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Sample records for aa sequence identity

  1. My Identical Twin Sequenced our Genome.

    PubMed

    Schilit, Samantha L P; Schilit Nitenson, Arielle

    2017-04-01

    With rapidly declining costs, whole genome sequencing is becoming feasible for widespread use. Although cost-effectiveness is driving increased use of the technology, comprehensive recommendations on how to handle ethical dilemmas have yet to reach a consensus. In this article, Sam shares her experience of undergoing whole genome sequencing. Despite the deeply private nature of the test, the results do not solely belong to Sam; her identical twin sister, Arielle, shares virtually the same genome and received results without a formal consent process. This article explores their parallel experiences as a way of highlighting the controversial ethics of a private test with familial implications.

  2. Some identities of generalized Fibonacci sequence

    NASA Astrophysics Data System (ADS)

    Chong, Chin-Yoon; Cheah, C. L.; Ho, C. K.

    2014-07-01

    We introduced the generalized Fibonacci sequence {Un} defined by U0 = 0, U1 = 1, and Un+2 = pUn+1+qUn for all p, q∈Z+ and for all non-negative integers n. In this paper, we obtained some recursive formulas of the sequence.

  3. Molecular identity of ramie germplasms using simple sequence repeat markers.

    PubMed

    Luan, M B; Chen, B F; Zou, Z Z; Zhu, J J; Wang, X F; Xu, Y; Sun, Z M; Chen, J H

    2015-03-27

    DNA identity is highly effective and efficient for distinguishing crop varieties regardless of their phenotypic similarities. To establish DNA identity in ramie, 21 simple sequence repeat primers were amplified in 108 accessions of domestic and exotic ramie germplasms. Sixty polymorphic bands were obtained, with an average of 2.9 bands per locus and 2-8 band types per primer locus (average of 5.19 band types). The Simpson's diversity index of the 21 simple sequence repeat loci ranged from 0.158 to 0.808 with an average of 0.612. There was large difference in the specific index in the germplasm tested, from 44.082 to 218.163, with an average of 83.620. Based on allele band type, 8 primer pairs were selected for DNA fingerprinting of the 108 genotypes. The combination of the 8 primer pairs were found to be very effective for distinguishing these genotypes, indicating that they can be used in the molecular DNA identity of ramie.

  4. Draft Genome Sequence of the Putrescine-Producing Strain Lactococcus lactis subsp. lactis 1AA59

    PubMed Central

    del Rio, Beatriz; Linares, Daniel M.; Fernandez, María; Mayo, Baltasar; Martín, M. Cruz

    2015-01-01

    We report here the 2,576,542-bp genome annotated draft assembly sequence of Lactococcus lactis subsp. lactis 1AA59. This strain—isolated from a traditional cheese—produces putrescine, one of the most frequently biogenic amines found in dairy products. PMID:26089428

  5. Bifunctional CYP81AA proteins catalyse identical hydroxylations but alternative regioselective phenol couplings in plant xanthone biosynthesis

    PubMed Central

    El-Awaad, Islam; Bocola, Marco; Beuerle, Till; Liu, Benye; Beerhues, Ludger

    2016-01-01

    Xanthones are natural products present in plants and microorganisms. In plants, their biosynthesis starts with regioselective cyclization of 2,3′,4,6-tetrahydroxybenzophenone to either 1,3,5- or 1,3,7-trihydroxyxanthones, catalysed by cytochrome P450 (CYP) enzymes. Here we isolate and express CYP81AA-coding sequences from Hypericum calycinum and H. perforatum in yeast. Microsomes catalyse two consecutive reactions, that is, 3′-hydroxylation of 2,4,6-trihydroxybenzophenone and C–O phenol coupling of the resulting 2,3′,4,6-tetrahydroxybenzophenone. Relative to the inserted 3′-hydroxyl, the orthologues Hc/HpCYP81AA1 cyclize via the para position to form 1,3,7-trihydroxyxanthone, whereas the paralogue HpCYP81AA2 directs cyclization to the ortho position, yielding the isomeric 1,3,5-trihydroxyxanthone. Homology modelling and reciprocal mutagenesis reveal the impact of S375, L378 and A483 on controlling the regioselectivity of HpCYP81AA2, which is converted into HpCYP81AA1 by sextuple mutation. However, the reciprocal mutations in HpCYP81AA1 barely affect its regiospecificity. Product docking rationalizes the alternative C–O phenol coupling reactions. Our results help understand the machinery of bifunctional CYPs. PMID:27145837

  6. How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity

    NASA Technical Reports Server (NTRS)

    Fox, G. E.; Wisotzkey, J. D.; Jurtshuk, P. Jr

    1992-01-01

    16S rRNA (genes coding for rRNA) sequence comparisons were conducted with the following three psychrophilic strains: Bacillus globisporus W25T (T = type strain) and Bacillus psychrophilus W16AT, and W5. These strains exhibited more than 99.5% sequence identity and within experimental uncertainty could be regarded as identical. Their close taxonomic relationship was further documented by phenotypic similarities. In contrast, previously published DNA-DNA hybridization results have convincingly established that these strains do not belong to the same species if current standards are used. These results emphasize the important point that effective identity of 16S rRNA sequences is not necessarily a sufficient criterion to guarantee species identity. Thus, although 16S rRNA sequences can be used routinely to distinguish and establish relationships between genera and well-resolved species, very recently diverged species may not be recognizable.

  7. Complete genome sequence of Bacillus thuringiensis tenebrionis 4AA1, a typical strain with toxicity to Coleopteran insects.

    PubMed

    Gao, Qiuling; Zheng, Jinshui; Zhu, Lei; Ruan, Lifang; Peng, Donghai; Sun, Ming

    2015-06-20

    Bacillus thuringiensis serovar morrisoni biovar tenebrionis has been developed as an bioinsecticide to control Coleopteran insects in agriculture and forestry for a few decades. Its major crystal protein Cry3Aa was also applied to transgenic crops. Here we report the complete genome sequence of strain tenebrionis 4AA1, which has one chromosome of 5,652,292bp and six plasmids. Two crystal protein genes, cry3Aa and cry15Aa, locate on one single plasmid named pBMB51. This strain also possesses plentiful virulence factors besides crystal proteins.

  8. Superior signal-to-noise ratio of a new AA1 sequence for random-modulation continuous-wave lidar.

    PubMed

    Rybaltowski, Adam; Taflove, Allen

    2004-08-01

    In an earlier work [Proc. SPIE 4484, 216 (2001)] we proposed a new AA1 modulation sequence for random-modulation continuous-wave lidar. It possesses significantly better signal properties than other pseudorandom codes (the M, A1, and A2 sequences). We derive and compare the signal-to-noise ratio (SNR) of the new AA1 sequence with those of previous modulation sequences. Using a figure of merit proposed for pseudorandom sequences in additive (and generally colored) noise, we show that the SNR of the AA1 sequence in 1/f noise can be as much as 50 times better than that of the commonly used M sequence. This improved SNR should permit as much as a 7:1 increase of the maximum lidar sensing range in baseband-modulation direct-detection infrared lidar with no significant changes to the transmitter and receiver.

  9. Vocal Generalization Depends on Gesture Identity and Sequence

    PubMed Central

    Sober, Samuel J.

    2014-01-01

    Generalization, the brain's ability to transfer motor learning from one context to another, occurs in a wide range of complex behaviors. However, the rules of generalization in vocal behavior are poorly understood, and it is unknown how vocal learning generalizes across an animal's entire repertoire of natural vocalizations and sequences. Here, we asked whether generalization occurs in a nonhuman vocal learner and quantified its properties. We hypothesized that adaptive error correction of a vocal gesture produced in one sequence would generalize to the same gesture produced in other sequences. To test our hypothesis, we manipulated the fundamental frequency (pitch) of auditory feedback in Bengalese finches (Lonchura striata var. domestica) to create sensory errors during vocal gestures (song syllables) produced in particular sequences. As hypothesized, error-corrective learning on pitch-shifted vocal gestures generalized to the same gestures produced in other sequential contexts. Surprisingly, generalization magnitude depended strongly on sequential distance from the pitch-shifted syllables, with greater adaptation for gestures produced near to the pitch-shifted syllable. A further unexpected result was that nonshifted syllables changed their pitch in the direction opposite from the shifted syllables. This apparently antiadaptive pattern of generalization could not be explained by correlations between generalization and the acoustic similarity to the pitch-shifted syllable. These findings therefore suggest that generalization depends on the type of vocal gesture and its sequential context relative to other gestures and may reflect an advantageous strategy for vocal learning and maintenance. PMID:24741046

  10. Vocal generalization depends on gesture identity and sequence.

    PubMed

    Hoffmann, Lukas A; Sober, Samuel J

    2014-04-16

    Generalization, the brain's ability to transfer motor learning from one context to another, occurs in a wide range of complex behaviors. However, the rules of generalization in vocal behavior are poorly understood, and it is unknown how vocal learning generalizes across an animal's entire repertoire of natural vocalizations and sequences. Here, we asked whether generalization occurs in a nonhuman vocal learner and quantified its properties. We hypothesized that adaptive error correction of a vocal gesture produced in one sequence would generalize to the same gesture produced in other sequences. To test our hypothesis, we manipulated the fundamental frequency (pitch) of auditory feedback in Bengalese finches (Lonchura striata var. domestica) to create sensory errors during vocal gestures (song syllables) produced in particular sequences. As hypothesized, error-corrective learning on pitch-shifted vocal gestures generalized to the same gestures produced in other sequential contexts. Surprisingly, generalization magnitude depended strongly on sequential distance from the pitch-shifted syllables, with greater adaptation for gestures produced near to the pitch-shifted syllable. A further unexpected result was that nonshifted syllables changed their pitch in the direction opposite from the shifted syllables. This apparently antiadaptive pattern of generalization could not be explained by correlations between generalization and the acoustic similarity to the pitch-shifted syllable. These findings therefore suggest that generalization depends on the type of vocal gesture and its sequential context relative to other gestures and may reflect an advantageous strategy for vocal learning and maintenance.

  11. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

    PubMed

    Muhire, Brejnev Muhizi; Varsani, Arvind; Martin, Darren Patrick

    2014-01-01

    The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).

  12. New complete mitochondrial DNA sequence of the lancelet Branchiostoma lanceolatum (Cephalochordata) and the identity of this species' sequences.

    PubMed

    Nohara, Masahiro; Nishida, Mutsumi; Nishikawa, Teruaki

    2005-06-01

    Three mitochondrial (mt) genes were sequenced for two Atlantic lancelet species, Branchiostoma lanceolatum and B. floridae, to examine a serious discrepancy among previously published results of molecular studies: substantial sequence difference in a nuclear gene vs. virtual identity in the mt genome sequence. The results revealed that three mt genes of B. lanceolatum, collected from Helgoland in the North Sea and Naples in the Mediterranean, were quite diverged from those of B. floridae, collected from Tampa Bay, Florida. Therefore, the previously recognized identity in the mt genome between the two species is attributable to misidentification of materials used. To correct this misleading information, the complete mtDNA sequence of B. lanceolatum was determined for an individual from Helgoland.

  13. Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences.

    PubMed

    Wambugu, Peterson W; Brozynska, Marta; Furtado, Agnelo; Waters, Daniel L; Henry, Robert J

    2015-09-10

    Rice is the most important crop in the world, acting as the staple food for over half of the world's population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.

  14. Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences

    PubMed Central

    Wambugu, Peterson W.; Brozynska, Marta; Furtado, Agnelo; Waters, Daniel L.; Henry, Robert J.

    2015-01-01

    Rice is the most important crop in the world, acting as the staple food for over half of the world’s population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation. PMID:26355750

  15. Identical ribosomal DNA sequence data from Pfiesteria piscicida (Dinophyceae) isolates with different toxicity phenotypes.

    PubMed

    Tengs, Torstein; Bowers, Holly A; Glasgow, Howard B; Burkholder, JoAnn M; Oldach, David W

    2003-09-01

    Complete small subunit ribosomal RNA, internal transcribed spacer 1 and 2, 5.8S, and partial large subunit ribosomal RNA gene sequences were generated from multiple isolates of Pfiesteria piscicida. Sequences were derived from isolates that have been shown to be ichthyotoxic as well as isolates that have no history of toxic behavior. All of the sequences generated were identical for the different cultures, and we therefore conclude that differences in toxicity seen between isolates of P. piscicida are linked to factors other than genetic strain variation detectable by ribosomal gene sequence analyses.

  16. Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir

    PubMed Central

    Sobolewski, Michele D.; Keele, Brandon F.; Spindler, Jonathan; Wiegand, Ann; Shao, Wei; Hughes, Stephen H.; Coffin, John M.; Kearney, Mary F.; Mellors, John W.

    2017-01-01

    The major obstacle to curing HIV infection is the persistence of cells with intact proviruses that can produce replication-competent virus. This HIV reservoir is believed to exist primarily in CD4+ T-cells and is stable despite years of suppressive antiretroviral therapy. A potential mechanism for HIV persistence is clonal expansion of infected cells, but how often such clones carry replication-competent proviruses has been controversial. Here, we used single-genome sequencing to probe for identical HIV sequence matches among viruses recovered in different viral outgrowth cultures and between the sequences of outgrowth viruses and proviral or intracellular HIV RNA sequences in uncultured blood mononuclear cells from eight donors on suppressive ART with diverse proviral populations. All eight donors had viral outgrowth virus that was fully susceptible to their current ART drug regimen. Six of eight donors studied had identical near full-length HIV RNA sequences recovered from different viral outgrowth cultures, and one of the two remaining donors had identical partial viral sequence matches between outgrowth virus and intracellular HIV RNA. These findings provide evidence that clonal expansion of HIV-infected cells is an important mechanism of reservoir persistence that should be targeted to cure HIV infection. PMID:28328934

  17. Proviruses with identical sequences comprise a large fraction of the replication-competent HIV reservoir.

    PubMed

    Bui, John K; Sobolewski, Michele D; Keele, Brandon F; Spindler, Jonathan; Musick, Andrew; Wiegand, Ann; Luke, Brian T; Shao, Wei; Hughes, Stephen H; Coffin, John M; Kearney, Mary F; Mellors, John W

    2017-03-01

    The major obstacle to curing HIV infection is the persistence of cells with intact proviruses that can produce replication-competent virus. This HIV reservoir is believed to exist primarily in CD4+ T-cells and is stable despite years of suppressive antiretroviral therapy. A potential mechanism for HIV persistence is clonal expansion of infected cells, but how often such clones carry replication-competent proviruses has been controversial. Here, we used single-genome sequencing to probe for identical HIV sequence matches among viruses recovered in different viral outgrowth cultures and between the sequences of outgrowth viruses and proviral or intracellular HIV RNA sequences in uncultured blood mononuclear cells from eight donors on suppressive ART with diverse proviral populations. All eight donors had viral outgrowth virus that was fully susceptible to their current ART drug regimen. Six of eight donors studied had identical near full-length HIV RNA sequences recovered from different viral outgrowth cultures, and one of the two remaining donors had identical partial viral sequence matches between outgrowth virus and intracellular HIV RNA. These findings provide evidence that clonal expansion of HIV-infected cells is an important mechanism of reservoir persistence that should be targeted to cure HIV infection.

  18. Identical genotype B3 sequences from measles patients in 4 countries, 2005.

    PubMed

    Rota, Jennifer; Lowe, Luis; Rota, Paul; Bellini, William; Redd, Susan; Dayan, Gustavo; van Binnendijk, Rob; Hahné, Susan; Tipples, Graham; Macey, Jeannette; Espinoza, Rita; Posey, Drew; Plummer, Andrew; Bateman, John; Gudiño, José; Cruz-Ramirez, Edith; Lopez-Martinez, Irma; Anaya-Lopez, Luis; Holy Akwar, Teneg; Giffin, Scott; Carrión, Verónica; de Filippis, Ana Maria Bispo; Vicari, Andrea; Tan, Christina; Wolf, Bruce; Wytovich, Katherine; Borus, Peter; Mbugua, Francis; Chege, Paul; Kombich, Janeth; Akoua-Koffi, Chantal; Smit, Sheilagh; Bukenya, Henry; Bwogi, Josephine; Baliraine, Frederick Ndhoga; Kremer, Jacques; Muller, Claude; Santibanez, Sabine

    2006-11-01

    Surveillance of measles virus detected an epidemiologic link between a refugee from Kenya and a Dutch tourist in New Jersey, USA. Identical genotype B3 sequences from patients with contemporaneous cases in the United States, Canada, and Mexico in November and December 2005 indicate that Kenya was likely to have been the common source of virus.

  19. Sequences of Citrus tristeza virus separated in time and space are essentially identical.

    PubMed

    Albiach-Martí, M R; Mawassi, M; Gowda, S; Satyanarayana, T; Hilf, M E; Shanker, S; Almira, E C; Vives, M C; López, C; Guerri, J; Flores, R; Moreno, P; Garnsey, S M; Dawson, W O

    2000-08-01

    The first Citrus tristeza virus (CTV) genomes completely sequenced (19.3-kb positive-sense RNA), from four biologically distinct isolates, are unexpectedly divergent in nucleotide sequence (up to 60% divergence). Understanding of whether these large sequence differences resulted from recent evolution is important for the design of disease management strategies, particularly the use of genetically engineered mild (essentially symptomless)-strain cross protection and RNA-mediated transgenic resistance. The complete sequence of a mild isolate (T30) which has been endemic in Florida for about a century was found to be nearly identical to the genomic sequence of a mild isolate (T385) from Spain. Moreover, samples of sequences of other isolates from distinct geographic locations, maintained in different citrus hosts and also separated in time (B252 from Taiwan, B272 from Colombia, and B354 from California), were nearly identical to the T30 sequence. The sequence differences between these isolates were within or near the range of variability of the T30 population. A possible explanation for these results is that the parents of isolates T30, T385, B252, B272, and B354 have a common origin, probably Asia, and have changed little since they were dispersed throughout the world by the movement of citrus. Considering that the nucleotide divergence among the other known CTV genomes is much greater than those expected for strains of the same virus, the remarkable similarity of these five isolates indicates a high degree of evolutionary stasis in some CTV populations.

  20. The amino acid sequence of protein AA from a burro (Equus asinus).

    PubMed

    Sletten, Knut; Johnson, Kenneth H; Westermark, Per

    2003-09-01

    The primary structure of amyloid fibril protein AA of a burro has been determined by Edman degradation. The 80 amino acid residue long protein shows strong resemblance to that of other mammalian AA-proteins and differs from equine protein AA at 5 positions: Burro/horse positions 20 (Q/N), 44 (R,Q, K/K,Q), 59 (G,L/G,A), 61 (Q/E) and 65 (N/R).

  1. Large distribution and high sequence identity of a Copia-type retrotransposon in angiosperm families.

    PubMed

    Dias, Elaine Silva; Hatt, Clémence; Hamon, Serge; Hamon, Perla; Rigoreau, Michel; Crouzillat, Dominique; Carareto, Claudia Marcia Aparecida; de Kochko, Alexandre; Guyot, Romain

    2015-09-01

    Retrotransposons are the main component of plant genomes. Recent studies have revealed the complexity of their evolutionary dynamics. Here, we have identified Copia25 in Coffea canephora, a new plant retrotransposon belonging to the Ty1-Copia superfamily. In the Coffea genomes analyzed, Copia25 is present in relatively low copy numbers and transcribed. Similarity sequence searches and PCR analyses show that this retrotransposon with LTRs (Long Terminal Repeats) is widely distributed among the Rubiaceae family and that it is also present in other distantly related species belonging to Asterids, Rosids and monocots. A particular situation is the high sequence identity found between the Copia25 sequences of Musa, a monocot, and Ixora, a dicot species (Rubiaceae). Our results reveal the complexity of the evolutionary dynamics of the ancient element Copia25 in angiosperm, involving several processes including sequence conservation, rapid turnover, stochastic losses and horizontal transfer.

  2. Folding pathways of proteins with increasing degree of sequence identities but different structure and function.

    PubMed

    Giri, Rajanish; Morrone, Angela; Travaglini-Allocatelli, Carlo; Jemth, Per; Brunori, Maurizio; Gianni, Stefano

    2012-10-30

    Much experimental work has been devoted in comparing the folding behavior of proteins sharing the same fold but different sequence. The recent design of proteins displaying very high sequence identities but different 3D structure allows the unique opportunity to address the protein-folding problem from a complementary perspective. Here we explored by Φ-value analysis the pathways of folding of three different heteromorphic pairs, displaying increasingly high-sequence identity (namely, 30%, 77%, and 88%), but different structures called G(A) (a 3-α helix fold) and G(B) (an α/β fold). The analysis, based on 132 site-directed mutants, is fully consistent with the idea that protein topology is committed very early along the pathway of folding. Furthermore, data reveals that when folding approaches a perfect two-state scenario, as in the case of the G(A) domains, the structural features of the transition state appear very robust to changes in sequence composition. On the other hand, when folding is more complex and multistate, as for the G(B)s, there are alternative nuclei or accessible pathways that can be alternatively stabilized by altering the primary structure. The implications of our results in the light of previous work on the folding of different members belonging to the same protein family are discussed.

  3. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments.

    PubMed

    Short, Cindy M; Suttle, Curtis A

    2005-01-01

    Primers were designed to amplify a 592-bp region within a conserved structural gene (g20) found in some cyanophages. The goal was to use this gene as a proxy to infer genetic richness in natural cyanophage communities and to determine if sequences were more similar in similar environments. Gene products were amplified from samples from the Gulf of Mexico, the Arctic, Southern, and Northeast and Southeast Pacific Oceans, an Arctic cyanobacterial mat, a catfish production pond, lakes in Canada and Germany, and a depth of ca. 3,246 m in the Chuckchi Sea. Amplicons were separated by denaturing gradient gel electrophoresis, and selected bands were sequenced. Phylogenetic analysis revealed four previously unknown groups of g20 clusters, two of which were entirely found in freshwater. Also, sequences with >99% identities were recovered from environments that differed greatly in temperature and salinity. For example, nearly identical sequences were recovered from the Gulf of Mexico, the Southern Pacific Ocean, an Arctic freshwater cyanobacterial mat, and Lake Constance, Germany. These results imply that closely related hosts and the viruses infecting them are distributed widely across environments or that horizontal gene exchange occurs among phage communities from very different environments. Moreover, the amplification of g20 products from deep in the cyanobacterium-sparse Chuckchi Sea suggests that this primer set targets bacteriophages other than those infecting cyanobacteria.

  4. Sequences encoding identical peptides for the analysis and manipulation of coding DNA

    PubMed Central

    Sánchez, Joaquín

    2013-01-01

    The use of sequences encoding identical peptides (SEIP) for the in silico analysis of coding DNA from different species has not been reported; the study of such sequences could directly reveal properties of coding DNA that are independent of peptide sequences. For practical purposes SEIP might also be manipulated for e.g. heterologous protein expression. We extracted 1,551 SEIP from human and E. coli and 2,631 SEIP from human and D. melanogaster. We then analyzed codon usage and intercodon dinucleotide tendencies and found differences in both, with more conspicuous disparities between human and E. coli than between human and D. melanogaster. We also briefly manipulated SEIP to find out if they could be used to create new coding sequences. We hence attempted replacement of human by E. coli codons via dicodon exchange but found that full replacement was not possible, this indicated robust species-specific dicodon tendencies. To test another form of codon replacement we isolated SEIP from human and the jellyfish green fluorescent protein (GFP) and we then re-constructed the GFP coding DNA with human tetra-peptide-coding sequences. Results provide proof-of-principle that SEIP may be used to reveal differences in the properties of coding DNA and to reconstruct in pieces a protein coding DNA with sequences from a different organism, the latter might be exploited in heterologous protein expression. PMID:23861567

  5. Sequences encoding identical peptides for the analysis and manipulation of coding DNA.

    PubMed

    Sánchez, Joaquín

    2013-01-01

    The use of sequences encoding identical peptides (SEIP) for the in silico analysis of coding DNA from different species has not been reported; the study of such sequences could directly reveal properties of coding DNA that are independent of peptide sequences. For practical purposes SEIP might also be manipulated for e.g. heterologous protein expression. We extracted 1,551 SEIP from human and E. coli and 2,631 SEIP from human and D. melanogaster. We then analyzed codon usage and intercodon dinucleotide tendencies and found differences in both, with more conspicuous disparities between human and E. coli than between human and D. melanogaster. We also briefly manipulated SEIP to find out if they could be used to create new coding sequences. We hence attempted replacement of human by E. coli codons via dicodon exchange but found that full replacement was not possible, this indicated robust species-specific dicodon tendencies. To test another form of codon replacement we isolated SEIP from human and the jellyfish green fluorescent protein (GFP) and we then re-constructed the GFP coding DNA with human tetra-peptide-coding sequences. Results provide proof-of-principle that SEIP may be used to reveal differences in the properties of coding DNA and to reconstruct in pieces a protein coding DNA with sequences from a different organism, the latter might be exploited in heterologous protein expression.

  6. Parameters of the proteome evolution from the distribution of sequence identities of paralogous proteins

    NASA Astrophysics Data System (ADS)

    Yan, Koon-Kiu; Axelsen, Jacob; Maslov, Sergei

    2006-03-01

    The evolution of the full repertoire of proteins encoded in a given genome is driven by gene duplications, deletions and modifications of amino-acid sequences of already existing proteins. The information about relative rates and other intrinsic parameters of these three basic processes is contained in the distribution of sequence identities of pairs of paralogous proteins. We introduced a simple mathematical framework that allows one to extract some of this hidden information. It was then applied to the proteome-wide set of paralogous proteins in H. pylori, E. coli, S. cerevisiae, C. elegans, D. melanogaster and H. sapiens. We estimated the stationary per-gene deletion and duplication rates, the distribution of amino-acid substitution rate of these organisms. The validity of our mathematical framework was further confirmed by numerical simulations of a simple evolutionary model of a fixed-size proteome.

  7. [Expression of mosquitocidal Cyt1Aa toxin from Bacillus thuringiensis subsp. israelensis in Asticcacaulis excentricus].

    PubMed

    Zheng, Da-sheng; Crickmore, Neil; Cai, Ya-jun; Yan, Jian-ping; Yuan, Zhi-ming

    2007-04-01

    Asticcacaulis excentricus, who lives in upper-layer waters providing food resource to the mosquito larvae and has been proven to be a successful host to produce the mosquitocidal binary toxins or Cry11Aa toxin from Bacilli (Liu et al., 1996, Nat Biotech 14: 343; Armengol, et al. , 2005, Curr Microbiol 51: 430), was developed to express cyt1Aa gene from Bacillus thuringiensis subsp. israelensis (Bti). Two A. excentricus transformants were constructed with the attempt of producing CytlAa alone and alongside with Cry11Aa, repectively. Detection of expressed Cry11Aa and CytlAa proteins by immunoblot in the recombinant A. excentricus clones showed that either cry11Aa or cyt1Aa was expressed well solely but not simultaneously although both restriction analyses of plasmid DNA and DNA sequencing showed that the transformed plasmid was identical to scheme. To investigate the reason why the recombinant A. excentricus harboring both genes and their ribosome binding site (RBS) sequences expressed only Cry11Aa, the total RNA of A. excentricus cells was extracted and revealed three-band pattern in which all RNA molecule weights are not greater than 16S RNA of Escherichia coli by formamide agarose gel electrophoresis, indicating that different RNA systems within these two Gram-negative strains required distinguishingly organised constructs to express multiple foreign genes. It is hypothesized that an extra promoter upstream of RBS sequence is required to express cyt1Aa in the cry11Aa-cyt1Aa tandom plasmid.

  8. Subdomain interactions foster the design of two protein pairs with ∼80% sequence identity but different folds.

    PubMed

    Porter, Lauren L; He, Yanan; Chen, Yihong; Orban, John; Bryan, Philip N

    2015-01-06

    Metamorphic proteins, including proteins with high levels of sequence identity but different folds, are exceptions to the long-standing rule-of-thumb that proteins with as little as 30% sequence identity adopt the same fold. Which topologies can be bridged by these highly identical sequences remains an open question. Here we bridge two 3-α-helix bundle proteins with two radically different folds. Using a straightforward approach, we engineered the sequences of one subdomain within maltose binding protein (MBP, α/β/α-sandwich) and another within outer surface protein A (OspA, β-sheet) to have high sequence identity (80 and 77%, respectively) with engineered variants of protein G (GA, 3-α-helix bundle). Circular dichroism and nuclear magnetic resonance spectra of all engineered variants demonstrate that they maintain their native conformations despite substantial sequence modification. Furthermore, the MBP variant (80% identical to GA) remained active. Thermodynamic analysis of numerous GA and MBP variants suggests that the key to our approach involved stabilizing the modified MBP and OspA subdomains via external interactions with neighboring substructures, indicating that subdomain interactions can stabilize alternative folds over a broad range of sequence variation. These findings suggest that it is possible to bridge one fold with many other topologies, which has implications for protein folding, evolution, and misfolding diseases.

  9. A SNP panel for identity and kinship testing using massive parallel sequencing.

    PubMed

    Grandell, Ida; Samara, Raed; Tillmar, Andreas O

    2016-07-01

    Within forensic genetics, there is still a need for supplementary DNA marker typing in order to increase the power to solve cases for both identity testing and complex kinship issues. One major disadvantage with current capillary electrophoresis (CE) methods is the limitation in DNA marker multiplex capability. By utilizing massive parallel sequencing (MPS) technology, this capability can, however, be increased. We have designed a customized GeneRead DNASeq SNP panel (Qiagen) of 140 previously published autosomal forensically relevant identity SNPs for analysis using MPS. One single amplification step was followed by library preparation using the GeneRead Library Prep workflow (Qiagen). The sequencing was performed on a MiSeq System (Illumina), and the bioinformatic analyses were done using the software Biomedical Genomics Workbench (CLC Bio, Qiagen). Forty-nine individuals from a Swedish population were genotyped in order to establish genotype frequencies and to evaluate the performance of the assay. The analyses showed to have a balanced coverage among the included loci, and the heterozygous balance showed to have less than 0.5 % outliers. Analyses of dilution series of the 2800M Control DNA gave reproducible results down to 0.2 ng DNA input. In addition, typing of FTA samples and bone samples was performed with promising results. Further studies and optimizations are, however, required for a more detailed evaluation of the performance of degraded and PCR-inhibited forensic samples. In summary, the assay offers a straightforward sample-to-genotype workflow and could be useful to gain information in forensic casework, for both identity testing and in order to solve complex kinship issues.

  10. Sequence comparisons of A/AA/6/60 influenza viruses: mutations which may contribute to attenuation.

    PubMed

    Herlocher, M L; Clavo, A C; Maassab, H F

    1996-06-01

    Influenza virus infection is a worldwide public health threat. Cold-adaptation was used to develop a vaccine line (ca A/AA/6/60 H2N2) which promised to reduce the morbidity and mortality associated with influenza and to serve as a model for other live virus vaccines. This study establishes that two distinct lines of wt A/AA/6/60 viruses exist with different phenotypic and genotypic characteristics. The two virus lines have the same parent but different passage histories. The first line is both temperature sensitive (ts) and attenuated in ferrets and the second line (after multiple passages in chick kidney cells, eggs and mice) is non-ts and virulent in ferrets. Both lines of viruses have been further differentiated by sequence analysis. We have identified point mutations common to all virulent viruses but absent from the attenuated viruses. This was accomplished by comparing the nucleotide sequences of the six internal genes in three different attenuated passages of A/AA/6/60 with those of five different virulent passages of the same virus. The corresponding nucleotides of the attenuated viruses, therefore, represent candidate attenuating lesions: 6 in the basic polymerase genes (5 in PB1, 1 in PB2), 2 in the acidic polymerase gene (PA), 1 in the matrix (M) gene, 2 in the non-structural (NS) gene, and none in the nucleoprotein (NP) gene. Two of the 5 attenuating lesions in PB1 are silent; 1/2 in PA is silent; and 1/2 in NS is silent. Further changes which might be identified by comparing nucleotide and amino acid sequences of the A/AA/6/60 viruses with those of other influenza viruses may also contribute to the attenuation of the ca virus. Our study identifies nucleotides which more precisely define virulence for this virus and suggests that growth of the virus at low temperature may have preserved a non-virulent virus population rather than attenuating a virulent one.

  11. Monoclonal antibodies raised against 167-180 aa sequence of human carbonic anhydrase XII inhibit its enzymatic activity.

    PubMed

    Dekaminaviciute, Dovile; Kairys, Visvaldas; Zilnyte, Milda; Petrikaite, Vilma; Jogaite, Vaida; Matuliene, Jurgita; Gudleviciene, Zivile; Vullo, Daniela; Supuran, Claudiu T; Zvirbliene, Aurelija

    2014-12-01

    Abstract Human carbonic anhydrase XII (CA XII) is a single-pass transmembrane protein with an extracellular catalytic domain. This enzyme is being recognized as a potential biomarker for different tumours. The current study was aimed to generate monoclonal antibodies (MAbs) neutralizing the enzymatic activity of CA XII. Bioinformatics analysis of CA XII structure revealed surface-exposed sequences located in a proximity of its catalytic centre. Two MAbs against the selected antigenic peptide spanning 167-180 aa sequence of CA XII were generated. The MAbs were reactive with recombinant catalytic domain of CA XII expressed either in E. coli or mammalian cells. Inhibitory activity of the MAbs was demonstrated by a stopped flow CO2 hydration assay. The study provides new data on the surface-exposed linear CA XII epitope that may serve as a target for inhibitory antibodies with a potential immunotherapeutic application.

  12. Comparative genomic analysis of equilibrative nucleoside transporters suggests conserved protein structure despite limited sequence identity.

    PubMed

    Sankar, Narendra; Machado, Jerry; Abdulla, Parween; Hilliker, Arthur J; Coe, Imogen R

    2002-10-15

    Equilibrative nucleoside transporters (ENTs) are a recently characterized and poorly understood group of membrane proteins that are important in the uptake of endogenous nucleosides required for nucleic acid and nucleoside triphosphate synthesis. Despite their central importance in cellular metabolism and nucleoside analog chemotherapy, no human ENT gene has been described and nothing is known about gene structure and function. To gain insight into the ENT gene family, we used experimental and in silico comparative genomic approaches to identify ENT genes in three evolutionarily diverse organisms with completely (or almost completely) sequenced genomes, Homo sapiens, Caenorhabditis elegans and Drosophila melanogaster. We describe the chromosomal location, the predicted ENT gene structure and putative structural topologies of predicted ENT proteins derived from the open reading frames. Despite variations in genomic layout and limited ortholog protein sequence identity (< or =27.45%), predicted topologies of ENT proteins are strikingly similar, suggesting an evolutionary conservation of a prototypic structure. In addition, a similar distribution of protein domains on exons is apparent in all three taxa. These data demonstrate that comparative sequence analyses should be combined with other approaches (such as genomic and proteomic analyses) to fully understand structure, function and evolution of protein families.

  13. Isolation and partial sequence of the A-protein gene of Thermus thermophilus cytochrome c/sub 1/aa/sub 3/

    SciTech Connect

    Fee, J.A.; Mather, M.W.; Springer, P.; Hensel, S.; Buse, G.

    1988-01-01

    Thermus thermophilus is a strictly aerobic eubacterium which grows optimally near 70/degree/C. Its respiratory system is very similar to that of eukaryotic mitochondria, and the organism has proven to be a particularly good source of stable, comparatively simple respiratory enzymes. There are at least two terminal oxidases: The recently discovered cytochrome ba/sub 3//sup 3/ and cytochrome c/sub 1/aa/sub 3//sup 2/. Cytochrome ba/sub 3/ is analog of aa/sub 3/ in which the heme A of cytochrome a is replaced with protoporphyrin IX (heme B) while its order redox components appear to be largely identical to those of the now classical mammalian cytochrome aa/sub 3/; it has only a single 35 kD protein subunit. Cytochrome c/sub 1/aa/sub 3/ consists of two polypeptides. The /approximately/33 kD C-protein covalently binds one heme C, while the /approximately/55 kD protein is thought to bind the four canonical redox centers of aa/sub 3/, two heme A, and two Cu. Toward our goal of unequivocally establishing the distribution of the metal centers in cytochrome c/sub 1/aa/sub 3/, we have isolated the structural gene of the A-protein. 20 refs., 4 figs.

  14. Influence of sequence identity and unique breakpoints on the frequency of intersubtype HIV-1 recombination

    PubMed Central

    Baird, Heather A; Gao, Yong; Galetto, Román; Lalonde, Matthew; Anthony, Reshma M; Giacomoni, Véronique; Abreha, Measho; Destefano, Jeffrey J; Negroni, Matteo; Arts, Eric J

    2006-01-01

    Background HIV-1 recombination between different subtypes has a major impact on the global epidemic. The generation of these intersubtype recombinants follows a defined set of events starting with dual infection of a host cell, heterodiploid virus production, strand transfers during reverse transcription, and then selection. In this study, recombination frequencies were measured in the C1-C4 regions of the envelope gene in the presence (using a multiple cycle infection system) and absence (in vitro reverse transcription and single cycle infection systems) of selection for replication-competent virus. Ugandan subtypes A and D HIV-1 env sequences (115-A, 120-A, 89-D, 122-D, 126-D) were employed in all three assay systems. These subtypes co-circulate in East Africa and frequently recombine in this human population. Results Increased sequence identity between viruses or RNA templates resulted in increased recombination frequencies, with the exception of the 115-A virus or RNA template. Analyses of the recombination breakpoints and mechanistic studies revealed that the presence of a recombination hotspot in the C3/V4 env region, unique to 115-A as donor RNA, could account for the higher recombination frequencies with the 115-A virus/template. Single-cycle infections supported proportionally less recombination than the in vitro reverse transcription assay but both systems still had significantly higher recombination frequencies than observed in the multiple-cycle virus replication system. In the multiple cycle assay, increased replicative fitness of one HIV-1 over the other in a dual infection dramatically decreased recombination frequencies. Conclusion Sequence variation at specific sites between HIV-1 isolates can introduce unique recombination hotspots, which increase recombination frequencies and skew the general observation that decreased HIV-1 sequence identity reduces recombination rates. These findings also suggest that the majority of intra- or intersubtype A

  15. Distinctive properties of identical twins' TCR repertoires revealed by high-throughput sequencing.

    PubMed

    Zvyagin, Ivan V; Pogorelyy, Mikhail V; Ivanova, Marina E; Komech, Ekaterina A; Shugay, Mikhail; Bolotin, Dmitry A; Shelenkov, Andrey A; Kurnosov, Alexey A; Staroverov, Dmitriy B; Chudakov, Dmitriy M; Lebedev, Yuri B; Mamedov, Ilgar Z

    2014-04-22

    Adaptive immunity in humans is provided by hypervariable Ig-like molecules on the surface of B and T cells. The final set of these molecules in each organism is formed under the influence of two forces: individual genetic traits and the environment, which includes the diverse spectra of alien and self-antigens. Here we assess the impact of individual genetic factors on the formation of the adaptive immunity by analyzing the T-cell receptor (TCR) repertoires of three pairs of monozygous twins by next-generation sequencing. Surprisingly, we found that an overlap between the TCR repertoires of monozygous twins is similar to an overlap between the TCR repertoires of nonrelated individuals. However, the number of identical complementary determining region 3 sequences in two individuals is significantly increased for twin pairs in the fraction of highly abundant TCR molecules, which is enriched by the antigen-experienced T cells. We found that the initial recruitment of particular TCR V genes for recombination and subsequent selection in the thymus is strictly determined by individual genetic factors. J genes of TCRs are selected randomly for recombination; however, the subsequent selection in the thymus gives preference to some α but not β J segments. These findings provide a deeper insight into the mechanism of TCR repertoire generation.

  16. Romidepsin-induced HIV-1 viremia during effective antiretroviral therapy contains identical viral sequences with few deleterious mutations

    PubMed Central

    Winckelmann, Anni; Barton, Kirston; Hiener, Bonnie; Schlub, Timothy E.; Shao, Wei; Rasmussen, Thomas A.; Østergaard, Lars; Søgaard, Ole S.; Tolstrup, Martin; Palmer, Sarah

    2017-01-01

    Objective: To investigate the origin of the HIV-1 viremia induced by the latency-reversing agent romidepsin. Design: Six individuals on suppressive antiretroviral therapy received romidepsin administered intravenously once weekly for 3 consecutive weeks. CD4+ T cells were obtained at baseline, following the second and third romidepsin infusion, and 10 weeks after the final romidepsin treatment. Plasma samples were collected 24 and 72 h after romidepsin infusions. Methods: Single-genome sequencing of the env and p24-RT region was used to genetically characterize the virus from proviral DNA, the transcribed cell-associated RNA and the plasma RNA pool. Results: In three of six participants with available plasma samples we identified plasma HIV-1 RNA sequences that were identical to DNA and/or cell-associated RNA sequences from peripheral blood CD4+ T cells. In two participants, plasma RNA sequences contained expansions of identical sequences, corresponding to 62 and 100% of the total sequences, respectively. Plasma HIV-1 RNA had very low amounts of defective viruses compared to cell-associated RNA (odds ratio 20.85, P < 0.001) and to DNA (odds ratio 7.07, P = 0.011) during romidepsin therapy. Conclusions: Romidepsin induced transcription from proviruses in peripheral blood cells, which contributed to viremia in patients on suppressive therapy. The intermingling of these cell-associated HIV-1 RNA with DNA sequences indicates transcription from a diverse range of proviruses, but the expansions of identical viral plasma sequences with few defects indicate that the romidepsin-induced viremia arises from intact proviruses with highly similar or identical genetic backgrounds. PMID:28272134

  17. NGSCheckMate: software for validating sample identity in next-generation sequencing studies within and across data types.

    PubMed

    Lee, Sejoon; Lee, Soohyun; Ouellette, Scott; Park, Woong-Yang; Lee, Eunjung A; Park, Peter J

    2017-03-23

    In many next-generation sequencing (NGS) studies, multiple samples or data types are profiled for each individual. An important quality control (QC) step in these studies is to ensure that datasets from the same subject are properly paired. Given the heterogeneity of data types, file types and sequencing depths in a multi-dimensional study, a robust program that provides a standardized metric for genotype comparisons would be useful. Here, we describe NGSCheckMate, a user-friendly software package for verifying sample identities from FASTQ, BAM or VCF files. This tool uses a model-based method to compare allele read fractions at known single-nucleotide polymorphisms, considering depth-dependent behavior of similarity metrics for identical and unrelated samples. Our evaluation shows that NGSCheckMate is effective for a variety of data types, including exome sequencing, whole-genome sequencing, RNA-seq, ChIP-seq, targeted sequencing and single-cell whole-genome sequencing, with a minimal requirement for sequencing depth (>0.5X). An alignment-free module can be run directly on FASTQ files for a quick initial check. We recommend using this software as a QC step in NGS studies.

  18. Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome.

    PubMed

    Krawitz, Peter M; Schweiger, Michal R; Rödelsperger, Christian; Marcelis, Carlo; Kölsch, Uwe; Meisel, Christian; Stephani, Friederike; Kinoshita, Taroh; Murakami, Yoshiko; Bauer, Sebastian; Isau, Melanie; Fischer, Axel; Dahl, Andreas; Kerick, Martin; Hecht, Jochen; Köhler, Sebastian; Jäger, Marten; Grünhagen, Johannes; de Condor, Birgit Jonske; Doelken, Sandra; Brunner, Han G; Meinecke, Peter; Passarge, Eberhard; Thompson, Miles D; Cole, David E; Horn, Denise; Roscioli, Tony; Mundlos, Stefan; Robinson, Peter N

    2010-10-01

    Hyperphosphatasia mental retardation (HPMR) syndrome is an autosomal recessive form of mental retardation with distinct facial features and elevated serum alkaline phosphatase. We performed whole-exome sequencing in three siblings of a nonconsanguineous union with HPMR and performed computational inference of regions identical by descent in all siblings to establish PIGV, encoding a member of the GPI-anchor biosynthesis pathway, as the gene mutated in HPMR. We identified homozygous or compound heterozygous mutations in PIGV in three additional families.

  19. Selection of target sequences as well as sequence identity determine the outcome of RNAi approach for resistance against cotton leaf curl geminivirus complex

    PubMed Central

    2011-01-01

    Cotton leaf curl disease is caused by a geminivirus complex that involves multiple distinct begomoviruses and a disease-specific DNA satellite, cotton leaf curl Multan betasatellite (CLCuMB), which is essential to induce disease symptoms. Here we have investigated the use of RNA interference (RNAi) for obtaining resistance against one of the viruses, Cotton leaf curl Multan virus (CLCuMV), associated with the disease. Three hairpin RNAi constructs were produced containing either complementary-sense genes essential for replication/pathogenicity or non-coding regulatory sequences of CLCuMV. In transient assays all three RNAi constructs significantly reduced the replication of the virus in inoculated tissues. However, only one of the constructs, that targeting the overlapping genes involved in virus replication and pathogenicity (the replication-associated protein (Rep), the transcriptional activator protein and the replication enhancer protein) was able to prevent systemic movement of the virus, although the other constructs significantly reduced the levels of virus in systemic tissues. In the presence of CLCuMB, however, a small number of plants co-inoculated with even the most efficient RNAi construct developed symptoms of virus infection, suggesting that the betasatellite may compromise resistance. Further analyses, using Rep gene sequences of distinct begomoviruses expressed from a PVX vector as the target, are consistent with the idea that the success of the RNAi approach depends on sequence identity to the target virus. The results show that selection of both the target sequence, as well as the levels of identity between the construct and target sequence, determine the outcome of RNAi-based resistance against geminivirus complexes. PMID:21410988

  20. Protein identities from 'Graphocephala atropunctata' expressed sequence tags: Expanding leafhopper vector biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Heat shock proteins and 44 protein sequences from the blue-green sharpshooter, BGSS, were produced and identified. The sequences were submitted and published under accession numbers: DQ445499-DQ445542, in the National Center for Biotechnology Information, NCBI, Public Database. The blue-green sharps...

  1. A protective protein antigen of Rickettsia rickettsii has tandemly repeated, near-identical sequences.

    PubMed Central

    Anderson, B E; McDonald, G A; Jones, D C; Regnery, R L

    1990-01-01

    The nucleotide sequence of a Rickettsia rickettsii gene that encodes a high-molecular-mass surface antigen (190 kilodaltons), which elicits protective immunity, was determined. The 6,747-nucleotide gene coded for a 2,249-amino-acid protein with a calculated molecular weight of 224,321. A 3.8-kilobase PstI fragment proximal to the 5' end of the gene was found to consist of 13 highly related tandem repeats which constituted over 40% of the coding region. The repeated sequences could be divided into either a 225-nucleotide, 75-amino-acid unit (type I) or a 216-nucleotide, 72-amino-acid unit (type II), with extensive homology between the two types of repeating units. The deduced amino acid sequence for these repeat units, overall, was slightly hydrophobic with short hydrophilic domains. The carboxy-terminal (nonrepetitive) portion of the deduced protein sequence was hydrophilic, with potential surface-exposed epitopes. The full-length reading frame was reconstructed in Escherichia coli, and transient expression of the 190-kilodalton antigen was demonstrated; however, the protein appeared to be severely degraded by proteases and was apparently toxic to E. coli. The conservation of this unique repetitive gene structure, coupled with results from previous reports showing the protective properties of the 190-kilodalton antigen, suggests that this protein plays an important role in the pathogenesis of and immunity to Rocky Mountain spotted fever. Images PMID:2117568

  2. Fostering Research Identities in Two-Course Writing Sequences: A Curricular Perspective

    ERIC Educational Resources Information Center

    Sura, Thomas

    2015-01-01

    Two-course writing sequences are valuable because they extend the time that students spend focused on developing as writers and researchers, yet they cannot rely on a "more is better" argument to justify their ongoing implementation, especially when general education curricula are shrinking and one course often looks much the same as the…

  3. Protein identities - Graphocephala atropunctata expressed sequenced tags: expanding leafhopper vector biology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A small heat shock protein was isolated and sequenced from the Blue-green sharpshooter, BGSS, Graphocephala atropunctata (Signoret) (Hemiptera: Cicadellidae). The BGSS has been the native vector of Pierce’s disease in vineyards in California for nearly a century. The importance of this vector spec...

  4. A molecular footprint of limb loss: sequence variation of the autopodial identity gene Hoxa-13.

    PubMed

    Kohlsdorf, Tiana; Cummings, Michael P; Lynch, Vincent J; Stopper, Geffrey F; Takahashi, Kazuhiko; Wagner, Günter P

    2008-12-01

    The homeobox gene Hoxa-13 codes for a transcription factor involved in multiple functions, including body axis and hand/foot development in tetrapods. In this study we investigate whether the loss of one function (e.g., limb loss in snakes) left a molecular footprint in exon 1 of Hoxa-13 that could be associated with the release of functional constraints caused by limb loss. Fragments of the Hoxa-13 exon 1 were sequenced from 13 species and analyzed, with additional published sequences of the same region, using relative rates and likelihood-ratio tests. Five amino acid sites in exon 1 of Hoxa-13 were detected as evolving under positive selection in the stem lineage of snakes. To further investigate whether there is an association between limb loss and sequence variation in Hoxa-13, we used the random forest method on an alignment that included shark, basal fish lineages, and "eu-tetrapods" such as mammals, turtle, alligator, and birds. The random forest method approaches the problem as one of classification, where we seek to predict the presence or absence of autopodium based on amino acid variation in Hoxa-13 sequences. Different alignments tested were associated with similar error rates (18.42%). The random forest method suggested that phenotypic states (autopodium present and absent) can often be correctly predicted based on Hoxa-13 sequences. Basal, nontetrapod gnat-hostomes that never had an autopodium were consistently classified as limbless together with the snakes, while eu-tetrapods without any history of limb loss in their phylogeny were also consistently classified as having a limb. Misclassifications affected mostly lizards, which, as a group, have a history of limb loss and limb re-evolution, and the urodele and caecilian in our sample. We conclude that a molecular footprint can be detected in Hoxa-13 that is associated with the lack of an autopodium; groups with classification ambiguity (lizards) are characterized by a history of repeated limb loss

  5. Bacillus thuringiensis Cry4Aa insecticidal protein: functional importance of the intrinsic stability of the unique α4-α5 loop comprising the Pro-rich sequence.

    PubMed

    Imtong, Chompounoot; Kanchanawarin, Chalermpol; Katzenmeier, Gerd; Angsuthanasombat, Chanan

    2014-06-01

    The long loop connecting transmembrane α4 and α5 of the Bacillus thuringiensis Cry4Aa toxin possesses a unique feature with Pro-rich sequence (Pro(193)Pro(194)_Pro(196)) which was shown to be crucial for toxicity. Here, the structural role in the intrinsic stability of the Pro-rich sequence toward toxin activity was investigated. Three Val-substituted mutants (P193V, P194V and P196V) and one Phe-substituted mutant (P193F) were generated and over-expressed in Escherichia coli as inclusions at levels equal to the wild-type. Bioassays demonstrated that all mutants, particularly P193V and P193F whose inclusions were hardly soluble in carbonate buffer (pH9.0), exhibited reduced toxicity, suggesting an essential role in toxin function by the specific cyclic structure of individual Pro residues. Analysis of the 65-kDa Cry4Aa structure from 10-ns molecular dynamics (MD) simulations revealed that the α4-α5 loop is substantially stable as it showed low structural fluctuation with a 1.2-Å RMSF value. When the flexibility of the α4-α5 loop was increased through P193G, P194G and P196G substitutions, decreased toxicity was also observed for all mutants, mostly for the P193G mutant with low alkali-solubility, suggesting a functional importance of loop-rigidity attributed by individual Pro-cyclic side-chains, particularly Pro(193). Further MD simulations revealed that the most critical residue-Pro(193) for which mutations vastly affect toxin solubility and larval toxicity is in close contact with several surrounding residues, thus playing an additional role in the structural arrangement of the Cry4Aa toxin molecule. Altogether, our data signify that the intrinsic stability of the unique Cry4Aa α4-α5 loop structure comprising the Pro-rich sequence plays an important role in toxin activity.

  6. Visual identity and uncertainty in repetition blindness.

    PubMed

    Brill, Gary A; Glass, Arnold L; Rashid, Hanin; Hussey, Erika

    2008-01-01

    Repetition blindness (RB) was investigated in 6 experiments. In the first 3 experiments participants detected vowel targets in 11-letter sequences. When all letters were uppercase, detection was poorer for same (e.g., AA) than for different (e.g., AO) targets. However, when one target was uppercase and the other lowercase, RB was found only for targets visually identical except for size (e.g., Oo), not for visually different pairs (e.g., Aa). Experiment 4 found RB for visually identical versus different consonant-vowel-consonant words. Experiments 5 and 6 replicated Kanwisher's (1987) experiment in which RB was insensitive to word case but revealed these effects to be artifacts of poor recognition of 5-letter words coupled with a biased guessing strategy. Overall, these experiments found RB only at a low level of visual information processing.

  7. Prevalence and Sequence-Based Identity of Rumen Fluke in Cattle and Deer in New Caledonia

    PubMed Central

    Cauquil, Laura; Hüe, Thomas; Hurlin, Jean-Claude; Mitchell, Gillian; Searle, Kate; Skuce, Philip; Zadoks, Ruth

    2016-01-01

    An abattoir survey was performed in the French Melanesian archipelago of New Caledonia to determine the prevalence of paramphistomes in cattle and deer and to generate material for molecular typing at species and subspecies level. Prevalence in adult cattle was high at animal level (70% of 387 adult cattle) and batch level (81%). Prevalence was lower in calves at both levels (33% of 484 calves, 51% at batch level). Animals from 2 of 7 deer farms were positive for rumen fluke, with animal-level prevalence of 41.4% (29/70) and 47.1% (33/70), respectively. Using ITS-2 sequencing, 3 species of paramphistomes were identified, i.e. Calicophoron calicophorum, Fischoederius elongatus and Orthocoelium streptocoelium. All three species were detected in cattle as well as deer, suggesting the possibility of rumen fluke transmission between the two host species. Based on heterogeneity in ITS-2 sequences, the C. calicophorum population comprises two clades, both of which occur in cattle as well as deer. The results suggest two distinct routes of rumen fluke introduction into this area. This approach has wider applicability for investigations of the origin of rumen fluke infections and for the possibility of parasite transmission at the livestock-wildlife interface. PMID:27043709

  8. Prevalence and Sequence-Based Identity of Rumen Fluke in Cattle and Deer in New Caledonia.

    PubMed

    Cauquil, Laura; Hüe, Thomas; Hurlin, Jean-Claude; Mitchell, Gillian; Searle, Kate; Skuce, Philip; Zadoks, Ruth

    2016-01-01

    An abattoir survey was performed in the French Melanesian archipelago of New Caledonia to determine the prevalence of paramphistomes in cattle and deer and to generate material for molecular typing at species and subspecies level. Prevalence in adult cattle was high at animal level (70% of 387 adult cattle) and batch level (81%). Prevalence was lower in calves at both levels (33% of 484 calves, 51% at batch level). Animals from 2 of 7 deer farms were positive for rumen fluke, with animal-level prevalence of 41.4% (29/70) and 47.1% (33/70), respectively. Using ITS-2 sequencing, 3 species of paramphistomes were identified, i.e. Calicophoron calicophorum, Fischoederius elongatus and Orthocoelium streptocoelium. All three species were detected in cattle as well as deer, suggesting the possibility of rumen fluke transmission between the two host species. Based on heterogeneity in ITS-2 sequences, the C. calicophorum population comprises two clades, both of which occur in cattle as well as deer. The results suggest two distinct routes of rumen fluke introduction into this area. This approach has wider applicability for investigations of the origin of rumen fluke infections and for the possibility of parasite transmission at the livestock-wildlife interface.

  9. A naturally occurring repeat protein with high internal sequence identity defines a new class of TPR-like proteins

    PubMed Central

    Marold, Jacob D.; Kavran, Jennifer M.; Bowman, Gregory D.; Barrick, Doug

    2016-01-01

    SUMMARY Linear repeat proteins often have high structural similarity and low (~25%) pairwise sequence identities (PSI) among modules. We identified a unique P. anserina (Pa) sequence with tetratricopeptide repeat (TPR) homology, which contains longer (42 residue) repeats (42PRs) with an average PSI >91%. We determined the crystal structure of five tandem Pa 42PRs to 1.6Å, and examined the stability and solution properties of constructs containing three to six Pa 42PRs. Compared to 34-residue TPRs (34PRs), Pa 42PRs have a one-turn extension of each helix, and bury more surface area. Unfolding transitions shift to higher denaturant concentration and become sharper as repeats are added. Fitted Ising models show Pa 42PRs to be more cooperative than consensus 34PRs, with increased magnitudes of intrinsic and interfacial free energies. These results demonstrate the tolerance of the TPR motif to length variation, and provide a basis to understand the effects of helix length on intrinsic/interfacial stability. PMID:26439765

  10. Rat androgen-binding protein: evidence for identical subunits and amino acid sequence homology with human sex hormone-binding globulin.

    PubMed

    Joseph, D R; Hall, S H; French, F S

    1987-01-01

    The cDNA for rat androgen-binding protein (ABP) was previously isolated from a bacteriophage lambda gt11 rat testis cDNA library and its identity was confirmed by epitope selection. Hybrid-arrested translation studies have now demonstrated the identity of the isolates. The nucleotide sequence of a near full-length cDNA encodes a 403-amino acid precursor (Mr = 44,539), which agrees in size with the cell-free translation product (Mr = 45,000) of ABP mRNA. Putative sites of N-glycosylation and signal peptide cleavage were identified. Comparison of the predicted amino acid sequence of rat ABP with the amino-terminal amino acid sequence of human sex hormone-binding globulin revealed that 17 of 25 residues are identical. On the basis of the predicted amino acid sequence the molecular weight of the primary translation product, lacking the signal peptide, was 41,183. Hybridization analyses indicated that the two subunits of ABP are coded for by a single gene and a single mRNA species. Our results suggest that ABP consists of two subunits with identical primary sequences and that differences in post-translational processing result in the production of 47,000 and 41,000 molecular weight monomers.

  11. IMGT/HighV-QUEST Statistical Significance of IMGT Clonotype (AA) Diversity per Gene for Standardized Comparisons of Next Generation Sequencing Immunoprofiles of Immunoglobulins and T Cell Receptors

    PubMed Central

    Aouinti, Safa; Malouche, Dhafer; Giudicelli, Véronique; Kossida, Sofia; Lefranc, Marie-Paule

    2015-01-01

    The adaptive immune responses of humans and of other jawed vertebrate species (gnasthostomata) are characterized by the B and T cells and their specific antigen receptors, the immunoglobulins (IG) or antibodies and the T cell receptors (TR) (up to 2.1012 different IG and TR per individual). IMGT, the international ImMunoGeneTics information system (http://www.imgt.org), was created in 1989 by Marie-Paule Lefranc (Montpellier University and CNRS) to manage the huge and complex diversity of these antigen receptors. IMGT built on IMGT-ONTOLOGY concepts of identification (keywords), description (labels), classification (gene and allele nomenclature) and numerotation (IMGT unique numbering), is at the origin of immunoinformatics, a science at the interface between immunogenetics and bioinformatics. IMGT/HighV-QUEST, the first web portal, and so far the only one, for the next generation sequencing (NGS) analysis of IG and TR, is the paradigm for immune repertoire standardized outputs and immunoprofiles of the adaptive immune responses. It provides the identification of the variable (V), diversity (D) and joining (J) genes and alleles, analysis of the V-(D)-J junction and complementarity determining region 3 (CDR3) and the characterization of the ‘IMGT clonotype (AA)’ (AA for amino acid) diversity and expression. IMGT/HighV-QUEST compares outputs of different batches, up to one million nucleotide sequencesfor the statistical module. These high throughput IG and TR repertoire immunoprofiles are of prime importance in vaccination, cancer, infectious diseases, autoimmunity and lymphoproliferative disorders, however their comparative statistical analysis still remains a challenge. We present a standardized statistical procedure to analyze IMGT/HighV-QUEST outputs for the evaluation of the significance of the IMGT clonotype (AA) diversity differences in proportions, per gene of a given group, between NGS IG and TR repertoire immunoprofiles. The procedure is generic and

  12. Molecular characterization of two Pepino mosaic virus variants from imported tomato seed reveals high levels of sequence identity between Chilean and US isolates.

    PubMed

    Ling, Kai-Shu

    2007-01-01

    Pepino mosaic virus (PepMV), a member of the genus Potexvirus, was first described in South America on pepino (Solanum muricatum A.). Only in recent years, it was reported to infect greenhouse-grown tomatoes. Genome nucleotide sequences from several European isolates showed extensive sequence identity (>99%). Recent genome nucleotide sequences from two US isolates (US1 and US2) however showed much greater sequence divergence from that of the European PepMV isolates. My interest in characterizing virus isolates from South America was due to an active commercial tomato seed production in Chile. Through genome sequence comparison and phylogenetic analyses, we may be able to understand the source of virus infection and control this devastating disease from further spreading into new tomato growing regions of the world. Complete genome nucleotide sequences from two PepMV variants (designated as Ch1 and Ch2) were determined from a virus isolate obtained from a commercial tomato seed lot produced in Chile. Using RT-PCR-based genome walking strategy, complete genome sequences from these two variants were determined. Excluding poly (A) tails, the genomes of PepMV Ch1 and Ch2 were 6414 and 6412 nucleotides (nt), respectively. Pairwise comparisons of PepMV Ch1 and Ch2 genomes with other PepMV isolates showed that the highest nucleotide sequence identity was with two US isolates, 98.7% between PepMV Ch1 and US1, and 90.7% between Ch2 and US2. Similar to PepMV US1 and US2, the two Chilean variants were the most divergent from one another (78% nt identity). These two Chilean PepMV variants also shared only 78-86% nucleotide sequence identity to that of five European isolates. The high level of nucleotide sequence identity between Chilean and US isolates suggests a common origin. Phylogenetic analyses with various gene products generated three distinct sequence clusters (or strains): US1 and Ch1 in the first group, US2 and Ch2 in the second, and the European tomato isolates in

  13. Presence of bacteriophage Aa phi 23 correlates with the population genetic structure of Actinobacillus actinomycetemcomitans.

    PubMed

    Haubek, D; Willi, K; Poulsen, K; Meyer, J; Kilian, M

    1997-02-01

    Several bacteriophages associated with the oral bacterium Actinobacillus actinomycetemcomitans have been identified. Lysogeny might affect the virulence of this bacterium, which has been implicated in the etiology of juvenile and adult periodontitis. We have determined the presence of bacteriophage Aa phi 23-related DNA sequences among 185 A. actinomycetemcomitans strains belonging to 2 well-characterized collections and have related the findings to the population genetic structure of the collections. 2 cloned Aa phi 23-specific DNA probes were used in Southern blot hybridization experiments to detect homologous sequences in whole-cell DNA of the strains. DNA from 65 (35%) of the 185 strains hybridized to either of the DNA probes. The majority (74%) of the hybridizing strains showed an identical hybridization pattern, indicating presence of phage Aa phi 23. Whole-cell DNA from the remaining hybridizing strains hybridized to the probes with different patterns, indicating that DNA sequences related to but different from phage Aa phi 23 occur in these strains. The majority (81%) of the strains which harbored phage Aa phi 23 were of serotype a, whereas serotype d strains appeared to be resistant to infection with this phage. There was a clear correlation between hybridization patterns and genetic subdivisions based on our previous population genetic analyses of A. actinomycetemcomitans. However, there was no significant correlation between occurrence of Aa phi 23 among A. actinomycetemcomitans strains and the periodontal status of the patients from whom the isolates were obtained, suggesting that this bacteriophage does not significantly influence the virulence of A. actinomycetemcomitans.

  14. Hibiscus virus S is a new subgroup II tobamovirus: evidence from its unique coat protein and movement protein sequences.

    PubMed

    Srinivasan, K G; Narendrakumar, R; Wong, S M

    2002-08-01

    The coat protein (CP) and movement protein (MP) sequences of a new tobamovirus infecting Hibiscus rosa-sinensis L were determined. The CP gene encodes 163 amino acid (aa) residues and with a theoretical molecular weight of 18.19 kDa. The MP gene encodes 282 amino acids and its theoretical molecular weight is 30.36 kDa. The nucleotide (nt) and aa sequences of the CP were 46.88 % to 51.63 % and 45.34 % to 57.06 % identical to other tobamoviruses, respectively. The nt and aa sequence identities of MP ranged from 38.81 % to 43.90 % and 30.85 % to 37.88 %, respectively. The predicted virion origin of assembly (OAS) was located in the CP gene. Phylogenetic trees generated based on the nt and aa sequences of both CP and MP genes indicate that this new virus clusters with members of subgroup II of tobamoviruses. Although this hibiscus virus shared a high nt and aa sequence identity with Sunn-hemp mosaic virus (SHMV), Western analysis showed that it is serologically unrelated to SHMV. We propose the name Hibiscus virus S (HVS) for this Singapore isolate. This is the first report on partial nt sequence of a tobamovirus that infects hibiscus.

  15. A case of orthologous sequences of hemocyanin subunits for an evolutionary study of horseshoe crabs: amino acid sequence comparison of immunologically identical subunits of Carcinoscorpius rotundicauda and Tachypleus tridentatus.

    PubMed

    Sugita, H; Shishikura, F

    1995-10-01

    About 83% of the amino acid sequence of hemocyanin subunit HR6 from the Southeast Asian horseshoe crab, Carcinoscorpius rotundicauda, has been determined. There is a difference of about 43% between HR6 and complete sequences of chelicerate hemocyanin subunits from the American horseshoe crab, Limulus polyphemus, and a tarantula, Eurypelma californicum. However, the immunologically identical subunits HR6 and HT6 from Tachypleus tridentatus (Japanese horseshoe crab) show 2.7% sequence difference. Based on the amino acid sequences of HR6 and HT6, the divergence between C. rotundicauda and T. tridentatus occurred about 9.6 million years ago. In the case of horseshoe crab hemocyanin subunits, it seems that the orthologous homologues in many homologous subunits between species are immunologically detectable.

  16. Code optimization of the subroutine to remove near identical matches in the sequence database homology search tool PSI-BLAST.

    PubMed

    Aspnäs, Mats; Mattila, Kimmo; Osowski, Kristoffer; Westerholm, Jan

    2010-06-01

    A central task in protein sequence characterization is the use of a sequence database homology search tool to find similar protein sequences in other individuals or species. PSI-BLAST is a widely used module of the BLAST package that calculates a position-specific score matrix from the best matching sequences and performs iterated searches using a method to avoid many similar sequences for the score. For some queries and parameter settings, PSI-BLAST may find many similar high-scoring matches, and therefore up to 80% of the total run time may be spent in this procedure. In this article, we present code optimizations that improve the cache utilization and the overall performance of this procedure. Measurements show that, for queries where the number of similar matches is high, the optimized PSI-BLAST program may be as much as 2.9 times faster than the original program.

  17. Ecological significance of microdiversity: identical 16S rRNA gene sequences can be found in bacteria with highly divergent genomes and ecophysiologies.

    PubMed

    Jaspers, Elke; Overmann, Jörg

    2004-08-01

    A combination of cultivation-based methods with a molecular biological approach was used to investigate whether planktonic bacteria with identical 16S rRNA gene sequences can represent distinct eco- and genotypes. A set of 11 strains of Brevundimonas alba were isolated from a bacterial freshwater community by conventional plating or by using a liquid most-probable-number (MPN) dilution series. These strains had identical 16S rRNA gene sequences and represented the dominant phylotype in the plateable fraction, as well as in the highest positive dilutions of the MPN series. However, internally transcribed spacer and enterobacterial repetitive intergenic consensus PCR fingerprinting analyses, as well as DNA-DNA hybridization analyses, revealed great genetic diversity among the 11 strains. Each strain utilized a specific combination of 59 carbon substrates, and the niche overlap indices were low, suggesting that each strain occupied a different ecological niche. In dialysis cultures incubated in situ, each strain had a different growth rate and cell yield. We thus demonstrated that the B. alba strains represent distinct populations with genetically determined adaptations and probably occupy different ecological niches. Our results have implications for assessment of the diversity and biogeography of bacteria and increase the perception of natural diversity beyond the level of 16S rRNA gene sequences.

  18. The Corynebacterium xerosis composite transposon Tn5432 consists of two identical insertion sequences, designated IS1249, flanking the erythromycin resistance gene ermCX.

    PubMed

    Tauch, A; Kassing, F; Kalinowski, J; Pühler, A

    1995-09-01

    Analysis of the 50-kb R-plasmid pTP10 from the clinical isolate Corynebacterium xerosis M82B revealed that the erythromycin resistance gene, ermCX, is located on a 4524-bp composite transposable element, Tn5432. The ends of Tn5432 are identical, direct repeats of an insertion sequence, designated IS1249, encoding a putative transposase of the IS256 family. IS1249 consists of 1385 bp with 45/42 imperfect terminal inverted repeats. The nucleotide sequence of the 1754-bp Tn5432 central region is 99% identical to the previously sequenced erythromycin resistance region of the Corynebacterium diphtheriae plasmid pNG2. It encodes the erythromycin resistance gene, ermCX, and an ORF homologous to the amino-terminal end of the transposase of IS31831 from Corynebacterium glutamicum. Transposons with regions flanking the insertion sites were recovered from the C. glutamicum chromosome by a plasmid rescue technique. Insertion of Tn5432 created 8-bp target site duplications. A Tn5432-induced isoleucine/valine-auxotrophic mutant was found to carry the transposon in the 5' region of the ilvBNC cluster; in pTP10 the transposon is inserted in a region similar to replication and partitioning functions of the Enterococcus faecalis plasmid pAD1 and the Agrobacterium tumefaciens plasmid pTAR.

  19. Identical amino acid sequence of the aroA(G) gene products of Bacillus subtilis 168 and B. subtilis Marburg strain.

    PubMed

    Bolotin, A; Khazak, V; Stoynova, N; Ratmanova, K; Yomantas, Y; Kozlov, Y

    1995-09-01

    A DNA fragment containing the aroA(G) gene of Bacillus subtilis 168, encoding 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase-chorismate mutase, was cloned and sequenced. The N-terminus of the protein encoded by aroA(G) showed homology with chorismate mutase encoded by aroH of B. subtilis and with the chorismate mutase parts of proteins encoded by the pheA and tyrA genes of Escherichia coli. The C-terminus of the aroA(G) product has sequence similarity with 3-deoxy-D-manno-octulosonate 8-phosphate synthase of E. coli. It was shown that the proteins encoded by the aroA(G) gene of B. subtilis 168 and the aroA gene of B. subtilis ATCC 6051 Marburg strain are identical, so the observed differences in DAHP synthase activity from these two strains must result from other changes.

  20. Identification of a gene sequence encoding a putative pyruvate oxidoreductase in Serpulina pilosicoli.

    PubMed

    Rayment, S J; Lee, B J; Hampson, D J; Livesley, M A

    1998-09-01

    Serpulina pilosicoli is a recently described species of intestinal spirochaete which can be identified using a species-specific monoclonal antibody BJL/AC1 reactive with a 29-kDa protein located in the cell envelope. A genomic library of the type strain of S. pilosicoli P43/6/78T was created in lambda zap express and screened using BJL/AC1. Single positive clones were isolated and excised into the phagemid vector pBK-CMV. Phagemid DNA was purified and a single clone was selected for sequencing. The size of spirochaetal DNA insert was determined by digestion with restriction endonucleases EcoRI and PstI as being approximately 2.6 kb. The nucleotide sequence of the gene encoding the protein with which the antibody reacted was determined by cycle sequencing. The insert contained an open reading frame of 285 nucleotides. Translation of the nucleotide sequence into amino acid (aa) residues showed a sequence of 275 aa. Comparison of this sequence with databases revealed homology to pyruvate oxidoreductases from various organisms found in the gastroinestinal tract. These included the pyruvate ferredoxin oxidoreductase (POR) alpha submit of Helicobacter pylori (38.8% identity in 250 aa), pyruvate-flavodoxin oxidoreductase of Escherichia coli (28.7% identify in 258 aa) and Giardia intestinalis (25.1% identity in 251 aa). A significant level of homology was also observed with hyperthermophilic bacteria such as the POR of Thermatoga maritima (38.6% in 254 aa) and the 2-ketovalerate-ferredoxin oxidoreductase of Pyrococcus furiosus (34% in 262 aa).

  1. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes.

    PubMed

    Kim, Mincheol; Oh, Hyun-Seok; Park, Sang-Cheol; Chun, Jongsik

    2014-02-01

    Among available genome relatedness indices, average nucleotide identity (ANI) is one of the most robust measurements of genomic relatedness between strains, and has great potential in the taxonomy of bacteria and archaea as a substitute for the labour-intensive DNA-DNA hybridization (DDH) technique. An ANI threshold range (95-96%) for species demarcation had previously been suggested based on comparative investigation between DDH and ANI values, albeit with rather limited datasets. Furthermore, its generality was not tested on all lineages of prokaryotes. Here, we investigated the overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla to see whether the suggested range can be applied to all species. There was an apparent distinction in the overall ANI distribution between intra- and interspecies relationships at around 95-96% ANI. We went on to determine which level of 16S rRNA gene sequence similarity corresponds to the currently accepted ANI threshold for species demarcation using over one million comparisons. A twofold cross-validation statistical test revealed that 98.65% 16S rRNA gene sequence similarity can be used as the threshold for differentiating two species, which is consistent with previous suggestions (98.2-99.0%) derived from comparative studies between DDH and 16S rRNA gene sequence similarity. Our findings should be useful in accelerating the use of genomic sequence data in the taxonomy of bacteria and archaea.

  2. Molecular detection and sequence analysis of human caliciviruses from acute gastroenteritis outbreaks in Hungary.

    PubMed

    Farkas, T; Berke, T; Reuter, G; Szûcs, G; Matson, D O; Jiang, X

    2002-08-01

    Three viral gastroenteritis (VGE) outbreaks that occurred in 1998-1999, in Hungary were investigated for the presence of human caliciviruses (HuCVs). HuCVs in stool specimens were detected by reverse transcription-polymerase chain reaction (RT-PCR) using primer pair 289/290, which was designed based on the RNA-dependent RNA polymerase (RdRp) sequence. RT-PCR results were confirmed by sequencing showing that all three outbreak strains belonged to genogroup II of "Norwalk-like viruses" (NLVs). Two strains had high sequence identity with strains in known genetic clusters (Hawaii and Lordsdale clusters). The third strain (MOH) had distinct RdRp sequence, sharing 77/86% (nt/aa) identity with Snow Mountain virus (SMV), the closest genogroup II virus. To characterize MOH further, we cloned, sequenced, and expressed in baculovirus its capsid gene. It had 75/79% (nt/aa) identity with SMV, but 97/98% (nt/aa) identity with NLV/Hillingdon/90/UK, a recently identified genetic cluster of HuCVs. The recombinant MOH (rMOH) capsid protein self-assembled into virus-like particles (VLPs), which is antigenically distinct from other recombinant HuCV capsid antigens available in our laboratory. Further study of this VLP will have important applications in antigenic characterization and diagnosis of HuCVs.

  3. Rating AAs.

    ERIC Educational Resources Information Center

    Carter, Susan J.

    2001-01-01

    Why alternative investments? In a word: performance. Many higher education endowment and foundation managers are making increasing commitments to alternative investments, or AAs, in order to obtain higher returns and broader diversification for their investment portfolios than public securities instruments can usually provide. Learn how to handle…

  4. Next generation sequencing of SNPs using the HID-Ion AmpliSeq™ Identity Panel on the Ion Torrent PGM™ platform.

    PubMed

    Guo, Fei; Zhou, Yishu; Song, He; Zhao, Jinling; Shen, Hongying; Zhao, Bin; Liu, Feng; Jiang, Xianhua

    2016-11-01

    The HID-Ion AmpliSeq™ Identity Panel (the HID Identity Panel) is designed to detect 124-plex single nucleotide polymorphisms (SNPs) with next generation sequencing (NGS) technology on the Ion Torrent PGM™ platform, including 90 individual identification SNPs (IISNPs) on autosomal chromosomes and 34 lineage informative SNPs (LISNPs) on Y chromosome. In this study, we evaluated performance for the HID Identity Panel to provide a reference for NGS-SNP application, focusing on locus strand balance, locus coverage balance, heterozygote balance, and background signals. Besides, several experiments were carried out to find out improvements and limitations of this panel, including studies of species specificity, repeatability and concordance, sensitivity, mixtures, case-type samples and degraded samples, population genetics and pedigrees following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. In addition, Southern and Northern Chinese Han were investigated to assess applicability of this panel. Results showed this panel led to cross-reactivity with primates to some extent but rarely with non-primate animals. Repeatable and concordant genotypes could be obtained in triplicate with one exception at rs7520386. Full profiles could be obtained from 100pg input DNA, but the optimal input DNA would be 1ng-200pg with 21 initial PCR cycles. A sample with ≥20% minor contributor could be considered as a mixture by the number of homozygotes, and full profiles belonging to minor contributors could be detected between 9:1 and 1:9 mixtures with known reference profiles. Also, this assay could be used for case-type samples and degraded samples. For autosomal SNPs (A-SNPs), FST across all 90loci was not significantly different between Southern and Northern Chinese Han or between male and female samples. All A-SNP loci were independent in Chinese Han population. Except for 18loci with He <0.4, most of the A-SNPs in the HID Identity Panel presented high

  5. Morphological Identities of Two Different Marine Stramenopile Environmental Sequence Clades: Bicosoeca kenaiensis (Hilliard, 1971) and Cantina marsupialis (Larsen and Patterson, 1990) gen. nov., comb. nov.

    PubMed

    Yubuki, Naoji; Pánek, Tomáš; Yabuki, Akinori; Čepička, Ivan; Takishita, Kiyotaka; Inagaki, Yuji; Leander, Brian S

    2015-01-01

    Although environmental DNA surveys improve our understanding of biodiversity, interpretation of unidentified lineages is limited by the absence of associated morphological traits and living cultures. Unidentified lineages of marine stramenopiles are called "MAST clades". Twenty-five MAST clades have been recognized: MAST-1 through MAST-25; seven of these have been subsequently discarded because the sequences representing those clades were found to either (1) be chimeric or (2) affiliate within previously described taxonomic groups. Eighteen MAST clades remain without a cellular identity. Moreover, the discarded "MAST-13" has been used in different studies to refer to two different environmental sequence clades. After establishing four cultures representing two different species of heterotrophic stramenopiles and then characterizing their morphology and molecular phylogenetic positions, we determined that the two different species represented the two different MAST-13 clades: (1) a lorica-bearing Bicosoeca kenaiensis and (2) a microaerophilic flagellate previously named "Cafeteria marsupialis". Both species were previously described with only light microscopy; no cultures, ultrastructural data or DNA sequences were available from these species prior to this study. The molecular phylogenetic position of three different "C. marsupialis" isolates was not closely related to the type species of Cafeteria; therefore, we established a new genus for these isolates, Cantina gen. nov.

  6. Sequence evolution and sex-specific expression patterns of the C class floral identity gene, SpAGAMOUS, in dioecious Spinacia oleracea L.

    PubMed

    Sather, D Noah; York, Amber; Pobursky, Kevin J; Golenberg, Edward M

    2005-10-01

    Development in dioecious cultivated spinach, Spinacia oleracea, is distinguished by the absence of alternative reproductive organ primordia in male and female flowers. Given the highly derived floral developmental program in spinach, we wished to characterize a spinach C class floral identity gene and to determine the patterns of sequence evolution as well as compare the spatial and temporal expression patterns with those of AGAMOUS. The isolated cDNA sequence clusters phylogenetically within the AGAMOUS/FARINELLI C class clade. In comparison with the SLM1 sequence from the related Silene latifolia, amino acid replacements are highly conservative and non-randomly distributed, being predominantly found in hinge regions or on exposed surfaces of helices. The spinach gene (SpAGAMOUS) appears to be exclusively expressed in reproductive tissues and not in vegetative organs. Initial expression of SpAGAMOUS is similar in male and female floral primordia. However, upon initiation of the first whorl organs, SpAGAMOUS becomes restricted to meristemic regions from which the reproductive primordia will develop. This results in an early gender-specific pattern. Thus, the spinach C class gene is differentially expressed prior to reproductive organ development and is, at least, correlated with, if not directly involved in, the sexual dimorphism in spinach.

  7. Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data.

    PubMed

    Blekhman, Ran; Tang, Karen; Archie, Elizabeth A; Barreiro, Luis B; Johnson, Zachary P; Wilson, Mark E; Kohn, Jordan; Yuan, Michael L; Gesquiere, Laurence; Grieneisen, Laura E; Tung, Jenny

    2016-08-16

    Field studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples-unique resources for understanding ecological, behavioral, and phylogenetic effects on the gut microbiome. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. Here, we extend previous work on storage methods for gut microbiome samples by comparing immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: lyophilization, storage in ethanol, and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods, and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts.

  8. Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data

    PubMed Central

    Blekhman, Ran; Tang, Karen; Archie, Elizabeth A.; Barreiro, Luis B.; Johnson, Zachary P.; Wilson, Mark E.; Kohn, Jordan; Yuan, Michael L.; Gesquiere, Laurence; Grieneisen, Laura E.; Tung, Jenny

    2016-01-01

    Field studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples—unique resources for understanding ecological, behavioral, and phylogenetic effects on the gut microbiome. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. Here, we extend previous work on storage methods for gut microbiome samples by comparing immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: lyophilization, storage in ethanol, and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods, and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts. PMID:27528013

  9. Reconstruction of cyclooxygenase evolution in animals suggests variable, lineage-specific duplications, and homologs with low sequence identity.

    PubMed

    Havird, Justin C; Kocot, Kevin M; Brannock, Pamela M; Cannon, Johanna T; Waits, Damien S; Weese, David A; Santos, Scott R; Halanych, Kenneth M

    2015-04-01

    Cyclooxygenase (COX) enzymatically converts arachidonic acid into prostaglandin G/H in animals and has importance during pregnancy, digestion, and other physiological functions in mammals. COX genes have mainly been described from vertebrates, where gene duplications are common, but few studies have examined COX in invertebrates. Given the increasing ease in generating genomic data, as well as recent, although incomplete descriptions of potential COX sequences in Mollusca, Crustacea, and Insecta, assessing COX evolution across Metazoa is now possible. Here, we recover 40 putative COX orthologs by searching publicly available genomic resources as well as ~250 novel invertebrate transcriptomic datasets. Results suggest the common ancestor of Cnidaria and Bilateria possessed a COX homolog similar to those of vertebrates, although such homologs were not found in poriferan and ctenophore genomes. COX was found in most crustaceans and the majority of molluscs examined, but only specific taxa/lineages within Cnidaria and Annelida. For example, all octocorallians appear to have COX, while no COX homologs were found in hexacorallian datasets. Most species examined had a single homolog, although species-specific COX duplications were found in members of Annelida, Mollusca, and Cnidaria. Additionally, COX genes were not found in Hemichordata, Echinodermata, or Platyhelminthes, and the few previously described COX genes in Insecta lacked appreciable sequence homology (although structural analyses suggest these may still be functional COX enzymes). This analysis provides a benchmark for identifying COX homologs in future genomic and transcriptomic datasets, and identifies lineages for future studies of COX.

  10. Coding sequences and levels of expression of Hsc70t are identical in mice with different Orch-1 alleles

    SciTech Connect

    Snoek, M.; Vugt, H. van; Olavesen, M.G.; Milner, C.M.; Campbell, R.D.; Teuscher, C.

    1994-12-31

    Experimental allergic orchitis (EAO) is an autoimmune disease of the testis that is controlled by multple genes. The use of recombinant mouse strains has defined the map position of the H-2-associated locus controlling disease susceptibility, Orch-1, within the H-2S/H-2D interval. Over the last few years the definition of the structural organization of the C4-H-2D segment and identification of the recombination sites of the various intra-H-2 recombinations has reduced the map position of Orch-1 to the Hsp70.1-G7 interval. Three Hsp70 genes, Hsp70.1, Hsp70.3, and Hsc70t, and the genes G7b and G7a are located in this segment of DNA. In order to investigate whether Hsc70t is a suitable candidate for Orch-1 we have compared the sequence of the gene from a susceptible and a resistant haplotype.

  11. Revealing the challenges of low template DNA analysis with the prototype Ion AmpliSeq™ Identity panel v2.3 on the PGM™ Sequencer.

    PubMed

    Elena, Salata; Alessandro, Agostino; Ignazio, Ciuna; Sharon, Wootton; Luigi, Ripani; Andrea, Berti

    2016-05-01

    Forensic scientists frequently have to deal with the analysis of challenging sources of DNA such as degraded and low template DNA (LtDNA). The capacity to genotype difficult biological traces has been facilitated by emerging technologies. Massive parallel sequencing (MPS) on microchip among other technologies promises high sensitivity and discrimination power. In this study we evaluated the combined use of the Quantifiler(®) Trio DNA Quantification Kit with the prototype Ion AmpliSeq™ Identity panel v2.3 and PGM™ platform in LtDNA samples. Coverage, allele balance, allele drop-out/in, consistency and variance were assessed. Overall, the results showed a great level of performance and consistency in terms of genotyping capability even under the most challenging conditions, making it possible to obtain consistent SNP profiles with 31 pg of DNA and partial informative profiles with as little as 5 pg or with severely degraded DNA. In addition, we demonstrated that the stochastic effects observed in some samples are due to the amplification of the library rather than sequencing. Based on our data, we proposed general recommendations for the analysis of casework samples starting from the use of quantification data, which proved to be critical in deciding whether to process the samples via STR (short tandem repeat) analysis or SNP MPS. In our experience, the use of the prototype Ion AmpliSeq™ Identity panel v2.3 has revealed a new applicable solution for processing LtDNAs. This approach provides users with an additional tool for analysis of traces that either would not give informative results with conventional STR-based techniques.

  12. Average nucleotide identity of genome sequences supports the description of Rhizobium lentis sp. nov., Rhizobium bangladeshense sp. nov. and Rhizobium binae sp. nov. from lentil (Lens culinaris) nodules.

    PubMed

    Rashid, M Harun-or; Young, J Peter W; Everall, Isobel; Clercx, Pia; Willems, Anne; Santhosh Braun, Markus; Wink, Michael

    2015-09-01

    Rhizobial strains isolated from effective root nodules of field-grown lentil (Lens culinaris) from different parts of Bangladesh were previously analysed using sequences of the 16S rRNA gene, three housekeeping genes (recA, atpD and glnII) and three nodulation genes (nodA, nodC and nodD), DNA fingerprinting and phenotypic characterization. Analysis of housekeeping gene sequences and DNA fingerprints indicated that the strains belonged to three novel clades in the genus Rhizobium. In present study, a representative strain from each clade was further characterized by determination of cellular fatty acid compositions, carbon substrate utilization patterns and DNA-DNA hybridization and average nucleotide identity (ANI) analyses from whole-genome sequences. DNA-DNA hybridization showed 50-62% relatedness to their closest relatives (the type strains of Rhizobium etli and Rhizobium phaseoli) and 50-60% relatedness to each other. These results were further supported by ANI values, based on genome sequencing, which were 87-92% with their close relatives and 88-89% with each other. On the basis of these results, three novel species, Rhizobium lentis sp. nov. (type strain BLR27(T) = LMG 28441(T) = DSM 29286(T)), Rhizobium bangladeshense sp. nov. (type strain BLR175(T) = LMG 28442(T) = DSM 29287(T)) and Rhizobium binae sp. nov. (type strain BLR195(T) = LMG 28443(T) = DSM 29288(T)), are proposed. These species share common nodulation genes (nodA, nodC and nodD) that are similar to those of the symbiovar viciae.

  13. A rhodopsin-like protein in Cyanophora paradoxa: gene sequence and protein immunolocalization.

    PubMed

    Frassanito, Anna Maria; Barsanti, Laura; Passarelli, Vincenzo; Evangelista, Valtere; Gualtieri, Paolo

    2010-03-01

    Here, we report the DNA sequence of the rhodopsin gene in the alga Cyanophora paradoxa (Glaucophyta). The primers were designed according to the conserved regions of prokaryotic and eukaryotic rhodopsin-like proteins deposited in the GenBank. The sequence consists of 1,272 bp comprised of 5 introns. The correspondent protein, named Cyanophopsin, showed high identity to rhodopsin-like proteins of Archea, Bacteria, Fungi, and Algae. At the N-terminal, the protein is characterized by a region with no transmembrane alpha-helices (80 aa), followed by a region with 7alpha-helices (219 aa) and a shorter 35-aa C-terminal region. The DNA sequence of the N-terminal region was expressed in E. coli and the recombinant purified peptide was used as antigen in hens to obtain polyclonal antibodies. Indirect immunofluorescence in C. paradoxa cells showed a marked labeling of the muroplast (aka cyanelle) membrane.

  14. Complete Genome Sequence of Mulberry Vein Banding Associated Virus, a New Tospovirus Infecting Mulberry.

    PubMed

    Meng, Jiaorong; Liu, Pingping; Zhu, Liling; Zou, Chengwu; Li, Jieqiu; Chen, Baoshan

    2015-01-01

    Mulberry vein banding associated virus (MVBaV) that infects mulberry plants with typical vein banding symptoms had been identified as a tentative species of the genus Tospovirus based on the homology of N gene sequence to those of tospoviruses. In this study, the complete sequence of the tripartite RNA genome of MVBaV was determined and analyzed. The L RNA has 8905 nucleotides (nt) and encodes the putative RNA-dependent RNA polymerase (RdRp) of 2877 aa amino acids (aa) in the viral complementary (vc) strand. The RdRp of MVBaV shares the highest aa sequence identity (85.9%) with that of Watermelon silver mottle virus (WSMoV), and contains conserved motifs shared with those of the species of the genus Tospovirus. The M RNA contains 4731 nt and codes in ambisense arrangement for the NSm protein of 309 aa in the sense strand and the Gn/Gc glycoprotein precursor (GP) of 1,124 aa in the vc strand. The NSm and GP of MVBaV share the highest aa sequence identities with those of Capsicum chlorosis virus (CaCV) and Groundnut bud necrosis virus (GBNV) (83.2% and 84.3%, respectively). The S RNA is 3294 nt in length and contains two open reading frames (ORFs) in an ambisense coding strategy, encoding a 439-aa non-structural protein (NSs) and the 277-aa nucleocapsid protein (N), respectively. The NSs and N also share the highest aa sequence identity (71.1% and 74.4%, respectively) with those of CaCV. Phylogenetic analysis of the RdRp, NSm, GP, NSs, and N proteins showed that MVBaV is most closely related to CaCV and GBNV and that these proteins cluster with those of the WSMoV serogroup, and that MVBaV seems to be a species bridging the two subgroups within the WSMoV serogroup of tospoviruses in evolutionary aspect, suggesting that MVBaV represents a distinct tospovirus. Analysis of S RNA sequence uncovered the highly conserved 5'-/3'-ends and the coding regions, and the variable region of IGR with divergent patterns among MVBaV isolates.

  15. Complete Genome Sequence of Mulberry Vein Banding Associated Virus, a New Tospovirus Infecting Mulberry

    PubMed Central

    Meng, Jiaorong; Liu, Pingping; Zhu, Liling; Zou, Chengwu; Li, Jieqiu; Chen, Baoshan

    2015-01-01

    Mulberry vein banding associated virus (MVBaV) that infects mulberry plants with typical vein banding symptoms had been identified as a tentative species of the genus Tospovirus based on the homology of N gene sequence to those of tospoviruses. In this study, the complete sequence of the tripartite RNA genome of MVBaV was determined and analyzed. The L RNA has 8905 nucleotides (nt) and encodes the putative RNA-dependent RNA polymerase (RdRp) of 2877 aa amino acids (aa) in the viral complementary (vc) strand. The RdRp of MVBaV shares the highest aa sequence identity (85.9%) with that of Watermelon silver mottle virus (WSMoV), and contains conserved motifs shared with those of the species of the genus Tospovirus. The M RNA contains 4731 nt and codes in ambisense arrangement for the NSm protein of 309 aa in the sense strand and the Gn/Gc glycoprotein precursor (GP) of 1,124 aa in the vc strand. The NSm and GP of MVBaV share the highest aa sequence identities with those of Capsicum chlorosis virus (CaCV) and Groundnut bud necrosis virus (GBNV) (83.2% and 84.3%, respectively). The S RNA is 3294 nt in length and contains two open reading frames (ORFs) in an ambisense coding strategy, encoding a 439-aa non-structural protein (NSs) and the 277-aa nucleocapsid protein (N), respectively. The NSs and N also share the highest aa sequence identity (71.1% and 74.4%, respectively) with those of CaCV. Phylogenetic analysis of the RdRp, NSm, GP, NSs, and N proteins showed that MVBaV is most closely related to CaCV and GBNV and that these proteins cluster with those of the WSMoV serogroup, and that MVBaV seems to be a species bridging the two subgroups within the WSMoV serogroup of tospoviruses in evolutionary aspect, suggesting that MVBaV represents a distinct tospovirus. Analysis of S RNA sequence uncovered the highly conserved 5’-/3’-ends and the coding regions, and the variable region of IGR with divergent patterns among MVBaV isolates. PMID:26291718

  16. Sinorhizobium meliloti strains TII7 and A5 by Multilocus Sequence Typing (MLST) have chromsomes identical with Rm1021 and form an effective and ineffective symbiosis with Medicago truncatula line Jemalong A17, respectively

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The strains TII7 and A5 formed an effective and ineffective symbiosis with Medicago truncatula Jemalong A17, respectively. Both were shown to have identical chromsomes with strains Rm1021 and RCR2011 using a Multilocus Sequence Typing method. The 2260 bp segments of DNA stretching from the 3’ end ...

  17. Activity of vegetative insecticidal proteins Vip3Aa58 and Vip3Aa59 of Bacillus thuringiensis against lepidopteran pests.

    PubMed

    Baranek, Jakub; Kaznowski, Adam; Konecka, Edyta; Naimov, Samir

    2015-09-01

    Vegetative insecticidal proteins (Vips) secreted by some isolates of Bacillus thuringiensis show activity against insects and are regarded as insecticides against pests. A number of B. thuringiensis strains harbouring vip3A genes were isolated from different sources and identified by using a PCR based approach. The isolates with the highest insecticidal activity were indicated in screening tests, and their vip genes were cloned and sequenced. The analysis revealed two polymorphic Vip protein forms, which were classified as Vip3Aa58 and Vip3Aa59. After expression of the vip genes, the proteins were isolated and characterized. The activity of both toxins was estimated against economically important lepidopteran pests of woodlands (Dendrolimus pini), orchards (Cydia pomonella) and field crops (Spodoptera exigua). Vip3Aa58 and Vip3Aa59 were highly toxic and their potency surpassed those of many Cry proteins used in commercial bioinsecticides. Vip3Aa59 revealed similar larvicidal activity as Vip3Aa58 against S. exigua and C. pomonella. Despite 98% similarity of amino acid sequences of both proteins, Vip3Aa59 was significantly more active against D. pini. Additionally the effect of proteolytic activation of Vip58Aa and Vip3Aa59 on toxicity of D. pini and S. exigua was studied. Both Vip3Aa proteins did not show any activity against Tenebrio molitor (Coleoptera) larvae. The results suggest that the Vip3Aa58 and Vip3Aa59 toxins might be useful for controlling populations of insect pests of crops and forests.

  18. The amino acid sequence of Canada goose (Branta canadensis) and mute swan (Cygnus olor) hemoglobins. Two different species with identical beta-chains.

    PubMed

    Oberthür, W; Godovac-Zimmermann, J; Braunitzer, G; Wiesner, H

    1982-08-01

    The amino acid sequences of the alpha- and beta-chains from the major hemoglobin component (HbA) of Canada goose (Branta canadensis) and mute swan (Cygnus olor) are given. The alpha-chains are of the alpha A-type, since alpha D-type was expressed but only found in low concentrations. By homologous comparison, greylag goose hemoglobin (Anser anser) and Canada goose hemoglobin alpha-chains differ by two exchanges, and beta-chains by three exchanges. A valine substitution for threonine was found at position alpha 34 (B15). This exchange is a result of a two point mutation. Thus, there are three nucleotide mutations in alpha-chains, as in beta-chains. Substitutions in positions alpha 34 (B15) and beta 125 (H3) have modified intersubunit contacts (alpha 1 beta 1-contacts). A comparison of mute swan hemoglobin with greylag goose hemoglobin shows four exchanges in alpha-chains and three in beta-chains. Canada goose and mute swan have identical beta-chains, while alpha-chains differ in two amino acids. One of these exchanges is implicated in one of the alpha 1 beta 1-contact points (alpha 34) where isoleucine substitution for valine was found. Comparison of hemoglobins from different species in the same tribe (Anserini) shows a high homology between Canada goose and mute swan hemoglobins.

  19. Sequence of the luxD gene encoding acyltransferase of the lux operon from Photobacterium leiognathi.

    PubMed

    Chao, Y F; Weng, S F; Lin, J W

    1993-04-15

    The nucleotide sequence of luxD (EMBL accession No. X65611), encoding acyltransferase (ACT), of the lux operon from Photobacterium leiognathi PL741 was determined, and the amino acid (aa) sequence was deduced. ACT is a component of the fatty acid reductase complex, which is responsible for converting fatty acid to aldehyde that serves as the substrate in the luciferase-catalyzed bioluminescent reactions. The protein has a calculated M(r) of 34,384 and comprises 305 aa residues. Alignment and comparison of the ACT of P. leiognathi with that of Vibrio fischeri ATCC7744, V. harveyi B392 and Xenorhabdus luminescens Hm shows that there is 66%, 59% and 61% aa identity, respectively.

  20. Is the serum amyloid A protein in acute phase plasma high density lipoprotein the precursor of AA amyloid fibrils?

    PubMed Central

    Baltz, M L; Rowe, I F; Caspi, D; Turnell, W G; Pepys, M B

    1986-01-01

    Serum amyloid A protein (SAA), an apolipoprotein of high density lipoprotein (HDL), is generally considered to be the precursor of AA protein, which forms the fibrils in reactive systemic amyloidosis in man and animals. This view is based on amino acid sequence identity between AA and the amino-terminal portion of SAA. However, in extensive and well-controlled studies of experimentally induced murine AA amyloidosis, we were unable to demonstrate a direct precursor-product relationship between SAA, in SAA-rich HDL preparations from acute phase or amyloidotic mouse or human serum, and AA protein in the amyloid deposits. This raises the possibility that SAA in its usual form, as an apolipoprotein of HDL synthesized during the acute phase response, may not be the major precursor of AA fibrils. The amyloidogenic forms of circulating SAA molecules may not be isolated during the preparation of HDL. Alternatively, particularly in the light of recent evidence that SAA mRNA is expressed in many different tissues throughout the body of appropriately stimulated animals, amyloidogenic SAA may be derived from sources other than the liver cells in which SAA-rich HDL is synthesized. PMID:3105937

  1. Exome sequencing identifies de novo gain of function missense mutation in KCND2 in identical twins with autism and seizures that slows potassium channel inactivation.

    PubMed

    Lee, Hane; Lin, Meng-chin A; Kornblum, Harley I; Papazian, Diane M; Nelson, Stanley F

    2014-07-01

    Numerous studies and case reports show comorbidity of autism and epilepsy, suggesting some common molecular underpinnings of the two phenotypes. However, the relationship between the two, on the molecular level, remains unclear. Here, whole exome sequencing was performed on a family with identical twins affected with autism and severe, intractable seizures. A de novo variant was identified in the KCND2 gene, which encodes the Kv4.2 potassium channel. Kv4.2 is a major pore-forming subunit in somatodendritic subthreshold A-type potassium current (ISA) channels. The de novo mutation p.Val404Met is novel and occurs at a highly conserved residue within the C-terminal end of the transmembrane helix S6 region of the ion permeation pathway. Functional analysis revealed the likely pathogenicity of the variant in that the p.Val404Met mutant construct showed significantly slowed inactivation, either by itself or after equimolar coexpression with the wild-type Kv4.2 channel construct consistent with a dominant effect. Further, the effect of the mutation on closed-state inactivation was evident in the presence of auxiliary subunits that associate with Kv4 subunits to form ISA channels in vivo. Discovery of a functionally relevant novel de novo variant, coupled with physiological evidence that the mutant protein disrupts potassium current inactivation, strongly supports KCND2 as the causal gene for epilepsy in this family. Interaction of KCND2 with other genes implicated in autism and the role of KCND2 in synaptic plasticity provide suggestive evidence of an etiological role in autism.

  2. Iranian johnsongrass mosaic virus: the complete genome sequence, molecular and biological characterization, and comparison of coat protein gene sequences.

    PubMed

    Moradi, Zohreh; Mehrvar, Mohsen; Nazifi, Ehsan; Zakiaghl, Mohammad

    2017-02-01

    Iranian johnsongrass mosaic virus (IJMV) is one of the most prevalent viruses causing maize mosaic disease in Iran. An IJMV isolate, Maz-Bah, was obtained from the maize showing mosaic symptoms in Mazandaran, north of Iran. The complete genomic sequence of Maz-Bah is 9544 nucleotides, excluding the poly(A) tail. It contains one single open reading frame of 9165 nucleotides and encodes a large polyprotein of 3054 amino acids, flanked by a 5'-untranslated region (UTR) of 143 nucleotides and a 3'-UTR of 236 nucleotides. The entire genomic sequence of Maz-Bah isolate shares identities of 84.9 and 94.2 % with the IJMV (Shz) isolate, the lone complete genome sequence available in the GenBank at the nucleotide (nt) and deduced amino acid (aa) levels, respectively. The whole genome sequences share identities of 51.5-69.8 and 44.9-74.3 % with those of other Sugarcane mosaic virus (SCMV) subgroup potyviruses at nt and aa levels, respectively. In phylogenetic trees based on the multiple alignments of the entire nt and aa sequences, IJMV isolates formed a separate sublineage of the tree with potyviruses infecting monocotyledons of cereals, indicating that IJMV is a member of SCMV subgroup of potyviruses. IJMV is most closely related to Sorghum mosaic virus and Maize dwarf mosaic virus and less closely related to the Johnsongrass mosaic virus and Cocksfoot streak virus. To further investigate the genetic relationship of IJMV, 9 other isolates from different hosts were cloned and sequenced. The identity of IJMV CP nt and aa sequences of 11 Iranian isolates ranged from 86.4 to 99.8 % and 90.5 to 99.7 %, respectively, indicating a high nt variability in CP gene. Furthermore, in the CP-based phylogenetic tree, IJMV isolates were clustered together with a maize potyvirus described as Zea mosaic virus from Israel (with 86-89 % nt identity), indicating that both isolates probably are the strains of the same virus.

  3. Screening of transgenic proteins expressed in transgenic food crops for the presence of short amino acid sequences identical to potential, IgE – binding linear epitopes of allergens

    PubMed Central

    Kleter, Gijs A; Peijnenburg, Ad ACM

    2002-01-01

    Background Transgenic proteins expressed by genetically modified food crops are evaluated for their potential allergenic properties prior to marketing, among others by identification of short identical amino acid sequences that occur both in the transgenic protein and allergenic proteins. A strategy is proposed, in which the positive outcomes of the sequence comparison with a minimal length of six amino acids are further screened for the presence of potential linear IgE-epitopes. This double track approach involves the use of literature data on IgE-epitopes and an antigenicity prediction algorithm. Results Thirty-three transgenic proteins have been screened for identities of at least six contiguous amino acids shared with allergenic proteins. Twenty-two transgenic proteins showed positive results of six- or seven-contiguous amino acids length. Only a limited number of identical stretches shared by transgenic proteins (papaya ringspot virus coat protein, acetolactate synthase GH50, and glyphosate oxidoreductase) and allergenic proteins could be identified as (part of) potential linear epitopes. Conclusion Many transgenic proteins have identical stretches of six or seven amino acids in common with allergenic proteins. Most identical stretches are likely to be false positives. As shown in this study, identical stretches can be further screened for relevance by comparison with linear IgE-binding epitopes described in literature. In the absence of literature data on epitopes, antigenicity prediction by computer aids to select potential antibody binding sites that will need verification of IgE binding by sera binding tests. Finally, the positive outcomes of this approach warrant further clinical testing for potential allergenicity. PMID:12477382

  4. Design and construction of a synthetic Bacillus thuringiensis Cry4Aa gene: hyperexpression in Escherichia coli.

    PubMed

    Hayakawa, Tohru; Howlader, Mohammad Tofazzal Hossain; Yamagiwa, Masashi; Sakai, Hiroshi

    2008-10-01

    Cry4Aa produced by Bacillus thuringiensis is a dipteran-specific toxin and is, therefore, of great interest for developing a bioinsecticide to control mosquitoes. However, the expression of Cry4Aa in Escherichia coli is relatively low, which is a major disadvantage in its development as a bioinsecticide. In this study, to establish an effective production system, a 1,914-bp modified gene (cry4Aa-S1) encoding Cry4Aa was designed and synthesized in accordance with the G + C content and codon preference of E. coli genes without altering the encoded amino acid sequence. The cry4Aa-S1 gene allowed a significant improvement in expression level, over five-fold, compared to that of the original cry4Aa gene. The product of the cry4Aa-S1 gene showed the same level of insecticidal activity against Culex pipiens larvae as that from cry4Aa. This suggested that unfavorable codon usage was one of the reasons for poor expression of cry4Aa in E. coli, and, therefore, changing the cry4Aa codons to accord with the codon usage in E. coli led to efficient production of Cry4Aa. Efficient production of Cry4Aa in E. coli can be a powerful measure to prepare a sufficient amount of Cry4Aa protein for both basic analytical and applied researches.

  5. Inkoo and Tahyna, the European California serogroup bunyaviruses: sequence and phylogeny of the S RNA segment.

    PubMed

    Vapalahti, O; Plyusnin, A; Cheng, Y; Manni, T; Brummer-Korvenkontio, M; Vaheri, A

    1996-08-01

    Inkoo (INK) and Tahyna (TAH) viruses, European representatives of the California serogroup (CAL), genus Bunyavirus, family Bunyaviridae, are transmitted by mosquitoes and frequently infect man. The S segments of INK and TAH prototype strains were amplified, cloned and sequenced. INK S consists of 986 and TAH S of 977 nucleotides (nt) coding for a nucleocapsid protein of 235 amino acids (aa) and, in an overlapping reading frame, for a nonstructural protein of 92 or 97 aa, respectively. By S segment sequences and phylogenetic analysis INK was seen to be most closely related to Jamestown Canyon virus, isolated in the USA (92.4% nt and 96.6% aa identity), which is currently classified in a different subcomplex within the CAL viruses. TAH was genetically closest to Lumbo virus, isolated in Mozambique (89.0% nt and 94.1% aa identity). The data suggest that genetic variation within the CAL viruses is less related to geographical distance than to similarity in ecological cycles.

  6. The cytochrome P450 2AA gene cluster in zebrafish (Danio rerio): Expression of CYP2AA1 and CYP2AA2 and response to phenobarbital-type inducers

    SciTech Connect

    Kubota, Akira; Bainy, Afonso C.D.; Woodin, Bruce R.; Goldstone, Jared V.; Stegeman, John J.

    2013-10-01

    The cytochrome P450 (CYP) 2 gene family is the largest and most diverse CYP gene family in vertebrates. In zebrafish, we have identified 10 genes in a new subfamily, CYP2AA, which does not show orthology to any human or other mammalian CYP genes. Here we report evolutionary and structural relationships of the 10 CYP2AA genes and expression of the first two genes, CYP2AA1 and CYP2AA2. Parsimony reconstruction of the tandem duplication pattern for the CYP2AA cluster suggests that CYP2AA1, CYP2AA2 and CYP2AA3 likely arose in the earlier duplication events and thus are most diverged in function from the other CYP2AAs. On the other hand, CYP2AA8 and CYP2AA9 are genes that arose in the latest duplication event, implying functional similarity between these two CYPs. A molecular model of CYP2AA1 showing the sequence conservation across the CYP2AA cluster reveals that the regions with the highest variability within the cluster map onto CYP2AA1 near the substrate access channels, suggesting differing substrate specificities. Zebrafish CYP2AA1 transcript was expressed predominantly in the intestine, while CYP2AA2 was most highly expressed in the kidney, suggesting differing roles in physiology. In the liver CYP2AA2 expression but not that of CYP2AA1, was increased by 1,4-bis [2-(3,5-dichloropyridyloxy)] benzene (TCPOBOP) and, to a lesser extent, by phenobarbital (PB). In contrast, pregnenolone 16α-carbonitrile (PCN) increased CYP2AA1 expression, but not CYP2AA2 in the liver. The results identify a CYP2 subfamily in zebrafish that includes genes apparently induced by PB-type chemicals and PXR agonists, the first concrete in vivo evidence for a PB-type response in fish. - Highlights: • A tandemly duplicated cluster of ten CYP2AA genes was described in zebrafish. • Parsimony and duplication analyses suggest pathways to CYP2AA diversity. • Homology models reveal amino acid positions possibly related to functional diversity. • The CYP2AA locus does not share synteny with

  7. Detecting authorized and unauthorized genetically modified organisms containing vip3A by real-time PCR and next-generation sequencing.

    PubMed

    Liang, Chanjuan; van Dijk, Jeroen P; Scholtens, Ingrid M J; Staats, Martijn; Prins, Theo W; Voorhuijzen, Marleen M; da Silva, Andrea M; Arisi, Ana Carolina Maisonnave; den Dunnen, Johan T; Kok, Esther J

    2014-04-01

    The growing number of biotech crops with novel genetic elements increasingly complicates the detection of genetically modified organisms (GMOs) in food and feed samples using conventional screening methods. Unauthorized GMOs (UGMOs) in food and feed are currently identified through combining GMO element screening with sequencing the DNA flanking these elements. In this study, a specific and sensitive qPCR assay was developed for vip3A element detection based on the vip3Aa20 coding sequences of the recently marketed MIR162 maize and COT102 cotton. Furthermore, SiteFinding-PCR in combination with Sanger, Illumina or Pacific BioSciences (PacBio) sequencing was performed targeting the flanking DNA of the vip3Aa20 element in MIR162. De novo assembly and Basic Local Alignment Search Tool searches were used to mimic UGMO identification. PacBio data resulted in relatively long contigs in the upstream (1,326 nucleotides (nt); 95 % identity) and downstream (1,135 nt; 92 % identity) regions, whereas Illumina data resulted in two smaller contigs of 858 and 1,038 nt with higher sequence identity (>99 % identity). Both approaches outperformed Sanger sequencing, underlining the potential for next-generation sequencing in UGMO identification.

  8. Bridging Identities

    ERIC Educational Resources Information Center

    Deaux, Kay; Burke, Peter

    2010-01-01

    Sociology and psychology are no strangers in the theoretical world of self and identity. Early works by William James (1890), a psychologist, and George Herbert Mead (1934), a sociologist, are often taken as a starting point by investigators in both fields. In more recent years, with the development of a number of identity theories in both fields,…

  9. Brand Identity.

    ERIC Educational Resources Information Center

    Lawlor, John

    1998-01-01

    Instead of differentiating themselves by building "brand identities," colleges and universities often focus on competing with price. As a result, fewer and fewer institutions base their identities on value, the combination of quality and price. Methods of building two concepts to influence customers' brand image and brand loyalty are…

  10. Molecular and biological changes in the cold-adapted "master strain" A/AA/6/60 (H2N2) influenza virus.

    PubMed Central

    Herlocher, M L; Maassab, H F; Webster, R G

    1993-01-01

    The live cold-adapted (ca) A/AA/6/60 influenza vaccine is being commercially developed for worldwide use in children and is being used as a model for other live vaccines. Although it has been proven safe and immunogenic, the molecular basis of cold adaptation has never been determined. To identify sequence changes responsible for cold adaptation, we have compared the sequence of the master ca vaccine strain to its progenitor wild-type virus, wt A/AA/6/60 E2 (wt2). Only 4 nt differences encoding 2 aa differences were found in three gene segments. Computer-predicted RNA folds project different secondary structures between the ca and wt2 molecules based on the two silent differences between them. Genes coding for the acidic polymerase, matrix, and nonstructural proteins are identical between the two viruses. The few differences found in the ca A/AA/6/60 virus after its long stepwise passage at 25 degrees C in primary chicken kidney cells suggest that cold adaptation resulted in greater genetic stability for the highly variable RNA genome. PMID:8327480

  11. The Escherichia coli orthologue of the Salmonella ushB gene (ushB(c)) produces neither UDP-sugar hydrolase activity nor detectable protein, but has an identical sequence to that of Escherichia coli cdh.

    PubMed

    Schroder, W; Burger, M; Edwards, C; Douglas, M; Innes, D; Beacham, I R; Burns, D M

    2001-09-11

    Salmonella ushB, which encodes a membrane-bound UDP-sugar hydrolase, has an Escherichia coli orthologue (ushB(c)) which does not detectably produce this activity. In this report, we show that ushB(c) does not produce any detectable protein either, despite being transcribed normally. Remarkably, ushB(c) is shown to have 100% sequence identity with E. coli cdh, previously characterised as encoding an active CDP-diglyceride hydrolase, an apparent contradiction with implications regarding enzyme evolution. We suggest that a useful gene designation is cdh (ushB(c)) rather than either ushB(c) or cdh, alone.

  12. Section AA Pre2004 Fire, Section AA 2009, Section AA, South ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Section A-A Pre-2004 Fire, Section A-A 2009, Section A-A, South Elevation - Boston & Maine Railroad, Berlin Branch Bridge #148.81, Formerly spanning Moose Brook at former Boston & Maine Railroad, Gorham, Coos County, NH

  13. AAS 227: Day 1

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    , 2016Naoz also showed applications of the Kozai-Lidov mechanisms to dark matter halos around black holes, triple black hole systems, and so-called blue stragglers: main-sequence stars in clusters that are brighter and bluer than they should be. Her body of work is an excellent example of how theorists can adapt general physics theories to a wonderful variety of astronomical problems.holy styrofoam planets batman naoz just explained everything. #aas227 August Muench (@augustmuench) January 5, 2016Harassment in the Astronomical Sciences Town Hall(by Caroline Morley)The Town Hall on Harassment in the Astronomical Sciences involved a sobering panel discussion on the current state on workplace climate in astronomy and the current steps that the AAS and federal agencies are taking to improve it. Christina Richey kicked it off by presenting preliminary results from the CSWA Survey on workplace climate. This survey involved 426 participants, and reveals that many people, especially junior members of the field, experience harassment including both verbal and physical harassment. These results will be published this year. Next up, Dara Norman, a Councilor of the AAS and a member of the AAS Ethics Task Force, spoke about the proposed changes to the current AAS Ethics Statement. These changes will focus on corrective policies to improve the state of the field; they will solicit community feedback this Spring and vote on the changes at the Summer AAS meeting. Last, Jim Ulvestad, representing the federal agencies including NSF, NASA, and the DOE, spoke about the current policies for reporting to federal funding agencies. He reminds us that if an institution accepts money from the federal government, they are required by law to follow laws such as Title VI (covering racial harassment) and Title IX (covering sexual harassment), and that breaches can be reported to the funding agency.Tools and Tips for Better Software (aka Pain Reduction for Code Authors)(by Caroline Morley

  14. Mulberry strains of Xylella fastidiosa contain a 25 kilobase pair plasmid with extensive sequence identity to a plasmid from Verminephrobacter eiseniae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A 25 kbp plasmid was present in each of four Californian strains of Xylella fastidiosa from mulberry affected with leaf scorch disease. Fragments of each plasmid were cloned into E. coli, sequenced, and assembled into circular contigs of 25,105 bp (pXF-RIV11 and pXF-RIV16) or 24,372 bp (pXF-RIV19 an...

  15. Xylella fastidiosa isolates from mulberry harbor a 25 kilobase pair plasmid with extensive sequence identity to a plasmid from Verminephrobacter eiseniae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A 25 kbp plasmid was present in each of four Californian isolates of Xylella fastidiosa from mulberry affected with leaf scorch disease. Fragments of each plasmid were cloned into E. coli, sequenced, and assembled into circular contigs of 25,105 bp (pXF-RIV11 and pXF-RIV16) or 24,372 bp (pXF-RIV19 a...

  16. Plasmids of Xylella fastidiosa Mulberry-Infecting Strains Share Extensive Sequence Identity and Gene Complement with pVEIS01 From the Earthworm Symbiont Verminephrobacter Eiseniae

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A ~25 kbp plasmid was present in each of four Californian strains of Xylella fastidiosa from mulberry affected with leaf scorch disease. Fragments of each plasmid were cloned into E. coli, sequenced, and assembled into circular contigs of 25,105 bp (pXF-RIV11 and pXF-RIV16) or 24,372 bp (pXF-RIV19 a...

  17. Exon-intron organization and sequence comparison of human and murine T11 (CD2) genes

    SciTech Connect

    Diamond, D.J.; Clayton, L.K.; Sayre, P.H.; Reinherz, E.L.

    1988-03-01

    Genomic DNA clones containing the human and murine genes coding for the 50-kDa T11 (CD2) T-cell surface glycoprotein were characterized. The human T11 gene is approx. = 12 kilobases long and comprised of five exons. A leader exon (L) contains the 5'-untranslated region and most of the nucleotides defining the signal peptide (amino acids (aa) -24 to -5). Two exons encode the extracellular segment; exon Ex1 is 321 base pairs (bp) long and codes for four residues of the leader peptide and aa 1-103 of the mature protein, and exon Ex2 is 231 bp long and encodes aa 104-180. Exon TM is 123 bp long and codes for the single transmembrane region of the molecule (aa 181-221). Exon C is a large 765-bp exon encoding virtually the entire cytoplasmic domain (aa 222-327) and the 3'-untranslated region. The murine region T11 gene has a similar organization with exon-intron boundaries essentially identical to the human gene. Substantial conservation of nucleotide sequences between species in both 5'- and 3'-gene flanking regions equivalent to that among homologous exons suggests that murine and human genes may be regulated in a similar fashion. The probable relationship of the individual T11 exons to functional and structural protein domains is discussed.

  18. Cytochrome aa3 in Haloferax volcanii

    PubMed Central

    Tanaka, Mikiei; Ogawa, Naohide; Ihara, Kunio; Sugiyama, Yasuo; Mukohata, Yasuo

    2002-01-01

    A cytochrome in an extremely halophilic archaeon, Haloferax volcanii, was purified to homogeneity. This protein displayed a redox difference spectrum that is characteristic of a-type cytochromes and a CN− complex spectrum that indicates the presence of heme a and heme a3. This cytochrome aa3 consisted of 44- and 35-kDa subunits. The amino acid sequence of the 44-kDa subunit was similar to that of the heme-copper oxidase subunit I, and critical amino acid residues for metal binding, such as histidines, were highly conserved. The reduced cytochrome c partially purified from the bacterial membrane fraction was oxidized by the cytochrome aa3, providing physiological evidence for electron transfer from cytochrome c to cytochrome aa3 in archaea. PMID:11790755

  19. Identities for the Fibonacci Powers

    ERIC Educational Resources Information Center

    Chen, Alex; Chen, Hongwei

    2008-01-01

    Based on the generating functions, for any positive integers "n" and "k", identities are established and the explicit formula for a[subscript i](k) in terms of Fibonomial coefficients are presented. The corresponding results are extended to some other famous sequences including Lucas and Pell sequences.

  20. Mitochondrial DNA and retroviral RNA analyses of archival oral polio vaccine (OPV CHAT) materials: evidence of macaque nuclear sequences confirms substrate identity.

    PubMed

    Berry, Neil; Jenkins, Adrian; Martin, Javier; Davis, Clare; Wood, David; Schild, Geoffrey; Bottiger, Margareta; Holmes, Harvey; Minor, Philip; Almond, Neil

    2005-02-25

    Inoculation of live experimental oral poliovirus vaccines (OPV CHAT) during the 1950s in central Africa has been proposed to account for the introduction of HIV into human populations. For this to have occurred, it would have been necessary for chimpanzee rather than macaque kidney epithelial cells to have been included in the preparation of early OPV materials. Theoretically, this could have led to contamination with a progenitor of HIV-1 derived from a related simian immunodeficiency virus of chimpanzees (SIVCPZ). In this article we present further detailed analyses of two samples of OPV, CHAT 10A-11 and CHAT 6039/Yugo, which were used in early human trials of poliovirus vaccination. Recovery of poliovirus by culture techniques confirmed the biological viability of the vaccines and sequence analysis of poliovirus RNA specifically identified the presence of the CHAT strain. Independent nested sets of oligonucleotide primers specific for HIV-1/SIVCPZ and HIV-2/SIVMAC/SIVSM phylogenetic lineages, respectively, indicated no evidence of HIV/SIV RNA in either vaccine preparation, at a sensitivity of 100 RNA equivalents/ml. Analysis of cellular substrate by the amplification of two distinct regions of mitochondrial DNA (D-loop control region and 12S ribosomal sequences) revealed no evidence of chimpanzee cellular sequences. However, this approach positively identified rhesus and cynomolgus macaque DNA for the CHAT 10A-11 and CHAT 6039/Yugo vaccine preparations, respectively. Analysis of multiple clones of mtDNA 12S rDNA indicated a relatively high number of nuclear mitochondrial DNA sequences (numts) in the CHAT 10A-11 material, but confirmed the macaque origin of cellular substrate used in vaccine preparation. These data reinforce earlier findings on this topic providing no evidence to support the contention that poliovirus vaccination was responsible for the introduction of HIV into humans and sparking the AIDS pandemic.

  1. Sequencing type material resolves the identity and distribution of the generitype Lithophyllum incrustans, and related European species L. hibernicum and L. bathyporum (Corallinales, Rhodophyta).

    PubMed

    Hernandez-Kantun, Jazmin J; Rindi, Fabio; Adey, Walter H; Heesch, Svenja; Peña, Viviana; Le Gall, Line; Gabrielson, Paul W

    2015-08-01

    DNA sequences from type material in the nongeniculate coralline genus Lithophyllum were used to unambiguously link some European species names to field-collected specimens, thus providing a great advance over morpho-anatomical identifi-cation. In particular, sequence comparisons of rbcL, COI and psbA genes from field-collected specimens allowed the following conclusion: the generitype species, L. incrustans, occurs mostly as subtidal rhodoliths and crusts on both Atlantic and Mediterranean coasts, and not as the common, NE Atlantic, epilithic, intertidal crust reported in the literature. The heterotypic type material of L. hibernicum was narrowed to one rhodolith belonging in Lithophyllum. As well as occurring as a subtidal rhodolith, L. hibernicum is a common, epilithic and epizoic crust in the intertidal zone from Ireland south to Mediterranean France. A set of four features distinguished L. incrustans from L. hibernicum, including epithallial cell diameter, pore canal shape of sporangial conceptacles and sporangium height and diameter. An rbcL sequence of the lectotype of Lithophyllum bathyporum, which was recently proposed to accommodate Atlantic intertidal collections of L. incrustans, corresponded to a distinct taxon hitherto known only from Brittany as the subtidal, bisporangial, lectotype, but also occurs intertidally in Atlantic Spain. Specimens from Ireland and France morpho-anatomically identified as L. fasciculatum and a specimen from Cornwall likewise identified as L. duckerae were resolved as L. incrustans and L. hibernicum, respectively.

  2. The AAS Workforce Survey

    NASA Astrophysics Data System (ADS)

    Postman, Marc; Norman, D. J.; Evans, N. R.; Ivie, R.

    2014-01-01

    The AAS Demographics Committee, on behalf of the AAS, was tasked with initiating a biennial survey to improve the Society's ability to serve its members and to inform the community about changes in the community's demographics. A survey, based in part on similar surveys for other scientific societies, was developed in the summer of 2012 and was publicly launched in January 2013. The survey randomly targeted 2500 astronomers who are members of the AAS. The survey was closed 4 months later (April 2013). The response rate was excellent - 63% (1583 people) completed the survey. I will summarize the results from this survey, highlighting key results and plans for their broad dissemination.

  3. AAS 228: Welcome!

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Greetings from the 228th American Astronomical Society meeting in San Diego, California! This week, along with a team of fellow authorsfrom astrobites, Iwill bewritingupdates on selectedevents at themeeting and posting twiceeach day. You can follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.If youre at the meeting, come stop by the AAS booth (Booth #211-213) to learn about the newly-announced partnership between AAS and astrobites and pick up some swag.And dont forget to visit the IOP booth in the Exhibit Hall (Booth #223) to learn more about the new corridors for AAS Journals and to pick up a badge pin to representyour corridor!

  4. AAS 227: Welcome!

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Greetings from the 227th American Astronomical Society meeting in Kissimmee, Florida! This week, along with several fellow authors from astrobites, Iwill bewritingupdates on selectedevents at themeeting and posting at the end of each day. You can follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.If youre an author or referee (or plan to be!) and youre here at the meeting, consider joining us at our Author and Referee Workshop on Wednesday in the Tallahassee room, where well be sharingsome of the exciting new features of the AAS journals. You can drop intoeither of the two-hour sessions(10 AM 12 PM or 1 PM 3 PM), and there will be afree buffet lunch at noon.Heres the agenda:Morning SessionTopic Speaker10:00 am 10:05 amIntroductionsJulie Steffen10:05 am 10:35 amChanges at AAS Journals; How to Be a Successful AAS AuthorEthan Vishniac10:35 am 11:00 amThe Peer Review ProcessButler Burton11:00 am 11:15 amAAS Nova: Sharing AAS Authors Research with the Broader CommunitySusanna Kohler11:15 am 11:30 amFixing Software and Instrumentation Publishing: New Paper Styles in AAS JournalsChris Lintott11:30 am 11:45 amMaking Article Writing Easier with the New AASTeX v6.0Greg Schwarz11:45 am 12:00 pmBringing JavaScript and Interactivity to Your AAS Journal FiguresGus MuenchLunch SessionTopic Speaker12:00 pm 12:15 pmUnified Astronomy ThesaurusKatie Frey12:15 pm 12:30 pmAAS/ADS ORCID Integration ToolAlberto Accomazzi12:30 pm 12:45 pmWorldWide Telescope and Video AbstractsJosh Peek12:45 pm 01:00 pmArizona Astronomical Data Hub (AADH)Bryan HeidornAfternoon SessionTopic Speaker01:00 pm 01:05 pmIntroductionsJulie Steffen01:05 pm 01:35 pmChanges at AAS Journals; How to Be a Successful AAS AuthorEthan Vishniac01:35 pm 02:00 pmThe Peer Review ProcessButler Burton02:00 pm 02:15 pmAAS Nova: Sharing AAS Authors Research with the Broader CommunitySusanna Kohler02:15 pm 02:30 pm

  5. 77 FR 72712 - Identity Theft Red Flags and Address Discrepancies Under the Fair and Accurate Credit...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-06

    ... CFR Part 681 RIN 3084-AA94 Identity Theft Red Flags and Address Discrepancies Under the Fair and... ``financial institutions'' and ``creditors'' to develop and implement a written identity theft program to identify, detect, and respond to possible risks of identity theft relevant to them. \\1\\ 72 FR 63718 (Nov....

  6. Morphologic and molecular study of hemoparasites in wild corvids and evidence of sequence identity with Plasmodium DNA detected in captive black-footed penguins (Spheniscus demersus).

    PubMed

    Leclerc, Antoine; Chavatte, Jean-Marc; Landau, Irène; Snounou, Georges; Petit, Thierry

    2014-09-01

    A morphologic and molecular epidemiologic investigation was conducted on a captive African black-footed penguin (Spheniscus demersus) colony with a history of Plasmodium infections at La Palmyre Zoo (France). Each penguin received 12.5 mg of pyrimethamine twice a week as a prophylaxis every year from April to November. Although Plasmodium parasites were not detected in blood smears and tissues collected from the penguins, various blood parasites were recorded in blood smears from wild Eurasian magpies (Pica pica) and carrion crows (Corvus corone) sampled at the same time in the study area. These parasites consisted of several Plasmodium spp. (P. lenoblei, P. dorsti, P bioccai, P. relictum, P. dherteae, P. beaucournui, P. maior, P. tranieri, and P. snounoui), Parahaemoproteus spp., Trypanosoma spp., and Leucocytozoon spp. On the other hand, nested polymerase chain reaction enabled detection of Plasmodium DNA in 28/44 (64%) penguins, 15/25 (60%) magpies, and 4/9 (44%) crows. Sequencing and phylogenetic analyses indicated that the parasite DNA amplified from the penguins, magpies, and crows were similar. Magpies and crows could therefore act as a reservoir for penguin Plasmodium infections, which may be more prevalent than previously thought. Morphologic characterization of the Plasmodium spp. detected in the penguins, as well as further biological and epidemiologic studies, are needed to fully understand the transmission of Plasmodium parasites to captive penguins.

  7. A comparison of quantitative-competitive and realtime PCR assays using an identical target sequence to detect Epstein-Barr virus viral load in the peripheral blood.

    PubMed

    Xu, Shushen; Green, Michael; Kingsley, Laurence; Webber, Steven; Rowe, David

    2006-11-01

    Monitoring the load of Epstein-Barr virus (EBV) in the peripheral blood by quantitative PCR has been accepted as a useful tool for predicting the onset of EBV related diseases, confirming an EBV disease diagnosis and following the response to treatment interventions. In the present study, the use of a realtime polymerase chain reaction (rt-PCR) assay developed for unpurified cell preparations was examined and the results of the realtime assay were compared to an EBV quantitative-competitive PCR assay (QC-PCR). Both assays use the same target sequence and the same method for determining the standard value for the copy number of EBV genomes present. A comparison of 572 PCR results reveals that the realtime assay gave 5-10-fold higher values than the QC-PCR. Fifty-one results (8.9%) were discordant between the two sets of data. The most commonly encountered discordant result was detection of low amounts of EBV DNA by the rt-PCR assay that were not detected in specimens by QC-PCR. The two assays had a high degree of correlation across the range of load detection allowing clinically relevant threshold values determined in the QC-PCR assay to be inferred for the rt-PCR assay. External normalization of the rt-PCR assay was determined to be an important tool for monitoring the quality and/or quantity of human DNA in the starting material. rt-PCR assays with unpurified cell lysates compare favorably with quantitative-competitive assays and when normalized offer real advantages in specimen preparation, assay manipulations and reproducibility over both quantitative-competitive assays and realtime assays that require purified nucleic acid inputs.

  8. Personal Construct Theory and the Transformation of Identity in Alcoholics Anonymous

    ERIC Educational Resources Information Center

    Young, Lance Brendan

    2011-01-01

    The dominant theoretical approach to alcoholism research presumes linear, causal relationships between individual cognitions and behavioral outcomes. This approach has largely failed to account for the recovery some alcoholics achieve in Alcoholics Anonymous (AA) because AA emphasizes the transformation of identity, framed in terms of…

  9. Ginger and turmeric expressed sequence tags identify signature genes for rhizome identity and development and the biosynthesis of curcuminoids, gingerols and terpenoids

    PubMed Central

    2013-01-01

    Background Ginger (Zingiber officinale) and turmeric (Curcuma longa) accumulate important pharmacologically active metabolites at high levels in their rhizomes. Despite their importance, relatively little is known regarding gene expression in the rhizomes of ginger and turmeric. Results In order to identify rhizome-enriched genes and genes encoding specialized metabolism enzymes and pathway regulators, we evaluated an assembled collection of expressed sequence tags (ESTs) from eight different ginger and turmeric tissues. Comparisons to publicly available sorghum rhizome ESTs revealed a total of 777 gene transcripts expressed in ginger/turmeric and sorghum rhizomes but apparently absent from other tissues. The list of rhizome-specific transcripts was enriched for genes associated with regulation of tissue growth, development, and transcription. In particular, transcripts for ethylene response factors and AUX/IAA proteins appeared to accumulate in patterns mirroring results from previous studies regarding rhizome growth responses to exogenous applications of auxin and ethylene. Thus, these genes may play important roles in defining rhizome growth and development. Additional associations were made for ginger and turmeric rhizome-enriched MADS box transcription factors, their putative rhizome-enriched homologs in sorghum, and rhizomatous QTLs in rice. Additionally, analysis of both primary and specialized metabolism genes indicates that ginger and turmeric rhizomes are primarily devoted to the utilization of leaf supplied sucrose for the production and/or storage of specialized metabolites associated with the phenylpropanoid pathway and putative type III polyketide synthase gene products. This finding reinforces earlier hypotheses predicting roles of this enzyme class in the production of curcuminoids and gingerols. Conclusion A significant set of genes were found to be exclusively or preferentially expressed in the rhizome of ginger and turmeric. Specific

  10. Complete nucleotide sequence of a novel strain of fig fleck-associated virus from China.

    PubMed

    He, Zhen; Mijit, Mahmut; Li, Shifang; Zhang, Zhixiang

    2017-04-01

    The complete nucleotide sequence of fig fleck-associated virus from Xinjiang Uygur Autonomous Region of China (FFkaV-CN) was determined. The 6,723-nucleotide-long viral genome, excluding a terminal poly(A) tail, contains three open reading frames (ORFs). Pairwise comparisons showed that FFkaV-CN shares 83% and 92% sequence identity with FFkaV-Italy based on the complete genomic sequence and CP aa sequence, respectively, slightly higher than the species demarcation criterion for the genus Maculavirus. Phylogenetic analysis showed that FFkaV-CN and FFkaV-Italy clustered into one group. These results indicate that FFkaV-CN is a novel strain of FFkaV with a genome organization somewhat different from what was reported for FFkaV-Italy.

  11. AAS Career Services

    NASA Astrophysics Data System (ADS)

    Marvel, Kevin B.

    2012-08-01

    The American Astronomical Society provides substantial programs in the area of Career Services.Motivated by the Society's mission to enhance and share humanity's understanding of the Universe, the AAS provides a central resource for advertising positions, interviewing opportunities at its annual winter meeting and information, workshops and networks to enable astronomers to find employment.The programs of the Society in this area are overseen by an active committee on employment and the AAS Council itself.Additional resources that help characterize the field, its growth and facts about employment such as salaries and type of jobs available are regularly summarized and reported on by the American Institute of Physics.

  12. Experimental immunologically mediated aplastic anemia (AA) in mice: cyclosporin A fails to protect against AA

    SciTech Connect

    Knospe, W.H.; Steinberg, D.; Gratwohl, A.; Speck, B.

    1984-07-01

    Immunologically mediated aplastic anemia (AA) in mice was induced by the i.v. injection of 10(7) lymph node cells (LNC) from H-2k identical but Mls mismatched CBA/J donor mice into previously irradiated (600 rad total body gamma) C3H/HeJ mice. Cyclosporin A (CsA), 25 mg/kg, was administered subcutaneously from day -1 to day 30. Control mice included C3H/HeJ mice which received 600 rad alone, C3H/HeJ mice which received 600 rad plus CsA as above, and C3H/HeJ mice which received 600 rad total body irradiation followed by 10(7) LNC from CBA/J donors. CsA failed to prevent lethal AA. These results suggest that the pathogenetic mechanisms operating in immunologically mediated AA differ from the mechanisms operating in rodents transplanted with allogeneically mismatched marrow or spleen cells which develop graft-versus-host disease. The results are consistent with a non-T cell-dependent mechanism causing the AA.

  13. A Quantitative Tool to Distinguish Isobaric Leucine and Isoleucine Residues for Mass Spectrometry-Based De Novo Monoclonal Antibody Sequencing

    NASA Astrophysics Data System (ADS)

    Poston, Chloe N.; Higgs, Richard E.; You, Jinsam; Gelfanova, Valentina; Hale, John E.; Knierman, Michael D.; Siegel, Robert; Gutierrez, Jesus A.

    2014-07-01

    De novo sequencing by mass spectrometry (MS) allows for the determination of the complete amino acid (AA) sequence of a given protein based on the mass difference of detected ions from MS/MS fragmentation spectra. The technique relies on obtaining specific masses that can be attributed to characteristic theoretical masses of AAs. A major limitation of de novo sequencing by MS is the inability to distinguish between the isobaric residues leucine (Leu) and isoleucine (Ile). Incorrect identification of Ile as Leu or vice versa often results in loss of activity in recombinant antibodies. This functional ambiguity is commonly resolved with costly and time-consuming AA mutation and peptide sequencing experiments. Here, we describe a set of orthogonal biochemical protocols, which experimentally determine the identity of Ile or Leu residues in monoclonal antibodies (mAb) based on the selectivity that leucine aminopeptidase shows for n-terminal Leu residues and the cleavage preference for Leu by chymotrypsin. The resulting observations are combined with germline frequencies and incorporated into a logistic regression model, called Predictor for Xle Sites (PXleS) to provide a statistical likelihood for the identity of Leu at an ambiguous site. We demonstrate that PXleS can generate a probability for an Xle site in mAbs with 96% accuracy. The implementation of PXleS precludes the expression of several possible sequences and, therefore, reduces the overall time and resources required to go from spectra generation to a biologically active sequence for a mAb when an Ile or Leu residue is in question.

  14. The complete nucleotide sequence of chrysanthemum stem necrosis virus.

    PubMed

    Dullemans, A M; Verhoeven, J Th J; Kormelink, R; van der Vlugt, R A A

    2015-02-01

    The complete genome sequence of chrysanthemum stem necrosis virus (CSNV) was determined using Roche 454 next-generation sequencing. CSNV is a tentative member of the genus Tospovirus within the family Bunyaviridae, whose members are arthropod-borne. This is the first report of the entire RNA genome sequence of a CSNV isolate. The large RNA of CSNV is 8955 nucleotides (nt) in size and contains a single open reading frame of 8625 nt in the antisense arrangement, coding for the putative RNA-dependent RNA polymerase (L protein) of 2874 aa with a predicted Mr of 331 kDa. Two untranslated regions of 397 and 33 nt are present at the 5' and 3' termini, respectively. The medium (M) and small (S) RNAs are 4830 and 2947 nt in size, respectively, and show 99 % identity to the corresponding genomic segments of previously partially characterized CSNV genomes. Protein sequences for the precursor of the Gn/Gc proteins, N and NSs, are identical in length in all of the analysed CSNV isolates.

  15. AAS Oral History Project

    NASA Astrophysics Data System (ADS)

    Buxner, Sanlyn; Holbrook, Jarita; AAS Oral History Team

    2016-06-01

    Now in its fourth year, the AAS Oral History Project has interviewed over 80 astronomers from all over the world. Led by the AAS Historical Astronomy Division (HAD) and partially funded by the American Institute of Physics Niels Bohr Library and ongoing support from the AAS, volunteers have collected oral histories from astronomers at professional meetings starting in 2015, including AAS, DPS, and the IAU general assembly. Each interview lasts one and a half to two hours and focuses on interviewees’ personal and professional lives. Questions include those about one’s family, childhood, strong influences on one’s scientific career, career path, successes and challenges, perspectives on how astronomy is changing as a field, and advice to the next generation. Each interview is audio recorded and transcribed, the content of which is checked with each interviewee. Once complete, interview transcripts are posted online as part of a larger oral history library at https://www.aip.org/history-programs/niels-bohr-library/oral-histories. Future analysis will reveal a rich story of astronomers and will help the community address issues of diversity, controversies, and the changing landscape of science. We are still recruiting individuals to be interviewed from all stages of career from undergraduate students to retired and emeritus astronomers. Contact Jarita Holbrook to schedule an interview or to find out more information about the project (astroholbrook@gmail.com). Also, contact Jarita Holbrook if you would like to become an interviewer for the project.

  16. Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes.

    PubMed

    Liu, Hongbo; Liu, Xiaojuan; Zhang, Shumei; Lv, Jie; Li, Song; Shang, Shipeng; Jia, Shanshan; Wei, Yanjun; Wang, Fang; Su, Jianzhong; Wu, Qiong; Zhang, Yan

    2016-01-08

    DNA methylation is a key epigenetic mark that is critical for gene regulation in multicellular eukaryotes. Although various human cell types may have the same genome, these cells have different methylomes. The systematic identification and characterization of methylation marks across cell types are crucial to understand the complex regulatory network for cell fate determination. In this study, we proposed an entropy-based framework termed SMART to integrate the whole genome bisulfite sequencing methylomes across 42 human tissues/cells and identified 757 887 genome segments. Nearly 75% of the segments showed uniform methylation across all cell types. From the remaining 25% of the segments, we identified cell type-specific hypo/hypermethylation marks that were specifically hypo/hypermethylated in a minority of cell types using a statistical approach and presented an atlas of the human methylation marks. Further analysis revealed that the cell type-specific hypomethylation marks were enriched through H3K27ac and transcription factor binding sites in cell type-specific manner. In particular, we observed that the cell type-specific hypomethylation marks are associated with the cell type-specific super-enhancers that drive the expression of cell identity genes. This framework provides a complementary, functional annotation of the human genome and helps to elucidate the critical features and functions of cell type-specific hypomethylation.

  17. Cloning and sequence analysis of FSH and LH in the giant panda (Ailuropoda melanoleuca).

    PubMed

    Liao, Ming-Juan; Zhu, Mu-Yuan; Zhang, Zhi-He; Zhang, An-Ju; Li, Guang-Han; Sheng, Fu-Jun

    2003-05-15

    The giant panda (Ailuropoda melanoleuca) is an endangered species and indigenous to China. It has been proposed that it has a highly specialized reproductive pattern with low fecundity, but little is known about its basic reproductive biology at the molecular level. In this report the genes encoding gonadotropin subunits alpha, follicle-stimulating hormone (FSH) beta and luteinizing hormone (LH) beta of the giant panda were amplified for the first time by RT-PCR from pituitary total RNA, and were cloned, sequenced and analyzed. The results revealed that the open reading region (ORF) of gonadotropin subunits alpha, FSH beta and LH beta are 363, 390 and 426 bp long, respectively. They displayed a reasonably high degree (74-94, 85-93, 75-91%, for alpha, FSH beta and LH beta subunits, respectively) of identity when deduced amino acids were compared with homologous sequences from partial available mammals including human, cattle, sheep, pig, rat, mouse. Three distinct differences were found at the site of 59 aa of the alpha subunit and 55 aa, 68 aa of FSH beta subunit. Our results provide an insight into understanding the mechanism of reproduction regulation and genetic characteristics of giant panda which will make an actual contribution to its conservation. In addition they lay a foundation for a further study towards producing recombinant panda FSH and LH which can be used in artificial breeding aimed to increase its captive reproductive efficiency.

  18. Structural characterization and biological activity of recombinant human epidermal growth factor proteins with different N-terminal sequences.

    PubMed

    Svoboda, M; Bauhofer, A; Schwind, P; Bade, E; Rasched, I; Przybylski, M

    1994-05-18

    The primary structures and molecular homogeneity of recombinant human epidermal growth factors from different suppliers were characterized and their biological activities evaluated by a standard DNA synthesis assay. Molecular weight determinations using 252Cf-plasma-desorption and electrospray mass spectrometry in combination with N- and C-terminal sequence analysis and determination of intramolecular disulfide bridges revealed that one recombinant protein had the correct human-identical structure (54 aa residues; 6347 Da). In contrast, a second recombinant protein (7020 Da) was found to contain a pentapeptide (KKYPR) insert following its N-terminal methionine. This structural variant showed a significant reduction in its capacity to stimulate DNA synthesis.

  19. Comparison of repair of DNA double-strand breaks in identical sequences in primary human fibroblast and immortal hamster-human hybrid cells harboring a single copy of human chromosome 11

    NASA Technical Reports Server (NTRS)

    Fouladi, B.; Waldren, C. A.; Rydberg, B.; Cooper, P. K.; Chatterjee, A. (Principal Investigator)

    2000-01-01

    We have optimized a pulsed-field gel electrophoresis assay that measures induction and repair of double-strand breaks (DSBs) in specific regions of the genome (Lobrich et al., Proc. Natl. Acad. Sci. USA 92, 12050-12054, 1995). The increased sensitivity resulting from these improvements makes it possible to analyze the size distribution of broken DNA molecules immediately after the introduction of DSBs and after repair incubation. This analysis shows that the distribution of broken DNA pieces after exposure to sparsely ionizing radiation is consistent with the distribution expected from randomly induced DSBs. It is apparent from the distribution of rejoined DNA pieces after repair incubation that DNA ends continue to rejoin between 3 and 24 h postirradiation and that some of these rejoining events are in fact misrejoining events, since novel restriction fragments both larger and smaller than the original fragment are generated after repair. This improved assay was also used to study the kinetics of DSB rejoining and the extent of misrejoining in identical DNA sequences in human GM38 cells and human-hamster hybrid A(L) cells containing a single human chromosome 11. Despite the numerous differences between these cells, which include species and tissue of origin, levels of TP53, expression of telomerase, and the presence or absence of a homologous chromosome for the restriction fragments examined, the kinetics of rejoining of radiation-induced DSBs and the extent of misrejoining were similar in the two cell lines when studied in the G(1) phase of the cell cycle. Furthermore, DSBs were removed from the single-copy human chromosome in the hamster A(L) cells with similar kinetics and misrejoining frequency as at a locus on this hybrid's CHO chromosomes.

  20. Molecular cloning of the cytochrome aa3 gene from the archaeon (Archaebacterium) Halobacterium halobium.

    PubMed

    Denda, K; Fujiwara, T; Seki, M; Yoshida, M; Fukumori, Y; Yamanaka, T

    1991-11-27

    A novel aa3-type cytochrome oxidase from the extremely halophilic archaeon, Halobacterium halobium, differs significantly from those of other prokaryotic and eukaryotic cytochrome oxidases (Fujiwara, T., Fukumori, Y., and Yamanaka, T. (1989) J. Biochem. 105, 287-292). In the present study, we cloned and sequenced the gene which encodes the cytochrome aa3 by using the polymerase chain reaction methods. The deduced amino acid sequence of subunit I of H. halobium cytochrome aa3 was more similar to that of subunit I of the eukaryotic cytochrome (44%, maize mitochondria) than that of the cytochrome from other bacteria (36%, Paracoccus denitrificans). The consensus sequence in putative metal binding residues is well-conserved also in H. halobium cytochrome aa3.

  1. Alternative Identities in Multicultural Schools in Israel: Emancipatory Identity, Mixed Identity and Transnational Identity

    ERIC Educational Resources Information Center

    Resnik, Julia

    2006-01-01

    Economic and technological processes of globalization and the increasing migrations of people in the world undermine dominant national identities. One of the main characteristics of our time is the instability of identities and the continuous invention of new/old identities. Traditions and ethnic identities are deconstructed and reconstructed.…

  2. Talkin' Musical Identities Blues

    ERIC Educational Resources Information Center

    Lamb, Roberta

    2004-01-01

    After reading the book "Musical Identities" (Raymond MacDonald, David Hargreaves, Dorothy Miell, eds.; Oxford and New York: Oxford University Press, 2002), this author states she finds it difficult to separate "identities in music" from "music in identities." In fact, she cannot conceive of music apart from identity.…

  3. Personal Identity in Italy

    ERIC Educational Resources Information Center

    Crocetti, Elisabetta; Rabaglietti, Emanuela; Sica, Luigia Simona

    2012-01-01

    This chapter discusses specifics of identity formation in Italian adolescents and emerging adults. We review consistent evidence illustrating that, in Italy, a progressive deferral of transition to adulthood strongly impacts youth identity development by stimulating identity exploration and postponement of identity commitments. We also consider…

  4. AAS 227: Day 2

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Welcome to Day 2 of the winter American Astronomical Society (AAS) meeting in Kissimmee! Several of us are attending the conference this year, and we will report highlights from each day here on astrobites. If youd like to see more timely updates during the day, we encourage you to follow @astrobites on twitter or search the #aas227 hashtag.Plenary Session: Black Hole Physics with the Event Horizon Telescope (by Susanna Kohler)If anyone needed motivation to wake up early this morning, they got it in the form of Feryal Ozel (University of Arizona) enthralling us all with exciting pictures, videos, and words about black holes and the Event Horizon Telescope. Ozel spoke to a packed room (at 8:30am!) about where the project currently stands, and where its heading in the future.The EHT has pretty much the coolest goal ever: actually image the event horizons of black holes in our universe. The problem is that the largest black hole we can look at (Sgr A*, in the center of our galaxy) has an event horizon size of 50 as. For this kind of resolution roughly equivalent to trying to image a DVD on the Moon! wed need an Earth-sized telescope. EHT has solved this problem by linking telescopes around the world, creating one giant, mm-wavelength effective telescope with a baseline the size of Earth.Besides producing awesome images, the EHT will be able to test properties of black-hole spacetime, the no-hair theorem, and general relativity (GR) in new regimes.Ozel walked us through some of the theory prep work we need to do now in order to get the most science out of the EHT, including devising new

  5. Complete genome sequences of a putative new alphapartitivirus detected in Rosa spp.

    PubMed

    Phelan, James; James, Delano

    2016-09-01

    A putative new alphapartitivirus was detected by next-generation sequencing (NGS) in Rosa spp. and identified as rose partitivirus isolate Phyllis Bide (RoPV-PB). The virus is bipartite with a dsRNA1 fragment (1937 bp) encoding a putative RdRp and a dsRNA2 fragment (1811 bp) encoding the putative CP subunit of the virus. dsRNA1 of RoPV-BP is closely related to Vicia faba partitivirus 1, with identities of 67 % and 72 % for the nucleotide (nt) and deduced amino acid (aa) sequences, respectively. In NGS analysis of RoPV-BP, coverage was uneven across both dsRNA fragments, with GC/AT content appearing to be a major determinant of depth of coverage.

  6. Bioinformatic Analysis Reveals Archaeal tRNATyr and tRNATrp Identities in Bacteria

    PubMed Central

    Mukai, Takahito; Reynolds, Noah M.; Crnković, Ana; Söll, Dieter

    2017-01-01

    The tRNA identity elements for some amino acids are distinct between the bacterial and archaeal domains. Searching in recent genomic and metagenomic sequence data, we found some candidate phyla radiation (CPR) bacteria with archaeal tRNA identity for Tyr-tRNA and Trp-tRNA synthesis. These bacteria possess genes for tyrosyl-tRNA synthetase (TyrRS) and tryptophanyl-tRNA synthetase (TrpRS) predicted to be derived from DPANN superphylum archaea, while the cognate tRNATyr and tRNATrp genes reveal bacterial or archaeal origins. We identified a trace of domain fusion and swapping in the archaeal-type TyrRS gene of a bacterial lineage, suggesting that CPR bacteria may have used this mechanism to create diverse proteins. Archaeal-type TrpRS of bacteria and a few TrpRS species of DPANN archaea represent a new phylogenetic clade (named TrpRS-A). The TrpRS-A open reading frames (ORFs) are always associated with another ORF (named ORF1) encoding an unknown protein without global sequence identity to any known protein. However, our protein structure prediction identified a putative HIGH-motif and KMSKS-motif as well as many α-helices that are characteristic of class I aminoacyl-tRNA synthetase (aaRS) homologs. These results provide another example of the diversity of molecular components that implement the genetic code and provide a clue to the early evolution of life and the genetic code. PMID:28230768

  7. AAS 227: Day 3

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Welcome to Day 3 of the winter American Astronomical Society (AAS) meeting in Kissimmee! Several of us are attending the conference this year, and we will report highlights from each day here on astrobites. If youd like to see more timely updates during the day, we encourage you to follow @astrobites on twitter or search the #aas227 hashtag.Henry Norris Russell Lecture: Viewing the Universe with Infrared Eyes: The Spitzer Space Telescope (by Erika Nesvold)The Henry Norris Russell Award is the highest honor given by the AAS, for a lifetime of eminence in astronomy research. This years award went to Giovanni Fazio of the Harvard-Smithsonian Center for Astrophysics. Fazio became a leader in gamma ray astronomy before switching mid-career to the study of infrared astronomy, and he gave his award lecture on the latter subject, specifically on the Spitzer Space Telescope, one of the most successful infrared telescopes of all time.Artists rendering of the Spitzer space telescope. [NASA/JPL-Caltech]Spitzer has been operating for more than twelve years, and has resulted in over six thousand papers in refereed journals in that time. The telescope sits in an Earth-trailing orbit around the Sun, and is now farther from the Earth (1.4 AU) than the Earth is from the Sun. Fazio gave the audience a fascinating overview of the science done by Spitzer over more than a decade. One of the most productive areas of research for Spitzer is the study of exoplanets, which hadnt even been discovered when the Spitzer Telescope was first conceived. Spitzers high sensitivity and ability to observe exoplanets over

  8. Literacy and Sexual Identity.

    ERIC Educational Resources Information Center

    Moje, Elizabeth Birr; MuQaribu, Mudhillun

    2003-01-01

    Calls for more attention to literacy teaching practices and teacher education that acknowledge sexual identity and orientation as key aspects of youth identity development. Discusses experience-based pedagogy and classroom interactions around sexual identities and texts. Notes the need for research and scholarship in the field of literacy and…

  9. Teachers' Interpersonal Role Identity

    ERIC Educational Resources Information Center

    van der Want, Anna C.; den Brok, Perry; Beijaard, Douwe; Brekelmans, Mieke; Claessens, Luce C. A.; Pennings, Helena J. M.

    2015-01-01

    This article investigates the link between teachers' appraisal of specific interpersonal situations in classrooms and their more general interpersonal identity standard, which together form their interpersonal role identity. Using semi-structured and video-stimulated interviews, data on teachers' appraisals and interpersonal identity standards…

  10. Identity security awareness.

    PubMed

    Philipsen, Nayna C

    2004-01-01

    Identity theft is an increasing concern when organizations, businesses, and even childbirth educators ask for a client's Social Security number for identification purposes. In this column, the author suggests ways to protect one's identity and, more importantly, decrease the opportunities for identity theft.

  11. Language, Power and Identity

    ERIC Educational Resources Information Center

    Wodak, Ruth

    2012-01-01

    How are identities constructed in discourse? How are national and European identities tied to language and communication? And what role does power have--power in discourse, over discourse and of discourse? This paper seeks to identify and analyse processes of identity construction within Europe and at its boundaries, particularly the diversity of…

  12. Observations of AA Tau requested to schedule XMM-Newton

    NASA Astrophysics Data System (ADS)

    Waagen, Elizabeth O.

    2013-08-01

    Dr. Hans Moritz Guenther (Harvard-Smithsonian Center for Astrophysics) has requested nightly observations of the classical T Tauri star AA Tau in order to schedule x-ray observations with XMM-Newton that have been planned for between 2013 August 15 and September 15. The purpose of the AAVSO observations is to determine whether AA Tau is at a suitable magnitude for the satellite observations. Taurus is difficult to observe during this time period but that is exactly why AAVSO assistance is needed! AA Tau is a morning object, and also, many of the professional ground-based telescopes are offline because of the US southwest monsoon season. Since it is critical to know the brightness of AA Tau, AAVSO observations will be truly essential. Nightly visual and snapshot (not more than once per night) observations beginning now and continuing through September 20 are needed. Coverage beginning ahead of the XMM window is requested because there is a one- to two-week lead time for the target to be inserted into the telescope schedule. Continuing the nightly observations a few days beyond the end of the XMM window will give better optical context for the x-ray data. AA Tau ranges between ~12.8V and ~16.1V; since December 2011 or earlier it has been at ~14.5V. The most recent observation in the AAVSO International Database shows it at 14.779V on 2013 Feb 5 (J. Roe, Bourbon, MO). Dr. Guenther writes, "AA Tau is surrounded by a thick accretion disk which is seen nearly edge-on. For decades the light curve of AA Tau showed regular eclipsing events when the accretion funnel rotated through the line of sight. However, earlier this year J. Bouvier and his group found that this behavior changed dramatically: AA Tau now seems to be deeply absorbed all the time (V band 14.5 mag). In collaboration with this group we will perform X-ray observations of AA Tau with the XMM-Newton satellite." Finder charts with sequence may be created using the AAVSO Variable Star Plo! tter (http

  13. Critical optical properties of AA-stacked multilayer graphenes

    NASA Astrophysics Data System (ADS)

    Chiu, Chih-Wei; Chen, Szu-Chao; Huang, Yuan-Cheng; Shyu, Feng-Lin; Lin, Ming-Fa

    2013-07-01

    The band structures and optical properties of AA-stacked multilayer graphenes are calculated by the tight-binding model and gradient approximation. For a nL-layer AA-stacked graphene, there are nL peaks at both low and middle frequencies. The threshold energy of odd-layer graphene is much lower than that of even-layer graphene for nL<10. The differences in the electronic structures and optical properties between the odd and even layers are reduced with increasing nL. When nL grows to 30 (200), the spectra of 2D graphene are almost identical to those of 3D graphite at middle (low) frequencies.

  14. Neurodegeneration and Identity.

    PubMed

    Strohminger, Nina; Nichols, Shaun

    2015-09-01

    There is a widespread notion, both within the sciences and among the general public, that mental deterioration can rob individuals of their identity. Yet there have been no systematic investigations of what types of cognitive damage lead people to appear to no longer be themselves. We measured perceived identity change in patients with three kinds of neurodegenerative disease: frontotemporal dementia, Alzheimer's disease, and amyotrophic lateral sclerosis. Structural equation models revealed that injury to the moral faculty plays the primary role in identity discontinuity. Other cognitive deficits, including amnesia, have no measurable impact on identity persistence. Accordingly, frontotemporal dementia has the greatest effect on perceived identity, and amyotrophic lateral sclerosis has the least. We further demonstrated that perceived identity change fully mediates the impact of neurodegenerative disease on relationship deterioration between patient and caregiver. Our results mark a departure from theories that ground personal identity in memory, distinctiveness, dispositional emotion, or global mental function.

  15. AAS 228: Day 4

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note: Lastweek we were at the 228th AAS Meeting in San Diego, CA. Here is a final post aboutselectedevents on the last day of the meeting, written by authors fromastrobites.com, a grad-student collaborative project with which we recently announced a new partnership! Starting in July,keep an eye out for astrobites postsat AAS Nova in between Highlights(i.e., on Tuesdays and Thursdays).Were excited to be working together to bring you more recent astronomy research from AAS journals!Extrasolar Planets: Detection (by Leonardo dos Santos)Thursdays first session on exoplanets was about detecting these distant worlds, and the opening talk was given by Robert Siverd (Las Cumbres Observatory). He describes the NRES, a network of spectrographs that will look for exoplanets using the radial velocity method. One of the coolest aspects of this instrument is that it will feature an on the fly scheduling system that will perform observations as efficiently as possible. The spectrograph is still being tested, but a unit will be deployed at CTIO later this year.@lcogt contracted by @NASA_TESS for follow up of their candidates. #aas228 Jessie Christiansen (@aussiastronomer) June 16, 2016Measuring the depths of transits and eclipses in Spitzer has been problematic in the past, since the Spitzer instrument IRAC (InfraRed Array Camera) has a non-uniform response in its detectors pixels. But, as reported by James Ingalls (Spitzer Science Center, Caltech), observers are circumventing this issue by using what they call the staring mode (avoiding large pointing jumps) and an algorithm to pick sweet spot pixels. Moreover, the results from the IRAC Data Challenge are helping to better understand its behavior. Giuseppe Morello (University College London), on the other hand, explained how his research group gets rid of instrumental effects from IRAC using machine learning. This method removes systematics from exoplanet transit data no matter if the noise source is from an instrument or

  16. AAS 227: Day 4

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-01-01

    Editors Note:This week were at the 227th AAS Meeting in Kissimmee, FL. Along with several fellow authors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting at the end of each day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Welcome to Day 4 of the winter American Astronomical Society (AAS) meeting in Kissimmee! Several of us are attending the conference this year, and we will report highlights from each day here on astrobites. If youd like to see more timely updates during the day, we encourage you to follow @astrobites on twitter or search the #aas227 hashtag.Helen B. Warner Prize: Origins of Structure in Planetary Systems (by Erika Nesvold)Another excellent prize lecture started off todays sessions. The Helen B. Warner Prize is awarded for achievement in observational or theoretical astrophysics by a young researcher (no more than eight years after their Ph.D.). This years Warner Prize was presented to Ruth Murray-Clay of UC Santa Barbara. For her award lecture, Murray-Clay told us all about planetary system architecture: the number, masses, and orbits of planets in a given system.Ruth Murray-Clay [photo from http://web.physics.ucsb.edu/ ~murray/biocv.html]The underlying question motivating this type of research is: How rare is the Solar System? In other words, how likely is it that a given planetary system will have rocky planets close to their star, gas giants farther out, and ice giants at the outer reaches of the system? Answering this question will help us solve the physics problem of how and where planets form, and will also help us on our search for other planets like Earth.The data on exoplanet population from transit and radial velocity observations and from direct imaging tell us that our Solar System is not common (many systems we observe have much more eccentric gas giants), but that doesnt

  17. Insertion Sequences

    PubMed Central

    Mahillon, Jacques; Chandler, Michael

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic elements and, for several of these, a detailed understanding of the transposition process at the chemical level. This review presents a general overview of the organization and function of insertion sequences of eubacterial, archaebacterial, and eukaryotic origins with particular emphasis on bacterial elements and on different aspects of the transposition mechanism. It also attempts to provide a framework for classification of these elements by assigning them to various families or groups. A total of 443 members of the collection have been grouped in 17 families based on combinations of the following criteria: (i) similarities in genetic organization (arrangement of open reading frames); (ii) marked identities or similarities in the enzymes which mediate the transposition reactions, the recombinases/transposases (Tpases); (iii) similar features of their ends (terminal IRs); and (iv) fate of the nucleotide sequence of their target sites (generation of a direct target duplication of determined length). A brief description of the mechanism(s) involved in the mobility of individual ISs in each family and of the structure-function relationships of the individual Tpases is included where available. PMID:9729608

  18. Genetics and identity.

    PubMed

    Nordgren, Anders

    2008-01-01

    For the last 20 years the concepts of identity and identification have been subject to much interest in the humanities and social sciences. However, the implications of genetics for identity and identification have been largely neglected. In this paper, I distinguish various conceptions of identity (as continuity over time, as basic kind of being, as unique set of properties, and as social role) and identification (as subjective experience of identity in various senses and as social ascription of identity in various senses), and investigate systematically genetic perspectives on each of these conceptions. I stress the importance of taking the genetic perspectives seriously but also their limitations. In particular, I pinpoint conceptual problems that arise when a genetic approach to identity is adopted.

  19. Exploring medical identity theft.

    PubMed

    Mancilla, Desla; Moczygemba, Jackie

    2009-09-16

    The crime of medical identity theft is a growing concern in healthcare institutions. A mixed-method study design including a two-stage electronic survey, telephone survey follow-up, and on-site observations was used to evaluate current practices in admitting and registration departments to reduce the occurrence of medical identity theft. Survey participants were chief compliance officers in acute healthcare organizations and members of the Health Care Compliance Association. Study results indicate variance in whether or how patient identity is confirmed in healthcare settings. The findings of this study suggest that information systems need to be designed for more efficient identity management. Admitting and registration staff must be trained, and compliance with medical identity theft policies and procedures must be monitored. Finally, biometric identity management solutions should be considered for stronger patient identification verification.

  20. Identical repeated backbone of the human genome

    PubMed Central

    2010-01-01

    Background Identical sequences with a minimal length of about 300 base pairs (bp) have been involved in the generation of various meiotic/mitotic genomic rearrangements through non-allelic homologous recombination (NAHR) events. Genomic disorders and structural variation, together with gene remodelling processes have been associated with many of these rearrangements. Based on these observations, we identified and integrated all the 100% identical repeats of at least 300 bp in the NCBI version 36.2 human genome reference assembly into non-overlapping regions, thus defining the Identical Repeated Backbone (IRB) of the reference human genome. Results The IRB sequences are distributed all over the genome in 66,600 regions, which correspond to ~2% of the total NCBI human genome reference assembly. Important structural and functional elements such as common repeats, segmental duplications, and genes are contained in the IRB. About 80% of the IRB bp overlap with known copy-number variants (CNVs). By analyzing the genes embedded in the IRB, we were able to detect some identical genes not previously included in the Ensembl release 50 annotation of human genes. In addition, we found evidence of IRB gene copy-number polymorphisms in raw sequence reads of two diploid sequenced genomes. Conclusions In general, the IRB offers new insight into the complex organization of the identical repeated sequences of the human genome. It provides an accurate map of potential NAHR sites which could be used in targeting the study of novel CNVs, predicting DNA copy-number variation in newly sequenced genomes, and improve genome annotation. PMID:20096123

  1. Evaluation of global sequence comparison and one-to-one FASTA local alignment in regulatory allergenicity assessment of transgenic proteins in food crops.

    PubMed

    Song, Ping; Herman, Rod A; Kumpatla, Siva

    2014-09-01

    To address the high false positive rate using >35% identity over 80 amino acids in the regulatory assessment of transgenic proteins for potential allergenicity and the change of E-value with database size, the Needleman-Wunsch global sequence alignment and a one-to-one (1:1) local FASTA search (one protein in the target database at a time) using FASTA were evaluated by comparing proteins randomly selected from Arabidopsis, rice, corn, and soybean with known allergens in a peer-reviewed allergen database (http://www.allergenonline.org/). Compared with the approach of searching >35%/80aa+, the false positive rate measured by specificity rate for identification of true allergens was reduced by a 1:1 global sequence alignment with a cut-off threshold of ≧30% identity and a 1:1 FASTA local alignment with a cut-off E-value of ≦1.0E-09 while maintaining the same sensitivity. Hence, a 1:1 sequence comparison, especially using the FASTA local alignment tool with a biological relevant E-value of 1.0E-09 as a threshold, is recommended for the regulatory assessment of sequence identities between transgenic proteins in food crops and known allergens.

  2. Microsolvation of the acetanilide cation (AA(+)) in a nonpolar solvent: IR spectra of AA(+)-L(n) clusters (L = He, Ar, N2; n ≤ 10).

    PubMed

    Schmies, Matthias; Patzer, Alexander; Schütz, Markus; Miyazaki, Mitsuhiko; Fujii, Masaaki; Dopfer, Otto

    2014-05-07

    Infrared photodissociation (IRPD) spectra of mass-selected cluster ions of acetanilide (N-phenylacetamide), AA(+)-Ln, with the ligands L = He (n = 1-2), Ar (n = 1-7), and N2 (n = 1-10) are recorded in the hydride stretch (amide A, νNH, νCH) and fingerprint (amide I-III) ranges of AA(+) in its (2)A'' ground electronic state. Cold AA(+)-Ln clusters are generated in an electron impact ion source, which predominantly produces the most stable isomer of a given cluster ion. Systematic vibrational frequency shifts of the N-H stretch fundamentals (νNH) provide detailed information about the sequential microsolvation process of AA(+) in a nonpolar (L = He and Ar) and quadrupolar (L = N2) solvent. In the most stable AA(+)-Ln clusters, the first ligand forms a hydrogen bond (H-bond) with the N-H proton of trans-AA(+) (t-AA(+)), whereas further ligands bind weakly to the aromatic ring (π-stacking). There is no experimental evidence for complexes with the less stable cis-AA(+) isomer. Quantum chemical calculations at the M06-2X/aug-cc-pVTZ level confirm the cluster growth sequence derived from the IR spectra. The calculated binding energies of De(H) = 720 and 1227 cm(-1) for H-bonded and De(π) = 585 and 715 cm(-1) for π-bonded Ar and N2 ligands in t-AA(+)-L are consistent with the observed photofragmentation branching ratios of AA(+)-Ln. Comparison between charged and neutral AA((+))-L dimers indicates that ionization switches the preferred ion-ligand binding motif from π-stacking to H-bonding. Electron removal from the HOMO of AA(+) delocalized over both the aromatic ring and the amide group significantly strengthens the C[double bond, length as m-dash]O bond and weakens the N-H bond of the amide group.

  3. The complete genome sequence of a double-stranded RNA mycovirus from Fusarium graminearum strain HN1.

    PubMed

    Wang, Luan; Wang, Shuangchao; Yang, Xiufen; Zeng, Hongmei; Qiu, Dewen; Guo, Lihua

    2017-03-15

    The complete nucleotide sequence of a double-stranded RNA (dsRNA) mycovirus, Fusarium graminearum dsRNA virus 5 (FgV5), was identified and characterized. The FgV5 genome comprises two dsRNA genome segments of 2030 bp and 1740 bp. FgV5 dsRNA1 contains a single open reading frame (ORF1), which is predicted to encode a protein of 613 amino acids (aa) with a molecular mass of 70.4 kDa and has a conserved RNA-dependent RNA polymerase (RdRp) motif. FgV5 dsRNA2 is predicted to contain two discontinuous ORFs (ORF2 and ORF3) that code for products of unknown function. Sequence comparisons showed that FgV5 has the highest aa sequence identities to Fusarium graminearum virus 4 (FgV4) (83.01% for ORF1, 78.70% for ORF2, and 76.27% for ORF3), suggesting that FgV5 and FgV4 should be regarded as members of different species. Phylogenetic analysis indicated that FgV5 belongs to a taxonomically unassigned dsRNA mycovirus group that is related to the families Amalgaviridae and Partitiviridae. Here, we propose that FgV5 and related viruses are members of a yet to be named and formally recognized new family.

  4. Optimal Compression for Identically Prepared Qubit States

    NASA Astrophysics Data System (ADS)

    Yang, Yuxiang; Chiribella, Giulio; Hayashi, Masahito

    2016-08-01

    We establish the ultimate limits to the compression of sequences of identically prepared qubits. The limits are determined by Holevo's information quantity and are attained through use of the optimal universal cloning machine, which finds here a novel application to quantum Shannon theory.

  5. Spectroscopic signatures of AA' and AB stacking of chemical vapor deposited bilayer MoS2

    DOE PAGES

    Xia, Ming; Li, Bo; Yin, Kuibo; ...

    2015-11-04

    We discuss prominent resonance Raman and photoluminescence spectroscopic differences between AA'and AB stacked bilayer molybdenum disulfide (MoS2) grown by chemical vapor deposition are reported. Bilayer MoS2 islands consisting of the two stacking orders were obtained under identical growth conditions. Also, resonance Raman and photoluminescence spectra of AA' and AB stacked bilayer MoS2 were obtained on Au nanopyramid surfaces under strong plasmon resonance. Both resonance Raman and photoluminescence spectra show distinct features indicating clear differences in interlayer interaction between these two phases. The implication of these findings on device applications based on spin and valley degrees of freedom.

  6. Multifunctional cellulolytic auxiliary activity protein HcAA10-2 from Hahella chejuensis enhances enzymatic hydrolysis of crystalline cellulose.

    PubMed

    Ghatge, Sunil S; Telke, Amar A; Waghmode, Tatoba R; Lee, Yuno; Lee, Keun-Woo; Oh, Doo-Byoung; Shin, Hyun-Dong; Kim, Seon-Won

    2015-04-01

    The modular auxiliary activity (AA) family of proteins is believed to cause amorphogenesis in addition to oxidative cleavage of crystalline cellulose although the supporting evidence is limited. HcAA10-2 is a modular AA10 family protein (58 kDa) composed of a AA10 module and a family two carbohydrate binding module (CBM2), joined by a long stretch of 222 amino acids of unknown function. The protein was expressed in Escherichia coli and purified to homogeneity. Scanning electron microscopy and X-ray diffraction analysis of Avicel treated with HcAA10-2 provided evidence for the disruption of the cellulose microfibrils ("amorphogenesis") and reduction of the crystallinity index, resulting in a twofold increase of cellulase adsorption on the polysaccharide surface. HcAA10-2 exhibited weak endoglucanase-like activity toward soluble cellulose and cello-oligosaccharides with an optimum at pH 6.5 and 45 °C. HcAA10-2 catalyzed oxidative cleavage of crystalline cellulose released native and oxidized cello-oligosaccharides in the presence of copper and an electron donor such as ascorbic acid. Multiple sequence alignment indicated that His1, His109, and Phe197 in the AA10 module formed the conserved copper-binding site. The reducing sugar released from Avicel by the endoglucanase Cel5 and Celluclast accompanying HcAA10-2 was increased by four- and sixfold, respectively. Moreover, HcAA10-2 and Celluclast acted synergistically on pretreated wheat straw biomass resulting in a threefold increase in reducing sugar than Celluclast alone. Taken together, these results suggest that HcAA10-2 is a novel multifunctional modular AA10 protein possessing amorphogenesis, weak endoglucanase, and oxidative cleavage activities useful for efficient degradation of crystalline cellulose.

  7. Evidence of mineralization activity and supramolecular assembly by the N-terminal sequence of ACCBP, a biomineralization protein that is homologous to the acetylcholine binding protein family.

    PubMed

    Amos, Fairland F; Ndao, Moise; Evans, John Spencer

    2009-12-14

    Several biomineralization proteins that exhibit intrinsic disorder also possess sequence regions that are homologous to nonmineral associated folded proteins. One such protein is the amorphous calcium carbonate binding protein (ACCBP), one of several proteins that regulate the formation of the oyster shell and exhibit 30% conserved sequence identity to the acetylcholine binding protein sequences. To gain a better understanding of the ACCBP protein, we utilized bioinformatic approaches to identify the location of disordered and folded regions within this protein. In addition, we synthesized a 50 AA polypeptide, ACCN, representing the N-terminal domain of the mature processed ACCBP protein. We then utilized this polypeptide to determine the mineralization activity and qualitative structure of the N-terminal region of ACCBP. Our bioinformatic studies indicate that ACCBP consists of a ten-stranded beta-sandwich structure that includes short disordered sequence blocks, two of which reside within the primarily helical and surface-accessible ACCN sequence. Circular dichroism studies reveal that ACCN is partially disordered in solution; however, ACCN can be induced to fold into an alpha helix in the presence of TFE. Furthermore, we confirm that the ACCN sequence is multifunctional; this sequence promotes radial calcite polycrystal growth on Kevlar threads and forms supramolecular assemblies in solution that contain amorphous-appearing deposits. We conclude that the partially disordered ACCN sequence is a putative site for mineralization activity within the ACCBP protein and that the presence of short disordered sequence regions within the ACCBP fold are essential for function.

  8. Replication mechanism and sequence analysis of the replicon of pAW63, a conjugative plasmid from Bacillus thuringiensis.

    PubMed

    Wilcks, A; Smidt, L; Okstad, O A; Kolsto, A B; Mahillon, J; Andrup, L

    1999-05-01

    A 5.8-kb fragment of the large conjugative plasmid pAW63 from Bacillus thuringiensis subsp. kurstaki HD73 containing all the information for autonomous replication was cloned and sequenced. By deletion analysis, the pAW63 replicon was reduced to a 4.1-kb fragment harboring four open reading frames (ORFs). Rep63A (513 amino acids [aa]), encoded by the largest ORF, displayed strong similarity (40% identity) to the replication proteins from plasmids pAMbeta1, pIP501, and pSM19035, indicating that the pAW63 replicon belongs to the pAMbeta1 family of gram-positive theta-replicating plasmids. This was confirmed by the facts that no single-stranded DNA replication intermediates could be detected and that replication was found to be dependent on host-gene-encoded DNA polymerase I. An 85-bp region downstream of Rep63A was also shown to have strong similarity to the origins of replication of pAMbeta1 and pIP501, and it is suggested that this region contains the bona fide pAW63 ori. The protein encoded by the second large ORF, Rep63B (308 aa), was shown to display similarity to RepB (34% identity over 281 aa) and PrgP (32% identity over 310 aa), involved in copy control of the Enterococcus faecalis plasmids pAD1 and pCF10, respectively. No significant similarity to known proteins or DNA sequences could be detected for the two smallest ORFs. However, the location, size, hydrophilicity, and orientation of ORF6 (107 codons) were analogous to those features of the putative genes repC and prgO, which encode stability functions on plasmids pAD1 and pCF10, respectively. The cloned replicon of plasmid pAW63 was stably maintained in Bacillus subtilis and B. thuringiensis and displayed incompatibility with the native pAW63. Hybridization experiments using the cloned replicon as a probe showed that pAW63 has similarity to large plasmids from other B. thuringiensis subsp. kurstaki strains and to a strain of B. thuringiensis subsp. alesti.

  9. Complete genomic sequence analysis of a highly virulent isolate revealed a novel strain of Sugarcane mosaic virus.

    PubMed

    Gao, Bo; Cui, Xiao-Wen; Li, Xiang-Dong; Zhang, Chun-Qing; Miao, Hong-Qin

    2011-12-01

    Sugarcane mosaic virus (SCMV) is the most prevalent virus causing maize dwarf mosaic disease in northern China. A SCMV isolate, BD8, was obtained from the maize showing dwarf and mosaic symptoms in Baoding, China. The complete genomic sequence of BD8 is 9,576 nucleotides (nt) excluding the poly(A) tail. It contains one single open reading frame of 9,192 nt and encodes a large polyprotein of 3,063 amino acids (aa), flanked by a 5'-untranslated region (UTR) of 148 nt and a 3'-UTR of 236 nt. The entire genomic sequence of BD8 shares identities of 79.1-80.8% with those of other 13 SCMV isolates available in the GenBank at nt level, while their CP genes share identities of 76.9-82.6 and 82.8-86.9% at nt and aa levels, respectively. Phylogenetic analysis of the complete genomic sequences reveals that SCMV can be clustered to four groups: group I includes isolates from maize, group II consists of isolates from sugarcane or maize, groups III and IV contain single isolate of AU-A (AJ278405) and BD8, respectively. Thus, BD8 represents a new strain of SCMV. Furthermore analysis of the CP gene sequences of more isolates shows that BD8 is clustered to a group with the isolates from Thailand and Vietnam, which implies that isolates of this strain have been distributed in South Asia. In the greenhouse, BD8 can cause severe symptoms in all the 12 maize varieties tested with high incidence, indicating that BD8 is highly virulent.

  10. Children's Social Identities

    ERIC Educational Resources Information Center

    Bennett, Mark

    2011-01-01

    This paper provides a brief overview of recent developmental research on themes related to children's social identities. Initially, consideration is given to the capacity for social categorization, following which attention is given to children's developing conceptions of social identities, their identification with social groups, and the…

  11. Personal Identity in Japan

    ERIC Educational Resources Information Center

    Sugimura, Kazumi; Mizokami, Shinichi

    2012-01-01

    This chapter explores characteristics of identity formation among Japanese adolescents and young adults living in a cultural context where individualism has been increasingly emphasized even while maintaining collectivism. We argue that, to develop a sense of identity in Japanese culture, adolescents and young adults carefully consider others'…

  12. Vip3Aa induces apoptosis in cultured Spodoptera frugiperda (Sf9) cells.

    PubMed

    Jiang, Kun; Mei, Si-Qi; Wang, Ting-Ting; Pan, Jin-Hua; Chen, Yue-Hua; Cai, Jun

    2016-09-15

    The vegetative insecticidal proteins (Vip) secreted by many Bacillus thuringiensis strains during their vegetative growth stage are regarded as second generation insecticidal proteins, as they share no sequence or structural homology with known crystal insecticidal proteins (Cry) and have a broad insecticidal spectrum. Compared with insecticidal crystal proteins (ICPs), the insecticidal mechanisms of Vips have been little studied. Here we investigated the mechanism responsible for Vip3Aa toxicity in cultured insect cells. Using, flow cytometry analyzes, TUNEL staining and DNA fragmentation assays, we show that Vip3Aa can induce apoptosis in Spodoptera frugiperda (Sf9) cells and cause cells to arrest at the G2/M phase. We also show that Vip3Aa can disrupt mitochondrial membrane potential (ΔΨm), leading to the activation of Sf-caspase-1, suggesting that a mitochondrial mediated and caspase dependent pathway may be involved in Vip3Aa-induced apoptosis in Sf9 cells.

  13. Cell volume regulation in hemoglobin CC and AA erythrocytes

    SciTech Connect

    Berkowitz, L.R.; Orringer, E.P.

    1987-03-01

    Swelling hemoglobin CC erythrocytes stimulates a ouabain-insensitive K flux that restores original cell volume. Studies were performed with the K analog, /sup 86/Rb. This volume regulatory pathway was characterized for its anion dependence, sensitivity to loop diuretics, and requirement for Na. The swelling-induced K flux was eliminated if intracellular chloride was replaced by nitrate and both swelling-activated K influx and efflux were partially inhibited by 1 mM furosemide or bumetanide. K influx in swollen hemoglobin CC cells was not diminished when Na in the incubation medium was replaced with choline, indicating Na independence of the swelling-induced flux. Identical experiments with hemoglobin AA cells also demonstrated a swelling-induced increase in K flux, but the magnitude and duration of this increase were considerably less than that seen with hemoglobin CC cells. The increased K flux in hemoglobin AA cells was likewise sensitive to anion replacement and to loop diuretics and did not require the presence of Na. These data indicate that a volume-activated K pathway with similar transport characteristics exists in both hemoglobin CC and AA red cells.

  14. The complete genome sequences of two naturally occurring recombinant isolates of Sugarcane mosaic virus from Iran.

    PubMed

    Moradi, Zohreh; Mehrvar, Mohsen; Nazifi, Ehsan; Zakiaghl, Mohammad

    2016-04-01

    Sugarcane mosaic virus (SCMV) is the most prevalent virus causing sugarcane mosaic and maize dwarf mosaic diseases. Here, we presented the first two complete genomic sequences of Iranian SCMV isolates, NRA and ZRA from sugarcane and maize. The complete genome sequences of NRA and ZRA were, respectively, 9571 and 9572 nucleotides (nt) in length, excluding the 3'-terminal poly(A) tail. Both isolates contained a 5'-untranslated region (UTR) of 149 nt, an open reading frame of 9192 nt encoding a polyprotein of 3063 amino acids (aa), and 3'-UTR of 230 nt for NRA and 231 nt for ZRA. SCMV-NRA and -ZRA genome nucleotide sequences were 97.3 % identical and shared nt identities of 79.1-92 % with those of other 21 SCMV isolates available in the GenBank, highest with the isolate Bris-A (AJ278405) (92 and 91.7 %) from Australia. When compared for separate genes, most of their genes shared the highest identities with Australian and Argentinean isolates. Phylogenetic analysis of the complete genomic sequences reveals that SCMV can be clustered to three groups. Both NRA and ZRA were clustered with sugarcane isolates from Australia and Argentina in group III but formed a separate sublineage. Recombination analysis showed that both isolates were intraspecific recombinants, and represented two novel recombination patterns of SCMV (in the P1 coding region). NRA had six recombination sites within the P1, HC-Pro, CI, NIa-Vpg, and NIa-pro coding regions, while ZRA had four within the P1, HC-Pro, NIa-Pro, and NIb coding regions.

  15. A.A., constructivism, and reflecting teams.

    PubMed

    Nevels, B

    1997-12-01

    Numerous studies and clinical anecdotes reveal a relationship between attendance at A.A. meetings and/or degree of involvement in A.A. and maintenance of sobriety. Hypotheses as to how A.A. and/or the A.A. meeting is helpful to its members have ranged from a focus on factors common to all therapy groups, to aspects of A.A. "treatment" which are behavioral in nature. Presented here is another way of understanding A.A.'s effectiveness within the frame of more recent, constructivistic approaches to family therapy. In particular, the A.A. topic meeting is compared to the reflecting team concept of Tom Anderson.

  16. Recognizing Sequences of Sequences

    PubMed Central

    Kiebel, Stefan J.; von Kriegstein, Katharina; Daunizeau, Jean; Friston, Karl J.

    2009-01-01

    The brain's decoding of fast sensory streams is currently impossible to emulate, even approximately, with artificial agents. For example, robust speech recognition is relatively easy for humans but exceptionally difficult for artificial speech recognition systems. In this paper, we propose that recognition can be simplified with an internal model of how sensory input is generated, when formulated in a Bayesian framework. We show that a plausible candidate for an internal or generative model is a hierarchy of ‘stable heteroclinic channels’. This model describes continuous dynamics in the environment as a hierarchy of sequences, where slower sequences cause faster sequences. Under this model, online recognition corresponds to the dynamic decoding of causal sequences, giving a representation of the environment with predictive power on several timescales. We illustrate the ensuing decoding or recognition scheme using synthetic sequences of syllables, where syllables are sequences of phonemes and phonemes are sequences of sound-wave modulations. By presenting anomalous stimuli, we find that the resulting recognition dynamics disclose inference at multiple time scales and are reminiscent of neuronal dynamics seen in the real brain. PMID:19680429

  17. [Diagnosing gender identity].

    PubMed

    Kaltiala-Heino, Riittakerttu; Mattila, Aino; Kärnä, Teemu; Joutsenneimi, Kaisla

    2015-01-01

    Transsexualism and other variations of gender identity are based on a stable sense of identity. The aetiology of this phenomenon is not fully known. Suffering caused by gender dysphoria is alleviated with sex reassignment. The psychiatric assessment of both adolescents and adults has been centralized in Finland to two university hospitals, the Helsinki University Hospital and Tampere University Hospital. In both hospitals, multidisciplinary teams aim at differential diagnosis by using well-known psychiatric and psychological instruments. Wishes for sex reassignment that are caused by a mental health disorder are excluded. Assessment in adolescence is challenging because the identity in youth is still forming.

  18. Dissociative Identity Disorder

    PubMed Central

    2009-01-01

    A brief description of the controversies surrounding the diagnosis of dissociative identity disorder is presented, followed by a discussion of the proposed similarities and differences between dissociative identity disorder and borderline personality disorder. The phenomenon of autohypnosis in the context of early childhood sexual trauma and disordered attachment is discussed, as is the meaning of alters or alternate personalities. The author describes recent neurosciences research that may relate the symptoms of dissociative identity disorder to demonstrable disordered attention and memory processes. A clinical description of a typical patient presentation is included, plus some recommendations for approaches to treatment. PMID:19724751

  19. Adolescence: Search for an Identity

    ERIC Educational Resources Information Center

    Kasinath, H. M.

    2013-01-01

    James Marcia (1991, 1994, 1999, 2002) expanded on Erikson's theory of identity formation. Specifically, he focused on two essential processes in achieving a mature identity: exploration and commitment. Erikson's observations about identity were extended by Marcia, who described four identity statuses: identity diffusion, foreclosure, moratorium…

  20. Identity verifier performance

    SciTech Connect

    Maxwell, R.

    1987-01-01

    This report is a transcript of a paper given at the Smart Card Applications and Technologies Conference, October 14, 1987. Identity verification techniques are identified and discussed, and statistical performance data is given. 20 figs. (JF)

  1. Native American Identity

    ERIC Educational Resources Information Center

    Horse, Perry G.

    2005-01-01

    Many issues and elements--including ethnic nomenclature, racial attitudes, and the legal and political status of American Indian nations and Indian people--influence Native American identity. (Contains 3 notes.)

  2. Autoethnography: Inquiry into Identity

    ERIC Educational Resources Information Center

    Hoppes, Steve

    2014-01-01

    This chapter provides guidelines and suggestions for assessing student development using autoethnography, a qualitative research method. Autoethnography guides students in examining the nexus between personal and professional identities, including skills, challenges, values, histories, and hopes for the future.

  3. Parasporal body formation via overexpression of the Cry10Aa toxin of Bacillus thuringiensis subsp. israelensis, and Cry10Aa-Cyt1Aa synergism.

    PubMed

    Hernández-Soto, Alejandro; Del Rincón-Castro, M Cristina; Espinoza, Ana M; Ibarra, Jorge E

    2009-07-01

    Bacillus thuringiensis subsp. israelensis is the most widely used microbial control agent against mosquitoes and blackflies. Its insecticidal success is based on an arsenal of toxins, such as Cry4A, Cry4B, Cry11A, and Cyt1A, harbored in the parasporal crystal of the bacterium. A fifth toxin, Cry10Aa, is synthesized at very low levels; previous attempts to clone and express Cry10Aa were limited, and no parasporal body was formed. By using a new strategy, the whole Cry10A operon was cloned in the pSTAB vector, where both open reading frames ORF1 and ORF2 (and the gap between the two) were located, under the control of the cyt1A operon and the STAB-SD stabilizer sequence characteristic of this vector. Once the acrystalliferous mutant 4Q7 of B. thuringiensis subsp. israelensis was transformed with this construct, parasporal bodies were observed by phase-contrast microscopy and transmission electron microscopy. Discrete, ca. 0.9-microm amorphous parasporal bodies were observed in the mature sporangia, which were readily purified by gradient centrifugation once autolysis had occurred. Pure parasporal bodies showed two major bands of ca. 68 and 56 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis. These bands were further characterized by N-terminal sequencing of tryptic fragments using matrix-assisted laser desorption ionization-time of flight mass spectrometry analysis, which identified both bands as the products of ORF1 and ORF2, respectively. Bioassays against fourth-instar larvae of Aedes aegypti of spore-crystal complex and pure crystals of Cry10Aa gave estimated 50% lethal concentrations of 2,061 ng/ml and 239 ng/ml, respectively. Additionally, synergism was clearly detected between Cry10A and Cyt1A, as the synergistic levels (potentiation rates) were estimated at 13.3 for the mixture of Cyt1A crystals and Cry10Aa spore-crystal complex and 12.6 for the combination of Cyt1A and Cry10Aa pure crystals.

  4. Story telling: crafting identities

    PubMed Central

    McMahon, Mary; Watson, Mark

    2013-01-01

    Career guidance clients are seeking to craft new identities that better position them in their careers. The focus of the present article is on narrative career counselling's potential contribution in providing a meaningful and useful experience for career guidance clients. To illustrate the potential of narrative career counselling, the story telling approach is offered as an example to illustrate how identity can be crafted in contextually and culturally sensitive ways. PMID:24009405

  5. Laboratory Astrophysics Division of The AAS (LAD)

    NASA Astrophysics Data System (ADS)

    Salama, Farid; Drake, R. P.; Federman, S. R.; Haxton, W. C.; Savin, D. W.

    2012-10-01

    The purpose of the Laboratory Astrophysics Division (LAD) is to advance our understanding of the Universe through the promotion of fundamental theoretical and experimental research into the underlying processes that drive the Cosmos. LAD represents all areas of astrophysics and planetary sciences. The first new AAS Division in more than 30 years, the LAD traces its history back to the recommendation from the scientific community via the White Paper from the 2006 NASA-sponsored Laboratory Astrophysics Workshop. This recommendation was endorsed by the Astronomy and Astrophysics Advisory Committee (AAAC), which advises the National Science Foundation (NSF), the National Aeronautics and Space Administration (NASA), and the U.S. Department of Energy (DOE) on selected issues within the fields of astronomy and astrophysics that are of mutual interest and concern to the agencies. In January 2007, at the 209th AAS meeting, the AAS Council set up a Steering Committee to formulate Bylaws for a Working Group on Laboratory Astrophysics (WGLA). The AAS Council formally established the WGLA with a five-year mandate in May 2007, at the 210th AAS meeting. From 2008 through 2012, the WGLA annually sponsored Meetings in-a-Meeting at the AAS Summer Meetings. In May 2011, at the 218th AAS meeting, the AAS Council voted to convert the WGLA, at the end of its mandate, into a Division of the AAS and requested draft Bylaws from the Steering Committee. In January 2012, at the 219th AAS Meeting, the AAS Council formally approved the Bylaws and the creation of the LAD. The inaugural gathering and the first business meeting of the LAD were held at the 220th AAS meeting in Anchorage in June 2012. You can learn more about LAD by visiting its website at http://lad.aas.org/ and by subscribing to its mailing list.

  6. Laboratory Astrophysics Division of the AAS (LAD)

    NASA Technical Reports Server (NTRS)

    Salama, Farid; Drake, R. P.; Federman, S. R.; Haxton, W. C.; Savin, D. W.

    2012-01-01

    The purpose of the Laboratory Astrophysics Division (LAD) is to advance our understanding of the Universe through the promotion of fundamental theoretical and experimental research into the underlying processes that drive the Cosmos. LAD represents all areas of astrophysics and planetary sciences. The first new AAS Division in more than 30 years, the LAD traces its history back to the recommendation from the scientific community via the White Paper from the 2006 NASA-sponsored Laboratory Astrophysics Workshop. This recommendation was endorsed by the Astronomy and Astrophysics Advisory Committee (AAAC), which advises the National Science Foundation (NSF), the National Aeronautics and Space Administration (NASA), and the U.S. Department of Energy (DOE) on selected issues within the fields of astronomy and astrophysics that are of mutual interest and concern to the agencies. In January 2007, at the 209th AAS meeting, the AAS Council set up a Steering Committee to formulate Bylaws for a Working Group on Laboratory Astrophysics (WGLA). The AAS Council formally established the WGLA with a five-year mandate in May 2007, at the 210th AAS meeting. From 2008 through 2012, the WGLA annually sponsored Meetings in-a-Meeting at the AAS Summer Meetings. In May 2011, at the 218th AAS meeting, the AAS Council voted to convert the WGLA, at the end of its mandate, into a Division of the AAS and requested draft Bylaws from the Steering Committee. In January 2012, at the 219th AAS Meeting, the AAS Council formally approved the Bylaws and the creation of the LAD. The inaugural gathering and the first business meeting of the LAD were held at the 220th AAS meeting in Anchorage in June 2012. You can learn more about LAD by visiting its website at http://lad.aas.org/ and by subscribing to its mailing list.

  7. On a New Trigonometric Identity

    ERIC Educational Resources Information Center

    Chen, Hongwei

    2002-01-01

    A new trigonometric identity derived from factorizations and partial fractions is given. This identity is used to evaluate the Poisson integral via Riemann sum and to establish some trigonometric summation identities.

  8. Orbit of 1976 AA. [asteroid

    NASA Technical Reports Server (NTRS)

    Marsden, B. G.; Williams, J. G.

    1977-01-01

    The orbit of Asteroid 1976 AA is described, with attention given to calculations of its period and its distance from earth, both of which could be accurately and quickly determined by measuring the minor planet's position over wide ranges of hour angle on one to three nights. The geometry of the asteroid's orbit is compared to that of earth's orbit, and the periodicity of the minor planet's approaches to earth is projected. The motion of 1976 AA over an interval of seven centuries into both past and future is also studied; the possibility of its libration with respect to earth or to Venus is examined. Some data on closest approaches of the asteroid to Mars and Venus, as well as to earth, are given.

  9. Inference for Identity Management

    DTIC Science & Technology

    2010-08-16

    proposal. Briefly, and following the spirit of the idea that Mallows [6] introduced for permutations, we define a measure of compatibility between a...A. The posterior p(x(0) | y(0)) can be computed by first determining high-likelihood esti- mates x̂(0) of x(0) from y(0). We can then use a Mallows ...Litow, and N. Bajema. Partition-distance via the assignment problem. Bioinformatics, 21(10):2463–2468, 2005. [6] C. L. Mallows . Non-null ranking models I

  10. Tools for Understanding Identity

    SciTech Connect

    Creese, Sadie; Gibson-Robinson, Thomas; Goldsmith, Michael; Hodges, Duncan; Kim, Dee DH; Love, Oriana J.; Nurse, Jason R.; Pike, William A.; Scholtz, Jean

    2013-12-28

    Identity attribution and enrichment is critical to many aspects of law-enforcement and intelligence gathering; this identity typically spans a number of domains in the natural-world such as biographic information (factual information – e.g. names, addresses), biometric information (e.g. fingerprints) and psychological information. In addition to these natural-world projections of identity, identity elements are projected in the cyber-world. Conversely, undesirable elements may use similar techniques to target individuals for spear-phishing attacks (or worse), and potential targets or their organizations may want to determine how to minimize the attack surface exposed. Our research has been exploring the construction of a mathematical model for identity that supports such holistic identities. The model captures the ways in which an identity is constructed through a combination of data elements (e.g. a username on a forum, an address, a telephone number). Some of these elements may allow new characteristics to be inferred, hence enriching the holistic view of the identity. An example use-case would be the inference of real names from usernames, the ‘path’ created by inferring new elements of identity is highlighted in the ‘critical information’ panel. Individual attribution exercises can be understood as paths through a number of elements. Intuitively the entire realizable ‘capability’ can be modeled as a directed graph, where the elements are nodes and the inferences are represented by links connecting one or more antecedents with a conclusion. The model can be operationalized with two levels of tool support described in this paper, the first is a working prototype, the second is expected to reach prototype by July 2013: Understanding the Model The tool allows a user to easily determine, given a particular set of inferences and attributes, which elements or inferences are of most value to an investigator (or an attacker). The tool is also able to take

  11. The 9aaTAD Is Exclusive Activation Domain in Gal4

    PubMed Central

    Havelka, Marek; Rezacova, Martina

    2017-01-01

    The Gal4 protein is a well-known prototypic acidic activator that has multiple activation domains. We have previously identified a new activation domain called the nine amino acid transactivation domain (9aaTAD) in Gal4 protein. The family of the 9aaTAD activators currently comprises over 40 members including p53, MLL, E2A and other members of the Gal4 family; Oaf1, Pip2, Pdr1 and Pdr3. In this study, we revised function of all reported Gal4 activation domains. Surprisingly, we found that beside of the activation domain 9aaTAD none of the previously reported activation domains had considerable transactivation potential and were not involved in the activation of transcription. Our results demonstrated that the 9aaTAD domain is the only decisive activation domain in the Gal4 protein. We found that the artificial peptides included in the original Gal4 constructs were results of an unintended consequence of cloning that were responsible for the artificial transcriptional activity. Importantly, the activation domain 9aaTAD, which is the exclusive activation domain in Gal4, is also the central part of a conserved sequence recognized by the inhibitory protein Gal80. We propose a revision of the Gal4 regulation, in which the activation domain 9aaTAD is directly linked to both activation function and Gal80 mediated inhibition. PMID:28056036

  12. Analysis of the complete sequences of two biologically distinct Zucchini yellow mosaic virus isolates further evidences the involvement of a single amino acid in the virus pathogenicity.

    PubMed

    Nováková, S; Svoboda, J; Glasa, M

    2014-01-01

    The complete genome sequences of two Slovak Zucchini yellow mosaic virus isolates (ZYMV-H and ZYMV-SE04T) were determined. These isolates differ significantly in their pathogenicity, producing either severe or very mild symptoms on susceptible cucurbit hosts. The viral genome of both isolates consisted of 9593 nucleotides in size, and contained an open reading frame encoding a single polyprotein of 3080 amino acids. Despite their different biological properties, an extremely high nucleotide identity could be noted (99.8%), resulting in differences of only 5 aa, located in the HC-Pro, P3, and NIb, respectively. In silico analysis including 5 additional fully-sequenced and phylogenetically closely-related isolates known to induce different symptoms in cucurbits was performed. This suggested that the key single mutation responsible for virus pathogenicity is likely located in the N-terminal part of P3, adjacent to the PIPO.

  13. When multiple identities interfere: the role of identity centrality.

    PubMed

    Settles, Isis H

    2004-04-01

    The current study extends research in the area of identity conflict or interference by focusing on a new identity combination, the woman and scientist identities. In addition, it examines the influence of identity centrality, or importance, as a predictor of interference and moderator of the relation between interference and well-being and science performance. Supporting hypotheses, greater identity interference was related to lower levels of performance and well-being. Furthermore, woman centrality was unrelated to interference for those with a central scientist identity, but for those without a central scientist identity, they were positively related. Although central identities were related to positive outcomes in the absence of interference, the outcomes of all women suffered when interference was high, contrary to the hypothesis. The implications of identity centrality for understanding the negotiation of potentially conflicting identities, and for the retention of women in the sciences, are discussed.

  14. AAS 228: Day 2 afternoon

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.The Limits of Scientific Cosmology: Setting the Stage: Accepted Facts, and Testing Limitations in Theory and Data (by Gourav Khullar)With a stellar lineup of speakers to talk about current and future prospects of cosmology and its limits (or lack thereof), the first session kicked off with talks by Risa Wechsler, Joseph Silk, and Sean Carroll (his talk on Multiverses is described below, by Nathan Sanders). Risa set the stage with an elaborate description of the current accepted facts in the era of precision cosmology including the standard model of concordance cosmology, described by seven parameters and an accepted Lambda-CDM paradigm (with a cosmological constant and cold dark matter). The talk stressed on the fact that all these parameters are understood to a percent order precision, which is a remarkable deviation from the time in 1990s when according to Risa, Alan Guth never thought that any of these numbers could be measured precisely!Risa Wechsler describing our current constraints on what Dark Matter could constitute.Joseph Silk discussing limits on cosmological parameters.The CMB measurements, Big Bang Nucleosynthesis estimates and galaxy clustering statistics all contribute to locking down the description of our universe. She emphasized on the tensions between different probes to measure expansion rate H0 of the universe, and small scale predictions of cold dark matter simulations, but she is hopeful that these shall be resolved eventually. Joe Silk followed this up with his interpretation of trying to understand our place in the universe and placing limits on different parameters and

  15. Nucleotide sequences of the coat protein genes of two Japanese zucchini yellow mosaic virus isolates.

    PubMed

    Kundu, A K; Ohshima, K; Sako, N

    1997-10-01

    The nucleotide (nt) sequences of the coat protein (CP) genes of two Japanese zucchini yellow mosaic virus (ZYMV) isolates (ZYMV-169 and ZYMV-M) were determined. The CP genes of both isolates were 837 nt long and encoded 279 amino acids (aa). The nt and deduced aa sequence similarities between the two isolates were 92% and 94.6%, respectively. The deduced aa sequences of CPs of the Japanese isolates were compared with those of previously reported ZYMV isolates by phylogenetic analysis. This comparison lead us to divide all ZMYV isolates into 3 groups in which ZYMV-169 formed its own distinct group.

  16. Draft genome sequences of two Bacillus thuringiensis strains and characterization of a putative 41.9-kDa insecticidal toxin.

    PubMed

    Palma, Leopoldo; Muñoz, Delia; Berry, Colin; Murillo, Jesús; Caballero, Primitivo

    2014-04-30

    In this work, we report the genome sequencing of two Bacillus thuringiensis strains using Illumina next-generation sequencing technology (NGS). Strain Hu4-2, toxic to many lepidopteran pest species and to some mosquitoes, encoded genes for two insecticidal crystal (Cry) proteins, cry1Ia and cry9Ea, and a vegetative insecticidal protein (Vip) gene, vip3Ca2. Strain Leapi01 contained genes coding for seven Cry proteins (cry1Aa, cry1Ca, cry1Da, cry2Ab, cry9Ea and two cry1Ia gene variants) and a vip3 gene (vip3Aa10). A putative novel insecticidal protein gene 1143 bp long was found in both strains, whose sequences exhibited 100% nucleotide identity. The predicted protein showed 57 and 100% pairwise identity to protein sequence 72 from a patented Bt strain (US8318900) and to a putative 41.9-kDa insecticidal toxin from Bacillus cereus, respectively. The 41.9-kDa protein, containing a C-terminal 6× HisTag fusion, was expressed in Escherichia coli and tested for the first time against four lepidopteran species (Mamestra brassicae, Ostrinia nubilalis, Spodoptera frugiperda and S. littoralis) and the green-peach aphid Myzus persicae at doses as high as 4.8 µg/cm2 and 1.5 mg/mL, respectively. At these protein concentrations, the recombinant 41.9-kDa protein caused no mortality or symptoms of impaired growth against any of the insects tested, suggesting that these species are outside the protein's target range or that the protein may not, in fact, be toxic. While the use of the polymerase chain reaction has allowed a significant increase in the number of Bt insecticidal genes characterized to date, novel NGS technologies promise a much faster, cheaper and efficient screening of Bt pesticidal proteins.

  17. Draft Genome Sequences of Two Bacillus thuringiensis Strains and Characterization of a Putative 41.9-kDa Insecticidal Toxin

    PubMed Central

    Palma, Leopoldo; Muñoz, Delia; Berry, Colin; Murillo, Jesús; Caballero, Primitivo

    2014-01-01

    In this work, we report the genome sequencing of two Bacillus thuringiensis strains using Illumina next-generation sequencing technology (NGS). Strain Hu4-2, toxic to many lepidopteran pest species and to some mosquitoes, encoded genes for two insecticidal crystal (Cry) proteins, cry1Ia and cry9Ea, and a vegetative insecticidal protein (Vip) gene, vip3Ca2. Strain Leapi01 contained genes coding for seven Cry proteins (cry1Aa, cry1Ca, cry1Da, cry2Ab, cry9Ea and two cry1Ia gene variants) and a vip3 gene (vip3Aa10). A putative novel insecticidal protein gene 1143 bp long was found in both strains, whose sequences exhibited 100% nucleotide identity. The predicted protein showed 57 and 100% pairwise identity to protein sequence 72 from a patented Bt strain (US8318900) and to a putative 41.9-kDa insecticidal toxin from Bacillus cereus, respectively. The 41.9-kDa protein, containing a C-terminal 6× HisTag fusion, was expressed in Escherichia coli and tested for the first time against four lepidopteran species (Mamestra brassicae, Ostrinia nubilalis, Spodoptera frugiperda and S. littoralis) and the green-peach aphid Myzus persicae at doses as high as 4.8 µg/cm2 and 1.5 mg/mL, respectively. At these protein concentrations, the recombinant 41.9-kDa protein caused no mortality or symptoms of impaired growth against any of the insects tested, suggesting that these species are outside the protein’s target range or that the protein may not, in fact, be toxic. While the use of the polymerase chain reaction has allowed a significant increase in the number of Bt insecticidal genes characterized to date, novel NGS technologies promise a much faster, cheaper and efficient screening of Bt pesticidal proteins. PMID:24784323

  18. Cellular identity at the single-cell level.

    PubMed

    Coskun, Ahmet F; Eser, Umut; Islam, Saiful

    2016-10-20

    A single cell creates surprising heterogeneity in a multicellular organism. While every organismal cell shares almost an identical genome, molecular interactions in cells alter the use of DNA sequences to modulate the gene of interest for specialization of cellular functions. Each cell gains a unique identity through molecular coding across the DNA, RNA, and protein conversions. On the other hand, loss of cellular identity leads to critical diseases such as cancer. Most cell identity dissection studies are based on bulk molecular assays that mask differences in individual cells. To probe cell-to-cell variability in a population, we discuss single cell approaches to decode the genetic, epigenetic, transcriptional, and translational mechanisms for cell identity formation. In combination with molecular instructions, the physical principles behind cell identity determination are examined. Deciphering and reprogramming cellular types impact biology and medicine.

  19. Origins of structural diversity within sequentially identical hexapeptides.

    PubMed Central

    Cohen, B. I.; Presnell, S. R.; Cohen, F. E.

    1993-01-01

    Efforts to predict protein secondary structure have been hampered by the apparent structural plasticity of local amino acid sequences. Kabsch and Sander (1984, Proc. Natl. Acad. Sci. USA 81, 1075-1078) articulated this problem by demonstrating that identical pentapeptide sequences can adopt distinct structures in different proteins. With the increased size of the protein structure database and the availability of new methods to characterize structural environments, we revisit this observation of structural plasticity. Within a set of proteins with less than 50% sequence identity, 59 pairs of identical hexapeptide sequences were identified. These local structures were compared and their surrounding structural environments examined. Within a protein structural class (alpha/alpha, beta/beta, alpha/beta, alpha + beta), the structural similarity of sequentially identical hexapeptides usually is preserved. This study finds eight pairs of identical hexapeptide sequences that adopt beta-strand structure in one protein and alpha-helical structure in the other. In none of the eight cases do the members of these sequences pairs come from proteins within the same folding class. These results have implications for class dependent secondary structure prediction algorithms. PMID:8298461

  20. Microstructural and Mechanical Characterization of a Dissimilar Friction Stir-Welded AA5083-AA7B04 Butt Joint

    NASA Astrophysics Data System (ADS)

    Chen, Yu; Ding, Hua; Cai, Zhihui; Zhao, Jingwei; Li, Jizhong

    2016-12-01

    Friction stir welding (FSW) has been used for joining AA5083 and AA7B04 alloy sheets with the aim of studying the microstructure and the mechanical properties of dissimilar FSW joints obtained by varying the initial base metal state of AA7B04 alloy. The results show that the initial base metal state has a significant impact on the material flow during dissimilar FSW. As compared with the joints placing hard alloy (artificially aged AA7B04-AA or naturally aged AA7B04-NA) on the retreating side, it becomes easier transporting AA5083 from advancing side to retreating side when soft alloy (annealed AA7B04-O) is placed on the retreating side. The atomic diffusion does not occur at the interface between AA5083 and AA7B04, indicating that the mixing of the two materials is merely mechanical. Grain refinement is observed in the stir zone. The failure location during tensile tests is different depending on the initial base metal state. The joints (AA5083/AA7B04-AA and AA5083/AA7B04-O) fail in the base metal on the soft material side which corresponds to the minimum values in hardness profiles. Differently, the joints (AA5083/AA5083 and AA5083/AA7B04-O) fail in the stir zone due to the presence of defects including "zigzag line," kissing bond and discontinuous voids.

  1. Microstructural and Mechanical Characterization of a Dissimilar Friction Stir-Welded AA5083-AA7B04 Butt Joint

    NASA Astrophysics Data System (ADS)

    Chen, Yu; Ding, Hua; Cai, Zhihui; Zhao, Jingwei; Li, Jizhong

    2017-02-01

    Friction stir welding (FSW) has been used for joining AA5083 and AA7B04 alloy sheets with the aim of studying the microstructure and the mechanical properties of dissimilar FSW joints obtained by varying the initial base metal state of AA7B04 alloy. The results show that the initial base metal state has a significant impact on the material flow during dissimilar FSW. As compared with the joints placing hard alloy (artificially aged AA7B04-AA or naturally aged AA7B04-NA) on the retreating side, it becomes easier transporting AA5083 from advancing side to retreating side when soft alloy (annealed AA7B04-O) is placed on the retreating side. The atomic diffusion does not occur at the interface between AA5083 and AA7B04, indicating that the mixing of the two materials is merely mechanical. Grain refinement is observed in the stir zone. The failure location during tensile tests is different depending on the initial base metal state. The joints (AA5083/AA7B04-AA and AA5083/AA7B04-O) fail in the base metal on the soft material side which corresponds to the minimum values in hardness profiles. Differently, the joints (AA5083/AA5083 and AA5083/AA7B04-O) fail in the stir zone due to the presence of defects including "zigzag line," kissing bond and discontinuous voids.

  2. Identities for generalized hypergeometric coefficients

    SciTech Connect

    Biedenharn, L.C.; Louck, J.D.

    1991-01-01

    Generalizations of hypergeometric functions to arbitrarily many symmetric variables are discussed, along with their associated hypergeometric coefficients, and the setting within which these generalizations arose. Identities generalizing the Euler identity for {sub 2}F{sub 1}, the Saalschuetz identity, and two generalizations of the {sub 4}F{sub 3} Bailey identity, among others, are given. 16 refs.

  3. Crustacean hyperglycemic hormones of two cold water crab species, Chionoecetes opilio and C. japonicus: isolation of cDNA sequences and localization of CHH neuropeptide in eyestalk ganglia.

    PubMed

    Chung, J Sook; Ahn, I S; Yu, O H; Kim, D S

    2015-04-01

    Crustacean hyperglycemic hormone (CHH) is primarily known for its prototypical function in hyperglycemia which is induced by the release of CHH. The CHH release takes place as an adaptive response to the energy demands of the animals experiencing stressful environmental, physiological or behavioral conditions. Although >63 decapod CHH nucleotide sequences are known (GenBank), the majority of them is garnered from the species inhabiting shallow and warm water. In order to understand the adaptive role of CHH in Chionoecetes opilio and Chionoecetes japonicus inhabiting deep water environments, we first aimed for the isolation of the full-length cDNA sequence of CHH from the eyestalk ganglia of C. opilio (ChoCHH) and C. japonicus (ChjCHH) using degenerate PCR and 5' and 3' RACE. Cho- and ChjCHH cDNA sequences are identical in 5' UTR and ORF with 100% sequence identity of the putative 138aa of preproCHHs. The length of 3' UTR ChjCHH cDNA sequence is 39 nucleotides shorter than that of ChoCHH. This is the first report in decapod crustaceans that two different species have the identical sequence of CHH. ChoCHH expression increases during embryogenesis of C. opilio and is significantly higher in adult males and females. C. japonicus males have slightly higher ChjCHH expression than C. opilio males, but no statistical difference. In both species, the immunostaining intensity of CHH is stronger in the sinus gland than that of X-organ cells. Future studies will enable us to gain better understanding of the comparative metabolic physiology and endocrinology of cold, deep water species of Chionoecetes spp.

  4. Cloning and sequencing of a cDNA encoding a heat-stable sweet protein, mabinlin II.

    PubMed

    Nirasawa, S; Masuda, Y; Nakaya, K; Kurihara, Y

    1996-11-28

    A cDNA clone encoding a heat-stable sweet protein, mabinlin II (MAB), was isolated and sequenced. The encoded precursor to MAB was composed of 155 amino acid (aa) residues, including a signal sequence of 20 aa, an N-terminal extension peptide of 15 aa, a linker peptide of 14 aa and one residue of C-terminal extension. Comparison of the proteolytic cleavage sites during post-translational processing of MAB precursor with those of like 2S seed-storage proteins of Arabidopsis thaliana, Brassica napus and Bertholletia excelsa shows that the three individual cleavage sites between respective species are conserved.

  5. Women and Identity.

    ERIC Educational Resources Information Center

    Coleman, Ann; And Others

    An interdisciplinary course on women and identity for college-level women's studies instructors is presented. Materials for the course are taken from myth, psychology, sociology, feminism, art, and other disciplines. It is divided into seven units: sexuality, fertility, work and family, fear and envy, women's networks, individuality, and social…

  6. The Visual Identity Project

    ERIC Educational Resources Information Center

    Tennant-Gadd, Laurie; Sansone, Kristina Lamour

    2008-01-01

    Identity is the focus of the middle-school visual arts program at Cambridge Friends School (CFS) in Cambridge, Massachusetts. Sixth graders enter the middle school and design a personal logo as their first major project in the art studio. The logo becomes a way for students to introduce themselves to their teachers and to represent who they are…

  7. Story Telling: Crafting Identities

    ERIC Educational Resources Information Center

    McMahon, Mary; Watson, Mark

    2013-01-01

    Career guidance clients are seeking to craft new identities that better position them in their careers. The focus of the present article is on narrative career counselling's potential contribution in providing a meaningful and useful experience for career guidance clients. To illustrate the potential of narrative career counselling, the story…

  8. Adoption and Identity.

    ERIC Educational Resources Information Center

    Lieberman, E. James

    1998-01-01

    Discusses how adoption responds to ancient questions about origins. Maintains that one's identity hinges on actual relationships more than on pedigree and genes. Discusses reasons for informing a child about his or her adoption. Suggests that adoption is a constructive process involving too many worrisome warnings and anxiety-raising advice by the…

  9. Identities in Flux

    ERIC Educational Resources Information Center

    Wagner, Tom

    2007-01-01

    Because people's vision of themselves and others is always changing, students wondered how pictures might show the effect of time and history on identity. They wondered how they might show two self-portraits in the same picture. This article describes a lesson on reconstructive self-portrait using a contrapuntal format. (Contains 5 resources and 3…

  10. Dissociative Identity Disorder

    ERIC Educational Resources Information Center

    Schmidt, Tom

    2007-01-01

    Few psychological disorders in the Diagnostic Statistical Manual have generated as much controversy as Dissociative Identity Disorder (DID). For the past 35 years diagnoses of DID, previously referred to as Multiple Personality Disorder (MPD), have increased exponentially, causing various psychological researchers and clinicians to question the…

  11. Identity conflicts in adoptees.

    PubMed

    Sorosky, A D; Baran, A; Pannor, R

    1975-01-01

    A review of the literature, and interviews with a large number of adoptees who have experienced reunions with their birth parents, indicates that adoptees are more vulnerable than the population at large to the development of identity problems in late adolescence and young adulthood.

  12. The Symbolic Identity Technique.

    ERIC Educational Resources Information Center

    Goud, Nelson H.

    2001-01-01

    Explains the role of symbols in attaining total psychic growth by applying concepts of C. Jung, R. Assagiolo, and L. Kubie. Describes a new strategy, the symbolic identity technique, which involves environmental exploration in a relaxed, receptive manner in order to discover something in the outer environment that reflects one's inner nature.…

  13. Language, Identity, and Exile

    ERIC Educational Resources Information Center

    Erdinast-Vulcan, Daphna

    2010-01-01

    The exilic mode of being, a living on boundary-lines, produces a constant relativization of one's home, one's culture, one's language, and one's self, through the acknowledgement of otherness. It is a homesickness without nostalgia, without the desire to return to the same, to be identical to oneself. The encounter with the other which produces a…

  14. Teaching European Identities

    ERIC Educational Resources Information Center

    Raento, Pauliina

    2008-01-01

    The political, cultural and social make-up of Europe is changing fast. A new European identity is under construction, but old contradictions and diversity challenge its contents, forms and boundaries. Migration, the changing role of the nation-state and Europe's regions, the reshaping of politico-administrative and perceptional boundaries, the…

  15. Interface Formation During Fusion™ Casting of AA3003/AA4045 Aluminum Alloy Ingots

    NASA Astrophysics Data System (ADS)

    Di Ciano, Massimo; Caron, E. J. F. R.; Weckman, D. C.; Wells, M. A.

    2015-12-01

    Fusion™ casting is a unique Direct Chill continuous casting process whereby two different alloys can be cast simultaneously, producing a laminated ingot for rolling into clad sheet metal such as AA3003/AA4045 brazing sheet. Better understanding of the wetting and interface formation process during Fusion™ casting is required to further improve process yields and also explore use of other alloy systems for new applications. In this research, AA3003-core/AA4045-clad ingots were cast using a well-instrumented lab-scale Fusion™ casting system. As-cast Fusion™ interfaces were examined metallurgically and by mechanical testing. Computational fluid dynamic analyses of the FusionTM casts were also performed. It was shown that the liquid AA4045-clad alloy was able to successfully wet and create an oxide-free, metallurgical, and mechanically sound interface with the lightly oxidized AA3003-core shell material. Based on the results of this study, it is proposed that the bond formation process at the alloys interface during casting is a result of discrete penetration of AA4045 liquid at defects in the preexisting AA3003 oxide, dissolution of underlying AA3003 by liquid AA4045, and subsequent bridging between penetration sites. Spot exudation on the AA3003 chill cast surface due to remelting and inverse segregation may also improve the wetting and bonding process.

  16. Generating matrix and sums of Fibonacci and Pell sequences

    NASA Astrophysics Data System (ADS)

    Ho, C. K.; Woon, H. S.; Chong, Chin-Yoon

    2014-07-01

    In this paper, we study the Fibonacci sequence and Pell sequence and developed generating matrices for them. First we proved two results on the even sum of the Fibonacci sequence and the Pell sequence, using the generating matrix approach. We then deduce the odd sums, some identities and recursive formulas for these two sequences.

  17. Bacillus thuringiensis insecticidal Cry1Aa toxin binds to a highly conserved region of aminopeptidase N in the host insect leading to its evolutionary success.

    PubMed

    Nakanishi, K; Yaoi, K; Shimada, N; Kadotani, T; Sato, R

    1999-06-15

    Bacillus thuringiensis insecticidal protein, Cry1Aa toxin, binds to a specific receptor in insect midguts and has insecticidal activity. Therefore, the structure of the receptor molecule is probably a key factor in determining the binding affinity of the toxin and insect susceptibility. The cDNA fragment (PX frg1) encoding the Cry1Aa toxin-binding region of an aminopeptidase N (APN) or an APN family protein from diamondback moth, Plutella xylostella midgut was cloned and sequenced. A comparison between the deduced amino acid sequence of PX frg1 and other insect APN sequences shows that Cry1Aa toxin binds to a highly conserved region of APN family protein. In this paper, we propose a model to explain the mechanism that causes B. thuringiensis evolutionary success and differing insect susceptibility to Cry1Aa toxin.

  18. Vector sequence contamination of the Plasmodium vivax sequence database in PlasmoDB and In silico correction of 26 parasite sequences.

    PubMed

    Tao, Zhi-Yong; Sui, Xu; Jun, Cao; Culleton, Richard; Fang, Qiang; Xia, Hui; Gao, Qi

    2015-06-12

    We found a 47 aa protein sequence that occurs 17 times in the Plasmodium vivax nucleotide database published on PlasmoDB. Coding sequence analysis showed multiple restriction enzyme sites within the 141 bp nucleotide sequence, and a His6 tag attached to the 3' end, suggesting cloning vector origins. Sequences with vector contamination were submitted to NCBI, and BLASTN was used to cross-examine whole-genome shotgun contigs (WGS) from four recently deposited P. vivax whole genome sequencing projects. There are at least 26 genes listed in the PlasmoDB database that incorporate this cloning vector sequence into their predicted provisional protein products.

  19. AAS 228: Day 3 afternoon

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Wikipedia Year of Science Editathon (by Meredith Rawls)Whats your first go-to source for an unfamiliar topic on the internet? If you said Wikipedia, youre not alone. For many people, Wikipedia is the primary source of information about astronomy and science. However, many Wikipedia articles about science topics are incomplete or missing, and women are underrepresented among scientists with biographies.To address this, the AAS Astronomy Education Board teamed up with the Wiki Education Foundation to host an edit-a-thon as part of the Wikipedia Year of Science. More than forty attendees spent the better part of three hours working through tutorials, creating new articles, and editing existing ones. The session was generously sponsored by the Simons Foundation.The Year of Science initiative seeks to bring Wikipedia editing skills to the classroom and help new editors find sustainable ways to contribute to Wikipedia in the long term. Anybody can create a free account and start editing!As a first-time Wikipedia contributor, I took the time to go through nearly all the tutorial exercises and familiarize myself with the process of editing a page. I decided to flesh out one section in an existing page about asteroseismology. Others created biography pages from scratch or selected various astronomical topics to write about. To me, the editing process felt like a cross between writing a blog post and a journal article, in a hack day type environment. Working through the tutorial and some examples renewed my empathy for learners who are tackling a new skill set for the first time. A full summary of our

  20. Entanglement by Path Identity.

    PubMed

    Krenn, Mario; Hochrainer, Armin; Lahiri, Mayukh; Zeilinger, Anton

    2017-02-24

    Quantum entanglement is one of the most prominent features of quantum mechanics and forms the basis of quantum information technologies. Here we present a novel method for the creation of quantum entanglement in multipartite and high-dimensional systems. The two ingredients are (i) superposition of photon pairs with different origins and (ii) aligning photons such that their paths are identical. We explain the experimentally feasible creation of various classes of multiphoton entanglement encoded in polarization as well as in high-dimensional Hilbert spaces-starting only from nonentangled photon pairs. For two photons, arbitrary high-dimensional entanglement can be created. The idea of generating entanglement by path identity could also apply to quantum entities other than photons. We discovered the technique by analyzing the output of a computer algorithm. This shows that computer designed quantum experiments can be inspirations for new techniques.

  1. Entanglement by Path Identity

    NASA Astrophysics Data System (ADS)

    Krenn, Mario; Hochrainer, Armin; Lahiri, Mayukh; Zeilinger, Anton

    2017-02-01

    Quantum entanglement is one of the most prominent features of quantum mechanics and forms the basis of quantum information technologies. Here we present a novel method for the creation of quantum entanglement in multipartite and high-dimensional systems. The two ingredients are (i) superposition of photon pairs with different origins and (ii) aligning photons such that their paths are identical. We explain the experimentally feasible creation of various classes of multiphoton entanglement encoded in polarization as well as in high-dimensional Hilbert spaces—starting only from nonentangled photon pairs. For two photons, arbitrary high-dimensional entanglement can be created. The idea of generating entanglement by path identity could also apply to quantum entities other than photons. We discovered the technique by analyzing the output of a computer algorithm. This shows that computer designed quantum experiments can be inspirations for new techniques.

  2. Implicit self and identity.

    PubMed

    Devos, Thierry; Banaji, Mahzarin R

    2003-10-01

    Recent advances in research on implicit social cognition offer an opportunity to challenge common assumptions about self and identity. In the present article, we critically review a burgeoning line of research on self-related processes known to occur outside conscious awareness or conscious control. Our discussion focuses on these implicit self-related processes as they unfold in the context of social group memberships. That is, we show that group memberships can shape thoughts, preferences, motives, goals, or behaviors without the actor's being aware of such an influence or having control over such expressions. As such, this research brings to the fore facets of the self that often contrast with experiences of reflexive consciousness and introspection. Far from being rigid or monolithic, these processes are highly flexible, context-sensitive, and deeply rooted in socio-structural realities. As such, work on implicit self and identity renew thinking about the interplay between the individual and the collective.

  3. FAB overlapping: a strategy for sequencing homologous proteins

    NASA Astrophysics Data System (ADS)

    Ferranti, P.; Malorni, A.; Marino, G.; Pucci, P.; di Luccia, A.; Ferrara, L.

    1991-12-01

    Extensive similarity has been shown to exist between the primary structures of closely related proteins from different species, the only differences being restricted to a few amino acid variations. A new mass spectrometric procedure, which has been called FAB-overlapping, has been developed for sequencing highly homologous proteins based on the detection of these small differences as compared with a known protein used as a reference. Several complementary peptide maps are constructed using fast atom bombardment mass spectrometry (FAB-MS) analysis of different proteolytic digests of the unknown protein and the mass values are related to those expected on the basis of the sequence of the reference protein. The mass signals exhibiting unusual mass values identify those regions where variations have taken place; fine location of the mutations can be obtained by coupling simple protein chemistry methodologies with FAB-MS. Using the FAB-overlapping procedure, it was possible to determine the sequence of [alpha]1, [alpha]3 and [beta] globins from water buffalo (Bubalus bubalis hemoglobins (phenotype AA). Two amino acid substitutions were detected in the buffalo [beta] chain (Lys16 --> His and Asn118 --> His) whereas the [alpha]1 chains were found the [alpha]1 and [alpha]3 chains were found to contain four amino acid replacements, three of which were identical (Glu23 --> Asp, Glu71 --> Gly, Phe117 --> Cys), and the insertion of an alanine residue in position 124. The only differences between [alpha]1 and [alpha]3 globins were identified in the C -terminal region; [alpha]1 contains a Phe residue at position 130 whereas [alpha]3 shows serine at position 132.

  4. Identity Styles and Religiosity: Examining the Role of Identity Commitment

    ERIC Educational Resources Information Center

    Grajales, Tevni E.; Sommers, Brittany

    2016-01-01

    This study observed the role of identity styles, identity commitment, and identity statuses in predicting religiosity in a sample of undergraduate students attending a Seventh-day Adventist university (N = 138). Two structural models were evaluated via path analysis. Results revealed two strong models for the prediction of religiosity. Identity…

  5. Does Everyone Have a Musical Identity?: Reflections on "Musical Identities"

    ERIC Educational Resources Information Center

    Gracyk, Theodore

    2004-01-01

    The book, "Musical Identities" (Raymond MacDonald, David Hargreaves, Dorothy Miell, eds.; Oxford and New York: Oxford University Press, 2002) consists of 11 essays on the psychology of music. The editors divided the essays into two groups: those on developing musical identities ("identities in music" involving recognizable…

  6. Identity Construction, Negotiation, and Resistance: Reconsideration of "Japanese" Identity

    ERIC Educational Resources Information Center

    Fukuda, Chie

    2010-01-01

    This dissertation explores identity construction, mainly focusing on the ethnonational identity of "Japanese," in contrast to that of "non-Japanese" from ethnomethodological and social constructionist perspectives. Within these approaches, identity is not given "a priori" but emerges through sociohistorical contexts…

  7. Genome Sequencing.

    PubMed

    Verma, Mansi; Kulshrestha, Samarth; Puri, Ayush

    2017-01-01

    Genome sequencing is an important step toward correlating genotypes with phenotypic characters. Sequencing technologies are important in many fields in the life sciences, including functional genomics, transcriptomics, oncology, evolutionary biology, forensic sciences, and many more. The era of sequencing has been divided into three generations. First generation sequencing involved sequencing by synthesis (Sanger sequencing) and sequencing by cleavage (Maxam-Gilbert sequencing). Sanger sequencing led to the completion of various genome sequences (including human) and provided the foundation for development of other sequencing technologies. Since then, various techniques have been developed which can overcome some of the limitations of Sanger sequencing. These techniques are collectively known as "Next-generation sequencing" (NGS), and are further classified into second and third generation technologies. Although NGS methods have many advantages in terms of speed, cost, and parallelism, the accuracy and read length of Sanger sequencing is still superior and has confined the use of NGS mainly to resequencing genomes. Consequently, there is a continuing need to develop improved real time sequencing techniques. This chapter reviews some of the options currently available and provides a generic workflow for sequencing a genome.

  8. AAS 228: Day 1 morning

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Come visit astrobites at the AAS booth we have swag!Things kicked off last night at our undergraduate reception booth. Thanks to all of you who stopped by we were delightedto hear from undergrads who already know and love the site, educators who want to use it in their classrooms, and students who had not yet been introduced to astrobites and were excited about a new resource!For the rest of the meeting we will be stationed at theAAS booth in the exhibit hall (booth #211-213), so drop by if you want to learn more (or pick up swag: weve got lots of stickers and sunglasses)!Mondaymorning was the official start of the meeting. Here are just a few of the talks and workshops astrobiters attended this morning.Opening Address(by Susanna Kohler)AAS President Meg Urry kicked off the meeting this morning at 8am with an overview of some of the great endeavors AAS is supporting. We astrobiters had personal motivation to drag ourselves out of bed that early: during this session, Urryannounced the new partnership between AAS and astrobites!Urry touched on some difficult topics in her welcome, including yesterdays tragedy in Orlando. Shereiteratedthe AASs support fortheCommittee for Sexual-Orientation and Gender Minorities in Astronomy (SGMA). She also reminded meeting attendees about the importance ofkeeping conference interactions professional, and pointed to the meetings anti-harassment policy.Partnership Announcement (by Michael Zevin)This morning, the American Astronomical Society announced the new partnership that it will have with Astrobites! We are beyond excited to embark on this new partnership with the

  9. John locke on personal identity.

    PubMed

    Nimbalkar, Namita

    2011-01-01

    John Locke speaks of personal identity and survival of consciousness after death. A criterion of personal identity through time is given. Such a criterion specifies, insofar as that is possible, the necessary and sufficient conditions for the survival of persons. John Locke holds that personal identity is a matter of psychological continuity. He considered personal identity (or the self) to be founded on consciousness (viz. memory), and not on the substance of either the soul or the body.

  10. Social Identity Simulation System (SISTEM)

    DTIC Science & Technology

    2014-03-31

    number of people G = identity group (e.g. gender, ethnicity, etc.) D = identity (e.g. male/ female , White/Black/Spanish/… etc.) R = real resources for an...actions as part of a collective. The collective actions are driven by social identity entrepreneurs (SIDs) (Haslam & Reicher, 2007; Lal, 1997). These...social identity entrepreneurs only advocate a collective action on behalf of the group when they perceive benefits of advocating being greater than

  11. Cloning and sequencing of a cDNA encoding a taste-modifying protein, miraculin.

    PubMed

    Masuda, Y; Nirasawa, S; Nakaya, K; Kurihara, Y

    1995-08-19

    A cDNA clone encoding a taste-modifying protein, miraculin (MIR), was isolated and sequenced. The encoded precursor to MIR was composed of 220 amino acid (aa) residues, including a possible signal sequence of 29 aa. Northern blot analysis showed that the mRNA encoding MIR was already expressed in fruits of Richadella dulcifica at 3 weeks after pollination and was present specifically in the pulp.

  12. Citizenship, Diversity and National Identity

    ERIC Educational Resources Information Center

    Crick, Bernard

    2008-01-01

    This article explores the issues of citizenship, diversity and national identity in the context of the introduction of citizenship education in the UK. It considers the historical context of national identity in the UK and notes that the "British national identity has historically implied diversity". It also analyses the views of British…

  13. Identity theft and your practice.

    PubMed

    Asbell, Lisa

    2010-01-01

    Medical identity theft is a growing problem in America. The federal government has passed laws to help "prevent" identity theft. However, several powerful medical associations are fighting the legislation. Americans need to know what is happening with these laws and why these laws are important to protect providers from lawsuits and consumers of healthcare from medical identity theft.

  14. Identity Development in Deaf Adolescents

    ERIC Educational Resources Information Center

    Kunnen, E. Saskia

    2014-01-01

    We studied identity development during 5 years in seven deaf adolescents who attended a school for deaf children in the highest level of regular secondary education (age between 14 and 18 years), administering identity interviews every year. Identity development is conceptualized as the processes of exploration and commitment formation (Bosma,…

  15. Mistaken identity: activating conservative political identities induces "conservative" financial decisions.

    PubMed

    Morris, Michael W; Carranza, Erica; Fox, Craig R

    2008-11-01

    Four studies investigated whether activating a social identity can lead group members to choose options that are labeled in words associated with that identity. When political identities were made salient, Republicans (but not Democrats) became more likely to choose the gamble or investment option labeled "conservative." This shift did not occur in a condition in which the same options were unlabeled. Thus, the mechanism underlying the effect appears to be not activated identity-related values prioritizing low risk, but rather activated identity-related language (the group label "conservative"). Indeed, when political identities were salient, Republicans favored options labeled "conservative" regardless of whether the options were low or high risk. Finally, requiring participants to explain the label "conservative" before making their choice did not diminish the effect, which suggests that it does not merely reflect inattention to content or construct accessibility. We discuss the implications of these results for the literatures on identity, priming, choice, politics, and marketing.

  16. Visual adaptation provides objective electrophysiological evidence of facial identity discrimination.

    PubMed

    Retter, Talia L; Rossion, Bruno

    2016-07-01

    Discrimination of facial identities is a fundamental function of the human brain that is challenging to examine with macroscopic measurements of neural activity, such as those obtained with functional magnetic resonance imaging (fMRI) and electroencephalography (EEG). Although visual adaptation or repetition suppression (RS) stimulation paradigms have been successfully implemented to this end with such recording techniques, objective evidence of an identity-specific discrimination response due to adaptation at the level of the visual representation is lacking. Here, we addressed this issue with fast periodic visual stimulation (FPVS) and EEG recording combined with a symmetry/asymmetry adaptation paradigm. Adaptation to one facial identity is induced through repeated presentation of that identity at a rate of 6 images per second (6 Hz) over 10 sec. Subsequently, this identity is presented in alternation with another facial identity (i.e., its anti-face, both faces being equidistant from an average face), producing an identity repetition rate of 3 Hz over a 20 sec testing sequence. A clear EEG response at 3 Hz is observed over the right occipito-temporal (ROT) cortex, indexing discrimination between the two facial identities in the absence of an explicit behavioral discrimination measure. This face identity discrimination occurs immediately after adaptation and disappears rapidly within 20 sec. Importantly, this 3 Hz response is not observed in a control condition without the single-identity 10 sec adaptation period. These results indicate that visual adaptation to a given facial identity produces an objective (i.e., at a pre-defined stimulation frequency) electrophysiological index of visual discrimination between that identity and another, and provides a unique behavior-free quantification of the effect of visual adaptation.

  17. Nucleotide sequence of a Proteus mirabilis DNA fragment homologous to the 60K-rnpA-rpmH-dnaA-dnaN-recF-gyrB region of Escherichia coli.

    PubMed

    Skovgaard, O

    1990-09-01

    A 6.5-kb DNA fragment from Proteus mirabilis hybridized to the Escherichia coli dnaA gene. This DNA fragment was cloned and the nucleotide (nt) sequence determined. The fragment is homologous to a region of the E. coli chromosome containing a part of the gene encoding a 60-kDa membrane-associated protein (60K), the rnpA-rpmH-dnaA-dnaN-recF genes, and the N-terminal part of the gyrB gene. The degree of homology is variable: the amino-acid (aa) sequence of a part of the 60K protein and a part of the DnaA protein is only minimally conserved, whereas the C-terminal 148 aa of DnaA are identical in the two species. The conservation of the nt sequence between the rnpA gene and the gene encoding the 60K protein suggests that this region encodes a hitherto unrecognized protein. The ORF for this protein partially overlaps the 3' end of the rnpA structural gene, and the degree of conservation suggests that this gene is important for these bacteria.

  18. Complete genome sequence of southern tomato virus identified from China using next generation sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complete genome sequence of a double-stranded RNA (dsRNA) virus, southern tomato virus (STV), on tomatoes in China, was elucidated using small RNAs deep sequencing. The identified STV_CN12 shares 99% sequence identity to other isolates from Mexico, France, Spain, and U.S. This is the first report ...

  19. The nucleotide sequence of metallothioneins (MT) in liver of the Kafue lechwe (Kobus leche kafuensis) and their potential as biomarkers of heavy metal pollution of the Kafue River.

    PubMed

    M'kandawire, Ethel; Syakalima, Michelo; Muzandu, Kaampwe; Pandey, Girja; Simuunza, Martin; Nakayama, Shouta M M; Kawai, Yusuke K; Ikenaka, Yoshinori; Ishizuka, Mayumi

    2012-09-15

    The study determined heavy metal concentrations and MT1 nucleotide sequence [phylogeny] in liver of the Kafue lechwe. Applicability of MT1 as a biomarker of pollution was assessed. cDNA-encoding sequences for lechwe MT1 were amplified by RT-PCR to characterize the sequence of MT1 which was subjected to BLAST searching at NCBI. Phylogenetic relationships were based on pairwise matrix of sequence divergences calculated by Clustal W. Phylogenetic tree was constructed by NJ method using PHILLIP program. Metals were extracted by acid digestion and concentrations of Cr, Co, Cu, Zn, Cd, Pb, and Ni were determined using an AAS. MT1 mRNA expression levels were measured by quantitative comparative real-time RT-PCR. Lechwe MT1 has a length of 183bp, which encode for MT1 proteins of 61AA, which include 20 cysteines. Nucleotide sequence of lechwe MT1 showed identity with sheep MT (97%) and cattle MT1E (97%). Phylogenetic tree revealed that lechwe MT1 was clustered with sheep MT and cattle MT1E. Cu and Ni concentrations and MT1 mRNA expression levels of lechwe from Blue Lagoon were significantly higher than those from Lochinvar (p<0.05). Concentrations of Cd and Cu, Co and Cu, Co and Pb, Ni and Cu, and Ni and Cr were positively correlated. Spearman's rank correlations also showed positive correlations between Cu and Co concentrations and MT mRNA expression. PCA further suggested that MT mRNA expression was related to Zn and Cd concentrations. Hepatic MT1 mRNA expression in lechwe can be used as biomarker of heavy metal pollution.

  20. 98% identical, 100% wrong: per cent nucleotide identity can lead plant virus epidemiology astray

    PubMed Central

    Duffy, Siobain; Seah, Yee Mey

    2010-01-01

    Short-form publications such as Plant Disease reports serve essential functions: the rapid dissemination of information on the geography of established plant pathogens, incidence and symptomology of pathogens in new hosts, and the discovery of novel pathogens. Many of these sentinel publications include viral sequence data, but most use that information only to confirm the virus' species. When researchers use the standard technique of per cent nucleotide identity to determine that the new sequence is closely related to another sequence, potentially erroneous conclusions can be drawn from the results. Multiple introductions of the same pathogen into a country are being ignored because researchers know fast-evolving plant viruses can accumulate substantial sequence divergence over time, even from a single introduction. An increased use of phylogenetic methods in short-form publications could speed our understanding of these cryptic second introductions and aid in control of epidemics. PMID:20478884

  1. Contextuality of identical particles

    NASA Astrophysics Data System (ADS)

    Kurzyński, Paweł

    2017-01-01

    There exist quantum phenomena that cannot be explained by noncontextual hidden-variable theories, yet the majority of them requires measurements that are performed on a single quantum system at a time. This fact constrains the phenomenon of contextuality to the microscopic domain. It is therefore natural to ask if quantum contextuality can be observed in measurements on collections of particles. Since particles in nature are identical, one can expect that such contextuality would be linked to bosonic and fermionic properties. Analysis of quantum contextuality in such scenarios would broaden our understanding of nonclassical effects in composite systems and perhaps would give us a hint on how to observe quantum phenomena in the macroscopic world. In this work I propose a generalization of quantum contextuality to the case of many identical particles. I show that a type of contextuality exhibited by a collection of particles (state dependent, state independent, or noncontextual) depends on their type and their number. I also discuss further properties of this generalization and identify major open questions.

  2. Online Identities and Social Networking

    NASA Astrophysics Data System (ADS)

    Maheswaran, Muthucumaru; Ali, Bader; Ozguven, Hatice; Lord, Julien

    Online identities play a critical role in the social web that is taking shape on the Internet. Despite many technical proposals for creating and managing online identities, none has received widespread acceptance. Design and implementation of online identities that are socially acceptable on the Internet remains an open problem. This chapter discusses the interplay between online identities and social networking. Online social networks (OSNs) are growing at a rapid pace and has millions of members in them. While the recent trend is to create explicit OSNs such as Facebook and MySpace, we also have implicit OSNs such as interaction graphs created by email and instant messaging services. Explicit OSNs allow users to create profiles and use them to project their identities on the web. There are many interesting identity related issues in the context of social networking including how OSNs help and hinder the definition of online identities.

  3. Chameleon sequences in neurodegenerative diseases.

    PubMed

    Bahramali, Golnaz; Goliaei, Bahram; Minuchehr, Zarrin; Salari, Ali

    2016-03-25

    Chameleon sequences can adopt either alpha helix sheet or a coil conformation. Defining chameleon sequences in PDB (Protein Data Bank) may yield to an insight on defining peptides and proteins responsible in neurodegeneration. In this research, we benefitted from the large PDB and performed a sequence analysis on Chameleons, where we developed an algorithm to extract peptide segments with identical sequences, but different structures. In order to find new chameleon sequences, we extracted a set of 8315 non-redundant protein sequences from the PDB with an identity less than 25%. Our data was classified to "helix to strand (HE)", "helix to coil (HC)" and "strand to coil (CE)" alterations. We also analyzed the occurrence of singlet and doublet amino acids and the solvent accessibility in the chameleon sequences; we then sorted out the proteins with the most number of chameleon sequences and named them Chameleon Flexible Proteins (CFPs) in our dataset. Our data revealed that Gly, Val, Ile, Tyr and Phe, are the major amino acids in Chameleons. We also found that there are proteins such as Insulin Degrading Enzyme IDE and GTP-binding nuclear protein Ran (RAN) with the most number of chameleons (640 and 405 respectively). These proteins have known roles in neurodegenerative diseases. Therefore it can be inferred that other CFP's can serve as key proteins in neurodegeneration, and a study on them can shed light on curing and preventing neurodegenerative diseases.

  4. Alkaline phosphatases and aminopeptidases are altered in a Cry11Aa resistant strain of Aedes aegypti

    PubMed Central

    Lee, Su-Bum; Aimanova, Karlygash G.; Gill, Sarjeet S.

    2014-01-01

    Bacillus thuringiensis subsp. israelensis (Bti) has been widely for the biological control of mosquito populations. However, the mechanism of Bti toxins is still not fully understood. To further elucidate the mechanism of Bti toxins, we developed an Aedes aegypti resistant strain that shows high-level resistance to Cry11Aa toxin. After 27 selections with Cry11Aa toxin, the larvae showed a 124-fold resistance ratio for Cry11Aa (strain G30). G30 larvae showed cross-resistance to Cry4Aa (66-fold resistance), less to Cry4Ba (13-fold), but not to Cry11Ba (2-fold). Midguts from these resistant larvae did not show detectable difference in the processing of the Cry11Aa toxin compared to that in susceptible larvae (WT). Brush border membrane vesicles (BBMV) from resistant larvae bound slightly less Cry11Aa compared to WT BBMV. To identify potential proteins associated with Cry11A resistance, not only transcript changes in the larval midgut were analyzed using Illumina sequencing and qPCR, but alterations of previously identified receptor proteins were investigated using immunoblots. The transcripts of 375 genes were significantly increased and those of 208 genes were down regulated in the resistant larvae midgut compared to the WT. None of the transcripts for previously identified receptors of Cry11Aa (Aedes cadherin, ALP1, APN1, and APN2) were altered in these analyses. The genes for the identified functional receptors in resistant larvae midgut did not contain any mutation in their sequences nor was there any change in their transcript expression levels compared to WT. However, ALP proteins were expressed at reduced levels (~40%) in the resistant strain BBMV. APN proteins and their activity were also slightly reduced in resistance strain. The transcript levels of ALPs (AAEL013330 and AAEL015070) and APNs (AAEL008158, AAEL008162) were significantly reduced. These results strongly suggest that ALPs and APNs could be associated with Cry11Aa resistance in Ae. aegypti. PMID

  5. The gender identity/gender dysphoria questionnaire for adolescents and adults.

    PubMed

    Deogracias, Joseph J; Johnson, Laurel L; Meyer-Bahlburg, Heino F L; Kessler, Suzanne J; Schober, Justine M; Zucker, Kenneth J

    2007-11-01

    The present study reports on the construction of a dimensional measure of gender identity (gender dysphoria) for adolescents and adults. The 27-item gender identity/gender dysphoria questionnaire for adolescents and adults (GIDYQ-AA) was administered to 389 university students (heterosexual and nonheterosexual) and 73 clinic-referred patients with gender identity disorder. Principal axis factor analysis indicated that a one-factor solution, accounting for 61.3% of the total variance, best fits the data. Factor loadings were all >or= .30 (median, .82; range, .34-.96). A mean total score (Cronbach's alpha, .97) was computed, which showed strong evidence for discriminant validity in that the gender identity patients had significantly more gender dysphoria than both the heterosexual and nonheterosexual university students. Using a cut-point of 3.00, we found the sensitivity was 90.4% for the gender identity patients and specificity was 99.7% for the controls. The utility of the GIDYQ-AA is discussed.

  6. IdentityMap Visualization of the Super Identity Model

    SciTech Connect

    2015-04-15

    The Super Identity Model is a collaboration with six United Kingdom universities to develop use cases used to piece together a person's identity across biological, cyber, psychological, and biographical domains. PNNL visualized the model in a web-based application called IdentityMap. This is the first step in a promising new field of research. Interested future collaborators are welcome to find out more by emailing superid@pnnl.gov.

  7. IdentityMap Visualization of the Super Identity Model

    ScienceCinema

    None

    2016-07-12

    The Super Identity Model is a collaboration with six United Kingdom universities to develop use cases used to piece together a person's identity across biological, cyber, psychological, and biographical domains. PNNL visualized the model in a web-based application called IdentityMap. This is the first step in a promising new field of research. Interested future collaborators are welcome to find out more by emailing superid@pnnl.gov.

  8. Expression, purification, kinetic, and structural characterization of an alpha-class carbonic anhydrase from Aedes aegypti (AaCA1).

    PubMed

    Fisher, S Zoë; Tariku, Iyerus; Case, Nicolette M; Tu, Chingkuang; Seron, Teri; Silverman, David N; Linser, Paul J; McKenna, Robert

    2006-08-01

    Carbonic anhydrases (CAs) are zinc-containing metalloenzymes that catalyze the interconversion of carbon dioxide and bicarbonate. The alpha-class CAs are found predominantly in vertebrates, but they are also expressed in insects like mosquitoes. Recently, an alpha-CA from the midgut of Aedes aegypti larvae (AaCA1) was identified, cloned, and subsequently shown to share high sequence homologous to human CA I (HCA I). This paper presents the bacterial expression, purification, and kinetic characterization of the soluble CA domain of AaCA1. The data show AaCA1 is a highly active CA that displays inhibition by methazolamide and ethoxzolamide with nM affinity. Additionally, a homology model of AaCA1, based on the crystal structure of HCA I, is presented and the overall structure, active site, and surface charge properties are compared to those of HCA I and II. Measurements of catalysis show that AaCA1 is more like HCA II in terms of proton transfer, but more similar to HCA I in terms of conversion of carbon dioxide to bicarbonate, and these differences are rationalized in terms of structure. These results also indicate that amino acid differences in the active site of AaCA1 compared to human CAs could be used to design specific CA inhibitors for the management of mosquito populations.

  9. Swiss identity smells like chocolate: Social identity shapes olfactory judgments

    PubMed Central

    Coppin, Géraldine; Pool, Eva; Delplanque, Sylvain; Oud, Bastiaan; Margot, Christian; Sander, David; Van Bavel, Jay J.

    2016-01-01

    There is extensive evidence that social identities can shape people’s attitudes and behavior, but what about sensory judgments? We examined the possibility that social identity concerns may also shape the judgment of non-social properties—namely, olfactory judgment. In two experiments, we presented Swiss and non-Swiss participants with the odor of chocolate, for which Switzerland is world-famous, and a control odor (popcorn). Swiss participants primed with Swiss identity reported the odor of chocolate (but not popcorn) as more intense than non-Swiss participants (Experiments 1 and 2) and than Swiss participants primed with individual identity or not primed (Experiment 2). The self-reported intensity of chocolate smell tended to increase as identity accessibility increased—but only among Swiss participants (Experiment 1). These results suggest that identity priming can counter-act classic sensory habituation effects, allowing identity-relevant smells to maintain their intensity after repeated presentations. This suggests that social identity dynamically influences sensory judgment. We discuss the potential implications for models of social identity and chemosensory perception. PMID:27725715

  10. Swiss identity smells like chocolate: Social identity shapes olfactory judgments.

    PubMed

    Coppin, Géraldine; Pool, Eva; Delplanque, Sylvain; Oud, Bastiaan; Margot, Christian; Sander, David; Van Bavel, Jay J

    2016-10-11

    There is extensive evidence that social identities can shape people's attitudes and behavior, but what about sensory judgments? We examined the possibility that social identity concerns may also shape the judgment of non-social properties-namely, olfactory judgment. In two experiments, we presented Swiss and non-Swiss participants with the odor of chocolate, for which Switzerland is world-famous, and a control odor (popcorn). Swiss participants primed with Swiss identity reported the odor of chocolate (but not popcorn) as more intense than non-Swiss participants (Experiments 1 and 2) and than Swiss participants primed with individual identity or not primed (Experiment 2). The self-reported intensity of chocolate smell tended to increase as identity accessibility increased-but only among Swiss participants (Experiment 1). These results suggest that identity priming can counter-act classic sensory habituation effects, allowing identity-relevant smells to maintain their intensity after repeated presentations. This suggests that social identity dynamically influences sensory judgment. We discuss the potential implications for models of social identity and chemosensory perception.

  11. Studies on cytochrome c oxidase activity of the cytochrome c1aa3 complex from Thermus thermophilus.

    PubMed

    Yoshida, T; Fee, J A

    1984-01-25

    Cytochrome oxidase from T. thermophilus is isolated as a noncovalent complex of cytochromes c1 and aa3 in which the four redox components of aa3 appear to be associated with a single approximately 55,000-D subunit while the heme C is associated with a approximately 33,000-D peptide (Yoshida, T., Lorence, R. M., Choc, M. G., Tarr, G. E., Findling, K. L., and Fee, J. A. (1983) J. Biol. Chem. 258, 112-123). We have examined the steady state transfer of electrons from ascorbate to oxygen by cytochrome c1aa3 as mediated by horse heart, Candida krusei, and T. thermophilus (c552) cytochromes c as well as tetramethylphenylenediamine (TMPD). These mediators exhibit simple Michaelis-Menten kinetic behavior yielding Vmax and KM values characteristic of the experimental conditions. Three classes of kinetic behavior were observed and are qualitatively discussed in terms of a reaction scheme. The data show that tetramethylphenyldiamine and cytochromes c react with the enzyme at independent sites; it is suggested that cytochrome c1 may efficiently transfer electrons to cytochrome aa3. When incorporated into phospholipid vesicles, the highly purified cytochrome c1aa3 was found to translocate one proton into the exterior medium for each molecule of cytochrome c552 oxidized. The combined results suggest that this bacterial enzyme functions in a manner generally identical with the more complex eucaryotic enzyme.

  12. Identity development in deaf adolescents.

    PubMed

    Kunnen, E Saskia

    2014-10-01

    We studied identity development during 5 years in seven deaf adolescents who attended a school for deaf children in the highest level of regular secondary education (age between 14 and 18 years), administering identity interviews every year. Identity development is conceptualized as the processes of exploration and commitment formation (Bosma, 1985). We started from the assumption that because deaf adolescents meet more challenges and also-in our sample-were stimulated in their identity development by school programs, they meet identity conflicts at a relatively early age. The findings were highly consistent with our hypotheses that-compared to a general sample-identity development proceeds faster than in a hearing group and that commitment formation in the domain "Being Deaf" starts earlier than in other domains. We did not find evidence for the hypothesis that commitment formation in this domain in the last year was more mature than in other domains due to a ceiling effect.

  13. AAS 228: Day 3 morning

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session 2015 Newton Lacy Pierce Prize Lecture: The Elephant in the Room: Effects of Distant, Massive Companions on Planetary System Architectures (by Leonardo dos Santos)The first session on Wednesday at 228th AAS Meeting was the Newton Lacy Pierce Prize Lecture by Heather Knutson (California Institute of Technology). This talk featured a broad range of research efforts on exoplanets, with the main focus on how we study the composition of their atmospheres, and how multi-body interactions carve the structure of the planetary systems we observe.One of her first points is the well-known idea that the Solar System is an oddball, compared to the exoplanet systems we have found so far: most of these systems contain hot Jupiters and mini-Neptunes at very close-in orbits around their host stars. Moreover, even when studying their transmission spectra, it is difficult to know the exact composition of their atmospheres.Knutson: it is difficult to constrain atmospheric composition of exoplanets (H-poor or H-rich+clouds?) #aas228pic.twitter.com/LdyN4o9RC7 astrobites (@astrobites) June 15, 2016The main proposal on how these systems formed is the migration scenario. In order to validate this idea, Dr. Knutson and her group The Friends of Hot Jupiters study systems with close-in gas giants and their frequency of binary companions, which are supposed to be the main culprits causing gas-giant migration. They found that approximately half of the observed systems have long-distance companions, providing strong validation of the migration scenario. Moreover, Dr. Knutson speculates that wide binaries have more

  14. Finding sequence motifs in groups of functionally related proteins.

    PubMed

    Smith, H O; Annau, T M; Chandrasegaran, S

    1990-01-01

    We have developed a method for rapidly finding patterns of conserved amino acid residues (motifs) in groups of functionally related proteins. All 3-amino acid patterns in a group of proteins of the type aa1 d1 aa2 d2 aa3, where d1 and d2 are distances that can be varied in a range up to 24 residues, are accumulated into an array. Segments of the proteins containing those patterns that occur most frequently are aligned on each other by a scoring method that obtains an average relatedness value for all the amino acids in each column of the aligned sequence block based on the Dayhoff relatedness odds matrix. The automated method successfully finds and displays nearly all of the sequence motifs that have been previously reported to occur in 33 reverse transcriptases, 18 DNA integrases, and 30 DNA methyltransferases.

  15. Men as Victims: "Victim" Identities, Gay Identities, and Masculinities

    ERIC Educational Resources Information Center

    Dunn, Peter

    2012-01-01

    The impact and meanings of homophobic violence on gay men's identities are explored with a particular focus on their identities as men and as gay men. Homosexuality can pose a challenge to conventional masculinities, and for some gay men, being victimized on account of sexual orientation reawakens conflicts about their masculinity that they…

  16. Threading "Stitches" to Approach Gender Identity, Sexual Identity, and Difference

    ERIC Educational Resources Information Center

    North, Connie E.

    2010-01-01

    As LGBTQI (lesbian, gay, bisexual, transgender, queer/questioning, and intersex) issues become increasingly integrated into multicultural education discourses, we as educators need to examine the implications of our pedagogies for teaching about gender and sexual identities. This article explores my teaching of non-conforming gender identities in…

  17. Identity Support, Identity Devaluation, and Well-Being among Lesbians

    ERIC Educational Resources Information Center

    Beals, Kristin P.; Peplau, Letitia Anne

    2005-01-01

    This research tested predictions about the association of identity support and identity devaluation with psychological well-being (self-esteem, life satisfaction, and depression). Lesbian women completed baseline surveys (N=42), then provided daily experience reports during a 2-week period (n=38), and completed a 2-month follow-up survey (n=34).…

  18. Social Identity Change: Shifts in Social Identity during Adolescence

    ERIC Educational Resources Information Center

    Tanti, Chris; Stukas, Arthur A.; Halloran, Michael J.; Foddy, Margaret

    2011-01-01

    This study investigated the proposition that adolescence involves significant shifts in social identity as a function of changes in social context and cognitive style. Using an experimental design, we primed either peer or gender identity with a sample of 380 early- (12-13 years), mid- (15-16 years), and late-adolescents (18-20 years) and then…

  19. Teacher Educator Identity Emerging from Identity as a Person

    ERIC Educational Resources Information Center

    Murphy, M. Shaun; Pinnegar, Stefinee

    2011-01-01

    Experience is fundamental in identity development. In research, concepts and issues around identity are shaped and confronted in moments of reflection. The act of reflection requires a backward attention to engender a present understanding and create future possibilities. Kim and Greene, and Young and Erickson capture this temporal aspect of…

  20. High School Identity Climate and Student Identity Development

    ERIC Educational Resources Information Center

    Rich, Yisrael; Schachter, Elli P.

    2012-01-01

    This research investigated whether schools characterized by high school students as being rich in identity promoting features contribute to student identity development. A theoretical model posited that student perceptions of teachers as caring role models and their school as cultivating the whole student will foster student exploration and…

  1. Evidence of the importance of the Met115 for Bacillus thuringiensis subsp. israelensis Cyt1Aa protein cytolytic activity in Escherichia coli.

    PubMed

    Zghal, Raida Zribi; Trigui, Hana; Ben Ali, Mamdouh; Jaoua, Samir

    2008-02-01

    Cyt1Aa is a cytolytic toxin, found together with the delta-endotoxins in Bacillus thuringiensis subsp. israelensis parasporal insecticidal crystals. The latter are used as an environmental friendly insecticide against mosquitoes and black flies. Contrary to Cry delta-endotoxin, the mode of action of Cyt1Aa is not completely understood. In the absence of direct structural data, a novel mutated cyt1Aa gene was used to obtain indirect informations on Cyt1Aa conformation changes in the lipid membrane environment. A mutated cyt1Aa gene named cyt1A97 has been isolated from a B. thuringiensis israelensis strain named BUPM97. The nucleotide sequence predicted a protein of 249 amino acids residues with a calculated molecular mass of 27 kDa. Both nucleotide and amino acid sequences similarity analysis revealed that cyt1A97 presents one amino acid different from the native cyt1Aa gene. This mutation was located in the helix alpha C corresponding to a substitution of Met(115) by a Thr. The heterologous expression of the cyt1A97 and another cyt1Aa-type gene called cyt1A98, not affected by such mutation used as control, was performed in Escherichia coli. It revealed that the mutated Cyt1A97 protein was over produced as inclusion bodies showing a very weak toxicity to E. coli contrarily to Cyt1A98 that stopped E. coli growth. Hence, hydrophobic residue Met at position 115 of Cyt1Aa should play a very important role for the maintenance of the structure and cytolytic functions of Cyt1Aa.

  2. AAS 228: Day 1 afternoon

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session: From Space Archeology to Serving the World Today: A 20-year Journey from the Jungles of Guatemala to a Network of Satellite Remote Sensing Facilities Around the World(by Michael Zevin)In the conferences second plenary session, NASAs Daniel Irwin turned the eyes of the conference back to Earth by highlighting the huge impact that NASA missions play in protecting and developing our own planet.Daniel Irwin: using satellite imagery to detect differences in vegetation and find ancient Mayan cities. #aas228 pic.twitter.com/9LFPQdCHTM astrobites (@astrobites) June 13, 2016Irwin came to be involved in NASA through his work mapping Guatemalan jungles, where he would spend 22 days at a time exploring the treacherous jungles on foot armed with a 1st generation GPS, a compass, and a machete. A colleague introduced Irwin to the satellite imagery thathe was exploring, demonstratinghow these images are a strong complement to field work. The sharing of this satellite data with nearby villages helped to show the encroachment of agriculture and the necessity of connecting space to the village. Satellite imagery also played a role in archeological endeavors, uncovering dozens of Mayan cities that have been buried for over a millennia by vegetation, and it provided evidence that the fall of the Mayan civilization may have been due to massive deforestation that ledto drought.Glacial retreat in Chile imaged by ISERV.Irwin displayed the constellation of NASAs Earth-monitoring satellites that have played an integral role in conserving our planet and alerting the world of natural disasters. He also showed

  3. Energy identity for harmonic maps into standard stationary Lorentzian manifolds

    NASA Astrophysics Data System (ADS)

    Han, Xiaoli; Zhao, Liang; Zhu, Miaomiao

    2017-04-01

    For a harmonic map from a closed Riemann surface into a standard stationary Lorentzian manifold, we prove that its Hopf differential is holomorphic. Moreover, we prove that for a sequence of such maps with their energy uniformly bounded, the Lorentzian energy identity holds during the blow-up process.

  4. Forensic aspects of DNA-based human identity testing.

    PubMed

    Roper, Stephen M; Tatum, Owatha L

    2008-01-01

    The forensic applications of DNA-based human identity laboratory testing are often underappreciated. Molecular biology has seen an exponential improvement in the accuracy and statistical power provided by identity testing in the past decade. This technology, dependent upon an individual's unique DNA sequence, has cemented the use of DNA technology in the forensic laboratory. This paper will discuss the state of modern DNA-based identity testing, describe the technology used to perform this testing, and describe its use as it relates to forensic applications. We will also compare individual technologies, including polymerase chain reaction (PCR) and Southern Blotting, that are used to detect the molecular differences that make all individuals unique. An increasing reliance on DNA-based identity testing dictates that healthcare providers develop an understanding of the background, techniques, and guiding principles of this important forensic tool.

  5. The genome sequence of parrot bornavirus 5.

    PubMed

    Guo, Jianhua; Tizard, Ian

    2015-12-01

    Although several new avian bornaviruses have recently been described, information on their evolution, virulence, and sequence are often limited. Here we report the complete genome sequence of parrot bornavirus 5 (PaBV-5) isolated from a case of proventricular dilatation disease in a Palm cockatoo (Probosciger aterrimus). The complete genome consists of 8842 nucleotides with distinct 5' and 3' end sequences. This virus shares nucleotide sequence identities of 69-74 % with other bornaviruses in the genomic regions excluding the 5' and 3' terminal sequences. Phylogenetic analysis based on the genomic regions demonstrated this new isolate is an isolated branch within the clade that includes the aquatic bird bornaviruses and the passerine bornaviruses. Based on phylogenetic analyses and its low nucleotide sequence identities with other bornavirus, we support the proposal that PaBV-5 be assigned to a new bornavirus species:- Psittaciform 2 bornavirus.

  6. Sequencing technologies and genome sequencing.

    PubMed

    Pareek, Chandra Shekhar; Smoczynski, Rafal; Tretyn, Andrzej

    2011-11-01

    The high-throughput - next generation sequencing (HT-NGS) technologies are currently the hottest topic in the field of human and animals genomics researches, which can produce over 100 times more data compared to the most sophisticated capillary sequencers based on the Sanger method. With the ongoing developments of high throughput sequencing machines and advancement of modern bioinformatics tools at unprecedented pace, the target goal of sequencing individual genomes of living organism at a cost of $1,000 each is seemed to be realistically feasible in the near future. In the relatively short time frame since 2005, the HT-NGS technologies are revolutionizing the human and animal genome researches by analysis of chromatin immunoprecipitation coupled to DNA microarray (ChIP-chip) or sequencing (ChIP-seq), RNA sequencing (RNA-seq), whole genome genotyping, genome wide structural variation, de novo assembling and re-assembling of genome, mutation detection and carrier screening, detection of inherited disorders and complex human diseases, DNA library preparation, paired ends and genomic captures, sequencing of mitochondrial genome and personal genomics. In this review, we addressed the important features of HT-NGS like, first generation DNA sequencers, birth of HT-NGS, second generation HT-NGS platforms, third generation HT-NGS platforms: including single molecule Heliscope™, SMRT™ and RNAP sequencers, Nanopore, Archon Genomics X PRIZE foundation, comparison of second and third HT-NGS platforms, applications, advances and future perspectives of sequencing technologies on human and animal genome research.

  7. Presence of glycosaminoglycans in purified AA type amyloid fibrils associated with juvenile rheumatoid arthritis.

    PubMed Central

    Magnus, J H; Husby, G; Kolset, S O

    1989-01-01

    Previous studies have strongly suggested an association between glycosaminoglycans and tissue deposits of amyloid. The present study was aimed at studying this association in purified preparations of hepatic amyloid fibrils obtained from human AA type secondary amyloidosis. Glycosaminoglycans were isolated by gradient ion exchange chromatography of purified amyloid fibrils treated with pronase. Degradation with specific enzymes identified the glycosaminoglycans as chondroitin sulphate, dermatan sulphate, and heparin/heparan sulphate. The total amount of glycosaminoglycans specifically coisolated with the amyloid fibrils was 15 micrograms/mg fibril weight. The presence of glycosaminoglycans in amyloid may play a part in the incorporation of structurally diverse protein precursors into amyloid fibrils of identical ultrastructure. PMID:2930277

  8. Play Memories and Place Identity.

    ERIC Educational Resources Information Center

    Sandberg, Anette

    2003-01-01

    This retrospective study examined play memories from childhood to adulthood of 478 university students between ages 20 and 62 as exhibited in drawings of play memories and questionnaire responses. The study focused on the role of the physical environment and place identity in play memories and individual identity development. Findings showed that…

  9. Teacher Investment in Learner Identity

    ERIC Educational Resources Information Center

    Reeves, Jenelle

    2009-01-01

    From a sociocultural perspective, teacher identity is constructed in relation to others, including other teachers and students. Drawing on positioning theory and the concept of investment, this study analyzed the case of a secondary English teacher who negotiated his teacher identity in relation to English language learners (ELLs). Findings…

  10. Exploring Our Complex Math Identities

    ERIC Educational Resources Information Center

    Leatham, Keith R.; Hill, Diane S.

    2010-01-01

    In this article, the authors discuss some of the dispositions that comprise students' (and teachers') relationships with mathematics--what they call a "mathematical identity." They define "mathematical identity" as an individual's "relationship" with mathematics. They present three reflective tasks that can be used with math students at all levels…

  11. Exploring Leader Identity and Development.

    PubMed

    Priest, Kerry L; Middleton, Eric

    2016-01-01

    Taking on a leader identity can be a motivating force for pursuing leader development. This chapter explores the reciprocal and recursive nature of identity development and leader development, emphasizing how shifting views of self influence one's motivation to develop as a leader.

  12. Ego Identity in Mature Women.

    ERIC Educational Resources Information Center

    Marcia, James E.; Miller, Elizabeth C.

    The relationship between psychosocial development and ego identity was explored among a group of 29 married women, 21-59 years old. After being interviewed, subjects were assigned to one of four categories of identity status, based on their statements regarding decision-making and commitment. There were significant differences between identity…

  13. Understanding Civic Identity in College

    ERIC Educational Resources Information Center

    Weerts, David J.; Cabrera, Alberto F.

    2015-01-01

    Past literature has examined ways in which college students adopt civic identities. However, little is known about characteristics of students that vary in their expression of these identities. Drawing on data from American College Testing (ACT), this study employs multinomial logistic regression to understand attributes of students who vary in…

  14. Gender identity development in adolescence.

    PubMed

    Steensma, Thomas D; Kreukels, Baudewijntje P C; de Vries, Annelou L C; Cohen-Kettenis, Peggy T

    2013-07-01

    This article is part of a Special Issue "Puberty and Adolescence".This article aims to provide an outline of what is currently known on trajectories, and contributing factors to gender identity development in adolescence. We give a historical overview of the concept of gender identity, and describe general identity development in adolescence, gender identity development in the general population and in gender variant youth. Possible psychosocial (such as child and parental characteristics) and biological factors (such as the effects of prenatal exposure to gonadal hormones and the role of genetics) contributing to a gender variant identity are discussed. Studies focusing on a number of psychosocial and biological factors separately, indicate that each of these factors influence gender identity formation, but little is known about the complex interplay between the factors, nor about the way individuals themselves contribute to the process. Research into normative and gender variant identity development of adolescents is clearly lagging behind. However, studies on persons with gender dysphoria and disorders of sex development, show that the period of adolescence, with its changing social environment and the onset of physical puberty, seems to be crucial for the development of a non-normative gender identity.

  15. Identity as a Mathematical Thinker

    ERIC Educational Resources Information Center

    Owens, Kay

    2008-01-01

    I argue in this article that identity as a mathematical thinker develops through self-directed learning within a supportive community of practice. The dynamic nature of identity as a mathematical thinker is illustrated by considering the experiences of primary pre-service teachers who undertook a mathematics and technology subject in their…

  16. Identity Research in Mathematics Education

    ERIC Educational Resources Information Center

    Darragh, Lisa

    2016-01-01

    This paper examines the literature on identity within mathematics education published in journals over the past two decades. It analyses the theoretical underpinnings, research methods and definitions of identity, providing a critique rather than a summary of the literature. A total of 188 articles from 85 different journals are reviewed in the…

  17. Fibonacci Identities, Matrices, and Graphs

    ERIC Educational Resources Information Center

    Huang, Danrun

    2005-01-01

    General strategies used to help discover, prove, and generalize identities for Fibonacci numbers are described along with some properties about the determinants of square matrices. A matrix proof for identity (2) that has received immense attention from many branches of mathematics, like linear algebra, dynamical systems, graph theory and others…

  18. Developing Professional Identity in LIS?

    ERIC Educational Resources Information Center

    Hussey, Lisa K.; Campbell-Meier, Jennifer

    2016-01-01

    Identity is the core of who we are as individuals. It shapes how we present ourselves, our expectations of how we interact with others and their treatment of us, and forms the basis of what we believe are our capabilities and potential. Identity is not limited to individuals, but also includes groups, such as clubs, organizations, and professions.…

  19. The Joint Accomplishment of Identity

    ERIC Educational Resources Information Center

    Hand, Victoria; Gresalfi, Melissa

    2015-01-01

    Identity has become a central concept in the analysis of learning from social perspectives. In this article, we draw on a situative perspective to conceptualize identity as a "joint accomplishment" between individuals and their interactions with norms, practices, cultural tools, relationships, and institutional and cultural contexts.…

  20. Supporting Biracial Children's Identity Development.

    ERIC Educational Resources Information Center

    Morrison, Johnetta Wade; Bordere, Tashel

    2001-01-01

    Discusses stages of identity development in early childhood, as well as ways teachers can be supportive of that development. Addresses components of identity development in young children, parental preferences, valuing diversity, and curriculum recommendations. Provides suggestions appropriate for children of any racial combination. (SD)

  1. Explanatory Identities and Conceptual Change

    ERIC Educational Resources Information Center

    Thagard, Paul

    2014-01-01

    Although mind-brain identity remains controversial, many other identities of ordinary things with scientific ones are well established. For example, air is a mixture of gases, water is H[subscript 2]O, and fire is rapid oxidation. This paper examines the history of 15 important identifications: air, blood, cloud, earth, electricity, fire, gold,…

  2. The Challenge of Hyphenated Identity

    ERIC Educational Resources Information Center

    Cheng, Li-Rong Lilly

    2004-01-01

    Hyphenated identity is a term that references the multiple socially bound features that individuals use to think about themselves. This article examines cultural and linguistic considerations in the understanding of hyphenated identity and discusses the merit of the concept for clinical use in speech-language pathology. The sources used consist of…

  3. 7 CFR 51.596 - U.S. Grade AA.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Consumer Standards for Celery Stalks Grades § 51.596 U.S. Grade AA. U.S. Grade AA shall consist of stalks of celery of similar varietal characteristics, which are well developed, and have good...

  4. 7 CFR 51.596 - U.S. Grade AA.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... Consumer Standards for Celery Stalks Grades § 51.596 U.S. Grade AA. U.S. Grade AA shall consist of stalks of celery of similar varietal characteristics, which are well developed, and have good...

  5. 7 CFR 51.596 - U.S. Grade AA.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Consumer Standards for Celery Stalks Grades § 51.596 U.S. Grade AA. U.S. Grade AA shall consist of stalks of celery of similar varietal characteristics, which are...

  6. 7 CFR 51.596 - U.S. Grade AA.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ..., CERTIFICATION, AND STANDARDS) United States Consumer Standards for Celery Stalks Grades § 51.596 U.S. Grade AA. U.S. Grade AA shall consist of stalks of celery of similar varietal characteristics, which are...

  7. Nucleotide sequencing and identification of some wild mushrooms.

    PubMed

    Das, Sudip Kumar; Mandal, Aninda; Datta, Animesh K; Gupta, Sudha; Paul, Rita; Saha, Aditi; Sengupta, Sonali; Dubey, Priyanka Kumari

    2013-01-01

    The rDNA-ITS (Ribosomal DNA Internal Transcribed Spacers) fragment of the genomic DNA of 8 wild edible mushrooms (collected from Eastern Chota Nagpur Plateau of West Bengal, India) was amplified using ITS1 (Internal Transcribed Spacers 1) and ITS2 primers and subjected to nucleotide sequence determination for identification of mushrooms as mentioned. The sequences were aligned using ClustalW software program. The aligned sequences revealed identity (homology percentage from GenBank data base) of Amanita hemibapha [CN (Chota Nagpur) 1, % identity 99 (JX844716.1)], Amanita sp. [CN 2, % identity 98 (JX844763.1)], Astraeus hygrometricus [CN 3, % identity 87 (FJ536664.1)], Termitomyces sp. [CN 4, % identity 90 (JF746992.1)], Termitomyces sp. [CN 5, % identity 99 (GU001667.1)], T. microcarpus [CN 6, % identity 82 (EF421077.1)], Termitomyces sp. [CN 7, % identity 76 (JF746993.1)], and Volvariella volvacea [CN 8, % identity 100 (JN086680.1)]. Although out of 8 mushrooms 4 could be identified up to species level, the nucleotide sequences of the rest may be relevant to further characterization. A phylogenetic tree is constructed using Neighbor-Joining method showing interrelationship between/among the mushrooms. The determined nucleotide sequences of the mushrooms may provide additional information enriching GenBank database aiding to molecular taxonomy and facilitating its domestication and characterization for human benefits.

  8. Nucleotide Sequencing and Identification of Some Wild Mushrooms

    PubMed Central

    Das, Sudip Kumar; Mandal, Aninda; Datta, Animesh K.; Gupta, Sudha; Paul, Rita; Saha, Aditi; Sengupta, Sonali; Dubey, Priyanka Kumari

    2013-01-01

    The rDNA-ITS (Ribosomal DNA Internal Transcribed Spacers) fragment of the genomic DNA of 8 wild edible mushrooms (collected from Eastern Chota Nagpur Plateau of West Bengal, India) was amplified using ITS1 (Internal Transcribed Spacers 1) and ITS2 primers and subjected to nucleotide sequence determination for identification of mushrooms as mentioned. The sequences were aligned using ClustalW software program. The aligned sequences revealed identity (homology percentage from GenBank data base) of Amanita hemibapha [CN (Chota Nagpur) 1, % identity 99 (JX844716.1)], Amanita sp. [CN 2, % identity 98 (JX844763.1)], Astraeus hygrometricus [CN 3, % identity 87 (FJ536664.1)], Termitomyces sp. [CN 4, % identity 90 (JF746992.1)], Termitomyces sp. [CN 5, % identity 99 (GU001667.1)], T. microcarpus [CN 6, % identity 82 (EF421077.1)], Termitomyces sp. [CN 7, % identity 76 (JF746993.1)], and Volvariella volvacea [CN 8, % identity 100 (JN086680.1)]. Although out of 8 mushrooms 4 could be identified up to species level, the nucleotide sequences of the rest may be relevant to further characterization. A phylogenetic tree is constructed using Neighbor-Joining method showing interrelationship between/among the mushrooms. The determined nucleotide sequences of the mushrooms may provide additional information enriching GenBank database aiding to molecular taxonomy and facilitating its domestication and characterization for human benefits. PMID:24489501

  9. Identity change and informed consent.

    PubMed

    Witt, Karsten

    2017-03-20

    In this paper, I focus on a kind of medical intervention that is at the same time fascinating and disturbing: identity-changing interventions. My guiding question is how such interventions can be ethically justified within the bounds of contemporary bioethical mainstream that places great weight on the patient's informed consent. The answer that is standardly given today is that patients should be informed about the identity effects, thus suggesting that changes in identity can be treated like 'normal' side effects. In the paper, I argue that this approach is seriously lacking because it misses important complexities going along with decisions involving identity changes and consequently runs into mistakes. As a remedy I propose a new approach, the 'perspective-sensitive account', which avoids these mistakes and thus provides the conceptual resources to systematically reflect on and give a valid consent to identity-changing interventions.

  10. National Development Generates National Identities

    PubMed Central

    2016-01-01

    The purpose of the article is to test the relationship between national identities and modernisation. We test the hypotheses that not all forms of identity are equally compatible with modernisation as measured by Human Development Index. The less developed societies are characterised by strong ascribed national identities based on birth, territory and religion, but also by strong voluntarist identities based on civic features selected and/or achieved by an individual. While the former decreases with further modernisation, the latter may either decrease or remain at high levels and coexist with instrumental supranational identifications, typical for the most developed countries. The results, which are also confirmed by multilevel regression models, thus demonstrate that increasing modernisation in terms of development contributes to the shifts from classical, especially ascribed, identities towards instrumental identifications. These findings are particularly relevant in the turbulent times increasingly dominated by the hardly predictable effects of the recent mass migrations. PMID:26841050

  11. The AAS: Its Next 100 Years

    NASA Astrophysics Data System (ADS)

    Wolff, S.

    1999-05-01

    The AAS: Its Next Hundred Years "We are probably nearing the limit of all we can know about astronomy."-- Simon Newcomb, 1888. The best way to celebrate the centennial of the AAS is to look forward, not backward, and to begin planning for the next 100 years. However, predicting the future is even more difficult than it was in Newcomb's time. We live in an era characterized by an unprecedented rate of change in the kinds of scientific questions we ask, the tools we use to answer them, and the way we communicate our results. This talk will highlight some of the issues that we will face as a community during the next 10--but not the next 100!--years and suggests that the AAS has a fundamental role to play in shaping the community response to these issues.

  12. Biochemical Properties and Atomic Resolution Structure of a Proteolytically Processed β-Mannanase from Cellulolytic Streptomyces sp. SirexAA-E

    PubMed Central

    Takasuka, Taichi E.; Acheson, Justin F.; Bianchetti, Christopher M.; Prom, Ben M.; Bergeman, Lai F.; Book, Adam J.; Currie, Cameron R.; Fox, Brian G.

    2014-01-01

    β-mannanase SACTE_2347 from cellulolytic Streptomyces sp. SirexAA-E is abundantly secreted into the culture medium during growth on cellulosic materials. The enzyme is composed of domains from the glycoside hydrolase family 5 (GH5), fibronectin type-III (Fn3), and carbohydrate binding module family 2 (CBM2). After secretion, the enzyme is proteolyzed into three different, catalytically active variants with masses of 53, 42 and 34 kDa corresponding to the intact protein, loss of the CBM2 domain, or loss of both the Fn3 and CBM2 domains. The three variants had identical N-termini starting with Ala51, and the positions of specific proteolytic reactions in the linker sequences separating the three domains were identified. To conduct biochemical and structural characterizations, the natural proteolytic variants were reproduced by cloning and heterologously expressed in Escherichia coli. Each SACTE_2347 variant hydrolyzed only β-1,4 mannosidic linkages, and also reacted with pure mannans containing partial galactosyl- and/or glucosyl substitutions. Examination of the X-ray crystal structure of the GH5 domain of SACTE_2347 suggests that two loops adjacent to the active site channel, which have differences in position and length relative to other closely related mannanases, play a role in producing the observed substrate selectivity. PMID:24710170

  13. AAS Nova and Astrobites: Making current astronomy research accessible

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna; Astrobites Team

    2016-10-01

    AAS Nova and Astrobites are two resources available for astronomers, astronomy students, and astronomy enthusiasts to keep up with some of the most recent research published across the field of astronomy. Both supported by the AAS, these two daily astrophysical literature blogs provide accessible summaries of recent publications on the arXiv and in AAS journals. We present the goals, content, and readership of AAS Nova and Astrobites, and discuss how they might be used as tools in the undergraduate classroom.

  14. Coming to an Asexual Identity: Negotiating Identity, Negotiating Desire

    PubMed Central

    Scherrer, Kristin S.

    2010-01-01

    Sexuality is generally considered an important aspect of self-hood. Therefore, individuals who do not experience sexual attraction, and embrace an asexual identity are in a unique position to inform the social construction of sexuality. This study explores the experiences of asexual individuals utilizing open ended Internet survey data from 102 self-identified asexual people. In this paper I describe several distinct aspects of asexual identities: the meanings of sexual, and therefore, asexual behaviors, essentialist characterizations of asexuality, and lastly, interest in romance as a distinct dimension of sexuality. These findings have implications not only for asexual identities, but also for the connections of asexuality with other marginalized sexualities. PMID:20593009

  15. The expression and crystallization of Cry65Aa require two C-termini, revealing a novel evolutionary strategy of Bacillus thuringiensis Cry proteins

    PubMed Central

    Peng, Dong-hai; Pang, Cui-yun; Wu, Han; Huang, Qiong; Zheng, Jin-shui; Sun, Ming

    2015-01-01

    The insecticidal crystal protein (Cry) genes of Bacillus thuringiensis are a key gene resource for generating transgenic crops with pest resistance. However, many cry genes cannot be expressed or form crystals in mother cells. Here, we report a novel Cry protein gene, cry65Aa1, which exists in an operon that contains a downstream gene encoding a hypothetical protein ORF2. We demonstrated that ORF2 is required for Cry65Aa1 expression and crystallization by function as a C-terminal crystallization domain. The orf2 sequence is also required for Cry65Aa expression, because orf2 transcripts have a stabilizing effect on cry65Aa1 transcripts. Furthermore, we found that the crystallization of Cry65Aa1 required the Cry65Aa1 C-terminus in addition to ORF2 or a typical Cry protein C-terminal region. Finally, we showed that Cry65Aa1 has a selective cytotoxic effect on MDA-MB231 cancer cells. This report is the first description of a 130-kDa mass range Cry protein requiring two C-termini for crystallization. Our findings reveal a novel evolutionary strategy of Cry proteins and provide an explanation for the existence of Cry protein genes that cannot form crystals in B. thuringiensis. This study also provides a potential framework for isolating novel cry genes from “no crystal” B. thuringiensis strains. PMID:25656389

  16. African American Racial Identity across the Lifespan: Identity Status, Identity Content, and Depressive Symptoms

    ERIC Educational Resources Information Center

    Yip, Tiffany; Seaton, Eleanor K.; Sellers, Robert M.

    2006-01-01

    Cluster analytic methods were used to create 4 theorized ethnic identity statuses (achieved, foreclosed, moratorium, and diffused) among 940 African American adolescents (13-17 years old), college students (18-23 years old), and adults (27-78 years old). Evidence for the existence of 4 identity statuses was found across the 3 age groups. The…

  17. Identity and Intimacy during Adolescence: Connections among Identity Styles, Romantic Attachment and Identity Commitment

    ERIC Educational Resources Information Center

    Kerpelman, Jennifer L.; Pittman, Joe F.; Cadely, Hans Saint-Eloi; Tuggle, Felicia J.; Harrell-Levy, Marinda K.; Adler-Baeder, Francesca M.

    2012-01-01

    Integration of adult attachment and psychosocial development theories suggests that adolescence is a time when capacities for romantic intimacy and identity formation are co-evolving. The current study addressed direct, indirect and moderated associations among identity and romantic attachment constructs with a diverse sample of 2178 middle…

  18. Complete genome sequence of Bacillus thuringiensis YC-10, a novel active strain against plant-parasitic nematodes.

    PubMed

    Cheng, Feixue; Wang, Jian; Song, Zhiqiang; Cheng, Ju'e; Zhang, Deyong; Liu, Yong

    2015-09-20

    Bacillus thuringiensis is an important microbial biopesticide for controlling agricultural pests by the production of toxic parasporal crystals proteins.Here,we report the finished annotated genome sequence of B. thuringiensis YC-10,which is highly toxic to nematodes.The complete genome sequence consists of a circular chromosome and nine circular plasmids,which the biggest plasmid harbors six parasporal crystals proteins genes consisting of cry1Aa, cry1Ac, cry1Ia, cry2Aa, cry2Ab and cryB1. The crystals proteins of Cry1Ia and Cry1Aa have high nematicidal activity against Meloidogyne incognita.

  19. 40 CFR Appendix A to Subpart Aa of... - Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... (40 CFR Part 63, Subpart A) to Subpart AA A Appendix A to Subpart AA of Part 63 Protection of... Hazardous Air Pollutants From Phosphoric Acid Manufacturing Plants Pt. 63, Subpt. AA, App. A Appendix A to Subpart AA of Part 63—Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA 40...

  20. 40 CFR Appendix A to Subpart Aa of... - Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... (40 CFR Part 63, Subpart A) to Subpart AA A Appendix A to Subpart AA of Part 63 Protection of... Hazardous Air Pollutants From Phosphoric Acid Manufacturing Plants Pt. 63, Subpt. AA, App. A Appendix A to Subpart AA of Part 63—Applicability of General Provisions (40 CFR Part 63, Subpart A) to Subpart AA 40...

  1. Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host-virus coevolution.

    PubMed

    Moniruzzaman, Mohammad; LeCleir, Gary R; Brown, Christopher M; Gobler, Christopher J; Bidle, Kay D; Wilson, William H; Wilhelm, Steven W

    2014-10-01

    Aureococcus anophagefferens causes economically and ecologically destructive "brown tides" in the United States, China and South Africa. Here we report the 370,920bp genomic sequence of AaV, a virus capable of infecting and lysing A. anophagefferens. AaV is a member of the nucleocytoplasmic large DNA virus (NCLDV) group, harboring 377 putative coding sequences and 8 tRNAs. Despite being an algal virus, AaV shows no phylogenetic affinity to the Phycodnaviridae family, to which most algae-infecting viruses belong. Core gene phylogenies, shared gene content and genome-wide similarities suggest AaV is the smallest member of the emerging clade "Megaviridae". The genomic architecture of AaV demonstrates that the ancestral virus had an even smaller genome, which expanded through gene duplication and assimilation of genes from diverse sources including the host itself - some of which probably modulate important host processes. AaV also harbors a number of genes exclusive to phycodnaviruses - reinforcing the hypothesis that Phycodna- and Mimiviridae share a common ancestor.

  2. Dna Sequencing

    DOEpatents

    Tabor, Stanley; Richardson, Charles C.

    1995-04-25

    A method for sequencing a strand of DNA, including the steps off: providing the strand of DNA; annealing the strand with a primer able to hybridize to the strand to give an annealed mixture; incubating the mixture with four deoxyribonucleoside triphosphates, a DNA polymerase, and at least three deoxyribonucleoside triphosphates in different amounts, under conditions in favoring primer extension to form nucleic acid fragments complementory to the DNA to be sequenced; labelling the nucleic and fragments; separating them and determining the position of the deoxyribonucleoside triphosphates by differences in the intensity of the labels, thereby to determine the DNA sequence.

  3. Gender identity in XY intersexuality.

    PubMed

    Sobel, Vivian; Imperato-McGinley, Julianne

    2004-07-01

    The following syndromes of XY intersexuality are reviewed: 5alpha-reductase-2 deficiency, 17beta-hydroxysteroid dehydrogenase-3 deficiency, and complete and partial androgen insensitivity with attention focused on issues of gender identity. Each syndrome, with its unique presentation, provides an opportunity to explore the relative effects of nature (androgens) versus nurture (sex of rearing) in gender identity development. The phenomenon of gender role reversal in these conditions is described and theories on the determinants of gender identity formation are proposed. Issues of importance to psychiatrists in treating patients who have these conditions also are discussed.

  4. Ward identities for Hall transport

    NASA Astrophysics Data System (ADS)

    Hoyos, Carlos; Kim, Bom Soo; Oz, Yaron

    2014-10-01

    We derive quantum field theory Ward identities based on linear area preserving and conformal transformations in 2+1 dimensions. The identities relate Hall viscosities, Hall conductivities and the angular momentum. They apply both for relativistic and non relativistic systems, at zero and at finite temperature. We consider systems with or without translation invariance, and introduce an external magnetic field and viscous drag terms. A special case of the identities yields the well known relation between the Hall conductivity and half the angular momentum density.

  5. Looking for Daisy: Constructing Teacher Identities

    ERIC Educational Resources Information Center

    Ritchie, Stephen M.

    2009-01-01

    Research on teacher identities is both important and increasing. In this forum contribution I re-interpret assertions about an African American science teacher's identities in terms of Jonathon Turner's ("2002") constructs of role identity and sub-identity. I contest the notion of renegotiation of identities, suggesting that particular role…

  6. Chicana Identity Construction: Pushing the Boundaries

    ERIC Educational Resources Information Center

    Vera, Helen; De Los Santos, Esmeralda

    2005-01-01

    Identity concepts that Chicana feminists have described as central to their developmental experience are not reflected in the traditional views of identity, feminist accounts of women's identity, or ethnic identity theory. Chicana feminist Gloria Anzaldua initially postulated that in the straddling of two cultures, a hybrid or mestiza identity is…

  7. Complete genome sequence of Bacillus thuringiensis subsp. chinensis strain CT-43.

    PubMed

    He, Jin; Wang, Jieping; Yin, Wen; Shao, Xiaohu; Zheng, Huajun; Li, Mingshun; Zhao, Youwen; Sun, Ming; Wang, Shengyue; Yu, Ziniu

    2011-07-01

    Bacillus thuringiensis has been widely used as an agricultural biopesticide for a long time. As a producing strain, B. thuringiensis subsp. chinensis strain CT-43 is highly toxic to lepidopterous and dipterous insects. It can form various parasporal crystals consisting of Cry1Aa3, Cry1Ba1, Cry1Ia14, Cry2Aa9, and Cry2Ab1. During fermentation, it simultaneously generates vegetative insecticidal protein Vip3Aa10 and the insecticidal nucleotide analogue thuringiensin. Here, we report the finished, annotated genome sequence of B. thuringiensis strain CT-43.

  8. Complete Genome Sequence of Bacillus thuringiensis subsp. chinensis Strain CT-43▿

    PubMed Central

    He, Jin; Wang, Jieping; Yin, Wen; Shao, Xiaohu; Zheng, Huajun; Li, Mingshun; Zhao, Youwen; Sun, Ming; Wang, Shengyue; Yu, Ziniu

    2011-01-01

    Bacillus thuringiensis has been widely used as an agricultural biopesticide for a long time. As a producing strain, B. thuringiensis subsp. chinensis strain CT-43 is highly toxic to lepidopterous and dipterous insects. It can form various parasporal crystals consisting of Cry1Aa3, Cry1Ba1, Cry1Ia14, Cry2Aa9, and Cry2Ab1. During fermentation, it simultaneously generates vegetative insecticidal protein Vip3Aa10 and the insecticidal nucleotide analogue thuringiensin. Here, we report the finished, annotated genome sequence of B. thuringiensis strain CT-43. PMID:21551307

  9. AAS 228: Day 2 morning

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2016-06-01

    Editors Note:This week were at the 228th AAS Meeting in San Diego, CA. Along with a team ofauthors from astrobites.com, I will bewritingupdates on selectedevents at themeeting and posting twiceeach day. Follow along here or atastrobites.com, or catch ourlive-tweeted updates from the@astrobites Twitter account. The usual posting schedule for AAS Nova will resumenext week.Plenary Session (Day 1) The Galaxy Zoo(by Benny Tsang)Galaxy Zoo was so hot that the servers hosting the galaxy images got melted down soon after being launched.Kevin Schawinski from ETH Zurich took us on a tour ofhis wonderful Galaxy Zoo. It is a huge zoo with about a quarter million zookeepers, they are citizen astronomers who collaboratively classify galaxies by their looks as an attempt to understand galaxy evolution. The big question that is being answered is: how do blue, actively star-forming galaxies evolve into red, quiescent (non-star-forming) galaxies? The Zoo helped reveal that blue galaxies turn into red galaxies via two possible paths galaxies might run out of supply of gas and shut off star formation slowly; or they could merge with one another and turn off star formation by destroying the gas reservoir rapidly!The Galaxy Zoo project also led to the discoveries of:Green Peas: they are the living fossils of galaxy evolution; compact, bright, green galaxies that are actively forming starsOverlapping galaxies: they are pairs of galaxies that are separated physically but happen to lie on the same line of sight; they provide excellent laboratories for studying dust extinctionHannys Voorwerp: an unusual object named after Hanny the discoverer, which is believed to be the first detection of quasar light echoThe idea of Galaxy Zoo in getting help from citizen scientists was further extended into an award-winningproject known as the Zooniverse, which is an online platform for streamlined crowd-sourcing for scientific research that requires human input. The future of astronomy is going to be

  10. The Development of Female Identity.

    ERIC Educational Resources Information Center

    Katz, Phyllis A.

    1979-01-01

    This article explores some of the major influences affecting the development of female sex-role identity and the psychological and social consequences of this deveopment during childhood and adolescence. (Author/EB)

  11. Digital Identity - The Legal Person?

    NASA Astrophysics Data System (ADS)

    Sullivan, Clare

    This paper examines the concept of digital identity which the author asserts is now evident in the United Kingdom as a consequence of the Identity Cards Act (UK) 2006 and the National Identity Scheme it establishes. The nature and functions of the concept, particularly the set of information which constitutes an individual’s transactional identity, are examined. The paper then considers the central question of who, or what, is the legal person in a transaction i.e. who or what enters into legal relations. The analysis presents some intriguing results which were almost certainly not envisaged by the legislature. The implications extend beyond the United Kingdom to similar schemes in other jurisdictions, and to countries, like Australia, which may implement such a scheme.

  12. Science Identity in Informal Education

    NASA Astrophysics Data System (ADS)

    Schon, Jennifer A.

    The national drive to increase the number of students pursuing Science Technology, Engineering, and Math (STEM) careers has brought science identity into focus for educators, with the need to determine what encourages students to pursue and persist in STEM careers. Science identity, the degree to which students think someone like them could be a scientist is a potential indicator of students pursuing and persisting in STEM related fields. Science identity, as defined by Carlone and Johnson (2007) consists of three constructs: competence, performance, and recognition. Students need to feel like they are good at science, can perform it well, and that others recognize them for these achievements in order to develop a science identity. These constructs can be bolstered by student visitation to informal education centers. Informal education centers, such as outdoor science schools, museums, and various learning centers can have a positive impact on how students view themselves as scientists by exposing them to novel and unique learning opportunities unavailable in their school. Specifically, the University of Idaho's McCall Outdoor Science School (MOSS) focuses on providing K-12 students with the opportunity to learn about science with a place-based, hands-on, inquiry-based curriculum that hopes to foster science identity development. To understand the constructs that lead to science identity formation and the impact the MOSS program has on science identity development, several questions were explored examining how students define the constructs and if the MOSS program impacted how they rate themselves within each construct. A mixed-method research approach was used consisting of focus group interviews with students and pre, post, one-month posttests for visiting students to look at change in science identity over time. Results from confirmatory factor analysis indicate that the instrument created is a good fit for examining science identity and the associated

  13. RNA Secondary Structures Having a Compatible Sequence of Certain Nucleotide Ratios.

    PubMed

    Barrett, Christopher L; Li, Thomas J X; Reidys, Christian M

    2016-11-01

    Given a random RNA secondary structure, S, we study RNA sequences having fixed ratios of nucleotides that are compatible with S. We perform this analysis for RNA secondary structures subject to various base-pairing rules and minimum arc- and stack-length restrictions. Our main result reads as follows: in the simplex of nucleotide ratios, there exists a convex region, in which, in the limit of long sequences, a random structure asymptotically almost surely (a.a.s.) has compatible sequence with these ratios and outside of which a.a.s. a random structure has no such compatible sequence. We localize this region for RNA secondary structures subject to various base-pairing rules and minimum arc- and stack-length restrictions. In particular, for GC-sequences (GC denoting the nucleotides guanine and cytosine, respectively) having a ratio of G nucleotides smaller than 1/3, a random RNA secondary structure without any minimum arc- and stack-length restrictions has a.a.s. no such compatible sequence. For sequences having a ratio of G nucleotides larger than 1/3, a random RNA secondary structure has a.a.s. such compatible sequences. We discuss our results in the context of various families of RNA structures.

  14. The Effect of Content Sequence on Student Learning.

    ERIC Educational Resources Information Center

    Rudnitsky, Alan N.; Posner, George J.

    This study investigates the effects of content sequence on student learning. The treatments, a spatial and conceptual instructional sequence each consisting of identical content elements, were administered to students in a two-year college Botany course. Hypotheses tested were that sequence would have an effect on student perceptions of the…

  15. Identity Theft: Trends and Issues

    DTIC Science & Technology

    2010-01-05

    as a result of a data breach.75 Synovate (2007) conducted a similar study on behalf of the Federal Trade Commission and found that about 12% of...February 2009, http://www.javelinstrategy.com. 76 Synovate , Federal Trade Commission: 2006 Identity Theft Survey Report, November 2007, http...Chairman of the FTC and Commissioner of the SSA. 88 Synovate , Federal Trade Commission: 2006 Identity Theft Survey Report, November 2007, http://www.ftc.gov

  16. Systemic AA amyloidosis: epidemiology, diagnosis, and management

    PubMed Central

    Real de Asúa, Diego; Costa, Ramón; Galván, Jose María; Filigheddu, María Teresa; Trujillo, Davinia; Cadiñanos, Julen

    2014-01-01

    The term “amyloidosis” encompasses the heterogeneous group of diseases caused by the extracellular deposition of autologous fibrillar proteins. The global incidence of amyloidosis is estimated at five to nine cases per million patient-years. While amyloid light-chain (AL) amyloidosis is more frequent in developed countries, amyloid A (AA) amyloidosis is more common in some European regions and in developing countries. The spectrum of AA amyloidosis has changed in recent decades owing to: an increase in the median age at diagnosis; a percent increase in the frequency of primary AL amyloidosis with respect to the AA type; and a substantial change in the epidemiology of the underlying diseases. Diagnosis of amyloidosis is based on clinical organ involvement and histological evidence of amyloid deposits. Among the many tinctorial characteristics of amyloid deposits, avidity for Congo red and metachromatic birefringence under unidirectional polarized light remain the gold standard. Once the initial diagnosis has been made, the amyloid subtype must be identified and systemic organ involvement evaluated. In this sense, the 123I-labeled serum amyloid P component scintigraphy is a safe and noninvasive technique that has revolutionized the diagnosis and monitoring of treatment in systemic amyloidosis. It can successfully identify anatomical patterns of amyloid deposition throughout the body and enables not only an initial estimation of prognosis, but also the monitoring of the course of the disease and the response to treatment. Given the etiologic diversity of AA amyloidosis, common therapeutic strategies are scarce. All treatment options should be based upon a greater control of the underlying disease, adequate organ support, and treatment of symptoms. Nevertheless, novel therapeutic strategies targeting the formation of amyloid fibrils and amyloid deposition may generate new expectations for patients with AA amyloidosis. PMID:25378951

  17. 7 CFR 52.771 - Identity.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... Cherries 1 Identity and Grades § 52.771 Identity. Canned red tart pitted cherries is the product represented as defined in the standard of identity for canned cherries (21 CFR 145.125(a)), issued pursuant...

  18. Visible periodicity of strong nucleosome DNA sequences.

    PubMed

    Salih, Bilal; Tripathi, Vijay; Trifonov, Edward N

    2015-01-01

    Fifteen years ago, Lowary and Widom assembled nucleosomes on synthetic random sequence DNA molecules, selected the strongest nucleosomes and discovered that the TA dinucleotides in these strong nucleosome sequences often appear at 10-11 bases from one another or at distances which are multiples of this period. We repeated this experiment computationally, on large ensembles of natural genomic sequences, by selecting the strongest nucleosomes--i.e. those with such distances between like-named dinucleotides, multiples of 10.4 bases, the structural and sequence period of nucleosome DNA. The analysis confirmed the periodicity of TA dinucleotides in the strong nucleosomes, and revealed as well other periodic sequence elements, notably classical AA and TT dinucleotides. The matrices of DNA bendability and their simple linear forms--nucleosome positioning motifs--are calculated from the strong nucleosome DNA sequences. The motifs are in full accord with nucleosome positioning sequences derived earlier, thus confirming that the new technique, indeed, detects strong nucleosomes. Species- and isochore-specific variations of the matrices and of the positioning motifs are demonstrated. The strong nucleosome DNA sequences manifest the highest hitherto nucleosome positioning sequence signals, showing the dinucleotide periodicities in directly observable rather than in hidden form.

  19. Complete genome sequence of Southern tomato virus naturally infecting tomatoes in Bangladesh using small RNA deep sequencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete genome sequence of a Southern tomato virus (STV) isolate on tomato plants in a seed production field in Bangladesh was obtained for the first time using next generation sequencing. The identified isolate STV_BD-13 shares high degree of sequence identity (99%) with several known STV isol...

  20. Short sequence motifs, overrepresented in mammalian conservednon-coding sequences

    SciTech Connect

    Minovitsky, Simon; Stegmaier, Philip; Kel, Alexander; Kondrashov,Alexey S.; Dubchak, Inna

    2007-02-21

    Background: A substantial fraction of non-coding DNAsequences of multicellular eukaryotes is under selective constraint. Inparticular, ~;5 percent of the human genome consists of conservednon-coding sequences (CNSs). CNSs differ from other genomic sequences intheir nucleotide composition and must play important functional roles,which mostly remain obscure.Results: We investigated relative abundancesof short sequence motifs in all human CNSs present in the human/mousewhole-genome alignments vs. three background sets of sequences: (i)weakly conserved or unconserved non-coding sequences (non-CNSs); (ii)near-promoter sequences (located between nucleotides -500 and -1500,relative to a start of transcription); and (iii) random sequences withthe same nucleotide composition as that of CNSs. When compared tonon-CNSs and near-promoter sequences, CNSs possess an excess of AT-richmotifs, often containing runs of identical nucleotides. In contrast, whencompared to random sequences, CNSs contain an excess of GC-rich motifswhich, however, lack CpG dinucleotides. Thus, abundance of short sequencemotifs in human CNSs, taken as a whole, is mostly determined by theiroverall compositional properties and not by overrepresentation of anyspecific short motifs. These properties are: (i) high AT-content of CNSs,(ii) a tendency, probably due to context-dependent mutation, of A's andT's to clump, (iii) presence of short GC-rich regions, and (iv) avoidanceof CpG contexts, due to their hypermutability. Only a small number ofshort motifs, overrepresented in all human CNSs are similar to bindingsites of transcription factors from the FOX family.Conclusion: Human CNSsas a whole appear to be too broad a class of sequences to possess strongfootprints of any short sequence-specific functions. Such footprintsshould be studied at the level of functional subclasses of CNSs, such asthose which flank genes with a particular pattern of expression. Overallproperties of CNSs are affected by patterns in

  1. Genetic characterization of Betacoronavirus lineage C viruses in bats reveals marked sequence divergence in the spike protein of pipistrellus bat coronavirus HKU5 in Japanese pipistrelle: implications for the origin of the novel Middle East respiratory syndrome coronavirus.

    PubMed

    Lau, Susanna K P; Li, Kenneth S M; Tsang, Alan K L; Lam, Carol S F; Ahmed, Shakeel; Chen, Honglin; Chan, Kwok-Hung; Woo, Patrick C Y; Yuen, Kwok-Yung

    2013-08-01

    While the novel Middle East respiratory syndrome coronavirus (MERS-CoV) is closely related to Tylonycteris bat CoV HKU4 (Ty-BatCoV HKU4) and Pipistrellus bat CoV HKU5 (Pi-BatCoV HKU5) in bats from Hong Kong, and other potential lineage C betacoronaviruses in bats from Africa, Europe, and America, its animal origin remains obscure. To better understand the role of bats in its origin, we examined the molecular epidemiology and evolution of lineage C betacoronaviruses among bats. Ty-BatCoV HKU4 and Pi-BatCoV HKU5 were detected in 29% and 25% of alimentary samples from lesser bamboo bat (Tylonycteris pachypus) and Japanese pipistrelle (Pipistrellus abramus), respectively. Sequencing of their RNA polymerase (RdRp), spike (S), and nucleocapsid (N) genes revealed that MERS-CoV is more closely related to Pi-BatCoV HKU5 in RdRp (92.1% to 92.3% amino acid [aa] identity) but is more closely related to Ty-BatCoV HKU4 in S (66.8% to 67.4% aa identity) and N (71.9% to 72.3% aa identity). Although both viruses were under purifying selection, the S of Pi-BatCoV HKU5 displayed marked sequence polymorphisms and more positively selected sites than that of Ty-BatCoV HKU4, suggesting that Pi-BatCoV HKU5 may generate variants to occupy new ecological niches along with its host in diverse habitats. Molecular clock analysis showed that they diverged from a common ancestor with MERS-CoV at least several centuries ago. Although MERS-CoV may have diverged from potential lineage C betacoronaviruses in European bats more recently, these bat viruses were unlikely to be the direct ancestor of MERS-CoV. Intensive surveillance for lineage C betaCoVs in Pipistrellus and related bats with diverse habitats and other animals in the Middle East may fill the evolutionary gap.

  2. Genetic Characterization of Betacoronavirus Lineage C Viruses in Bats Reveals Marked Sequence Divergence in the Spike Protein of Pipistrellus Bat Coronavirus HKU5 in Japanese Pipistrelle: Implications for the Origin of the Novel Middle East Respiratory Syndrome Coronavirus

    PubMed Central

    Lau, Susanna K. P.; Li, Kenneth S. M.; Tsang, Alan K. L.; Lam, Carol S. F.; Ahmed, Shakeel; Chen, Honglin; Chan, Kwok-Hung

    2013-01-01

    While the novel Middle East respiratory syndrome coronavirus (MERS-CoV) is closely related to Tylonycteris bat CoV HKU4 (Ty-BatCoV HKU4) and Pipistrellus bat CoV HKU5 (Pi-BatCoV HKU5) in bats from Hong Kong, and other potential lineage C betacoronaviruses in bats from Africa, Europe, and America, its animal origin remains obscure. To better understand the role of bats in its origin, we examined the molecular epidemiology and evolution of lineage C betacoronaviruses among bats. Ty-BatCoV HKU4 and Pi-BatCoV HKU5 were detected in 29% and 25% of alimentary samples from lesser bamboo bat (Tylonycteris pachypus) and Japanese pipistrelle (Pipistrellus abramus), respectively. Sequencing of their RNA polymerase (RdRp), spike (S), and nucleocapsid (N) genes revealed that MERS-CoV is more closely related to Pi-BatCoV HKU5 in RdRp (92.1% to 92.3% amino acid [aa] identity) but is more closely related to Ty-BatCoV HKU4 in S (66.8% to 67.4% aa identity) and N (71.9% to 72.3% aa identity). Although both viruses were under purifying selection, the S of Pi-BatCoV HKU5 displayed marked sequence polymorphisms and more positively selected sites than that of Ty-BatCoV HKU4, suggesting that Pi-BatCoV HKU5 may generate variants to occupy new ecological niches along with its host in diverse habitats. Molecular clock analysis showed that they diverged from a common ancestor with MERS-CoV at least several centuries ago. Although MERS-CoV may have diverged from potential lineage C betacoronaviruses in European bats more recently, these bat viruses were unlikely to be the direct ancestor of MERS-CoV. Intensive surveillance for lineage C betaCoVs in Pipistrellus and related bats with diverse habitats and other animals in the Middle East may fill the evolutionary gap. PMID:23720729

  3. Memory and learning with rapid audiovisual sequences

    PubMed Central

    Keller, Arielle S.; Sekuler, Robert

    2015-01-01

    We examined short-term memory for sequences of visual stimuli embedded in varying multisensory contexts. In two experiments, subjects judged the structure of the visual sequences while disregarding concurrent, but task-irrelevant auditory sequences. Stimuli were eight-item sequences in which varying luminances and frequencies were presented concurrently and rapidly (at 8 Hz). Subjects judged whether the final four items in a visual sequence identically replicated the first four items. Luminances and frequencies in each sequence were either perceptually correlated (Congruent) or were unrelated to one another (Incongruent). Experiment 1 showed that, despite encouragement to ignore the auditory stream, subjects' categorization of visual sequences was strongly influenced by the accompanying auditory sequences. Moreover, this influence tracked the similarity between a stimulus's separate audio and visual sequences, demonstrating that task-irrelevant auditory sequences underwent a considerable degree of processing. Using a variant of Hebb's repetition design, Experiment 2 compared musically trained subjects and subjects who had little or no musical training on the same task as used in Experiment 1. Test sequences included some that intermittently and randomly recurred, which produced better performance than sequences that were generated anew for each trial. The auditory component of a recurring audiovisual sequence influenced musically trained subjects more than it did other subjects. This result demonstrates that stimulus-selective, task-irrelevant learning of sequences can occur even when such learning is an incidental by-product of the task being performed. PMID:26575193

  4. Multilocus sequence analysis provides insights into molecular epidemiology of Chlamydia pecorum infections in Australian sheep, cattle, and koalas.

    PubMed

    Jelocnik, Martina; Frentiu, Francesca D; Timms, Peter; Polkinghorne, Adam

    2013-08-01

    Chlamydia pecorum is a significant pathogen of domestic livestock and wildlife. We have developed a C. pecorum-specific multilocus sequence analysis (MLSA) scheme to examine the genetic diversity of and relationships between Australian sheep, cattle, and koala isolates. An MLSA of seven concatenated housekeeping gene fragments was performed using 35 isolates, including 18 livestock isolates (11 Australian sheep, one Australian cow, and six U.S. livestock isolates) and 17 Australian koala isolates. Phylogenetic analyses showed that the koala isolates formed a distinct clade, with limited clustering with C. pecorum isolates from Australian sheep. We identified 11 MLSA sequence types (STs) among Australian C. pecorum isolates, 10 of them novel, with koala and sheep sharing at least one identical ST (designated ST2013Aa). ST23, previously identified in global C. pecorum livestock isolates, was observed here in a subset of Australian bovine and sheep isolates. Most notably, ST23 was found in association with multiple disease states and hosts, providing insights into the transmission of this pathogen between livestock hosts. The complexity of the epidemiology of this disease was further highlighted by the observation that at least two examples of sheep were infected with different C. pecorum STs in the eyes and gastrointestinal tract. We have demonstrated the feasibility of our MLSA scheme for understanding the host relationship that exists between Australian C. pecorum strains and provide the first molecular epidemiological data on infections in Australian livestock hosts.

  5. Origin and identity of Fejervarya (Anura: Dicroglossidae) on Guam

    USGS Publications Warehouse

    Wostl, Elijah; Smith, Eric N.; Reed, Robert

    2016-01-01

    We used morphological and molecular data to infer the identity and origin of frogs in the genus Fejervarya that have been introduced to the island of Guam. Mensural and meristic data were collected from 96 specimens from throughout their range on the island and a principal component analysis was used to investigate the distribution of these data in morphological space. We also amplified a fragment of the 16S ribosomal ribonucleic acid mitochondrial gene from 27 of these specimens and compared it to 63 published sequences of Fejervarya and the morphologically similar Zakerana. All examined Fejervarya from Guam are morphologically indistinguishable and share an identical haplotype. The molecular data identify them as Fejervarya cancrivora with a haplotype identical to F. cancrivora from Taiwan.

  6. The gender identity/gender dysphoria questionnaire for adolescents and adults: further validity evidence.

    PubMed

    Singh, Devita; Deogracias, Joseph J; Johnson, Laurel L; Bradley, Susan J; Kibblewhite, Sarah J; Owen-Anderson, Allison; Peterson-Badali, Michele; Meyer-Bahlburg, Heino F L; Zucker, Kenneth J

    2010-01-01

    This study aimed to provide further validity evidence for the dimensional measurement of gender identity and gender dysphoria in both adolescents and adults. Adolescents and adults with gender identity disorder (GID) were compared to clinical control (CC) adolescents and adults on the Gender Identity/Gender Dysphoria Questionnaire for Adolescents and Adults (GIDYQ-AA), a 27-item scale originally developed by Deogracias et al. (2007). In Study 1, adolescents with GID (n = 44) were compared to CC adolescents (n = 98); and in Study 2, adults with GID (n = 41) were compared to CC adults (n = 94). In both studies, clients with GID self-reported significantly more gender dysphoria than did the CCs, with excellent sensitivity and specificity rates. In both studies, degree of self-reported gender dysphoria was significantly correlated with recall of cross-gender behavior in childhood-a test of convergent validity. The research and clinical utility of the GIDYQ-AA is discussed, including directions for further research in distinct clinical populations.

  7. Characterization of an Insertion Sequence Element Associated with Genetically Diverse Plant Pathogenic Streptomyces spp.

    PubMed Central

    Healy, Frank G.; Bukhalid, Raghida A.; Loria, Rosemary

    1999-01-01

    Streptomycetes are common soil inhabitants, yet few described species are plant pathogens. While the pathogenicity mechanisms remain unclear, previous work identified a gene, nec1, which encodes a putative pathogenicity or virulence factor. nec1 and a neighboring transposase pseudogene, ORFtnp, are conserved among unrelated plant pathogens and absent from nonpathogens. The atypical GC content of nec1 suggests that it was acquired through horizontal transfer events. Our investigation of the genetic organization of regions adjacent to the 3′ end of nec1 in Streptomyces scabies 84.34 identified a new insertion sequence (IS) element, IS1629, with homology to other IS elements from prokaryotic animal pathogens. IS1629 is 1,462 bp with 26-bp terminal inverted repeats and encodes a putative 431-amino-acid (aa) transposase. Transposition of IS1629 generates a 10-bp target site duplication. A 77-nucleotide (nt) sequence encompassing the start codon and upstream region of the transposase was identified which could function in the posttranscritpional regulation of transposase synthesis. A functional copy of IS1629 from S. turgidiscabies 94.09 (Hi-C-13) was selected in the transposon trap pCZA126, through its insertion into the λ cI857 repressor. IS1629 is present in multiple copies in some S. scabies strains and is present in all S. acidiscabies and S. turgidiscabies strains examined. A second copy of IS1629 was identified between ORFtnp and nec1 in S. acidiscabies strains. The diversity of IS1629 hybridization profiles was greatest within S. scabies. IS1629 was absent from the 27 nonpathogenic Streptomyces strains tested. The genetic organization and nucleotide sequence of the nec1-IS1629 region was conserved and identical among representatives of S. acidiscabies and S. turgidiscabies. These findings support our current model for the unidirectional transfer of the ORFtnp-nec1-IS1629 locus from IS1629-containing S. scabies (type II) to S. acidiscabies and S. turgidiscabies

  8. Tracing the identity of objects.

    PubMed

    Rips, Lance J; Blok, Sergey; Newman, George

    2006-01-01

    This article considers how people judge the identity of objects (e.g., how people decide that a description of an object at one time, t(0), belongs to the same object as a description of it at another time, t(1)). The authors propose a causal continuer model for these judgments, based on an earlier theory by Nozick (1981). According to this model, the 2 descriptions belong to the same object if (a) the object at t(1) is among those that are causally close enough to be genuine continuers of the original and (b) it is the closest of these close-enough contenders. A quantitative version of the model makes accurate predictions about judgments of which a pair of objects is identical to an original (Experiments 1 and 2). The model makes correct qualitative predictions about identity across radical disassembly (Experiment 1) as well as more ordinary transformations (Experiments 2 and 3).

  9. 'Chronic' identities in mental illness.

    PubMed

    von Peter, Sebastian

    2013-04-01

    The term 'chronicity' is still widely used in psychiatric discourse and practice. A category employed in political, administrative and therapeutic contexts, it guides practitioners' beliefs and actions. This paper attempts a review of the attitudes and procedures that result as a consequence of identifying 'chronically' disturbed identities in clinical practice. An essentially social, relational and materialist understanding of mental illness is used to highlight the kind of thinking underlying the notion of 'chronic' identities in day-to-day psychiatric routines. Problematising the notions of singularity and expressiveness, as well as mind/body- and self/other-distinctions, it claims the category itself is responsible for creating a 'chronic' kind of being. A spatial metaphor is presented in the conclusion, illustrating a mental strategy by which we can re-shape our thinking about 'chronic' identities. It attempts to describe how the shift from an epistemological to a praxeographic approach could build a more complete understanding of mental illness.

  10. Social Trust of Virtual Identities

    NASA Astrophysics Data System (ADS)

    Seigneur, Jean-Marc

    Most other chapters of this book discuss computational models of trust in broader terms, giving definitions of trust, explaining how trust should evolve over time, surveying the different facets of trust .On the other hand, this chapter has a clear focus on the important element of identity in computational trust mechanisms. Trust and reputation are easier to form in face-to-face situations than in situations involving the use of computers and networks because the identity of the trustee is more difficult to verify. In this chapter, the different means to recognise virtual identities are surveyed. Next, their integration into computational trust engines is discussed, especially according to four main requirements: Adaptability, Security, Usability and Privacy (ASUP).

  11. High cycle fatigue of AA6082 and AA6063 aluminum extrusions

    NASA Astrophysics Data System (ADS)

    Nanninga, Nicholas E.

    The high cycle fatigue behavior of hollow extruded AA6082 and AA6063 aluminum extrusions has been studied. Hollow extruded aluminum profiles can be processed into intricate shapes, and may be suitable replacements for fatigue critical automotive applications requiring reduced weight. There are several features inherent in hollow aluminum extrusions, such as seam welds, charge welds, microstructural variations and die lines. The effects of such extrusion variables on high cycle fatigue properties were studied by taking specimens from an actual car bumper extrusion. It appears that extrusion die lines create large anisotropy differences in fatigue properties, while welds themselves have little effect on fatigue lives. Removal of die lines greatly increased fatigue properties of AA6082 specimens taken transverse to the extrusion direction. Without die lines, anisotropy in fatigue properties between AA6082 specimens taken longitudinal and transverse to the extrusion direction, was significantly reduced, and properties associated with the orientation of the microstructure appears to be isotropic. A fibrous microstructure for AA6082 specimens showed great improvements in fatigue behavior. The effects of elevated temperatures and exposure of specimens to NaCl solutions was also studied. Exposure to the salt solution greatly reduced the fatigue lives of specimens, while elevated temperatures showed more moderate reductions in fatigue lives.

  12. Colchicine use in isolated renal AA amyloidosis.

    PubMed

    Meneses, Carlos F; Egües, César A; Uriarte, Miren; Belzunegui, Joaquín; Rezola, Marta

    2015-01-01

    We present the case of a 45-year-old woman, with two-year history of chronic renal insufficiency and proteinuria. A kidney biopsy showed the presence of AA amyloidosis (positive Congo red staining and immunohistochemistry). There was no evidence of amyloid deposits in other organs and there was no underlying disease. AA amyloidosis normally is secondary to chronic inflammatory or infectious diseases. High levels of IL-1, IL-6 and TNF-α play a role in the pathogenesis of amyloidosis and induce the synthesis of serum amyloid A protein (SAA), a precursor of tissue amyloid deposits. We empirically treated the patient with a low dose colchicine. The patient responded well. Colchicine has been used for the treatment of Familiar Mediterranean Fever and related auto-inflammatory diseases. To monitor treatment responses, we measured SAA finding low titers. Soon after treatment onset there were signs of improvement pertaining to proteinuria and stabilization of renal function.

  13. Split Identity: Intransitive Judgments of the Identity of Objects

    ERIC Educational Resources Information Center

    Rips, Lance J.

    2011-01-01

    Identity is a transitive relation, according to all standard accounts. Necessarily, if "x = y" and "y = z," then "x = z." However, people sometimes say that two objects, "x" and "z," are the same as a third, "y," even when "x" and "z" have different properties (thus,…

  14. Drawing Identity: Beginning Pre-Service Teachers' Professional Identities

    ERIC Educational Resources Information Center

    Beltman, Susan; Glass, Christine; Dinham, Judith; Chalk, Beryl; Nguyen, Bich

    2015-01-01

    Developing a professional teacher identity can be complex as pre-service teachers engage with a process informed by their previous experiences of teachers and teaching, by learning in their pre-service course, by field placements, and by societal expectations. Using drawing as the method for gathering data, pre-service teachers in an Australian…

  15. "Doing Identity" in the Botswana Classroom: Negotiating Gendered Institutional Identities

    ERIC Educational Resources Information Center

    Humphreys, Sara

    2013-01-01

    Drawing on post-structural and post-colonial conceptions of gender, this paper explores multiple student masculinities and femininities in the classrooms of four junior secondary schools in Botswana. These gendered identities, it is argued, are negotiated within broader institutional constraints that have been socio-historically produced. Such…

  16. Blended Identities: Identity Work, Equity and Marginalization in Blended Learning

    ERIC Educational Resources Information Center

    Heikoop, Will

    2013-01-01

    This article is a theoretical study of the self-presentation strategies employed by higher education students online; it examines student identity work via profile information and avatars in a blended learning environment delivered through social networking sites and virtual worlds. It argues that students are faced with difficult choices when…

  17. Integrating Identities: Ethnic and Academic Identities among Diverse College Students

    ERIC Educational Resources Information Center

    Walker, Lovey H. M.; Syed, Moin

    2013-01-01

    Background/Context: Students of Color continue to be underrepresented at the undergraduate level. Recent research has demonstrated the importance of non-academic psychosocial factors for understanding college experiences. One factor, identity, is a broad, multidimensional construct that comprises numerous distinct domains, including political,…

  18. Identity in Flux: Negotiating Identity While Studying Abroad

    ERIC Educational Resources Information Center

    Young, Jennifer T.; Natrajan-Tyagi, Rajeswari; Platt, Jason J.

    2015-01-01

    Study abroad is one aspect of global movement that connects individuals of diverse backgrounds. Individuals studying abroad are proffered to negotiate self-identity when they confront novelty and new contexts. This study chose to use the qualitative method of phenomenological interviews to examine how individuals experience themselves and others…

  19. Spectroscopic signatures of AA' and AB stacking of chemical vapor deposited bilayer MoS2

    SciTech Connect

    Xia, Ming; Li, Bo; Yin, Kuibo; Capellini, Giovanni; Niu, Gang; Gong, Yongji; Zhou, Wu; Ajayan, Pulickel M.; Xie, Ya -Hong

    2015-11-04

    We discuss prominent resonance Raman and photoluminescence spectroscopic differences between AA'and AB stacked bilayer molybdenum disulfide (MoS2) grown by chemical vapor deposition are reported. Bilayer MoS2 islands consisting of the two stacking orders were obtained under identical growth conditions. Also, resonance Raman and photoluminescence spectra of AA' and AB stacked bilayer MoS2 were obtained on Au nanopyramid surfaces under strong plasmon resonance. Both resonance Raman and photoluminescence spectra show distinct features indicating clear differences in interlayer interaction between these two phases. The implication of these findings on device applications based on spin and valley degrees of freedom.

  20. AAS Oral History Project - Seeking Planetary Scientist

    NASA Astrophysics Data System (ADS)

    Buxner, Sanlyn; Holbrook, Jarita

    2016-10-01

    Now in its fourth year, the AAS Oral History Project has interviewed over 100 space scientists from all over the world. Led by the AAS Historical Astronomy Division (HAD) and partially funded by the American Institute of Physics Niels Bohr Library and ongoing support from the AAS, volunteers have collected oral histories from space scientists at professional meetings starting in 2015, including AAS, DPS, and the IAU general assembly. Each interview lasts one and a half to two hours and focuses on interviewees' personal and professional lives. Questions include those about one's family, childhood, strong influences on one's scientific career, career path, successes and challenges, perspectives on how astronomy is changing as a field, and advice to the next generation. Each interview is audio recorded and transcribed, the content of which is checked with each interviewee. Once complete, interview transcripts are posted online as part of a larger oral history library at https://www.aip.org/history-programs/niels-bohr-library/oral-histories. We will present preliminary analysis of those interviewed including characterizing career status, age range, nationality, and primary field. Additionally, we will discuss trends beginning to emerge in analysis of participants' responses about data driven science and advice to the next generation. Future analysis will reveal a rich story of space scientists and will help the community address issues of diversity, controversies, and the changing landscape of science. We are actively recruiting individuals to be interviewed at this meeting from all stages of career from undergraduate students to retired and emeritus astronomers. We are especially interested in interviewing 40+E members of DPS. Contact Sanlyn Buxner to schedule an interview or to find out more information about the project (buxner@psi.edu). Contact Jarita Holbrook if you would like to become an interviewer for the project (astroholbrook@gmail.com).

  1. The Effectiveness of the AAS REU Program

    NASA Astrophysics Data System (ADS)

    Hemenway, M. K.; Boyce, P. B.; Milkey, R. W.

    1996-05-01

    In an attempt to address the particular needs of astronomy faculty and undergraduate students, in 1991 the Education Office of the American Astronomical Society approached the National Science Foundation with a unique proposal for funding through the Research Experiences for Undergraduates program. The goals of the AAS program were to "slow the hemorrhage of students out of science...", extend the REU program to non-NSF-funded scientists, to reach under-represented women and minority students particularly in small educational institutions, and to encourage research scientists there to mentor students. As this grant has now expired, the AAS has surveyed the 44 mentors and their students to assess the program's effect on the mentor and the mentor's career; the educational institution; and the student's education and career choices. More than half the mentors responded by the abstract deadline. The program clearly had an effect upon the individuals involved. The greatest effect (in 85% of the cases) was to develop more interest in the mentor's research project both among the students and among the mentor's faculty colleagues. The mentors rated the grant to be a medium or strong factor in their student's decision to pursue graduate study, which 90% of them did. All but one of the AAS-REU students attended an AAS meeting and 3/4 of those gave a paper on their project research. Over 90% of the mentors felt that the research experience strongly promoted a greater interest in science, a greater understanding of science and a desire to continue in science. According to the mentors, this was a very positive and beneficial program for the students as well as for themselves.

  2. RFID identity theft and countermeasures

    NASA Astrophysics Data System (ADS)

    Herrigel, Alexander; Zhao, Jian

    2006-02-01

    This paper reviews the ICAO security architecture for biometric passports. An attack enabling RFID identity theft for a later misuse is presented. Specific countermeasures against this attack are described. Furthermore, it is shown that robust high capacity digital watermarking for the embedding and retrieving of binary digital signature data can be applied as an effective mean against RFID identity theft. This approach requires only minimal modifications of the passport manufacturing process and is an enhancement of already proposed solutions. The approach may also be applied in combination with a RFID as a backup solution (damaged RFID chip) to verify with asymmetric cryptographic techniques the authenticity and the integrity of the passport data.

  3. Representing Identity and Equivalence for Scientific Data

    NASA Astrophysics Data System (ADS)

    Wickett, K. M.; Sacchi, S.; Dubin, D.; Renear, A. H.

    2012-12-01

    Matters of equivalence and identity are central to the stewardship of scientific data. In order to properly prepare for and manage the curation, preservation and sharing of digitally-encoded data, data stewards must be able to characterize and assess the relationships holding between data-carrying digital resources. However, identity-related questions about resources and their information content may not be straightforward to answer: for example, what exactly does it mean to say that two files contain the same data, but in different formats? Information content is frequently distinguished from particular representations, but there is no adequately developed shared understanding of what this really means and how the relationship between content and its representations hold. The Data Concepts group at the Center for Informatics Research in Science and Scholarship (CIRSS), University of Illinois at Urbana Champaign, is developing a logic-based framework of fundamental concepts related to scientific data to support curation and integration. One project goal is to develop precise accounts of information resources carrying the same data. We present two complementary conceptual models for information representation: the Basic Representation Model (BRM) and the Systematic Assertion Model (SAM). We show how these models provide an analytical account of digitally-encoded scientific data and a precise understanding of identity and equivalence. The Basic Representation Model identifies the core entities and relationships involved in representing information carried by digital objects. In BRM, digital objects are symbol structures that express propositional content, and stand in layered encoding relationships. For example, an RDF description may be serialized as either XML or N3, and those expressions in turn may be encoded as either UTF-8 or UTF-16 sequences. Defining this encoding stack reveals distinctions necessary for a precise account of identity and equivalence

  4. MSLICE Sequencing

    NASA Technical Reports Server (NTRS)

    Crockett, Thomas M.; Joswig, Joseph C.; Shams, Khawaja S.; Norris, Jeffrey S.; Morris, John R.

    2011-01-01

    MSLICE Sequencing is a graphical tool for writing sequences and integrating them into RML files, as well as for producing SCMF files for uplink. When operated in a testbed environment, it also supports uplinking these SCMF files to the testbed via Chill. This software features a free-form textural sequence editor featuring syntax coloring, automatic content assistance (including command and argument completion proposals), complete with types, value ranges, unites, and descriptions from the command dictionary that appear as they are typed. The sequence editor also has a "field mode" that allows tabbing between arguments and displays type/range/units/description for each argument as it is edited. Color-coded error and warning annotations on problematic tokens are included, as well as indications of problems that are not visible in the current scroll range. "Quick Fix" suggestions are made for resolving problems, and all the features afforded by modern source editors are also included such as copy/cut/paste, undo/redo, and a sophisticated find-and-replace system optionally using regular expressions. The software offers a full XML editor for RML files, which features syntax coloring, content assistance and problem annotations as above. There is a form-based, "detail view" that allows structured editing of command arguments and sequence parameters when preferred. The "project view" shows the user s "workspace" as a tree of "resources" (projects, folders, and files) that can subsequently be opened in editors by double-clicking. Files can be added, deleted, dragged-dropped/copied-pasted between folders or projects, and these operations are undoable and redoable. A "problems view" contains a tabular list of all problems in the current workspace. Double-clicking on any row in the table opens an editor for the appropriate sequence, scrolling to the specific line with the problem, and highlighting the problematic characters. From there, one can invoke "quick fix" as described

  5. Data Behind the Figures in AAS Journals

    NASA Astrophysics Data System (ADS)

    Biemesderfer, Chris

    2013-01-01

    Substantial amounts of digital data are produced in the scientific enterprise, and much of it is carefully analyzed and processed. Often resulting from a good deal of intellectual effort, many of these highly-processed products are published in the scholarly literature. Many of these data - or more precisely, representations of these data - are committed to the scholarly record in the forms of figures and tables that appear within articles: the AAS journals publish more than 30,000 figures and nearly 10,000 tables each year. For more than a decade, the AAS journals have accepted machine-readable tables that provide the data behind (some of) the tables, and recently the journals have started to encourage the submission of the data behind figures. (See the related poster by Greg Schwarz.) During this time, the journals have been refining techniques for acquiring and managing the digital data that underlie figures and tables. In 2012 the AAS was awarded a grant by the US NSF so that the journals can extend the methods for providing access to these data objects, through a deeper collaboration with the VO and with organizations like DataCite, and by spearheading discussions about the formats and metadata that will best facilitate long-term data management and access. An important component of these activities is educating scientists about the importance and benefits of making such data sets available.

  6. Introducing the AAS Astronomy Ambassadors Program

    NASA Astrophysics Data System (ADS)

    Gurton, S.; Fienberg, R. T.; Fraknoi, A.; Prather, E. E.

    2013-04-01

    Newly established by the American Astronomical Society (AAS), the Astronomy Ambassadors program is designed to support early-career AAS members with training in resources and techniques for effective outreach to students and/or the public. A pilot Astronomy Ambassadors workshop will be held at the January 2013 AAS meeting. Workshop participants will learn to communicate effectively with public and school audiences; find outreach opportunities and establish ongoing partnerships with local schools, science centers, museums, parks, and/or community centers; reach audiences with personal stories, hands-on activities, and jargon-free language; identify strategies and techniques to improve their presentation skills; gain access to a menu of outreach resources that work in a variety of settings; and become part of an active community of astronomers who do outreach. Applications are welcome from advanced undergraduates (those doing research and committed to continuing in astronomy), graduate students, and postdocs and new faculty in their first two years after receipt of the PhD. We especially encourage applications from members of groups that are presently underrepresented in science.

  7. AAS Publishing News: Astronomical Software Citation Workshop

    NASA Astrophysics Data System (ADS)

    Kohler, Susanna

    2015-07-01

    Do you write code for your research? Use astronomical software? Do you wish there were a better way of citing, sharing, archiving, or discovering software for astronomy research? You're not alone! In April 2015, AAS's publishing team joined other leaders in the astronomical software community in a meeting funded by the Sloan Foundation, with the purpose of discussing these issues and potential solutions. In attendance were representatives from academic astronomy, publishing, libraries, for-profit software sharing platforms, telescope facilities, and grantmaking institutions. The goal of the group was to establish “protocols, policies, and platforms for astronomical software citation, sharing, and archiving,” in the hopes of encouraging a set of normalized standards across the field. The AAS is now collaborating with leaders at GitHub to write grant proposals for a project to develop strategies for software discoverability and citation, in astronomy and beyond. If this topic interests you, you can find more details in this document released by the group after the meeting: http://astronomy-software-index.github.io/2015-workshop/ The group hopes to move this project forward with input and support from the broader community. Please share the above document, discuss it on social media using the hashtag #astroware (so that your conversations can be found!), or send private comments to julie.steffen@aas.org.

  8. An Existentialist Account of Identity Formation.

    ERIC Educational Resources Information Center

    Bilsker, Dan

    1992-01-01

    Gives account of Marcia's identity formation model in language of existentialist philosophy. Examines parallels between ego-identity and existentialist approaches. Describes identity in terms of existentialist concepts of Heidegger and Sartre. Argues that existentialist account of identity formation has benefits of clarification of difficult…

  9. Teacher Educators' Identity: A Review of Literature

    ERIC Educational Resources Information Center

    Izadinia, Mahsa

    2014-01-01

    Research suggests that the development of a teacher educator identity is a central process in becoming a teacher educator. Recently, there has been an increasing interest in the concept of teacher identity. However, teacher educator identity seems to be still under-researched. In this article, a review of literature on teacher educator identity is…

  10. Problems of Identity Development of Deaf Children.

    ERIC Educational Resources Information Center

    Ahrbeck, Bernd

    This paper considers theory and research on identity development in deaf children and concludes that the exclusively oral method of instruction is not conducive to healthy identity development. The importance of interpersonal communication in identity development from the viewpoints of both sociological and psychoanalytical theories of identity is…

  11. 7 CFR 52.771 - Identity.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 2 2014-01-01 2014-01-01 false Identity. 52.771 Section 52.771 Agriculture... Cherries 1 Identity and Grades § 52.771 Identity. Canned red tart pitted cherries is the product represented as defined in the standard of identity for canned cherries (21 CFR 145.125(a)), issued pursuant...

  12. Teacher Identity Work in Mathematics Teacher Education

    ERIC Educational Resources Information Center

    Neumayer-Depiper, Jill

    2013-01-01

    Becoming a teacher is not developing an identity, but is developing identity as a continuous process of constructing and deconstructing understandings within the complexities of social practice, beliefs, experiences, and social norms. I take up this stance on identity as articulated in Judith Butler's (1999) work with gender identity and…

  13. A Dialogical Approach to Conceptualizing Teacher Identity

    ERIC Educational Resources Information Center

    Akkerman, Sanne F.; Meijer, Paulien C.

    2011-01-01

    In recent attempts to address the notion of teacher identity, scholars have stressed how identity is dynamically evolving, intrinsically related to others, and consists of multiple identities. Though these postmodern characterizations represent radically new perceptions of identity, they are not extensively discussed in relation to previous…

  14. The Moral Self: Applying Identity Theory

    ERIC Educational Resources Information Center

    Stets, Jan E.; Carter, Michael J.

    2011-01-01

    This research applies identity theory to understand the moral self. In identity theory, individuals act on the basis of their identity meanings, and they regulate the meanings of their behavior so that those meanings are consistent with their identity meanings. An inconsistency produces negative emotions and motivates individuals to behave…

  15. Genome sequence of vanilla distortion mosaic virus infecting Coriandrum sativum.

    PubMed

    Adams, I P; Rai, S; Deka, M; Harju, V; Hodges, T; Hayward, G; Skelton, A; Fox, A; Boonham, N

    2014-12-01

    The 9573-nucleotide genome of a potyvirus was sequenced from a Coriandrum sativum plant from India with viral symptoms. On analysis, this virus was shown to have greater than 85 % nucleotide sequence identity to vanilla distortion mosaic virus (VDMV). Analysis of the putative coat protein sequence confirmed that this virus was in fact VDMV, with greater than 91 % amino acid sequence identity. The genome appears to encode a 3083-amino-acid polyprotein potentially cleaved into the 10 mature proteins expected in potyviruses. Phylogenetic analysis confirmed that VDMV is a distinct but ungrouped member of the genus Potyvirus.

  16. The primary transcriptome of the Escherichia coli O104:H4 pAA plasmid and novel insights into its virulence gene expression and regulation

    PubMed Central

    Berger, Petya; Knödler, Michael; Förstner, Konrad U.; Berger, Michael; Bertling, Christian; Sharma, Cynthia M.; Vogel, Jörg; Karch, Helge; Dobrindt, Ulrich; Mellmann, Alexander

    2016-01-01

    Escherichia coli O104:H4 (E. coli O104:H4), which caused a massive outbreak of acute gastroenteritis and hemolytic uremic syndrome in 2011, carries an aggregative adherence fimbriae I (AAF/I) encoding virulence plasmid, pAA. The importance of pAA in host-pathogen interaction and disease severity has been demonstrated, however, not much is known about its transcriptional organization and gene regulation. Here, we analyzed the pAA primary transcriptome using differential RNA sequencing, which allows for the high-throughput mapping of transcription start site (TSS) and non-coding RNA candidates. We identified 248 TSS candidates in the 74-kb pAA and only 21% of them could be assigned as TSS of annotated genes. We detected TSS for the majority of pAA-encoded virulence factors. Interestingly, we mapped TSS, which could allow for the transcriptional uncoupling of the AAF/I operon, and potentially regulatory antisense RNA candidates against the genes encoding dispersin and the serine protease SepA. Moreover, a computational search for transcription factor binding sites suggested for AggR-mediated activation of SepA expression, which was additionally experimentally validated. This work advances our understanding of the molecular basis of E. coli O104:H4 pathogenicity and provides a valuable resource for further characterization of pAA virulence gene regulation. PMID:27748404

  17. Effects of identity disequilibrium and linkage on quantitative variation in finite populations.

    PubMed

    Tachida, H; Cockerham, C C

    1989-02-01

    Identity disequilibrium, ID, is the difference between joint identity by descent and the product of the separate probabilities of identity by descent for two loci. The effects of ID on the additive by additive (a*a) epistatic variance and joint dominance component between populations and in the additive, dominance and a*a variance within populations, including the effects on covariances of relatives within populations, were studied for finite monoecious populations. The effects are formulated in terms of three additive partitions, eta b, eta a and eta d, of the total ID, each of which increases from zero to a maximum at some generation dependent upon linkage and population size and decreases thereafter. eta d is about four times the magnitude of the other two but none is of any consequence except for tight linkage and very small populations. For single-generation bottleneck populations only eta d is not zero. With random mating of expanded populations eta b remains constant and eta a and eta d go to zero at a rate dependent upon linkage, very fast with free recombination. The contributions of joint dominance to the genetic components of variance within and between populations are entirely a function of the eta's while those of a*a variance to the components are functions mainly of the coancestry coefficient and only modified by the eta's. The contributions of both to the covariances of half-sibs, full-sibs and parent-offspring follow the pattern expected from their contributions to the genetic components of variance within populations except for minor terms which most likely are of little importance.

  18. The Ontogeny of Face Identity

    ERIC Educational Resources Information Center

    Blass, Elliott M.; Camp, Carole Ann

    2004-01-01

    A paradigm was designed to study how infants identify live faces. Eight- to 21-week-old infants were seated comfortably and were presented an adult female, dressed in a white laboratory coat and a white turtle neck sweater, until habituation ensued. The adult then left the room. One minute later either she or an identically garbed confederate…

  19. Brand: Identity, Image, and Relationships

    ERIC Educational Resources Information Center

    Danker, Stephanie Harvey

    2014-01-01

    Adolescents face complex dilemmas such as challenging issues of identity and self-concept, and struggles with building and maintaining relationships. These issues must be embraced in the art classroom. This Instructional Resource will focus on the concept of brand--connecting visual art, marketing, and psychology--and center on ideas found in the…

  20. The Identity of Problem Solving

    ERIC Educational Resources Information Center

    Mamona-Downs, Joanna; Downs, Martin

    2005-01-01

    This paper raises issues motivated by considering the "identity" of problem solving. This means that we are concerned with how other mathematics education topics impinge on problem solving, and with themes that naturally arise within the problem-solving agenda. We claim that some of these issues need more attention by educational research, while…

  1. 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.

  2. [Identity and narration: autobiographical quests].

    PubMed

    Arfuch, Leonor

    2013-01-01

    This paper aims to tackle the subtle relation between autobiographical narratives and identity construction, from a non essentialist conception of identity. In a perspective that articulates philosophy of language, psychoanalysis, semiotics and literary critique, we posit the concept of biographical space as an analytical instrument to make a critical update of the reconfiguration of identities and subjectivities in contemporary culture, marked by the predominance of the biographical, the private and a kind of "public intimacy". This look is more symptomatic than descriptive: it intends to account for the rise of auto/biographical narratives and life-stories, from canonic genres to their multiple derivations in the media, social networks and the most diverse artistic practices, a phenomenon that seems to reaffirm the notion of narrative identities by Ricoeur. Our analysis here, from an ethic, aesthetic and political point of view, will focus on two visual arts experiences that have recently taken place for the first time in Buenos Aires: Christian Boltanski's and Tracey Emin's, solo exhibitions, each of them with a different biographical approach.

  3. 6 Keys to Identity Management

    ERIC Educational Resources Information Center

    Shoham, Idan

    2011-01-01

    An Identity and Access Management (IAM) project on campus can feel like a Sisyphean task: Just when access rights have finally been sorted out, the semester ends--and users change roles, leave campus, or require new processes. IT departments face a constantly changing technical landscape: (1) integrating new applications and retiring old ones; (2)…

  4. Gender Identity Disorder in Children.

    ERIC Educational Resources Information Center

    Redmond, Dionne; Flauto, Phil

    Identity formation involves the development of self esteem, social skills, and a sense of self. Many gay and lesbian adults have noted that they were aware of their attraction to members of the same sex as early as five- and six-years-old. Reactions they received from parents and others often added to their stress. Following a description of the…

  5. Cultural Identity in Tibetan Diasporas

    ERIC Educational Resources Information Center

    Giles, Howard; Dorjee, Tenzin

    2005-01-01

    Tibetan civilisation is over two millenniums old and, today, its struggles in diaspora open up a new chapter in Tibetan history. Diasporic Tibetans (e.g. in India and the USA) have made tremendous efforts over the last few decades to maintain their way of life. We focus on cultural identity in the Tibetan diasporas, with special attention focused…

  6. Imperialism and Samoan National Identity.

    ERIC Educational Resources Information Center

    Milford, Sereisa

    1986-01-01

    Political division and domination by different foreign powers have given birth to national identity problems which Samoans face both at home and abroad. Community leaders should put aside antagonistic feelings among themselves and restore appreciation for the "faasamoa," that body of customs and traditions once shared by all Samoans. (GC)

  7. Developing Designer Identity through Reflection

    ERIC Educational Resources Information Center

    Tracey, Monica W.; Hutchinson, Alisa

    2013-01-01

    As designers utilize design thinking while moving through a design space between problem and solution, they must rely on design intelligence, precedents, and intuition in order to arrive at meaningful and inventive outcomes. Thus, instructional designers must constantly re-conceptualize their own identities and what it means to be a designer.…

  8. Trig Integrals without Trig Identities

    ERIC Educational Resources Information Center

    Sprows, David J.

    2008-01-01

    The standard approach to finding antiderivatives of trigonometric expressions such as sin(ax) cos(bx) is to make use of certain trigonometric identities. The disadvantage of this technique is that it gives no insight into the problem, but relies on students using a memorized formula. This note considers a technique for finding antiderivatives of…

  9. Understanding, Personal Identity and Education

    ERIC Educational Resources Information Center

    Godon, Rafal

    2004-01-01

    Analysing the triad understanding-personal identity-education in three different contexts (scientism, historicism, hermeneutics) make it possible to investigate the kind of thinking that is emphasised most in each context. The implications of thinking to educational practice are stressed at each level of interpretation. The chief shortfalls in the…

  10. Developing Students' Professional Digital Identity

    ERIC Educational Resources Information Center

    Cochrane, Thomas; Antonczak, Laurent

    2015-01-01

    In contrast to the myth of the "Digital Native" and the ubiquity of Facebook use, we have found that students' digital identities are predominantly social with their online activity beyond Facebook limited to being social media consumers rather than producers. Within a global economy students need to learn new digital literacy skills to…

  11. Feminist Identity among Latina Adolescents

    ERIC Educational Resources Information Center

    Manago, Adriana M.; Brown, Christia Spears; Leaper, Campbell

    2009-01-01

    This study explores developing conceptions of feminism among Latina adolescents, their prevalence of feminist endorsement, and whether home environment and well-being are related to feminist identity. One hundred and forty Latina girls (Grades 9 to 12, M age = 15) wrote personal narratives of their understanding of feminism and whether they…

  12. Understanding Academic Identity through Metaphor

    ERIC Educational Resources Information Center

    Billot, Jennie; King, Virginia

    2015-01-01

    Metaphors used by higher education teachers in their narratives of academic life provide insight into aspects of academic identity. Drawing on an international study of leader/follower dynamics, the teachers' narratives reveal how academics interpret their interactions with leaders; the perceived distance between expectations and experience, and…

  13. Personal Identity: Moving beyond Essence

    ERIC Educational Resources Information Center

    Webster, R. Scott

    2005-01-01

    Education's ancient and profoundly important pursuit to "know thyself", is often realised through engaging with the question "who am I?" In order to the identify "who" in this search, it is argued in this paper that personal identity should be understood to be embedded in the purposes one has for one's life through "how" one relates, and is…

  14. Immigrant Identity in Teacher Preparation

    ERIC Educational Resources Information Center

    Carter, Candice C.

    2012-01-01

    In this article, I report research on representations of immigrant identities in one university where teacher candidates matriculated in undergraduate and graduate degree programs. The case study occurred in a community where immigrants were highly visible. A content analysis of curriculum for teacher preparation provided a view of factors that…

  15. Identity, causality, and pronoun ambiguity.

    PubMed

    Sagi, Eyal; Rips, Lance J

    2014-10-01

    This article looks at the way people determine the antecedent of a pronoun in sentence pairs, such as: Albert invited Ron to dinner. He spent hours cleaning the house. The experiment reported here is motivated by the idea that such judgments depend on reasoning about identity (e.g., the identity of the he who cleaned the house). Because the identity of an individual over time depends on the causal-historical path connecting the stages of the individual, the correct antecedent will also depend on causal connections. The experiment varied how likely it is that the event of the first sentence (e.g., the invitation) would cause the event of the second (the house cleaning) for each of the two individuals (the likelihood that if Albert invited Ron to dinner, this would cause Albert to clean the house, versus cause Ron to clean the house). Decisions about the antecedent followed causal likelihood. A mathematical model of causal identity accounted for most of the key aspects of the data from the individual sentence pairs.

  16. Effect of adding amino acids residues in N- and C-terminus of Vip3Aa16 (L121I) toxin.

    PubMed

    Sellami, Sameh; Cherif, Marwa; Jamoussi, Kaïs

    2016-06-01

    To study the importance of N- and C-terminus of Bacillus thuringiensis Vip3Aa16 (L121I) toxin (88 kDa), a number of mutants were generated. The addition of two (2R: RS) or eleven (11R: RSRPGHHHHHH) amino acid residues at the Vip3Aa16 (L121I) C-terminus allowed to an unappropriated folding illustrated by the abundant presence of the 62 kDa proteolytic form. The produced Vip3Aa16 (L121I) full length form was less detected when increasing the number of amino acids residues in the C-terminus. Bioassays demonstrated that the growth of the lepidopteran Ephestia kuehniella was slightly affected by Vip3Aa16 (L121I)-2R and not affected by Vip3Aa16 (L121I)-11R. Additionally, the fusion at the Vip3Aa16 (L121I) N-terminus of 39 amino acids harboring the E. coli OmpA leader peptide and the His-tag sequence allowed to the increase of protease sensitivity of Vip3Aa16 (L121I) full length form, as only the 62 kDa proteolysis form was detected. Remarkably, this fused protein produced in Escherichia coli (E. coli) was biologically inactive toward Ephestia kuehniella larvae. Thus, the N-terminus of the protein is required to the accomplishment of the insecticidal activity of Vip3 proteins. This report serves as guideline for the study of Vip3Aa16 (L121I) protein stability and activity.

  17. Waldenström's macroglobulinemia associated with AA amyloidosis.

    PubMed

    Gardyn, J; Schwartz, A; Gal, R; Lewinski, U; Kristt, D; Cohen, A M

    2001-07-01

    It is widely accepted that amyloidosis in Waldenström's macroglobulinemia (WM) is exclusively due to amyloid light-chain deposition. However, only a small number of previous reports have actually characterized the type of amyloid in WM. We now report the third patient with WM and amyloid A protein (AA) amyloidosis. This patient developed malabsorption, nephrotic syndrome, and orthostatic hypotension. AA was immunohistochemically demonstrated in the rectal biopsy. In conjunction with previous examples of AA amyloidosis, the present report raises the possibility that AA amyloidosis may also occur in WM patients.

  18. Bounds for the discrete correlation of infinite sequences on k symbols and generalized Rudin-Shapiro sequences

    NASA Astrophysics Data System (ADS)

    Grant, E.; Shallit, J.; Stoll, T.

    Motivated by the known autocorrelation properties of the Rudin-Shapiro sequence, we study the discrete correlation among infinite sequences over a finite alphabet, where we just take into account whether two symbols are identical. We show by combinatorial means that sequences cannot be "too" different, and by an explicit construction generalizing the Rudin-Shapiro sequence, we show that we can achieve the maximum possible difference.

  19. New variants of lepidoptericidal toxin genes encoding Bacillus thuringiensis Vip3Aa proteins.

    PubMed

    Sauka, Diego H; Rodriguez, Sonia E; Benintende, Graciela B

    2012-01-01

    Bacillus thuringiensis is an entomopathogenic bacterium characterized by producing parasporal proteinaceous insecticidal crystal inclusions during sporulation. Many strains are capable of also expressing other insecticidal proteins called Vip during the vegetative growing phase. Particularly, Vip3A proteins have activity against certain Lepidoptera species through a unique mechanism of action which emphasized their possible use in resistance management strategies against resistant pests. The aim of the work was to develop a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method that can distinguish between vip3A genes from B. thuringiensis strains. In addition, 4 novel vip3Aa genes were cloned and sequenced. The method was originally based on amplification of a single PCR amplicon and the use of 2 restriction enzymes with recognition sites that facilitate simultaneous detection. Subsequently, a third restriction enzyme was used to distinguish between vip3A variants. Thirteen vip3Aa genes were identified in strains belonging to 10 different B. thuringiensis serovars. Three intra-subclass variants of vip3Aa genes could be differentiated. The presented method can serve as an invaluable tool for the investigation of known and novel vip3A genes in B. thuringiensis strains. To the best of our knowledge, this is the first report where variants of a same subclass of insecticidal genes could be distinguished following PCR-RFLP.

  20. Identity

    ERIC Educational Resources Information Center

    Ransom, Liz

    2012-01-01

    The National Association of Hispanic Journalists tracks the presence of Latinos in the news. It reports that news stories in which Latinos are the subject most often concern immigration, poverty and crime. And Hollywood does no better in reflecting the broad reality of Latino life. Latino characters are often portrayed as poor and uneducated. In…

  1. Numerical and experimental study of Bauschinger effect on AA5182 sheets

    NASA Astrophysics Data System (ADS)

    Talla, Abhinav

    For stamping process, most of the sheet metal elements undergo a complicated deformation process that may comprise a sequence of stretching, bending, unbending and reverse bending processes. For this kind of deformation, the Bauschinger effect must be considered in order to calculate the internal stress within the parts before springback. To understand the Bauschinger effect phenomenon on AA5182-O temper, a fixture for cyclic double-shear test has been designed and manufactured. This test can induce cyclic shear loading on the specimen during experiment. LS-Dyna has also been used to simulate this experiment.

  2. Complete De Novo Assembly of Monoclonal Antibody Sequences

    PubMed Central

    Tran, Ngoc Hieu; Rahman, M. Ziaur; He, Lin; Xin, Lei; Shan, Baozhen; Li, Ming

    2016-01-01

    De novo protein sequencing is one of the key problems in mass spectrometry-based proteomics, especially for novel proteins such as monoclonal antibodies for which genome information is often limited or not available. However, due to limitations in peptides fragmentation and coverage, as well as ambiguities in spectra interpretation, complete de novo assembly of unknown protein sequences still remains challenging. To address this problem, we propose an integrated system, ALPS, which for the first time can automatically assemble full-length monoclonal antibody sequences. Our system integrates de novo sequencing peptides, their quality scores and error-correction information from databases into a weighted de Bruijn graph to assemble protein sequences. We evaluated ALPS performance on two antibody data sets, each including a heavy chain and a light chain. The results show that ALPS was able to assemble three complete monoclonal antibody sequences of length 216–441 AA, at 100% coverage, and 96.64–100% accuracy. PMID:27562653

  3. Taxonomic evaluation of Streptomyces albus and related species using multilocus sequence analysis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In phylogenetic analyses of the genus Streptomyces using 16S rRNA gene sequences, Streptomyces albus subsp. albus NRRL B-1811T formed a cluster with 5 other species having identical or nearly identical 16S rRNA gene sequences. Moreover, the morphological and physiological characteristics of these ot...

  4. Amino acid sequence of mouse submaxillary gland renin.

    PubMed Central

    Misono, K S; Chang, J J; Inagami, T

    1982-01-01

    The complete amino acid sequences of the heavy chain and light chain of mouse submaxillary gland renin have been determined. The heavy chain consists of 288 amino acid residues having a Mr of 31,036 calculated from the sequence. The light chain contains 48 amino acid residues with a Mr of 5,458. The sequence of the heavy chain was determined by automated Edman degradations of the cyanogen bromide peptides and tryptic peptides generated after citraconylation, as well as other peptides generated therefrom. The sequence of the light chain was derived from sequence analyses of the peptides generated by cyanogen bromide cleavage or by digestion with Staphylococcus aureus protease. The sequences in the active site regions in renin containing two catalytically essential aspartyl residues 32 and 215 were found identical with those in pepsin, chymosin, and penicillopepsin. Comparison of the amino acid sequence of renin with that of porcine pepsin indicated a 42% sequence identity of the heavy chain with the amino-terminal and middle regions and a 46% identity of the light chain with the carboxyl-terminal region of the porcine pepsin sequence. Residues identical in renin and pepsin are distributed throughout the length of the molecules, suggesting a similarity in their overall structures. PMID:6812055

  5. Complete Genome Sequence of Bacillus thuringiensis subsp. thuringiensis Strain IS5056, an Isolate Highly Toxic to Trichoplusia ni

    PubMed Central

    Murawska, Emilia; Fiedoruk, Krzysztof; Bideshi, Dennis K.

    2013-01-01

    The genome sequence of the entomopathogen Bacillus thuringiensis subsp. thuringiensis strain IS5056 was determined. The chromosome is composed of 5,491,935 bp. In addition, IS5056 harbors 14 plasmids ranging from 6,880 to 328,151 bp, four of which contain nine insecticidal protein genes, cry1Aa3, cry1Ab21, cry1Ba1, cry1Ia14, cry2Aa9, cry2Ab1, vip1, vip2, and vip3Aa10. PMID:23516221

  6. Draft Genome Sequence of Bacillus thuringiensis Serovar Tolworthi Strain Na205-3, an Isolate Toxic for Helicoverpa armigera

    PubMed Central

    Palma, Leopoldo; Muñoz, Delia; Murillo, Jesús

    2014-01-01

    We report here the complete annotated 6,510,053-bp draft genome sequence of Bacillus thuringiensis serovar tolworthi strain Na205-3, which is toxic for Helicoverpa armigera. This strain potentially contains nine insecticidal toxin genes homologous to cry1Aa12, cry1Ab1, cry1Ab8, cry1Ba1, cry1Af1, cry1Ia10, vip1Bb1, vip2Ba2, and vip3Aa6. PMID:24625875

  7. Study on Fabrication of AA4032/AA6069 Cladding Billet Using Direct Chill Casting Process

    NASA Astrophysics Data System (ADS)

    Han, Xing; Zhang, Haitao; Shao, Bo; Li, Lei; Liu, Xuan; Cui, Jianzhong

    2016-04-01

    AA4032/AA6069 cladding billet in size of φ130 mm/φ110 mm was prepared by the modified direct chill casting process, and the parametric effect on casting performance was investigated using numerical simulation. Microstructures, elements distribution, and mechanical properties of the bonding interface were examined. The results show that metallurgical bonding interface can be obtained with the optimal parameters: the casting speed of 130 to 140 mm/min, the internal liquid level height of 50 to 60 mm, and the contact height of 40 to 50 mm. The metallurgical bonding interface is free of any discontinuities due to the fact that the alloying elements diffused across the interface and formed Ni-containing phase. Tensile strength of the cladding billet reaches 225.3 MPa, and the fracture position was located in AA6069 side, suggesting that the interface bonding strength is higher than the strength of AA6069. The interfacial shearing strength is 159.3 MPa, indicating excellent metallurgical bonding.

  8. Complete genome sequence of a new tobamovirus naturally infecting tomatoes in Mexico

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete genomic sequence of a new tobamovirus in tomato was determined through deep sequencing and assembly of small RNAs, thenvalidated through Sanger sequencing of the overlapping RT-PCR products and rapid amplification of cDNA ends (RACE). Based on the genomic sequence identity (85%) to kn...

  9. Complete genome sequence of a new tobamovirus naturally infecting tomatoes in Mexico.

    PubMed

    Li, Rugang; Gao, Shan; Fei, Zhangjun; Ling, Kai-Shu

    2013-10-03

    The complete genomic sequence of a new tobamovirus in tomatoes was determined through deep sequencing and assembly of small RNAs, then validated through Sanger sequencing. Based on the low sequence identity (≤85%) to known viruses and a close phylogenetic relationship to tobamoviruses, it was identified as a new species.

  10. Complete genome sequence of an emerging genotype of tobacco streak virus in the U.S.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report the complete genome sequence of an emerging genotype of Tobacco streak virus (TSV) infecting zucchini squash in Florida (TSV_FL13-07), through deep sequencing of sRNAs and validation by Sanger sequencing. TSV_FL13-07 only shares less than 90% sequence identity in three genomic ribonucleic...

  11. Complete Genome Sequence of Human Coronavirus OC43 Isolated from Mexico

    PubMed Central

    Isa, P.; Espinoza, M. A.; Aponte, F. E.; Arias-Ortiz, M. A.; Monge-Martínez, J.; Rodríguez-Vázquez, R.; Díaz-Hernández, F.; Zárate-Vidal, F.; Wong-Chew, R. M.; Firo-Reyes, V.; del Río-Almendárez, C. N.; Gaitán-Meza, J.; Villaseñor-Sierra, A.; Martínez-Aguilar, G.; García-Borjas, M.; Noyola, D. E.; Pérez-Gónzalez, L. F.; López, S.; Santos-Preciado, J. I.

    2016-01-01

    We report the complete genome sequence of the first Mexican human coronavirus (HCoV) OC43, obtained by new-generation sequencing and a metagenomic approach, isolated from a child hospitalized with pneumonia. The genome is closely related to the other OC43 genome sequences available, ranging from 99.8% to 98.2% nucleotide sequence identity. PMID:27834708

  12. AAS Special Session: Policy Making in Astronomy

    NASA Astrophysics Data System (ADS)

    Cardelli, J. A.; Massa, D.

    1995-12-01

    The professional astronomical community today is more diverse than at any time in its history. Individuals participating in creative research programs can be found in a wide range of positions. This type of diversity, which mixes research, education, and service (e.g. contract) work, represents the strength of contemporary astronomy. While recognizing the unavoidable reductions in funding and restructuring of organizations like NASA, it is imperative that the significance of the current diversity be considered during these processes. Creative ideas are one of the cornerstones of quality research, and they can originate anywhere. Consequently, it is essential that adequate research resources remain available for free and open competition by all astronomers. Our goal in this session is to bring together officials from the AAS, NASA, and the NSF to discuss how the policy and decision making process operates and whether it should be changed to better serve the general needs of the professional astronomical community. Examples of the issues we believe are important include: In establishing new policy, how can the needs of the average research astronomer be better addressed? How could input from such astronomers be provided to those who craft NASA/NSF policy? How can/should the AAS serve as an interface between policy/decision making bodies and its membership? Should the AAS membership become more actively/effectively involved in the decision making process and, if so, how? More information on this session and related issues can be found at the Association of Research Astronomers Home Page: http://www.phy.vill.edu/astro/faculty/ara/ara_home.htm

  13. Tracing the Identity of Objects

    ERIC Educational Resources Information Center

    Rips, Lance J.; Blok, Sergey; Newman, George

    2006-01-01

    This article considers how people judge the identity of objects (e.g., how people decide that a description of an object at one time, t-sub-0, belongs to the same object as a description of it at another time, t-sub-1). The authors propose a causal continuer model for these judgments, based on an earlier theory by Nozick (1981). According to this…

  14. Identity Theft: Trends and Issues

    DTIC Science & Technology

    2010-05-27

    been stolen, and some proportion of these could have occurred as a result of a data breach.76 Synovate (2007) conducted a similar study on behalf of...continued) http://www.javelinstrategy.com. 77 Synovate , Federal Trade Commission: 2006 Identity Theft Survey...rulemaking authority to the Attorney General, in conjunction with the Chairman of the FTC and Commissioner of the SSA. 89 Synovate , Federal Trade Commission

  15. Macroscopic anisotropy in AA5019A sheets

    SciTech Connect

    Choi, S.H.; Brem, J.C.; Barlat, F.; Oh, K.H.

    2000-05-11

    The macroscopic anisotropy for typical texture components in aluminum alloys and AA5019A sheet samples (H48 and O temper conditions) were investigated. In order to simultaneously consider the effects of morphological texture and crystallographic texture on macroscopic anisotropy, predictions of plastic properties were carried out using a full-constraints Taylor model and a visco-plastic self-consistent (VPSC) polycrystal model. The yield stress and r-value (width-to-thickness plastic strain ratio in uniaxial tension) anisotropy predicted using the VPSC model were in good agreement with experimental data.

  16. Swift Observations of SN 2007aa

    NASA Astrophysics Data System (ADS)

    Immler, S.; Brown, P. J.; Milne, P.

    2007-03-01

    Swift Ultraviolet/Optical Telescope (UVOT) and X-Ray Telescope (XRT) observed the type II SN 2007aa (CBET #850, IAUC #8814) on 2007-02-24.63 UT. The following UVOT magnitudes were measured: V = 15.8 (322 s exposure time), B = 16.4 (367 s), U = 16.9 (367 s), UVW1 [181-321nm] = 18.6 (737 s), UVM2 [166-268 nm] > 19.5 (3-sigma upper limit; 236 s), and UVW2 [112-264 nm] = 19.7 (725 s). The magnitudes have not been corrected for extinction.

  17. Affective temperament and personal identity.

    PubMed

    Stanghellini, Giovanni; Rosfort, René

    2010-10-01

    The complex relationship between temperament and personal identity, and between these and mental disorders, is of critical interest to both philosophy and psychopathology. More than other living creatures, human beings are constituted and characterized by the interplay of their genotype and phenotype. There appears to be an explanatory gap between the almost perfect genetic identity and the individual differences among humans. One reason for this gap is that a human being is a person besides a physiological organism. We propose an outline of a theoretical model that might somewhat mitigate the explanatory discrepancies between physiological mechanisms and individual human emotional experience and behaviour. Arguing for the pervasive nature of human affectivity, i.e., for the assumption that human consciousness and behaviour is characterised by being permeated by affectivity; to envisage the dynamics of emotional experience, we make use of a three-levelled model of human personal identity that differentiates between factors that are simultaneously at work in the constitution of the individual human person: 1) core emotions, 2) affective temperament types/affective character traits, and 3) personhood. These levels are investigated separately in order to respect the methodological diversity among them (neuroscience, psychopathology, and philosophy), but they are eventually brought together in a hermeneutical account of human personhood.

  18. Vasospastic Angina in Identical Twins

    PubMed Central

    Yoshioka, Takayuki; Otsui, Kazunori; Suzuki, Atsushi; Ozawa, Toru; Iwata, Sachiyo; Takei, Asumi; Inoue, Nobutaka

    2015-01-01

    Patient: Male, 58 Final Diagnosis: Vasospastic angina Symptoms: Chest pain Medication: — Clinical Procedure: Medical treatment Specialty: Cardiology Objective: Rare disease Background: The clinical conditions of various diseases, including coronary artery disease, are determined by genetics and the environment. Previous investigations noted the significance of genetic mutations and polymorphisms in cases of coronary spasm. Case Report: We report on monozygotic identical twins who almost simultaneously presented with vasospastic angina. The 58-year-old younger twin was admitted to our hospital because of persistent chest pain. An electrocardiogram showed an inverted T wave in the left precordial leads. Coronary angiographies revealed a short left main trunk (LMT) and 50% stenosis at the proximal portion of the left anterior descending artery (LAD). Infusion of acetylcholine to his left coronary artery caused marked vasoconstriction associated with a sensation of chest oppression. Nitroglycerine completely reversed this response. Based on these findings, we diagnosed Twin A with vasospastic angina. At nearly the same time, his identical twin brother was diagnosed with vasospastic angina at another hospital. Comparison of both coronary angiograms indicated similar structure of coronary vessels, including short LMT and mild stenosis at the proximal portion of LAD. Conclusions: These 2 cases highlight the importance of genetic factors in the pathogenesis of vasospastic angina. It may be important for individuals to receive medical attention if their identical twin presents with vasospastic angina. PMID:26347942

  19. The complete amino acid sequence of prochymosin.

    PubMed Central

    Foltmann, B; Pedersen, V B; Jacobsen, H; Kauffman, D; Wybrandt, G

    1977-01-01

    The total sequence of 365 amino acid residues in bovine prochymosin is presented. Alignment with the amino acid sequence of porcine pepsinogen shows that 204 amino acid residues are common to the two zymogens. Further comparison and alignment with the amino acid sequence of penicillopepsin shows that 66 residues are located at identical positions in all three proteases. The three enzymes belong to a large group of proteases with two aspartate residues in the active center. This group forms a family derived from one common ancestor. PMID:329280

  20. Idiopathic systemic AA-amyloidosis in a skunk (Mephitis mephitis).

    PubMed

    Elhensheri, Mohamed; Linke, Reinhold P; Blankenburg, Anja; Beineke, Andreas

    2012-03-01

    This report describes a case of systemic amyloidosis in a captive striped skunk. At necropsy, bilateral alopecia, as well as reno-, hepato-, and splenomegaly were present. Congo red staining and immunohistochemistry revealed depositions of AA-amyloid in different organs. The lack of a predisposing disease is suggestive of idiopathic systemic AA-amyloidosis.

  1. Floor Plans: Section "AA", Section "BB"; Floor Framing Plans: Section ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Floor Plans: Section "A-A", Section "B-B"; Floor Framing Plans: Section "A-A", Section "B-B" - Fort Washington, Fort Washington Light, Northeast side of Potomac River at Fort Washington Park, Fort Washington, Prince George's County, MD

  2. Distinguishing Proteins From Arbitrary Amino Acid Sequences

    PubMed Central

    Yau, Stephen S.-T.; Mao, Wei-Guang; Benson, Max; He, Rong Lucy

    2015-01-01

    What kinds of amino acid sequences could possibly be protein sequences? From all existing databases that we can find, known proteins are only a small fraction of all possible combinations of amino acids. Beginning with Sanger's first detailed determination of a protein sequence in 1952, previous studies have focused on describing the structure of existing protein sequences in order to construct the protein universe. No one, however, has developed a criteria for determining whether an arbitrary amino acid sequence can be a protein. Here we show that when the collection of arbitrary amino acid sequences is viewed in an appropriate geometric context, the protein sequences cluster together. This leads to a new computational test, described here, that has proved to be remarkably accurate at determining whether an arbitrary amino acid sequence can be a protein. Even more, if the results of this test indicate that the sequence can be a protein, and it is indeed a protein sequence, then its identity as a protein sequence is uniquely defined. We anticipate our computational test will be useful for those who are attempting to complete the job of discovering all proteins, or constructing the protein universe. PMID:25609314

  3. Pittosporum cryptic virus 1: genome sequence completion using next-generation sequencing.

    PubMed

    Elbeaino, Toufic; Kubaa, Raied Abou; Tuzlali, Hasan Tuna; Digiaro, Michele

    2016-07-01

    Next-generation sequencing (NGS) was applied to dsRNAs extracted from an Italian pittosporum plant infected with pittosporum cryptic virus 1 (PiCV1). NGS allowed assembly of the full genome sequence of PiCV1, comprising dsRNA1 (1.9 kbp) and dsRNA2 (1.5 kbp), which encode the RNA-dependent RNA polymerase and capsid protein genes, respectively. Phylogenetic and sequence analyses confirmed that PiCV1 is a new member of the genus Deltapartitivirus, family Partiviridae. From the same plant, NSG also permitted assembly of the complete genome sequence of eggplant mottled dwarf virus (EMDV), which shared 86 % to 98 % nucleotide sequence identity with complete and partial sequences (ca 6750 nt) of other known EMDV isolates with sequences available in the GenBank database.

  4. Sequential on-line C-terminal sequencing of peptides based on carboxypeptidase Y digestion and optically gated capillary electrophoresis with laser-induced fluorescence detection.

    PubMed

    Tian, Miaomiao; Zhang, Ning; Liu, Xiaoxia; Guo, Liping; Yang, Li

    2016-08-12

    We report a novel method for sequential on-line C-terminal sequencing of peptides, which combines carboxypeptidase Y (CPY) digestion with on-line derivatization and optically gated capillary electrophoresis with laser-induced fluorescence detection (OGCE-LIF). Various factors that may affect the C-terminal sequencing were investigated and optimized. High repeatability of on-line derivatization and the sequential OGCE-LIF assay of amino acids (AAs) was achieved with relative standard deviation (RSD) (n=20) less than 1.5% and 3.2% for migration time and peak height, respectively. A total of 13 AAs was efficiently separated in the present study, indicating that the method can be used for sequencing of peptides consisting of the 13 AAs studied. Using two synthesized N-terminally blocked peptides as test examples, we show that the present method can on-line monitor the released AAs with a temporal resolution of 50s during the entire CPY digestion process. The rates of AA release as a function of digestion time were easily measured; thus, the AA sequence of the peptide was determined with just one OGCE assay. Our study indicates the present approach is an effective, reliable, and convenient method for rapid analysis of the C-terminal sequence of peptides, with potential application in peptide analysis and proteome research.

  5. Dicer maintains the identity and function of proprioceptive sensory neurons.

    PubMed

    O'Toole, Sean M; Ferrer, Monica M; Mekonnen, Jennifer; Zhang, Haihan; Shima, Yasuyuki; Ladle, David R; Nelson, Sacha B

    2017-03-01

    Neuronal cell identity is established during development and must be maintained throughout an animal's life (Fishell G, Heintz N. Neuron 80: 602-612, 2013). Transcription factors critical for establishing neuronal identity can be required for maintaining it (Deneris ES, Hobert O. Nat Neurosci 17: 899-907, 2014). Posttranscriptional regulation also plays an important role in neuronal differentiation (Bian S, Sun T. Mol Neurobiol 44: 359-373, 2011), but its role in maintaining cell identity is less established. To better understand how posttranscriptional regulation might contribute to cell identity, we examined the proprioceptive neurons in the dorsal root ganglion (DRG), a highly specialized sensory neuron class, with well-established properties that distinguish them from other neurons in the ganglion. By conditionally ablating Dicer in mice, using parvalbumin (Pvalb)-driven Cre recombinase, we impaired posttranscriptional regulation in the proprioceptive sensory neuron population. Knockout (KO) animals display a progressive form of ataxia at the beginning of the fourth postnatal week that is accompanied by a cell death within the DRG. Before cell loss, expression profiling shows a reduction of proprioceptor specific genes and an increased expression of nonproprioceptive genes normally enriched in other ganglion neurons. Furthermore, although central connections of these neurons are intact, the peripheral connections to the muscle are functionally impaired. Posttranscriptional regulation is therefore necessary to retain the transcriptional identity and support functional specialization of the proprioceptive sensory neurons.NEW & NOTEWORTHY We have demonstrated that selectively impairing Dicer in parvalbumin-positive neurons, which include the proprioceptors, triggers behavioral changes, a lack of muscle connectivity, and a loss of transcriptional identity as observed through RNA sequencing. These results suggest that Dicer and, most likely by extension, micro

  6. Dissimilar plasmids isolated from Pseudomonas diminuta MG and a Flavobacterium sp. (ATCC 27551) contain identical opd genes.

    PubMed

    Harper, L L; McDaniel, C S; Miller, C E; Wild, J R

    1988-10-01

    The opd (organophosphate-degrading) gene derived from a 43-kilobase-pair plasmid (pSM55) of a Flavobacterium sp. (ATCC 27551) has a sequence identical to that of the plasmid-borne gene of Pseudomonas diminuta. Hybridization studies with DNA fragments obtained by restriction endonuclease digestion of plasmid DNAs demonstrated that the identical opd sequences were encoded on dissimilar plasmids from the two sources.

  7. Dissimilar plasmids isolated from Pseudomonas diminuta MG and a Flavobacterium sp. (ATCC 27551) contain identical opd genes.

    PubMed Central

    Harper, L L; McDaniel, C S; Miller, C E; Wild, J R

    1988-01-01

    The opd (organophosphate-degrading) gene derived from a 43-kilobase-pair plasmid (pSM55) of a Flavobacterium sp. (ATCC 27551) has a sequence identical to that of the plasmid-borne gene of Pseudomonas diminuta. Hybridization studies with DNA fragments obtained by restriction endonuclease digestion of plasmid DNAs demonstrated that the identical opd sequences were encoded on dissimilar plasmids from the two sources. Images PMID:3202637

  8. Perception, experience and body identity.

    PubMed

    López-Ibor, Juan J; Ortiz, Tomás; López-Ibor, María I

    2011-12-01

    Physician has to know the patient in the disease and not only the disease in the patient, from the dual perspective of the body as object and the body as subject. This also affects the patient who has to cope with the reality of having a body that bursts into the subject's consciousness as a vital threat, as source of discomfort and inability and being a body (Marcel). The human body in its dual aspect has been and is a great unknown, if not a great outrage in spite of the fact that we are our body and our body is each of us. We sometimes do not feel as we are and thus a confrontation arises, sometimes more normal, others more morbid. This forces the physician to face complex ethics considerations and the scientist to accept a personal identity disorder. Dualism considers that there are two substances in us, one that distinguishes us from other beings and from the rest of the individuals of the human species, the soul, the psychic life, mind or consciousness, and another more insubstancial one, the body. The aim of the first substance is to dominate the body, to survive it after death when it is, already a corpse is meant to become putrefied, is buried, incinerated or thrown to the depth of the sea. This dualism aims to explain the origin of the evil and the attitude to defeat it and it does so efficiently. This anthropology has very ancient roots (the Upvanishads, in the orphic texts, in Plato), it is the core of Gnostic thought and the foundation of the modern science since Descartes. Some monist perspectives are a masked dualism or a mereologic fallacy, according to which, the brain is conscious, when that what is conscious is the subject, although the subject, with the brain could not be conscious. Therefore, a new perspective is proposed, chiasmatic or janicular monism, that considers the adaptive value of focusing on the reality from two perspectives, as physical universe and the world of interpersonal relationships. In the agnosias and in the phantom limb

  9. Correlation between relatives given complete genotypes: from identity by descent to identity by function.

    PubMed

    Sverdlov, Serge; Thompson, Elizabeth A

    2013-09-01

    In classical quantitative genetics, the correlation between the phenotypes of individuals with unknown genotypes and a known pedigree relationship is expressed in terms of probabilities of IBD states. In existing approaches to the inverse problem where genotypes are observed but pedigree relationships are not, dependence between phenotypes is either modeled as Bayesian uncertainty or mapped to an IBD model via inferred relatedness parameters. Neither approach yields a relationship between genotypic similarity and phenotypic similarity with a probabilistic interpretation corresponding to a generative model. We introduce a generative model for diploid allele effect based on the classic infinite allele mutation process. This approach motivates the concept of IBF (Identity by Function). The phenotypic covariance between two individuals given their diploid genotypes is expressed in terms of functional identity states. The IBF parameters define a genetic architecture for a trait without reference to specific alleles or population. Given full genome sequences, we treat a gene-scale functional region, rather than a SNP, as a QTL, modeling patterns of dominance for multiple alleles. Applications demonstrated by simulation include phenotype and effect prediction and association, and estimation of heritability and classical variance components. A simulation case study of the Missing Heritability problem illustrates a decomposition of heritability under the IBF framework into Explained and Unexplained components.

  10. Enterotoxigenic Escherichia coli Multilocus Sequence Types in Guatemala and Mexico

    PubMed Central

    Klena, John; Rodas, Claudia; Bourgeois, August Louis; Torres, Olga; Svennerholm, Ann-Mari; Sjöling, Åsa

    2010-01-01

    The genetic backgrounds of 24 enterotoxigenic Escherichia coli (ETEC) strains from Mexico and Guatemala expressing heat-stable toxin (ST) and coli surface antigen 6 (CS6) were analyzed. US travelers to these countries and resident children in Guatemala were infected by ETEC strains of sequence type 398, expressing STp and carrying genetically identical CS6 sequences. PMID:20031063

  11. Complete Genome Sequence of Spiroplasma sp. NBRC 100390

    PubMed Central

    Haryono, Mindia; Lo, Wen-Sui; Gasparich, Gail E.

    2017-01-01

    ABSTRACT Spiroplasma sp. NBRC 100390 was initially described as a duplicate of S. atrichopogonis GNAT3597T (=ATCC BAA-520T) but later found to be different in the 16S rDNA sequences. Here, we report the complete genome sequence of this bacterium to establish its identity and to facilitate future investigation. PMID:28280009

  12. Transfer in Motor Sequence Learning: Effects of Practice Schedule and Sequence Context

    PubMed Central

    Müssgens, Diana M.; Ullén, Fredrik

    2015-01-01

    Transfer (i.e., the application of a learned skill in a novel context) is an important and desirable outcome of motor skill learning. While much research has been devoted to understanding transfer of explicit skills the mechanisms of skill transfer after incidental learning remain poorly understood. The aim of this study was to (1) examine the effect of practice schedule on transfer and (2) investigate whether sequence-specific knowledge can transfer to an unfamiliar sequence context. We trained two groups of participants on an implicit serial response time task under a Constant (one sequence for 10 blocks) or Variable (alternating between two sequences for a total of 10 blocks) practice schedule. We evaluated response times for three types of transfer: task-general transfer to a structurally non-overlapping sequence, inter-manual transfer to a perceptually identical sequence, and sequence-specific transfer to a partially overlapping (three shared triplets) sequence. Results showed partial skill transfer to all three sequences and an advantage of Variable practice only for task-general transfer. Further, we found expression of sequence-specific knowledge for familiar sub-sequences in the overlapping sequence. These findings suggest that (1) constant practice may create interference for task-general transfer and (2) sequence-specific knowledge can transfer to a new sequential context. PMID:26635591

  13. Rational recovery: alternative to AA for addiction?

    PubMed

    Galanter, M; Egelko, S; Edwards, H

    1993-01-01

    Rational Recovery (RR) is a new self-help movement for substance abusers, with a cognitive orientation. It has been suggested as an alternative to Alcoholics Anonymous. This study was designed to examine the nature of RR and its impact on those who join. A national sample of 433 substance-abusing people attending 63 established RR groups was evaluated, using codable self-report questionnaires completed at RR meetings. Members were mostly men with college experience who had previously attended AA. Among recruits who attended their first RR meeting in the last month, 38% were abstinent in the last month. Among members who had joined 3 or more months before, 73% were abstinent in the last month; they had attended an average of 4.1 RR meetings in that month, and carried out exercises at home based on Rational Emotive Therapy. Among those who joined 6 or more months before, 58% reported at least 6 months of abstinence. Among members with a history of heavy cocaine use, the portion reporting abstinence in the last month was not significantly different from those who had never used cocaine. The minority of members who were engaged for 3 months were still drinking, though, and did so on an average of 9.9 days in the last month. RR succeeded in engaging substance abusers and promoting abstinence among many of them while presenting a cognitive orientation that is different from the spiritual one of AA. Its utility in substance abuse treatment warrants further assessment.

  14. States' Flexibility Waiver Plans for Alternate Assessments Based on Alternate Achievement Standards (AA-AAS). Synthesis Report 96

    ERIC Educational Resources Information Center

    Lazarus, Sheryl S.; Edwards, Lynn M.; Thurlow, Martha L.; Hodgson, Jennifer R.

    2014-01-01

    All states have alternate assessments based on alternate achievement standards (AA-AAS) for students with the most significant cognitive disabilities. For accountability purposes, the Elementary and Secondary Education Act (ESEA) allows up to 1% of students to be counted as proficient with this assessment option. In 2011 the U.S. Department of…

  15. The AAS Working Group on Accessibility and Disability (WGAD): Year 1 Highlights

    NASA Astrophysics Data System (ADS)

    Aarnio, Alicia; Monkiewicz, Jacqueline; Murphy, Nicholas Arnold; Nordhaus, Jason; Tuttle, Sarah E.

    2017-01-01

    The AAS Working Group on Accessibility and Disability (WGAD) was formed in January of 2016 with the express purpose of seeking equity of opportunity and building inclusive practices for disabled astronomers at all career stages. In our first year, the WGAD has been actively developing resources and the online infrastructure for the dissemination of information and engagement with the astronomy community. Our official WGAD website has gone live, and we have used both the access: astronomy google group and blog to discuss specific issues of disability justice and to raise awareness for less-discussed barriers to access. The WGAD has developed relationships and collaboration with AAS inclusion committees (SGMA, CSMA, CSWA) so our work can recognize and address the intersections of identity astronomers occupy. In this presentation, we summarize our year one activities, focusing on our recently developed set of recommendations for journal accessibility to ensure everyone can engage with journal content and navigate the submission process. We will also discuss ongoing and future endeavors: a best practices guide for accessibility to be available via our website, and a site visit program.

  16. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST

    PubMed Central

    Aouinti, Safa; Giudicelli, Véronique; Duroux, Patrice; Malouche, Dhafer; Kossida, Sofia; Lefranc, Marie-Paule

    2016-01-01

    There is a huge need for standardized analysis and statistical procedures in order to compare the complex immune repertoires of antigen receptors immunoglobulins (IG) and T cell receptors (TR) obtained by next generation sequencing (NGS). NGS technologies generate millions of nucleotide sequences and have led to the development of new tools. The IMGT/HighV-QUEST, available since 2010, is the first global web portal for the analysis of IG and TR high throughput sequences. IMGT/HighV-QUEST provides standardized outputs for the characterization of the “IMGT clonotype (AA)” (AA for amino acids) and their comparison in up to one million sequences. Standardized statistical procedures for “IMGT clonotype (AA)” diversity or expression comparisons have recently been described, however, no tool was yet available. IMGT/StatClonotype, a new IMGT® tool, evaluates and visualizes statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per V (variable), D (diversity), and J (joining) gene of a given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. IMGT/StatClonotype tool is incorporated in the R package “IMGTStatClonotype,” with a user-friendly interface. IMGT/StatClonotype is downloadable at IMGT®1 for users to evaluate pairwise comparison of IG and TR NGS statistical output from IMGT/HighV-QUEST and to visualize, on their web browser, the statistical significance of IMGT clonotype (AA) diversity or expression, per gene, the comparative analysis of CDR-IMGT and the V–D–J associations, in immunoprofiles from normal or pathological immune responses. PMID:27667992

  17. Identity Verification, Control, and Aggression in Marriage

    ERIC Educational Resources Information Center

    Stets, Jan E.; Burke, Peter J.

    2005-01-01

    In this research we study the identity verification process and its effects in marriage. Drawing on identity control theory, we hypothesize that a lack of verification in the spouse identity (1) threatens stable self-meanings and interaction patterns between spouses, and (2) challenges a (nonverified) spouse's perception of control over the…

  18. Positional Identity and Science Teacher Professional Development

    ERIC Educational Resources Information Center

    Moore, Felicia M.

    2008-01-01

    The aim of this study was to understand the positional identity of three African American secondary science teachers. Positional identity was operationally defined in terms of race, ethnicity, economic status, gender, religion, and age. Positional identity was posited to inform why diverse teachers with differing knowledge and experiences in…

  19. Foreign Language Teaching and Cultural Identity.

    ERIC Educational Resources Information Center

    Nasr, Raja T., Ed.; And Others

    A collection of works on the role of cultural identity in second language learning and teaching includes: "Linguas estrangeiras e ideologia" (Roberto Ballalai); "Cultural Identity and Bilinguality" (Josiane F. Hamers, Michel Blanc); "Foreign Language Teaching and Cultural Identity" (Lakshmie K. Cumaranatunge);…

  20. Racial and Ethnic Identities in American Society.

    ERIC Educational Resources Information Center

    Yin, Robert K.

    The investigation of race relations, of social problems related to race and ethnicity, and of different racial and social groups, all presume prior information about the definition of racial or ethnic group identity, about the formation, maintenance, and dissolution of such identities, and about the importance of such identities in American…

  1. The Development of Ethnic Identity during Adolescence

    ERIC Educational Resources Information Center

    French, Sabine Elizabeth; Seidman, Edward; Allen, LaRue; Aber, J. Lawrence

    2006-01-01

    The development of ethnic identity is a critical facet of adolescence, particularly for adolescents of color. In order to examine the developmental trajectory of ethnic identity, African American, Latino American, and European American early and middle adolescents (N=420) were assessed over 3 years. Two components of ethnic identity were…

  2. Identity Tensions in Lesbian Intercollegiate Coaches

    ERIC Educational Resources Information Center

    Krane, Vikki; Barber, Heather

    2005-01-01

    Using social identity perspective, the authors investigated the experiences of 13 lesbian college coaches. Through semistructured interviews, the coaches revealed the daily identity tensions they experienced. There was constant negotiation between their social identities of "coach" and "lesbian." The social context of intercollegiate women's…

  3. Identities, Social Representations and Critical Thinking

    ERIC Educational Resources Information Center

    Lopez-Facal, Ramon; Jimenez-Aleixandre, Maria Pilar

    2009-01-01

    This comment on L. Simonneaux and J. Simonneaux paper focuses on the role of "identities" in dealing with socio-scientific issues. We argue that there are two types of identities (social representations) influencing the students' positions: On the one hand their social representations of the bears' and wolves' identities as belonging to…

  4. American Identity in the USA: Youth Perspectives

    ERIC Educational Resources Information Center

    Jahromi, Parissa

    2011-01-01

    National identity, how one sees oneself as a member of a given nation, is an important form of social identity. Feelings toward one's country are a matter of both individual and collective concern. In an increasingly diverse world, the issue of identifying with a nation is complex and consequential for individual identity formation as well as…

  5. 21 CFR 610.14 - Identity.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Identity. 610.14 Section 610.14 Food and Drugs FOOD... BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.14 Identity. The contents of a final container of each filling of each lot shall be tested for identity after all labeling operations shall have been...

  6. 21 CFR 610.14 - Identity.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 21 Food and Drugs 7 2012-04-01 2012-04-01 false Identity. 610.14 Section 610.14 Food and Drugs... BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.14 Identity. The contents of a final container of each filling of each lot shall be tested for identity after all labeling operations shall have been...

  7. 7 CFR 782.14 - Identity preservation.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 7 2013-01-01 2013-01-01 false Identity preservation. 782.14 Section 782.14... § 782.14 Identity preservation. (a) The importer and all subsequent buyers of the imported wheat shall preserve the identity of the Canadian-produced wheat. (b) Canadian-produced wheat may only be...

  8. 21 CFR 610.14 - Identity.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 7 2010-04-01 2010-04-01 false Identity. 610.14 Section 610.14 Food and Drugs... BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.14 Identity. The contents of a final container of each filling of each lot shall be tested for identity after all labeling operations shall have been...

  9. 21 CFR 610.14 - Identity.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 7 2014-04-01 2014-04-01 false Identity. 610.14 Section 610.14 Food and Drugs... BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.14 Identity. The contents of a final container of each filling of each lot shall be tested for identity after all labeling operations shall have been...

  10. 7 CFR 52.771 - Identity.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Identity. 52.771 Section 52.771 Agriculture... United States Standards for Grades of Canned Red Tart Pitted Cherries 1 Identity and Grades § 52.771 Identity. Canned red tart pitted cherries is the product represented as defined in the standard of...

  11. 21 CFR 610.14 - Identity.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 21 Food and Drugs 7 2013-04-01 2013-04-01 false Identity. 610.14 Section 610.14 Food and Drugs... BIOLOGICAL PRODUCTS STANDARDS General Provisions § 610.14 Identity. The contents of a final container of each filling of each lot shall be tested for identity after all labeling operations shall have been...

  12. Fibonacci Identities via the Determinant Sum Property

    ERIC Educational Resources Information Center

    Spivey, Michael

    2006-01-01

    We use the sum property for determinants of matrices to give a three-stage proof of an identity involving Fibonacci numbers. Cassini's and d'Ocagne's Fibonacci identities are obtained at the ends of stages one and two, respectively. Catalan's Fibonacci identity is also a special case.

  13. Pre-Service Teacher Cultural Identity Development

    ERIC Educational Resources Information Center

    Cunningham, Maurella Louise

    2013-01-01

    The main purpose of this study is to conduct exploratory qualitative research to investigate how PSTs and practicing teachers experience cultural and racial identity development or changes in identity. Rather than examine the "what" or contributors to identity development, I will explore the "how" or processes of identity…

  14. Gender, Legitimation, and Identity Verification in Groups

    ERIC Educational Resources Information Center

    Burke, Peter J.; Stets, Jan E.; Cerven, Christine

    2007-01-01

    Drawing upon identity theory, expectation states theory, and legitimation theory, we examine how the task leader identity in task-oriented groups is more likely to be verified for persons with high status characteristics. We hypothesize that identity verification will be accomplished more readily for male group members and legitimated task leaders…

  15. Identity Construction in Powerful Institutions: A Commentary

    ERIC Educational Resources Information Center

    Philips, Susan U.

    2010-01-01

    The articles in this issue focus on the collaborative and negotiated construction of identities in interaction. Most of the articles are concerned with the constitution of identities through time in powerful educational and legal institutional contexts. Here the emphasis is on the emergence of new identities being learned by some participants…

  16. Dehistoricized Cultural Identity and Cultural Othering

    ERIC Educational Resources Information Center

    Weiguo, Qu

    2013-01-01

    The assumption that each culture has its own distinctive identity has been generally accepted in the discussion of cultural identities. Quite often identity formation is not perceived as a dynamic and interactive ongoing process that engages other cultures and involves change in its responses to different challenges at different times. I will…

  17. 7 CFR 52.771 - Identity.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... United States Standards for Grades of Canned Red Tart Pitted Cherries 1 Identity and Grades § 52.771 Identity. Canned red tart pitted cherries is the product represented as defined in the standard of identity for canned cherries (21 CFR 145.125(a)), issued pursuant to the Federal Food, Drug, and Cosmetic...

  18. The Formation of Adult Identity: A Review.

    ERIC Educational Resources Information Center

    Johnson, William L.

    This paper examines the concept of identity from philosophical, personal, and territorial perspectives. In the first section an historical perspective on identity is explored through the writings of Plato, Dupius, Josephus, and Thut. Twentieth century models of identity are related to the concepts of these writers of ancient Greece. In the second…

  19. Career Identity among Community College Students

    ERIC Educational Resources Information Center

    Stringer, Kate J.; Kerpelman, Jennifer L.

    2014-01-01

    Career identity development is salient in adolescence and young adulthood, but little research has assessed career identity in populations other than four-year college students. Context should be considered when examining career identity, and to address this gap in the literature, the current study examined the extent to which parental support for…

  20. 7 CFR 52.771 - Identity.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 2 2012-01-01 2012-01-01 false Identity. 52.771 Section 52.771 Agriculture... United States Standards for Grades of Canned Red Tart Pitted Cherries 1 Identity and Grades § 52.771 Identity. Canned red tart pitted cherries is the product represented as defined in the standard of...

  1. Synchronization of two identical and non-identical Rulkov models

    NASA Astrophysics Data System (ADS)

    Sun, Huijing; Cao, Hongjun

    2016-11-01

    In this paper, the synchronization of two chaotic Rulkov map-based neurons is taken into account. Firstly, based on the master stability function (MSF) analysis, the complete synchronization of two electrical coupled chaotic Rulkov neurons is investigated in detail. The two-dimensional parameter-space plot that displays directly the values of the MSF in different colors is numerically obtained. The numerical values of the MSF show that the two electrical coupled Rulkov neurons are likely to achieve the complete synchronization when each single neuron is in a silent state or a period-1 bursting state, while are unable to reach the complete synchronous state when each single neuron is in a chaotic bursting state or a spiking state. Secondly, Pearson's correlation coefficient is employed to measure the synchronization degree, which demonstrates the nonexistence of the complete synchronization for non-identical electrical coupled Rulkov neurons. Importantly, the complete synchronization can not be reached with the increase of the electrical coupling strength, which is different from the continuous-time neuronal models. Finally, based on the active control method, a synchronization scheme is presented to study the complete synchronization for two Rulkov neurons no matter whether they are identical or not. The scheme is also applied to investigate the anticipated synchronization and the lag synchronization for any two Rulkov neurons. Numerical simulations verify the correctness of our analytical results and the effectiveness of our methods.

  2. Single molecule real-time sequencing of Xanthomonas oryzae genomes reveals a dynamic structure and complex TAL (transcription activator-like) effector gene relationships

    PubMed Central

    Booher, Nicholas J.; Carpenter, Sara C. D.; Sebra, Robert P.; Wang, Li; Salzberg, Steven L.; Leach, Jan E.; Bogdanove, Adam J.

    2016-01-01

    Pathogen-injected, direct transcriptional activators of host genes, TAL (transcription activator-like) effectors play determinative roles in plant diseases caused by Xanthomonas spp. A large domain of nearly identical, 33–35 aa repeats in each protein mediates DNA recognition. This modularity makes TAL effectors customizable and thus important also in biotechnology. However, the repeats render TAL effector (tal) genes nearly impossible to assemble using next-generation, short reads. Here, we demonstrate that long-read, single molecule real-time (SMRT) sequencing solves this problem. Taking an ensemble approach to first generate local, tal gene contigs, we correctly assembled de novo the genomes of two strains of the rice pathogen X. oryzae completed previously using the Sanger method and even identified errors in those references. Sequencing two more strains revealed a dynamic genome structure and a striking plasticity in tal gene content. Our results pave the way for population-level studies to inform resistance breeding, improve biotechnology and probe TAL effector evolution. PMID:27148456

  3. Practicing Identity: A Crafty Ideal?

    NASA Astrophysics Data System (ADS)

    Brysbaert, A.; Vetters, M.

    This paper focuses on the materialization of technological practices as a form of identity expression. Contextual analyses of a Mycenaean workshop area in the Late Bronze Age citadel of Tiryns (Argolis, Greece) are presented to investigate the interaction of different artisans under changing socio-political and economic circumstances. The case study indicates that although certain technological practices are often linked to specific crafts, they do not necessarily imply the separation of job tasks related to the working of one specific material versus another. Shared technological practices and activities, therefore, may be a factor in shaping cohesive group identities of specialized artisans. Since tracing artisans' identities is easier said than done on the basis of excavated materials alone, we employ the concepts of multiple chaînes opératoires combined with cross-craft interactions as a methodology in order to retrieve distinctive sets of both social and technological practices from the archaeological remains. These methodological concepts are not restricted to a specific set of steps in the production cycle, but ideally encompass reconstructing contexts of extraction, manufacture, distribution and discard/reuse for a range of artefacts. Therefore, these concepts reveal both technological practices, and, by contextualising these technological practices in their spatial layout, equally focus on social contacts that would have taken place during any of these actions. Our detailed contextual study demonstrates that the material remains when analysed in their entirety are complementary to textual evidence. In this case study they even form a source of information on palatial spheres of life about which the fragmentary Linear B texts, so far, remain silent.

  4. [Dissociative identity disorder or schizophrenia?].

    PubMed

    Tschöke, S; Steinert, T

    2010-01-01

    We present a case of dissociative identity disorder in which Schneiderian first rank symptoms were present besides of various states of consciousness. Thus the diagnosis of schizophrenia had to be considered. Formally, the symptoms met ICD-10 criteria for schizophrenia. However, taking into account the lack of formal thought disorder and of negative symptoms as well as a typical history of severe and prolonged traumatisation, we did not diagnose a co-morbid schizophrenic disorder. There is good evidence for the existence of psychotic symptoms among patients with dissociative disorders. However, in clinical practice this differential diagnosis is rarely considered.

  5. Agrotis segetum midgut putative receptor of Bacillus thuringiensis vegetative insecticidal protein Vip3Aa16 differs from that of Cry1Ac toxin.

    PubMed

    Ben Hamadou-Charfi, Dorra; Boukedi, Hanen; Abdelkefi-Mesrati, Lobna; Tounsi, Slim; Jaoua, Samir

    2013-10-01

    Considering the fact that Agrotis segetum is one of the most pathogenic insects to vegetables and cereals in the world, particularly in Africa, the mode of action of Vip3Aa16 of Bacillus thuringiensis BUPM95 and Cry1Ac of the recombinant strain BNS3Cry-(pHTcry1Ac) has been examined in this crop pest. A. segetum proteases activated the Vip3Aa16 protoxin (90kDa) yielding three bands of about 62, 45, 22kDa and the activated form of the toxin was active against this pest with an LC50 of about 86ng/cm(2). To be active against A. segetum, Cry1Ac protoxin was activated to three close bands of about 60-65kDa. Homologous and heterologous competition binding experiments demonstrated that Vip3Aa16 bound specifically to brush border membrane vesicles (BBMV) prepared from A. segetum midgut and that it does not inhibit the binding of Cry1Ac. Moreover, BBMV protein blotting experiments showed that the receptor of Vip3Aa16 toxin in A. segetum midgut differs from that of Cry1Ac. In fact, the latter binds to a 120kDa protein whereas the Vip3Aa16 binds to a 65kDa putative receptor. The midgut histopathology of Vip3Aa16 fed larvae showed vacuolization of the cytoplasm, brush border membrane lysis, vesicle formation in the goblet cells and disintegration of the apical membrane. The distinct binding properties and the unique protein sequence of Vip3Aa16 support its use as a novel insecticidal agent to control the crop pest A. segetum.

  6. Examining the psychometric validity of the Multigroup Ethnic Identity Measure-Revised (MEIM-R) in a community sample of African American and European American adults.

    PubMed

    Chakawa, Ayanda; Butler, Robert C; Shapiro, Steven K

    2015-10-01

    The purpose of this study was to examine the psychometric properties of the Multigroup Ethnic Identity Measure-Revised (MEIM-R), focusing on a sample drawn from a geographic region in the United States that has not been included in previously published research on the MEIM-R. Data were obtained from a community-based sample of 105 African American (AA) and 91 European American (EA) adults located in the state of Alabama. The MEIM-R was best represented by two constructs-exploration and commitment. AA adults reported higher levels of racial/ethnic identity exploration and commitment than EA adults. Differential item functioning was found among 1 of the exploration items. The current study provides additional support for the structural validity of the MEIM-R. Further research on the invariance of responses to the MEIM-R across a variety of sociodemographic factors is still necessary.

  7. The sequence of sequencers: The history of sequencing DNA.

    PubMed

    Heather, James M; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way.

  8. Teacher Educators: Their Identities, Sub-Identities and Implications for Professional Development

    ERIC Educational Resources Information Center

    Swennen, Anja; Jones, Ken; Volman, Monique

    2010-01-01

    In this article we address the question: "What sub-identities of teacher educators emerge from the research literature about teacher educators and what are the implications of the sub-identities for the professional development of teacher educators?" Like other professional identities, the identity of teacher educators is a construction of various…

  9. Identity salience model: A paradigm for integrating multiple identities in clinical practice.

    PubMed

    Yakushko, Oksana; Davidson, Meghan M; Williams, Elizabeth Nutt

    2009-06-01

    The manuscript presents an identity salience model for clinical practice and psychotherapy research. The model seeks to incorporate contemporary social identity theory and ecological theory, as well as an appreciation of individuals' multiple identities without necessitating a hierarchy of oppression. A clinical case example utilizing the identity salience model is presented. (PsycINFO Database Record (c) 2010 APA, all rights reserved).

  10. Ambivalent Urban, Immigrant Identities: The Incompleteness of Lao American Student Identities

    ERIC Educational Resources Information Center

    Ngo, Bic

    2009-01-01

    In this article, the author elucidates the identity work of Lao American urban, immigrant students, highlighting ambivalent identities that do not fit into notions of bicultural or binary identities. It examines the various discourses and practices that inform and shape the experiences and identities of urban, Lao American high school students. It…

  11. Racial Identity Attitudes and Ego Identity Statuses in Dominican and Puerto Rican College Students

    ERIC Educational Resources Information Center

    Sanchez, Delida

    2013-01-01

    This study explored the relation between racial identity attitudes and ego identity statuses in 94 Dominican and Puerto Rican Latino college students in an urban public college setting. Simultaneous regression analyses were conducted to test the relation between racial identity attitudes and ego identity statuses, and findings indicated that…

  12. Conceptualizing Identity Development: Unmasking the Assumptions within Inventories Measuring Identity Development

    ERIC Educational Resources Information Center

    Moran, Christy D.

    2009-01-01

    The purpose of this qualitative research was to analyze the dimensions and manifestations of identity development embedded within commonly used instruments measuring student identity development. To this end, a content analysis of ten identity assessment tools was conducted to determine the assumptions about identity development contained therein.…

  13. Identities in Harmony: Gender-Work Identity Integration Moderates Frame Switching in Cognitive Processing

    ERIC Educational Resources Information Center

    Sacharin, Vera; Lee, Fiona; Gonzalez, Richard

    2009-01-01

    Professional women's identity integration--the perceived compatibility between work and gender identities--plays a role in how task or relationship information is processed. Seventy female business school students were primed with either their professional or their gender identity. Business women with higher identity integration showed an…

  14. Convergent paradigms for visual neuroscience and dissociative identity disorder.

    PubMed

    Manning, Mark L; Manning, Rana L

    2009-01-01

    Although dissociative identity disorder, a condition in which multiple individuals appear to inhabit a single body, is a recognized psychiatric disorder, patients may yet encounter health professionals who declare that they simply "do not believe in multiple personalities." This article explores the proposal that resistance to the disorder represents a failure to apply an appropriate paradigm from which the disorder should be interpreted. Trauma and sociocognitive explanations of dissociative identity disorder are contrasted. The trauma hypothesis is further differentiated into paradigms in which trauma affects a defense mechanism, and one in which trauma serves to inhibit the normal integration sequence of parallel processes of the self in childhood. This latter paradigm is shown to be broadly consistent with current models of cortical processing in another system, the cortical visual system.

  15. Nephrotic Syndrome Associated with Lung Cancer: A Rare Case of Malignancy Associated with AA Amyloidosis.

    PubMed

    Gueutin, Victor; Langlois, Anne-Lyse; Shehwaro, Nathalie; Elharraqui, Ryme; Rouvier, Philippe; Izzedine, Hassane

    2013-01-01

    Nonhematologic malignancies are rarely reported to be associated with AA amyloidosis. Although the association between renal cell carcinoma and systemic AA amyloidosis has been established, the evidence linking pulmonary cancer to AA amyloidosis is scarce. Here, a case of biopsy-proven renal AA amyloidosis complicated with nephrotic syndrome associated with lung carcinoma is reported.

  16. Nephrotic Syndrome Associated with Lung Cancer: A Rare Case of Malignancy Associated with AA Amyloidosis

    PubMed Central

    Gueutin, Victor; Langlois, Anne-Lyse; Shehwaro, Nathalie; Elharraqui, Ryme; Rouvier, Philippe; Izzedine, Hassane

    2013-01-01

    Nonhematologic malignancies are rarely reported to be associated with AA amyloidosis. Although the association between renal cell carcinoma and systemic AA amyloidosis has been established, the evidence linking pulmonary cancer to AA amyloidosis is scarce. Here, a case of biopsy-proven renal AA amyloidosis complicated with nephrotic syndrome associated with lung carcinoma is reported. PMID:24558629

  17. New graduate identity: discursive mismatch.

    PubMed

    Hamilton, Helen

    2005-09-01

    For many new graduates the transition from nursing student to a professional in practice is marked by conflict and tension. Given that conflict may ensue from differing discursive constructions of new graduates, this article reports a review of discursive construction between new graduates from two institutions with vested interests in nursing graduates--comparing health service organisations and educational institutions in Victoria. Four discourses, common to both sets of texts and constitutive of new graduate identity were identified: these were the discourse of nursing practice; the discourse of the good nurse; the discourse of knowing and thinking; and the discourse of statute and regulation. A discourse peculiar to health service organisations only was identified as an organisational and bureaucratic discourse. This review reports the new graduate, as constructed in education texts, as a rational, independent, critically thinking and knowing care giver. In contrast, in health service organisation texts, the new graduate is constructed as a functional, efficient, organisational operative, providing a nursing service. New graduates are concluded to experience multiple discursive dissonances in their first employment which stem from differing constructions of new graduate identity within institutional discourses. If tensions experienced in the transition as discursively generated are understood, previously unthought of ways preparing and introducing nurses to the work place may ensue.

  18. Categorizing identity from facial motion.

    PubMed

    Girges, Christine; Spencer, Janine; O'Brien, Justin

    2015-01-01

    Advances in marker-less motion capture technology now allow the accurate replication of facial motion and deformation in computer-generated imagery (CGI). A forced-choice discrimination paradigm using such CGI facial animations showed that human observers can categorize identity solely from facial motion cues. Animations were generated from motion captures acquired during natural speech, thus eliciting both rigid (head rotations and translations) and nonrigid (expressional changes) motion. To limit interferences from individual differences in facial form, all animations shared the same appearance. Observers were required to discriminate between different videos of facial motion and between the facial motions of different people. Performance was compared to the control condition of orientation-inverted facial motion. The results show that observers are able to make accurate discriminations of identity in the absence of all cues except facial motion. A clear inversion effect in both tasks provided consistency with previous studies, supporting the configural view of human face perception. The accuracy of this motion capture technology thus allowed stimuli to be generated that closely resembled real moving faces. Future studies may wish to implement such methodology when studying human face perception.

  19. Biochemical determinants in Gender identity.

    PubMed

    Hamilton, W; Chapman, P H

    1977-01-01

    The purpose of this communication is to report cognate studies which suggest that the nature of the peripheral metabolism of testosterone may impart gender direction to thought construction and motive. In patients with the complete testicular feminizing syndrome [4], the XO/XY syndrome [4], female trans-sexualism [4] and testicular agenesis [5] HCG-tests of 3 days duration were performed, and plasma and urinary testosterone, urinary excretion of 5 alpha-androstane, 3 alpha, 17 beta-diol (5 alpha-diol), 5 beta-androstane, 3 alpha, 17 beta-diol (5 beta-diol) and epiandrosterone before and after stimulation were measured. In addition steroid transformation was examined by incubation studies with human fetal brain tissue. The results of the latter method presented here are in agreement with published work. It seems clear therefore that the peripheral levels of androgens, oestrogens and their metabolites combine with cerebral steroid transformation, metabolism and possible also synthesis in order to establish gender identity. Exploration of the role of peripheral hormones as stimulators of both gender identity and gender function has dictated the need for a new approach to therapy for gender abnormalities in psyche and soma.

  20. Crystal structure of Cry6Aa: A novel nematicidal ClyA-type α-pore-forming toxin from Bacillus thuringiensis.

    PubMed

    Huang, Jinbo; Guan, Zeyuan; Wan, Liting; Zou, Tingting; Sun, Ming

    2016-09-09

    Crystal (Cry) proteins from Bacillus thuringiensis (Bt) are globally used in agriculture as proteinaceous insecticides. Numerous crystal structures have been determined, and most exhibit conserved three-dimensional architectures. Recently, we have identified a novel nematicidal mechanism by which Cry6Aa triggers cell death through a necrosis-signaling pathway via an interaction with the host protease ASP-1. However, we found little sequence conservation of Cry6Aa in our functional study. Here, we report the 1.90 angstrom (Å) resolution structure of the proteolytic form of Cry6Aa (1-396), determined by X-ray crystallography. The structure of Cry6Aa is highly similar to those of the pathogenic toxin family of ClyA-type α-pore-forming toxins (α-PFTs), which are characterized by a bipartite structure comprising a head domain and a tail domain, thus suggesting that Cry6Aa exhibits a previously undescribed nematicidal mode of action. This structure also provides a framework for the functional study of other nematicidal toxins.

  1. The relationships among caregiver and adolescent identity status, identity distress and psychological adjustment.

    PubMed

    Wiley, Rachel E; Berman, Steven L

    2012-10-01

    The present study addresses the relationships of caregiver identity status on their adolescent children's identity distress and psychological symptom severity among a sample of adolescents (age 12-19) in treatment at a community mental health center (N = 60 caregiver-child dyads). A significant proportion of caregivers (10%) and their adolescent children (21.7%) met DSM-IV criteria for Identity Problem. Caregiver identity commitment, significantly predicted adolescent identity distress over and above the adolescents' identity variables, while caregiver identity exploration significantly predicted adolescent psychological symptom severity. These findings and implications are discussed in further detail.

  2. Recognizing Moral Identity as a Cultural Construct

    PubMed Central

    Jia, Fanli; Krettenauer, Tobias

    2017-01-01

    Current research on moral identity shows that moral identity predicts moral action in Western cultures but not in non-Western cultures. The present paper argues that this may be due to the fact that the concept of moral identity is culturally biased. In order to remedy this situation, we argue that researchers should broaden their scopes of inquiry by adding a cultural lens to their studies of moral identity. This change is important because although some concept of moral identity likely exists in all cultures, it may function in different ways and at different levels in each place. We propose that moral identity is a context-dependent construct tied to varying social and cultural obligations. We argue that Western moral identity stresses an individually oriented morality, whereas, people from Eastern cultures consider a highly moral person to be societally oriented. We conclude by discussing the implications of this view for future research. PMID:28377737

  3. Three quantitative studies of gender and identity in psychotherapy consultations.

    PubMed

    Langs, R; Rapp, P E; Pinto, A; Cramer, G; Badalamenti, A

    1992-04-01

    This paper details the application of three distinctive approaches to the analysis of line-by-line scores for themes of gender and identity in recorded psychotherapy consultations conducted by three male analysts with a female patient. The first method involved commonly used statistical comparisons of the frequency with which gender subthemes and allusions to identity appeared in each consultation session. The results of this study indicate three significantly different patterns of gender material in the communications from the patient with each of the analysts who interviewed her--and from each analyst and patient/analyst system as well. Therapist dominance in this area appeared to be quite strong. The second study involved measures of overall informational complexity for various aspects of the gender/identity sequence of communications. Here too, individual differences emerged. They not only add to the evidence for therapist dominance in these protocols, but also provide indications that sessions differ in respect to the extent to which the information they contain is ordered and repetitive or redundant, as compared to disordered, complex, and varied. The third study availed itself of stochastic methods in which the Box-Jenkins models were used to define mathematically and post hoc, the deeper structure of aspects of the vicissitudes of gender/identity expressions in the course of these consultations. The main finding was that change in speaker role in respect to these themes accelerated in response to random interventional shocks to the system that occurred at the time of measurement and inversely with shocks to the system sustained the previous second. This look into the deeper structure of these sequences revealed considerable sensitivity to recent shocks to the patient/therapist system, much underlying instability, and strong tendencies toward establishing stability or equilibrium when the system destabilized. Of note is the finding that all three

  4. Perspectives on Sexual Identity Formation, Identity Practices, and Identity Transitions Among Men Who Have Sex With Men in India.

    PubMed

    Tomori, Cecilia; Srikrishnan, Aylur K; Ridgeway, Kathleen; Solomon, Sunil S; Mehta, Shruti H; Solomon, Suniti; Celentano, David D

    2016-07-08

    Men who have sex with men (MSM) remain at high risk for HIV infection. Culturally specific sexual identities, encompassing sexual roles, behavior, and appearance, may shape MSM's experiences of stigmatization and discrimination, and affect their vulnerability to HIV. This multi-site qualitative study (n = 363) encompassing 31 focus group discussions (FGDs) and 121 in-depth interviews (IDIs) across 15 sites in India investigated sexual identity formation, identity practices, and transitions and their implications for HIV prevention. IDIs and FGDs were transcribed, translated, and underwent thematic analysis. Our findings document heterogeneous sexual identity formation, with MSM who have more gender nonconforming behaviors or appearance reporting greater family- and community-level disapproval, harassment, violence, and exclusion. Concealing feminine aspects of sexual identities was important in daily life, especially for married MSM. Some participants negotiated their identity practices in accordance with socioeconomic and cultural pressures, including taking on identity characteristics to suit consumer demand in sex work and on extended periods of joining communities of hijras (sometimes called TG or transgender women). Participants also reported that some MSM transition toward more feminine and hijra or transgender women identities, motivated by intersecting desires for feminine gender expression and by social exclusion and economic marginalization. Future studies should collect information on gender nonconformity stigma, and any changes in sexual identity practices or plans for transitions to other identities over time, in relation to HIV risk behaviors and outcomes.

  5. A naturally occurring -263G/C variant of the human AA-NAT gene and overnight melatonin production.

    PubMed

    Ying, Grace Wang; Lee, Caroline Guat Lay; Lee, Edmund Jon Deoon

    2004-01-01

    Several lines of evidence show that the daily amount of melatonin produced differs greatly between individuals. Any polymorphism in the gene of arylalkylamine N-acetyltransferase (AA-NAT), a critical enzyme involved in melatonin biosynthesis, may contribute to the variability of melatonin production. The present study investigated the possible association between overnight melatonin excretion and a commonly occurring -263G/C polymorphism in the promoter region of the human AA-NAT gene. However, we found that -263G/C variant had no effect on the overnight 6-OHMS excretion. In this study, individual genotyping for -263G/C was determined by denaturing high performance liquid chromatography (DHPLC) and confirmed by sequencing. The overnight urinary 6-hydroxymelatonin sulfate (6-OHMS) excretion was quantified by enzyme-linked immunosorbent assay (ELISA).

  6. Sequence diversity of wheat mosaic virus isolates.

    PubMed

    Stewart, Lucy R

    2016-02-02

    Wheat mosaic virus (WMoV), transmitted by eriophyid wheat curl mites (Aceria tosichella) is the causal agent of High Plains disease in wheat and maize. WMoV and other members of the genus Emaravirus evaded thorough molecular characterization for many years due to the experimental challenges of mite transmission and manipulating multisegmented negative sense RNA genomes. Recently, the complete genome sequence of a Nebraska isolate of WMoV revealed eight segments, plus a variant sequence of the nucleocapsid protein-encoding segment. Here, near-complete and partial consensus sequences of five more WMoV isolates are reported and compared to the Nebraska isolate: an Ohio maize isolate (GG1), a Kansas barley isolate (KS7), and three Ohio wheat isolates (H1, K1, W1). Results show two distinct groups of WMoV isolates: Ohio wheat isolate RNA segments had 84% or lower nucleotide sequence identity to the NE isolate, whereas GG1 and KS7 had 98% or higher nucleotide sequence identity to the NE isolate. Knowledge of the sequence variability of WMoV isolates is a step toward understanding virus biology, and potentially explaining observed biological variation.

  7. Hot stamping of AA7075 aluminum sheets

    NASA Astrophysics Data System (ADS)

    Mendiguren, J.; Saenz de Argandona, E.; Galdos, L.

    2016-11-01

    In this work the formability of a high strength aluminium alloy (AA7075-T6) for the stamping of an automotive component has been studied. Due to the low formability of the selected alloy, two different heat assisted forming strategies have been analysed. On the one hand, the W-temper process, where the thermal process is carried out prior to the forming operation. On the other hand, the hot stamping process, where the thermal process is carried out at the same time as the forming. The results showed that both technology were able to form the component avoiding any failure of the material. On the contrary, both processes reduced the final mechanical properties of the material compared to the as received material condition. However, the obtained mechanical properties doubled the strength of commonly used 5xxx and 6xxx aluminium alloys.

  8. The expression pattern of the murine Hoxa-10 gene and the sequence recognition of its homeodomain reveal specific properties of Abdominal B-like genes.

    PubMed Central

    Benson, G V; Nguyen, T H; Maas, R L

    1995-01-01

    Homeobox genes of the Abdominal B (AbdB) family constitute a distinct subset of vertebrate Hox genes. Analysis of the murine Hoxa-10 gene, one member of this family, revealed several properties specific to this class. Two transcripts of Hoxa-10, a10-1 and a10-2, encode homeodomain proteins of 55 kDa (399 amino acids) and 16 kDa (96 amino acids), respectively. These proteins have identical homeodomains and C-terminal regions encoded by a common 3' exon but differ significantly in the sizes of their N-terminal regions because of the usage of alternative 5' exons. The 5' exon of the a10-2 form is also present in transcripts of Hoxa-9, the next 3' gene, indicating that splicing can occur between adjacent AbdB Hox genes within a cluster. Both Hoxa-10 transcripts demonstrated identical patterns of expression in the posterior body and proximal limb bud, differentiating them from AbdB morphogenetic and regulatory transcripts and suggesting a role with other AbdB Hox genes in the patterning of these structures. Finally, a binding site selection identified the sequence AA(A/T)TTTTATTAC as the Hoxa-10 homeodomain consensus binding site, with a TTAT core sequence. Preferential recognition of a TTAT core therefore differentiates the AbdB class from Antennapedia (Antp) class gene products which bind a TAAT core. Thus, in vertebrates, structural similarities, coordinate transcriptional regulation, sites of expression, and binding site preferences all serve to distinguish AbdB from Antp Hox genes. PMID:7862151

  9. Classification of mouse VK groups based on the partial amino acid sequence to the first invariant tryptophan: impact of 14 new sequences from IgG myeloma proteins.

    PubMed

    Potter, M; Newell, J B; Rudikoff, S; Haber, E

    1982-12-01

    Fourteen new VK sequences derived from BALB/c IgG myeloma proteins were determined to the first invariant tryptophan (Trp 35). These partial sequences were compared with 65 other published VK sequences using a computer program. The 79 sequences were organized according to the length of the sequence from the amino terminus to the first invariant tryptophan (Trp 35), into seven groups (33, 34, 35, 36, 39, 40 and 41aa). A distance matrix of all 79 sequences was then computed, i.e. the number of amino acid substitutions necessary to convert one sequence to another was determined. From these data a dendrogram was constructed. Most of the VK sequences fell into clusters or closely related groups. The definition of a sequence group is arbitrary but facilitates the classification of VK proteins. We used 12 substitutions as the basis for defining a sequence group based on the known number of substitutions that are found in the VK21 proteins. By this criterion there were 18 groups in the Trp 35 dendrogram. Twelve of the 14 new sequences fell into one of these sequence groups; two formed new sequence groups. Collective amino acid sequencing is still encountering new VK structures indicating more sequences will be required to attain an accurate estimate of the total number of VK groups. Updated dendrograms can be quickly generated to include newly generated sequences.

  10. The college journey and academic engagement: how metaphor use enhances identity-based motivation.

    PubMed

    Landau, Mark J; Oyserman, Daphna; Keefer, Lucas A; Smith, George C

    2014-05-01

    People commonly talk about goals metaphorically as destinations on physical paths extending into the future or as contained in future periods. Does metaphor use have consequences for people's motivation to engage in goal-directed action? Three experiments examine the effect of metaphor use on students' engagement with their academic possible identity: their image of themselves as academically successful graduates. Students primed to frame their academic possible identity using the goal-as-journey metaphor reported stronger academic intention, and displayed increased effort on academic tasks, compared to students primed with a nonacademic possible identity, a different metaphoric framing (goal-as-contained-entity), and past academic achievements (Studies 1-2). This motivating effect persisted up to a week later as reflected in final exam performance (Study 3). Four experiments examine the cognitive processes underlying this effect. Conceptual metaphor theory posits that an accessible metaphor transfers knowledge between dissimilar concepts. As predicted in this paradigm, a journey-metaphoric framing of a possible academic identity transferred confidence in the procedure, or action sequence, required to attain that possible identity, which in turn led participants to perceive that possible identity as more connected to their current identity (Study 4). Drawing on identity-based motivation theory, we hypothesized that strengthened current/possible identity connection would mediate the journey framing's motivating effect. This mediational process predicted students' academic engagement (Study 5) and an online sample's engagement with possible identities in other domains (Study 6). Also as predicted, journey framing increased academic engagement particularly among students reporting a weak connection to their academic possible identity (Study 7).

  11. Mitochondrial Replacement: Ethics and Identity.

    PubMed

    Wrigley, Anthony; Wilkinson, Stephen; Appleby, John B

    2015-11-01

    Mitochondrial replacement techniques (MRTs) have the potential to allow prospective parents who are at risk of passing on debilitating or even life-threatening mitochondrial disorders to have healthy children to whom they are genetically related. Ethical concerns have however been raised about these techniques. This article focuses on one aspect of the ethical debate, the question of whether there is any moral difference between the two types of MRT proposed: Pronuclear Transfer (PNT) and Maternal Spindle Transfer (MST). It examines how questions of identity impact on the ethical evaluation of each technique and argues that there is an important difference between the two. PNT, it is argued, is a form of therapy based on embryo modification while MST is, instead, an instance of selective reproduction. The article's main ethical conclusion is that, in some circumstances, there is a stronger obligation to use PNT than MST.

  12. Historic Cosmology Identity and Exploration

    NASA Astrophysics Data System (ADS)

    Nebergall, K.

    The role of the soul and spirit in the composition of human endeavour generally takes the form of motivational poster catch phrases or third-hand quotes. If the spirit equals the life of a creature, and one of the signs of life is locomotion, are humans not obliged by something even deeper than our humanity to explore the universe? This paper examines the roots and perspectives of our worldviews on identity, exploration, and the limitations and capacities of humanity. It will equip the reader to discuss the nature of exploration with audiences across a wide range of worldviews. Current cultures, regardless of religion or politics, are looped into a series of nihilistic patterns that must be broken by rediscovering our nature as living beings, and our obligations as human beings.

  13. Best packing of identical helices

    NASA Astrophysics Data System (ADS)

    Huh, Youngsik; Hong, Kyungpyo; Kim, Hyoungjun; No, Sungjong; Oh, Seungsang

    2016-10-01

    In this paper we prove the unique existence of a ropelength-minimizing conformation of the θ-spun double helix in a mathematically rigorous way, and find the minimal ropelength {{{Rop}}}* (θ )=-\\tfrac{8π }{t} where t is the unique solution in [-θ ,0] of the equation 2-2\\cos (t+θ )={t}2. Using this result, the pitch angles of the standard, triple and quadruple helices are around 39.3771^\\circ , 42.8354^\\circ and 43.8351^\\circ , respectively, which are almost identical with the approximated pitch angles of the zero-twist structures previously known by Olsen and Bohr. We also find the ropelength of the standard N-helix.

  14. Mitochondrial Replacement: Ethics and Identity

    PubMed Central

    Wilkinson, Stephen; Appleby, John B.

    2015-01-01

    Abstract Mitochondrial replacement techniques (MRTs) have the potential to allow prospective parents who are at risk of passing on debilitating or even life‐threatening mitochondrial disorders to have healthy children to whom they are genetically related. Ethical concerns have however been raised about these techniques. This article focuses on one aspect of the ethical debate, the question of whether there is any moral difference between the two types of MRT proposed: Pronuclear Transfer (PNT) and Maternal Spindle Transfer (MST). It examines how questions of identity impact on the ethical evaluation of each technique and argues that there is an important difference between the two. PNT, it is argued, is a form of therapy based on embryo modification while MST is, instead, an instance of selective reproduction. The article's main ethical conclusion is that, in some circumstances, there is a stronger obligation to use PNT than MST. PMID:26481204

  15. Stop identity cue as a cue to language identity

    NASA Astrophysics Data System (ADS)

    Castonguay, Paula Lisa

    The purpose of the present study was to determine whether language membership could potentially be cued by the acoustic-phonetic detail of word-initial stops and retained all the way through the process of lexical access to aid in language identification. Of particular interest were language-specific differences in CE and CF word-initial stops. Experiment 1 consisted of an interlingual homophone production task. The purpose of this study was to examine how word-initial stop consonants differ in terms of acoustic properties in Canadian English (CE) and Canadian French (CF) interlingual homophones. The analyses from the bilingual speakers in Experiment 1 indicate that bilinguals do produce language-specific differences in CE and CF word-initial stops, and that closure duration, voice onset time, and burst spectral SD may provide cues to language identity in CE and CF stops. Experiment 2 consisted of a Phoneme and Language Categorization task. The purpose of this study was to examine how stop identity cues, such as VOT and closure duration, influence a listener to identify word-initial stop consonants as belonging to Canadian English (CE) or Canadian French (CF). The RTs from the bilingual listeners in this study indicate that bilinguals do perceive language-specific differences in CE and CF word-initial stops, and that voice onset time may provide cues to phoneme and language membership in CE and CF stops. Experiment 3 consisted of a Phonological-Semantic priming task. The purpose of this study was to examine how subphonetic variations, such as changes in the VOT, affect lexical access. The results of Experiment 3 suggest that language-specific cues, such as VOT, affects the composition of the bilingual cohort and that the extent to which English and/or French words are activated is dependent on the language-specific cues present in a word. The findings of this study enhanced our theoretical understanding of lexical structure and lexical access in bilingual speakers

  16. Ethnic identity, identity coherence, and psychological functioning: testing basic assumptions of the developmental model.

    PubMed

    Syed, Moin; Juang, Linda P

    2014-04-01

    The purpose of the present study was to test three fundamental theoretical propositions from Phinney's (1990) developmental model about the relations among ethnic identity, identity coherence, and psychological functioning: (a) ethnic identity is more strongly related to identity coherence for ethnic minorities than for Whites; (b) ethnic identity is more strongly related to psychological functioning for ethnic minorities than for Whites; and (c) identity coherence mediates the association between ethnic identity and psychological functioning for ethnic minorities, but not for Whites. These hypotheses were tested in three independent samples of ethnically diverse youth. In general, we found weak to moderate support for these three hypotheses, suggesting that the theoretically proposed differences in ethnic identity between ethnic minorities and Whites may not be supported by data. Implications for theory and measurement of ethnic identity are discussed.

  17. A&A Painting and Restoration Co., Inc. Information Sheet

    EPA Pesticide Factsheets

    A&A Painting and Restoration Co., Inc. (the Company) is located in Great Mills, Maryland. The settlement involves renovation activities conducted at properties constructed prior to 1978, located in Drayden, Maryland.

  18. Large-scale mapping of transposable element insertion sites using digital encoding of sample identity.

    PubMed

    Gohl, Daryl M; Freifeld, Limor; Silies, Marion; Hwa, Jennifer J; Horowitz, Mark; Clandinin, Thomas R

    2014-03-01

    Determining the genomic locations of transposable elements is a common experimental goal. When mapping large collections of transposon insertions, individualized amplification and sequencing is both time consuming and costly. We describe an approach in which large numbers of insertion lines can be simultaneously mapped in a single DNA sequencing reaction by using digital error-correcting codes to encode line identity in a unique set of barcoded pools.

  19. 40 CFR Table Aa-2 to Subpart Aa of... - Kraft Lime Kiln and Calciner Emissions Factors for CH4 and N2O

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Kraft Lime Kiln and Calciner Emissions... Manufacturing Pt. 98, Subpt. AA, Table AA -2 Table AA-2 to Subpart AA of Part 98—Kraft Lime Kiln and Calciner... CH4 N2O Kraft calciners CH4 N2O Residual Oil (any type) 0.0027 0 0.0027 0.0003 Distillate Oil...

  20. Section AA through main entrance gates & west stairs. San ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Section AA through main entrance gates & west stairs. San Bernardino Valley Union Junior College, Science Building. Also includes plans and sections of boys' and girls' toilets. Howard E. Jones, Architect, San Bernardino, California. Sheet 5, job no. 311. Scales 1/4 inch to the foot (section AA) and 1/2 inch to the foot (toilet rooms). February 15, 1927. - San Bernardino Valley College, Life Science Building, 701 South Mount Vernon Avenue, San Bernardino, San Bernardino County, CA

  1. Preventing and responding to medical identity theft.

    PubMed

    Amori, Geraldine

    2008-01-01

    Medical identity theft is a crime with two victims: patients and providers. It is easy to commit and lucrative because healthcare record keeping and business interactions are complex and mainly electronic. Patients whose identity has been stolen are vulnerable to both medical error and financial loss. Providers may suffer both reputation loss and financial loss. There are steps to help prevent and to respond appropriately to medical identity theft.

  2. Ethnic identity in everyday life: the influence of identity development status.

    PubMed

    Yip, Tiffany

    2014-01-01

    The current study explores the intersection of ethnic identity development and significance in a sample of 354 diverse adolescents (mean age 14). Adolescents completed surveys five times a day for 1 week. Cluster analyses revealed four identity clusters: diffused, foreclosed, moratorium, and achieved. Achieved adolescents reported the highest levels of identity salience across situations, followed by moratorium adolescents. Achieved and moratorium adolescents also reported a positive association between identity salience and private regard. For foreclosed and achieved adolescents reporting low levels of centrality, identity salience was associated with lower private regard. For foreclosed and achieved adolescents reporting high levels of centrality, identity salience was associated with higher private regard.

  3. Contrasting Sequence Groups by Emerging Sequences

    NASA Astrophysics Data System (ADS)

    Deng, Kang; Zaïane, Osmar R.

    Group comparison per se is a fundamental task in many scientific endeavours but is also the basis of any classifier. Contrast sets and emerging patterns contrast between groups of categorical data. Comparing groups of sequence data is a relevant task in many applications. We define Emerging Sequences (ESs) as subsequences that are frequent in sequences of one group and less frequent in the sequences of another, and thus distinguishing or contrasting sequences of different classes. There are two challenges to distinguish sequence classes: the extraction of ESs is not trivially efficient and only exact matches of sequences are considered. In our work we address those problems by a suffix tree-based framework and a similar matching mechanism. We propose a classifier based on Emerging Sequences. Evaluating against two learning algorithms based on frequent subsequences and exact matching subsequences, the experiments on two datasets show that our model outperforms the baseline approaches by up to 20% in prediction accuracy.

  4. Identity theory and personality theory: mutual relevance.

    PubMed

    Stryker, Sheldon

    2007-12-01

    Some personality psychologists have found a structural symbolic interactionist frame and identity theory relevant to their work. This frame and theory, developed in sociology, are first reviewed. Emphasized in the review are a multiple identity conception of self, identities as internalized expectations derived from roles embedded in organized networks of social interaction, and a view of social structures as facilitators in bringing people into networks or constraints in keeping them out, subsequently, attention turns to a discussion of the mutual relevance of structural symbolic interactionism/identity theory and personality theory, looking to extensions of the current literature on these topics.

  5. Smoker Identity Development among Adolescents who Smoke

    PubMed Central

    Hertel, Andrew W.; Mermelstein, Robin J.

    2016-01-01

    Adolescents who smoke are more likely to escalate their smoking frequency if they believe smoking is self-defining. Knowing factors that are associated with development of a smoker identity among adolescents who smoke may help to identify who will become a regular smoker. We investigated whether smoker identity development is associated with internal and external motives for smoking. For comparison, we also investigated whether social smoker identity development is associated with internal and external motives for smoking. Adolescents who smoke (n = 292) completed measures of smoker and social smoker identity, internal motives for smoking (negative affect coping, positive affect enhancement), and external motives for smoking (social fit) at baseline, 6-, 15-, and 24-month assessments of an ongoing longitudinal study of smoking patterns. We examined whether change in smoker and social smoker identity from 6 to 24 months was associated with change in motives at earlier assessment waves. We also explored whether gender moderated these relationships. Increases in negative affect coping motives were associated with smoker identity development among both males and females. Increases in social motives were associated with smoker identity development among males, and increases in negative affect coping motives were associated with social smoker identity development among females. Smoker and social smoker identities are signaled by negative affect coping as well as social motives for smoking. PMID:27136374

  6. An existentialist account of identity formation.

    PubMed

    Bilsker, D

    1992-06-01

    An account of James Marcia's identity formation model is given in the language of existentialist philosophy. Parallels between ego-identity and existentialist approaches are examined and identity is described in terms of existentialist concepts formulated by Martin Heidegger (Being and Time) and Jean-Paul Sartre (Being and Nothingness). While identity formation has previously been formulated in terms of ego-analytic theory, this paper argues and seeks to demonstrate that significant benefits accrue from an existentialist account. These benefits include clarification of difficult theoretical issues, delineation of specific research directions and enrichment of clinical understanding.

  7. Smoker identity development among adolescents who smoke.

    PubMed

    Hertel, Andrew W; Mermelstein, Robin J

    2016-06-01

    Adolescents who smoke are more likely to escalate their smoking frequency if they believe smoking is self-defining. Knowing factors that are associated with development of a smoker identity among adolescents who smoke may help to identify who will become a regular smoker. We investigated whether smoker identity development is associated with internal and external motives for smoking. For comparison, we also investigated whether social smoker identity development is associated with internal and external motives for smoking. Adolescents who smoke (n = 292) completed measures of smoker and social smoker identity, internal motives for smoking (negative affect coping, positive affect enhancement), and external motives for smoking (social fit) at baseline, 6-, 15-, and 24-month assessments of an ongoing longitudinal study of smoking patterns. We examined whether change in smoker and social smoker identity from 6 to 24 months was associated with change in motives at earlier assessment waves. We also explored whether gender moderated these relationships. Increases in negative affect coping motives were associated with smoker identity development among both males and females. Increases in social motives were associated with smoker identity development among males, and increases in negative affect coping motives were associated with social smoker identity development among females. Smoker and social smoker identities are signaled by negative affect coping as well as social motives for smoking. (PsycINFO Database Record

  8. Genome sequence and characterization of a new virus infecting Mikania micrantha H.B.K.

    PubMed

    Wang, Rui-Long; Ding, Ling-Wen; Sun, Qiao-Yang; Li, Jing; Xu, Zeng-Fu; Peng, Shao-Lin

    2008-01-01

    The complete RNA genomic sequence of a new virus infecting Mikania micrantha, designated as Mikania micrantha wilt virus (MMWV), has been determined. The genomic sequence and the predicted gene products of MMWV were similar to those of the other viruses of the genus Fabavirus. The MMWV nucleotide sequence showed 75.6% identity to that of gentian mosaic virus, 56.6 and 57% identity to those of two Broad bean wilt virus 1 isolates, and between 55.7 and 58% identity to those of seven Broad bean wilt virus 2 isolates. Our results suggested that MMWV represents a distinct isolate of the candidate species Gentian mosaic virus.

  9. Shotgun protein sequencing.

    SciTech Connect

    Faulon, Jean-Loup Michel; Heffelfinger, Grant S.

    2009-06-01

    A novel experimental and computational technique based on multiple enzymatic digestion of a protein or protein mixture that reconstructs protein sequences from sequences of overlapping peptides is described in this SAND report. This approach, analogous to shotgun sequencing of DNA, is to be used to sequence alternative spliced proteins, to identify post-translational modifications, and to sequence genetically engineered proteins.

  10. Complete Genome Sequence of Southern tomato virus Naturally Infecting Tomatoes in Bangladesh

    PubMed Central

    Padmanabhan, Chellappan; Zheng, Yi; Li, Rugang; Fei, Zhangjun

    2015-01-01

    The complete genome sequence of a Southern tomato virus (STV) isolate on tomato plants in a seed production field in Bangladesh was obtained for the first time using next-generation sequencing. The identified isolate, STV_BD-13, shares a high degree of sequence identity (99%) with several known STV isolates worldwide. PMID:26722014

  11. First complete genome sequence of an emerging cucumber green mottle mosaic virus isolate in North America

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The complete genome sequence (6,423 nt) of an emerging Cucumber green mottle mosaic virus (CGMMV) isolate on cucumber in North America was determined through deep sequencing of sRNA and rapid amplification of cDNA ends. It shares 99% nucleotide sequence identity to the Asian genotype, but only 90% t...

  12. Complete Genome Sequence of Seneca Valley Virus CH-01-2015 Identified in China.

    PubMed

    Wu, Qiwen; Zhao, Xiaoya; Chen, Yanshan; He, Xiaoming; Zhang, Guanqun; Ma, Jingyun

    2016-01-21

    The complete genome sequence of Seneca Valley virus (SVV), a single-stranded RNA virus that causes porcine vesicular disease in China, has been sequenced and analyzed. This Chinese isolate shares 94.4 to 97.1% sequence identity to another 8 strains from Canada, Brazil, and the United States. This is the first report of SVV infecting swine in China.

  13. Complete Genome Sequence of a Tomato-Infecting Tomato Mottle Mosaic Virus in New York

    PubMed Central

    Padmanabhan, Chellappan; Zheng, Yi; Li, Rugang; Martin, Gregory B.; Fei, Zhangjun

    2015-01-01

    The complete genome sequence of an isolate of tomato mottle mosaic virus (ToMMV) infecting tomatoes in New York was obtained using small RNA (sRNA) deep sequencing. ToMMV_NY-13 shared 99% sequence identity with isolates from Mexico and Florida. Broader distribution of this emerging virus is a cause for concern to the tomato industry. PMID:26701086

  14. Complete Genome Sequence of a Tomato Isolate of Parietaria Mottle Virus from Italy.

    PubMed

    Martínez, Carolina; Aramburu, José; Rubio, Luis; Galipienso, Luis

    2015-12-17

    We report here the complete genome sequence of isolate T32 of parietaria mottle virus (PMoV) infecting tomato plants in Turin, Italy, obtained by Sanger sequencing. T32 shares 90.48 to 96.69% nucleotide identity with other two PoMV isolates, CR8 and Pe1, respectively, whose complete genome sequences are available.

  15. Complete Genome Sequence of a Tomato Isolate of Parietaria Mottle Virus from Italy

    PubMed Central

    Martínez, Carolina; Aramburu, José; Rubio, Luis

    2015-01-01

    We report here the complete genome sequence of isolate T32 of parietaria mottle virus (PMoV) infecting tomato plants in Turin, Italy, obtained by Sanger sequencing. T32 shares 90.48 to 96.69% nucleotide identity with other two PoMV isolates, CR8 and Pe1, respectively, whose complete genome sequences are available. PMID:26679580

  16. Complete genome sequence of a novel genotype of squash mosaic virus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complete genome sequence of a novel genotype of Squash mosaic virus (SqMV) infecting squash plants in Spain was obtained using deep sequencing of small ribonucleic acids and assembly. The low nucleotide sequence identities, with 87-88% on RNA1 and 84-86% on RNA2 to known SqMV isolates, suggest a new...

  17. Resolving the database sequence discrepancies for the Staphylococcus aureus bacteriophage phi 11 amidase.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    There are two conflicting primary nucleotide sequences of the Staphylococcus aureus bacteriophage '11 amidase gene in public databases. Nucleotide sequence differences as well as alternative translational start site assignments result in three non-identical protein sequence predictions in Genbank f...

  18. Complete genome sequence of a tomato infecting tomato mottle mosaic virus in New York

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complete genome sequence of an emerging isolate of tomato mottle mosaic virus (ToMMV) infecting experimental nicotianan benthamiana plants in up-state New York was obtained using small RNA deep sequencing. ToMMV_NY-13 shared 99% sequence identity to ToMMV isolates from Mexico and Florida. Broader d...

  19. Complete genome sequence of Bacillus thuringiensis YBT-1518, a typical strain with high toxicity to nematodes.

    PubMed

    Wang, Pengxia; Zhang, Chunyi; Guo, Mengmeng; Guo, Suxia; Zhu, Yiguang; Zheng, Jinshui; Zhu, Lei; Ruan, Lifang; Peng, Donghai; Sun, Ming

    2014-02-10

    Bacillus thuringiensis is a ubiquitous spore-forming bacterium and has been widely used as a biopesticide for controlling agricultural insects by the production of insecticidal crystal proteins (ICPs). B. thuringiensis YBT-1518 displays effective toxicity to nematodes. This strain harbors three nematicidal crystal protein genes, including cry55Aa1, cry6Aa2 and cry5Ba2, and also contains multiple potential virulence factors. Here, we report the complete genome sequence of B. thuringiensis YBT-1518, which consists of one circular chromosome and six circular plasmids.

  20. Non-virulence of a recombinant shrimp nidovirus is associated with its non structural gene sequence and not a large structural gene deletion

    SciTech Connect

    Gangnonngiw, Warachin; Anantasomboon, Gun; Sang-oum, Wiwat; Sriurairatana, Siriporn; Sritunyalucksana, Kallaya; Flegel, Timothy W.

    2009-03-01

    RT-PCR using a commercial kit for yellow head virus (YHV) detection in growth-retarded shrimp yielded an unusual 777 bp amplicon instead of expected amplicons of 277 bp for YHV type-1 (YHV-1) or 406 bp for YHV type-2 (YHV-2). Cloning and sequencing (GenBank (EU170438)) revealed approximately 80% identity to non-structural (NS) ORF1b sequences of both YHV-1 (GenBank (AA083987)) and YHV-2 (GenBank (AF227196)), indicating an atypical YHV type (A-YHV) phylogenetically equidistant from both types. An RT-PCR test specifically designed for A-YHV revealed that it was uncommon and that its occurrence in shrimp culture ponds did not correlate with growth retardation or mortality. By immunohistochemistry with YHV-specific monoclonal antibodies, the A-YHV gave positive reactions for envelope protein gp64 and capsid protein p20, but not for envelope protein gp116, even though gp116 and gp64 originate from a polyprotein of ORF3. Lack of gp116 immunoreactivity correlated with a large ORF3 deletion (GenBank (EU123854)) in the region of the protein targeted by an MAb against gp116. Transmission electron microscopy of A-YHV-infected shrimp revealed only unenveloped pre-virions. During manuscript revision, information received revealed that typing of YHV isolates based on sequences of ORF1b and ORF3 had yielded several geographical types, including one virulent type (YHV-1b) with an ORF3 deletion sequence that matched the sequence of A-YHV. Using these sequences and an additional A-YHV sequence ( (EU853170)) from the ORF1b typing region, A-YHV potentially represents a recombinant between type 1b and type 5. SDS-PAGE and Western blot analysis revealed that type 1b produced a gp116 deletion protein that did not bind with the MAb or polyclonal Ab to normal gp116. Overall, the information suggested that lack of A-YHV virulence was associated with the NS gene sequence linked to ORF1b rather than the deletion in ORF3.

  1. Temporal identity in axonal target layer recognition.

    PubMed

    Petrovic, Milan; Hummel, Thomas

    2008-12-11

    The segregation of axon and dendrite projections into distinct synaptic layers is a fundamental principle of nervous system organization and the structural basis for information processing in the brain. Layer-specific recognition molecules that allow projecting neurons to stabilize transient contacts and initiate synaptogenesis have been identified. However, most of the neuronal cell-surface molecules critical for layer organization are expressed broadly in the developing nervous system, raising the question of how these so-called permissive adhesion molecules support synaptic specificity. Here we show that the temporal expression dynamics of the zinc-finger protein sequoia is the major determinant of Drosophila photoreceptor connectivity into distinct synaptic layers. Neighbouring R8 and R7 photoreceptors show consecutive peaks of elevated sequoia expression, which correspond to their sequential target-layer innervation. Loss of sequoia in R7 leads to a projection switch into the R8 recipient layer, whereas a prolonged expression in R8 induces a redirection of their axons into the R7 layer. The sequoia-induced axon targeting is mediated through the ubiquitously expressed Cadherin-N cell adhesion molecule. Our data support a model in which recognition specificity during synaptic layer formation is generated through a temporally restricted axonal competence to respond to broadly expressed adhesion molecules. Because developing neurons innervating the same target area often project in a distinct, birth-order-dependent sequence, temporal identity seems to contain crucial information in generating not only cell type diversity during neuronal division but also connection diversity of projecting neurons.

  2. Comparison of RNAi Sequences in Insect-Resistant Plants to Expressed Sequences of a Beneficial Lady Beetle: A Closer Look at Off-Target Considerations

    PubMed Central

    Allen, Margaret L.

    2017-01-01

    Sequences obtained from transcriptomes of the lady beetle Coleomegilla maculata were compared to those designed for incorporation into crops. Searches of the transcriptomes identified sequences as the most likely to be closely similar to the sequences described in RNAi plant incorporated products. Some proposed prime RNAi pest management targets were also used to identify predicted orthologs from C. maculata. The lady beetle sequences were aligned with sequences from corn rootworms and Colorado potato beetles and, as appropriate in the case of targets, regions of similarity were compared with the genetic model organism for beetles, Tribolium castaneum. Some high levels of nucleotide identity were identified, particularly with an actin-derived sequence from Colorado potato beetle. This actin-derived sequence shared identical sequences with the lady beetle and a parasitic wasp. PMID:28257058

  3. Comparison of RNAi Sequences in Insect-Resistant Plants to Expressed Sequences of a Beneficial Lady Beetle: A Closer Look at Off-Target Considerations.

    PubMed

    Allen, Margaret L

    2017-03-01

    Sequences obtained from transcriptomes of the lady beetle Coleomegilla maculata were compared to those designed for incorporation into crops. Searches of the transcriptomes identified sequences as the most likely to be closely similar to the sequences described in RNAi plant incorporated products. Some proposed prime RNAi pest management targets were also used to identify predicted orthologs from C. maculata. The lady beetle sequences were aligned with sequences from corn rootworms and Colorado potato beetles and, as appropriate in the case of targets, regions of similarity were compared with the genetic model organism for beetles, Tribolium castaneum. Some high levels of nucleotide identity were identified, particularly with an actin-derived sequence from Colorado potato beetle. This actin-derived sequence shared identical sequences with the lady beetle and a parasitic wasp.

  4. The sequence of sequencers: The history of sequencing DNA

    PubMed Central

    Heather, James M.; Chain, Benjamin

    2016-01-01

    Determining the order of nucleic acid residues in biological samples is an integral component of a wide variety of research applications. Over the last fifty years large numbers of researchers have applied themselves to the production of techniques and technologies to facilitate this feat, sequencing DNA and RNA molecules. This time-scale has witnessed tremendous changes, moving from sequencing short oligonucleotides to millions of bases, from struggling towards the deduction of the coding sequence of a single gene to rapid and widely available whole genome sequencing. This article traverses those years, iterating through the different generations of sequencing technology, highlighting some of the key discoveries, researchers, and sequences along the way. PMID:26554401

  5. Fecal transmission of AA amyloidosis in the cheetah contributes to high incidence of disease.

    PubMed

    Zhang, Beiru; Une, Yumi; Fu, Xiaoying; Yan, Jingmin; Ge, FengXia; Yao, Junjie; Sawashita, Jinko; Mori, Masayuki; Tomozawa, Hiroshi; Kametani, Fuyuki; Higuchi, Keiichi

    2008-05-20

    AA amyloidosis is one of the principal causes of morbidity and mortality in captive cheetahs (Acinonyx jubatus), which are in danger of extinction, but little is known about the underlying mechanisms. Given the transmissible characteristics of AA amyloidosis, transmission between captive cheetahs may be a possible mechanism involved in the high incidence of AA amyloidosis. In this study of animals with AA amyloidosis, we found that cheetah feces contained AA amyloid fibrils that were different from those of the liver with regard to molecular weight and shape and had greater transmissibility. The infectious activity of fecal AA amyloid fibrils was reduced or abolished by the protein denaturants 6 M guanidine.HCl and formic acid or by AA immunodepletion. Thus, we propose that feces are a vehicle of transmission that may accelerate AA amyloidosis in captive cheetah populations. These results provide a pathogenesis for AA amyloidosis and suggest possible measures for rescuing cheetahs from extinction.

  6. In silico detection of tRNA sequence features characteristic to aminoacyl-tRNA synthetase class membership

    PubMed Central

    Jakó, Éena; Ittzés, Péter; Szenes, Áron; Kun, Ádám; Szathmáry, Eörs; Pál, Gábor

    2007-01-01

    Aminoacyl tRNA synthetases (aaRS) are grouped into Class I and II based on primary and tertiary structure and enzyme properties suggesting two independent phylogenetic lineages. Analogously, tRNA molecules can also form two respective classes, based on the class membership of their corresponding aaRS. Although some aaRS–tRNA interactions are not extremely specific and require editing mechanisms to avoid misaminoacylation, most aaRS–tRNA interactions are rather stereospecific. Thus, class-specific aaRS features could be mirrored by class-specific tRNA features. However, previous investigations failed to detect conserved class-specific nucleotides. Here we introduce a discrete mathematical approach that evaluates not only class-specific ‘strictly present’, but also ‘strictly absent’ nucleotides. The disjoint subsets of these elements compose a unique partition, named extended consensus partition (ECP). By analyzing the ECP for both Class I and II tDNA sets from 50 (13 archaeal, 30 bacterial and 7 eukaryotic) species, we could demonstrate that class-specific tRNA sequence features do exist, although not in terms of strictly conserved nucleotides as it had previously been anticipated. This finding demonstrates that important information was hidden in tRNA sequences inaccessible for traditional statistical methods. The ECP analysis might contribute to the understanding of tRNA evolution and could enrich the sequence analysis tool repertoire. PMID:17704131

  7. Molecular characterization of subgenotype A1 (subgroup Aa) of hepatitis B virus.

    PubMed

    Kramvis, Anna; Kew, Michael C

    2007-07-01

    Subgenotypes of hepatitis B virus (HBV) were first recognized after a unique segment of genotype A was identified when sequencing the preS2/S region of southern African HBV isolates. Originally named subgroup A', subsequently called subgroup Aa (for Africa) or subgenotype A1, this subgenotype is found in South Africa, Malawi, Uganda, Tanzania, Somalia, Yemen, India, Nepal, the Philippines and Brazil. The relatively higher mean nucleotide divergence of subgenotype A1 suggests that it has been endemic and has a long evolutionary history in the populations where it prevails. Distinctive sequence characteristics could account for the high hepatitis B e-antigen (HBeAg) negativity and low HBV DNA levels in carriers of this subgenotype. Substitutions or mutations can reduce HBeAg expression at three levels: (i) 1762T1764A atthe transcriptional level; (ii) substitutions at nt 1809-1812 at the translational level; and (iii) 1862T at the post-translational level. Co-existence of 1762T1764A and nt 1809-1812 mutations reduces HBeAg expression in an additive manner. In addition, subgenotype A1 has unique sequence alterations in the transcriptional regulatory elements and the polymerase coding region. The distinct sequence characteristics of subgenotype A1 may contribute to the 4.5-fold increased risk of heptocellular carcinoma in HBV carriers infected with genotype A, which is entirely attributable to subgenotype A1.

  8. Optimization of identity operation in NMR spectroscopy via genetic algorithm: Application to the TEDOR experiment

    NASA Astrophysics Data System (ADS)

    Manu, V. S.; Veglia, Gianluigi

    2016-12-01

    Identity operation in the form of π pulses is widely used in NMR spectroscopy. For an isolated single spin system, a sequence of even number of π pulses performs an identity operation, leaving the spin state essentially unaltered. For multi-spin systems, trains of π pulses with appropriate phases and time delays modulate the spin Hamiltonian to perform operations such as decoupling and recoupling. However, experimental imperfections often jeopardize the outcome, leading to severe losses in sensitivity. Here, we demonstrate that a newly designed Genetic Algorithm (GA) is able to optimize a train of π pulses, resulting in a robust identity operation. As proof-of-concept, we optimized the recoupling sequence in the transferred-echo double-resonance (TEDOR) pulse sequence, a key experiment in biological magic angle spinning (MAS) solid-state NMR for measuring multiple carbon-nitrogen distances. The GA modified TEDOR (GMO-TEDOR) experiment with improved recoupling efficiency results in a net gain of sensitivity up to 28% as tested on a uniformly 13C, 15N labeled microcrystalline ubiquitin sample. The robust identity operation achieved via GA paves the way for the optimization of several other pulse sequences used for both solid- and liquid-state NMR used for decoupling, recoupling, and relaxation experiments.

  9. Native Speaker and Nonnative Speaker Identities in Repair Practices of English Conversation

    ERIC Educational Resources Information Center

    Bae, Eun Young; Oh, Sun-Young

    2013-01-01

    Within the theoretical and methodological framework of Conversation Analysis, the present study explores the nature of the native speaker (NS) and nonnative speaker (NNS) identities in repair practices of English conversation. It has identified and analyzed in detail repair sequences in the data and has also conducted quantitative analyses in…

  10. Dissociative identity disorder: Medicolegal challenges.

    PubMed

    Farrell, Helen M

    2011-01-01

    Persons with dissociative identity disorder (DID) often present in the criminal justice system rather than the mental health system and perplex experts in both professions. DID is a controversial diagnosis with important medicolegal implications. Defendants have claimed that they committed serious crimes, including rape or murder, while they were in a dissociated state. Asserting that their alter personality committed the bad act, defendants have pleaded not guilty by reason of insanity (NGRI). In such instances, forensic experts are asked to assess the defendant for DID and provide testimony in court. Debate continues over whether DID truly exists, whether expert testimony should be allowed into evidence, and whether it should exculpate defendants for their criminal acts. This article reviews historical and theoretical perspectives on DID, presents cases that illustrate the legal implications and controversies of raising an insanity defense based on multiple personalities, and examines the role of forensic experts asked to comment on DID with the goal of assisting clinicians in the medicolegal assessment of DID in relation to crimes.

  11. Fingerprint recognition with identical twin fingerprints.

    PubMed

    Tao, Xunqiang; Chen, Xinjian; Yang, Xin; Tian, Jie

    2012-01-01

    Fingerprint recognition with identical twins is a challenging task due to the closest genetics-based relationship existing in the identical twins. Several pioneers have analyzed the similarity between twins' fingerprints. In this work we continue to investigate the topic of the similarity of identical twin fingerprints. Our study was tested based on a large identical twin fingerprint database that contains 83 twin pairs, 4 fingers per individual and six impressions per finger: 3984 (83*2*4*6) images. Compared to the previous work, our contributions are summarized as follows: (1) Two state-of-the-art fingerprint identification methods: P071 and VeriFinger 6.1 were used, rather than one fingerprint identification method in previous studies. (2) Six impressions per finger were captured, rather than just one impression, which makes the genuine distribution of matching scores more realistic. (3) A larger sample (83 pairs) was collected. (4) A novel statistical analysis, which aims at showing the probability distribution of the fingerprint types for the corresponding fingers of identical twins which have same fingerprint type, has been conducted. (5) A novel analysis, which aims at showing which finger from identical twins has higher probability of having same fingerprint type, has been conducted. Our results showed that: (a) A state-of-the-art automatic fingerprint verification system can distinguish identical twins without drastic degradation in performance. (b) The chance that the fingerprints have the same type from identical twins is 0.7440, comparing to 0.3215 from non-identical twins. (c) For the corresponding fingers of identical twins which have same fingerprint type, the probability distribution of five major fingerprint types is similar to the probability distribution for all the fingers' fingerprint type. (d) For each of four fingers of identical twins, the probability of having same fingerprint type is similar.

  12. Characterization of the radical-scavenging reaction of 2-O-substituted ascorbic acid derivatives, AA-2G, AA-2P, and AA-2S: a kinetic and stoichiometric study.

    PubMed

    Takebayashi, Jun; Tai, Akihiro; Gohda, Eiichi; Yamamoto, Itaru

    2006-04-01

    The aim of this study was to characterize the antioxidant activity of three ascorbic acid (AA) derivatives O-substituted at the C-2 position of AA: ascorbic acid 2-glucoside (AA-2G), ascorbic acid 2-phosphate (AA-2P), and ascorbic acid 2-sulfate (AA-2S). The radical-scavenging activities of these AA derivatives and some common low molecular-weight antioxidants such as uric acid or glutathione against 1,1-diphenyl-picrylhydrazyl (DPPH) radical, 2,2'-azinobis(3-ethylbenzothiazoline-6-sulfonic acid) radical cation (ABTS+), or galvinoxyl radical were kinetically and stoichiometrically evaluated under pH-controlled conditions. Those AA derivatives slowly and continuously reacted with DPPH radical and ABTS+, but not with galvinoxyl radical. They effectively reacted with DPPH radical under acidic conditions and with ABTS+ under neutral conditions. In contrast, AA immediately quenched all species of radicals tested at all pH values investigated. The reactivity of Trolox, a water-soluble vitamin E analogue, was comparable to that of AA in terms of kinetics and stoichiometrics. Uric acid and glutathione exhibited long-lasting radical-scavenging activity against these radicals under certain pH conditions. The radical-scavenging profiles of AA derivatives were closer to those of uric acid and glutathione rather than to that of AA. The number of radicals scavenged by one molecule of AA derivatives, uric acid, or glutathione was equal to or greater than that by AA or Trolox under the appropriate conditions. These data suggest the potential usage of AA derivatives as radical scavengers.

  13. Multimodal sequence learning.

    PubMed

    Kemény, Ferenc; Meier, Beat

    2016-02-01

    While sequence learning research models complex phenomena, previous studies have mostly focused on unimodal sequences. The goal of the current experiment is to put implicit sequence learning into a multimodal context: to test whether it can operate across different modalities. We used the Task Sequence Learning paradigm to test whether sequence learning varies across modalities, and whether participants are able to learn multimodal sequences. Our results show that implicit sequence learning is very similar regardless of the source modality. However, the presence of correlated task and response sequences was required for learning to take place. The experiment provides new evidence for implicit sequence learning of abstract conceptual representations. In general, the results suggest that correlated sequences are necessary for implicit sequence learning to occur. Moreover, they show that elements from different modalities can be automatically integrated into one unitary multimodal sequence.

  14. Recrystallization behaviour of AA6063 extrusions

    NASA Astrophysics Data System (ADS)

    Zhang, K.; Pettersen, T.; Paulsen, C. O.; Marthinsen, K.; Holmedal, B.; Segatori, A.

    2015-08-01

    Cylindrical profiles of an AA6063 aluminium alloy were produced in a lab-scale direct extrusion set-up. The extrusion was performed at 300 °C, 450 °C and 550 °C, respectively, with the same ram speed. Immediate water quenching was applied to the profiles and the end of billet (butt-end) after extrusion. Microstructure and texture of the material in different states were measured by electron back-scattered diffraction. Only the profile extruded at 300 °C, was found in the deformed state after extrusion, featuring a fibrous grain structure and a strong <111> and weak <100> double fibre texture. Post-extrusion annealing of this profile at 450 °C resulted in an almost fully recrystallized structure (recrystallized fraction of 87%) and with a texture similar to that of the as-deformed state. The profile extruded at 450 °C was almost fully recrystallized (recrystallization fraction 91%) already after quenching, and with a texture characterized by a weak <111> and strong <100> double fibre. The profile extruded at 550 °C showed a partially recrystallized grain structure with recrystallization fraction of 71%, and with a texture dominated by a <100> fibre. The influence of the deformation conditions on the recrystallization behaviour, in terms of recrystallization kinetics and mechanisms, are discussed in view of these results.

  15. Coordinate cytokine regulatory sequences

    DOEpatents

    Frazer, Kelly A.; Rubin, Edward M.; Loots, Gabriela G.

    2005-05-10

    The present invention provides CNS sequences that regulate the cytokine gene expression, expression cassettes and vectors comprising or lacking the CNS sequences, host cells and non-human transgenic animals comprising the CNS sequences or lacking the CNS sequences. The present invention also provides methods for identifying compounds that modulate the functions of CNS sequences as well as methods for diagnosing defects in the CNS sequences of patients.

  16. Identity, Language Learning, and Social Change

    ERIC Educational Resources Information Center

    Norton, Bonny; Toohey, Kelleen

    2011-01-01

    In this review article on identity, language learning, and social change, we argue that contemporary poststructuralist theories of language, identity, and power offer new perspectives on language learning and teaching, and have been of considerable interest in our field. We first review poststructuralist theories of language, subjectivity, and…

  17. I Alumnus: Understanding Early Alumni Identity

    ERIC Educational Resources Information Center

    Pung, Barnaby

    2013-01-01

    This dissertation sought to provide a better understanding of early alumnus identity at a public Midwestern university. Unlike a majority of alumni studies, this study used a qualitative case study methodology to examine alumni identity among participants through the use of personal interviews. Participants were 10-11 years post graduation from…

  18. 40 CFR 725.85 - Microorganism identity.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Microorganism identity. 725.85 Section... ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS Confidentiality and Public Access to Information § 725.85 Microorganism identity. (a) Claims applicable to the period prior...

  19. 40 CFR 725.85 - Microorganism identity.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Microorganism identity. 725.85 Section... ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS Confidentiality and Public Access to Information § 725.85 Microorganism identity. (a) Claims applicable to the period prior...

  20. 40 CFR 725.85 - Microorganism identity.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Microorganism identity. 725.85 Section... ACT REPORTING REQUIREMENTS AND REVIEW PROCESSES FOR MICROORGANISMS Confidentiality and Public Access to Information § 725.85 Microorganism identity. (a) Claims applicable to the period prior...