each genotype in a population, which determines body and trait size expressed by each individual, depending on developmental nutrition. We find that populations may have identical population-level allometries but very different underlying patterns of cryptic individual scaling relationships. Consequently, two populations with apparently the same morphological scaling relationship may respond very differently to the same form of selection. By focusing on the developmental mechanisms that regulate trait size and the patterns of cryptic individual scaling relationships they produce, our approach reveals the forms of selection that should be most effective in altering morphological scaling, and directs researcher attention on the actual, hitherto overlooked, targets of selection.

  2. Sperm storage mediated by cryptic female choice for nuptial gifts.

    PubMed

    Albo, Maria J; Bilde, Trine; Uhl, Gabriele

    2013-12-07

    Polyandrous females are expected to discriminate among males through postcopulatory cryptic mate choice. Yet, there is surprisingly little unequivocal evidence for female-mediated cryptic sperm choice. In species in which nuptial gifts facilitate mating, females may gain indirect benefits through preferential storage of sperm from gift-giving males if the gift signals male quality. We tested this hypothesis in the spider Pisaura mirabilis by quantifying the number of sperm stored in response to copulation with males with or without a nuptial gift, while experimentally controlling copulation duration. We further assessed the effect of gift presence and copulation duration on egg-hatching success in matings with uninterrupted copulations with gift-giving males. We show that females mated to gift-giving males stored more sperm and experienced 17% higher egg-hatching success, compared with those mated to no-gift males, despite matched copulation durations. Uninterrupted copulations resulted in both increased sperm storage and egg-hatching success. Our study confirms the prediction that the nuptial gift as a male signal is under positive sexual selection by females through cryptic sperm storage. In addition, the gift facilitates longer copulations and increased sperm transfer providing two different types of advantage to gift-giving in males.

  3. Sperm storage mediated by cryptic female choice for nuptial gifts

    PubMed Central

    Albo, Maria J.; Bilde, Trine; Uhl, Gabriele

    2013-01-01

    Polyandrous females are expected to discriminate among males through postcopulatory cryptic mate choice. Yet, there is surprisingly little unequivocal evidence for female-mediated cryptic sperm choice. In species in which nuptial gifts facilitate mating, females may gain indirect benefits through preferential storage of sperm from gift-giving males if the gift signals male quality. We tested this hypothesis in the spider Pisaura mirabilis by quantifying the number of sperm stored in response to copulation with males with or without a nuptial gift, while experimentally controlling copulation duration. We further assessed the effect of gift presence and copulation duration on egg-hatching success in matings with uninterrupted copulations with gift-giving males. We show that females mated to gift-giving males stored more sperm and experienced 17% higher egg-hatching success, compared with those mated to no-gift males, despite matched copulation durations. Uninterrupted copulations resulted in both increased sperm storage and egg-hatching success. Our study confirms the prediction that the nuptial gift as a male signal is under positive sexual selection by females through cryptic sperm storage. In addition, the gift facilitates longer copulations and increased sperm transfer providing two different types of advantage to gift-giving in males. PMID:24266042

  4. Hiding in Plain Sight: A Case for Cryptic Metapopulations in Brook Trout (Salvelinus fontinalis).

    PubMed

    Kazyak, David C; Hilderbrand, Robert H; King, Tim L; Keller, Stephen R; Chhatre, Vikram E

    2016-01-01

    A fundamental issue in the management and conservation of biodiversity is how to define a population. Spatially contiguous fish occupying a stream network have often been considered to represent a single, homogenous population. However, they may also represent multiple discrete populations, a single population with genetic isolation-by-distance, or a metapopulation. We used microsatellite DNA and a large-scale mark-recapture study to assess population structure in a spatially contiguous sample of Brook Trout (Salvelinus fontinalis), a species of conservation concern. We found evidence for limited genetic exchange across small spatial scales and in the absence of barriers to physical movement. Mark-recapture and stationary passive integrated transponder antenna records demonstrated that fish from two tributaries very seldom moved into the opposite tributary, but movements between the tributaries and mainstem were more common. Using Bayesian genetic clustering, we identified two genetic groups that exhibited significantly different growth rates over three years of study, yet survival rates were very similar. Our study highlights the importance of considering the possibility of multiple genetically distinct populations occurring within spatially contiguous habitats, and suggests the existence of a cryptic metapopulation: a spatially continuous distribution of organisms exhibiting metapopulation-like behaviors.

  5. Hiding in Plain Sight: A Case for Cryptic Metapopulations in Brook Trout (Salvelinus fontinalis)

    PubMed Central

    Kazyak, David C.; Hilderbrand, Robert H.; King, Tim L.; Keller, Stephen R.; Chhatre, Vikram E.

    2016-01-01

    A fundamental issue in the management and conservation of biodiversity is how to define a population. Spatially contiguous fish occupying a stream network have often been considered to represent a single, homogenous population. However, they may also represent multiple discrete populations, a single population with genetic isolation-by-distance, or a metapopulation. We used microsatellite DNA and a large-scale mark-recapture study to assess population structure in a spatially contiguous sample of Brook Trout (Salvelinus fontinalis), a species of conservation concern. We found evidence for limited genetic exchange across small spatial scales and in the absence of barriers to physical movement. Mark-recapture and stationary passive integrated transponder antenna records demonstrated that fish from two tributaries very seldom moved into the opposite tributary, but movements between the tributaries and mainstem were more common. Using Bayesian genetic clustering, we identified two genetic groups that exhibited significantly different growth rates over three years of study, yet survival rates were very similar. Our study highlights the importance of considering the possibility of multiple genetically distinct populations occurring within spatially contiguous habitats, and suggests the existence of a cryptic metapopulation: a spatially continuous distribution of organisms exhibiting metapopulation-like behaviors. PMID:26730588

  6. Differential Responses to Woodland Character and Landscape Context by Cryptic Bats in Urban Environments

    PubMed Central

    Lintott, Paul R.; Bunnefeld, Nils; Minderman, Jeroen; Fuentes-Montemayor, Elisa; Mayhew, Rebekah J.; Olley, Lena; Park, Kirsty J.

    2015-01-01

    Urbanisation is one of the most dramatic forms of land use change which relatively few species can adapt to. Determining how and why species respond differently to urban habitats is important in predicting future biodiversity loss as urban areas rapidly expand. Understanding how morphological or behavioural traits can influence species adaptability to the built environment may enable us to improve the effectiveness of conservation efforts. Although many bat species are able to exploit human resources, bat species richness generally declines with increasing urbanisation and there is considerable variation in the responses of different bat species to urbanisation. Here, we use acoustic recordings from two cryptic, and largely sympatric European bat species to assess differential responses in their use of fragmented urban woodland and the surrounding urban matrix. There was a high probability of P. pygmaeus activity relative to P. pipistrellus in woodlands with low clutter and understory cover which were surrounded by low levels of built environment. Additionally, the probability of recording P. pygmaeus relative to P. pipistrellus was considerably higher in urban woodland interior or edge habitat in contrast to urban grey or non-wooded green space. These results show differential habitat use occurring between two morphologically similar species; whilst the underlying mechanism for this partitioning is unknown it may be driven by competition avoidance over foraging resources. Their differing response to urbanisation indicates the difficulties involved when attempting to assess how adaptable a species is to urbanisation for conservation purposes. PMID:25978034

  7. Identification of cryptic species within liverwort Conocephalum conicum based on the volatile components.

    PubMed

    Ludwiczuk, Agnieszka; Odrzykoski, Ireneusz J; Asakawa, Yoshinori

    2013-11-01

    Cryptic speciation refers to cases where species are clearly genetically differentiated, but show little or no morphological differences. This study investigated whether volatile components can be used to distinguish the cryptic species within the Conocephalum conicum complex. Thirteen samples were included in this study representing four cryptic species (A, F, J, L) and the recently described Conocephalum salebrosum (formerly cryptic species S) detected in a worldwide collection. Results received from GC-MS analyses showed some differences between samples, indicating the existence of chemical polymorphism. It is evident from both statistical analyses (CA and PCA), that cryptic species L appears to be the most differentiated species, with the volatile components not significantly shared with the rest of the types. The most characteristic compound of this type is the sesquiterpene alcohol, conocephalenol. Distinction between other examined cryptic species were also indicated. However species F and J, as well as species A and C. salebrosum, share a great similarity in their volatile composition and are grouped together in both CA and PCA. Despite their similarities, we were able to find chemical markers which can describe each species. Cubebol is characteristic for C. salebrosum, while cryptic species A produces (E)-methylcinnamate. The presence of a large amount of the monoterpene hydrocarbon, sabinene, is characteristic for cryptic species J. In one of the analyzed specimens belonging to the cryptic species F, a large amount of cyclocolorenone was detected. Chemical differentiation was correlated with the geographical distribution of the analyzed samples.

  8. Mitochondrial DNA sequences support allozyme evidence for cryptic radiation of New Zealand Peripatoides (Onychophora).

    PubMed

    Trewick, S A

    2000-03-01

    A combination of single-strand conformation polymorphism analysis (SSCP) and sequencing were used to survey cytochrome oxidase I (COI) mitochondrial DNA (mtDNA) diversity among New Zealand ovoviviparous Onychophora. Most of the sites and individuals had previously been analysed using allozyme electrophoresis. A total of 157 peripatus collected at 54 sites throughout New Zealand were screened yielding 62 different haplotypes. Comparison of 540-bp COI sequences from Peripatoides revealed mean among-clade genetic distances of up to 11. 4% using Kimura 2-parameter (K2P) analysis or 17.5% using general time-reversible (GTR + I + Gamma) analysis. Phylogenetic analysis revealed eight well-supported clades that were consistent with the allozyme analysis. Five of the six cryptic peripatus species distinguished by allozymes were confirmed by mtDNA analysis. The sixth taxon appeared to be paraphyletic, but genetic and geographical evidence suggested recent speciation. Two additional taxa were evident from the mtDNA data but neither occurred within the areas surveyed using allozymes. Among the peripatus surveyed with both mtDNA and allozymes, only one clear instance of recent introgression was evident, even though several taxa occurred in sympatry. This suggests well-developed mate recognition despite minimal morphological variation and low overall genetic diversity.

  9. Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity.

    PubMed

    Kumar, Atul; Chaugule, Viduth K; Condos, Tara E C; Barber, Kathryn R; Johnson, Clare; Toth, Rachel; Sundaramoorthy, Ramasubramanian; Knebel, Axel; Shaw, Gary S; Walden, Helen

    2017-05-01

    RING-between-RING (RBR) E3 ligases are a class of ubiquitin ligases distinct from RING or HECT E3 ligases. An important RBR ligase is Parkin, mutations in which lead to early-onset hereditary Parkinsonism. Parkin and other RBR ligases share a catalytic RBR module but are usually autoinhibited and activated via distinct mechanisms. Recent insights into Parkin regulation predict large, unknown conformational changes during Parkin activation. However, current data on active RBR ligases reflect the absence of regulatory domains. Therefore, it remains unclear how individual RBR ligases are activated, and whether they share a common mechanism. We now report the crystal structure of a human Parkin-phosphoubiquitin complex, which shows that phosphoubiquitin binding induces movement in the 'in-between RING' (IBR) domain to reveal a cryptic ubiquitin-binding site. Mutation of this site negatively affects Parkin's activity. Furthermore, ubiquitin binding promotes cooperation between Parkin molecules, which suggests a role for interdomain association in the RBR ligase mechanism.

  10. First description of a new cryptic species, Simulium vanluni from Peninsular Malaysia: An integrated morpho-taxonomical and genetic approach for naming cryptic species in the family Simuliidae.

    PubMed

    Ya'cob, Zubaidah; Takaoka, Hiroyuki; Low, Van Lun; Sofian-Azirun, Mohd

    2017-03-01

    In recent decades, the numbers of cryptic taxa have increased significantly with current progress in DNA barcoding, yet, most of these cryptic taxa have not been formally named and recognized as valid species. To address this issue, we provide a guide for applying the procedure of describing new cryptic species in the family Simuliidae. Simulium (Simulium) vanluni from Pahang, Peninsular Malaysia, previously treated as S. nobile De Meijere, is described as a new species by using an integrated morpho-taxonomical and genetic approach. This new species is morphologically identical to S. nobile from Java and S. kiuliense Smart & Clifford from Borneo, but their distinctiveness is supported by an expanded multigene phylogeny analysis.

  11. Diagnostic description and geographic distribution of four new cryptic species of the blue-spotted maskray species complex (Myliobatoidei: Dasyatidae; Neotrygon spp.) based on DNA sequences

    NASA Astrophysics Data System (ADS)

    Borsa, Philippe; Arlyza, Irma S.; Hoareau, Thierry B.; Shen, Kang-Ning

    2017-08-01

    Nine morphologically similar but genetically distinct lineages in the blue-spotted maskray species complex, previously Neotrygon kuhlii (Müller and Henle) qualify as cryptic species. Four of these lineages have been previously described as Neotrygon australiae Last, White and Séret, Neotrygon caeruleopunctata Last, White and Séret, Neotrygon orientale Last, White and Séret, and Neotrygon varidens (Garman), but the morphological characters used in the descriptions offered poor diagnoses and their geographic distributions were not delineated precisely. The objective of the present work is to complete the description of the cryptic species in the complex. Here, an additional four lineages are described as new species on the basis of their mitochondrial DNA sequences: Neotrygon bobwardi, whose distribution extends from the northern tip of Aceh to the western coast of Sumatera; Neotrygon malaccensis, sampled from the eastern part of the Andaman Sea and from the Malacca Strait; Neotrygon moluccensis, from the eastern half of the Banda Sea; and Neotrygon westpapuensis from the central portion of northern West Papua. The geographic distributions of N. australiae, N. coeruleopunctata, N. orientale, and N. varidens are updated. For each species, a diagnosis is provided in the form of a combination of private or partly-private nucleotides at 2-4 nucleotide sites along a 519-base pair fragment of the CO1 gene. We believe that the present taxonomic revision will provide information relevant to the sound management and conservation of cryptic species of the blue-spotted maskray in the Coral Triangle region.

  12. Cold adaptation regulated by cryptic prophage excision in Shewanella oneidensis

    PubMed Central

    Zeng, Zhenshun; Liu, Xiaoxiao; Yao, Jianyun; Guo, Yunxue; Li, Baiyuan; Li, Yangmei; Jiao, Nianzhi; Wang, Xiaoxue

    2016-01-01

    Among the environmental stresses experienced by bacteria, temperature shifts are one of the most important. In this study, we discovered a novel cold adaptation mechanism in Shewanella oneidensis that occurs at the DNA level and is regulated by cryptic prophage excision. Previous studies on bacterial cold tolerance mainly focus on the structural change of cell membrane and changes at the RNA and protein levels. Whether or not genomic change can also contribute to this process has not been explored. Here we employed a whole-genome deep-sequencing method to probe the changes at DNA level in a model psychrotrophic bacteria strain. We found that temperature downshift induced a 10 000-fold increase of the excision of a novel P4-like cryptic prophage. Importantly, although prophage excision only occurred in a relatively small population of bacteria, it was able to facilitate biofilm formation and promote the survival of the entire population. This prophage excision affected cell physiology by disrupting a critical gene encoding transfer-messenger RNA (tmRNA). In addition, we found that the histone-like nucleoid-structuring protein (H-NS) could silence prophage excision via binding to the promoter of the putative excisionase gene at warm temperatures. H-NS level was reduced at cold temperatures, leading to de-repression of prophage excision. Collectively, our results reveal that cryptic prophage excision acts as a regulatory switch to enable the survival of the host at low temperature by controlling the activity of tmRNA and biofilm formation. PMID:27482926

  13. Cold adaptation regulated by cryptic prophage excision in Shewanella oneidensis.

    PubMed

    Zeng, Zhenshun; Liu, Xiaoxiao; Yao, Jianyun; Guo, Yunxue; Li, Baiyuan; Li, Yangmei; Jiao, Nianzhi; Wang, Xiaoxue

    2016-12-01

    Among the environmental stresses experienced by bacteria, temperature shifts are one of the most important. In this study, we discovered a novel cold adaptation mechanism in Shewanella oneidensis that occurs at the DNA level and is regulated by cryptic prophage excision. Previous studies on bacterial cold tolerance mainly focus on the structural change of cell membrane and changes at the RNA and protein levels. Whether or not genomic change can also contribute to this process has not been explored. Here we employed a whole-genome deep-sequencing method to probe the changes at DNA level in a model psychrotrophic bacteria strain. We found that temperature downshift induced a 10 000-fold increase of the excision of a novel P4-like cryptic prophage. Importantly, although prophage excision only occurred in a relatively small population of bacteria, it was able to facilitate biofilm formation and promote the survival of the entire population. This prophage excision affected cell physiology by disrupting a critical gene encoding transfer-messenger RNA (tmRNA). In addition, we found that the histone-like nucleoid-structuring protein (H-NS) could silence prophage excision via binding to the promoter of the putative excisionase gene at warm temperatures. H-NS level was reduced at cold temperatures, leading to de-repression of prophage excision. Collectively, our results reveal that cryptic prophage excision acts as a regulatory switch to enable the survival of the host at low temperature by controlling the activity of tmRNA and biofilm formation.

  14. Cryptic species of planktonic foraminifera: their effect on palaeoceanographic reconstructions.

    PubMed

    Kucera, Michal; Darling, Kate F

    2002-04-15

    Shells of planktonic foraminifera recovered from marine sediments provide a multitude of important palaeoproxies. Most of these proxies are based on the assumption that each morphospecies of planktonic foraminifera represents a genetically continuous species with a unique habitat. Recent discovery of hitherto hidden genetic diversity among modern planktonic foraminifera has significant repercussions on palaeoproxies derived from their fossil shells. We have compiled all available data on this genetic diversity. To date, 33 cryptic genetic types were found in 9 out of the 22 sequenced morphospecies of modern planktonic foraminifera. An examination of this database suggests that cryptic genetic diversity may be a prevalent pattern among modern planktonic foraminifera, but that the total number of cryptic genetic types per morphospecies is not large and that most genetic types show a non-random pattern of distribution in the oceans. Using modern distribution data from the Atlantic Ocean as constraints, the relationship between abundances of three genetic types of Globigerina bulloides and sea-surface temperature has been modelled and this model has been applied to a database of species counts in Atlantic coretops (761 samples). Trials with artificial neural networks (ANNs), the modern analogue technique and Imbrie-Kipp transfer functions showed that the splitting of G. bulloides into three genetic types resulted in substantial reduction in the prediction error rate (by 5 to 34%) and that this improvement was by far greatest in ANN trials (on average more than 20%). We conclude that such a large reduction in error rate occurred because the models resonated with a real pattern in the original data. This study indicates that genetic diversity among planktonic foraminifera may become more of a gift than malaise to palaeoproxies. If it becomes possible to distinguish these genetic types in the fossil record, the accuracy of proxies based on planktonic foraminifera will

  15. What we don't recognize can hurt us: a plea for awareness about cryptic species.

    PubMed

    de León, Gerardo Pérez-Ponce; Nadler, Steven A

    2010-04-01

    We conducted an extensive literature review on studies that have used DNA sequences to detect cryptic species of parasites during the last decade. Each literature citation that included the term "cryptic" or "sibling" species was analyzed to determine the approach used by the author(s). Reports were carefully filtered to retain only those that recognized the existence of cryptic species centered on the use of DNA sequences. Based on analysis of these papers, we comment on the different ways that parasite cryptic species are discovered in studies focusing on different aspects of the host-parasite relationship, or disciplines, within parasitology. We found a lack of methodological and theoretical uniformity in the discipline for finding and delimiting cryptic species, and we draw attention to the need for standardizing these approaches. We suggest that cryptic species, in the strict sense, are always provisionally cryptic, in that the possibility does exist that new morphological studies or techniques will reveal previously unknown diagnostic structural differences which will permit rapid and practical morphological diagnosis. To avoid future taxonomic confusion, we recommend that parasitologists describe (and formally name) cryptic species following standard taxonomic practice.

  16. Complete sequence of a cryptic virus from hemp (Cannabis sativa).

    PubMed

    Ziegler, Angelika; Matoušek, Jaroslav; Steger, Gerhard; Schubert, Jörg

    2012-02-01

    Hemp (Cannabis sativa) was found to be a useful propagation host for hop latent virus, a carlavirus. However, when virus preparations were analysed by electron microscopy, along with the expected filamentous particles, spherical particles with a diameter of around 34 nm were found. RNA from virus preparations was purified, and cDNA was prepared and cloned. Sequence information was used to search databases, and the greatest similarity was found with Primula malacoides virus 1, a putative new member of the genus Partitivirus. The full sequences of RNA 1 and RNA 2 of this new hemp cryptic virus were obtained.

  17. Conformal Vortex Crystals.

    PubMed

    Menezes, Raí M; Silva, Clécio C de Souza

    2017-10-06

    We investigate theoretically globally nonuniform configurations of quantized-flux vortices in clean superconductors trapped by an external force field that induces a nonuniform vortex density profile. Using an extensive series of numerical simulations, we demonstrate that, for suitable choices of the force field, and bellow a certain transition temperature, the vortex system self-organizes into highly inhomogeneous conformal crystals in a way as to minimize the total energy. These nonuniform structures are topologically ordered and can be mathematically mapped into a triangular Abrikosov lattice via a conformal transformation. Above the crystallization temperature, the conformal vortex crystal becomes unstable and gives place to a nonuniform polycrystalline structure. We propose a simple method to engineer the potential energy profile necessary for the observation of conformal crystals of vortices, which can also be applied to other 2D particle systems, and suggest possible experiments in which conformal or quasi-conformal vortex crystals could be observed in bulk superconductors and in thin films.

  18. Cryptic habitats and cryptic diversity: unexpected patterns of connectivity and phylogeographical breaks in a Mediterranean endemic marine cave mysid.

    PubMed

    Rastorgueff, Pierre-Alexandre; Chevaldonné, Pierre; Arslan, Defne; Verna, Caroline; Lejeusne, Christophe

    2014-06-01

    The marine cave-dwelling mysid Hemimysis margalefi is distributed over the whole Mediterranean Sea, which contrasts with the poor dispersal capabilities of this brooding species. In addition, underwater marine caves are a highly fragmented habitat which further promotes strong genetic structuring, therefore providing highly informative data on the levels of marine population connectivity across biogeographical regions. This study investigates how habitat and geography have shaped the connectivity network of this poor disperser over the entire Mediterranean Sea through the use of several mitochondrial and nuclear markers. Five deeply divergent lineages were observed among H. margalefi populations resulting from deep phylogeographical breaks, some dating back to the Oligo-Miocene. Whether looking at the intralineage or interlineage levels, H. margalefi populations present a high genetic diversity and population structuring. This study suggests that the five distinct lineages observed in H. margalefi actually correspond to as many separate cryptic taxa. The nominal species, H. margalefi sensu stricto, corresponds to the westernmost lineage here surveyed from the Alboran Sea to southeastern Italy. Typical genetic breaks such as the Almeria-Oran Front or the Siculo-Tunisian Strait do not appear to be influential on the studied loci in H. margalefi sensu stricto. Instead, population structuring appears more complex and subtle than usually found for model species with a pelagic dispersal phase. The remaining four cryptic taxa are all found in the eastern basin, but incomplete lineage sorting is suspected and speciation might still be in process. Present-day population structure of the different H. margalefi cryptic species appears to result from past vicariance events started in the Oligo-Miocene and maintained by present-day coastal topography, water circulation and habitat fragmentation.

  19. The Conformal Bootstrap

    NASA Astrophysics Data System (ADS)

    Simmons-Duffin, David

    These notes are from courses given at TASI and the Advanced Strings School in summer 2015. Starting from principles of quantum field theory and the assumption of a traceless stress tensor, we develop the basics of conformal field theory, including conformal Ward identities, radial quantization, reection positivity, the operator product expansion, and conformal blocks. We end with an introduction to numerical bootstrap methods, focusing on the 2d and 3d Ising models.

  20. Allopatric speciation within a cryptic species complex of Australasian octopuses.

    PubMed

    Amor, Michael D; Norman, Mark D; Cameron, Hayley E; Strugnell, Jan M

    2014-01-01

    Despite extensive revisions over recent decades, the taxonomy of benthic octopuses (Family Octopodidae) remains in a considerable flux. Among groups of unresolved status is a species complex of morphologically similar shallow-water octopods from subtropical Australasia, including: Allopatric populations of Octopus tetricus on the eastern and western coasts of Australia, of which the Western Australian form is speculated to be a distinct or sub-species; and Octopus gibbsi from New Zealand, a proposed synonym of Australian forms. This study employed a combination of molecular and morphological techniques to resolve the taxonomic status of the 'tetricus complex'. Phylogenetic analyses (based on five mitochondrial genes: 12S rRNA, 16S rRNA, COI, COIII and Cytb) and Generalised Mixed Yule Coalescent (GMYC) analysis (based on COI, COIII and Cytb) distinguished eastern and Western Australian O. tetricus as distinct species, while O. gibbsi was found to be synonymous with the east Australian form (BS = >97, PP = 1; GMYC p = 0.01). Discrete morphological differences in mature male octopuses (based on sixteen morphological traits) provided further evidence of cryptic speciation between east (including New Zealand) and west coast populations; although females proved less useful in morphological distinction among members of the tetricus complex. In addition, phylogenetic analyses suggested populations of octopuses currently treated under the name Octopus vulgaris are paraphyletic; providing evidence of cryptic speciation among global populations of O. vulgaris, the most commercially valuable octopus species worldwide.

  1. Aspergillus niger contains the cryptic phylogenetic species A. awamori.

    PubMed

    Perrone, Giancarlo; Stea, Gaetano; Epifani, Filomena; Varga, János; Frisvad, Jens C; Samson, Robert A

    2011-11-01

    Aspergillus section Nigri is an important group of species for food and medical mycology, and biotechnology. The Aspergillus niger 'aggregate' represents its most complicated taxonomic subgroup containing eight morphologically indistinguishable taxa: A. niger, Aspergillus tubingensis, Aspergillus acidus, Aspergillus brasiliensis, Aspergillus costaricaensis, Aspergillus lacticoffeatus, Aspergillus piperis, and Aspergillus vadensis. Aspergillus awamori, first described by Nakazawa, has been compared taxonomically with other black aspergilli and recently it has been treated as a synonym of A. niger. Phylogenetic analyses of sequences generated from portions of three genes coding for the proteins β-tubulin (benA), calmodulin (CaM), and the translation elongation factor-1 alpha (TEF-1α) of a population of A. niger strains isolated from grapes in Europe revealed the presence of a cryptic phylogenetic species within this population, A. awamori. Morphological, physiological, ecological and chemical data overlap occurred between A. niger and the cryptic A. awamori, however the splitting of these two species was also supported by AFLP analysis of the full genome. Isolates in both phylospecies can produce the mycotoxins ochratoxin A and fumonisin B₂, and they also share the production of pyranonigrin A, tensidol B, funalenone, malformins, and naphtho-γ-pyrones. In addition, sequence analysis of four putative A. awamori strains from Japan, used in the koji industrial fermentation, revealed that none of these strains belong to the A. awamori phylospecies.

  2. Long-Term Coexistence of Rotifer Cryptic Species

    PubMed Central

    Serra, Manuel; Gómez, Africa

    2011-01-01

    Despite their high morphological similarity, cryptic species often coexist in aquatic habitats presenting a challenge in the framework of niche differentiation theory and coexistence mechanisms. Here we use a rotifer species complex inhabiting highly unpredictable and fluctuating salt lakes to gain insights into the mechanisms involved in stable coexistence in cryptic species. We combined molecular barcoding surveys of planktonic populations and paleogenetic analysis of diapausing eggs to reconstruct the current and historical coexistence dynamics of two highly morphologically similar rotifer species, B. plicatilis and B. manjavacas. In addition, we carried out laboratory experiments using clones isolated from eight lakes where both species coexist to explore their clonal growth responses to salinity, a challenging, highly variable and unpredictable condition in Mediterranean salt lakes. We show that both species have co-occurred in a stable way in one lake, with population fluctuations in which no species was permanently excluded. The seasonal occurrence patterns of the plankton in two lakes agree with laboratory experiments showing that both species differ in their optimal salinity. These results suggest that stable species coexistence is mediated by differential responses to salinity and its fluctuating regime. We discuss the role of fluctuating salinity and a persistent diapausing egg banks as a mechanism for species coexistence in accordance with the ‘storage effect’. PMID:21738691

  3. Minimized state complexity of quantum-encoded cryptic processes

    NASA Astrophysics Data System (ADS)

    Riechers, Paul M.; Mahoney, John R.; Aghamohammadi, Cina; Crutchfield, James P.

    2016-05-01

    The predictive information required for proper trajectory sampling of a stochastic process can be more efficiently transmitted via a quantum channel than a classical one. This recent discovery allows quantum information processing to drastically reduce the memory necessary to simulate complex classical stochastic processes. It also points to a new perspective on the intrinsic complexity that nature must employ in generating the processes we observe. The quantum advantage increases with codeword length: the length of process sequences used in constructing the quantum communication scheme. In analogy with the classical complexity measure, statistical complexity, we use this reduced communication cost as an entropic measure of state complexity in the quantum representation. Previously difficult to compute, the quantum advantage is expressed here in closed form using spectral decomposition. This allows for efficient numerical computation of the quantum-reduced state complexity at all encoding lengths, including infinite. Additionally, it makes clear how finite-codeword reduction in state complexity is controlled by the classical process's cryptic order, and it allows asymptotic analysis of infinite-cryptic-order processes.

  4. Cryptic female preference for colorful males in guppies.

    PubMed

    Pilastro, Andrea; Simonato, Martina; Bisazza, Angelo; Evans, Jonathan P

    2004-03-01

    Cryptic female choice (CFC) refers to female-mediated processes occurring during or after copulation that result in biased sperm use in favor of preferred or compatible males. Despite recent empirical support for this hypothesis, evidence that CFC contributes towards the evolution of male body ornaments, in the same way that precopulatory female choice does, is currently lacking. Here, we tested the possibility that CFC selects for increased male attractiveness in the guppy Poecilia reticulata, a freshwater fish exhibiting internal fertilization. Specifically, we examined whether females are able to manipulate the number of sperm transferred or retained at copulation in favor of relatively attractive males. In support of this prediction, we found that following solicited copulations the number of sperm inseminated is influenced exclusively by the female's perception of relative male coloration, independent of any direct manipulation of males themselves. Because females prefer brightly colored males during precopulatory mate choice, our finding that colorful males are also favored as a consequence of enhanced insemination success indicates that cryptic female choice can reinforce precopulatory preferences for extravagant male ornaments.

  5. Uncovering Cryptic Parasitoid Diversity in Horismenus (Chalcidoidea, Eulophidae)

    PubMed Central

    Hansson, Christer; Alvarez, Nadir; Benrey, Betty

    2015-01-01

    Horismenus parasitoids are an abundant and understudied group of eulophid wasps found mainly in the New World. Recent surveys based on morphological analyses in Costa Rica have quadrupled the number of named taxa, with more than 400 species described so far. This recent revision suggests that there is still a vast number of unknown species to be identified. As Horismenus wasps have been widely described as parasitoids of insect pests associated with crop plants, it is of high importance to properly establish the extant diversity of the genus, in order to provide biological control practitioners with an exhaustive catalog of putative control agents. In this study, we first collected Horismenus wasps from wild Phaseolus bean seeds in Central Mexico and Arizona to assess the genetic relatedness of three morphologically distinct species with overlapping host and geographical ranges. Sequence data from two nuclear and two mitochondrial gene regions uncovered three cryptic species within each of the three focal species (i.e., H. missouriensis, H. depressus and H. butcheri). The monophyly of each cryptic group is statistically supported (except in two of them represented by one single tip in which monophyly cannot be tested). The phylogenetic reconstruction is discussed with respect to differences between gene regions as well as likely reasons for the differences in variability between species. PMID:26352700

  6. Allopatric Speciation within a Cryptic Species Complex of Australasian Octopuses

    PubMed Central

    Amor, Michael D.; Norman, Mark D.; Cameron, Hayley E.; Strugnell, Jan M.

    2014-01-01

    Despite extensive revisions over recent decades, the taxonomy of benthic octopuses (Family Octopodidae) remains in a considerable flux. Among groups of unresolved status is a species complex of morphologically similar shallow-water octopods from subtropical Australasia, including: Allopatric populations of Octopus tetricus on the eastern and western coasts of Australia, of which the Western Australian form is speculated to be a distinct or sub-species; and Octopus gibbsi from New Zealand, a proposed synonym of Australian forms. This study employed a combination of molecular and morphological techniques to resolve the taxonomic status of the ‘tetricus complex’. Phylogenetic analyses (based on five mitochondrial genes: 12S rRNA, 16S rRNA, COI, COIII and Cytb) and Generalised Mixed Yule Coalescent (GMYC) analysis (based on COI, COIII and Cytb) distinguished eastern and Western Australian O. tetricus as distinct species, while O. gibbsi was found to be synonymous with the east Australian form (BS = >97, PP = 1; GMYC p = 0.01). Discrete morphological differences in mature male octopuses (based on sixteen morphological traits) provided further evidence of cryptic speciation between east (including New Zealand) and west coast populations; although females proved less useful in morphological distinction among members of the tetricus complex. In addition, phylogenetic analyses suggested populations of octopuses currently treated under the name Octopus vulgaris are paraphyletic; providing evidence of cryptic speciation among global populations of O. vulgaris, the most commercially valuable octopus species worldwide. PMID:24964133

  7. Monitoring cryptic amphibians and reptiles in a Florida state park.

    PubMed

    Engeman, Richard M; Meshaka, Walter E; Severson, Robert; Severson, Mary Ann; Kaufman, Greg; Groninger, N Paige; Smith, Henry T

    2016-04-01

    We monitored cryptic herpetofauna at Savannas Preserve State Park, Florida, by combining artificial cover counts with a quantitative paradigm for constructing and calculating population indices. Weekly indices were calculated from two consecutive days of data collection each week for 7 months from mid-winter to mid-summer in three habitats. Seventeen species were observed at least once, and time trends using index values were followed for six species. Among these, abundance and seasonal pattern information were obtained for an exotic species (greenhouse frog) and a species identified by the Florida Committee on Rare and Endangered Plants and Animals as threatened (Florida scrub lizard). We identified winter as the optimal time in this area to monitor populations for conducting annual assessments. This combined observation and indexing approach could provide managers or researchers with an economical means to quantitatively index population trends for multiple cryptic herpetofauna species simultaneously. Using artificial cover to sample within a population indexing design can be generalized beyond monitoring herpetofauna. Other forms of artificial cover that can be used as observation stations include aquatic artificial substrates, artificial tree cavities, artificial reefs, and other artificial aquatic structures and artificial sea grass units, among many others, and a wide range of taxa are suitable for population monitoring using artificial cover as observation stations in the approach we present, including insects, soil invertebrates, micro and macro aquatic invertebrates, fish, crustaceans, and small mammals.

  8. Placing an upper limit on cryptic marine sulphur cycling.

    PubMed

    Johnston, D T; Gill, B C; Masterson, A; Beirne, E; Casciotti, K L; Knapp, A N; Berelson, W

    2014-09-25

    A quantitative understanding of sources and sinks of fixed nitrogen in low-oxygen waters is required to explain the role of oxygen-minimum zones (OMZs) in controlling the fixed nitrogen inventory of the global ocean. Apparent imbalances in geochemical nitrogen budgets have spurred numerous studies to measure the contributions of heterotrophic and autotrophic N2-producing metabolisms (denitrification and anaerobic ammonia oxidation, respectively). Recently, 'cryptic' sulphur cycling was proposed as a partial solution to the fundamental biogeochemical problem of closing marine fixed-nitrogen budgets in intensely oxygen-deficient regions. The degree to which the cryptic sulphur cycle can fuel a loss of fixed nitrogen in the modern ocean requires the quantification of sulphur recycling in OMZ settings. Here we provide a new constraint for OMZ sulphate reduction based on isotopic profiles of oxygen ((18)O/(16)O) and sulphur ((33)S/(32)S, (34)S/(32)S) in seawater sulphate through oxygenated open-ocean and OMZ-bearing water columns. When coupled with observations and models of sulphate isotope dynamics and data-constrained model estimates of OMZ water-mass residence time, we find that previous estimates for sulphur-driven remineralization and loss of fixed nitrogen from the oceans are near the upper limit for what is possible given in situ sulphate isotope data.

  9. Cryptic diversity in vertebrates: molecular data double estimates of species diversity in a radiation of Australian lizards (Diplodactylus, Gekkota)

    PubMed Central

    Oliver, Paul M.; Adams, Mark; Lee, Michael S.Y.; Hutchinson, Mark N.; Doughty, Paul

    2009-01-01

    A major problem for biodiversity conservation and management is that a significant portion of species diversity remains undocumented (the ‘taxonomic impediment’). This problem is widely acknowledged to be dire among invertebrates and in developing countries; here, we demonstrate that it can be acute even in conspicuous animals (reptiles) and in developed nations (Australia). A survey of mtDNA, allozyme and chromosomal variation in the Australian gecko, genus Diplodactylus, increases overall species diversity estimates from 13 to 29. Four nominal species each actually represent multi-species complexes; three of these species complexes are not even monophyletic. The high proportion of cryptic species discovered emphasizes the importance of continuing detailed assessments of species diversity, even in apparently well-known taxa from industrialized countries. PMID:19324781

  10. Synergistic requirement of orphan nonamer-like elements and DNA bending enhanced by HMGB1 for RAG-mediated nicking at cryptic 12-RSS but not authentic 12-RSS.

    PubMed

    Numata, Masashi; Nagata, Kyosuke

    2011-08-01

    V(D)J recombination is initiated by the specific binding of the recombination activating gene (RAG) complex to the heptamer and nonamer elements within recombination signal sequence (RSS). The break points associated with some chromosomal translocations contain cryptic RSSs, and mistargeting of RAG proteins to these less conserved elements could contribute to an aberrant V(D)J recombination. Recently, we found RAG-dependent recombination in the hotspots of TEL-AML1 t(12;21)(p13;q22) chromosomal translocation by an extrachromosomal recombination assay. Here, we describe using in vitro cleavage assays that RAG proteins directly bind to and introduce nicks into TEL and AML1 translocation regions, which contain several heptamer-like sequences. The cryptic nicking site within the TEL fragment was cleaved by RAG proteins essentially depending on a 12-RSS framework, and the nicking activity was enhanced synergistically by both HMGB1 and orphan nonamer-like (NL) sequences, which do not possess counterpart heptamers. In addition, we found that DNA bending stimulated by HMGB1 is indispensable for the HMGB1- and orphan NL element-dependent enhancement of RAG-mediated nicking at the cryptic 12-RSS. Collectively, we would propose the mechanism of HMGB1-dependent enhancement of RAG-mediated nicking at a cryptic RSS through enhanced DNA bending.

  11. Phylogeography of a Morphologically Cryptic Golden Mole Assemblage from South-Eastern Africa

    PubMed Central

    Mynhardt, Samantha; Maree, Sarita; Pelser, Illona; Bennett, Nigel C.; Bronner, Gary N.; Wilson, John W.; Bloomer, Paulette

    2015-01-01

    The Greater Maputaland-Pondoland-Albany (GMPA) region of southern Africa was recently designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa occupying this region may provide insights into the evolution of faunal endemism in south-eastern Africa. Here we investigate the phylogeographic patterns of an understudied small mammal species assemblage (Amblysomus) endemic to the GMPA, to test for cryptic diversity within the genus, and to better understand diversification across the region. We sampled specimens from 50 sites across the distributional range of Amblysomus, with emphasis on the widespread A. hottentotus, to analyse geographic patterns of genetic diversity using mitochondrial DNA (mtDNA) and nuclear intron data. Molecular dating was used to elucidate the evolutionary and phylogeographic history of Amblysomus. Our phylogenetic reconstructions show that A. hottentotus comprises several distinct lineages, or evolutionarily significant units (ESUs), some with restricted geographic ranges and thus worthy of conservation attention. Divergence of the major lineages dated to the early Pliocene, with later radiations in the GMPA during the late-Pliocene to early-Pleistocene. Evolutionary diversification within Amblysomus may have been driven by uplift of the Great Escarpment c. 5–3 million years ago (Ma), habitat changes associated with intensification of the east-west rainfall gradient across South Africa and the influence of subsequent global climatic cycles. These drivers possibly facilitated geographic spread of ancestral lineages, local adaptation and vicariant isolation. Our study adds to growing empirical evidence identifying East and southern Africa as cradles of vertebrate diversity. PMID:26683828

  12. Barcoding of ancient lake ostracods (crustacea) reveals cryptic speciation with extremely low distances.

    PubMed

    Karanovic, Ivana

    2015-01-01

    Ostracods are drastically reduced crustaceans, with never more than eight appendages enclosed between two valves, leaving only a limited number of morphological characters for species delineation. Conservative morphology of characters used to define genera, along with high variability of characters used to define species are creating problems in applying a morphospecies concept. A high intraspecific variability in a Lake Biwa (Japan) endemic, Physocypria biwaensis (Okubo, 1990), has been observed previously but was never studied in detail. Two sympatric forms, differing in pigmentation and size, suggest a presence of reproductive isolation. The aim of this study is to employ molecular and morphometric tools to aid in species delineation within P. biwaensis complex and reconstruct their phylogenetic relationships. A fragment of the mtCOI gene was amplified from 30 specimens, and an additional 37 specimens were studied for morphological characters. Resulting phylogenies showed that each morphologically distinct form is associated with a distinct phylogenetic group based on mtDNA. The average pairwise distance is very low (5%), indicating a recent divergence time. I speculate that there is a possibility that one of them originated in the lake, while the other probably colonized it afterwards. This seems to be supported with an apparent niche partitioning at different depths. In spite of the fact that traditionally used sexual characters are highly variable in these two species, the morphometric analysis of shell and soft part related characters clearly delineates them and suggests that such characters may be useful for future detection of seemingly cryptic ostracod species.

  13. Heterogeneous rates of molecular evolution among cryptic species of the ciliate morphospecies Chilodonella uncinata

    PubMed Central

    Katz, Laura A.; DeBerardinis, Jennifer; Hall, Meaghan S.; Kovner, Alexandra M.; Dunthorn, Micah; Muse, Spencer V.

    2012-01-01

    While molecular analyses have provided insight into the phylogeny of ciliates, the few studies assessing intraspecific variation have largely relied on just a single locus (e.g. nuclear small subunit rDNA (nSSU-rDNA) or mitochondrial cytochrome oxidase I). In this study, we characterize the diversity of several nuclear protein-coding genes plus both nSSU-rDNA and mitochondrial small subunit rDNA (mtSSU-rDNA) of five isolates of the ciliate morphospecies Chilodonella uncinata. Although these isolates have nearly identical nSSU-rDNA sequences, they differ by up to 8.0% in mtSSU-rDNA. Comparative analyses of all loci, including β-tubulin paralogs, indicate a lack of recombination between strains, demonstrating that the morphospecies C. uncinata consists of multiple cryptic species. Further, there is considerable variation in substitution rates among loci as some protein-coding domains are nearly identical between isolates while others differ by up to 13.2% at the amino acid level. Combining insights on macronuclear variation among isolates, the focus of this study, with published data from the micronucleus of two of these isolates indicates that C. uncinata lineages are able to maintain both highly divergent and highly conserved genes within a rapidly evolving germline genome. PMID:22258433

  14. Phylogeography of a Morphologically Cryptic Golden Mole Assemblage from South-Eastern Africa.

    PubMed

    Mynhardt, Samantha; Maree, Sarita; Pelser, Illona; Bennett, Nigel C; Bronner, Gary N; Wilson, John W; Bloomer, Paulette

    2015-01-01

    The Greater Maputaland-Pondoland-Albany (GMPA) region of southern Africa was recently designated as a centre of vertebrate endemism. The phylogeography of the vertebrate taxa occupying this region may provide insights into the evolution of faunal endemism in south-eastern Africa. Here we investigate the phylogeographic patterns of an understudied small mammal species assemblage (Amblysomus) endemic to the GMPA, to test for cryptic diversity within the genus, and to better understand diversification across the region. We sampled specimens from 50 sites across the distributional range of Amblysomus, with emphasis on the widespread A. hottentotus, to analyse geographic patterns of genetic diversity using mitochondrial DNA (mtDNA) and nuclear intron data. Molecular dating was used to elucidate the evolutionary and phylogeographic history of Amblysomus. Our phylogenetic reconstructions show that A. hottentotus comprises several distinct lineages, or evolutionarily significant units (ESUs), some with restricted geographic ranges and thus worthy of conservation attention. Divergence of the major lineages dated to the early Pliocene, with later radiations in the GMPA during the late-Pliocene to early-Pleistocene. Evolutionary diversification within Amblysomus may have been driven by uplift of the Great Escarpment c. 5-3 million years ago (Ma), habitat changes associated with intensification of the east-west rainfall gradient across South Africa and the influence of subsequent global climatic cycles. These drivers possibly facilitated geographic spread of ancestral lineages, local adaptation and vicariant isolation. Our study adds to growing empirical evidence identifying East and southern Africa as cradles of vertebrate diversity.

  15. Molecular phylogeny of Orthetrum dragonflies reveals cryptic species of Orthetrum pruinosum.

    PubMed

    Yong, Hoi Sen; Lim, Phaik-Eem; Tan, Ji; Ng, Yong Foo; Eamsobhana, Praphathip; Suana, I Wayan

    2014-07-03

    Dragonflies of the genus Orthetrum are members of the suborder Anisoptera, family Libellulidae. There are species pairs whose members are not easily separated from each other by morphological characters. In the present study, the DNA nucleotide sequences of mitochondrial and nuclear genes were employed to elucidate the phylogeny and systematics of Orthetrum dragonflies. Phylogenetic analyses could not resolve the various subfamilies of the family Libellulidae unequivocally. The nuclear 28S rRNA gene is highly conserved and could not resolve congeneric species of Orthetrum. Individual mitochondrial genes (COI, COII, and 16S rRNA) and combination of these genes as well as the nuclear ITS1&2 genes clearly differentiate morphologically similar species, such as the reddish species pairs O. chrysis and O. testaceum, and the bluish-coloured species O. glaucum and O. luzonicum. This study also reveals distinct genetic lineages between O. pruinosum schneideri (occurring in Malaysia) and O. pruinosum neglectum (occurring north of Peninsular Malaysia from India to Japan), indicating these taxa are cryptic species.

  16. Exceptionally preserved crustaceans from western Canada reveal a cryptic Cambrian radiation.

    PubMed

    Harvey, Thomas H P; Vélez, Maria I; Butterfield, Nicholas J

    2012-01-31

    The early history of crustaceans is obscured by strong biases in fossil preservation, but a previously overlooked taphonomic mode yields important complementary insights. Here we describe diverse crustacean appendages of Middle and Late Cambrian age from shallow-marine mudstones of the Deadwood Formation in western Canada. The fossils occur as flattened and fragmentary carbonaceous cuticles but provide a suite of phylogenetic and ecological data by virtue of their detailed preservation. In addition to an unprecedented range of complex, largely articulated filtering limbs, we identify at least four distinct types of mandible. Together, these fossils provide the earliest evidence for crown-group branchiopods and total-group copepods and ostracods, extending the respective ranges of these clades back from the Devonian, Pennsylvanian, and Ordovician. Detailed similarities with living forms demonstrate the early origins and subsequent conservation of various complex food-handling adaptations, including a directional mandibular asymmetry that has persisted through half a billion years of evolution. At the same time, the Deadwood fossils indicate profound secular changes in crustacean ecology in terms of body size and environmental distribution. The earliest radiation of crustaceans is largely cryptic in the fossil record, but "small carbonaceous fossils" reveal organisms of surprisingly modern aspect operating in an unfamiliar biosphere.

  17. Molecular phylogeny of Orthetrum dragonflies reveals cryptic species of Orthetrum pruinosum

    PubMed Central

    Yong, Hoi Sen; Lim, Phaik-Eem; Tan, Ji; Ng, Yong Foo; Eamsobhana, Praphathip; Suana, I. Wayan

    2014-01-01

    Dragonflies of the genus Orthetrum are members of the suborder Anisoptera, family Libellulidae. There are species pairs whose members are not easily separated from each other by morphological characters. In the present study, the DNA nucleotide sequences of mitochondrial and nuclear genes were employed to elucidate the phylogeny and systematics of Orthetrum dragonflies. Phylogenetic analyses could not resolve the various subfamilies of the family Libellulidae unequivocally. The nuclear 28S rRNA gene is highly conserved and could not resolve congeneric species of Orthetrum. Individual mitochondrial genes (COI, COII, and 16S rRNA) and combination of these genes as well as the nuclear ITS1&2 genes clearly differentiate morphologically similar species, such as the reddish species pairs O. chrysis and O. testaceum, and the bluish-coloured species O. glaucum and O. luzonicum. This study also reveals distinct genetic lineages between O. pruinosum schneideri (occurring in Malaysia) and O. pruinosum neglectum (occurring north of Peninsular Malaysia from India to Japan), indicating these taxa are cryptic species. PMID:24989852

  18. Vietnam, a Hotspot for Chromosomal Diversity and Cryptic Species in Black Flies (Diptera: Simuliidae)

    PubMed Central

    Takaoka, Hiroyuki; Sofian-Azirun, Mohd; Low, Van Lun; Ya’cob, Zubaidah; Chen, Chee Dhang; Lau, Koon Weng; Pham, Xuan Da

    2016-01-01

    The increasing attention on Vietnam as a biodiversity hotspot prompted an investigation of the potential for cryptic diversity in black flies, a group well known elsewhere for its high frequency of isomorphic species. We analyzed the banding structure of the larval polytene chromosomes in the Simulium tuberosum species group to probe for diversity beyond the morphological level. Among 272 larvae, 88 different chromosomal rearrangements, primarily paracentric inversions, were discovered in addition to 25 already known in the basic sequences of the group in Asia. Chromosomal diversity in Vietnam far exceeds that known for the group in Thailand, with only about 5% of the rearrangements shared between the two countries. Fifteen cytoforms and nine morphoforms were revealed among six nominal species in Vietnam. Chromosomal evidence, combined with available molecular and morphological evidence, conservatively suggests that at least five of the cytoforms are valid species, two of which require formal names. The total chromosomal rearrangements and species (15) now known from the group in Vietnam far exceed those of any other area of comparable size in the world, supporting the country’s status as a biodiversity hotspot. Phylogenetic inference based on uniquely shared, derived chromosomal rearrangements supports the clustering of cytoforms into two primary lineages, the Simulium tani complex and the Southeast Asian Simulium tuberosum subgroup. Some of these taxa could be threatened by habitat destruction, given their restricted geographical distributions and the expanding human population of Vietnam. PMID:27695048

  19. Vietnam, a Hotspot for Chromosomal Diversity and Cryptic Species in Black Flies (Diptera: Simuliidae).

    PubMed

    Adler, Peter H; Takaoka, Hiroyuki; Sofian-Azirun, Mohd; Low, Van Lun; Ya'cob, Zubaidah; Chen, Chee Dhang; Lau, Koon Weng; Pham, Xuan Da

    2016-01-01

    The increasing attention on Vietnam as a biodiversity hotspot prompted an investigation of the potential for cryptic diversity in black flies, a group well known elsewhere for its high frequency of isomorphic species. We analyzed the banding structure of the larval polytene chromosomes in the Simulium tuberosum species group to probe for diversity beyond the morphological level. Among 272 larvae, 88 different chromosomal rearrangements, primarily paracentric inversions, were discovered in addition to 25 already known in the basic sequences of the group in Asia. Chromosomal diversity in Vietnam far exceeds that known for the group in Thailand, with only about 5% of the rearrangements shared between the two countries. Fifteen cytoforms and nine morphoforms were revealed among six nominal species in Vietnam. Chromosomal evidence, combined with available molecular and morphological evidence, conservatively suggests that at least five of the cytoforms are valid species, two of which require formal names. The total chromosomal rearrangements and species (15) now known from the group in Vietnam far exceed those of any other area of comparable size in the world, supporting the country's status as a biodiversity hotspot. Phylogenetic inference based on uniquely shared, derived chromosomal rearrangements supports the clustering of cytoforms into two primary lineages, the Simulium tani complex and the Southeast Asian Simulium tuberosum subgroup. Some of these taxa could be threatened by habitat destruction, given their restricted geographical distributions and the expanding human population of Vietnam.

  20. 18 CFR 1309.9 - How does TVA provide financial assistance in conformity with the Act?

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 18 Conservation of Power and Water Resources 2 2011-04-01 2011-04-01 false How does TVA provide financial assistance in conformity with the Act? 1309.9 Section 1309.9 Conservation of Power and Water... financial assistance in conformity with the Act? (a) TVA contributes financial assistance only...

  1. 18 CFR 1309.9 - How does TVA provide financial assistance in conformity with the Act?

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false How does TVA provide financial assistance in conformity with the Act? 1309.9 Section 1309.9 Conservation of Power and Water... financial assistance in conformity with the Act? (a) TVA contributes financial assistance only...

  2. Collections Conservation.

    ERIC Educational Resources Information Center

    DeCandido, Robert

    Collections conservation is an approach to the preservation treatment of books and book-like materials that is conceptualized and organized in terms of large groups of materials. This guide is intended to enable a library to evaluate its current collections conservation activities. The introduction describes collections conservation and gives…

  3. [Dosimetric evaluation of conformal radiotherapy: conformity factor].

    PubMed

    Oozeer, R; Chauvet, B; Garcia, R; Berger, C; Felix-Faure, C; Reboul, F

    2000-01-01

    The aim of three-dimensional conformal therapy (3DCRT) is to treat the Planning Target Volume (PTV) to the prescribed dose while reducing doses to normal tissues and critical structures, in order to increase local control and reduce toxicity. The evaluation tools used for optimizing treatment techniques are three-dimensional visualization of dose distributions, dose-volume histograms, tumor control probabilities (TCP) and normal tissue complication probabilities (NTCP). These tools, however, do not fully quantify the conformity of dose distributions to the PTV. Specific tools were introduced to measure this conformity for a given dose level. We have extended those definitions to different dose levels, using a conformity index (CI). CI is based on the relative volumes of PTV and outside the PTV receiving more than a given dose. This parameter has been evaluated by a clinical study including 82 patients treated for lung cancer and 82 patients treated for prostate cancer. The CI was low for lung dosimetric studies (0.35 at the prescribed dose 66 Gy) due to build-up around the GTV and to spinal cord sparing. For prostate dosimetric studies, the CI was higher (0.57 at the prescribed dose 70 Gy). The CI has been used to compare treatment plans for lung 3DCRT (2 vs 3 beams) and prostate 3DCRT (4 vs 7 beams). The variation of CI with dose can be used to optimize dose prescription.

  4. Conformations of Substituted Ethanes.

    ERIC Educational Resources Information Center

    Kingsbury, Charles A.

    1979-01-01

    Reviews state-of-the-art of conformational analysis and factors which affect it. Emphasizes sp-3 hybridized acrylic molecules. Provides examples on the importance of certain factors in determining conformation. Purpose, is to provide examples for examination questions. (Author/SA)

  5. Conformal differential invariants

    NASA Astrophysics Data System (ADS)

    Kruglikov, Boris

    2017-03-01

    We compute the Hilbert polynomial and the Poincaré function counting the number of fixed jet-order differential invariants of conformal metric structures modulo local diffeomorphisms, and we describe the field of rational differential invariants separating generic orbits of the diffeomorphism pseudogroup action. This resolves the local recognition problem for conformal structures.

  6. Conformations of Substituted Ethanes.

    ERIC Educational Resources Information Center

    Kingsbury, Charles A.

    1979-01-01

    Reviews state-of-the-art of conformational analysis and factors which affect it. Emphasizes sp-3 hybridized acrylic molecules. Provides examples on the importance of certain factors in determining conformation. Purpose, is to provide examples for examination questions. (Author/SA)

  7. CONSENSUS AND CONFORMITY.

    ERIC Educational Resources Information Center

    ALLEN, VERNON L.; LEVINE, JOHN M.

    IN THIS STUDY, PROFESSOR ALLEN EMPLOYS TWO METHODS OF BREAKING GROUP CONSENSUS, AND HE MEASURES THE EFFECTS ON THE RESPONSES OF COLLEGE SUBJECTS TO BOTH OBJECTIVE AND SUBJECTIVE STIMULI. THE RESULTS SUGGEST THE NEED FOR MODIFICATION OF EXISTING THEORIES OF CONFORMITY BEHAVIOR. IN ADDITION, THESE RESULTS EMPHASIZE THE DIFFERENCES IN CONFORMITY OF…

  8. Conformity index: a review.

    PubMed

    Feuvret, Loïc; Noël, Georges; Mazeron, Jean-Jacques; Bey, Pierre

    2006-02-01

    We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear.

  9. Conformity index: A review

    SciTech Connect

    Feuvret, Loic . E-mail: loic.feuvret@cpo.curie.net; Noel, Georges; Mazeron, Jean-Jacques; Bey, Pierre

    2006-02-01

    We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear.

  10. Effects of cryptic mortality and the hidden costs of using length limits in fishery management

    USGS Publications Warehouse

    Coggins, L.G.; Catalano, M.J.; Allen, M.S.; Pine, William E.; Walters, C.J.

    2007-01-01

    Fishery collapses cause substantial economic and ecological harm, but common management actions often fail to prevent overfishing. Minimum length limits are perhaps the most common fishing regulation used in both commercial and recreational fisheries, but their conservation benefits can be influenced by discard mortality of fish caught and released below the legal length. We constructed a computer model to evaluate how discard mortality could influence the conservation utility of minimum length regulations. We evaluated policy performance across two disparate fish life-history types: short-lived high-productivity (SLHP) and long-lived low-productivity (LLLP) species. For the life-history types, fishing mortality rates and minimum length limits that we examined, length limits alone generally failed to achieve sustainability when discard mortality rate exceeded about 0.2 for SLHP species and 0.05 for LLLP species. At these levels of discard mortality, reductions in overall fishing mortality (e.g. lower fishing effort) were required to prevent recruitment overfishing if fishing mortality was high. Similarly, relatively low discard mortality rates (>0.05) rendered maximum yield unobtainable and caused a substantial shift in the shape of the yield response surfaces. An analysis of fishery efficiency showed that length limits caused the simulated fisheries to be much less efficient, potentially exposing the target species and ecosystem to increased negative effects of the fishing process. Our findings suggest that for overexploited fisheries with moderate-to-high discard mortality rates, reductions in fishing mortality will be required to meet management goals. Resource managers should carefully consider impacts of cryptic mortality sources (e.g. discard mortality) on fishery sustainability, especially in recreational fisheries where release rates are high and effort is increasing in many areas of the world. ?? 2007 Blackwell Publishing Ltd.

  11. Cosmological particle creation in conformal gravity

    NASA Astrophysics Data System (ADS)

    Berezin, Victor; Dokuchaev, Vyacheslav; Eroshenko, Yury

    2016-10-01

    We constructed the conformally invariant model for scalar particle creation induced by strong gravitational fields. Starting from the "usual" hydrodynamical description of the particle motion written in the Eulerian coordinates we substituted the particle number conservation law (which enters the formalism) by "the particle creation law", proportional to the square of the Weyl tensor (following the famous result by Ya. B. Zel`dovich and A. A. Starobinsky). Then, demanding the conformal invariance of the whole dynamical system, we have got both the (Weyl)-conformal gravity and the Einstein-Hilbert-dilaton gravity action integral. Thus, we obtained something like the induced gravity suggested first by A. D. Sakharov. It is shown that the resulting system is self-consistent. Some future developments of the theory are discussed in the concluding Chapter.

  12. Causality constraints in conformal field theory

    SciTech Connect

    Hartman, Thomas; Jain, Sachin; Kundu, Sandipan

    2016-05-17

    Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well known sign constraint on the (Φ)4 coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. As a result, our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinning operators

  13. Causality constraints in conformal field theory

    NASA Astrophysics Data System (ADS)

    Hartman, Thomas; Jain, Sachin; Kundu, Sandipan

    2016-05-01

    Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well known sign constraint on the (∂ ϕ)4 coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. Our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinning operators.

  14. Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

    PubMed Central

    Sheppard, Samuel K; Cheng, Lu; Méric, Guillaume; de Haan, Caroline P A; Llarena, Ann-Katrin; Marttinen, Pekka; Vidal, Ana; Ridley, Anne; Clifton-Hadley, Felicity; Connor, Thomas R; Strachan, Norval J C; Forbes, Ken; Colles, Frances M; Jolley, Keith A; Bentley, Stephen D; Maiden, Martin C J; Hänninen, Marja-Liisa; Parkhill, Julian; Hanage, William P; Corander, Jukka

    2014-01-01

    Homologous recombination between bacterial strains is theoretically capable of preventing the separation of daughter clusters, and producing cohesive clouds of genotypes in sequence space. However, numerous barriers to recombination are known. Barriers may be essential such as adaptive incompatibility, or ecological, which is associated with the opportunities for recombination in the natural habitat. Campylobacter jejuni is a gut colonizer of numerous animal species and a major human enteric pathogen. We demonstrate that the two major generalist lineages of C. jejuni do not show evidence of recombination with each other in nature, despite having a high degree of host niche overlap and recombining extensively with specialist lineages. However, transformation experiments show that the generalist lineages readily recombine with one another in vitro. This suggests ecological rather than essential barriers to recombination, caused by a cryptic niche structure within the hosts. PMID:24689900

  15. Mitochondrial DNA data reveal cryptic species within Taenia krabbei.

    PubMed

    Lavikainen, Antti; Haukisalmi, Voitto; Lehtinen, Markus J; Laaksonen, Sauli; Holmström, Sauli; Isomursu, Marja; Oksanen, Antti; Meri, Seppo

    2010-06-01

    Cysticerci of Taenia sp. from two elks (Alces alces) in Finland were characterized using morphological criteria and sequences of two mitochondrial DNA regions. The host species, size, structure and location of the cysticerci indicated that they might belong to Taenia krabbei, a circumpolar species occurring in a sylvatic life cycle in wild canids and cervids. Based on the number, length and shape of the rostellar hooks, the specimens could not be unambiguously defined as belonging to T. krabbei, T. cervi, T. ovis or T. solium. In the phylogenetic analysis, based on mitochondrial nucleotide sequence data, Taenia sp. was placed as a sister species of T. solium, distant from T. krabbei isolates previously characterized from Svalbard. This indicates that the Finnish and the Svalbard isolates, resembling T. krabbei, cannot represent a single species. The results suggest that careful morphological and genetic analyses of further isolates from intermediate and definitive hosts are required to define the taxonomic status of these two cryptic species.

  16. Genomic footprints of a cryptic plastid endosymbiosis in diatoms.

    PubMed

    Moustafa, Ahmed; Beszteri, Bánk; Maier, Uwe G; Bowler, Chris; Valentin, Klaus; Bhattacharya, Debashish

    2009-06-26

    Diatoms and other chromalveolates are among the dominant phytoplankters in the world's oceans. Endosymbiosis was essential to the success of chromalveolates, and it appears that the ancestral plastid in this group had a red algal origin via an ancient secondary endosymbiosis. However, recent analyses have turned up a handful of nuclear genes in chromalveolates that are of green algal derivation. Using a genome-wide approach to estimate the "green" contribution to diatoms, we identified >1700 green gene transfers, constituting 16% of the diatom nuclear coding potential. These genes were probably introduced into diatoms and other chromalveolates from a cryptic endosymbiont related to prasinophyte-like green algae. Chromalveolates appear to have recruited genes from the two major existing algal groups to forge a highly successful, species-rich protist lineage.

  17. Ovarian fluid allows directional cryptic female choice despite external fertilization

    PubMed Central

    Alonzo, Suzanne H.; Stiver, Kelly A.; Marsh-Rollo, Susan E.

    2016-01-01

    In species with internal fertilization, females can favour certain males over others, not only before mating but also within the female's reproductive tract after mating. Here, we ask whether such directional post-mating (that is, cryptic) female mate choice can also occur in species with external fertilization. Using an in vitro sperm competition experiment, we demonstrate that female ovarian fluid (ovarian fluid) changes the outcome of sperm competition by decreasing the importance of sperm number thereby increasing the relative importance of sperm velocity. We further show that ovarian fluid does not differentially affect sperm from alternative male phenotypes, but generally enhances sperm velocity, motility, straightness and chemoattraction. Under natural conditions, female ovarian fluid likely increases the paternity of the preferred parental male phenotype, as these males release fewer but faster sperm. These results imply females have greater control over fertilization and potential to exert selection on males in species with external fertilization than previously thought possible. PMID:27529581

  18. Ovarian fluid allows directional cryptic female choice despite external fertilization.

    PubMed

    Alonzo, Suzanne H; Stiver, Kelly A; Marsh-Rollo, Susan E

    2016-08-16

    In species with internal fertilization, females can favour certain males over others, not only before mating but also within the female's reproductive tract after mating. Here, we ask whether such directional post-mating (that is, cryptic) female mate choice can also occur in species with external fertilization. Using an in vitro sperm competition experiment, we demonstrate that female ovarian fluid (ovarian fluid) changes the outcome of sperm competition by decreasing the importance of sperm number thereby increasing the relative importance of sperm velocity. We further show that ovarian fluid does not differentially affect sperm from alternative male phenotypes, but generally enhances sperm velocity, motility, straightness and chemoattraction. Under natural conditions, female ovarian fluid likely increases the paternity of the preferred parental male phenotype, as these males release fewer but faster sperm. These results imply females have greater control over fertilization and potential to exert selection on males in species with external fertilization than previously thought possible.

  19. Postmating Female Control: 20 Years of Cryptic Female Choice.

    PubMed

    Firman, Renée C; Gasparini, Clelia; Manier, Mollie K; Pizzari, Tommaso

    2017-03-16

    Cryptic female choice (CFC) represents postmating intersexual selection arising from female-driven mechanisms at or after mating that bias sperm use and impact male paternity share. Although biologists began to study CFC relatively late, largely spurred by Eberhard's book published 20 years ago, the field has grown rapidly since then. Here, we review empirical progress to show that numerous female processes offer potential for CFC, from mating through to fertilization, although seldom has CFC been clearly demonstrated. We then evaluate functional implications, and argue that, under some conditions, CFC might have repercussions for female fitness, sexual conflict, and intersexual coevolution, with ramifications for related evolutionary phenomena, such as speciation. We conclude by identifying directions for future research in this rapidly growing field.

  20. Hyper-Cryptic Marine Meiofauna: Species Complexes in Nemertodermatida

    PubMed Central

    Meyer-Wachsmuth, Inga; Curini Galletti, Marco; Jondelius, Ulf

    2014-01-01

    Nemertodermatida are microscopically small, benthic marine worms. Specimens of two nominal species, Sterreria psammicola and Nemertinoides elongatus from 33 locations worldwide were sequenced for three molecular markers. Species delimitation and validation was done using gene trees, haplotype networks and multilocus Bayesian analysis. We found 20 supported species of which nine: Nemertinoides glandulosum n.sp., N. wolfgangi n.sp., Sterreria boucheti n.sp., S. lundini n.sp., S. martindalei n.sp., S. monolithes n.sp., S. papuensis n.sp., S. variabilis n.sp. and S. ylvae n.sp., are described including nucleotide-based diagnoses. The distribution patterns indicate transoceanic dispersal in some of the species. Sympatric species were found in many cases. The high level of cryptic diversity in this meiofauna group implies that marine diversity may be higher than previously estimated. PMID:25225981

  1. Is the Kapuskasing structure the site of a cryptic suture

    NASA Technical Reports Server (NTRS)

    Burke, K.

    1983-01-01

    The demonstration that the Kapuskasing structure involves substantial thrusting of deep continental crustal rocks over shallower continental rocks calls into question an earlier suggestion (by Wilson) that the Circum-Ungaua suture zone continued through the Kapuskasing to join the Penokean fold belt (implying that the Kapuskasing marked the site of what has since come to be called a cryptic suture). Problems are discussed which arose in attempting to reconcile Wilson's idea with data from more recent studies: whether the Kapuskasing and the Thompson belt both mark sutures of about 1700 Ma age; why there is no age difference across the Kapuskasing if it does mark the site of continental collision, and why there is no offset of Superior subprovinces across the Kapuskasing.

  2. Prone Whole-Breast Irradiation Using Three-Dimensional Conformal Radiotherapy in Women Undergoing Breast Conservation for Early Disease Yields High Rates of Excellent to Good Cosmetic Outcomes in Patients With Large and/or Pendulous Breasts

    SciTech Connect

    Bergom, Carmen; Kelly, Tracy; Morrow, Natalya; Wilson, J. Frank; Walker, Alonzo; Xiang Qun; Ahn, Kwang Woo; White, Julia

    2012-07-01

    Purpose: To report our institution's experience using prone positioning for three-dimensional conformal radiotherapy (3D-CRT) to deliver post-lumpectomy whole breast irradiation (WBI) in a cohort of women with large and/or pendulous breasts, to determine the rate of acute and late toxicities and, more specifically, cosmetic outcomes. We hypothesized that using 3D-CRT for WBI in the prone position would reduce or eliminate patient and breast size as negative prognostic indicators for toxicities associated with WBI. Methods and Materials: From 1998 to 2006, 110 cases were treated with prone WBI using 3D-CRT. The lumpectomy, breast target volumes, heart, and lung were contoured on all computed tomography scans. A dose of 45-50 Gy was prescribed to the breast volume using standard fractionation schemes. The planning goals were {>=}95% of prescription to 95% of the breast volume, and 100% of boost dose to 95% of lumpectomy planning target volume. Toxicities and cosmesis were prospectively scored using the Common Terminology Criteria for Adverse Effects Version 3.0 and the Harvard Scale. The median follow-up was 40 months. Results: The median body mass index (BMI) was 33.6 kg/m{sup 2}, and median breast volume was 1396 cm{sup 3}. The worst toxicity encountered during radiation was Grade 3 dermatitis in 5% of our patient population. Moist desquamation occurred in 16% of patients, with only 2% of patients with moist desquamation outside the inframammary/axillary folds. Eleven percent of patients had Grade {>=}2 late toxicities, including Grade 3 induration/fibrosis in 2%. Excellent to good cosmesis was achieved in 89%. Higher BMI was associated with moist desquamation and breast pain, but BMI and breast volume did not impact fibrosis or excellent to good cosmesis. Conclusion: In patients with higher BMI and/or large-pendulous breasts, delivering prone WBI using 3D-CRT results in favorable toxicity profiles and high excellent to good cosmesis rates. Higher BMI was

  3. Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago

    PubMed Central

    Simó-Riudalbas, Marc; Sindaco, Roberto; Santos, Xavier; Fasola, Mauro; Llorente, Gustavo; Razzetti, Edoardo; Carranza, Salvador

    2016-01-01

    Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra’s most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8–54.4%. This has implications in the species’ ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework. PMID:26930572

  4. Unexpectedly High Levels of Cryptic Diversity Uncovered by a Complete DNA Barcoding of Reptiles of the Socotra Archipelago.

    PubMed

    Vasconcelos, Raquel; Montero-Mendieta, Santiago; Simó-Riudalbas, Marc; Sindaco, Roberto; Santos, Xavier; Fasola, Mauro; Llorente, Gustavo; Razzetti, Edoardo; Carranza, Salvador

    2016-01-01

    Few DNA barcoding studies of squamate reptiles have been conducted. Due to the significance of the Socotra Archipelago (a UNESCO Natural World Heritage site and a biodiversity hotspot) and the conservation interest of its reptile fauna (94% endemics), we performed the most comprehensive DNA barcoding study on an island group to date to test its applicability to specimen identification and species discovery. Reptiles constitute Socotra's most important vertebrate fauna, yet their taxonomy remains under-studied. We successfully DNA-barcoded 380 individuals of all 31 presently recognized species. The specimen identification success rate is moderate to high, and almost all species presented local barcoding gaps. The unexpected high levels of intra-specific variability found within some species suggest cryptic diversity. Species richness may be under-estimated by 13.8-54.4%. This has implications in the species' ranges and conservation status that should be considered for conservation planning. Other phylogenetic studies using mitochondrial and nuclear markers are congruent with our results. We conclude that, despite its reduced length (663 base pairs), cytochrome c oxidase 1, COI, is very useful for specimen identification and for detecting intra-specific diversity, and has a good phylogenetic signal. We recommend DNA barcoding to be applied to other biodiversity hotspots for quickly and cost-efficiently flagging species discovery, preferentially incorporated into an integrative taxonomic framework.

  5. Cryptic trace-element alteration of Anorthosite, Stillwater complex, Montana

    USGS Publications Warehouse

    Czamanske, G.K.; Loferski, P.J.

    1996-01-01

    Evidence of cryptic alteration and correlations among K, Ba, and LREE concentrations indicate that a post-cumulus, low-density aqueous fluid phase significantly modified the trace-element contents of samples from Anorthosite zones I and II of the Stillwater Complex, Montana. Concentrations of Ba, Ca, Co, Cr, Cu, Fe, Hf, K, Li, Mg, Mn, Na, Ni, Sc, Sr, Th, Zn, and the rare-earth elements (REE) were measured in whole rocks and plagioclase separates from five traverses across the two main plagioclase cumulate (anorthosite) zones and the contiguous cumulates of the Stillwater Complex in an attempt to better understand the origin and solidification of the anorthosites. However, nearly the entire observed compositional range for many trace elements can be duplicated at a single locality by discriminating between samples rich in oikocrystic pyroxene and those which are composed almost entirely of plagioclase and show anhedral-granular texture. Plagioclase separates with high trace-element contents were obtained from the pyroxene-poor samples, for which maps of K concentration show plagioclase grains to contain numerous fractures hosting a fine-grained, K-rich phase, presumed to be sericite. Secondary processes in layered intrusions have the potential to cause cryptic disturbance, and the utmost care must be taken to ensure that samples provide information about primary processes. Although plagioclase from Anorthosite zones I and II shows significant compositional variation, there are no systematic changes in the major- or trace-element compositions of plagioclase over as much as 630 m of anorthosite thickness or 18 km of strike length. Plagioclase in the two major anorthosite zones shows little distinction in trace-element concentrations from plagioclase in the cumulates immediately below, between, and above these zones.

  6. Differential responses of cryptic bat species to the urban landscape.

    PubMed

    Lintott, Paul R; Barlow, Kate; Bunnefeld, Nils; Briggs, Philip; Gajas Roig, Clara; Park, Kirsty J

    2016-04-01

    Urbanization is a key global driver in the modification of land use and has been linked to population declines even in widespread and relatively common species. Cities comprise a complex assortment of habitat types yet we know relatively little about the effects of their composition and spatial configuration on species distribution. Although many bat species exploit human resources, the majority of species are negatively impacted by urbanization. Here, we use data from the National Bat Monitoring Programme, a long-running citizen science scheme, to assess how two cryptic European bat species respond to the urban landscape. A total of 124 × 1 km(2) sites throughout Britain were surveyed. The landscape surrounding each site was mapped and classified into discrete biotope types (e.g., woodland). Generalized linear models were used to assess differences in the response to the urban environment between the two species, and which landscape factors were associated with the distributions of P. pipistrellus and P. pygmaeus. The relative prevalence of P. pygmaeus compared to P. pipistrellus was greater in urban landscapes with a higher density of rivers and lakes, whereas P. pipistrellus was frequently detected in landscapes comprising a high proportion of green space (e.g., parklands). Although P. pipistrellus is thought to be well adapted to the urban landscape, we found a strong negative response to urbanization at a relatively local scale (1 km), whilst P. pygmaeus was detected more regularly in wooded urban landscapes containing freshwater. These results show differential habitat use at a landscape scale of two morphologically similar species, indicating that cryptic species may respond differently to anthropogenic disturbance. Even species considered relatively common and well adapted to the urban landscape may respond negatively to the built environment highlighting the future challenges involved in maintaining biodiversity within an increasingly urbanized

  7. Cryptic Recanalization of Chronic Vertebral Artery Occlusion by Head Rotation.

    PubMed

    Yagi, Kenji; Nakagawa, Hiroshi; Mure, Hideo; Okita, Shinya; Nagahiro, Shinji

    2017-04-01

    Chronic vertebral artery occlusion (VAO) can be associated with ischemic stroke, as thrombi formed under blood flow stagnation around the stump of the VAO may migrate into the brain. We report a new mechanism of chronic VAO-associated ischemic stroke and a patient with cryptic recanalization of chronic VAO by head rotation. A 74-year-old man presented with chronic right VAO and repeated ischemic embolic stroke in the posterior circulation despite antiplatelet therapy. He also manifested vertigo with 30° leftward head rotation, indicative of rotational vertebrobasilar insufficiency due to mechanical compression of the patent left vertebral artery (VA) at the C4-C5 level. Surgical decompression of the vessel via the anterior approach resulted in the disappearance of his rotational vertebrobasilar insufficiency. Adequate decompression of the VA on the left side was confirmed on postoperative computed tomography angiography scans obtained with his head rotated more to the left than on preoperative scans. Unexpected partial recanalization of his right chronic VAO was observed at the C5-C6 level. VAO was due to VA compression by osteophytes at neutral head position; it was released by head rotation. We suspected that his repeated brain infarcts were attributable to head rotation-related opening and closing of the VA lumen and these decompressed the left VA by removing the implicated osteophyte via the anterior approach. Cryptic recanalization of chronic VAO by head rotation contributed to repeated infarcts in the posterior circulation and was resolved by surgical decompression. Copyright © 2017 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  8. Cryptic diversity and patterns of host specificity in trematode flatworms.

    PubMed

    Hayward, Alexander

    2010-07-01

    The widespread utilization of molecular markers has revealed that a broad spectrum of taxa contain sets of morphologically cryptic, but genetically distinct lineages (Bickford et al. 2007). The identification of cryptic taxa is important as an accurate appreciation of diversity is crucial for a proper understanding of evolutionary and ecological processes. An example is the study of host specificity in parasitic taxa, where an apparent generalist may be found to contain a complex of several more specific species (Smith et al. 2006). Host specificity is a key life history trait that varies greatly among parasites (Poulin & Keeney 2007). While some can exploit a wide range of hosts, others are confined to just a single species. Access to additional hosts increases the resources available to a parasite. However, physiological or ecological constraints can restrict the extension of host range. Furthermore, there may be a trade-off between relaxed specificity and performance: generalism can decrease a parasites ability to adapt to each individual host species, and increase exposure to competition from other parasites (Poulin 1998). Despite the central role that host specificity plays in parasite life history, relatively little is known about how host range is determined in natural systems, and data from field studies are required to evaluate among competing ideas. In this issue, an exciting paper by Locke et al. (2010) makes a valuable contribution toward the understanding of host specificity in an important group of trematode flatworms. Using molecular methods, Locke et al. reveal an almost four-fold increase in the appreciated diversity of their focal group. In combination with a large and elegant sampling design this allows them to accurately assess host specificity for each taxon, and thus draw key insights into the factors that control host range in a dominant parasite group.

  9. EC declaration of conformity.

    PubMed

    Donawa, M E

    1996-05-01

    The CE-marking procedure requires that manufacturers draw up a written declaration of conformity before placing their products on the market. However, some companies do not realize that this is a requirement for all devices. Also, there is no detailed information concerning the contents and format of the EC declaration of conformity in the medical device Directives or in EC guidance documentation. This article will discuss some important aspects of the EC declaration of conformity and some of the guidance that is available on its contents and format.

  10. Γ-conformal algebras

    NASA Astrophysics Data System (ADS)

    Golenishcheva-Kutuzova, Maria I.; Kac, Victor G.

    1998-04-01

    Γ-conformal algebra is an axiomatic description of the operator product expansion of chiral fields with simple poles at finitely many points. We classify these algebras and their representations in terms of Lie algebras and their representations with an action of the group Γ. To every Γ-conformal algebra and a character of Γ we associate a Lie algebra generated by fields with the OPE with simple poles. Examples include twisted affine Kac-Moody algebras, the sin algebra (which is a "Γ-conformal" analogue of the general linear algebra) and its analogues, the algebra of pseudodifferential operators on the circle, etc.

  11. Conformal Carroll groups

    NASA Astrophysics Data System (ADS)

    Duval, C.; Gibbons, G. W.; Horvathy, P. A.

    2014-08-01

    Conformal extensions of Lévy-Leblond's Carroll group, based on geometric properties analogous to those of Newton-Cartan space-time are proposed. The extensions are labeled by an integer k. This framework includes and extends our recent study of the Bondi-Metzner-Sachs (BMS) and Newman-Unti (NU) groups. The relation to conformal Galilei groups is clarified. Conformal Carroll symmetry is illustrated by ‘Carrollian photons’. Motion both in the Newton-Cartan and Carroll spaces may be related to that of strings in the Bargmann space.

  12. Conformance Testing: Measurement Decision Rules

    NASA Technical Reports Server (NTRS)

    Mimbs, Scott M.

    2010-01-01

    The goal of a Quality Management System (QMS) as specified in ISO 9001 and AS9100 is to provide assurance to the customer that end products meet specifications. Measuring devices, often called measuring and test equipment (MTE), are used to provide the evidence of product conformity to specified requirements. Unfortunately, processes that employ MTE can become a weak link to the overall QMS if proper attention is not given to the measurement process design, capability, and implementation. Documented "decision rules" establish the requirements to ensure measurement processes provide the measurement data that supports the needs of the QMS. Measurement data are used to make the decisions that impact all areas of technology. Whether measurements support research, design, production, or maintenance, ensuring the data supports the decision is crucial. Measurement data quality can be critical to the resulting consequences of measurement-based decisions. Historically, most industries required simplistic, one-size-fits-all decision rules for measurements. One-size-fits-all rules in some cases are not rigorous enough to provide adequate measurement results, while in other cases are overly conservative and too costly to implement. Ideally, decision rules should be rigorous enough to match the criticality of the parameter being measured, while being flexible enough to be cost effective. The goal of a decision rule is to ensure that measurement processes provide data with a sufficient level of quality to support the decisions being made - no more, no less. This paper discusses the basic concepts of providing measurement-based evidence that end products meet specifications. Although relevant to all measurement-based conformance tests, the target audience is the MTE end-user, which is anyone using MTE other than calibration service providers. Topics include measurement fundamentals, the associated decision risks, verifying conformance to specifications, and basic measurement

  13. Conservation Laws

    NASA Astrophysics Data System (ADS)

    Dewitt, Bryce; Christensen, Steven M.

    In the case of the free particle, we interpreted various components of the energy-momentum-stress density as fluxes of energy and momentum. This interpretation can obviously be extended also to particle ensembles and gases. When we speak of fluxes we usually think of quantities that are conserved. In special relativity, energy and momentum are conserved. In general relativity, they are no longer generally conserved, at least if we do not include the energy and momentum of the gravitational field itself. Nevertheless, their densities and fluxes satisfy a covariant generalization of a true conservation law, which is quite easy to obtain.

  14. Animal culture: chimpanzee conformity?

    PubMed

    van Schaik, Carel P

    2012-05-22

    Culture-like phenomena in wild animals have received much attention, but how good is the evidence and how similar are they to human culture? New data on chimpanzees suggest their culture may even have an element of conformity.

  15. Assemblies of Conformal Tanks

    NASA Technical Reports Server (NTRS)

    DeLay, Tom

    2009-01-01

    Assemblies of tanks having shapes that conform to each other and/or conform to other proximate objects have been investigated for use in storing fuels and oxidizers in small available spaces in upper stages of spacecraft. Such assemblies might also prove useful in aircraft, automobiles, boats, and other terrestrial vehicles in which space available for tanks is limited. The basic concept of using conformal tanks to maximize the utilization of limited space is not new in itself: for example, conformal tanks are used in some automobiles to store windshield -washer liquid and coolant that overflows from radiators. The novelty of the present development lies in the concept of an assembly of smaller conformal tanks, as distinguished from a single larger conformal tank. In an assembly of smaller tanks, it would be possible to store different liquids in different tanks. Even if the same liquid were stored in all the tanks, the assembly would offer an advantage by reducing the mechanical disturbance caused by sloshing of fuel in a single larger tank: indeed, the requirement to reduce sloshing is critical in some applications. The figure shows a prototype assembly of conformal tanks. Each tank was fabricated by (1) copper plating a wax tank mandrel to form a liner and (2) wrapping and curing layers of graphite/epoxy composite to form a shell supporting the liner. In this case, the conformal tank surfaces are flat ones where they come in contact with the adjacent tanks. A band of fibers around the outside binds the tanks together tightly in the assembly, which has a quasi-toroidal shape. For proper functioning, it would be necessary to maintain equal pressure in all the tanks.

  16. Cryptic speciation in the mesopelagic environment: molecular phylogenetics of the lanternfish genus Benthosema.

    PubMed

    Zahuranec, Bernard; Karuppasamy, P K; Valinassab, Tooraj; Kidwai, Samina; Bernardi, Jeremy; Bernardi, Giacomo

    2012-09-01

    The presence of morphologically identical individuals that are genetically divergent, known as cryptic species, is a phenomenon that is likely to be of importance at the theoretical level, for speciation studies, and at the applied level, for management purposes. Cryptic species are probably common in the marine environment, and they have been described in a variety of habitats. Here we present the first case of cryptic speciation in the mesopelagic environment for the Benthosema lanternfishes. Based on mitochondrial and nuclear sequences, we describe the presence of widely divergent Benthosema pterotum cryptic species that diverged at least 5 million years ago. Our results have important theoretical, as well as practical implications, related to developing mesopelagic fisheries. Copyright © 2012 Elsevier B.V. All rights reserved.

  17. Global haplotype analysis of the whitefly Bemisia tabaci cryptic species Asia I in Asia.

    PubMed

    Hu, Jian; Chen, Yong-Dui; Jiang, Zhi-Lin; Nardi, Francesco; Yang, Tai-Yuan; Jin, Jie; Zhang, Zhong-Kai

    2015-04-01

    The whitefly, Bemisia tabaci (Hemiptera: Aleyrodidiae), is a cryptic species complex comprising a minimum of 24 cryptic species. Some members of this complex are important agricultural pests, causing considerable damage to vegetable as well as ornamental and horticultural crops. Asia I, one of the cryptic species of B. tabaci, is widely distributed in Asia. One hundred and sixty mitochondrial cytochrome oxidase I (COI) sequences from eight countries have been analyzed to investigate the geographic origin and current genetic structure of this cryptic species. Sixty different haplotypes were identified, with levels of genetic distances ranging from 0.001 to 0.021. A sign of possible genetic differentiation emerges from the differential distribution of dominant haplotypes in Indonesia and India compared to China. A possible ancient separation between Asia I in India and Indonesia and secondary contact in China has been hypothesized.

  18. Homology of cryptic plasmid of Neisseria gonorrhoeae with plasmids from Neisseria meningitidis and Neisseria lactamica.

    PubMed

    Ison, C A; Bellinger, C M; Walker, J

    1986-10-01

    DNA probe hybridisation was used to examine the relation between the cryptic plasmid from Neisseria gonorrhoeae and plasmids carried by pharyngeal isolates of Neisseria meningitidis and Neisseria lactamica. The complete gonococcal cryptic plasmid and HinfI derived digestion fragments subcloned into Escherichia coli were used to probe Southern blots of plasmid extracts. Homology was found to a plasmid of approximate molecular weight 4.5 kilobase pairs (Kb) but not to plasmids of less than 3.2 Kb or 6.5 Kb. Eleven of 16 strains of N meningitidis and two of six strains of N lactamica carried plasmids that showed strong hybridisation with the 4.2 Kb gonococcal plasmid. Hybridisation of plasmids from non-gonococcal species of neisseria with the gonococcal cryptic plasmid indicates that caution should be taken when using the cryptic plasmid as a diagnostic probe for gonorrhoea.

  19. Shock Condition Forensics and Cryptic Phase Transformations from Crystallographic Orientation Relationships in Zircon

    NASA Astrophysics Data System (ADS)

    Timms, N. E.; Erickson, T. M.; Cavosie, A. J.; Pearce, M. A.; Reddy, S. M.; Zanetti, M.; Tohver, E.; Schmieder, M.; Nemchin, A. A.; Wittmann, A.

    2016-08-01

    We present an approach to constrain pressure and temperature conditions during impact events involving identification of cryptic histories of phase transformations from orientation relationships in shocked zircon, linked to new P-T phase diagrams.

  20. Conformational sampling techniques.

    PubMed

    Hatfield, Marcus P D; Lovas, Sándor

    2014-01-01

    The potential energy hyper-surface of a protein relates the potential energy of the protein to its conformational space. This surface is useful in determining the native conformation of a protein or in examining a statistical-mechanical ensemble of structures (canonical ensemble). In determining the potential energy hyper-surface of a protein three aspects must be considered; reducing the degrees of freedom, a method to determine the energy of each conformation and a method to sample the conformational space. For reducing the degrees of freedom the choice of solvent, coarse graining, constraining degrees of freedom and periodic boundary conditions are discussed. The use of quantum mechanics versus molecular mechanics and the choice of force fields are also discussed, as well as the sampling of the conformational space through deterministic and heuristic approaches. Deterministic methods include knowledge-based statistical methods, rotamer libraries, homology modeling, the build-up method, self-consistent electrostatic field, deformation methods, tree-based elimination and eigenvector following routines. The heuristic methods include Monte Carlo chain growing, energy minimizations, metropolis monte carlo and molecular dynamics. In addition, various methods to enhance the conformational search including the deformation or smoothing of the surface, scaling of system parameters, and multi copy searching are also discussed.

  1. The effect of cryptic female choice on sex allocation in simultaneous hermaphrodites.

    PubMed

    van Velzen, Ellen; Schärer, Lukas; Pen, Ido

    2009-09-07

    Sex allocation theory for simultaneous hermaphrodites has focused primarily on the effects of sperm competition, but the role of mate choice has so far been neglected. We present a model to study the coevolution of cryptic female choice and sex allocation in simultaneous hermaphrodites. We show that the mechanism of cryptic female choice has a strong effect on the evolutionary outcome: if individuals remove a fixed proportion of less-preferred sperm, the optimal sex allocation is more female biased (i.e. more biased towards egg production) than without cryptic female choice; conversely, if a fixed amount of sperm is removed, sex allocation is less female-biased than without cryptic female choice, and can easily become male biased (i.e. biased towards sperm production). Under male-biased sex allocation, hermaphroditism can become unstable and the population can split into pure males and hermaphrodites with a female-biased allocation. We discuss the idea that the evolution of sex allocation may depend on the outcome of sexual conflict over the fate of received sperm: the sperm donor may attempt to manipulate or by-pass cryptic female choice and the sperm recipient is expected to resist such manipulation. We conclude that cryptic female choice can have a strong influence on sex allocation in simultaneous hermaphrodites and strongly encourage empirical work on this question.

  2. Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex.

    PubMed

    Dincă, V; Wiklund, C; Lukhtanov, V A; Kodandaramaiah, U; Norén, K; Dapporto, L; Wahlberg, N; Vila, R; Friberg, M

    2013-10-01

    Molecular studies of natural populations are often designed to detect and categorize hidden layers of cryptic diversity, and an emerging pattern suggests that cryptic species are more common and more widely distributed than previously thought. However, these studies are often decoupled from ecological and behavioural studies of species divergence. Thus, the mechanisms by which the cryptic diversity is distributed and maintained across large spatial scales are often unknown. In 1988, it was discovered that the common Eurasian Wood White butterfly consisted of two species (Leptidea sinapis and Leptidea reali), and the pair became an emerging model for the study of speciation and chromosomal evolution. In 2011, the existence of a third cryptic species (Leptidea juvernica) was proposed. This unexpected discovery raises questions about the mechanisms preventing gene flow and about the potential existence of additional species hidden in the complex. Here, we compare patterns of genetic divergence across western Eurasia in an extensive data set of mitochondrial and nuclear DNA sequences with behavioural data on inter- and intraspecific reproductive isolation in courtship experiments. We show that three species exist in accordance with both the phylogenetic and biological species concepts and that additional hidden diversity is unlikely to occur in Europe. The Leptidea species are now the best studied cryptic complex of butterflies in Europe and a promising model system for understanding the formation of cryptic species and the roles of local processes, colonization patterns and heterospecific interactions for ecological and evolutionary divergence.

  3. Tracing shifts of oceanic fronts using the cryptic diversity of the planktonic foraminifera Globorotalia inflata

    NASA Astrophysics Data System (ADS)

    Morard, Raphaël.; Reinelt, Melanie; Chiessi, Cristiano M.; Groeneveld, Jeroen; Kucera, Michal

    2016-09-01

    The use of planktonic foraminifera in paleoceanographic studies relies on the assumption that morphospecies represent biological species with ecological preferences that are stable through time and space. However, genetic surveys unveiled a considerable level of diversity in most morphospecies of planktonic foraminifera. This diversity is significant for paleoceanographic applications because cryptic species were shown to display distinct ecological preferences that could potentially help refine paleoceanographic proxies. Subtle morphological differences between cryptic species of planktonic foraminifera have been reported, but so far, their applicability within paleoceanographic studies remains largely unexplored. Here we show how information on genetic diversity can be transferred to paleoceanography using Globorotalia inflata as a case study. The two cryptic species of G. inflata are separated by the Brazil-Malvinas Confluence (BMC), a major oceanographic feature in the South Atlantic. Based on this observation, we developed a morphological model of cryptic species detection in core top material. The application of the cryptic species detection model to Holocene samples implies latitudinal oscillations in the position of the confluence that are largely consistent with reconstructions obtained from stable isotope data. We show that the occurrence of cryptic species in G. inflata can be detected in the fossil record and used to trace the migration of the BMC. Since a similar degree of morphological separation as in G. inflata has been reported from other species of planktonic foraminifera, the approach presented in this study can potentially yield a wealth of new paleoceanographical proxies.

  4. Volatile compounds in cryptic species of the Aneura pinguis complex and Aneura maxima (Marchantiophyta, Metzgeriidae).

    PubMed

    Wawrzyniak, Rafał; Wasiak, Wiesław; Bączkiewicz, Alina; Buczkowska, Katarzyna

    2014-09-01

    Aneura pinguis is one of the liverwort species complexes that consist of several cryptic species. Ten samples collected from different regions in Poland are in the focus of our research. Eight of the A. pinguis complex belonging to four cryptic species (A, B, C, E) and two samples of closely related species Aneura maxima were tested for the composition of volatile compounds. The HS-SPME technique coupled to GC/FID and GC/MS analysis has been applied. The fiber coated with DVB/CAR/PDMS has been used. The results of the present study, revealed the qualitative and quantitative differences in the composition of the volatile compounds between the studied species. Mainly they are from the group of sesquiterpenoids, oxygenated sesquiterpenoids and aliphatic hydrocarbons. The statistical methods (CA and PCA) showed that detected volatile compounds allow to distinguish cryptic species of A. pinguis. All examined cryptic species of the A. pinguis complex differ from A. maxima. Species A and E of A. pinguis, in CA and PCA, form separate clusters remote from two remaining cryptic species of A. pinguis (B and C) and A. maxima. Relationship between the cryptic species appeared from the chemical studies are in accordance with that revealed on the basis of DNA sequences.

  5. Conservation Tillage

    NASA Astrophysics Data System (ADS)

    Gebhardt, Maurice R.; Daniel, Tommy C.; Schweizer, Edward E.; Allmaras, Raymond R.

    1985-11-01

    Conservation production systems combine tillage and planting practices to reduce soil erosion and loss of water from farmland. Successful conservation tillage practices depend on the ability of farm managers to integrate sound crop production practices with effective pest management systems. More scientific information is needed to determine the relations between tillage practices and physical, chemical, and biological soil factors that affect plant and pest ecology. There is a need to devise improved pest management strategies for conservation tillage and to better understand the impact of conservation tillage on water quality, especially as it is related to use of agricultural chemicals. While savings in fuel, labor, and soil have induced many farmers to adopt conservation tillage, improved methods and equipment should increase adoption even more.

  6. Molecular phylogeny of the Afroedura nivaria (Reptilia: Gekkonidae) species complex in South Africa provides insight on cryptic speciation.

    PubMed

    Makhubo, Buyisile G; Tolley, Krystal A; Bates, Michael F

    2015-01-01

    The Afroedura nivaria species complex (A. nivaria, A. karroica, A. amatolica, A. tembulica and A. halli) is a morphologically conservative group of medium-sized flat geckos endemic to South Africa and Lesotho. Species are allopatric, as are some populations within species that are separated by large expanses of unsuitable habitat. Because of this isolation of populations we hypothesised that several cryptic species may be present. To investigate this hypothesis we constructed a molecular phylogeny using multiple markers, and included representatives of other Afroedura species. Bayesian inference and maximum likelihood analyses (439bp 16S, 593bp ND4, 948bp RAG1) strongly supported the genetic distinctiveness of the five described species. However, the A. nivaria species complex as currently described is not monophyletic, as A. karroica was positioned outside a clade containing all other Afroedura species, and A. pondolia (which was presumed to belong to a different species complex) was recovered within the A. nivaria complex. Several distinct clades within A. halli and A. nivaria were also recovered, and the narrowly-distributed A. amatolica consisted of two highly divergent clades. We also conducted a multivariate analysis using 19 morphological characters to investigate whether the clades recovered by the phylogeny were distinct in terms of head, body and limb shape. The analysis showed some variation between clades in terms of locomotor apparatus (forelimbs and feet), head and body dimensions, but overall the morphological differences were minor. This morphological conservatism in the A. nivaria complex may be a result of adaptation to similar microhabitats. Exclusive of A. karroica, the results suggest that there are at least nine species in this complex, of which four are cryptic and undescribed. Copyright © 2014 Elsevier Inc. All rights reserved.

  7. The Cryptic dsdA Gene Encodes a Functional D-Serine Dehydratase in Pseudomonas aeruginosa PAO1.

    PubMed

    Li, Guoqing; Lu, Chung-Dar

    2016-06-01

    D-Serine, an important neurotransmitter, also contributes to bacterial adaptation and virulence in humans. It was reported that Pseudomonas aeruginosa PAO1 can grow on D-serine as the sole nitrogen source, and growth was severely reduced in the dadA mutant devoid of the D-alanine dehydrogenase with broad substrate specificity. In this study, the dsdA gene (PA3357) encoding a putative D-serine dehydratase was subjected to further characterization. Growth on D-serine as the sole source of nitrogen was retained in the ∆dsdA mutant and was abolished completely in the ∆dadA and ∆dadA-∆dsdA mutants. However, when complemented by dsdA on a plasmid, the double mutant was able to grow on D-serine as the sole source of carbon and nitrogen, supporting the proposed biochemical function of DsdA in the conversion of D-serine into pyruvate and ammonia. Among D- and L-amino acids tested, only D-serine and D-threonine could serve as the substrates of DsdA, and the Km of DsdA with D-serine was calculated to be 330 μM. Comparative genomics revealed that this cryptic dsdA gene was highly conserved in strains of P. aeruginosa, and that most strains of Pseudomonas putida possess putative dsdCAX genes encoding a transcriptional regulator DsdC and a D-serine transporter DsdX as in enteric bacteria. In conclusion, this study supports the presence of a cryptic dsdA gene encoding a functional D-serine dehydratase in P. aeruginosa, and the absence of dsdA expression in response to exogenous D-serine might be due to the loss of regulatory elements for gene activation during evolution.

  8. 50 CFR 635.40 - Restrictions to enhance conservation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... products of an American fishery and were lawfully taken in conformity with applicable conservation laws and... 50, Code of Federal Regulations, and such other conservation laws and regulations as were applicable... 50 Wildlife and Fisheries 12 2013-10-01 2013-10-01 false Restrictions to enhance conservation....

  9. 50 CFR 635.40 - Restrictions to enhance conservation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... products of an American fishery and were lawfully taken in conformity with applicable conservation laws and... 50, Code of Federal Regulations, and such other conservation laws and regulations as were applicable... 50 Wildlife and Fisheries 10 2011-10-01 2011-10-01 false Restrictions to enhance conservation....

  10. 50 CFR 635.40 - Restrictions to enhance conservation.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... products of an American fishery and were lawfully taken in conformity with applicable conservation laws and... 50, Code of Federal Regulations, and such other conservation laws and regulations as were applicable... 50 Wildlife and Fisheries 12 2012-10-01 2012-10-01 false Restrictions to enhance conservation....

  11. 50 CFR 635.40 - Restrictions to enhance conservation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... products of an American fishery and were lawfully taken in conformity with applicable conservation laws and... 50, Code of Federal Regulations, and such other conservation laws and regulations as were applicable... 50 Wildlife and Fisheries 8 2010-10-01 2010-10-01 false Restrictions to enhance conservation....

  12. 50 CFR 635.40 - Restrictions to enhance conservation.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... products of an American fishery and were lawfully taken in conformity with applicable conservation laws and... 50, Code of Federal Regulations, and such other conservation laws and regulations as were applicable... 50 Wildlife and Fisheries 12 2014-10-01 2014-10-01 false Restrictions to enhance conservation....

  13. Cryptic protein-protein interaction motifs in the cytoplasmic domain of MHCI proteins.

    PubMed

    Frietze, Karla K; Pappy, Adlai L; Melson, Jack W; O'Driscoll, Emily E; Tyler, Carolyn M; Perlman, David H; Boulanger, Lisa M

    2016-07-19

    -1, and identify a conserved PDZ ligand motif in the classical MHCI H2-K that is required for this interaction. These results identify cryptic protein interaction motifs in the cytoplasmic domain of MHCI. In so doing, they suggest that the cytoplasmic domain of MHCI could participate in previously unsuspected PDZ mediated protein-protein interactions at neuronal as well as immunological synapses.

  14. Hydrology and Conservation Ecology

    NASA Astrophysics Data System (ADS)

    Narayanan, M.

    2006-12-01

    Responses to change in the behavior of ecological systems are largely governed by interactions at different levels. Research is essential and is to be necessarily designed to gain insights into various interactions at the community level. Sustainable resource management is only possible if conservation of biodiversity can be accomplished by properly using the knowledge discovered. It is well known that the United States Department of Agriculture provides technical information, resources, and data necessary to assist the researchers in addressing their conservation needs. Conservation aims to protect, preserve and conserve the earth's natural resources. These include, but not limited to the conservation of soil, water, minerals, air, plants and all living beings. The United States Department of Agriculture also encourages farmers and ranchers to voluntarily address threats to soil and water. Protection of wetlands and wildlife habitat has been on the radar screen of conservation experts for a very long time. The main objective has always been to help farmers and landowners conform and comply with federal and state environmental laws. During the implementation phase, farmers should be encouraged to make beneficial, cost-effective changes to methods of irrigation systems. In some cases, the hydrologic regime of the project area can be thought of as principally an issue of river flow regimes for floodplain forests. In this presentation, the author tries to focus on the impact of hydrology and conservation ecology on global warming. He also discusses the impact of hydrology and conservation ecology global air concerns such as greenhouse gas concentrations in the atmosphere. References: Chow, V. T, D. R. Maidment, and L. W. Mays. 1988. Applied Hydrology. McGraw-Hill, Inc. U.S. Soil Conservation Service. Technical Release 55: Urban Hydrology for Small Watersheds. USDA (U.S. Department of Agriculture). June 1986. Lehner, B. and P. Döll (2004). Development and validation

  15. Resolving cryptic species complexes of major tephritid pests

    PubMed Central

    Hendrichs, Jorge; Vera, M. Teresa; De Meyer, Marc; Clarke, Anthony R.

    2015-01-01

    Abstract An FAO/IAEA Co-ordinated Research Project (CRP) on “Resolution of Cryptic Species Complexes of Tephritid Pests to Overcome Constraints to SIT Application and International Trade” was conducted from 2010 to 2015. As captured in the CRP title, the objective was to undertake targeted research into the systematics and diagnostics of taxonomically challenging fruit fly groups of economic importance. The scientific output was the accurate alignment of biological species with taxonomic names; which led to the applied outcome of assisting FAO and IAEA Member States in overcoming technical constraints to the application of the Sterile Insect Technique (SIT) against pest fruit flies and the facilitation of international agricultural trade. Close to 50 researchers from over 20 countries participated in the CRP, using coordinated, multidisciplinary research to address, within an integrative taxonomic framework, cryptic species complexes of major tephritid pests. The following progress was made for the four complexes selected and studied: Anastrepha fraterculus complex – Eight morphotypes and their geographic and ecological distributions in Latin America were defined. The morphotypes can be considered as distinct biological species on the basis of differences in karyotype, sexual incompatibility, post-mating isolation, cuticular hydrocarbon, pheromone, and molecular analyses. Discriminative taxonomic tools using linear and geometric morphometrics of both adult and larval morphology were developed for this complex. Bactrocera dorsalis complex – Based on genetic, cytogenetic, pheromonal, morphometric, and behavioural data, which showed no or only minor variation between the Asian/African pest fruit flies Bactrocera dorsalis, Bactrocera papayae, Bactrocera philippinensis and Bactrocera invadens, the latter three species were synonymized with Bactrocera dorsalis. Of the five target pest taxa studied, only Bactrocera dorsalis and Bactrocera carambolae remain as

  16. Resolving cryptic species complexes of major tephritid pests.

    PubMed

    Hendrichs, Jorge; Vera, M Teresa; De Meyer, Marc; Clarke, Anthony R

    2015-01-01

    An FAO/IAEA Co-ordinated Research Project (CRP) on "Resolution of Cryptic Species Complexes of Tephritid Pests to Overcome Constraints to SIT Application and International Trade" was conducted from 2010 to 2015. As captured in the CRP title, the objective was to undertake targeted research into the systematics and diagnostics of taxonomically challenging fruit fly groups of economic importance. The scientific output was the accurate alignment of biological species with taxonomic names; which led to the applied outcome of assisting FAO and IAEA Member States in overcoming technical constraints to the application of the Sterile Insect Technique (SIT) against pest fruit flies and the facilitation of international agricultural trade. Close to 50 researchers from over 20 countries participated in the CRP, using coordinated, multidisciplinary research to address, within an integrative taxonomic framework, cryptic species complexes of major tephritid pests. The following progress was made for the four complexes selected and studied: Anastrepha fraterculus complex - Eight morphotypes and their geographic and ecological distributions in Latin America were defined. The morphotypes can be considered as distinct biological species on the basis of differences in karyotype, sexual incompatibility, post-mating isolation, cuticular hydrocarbon, pheromone, and molecular analyses. Discriminative taxonomic tools using linear and geometric morphometrics of both adult and larval morphology were developed for this complex. Bactrocera dorsalis complex - Based on genetic, cytogenetic, pheromonal, morphometric, and behavioural data, which showed no or only minor variation between the Asian/African pest fruit flies Bactrocera dorsalis, Bactrocera papayae, Bactrocera philippinensis and Bactrocera invadens, the latter three species were synonymized with Bactrocera dorsalis. Of the five target pest taxa studied, only Bactrocera dorsalis and Bactrocera carambolae remain as scientifically valid

  17. Conformity: Implications for ABE Instruction

    ERIC Educational Resources Information Center

    Long, Huey B.

    1977-01-01

    Provides an interpretative review of the literature of conforming behavior with special attention to implications for adult education. Eight different research areas of conformity research are summarized, and five reasons for conformity and three different kinds of conforming behavior are identified and discussed. (SH)

  18. Conformational kinetics reveals affinities of protein conformational states.

    PubMed

    Daniels, Kyle G; Suo, Yang; Oas, Terrence G

    2015-07-28

    Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein's affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states.

  19. Conformational kinetics reveals affinities of protein conformational states

    PubMed Central

    Daniels, Kyle G.; Suo, Yang; Oas, Terrence G.

    2015-01-01

    Most biological reactions rely on interplay between binding and changes in both macromolecular structure and dynamics. Practical understanding of this interplay requires detection of critical intermediates and determination of their binding and conformational characteristics. However, many of these species are only transiently present and they have often been overlooked in mechanistic studies of reactions that couple binding to conformational change. We monitored the kinetics of ligand-induced conformational changes in a small protein using six different ligands. We analyzed the kinetic data to simultaneously determine both binding affinities for the conformational states and the rate constants of conformational change. The approach we used is sufficiently robust to determine the affinities of three conformational states and detect even modest differences in the protein’s affinities for relatively similar ligands. Ligand binding favors higher-affinity conformational states by increasing forward conformational rate constants and/or decreasing reverse conformational rate constants. The amounts by which forward rate constants increase and reverse rate constants decrease are proportional to the ratio of affinities of the conformational states. We also show that both the affinity ratio and another parameter, which quantifies the changes in conformational rate constants upon ligand binding, are strong determinants of the mechanism (conformational selection and/or induced fit) of molecular recognition. Our results highlight the utility of analyzing the kinetics of conformational changes to determine affinities that cannot be determined from equilibrium experiments. Most importantly, they demonstrate an inextricable link between conformational dynamics and the binding affinities of conformational states. PMID:26162682

  20. Conformers of Gaseous Serine.

    PubMed

    He, Kedan; Allen, Wesley D

    2016-08-09

    The myriad conformers of the neutral form of natural amino acid serine (Ser) have been investigated by systematic computations with reliable electronic wave function methods. A total of 85 unique conformers were located using the MP2/cc-pVTZ level of theory. The 12 lowest-energy conformers of serine fall within a 8 kJ mol(-1) window, and for these species, geometric structures, precise relative energies, equilibrium and vibrationally averaged rotational constants, anharmonic vibrational frequencies, infrared intensities, quartic and sextic centrifugal distortion constants, dipole moments, and (14)N nuclear quadrupole coupling constants were computed. The relative energies were refined through composite focal-point analyses employing basis sets as large as aug-cc-pV5Z and correlation treatments through CCSD(T). The rotational constants for seven conformers measured by Fourier-transform microwave spectroscopy are in good agreement with the vibrationally averaged rotational constants computed in this study. Our anharmonic vibrational frequencies are compared to the large number of experimental vibrational absorptions attributable to at least six conformers.

  1. Cryptic diversity, geographical endemism and allopolyploidy in NE Pacific seaweeds.

    PubMed

    Neiva, João; Serrão, Ester A; Anderson, Laura; Raimondi, Peter T; Martins, Neusa; Gouveia, Licínia; Paulino, Cristina; Coelho, Nelson C; Miller, Kathy Ann; Reed, Daniel C; Ladah, Lydia B; Pearson, Gareth A

    2017-01-23

    Molecular markers are revealing a much more diverse and evolutionarily complex picture of marine biodiversity than previously anticipated. Cryptic and/or endemic marine species are continually being found throughout the world oceans, predominantly in inconspicuous tropical groups but also in larger, canopy-forming taxa from well studied temperate regions. Interspecific hybridization has also been found to be prevalent in many marine groups, for instance within dense congeneric assemblages, with introgressive gene-flow being the most common outcome. Here, using a congeneric phylogeographic approach, we investigated two monotypic and geographically complementary sister genera of north-east Pacific intertidal seaweeds (Hesperophycus and Pelvetiopsis), for which preliminary molecular tests revealed unexpected conflicts consistent with unrecognized cryptic diversity and hybridization. The three recovered mtDNA clades did not match a priori species delimitations. H. californicus was congruent, whereas widespread P. limitata encompassed two additional narrow-endemic species from California - P. arborescens (here genetically confirmed) and P. hybrida sp. nov. The congruence between the genotypic clusters and the mtDNA clades was absolute. Fixed heterozygosity was apparent in a high proportion of loci in P. limitata and P. hybrida, with genetic analyses showing that the latter was composed of both H. californicus and P. arborescens genomes. All four inferred species could be distinguished based on their general morphology. This study confirmed additional diversity and reticulation within NE Pacific Hesperophycus/Pelvetiopsis, including the validity of the much endangered, modern climatic relict P. arborescens, and the identification of a new, stable allopolyploid species (P. hybrida) with clearly discernable ancestry (♀ H. californicus x ♂ P. arborescens), morphology, and geographical distribution. Allopolyploid speciation is otherwise completely unknown in brown

  2. Early Miocene origin and cryptic diversification of South American salamanders

    PubMed Central

    2013-01-01

    Background The currently recognized species richness of South American salamanders is surprisingly low compared to North and Central America. In part, this low richness may be due to the salamanders being a recent arrival to South America. Additionally, the number of South American salamander species may be underestimated because of cryptic diversity. The aims of our present study were to infer evolutionary relationships, lineage diversity, and timing of divergence of the South American Bolitoglossa using mitochondrial and nuclear sequence data from specimens primarily from localities in the Andes and upper Amazon Basin. We also estimated time of colonization of South America to test whether it is consistent with arrival via the Panamanian Isthmus, or land bridge connection, at its traditionally assumed age of 3 million years. Results Divergence time estimates suggest that Bolitoglossa arrived in South America from Central America by at least the Early Miocene, ca. 23.6 MYA (95% HPD 15.9-30.3 MYA), and subsequently diversified. South American salamanders of the genus Bolitoglossa show strong phylogeographic structure at fine geographic scales and deep divergences at the mitochondrial gene cytochrome b (Cytb) and high diversity at the nuclear recombination activating gene-1 (Rag1). Species often contain multiple genetically divergent lineages that are occasionally geographically overlapping. Single specimens from two southeastern localities in Ecuador are sister to the equatoriana-peruviana clade and genetically distinct from all other species investigated to date. Another single exemplar from the Andes of northwestern Ecuador is highly divergent from all other specimens and is sister to all newly studied samples. Nevertheless, all sampled species of South American Bolitoglossa are members of a single clade that is one of several constituting the subgenus Eladinea, one of seven subgenera in this large genus. Conclusions The ancestors of South American salamanders

  3. Cryptic zooplankton ``swimmers'' in upper ocean sediment traps

    NASA Astrophysics Data System (ADS)

    Michaels, Anthony F.; Silver, Mary W.; Gowing, Marcia M.; Knauer, George A.

    1990-08-01

    Sediment traps are the major oceanographic tool for collecting passively sinking particulate material (the "particle flux") in the ocean. Sediment traps in the upper ocean also collect actively sinking zooplankton that are usually manually removed prior to analysis. Microscospic analysis of sediment trap samples collected over a 19-month period in the eastern North Pacific reveals that zooplankton "swimmers" are a larger problem than previously recognized. Zooplankton that are cryptic (i.e. difficult to see or distinguish from the detrital material) and difficult to remove (principally gelatinous zooplankton) may have contributed up to 20 mg C m -2 day -1 to the "particulate flux", with the highest values in the upper 150 m. This swimmer problem is in addition to the previously recognized presence of crustaceans and other large metazoans in traps. Additionally, the detritus-laden, mucous-feeding structures (houses)of larvaceans probably enter the traps with the larvaceans and would be impossible to remove. We estimate that the contribution of the cryptic swimmers and larvacean houses could be as much as 96% of the measured carbon flux. The contribution is greatest in the euphotic zone and drops sharply below 200 m. Subtracting out this potential artifact at the VERTEX station results in vertical profiles of organic carbon flux that differ dramatically from the standard flux profile for carbon in the upper ocean: specifically, the implied "regeneration" rate is greatly reduced. Screened traps (300 μm screens below the baffles) contained numerous metazoans smaller than the screen mesh size. These traps also contained lower levels of other types of sinking particles, and it is unclear to what extent the screens reduced the relative contribution of swimmers to the trap-collected carbon. Although the expanded swimmer problem presented here is now documented at just the VERTEX site, we expect it exists elsewhere. The extent of this swimmer problem requires resolution

  4. A Novel lux Operon in the Cryptically Bioluminescent Fish Pathogen Vibrio salmonicida Is Associated with Virulence▿

    PubMed Central

    Nelson, Eric J.; Tunsjø, Hege S.; Fidopiastis, Pat M.; Sørum, Henning; Ruby, Edward G.

    2007-01-01

    The cold-water-fish pathogen Vibrio salmonicida expresses a functional bacterial luciferase but produces insufficient levels of its aliphatic-aldehyde substrate to be detectably luminous in culture. Our goals were to (i) better explain this cryptic bioluminescence phenotype through molecular characterization of the lux operon and (ii) test whether the bioluminescence gene cluster is associated with virulence. Cloning and sequencing of the V. salmonicida lux operon revealed that homologs of all of the genes required for luminescence are present: luxAB (luciferase) and luxCDE (aliphatic-aldehyde synthesis). The arrangement and sequence of these structural lux genes are conserved compared to those in related species of luminous bacteria. However, V. salmonicida strains have a novel arrangement and number of homologs of the luxR and luxI quorum-sensing regulatory genes. Reverse transcriptase PCR analysis suggests that this novel arrangement of quorum-sensing genes generates antisense transcripts that may be responsible for the reduced production of bioluminescence. In addition, infection with a strain in which the luxA gene was mutated resulted in a marked delay in mortality among Atlantic salmon relative to infection with the wild-type parent in single-strain challenge experiments. In mixed-strain competition between the luxA mutant and the wild type, the mutant was attenuated up to 50-fold. It remains unclear whether the attenuation results from a direct loss of luciferase or a polar disturbance elsewhere in the lux operon. Nevertheless, these findings document for the first time an association between a mutation in a structural lux gene and virulence, as well as provide a new molecular system to study Vibrio pathogenesis in a natural host. PMID:17277225

  5. Resolving the trophic relations of cryptic species: an example using stable isotope analysis of dolphin teeth.

    PubMed

    Owen, Kylie; Charlton-Robb, Kate; Thompson, Ross

    2011-02-18

    Understanding the foraging ecology and diet of animals can play a crucial role in conservation of a species. This is particularly true where species are cryptic and coexist in environments where observing feeding behaviour directly is difficult. Here we present the first information on the foraging ecology of a recently identified species of dolphin (Southern Australian bottlenose dolphin (SABD)) and comparisons to the common bottlenose dolphin (CBD) in Victoria, Australia, using stable isotope analysis of teeth. Stable isotope signatures differed significantly between SABD and CBD for both δ(13)C (-14.4‰ vs. -15.5‰ respectively) and δ(15)N (15.9‰ vs. 15.0‰ respectively), suggesting that the two species forage in different areas and consume different prey. This finding supports genetic and morphological data indicating that SABD are distinct from CBD. In Victoria, the SABD is divided into two distinct populations, one in the large drowned river system of Port Phillip Bay and the other in a series of coastal lakes and lagoons called the Gippsland Lakes. Within the SABD species, population differences were apparent. The Port Phillip Bay population displayed a significantly higher δ(15)N than the Gippsland Lakes population (17.0‰ vs. 15.5‰), suggesting that the Port Phillip Bay population may feed at a higher trophic level--a result which is supported by analysis of local food chains. Important future work is required to further understand the foraging ecology and diet of this newly described, endemic, and potentially endangered species of dolphin.

  6. Morphological and molecular evidence for cryptic species of springsnails [genus Pseudamnicola ( Corrosella) (Mollusca, Caenogastropoda, Hydrobiidae)

    PubMed Central

    Delicado, Diana; Ramos, Marian A.

    2012-01-01

    Abstract Several Pseudamnicola (Corrosella) populations of the central and eastern Iberian Peninsula have been ascribed to Pseudamnicola (Corrosella) astieri (Dupuy, 1851), though recent evidence demonstrates the species could be endemic to the departments of Var and Alpes-Maritimes in France. Through the identification of cryptic species using a combined morphological and phylogenetic approach, this paper provides a detailed morphological description of Pseudamnicola (Corrosella) astieri, clarifying its taxonomic boundaries and confirming it as a French endemic. In parallel, by comparing Pseudamnicola (Corrosella) populations from the provinces of Castellón and Valencia in Eastern Spain, it was observed that rather than Pseudamnicola (Corrosella) astieri they represented a new species here described as Pseudamnicola (Corrosella) hauffei sp. n. Among other characters, the two species show marked differences in shell shape, male and female genital systems, radular formula and concentration of the nervous system. Pseudamnicola (Corrosella) hauffei sp. n. was also compared morphologically to another two Pseudamnicola (Corrosella) species living in nearby areas [Pseudamnicola (Corrosella) hinzi Boeters, 1986 and Pseudamnicola (Corrosella) navasiana (Fagot, 1907)], molecularly to Pseudamnicola (Corrosella) falkneri (Boeters, 1970), the type species of the subgenus, and to the rest of the Pseudamnicola (Corrosella) species described so far. Morphological differentiation between the species is supported by a genetic divergence of 7.4% inferred from a partial sequence (658 bp) of the mitochondrial gene cytochrome c oxidase subunit I (COI). On the basis of an average 8% (5.39 to 11.15%) divergence estimated for the COI gene in other Pseudamnicola (Corrosella) species reported in GenBank, the existence of two specific entities is here proposed, which will have impact on conservation policies both in France and in Spain. PMID:22639531

  7. Resolving the Trophic Relations of Cryptic Species: An Example Using Stable Isotope Analysis of Dolphin Teeth

    PubMed Central

    Owen, Kylie; Charlton-Robb, Kate; Thompson, Ross

    2011-01-01

    Understanding the foraging ecology and diet of animals can play a crucial role in conservation of a species. This is particularly true where species are cryptic and coexist in environments where observing feeding behaviour directly is difficult. Here we present the first information on the foraging ecology of a recently identified species of dolphin (Southern Australian bottlenose dolphin (SABD)) and comparisons to the common bottlenose dolphin (CBD) in Victoria, Australia, using stable isotope analysis of teeth. Stable isotope signatures differed significantly between SABD and CBD for both δ13C (−14.4‰ vs. −15.5‰ respectively) and δ15N (15.9‰ vs. 15.0‰ respectively), suggesting that the two species forage in different areas and consume different prey. This finding supports genetic and morphological data indicating that SABD are distinct from CBD. In Victoria, the SABD is divided into two distinct populations, one in the large drowned river system of Port Phillip Bay and the other in a series of coastal lakes and lagoons called the Gippsland Lakes. Within the SABD species, population differences were apparent. The Port Phillip Bay population displayed a significantly higher δ15N than the Gippsland Lakes population (17.0‰ vs. 15.5‰), suggesting that the Port Phillip Bay population may feed at a higher trophic level - a result which is supported by analysis of local food chains. Important future work is required to further understand the foraging ecology and diet of this newly described, endemic, and potentially endangered species of dolphin. PMID:21364748

  8. The importance of data quality for generating reliable distribution models for rare, elusive, and cryptic species.

    PubMed

    Aubry, Keith B; Raley, Catherine M; McKelvey, Kevin S

    2017-01-01

    The availability of spatially referenced environmental data and species occurrence records in online databases enable practitioners to easily generate species distribution models (SDMs) for a broad array of taxa. Such databases often include occurrence records of unknown reliability, yet little information is available on the influence of data quality on SDMs generated for rare, elusive, and cryptic species that are prone to misidentification in the field. We investigated this question for the fisher (Pekania pennanti), a forest carnivore of conservation concern in the Pacific States that is often confused with the more common Pacific marten (Martes caurina). Fisher occurrence records supported by physical evidence (verifiable records) were available from a limited area, whereas occurrence records of unknown quality (unscreened records) were available from throughout the fisher's historical range. We reserved 20% of the verifiable records to use as a test sample for both models and generated SDMs with each dataset using Maxent. The verifiable model performed substantially better than the unscreened model based on multiple metrics including AUCtest values (0.78 and 0.62, respectively), evaluation of training and test gains, and statistical tests of how well each model predicted test localities. In addition, the verifiable model was consistent with our knowledge of the fisher's habitat relations and potential distribution, whereas the unscreened model indicated a much broader area of high-quality habitat (indices > 0.5) that included large expanses of high-elevation habitat that fishers do not occupy. Because Pacific martens remain relatively common in upper elevation habitats in the Cascade Range and Sierra Nevada, the SDM based on unscreened records likely reflects primarily a conflation of marten and fisher habitat. Consequently, accurate identifications are far more important than the spatial extent of occurrence records for generating reliable SDMs for the

  9. Conformal perturbation theory

    NASA Astrophysics Data System (ADS)

    Amoretti, Andrea; Magnoli, Nicodemo

    2017-08-01

    Statistical systems near a classical critical point have been intensively studied from both theoretical and experimental points of view. In particular, correlation functions are of relevance in comparing theoretical models with the experimental data of real systems. In order to compute physical quantities near a critical point, one needs to know the model at the critical (conformal) point. In this line, recent progress in the knowledge of conformal field theories, through the conformal bootstrap, gives the hope of getting some interesting results also outside of the critical point. In this paper, we will review and clarify how, starting from the knowledge of the critical correlators, one can calculate in a safe way their behavior outside the critical point. The approach illustrated requires the model to be just scale invariant at the critical point. We will clarify the method by applying it to different kind of perturbations of the 2D Ising model.

  10. The use of photographic rates to estimate densities of tigers and other cryptic mammals: a comment on misleading conclusions

    USGS Publications Warehouse

    Jennelle, C.S.; Runge, M.C.; MacKenzie, D.I.

    2002-01-01

    The search for easy-to-use indices that substitute for direct estimation of animal density is a common theme in wildlife and conservation science, but one fraught with well-known perils (Nichols & Conroy, 1996; Yoccoz, Nichols & Boulinier, 2001; Pollock et al., 2002). To establish the utility of an index as a substitute for an estimate of density, one must: (1) demonstrate a functional relationship between the index and density that is invariant over the desired scope of inference; (2) calibrate the functional relationship by obtaining independent measures of the index and the animal density; (3) evaluate the precision of the calibration (Diefenbach et al., 1994). Carbone et al. (2001) argue that the number of camera-days per photograph is a useful index of density for large, cryptic, forest-dwelling animals, and proceed to calibrate this index for tigers (Panthera tigris). We agree that a properly calibrated index may be useful for rapid assessments in conservation planning. However, Carbone et al. (2001), who desire to use their index as a substitute for density, do not adequately address the three elements noted above. Thus, we are concerned that others may view their methods as justification for not attempting directly to estimate animal densities, without due regard for the shortcomings of their approach.

  11. From Cryptic Toward Canonical Pre-mRNA Splicing in Pompe Disease: a Pipeline for the Development of Antisense Oligonucleotides

    PubMed Central

    Bergsma, Atze J; in ‘t Groen, Stijn LM; Verheijen, Frans W; van der Ploeg, Ans T; Pijnappel, WWM Pim

    2016-01-01

    While 9% of human pathogenic variants have an established effect on pre-mRNA splicing, it is suspected that an additional 20% of otherwise classified variants also affect splicing. Aberrant splicing includes disruption of splice sites or regulatory elements, or creation or strengthening of cryptic splice sites. For the majority of variants, it is poorly understood to what extent and how these may affect splicing. We have identified cryptic splicing in an unbiased manner. Three types of cryptic splicing were analyzed in the context of pathogenic variants in the acid α-glucosidase gene causing Pompe disease. These involved newly formed deep intronic or exonic cryptic splice sites, and a natural cryptic splice that was utilized due to weakening of a canonical splice site. Antisense oligonucleotides that targeted the identified cryptic splice sites repressed cryptic splicing at the expense of canonical splicing in all three cases, as shown by reverse-transcriptase-quantitative polymerase chain reaction analysis and by enhancement of acid α-glucosidase enzymatic activity. This argues for a competition model for available splice sites, including intact or weakened canonical sites and natural or newly formed cryptic sites. The pipeline described here can detect cryptic splicing and correct canonical splicing using antisense oligonucleotides to restore the gene defect. PMID:27623443

  12. Conservation Presentation.

    ERIC Educational Resources Information Center

    Friday, Gerald

    2001-01-01

    Introduces a project in which students teach about the importance of recycling and conservation by presenting demonstrations. Includes demonstrations on water, plastic, and other recycling products such as steel. (YDS)

  13. Energy Conservation

    ERIC Educational Resources Information Center

    Abelson, Philip H.

    1972-01-01

    Comments on The Potential for Energy Conservation,'' a study by the Office of Emergency Preparedness, emphasizing the coming dependence on foreign oil, and presses for government influence to encourage development of more efficient cars. (AL)

  14. Charged conformal Killing spinors

    SciTech Connect

    Lischewski, Andree

    2015-01-15

    We study the twistor equation on pseudo-Riemannian Spin{sup c}-manifolds whose solutions we call charged conformal Killing spinors (CCKSs). We derive several integrability conditions for the existence of CCKS and study their relations to spinor bilinears. A construction principle for Lorentzian manifolds admitting CCKS with nontrivial charge starting from CR-geometry is presented. We obtain a partial classification result in the Lorentzian case under the additional assumption that the associated Dirac current is normal conformal and complete the classification of manifolds admitting CCKS in all dimensions and signatures ≤5 which has recently been initiated in the study of supersymmetric field theories on curved space.

  15. Characterization of the cryptic plasmid pBGR1 from Bartonella grahamii and construction of a versatile Escherichia coli-Bartonella spp. shuttle cloning vector.

    PubMed

    Seubert, Anja; Falch, Christine; Birtles, Richard J; Schulein, Ralf; Dehio, Christoph

    2003-01-01

    We report herein the isolation and molecular characterization of pBGR1, the first native plasmid isolated from the genus Bartonella. Cloning and sequencing revealed a 2725-base pair (bp) cryptic plasmid comprising two open reading frames of considerable length, which were designated rep and mob. The regions containing rep and mob are separated by 140-bp inverted repeat sequences and display a difference in G + C content from one another. A 1435-bp SacI-BclI fragment containing the rep gene is sufficient to mediate replication in the species Bartonella henselae and Bartonella tribocorum, while this replicon does not appear to be functional in Escherichia coli. The Rep protein of 190 amino acids (aa) shares homology to putative replication proteins of cryptic plasmids of Gram-negative origin, which form a subgroup of the rolling-circle replication proteins of the pSN2 plasmid superfamily of Gram-positive bacteria. The Mob protein of 333 aa is related to mobilization proteins of several cryptic plasmids and is associated with a conserved recombination site A. The tra functions of RP4 can mobilize pBGR1 derivatives in a mob-dependent manner. Mobilizable pBGR1-based E. coli-Bartonella spp. shuttle vectors were constructed and were shown to be maintained in B. tribocorum during in vivo passage in a rat model in the absence of antibiotic selection. The small size and stability of these shuttle cloning vectors should render them particularly valuable for genetic studies in Bartonella spp.

  16. Cryptic microsporidian parasites differentially affect invasive and native Artemia spp.

    PubMed

    Rode, Nicolas O; Lievens, Eva J P; Segard, Adeline; Flaven, Elodie; Jabbour-Zahab, Roula; Lenormand, Thomas

    2013-09-01

    We investigated the host specificity of two cryptic microsporidian species (Anostracospora rigaudi and Enterocytospora artemiae) infecting invasive (Artemia franciscana) and native (Artemia parthenogenetica) hosts in sympatry. Anostracospora rigaudi was on average four times more prevalent in the native host, whereas E. artemiae was three times more prevalent in the invasive host. Infection with An. rigaudi strongly reduced female reproduction in both host species, whereas infection with E. artemiae had weaker effects on female reproduction. We contrasted microsporidian prevalence in native A. franciscana populations (New World) and in both invaded and non-invaded Artemia populations (Old World). At a community level, microsporidian prevalence was twice as high in native compared with invasive hosts, due to the contrasting host-specificity of An. rigaudi and E. artemiae. At a higher biogeographical level, microsporidian prevalence in A. franciscana did not differ between the invaded populations and the native populations used for the introduction. Although E. artemiae was the only species found both in New and Old World populations, no evidence of its co-introduction with the invasive host was found in our experimental and phylogeographic tests. These results suggest that the success of A. franciscana invasion is probably due to a lower susceptibility to virulent microsporidian parasites rather than to decreased microsporidian prevalence compared with A. parthenogenetica or to lower microsporidian virulence in introduced areas. Published by Elsevier Ltd.

  17. Cryptic adaptive radiation in tropical forest trees in New Caledonia.

    PubMed

    Pillon, Yohan; Hopkins, Helen C F; Rigault, Frédéric; Jaffré, Tanguy; Stacy, Elizabeth A

    2014-04-01

    The causes of the species richness of tropical trees are poorly understood, in particular the roles of ecological factors such as soil composition. The nickel(Ni)-hyperaccumulating tree genus Geissois (Cunoniaceae) from the South-west Pacific was chosen as a model of diversification on different substrates. Here, we investigated the leaf element compositions, spatial distributions and phylogeny of all species of Geissois occurring on New Caledonia. We found that New Caledonian Geissois descended from a single colonist and diversified relatively quickly into 13 species. Species on ultramafic and nonultramafic substrates showed contrasting patterns of leaf element composition and range overlap. Those on nonultramafic substrates were largely sympatric but had distinct leaf element compositions. By contrast, species on ultramafic substrates showed similar leaf element composition, but occurred in many cases exclusively in allopatry. Further, earlier work showed that at least three out of these seven species use different molecules to bind Ni. Geissois qualifies as a cryptic adaptive radiation, and may be the first such example in a lineage of tropical forest trees. Variation in biochemical strategies for coping with both typical and adverse soil conditions may help to explain the diversification and coexistence of tropical forest trees on similar soil types.

  18. Species diversity in the cryptic abyssal holothurian Psychropotes longicauda (Echinodermata)

    NASA Astrophysics Data System (ADS)

    Gubili, Chrysoula; Ross, Elizabeth; Billett, David S. M.; Yool, Andrew; Tsairidis, Charalampos; Ruhl, Henry A.; Rogacheva, Antonina; Masson, Doug; Tyler, Paul A.; Hauton, Chris

    2017-03-01

    Despite the plethora of studies on swallow-water invertebrates, almost nothing is known about the evolution and population structure of deep-sea species at the global scale. The aim of this study was to assess phylogeographic patterns of a common and cosmopolitan, predominantly abyssal sea cucumber, Psychropotes longicauda, based on samples from the Atlantic, Southern, Indian and Pacific oceans. Sequences of the mitochondrial COI and 16S genes were analysed for 128 specimens of P. longicauda. In addition, temporal genetic variation was investigated at one site, the Porcupine Abyssal Plain, NE Atlantic Ocean over a period of 34 years. Two distinct lineages within the global distribution were identified. The sister clades probably could be classified as separate species based on the observed genetic divergence (>5.0%) and phylogenetic reconstruction with indications of a Southern Hemisphere origin. Moreover, significant population differentiation was detected between the North Atlantic and localities in both the Pacific and Indian oceans. No bathymetric structuring was detected among lineages. Temporal genetic shifts were detected in a time series of samples from 1977 to 2011. Our data confirm the previously suspected cryptic species diversity throughout the wide distributional range previously attributed to the single species P. longicauda. The presence of sympatric species in the North Pacific and Indian Oceans has been underestimated by previous morphological analyses. The differentiation at the population level detected in the main lineages among the four oceans could suggest restricted gene flow despite wide-scale dispersal potential of the species.

  19. Cryptic polyketide synthase genes in non-pathogenic Clostridium SPP.

    PubMed

    Behnken, Swantje; Hertweck, Christian

    2012-01-01

    Modular type I polyketide synthases (PKS) produce a vast array of bacterial metabolites with highly diverse biological functions. Notably, all known polyketides were isolated from aerobic bacteria, and yet no example has been reported for strict anaerobes. In this study we explored the diversity and distribution of PKS genes in the genus Clostridium. In addition to comparative genomic analyses combined with predictions of modular type I polyketide synthase (PKS) gene clusters in sequenced genomes of Clostridium spp., a representative selection of other species inhabiting a variety of ecological niches was investigated by PCR screening for PKS genes. Our data reveal that all studied pathogenic Clostridium spp. are devoid of putative PKS genes. In stark contrast, cryptic PKS genes are widespread in genomes of non-pathogenic Clostridium species. According to phylogenetic analyses, the Clostridium PKS genes have unusual and diverse origins. However, reverse transcription quantitative PCR demonstrates that these genes are silent under standard cultivation conditions, explaining why the related metabolites have been overlooked until now. This study presents clostridia as a putative source for novel bioactive polyketides.

  20. Cryptic biodiversity loss linked to global climate change

    NASA Astrophysics Data System (ADS)

    Bálint, M.; Domisch, S.; Engelhardt, C. H. M.; Haase, P.; Lehrian, S.; Sauer, J.; Theissinger, K.; Pauls, S. U.; Nowak, C.

    2011-09-01

    Global climate change (GCC) significantly affects distributional patterns of organisms, and considerable impacts on biodiversity are predicted for the next decades. Inferred effects include large-scale range shifts towards higher altitudes and latitudes, facilitation of biological invasions and species extinctions. Alterations of biotic patterns caused by GCC have usually been predicted on the scale of taxonomically recognized morphospecies. However, the effects of climate change at the most fundamental level of biodiversity--intraspecific genetic diversity--remain elusive. Here we show that the use of morphospecies-based assessments of GCC effects will result in underestimations of the true scale of biodiversity loss. Species distribution modelling and assessments of mitochondrial DNA variability in nine montane aquatic insect species in Europe indicate that future range contractions will be accompanied by severe losses of cryptic evolutionary lineages and genetic diversity within these lineages. These losses greatly exceed those at the scale of morphospecies. We also document that the extent of range reduction may be a useful proxy when predicting losses of genetic diversity. Our results demonstrate that intraspecific patterns of genetic diversity should be considered when estimating the effects of climate change on biodiversity.

  1. Cryptic species of Paracoccidioides brasiliensis: impact on paracoccidioidomycosis immunodiagnosis

    PubMed Central

    Machado, Gabriel Capella; Moris, Daniela Vanessa; Arantes, Thales Domingos; Silva, Luciane Regina Franciscone; Theodoro, Raquel Cordeiro; Mendes, Rinaldo Pôncio; Vicentini, Adriana Pardini; Bagagli, Eduardo

    2013-01-01

    We aimed to evaluate whether the occurrence of cryptic species of Paracoccidioides brasiliensis, S1, PS2, PS3 and Paracoccidioides lutzii, has implications in the immunodiagnosis of paracoccidioidomycosis (PCM). Small quantities of the antigen gp43 were found in culture filtrates of P. lutzii strains and this molecule appeared to be more variable within P. lutzii because the synonymous-nonsynonymous mutation rate was lower, indicating an evolutionary process different from that of the remaining genotypes. The production of gp43 also varied between isolates belonging to the same species, indicating that speciation events are important, but not sufficient to fully explain the diversity in the production of this antigen. The culture filtrate antigen AgEpm83, which was obtained from a PS3 isolate, showed large quantities of gp43 and reactivity by immunodiffusion assays, similar to the standard antigen (AgB-339) from an S1 isolate. Furthermore, AgEpm83 was capable of serologically differentiating five serum samples from patients from the Botucatu and Jundiaí regions. These patients had confirmed PCM but, were non-reactive to the standard antigen, thus demonstrating an alternative for serological diagnosis in regions in which S1 and PS2 occur. We also emphasise that it is not advisable to use a single antigen preparation to diagnose PCM, a disease that is caused by highly diverse pathogens. PMID:23903981

  2. Copepod Behavior in ``Cryptic Blooms'' of Toxic Algae

    NASA Astrophysics Data System (ADS)

    True, A. C.; Webster, D. R.; Weissburg, M. J.; Yen, J.

    2014-11-01

    Copepods,Acartia tonsa and Temora longicornis, were exposed to thin layers of exudates from the toxic dinoflagellate Karenia brevis (1 - 10,000 cells/mL) (i.e. models of ``cryptic blooms'' of toxic phytoplankton). Planar laser-induced fluorescence (PLIF) was used to quantify the spatiotemporal structure of the layer allowing for correlation of behavioral responses with toxin levels. Both species explicitly avoided the exudate layer and the vicinity of the layer. Measures of path kinematics (swimming speed, turn frequency) by location (in-layer vs. out-of-layer) and exposure (pre-contact vs. post-contact) revealed some similarities, but also significant differences, in trends for each species. A. tonsa significantly increases swimming speed and swimming speed variability in the exudate layer and post-contact, whereas T. longicornis slightly increases both in-layer and slightly reduces both post-contact. Both species increase turn frequency in-layer and post-contact with increasing K. brevis exudate concentration. Path fracticality indicates that A. tonsatrajectories became more diffuse/sinuous and T. longicornis trajectories became more linear/ballistic (trending effects). Regression analyses revealed that the rate of change of behavior with increasing exudate concentration for A. tonsa was thrice to fifty times that of T. longicornis. Toxic K. brevis can essentially eliminate top-down grazer control ,another sinister means by which it gains a competitive advantage over the local phytoplankton taxa.

  3. Two sisters in the same dress: Heliconius cryptic species

    PubMed Central

    2008-01-01

    Background Sister species divergence and reproductive isolation commonly results from ecological adaptation. In mimetic Heliconius butterflies, shifts in colour pattern contribute to pre- and post-mating reproductive isolation and are commonly correlated with speciation. Closely related mimetic species are therefore not expected, as they should lack several important sources of reproductive isolation. Results Here we present phenotypic, behavioral and genetic evidence for the coexistence of two sympatric 'cryptic' species near Florencia in the eastern Andes of Colombia that share the same orange rayed colour pattern. These represent H. melpomene malleti and a novel taxon in the H. cydno group, here designated as novel race of Heliconius timareta, Heliconius timareta florencia. No-choice mating experiments show that these sympatric forms have strong assortative mating (≈96%) despite great similarity in colour pattern, implying enhanced divergence in pheromonal signals. Conclusion We hypothesize that these species might have resulted from recent convergence in colour pattern, perhaps facilitated by hybrid introgression of wing pattern genes. PMID:19040737

  4. Cryptic Polyketide Synthase Genes in Non-Pathogenic Clostridium SPP

    PubMed Central

    Behnken, Swantje; Hertweck, Christian

    2012-01-01

    Modular type I polyketide synthases (PKS) produce a vast array of bacterial metabolites with highly diverse biological functions. Notably, all known polyketides were isolated from aerobic bacteria, and yet no example has been reported for strict anaerobes. In this study we explored the diversity and distribution of PKS genes in the genus Clostridium. In addition to comparative genomic analyses combined with predictions of modular type I polyketide synthase (PKS) gene clusters in sequenced genomes of Clostridium spp., a representative selection of other species inhabiting a variety of ecological niches was investigated by PCR screening for PKS genes. Our data reveal that all studied pathogenic Clostridium spp. are devoid of putative PKS genes. In stark contrast, cryptic PKS genes are widespread in genomes of non-pathogenic Clostridium species. According to phylogenetic analyses, the Clostridium PKS genes have unusual and diverse origins. However, reverse transcription quantitative PCR demonstrates that these genes are silent under standard cultivation conditions, explaining why the related metabolites have been overlooked until now. This study presents clostridia as a putative source for novel bioactive polyketides. PMID:22235310

  5. Role of Pleiotropy in the Evolution of a Cryptic Developmental Variation in Caenorhabditis elegans

    PubMed Central

    Duveau, Fabien; Félix, Marie-Anne

    2012-01-01

    Robust biological systems are expected to accumulate cryptic genetic variation that does not affect the system output in standard conditions yet may play an evolutionary role once phenotypically expressed under a strong perturbation. Genetic variation that is cryptic relative to a robust trait may accumulate neutrally as it does not change the phenotype, yet it could also evolve under selection if it affects traits related to fitness in addition to its cryptic effect. Cryptic variation affecting the vulval intercellular signaling network was previously uncovered among wild isolates of Caenorhabditis elegans. Using a quantitative genetic approach, we identify a non-synonymous polymorphism of the previously uncharacterized nath-10 gene that affects the vulval phenotype when the system is sensitized with different mutations, but not in wild-type strains. nath-10 is an essential protein acetyltransferase gene and the homolog of human NAT10. The nath-10 polymorphism also presents non-cryptic effects on life history traits. The nath-10 allele carried by the N2 reference strain leads to a subtle increase in the egg laying rate and in the total number of sperm, a trait affecting the trade-off between fertility and minimal generation time in hermaphrodite individuals. We show that this allele appeared during early laboratory culture of N2, which allowed us to test whether it may have evolved under selection in this novel environment. The derived allele indeed strongly outcompetes the ancestral allele in laboratory conditions. In conclusion, we identified the molecular nature of a cryptic genetic variation and characterized its evolutionary history. These results show that cryptic genetic variation does not necessarily accumulate neutrally at the whole-organism level, but may evolve through selection for pleiotropic effects that alter fitness. In addition, cultivation in the laboratory has led to adaptive evolution of the reference strain N2 to the laboratory environment

  6. Conformal cloak for waves

    SciTech Connect

    Chen Huanyang; Leonhardt, Ulf; Tyc, Tomas

    2011-05-15

    Conformal invisibility devices are only supposed to work within the valid range of geometrical optics. Here, we show by numerical simulations and analytical arguments that for certain quantized frequencies, they are nearly perfect even in a regime that clearly violates geometrical optics. The quantization condition follows from the analogy between the Helmholtz equation and the stationary Schroedinger equation.

  7. Conformational properties of pyrethroids

    NASA Astrophysics Data System (ADS)

    Mullaley, Anne; Taylor, Robin

    1994-04-01

    X-ray database searches and theoretical potential-energy calculations indicate that the acid moieties of pyrethroid cyclopropanecarboxylate esters adopt a well-defined, relatively inflexible conformation. In contrast, the alcohol moieties can exist in many low-energy geometries. One of the least conformationally flexible pyrethroid alcohols is 4-phenylindan-2-ol. The approximate overall conformation adopted at the biological binding site by insecticidal esters of this alcohol can be deduced with reasonable confidence by molecular modelling. Graphics superposition of a variety of pyrethroid acids suggests the existence of a large but rather narrow pocket at the binding site, in which substituents at the 3-position of the cyclopropane ring can be accommodated. This pocket is asymmetric with respect to the plane of the cyclopropane ring, extending further on the side remote from the ester group. The effects of α-substitution on the insecticidal activity of pyrethroid esters may be due to the influence of substituents on the preferred conformations of the molecules. This hypothesis rationalises the paradoxical dependence on absolute stereochemistry of the activities of various allylbenzyl and cinnamyl alcohol derivatives.

  8. Conformal Image Warping

    DTIC Science & Technology

    1988-10-01

    the unit disk Henrici has recently surveyed existing numerical conformal mapping algorithms [8]. For arbitrary shaped regions (which are approximated...22, 3 (August 1988),. 8. Henrici , P., in Applied and computational complex analysis, vol. 3, Wiley, New York,NY, 1986, 402-413. 9. Preparata, F. P

  9. PERSONALITY AND CONFORMITY.

    ERIC Educational Resources Information Center

    BAROCAS, RALPH; GORLOW, LEON

    AN INVESTIGATION WAS MADE OF THE RELATIONSHIP BETWEEN PERSONALITY FACTORS AND CONFORMITY. THE SUBJECTS WERE 243 RANDOMLY SELECTED STUDENTS ENROLLED IN COLLEGE PSYCHOLOGY COURSES WHO WERE DIVIDED INTO GROUPS OF 97, 96, AND 50 SUBJECTS. A PERSONALITY FACTOR INVENTORY WAS OBTAINED FROM RESPONSES TO A LARGE LIST OF TRUE-FALSE PERSONALITY ITEM…

  10. Conformational changes in biopolymers

    NASA Astrophysics Data System (ADS)

    Ivanov, Vassili

    2005-12-01

    Biopolymer conformational changes are involved in many biological processes. This thesis summarizes some theoretical and experimental approaches which I have taken at UCLA to explore conformational changes in biopolymers. The reversible thermal denaturation of the DNA double helix is, perhaps, the simplest example of biopolymer conformational change. I have developed a statistical mechanics model of DNA melting with reduced degrees of freedom, which allows base stacking interaction to be taken into account and treat base pairing and stacking separately. Unlike previous models, this model describes both the unpairing and unstacking parts of the experimental melting curves and explains the observed temperature dependence of the effective thermodynamic parameters used in models of the nearest neighbor type. I developed a basic kinetic model for irreversible thermal denaturation of F-actin, which incorporates depolymerization of F-actin from the ends and breaking of F-actin fiber in the middle. The model explains the cooperativity of F-actin thermal denaturation observed by D. Pavlov et al. in differential calorimetry measurements. CG-rich DNA sequences form left-handed Z-DNA at high ionic strength or upon binding of polyvalent ions and some proteins. I studied experimentally the B-to-Z transition of the (CG)6 dodecamer. Improvement of the locally linearized model used to interpret the data gives evidence for an intermediate state in the B-to-Z transition of DNA, contrary to previous research on this subject. In the past 15 years it has become possible to study the conformational changes of biomolecules using single-molecule techniques. In collaboration with other lab members I performed a single-molecule experiment, where we monitored the displacement of a micrometer-size bead tethered to a surface by a DNA probe undergoing the conformational change. This technique allows probing of conformational changes with subnanometer accuracy. We applied the method to detect

  11. Galilean conformal and superconformal symmetries

    SciTech Connect

    Lukierski, J.

    2012-10-15

    Firstly we discuss briefly three different algebras named as nonrelativistic (NR) conformal: Schroedinger, Galilean conformal, and infinite algebra of local NR conformal isometries. Further we shall consider in some detail Galilean conformal algebra (GCA) obtained in the limit c{yields}{infinity} from relativistic conformal algebraO(d+1, 2) (d-number of space dimensions). Two different contraction limits providing GCA and some recently considered realizations will be briefly discussed. Finally by considering NR contraction of D = 4 superconformal algebra the Galilei conformal superalgebra (GCSA) is obtained, in the formulation using complexWeyl supercharges.

  12. Cryptic species diversity reveals biogeographic support for the 'mountain passes are higher in the tropics' hypothesis.

    PubMed

    Gill, B A; Kondratieff, B C; Casner, K L; Encalada, A C; Flecker, A S; Gannon, D G; Ghalambor, C K; Guayasamin, J M; Poff, N L; Simmons, M P; Thomas, S A; Zamudio, K R; Funk, W C

    2016-06-15

    The 'mountain passes are higher in the tropics' (MPHT) hypothesis posits that reduced climate variability at low latitudes should select for narrower thermal tolerances, lower dispersal and smaller elevational ranges compared with higher latitudes. These latitudinal differences could increase species richness at low latitudes, but that increase may be largely cryptic, because physiological and dispersal traits isolating populations might not correspond to morphological differences. Yet previous tests of the MPHT hypothesis have not addressed cryptic diversity. We use integrative taxonomy, combining morphology (6136 specimens) and DNA barcoding (1832 specimens) to compare the species richness, cryptic diversity and elevational ranges of mayflies (Ephemeroptera) in the Rocky Mountains (Colorado; approx. 40°N) and the Andes (Ecuador; approx. 0°). We find higher species richness and smaller elevational ranges in Ecuador than Colorado, but only after quantifying and accounting for cryptic diversity. The opposite pattern is found when comparing diversity based on morphology alone, underscoring the importance of uncovering cryptic species to understand global biodiversity patterns. © 2016 The Author(s).

  13. DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes

    PubMed Central

    Wiklund, Helena; Neal, Lenka; Jeffreys, Rachel; Linse, Katrin; Ruhl, Henry; Glover, Adrian G.

    2016-01-01

    The Antarctic marine environment is a diverse ecosystem currently experiencing some of the fastest rates of climatic change. The documentation and management of these changes requires accurate estimates of species diversity. Recently, there has been an increased recognition of the abundance and importance of cryptic species, i.e. those that are morphologically identical but genetically distinct. This article presents the largest genetic investigation into the prevalence of cryptic polychaete species within the deep Antarctic benthos to date. We uncover cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%. Our ability to describe universal rules for the detection of cryptic species within polychaetes, or normalization to expected number of species based on genetic data is prevented by taxon-specific differences in phylogenetic outputs and genetic variation between and within potential cryptic species. These data provide the foundation for biogeographic and functional analysis that will provide insight into the drivers of species diversity and its role in ecosystem function. PMID:28018624

  14. Integrating molecular and morphological approaches for characterizing parasite cryptic species: implications for parasitology.

    PubMed

    Nadler, Steven A; DE León, Gerardo Pérez-Ponce

    2011-11-01

    Herein we review theoretical and methodological considerations important for finding and delimiting cryptic species of parasites (species that are difficult to recognize using traditional systematic methods). Applications of molecular data in empirical investigations of cryptic species are discussed from an historical perspective, and we evaluate advantages and disadvantages of approaches that have been used to date. Developments concerning the theory and practice of species delimitation are emphasized because theory is critical to interpretation of data. The advantages and disadvantages of different molecular methodologies, including the number and kind of loci, are discussed relative to tree-based approaches for detecting and delimiting cryptic species. We conclude by discussing some implications that cryptic species have for research programmes in parasitology, emphasizing that careful attention to the theory and operational practices involved in finding, delimiting, and describing new species (including cryptic species) is essential, not only for fully characterizing parasite biodiversity and broader aspects of comparative biology such as systematics, evolution, ecology and biogeography, but to applied research efforts that strive to improve development and understanding of epidemiology, diagnostics, control and potential eradication of parasitic diseases.

  15. DNA barcoding uncovers cryptic diversity in 50% of deep-sea Antarctic polychaetes.

    PubMed

    Brasier, Madeleine J; Wiklund, Helena; Neal, Lenka; Jeffreys, Rachel; Linse, Katrin; Ruhl, Henry; Glover, Adrian G

    2016-11-01

    The Antarctic marine environment is a diverse ecosystem currently experiencing some of the fastest rates of climatic change. The documentation and management of these changes requires accurate estimates of species diversity. Recently, there has been an increased recognition of the abundance and importance of cryptic species, i.e. those that are morphologically identical but genetically distinct. This article presents the largest genetic investigation into the prevalence of cryptic polychaete species within the deep Antarctic benthos to date. We uncover cryptic diversity in 50% of the 15 morphospecies targeted through the comparison of mitochondrial DNA sequences, as well as 10 previously overlooked morphospecies, increasing the total species richness in the sample by 233%. Our ability to describe universal rules for the detection of cryptic species within polychaetes, or normalization to expected number of species based on genetic data is prevented by taxon-specific differences in phylogenetic outputs and genetic variation between and within potential cryptic species. These data provide the foundation for biogeographic and functional analysis that will provide insight into the drivers of species diversity and its role in ecosystem function.

  16. HIGH-RESOLUTION GENOMIC ARRAYS FACILITATE DETECTION OF NOVEL CRYPTIC CHROMOSOMAL LESIONS IN MYELODYSPLASTIC SYNDROMES

    PubMed Central

    O’Keefe, Christine L.; Tiu, Ramon; Gondek, Lukasz P.; Powers, Jennifer; Theil, Karl S.; Kalaycio, Matt; Lichtin, Alan; Sekeres, Mikkael A.; Maciejewski, Jaroslaw P.

    2008-01-01

    Objective Unbalanced chromosomal aberrations are common in myelodysplastic syndromes, and have prognostic implications. An increased frequency of cytogenetic changes may reflect an inherent chromosomal instability due to failure of DNA repair. Therefore, it is likely that chromosomal defects in myelodysplastic syndromes may be more frequent than predicted by metaphase cytogenetics and new cryptic lesions may be revealed by precise analysis methods. Methods We used a novel high-resolution karyotyping technique, array-based comparative genomic hybridization, to investigate the frequency of cryptic chromosomal lesions in a cohort of 38 well-characterized myelodysplastic syndromes patients; results were confirmed by microsatellite quantitative PCR or single nucleotide polymorphism analysis. Results As compared to metaphase karyotyping, chromosomal abnormalities detected by array-based analysis were encountered more frequently and in a higher proportion of patients. For example, chromosomal defects were found in patients with a normal karyotype by traditional cytogenetics. In addition to verifying common abnormalities, previously cryptic defects were found in new regions of the genome. Cryptic changes often overlapped chromosomes and regions frequently identified as abnormal by metaphase cytogenetics. Conclusion The results underscore the instability of the myelodysplastic syndromes genome and highlight the utility of array-based karyotyping to study cryptic chromosomal changes which may provide new diagnostic information. PMID:17258073

  17. Testing dispersal and cryptic diversity in a widely distributed groundwater amphipod (Niphargus rhenorhodanensis).

    PubMed

    Lefébure, T; Douady, C J; Malard, F; Gibert, J

    2007-03-01

    Theories about colonization and evolution in groundwater have assumed that the fragmented structure of groundwater strongly limits dispersal. The high number of endemic and allopatric species in groundwater supports this hypothesis, but the occurrence of widely distributed groundwater taxa calls into question its universality. These widely distributed taxa might also be sets of cryptic species because extreme conditions of life in groundwater promote cryptic diversity by inducing convergent morphological evolution. Niphargus rhenorhodanensis is a widely distributed and ubiquitous groundwater amphipod which supposedly colonized the Alps after Quaternary glaciations. We tested the dispersal and the cryptic species hypotheses within this species using a phylogeographic approach based on two mitochondrial genes (COI and 16S) and a nuclear gene (28S). Results support the view that poor dispersal is a main evolutionary factor in groundwater. All genes independently supported the existence of numerous cryptic and mostly allopatric units within N. rhenorhodanensis, indicating that its apparently wide distribution range is an artefact generated by cryptic diversity. We reject the hypothesis of a recent and global colonization of the Alps and argue that some N. rhenorhodanensis lineages probably survived glaciations near or within the Alps.

  18. Cryptic diversity and ecosystem functioning: a complex tale of differential effects on decomposition.

    PubMed

    De Meester, N; Gingold, R; Rigaux, A; Derycke, S; Moens, T

    2016-10-01

    Marine ecosystems are experiencing accelerating population and species loss. Some ecosystem functions are decreasing and there is growing interest in the link between biodiversity and ecosystem functioning. The role of cryptic (morphologically identical but genetically distinct) species in this biodiversity-ecosystem functioning link is unclear and has not yet been formally tested. We tested if there is a differential effect of four cryptic species of the bacterivorous nematode Litoditis marina on the decomposition process of macroalgae. Bacterivorous nematodes can stimulate or slow down bacterial activity and modify the bacterial assemblage composition. Moreover, we tested if interspecific interactions among the four cryptic species influence the decomposition process. A laboratory experiment with both mono- and multispecific nematode cultures was conducted, and loss of organic matter and the activity of two key extracellular enzymes for the degradation of phytodetritus were assessed. L. marina mainly influenced qualitative aspects of the decomposition process rather than its overall rate: an effect of the nematodes on the enzymatic activities became manifest, although no clear nematode effect on bulk organic matter weight loss was found. We also demonstrated that species-specific effects on the decomposition process existed. Combining the four cryptic species resulted in high competition, with one dominant species, but without complete exclusion of other species. These interspecific interactions translated into different effects on the decomposition process. The species-specific differences indicated that each cryptic species may play an important and distinct role in ecosystem functioning. Functional differences may result in coexistence among very similar species.

  19. Speed-accuracy tradeoffs and false alarms in bee responses to cryptic predators.

    PubMed

    Ings, Thomas C; Chittka, Lars

    2008-10-14

    Learning plays a crucial role in predator avoidance [1-3], but little is known about how the type of experience with predators molds future prey behavior. Specifically, is predator-avoidance learning and memory retention disrupted by cryptic coloration of predators, such as crab spiders [4, 5]? How does experience with different predators affect foraging decisions? We evaluated these questions by exposing foraging bumblebees to controlled predation risk from predators (robotic crab spiders) that were either cryptic or highly contrasting, as assessed by a quantitative model of bee color perception [6]. Our results from 3D tracking software reveal a speed-accuracy tradeoff [7]: Bees slow their inspection flights after learning that there is a risk from cryptic spiders. The adjustment of inspection effort results in accurate predator detection, leveling out predation risk at the expense of foraging time. Overnight-retention tests reveal no decline in performance, but bees that had experienced cryptic predators are more prone to "false alarms" (rejection of foraging opportunities on safe flowers) than those that had experienced conspicuous predators. Therefore, bees in the cryptic-spider treatment made a functional decision to trade off reduced foraging efficiency via increased inspection times and false-alarm rates against higher potential fitness loss from being injured or eaten.

  20. Exploration of the relationship between topology and designability of conformations.

    PubMed

    Leelananda, Sumudu P; Towfic, Fadi; Jernigan, Robert L; Kloczkowski, Andrzej

    2011-06-21

    Protein structures are evolutionarily more conserved than sequences, and sequences with very low sequence identity frequently share the same fold. This leads to the concept of protein designability. Some folds are more designable and lots of sequences can assume that fold. Elucidating the relationship between protein sequence and the three-dimensional (3D) structure that the sequence folds into is an important problem in computational structural biology. Lattice models have been utilized in numerous studies to model protein folds and predict the designability of certain folds. In this study, all possible compact conformations within a set of two-dimensional and 3D lattice spaces are explored. Complementary interaction graphs are then generated for each conformation and are described using a set of graph features. The full HP sequence space for each lattice model is generated and contact energies are calculated by threading each sequence onto all the possible conformations. Unique conformation giving minimum energy is identified for each sequence and the number of sequences folding to each conformation (designability) is obtained. Machine learning algorithms are used to predict the designability of each conformation. We find that the highly designable structures can be distinguished from other non-designable conformations based on certain graphical geometric features of the interactions. This finding confirms the fact that the topology of a conformation is an important determinant of the extent of its designability and suggests that the interactions themselves are important for determining the designability. © 2011 American Institute of Physics

  1. Exploration of the relationship between topology and designability of conformations

    NASA Astrophysics Data System (ADS)

    Leelananda, Sumudu P.; Towfic, Fadi; Jernigan, Robert L.; Kloczkowski, Andrzej

    2011-06-01

    Protein structures are evolutionarily more conserved than sequences, and sequences with very low sequence identity frequently share the same fold. This leads to the concept of protein designability. Some folds are more designable and lots of sequences can assume that fold. Elucidating the relationship between protein sequence and the three-dimensional (3D) structure that the sequence folds into is an important problem in computational structural biology. Lattice models have been utilized in numerous studies to model protein folds and predict the designability of certain folds. In this study, all possible compact conformations within a set of two-dimensional and 3D lattice spaces are explored. Complementary interaction graphs are then generated for each conformation and are described using a set of graph features. The full HP sequence space for each lattice model is generated and contact energies are calculated by threading each sequence onto all the possible conformations. Unique conformation giving minimum energy is identified for each sequence and the number of sequences folding to each conformation (designability) is obtained. Machine learning algorithms are used to predict the designability of each conformation. We find that the highly designable structures can be distinguished from other non-designable conformations based on certain graphical geometric features of the interactions. This finding confirms the fact that the topology of a conformation is an important determinant of the extent of its designability and suggests that the interactions themselves are important for determining the designability.

  2. Conformational flexibility of bacterial RNA polymerase

    PubMed Central

    Darst, Seth A.; Opalka, Natacha; Chacon, Pablo; Polyakov, Andrey; Richter, Catherine; Zhang, Gongyi; Wriggers, Willy

    2002-01-01

    The structure of Escherichia coli core RNA polymerase (RNAP) was determined by cryo-electron microscopy and image processing of helical crystals to a nominal resolution of 15 Å. Because of the high sequence conservation between the core RNAP subunits, we were able to interpret the E. coli structure in relation to the high-resolution x-ray structure of Thermus aquaticus core RNAP. A very large conformational change of the T. aquaticus RNAP x-ray structure, corresponding to opening of the main DNA/RNA channel by nearly 25 Å, was required to fit the E. coli map. This finding reveals, at least partially, the range of conformational flexibility of the RNAP, which is likely to have functional implications for the initiation of transcription, where the DNA template must be loaded into the channel. PMID:11904365

  3. Conservation endocrinology

    USGS Publications Warehouse

    McCormick, Stephen; Romero, L. Michael

    2017-01-01

    Endocrinologists can make significant contributions to conservation biology by helping to understand the mechanisms by which organisms cope with changing environments. Field endocrine techniques have advanced rapidly in recent years and can provide substantial information on the growth, stress, and reproductive status of individual animals, thereby providing insight into current and future responses of populations to changes in the environment. Environmental stressors and reproductive status can be detected nonlethally by measuring a number of endocrine-related endpoints, including steroids in plasma, living and nonliving tissue, urine, and feces. Information on the environmental or endocrine requirements of individual species for normal growth, development, and reproduction will provide critical information for species and ecosystem conservation. For many taxa, basic information on endocrinology is lacking, and advances in conservation endocrinology will require approaches that are both “basic” and “applied” and include integration of laboratory and field approaches.

  4. Evidence of cryptic individual specialization in an opportunistic insectivorous bat

    USGS Publications Warehouse

    Cryan, Paul M.; Stricker, Craig A.; Wunder, Michael B.

    2012-01-01

    Habitat use and feeding behaviors of cryptic animals are often poorly understood. Analyses of stable isotope ratios in animal body tissues can help reveal an individual's location and resource use during tissue growth. We investigated variation in stable isotope ratios of 4 elements (H, C, N, and S) in the hair of a sedentary species of insectivorous bat (Eptesicus fuscus) inhabiting a chemically complex urban landscape. Our objective was to quantify population-level isotopic variation and test for evidence of resource specialization by individuals. Bats were sampled over 3 annual molt cycles at maternity roosts in buildings and variance components analysis was used to test whether intraindividual isotopic variation among molts differed from interindividual variation, after controlling for year and roost-group effects. Consistent with prior evidence that E. fuscus is opportunistic in its habitat use and foraging at the population level, we observed wide population-level variation for all isotopes. This variation likely reflects the chemical complexity of the urban landscape studied. However, isotopic variation among years within marked individuals was lower than variation among marked individuals within year for all isotopes, and carbon signatures indicated resource specialization by roost groups and individuals. This is the 1st study to examine variation in stable isotope ratios of individual wild bats over multiple years. Although our results suggest this population tends toward opportunistic habitat use or prey selection, or both, during molt periods, results also indicate that individuals and groups of bats composing the population might be habitat or dietary specialists—a novel finding for insectivorous bats.

  5. "Cryptic" diagenesis and its implications for speleothem geochronologies

    NASA Astrophysics Data System (ADS)

    Bajo, Petra; Hellstrom, John; Frisia, Silvia; Drysdale, Russell; Black, Jay; Woodhead, Jon; Borsato, Andrea; Zanchetta, Giovanni; Wallace, Malcolm W.; Regattieri, Eleonora; Haese, Ralf

    2016-09-01

    Speleothems are usually considered as one of the most amenable palaeoclimate archives for U-series dating. A number of studies in recent years, however, report cases of diagenetic alteration which compromises the use of U-series systematics in speleothems, resulting in inaccurate U-Th ages. Here we present the results of a high-resolution U-Th dating study of a stalagmite (CC26) from Corchia Cave in Italy where we document a number of departures from an otherwise well-defined age-depth model, and explore potential causes for these outliers. Unlike examples illustrated in previous studies, CC26 contains no visible evidence of neomorphism, and appears, at least superficially, ideally suited to dating. Good reproducibility obtained between multi-aliquot U-Th analyses removes any possibility of analytical issues contributing to these outliers. Furthermore, replicate analyses of samples from the same stratigraphic layer yielded ages in stratigraphic sequence, implying very localized open-system behavior. Uranium loss is suggested as a causative mechanism on account of the fact that all the outliers are older than their assumed true age. A limited number of micro-voids were observed under micro-CT analyses, and it is proposed that these were pathways for U loss. Uranium-loss modelling allows us to constrain the possible timing of diagenetic alteration and indicates that the precursor for the outlier with the largest age discrepancy (309%) must have been aragonite. This study indicates that visibly unaltered speleothems may still contain small domains that have experienced post-depositional alteration. Such ;cryptic; diagenesis, as recorded in this stalagmite, has implications for the constancy of accuracy of the U-series dating technique, and suggests a need for careful examination of speleothems prior to dating, particularly in low-resolution U-Th studies.

  6. Cryptic diversity and symbiont interactions in rock-posy lichens.

    PubMed

    Leavitt, Steven D; Kraichak, Ekaphan; Vondrak, Jan; Nelsen, Matthew P; Sohrabi, Mohammad; Perez-Ortega, Sergio; St Clair, Larry L; Lumbsch, H Thorsten

    2016-06-01

    Identifying factors that influence species interactions is central to research in symbiotic systems. While lichens represent iconic models of symbiosis and play important roles in understanding the biology of symbiotic interactions, patterns of interactions in lichen symbionts and mechanisms governing these relationships are not well characterized. This is due, in part to the fact that current taxonomic approaches for recognizing diversity in lichen symbionts commonly fail to accurately reflect actual species diversity. In this study, we employed DNA-based approaches to circumscribed candidate species-level lineages in rock-posy lichen symbionts (mycobiont=Rhizoplaca s. lat. species; photobiont=Trebouxia species). Our results revealed a high degree of cryptic diversity in both the myco- and photobionts in these lichens. Using the candidate species circumscribed here, we investigated the specificity of the symbionts toward their partners and inferred the relative importance of various factors influencing symbiont interactions. Distinct mycobiont species complexes, ecozones, and biomes are significantly correlated with the occurrence of photobiont OTUs, indicating that complex interactions among mycobiont lineages, ecogeography, and microhabitat determine interactions between photobionts and their mycobionts in lichen symbiosis. One-to-one specificity between mycobiont and photobiont species was not found, with the exception of R. maheui that associated with a single Trebouxia OTU that was not found with other Rhizoplaca s. lat. species. We estimated the most recent common ancestor of the core Rhizoplaca group at c. 62.5Ma, similar in age to the diverse parmelioid core group in the well-studied family Parmeliaceae. However, in contrast to Parmeliaceae, species in Rhizoplaca were found to associate with a narrow range of photobionts. Our study provides important perspectives into species diversity and interactions in iconic lichen symbiotic systems and establishes a

  7. Cryptic impacts of temperature variability on amphibian immune function.

    PubMed

    Terrell, Kimberly A; Quintero, Richard P; Murray, Suzan; Kleopfer, John D; Murphy, James B; Evans, Matthew J; Nissen, Bradley D; Gratwicke, Brian

    2013-11-15

    Ectothermic species living in temperate regions can experience rapid and potentially stressful changes in body temperature driven by abrupt weather changes. Yet, among amphibians, the physiological impacts of short-term temperature variation are largely unknown. Using an ex situ population of Cryptobranchus alleganiensis, an aquatic North American salamander, we tested the hypothesis that naturally occurring periods of temperature variation negatively impact amphibian health, either through direct effects on immune function or by increasing physiological stress. We exposed captive salamanders to repeated cycles of temperature fluctuations recorded in the population's natal stream and evaluated behavioral and physiological responses, including plasma complement activity (i.e. bacteria killing) against Pseudomonas aeruginosa, Escherichia coli and Aeromonas hydrophila. The best-fit model (ΔAICc=0, wi=0.9992) revealed 70% greater P. aeruginosa killing after exposure to variable temperatures and no evidence of thermal acclimation. The same model predicted 50% increased E. coli killing, but had weaker support (ΔAICc=1.8, wi=0.2882). In contrast, plasma defenses were ineffective against A. hydrophila, and other health indicators (leukocyte ratios, growth rates and behavioral patterns) were maintained at baseline values. Our data suggest that amphibians can tolerate, and even benefit from, natural patterns of rapid warming/cooling. Specifically, temperature variation can elicit increased activity of the innate immune system. This immune response may be adaptive in an unpredictable environment, and is undetectable by conventional health indicators (and hence considered cryptic). Our findings highlight the need to consider naturalistic patterns of temperature variation when predicting species' susceptibility to climate change.

  8. Uncovering Cryptic Asexuality in Daphnia magna by RAD Sequencing.

    PubMed

    Svendsen, Nils; Reisser, Celine M O; Dukić, Marinela; Thuillier, Virginie; Ségard, Adeline; Liautard-Haag, Cathy; Fasel, Dominique; Hürlimann, Evelin; Lenormand, Thomas; Galimov, Yan; Haag, Christoph R

    2015-11-01

    The breeding systems of many organisms are cryptic and difficult to investigate with observational data, yet they have profound effects on a species' ecology, evolution, and genome organization. Genomic approaches offer a novel, indirect way to investigate breeding systems, specifically by studying the transmission of genetic information from parents to offspring. Here we exemplify this method through an assessment of self-fertilization vs. automictic parthenogenesis in Daphnia magna. Self-fertilization reduces heterozygosity by 50% compared to the parents, but under automixis, whereby two haploid products from a single meiosis fuse, the expected heterozygosity reduction depends on whether the two meiotic products are separated during meiosis I or II (i.e., central vs. terminal fusion). Reviewing the existing literature and incorporating recombination interference, we derive an interchromosomal and an intrachromosomal prediction of how to distinguish various forms of automixis from self-fertilization using offspring heterozygosity data. We then test these predictions using RAD-sequencing data on presumed automictic diapause offspring of so-called nonmale producing strains and compare them with "self-fertilized" offspring produced by within-clone mating. The results unequivocally show that these offspring were produced by automixis, mostly, but not exclusively, through terminal fusion. However, the results also show that this conclusion was only possible owing to genome-wide heterozygosity data, with phenotypic data as well as data from microsatellite markers yielding inconclusive or even misleading results. Our study thus demonstrates how to use the power of genomic approaches for elucidating breeding systems, and it provides the first demonstration of automictic parthenogenesis in Daphnia.

  9. Conformational switch triggered by [alpha]-ketoglutarate in a halogenase of curacin A biosynthesis

    SciTech Connect

    Khare, Dheeraj; Wang, Bo; Gu, Liangcai; Razelun, Jamie; Sherman, David H.; Gerwick, William H.; Håkansson, Kristina; Smith, Janet L.

    2010-08-12

    The CurA halogenase (Hal) catalyzes a cryptic chlorination leading to cyclopropane ring formation in the synthesis of the natural product curacin A. Hal belongs to a family of enzymes that use Fe{sup 2+}, O{sub 2} and {alpha}-ketoglutarate ({alpha}KG) to perform a variety of halogenation reactions in natural product biosynthesis. Crystal structures of the enzyme in five ligand states reveal strikingly different open and closed conformations dependent on {alpha}KG binding. The open form represents ligand-free enzyme, preventing substrate from entering the active site until both {alpha}KG and chloride are bound, while the closed form represents the holoenzyme with {alpha}KG and chloride coordinated to iron. Candidate amino acid residues involved in substrate recognition were identified by site-directed mutagenesis. These new structures provide direct evidence of a conformational switch driven by {alpha}KG leading to chlorination of an early pathway intermediate.

  10. Transportation Conformity Training and Presentations

    EPA Pesticide Factsheets

    EPA's OTAQ has provided multiple conformity training sessions in the past to assist state and local governments in implementing conformity requirements. As training information is prepared for other venues, it will be posted on this page.

  11. ELECTROMAGNETISM, OPTICS, ACOUSTICS, HEAT TRANSFER, CLASSICAL MECHANICS, AND FLUID DYNAMICS: Conformal Invariance and Noether Symmetry, Lie Symmetry of Birkhoffian Systems in Event Space

    NASA Astrophysics Data System (ADS)

    Zhang, Yi

    2010-01-01

    This paper focuses on studying a conformal invariance and a Noether symmetry, a Lie symmetry for a Birkhoffian system in event space. The definitions of the conformal invariance of the system are given. By investigation on the relations between the conformal invariance and the Noether symmetry, the conformal invariance and the Lie symmetry, the expressions of conformal factors of the system under these circumstances are obtained. The Noether conserved quantities and the Hojman conserved quantities directly derived from the conformal invariance are given. Two examples are given to illustrate the application of the results.

  12. Cryptic exon incorporation occurs in Alzheimer's brain lacking TDP-43 inclusion but exhibiting nuclear clearance of TDP-43.

    PubMed

    Sun, Mingkuan; Bell, William; LaClair, Katherine D; Ling, Jonathan P; Han, Heather; Kageyama, Yusuke; Pletnikova, Olga; Troncoso, Juan C; Wong, Philip C; Chen, Liam L

    2017-06-01

    Abnormal accumulation of TDP-43 into cytoplasmic or nuclear inclusions with accompanying nuclear clearance, a common pathology initially identified in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), has also been found in Alzheimer' disease (AD). TDP-43 serves as a splicing repressor of nonconserved cryptic exons and that such function is compromised in brains of ALS and FTD patients, suggesting that nuclear clearance of TDP-43 underlies its inability to repress cryptic exons. However, whether TDP-43 cytoplasmic aggregates are a prerequisite for the incorporation of cryptic exons is not known. Here, we assessed hippocampal tissues from 34 human postmortem brains including cases with confirmed diagnosis of AD neuropathologic changes along with age-matched controls. We found that cryptic exon incorporation occurred in all AD cases exhibiting TDP-43 pathology. Furthermore, incorporation of cryptic exons was observed in the hippocampus when TDP-43 inclusions was restricted only to the amygdala, the earliest stage of TDP-43 progression. Importantly, cryptic exon incorporation could be detected in AD brains lacking TDP-43 inclusion but exhibiting nuclear clearance of TDP-43. These data supports the notion that the functional consequence of nuclear depletion of TDP-43 as determined by cryptic exon incorporation likely occurs as an early event of TDP-43 proteinopathy and may have greater contribution to the pathogenesis of AD than currently appreciated. Early detection and effective repression of cryptic exons in AD patients may offer important diagnostic and therapeutic implications for this devastating illness of the elderly.

  13. Botrytis californica, a new cryptic species in the B. cinerea species complex causing gray mold in blueberries and table grapes

    USDA-ARS?s Scientific Manuscript database

    Botrytis cinerea consists of two cryptic species, referred to as Group I and Group II based on Bc-hch gene RFLP haplotyping, and Group I has been described as a new cryptic species B. pseudocinerea. During a survey for Botrytis spp. causing gray mold in blueberries and table grapes in the Central Va...

  14. Multiscale conformal pattern transfer

    NASA Astrophysics Data System (ADS)

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-06-01

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics.

  15. Conformal ALON® windows

    NASA Astrophysics Data System (ADS)

    Goldman, Lee M.; Balasubramanian, Sreeram; Smith, Mark; Nag, Nagendra; Foti, Robyn; Jha, Santosh; Sastri, Suri

    2014-05-01

    Aluminum Oxynitride (ALON® Optical Ceramic) combines broadband transparency with excellent mechanical properties. ALON's cubic structure means that it is transparent in its polycrystalline form, allowing it to be manufactured by conventional powder processing techniques. Surmet controls every aspect of the manufacturing process, beginning with synthesis of ALON® powder, continuing through forming/heat treatment of blanks, ending with optical fabrication of ALON® windows. Surmet has made significant progress in its production capability in recent years. Additional scale up of Surmet's manufacturing capability, for complex geometries, larger sizes and higher quantities, is underway. The requirements for modern aircraft are driving the need for conformal windows for future sensor systems. However, limitations on optical systems and the ability to produce windows in complex geometries currently limit the geometry of existing windows and window assemblies to faceted assemblies of flat windows. Surmet's ability to produce large curved ALON® blanks is an important step in the development of conformal windows for future aircraft applications.

  16. Multiscale conformal pattern transfer

    PubMed Central

    Lodewijks, Kristof; Miljkovic, Vladimir; Massiot, Inès; Mekonnen, Addis; Verre, Ruggero; Olsson, Eva; Dmitriev, Alexandre

    2016-01-01

    We demonstrate a method for seamless transfer from a parent flat substrate of basically any lithographic top-down or bottom-up pattern onto essentially any kind of surface. The nano- or microscale patterns, spanning macroscopic surface areas, can be transferred with high conformity onto a large variety of surfaces when such patterns are produced on a thin carbon film, grown on top of a sacrificial layer. The latter allows lifting the patterns from the flat parent substrate onto a water-air interface to be picked up by the host surface of choice. We illustrate the power of this technique by functionalizing broad range of materials including glass, plastics, metals, rough semiconductors and polymers, highlighting the potential applications in in situ colorimetry of the chemistry of materials, anti-counterfeit technologies, biomolecular and biomedical studies, light-matter interactions at the nanoscale, conformal photovoltaics and flexible electronics. PMID:27329824

  17. Conformal gripping device

    NASA Technical Reports Server (NTRS)

    Vranish, John M. (Inventor)

    2009-01-01

    The present invention relates to a conformal gripping device. In an embodiment of the present invention a conformal gripper device may be disclosed comprising a frame that includes an array of movable pins. The device may also include a roller locking and unlocking system within the frame. The system may comprise a pair of locking rollers for each row of gripper pins to facilitate locking and unlocking the array of gripper pins on a column-by-column basis. The system may also include a striker element that may force the locking rollers to roll along an angled roll surface to facilitate unlocking of the array of pins on a column-by-column basis. The system may further include an electromagnetic actuator or solenoid and permanent magnets to facilitate movement of the striker element and the locking rollers.

  18. Conformational flexibility of aspartame.

    PubMed

    Toniolo, Claudio; Temussi, Pierandrea

    2016-05-01

    L-Aspartyl-L-phenylalanine methyl ester, better known as aspartame, is not only one of the most used artificial sweeteners, but also a very interesting molecule with respect to the correlation between molecular structure and taste. The extreme conformational flexibility of this dipeptide posed a huge difficulty when researchers tried to use it as a lead compound to design new sweeteners. In particular, it was difficult to take advantage of its molecular model as a mold to infer the shape of the, then unknown, active site of the sweet taste receptor. Here, we follow the story of the 3D structural aspects of aspartame from early conformational studies to recent docking into homology models of the receptor. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 376-384, 2016. © 2016 Wiley Periodicals, Inc.

  19. Cuticular hydrocarbon phenotypes do not indicate cryptic species in fungus-growing termites (Isoptera: Macrotermitinae).

    PubMed

    Marten, Andreas; Kaib, Manfred; Brandl, Roland

    2009-05-01

    In several termite species, distinct differences in the composition of cuticular hydrocarbons among colonies correspond to high genetic divergence of mitochondrial DNA sequences. These observations suggest that hydrocarbon phenotypes represent cryptic species. Different cuticular hydrocarbon phenotypes also are found among colonies of fungus-growing termites of the genus Macrotermes. To determine if these hydrocarbon differences in Macrotermes also indicate cryptic species, we sequenced the mitochondrial CO I gene from species in West and East Africa. Among individuals of a supposed species but belonging to different cuticular hydrocarbon phenotypes, the genetic distances are much smaller than distances between species. Unlike what has been observed in other termites, Macrotermes hydrocarbon phenotypes do not represent cryptic species. Our findings suggest fundamental differences in the evolution and/or function of cuticular hydrocarbons among different termite lineages.

  20. Features of Cryptic Promoters and Their Varied Reliance on Bromodomain-Containing Factors

    PubMed Central

    Pattenden, Samantha G.; Gogol, Madelaine M.; Workman, Jerry L.

    2010-01-01

    The Set2-Rpd3S pathway is important for the control of transcription memory. Mutation of components of this pathway results in cryptic transcription initiation within the coding region of approximately 30% of yeast genes. Specifically, deletion of the Set2 histone methyltransferase or Rco1, a component of the Rpd3S histone deacetylase complex leads to hyperacetylation of certain open reading frames (ORFs). We used this mutant as a system to study the role of histone modifications and co-activator recruitment in preinitiation complex (PIC) formation. Specifically, we looked at the dependence of promoters on the bromodomain-containing RSC complex and the Bdf1 protein. We found that the dependence of cryptic promoters for these proteins varied. Overall, our data indicate that cryptic promoters are independently regulated, and their activation is dependent on factors that govern gene activation at canonical promoters. PMID:20886085

  1. Co-occurrence of ecologically equivalent cryptic species of spider wasps

    PubMed Central

    Kurushima, Hiroaki; Kim, Jeong-Kyu; Kim, Jong-Kuk; Nishimoto, Yutaka; Sayama, Katsuhiko; Kato, Manabu; Watanabe, Kenta; Hasegawa, Eisuke; Roff, Derek A.; Shimizu, Akira

    2016-01-01

    Many cryptic species have been discovered in various taxonomic groups based on molecular phylogenetic analyses and mating experiments. Some sympatric cryptic species share equivalent resources, which contradicts the competitive exclusion principle. Two major theories have been proposed to explain the apparent lack of competitive exclusion, i.e. niche-based coexistence and neutral model, but a conclusive explanation is lacking. Here, we report the co-occurrence of cryptic spider wasp species appearing to be ecologically equivalent. Molecular phylogenetic analyses and mating experiments revealed that three phylogenetically closely related species are found sympatrically in Japan. These species share the same resources for larval food, and two of the species have the same niche for nesting sites, indicating a lack of competitive exclusion. This evidence may suggest that ecologically equivalent species can co-occur stably if their shared resources are sufficiently abundant that they cannot be over-exploited. PMID:27853590

  2. Cryptic female exaggeration: the asymmetric female internal genitalia of Kaliana yuruani (Araneae: Pholcidae).

    PubMed

    Huber, Bernhard A

    2006-06-01

    Males of the Venezuelan pholcid spider Kaliana yuruani have unique genitalia, with the procursi about six times as long as usual in the family. The present article describes the previously unknown female, searching for a morphological correlate in the female genitalia to the male's exaggeration. Reconstruction of histological serial sections reveals an internal female complexity that is unequalled in pholcid spiders. An intricate system of ducts and folds is arranged in an asymmetric way, making this the third known case of genital asymmetry in spiders. The term "cryptic female exaggeration" is used in analogy to cryptic female choice, pointing to the fact that from the outside, the female genitalia do not appear unusual. I propose that cryptic female exaggeration may be relatively common in copulatory structures if male exaggerations need to be evaluated according to the female choice by mechanical fit model. Finally, the evolution of genital asymmetry in spiders is contrasted with that in insects.

  3. Cryptic speciation or global spread? The case of a cosmopolitan marine invertebrate with limited dispersal capabilities

    PubMed Central

    R., Pérez-Portela; V., Arranz; M., Rius; X., Turon

    2013-01-01

    The existence of globally-distributed species with low dispersal capabilities is a paradox that has been explained as a result of human-mediated transport and by hidden diversity in the form of unrecognized cryptic species. Both factors are not mutually exclusive, but relatively few studies have demonstrated the presence of both. Here we analyse the genetic patterns of the colonial ascidian Diplosoma listerianum, a species nowadays distributed globally. The study of a fragment of a mitochondrial gene in localities worldwide revealed the existence of multiple cryptic species. In addition, we found a complex geographic structure and multiple clades occurred in sympatry. One of the species showed strong population structure irrespective of geographical distances, which is coherent with stochastic dispersal linked to human transport. The present study shows the complexity of discerning the role of cryptic diversity from human-driven range shifts worldwide, as well as disentangling the effects of natural and artificial dispersal. PMID:24217373

  4. Early embryogenesis of planaria: a cryptic larva feeding on maternal resources.

    PubMed

    Cardona, Albert; Hartenstein, Volker; Romero, Rafael

    2006-11-01

    The early planarian embryo presents a complete ciliated epidermis and a pharynx and feeds on maternal yolk cells. In this paper, we report on all the elements involved in the formation of such an autonomous embryo, which we name cryptic larva. First, we provide a description of the spherical and fusiform yolk cells and their relationship with the blastomeres, from the laying of the egg capsule up to their final fate in mid embryonic stages. Then, we describe the early cleavage and the subsequent development of the tissues of the cryptic larva, namely, the primary epidermis, the embryonic pharynx, and a new cell type, the star cells. Finally, we discuss the possibility that the cryptic larva either constitutes a vestigial larva or, more likely, is the evolutionary result of the competition between multiple embryos for the limited and shared maternal resources in the egg capsule.

  5. Effect of distal sugars and interglycosidic linkage on the N-glycoprotein linkage region conformation: synthesis and X-ray crystallographic investigation of β-1-N-alkanamide derivatives of cellobiose and maltose as disaccharide analogs of the conserved chitobiosylasparagine linkage.

    PubMed

    Mathiselvam, Manoharan; Ramkumar, Venkatachalam; Loganathan, Duraikkannu; Pérez, Serge

    2014-01-01

    The linkage region constituents, 2-deoxy-2-acetamido-β-D-glucopyranose (GlcNAc) and L-asparagine (Asn) are conserved in the N-glycoproteins of all eukaryotes. Elucidation of the structure and conformation of the linkage region of glycoproteins is important to understand the presentation and dynamics of the carbohydrate chain at the protein/cell surface. Earlier crystallographic studies using monosaccharide models and analogs of N-glycoprotein linkage region have shown that the N-glycosidic torsion, ϕN, is more influenced by the structural variation in the sugar part than that of the aglycon moiety. To access the influence of distal sugar as well as interglycosidic linkage (α or β) on the N-glycosidic torsion angles, cellobiosyl and maltosyl alkanamides have been synthesized and structural features of seven of these analogs have been characterized by X-ray crystallography. Comparative analysis of the seven disaccharide analogs with the reported monosaccharide analogs showed that the ϕN value of cellobiosyl analogs deviate ~9° with respect to GlcβNHAc. In the case of maltosyl analogs, deviation is more than 18°. These deviations indicate that the N-glycosidic torsion is influenced by addition of distal sugar as well as with respect to inter glycosidic linkage (α or β); it is less influenced by changes occurring at the aglycon. The χ₂ value of alkanamide derived from glucose, cellobiose and maltose exhibit a large range of variations (from 1.6° to -109.9°). This large span of χ₂ value suggests the greater degree of rotational freedom around C1'-C2' bond which is restricted in GlcNAc alkanamides. The present finding explicitly proved the importance of molecular architecture in the N-glycoproteins linkage region to maintain the linearity, planarity and rigidity. These factors are necessary for N-glycan to serve role in inter- as well as intramolecular carbohydrate-protein interactions.

  6. [Conservation Units.

    ERIC Educational Resources Information Center

    Texas Education Agency, Austin.

    Each of the six instructional units deals with one aspect of conservation: forests, water, rangeland, minerals (petroleum), and soil. The area of the elementary school curriculum with which each correlates is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the…

  7. [Conservation Units.

    ERIC Educational Resources Information Center

    Texas Education Agency, Austin.

    Instructional units deal with each aspect of conservation: forests, wildlife, rangelands, water, minerals, and soil. The area of the secondary school curriculum with which each is correlated is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the topic, questions to…

  8. Marketing Conservation.

    ERIC Educational Resources Information Center

    Ellis, William B.

    1987-01-01

    In 1986, Northeast Utilities began helping shool administrators combat school building energy wastage through a program called Energy Alliance. The typical school can reduce its energy bill by 30 percent by adopting a wide range of conservation measures, including cogeneration, relamping, and energy audits. (MLH)

  9. Lighting Conservation

    ERIC Educational Resources Information Center

    Arnold, Frank D.

    1975-01-01

    With the energy crisis has come an awareness of wasteful consumption practices. One area where research is being done is in lighting conservation. Information in this article is concerned with finding more effective and efficient lighting designs which include daylight utilization, task-oriented lighting, and lighting controls. (MA)

  10. Energy Conservation.

    ERIC Educational Resources Information Center

    Land, Amy A.

    This selection of class activities involves a sequence of 10 class sessions. The goal of the collection is to aid students in learning the concepts of energy conservation and to put this knowledge into practice. Attention is also given to the development of alternate energy sources. Each lesson includes an activity title, motivational hints,…

  11. Colorful Conservation

    ERIC Educational Resources Information Center

    Skophammer, Karen

    2011-01-01

    Some people only think about conservation on Earth Day. Being in the "art business" however, this author is always conscious of the many products she thinks get wasted when they could be reused, recycled, and restored--especially in a school building and art room. In this article, she describes an art lesson that allows students to paint…

  12. Colorful Conservation

    ERIC Educational Resources Information Center

    Skophammer, Karen

    2011-01-01

    Some people only think about conservation on Earth Day. Being in the "art business" however, this author is always conscious of the many products she thinks get wasted when they could be reused, recycled, and restored--especially in a school building and art room. In this article, she describes an art lesson that allows students to paint…

  13. Conformal scalar field wormholes

    NASA Technical Reports Server (NTRS)

    Halliwell, Jonathan J.; Laflamme, Raymond

    1989-01-01

    The Euclidian Einstein equations with a cosmological constant and a conformally coupled scalar field are solved, taking the metric to be of the Robertson-Walker type. In the case Lambda = 0, solutions are found which represent a wormhole connecting two asymptotically flat Euclidian regions. In the case Lambda greater than 0, the solutions represent tunneling from a small Tolman-like universe to a large Robertson-Walker universe.

  14. Ordering in Conformal Crystals

    NASA Astrophysics Data System (ADS)

    Soni, Vishal; Gomez, Leopoldo; Irvine, William

    2014-03-01

    Condensed matter systems commonly undergo ordering processes that are frustrated by geometric constraints. Experiments on interfacial colloidal systems have resulted in several recent insights into the two dimensional ordering of crystalline lattices frustrated by Gaussian curvature. We study the ordering of flat colloidal Wigner crystals immersed in an axially symmetric potential. By relating the resulting inhomogenous structure to a lattice with Gaussian curvature, we investigate the role of topological defects in organizing the conformal crystal-like ground state.

  15. Conformal scalar field wormholes

    NASA Technical Reports Server (NTRS)

    Halliwell, Jonathan J.; Laflamme, Raymond

    1989-01-01

    The Euclidian Einstein equations with a cosmological constant and a conformally coupled scalar field are solved, taking the metric to be of the Robertson-Walker type. In the case Lambda = 0, solutions are found which represent a wormhole connecting two asymptotically flat Euclidian regions. In the case Lambda greater than 0, the solutions represent tunneling from a small Tolman-like universe to a large Robertson-Walker universe.

  16. The conformal bootstrap

    NASA Astrophysics Data System (ADS)

    Poland, David; Simmons-Duffin, David

    2016-06-01

    The conformal bootstrap was proposed in the 1970s as a strategy for calculating the properties of second-order phase transitions. After spectacular success elucidating two-dimensional systems, little progress was made on systems in higher dimensions until a recent renaissance beginning in 2008. We report on some of the main results and ideas from this renaissance, focusing on new determinations of critical exponents and correlation functions in the three-dimensional Ising and O(N) models.

  17. 18 CFR 415.51 - Prior non-conforming structures.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... structures. 415.51 Section 415.51 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION... structures. A structure which was lawful before the adoption of this regulation but which is not in... this part): (a) A non-conforming structure in the floodway may not be expanded, except that it may be...

  18. 18 CFR 415.51 - Prior non-conforming structures.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... structures. 415.51 Section 415.51 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION... structures. A structure which was lawful before the adoption of this regulation but which is not in... this part): (a) A non-conforming structure in the floodway may not be expanded, except that it may be...

  19. On gravitational energy in conformal teleparallel gravity

    NASA Astrophysics Data System (ADS)

    da Silva, J. G.; Ulhoa, S. C.

    2017-07-01

    The paper deals with the definition of gravitational energy in conformal teleparallel gravity. The total energy is defined by means of the field equations which allow a local conservation law. Then such an expression is analyzed for a homogeneous and isotropic Universe. This model is implemented by the Friedmann-Robertson-Walker (FRW) line element. The energy of the Universe in the absence of matter is identified with the dark energy, however it can be expanded for curved models defining such an energy as the difference between the total energy and the energy of the perfect fluid which is the matter field in the FRW model.

  20. Conformations of organophosphine oxides

    SciTech Connect

    De Silva, Nuwan; Zahariev, Federico; Hay, Benjamin P.; Gordon, Mark S.; Windus, Theresa L.

    2015-07-17

    The conformations of a series of organophosphine oxides, OP(CH3)2R, where R = methyl, ethyl, isopropyl, tert-butyl, vinyl, and phenyl, are predicted using the MP2/cc-pVTZ level of theory. Comparison of potential energy surfaces for rotation about P–C bonds with crystal structure data reveals a strong correlation between predicted location and energetics of minima and histograms of dihedral angle distributions observed in the solid state. In addition, the most stable conformers are those that minimize the extent of steric repulsion between adjacent rotor substituents, and the torsional barriers tend to increase with the steric bulk of the rotating alkyl group. MM3 force field parameters were adjusted to fit the MP2 results, providing a fast and accurate model for predicting organophosphine oxides shapes—an essential part of understanding the chemistry of these compounds. As a result, the predictive power of the modified MM3 model was tested against MP2/cc-pVTZ conformations for triethylphosphine oxide, OP(CH2CH3)3, and triphenylphosphine oxide, OP(Ph)3.

  1. Conformations of organophosphine oxides

    DOE PAGES

    De Silva, Nuwan; Zahariev, Federico; Hay, Benjamin P.; ...

    2015-07-17

    The conformations of a series of organophosphine oxides, OP(CH3)2R, where R = methyl, ethyl, isopropyl, tert-butyl, vinyl, and phenyl, are predicted using the MP2/cc-pVTZ level of theory. Comparison of potential energy surfaces for rotation about P–C bonds with crystal structure data reveals a strong correlation between predicted location and energetics of minima and histograms of dihedral angle distributions observed in the solid state. In addition, the most stable conformers are those that minimize the extent of steric repulsion between adjacent rotor substituents, and the torsional barriers tend to increase with the steric bulk of the rotating alkyl group. MM3 forcemore » field parameters were adjusted to fit the MP2 results, providing a fast and accurate model for predicting organophosphine oxides shapes—an essential part of understanding the chemistry of these compounds. As a result, the predictive power of the modified MM3 model was tested against MP2/cc-pVTZ conformations for triethylphosphine oxide, OP(CH2CH3)3, and triphenylphosphine oxide, OP(Ph)3.« less

  2. Hot conformal gauge theories

    NASA Astrophysics Data System (ADS)

    Mojaza, Matin; Pica, Claudio; Sannino, Francesco

    2010-12-01

    We compute the nonzero temperature free energy up to the order g6ln⁡(1/g) in the coupling constant for vectorlike SU(N) gauge theories featuring matter transforming according to different representations of the underlying gauge group. The number of matter fields, i.e. flavors, is arranged in such a way that the theory develops a perturbative stable infrared fixed point at zero temperature. Because of large distance conformality we trade the coupling constant with its fixed point value and define a reduced free energy which depends only on the number of flavors, colors, and matter representation. We show that the reduced free energy changes sign, at the second, fifth, and sixth order in the coupling, when decreasing the number of flavors from the upper end of the conformal window. If the change in sign is interpreted as a signal of an instability of the system then we infer a critical number of flavors. Surprisingly this number, if computed to the order g2, agrees with previous predictions for the lower boundary of the conformal window for nonsupersymmetric gauge theories. The higher order results tend to predict a higher number of critical flavors. These are universal properties, i.e. they are independent of the specific matter representation.

  3. Extensive cryptic splicing upon loss of RBM17 and TDP43 in neurodegeneration models.

    PubMed

    Tan, Qiumin; Yalamanchili, Hari Krishna; Park, Jeehye; De Maio, Antonia; Lu, Hsiang-Chih; Wan, Ying-Wooi; White, Joshua J; Bondar, Vitaliy V; Sayegh, Layal S; Liu, Xiuyun; Gao, Yan; Sillitoe, Roy V; Orr, Harry T; Liu, Zhandong; Zoghbi, Huda Y

    2016-12-01

    Splicing regulation is an important step of post-transcriptional gene regulation. It is a highly dynamic process orchestrated by RNA-binding proteins (RBPs). RBP dysfunction and global splicing dysregulation have been implicated in many human diseases, but the in vivo functions of most RBPs and the splicing outcome upon their loss remain largely unexplored. Here we report that constitutive deletion of Rbm17, which encodes an RBP with a putative role in splicing, causes early embryonic lethality in mice and that its loss in Purkinje neurons leads to rapid degeneration. Transcriptome profiling of Rbm17-deficient and control neurons and subsequent splicing analyses using CrypSplice, a new computational method that we developed, revealed that more than half of RBM17-dependent splicing changes are cryptic. Importantly, RBM17 represses cryptic splicing of genes that likely contribute to motor coordination and cell survival. This finding prompted us to re-analyze published datasets from a recent report on TDP-43, an RBP implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), as it was demonstrated that TDP-43 represses cryptic exon splicing to promote cell survival. We uncovered a large number of TDP-43-dependent splicing defects that were not previously discovered, revealing that TDP-43 extensively regulates cryptic splicing. Moreover, we found a significant overlap in genes that undergo both RBM17- and TDP-43-dependent cryptic splicing repression, many of which are associated with survival. We propose that repression of cryptic splicing by RBPs is critical for neuronal health and survival. CrypSplice is available at www.liuzlab.org/CrypSplice. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  4. Risk of Gonadoblastoma Development in Patients with Turner Syndrome with Cryptic Y Chromosome Material.

    PubMed

    Kwon, Ahreum; Hyun, Sei Eun; Jung, Mo Kyung; Chae, Hyun Wook; Lee, Woo Jung; Kim, Tae Hyuk; Kim, Duk Hee; Kim, Ho-Seong

    2017-03-27

    Current guidelines recommend that testing for Y chromosome material should be performed only in patients with Turner syndrome harboring a marker chromosome and exhibiting virilization in order to detect individuals who are at high risk of gonadoblastoma. However, cryptic Y chromosome material is suggested to be a risk factor for gonadoblastoma in patients with Turner syndrome. Here, we aimed to estimate the frequency of cryptic Y chromosome material in patients with Turner syndrome and determine whether Y chromosome material increased the risk for development of gonadoblastoma. A total of 124 patients who were diagnosed with Turner syndrome by conventional cytogenetic techniques underwent additional molecular analysis to detect cryptic Y chromosome material. In addition, patients with Turner syndrome harboring Y chromosome cell lines had their ovaries removed prophylactically. Finally, we assessed the occurrence of gonadoblastoma in patients with Turner syndrome. Molecular analysis demonstrated that 10 patients had Y chromosome material among 118 patients without overt Y chromosome (8.5%). Six patients with overt Y chromosome and four patients with cryptic Y chromosome material underwent oophorectomy. Histopathological analysis revealed that the occurrence of gonadoblastoma in the total group was 2.4%, and gonadoblastoma occurred in one of six patients with an overt Y chromosome (16.7%) and 2 of 10 patients with cryptic Y chromosome material (20.0%). The risk of developing gonadoblastoma in patients with cryptic Y chromosome material was similar to that in patients with overt Y chromosome. Therefore, molecular screening for Y chromosome material should be recommended for all patients with Turner syndrome to detect individuals at a high risk of gonadoblastoma and to facilitate proper management of the disease.

  5. Electrical control of protein conformation.

    PubMed

    Wan, Alwin M D; Schur, Rebecca M; Ober, Christopher K; Fischbach, Claudia; Gourdon, Delphine; Malliaras, George G

    2012-05-08

    Conducting polymer devices that enable precise control of fibronectin conformation over macroscopic areas are reported. Single conformations as well as conformation gradients are achieved by applying an appropriate potential. These surfaces remain biologically relevant and support cell culture; hence, they may serve as a model to understand and control cell-surface interactions, with applications in basic research, medical diagnostics, and tissue engineering.

  6. Conformal killing tensors and covariant Hamiltonian dynamics

    SciTech Connect

    Cariglia, M.; Gibbons, G. W.; Holten, J.-W. van; Horvathy, P. A.; Zhang, P.-M.

    2014-12-15

    A covariant algorithm for deriving the conserved quantities for natural Hamiltonian systems is combined with the non-relativistic framework of Eisenhart, and of Duval, in which the classical trajectories arise as geodesics in a higher dimensional space-time, realized by Brinkmann manifolds. Conserved quantities which are polynomial in the momenta can be built using time-dependent conformal Killing tensors with flux. The latter are associated with terms proportional to the Hamiltonian in the lower dimensional theory and with spectrum generating algebras for higher dimensional quantities of order 1 and 2 in the momenta. Illustrations of the general theory include the Runge-Lenz vector for planetary motion with a time-dependent gravitational constant G(t), motion in a time-dependent electromagnetic field of a certain form, quantum dots, the Hénon-Heiles and Holt systems, respectively, providing us with Killing tensors of rank that ranges from one to six.

  7. In silico Exploration of the Conformational Universe of GPCRs.

    PubMed

    Rodríguez-Espigares, Ismael; Kaczor, Agnieszka A; Selent, Jana

    2016-07-01

    The structural plasticity of G protein coupled receptors (GPCRs) leads to a conformational universe going from inactive to active receptor states with several intermediate states. Many of them have not been captured yet and their role for GPCR activation is not well understood. The study of this conformational space and the transition dynamics between different receptor populations is a major challenge in molecular biophysics. The rational design of effector molecules that target such receptor populations allows fine-tuning receptor signalling with higher specificity to produce drugs with safer therapeutic profiles. In this minireview, we outline highly conserved receptor regions which are considered determinant for the establishment of distinct receptor states. We then discuss in-silico approaches such as dimensionality reduction methods and Markov State Models to explore the GPCR conformational universe and exploit the obtained conformations through structure-based drug design.

  8. Conformal Janus on Euclidean sphere

    NASA Astrophysics Data System (ADS)

    Bak, Dongsu; Gustavsson, Andreas; Rey, Soo-Jong

    2016-12-01

    We interpret Janus as an interface in a conformal field theory and study its properties. The Janus is created by an exactly marginal operator and we study its effect on the interface conformal field theory on the Janus. We do this by utilizing the AdS/CFT correspondence. We compute the interface free energy both from leading correction to the Euclidean action in the dual gravity description and from conformal perturbation theory in the conformal field theory. We find that the two results agree each other and that the interface free energy scales precisely as expected from the conformal invariance of the Janus interface.

  9. Conformal vectors and stellar models

    NASA Astrophysics Data System (ADS)

    Manjonjo, A. M.; Maharaj, S. D.; Moopanar, S.

    2017-02-01

    The relationship between conformal symmetries and relativistic spheres in astrophysics is studied. We use the nonvanishing components of the Weyl tensor to classify the conformal symmetries in static spherical spacetimes. It is possible to find an explicit connection between the two gravitational potentials for both conformally flat and nonconformally flat cases. We show that the conformal Killing vector admits time dependence in terms of quadratic, trigonometric and hyperbolic functions. The Einstein and Einstein-Maxwell field equations can be written in terms of a single potential, any choice of which leads to an exact solution. Previous results of conformally invariant static spheres are contained in our treatment.

  10. Comprehensive Analysis of Contributions from Protein Conformational Stability and Major Histocompatibility Complex Class II-Peptide Binding Affinity to CD4+ Epitope Immunogenicity in HIV-1 Envelope Glycoprotein

    PubMed Central

    Li, Tingfeng; Steede, N. Kalaya; Nguyen, Hong-Nam P.; Freytag, Lucy C.; McLachlan, James B.; Mettu, Ramgopal R.; Robinson, James E.

    2014-01-01

    ABSTRACT Helper T-cell epitope dominance in human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 is not adequately explained by peptide binding to major histocompatibility complex (MHC) proteins. Antigen processing potentially influences epitope dominance, but few, if any, studies have attempted to reconcile the influences of antigen processing and MHC protein binding for all helper T-cell epitopes of an antigen. Epitopes of gp120 identified in both humans and mice occur on the C-terminal flanks of flexible segments that are likely to be proteolytic cleavage sites. In this study, the influence of gp120 conformation on the dominance pattern in gp120 from HIV strain 89.6 was examined in CBA mice, whose MHC class II protein has one of the most well defined peptide-binding preferences. Only one of six dominant epitopes contained the most conserved element of the I-Ak binding motif, an aspartic acid. Destabilization of the gp120 conformation by deletion of single disulfide bonds preferentially enhanced responses to the cryptic I-Ak motif-containing sequences, as reported by T-cell proliferation or cytokine secretion. Conversely, inclusion of CpG in the adjuvant with gp120 enhanced responses to the dominant CD4+ T-cell epitopes. The gp120 destabilization affected secretion of some cytokines more than others, suggesting that antigen conformation could modulate T-cell functions through mechanisms of antigen processing. IMPORTANCE CD4+ helper T cells play an essential role in protection against HIV and other pathogens. Thus, the sites of helper T-cell recognition, the dominant epitopes, are targets for vaccine design; and the corresponding T cells may provide markers for monitoring infection and immunity. However, T-cell epitopes are difficult to identify and predict. It is also unclear whether CD4+ T cells specific for one epitope are more protective than T cells specific for other epitopes. This work shows that the three-dimensional (3D) structure of an

  11. Energy conservation

    SciTech Connect

    Not Available

    1990-05-01

    Under the Warner Amendment, oil overcharge funds are designated for states' use in certain authorized energy conservation and assistance programs. During FY 1982-87 Warner funds accounted for $200 million of the $3.3 billion states received from the oil overcharge escrow account. The $3.3 billion was in addition to the $13.3 billion that the Congress appropriated for the conservation and assistance programs. More than 4 years after their distribution, states had not used all the Warner funds. This report provides the status of all oil overcharge funds; the use of Warner funds and the time it is taking to spend the funds in Arizona, California, and Illinois.

  12. Heron conservation

    USGS Publications Warehouse

    Kushlan, J.A.; Hafner, H.

    2000-01-01

    Herons are large, popular and, in many cases, spectacular birds found in wetlands world-wide, both tropical and temperate, natural and man-made. Some populations are very small and localized, some have decreased, some have expanded their ranges, and a few are pests of human activities. In the fifteen years since the publication of the latest monographic treatment of the family, The Herons Handbook, there has been a tremendous increase in our knowledge of heron status and conservation requirements, set against a backdrop of increasing concern about the future of the world?s wetland habitats. This book provides a comprehensive update following two distinct threads. The status and conservation needs of herons are first presented on a regional basis, in a series of chapters set at a continental or subcontinental scale. Over 200 biologists and heron conservationists have contributed to the data summarized here, and the very latest census and survey results provide the most up-to-date and detailed picture of heron populations currently available. Chapters discussing several critical issues in heron conservation follow, tending to focus on the international nature of the problems.

  13. Restriction fragment length analysis of the cytochrome b gene and muscle fatty acid composition differentiate the cryptic flatfish species Solea solea and Solea aegyptiaca.

    PubMed

    Boukouvala, Evridiki; Cariani, Alessia; Maes, Gregory E; Sevilla, Rafael G; Verrez-Bagnis, Véronique; Jérôme, Marc; Guarniero, Ilaria; Monios, Georgios; Tinti, Fausto; Volckaert, Filip A M; Bautista, José M; Krey, Grigorios

    2012-08-15

    Overlapping external morphometric characters easily confound the flatfishes Solea aegyptiaca and Solea solea (Soleidae) in areas of the Mediterranean Sea where both species live in sympatry. This leads to uncertainties in the fisheries and marketing of the species, in addition to misinterpretations in biogeography and conservation studies. This paper describes a simple restriction fragment length-based diagnostic test that differentiates S. solea from S. aegyptiaca, as well as from other species of the Soleidae family. Furthermore, the two species living in sympatry in the Gulf of Kavala (North Aegean Sea, Greece) present significant qualitative differences in muscle fatty acid composition, a property that can also be used to distinguish the two cryptic species.

  14. Implication of nifA in regulation of genes located on a Rhizobium meliloti cryptic plasmid that affect nodulation efficiency.

    PubMed Central

    Sanjuan, J; Olivares, J

    1989-01-01

    We examined the contribution of a cryptic plasmid, pRmeGR4b, to the nodulation of Medicago sativa by strain GR4 of Rhizobium meliloti. A 905-base-pair PstI DNA fragment in pRmeGR4b was found to hybridize DNA of the R. meliloti fixA promoter region as a probe. Sequence analysis of the PstI fragment showed a 206-base-pair region displaying high homology with the DNA upstream of the RNA start points of the P1 and P2 symbiotic promoters. Putative nif promoter consensus sequences were conserved in this DNA segment. Expression of DNA downstream of the nif promoterlike sequence, monitored by beta-galactosidase activity of different lacZ fusions, was demonstrated to depend on a functional nifA gene, both in microaerobically free-living cells and in nodules. Individual transposon Tn3-HoHo1 insertions in this DNA region caused a reduced nodulation competitiveness. This new symbiotic region, occupying approximately 5 kilobases of pRmeGR4b DNA, was called nfe (nodule formation efficiency). Images PMID:2546913

  15. The genome of the xerotolerant mold Wallemia sebi reveals adaptations to osmotic stress and suggests cryptic sexual reproduction

    SciTech Connect

    Mahajabeen, Padamsee; Kumas, T. K. Arun; Riley, Robert; Binder, Manfred; Boyd, Alex; Calvo, Ann M.; Furukawa, Kentaro; Hesse, Cedar; Hohmann, Stefan; James, Tim Y.; LaButti, Kurt; Lapidus, Alla; Lindquist, Erika; Lucas, Susan; Miller, Kari; Shantappa, Sourabha; Grigoriev, Igor V.; Hibbett, David S.; McLaughlin, David J.; Spatafora, Joseph W.; Aime, Mary C.

    2011-09-03

    Wallemia (Wallemiales, Wallemiomycetes) is a genus of xerophilic Fungi of uncertain phylogenetic position within Basidiomycota. Most commonly found as food contaminants, species of Wallemia have also been isolated from hypersaline environments. The ability to tolerate environments with reduced water activity is rare in Basidiomycota. We sequenced the genome of W. sebi in order to understand its adaptations for surviving in osmotically challenging environments, and we performed phylogenomic and ultrastructural analyses to address its systematic placement and reproductive biology. W. sebi has a compact genome (9.8 Mb), with few repeats and the largest fraction of genes with functional domains compared with other Basidiomycota. We applied several approaches to searching for osmotic stress-related proteins. In silico analyses identied 93 putative osmotic stress proteins; homology searches showed the HOG (High Osmolarity Glycerol) pathway to be mostly conserved. Despite the seemingly reduced genome, several gene family expansions and a high number of transporters (549) were found that also provide clues to the ability of W. sebito colonize harsh environments. Phylogenetic analyses of a 71-protein dataset support the position of Wallemia as the earliest diverging lineage of Agaricomycotina, which is conrmed by septal pore ultrastructure that shows the septal pore apparatus as a variant of the Tremella-type. Mating type gene homologs were idented although we found no evidence of meiosis during conidiogenesis, suggesting there may be aspects of the life cycle of W. sebi that remain cryptic

  16. The Cryptic African Wolf: Canis aureus lupaster Is Not a Golden Jackal and Is Not Endemic to Egypt

    PubMed Central

    Rueness, Eli Knispel; Asmyhr, Maria Gulbrandsen; Sillero-Zubiri, Claudio; Macdonald, David W.; Bekele, Afework; Atickem, Anagaw; Stenseth, Nils Chr.

    2011-01-01

    The Egyptian jackal (Canis aureus lupaster) has hitherto been considered a large, rare subspecies of the golden jackal (C. aureus). It has maintained its taxonomical status to date, despite studies demonstrating morphological similarities to the grey wolf (C. lupus). We have analyzed 2055 bp of mitochondrial DNA from C. a. lupaster and investigated the similarity to C. aureus and C. lupus. Through phylogenetic comparison with all wild wolf-like canids (based on 726 bp of the Cytochrome b gene) we conclusively (100% bootstrap support) place the Egyptian jackal within the grey wolf species complex, together with the Holarctic wolf, the Indian wolf and the Himalayan wolf. Like the two latter taxa, C. a. lupaster seems to represent an ancient wolf lineage which most likely colonized Africa prior to the northern hemisphere radiation. We thus refer to C. a. lupaster as the African wolf. Furthermore, we have detected C. a. lupaster individuals at two localities in the Ethiopian highlands, extending the distribution by at least 2,500 km southeast. The only grey wolf species to inhabit the African continent is a cryptic species for which the conservation status urgently needs assessment. PMID:21298107

  17. The structure of the plk4 cryptic polo box reveals two tandem polo boxes required for centriole duplication.

    PubMed

    Slevin, Lauren K; Nye, Jonathan; Pinkerton, Derek C; Buster, Daniel W; Rogers, Gregory C; Slep, Kevin C

    2012-11-07

    Centrioles are key microtubule polarity determinants. Centriole duplication is tightly controlled to prevent cells from developing multipolar spindles, a situation that promotes chromosomal instability. A conserved component in the duplication pathway is Plk4, a polo kinase family member that localizes to centrioles in M/G1. To limit centriole duplication, Plk4 levels are controlled through trans-autophosphorylation that primes ubiquitination. In contrast to Plks 1-3, Plk4 possesses a unique central region called the "cryptic polo box." Here, we present the crystal structure of this region at 2.3 Å resolution. Surprisingly, the structure reveals two tandem homodimerized polo boxes, PB1-PB2, that form a unique winged architecture. The full PB1-PB2 cassette is required for binding the centriolar protein Asterless as well as robust centriole targeting. Thus, with its C-terminal polo box (PB3), Plk4 has a triple polo box architecture that facilitates oligomerization, targeting, and promotes trans-autophosphorylation, limiting centriole duplication to once per cell cycle.

  18. A multiplex PCR assay that separates Rhodnius prolixus from members of the Rhodnius robustus cryptic species complex (Hemiptera: Reduviidae).

    PubMed

    Pavan, M G; Monteiro, F A

    2007-06-01

    Rhodnius prolixus is one of the most important primary vectors of human Chagas disease in Latin America. Its morphology is, however, identical to that of the members of the Rhodnius robustus cryptic species complex, which includes secondary vectors. The correct identification of these taxa with differential vector competence is, therefore, of great epidemiological relevance. We used the alignment of 26 mitochondrial cytochrome b haplotypes (663 bp) to select for PCR-amplifiable species-specific regions. We designed one forward primer on a region conserved across all haplotypes, and three reverse primers that anneal to species-specific regions and amplify fragments of different lengths for R. prolixus (285 bp) and for members of the two major R. robustus lineages: group I (349 bp) and groups II-IV (239 bp). These fragments were easily identifiable on regular 1.5% agarose gels. This multiplex PCR assay was successfully tested on 81 specimens from six Latin American countries, and used to determine the phylogeographic boundaries for each species. It is a simple, objective, and cost-effective assay. Its PCR-based nature makes it applicable to any insect developmental stage, as well as to dried specimens, and insect remains. It should be particularly useful in areas where representatives of these Rhodnius species occur in sympatry.

  19. Metabolomics Reveals Cryptic Interactive Effects of Species Interactions and Environmental Stress on Nitrogen and Sulfur Metabolism in Seagrass.

    PubMed

    Hasler-Sheetal, Harald; Castorani, Max C N; Glud, Ronnie N; Canfield, Donald E; Holmer, Marianne

    2016-11-01

    Eutrophication of estuaries and coastal seas is accelerating, increasing light stress on subtidal marine plants and changing their interactions with other species. To date, we have limited understanding of how such variations in environmental and biological stress modify the impact of interactions among foundational species and eventually affect ecosystem health. Here, we used metabolomics to assess the impact of light reductions on interactions between the seagrass Zostera marina, an important habitat-forming marine plant, and the abundant and commercially important blue mussel Mytilus edulis. Plant performance varied with light availability but was unaffected by the presence of mussels. Metabolomic analysis, on the other hand, revealed an interaction between light availability and presence of M. edulis on seagrass metabolism. Under high light, mussels stimulated seagrass nitrogen and energy metabolism. Conversely, in low light mussels impeded nitrogen and energy metabolism, and enhanced responses against sulfide toxicity, causing inhibited oxidative energy metabolism and tissue degradation. Metabolomic analysis thereby revealed cryptic changes to seagrass condition that could not be detected by traditional approaches. Our findings suggest that coastal eutrophication and associated reductions in light may shift seagrass-bivalve interactions from mutualistic to antagonistic, which is important for conservation management of seagrass meadows.

  20. Cryptic confounding compounds: A brief consideration of the influences of anthropogenic contaminants on courtship and mating behavior.

    PubMed

    Blocker, Tomica D; Ophir, Alexander G

    2013-06-01

    Contaminants, like pesticides, polychlorinated biphenyls (PCBs), dioxins and metals, are persistent and ubiquitous and are known to threaten the environment. Traditionally, scientists have considered the direct physiological risks that these contaminants pose. However, scientists have just begun to integrate ethology and toxicology to investigate the effects that contaminants have on behavior. This review considers the potential for contaminant effects on mating behavior. Here we assess the growing body of research concerning disruptions in sexual differentiation, courtship, sexual receptivity, arousal, and mating. We discuss the implications of these disruptions on conservation efforts and highlight the importance of recognizing the potential for environmental stressors to affect behavioral experimentation. More specifically, we consider the negative implications for anthropogenic contaminants to affect the immediate behavior of animals, and their potential to have cascading and/or long-term effects on the behavioral ecology and evolution of populations. Overall, we aim to raise awareness of the confounding influence that contaminants can have, and promote caution when interpreting results where the potential for cryptic affects are possible.

  1. Cryptic confounding compounds: A brief consideration of the influences of anthropogenic contaminants on courtship and mating behavior

    PubMed Central

    Blocker, Tomica D.; Ophir, Alexander G.

    2012-01-01

    Contaminants, like pesticides, polychlorinated biphenyls (PCBs), dioxins and metals, are persistent and ubiquitous and are known to threaten the environment. Traditionally, scientists have considered the direct physiological risks that these contaminants pose. However, scientists have just begun to integrate ethology and toxicology to investigate the effects that contaminants have on behavior. This review considers the potential for contaminant effects on mating behavior. Here we assess the growing body of research concerning disruptions in sexual differentiation, courtship, sexual receptivity, arousal, and mating. We discuss the implications of these disruptions on conservation efforts and highlight the importance of recognizing the potential for environmental stressors to affect behavioral experimentation. More specifically, we consider the negative implications for anthropogenic contaminants to affect the immediate behavior of animals, and their potential to have cascading and/or long-term effects on the behavioral ecology and evolution of populations. Overall, we aim to raise awareness of the confounding influence that contaminants can have, and promote caution when interpreting results where the potential for cryptic affects are possible. PMID:24244068

  2. The cryptic African wolf: Canis aureus lupaster is not a golden jackal and is not endemic to Egypt.

    PubMed

    Rueness, Eli Knispel; Asmyhr, Maria Gulbrandsen; Sillero-Zubiri, Claudio; Macdonald, David W; Bekele, Afework; Atickem, Anagaw; Stenseth, Nils Chr

    2011-01-26

    The Egyptian jackal (Canis aureus lupaster) has hitherto been considered a large, rare subspecies of the golden jackal (C. aureus). It has maintained its taxonomical status to date, despite studies demonstrating morphological similarities to the grey wolf (C. lupus). We have analyzed 2055 bp of mitochondrial DNA from C. a. lupaster and investigated the similarity to C. aureus and C. lupus. Through phylogenetic comparison with all wild wolf-like canids (based on 726 bp of the Cytochrome b gene) we conclusively (100% bootstrap support) place the Egyptian jackal within the grey wolf species complex, together with the Holarctic wolf, the Indian wolf and the Himalayan wolf. Like the two latter taxa, C. a. lupaster seems to represent an ancient wolf lineage which most likely colonized Africa prior to the northern hemisphere radiation. We thus refer to C. a. lupaster as the African wolf. Furthermore, we have detected C. a. lupaster individuals at two localities in the Ethiopian highlands, extending the distribution by at least 2,500 km southeast. The only grey wolf species to inhabit the African continent is a cryptic species for which the conservation status urgently needs assessment.

  3. OSI Conformance Testing for Bibliographic Applications.

    ERIC Educational Resources Information Center

    Arbez, Gilbert; Swain, Leigh

    1990-01-01

    Describes the development of Open Systems Interconnection (OSI) conformance testing sites, conformance testing tools, and conformance testing services. Discusses related topics such as interoperability testing, arbitration testing, and international harmonization of conformance testing. A glossary is included. (24 references) (SD)

  4. OSI Conformance Testing for Bibliographic Applications.

    ERIC Educational Resources Information Center

    Arbez, Gilbert; Swain, Leigh

    1990-01-01

    Describes the development of Open Systems Interconnection (OSI) conformance testing sites, conformance testing tools, and conformance testing services. Discusses related topics such as interoperability testing, arbitration testing, and international harmonization of conformance testing. A glossary is included. (24 references) (SD)

  5. Leaf growth is conformal

    NASA Astrophysics Data System (ADS)

    Alim, Karen; Armon, Shahaf; Shraiman, Boris I.; Boudaoud, Arezki

    2016-10-01

    Growth pattern dynamics lie at the heart of morphogenesis. Here, we investigate the growth of plant leaves. We compute the conformal transformation that maps the contour of a leaf at a given stage onto the contour of the same leaf at a later stage. Based on the mapping we predict the local displacement field in the leaf blade and find it to agree with the experimentally measured displacement field to 92%. This approach is applicable to any two-dimensional system with locally isotropic growth, enabling the deduction of the whole growth field just from observation of the tissue contour.

  6. Metamaterials with conformational nonlinearity

    PubMed Central

    Lapine, Mikhail; Shadrivov, Ilya V.; Powell, David A.; Kivshar, Yuri S.

    2011-01-01

    Within a decade of fruitful development, metamaterials became a prominent area of research, bridging theoretical and applied electrodynamics, electrical engineering and material science. Being man-made structures, metamaterials offer a particularly useful playground to develop interdisciplinary concepts. Here we demonstrate a novel principle in metamaterial assembly which integrates electromagnetic, mechanical, and thermal responses within their elements. Through these mechanisms, the conformation of the meta-molecules changes, providing a dual mechanism for nonlinearity and offering nonlinear chirality. Our proposal opens a wide road towards further developments of nonlinear metamaterials and photonic structures, adding extra flexibility to their design and control. PMID:22355655

  7. Technidilaton at the conformal edge

    SciTech Connect

    Hashimoto, Michio; Yamawaki, Koichi

    2011-01-01

    Technidilaton (TD) was proposed long ago in the technicolor near criticality/conformality. To reveal the critical behavior of TD, we explicitly compute the nonperturbative contributions to the scale anomaly <{theta}{sub {mu}}{sup {mu}>} and to the technigluon condensate <{alpha}G{sub {mu}{nu}}{sup 2}>, which are generated by the dynamical mass m of the technifermions. Our computation is based on the (improved) ladder Schwinger-Dyson equation, with the gauge coupling {alpha} replaced by the two-loop running coupling {alpha}({mu}) having the Caswell-Banks-Zaks infrared fixed point {alpha}{sub *}: {alpha}({mu}){approx_equal}{alpha}={alpha}{sub *} for the infrared region m<{mu}<{Lambda}{sub TC}, where {Lambda}{sub TC} is the intrinsic scale (analogue of {Lambda}{sub QCD} of QCD) relevant to the perturbative scale anomaly. We find that -<{theta}{sub {mu}}{sup {mu}}>/m{sup 4}{yields}const{ne}0 and <{alpha}G{sub {mu}}{nu}{sup 2}>/m{sup 4}{yields}({alpha}/{alpha}{sub cr}-1){sup -3/2}{yields}{infinity} in the criticality limit m/{Lambda}{sub TC}{approx}exp(-{pi}/({alpha}/{alpha}{sub cr}-1){sup 1/2}){yields}0 ({alpha}={alpha}{sub *}=>{alpha}{sub cr}, or N{sub f} approaches N{sub f}{sup cr}) ('conformal edge'). Our result precisely reproduces the formal identity <{theta}{sub {mu}}{sup {mu}>}=({beta}({alpha})/4{alpha}{sup 2})<{alpha}G{sub {mu}{nu}}{sup 2}>, where {beta}({alpha})={Lambda}{sub TC}({partial_derivative}{alpha}/{partial_derivative}{Lambda}{sub TC})=-(2{alpha}{sub cr}/{pi}){center_dot}({alpha}/{alpha}{sub cr}-1){sup 3/2} is the nonperturbative beta function corresponding to the above essential singularity scaling of m/{Lambda}{sub TC}. Accordingly, the partially conserved dilatation current implies (M{sub TD}/m){sup 2}(F{sub TD}/m){sup 2}=-4<{theta}{sub {mu}}{sup {mu}}>/m{sup 4}{yields}const{ne}0 at criticality limit, where M{sub TD} is the mass of TD and F{sub TD} the decay constant of TD. We thus conclude that at criticality limit the TD could become a ''true

  8. Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles

    PubMed Central

    2012-01-01

    Background Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. Results Each marker was mapped with high confidence (e<1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. Conclusion Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive

  9. Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles.

    PubMed

    Labate, Joanne A; Robertson, Larry D

    2012-08-07

    Many highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions. Each marker was mapped with high confidence (e<1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles. Of the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed

  10. The importance of data quality for generating reliable distribution models for rare, elusive, and cryptic species

    PubMed Central

    Aubry, Keith B.; Raley, Catherine M.; McKelvey, Kevin S.

    2017-01-01

    The availability of spatially referenced environmental data and species occurrence records in online databases enable practitioners to easily generate species distribution models (SDMs) for a broad array of taxa. Such databases often include occurrence records of unknown reliability, yet little information is available on the influence of data quality on SDMs generated for rare, elusive, and cryptic species that are prone to misidentification in the field. We investigated this question for the fisher (Pekania pennanti), a forest carnivore of conservation concern in the Pacific States that is often confused with the more common Pacific marten (Martes caurina). Fisher occurrence records supported by physical evidence (verifiable records) were available from a limited area, whereas occurrence records of unknown quality (unscreened records) were available from throughout the fisher’s historical range. We reserved 20% of the verifiable records to use as a test sample for both models and generated SDMs with each dataset using Maxent. The verifiable model performed substantially better than the unscreened model based on multiple metrics including AUCtest values (0.78 and 0.62, respectively), evaluation of training and test gains, and statistical tests of how well each model predicted test localities. In addition, the verifiable model was consistent with our knowledge of the fisher’s habitat relations and potential distribution, whereas the unscreened model indicated a much broader area of high-quality habitat (indices > 0.5) that included large expanses of high-elevation habitat that fishers do not occupy. Because Pacific martens remain relatively common in upper elevation habitats in the Cascade Range and Sierra Nevada, the SDM based on unscreened records likely reflects primarily a conflation of marten and fisher habitat. Consequently, accurate identifications are far more important than the spatial extent of occurrence records for generating reliable SDMs for the

  11. Causality constraints in conformal field theory

    DOE PAGES

    Hartman, Thomas; Jain, Sachin; Kundu, Sandipan

    2016-05-17

    Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well knownmore » sign constraint on the (Φ)4 coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. As a result, our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinning operators« less

  12. Acoustic analysis reveals a new cryptic bush-cricket in the Carpathian Mountains (Orthoptera, Phaneropteridae).

    PubMed

    Iorgu, Ionuţ Ştefan

    2012-01-01

    A new morphologically cryptic species of phaneropterid bush-cricket from the genus Isophya is described from the Eastern Carpathian Mountains: Isophya dochiasp. n. Sound analysis and morphological details are discussed in the paper comparing the new species with several Isophya species having similar morphology and acoustic behavior.

  13. First report of Persimmon cryptic virus and Persimmon virus A in Korea

    USDA-ARS?s Scientific Manuscript database

    In 2014, a total of 77 persimmon (Diospyros kaki Thunb.) trees from Korean commercial persimmon orchards were surveyed for Persimmon cryptic virus (PeCV) and Persimmon virus A (PeVA). Leaf samples were collected from symptomatic trees with necrosis (two), or mosaic and leaf malformations (one) and 7...

  14. Cryptic speciation in the Acari: a function of species lifestyles or our ability to separate species?

    USDA-ARS?s Scientific Manuscript database

    There are approximately 55,000 described Acari species, accounting for almost half of all known Arachnida species, but total estimated Acari diversity is reckoned to be far greater. One important source of currently hidden Acari diversity is cryptic speciation, which poses challenges to taxonomists ...

  15. ACTIVATION OF A CRYPTIC D-SERINE DEAMINASE (DSD) GENE FROM PSEUDOMONAS CEPACIA 17616

    EPA Science Inventory

    D-serine inhibits growth of P. cepacia 17616; however, resistant mutants able to express an ordinarily cryptic D-serine deaminase (dsd) gene were isolated readily. The resistant strains formed high levels of a D-serine deaminase active on D-threonine as well as D-serine. IS eleme...

  16. A cryptic wheat–Aegilops triuncialis translocation with leaf rust resistance gene Lr58

    USDA-ARS?s Scientific Manuscript database

    Genes transferred to crop plants from wild species are often associated with deleterious traits. Using molecular markers, we detected a cryptic introgression with a leaf rust resistance gene transferred from Aegilops triuncialis L. into common wheat (Triticum aestivum L.). One agronomically desirabl...

  17. Temporal Exposure of Cryptic Collagen Epitopes within Ischemic Muscle during Hindlimb Reperfusion

    PubMed Central

    Gagne, Paul J.; Tihonov, Nikita; Li, Xialou; Glaser, Joseph; Qiao, Jhenrong; Silberstein, Michael; Yee, Herman; Gagne, Elizabeth; Brooks, Peter

    2005-01-01

    Chronic limb-threatening ischemia is a devastating disease with limited surgical options. However, inducing controlled angiogenesis and enhancing reperfusion holds therapeutic promise. To gain a better understanding of the mechanisms that contribute to limb reperfusion, we examined the temporal biochemical and structural changes occurring within the extracellular matrix of ischemic skeletal muscle. Both the latent and active forms of MMP-2 and -9 significantly increased during the active phase of limb reperfusion. Moreover, small but significant alterations in tissue inhibitors of metalloproteinase levels also occurred during a similar time course, consistent with a net increase in extracellular matrix remodeling. This temporal increase in MMP activity coincided with enhanced exposure of the unique HU177 cryptic collagen epitope. Although the HUIV26 cryptic collagen epitope has been implicated in angiogenesis, little is known concerning such epitopes within ischemic muscle tissue. Here, we provide the first evidence that a functionally distinct cryptic collagen epitope (HU177) is temporally exposed in ischemic muscle tissue during the active phase of reperfusion. Interestingly, the exposure of the HU177 epitope was greatly diminished in MMP-9 null mice, corresponding with significantly reduced limb reperfusion. Therefore, the regulated exposure of a unique cryptic collagen epitope within ischemic muscle suggests an important role for collagen remodeling during the active phase of ischemic limb reperfusion. PMID:16251419

  18. A near-infrared spectroscopy routine for unambiguous identification of cryptic ant species

    USDA-ARS?s Scientific Manuscript database

    The identification of species – of importance for most biological disciplines – is not always straightforward as cryptic species present a hurdle for traditional species discrimination. Fibre-optic near-infrared spectroscopy (NIRS) is a rapid and cheap method for a wide range of different applicatio...

  19. Spatial Distribution of Cryptic Species Diversity in European Freshwater Amphipods (Gammarus fossarum) as Revealed by Pyrosequencing

    PubMed Central

    Westram, Anja Marie; Jokela, Jukka; Baumgartner, Caroline; Keller, Irene

    2011-01-01

    In order to understand and protect ecosystems, local gene pools need to be evaluated with respect to their uniqueness. Cryptic species present a challenge in this context because their presence, if unrecognized, may lead to serious misjudgement of the distribution of evolutionarily distinct genetic entities. In this study, we describe the current geographical distribution of cryptic species of the ecologically important stream amphipod Gammarus fossarum (types A, B and C). We use a novel pyrosequencing assay for molecular species identification and survey 62 populations in Switzerland, plus several populations in Germany and eastern France. In addition, we compile data from previous publications (mainly Germany). A clear transition is observed from type A in the east (Danube and Po drainages) to types B and, more rarely, C in the west (Meuse, Rhone, and four smaller French river systems). Within the Rhine drainage, the cryptic species meet in a contact zone which spans the entire G. fossarum distribution range from north to south. This large-scale geographical sorting indicates that types A and B persisted in separate refugia during Pleistocene glaciations. Within the contact zone, the species rarely co-occur at the same site, suggesting that ecological processes may preclude long-term coexistence. The clear phylogeographical signal observed in this study implies that, in many parts of Europe, only one of the cryptic species is present. PMID:21909373

  20. ACTIVATION OF A CRYPTIC D-SERINE DEAMINASE (DSD) GENE FROM PSEUDOMONAS CEPACIA 17616

    EPA Science Inventory

    D-serine inhibits growth of P. cepacia 17616; however, resistant mutants able to express an ordinarily cryptic D-serine deaminase (dsd) gene were isolated readily. The resistant strains formed high levels of a D-serine deaminase active on D-threonine as well as D-serine. IS eleme...

  1. Cryptic species diversity in sub-Antarctic islands: A case study of Lepidonotothen.

    PubMed

    Dornburg, Alex; Federman, Sarah; Eytan, Ron I; Near, Thomas J

    2016-11-01

    The marine fauna of the Southern Ocean is well known for an impressive adaptive radiation of fishes, the notothenioids. However, when compared to other marine areas, the frigid waters of the Southern Ocean also contain a seemingly large proportion of cryptic species. The documented instances of speciation in the absence of morphological change are largely observed in invertebrate taxa, in particular around peri- and sub-Antarctic islands such as South Georgia, which has been dubbed a cryptic species hotspot. This prevalence of cryptic species raises the question of how generalizable these patterns are for Antarctic vertebrates. Here we examine aspects of genotype and phenotype in an Antarctic notothenioid fish species, Lepidonotothen nudifrons, which is distributed in near shore habitats of the Antarctic Peninsula, South Orkney Islands, South Georgia, and the South Sandwich Islands. The results of our analyses show that L. nudifrons comprises two species. We highlight that cryptic species are phenomena not restricted to invertebrate lineages, raising the possibility that the species diversity of notothenioids and other Southern Ocean fishes is under-described. In addition, our findings raise several questions about the evolutionary origin and maintenance of morphological stasis in one of the most extreme habitats on earth. Copyright © 2016 Elsevier Inc. All rights reserved.

  2. Population genetics of invasive Bemisia tabaci cryptic species in the United States based on microsatellite markers

    USDA-ARS?s Scientific Manuscript database

    The Bemisia tabaci cryptic species complex of whiteflies contains two species, MEAM1 and MED, that are highly invasive in supportive climates the world over. In the United States MEAM1 occurs both in the field and in the greenhouse, but MED is only found in the greenhouse. In order to make inference...

  3. Population genetics of invasive Bemisia tabaci cryptic species in the United States based on microsatellite markers

    USDA-ARS?s Scientific Manuscript database

    The Bemisia tabaci cryptic species complex of whiteflies contains two species, MEAM1 and MED, that are highly invasive in supportive climates the world over. In the U.S. MEAM1 occurs both in the field and in the greenhouse but MED is only found in the greenhouse. In order to make inferences about th...

  4. Formal nomenclature and description of cryptic species of the Encyrtus sasakii complex (Hymenoptera: Encyrtidae)

    PubMed Central

    Wang, Ying; Zhou, Qing-Song; Qiao, Hui-Jie; Zhang, Ai-Bing; Yu, Fang; Wang, Xu-Bo; Zhu, Chao-Dong; Zhang, Yan-Zhou

    2016-01-01

    With the recent development of molecular approaches to species delimitation, a growing number of cryptic species have been discovered in what had previously been thought to be single morpho-species. Molecular methods, such as DNA barcoding, have greatly enhanced our knowledge of taxonomy, but taxonomy remains incomplete and needs a formal species nomenclature and description to facilitate its use in other scientific fields. A previous study using DNA barcoding, geometric morphometrics and mating tests revealed at least two cryptic species in the Encyrtus sasakii complex. (Hymenoptera: Encyrtidae). To describe these two new species formally (Encyrtus eulecaniumiae sp. nov. and Encyrtus rhodococcusiae sp. nov.), a detailed morphometric study of Encyrtus spp. was performed in addition to the molecular analysis and evaluation of biological data. Morphometric analyses, a multivariate ratio analysis (MRA) and a geometric morphometric analysis (GMA) revealed a great number of differences between the species, but reliable characteristics were not observed for diagnosing the cryptic species. We thus diagnosed these three Encyrtus species on the basis of the characteristics that resulted from genetic markers (mitochondrial cytochrome c oxidase subunit I and nuclear 28S rRNA) and biological data. A formal nomenclature and description of cryptic species was provided on the basis of an integrated taxonomy. PMID:27698441

  5. Cryptic female Strawberry poison frogs experience elevated predation risk when associating with an aposematic partner.

    PubMed

    Segami Marzal, Julia Carolina; Rudh, Andreas; Rogell, Björn; Ödeen, Anders; Løvlie, Hanne; Rosher, Charlotte; Qvarnström, Anna

    2017-01-01

    Population divergence in sexual signals may lead to speciation through prezygotic isolation. Sexual signals can change solely due to variation in the level of natural selection acting against conspicuousness. However, directional mate choice (i.e., favoring conspicuousness) across different environments may lead to gene flow between populations, thereby delaying or even preventing the evolution of reproductive barriers and speciation. In this study, we test whether natural selection through predation upon mate-choosing females can favor corresponding changes in mate preferences. Our study system, Oophaga pumilio, is an extremely color polymorphic neotropical frog with two distinctive antipredator strategies: aposematism and crypsis. The conspicuous coloration and calling behavior of aposematic males may attract both cryptic and aposematic females, but predation may select against cryptic females choosing aposematic males. We used an experimental approach where domestic fowl were encouraged to find digitized images of cryptic frogs at different distances from aposematic partners. We found that the estimated survival time of a cryptic frog was reduced when associating with an aposematic partner. Hence, predation may act as a direct selective force on female choice, favoring evolution of color assortative mating that, in turn, may strengthen the divergence in coloration that natural selection has generated.

  6. The evolution of alternative cryptic female choice strategies in age-structured populations.

    PubMed

    Jones, Adam G

    2002-12-01

    Cryptic female choice is a potentially important aspect of the sexual selection process. According to the theory of sexual dialectics, postcopulation manipulation of relative male fertilization success can provide an avenue by which females can circumvent attempts by males to control female reproduction. Here I use stochastic models to investigate the evolution of cryptic female choice in populations with and without age structure. In populations without age structure, cryptic female choice will evolve only when (1) precopulatory mate choice by females is inefficient, (2) variation in male fitness is correlated with a trait upon which a female can base her choice of mates, and (3) the cost of multiple mating is not too high. In populations with age structure, similar conditions apply. However, selection sometimes favors females that employ alternative strategies of female choice at different ages. These results help to define the types of biological systems in which we should expect to see the evolution of cryptic female choice. They also illustrate that the evolution of choice strategies in females may be complex and may mirror in some important respects the evolution of alternative mating tactics in males.

  7. Predator experience on cryptic prey affects the survival of conspicuous aposematic prey.

    PubMed Central

    Lindström, L.; Alatalo, R. V.; Lyytinen, A.; Mappes, J.

    2001-01-01

    Initially, aposematism, which is an unprofitable trait, e.g. noxiousness conspicuously advertised to predators, appears to be a paradox since conspicuousness should increase predation by naive predators. However, reluctance of predators for eating novel prey (e.g. neophobia) might balance the initial predation caused by inexperienced predators. We tested the novelty effects on initial predation and avoidance learning in two separate conspicuousness levels of aposematic prey by using a 'novel world' method. Half of the wild great tits (Parus major) were trained to eat cryptic prey prior to the introduction of an aposematic prey, which potentially creates a bias against the aposematic morph. Both prey types were equally novel for control birds and they should not have shown any biased reluctance for eating an aposematic prey. Knowledge of cryptic prey reduced the expected initial mortality of the conspicuous morph to a random level whereas control birds initially ate the conspicuous morph according to the visibility risk. Birds learned to avoid conspicuous prey in both treatments but knowledge of cryptic prey did not increase the rate of avoidance learning. Predators' knowledge of cryptic prey did not reduce the predation of the less conspicuous aposematic prey and additionally predators did not learn to avoid the less conspicuous prey. These results indicate that predator psychology, which was shown as reluctance for attacking novel conspicuous prey, might have been important in the evolution of aposematism. PMID:11270431

  8. Field identification of the cryptic vespertilionid bats, Myotis lucifugus and M. yumanensis

    Treesearch

    Theodore J. Weller; Shonene A. Scott; Thomas J. Rodhouse; Patricia C. Ormsbee; Jan M. Zinck

    2007-01-01

    Recent advances in molecular techniques have provided new tools for confirming species identities, however they can be expensive and results are not immediately available. Myotis lucificugus and M. yumanensis are morphologically cryptic species of bats sympatric in western North America that can be difficult to distinguish in the...

  9. Acoustic analysis reveals a new cryptic bush–cricket in the Carpathian Mountains (Orthoptera, Phaneropteridae)

    PubMed Central

    Iorgu, Ionuţ Ştefan

    2012-01-01

    Abstract A new morphologically cryptic species of phaneropterid bush–cricket from the genus Isophya is described from the Eastern Carpathian Mountains: Isophya dochia sp. n. Sound analysis and morphological details are discussed in the paper comparing the new species with several Isophya species having similar morphology and acoustic behavior. PMID:23378813

  10. Activation of cryptic 3' splice sites within introns of cellular genes following gene entrapment.

    PubMed

    Osipovich, Anna B; White-Grindley, Erica K; Hicks, Geoffrey G; Roshon, Michael J; Shaffer, Christian; Moore, Jason H; Ruley, H Earl

    2004-01-01

    Gene trap vectors developed for genome-wide mutagenesis can be used to study factors governing the expression of exons inserted throughout the genome. For example, entrapment vectors consisting of a partial 3'-terminal exon [i.e. a neomycin resistance gene (Neo), a poly(A) site, but no 3' splice site] were typically expressed following insertion into introns, from cellular transcripts that spliced to cryptic 3' splice sites present either within the targeting vector or in the adjacent intron. A vector (U3NeoSV1) containing the wild-type Neo sequence preferentially disrupted genes that spliced in-frame to a cryptic 3' splice site in the Neo coding sequence and expressed functional neomycin phosphotransferase fusion proteins. Removal of the cryptic Neo 3' splice site did not reduce the proportion of clones with inserts in introns; rather, the fusion transcripts utilized cryptic 3' splice sites present in the adjacent intron or generated by virus integration. However, gene entrapment with U3NeoSV2 was considerably more random than with U3NeoSV1, consistent with the widespread occurrence of potential 3' splice site sequences in the introns of cellular genes. These results clarify the mechanisms of gene entrapment by U3 gene trap vectors and illustrate features of exon definition required for 3' processing and polyadenylation of cellular transcripts.

  11. Activation of cryptic 3′ splice sites within introns of cellular genes following gene entrapment

    PubMed Central

    Osipovich, Anna B.; White-Grindley, Erica K.; Hicks, Geoffrey G.; Roshon, Michael J.; Shaffer, Christian; Moore, Jason H.; Ruley, H. Earl

    2004-01-01

    Gene trap vectors developed for genome-wide mutagenesis can be used to study factors governing the expression of exons inserted throughout the genome. For example, entrapment vectors consisting of a partial 3′-terminal exon [i.e. a neomycin resistance gene (Neo), a poly(A) site, but no 3′ splice site] were typically expressed following insertion into introns, from cellular transcripts that spliced to cryptic 3′ splice sites present either within the targeting vector or in the adjacent intron. A vector (U3NeoSV1) containing the wild-type Neo sequence preferentially disrupted genes that spliced in-frame to a cryptic 3′ splice site in the Neo coding sequence and expressed functional neomycin phosphotransferase fusion proteins. Removal of the cryptic Neo 3′ splice site did not reduce the proportion of clones with inserts in introns; rather, the fusion transcripts utilized cryptic 3′ splice sites present in the adjacent intron or generated by virus integration. However, gene entrapment with U3NeoSV2 was considerably more random than with U3NeoSV1, consistent with the widespread occurrence of potential 3′ splice site sequences in the introns of cellular genes. These results clarify the mechanisms of gene entrapment by U3 gene trap vectors and illustrate features of exon definition required for 3′ processing and polyadenylation of cellular transcripts. PMID:15155860

  12. Restricted Gene Flow among Lineages of Thrips tabaci Supports Genetic Divergence Among Cryptic Species Groups

    PubMed Central

    Jacobson, Alana L.; Nault, Brian A.; Vargo, Edward L.; Kennedy, George G.

    2016-01-01

    Knowledge of the relative influence of population- versus species-level genetic variation is important to understand patterns of phenotypic variation and ecological relationships that exist among and within morphologically indistinguishable cryptic species and subspecies. In the case of cryptic species groups that are pests, such knowledge is also essential for devising effective population management strategies. The globally important crop pest Thrips tabaci is a taxonomically difficult group of putatively cryptic species. This study examines population genetic structure of T. tabaci and reproductive isolation among lineages of this species complex using microsatellite markers and mitochondrial COI sequences. Overall, genetic structure supports T. tabaci as a cryptic species complex, although limited interbreeding occurs between different clonal groups from the same lineage as well as between individuals from different lineages. These results also provide evidence that thelytoky and arrhenotoky are not fixed phenotypes among members of different T. tabaci lineages that have been generally associated with either reproductive mode. Possible biological and ecological factors contributing to these observations are discussed. PMID:27690317

  13. A nearly cryptic scorpionfly, Panorpa cryptica n sp.(Mecoptera: Panorpidae) from North America

    Treesearch

    Wesley Bicha; Nathan Schiff; Aaron Lancaster; Brian Scheffler

    2015-01-01

    The first nearly cryptic species of scorpionfly from the United States, Strong>Panorpa cryptica Bicha and Schiff, n. sp., is described from northern Georgia, southwestern North Carolina and northwestern South Carolina. This insect was initially differentiated from the very similar Panorpa nebulosa Westwood by its unique cytochrome...

  14. Molecular species identification of cryptic apple and snowberry maggots (Diptera: Tephritidae) in Western and Central Washington

    USDA-ARS?s Scientific Manuscript database

    In Washington state, identification of the quarantine apple pest Rhagoletis pomonella (Walsh) is complicated by the presence of the cryptic species R. zephyria Snow (Diptera: Tephritidae). Distinguishing the two flies is important because there is a zero tolerance policy for R. pomonella in apple p...

  15. Near-infrared imaging spectroscopy as a tool to discriminate two cryptic Tetramorium ant species

    USDA-ARS?s Scientific Manuscript database

    Correct species identification is a precondition for many ecological studies. Morphologically highly similar, i.e. cryptic, species are an important component of biodiversity but particularly difficult to discriminate and therefore understudied ecologically. To find new methods for their rapid ident...

  16. Predation cues rather than resource availability promote cryptic behaviour in a habitat-forming sea urchin.

    PubMed

    Spyksma, Arie J P; Taylor, Richard B; Shears, Nick T

    2017-03-01

    It is well known that predators often influence the foraging behaviour of prey through the so-called "fear effect". However, it is also possible that predators could change prey behaviour indirectly by altering the prey's food supply through a trophic cascade. The predator-sea urchin-kelp trophic cascade is widely assumed to be driven by the removal of sea urchins by predators, but changes in sea urchin behaviour in response to predators or increased food availability could also play an important role. We tested whether increased crevice occupancy by herbivorous sea urchins in the presence of abundant predatory fishes and lobsters is a response to the increased risk of predation, or an indirect response to higher kelp abundances. Inside two New Zealand marine reserves with abundant predators and kelp, individuals of the sea urchin Evechinus chloroticus were rarer and remained cryptic (i.e. found in crevices) to larger sizes than on adjacent fished coasts where predators and kelp are rare. In a mesocosm experiment, cryptic behaviour was induced by simulated predation (the addition of crushed conspecifics), but the addition of food in the form of drift kelp did not induce cryptic behaviour. These findings demonstrate that the 'fear' of predators is more important than food availability in promoting sea urchin cryptic behaviour and suggest that both density- and behaviourally mediated interactions are important in the predator-sea urchin-kelp trophic cascade.

  17. Eikonalization of conformal blocks

    DOE PAGES

    Fitzpatrick, A. Liam; Kaplan, Jared; Walters, Matthew T.; ...

    2015-09-03

    Classical field configurations such as the Coulomb potential and Schwarzschild solution are built from the t-channel exchange of many light degrees of freedom. We study the CFT analog of this phenomenon, which we term the 'eikonalization' of conformal blocks. We show that when an operator T appears in the OPE Ο(x)Ο(0), then the large spin Fock space states [TT···T]ℓ also appear in this OPE with a computable coefficient. The sum over the exchange of these Fock space states in an correlator build the classical 'T field' in the dual AdS description. In some limits the sum of all Fock spacemore » exchanges can be represented as the exponential of a single T exchange in the 4-pt correlator of O. Our results should be useful for systematizing 1/ℓ perturbation theory in general CFTs and simplifying the computation of large spin OPE coefficients. As examples we obtain the leading log ℓ dependence of Fock space conformal block coefficients, and we directly compute the OPE coefficients of the simplest ‘triple-trace’ operators.« less

  18. Eikonalization of conformal blocks

    SciTech Connect

    Fitzpatrick, A. Liam; Kaplan, Jared; Walters, Matthew T.; Wang, Junpu

    2015-09-03

    Classical field configurations such as the Coulomb potential and Schwarzschild solution are built from the t-channel exchange of many light degrees of freedom. We study the CFT analog of this phenomenon, which we term the 'eikonalization' of conformal blocks. We show that when an operator T appears in the OPE Ο(x)Ο(0), then the large spin Fock space states [TT···T] also appear in this OPE with a computable coefficient. The sum over the exchange of these Fock space states in an correlator build the classical 'T field' in the dual AdS description. In some limits the sum of all Fock space exchanges can be represented as the exponential of a single T exchange in the 4-pt correlator of O. Our results should be useful for systematizing 1/ℓ perturbation theory in general CFTs and simplifying the computation of large spin OPE coefficients. As examples we obtain the leading log ℓ dependence of Fock space conformal block coefficients, and we directly compute the OPE coefficients of the simplest ‘triple-trace’ operators.

  19. Supergravitational conformal Galileons

    NASA Astrophysics Data System (ADS)

    Deen, Rehan; Ovrut, Burt

    2017-08-01

    The worldvolume actions of 3+1 dimensional bosonic branes embedded in a five-dimensional bulk space can lead to important effective field theories, such as the DBI conformal Galileons, and may, when the Null Energy Condition is violated, play an essential role in cosmological theories of the early universe. These include Galileon Genesis and "bouncing" cosmology, where a pre-Big Bang contracting phase bounces smoothly to the presently observed expanding universe. Perhaps the most natural arena for such branes to arise is within the context of superstring and M -theory vacua. Here, not only are branes required for the consistency of the theory, but, in many cases, the exact spectrum of particle physics occurs at low energy. However, such theories have the additional constraint that they must be N = 1 supersymmetric. This motivates us to compute the worldvolume actions of N = 1 supersymmetric three-branes, first in flat superspace and then to generalize them to N = 1 supergravitation. In this paper, for simplicity, we begin the process, not within the context of a superstring vacuum but, rather, for the conformal Galileons arising on a co-dimension one brane embedded in a maximally symmetric AdS 5 bulk space. We proceed to N = 1 supersymmetrize the associated worldvolume theory and then generalize the results to N = 1 supergravity, opening the door to possible new cosmological scenarios

  20. Conformally symmetric traversable wormholes

    SciTech Connect

    Boehmer, Christian G.; Harko, Tiberiu; Lobo, Francisco S. N.

    2007-10-15

    Exact solutions of traversable wormholes are found under the assumption of spherical symmetry and the existence of a nonstatic conformal symmetry, which presents a more systematic approach in searching for exact wormhole solutions. In this work, a wide variety of solutions are deduced by considering choices for the form function, a specific linear equation of state relating the energy density and the pressure anisotropy, and various phantom wormhole geometries are explored. A large class of solutions impose that the spatial distribution of the exotic matter is restricted to the throat neighborhood, with a cutoff of the stress-energy tensor at a finite junction interface, although asymptotically flat exact solutions are also found. Using the 'volume integral quantifier', it is found that the conformally symmetric phantom wormhole geometries may, in principle, be constructed by infinitesimally small amounts of averaged null energy condition violating matter. Considering the tidal acceleration traversability conditions for the phantom wormhole geometry, specific wormhole dimensions and the traversal velocity are also deduced.

  1. Amitriptylinium picrate: conformational disorder.

    PubMed

    Bindya, S; Wong, Wing-Tak; Ashok, M A; Yathirajan, H S; Rathore, R S

    2007-09-01

    In the structure of the title salt [systematic name: 3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-ylidene)-N,N-dimethylpropan-1-aminium 2,4,6-trinitrophenolate] of a tricyclic antidepressant, C(20)H(24)N+.C(6)H(2)N(3)O(7)-, the dimethylaminopropyl subunit possesses a classical static conformational disorder. The central cycloheptadiene ring adopts a bent conformation that is intermediate between boat and chair forms, leading to a butterfly shape for the hetero-tricyclic moiety. In a complementary fashion, donors from amitriptyline and acceptors from picrate form intermolecular C-H...O hydrogen bonds and N-H...O salt bridges. These hydrogen bonds cluster amitriptyline and picrate ions into a closed R4(4)(36) hetero-tetramer, whereas intermolecular C-H...pi interactions between amitriptyline ions cluster them into homo-dimers. Significant pi-pi stacking interactions are also observed between aromatic rings of amitriptyline and picrate, and these, combined with the C-H...pi interactions, associate molecules into linear arrays along the [111] direction.

  2. Phylogeography of the dark kangaroo mouse, Microdipodops megacephalus: cryptic lineages and dispersal routes in North America's Great Basin.

    PubMed

    Hafner, John C; Upham, Nathan S

    2011-06-01

    AIM: The rodent genus Microdipodops (kangaroo mice) includes two sand-obligate endemics of the Great Basin Desert: M. megacephalus and M. pallidus. The dark kangaroo mouse, M. megacephalus, is distributed throughout the Great Basin and our principal aims were to formulate phylogenetic hypotheses for this taxon and make phylogeographical comparisons with its congener. LOCATION: The Great Basin Desert of western North America. METHODS: DNA sequence data from three mitochondrial genes were examined from 186 individuals of M. megacephalus, representing 47 general localities. Phylogenetic inference was used to analyse the sequence data. Directional analysis of phylogeographical patterns was used to examine haplotype sharing patterns and recover routes of gene exchange. Haplotype-area curves were constructed to evaluate the relationship between genetic variation and distributional island size for M. megacephalus and M. pallidus. RESULTS: Microdipodops megacephalus is a rare desert rodent (trapping success was 2.67%). Temporal comparison of trapping data shows that kangaroo mice are becoming less abundant in the study area. The distribution has changed slightly since the 1930s but many northern populations now appear to be small, fragmented, or locally extinct. Four principal phylogroups (the Idaho isolate and the western, central and eastern clades) are evident; mean sequence divergence between phylogroups for cytochrome b is c. 8%. Data from haplotype sharing show two trends: a north-south trend and a web-shaped trend. Analyses of haplotype-area curves reveal significant positive relationships. MAIN CONCLUSIONS: The four phylogroups of M. megacephalus appear to represent morphologically cryptic species; in comparison, a companion study revealed two cryptic lineages in M. pallidus. Estimated divergence times of the principal clades of M. megacephalus (c. 2-4 Ma) indicate that these kangaroo mice were Pleistocene invaders into the Great Basin coincident with the formation

  3. Phylogeography of the dark kangaroo mouse, Microdipodops megacephalus: cryptic lineages and dispersal routes in North America's Great Basin

    PubMed Central

    Hafner, John C; Upham, Nathan S

    2011-01-01

    Aim The rodent genus Microdipodops (kangaroo mice) includes two sand-obligate endemics of the Great Basin Desert: M. megacephalus and M. pallidus. The dark kangaroo mouse, M. megacephalus, is distributed throughout the Great Basin and our principal aims were to formulate phylogenetic hypotheses for this taxon and make phylogeographical comparisons with its congener. Location The Great Basin Desert of western North America. Methods DNA sequence data from three mitochondrial genes were examined from 186 individuals of M. megacephalus, representing 47 general localities. Phylogenetic inference was used to analyse the sequence data. Directional analysis of phylogeographical patterns was used to examine haplotype sharing patterns and recover routes of gene exchange. Haplotype–area curves were constructed to evaluate the relationship between genetic variation and distributional island size for M. megacephalus and M. pallidus. Results Microdipodops megacephalus is a rare desert rodent (trapping success was 2.67%). Temporal comparison of trapping data shows that kangaroo mice are becoming less abundant in the study area. The distribution has changed slightly since the 1930s but many northern populations now appear to be small, fragmented, or locally extinct. Four principal phylogroups (the Idaho isolate and the western, central and eastern clades) are evident; mean sequence divergence between phylogroups for cytochrome b is c. 8%. Data from haplotype sharing show two trends: a north–south trend and a web-shaped trend. Analyses of haplotype–area curves reveal significant positive relationships. Main conclusions The four phylogroups of M. megacephalus appear to represent morphologically cryptic species; in comparison, a companion study revealed two cryptic lineages in M. pallidus. Estimated divergence times of the principal clades of M. megacephalus (c. 2–4 Ma) indicate that these kangaroo mice were Pleistocene invaders into the Great Basin coincident with the

  4. Targeting a Hidden Enemy: Pyriproxyfen Autodissemination Strategy for the Control of the Container Mosquito Aedes albopictus in Cryptic Habitats.

    PubMed

    Chandel, Kshitij; Suman, Devi Shankar; Wang, Yi; Unlu, Isik; Williges, Eric; Williams, Gregory M; Gaugler, Randy

    2016-12-01

    The Asian tiger mosquito, Aedes albopictus, is a vector of dengue, Chikungunya, and Zika viruses. This mosquito inhabits a wide range of artificial water-holding containers in urban and suburban areas making it difficult to control. We tested the hypothesis that female-driven autodissemination of an insect growth regulator could penetrate cryptic oviposition habitats difficult to treat with conventional insecticidal sprays. Oviposition preferences of Ae. albopictus females for open and cryptic cups were tested in semi-field experiments. Two conventional larvicidal sprayers were tested to determine droplet penetration and larvicidal efficacy in open and cryptic habitats using Bacillus thuringiensis var. israelensis (Bti) in the field. Finally, the efficacy of pyriproxyfen autodissemination stations was assessed in cryptic and open cups in residential areas during 2013 and 2014. Gravid females strongly preferred cryptic (53.1±12.9 eggs/cup) over open (10.3±4.3 eggs/cup) cups for oviposition. Cryptic cups showed limited droplet penetration and produced 0.1-0.3% larval mortality with a conventional backpack and low-volume sprays of Bti. The autodissemination stations effectively contaminated these cryptic cups (59.3-84.6%) and produced 29.7-40.8% pupal mortality during 2013-2014. Significant pupal mortality was also observed in open cups. The autodissemination station effectively exploits the oviposition behavior of wild gravid females to deliver pyriproxyfen to targeted oviposition habitats. Although the pupal mortality in cryptic cups was relatively lower than expected for the effective vector control. Autodissemination approach may be a suitable supporting tool to manage Ae. albopictus immatures in the cryptic habitats those are less accessible to conventional larvicidal sprays.

  5. Targeting a Hidden Enemy: Pyriproxyfen Autodissemination Strategy for the Control of the Container Mosquito Aedes albopictus in Cryptic Habitats

    PubMed Central

    Suman, Devi Shankar; Wang, Yi; Unlu, Isik; Williges, Eric; Williams, Gregory M.; Gaugler, Randy

    2016-01-01

    Background The Asian tiger mosquito, Aedes albopictus, is a vector of dengue, Chikungunya, and Zika viruses. This mosquito inhabits a wide range of artificial water-holding containers in urban and suburban areas making it difficult to control. We tested the hypothesis that female-driven autodissemination of an insect growth regulator could penetrate cryptic oviposition habitats difficult to treat with conventional insecticidal sprays. Methodology Oviposition preferences of Ae. albopictus females for open and cryptic cups were tested in semi-field experiments. Two conventional larvicidal sprayers were tested to determine droplet penetration and larvicidal efficacy in open and cryptic habitats using Bacillus thuringiensis var. israelensis (Bti) in the field. Finally, the efficacy of pyriproxyfen autodissemination stations was assessed in cryptic and open cups in residential areas during 2013 and 2014. Principal Findings Gravid females strongly preferred cryptic (53.1±12.9 eggs/cup) over open (10.3±4.3 eggs/cup) cups for oviposition. Cryptic cups showed limited droplet penetration and produced 0.1–0.3% larval mortality with a conventional backpack and low-volume sprays of Bti. The autodissemination stations effectively contaminated these cryptic cups (59.3–84.6%) and produced 29.7–40.8% pupal mortality during 2013–2014. Significant pupal mortality was also observed in open cups. Conclusions The autodissemination station effectively exploits the oviposition behavior of wild gravid females to deliver pyriproxyfen to targeted oviposition habitats. Although the pupal mortality in cryptic cups was relatively lower than expected for the effective vector control. Autodissemination approach may be a suitable supporting tool to manage Ae. albopictus immatures in the cryptic habitats those are less accessible to conventional larvicidal sprays. PMID:28033379

  6. DM determines the cryptic and immunodominant fate of T cell epitopes.

    PubMed

    Nanda, N K; Sant, A J

    2000-09-18

    The ability of the immune system to focus T cell responses against a select number of potential epitopes of a complex antigen is termed immunodominance. Epitopes that trigger potent T cell activation, after in vivo priming, are classified as immunodominant. By contrast, determinants that fail to elicit any response are called cryptic. DM, a major histocompatibility complex (MHC) heterodimer, plays a pivotal role in the presentation of MHC class II-restricted epitopes by catalyzing the exchange of class II-associated invariant chain peptide with the antigen-derived peptides within the MHC class II binding groove. Using L cells transfected with genes for MHC class II, invariant chain, and DM, we have studied the contribution of DM in the presentation of two cryptic (peptide 11-25 and peptide 20-35) and one dominant (peptide 106-116) epitope of hen egg white lysozyme (HEL). Cells lacking DM heterodimers efficiently display the determinants HEL 11-25 and HEL 20-35 to T cells. Strikingly, however, cells expressing DM are severely compromised in their ability to present the cryptic HEL 11-25/A(d) and 20-35/A(d) epitopes. DM-mediated antagonism of HEL 11-25/A(d) and 20-35/A(d) presentation could thus be central to 11-25/A(d) and 20-35/A(d) being cryptic epitopes in the HEL system. Interestingly, the display of the immunodominant epitope of HEL, 106-116/E(d), and of a dominant epitope of sperm whale myoglobin (SWM), 102-118/A(d), is entirely dependent on the expression of DM. Thus, cells lacking DM molecules are unable to efficiently express HEL 106-116/E(d) and SWM 102-118/A(d) determinants. We conclude that the DM heterodimers direct the immunodominant and cryptic fate of antigenic epitopes in vivo.

  7. Dm Determines the Cryptic and Immunodominant Fate of T Cell Epitopes

    PubMed Central

    Nanda, Navreet K.; Sant, Andrea J.

    2000-01-01

    The ability of the immune system to focus T cell responses against a select number of potential epitopes of a complex antigen is termed immunodominance. Epitopes that trigger potent T cell activation, after in vivo priming, are classified as immunodominant. By contrast, determinants that fail to elicit any response are called cryptic. DM, a major histocompatibility complex (MHC) heterodimer, plays a pivotal role in the presentation of MHC class II–restricted epitopes by catalyzing the exchange of class II–associated invariant chain peptide with the antigen-derived peptides within the MHC class II binding groove. Using L cells transfected with genes for MHC class II, invariant chain, and DM, we have studied the contribution of DM in the presentation of two cryptic (peptide 11–25 and peptide 20–35) and one dominant (peptide 106–116) epitope of hen egg white lysozyme (HEL). Cells lacking DM heterodimers efficiently display the determinants HEL 11–25 and HEL 20–35 to T cells. Strikingly, however, cells expressing DM are severely compromised in their ability to present the cryptic HEL 11–25/Ad and 20–35/Ad epitopes. DM-mediated antagonism of HEL 11–25/Ad and 20–35/Ad presentation could thus be central to 11–25/Ad and 20–35/Ad being cryptic epitopes in the HEL system. Interestingly, the display of the immunodominant epitope of HEL, 106–116/Ed, and of a dominant epitope of sperm whale myoglobin (SWM), 102–118/Ad, is entirely dependent on the expression of DM. Thus, cells lacking DM molecules are unable to efficiently express HEL 106–116/Ed and SWM 102–118/Ad determinants. We conclude that the DM heterodimers direct the immunodominant and cryptic fate of antigenic epitopes in vivo. PMID:10993909

  8. Variation in Phenotype, Parasite Load and Male Competitive Ability across a Cryptic Hybrid Zone

    PubMed Central

    Stuart-Fox, Devi; Godinho, Raquel; Goüy de Bellocq, Joëlle; Irwin, Nancy R.; Brito, José Carlos; Moussalli, Adnan; Široký, Pavel; Hugall, Andrew F.; Baird, Stuart J. E.

    2009-01-01

    Background Molecular genetic studies are revealing an increasing number of cryptic lineages or species, which are highly genetically divergent but apparently cannot be distinguished morphologically. This observation gives rise to three important questions: 1) have these cryptic lineages diverged in phenotypic traits that may not be obvious to humans; 2) when cryptic lineages come into secondary contact, what are the evolutionary consequences: stable co-existence, replacement, admixture or differentiation and 3) what processes influence the evolutionary dynamics of these secondary contact zones? Methodology/Principal Findings To address these questions, we first tested whether males of the Iberian lizard Lacerta schreiberi from two highly genetically divergent, yet morphologically cryptic lineages on either side of an east-west secondary contact could be differentiated based on detailed analysis of morphology, coloration and parasite load. Next, we tested whether these differences could be driven by pre-copulatory intra-sexual selection (male-male competition). Compared to eastern males, western males had fewer parasites, were in better body condition and were more intensely coloured. Although subtle environmental variation across the hybrid zone could explain the differences in parasite load and body condition, these were uncorrelated with colour expression, suggesting that the differences in coloration reflect heritable divergence. The lineages did not differ in their aggressive behaviour or competitive ability. However, body size, which predicted male aggressiveness, was positively correlated with the colour traits that differed between genetic backgrounds. Conclusions/Significance Our study confirms that these cryptic lineages differ in several aspects that are likely to influence fitness. Although there were no clear differences in male competitive ability, our results suggest a potential indirect role for intra-sexual selection. Specifically, if lizards use

  9. Energy Conservation

    SciTech Connect

    Simpson, P.

    1995-06-01

    There are two fundamental reasons or motivations for energy conservation: (1) economics; and (2) consideration of energy - its sources and availability. Economics speaks for itself and needs little explanation: a project is undertaken, the cost is recovered in a given period of time (we hope) and our company realizes cost savings thereafter. We study and propose a project; we estimate the payback. If approved, we implement the project. Then, we eagerly watch for its effectiveness - for the proposed payback. The second consideration in regard to energy conservation might - in the foreseeable future - become by far the most important - that of availability. Very knowledgeable persons have stated that this - in reality - is the most serious problem facing our nation today. Readily available, reasonably priced energy has given to the US the high form of living experienced today. An interruption in this flow could catapult our nation in an awesome catastrophe. The energy shortage of the late 70`s might be a forerunner of such an experience.

  10. Recent Advances in Conformal Gravity

    NASA Astrophysics Data System (ADS)

    O'Brien, James; Chaykov, Spasen

    2016-03-01

    In recent years, significant advances have been made in alternative gravitational theories. Although MOND remains the leading candidate among the alternative models, Conformal Gravity has been studied by Mannheim and O'Brien to solve the rotation curve problem without the need for dark matter. Recently, Mannheim, O'Brien and Chaykov have begun solving other gravitational questions in Conformal Gravity. In this presentation, we highlight the new work of Conformal Gravity's application to random motions of clusters (the original Zwicky problem), gravitational bending of light, gravitational lensing and a very recent survey of dwarf galaxy rotation curves. We will show in each case that Conformal Gravity can provide an accurate explanation and prediction of the data without the need for dark matter. Coupled with the fact that Conformal Gravity is a fully re-normalizable metric theory of gravity, these results help to push Conformal Gravity onto a competitive stage against other alternative models.

  11. Fermion-scalar conformal blocks

    DOE PAGES

    Iliesiu, Luca; Kos, Filip; Poland, David; ...

    2016-04-13

    In this study, we compute the conformal blocks associated with scalar-scalar-fermionfermion 4-point functions in 3D CFTs. Together with the known scalar conformal blocks, our result completes the task of determining the so-called ‘seed blocks’ in three dimensions. In addition, conformal blocks associated with 4-point functions of operators with arbitrary spins can now be determined from these seed blocks by using known differential operators.

  12. Fermion-scalar conformal blocks

    SciTech Connect

    Iliesiu, Luca; Kos, Filip; Poland, David; Pufu, Silviu S.; Simmons-Duffin, David; Yacoby, Ran

    2016-04-13

    In this study, we compute the conformal blocks associated with scalar-scalar-fermionfermion 4-point functions in 3D CFTs. Together with the known scalar conformal blocks, our result completes the task of determining the so-called ‘seed blocks’ in three dimensions. In addition, conformal blocks associated with 4-point functions of operators with arbitrary spins can now be determined from these seed blocks by using known differential operators.

  13. Loop Virasoro Lie conformal algebra

    SciTech Connect

    Wu, Henan Chen, Qiufan; Yue, Xiaoqing

    2014-01-15

    The Lie conformal algebra of loop Virasoro algebra, denoted by CW, is introduced in this paper. Explicitly, CW is a Lie conformal algebra with C[∂]-basis (L{sub i} | i∈Z) and λ-brackets [L{sub i} {sub λ} L{sub j}] = (−∂−2λ)L{sub i+j}. Then conformal derivations of CW are determined. Finally, rank one conformal modules and Z-graded free intermediate series modules over CW are classified.

  14. Conformal array antenna subsystem

    NASA Astrophysics Data System (ADS)

    1985-04-01

    An antenna subsystem to communicate between Ariane 4 and a data relay satellite was studied, concluding that the original ideas on ring antennas should be corrected due to the wide margin of coverage required in elevation for such antennas, which implies the need of splitting the coverage. Nevertheless, the study of cylindrical and conical conformal arrays was continued in view of their intrinsic interest. Needed coverages with specified gain can be obtained with a set of microstrip circular patch antennas. For the lower stage, a single patch is enough. For geostationary missions, one horizontal array is used, and for heliosynchronous missions two horizontal arrays and a vertical one. The numerical study carried out on omniazimuthal ring antennas shows that a tendency to omnidirectional pattern exists in spite of the directivity of the elementary radiators. A small pointing improvement of the meridian pattern can be obtained by means of conical arrays instead of the cylindrical ones.

  15. Capturing Chromosome Conformation

    NASA Astrophysics Data System (ADS)

    Dekker, Job; Rippe, Karsten; Dekker, Martijn; Kleckner, Nancy

    2002-02-01

    We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G1 stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.

  16. Thermal insulating conformal blanket

    NASA Technical Reports Server (NTRS)

    Barney, Andrea (Inventor); Whittington, Charles A (Inventor); Eilertson, Bryan (Inventor); Siminski, Zenon (Inventor)

    2003-01-01

    The conformal thermal insulating blanket may have generally rigid batting material covered by an outer insulating layer formed of a high temperature resistant woven ceramic material and an inner insulating layer formed of a woven ceramic fiber material. The batting and insulating layers may be fastened together by sewing or stitching using an outer mold layer thread fabricated of a high temperature resistant material and an inner mold layer thread of a ceramic fiber material. The batting may be formed to a composite structure that may have a firmness factor sufficient to inhibit a pillowing effect after the stitching to not more than 0.03 inch. The outer insulating layer and an upper portion of the batting adjacent the outer insulating layer may be impregnated with a ceramic coating material.

  17. Conformally symmetric relativistic star

    NASA Astrophysics Data System (ADS)

    Rahaman, Farook; Maharaj, Sunil D.; Sardar, Iftikar Hossain; Chakraborty, Koushik

    2017-03-01

    We investigate whether compact stars having Tolman-like interior geometry admit conformal symmetry. Taking anisotropic pressure along the two principal directions within the compact object, we obtain physically relevant quantities such as transverse and radial pressure, density and redshift function. We study the equation of state (EOS) for the matter distribution inside the star. From the relation between pressure and density function of the constituent matter, we explore the nature and properties of the interior matter. The redshift function and compactness parameter are found to be physically reasonable. The matter inside the star satisfies the null, weak and strong energy conditions. Finally, we compare the masses and radii predicted from the model with corresponding values in some observed stars.

  18. Conformal model of gravitons

    NASA Astrophysics Data System (ADS)

    Donoghue, John F.

    2017-08-01

    In the description of general covariance, the vierbein and the Lorentz connection can be treated as independent fundamental fields. With the usual gauge Lagrangian, the Lorentz connection is characterized by an asymptotically free running coupling. When running from high energy, the coupling gets large at a scale which can be called the Planck mass. If the Lorentz connection is confined at that scale, the low energy theory can have the Einstein Lagrangian induced at low energy through dimensional transmutation. However, in general there will be new divergences in such a theory and the Lagrangian basis should be expanded. I construct a conformally invariant model with a larger basis size which potentially may have the same property.

  19. Conformal Aspects of QCD

    SciTech Connect

    Brodsky, S

    2003-11-19

    Theoretical and phenomenological evidence is now accumulating that the QCD coupling becomes constant at small virtuality; i.e., {alpha}{sub s}(Q{sup 2}) develops an infrared fixed point in contradiction to the usual assumption of singular growth in the infrared. For example, the hadronic decays of the {tau} lepton can be used to determine the effective charge {alpha}{sub {tau}}(m{sub {tau}{prime}}{sup 2}) for a hypothetical {tau}-lepton with mass in the range 0 < m{sub {tau}{prime}} < m{sub {tau}}. The {tau} decay data at low mass scales indicates that the effective charge freezes at a value of s = m{sub {tau}{prime}}{sup 2} of order 1 GeV{sup 2} with a magnitude {alpha}{sub {tau}} {approx} 0.9 {+-} 0.1. The near-constant behavior of effective couplings suggests that QCD can be approximated as a conformal theory even at relatively small momentum transfer and why there are no significant running coupling corrections to quark counting rules for exclusive processes. The AdS/CFT correspondence of large N{sub c} supergravity theory in higher-dimensional anti-de Sitter space with supersymmetric QCD in 4-dimensional space-time also has interesting implications for hadron phenomenology in the conformal limit, including an all-orders demonstration of counting rules for exclusive processes and light-front wavefunctions. The utility of light-front quantization and light-front Fock wavefunctions for analyzing nonperturbative QCD and representing the dynamics of QCD bound states is also discussed.

  20. Replacement between conformity and counter-conformity in consumption decisions.

    PubMed

    Chou, Ting-Jui; Chang, En-Chung; Dai, Qi; Wong, Veronica

    2013-02-01

    This study assessed, in a Chinese context, how self-esteem interacts with perceived similarity and uniqueness to yield cognitive dissonance, and whether the dissonance leads to self-reported conformity or counter-conformity behavior. Participants were 408 respondents from 4 major Chinese cities (M age = 33.0 yr., SD = 4.3; 48% men). Self-perceptions of uniqueness, similarity, cognitive dissonance, self-esteem and need to behave in conformity or counter-conformity were measured. A theoretical model was assessed in four situations, relating the ratings of self-esteem and perceived similarity/uniqueness to the way other people at a wedding were dressed, and the resultant cognitive dissonance and conformity/ counter-conformity behavior. Regardless of high or low self-esteem, all participants reported cognitive dissonance when they were told that they were dressed extremely similarly to or extremely differently from the other people attending the wedding. However, the conforming/counter-conforming strategies used by participants to resolve the cognitive dissonance differed. When encountering dissonance induced by the perceived extreme uniqueness of dress, participants with low self-esteem tended to say they would dress next time so as to conform with the way others were dressed, while those with high self-esteem indicated they would continue their counter-conformity in attire. When encountering dissonance induced by the perceived extreme similarity to others, both those with high and low self-esteem tended to say they would dress in an unorthodox manner to surprise other people in the future.

  1. Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, aliatypus).

    PubMed

    Satler, Jordan D; Carstens, Bryan C; Hedin, Marshal

    2013-11-01

    Species are a fundamental unit for biological studies, yet no uniform guidelines exist for determining species limits in an objective manner. Given the large number of species concepts available, defining species can be both highly subjective and biased. Although morphology has been commonly used to determine species boundaries, the availability and prevalence of genetic data has allowed researchers to use such data to make inferences regarding species limits. Genetic data also have been used in the detection of cryptic species, where other lines of evidence (morphology in particular) may underestimate species diversity. In this study, we investigate species limits in a complex of morphologically conserved trapdoor spiders (Mygalomorphae, Antrodiaetidae, Aliatypus) from California. Multiple approaches were used to determine species boundaries in this highly genetically fragmented group, including both multilocus discovery and validation approaches (plus a chimeric approach). Additionally, we introduce a novel tree-based discovery approach using species trees. Results suggest that this complex includes multiple cryptic species, with two groupings consistently recovered across analyses. Due to incongruence across analyses for the remaining samples, we take a conservative approach and recognize a three species complex, and formally describe two new species (Aliatypus roxxiae, sp. nov. and Aliatypus starretti, sp. nov.). This study helps to clarify species limits in a genetically fragmented group and provides a framework for identifying and defining the cryptic lineage diversity that prevails in many organismal groups.

  2. Activation of a cryptic splice site in the growth hormone receptor associated with growth hormone insensitivity syndrome in a genetic isolate of Laron Syndrome

    SciTech Connect

    Schiavi, A.; Bartlett, R.; Brown, M.

    1994-09-01

    Laron syndrome (LS) is a rare, autosomal recessive disease found worldwide. Despite various ethnic differences, all patients with LS described display classic dysmorphic features and extreme short stature due to defects in the growth hormone receptor (GHR). The vast majority of these patients are sporadic occurrences resulting from consanguineous matings; however, an Ecuadorian genetic isolate of LS has been reported. Our investigations have identified a genetic isolate of LS of Anglo Saxon origin. Seven individuals, by all clinical and biochemical criteria, have LS. As a result of extensive review of family and medical histories we have constructed a pedigree tracing the lineage of our affected patients through the 17th century. No GHR gross deletions were detected using an exon-specific PCR assay developed in our laboratory. Previous molecular analyses have identified mutations in exons 2-7 in numerous patients with classical LS. Single strand conformational polymorphism (SSCP) analysis was performed on GHR exons 2-7, and a marked conformational shift was noted in exon 7. Cycle sequencing of exon 7 from three affected individuals, and from four first-degree relatives, revealed a C{r_arrow}T transition at position 766 of the cDNA, and a heterozygous C{r_arrow}T transition at the identical position in the obligate carriers studied. This mutation is predicted to activate a cryptic donor splice site 63 base pairs upstream from the 3{prime} end of exon 7, effectively truncating the GHR cDNA without changing the reading frame. The resultant GHR protein is shortened by a proposed 21 amino acids. The identification and conformation of this mutation not only identifies a novel mutation in the GHR, and the first to be described in LS patients of English descent, but also allows for comparisons between genotypes and phenotypes in an inbred population.

  3. Counselor Identity: Conformity or Distinction?

    ERIC Educational Resources Information Center

    McLaughlin, Jerry E.; Boettcher, Kathryn

    2009-01-01

    The authors explore 3 debates in other disciplines similar to counseling's identity debate in order to learn about common themes and outcomes. Conformity, distinction, and cohesion emerged as common themes. They conclude that counselors should retain their distinctive, humanistic approach rather than conforming to the dominant, medical approach.

  4. Recent advancements in conformal gravity

    NASA Astrophysics Data System (ADS)

    O'Brien, James G.; Chaykov, Spasen S.; Dentico, Jeremy; Stulge, Modestas; Stefanski, Brian; Moss, Robert J.

    2017-05-01

    In recent years, due to the lack of direct observed evidence of cold dark matter, coupled with the shrinking parameter space to search for new dark matter particles, there has been increased interest in Alternative Gravitational theories. This paper, addresses three recent advances in conformal gravity, a fourth order renormalizable metric theory of gravitation originally formulated by Weyl, and later advanced by Mannheim and Kazanas. The first section of the paper applies conformal gravity to the rotation curves of the LITTLE THINGS survey, extending the total number of rotation curves successfully fit by conformal gravity to well over 200 individual data sets without the need for additional dark matter. Further, in this rotation curve study, we show how MOND and conformal gravity compare for each galaxy in the sample. Second, we look at the original Zwicky problem of applying the virial theorem to the Coma cluster in order to get an estimate for the cluster mass. However, instead of using the standard Newtonian potential, here we use the weak field approximation of conformal gravity. We show that in the conformal case we can get a much smaller mass estimate and thus there is no apparent need to include dark matter. We then show that this calculation is in agreement with the observational data from other well studied clusters. Last, we explore the calculation of the deflection of starlight through conformal gravity, as a first step towards applying conformal gravity to gravitaitonal lensing.

  5. Conformal Transformations and Space Travel.

    PubMed

    Gupta, S N

    1961-10-27

    Conformal transformations are applied to the motion of a space ship experiencing a constant acceleration. The role of proper time is interpreted in terms of atomic periods, and the relationship between the conformal transformations and the general theory of relativity is clarified.

  6. Cloning vectors based on cryptic plasmids isolated from lactic acid bacteria: their characteristics and potential applications in biotechnology.

    PubMed

    Shareck, Julie; Choi, Young; Lee, Byong; Miguez, Carlos B

    2004-01-01

    Lactic acid bacteria (LAB) are Gram positive bacteria, widely distributed in nature, and industrially important as they are used in a variety of industrial food fermentations. The use of genetic engineering techniques is an effective means of enhancing the industrial applicability of LAB. However, when using genetic engineering technology, safety becomes an essential factor for the application of improved LAB to the food industry. Cloning and expression systems should be derived preferably from LAB cryptic plasmids that generally encode genes for which functions can be proposed, but no phenotypes can be observed. However, some plasmid-encoded functions have been discovered in cryptic plasmids originating from Lactobacillus, Streptococcus thermophilus, and Pediococcus spp. and can be used as selective marker systems in vector construction. This article presents information concerning LAB cryptic plasmids, and their structures, functions, and applications. A total of 134 cryptic plasmids collated are discussed.

  7. Nest Construction by a Ground-nesting Bird Represents a Potential Trade-off Between Egg Crypticity and Thermoregulation

    EPA Science Inventory

    Predation selects against conspicuous colors in bird eggs and nests, while thermoregulatory constraints select for nest building behavior that regulates incubation temperatures. We present results that reveal a trade-off between nest crypticity and thermoregulation of eggs base...

  8. Nest Construction by a Ground-nesting Bird Represents a Potential Trade-off Between Egg Crypticity and Thermoregulation

    EPA Science Inventory

    Predation selects against conspicuous colors in bird eggs and nests, while thermoregulatory constraints select for nest building behavior that regulates incubation temperatures. We present results that reveal a trade-off between nest crypticity and thermoregulation of eggs base...

  9. Characterization of the patterns of polymorphism in a [open quotes]cryptic repeat[close quotes] reveals a novel type of hypervariable sequence

    SciTech Connect

    Jacobson, D.P.; Schmeling, P.; Sommer, S.S. )

    1993-08-01

    Alternating purine and pyrimidine repeats (RY(i)) are an abundant source of polymorphism. The subset with long tandem repeats of GT or AC (GT(i)) have been studied extensively, but cryptic RY(i) (i.e., no single tandem repeat predominates) have received little attention. The factor IX gene has a polymorphic cryptic RY(i) of 142-216 bp. Previously, there were four known polymorphic alleles, of the form AB, A[sub 2]B, A[sub 2]B[sub 2], and A[sub 3]B[sub 2], where A = (GT)(AC)[sub 3](AT)[sub 3](GT)(AT)[sub 4] and B = A with an additional 3' AT dinucleotide. To further characterize this locus, the authors examined more than 1,700 additional human chromosomes and determined the sequences of the homologous sites in orangutans and chimpanzees. The novel alleles found in humans expand the repertoire of A/B alleles to A[sub 0-4]B[sub 1] and A[sub 1-3]B[sub 2]. The A[sub n]B[sub 2] series are abundant in Caucasians but are absent in blacks and Asians. Conversely, the A[sub 0]B[sub 1] allele is common in blacks but is not found in more than 1,700 Caucasian chromosomes. The data are compatible with a model in which recombination is more frequent than polymerase slippage at this locus. In orangutans, the RY(i) is present, but the sequence is markedly different. An A/B-type of pattern was discerned in which B differs from A by an additional six (AT) dinucleotides at the 3' end. In chimpanzees, the size of the RY(i) locus was greatly expanded, and the sequence showed a novel pattern of hypervariability in which there are many tandem repeats of the form (GT)[sub n](AC)[sub 0](AT)[sub p](GT)[sub q](AT)[sub s], where n, o, p, q, and s are different integers. The sequences of the factor IX intron 1 cryptic RY(i) in three primates provide perspective on the range of possible patterns of polymorphism. Analysis of the patterns suggests how the RY(i) can be conserved during evolution, while the precise sequence varies. 25 refs., 5 figs., 3 tabs.

  10. Remarks on Polyelectrolyte Conformation

    NASA Astrophysics Data System (ADS)

    de Gennes, P. G.; Pincus, P.; Velasco, R. M.; Brochard, F.

    Nous discutons des conformations de polymères linéaires chargés en faisant les hypothèses suivantes : a) la chaĬne sans charge est flexible, b) la force éctrostatique domine les interactions monomère-monomère c) il n'y a pas de sels. 1) Pour le cas dilué (chaĬne non enchevetrees) en corrigeant le calcul self-consistant fait récemment par Richmond [1a], on trouve une taille des polyions égale a = R ND, qui est une fonction linéaire de l'indice de polymérisation N. Ce rèsultat est en accord avec les prècèdents travaux de Hermans et Overbeek [1b], Kuhn, Kunzle et Katchalsky [1c]. 2) Il existe un domaine pour des concentrations très petites c (c** < c < c*) oò les interactions èlectrostatiques entre les polyions sont supèrieures aux ènergies thermiques, il semble donc possible que les polyions puissent former un rèseau pèriodique à trois dimensions. Nèanmoins, il semble difficile de mettre en èvidence un rèseau si diluè. 3) Jusqu'ici toutes les expériences avec les polyélectrolytes sans sels ont été pratiquement faites à des concentrations c > c*, pour lesquelles les différentes cha.nes sont enchevêtrées. Pour discuter ce régime on s.intéresse uniquement au cas où la charge par unité de longueur est près du (ou audessus du) seuil de condensation, donc il existe une seule longueur ξ(c) caractérisant les corrélations; à trois dimensions 03BE a le même comportement que le rayon de Debye pour les contre-ions. On a considéré quelques conformations possibles : a) un réseau hexagonal de batonnets; b) un réseau cubique de batonnets; c) une phase isotrope de cha.nes partiellement flexibles. Les différentes structures formées de batonnets semblent avoir la même énergie électrostatique. Ce fait suggère que la phase isotrope peut être la plus favorable. On analyse cette dernière phase en utilisant les mêmes méthodes qui se sont révélées efficaces pour les solutions des polymères neutres. Dans le modèle isotrope

  11. Conformal Fermi Coordinates

    SciTech Connect

    Dai, Liang; Pajer, Enrico; Schmidt, Fabian E-mail: Enrico.pajer@gmail.com

    2015-11-01

    Fermi Normal Coordinates (FNC) are a useful frame for isolating the locally observable, physical effects of a long-wavelength spacetime perturbation. Their cosmological application, however, is hampered by the fact that they are only valid on scales much smaller than the horizon. We introduce a generalization that we call Conformal Fermi Coordinates (CFC). CFC preserve all the advantages of FNC, but in addition are valid outside the horizon. They allow us to calculate the coupling of long- and short-wavelength modes on all scales larger than the sound horizon of the cosmological fluid, starting from the epoch of inflation until today, by removing the complications of the second order Einstein equations to a large extent, and eliminating all gauge ambiguities. As an application, we present a calculation of the effect of long-wavelength tensor modes on small scale density fluctuations. We recover previous results, but clarify the physical content of the individual contributions in terms of locally measurable effects and ''projection'' terms.

  12. Imaging of conformational changes

    SciTech Connect

    Michl, Josef

    2016-03-13

    Control of intramolecular conformational change in a small number of molecules or even a single one by an application of an outside electric field defined by potentials on nearby metal or dielectric surfaces has potential applications in both 3-D and 2-D nanotechnology. Specifically, the synthesis, characterization, and understanding of designed solids with controlled built-in internal rotational motion of a dipole promises a new class of materials with intrinsic dielectric, ferroelectric, optical and optoelectronic properties not found in nature. Controlled rotational motion is of great interest due to its expected utility in phenomena as diverse as transport, current flow in molecular junctions, diffusion in microfluidic channels, and rotary motion in molecular machines. A direct time-resolved observation of the dynamics of motion on ps or ns time scale in a single molecule would be highly interesting but is also very difficult and has yet to be accomplished. Much can be learned from an easier but still challenging comparison of directly observed initial and final orientational states of a single molecule, which is the basis of this project. The project also impacts the understanding of surface-enhanced Raman spectroscopy (SERS) and single-molecule spectroscopic detection, as well as the synthesis of solid-state materials with tailored properties from designed precursors.

  13. Dynamics of protein conformations

    NASA Astrophysics Data System (ADS)

    Stepanova, Maria

    2010-10-01

    A novel theoretical methodology is introduced to identify dynamic structural domains and analyze local flexibility in proteins. The methodology employs a multiscale approach combining identification of essential collective coordinates based on the covariance analysis of molecular dynamics trajectories, construction of the Mori projection operator with these essential coordinates, and analysis of the corresponding generalized Langevin equations [M.Stepanova, Phys.Rev.E 76(2007)051918]. Because the approach employs a rigorous theory, the outcomes are physically transparent: the dynamic domains are associated with regions of relative rigidity in the protein, whereas off-domain regions are relatively soft. This also allows scoring the flexibility in the macromolecule with atomic-level resolution [N.Blinov, M.Berjanskii, D.S.Wishart, and M.Stepanova, Biochemistry, 48(2009)1488]. The applications include the domain coarse-graining and characterization of conformational stability in protein G and prion proteins. The results are compared with published NMR experiments. Potential applications for structural biology, bioinformatics, and drug design are discussed.

  14. Lipids modulate the conformational dynamics of a secondary multidrug transporter

    PubMed Central

    Martens, Chloé; Stein, Richard A; Masureel, Matthieu; Roth, Aurélie; Mishra, Smriti; Dawaliby, Rosie; Konijnenberg, Albert; Sobott, Frank; Govaerts, Cédric; Mchaourab, Hassane S

    2017-01-01

    Direct interactions with lipids have emerged as key determinants of the folding, structure and function of membrane proteins, but an understanding of how lipids modulate protein dynamics is still lacking. Here, we systematically explored the effects of lipids on the conformational dynamics of the proton-powered, multidrug transporter LmrP from Lactococcus lactis utilizing the pattern of distances between spin label pairs previously shown to fingerprint alternating access of the protein. We uncover at the molecular level how the lipid headgroups shape the conformational energy landscape of the transporter. The model emerging from our data hypothesizes a direct interaction between lipid headgroups and a conserved motif of charged residues that control the conformational equilibrium through an interplay of electrostatic interactions within the protein. Together, our data lay the foundation for a comprehensive model of secondary multidrug transport in lipid bilayers. PMID:27399258

  15. A conformational transition at the N terminus of the prion protein features in formation of the scrapie isoform.

    PubMed

    Peretz, D; Williamson, R A; Matsunaga, Y; Serban, H; Pinilla, C; Bastidas, R B; Rozenshteyn, R; James, T L; Houghten, R A; Cohen, F E; Prusiner, S B; Burton, D R

    1997-10-31

    The scrapie prion protein (PrPSc) is formed from the cellular isoform (PrPC) by a post-translational process that involves a profound conformational change. Linear epitopes for recombinant antibody Fab fragments (Fabs) on PrPC and on the protease-resistant core of PrPSc, designated PrP 27-30, were identified using ELISA and immunoprecipitation. An epitope region at the C terminus was accessible in both PrPC and PrP 27-30; in contrast, epitopes towards the N-terminal region (residues 90 to 120) were accessible in PrPC but largely cryptic in PrP 27-30. Denaturation of PrP 27-30 exposed the epitopes of the N-terminal domain. We argue from our findings that the major conformational change underlying PrPSc formation occurs within the N-terminal segment of PrP 27-30.

  16. Arboreal Ant Colonies as ‘Hot-Points’ of Cryptic Diversity for Myrmecophiles: The Weaver Ant Camponotus sp. aff. textor and Its Interaction Network with Its Associates

    PubMed Central

    Pérez-Lachaud, Gabriela; Lachaud, Jean-Paul

    2014-01-01

    Introduction Systematic surveys of macrofaunal diversity within ant colonies are lacking, particularly for ants nesting in microhabitats that are difficult to sample. Species associated with ants are generally small and rarely collected organisms, which makes them more likely to be unnoticed. We assumed that this tendency is greater for arthropod communities in microhabitats with low accessibility, such as those found in the nests of arboreal ants that may constitute a source of cryptic biodiversity. Materials and Methods We investigated the invertebrate diversity associated with an undescribed, but already threatened, Neotropical Camponotus weaver ant. As most of the common sampling methods used in studies of ant diversity are not suited for evaluating myrmecophile diversity within ant nests, we evaluated the macrofauna within ant nests through exhaustive colony sampling of three nests and examination of more than 80,000 individuals. Results We identified invertebrates from three classes belonging to 18 taxa, some of which were new to science, and recorded the first instance of the co-occurrence of two brood parasitoid wasp families attacking the same ant host colony. This diversity of ant associates corresponded to a highly complex interaction network. Agonistic interactions prevailed, but the prevalence of myrmecophiles was remarkably low. Conclusions Our data support the hypothesis of the evolution of low virulence in a variety of symbionts associated with large insect societies. Because most myrmecophiles found in this work are rare, strictly specific, and exhibit highly specialized biology, the risk of extinction for these hitherto unknown invertebrates and their natural enemies is high. The cryptic, far unappreciated diversity within arboreal ant nests in areas at high risk of habitat loss qualifies these nests as ‘hot-points’ of biodiversity that urgently require special attention as a component of conservation and management programs. PMID:24941047

  17. Cryptic diversity in Indo-Pacific coral-reef fishes revealed by DNA-barcoding provides new support to the centre-of-overlap hypothesis.

    PubMed

    Hubert, Nicolas; Meyer, Christopher P; Bruggemann, Henrich J; Guérin, Fabien; Komeno, Roberto J L; Espiau, Benoit; Causse, Romain; Williams, Jeffrey T; Planes, Serge

    2012-01-01

    Diversity in coral reef fishes is not evenly distributed and tends to accumulate in the Indo-Malay-Philippines Archipelago (IMPA). The comprehension of the mechanisms that initiated this pattern is in its infancy despite its importance for the conservation of coral reefs. Considering the IMPA either as an area of overlap or a cradle of marine biodiversity, the hypotheses proposed to account for this pattern rely on extant knowledge about taxonomy and species range distribution. The recent large-scale use of standard molecular data (DNA barcoding), however, has revealed the importance of taking into account cryptic diversity when assessing tropical biodiversity. We DNA barcoded 2276 specimens belonging to 668 coral reef fish species through a collaborative effort conducted concomitantly in both Indian and Pacific oceans to appraise the importance of cryptic diversity in species with an Indo-Pacific distribution range. Of the 141 species sampled on each side of the IMPA, 62 presented no spatial structure whereas 67 exhibited divergent lineages on each side of the IMPA with K2P distances ranging between 1% and 12%, and 12 presented several lineages with K2P distances ranging between 3% and 22%. Thus, from this initial pool of 141 nominal species with Indo-Pacific distribution, 79 dissolved into 165 biological units among which 162 were found in a single ocean. This result is consistent with the view that the IMPA accumulates diversity as a consequence of its geological history, its location on the junction between the two main tropical oceans and the presence of a land bridge during glacial times in the IMPA that fostered allopatric divergence and secondary contacts between the Indian and Pacific oceans.

  18. A novel field method to distinguish between cryptic carcharhinid sharks, Australian blacktip shark Carcharhinus tilstoni and common blacktip shark C. limbatus, despite the presence of hybrids.

    PubMed

    Johnson, G J; Buckworth, R C; Lee, H; Morgan, J A T; Ovenden, J R; McMahon, C R

    2017-01-01

    Multivariate and machine-learning methods were used to develop field identification techniques for two species of cryptic blacktip shark. From 112 specimens, precaudal vertebrae (PCV) counts and molecular analysis identified 95 Australian blacktip sharks Carcharhinus tilstoni and 17 common blacktip sharks Carcharhinus limbatus. Molecular analysis also revealed 27 of the 112 were C. tilstoni × C. limbatus hybrids, of which 23 had C. tilstoni PCV counts and four had C. limbatus PCV counts. In the absence of further information about hybrid phenotypes, hybrids were assigned as either C. limbatus or C. tilstoni based on PCV counts. Discriminant analysis achieved 80% successful identification, but machine-learning models were better, achieving 100% successful identification, using six key measurements (fork length, caudal-fin peduncle height, interdorsal space, second dorsal-fin height, pelvic-fin length and pelvic-fin midpoint to first dorsal-fin insertion). Furthermore, pelvic-fin markings could be used for identification: C. limbatus has a distinct black mark >3% of the total pelvic-fin area, while C. tilstoni has markings with diffuse edges, or has smaller or no markings. Machine learning and pelvic-fin marking identification methods were field tested achieving 87 and 90% successful identification, respectively. With further refinement, the techniques developed here will form an important part of a multi-faceted approach to identification of C. tilstoni and C. limbatus and have a clear management and conservation application to these commercially important sharks. The methods developed here are broadly applicable and can be used to resolve species identities in many fisheries where cryptic species exist. © 2016 The Fisheries Society of the British Isles.

  19. How many remnant gibbon populations are left on Hainan? Testing the use of local ecological knowledge to detect cryptic threatened primates.

    PubMed

    Turvey, Samuel T; Bryant, Jessica V; Duncan, Clare; Wong, Michelle H G; Guan, Zhenhua; Fei, Hanlan; Ma, Changyong; Hong, Xiaojiang; Nash, Helen C; Chan, Bosco P L; Xu, Yang; Fan, Pengfei

    2017-02-01

    For Critically Endangered "species of extreme rarity," there is an urgent need to clarify the potential survival of remnant populations. Such populations can be difficult to detect using standard field methods. Local ecological knowledge (LEK) represents an important alternative source of information, but anecdotal reports of rare or possibly extinct species can contain uncertainty and error. The Hainan gibbon (Nomascus hainanus), the world's rarest primate species, is confirmed to only survive as a tiny remnant population in Bawangling National Nature Reserve, China, but unverified gibbon sightings have been reported from other forest areas on Hainan. We conducted a large-scale community interview survey to gather new data on patterns of primate LEK from 709 respondents around seven reserves across Hainan, to investigate the possibility of gibbon survival outside Bawangling and assess whether LEK can provide useful information for conservation management of cryptic remnant populations. Comparative LEK data for gibbons and macaques are consistent with independent data on the relative status of these species across Hainan. Local awareness and experience of gibbons was low across Hainan, including at Bawangling, but we recorded recent anecdotal gibbon reports from most reserves. A follow-up field survey at Limushan Provincial Nature Reserve did not detect gibbons, however, and documented intensive wildlife exploitation within this reserve. All other surveyed landscapes showed some statistically lower levels of respondent awareness, experience, or sighting histories of gibbons compared to Bawangling, and are therefore considered biologically unlikely to support gibbons. Unverified LEK data can provide important insights into the possible status of cryptic remnant populations when assessed carefully and critically in relation to data from known populations.

  20. Population structure and cryptic speciation in bonnethead sharks Sphyrna tiburo in the south-eastern U.S.A. and Caribbean.

    PubMed

    Fields, A T; Feldheim, K A; Gelsleichter, J; Pfoertner, C; Chapman, D D

    2016-11-01

    Population structure and lineage diversification within a small, non-dispersive hammerhead shark species, the bonnethead shark Sphyrna tiburo, was assessed. Sphyrna tiburo is currently described as one continuously distributed species along the Atlantic continental margins of North, Central and South America, but recent genetic analysis of an insular population (Trinidad) suggests the possibility of cryptic speciation. To address this issue S. tiburo were sampled at six sites along c. 6200 km of continuous, continental coastline and from one island location (Grand Bahama) across a discontinuity in their distribution (the Straits of Florida), in order to test if they constitute a single lineage over this distribution. A total of 1030 bp of the mitochondrial control region (CR) was obtained for 239 S. tiburo, revealing 73 distinct haplotypes, high nucleotide diversity (0·01089) and a pair of highly divergent lineages estimated to have separated 3·61-5·62 million years ago. Mitochondrial cytochrome oxidase I and nuclear internal transcribed spacer loci show the same pattern. Divergence is similar within S. tiburo to that observed between established elasmobranch sister species, providing further evidence of cryptic speciation. A global AMOVA based on CR confirms that genetic diversity is primarily partitioned among populations (ΦST = 0·828, P < 0·001) because the divergent lineages are almost perfectly segregated between Belize and North America-The Bahamas. An AMOVA consisting solely of the North American and Bahamian samples is also significantly different from zero (ΦST = 0·088, P < 0·001) and pairwise FST is significantly different between all sites. These findings suggest that S. tiburo comprises a species complex and supports previous research indicating fine population structure, which has implications for fisheries management and biodiversity conservation.

  1. The r1162 mob proteins can promote conjugative transfer from cryptic origins in the bacterial chromosome.

    PubMed

    Meyer, Richard

    2009-03-01

    The mobilization proteins of the broad-host-range plasmid R1162 can initiate conjugative transfer of a plasmid from a 19-bp locus that is partially degenerate in sequence. Such loci are likely to appear by chance in the bacterial chromosome and could act as cryptic sites for transfer of chromosomal DNA when R1162 is present. The R1162-dependent transfer of chromosomal DNA, initiated from one such potential site in Pectobacterium atrosepticum, is shown here. A second active site was identified in Escherichia coli, where it is also shown that large amounts of DNA are transferred. This transfer probably reflects the combined activity of the multiple cryptic origins in the chromosome. Transfer of chromosomal DNA due to the presence of a plasmid in the cytoplasm describes a previously unrecognized potential for the exchange of bacterial DNA.

  2. Is Esterase-P Encoded by a Cryptic Pseudogene in Drosophila Melanogaster?

    PubMed Central

    Balakirev, E. S.; Ayala, F. J.

    1996-01-01

    We have amplified and sequenced the gene encoding Esterase-P (Est-P) in 10 strains of Drosophila melanogaster. Three premature termination codons occur in the coding region of the gene in two strains. This observation, together with other indirect evidence, leads us to propose that Est-P may be a pseudogene in D. melanogaster. Est-P would be a ``cryptic'' pseudogene, in the sense that it retains intact the coding sequence (without stop codons and other alterations usually observed in pseudogenes) in most D. melanogaster strains. We conjecture that the β-esterase cluster may consist in other Drosophila species of functional and nonfunctional genes. We also conjecture that the rarity of detected pseudogenes in Drosophila may be due to the difficulty of discovering them, because most of them are cryptic. PMID:8978040

  3. Complex genital structures indicate cryptic female choice in a haplogyne spider (Arachnida, Araneae, Oonopidae, Gamasomorphinae).

    PubMed

    Burger, Matthias; Nentwig, Wolfgang; Kropf, Christian

    2003-01-01

    Female genital structures with their allied muscles of the haplogyne spider Opopaea fosuma are described. A functional explanation of this system is given, which indicates that cryptic female choice may occur in these spiders: the anterior wall of their spermatheca is strongly sclerotized and possesses a cone-shaped hole in its upper part. A transverse sclerite that serves as muscle attachment bears a nail-like structure and lies in a chitinized area of the anterior wall of the uterus externus. Muscle contraction presses this nail into the hole of the spermatheca. In this way, the uterus externus gets both locked and fixed. Furthermore, as this occurs the copulatory orifice is enlarged and the resulting suction probably leads to previously deposited sperm being drawn from the spermatheca and dumped. This is a common mechanism used by females to influence a male's chances of fathering their offspring in a process known as cryptic female choice.

  4. Three sisters in the same dress: cryptic speciation in African odonates.

    PubMed

    Cordero-Rivera, A; Lorenzo-Carballa, M O

    2010-09-01

    The discovery of cryptic species (i.e. two or more distinct but morphologically undistinguishable species) has grown exponentially in the last two decades, due mainly to the increasing availability of DNA sequences. This suggests that hidden in the known species, many of which have been described based solely on morphological information, there might be a high number of species waiting to be discovered. In this issue Damm et al. (2010) use a combination of genetic, morphological and ecological evidence to identify the first cryptic species complex found within dragonflies (insect order Odonata). Their findings add more evidence for the importance of combining information from different disciplines to new species' discovery (DeSalle et al. 2005).

  5. Cryptic or mystic? Glacial tree refugia in northern Europe.

    PubMed

    Tzedakis, P C; Emerson, B C; Hewitt, G M

    2013-12-01

    Here, we examine the evidence for tree refugia in northern Europe during the Late Pleniglacial (LPG) interval of maximum tree-range contraction. Our review highlights the often equivocal nature of genetic data and a tendency to overestimate potential tree distributions due to warm climate-model bias, and also reveals a convergence of macrofossil and pollen evidence. What emerges is the absence of temperate trees north of 45°N and a west-east (W-E) asymmetry in boreal tree distribution, with a treeless Western Europe north of 46°N, while restricted boreal populations persisted in Eastern Europe up to 49°N, and higher latitudes east of the Fennoscandian ice-sheet. These results have implications for current thinking on European genetic diversity patterns, species migration capacity, and conservation strategies.

  6. Benchmarking Commercial Conformer Ensemble Generators.

    PubMed

    Friedrich, Nils-Ole; de Bruyn Kops, Christina; Flachsenberg, Florian; Sommer, Kai; Rarey, Matthias; Kirchmair, Johannes

    2017-10-02

    We assess and compare the performance of eight commercial conformer ensemble generators (ConfGen, ConfGenX, cxcalc, iCon, MOE LowModeMD, MOE Stochastic, MOE Conformation Import and OMEGA) and one leading free algorithm, the distance geometry (DG) algorithm implemented in RDKit. The comparative study is based on a new version of the Platinum Diverse Dataset, a high-quality benchmarking dataset of 2859 protein-bound ligand conformations extracted from the PDB. Differences in the performance of commercial algorithms are much smaller than those observed for free algorithms in our previous study (J. Chem. Inf. 2017, 57, 529-539). For commercial algorithms the median minimum RMSDs measured between protein-bound ligand conformations and ensembles of a maximum of 250 conformers are between 0.46 and 0.61 Å. Commercial conformer ensemble generators are characterized by their high robustness, with at least 99% of all input molecules successfully processed and few or even no substantial geometrical errors detectable in their output conformations. The RDKit DG algorithm (with minimization enabled) appears to be a good free alternative since its performance is comparable to that of the mid-ranked commercial algorithms. Based on a statistical analysis, we elaborate on which algorithms to use and how to parameterize them for best performance in different application scenarios.

  7. Conformal optics risk reduction demonstration

    NASA Astrophysics Data System (ADS)

    Knapp, David J.; Mills, James P.; Hegg, Ronald G.; Trotta, Patrick A.; Smith, Christopher B.

    2001-09-01

    For the past three years, the Precision Conformal Optics Consortium has been developing a revolutionary new class of optics. These optics are characterized by outer window elements that conform to aerodynamic rather than optical requirements. Conformal optical elements can greatly improve the aerodynamic performance of the host platform. To make conformal optics a reality, challenges had to be overcome in design, fabrication, and testing. This was accomplished in October 1999 when Raytheon demonstrated the world's first conformal optical system. This fineness ratio one system was a risk reduction effort to develop technology for later systems. It is comprised of a calcium fluoride conformal optical dome, a TI-1173 aspheric corrector, and a calcium fluoride solid catadioptric telescope. The design involved overcoming large amounts of aberration that varied with gimbal look angle. Efforts also included aligning the system to tight tolerances and testing highly aspheric optical elements. Overall, the actual system performance compared very favorably with the design model. With the proven success of this risk reduction demonstration, the path was cleared for new higher performance conformal optical systems.

  8. "Nested" cryptic diversity in a widespread marine ecosystem engineer: a challenge for detecting biological invasions

    PubMed Central

    2011-01-01

    Background Ecosystem engineers facilitate habitat formation and enhance biodiversity, but when they become invasive, they present a critical threat to native communities because they can drastically alter the receiving habitat. Management of such species thus needs to be a priority, but the poorly resolved taxonomy of many ecosystem engineers represents a major obstacle to correctly identifying them as being either native or introduced. We address this dilemma by studying the sea squirt Pyura stolonifera, an important ecosystem engineer that dominates coastal communities particularly in the southern hemisphere. Using DNA sequence data from four independently evolving loci, we aimed to determine levels of cryptic diversity, the invasive or native status of each regional population, and the most appropriate sampling design for identifying the geographic ranges of each evolutionary unit. Results Extensive sampling in Africa, Australasia and South America revealed the existence of "nested" levels of cryptic diversity, in which at least five distinct species can be further subdivided into smaller-scale genetic lineages. The ranges of several evolutionary units are limited by well-documented biogeographic disjunctions. Evidence for both cryptic native diversity and the existence of invasive populations allows us to considerably refine our view of the native versus introduced status of the evolutionary units within Pyura stolonifera in the different coastal communities they dominate. Conclusions This study illustrates the degree of taxonomic complexity that can exist within widespread species for which there is little taxonomic expertise, and it highlights the challenges involved in distinguishing between indigenous and introduced populations. The fact that multiple genetic lineages can be native to a single geographic region indicates that it is imperative to obtain samples from as many different habitat types and biotic zones as possible when attempting to identify the

  9. Temperature Effects on Gametophyte Life-History Traits and Geographic Distribution of Two Cryptic Kelp Species

    PubMed Central

    Oppliger, L. Valeria; Correa, Juan A.; Engelen, Aschwin H.; Tellier, Florence; Vieira, Vasco; Faugeron, Sylvain; Valero, Myriam; Gomez, Gonzalo; Destombe, Christophe

    2012-01-01

    A major determinant of the geographic distribution of a species is expected to be its physiological response to changing abiotic variables over its range. The range of a species often corresponds to the geographic extent of temperature regimes the organism can physiologically tolerate. Many species have very distinct life history stages that may exhibit different responses to environmental factors. In this study we emphasized the critical role of the haploid microscopic stage (gametophyte) of the life cycle to explain the difference of edge distribution of two related kelp species. Lessonia nigrescens was recently identified as two cryptic species occurring in parapatry along the Chilean coast: one located north and the other south of a biogeographic boundary at latitude 29–30°S. Six life history traits from microscopic stages were identified and estimated under five treatments of temperature in eight locations distributed along the Chilean coast in order to (1) estimate the role of temperature in the present distribution of the two cryptic L. nigrescens species, (2) compare marginal populations to central populations of the two cryptic species. In addition, we created a periodic matrix model to estimate the population growth rate (λ) at the five temperature treatments. Differential tolerance to temperature was demonstrated between the two species, with the gametophytes of the Northern species being more tolerant to higher temperatures than gametophytes from the south. Second, the two species exhibited different life history strategies with a shorter haploid phase in the Northern species contrasted with considerable vegetative growth in the Southern species haploid stage. These results provide strong ecological evidence for the differentiation process of the two cryptic species and show local adaptation of the life cycle at the range limits of the distribution. Ecological and evolutionary implications of these findings are discussed. PMID:22723987

  10. Study of biological rhythms of small intestinal cryptic epithelial mitosis of different periodicity by fourier analysis.

    PubMed

    Romanov, Yu A; Zharkova, N A; Antochin, A I; Zakharchenko, A V

    2009-05-01

    Rhythms of cell division with different periods in the mouse small intestinal cryptic epithelium were studied using Fourier analysis. It was found that the proliferative system of the crypt is characterized by an intricate spatial and temporal organization. The amplitude of low-frequency rhythms increases, while the amplitude of high-frequency rhythms decreased in the direction from the crypt bottom to the neck.

  11. Hidden Biodiversity in an Ecologically Important Freshwater Amphipod: Differences in Genetic Structure between Two Cryptic Species

    PubMed Central

    Westram, Anja Marie; Jokela, Jukka; Keller, Irene

    2013-01-01

    Cryptic species, i.e. species that are morphologically hard to distinguish, have been detected repeatedly in various taxa and ecosystems. In order to evaluate the importance of this finding, we have to know in how far cryptic species differ in various aspects of their biology. The amphipod Gammarus fossarum is a key invertebrate in freshwater streams and contains several cryptic species. We examined the population genetic structure, genetic diversity and demographic history of two of them (type A and type B) using microsatellite markers and asked whether they show significant differences. We present results of population genetic analyses based on a total of 37 populations from the headwaters of two major European drainages, Rhine and Rhone. We found that, in both species, genetic diversity was geographically structured among and within drainages. For type A in the Rhine and type B in the Rhone, we detected significant patterns of isolation by distance. The increase of genetic differentiation with geographical distance, however, was much higher in type A than in type B. This result indicates substantial interspecific differences in population history and/or the extent of current gene flow between populations. In the Rhine, type B does not show evidence of isolation by distance, and population differentiation is relatively low across hundreds of kilometres. The majority of these populations also show signatures of recent bottlenecks. These patterns are consistent with a recent expansion of type B into the Rhine drainage. In summary, our results suggest considerable and previously unrecognized interspecific differences in the genetic structure of these cryptic keystone species. PMID:23967060

  12. Hidden biodiversity in an ecologically important freshwater amphipod: differences in genetic structure between two cryptic species.

    PubMed

    Westram, Anja Marie; Jokela, Jukka; Keller, Irene

    2013-01-01

    Cryptic species, i.e. species that are morphologically hard to distinguish, have been detected repeatedly in various taxa and ecosystems. In order to evaluate the importance of this finding, we have to know in how far cryptic species differ in various aspects of their biology. The amphipod Gammarus fossarum is a key invertebrate in freshwater streams and contains several cryptic species. We examined the population genetic structure, genetic diversity and demographic history of two of them (type A and type B) using microsatellite markers and asked whether they show significant differences. We present results of population genetic analyses based on a total of 37 populations from the headwaters of two major European drainages, Rhine and Rhone. We found that, in both species, genetic diversity was geographically structured among and within drainages. For type A in the Rhine and type B in the Rhone, we detected significant patterns of isolation by distance. The increase of genetic differentiation with geographical distance, however, was much higher in type A than in type B. This result indicates substantial interspecific differences in population history and/or the extent of current gene flow between populations. In the Rhine, type B does not show evidence of isolation by distance, and population differentiation is relatively low across hundreds of kilometres. The majority of these populations also show signatures of recent bottlenecks. These patterns are consistent with a recent expansion of type B into the Rhine drainage. In summary, our results suggest considerable and previously unrecognized interspecific differences in the genetic structure of these cryptic keystone species.

  13. Two Large, Related, Cryptic Plasmids from Geographically Distinct Isolates of Sulfobacillus thermotolerans▿†

    PubMed Central

    Deane, S. M.; Rawlings, D. E.

    2011-01-01

    Two large cryptic plasmids (59.2 and 65.9 kb) from isolates of Sulfobacillus thermotolerans from Yellowstone National Park (United States) and the Caribbean island of Montserrat were isolated and sequenced. This analysis revealed a common “backbone” region coding for a potential plasmid stability system plus a nonpheromone conjugation system containing homologues of both type IV and type II (tight adherence, or Tad-like) secretion systems. PMID:21926204

  14. Parallel evolution in ecological and reproductive traits to produce cryptic damselfly species across the holarctic.

    PubMed

    Stoks, Robby; Nystrom, Jennifer L; May, Michael L; McPeek, Mark A

    2005-09-01

    The damselfly genus Enallagma originated in the Nearctic, and two Nearctic lineages recently underwent radiations partly associated with multiple independent habitat shifts from lakes dominated by fish predators into lakes dominated by dragonfly predators. A previous molecular study of four Palearctic morphospecies and all representative Nearctic species identified the presence of two cryptic species sets, with each set having Palearctic and Nearctic representatives. However, the cryptic species within each set are not sibling species. Here, we present quantitative data on ecologically important larval morphologies and behaviors involved in predator avoidance and on adult male morphological structures involved in mate recognition to quantify the phenotypic relationships among these cryptic species sets. For the adult stage, our data indicate strong parallel evolution of the structures involved in specific mate recognition-the male cerci. For the larval stage, morphometric analyses show that the Palearctic species evolved a nearly identical morphology to the sibling-clade members in the Nearctic that live in waters where dragonflies are the top predators. This implicates the importance of dragonfly predation in the history of the Palearctic clade. Behavioral analyses suggest population differentiation in response to the actual predator environment in the Palearctic clade, consistent with the species differentiation seen in the Nearctic. Our results suggest parallel evolution of adult traits that influence specific mate choice and larval traits that influence ecological performance underlie the striking similarity of Enallagma species across continents. This concurrent parallel evolution in both stages of a complex life cycle, especially when both stages do not share the same selective environment, may be a very unusual mechanism generating cryptic species.

  15. Evidence for Cryptic Speciation in Directly Transmitted Gyrodactylid Parasites of Trinidadian Guppies

    PubMed Central

    Xavier, Raquel; Faria, Patricia J.; Paladini, Giuseppe; van Oosterhout, Cock; Johnson, Mireille; Cable, Jo

    2015-01-01

    Cryptic species complexes are common among parasites, which tend to have large populations and are subject to rapid evolution. Such complexes may arise through host-parasite co-evolution and/or host switching. For parasites that reproduce directly on their host, there might be increased opportunities for sympatric speciation, either by exploiting different hosts or different micro-habitats within the same host. The genus Gyrodactylus is a specious group of viviparous monogeneans. These ectoparasites transfer between teleosts during social contact and cause significant host mortality. Their impact on the guppy (Poecilia reticulata), an iconic evolutionary and ecological model species, is well established and yet the population genetics and phylogenetics of these parasites remains understudied. Using mtDNA sequencing of the host and its parasites, we provide evidence of cryptic speciation in Gyrodactylus bullatarudis, G. poeciliae and G. turnbulli. For the COII gene, genetic divergence of lineages within each parasite species ranged between 5.7 and 17.2%, which is typical of the divergence observed between described species in this genus. Different lineages of G. turnbulli and G. poeciliae appear geographically isolated, which could imply allopatric speciation. In addition, for G. poeciliae, co-evolution with a different host species cannot be discarded due to its host range. This parasite was originally described on P. caucana, but for the first time here it is also recorded on the guppy. The two cryptic lineages of G. bullatarudis showed considerable geographic overlap. G. bullatarudis has a known wide host range and it can also utilize a killifish (Anablepsoides hartii) as a temporary host. This killifish is capable of migrating overland and it could act as a transmission vector between otherwise isolated populations. Additional genetic markers are needed to confirm the presence of these cryptic Gyrodactylus species complexes, potentially leading to more in

  16. Random Amplified Polymorphic DNA (RAPD) Markers Readily Distinguish Cryptic Mosquito Species (Diptera: Culicidae: Anopheles)

    DTIC Science & Technology

    1993-01-01

    Paskewitz & Collins. 1990; approaches to overcome these are suggested. J. Scott , W. Brogden and F. Collins, pers. comm.). Even though this is an...characterized, yet morphologically cryptic, mosquito Bowditch et al (1993). Total reaction volumes of 25 11l were used species portend that RAPD analysis...Institutes of Health, Bethesda, Mary- Acknowledgements land, USA. The identities of the species were confirmed using PCR primers supplied by J. Scott , W

  17. Nucleotide sequence and replication properties of the Bacillus borstelensis cryptic plasmid pHT926.

    PubMed Central

    Ebisu, S; Murahashi, Y; Takagi, H; Kadowaki, K; Yamaguchi, K; Yamagata, H; Udaka, S

    1995-01-01

    The nucleotide sequence of pHT926, a cryptic plasmid found in Bacillus borstelensis HP926, was determined. pHT926 replicates by a rolling-circle mechanism and belongs to the pC194 plasmid family. The copy number of pHT926 was fourfold higher than that of pUB110 and very stably maintained in Bacillus choshinensis. PMID:7487045

  18. Increased Furan Tolerance in Escherichia coli Due to a Cryptic ucpA Gene

    PubMed Central

    Wang, Xuan; Miller, Elliot N.; Yomano, Lorraine P.; Shanmugam, K. T.

    2012-01-01

    Expression arrays were used to identify 4 putative oxidoreductases that were upregulated (>3-fold) by furfural (15 mM, 15 min). Plasmid expression of one (ucpA) increased furan tolerance in ethanologenic strain LY180 and wild-type strain W. Deleting ucpA decreased furfural tolerance. Although the mechanism remains unknown, the cryptic ucpA gene is now associated with a phenotype: furan resistance. PMID:22267665

  19. Widespread prevalence of cryptic Symbiodinium D in the key Caribbean reef builder, Orbicella annularis

    NASA Astrophysics Data System (ADS)

    Kennedy, Emma V.; Foster, Nicola L.; Mumby, Peter J.; Stevens, Jamie R.

    2015-06-01

    Symbiodinium D, a relatively rare clade of algal endosymbiont with a global distribution, has attracted interest as some of its sub-cladal types induce increased thermal tolerance and associated trade-offs, including reduced growth rate in its coral hosts. Members of Symbiodinium D are increasingly reported to comprise low-abundance `cryptic' (<10 %) proportions of mixed coral endosymbiont communities, with unknown ecological implications. Real-time PCR (RT-PCR) targeted to specific types is sufficiently sensitive to detect these background symbiont levels. In this study, RT-PCR was employed to screen 552 colonies of the key Caribbean reef builder Orbicella annularis sampled across a 5.4 million km2 range for the presence of cryptic Symbiodinium `D1' (i.e., the principal Caribbean ITS2 variants, D1 and D1-4). All but one out of 33 populations analysed were shown to host low abundances of Symbiodinium D1, with an average of >30 % of corals per site found to harbour the symbiont. When the same samples were analysed using the conventional screening technique, denaturing gradient gel electrophoresis, Symbiodinium D1 was only detected in 12 populations and appeared to be hosted by <12 % of colonies where present (in agreement with other reported low prevalence/absences in O. annularis). Cryptic Symbiodinium D1 showed a mainly uniform distribution across the wider Caribbean region, although significantly more Mesoamerican Barrier Reef corals hosted cryptic Symbiodinium D1 than might be expected by chance, possibly as a consequence of intense warming in the region in 1998. Widespread prevalence of thermally tolerant Symbiodinium in O. annularis may potentially reflect a capacity for the coral to temporarily respond to warming events through symbiont shuffling. However, association with reduced coral calcification means that the ubiquitous nature of Symbiodinium D1 in O. annularis populations is unlikely to prevent long-term declines in reef health, at a time when

  20. "Nested" cryptic diversity in a widespread marine ecosystem engineer: a challenge for detecting biological invasions.

    PubMed

    Teske, Peter R; Rius, Marc; McQuaid, Christopher D; Styan, Craig A; Piggott, Maxine P; Benhissoune, Saïd; Fuentes-Grünewald, Claudio; Walls, Kathy; Page, Mike; Attard, Catherine Rm; Cooke, Georgina M; McClusky, Claire F; Banks, Sam C; Barker, Nigel P; Beheregaray, Luciano B

    2011-06-21

    Ecosystem engineers facilitate habitat formation and enhance biodiversity, but when they become invasive, they present a critical threat to native communities because they can drastically alter the receiving habitat. Management of such species thus needs to be a priority, but the poorly resolved taxonomy of many ecosystem engineers represents a major obstacle to correctly identifying them as being either native or introduced. We address this dilemma by studying the sea squirt Pyura stolonifera, an important ecosystem engineer that dominates coastal communities particularly in the southern hemisphere. Using DNA sequence data from four independently evolving loci, we aimed to determine levels of cryptic diversity, the invasive or native status of each regional population, and the most appropriate sampling design for identifying the geographic ranges of each evolutionary unit. Extensive sampling in Africa, Australasia and South America revealed the existence of "nested" levels of cryptic diversity, in which at least five distinct species can be further subdivided into smaller-scale genetic lineages. The ranges of several evolutionary units are limited by well-documented biogeographic disjunctions. Evidence for both cryptic native diversity and the existence of invasive populations allows us to considerably refine our view of the native versus introduced status of the evolutionary units within Pyura stolonifera in the different coastal communities they dominate. This study illustrates the degree of taxonomic complexity that can exist within widespread species for which there is little taxonomic expertise, and it highlights the challenges involved in distinguishing between indigenous and introduced populations. The fact that multiple genetic lineages can be native to a single geographic region indicates that it is imperative to obtain samples from as many different habitat types and biotic zones as possible when attempting to identify the source region of a putative

  1. Diverse Borrelia burgdorferi Strains in a Bird-Tick Cryptic Cycle ▿ †

    PubMed Central

    Hamer, Sarah A.; Hickling, Graham J.; Sidge, Jennifer L.; Rosen, Michelle E.; Walker, Edward D.; Tsao, Jean I.

    2011-01-01

    The blacklegged tick Ixodes scapularis is the primary vector of the most prevalent vector-borne zoonosis in North America, Lyme disease (LD). Enzootic maintenance of the pathogen Borrelia burgdorferi by I. scapularis and small mammals is well documented, whereas its “cryptic” maintenance by other specialist ticks and wildlife hosts remains largely unexplored because these ticks rarely bite humans. We quantified B. burgdorferi infection in a cryptic bird-rabbit-tick cycle. Furthermore, we explored the role of birds in maintaining and moving B. burgdorferi strains by comparing their genetic diversity in this cryptic cycle to that found in cycles vectored by I. scapularis. We examined birds, rabbits, and small mammals for ticks and infection over a 4-year period at a focal site in Michigan, 90 km east of a zone of I. scapularis invasion. We mist netted 19,631 birds that yielded 12,301 ticks, of which 86% were I. dentatus, a bird-rabbit specialist. No resident wildlife harbored I. scapularis, and yet 3.5% of bird-derived ticks, 3.6% of rabbit-derived ticks, and 20% of rabbit ear biopsy specimens were infected with B. burgdorferi. We identified 25 closely related B. burgdorferi strains using an rRNA gene intergenic spacer marker, the majority (68%) of which had not been reported previously. The presence of strains common to both cryptic and endemic cycles strongly implies bird-mediated dispersal. Given continued large-scale expansion of I. scapularis populations, we predict that its invasion into zones of cryptic transmission will allow for bridging of novel pathogen strains to humans and animals. PMID:21257811

  2. Through thick and thin: cryptic sympatric speciation in the submersed genus Najas (Hydrocharitaceae).

    PubMed

    Les, Donald H; Peredo, Elena L; King, Ursula M; Benoit, Lori K; Tippery, Nicholas P; Ball, Cassandra J; Shannon, Robynn K

    2015-01-01

    Cryptic sympatric species arise when reproductive isolation is established in sympatry, leading to genetically divergent lineages that are highly similar morphologically or virtually indistinguishable. Although cryptic sympatric species have been reported in various animals, fungi, and protists, there are few compelling examples for plants. This investigation presents a case for cryptic sympatric speciation in Najas flexilis, a widespread aquatic plant, which extends throughout northern North America and Eurasia. The taxon is noted for its variable seed morphology, which earlier research associated with cytotypes; i.e., diploids were characterized by thicker seeds and tetraploids by thinner seeds. However, cytotypes are not patterned geographically with diploid and tetraploid plants often found in close proximity within the same lake. Using digital image and DNA sequence analyses, we found that diploids and tetraploids are well-isolated and remain genetically distinct throughout their sympatric range, where sterile hybrids occur frequently. Incorporation of sequence data from the single-copy nuclear phytoene desaturase locus revealed further that the tetraploids are allopolyploid derivatives of N. flexilis and N. guadalupensis, the latter a closely related species with an overlapping distribution. We conclude that the taxon widely known as N. flexilis actually comprises two cryptic, sibling species, which diverged in sympatry by interspecific hybridization and subsequent chromosomal isolation. By comparing seed morphology of type specimens, we associated the names N. flexilis and N. canadensis to the diploids and tetraploids respectively. Additionally, the narrowly restricted taxon known formerly as N. muenscheri is shown via morphological and genetic evidence to be synonymous with N. canadensis. Copyright © 2014 Elsevier Inc. All rights reserved.

  3. Evidence for cryptic speciation in directly transmitted gyrodactylid parasites of Trinidadian guppies.

    PubMed

    Xavier, Raquel; Faria, Patricia J; Paladini, Giuseppe; van Oosterhout, Cock; Johnson, Mireille; Cable, Jo

    2015-01-01

    Cryptic species complexes are common among parasites, which tend to have large populations and are subject to rapid evolution. Such complexes may arise through host-parasite co-evolution and/or host switching. For parasites that reproduce directly on their host, there might be increased opportunities for sympatric speciation, either by exploiting different hosts or different micro-habitats within the same host. The genus Gyrodactylus is a specious group of viviparous monogeneans. These ectoparasites transfer between teleosts during social contact and cause significant host mortality. Their impact on the guppy (Poecilia reticulata), an iconic evolutionary and ecological model species, is well established and yet the population genetics and phylogenetics of these parasites remains understudied. Using mtDNA sequencing of the host and its parasites, we provide evidence of cryptic speciation in Gyrodactylus bullatarudis, G. poeciliae and G. turnbulli. For the COII gene, genetic divergence of lineages within each parasite species ranged between 5.7 and 17.2%, which is typical of the divergence observed between described species in this genus. Different lineages of G. turnbulli and G. poeciliae appear geographically isolated, which could imply allopatric speciation. In addition, for G. poeciliae, co-evolution with a different host species cannot be discarded due to its host range. This parasite was originally described on P. caucana, but for the first time here it is also recorded on the guppy. The two cryptic lineages of G. bullatarudis showed considerable geographic overlap. G. bullatarudis has a known wide host range and it can also utilize a killifish (Anablepsoides hartii) as a temporary host. This killifish is capable of migrating overland and it could act as a transmission vector between otherwise isolated populations. Additional genetic markers are needed to confirm the presence of these cryptic Gyrodactylus species complexes, potentially leading to more in

  4. Conformal Lorentz geometry revisited

    NASA Astrophysics Data System (ADS)

    Teleman, Kostake

    1996-02-01

    The group U(2,2) and its subgroup SU(2,2) were considered by Penrose in his study of the conformal compactification M of the Minkowski space M [R. Penrose and W. Rindler, Spinors and Space-Time (Cambridge University, Cambridge, 1986) and R. O. Wells, Jr., Bull. Am. Math. Soc. I, 2 (1979)]. The standard representation of SU(2,2) in C4 and in M are the corner stones of twistor theory, which was created by Penrose to the double purpose of obtaining new solutions of Einstein equations and new insights on gravitational radiation. We think that other representations of SU(2,2) or U(2,2) could also bring some information in relativity [see also, Barut O. Asjim, in Noncompact Lie Groups and some of their Applications, edited by E. A. Tanner and R. Wilson (Kluwer Academic, Dordrecht, 1994), p. 103] and, accordingly, we propose an extension of Penrose twistor program. In this paper we deal with a new U(2,2)-space, which we denote by W. We show first that the SU(2,2)-space M introduced by Penrose is isomorphic to U(2), endowed with an action of SU(2,2) given by non-Abelian homographic transformations. These transformations keep invariant the equation det(u-v)=0, characterizing the pairs (u,v)∈U(2)×U(2) such that ``u lies on the light-cone of v.'' By definition, our space W consists of all pairs (u,v)∈U(2)×U(2) satisfying the condition det(u-v)≠0. The starting point of this article is the observation that W carries an SU(2,2)-invariant pseudo-Riemannian metric L:=Tr[(u-v)-1u˙ ×(u-v)-1v˙], of signature (4,4). (W,L) is in fact an irreducible symmetric space in Cartan's sense, which is isomorphic to the quotient SO(2,4)/S[O(1,1)×O(1,3)]. As an irreducible symmetric space, it is an 8-dimensional Einstein space, whose Ricci tensor is proportional to the metric tensor. We study the geodesic paths of this space giving the general solutions in terms of initial data and studying the constants of motion. In particular we determine the geodesic paths which exhibit two periods

  5. Aubry-Mather Theory for Conformally Symplectic Systems

    NASA Astrophysics Data System (ADS)

    Marò, Stefano; Sorrentino, Alfonso

    2017-09-01

    In this article we develop an analogue of Aubry-Mather theory for a class of dissipative systems, namely conformally symplectic systems, and prove the existence of interesting invariant sets, which, in analogy to the conservative case, will be called the Aubry and the Mather sets. Besides describing their structure and their dynamical significance, we shall analyze their attracting/repelling properties, as well as their noteworthy role in driving the asymptotic dynamics of the system.

  6. CONFORMANCE IMPROVEMENT USING GELS

    SciTech Connect

    Randall S. Seright

    2002-02-28

    This technical progress report describes work performed from June 20 through December 19, 2001, for the project, ''Conformance Improvement Using Gels''. Interest has increased in some new polymeric products that purport to substantially reduce permeability to water while causing minimum permeability reduction to oil. In view of this interest, we are currently studying BJ's Aqua Con. Results from six corefloods revealed that the Aqua Con gelant consistently reduced permeability to water more than that to oil. However, the magnitude of the disproportionate permeability reduction varied significantly for the various experiments. Thus, as with most materials tested to date, the issue of reproducibility and control of the disproportionate permeability remains to be resolved. Concern exists about the ability of gels to resist washout after placement in fractures. We examined whether a width constriction in the middle of a fracture would cause different gel washout behavior upstream versus downstream of the constriction. Tests were performed using a formed Cr(III)-acetate-HPAM gel in a 48-in.-long fracture with three sections of equal length, but with widths of 0.08-, 0.02-, and 0.08-in., respectively. The pressure gradients during gel extrusion (i.e., placement) were similar in the two 0.08-in.-wide fracture sections, even though they were separated by a 0.02-in.-wide fracture section. The constriction associated with the middle fracture section may have inhibited gel washout during the first pulse of brine injection after gel placement. However, during subsequent phases of brine injection, the constriction did not inhibit washout in the upstream fracture section any more than in the downstream section.

  7. Classification of finite irreducible conformal modules over some Lie conformal algebras related to the Virasoro conformal algebra

    NASA Astrophysics Data System (ADS)

    Wu, Henan; Yuan, Lamei

    2017-04-01

    In this paper, we classify all finite irreducible conformal modules over a class of Lie conformal algebras W (b ) with b ∈ℂ related to the Virasoro conformal algebra. Explicitly, any finite irreducible conformal module over W (b ) is proved to be isomorphic to MΔ ,α ,β with Δ ≠0 or β ≠0 if b = 0, or MΔ ,α with Δ ≠0 if b ≠0 . As a byproduct, all finite irreducible conformal modules over the Heisenberg-Virasoro conformal algebra and the W(2, 2) Lie conformal algebra are classified. Finally, the same thing is done for the Schrödinger-Virasoro conformal algebra.

  8. Population structure and cryptic genetic variation in the mango fruit fly, Ceratitis cosyra (Diptera, Tephritidae)

    PubMed Central

    Virgilio, Massimiliano; Delatte, Hélène; Nzogela, Yasinta Beda; Simiand, Christophe; Quilici, Serge; De Meyer, Marc; Mwatawala, Maulid

    2015-01-01

    Abstract The fruit fly Ceratitis cosyra is an important agricultural pest negatively affecting the mango crop production throughout Africa and also feeding on a variety of other wild and cultivated hosts. The occurrence of deeply divergent haplotypes, as well as extensive morphological variability, previously suggested possible cryptic speciation within Ceratitis cosyra. Here we provide the first large-scale characterisation of the population structure of Ceratitis cosyra with the main objective of verifying cryptic genetic variation. A total of 348 specimens from 13 populations were genotyped at 16 polymorphic microsatellite loci. Hardy-Weinberg equilibrium (HWE) deviations were observed in 40.4% of locus-population combinations and suggested the occurrence of genetic substructuring within populations. Discriminant Analysis of Principal Components (DAPC) showed genetic divergence between the vast majority of vouchers from Burundi and Tanzania (plus a few outliers from other African countries) and all other specimens sampled. Individual Bayesian assignments confirmed the existence of two main genotypic groups also occurring in sympatry. These data provided further support to the hypothesis that Ceratitis cosyra might include cryptic species. However, additional integrative taxonomy, possibly combining morphological, ecological and physiological approaches, is required to provide the necessary experimental support to this model. PMID:26798276

  9. Cryptic Photosynthesis-Extrasolar Planetary Oxygen Without a Surface Biological Signature

    NASA Astrophysics Data System (ADS)

    Cockell, Charles S.; Kaltenegger, Lisa; Raven, John A.

    2009-09-01

    On Earth, photosynthetic organisms are responsible for the production of virtually all the oxygen in the atmosphere. On land, vegetation reflects in the visible and leads to a "red edge," which developed about 450 million years ago on Earth and has been proposed as a biosignature for life on extrasolar planets. However, in many regions on Earth, particularly where surface conditions are extreme -- in hot and cold deserts, for example -- photosynthetic organisms can be driven into and under substrates where light is still sufficient for photosynthesis. These communities exhibit no detectable surface spectral signature to indicate life. The same is true of the assemblages of photosynthetic organisms at more than a few meters' depth in water bodies. These communities are widespread and dominate local photosynthetic productivity. We review known cryptic photosynthetic communities and their productivity. We have linked geomicrobiology with observational astronomy by calculating the disk-averaged spectra of cryptic habitats and identifying detectable features on an exoplanet dominated by such a biota. The hypothetical cryptic photosynthesis worlds discussed here are Earth analogues that show detectable atmospheric biosignatures like our own planet but do not exhibit a discernable biological surface feature in the disc-averaged spectrum.

  10. CRYPTIC CHOICE OF CONSPECIFIC SPERM CONTROLLED BY THE IMPACT OF OVARIAN FLUID ON SPERM SWIMMING BEHAVIOR

    PubMed Central

    Yeates, Sarah E; Diamond, Sian E; Einum, Sigurd; Emerson, Brent C; Holt, William V; Gage, Matthew J G

    2013-01-01

    Despite evidence that variation in male–female reproductive compatibility exists in many fertilization systems, identifying mechanisms of cryptic female choice at the gamete level has been a challenge. Here, under risks of genetic incompatibility through hybridization, we show how salmon and trout eggs promote fertilization by conspecific sperm. Using in vitro fertilization experiments that replicate the gametic microenvironment, we find complete interfertility between both species. However, if either species’ ova were presented with equivalent numbers of both sperm types, conspecific sperm gained fertilization precedence. Surprisingly, the species’ identity of the eggs did not explain this cryptic female choice, which instead was primarily controlled by conspecific ovarian fluid, a semiviscous, protein-rich solution that bathes the eggs and is released at spawning. Video analyses revealed that ovarian fluid doubled sperm motile life span and straightened swimming trajectory, behaviors allowing chemoattraction up a concentration gradient. To confirm chemoattraction, cell migration tests through membranes containing pores that approximated to the egg micropyle showed that conspecific ovarian fluid attracted many more spermatozoa through the membrane, compared with heterospecific fluid or water. These combined findings together identify how cryptic female choice can evolve at the gamete level and promote reproductive isolation, mediated by a specific chemoattractive influence of ovarian fluid on sperm swimming behavior. PMID:24299405

  11. Multiple cryptic species in the blue-spotted maskray (Myliobatoidei: Dasyatidae: Neotrygon spp.): An update.

    PubMed

    Borsa, Philippe; Shen, Kang-Ning; Arlyza, Irma S; Hoareau, Thierry B

    2016-01-01

    Previous investigations have uncovered divergent mitochondrial clades within the blue-spotted maskray, previously Neotrygon kuhlii (Müller and Henle). The hypothesis that the blue-spotted maskray may consist of a complex of multiple cryptic species has been proposed, and four species have been recently described or resurrected. To test the multiple cryptic species hypothesis, we investigated the phylogenetic relationships and coalescence patterns of mitochondrial sequences in a sample of 127 new individuals from the Indian Ocean and the Coral Triangle region, sequenced at both the CO1 and cytochrome b loci. The maximum-likelihood (ML) tree of concatenated CO1+cytochrome b gene sequences, rooted by the New Caledonian maskray N. trigonoides, yielded 9 strongly supported, main clades. Puillandre's ABGD algorithm detected gaps in nucleotide distance consistent with the ML phylogeny. The general mixed Yule-coalescent algorithm partitioned the dataset into putative species generally consistent with the ML phylogeny. Nuclear markers generally confirmed that distinct mitochondrial clades correspond to genetically isolated lineages. The nine main lineages identified by ML analysis were geographically distributed in a parapatric fashion, indicating reproductive isolation. The hypothesis of multiple cryptic species is thus validated.

  12. Nuclear genomes distinguish cryptic species suggested by their DNA barcodes and ecology.

    PubMed

    Janzen, Daniel H; Burns, John M; Cong, Qian; Hallwachs, Winnie; Dapkey, Tanya; Manjunath, Ramya; Hajibabaei, Mehrdad; Hebert, Paul D N; Grishin, Nick V

    2017-08-01

    DNA sequencing brings another dimension to exploration of biodiversity, and large-scale mitochondrial DNA cytochrome oxidase I barcoding has exposed many potential new cryptic species. Here, we add complete nuclear genome sequencing to DNA barcoding, ecological distribution, natural history, and subtleties of adult color pattern and size to show that a widespread neotropical skipper butterfly known as Udranomia kikkawai (Weeks) comprises three different species in Costa Rica. Full-length barcodes obtained from all three century-old Venezuelan syntypes of U. kikkawai show that it is a rainforest species occurring from Costa Rica to Brazil. The two new species are Udranomia sallydaleyae Burns, a dry forest denizen occurring from Costa Rica to Mexico, and Udranomia tomdaleyi Burns, which occupies the junction between the rainforest and dry forest and currently is known only from Costa Rica. Whereas the three species are cryptic, differing but slightly in appearance, their complete nuclear genomes totaling 15 million aligned positions reveal significant differences consistent with their 0.00065-Mbp (million base pair) mitochondrial barcodes and their ecological diversification. DNA barcoding of tropical insects reared by a massive inventory suggests that the presence of cryptic species is a widespread phenomenon and that further studies will substantially increase current estimates of insect species richness.

  13. Standardised molecular diagnostic tool for the identification of cryptic species within the Bemisia tabaci complex.

    PubMed

    Elfekih, S; Tay, W T; Gordon, K; Court, L; De Barro, P

    2017-07-23

    The whitefly Bemisia tabaci complex harbours over 40 cryptic species that have been placed in 11 phylogenetically distinct clades based on the molecular characterisation of partial mitochondrial DNA COI (mtCOI) gene region. Four cryptic species are currently within the invasive clade i.e. 'MED', 'MEAM1', 'MEAM2' and IO'. Correct identification of these species is a critical step towards implementing reliable measures for plant biosecurity and border protection, however no standardised B. tabaci-specific primers are currently available which has caused inconsistencies in the species identification processes. We report three sets of PCR primers developed to amplify the mtCOI region which can be used for genotyping 'MED', 'MEAM1', and 'IO' species and tested these primers on 91 MED, 35 MEAM1 and five IO individuals. PCR and sequencing of amplicons identified a total of 21, six and one haplotypes in MED, MEAM1 and IO respectively, of which six haplotypes were new to the B. tabaci database. These primer pairs enabled standardisation and robust molecular species identification via mtCOI screening of the targeted invasive cryptic species and will improve quarantine decisions. The use of this diagnostic tool could be extended to other species within the complex. This article is protected by copyright. All rights reserved.

  14. Evidence of cryptic and pseudocryptic speciation in the Paracalanus parvus species complex (Crustacea, Copepoda, Calanoida)

    PubMed Central

    2014-01-01

    Introduction Many marine planktonic crustaceans such as copepods have been considered as widespread organisms. However, the growing evidence for cryptic and pseudo-cryptic speciation has emphasized the need of re-evaluating the status of copepod species complexes in molecular and morphological studies to get a clearer picture about pelagic marine species as evolutionary units and their distributions. This study analyses the molecular diversity of the ecologically important Paracalanus parvus species complex. Its seven currently recognized species are abundant and also often dominant in marine coastal regions worldwide from temperate to tropical oceans. Results COI and Cytochrome b sequences of 160 specimens of the Paracalanus parvus complex from all oceans were obtained. Furthermore, 42 COI sequences from GenBank were added for the genetic analyses. Thirteen distinct molecular operational taxonomic units (MOTU) and two single sequences were revealed with cladistic analyses (Maximum Likelihood, Bayesian Inference), of which seven were identical with results from species delimitation methods (barcode gaps, ABDG, GMYC, Rosenberg’s P(AB)). In total, 10 to 12 putative species were detected and could be placed in three categories: (1) temperate geographically isolated, (2) warm-temperate to tropical wider spread and (3) circumglobal warm-water species. Conclusions The present study provides evidence of cryptic or pseudocryptic speciation in the Paracalanus parvus complex. One major insight is that the species Paracalanus parvus s.s. is not panmictic, but may be restricted in its distribution to the northeastern Atlantic. PMID:24581044

  15. Diversity of sponges (Porifera) from cryptic habitats on the Belize barrier reef near Carrie Bow Cay.

    PubMed

    Rützler, Klaus; Piantoni, Carla; Van Soest, Rob W M; Díaz, M Cristina

    2014-05-29

    The Caribbean barrier reef near Carrie Bow Cay, Belize, has been a focus of Smithsonian Institution (Washington) reef and mangrove investigations since the early 1970s. Systematics and biology of sponges (Porifera) were addressed by several researchers but none of the studies dealt with cryptic habitats, such as the shaded undersides of coral rubble, reef crevices, and caves, although a high species diversity was recognized and samples were taken for future reference and study. This paper is the result of processing samples taken between 1972 and 2012. In all, 122 species were identified, 14 of them new (including one new genus). The new species are Tetralophophora (new genus) mesoamericana, Geodia cribrata, Placospongia caribica, Prosuberites carriebowensis, Timea diplasterina, Timea oxyasterina, Rhaphidhistia belizensis, Wigginsia curlewensis, Phorbas aurantiacus, Myrmekioderma laminatum, Niphates arenata, Siphonodictyon occultum, Xestospongia purpurea, and Aplysina sciophila. We determined that about 75 of the 122 cryptic sponge species studied (61%) are exclusive members of the sciophilic community, 47 (39 %) occur in both, light-exposed and shaded or dark habitats. Since we estimate the previously known sponge population of Carrie Bow reefs and mangroves at about 200 species, the cryptic fauna makes up 38 % of total diversity.

  16. No evidence for external genital morphology affecting cryptic female choice and reproductive isolation in Drosophila.

    PubMed

    LeVasseur-Viens, Hélène; Polak, Michal; Moehring, Amanda J

    2015-07-01

    Genitalia are one of the most rapidly diverging morphological features in animals. The evolution of genital morphology is proposed to be driven by sexual selection via cryptic female choice, whereby a female selectively uptakes and uses a particular male's sperm on the basis of male genital morphology. The resulting shifts in genital morphology within a species can lead to divergence in genitalia between species, and consequently to reproductive isolation and speciation. Although this conceptual framework is supported by correlative data, there is little direct empirical evidence. Here, we used a microdissection laser to alter the morphology of the external male genitalia in Drosophila, a widely used genetic model for both genital shape and cryptic female choice. We evaluate the effect of precision alterations to lobe morphology on both interspecific and intraspecific mating, and demonstrate experimentally that the male genital lobes do not affect copulation duration or cryptic female choice, contrary to long-standing assumptions regarding the role of the lobes in this model system. Rather, we demonstrate that the lobes are essential for copulation to occur. Moreover, slight alterations to the lobes significantly reduced copulatory success only in competitive environments, identifying precopulatory sexual selection as a potential contributing force behind genital diversification.

  17. Cryptic female choice during spermatophore transfer in Tribolium castaneum (Coleoptera: Tenebrionidae).

    PubMed

    Fedina, Tatyana Y

    2007-01-01

    Sexual selection in both males and females promotes traits and behaviors that allow control over paternity when female mates with multiple males. Nonetheless, mechanisms of cryptic female choice have been consistently overlooked, due to traditional focus on sperm competition as well as difficulty in distinguishing male vs. female influence over processes occurring during and after mating. The first part of this study describes morphology and transformation of Tribolium castaneum spermatophores inferred from dissecting females immediately after normal or interrupted copulations. T. castaneum males are found to transfer spermatophores as an invaginated tube that everts inside the female bursa and which is filled with sperm during copulation. This sequence of events makes it feasible for females to control the sperm quantity transferred in each spermatophore. Through manipulation of the male phenotypic quality (by starvation) and manipulation of female control over sperm transfer (by killing a subset of females), the second part of this study examines whether females use control over transferred sperm quantity as a cryptic choice mechanism. Fed males transferred significantly more sperm per spermatophore than starved males but only when mating with live females. These results suggest an active differentiation by live females against starved males and provide an evidence for the proposed cryptic female choice mechanism.

  18. Experimental demonstration of possible cryptic female choice on male tsetse fly genitalia.

    PubMed

    Briceño, R D; Eberhard, W G

    2009-11-01

    A possible explanation for one of the most general trends in animal evolution - rapid divergent evolution of animal genitalia - is that male genitalia are used as courtship devices that influence cryptic female choice. But experimental demonstrations of stimulatory effects of male genitalia on female reproductive processes have generally been lacking. Previous studies of female reproductive physiology in the tsetse fly Glossina morsitans suggested that stimulation during copulation triggers ovulation and resistance to remating. In this study we altered the form of two male genital structures that squeeze the female's abdomen rhythmically in G. morsitans centralis and induced, as predicted, cryptic female choice against the male: sperm storage decreased, while female remating increased. Further experiments in which we altered the female sensory abilities at the site contacted by these male structures during copulation, and severely altered or eliminated the stimuli the male received from this portion of his genitalia, suggested that the effects of genital alteration on sperm storage were due to changes in tactile stimuli received by the female, rather than altered male behavior. These data support the hypothesis that sexual selection by cryptic female choice has been responsible for the rapid divergent evolution of male genitalia in Glossina; limitations of this support are discussed. It appears that a complex combination of stimuli trigger female ovulation, sperm storage, and remating, and different stimuli affect different processes in G. morsitans, and that the same processes are controlled differently in G. pallidipes. This puzzling diversity in female triggering mechanisms may be due to the action of sexual selection.

  19. Cryptic female choice favours sperm from major histocompatibility complex-dissimilar males.

    PubMed

    Løvlie, Hanne; Gillingham, Mark A F; Worley, Kirsty; Pizzari, Tommaso; Richardson, David S

    2013-10-22

    Cryptic female choice may enable polyandrous females to avoid inbreeding or bias offspring variability at key loci after mating. However, the role of these genetic benefits in cryptic female choice remains poorly understood. Female red junglefowl, Gallus gallus, bias sperm use in favour of unrelated males. Here, we experimentally investigate whether this bias is driven by relatedness per se, or by similarity at the major histocompatibility complex (MHC), genes central to vertebrate acquired immunity, where polymorphism is critical to an individual's ability to combat pathogens. Through experimentally controlled natural matings, we confirm that selection against related males' sperm occurs within the female reproductive tract but demonstrate that this is more accurately predicted by MHC similarity: controlling for relatedness per se, more sperm reached the eggs when partners were MHC--dissimilar. Importantly, this effect appeared largely owing to similarity at a single MHC locus (class I minor). Further, the effect of MHC similarity was lost following artificial insemination, suggesting that male phenotypic cues might be required for females to select sperm differentially. These results indicate that postmating mechanisms that reduce inbreeding may do so as a consequence of more specific strategies of cryptic female choice promoting MHC diversity in offspring.

  20. Strategic male mating effort and cryptic male choice in a scorpionfly.

    PubMed

    Engqvist, L; Sauer, K P

    2001-04-07

    In animal species with high male mating effort, males often find themselves in a dilemma: by increasing their mating effort, the gain from each copulation increases but simultaneously reduces available resources and, thus, the opportunity for future copulations. Therefore, we expect males to spend less reproductive resources on matings that provide low reproductive potential, thereby saving resources for future copulations, possibly with high-quality females, a sort of cryptic male choice. However, the strength of the trade-off between investment in a current mating and resources available for future matings must not be the same for all males. Males with relatively high mating costs should allocate their limited resources more cautiously than males with more plentiful resources. Here, we examine this prediction in the scorpionfly Panorpa cognata. Prior to copulation, males produce a large salivary mass on which females feed during copulation. We show that the production of larger salivary masses leads to longer copulations. Moreover, the size of the salivary gland and salivary mass increases with increasing male condition. However, males in poor condition make a relatively higher mating investment than males in good condition. We therefore expect male condition to influence cryptic male choice. In accordance with our hypothesis, only males in poor condition choose cryptically, producing larger salivary masses in copulations with females of high fecundity.