Transposable elements in Drosophila

PubMed Central

McCullers, Tabitha J.; Steiniger, Mindy

2017-01-01

ABSTRACT Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster. PMID:28580197

Generation of Tandem Direct Duplications by Reversed-Ends Transposition of Maize Ac Elements

PubMed Central

Peterson, Thomas

2013-01-01

Tandem direct duplications are a common feature of the genomes of eukaryotes ranging from yeast to human, where they comprise a significant fraction of copy number variations. The prevailing model for the formation of tandem direct duplications is non-allelic homologous recombination (NAHR). Here we report the isolation of a series of duplications and reciprocal deletions isolated de novo from a maize allele containing two Class II Ac/Ds transposons. The duplication/deletion structures suggest that they were generated by alternative transposition reactions involving the termini of two nearby transposable elements. The deletion/duplication breakpoint junctions contain 8 bp target site duplications characteristic of Ac/Ds transposition events, confirming their formation directly by an alternative transposition mechanism. Tandem direct duplications and reciprocal deletions were generated at a relatively high frequency (∼0.5 to 1%) in the materials examined here in which transposons are positioned nearby each other in appropriate orientation; frequencies would likely be much lower in other genotypes. To test whether this mechanism may have contributed to maize genome evolution, we analyzed sequences flanking Ac/Ds and other hAT family transposons and identified three small tandem direct duplications with the structural features predicted by the alternative transposition mechanism. Together these results show that some class II transposons are capable of directly inducing tandem sequence duplications, and that this activity has contributed to the evolution of the maize genome. PMID:23966872

Interspecific hybridization as a genomic stressor inducing mobilization of transposable elements in Drosophila

PubMed Central

Guerreiro, Maria Pilar García

2014-01-01

Transposable elements (TEs) are DNA sequences able to be mobilized in host genomes. They are currently recognized as the major mutation inducers because of their insertion in the target, their effect on neighboring regions, or their ectopic recombination. A large number of factors including chemical and physical factors as well as intraspecific crosses have traditionally been identified as inducers of transposition. Besides environmental factors, interspecific crosses have also been proposed as promoters of transposition of particular TEs in plants and different animals. Our previous published work includes a genome-wide survey with the set of genomic TEs and shows that interspecific hybridization between the species Drosophila buzzatii and Drosophila koepferae induces genomic instability by transposition bursts. A high percentage of this instability corresponds to TEs belonging to classes I and II. The detailed study of three TEs (Osvaldo, Helena, and Galileo), representative of the different TE families, shows an increase of transposition in hybrids compared with parental species, that varies depending on the element. This study suggests ample variation in TE regulation mechanisms and the question is why this variation occurs. Interspecific hybridization is a genomic stressor that disrupts the stability of TEs probably contributing to a relaxation of the mechanisms controlling TEs in the Drosophila genome. In this commentary paper we will discuss these results and the molecular mechanisms that could explain these increases of transposition rates observed in interspecific Drosophila hybrids. PMID:25136509

The Evolution of Tyrosine-Recombinase Elements in Nematoda

PubMed Central

Szitenberg, Amir; Koutsovoulos, Georgios; Blaxter, Mark L.; Lunt, David H.

2014-01-01

Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1-like elements were found to be a derived form of another Pat1-like element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum. PMID:25197791

The evolution of tyrosine-recombinase elements in Nematoda.

PubMed

Szitenberg, Amir; Koutsovoulos, Georgios; Blaxter, Mark L; Lunt, David H

2014-01-01

Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1-like elements were found to be a derived form of another Pat1-like element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum.

Dynamics and Differential Proliferation of Transposable Elements During the Evolution of the B and A Genomes of Wheat

PubMed Central

Charles, Mathieu; Belcram, Harry; Just, Jérémy; Huneau, Cécile; Viollet, Agnès; Couloux, Arnaud; Segurens, Béatrice; Carter, Meredith; Huteau, Virginie; Coriton, Olivier; Appels, Rudi; Samain, Sylvie; Chalhoub, Boulos

2008-01-01

Transposable elements (TEs) constitute >80% of the wheat genome but their dynamics and contribution to size variation and evolution of wheat genomes (Triticum and Aegilops species) remain unexplored. In this study, 10 genomic regions have been sequenced from wheat chromosome 3B and used to constitute, along with all publicly available genomic sequences of wheat, 1.98 Mb of sequence (from 13 BAC clones) of the wheat B genome and 3.63 Mb of sequence (from 19 BAC clones) of the wheat A genome. Analysis of TE sequence proportions (as percentages), ratios of complete to truncated copies, and estimation of insertion dates of class I retrotransposons showed that specific types of TEs have undergone waves of differential proliferation in the B and A genomes of wheat. While both genomes show similar rates and relatively ancient proliferation periods for the Athila retrotransposons, the Copia retrotransposons proliferated more recently in the A genome whereas Gypsy retrotransposon proliferation is more recent in the B genome. It was possible to estimate for the first time the proliferation periods of the abundant CACTA class II DNA transposons, relative to that of the three main retrotransposon superfamilies. Proliferation of these TEs started prior to and overlapped with that of the Athila retrotransposons in both genomes. However, they also proliferated during the same periods as Gypsy and Copia retrotransposons in the A genome, but not in the B genome. As estimated from their insertion dates and confirmed by PCR-based tracing analysis, the majority of differential proliferation of TEs in B and A genomes of wheat (87 and 83%, respectively), leading to rapid sequence divergence, occurred prior to the allotetraploidization event that brought them together in Triticum turgidum and Triticum aestivum, <0.5 million years ago. More importantly, the allotetraploidization event appears to have neither enhanced nor repressed retrotranspositions. We discuss the apparent proliferation of TEs as resulting from their insertion, removal, and/or combinations of both evolutionary forces. PMID:18780739

Transposable elements as genetic regulatory substrates in early development.

PubMed

Gifford, Wesley D; Pfaff, Samuel L; Macfarlan, Todd S

2013-05-01

The abundance and ancient origins of transposable elements (TEs) in eukaryotic genomes has spawned research into the potential symbiotic relationship between these elements and their hosts. In this review, we introduce the diversity of TEs, discuss how distinct classes are uniquely regulated in development, and describe how they appear to have been coopted for the purposes of gene regulation and the orchestration of a number of processes during early embryonic development. Although young, active TEs play an important role in somatic tissues and evolution, we focus mostly on the contributions of the older, fixed elements in mammalian genomes. We also discuss major challenges inherent in the study of TEs and contemplate future experimental approaches to further investigate how they coordinate developmental processes. Published by Elsevier Ltd.

Transposable elements as genetic regulatory substrates in early development

PubMed Central

Gifford, Wesley D.; Pfaff, Samuel L.; Macfarlan, Todd S.

2014-01-01

The abundance and ancient origins of transposable elements (TEs) in eukaryotic genomes has spawned research into the potential symbiotic relationship between these elements and their hosts. In this review, we introduce the diversity of TEs, discuss how distinct classes are uniquely regulated in development, and describe how they appear to have been coopted for the purposes of gene regulation and the orchestration of a number of processes during early embryonic development. Although young, active TEs play an important role in somatic tissues and evolution, we focus mostly on the contributions of the older, fixed elements in mammalian genomes. We also discuss major challenges inherent in the study of TEs and contemplate future experimental approaches to further investigate how they coordinate developmental processes. PMID:23411159

Genetic and DNA sequence analysis of the kanamycin resistance transposon Tn903.

PubMed Central

Grindley, N D; Joyce, C M

1980-01-01

The kanamycin resistance transposon Tn903 consists of a unique region of about 1000 base pairs bounded by a pair of 1050-base-pair inverted repeat sequences. Each repeat contains two Pvu II endonuclease cleavage sites separated by 520 base pairs. We have constructed derivatives of Tn903 in which this 520-base-pair fragment is deleted from one or both repeats. Those derivatives that lack both 520-base-pair fragments cannot transpose, whereas those that lack just one remain transposition proficient. One such transposable derivative, Tn903 delta I, has been selected for further study. We have determined the sequence of the intact inverted repeat. The 18 base pairs at each end are identical and inverted relative to one another, a structure characteristic of insertion sequences. Additional experiments indicate that a single inverted repeat from Tn903 can, in fact, transpose; we propose that this element be called IS903. To correlate the DNA sequence with genetic activities, we have created mutations by inserting a 10-base-pair DNA fragment at several sites within the intact repeat of Tn903 delta 1, and we have examined the effect of such insertions on transposability. The results suggest that IS903 encodes a 307-amino-acid polypeptide (a "transposase") that is absolutely required for transposition of IS903 or Tn903. Images PMID:6261245

The expanding universe of transposon technologies for gene and cell engineering.

PubMed

Ivics, Zoltán; Izsvák, Zsuzsanna

2010-12-07

Transposable elements can be viewed as natural DNA transfer vehicles that, similar to integrating viruses, are capable of efficient genomic insertion. The mobility of class II transposable elements (DNA transposons) can be controlled by conditionally providing the transposase component of the transposition reaction. Thus, a DNA of interest (be it a fluorescent marker, a small hairpin (sh)RNA expression cassette, a mutagenic gene trap or a therapeutic gene construct) cloned between the inverted repeat sequences of a transposon-based vector can be used for stable genomic insertion in a regulated and highly efficient manner. This methodological paradigm opened up a number of avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture, the production of germline transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species, and therapy of genetic disorders in humans. Sleeping Beauty (SB) was the first transposon shown to be capable of gene transfer in vertebrate cells, and recent results confirm that SB supports a full spectrum of genetic engineering including transgenesis, insertional mutagenesis, and therapeutic somatic gene transfer both ex vivo and in vivo. The first clinical application of the SB system will help to validate both the safety and efficacy of this approach. In this review, we describe the major transposon systems currently available (with special emphasis on SB), discuss the various parameters and considerations pertinent to their experimental use, and highlight the state of the art in transposon technology in diverse genetic applications.

Transposon based functional characterization of soybean genes

USDA-ARS?s Scientific Manuscript database

Type II transposable elements that use cut and paste mechanism for jumping from one genomic region to another is ideal in tagging and cloning genes. Precise excision from an insertion site in a mutant gene leads to regaining the wild-type function. Thus, function of a gene can be established based o...

The Tgm9-induced indexed insertional mutant collection to conduct community-based reverse genetics studies in soybean

USDA-ARS?s Scientific Manuscript database

Until now, functional analyses of soybean genes have been very arduous because of the lack of a rapid transformation procedure. Recently identified the active endogenous type II transposable element, Tgm9, excises from insertion sites and restores wild-type phenotypes. Thus, this element provides a ...

The processing of consonants and vowels during letter identity and letter position assignment in visual-word recognition: an ERP study.

PubMed

Vergara-Martínez, Marta; Perea, Manuel; Marín, Alejandro; Carreiras, Manuel

2011-09-01

Recent research suggests that there is a processing distinction between consonants and vowels in visual-word recognition. Here we conjointly examine the time course of consonants and vowels in processes of letter identity and letter position assignment. Event related potentials (ERPs) were recorded while participants read words and pseudowords in a lexical decision task. The stimuli were displayed under different conditions in a masked priming paradigm with a 50-ms SOA: (i) identity/baseline condition e.g., chocolate-CHOCOLATE); (ii) vowels-delayed condition (e.g., choc_l_te-CHOCOLATE); (iii) consonants-delayed condition (cho_o_ate-CHOCOLATE); (iv) consonants-transposed condition (cholocate-CHOCOLATE); (v) vowels-transposed condition (chocalote-CHOCOLATE), and (vi) unrelated condition (editorial-CHOCOLATE). Results showed earlier ERP effects and longer reaction times for the delayed-letter compared to the transposed-letter conditions. Furthermore, at early stages of processing, consonants may play a greater role during letter identity processing. Differences between vowels and consonants regarding letter position assignment are discussed in terms of a later phonological level involved in lexical retrieval. Copyright © 2010 Elsevier Inc. All rights reserved.

Evolutionary dynamics of hAT DNA transposon families in Saccharomycetaceae.

PubMed

Sarilar, Véronique; Bleykasten-Grosshans, Claudine; Neuvéglise, Cécile

2014-12-21

Transposable elements (TEs) are widespread in eukaryotes but uncommon in yeasts of the Saccharomycotina subphylum, in terms of both host species and genome fraction. The class II elements are especially scarce, but the hAT element Rover is a noteworthy exception that deserves further investigation. Here, we conducted a genome-wide analysis of hAT elements in 40 ascomycota. A novel family, Roamer, was found in three species, whereas Rover was detected in 15 preduplicated species from Kluyveromyces, Eremothecium, and Lachancea genera, with up to 41 copies per genome. Rover acquisition seems to have occurred by horizontal transfer in a common ancestor of these genera. The detection of remote Rover copies in Naumovozyma dairenensis and in the sole Saccharomyces cerevisiae strain AWRI1631, without synteny, suggests that two additional independent horizontal transfers took place toward these genomes. Such patchy distribution of elements prevents any anticipation of TE presence in incoming sequenced genomes, even closely related ones. The presence of both putative autonomous and defective Rover copies, as well as their diversification into five families, indicate particular dynamics of Rover elements in the Lachancea genus. Especially, we discovered the first miniature inverted-repeat transposable elements (MITEs) to be described in yeasts, together with their parental autonomous copies. Evidence of MITE insertion polymorphism among Lachancea waltii strains suggests their recent activity. Moreover, 40% of Rover copies appeared to be involved in chromosome rearrangements, showing the large structural impact of TEs on yeast genome and opening the door to further investigations to understand their functional and evolutionary consequences. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis

PubMed Central

2013-01-01

Background Galileo is a transposable element responsible for the generation of three chromosomal inversions in natural populations of Drosophila buzzatii. Although the most characteristic feature of Galileo is the long internally-repetitive terminal inverted repeats (TIRs), which resemble the Drosophila Foldback element, its transposase-coding sequence has led to its classification as a member of the P-element superfamily (Class II, subclass 1, TIR order). Furthermore, Galileo has a wide distribution in the genus Drosophila, since it has been found in 6 of the 12 Drosophila sequenced genomes. Among these species, D. mojavensis, the one closest to D. buzzatii, presented the highest diversity in sequence and structure of Galileo elements. Results In the present work, we carried out a thorough search and annotation of all the Galileo copies present in the D. mojavensis sequenced genome. In our set of 170 Galileo copies we have detected 5 Galileo subfamilies (C, D, E, F, and X) with different structures ranging from nearly complete, to only 2 TIR or solo TIR copies. Finally, we have explored the structural and length variation of the Galileo copies that point out the relatively frequent rearrangements within and between Galileo elements. Different mechanisms responsible for these rearrangements are discussed. Conclusions Although Galileo is a transposable element with an ancient history in the D. mojavensis genome, our data indicate a recent transpositional activity. Furthermore, the dynamism in sequence and structure, mainly affecting the TIRs, suggests an active exchange of sequences among the copies. This exchange could lead to new subfamilies of the transposon, which could be crucial for the long-term survival of the element in the genome. PMID:23374229

Transposable Elements as Stress Adaptive Capacitors Induce Genomic Instability in Fungal Pathogen Magnaporthe oryzae

PubMed Central

Chadha, Sonia; Sharma, Mradul

2014-01-01

A fundamental problem in fungal pathogenesis is to elucidate the evolutionary forces responsible for genomic rearrangements leading to races with fitter genotypes. Understanding the adaptive evolutionary mechanisms requires identification of genomic components and environmental factors reshaping the genome of fungal pathogens to adapt. Herein, Magnaporthe oryzae, a model fungal plant pathogen is used to demonstrate the impact of environmental cues on transposable elements (TE) based genome dynamics. For heat shock and copper stress exposed samples, eight TEs belonging to class I and II family were employed to obtain DNA profiles. Stress induced mutant bands showed a positive correlation with dose/duration of stress and provided evidences of TEs role in stress adaptiveness. Further, we demonstrate that genome dynamics differ for the type/family of TEs upon stress exposition and previous reports of stress induced MAGGY transposition has underestimated the role of TEs in M. oryzae. Here, we identified Pyret, MAGGY, Pot3, MINE, Mg-SINE, Grasshopper and MGLR3 as contributors of high genomic instability in M. oryzae in respective order. Sequencing of mutated bands led to the identification of LTR-retrotransposon sequences within regulatory regions of psuedogenes. DNA transposon Pot3 was identified in the coding regions of chromatin remodelling protein containing tyrosinase copper-binding and PWWP domains. LTR-retrotransposons Pyret and MAGGY are identified as key components responsible for the high genomic instability and perhaps these TEs are utilized by M. oryzae for its acclimatization to adverse environmental conditions. Our results demonstrate how common field stresses change genome dynamics of pathogen and provide perspective to explore the role of TEs in genome adaptability, signalling network and its impact on the virulence of fungal pathogens. PMID:24709911

Striking structural dynamism and nucleotide sequence variation of the transposon Galileo in the genome of Drosophila mojavensis.

PubMed

Marzo, Mar; Bello, Xabier; Puig, Marta; Maside, Xulio; Ruiz, Alfredo

2013-02-04

Galileo is a transposable element responsible for the generation of three chromosomal inversions in natural populations of Drosophila buzzatii. Although the most characteristic feature of Galileo is the long internally-repetitive terminal inverted repeats (TIRs), which resemble the Drosophila Foldback element, its transposase-coding sequence has led to its classification as a member of the P-element superfamily (Class II, subclass 1, TIR order). Furthermore, Galileo has a wide distribution in the genus Drosophila, since it has been found in 6 of the 12 Drosophila sequenced genomes. Among these species, D. mojavensis, the one closest to D. buzzatii, presented the highest diversity in sequence and structure of Galileo elements. In the present work, we carried out a thorough search and annotation of all the Galileo copies present in the D. mojavensis sequenced genome. In our set of 170 Galileo copies we have detected 5 Galileo subfamilies (C, D, E, F, and X) with different structures ranging from nearly complete, to only 2 TIR or solo TIR copies. Finally, we have explored the structural and length variation of the Galileo copies that point out the relatively frequent rearrangements within and between Galileo elements. Different mechanisms responsible for these rearrangements are discussed. Although Galileo is a transposable element with an ancient history in the D. mojavensis genome, our data indicate a recent transpositional activity. Furthermore, the dynamism in sequence and structure, mainly affecting the TIRs, suggests an active exchange of sequences among the copies. This exchange could lead to new subfamilies of the transposon, which could be crucial for the long-term survival of the element in the genome.

Transposable element evolution in Heliconius suggests genome diversity within Lepidoptera

PubMed Central

2013-01-01

Background Transposable elements (TEs) have the potential to impact genome structure, function and evolution in profound ways. In order to understand the contribution of transposable elements (TEs) to Heliconius melpomene, we queried the H. melpomene draft sequence to identify repetitive sequences. Results We determined that TEs comprise ~25% of the genome. The predominant class of TEs (~12% of the genome) was the non-long terminal repeat (non-LTR) retrotransposons, including a novel SINE family. However, this was only slightly higher than content derived from DNA transposons, which are diverse, with several families having mobilized in the recent past. Compared to the only other well-studied lepidopteran genome, Bombyx mori, H. melpomene exhibits a higher DNA transposon content and a distinct repertoire of retrotransposons. We also found that H. melpomene exhibits a high rate of TE turnover with few older elements accumulating in the genome. Conclusions Our analysis represents the first complete, de novo characterization of TE content in a butterfly genome and suggests that, while TEs are able to invade and multiply, TEs have an overall deleterious effect and/or that maintaining a small genome is advantageous. Our results also hint that analysis of additional lepidopteran genomes will reveal substantial TE diversity within the group. PMID:24088337

Bipartite separability and nonlocal quantum operations on graphs

NASA Astrophysics Data System (ADS)

Dutta, Supriyo; Adhikari, Bibhas; Banerjee, Subhashish; Srikanth, R.

2016-07-01

In this paper we consider the separability problem for bipartite quantum states arising from graphs. Earlier it was proved that the degree criterion is the graph-theoretic counterpart of the familiar positive partial transpose criterion for separability, although there are entangled states with positive partial transpose for which the degree criterion fails. Here we introduce the concept of partially symmetric graphs and degree symmetric graphs by using the well-known concept of partial transposition of a graph and degree criteria, respectively. Thus, we provide classes of bipartite separable states of dimension m ×n arising from partially symmetric graphs. We identify partially asymmetric graphs that lack the property of partial symmetry. We develop a combinatorial procedure to create a partially asymmetric graph from a given partially symmetric graph. We show that this combinatorial operation can act as an entanglement generator for mixed states arising from partially symmetric graphs.

Transposable elements in sexual and ancient asexual taxa

PubMed Central

Arkhipova, Irina; Meselson, Matthew

2000-01-01

Sexual reproduction allows deleterious transposable elements to proliferate in populations, whereas the loss of sex, by preventing their spread, has been predicted eventually to result in a population free of such elements [Hickey, D. A. (1982) Genetics 101, 519–531]. We tested this expectation by screening representatives of a majority of animal phyla for LINE-like and gypsy-like reverse transcriptases and mariner/Tc1-like transposases. All species tested positive for reverse transcriptases except rotifers of the class Bdelloidea, the largest eukaryotic taxon in which males, hermaphrodites, and meiosis are unknown and for which ancient asexuality is supported by molecular genetic evidence. Mariner-like transposases are distributed sporadically among species and are present in bdelloid rotifers. The remarkable lack of LINE-like and gypsy-like retrotransposons in bdelloids and their ubiquitous presence in other taxa support the view that eukaryotic retrotransposons are sexually transmitted nuclear parasites and that bdelloid rotifers evolved asexually. PMID:11121049

Carnivore-specific SINEs (Can-SINEs): distribution, evolution, and genomic impact.

PubMed

Walters-Conte, Kathryn B; Johnson, Diana L E; Allard, Marc W; Pecon-Slattery, Jill

2011-01-01

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics.

Carnivore-Specific SINEs (Can-SINEs): Distribution, Evolution, and Genomic Impact

PubMed Central

Johnson, Diana L.E.; Allard, Marc W.; Pecon-Slattery, Jill

2011-01-01

Short interspersed nuclear elements (SINEs) are a type of class 1 transposable element (retrotransposon) with features that allow investigators to resolve evolutionary relationships between populations and species while providing insight into genome composition and function. Characterization of a Carnivora-specific SINE family, Can-SINEs, has, has aided comparative genomic studies by providing rare genomic changes, and neutral sequence variants often needed to resolve difficult evolutionary questions. In addition, Can-SINEs constitute a significant source of functional diversity with Carnivora. Publication of the whole-genome sequence of domestic dog, domestic cat, and giant panda serves as a valuable resource in comparative genomic inferences gleaned from Can-SINEs. In anticipation of forthcoming studies bolstered by new genomic data, this review describes the discovery and characterization of Can-SINE motifs as well as describes composition, distribution, and effect on genome function. As the contribution of noncoding sequences to genomic diversity becomes more apparent, SINEs and other transposable elements will play an increasingly large role in mammalian comparative genomics. PMID:21846743

Zaba: a novel miniature transposable element present in genomes of legume plants.

PubMed

Macas, J; Neumann, P; Pozárková, D

2003-08-01

A novel family of miniature transposable elements, named Zaba, was identified in pea (Pisum sativum) and subsequently also in other legume species using computer analysis of their DNA sequences. Zaba elements are 141-190 bp long, generate 10-bp target site duplications, and their terminal inverted repeats make up most of the sequence. Zaba elements thus resemble class 3 foldback transposons. The elements are only moderately repetitive in pea (tens to hundreds copies per haploid genome), but they are present in up to thousands of copies in the genomes of several Medicago and Vicia species. More detailed analysis of the elements from pea, including isolation of new sequences from a genomic library, revealed that a fraction of these elements are truncated, and that their last transposition probably did not occur recently. A search for Zaba sequences in EST databases showed that at least some elements are transcribed, most probably due to their association with genic regions.

Krylov Deferred Correction Accelerated Method of Lines Transpose for Parabolic Problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jia, Jun; Jingfang, Huang

2008-01-01

In this paper, a new class of numerical methods for the accurate and efficient solutions of parabolic partial differential equations is presented. Unlike traditional method of lines (MoL), the new {\\bf \\it Krylov deferred correction (KDC) accelerated method of lines transpose (MoL^T)} first discretizes the temporal direction using Gaussian type nodes and spectral integration, and symbolically applies low-order time marching schemes to form a preconditioned elliptic system, which is then solved iteratively using Newton-Krylov techniques such as Newton-GMRES or Newton-BiCGStab method. Each function evaluation in the Newton-Krylov method is simply one low-order time-stepping approximation of the error by solving amore » decoupled system using available fast elliptic equation solvers. Preliminary numerical experiments show that the KDC accelerated MoL^T technique is unconditionally stable, can be spectrally accurate in both temporal and spatial directions, and allows optimal time-step sizes in long-time simulations.« less

The role of Transposable Elements in shaping the combinatorial interaction of Transcription Factors

PubMed Central

2012-01-01

Background In the last few years several studies have shown that Transposable Elements (TEs) in the human genome are significantly associated with Transcription Factor Binding Sites (TFBSs) and that in several cases their expansion within the genome led to a substantial rewiring of the regulatory network. Another important feature of the regulatory network which has been thoroughly studied is the combinatorial organization of transcriptional regulation. In this paper we combine these two observations and suggest that TEs, besides rewiring the network, also played a central role in the evolution of particular patterns of combinatorial gene regulation. Results To address this issue we searched for TEs overlapping Estrogen Receptor α (ERα) binding peaks in two publicly available ChIP-seq datasets from the MCF7 cell line corresponding to different modalities of exposure to estrogen. We found a remarkable enrichment of a few specific classes of Transposons. Among these a prominent role was played by MIR (Mammalian Interspersed Repeats) transposons. These TEs underwent a dramatic expansion at the beginning of the mammalian radiation and then stabilized. We conjecture that the special affinity of ERα for the MIR class of TEs could be at the origin of the important role assumed by ERα in Mammalians. We then searched for TFBSs within the TEs overlapping ChIP-seq peaks. We found a strong enrichment of a few precise combinations of TFBS. In several cases the corresponding Transcription Factors (TFs) were known cofactors of ERα, thus supporting the idea of a co-regulatory role of TFBS within the same TE. Moreover, most of these correlations turned out to be strictly associated to specific classes of TEs thus suggesting the presence of a well-defined "transposon code" within the regulatory network. Conclusions In this work we tried to shed light into the role of Transposable Elements (TEs) in shaping the regulatory network of higher eukaryotes. To test this idea we focused on a particular transcription factor: the Estrogen Receptor α (ERα) and we found that ERα preferentially targets a well defined set of TEs and that these TEs host combinations of transcriptional regulators involving several of known co-regulators of ERα. Moreover, a significant number of these TEs turned out to be conserved between human and mouse and located in the vicinity (and thus candidate to be regulators) of important estrogen-related genes. PMID:22897927

Genomic patterns associated with paternal/maternal distribution of transposable elements

NASA Astrophysics Data System (ADS)

Jurka, Jerzy

2003-03-01

Transposable elements (TEs) are specialized DNA or RNA fragments capable of surviving in intragenomic niches. They are commonly, perhaps unjustifiably referred to as "selfish" or "parasitic" elements. TEs can be divided in two major classes: retroelements and DNA transposons. The former include non-LTR retrotransposons and retrovirus-like elements, using reverse transriptase for their reproduction prior to integration into host DNA. The latter depend mostly on host DNA replication, with possible exception of rolling-circle transposons recently discovered by our team. I will review basic information on TEs, with emphasis on human Alu and L1 retroelements discussed in the context of genomic organization. TEs are non-randomly distributed in chromosomal DNA. In particular, human Alu elements tend to prefer GC-rich regions, whereas L1 accumulate in AT-rich regions. Current explanations of this phenomenon focus on the so called "target effects" and post-insertional selection. However, the proposed models appear to be unsatisfactory and alternative explanations invoking "channeling" to different chromosomal regions will be a major focus of my presentation. Transposable elements (TEs) can be expressed and integrated into host DNA in the male or female germlines, or both. Different models of expression and integration imply different proportions of TEs on sex chromosomes and autosomes. The density of recently retroposed human Alu elements is around three times higher on chromosome Y than on chromosome X, and over two times higher than the average density for all human autosomes. This implies Alu activity in paternal germlines. Analogous inter-chromosomal proportions for other repeat families should determine their compatibility with one of the three basic models describing the inheritance of TEs. Published evidence indicates that maternally and paternally imprinted genes roughly correspond to GC-rich and AT-rich DNA. This may explain the observed chromosomal distribution of Alu and L1 elements. Finally, paternal models of inheritance predict rapid accumulation of active TEs on chromosome Y. I will discuss potential implications of this phenomenon for evolution of chromosome Y and transposable elements.

Insights into the transposable mobilome of Paracoccus spp. (Alphaproteobacteria).

PubMed

Dziewit, Lukasz; Baj, Jadwiga; Szuplewska, Magdalena; Maj, Anna; Tabin, Mateusz; Czyzkowska, Anna; Skrzypczyk, Grazyna; Adamczuk, Marcin; Sitarek, Tomasz; Stawinski, Piotr; Tudek, Agnieszka; Wanasz, Katarzyna; Wardal, Ewa; Piechucka, Ewa; Bartosik, Dariusz

2012-01-01

Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial evolution.

Insights into the Transposable Mobilome of Paracoccus spp. (Alphaproteobacteria)

PubMed Central

Dziewit, Lukasz; Baj, Jadwiga; Szuplewska, Magdalena; Maj, Anna; Tabin, Mateusz; Czyzkowska, Anna; Skrzypczyk, Grazyna; Adamczuk, Marcin; Sitarek, Tomasz; Stawinski, Piotr; Tudek, Agnieszka; Wanasz, Katarzyna; Wardal, Ewa; Piechucka, Ewa; Bartosik, Dariusz

2012-01-01

Several trap plasmids (enabling positive selection of transposition events) were used to identify a pool of functional transposable elements (TEs) residing in bacteria of the genus Paracoccus (Alphaproteobacteria). Complex analysis of 25 strains representing 20 species of this genus led to the capture and characterization of (i) 37 insertion sequences (ISs) representing 9 IS families (IS3, IS5, IS6, IS21, IS66, IS256, IS1182, IS1380 and IS1634), (ii) a composite transposon Tn6097 generated by two copies of the ISPfe2 (IS1634 family) containing two predicted genetic modules, involved in the arginine deiminase pathway and daunorubicin/doxorubicin resistance, (iii) 3 non-composite transposons of the Tn3 family, including Tn5393 carrying streptomycin resistance and (iv) a transposable genomic island TnPpa1 (45 kb). Some of the elements (e.g. Tn5393, Tn6097 and ISs of the IS903 group of the IS5 family) were shown to contain strong promoters able to drive transcription of genes placed downstream of the target site of transposition. Through the application of trap plasmid pCM132TC, containing a promoterless tetracycline resistance reporter gene, we identified five ways in which transposition can supply promoters to transcriptionally silent genes. Besides highlighting the diversity and specific features of several TEs, the analyses performed in this study have provided novel and interesting information on (i) the dynamics of the process of transposition (e.g. the unusually high frequency of transposition of TnPpa1) and (ii) structural changes in DNA mediated by transposition (e.g. the generation of large deletions in the recipient molecule upon transposition of ISPve1 of the IS21 family). We also demonstrated the great potential of TEs and transposition in the generation of diverse phenotypes as well as in the natural amplification and dissemination of genetic information (of adaptative value) by horizontal gene transfer, which is considered the driving force of bacterial evolution. PMID:22359677

Transposable genetic elements in Spirulina and potential applications for genetic engineering

NASA Astrophysics Data System (ADS)

Hiroyuki, Kojima; Qin, Song; Thankappan, Ajith Kumar; Yoshikazu, Kawata; Shin-Ichi, Yano

1998-03-01

Transposable elements in cyanobacteria are briefly reviewed. Evidence is presented to show that transposable elements in Spirulina platensis is actually reflected on the phenotype change, i e., helical to straight filaments. Transposition intermediates of DNA were isolated from the extrachromosome and the transposition was related to helical variations in Spirulina. Uses of transposable elements for microalgal recombination are discussed based on the transposition mechanism.

An Insertional Translocation in Neurospora That Generates Duplications Heterozygous for Mating Type

PubMed Central

Perkins, David D.

1972-01-01

In strain T(I→II)39311 a long interstitial segment is transposed from IL to IIR, where it is inserted in reversed order with respect to the centromere. In crosses of T x T essentially all asci have eight viable, black spores, and all progeny are phenotypically normal. When T(I→II)39311 is crossed by Normal sequence (N), the expected duplication class is viable while the corresponding deficiency is lethal; 44% of the asci have 8 Black (viable) spores and 0 White (inviable) spores, 41% have 4 Black: 4 White, and 10% have 6 Black: 2 White. These are the ascus types expected from normal centromere disjunction without crossing over (8B:0W and 4B:4W equally probable), and with crossing over between centromere and break point (6B:2W). On germination, 8B:0W asci give rise to only parental types—4 T and 4 N; 4B:4W asci usually give four duplication (Dup) progeny; and 6B:2W asci usually give 2 T, 2 N, 2 Dup. Thus one third of all viable, black ascospores contain duplications.—Recessive markers in the donor chromosome which contributes the translocated segment can be mapped by duplication coverage. Ratios of 2 Dominant: 1 Recessive vs. 1 Dominant: 2 Recessive distinguish location in or outside the transposed segment. Eleven loci including mating type have been shown to lie within the segment, and markers at four loci have been transferred into the segment by meiotic recombination. The frequency of marker transfer indicates that the inserted segment usually pairs with its homologue. Ascus types that would result from single exchanges within the insertion are infrequent, as expected if asci containing dicentric bridges usually do not survive.—Duplication ascospores germinate to produce distinctive inhibited colonies. Later these "escape" to grow like wild type, and genes that were initially heterozygous in the duplication segregate when escape occurs. As with duplications from pericentric inversion In(IL→IR)H4250 (Newmeyer and Taylor 1967), the initial inhibition is attributed to mating-type heterozygosity, and escape to a somatic event that makes mating type homoor hemizygous.—Twenty additional duplication-generating Neurospora rearrangements are listed and described briefly in an Appendix. PMID:17248574

Transposition of a Ds element from a plasmid into the plant genome in Nicotiana plumbaginifolia protoplast-derived cells.

PubMed

Houba-Hérin, N; Domin, M; Pédron, J

1994-07-01

Nicotiana plumbaginifolia haploid protoplasts were co-transformed with two plasmids, one with a NPT-II/Ds element and one with a gene encoding an amino-terminal truncated Ac transposase. It is shown that Ds can efficiently transpose from extrachromosomal DNA to N. plumbaginifolia chromosomes when the Ac transposase gene is present in trans. Ds has been shown to have transposed into the plant genome in a limited number of copies (1.9 copies per genome), for 21/32 transgenic lines tested. The flanking sequences present in the original plasmid are missing in these 21 plants. In only two of 21 plants was part of the transposase construct integrated. By segregation analysis of transgenic progeny, Ds was shown to be present in the heterozygous state in 10 lines even though haploid protoplasts had been originally transformed. This observation could indicate that integration occurred after or during DNA replication that leads to protoplast diploidization.

DNA transposon dynamics in populations of Daphnia pulex with and without sex.

PubMed

Schaack, Sarah; Pritham, Ellen J; Wolf, Abby; Lynch, Michael

2010-08-07

We investigate the role of recombination in transposable element (TE) proliferation in the cyclical parthenogen, Daphnia pulex. Recombination provides a mechanism by which the rate of both TE gain and loss can be accelerated, a duality that has long intrigued many biologists interested in the influence of sex on mutation accumulation. We compared TE loads among populations of D. pulex where sex occurs regularly (cyclical parthenogens or 'sexuals') with those in which the ability to reproduce sexually has been completely lost (obligate 'asexuals') for six different families of DNA transposons. Transposon display assays showed that sexuals have more TEs than asexuals, contrary to the expectations under Muller's ratchet but consistent with the idea that sex facilitates TE spread. Sexuals also exhibit higher insertion site polymorphism among lineages, as predicted because recombination accelerates rates of loss and gain. Asexuals, however, have proportionally more singletons (loci occupied in a single isolate), which differs from previous studies where selfing and outcrossing were used as a proxy for high and low recombination. Our multi-element survey reveals that the impact of sex on TE proliferation is consistent among different Class II TE families and we discuss the genomic consequences of different reproductive strategies over long time periods.

Splicing-independent loading of TREX on nascent RNA is required for efficient expression of dual-strand piRNA clusters in Drosophila

PubMed Central

Hur, Junho K.; Luo, Yicheng; Moon, Sungjin; Ninova, Maria; Marinov, Georgi K.; Chung, Yun D.; Aravin, Alexei A.

2016-01-01

The conserved THO/TREX (transcription/export) complex is critical for pre-mRNA processing and mRNA nuclear export. In metazoa, TREX is loaded on nascent RNA transcribed by RNA polymerase II in a splicing-dependent fashion; however, how TREX functions is poorly understood. Here we show that Thoc5 and other TREX components are essential for the biogenesis of piRNA, a distinct class of small noncoding RNAs that control expression of transposable elements (TEs) in the Drosophila germline. Mutations in TREX lead to defects in piRNA biogenesis, resulting in derepression of multiple TE families, gametogenesis defects, and sterility. TREX components are enriched on piRNA precursors transcribed from dual-strand piRNA clusters and colocalize in distinct nuclear foci that overlap with sites of piRNA transcription. The localization of TREX in nuclear foci and its loading on piRNA precursor transcripts depend on Cutoff, a protein associated with chromatin of piRNA clusters. Finally, we show that TREX is required for accumulation of nascent piRNA precursors. Our study reveals a novel splicing-independent mechanism for TREX loading on nascent RNA and its importance in piRNA biogenesis. PMID:27036967

Lateralization of high-frequency transposed stimuli under conditions of binaural interference

NASA Astrophysics Data System (ADS)

Bernstein, Leslie R.; Trahiotis, Constantine

2005-04-01

The purpose of this study was to determine whether binaural interference would occur if ITD-based extents of laterality were measured using high-frequency transposed stimuli as targets. The results of an earlier study [L. R. Bernstein and C. Trahiotis, J. Acoust. Soc. Am. 116, 3062-3069 (2004)], which focused on threshold-ITDs rather than extents of laterality, suggested that high-frequency transposed stimuli might be immune to binaural interference effects resulting from the addition of a spectrally-remote, low-frequency interferer. In contrast to the earlier findings, the data from this study indicate that high-frequency transposed targets can, indeed, be susceptible to binaural interference. High-frequency transposed targets, even when presented along with an interferer, yielded greater extents of ITD-based laterality than did Gaussian noise targets presented in isolation. That is, the enhanced potency of ITDs conveyed by transposed stimuli persisted even in the presence of a low-frequency interferer. Predictions made using an extension of the model of Heller and Trahiotis [L. M. Heller and C. Trahiotis, J. Acoust. Soc. Am. 99, 3632-3637 (1996)] accounted well for binaural interference obtained with conventional Gaussian noise targets but generally over-predicted the amounts of interference found with the transposed targets.

There is no clam with coats in the calm coast: delimiting the transposed-letter priming effect.

PubMed

Duñabeitia, Jon Andoni; Perea, Manuel; Carreiras, Manuel

2009-10-01

In this article, we explore the transposed-letter priming effect (e.g., jugde-JUDGE vs. jupte-JUDGE), a phenomenon that taps into some key issues on how the brain encodes letter positions and has favoured the creation of new input coding schemes. However, almost all the empirical evidence from transposed-letter priming experiments comes from nonword primes (e.g., jugde-JUDGE). Indeed, previous evidence when using word-word pairs (e.g., causal-CASUAL) is not conclusive. Here, we conducted five masked priming lexical decision experiments that examined the relationship between pairs of real words that differed only in the transposition of two of their letters (e.g., CASUAL vs. CAUSAL). Results showed that, unlike transposed-letter nonwords, transposed-letter words do not seem to affect the identification time of their transposed-letter mates. Thus, prime lexicality is a key factor that modulates the magnitude of transposed-letter priming effects. These results are interpreted under the assumption of the existence of lateral inhibition processes occurring within the lexical level-which cancels out any orthographic facilitation due to the overlapping letters. We examine the implications of these findings for models of visual-word recognition.

Functional characterization of piggyBat from the bat Myotis lucifugus unveils an active mammalian DNA transposon.

PubMed

Mitra, Rupak; Li, Xianghong; Kapusta, Aurélie; Mayhew, David; Mitra, Robi D; Feschotte, Cédric; Craig, Nancy L

2013-01-02

A revelation of the genomic age has been the contributions of the mobile DNA segments called transposable elements to chromosome structure, function, and evolution in virtually all organisms. Substantial fractions of vertebrate genomes derive from transposable elements, being dominated by retroelements that move via RNA intermediates. Although many of these elements have been inactivated by mutation, several active retroelements remain. Vertebrate genomes also contain substantial quantities and a high diversity of cut-and-paste DNA transposons, but no active representative of this class has been identified in mammals. Here we show that a cut-and-paste element called piggyBat, which has recently invaded the genome of the little brown bat (Myotis lucifugus) and is a member of the piggyBac superfamily, is active in its native form in transposition assays in bat and human cultured cells, as well as in the yeast Saccharomyces cerevisiae. Our study suggests that some DNA transposons are still actively shaping some mammalian genomes and reveals an unprecedented opportunity to study the mechanism, regulation, and genomic impact of cut-and-paste transposition in a natural mammalian host.

Irreversibility of Asymptotic Entanglement Manipulation Under Quantum Operations Completely Preserving Positivity of Partial Transpose.

PubMed

Wang, Xin; Duan, Runyao

2017-11-03

We demonstrate the irreversibility of asymptotic entanglement manipulation under quantum operations that completely preserve the positivity of partial transpose (PPT), resolving a major open problem in quantum information theory. Our key tool is a new efficiently computable additive lower bound for the asymptotic relative entropy of entanglement with respect to PPT states, which can be used to evaluate the entanglement cost under local operations and classical communication (LOCC). We find that for any rank-two mixed state supporting on the 3⊗3 antisymmetric subspace, the amount of distillable entanglement by PPT operations is strictly smaller than one entanglement bit (ebit) while its entanglement cost under PPT operations is exactly one ebit. As a by-product, we find that for this class of states, both the Rains's bound and its regularization are strictly less than the asymptotic relative entropy of entanglement. So, in general, there is no unique entanglement measure for the manipulation of entanglement by PPT operations. We further show a computable sufficient condition for the irreversibility of entanglement distillation by LOCC (or PPT) operations.

Orthographic Reading Deficits in Dyslexic Japanese Children: Examining the Transposed-Letter Effect in the Color-Word Stroop Paradigm

PubMed Central

Ogawa, Shino; Shibasaki, Masahiro; Isomura, Tomoko; Masataka, Nobuo

2016-01-01

In orthographic reading, the transposed-letter effect (TLE) is the perception of a transposed-letter position word such as “cholocate” as the correct word “chocolate.” Although previous studies on dyslexic children using alphabetic languages have reported such orthographic reading deficits, the extent of orthographic reading impairment in dyslexic Japanese children has remained unknown. This study examined the TLE in dyslexic Japanese children using the color-word Stroop paradigm comprising congruent and incongruent Japanese hiragana words with correct and transposed-letter positions. We found that typically developed children exhibited Stroop effects in Japanese hiragana words with both correct and transposed-letter positions, thus indicating the presence of TLE. In contrast, dyslexic children indicated Stroop effects in correct letter positions in Japanese words but not in transposed, which indicated an absence of the TLE. These results suggest that dyslexic Japanese children, similar to dyslexic children using alphabetic languages, may also have a problem with orthographic reading. PMID:27303331

Orthographic Reading Deficits in Dyslexic Japanese Children: Examining the Transposed-Letter Effect in the Color-Word Stroop Paradigm.

PubMed

Ogawa, Shino; Shibasaki, Masahiro; Isomura, Tomoko; Masataka, Nobuo

2016-01-01

In orthographic reading, the transposed-letter effect (TLE) is the perception of a transposed-letter position word such as "cholocate" as the correct word "chocolate." Although previous studies on dyslexic children using alphabetic languages have reported such orthographic reading deficits, the extent of orthographic reading impairment in dyslexic Japanese children has remained unknown. This study examined the TLE in dyslexic Japanese children using the color-word Stroop paradigm comprising congruent and incongruent Japanese hiragana words with correct and transposed-letter positions. We found that typically developed children exhibited Stroop effects in Japanese hiragana words with both correct and transposed-letter positions, thus indicating the presence of TLE. In contrast, dyslexic children indicated Stroop effects in correct letter positions in Japanese words but not in transposed, which indicated an absence of the TLE. These results suggest that dyslexic Japanese children, similar to dyslexic children using alphabetic languages, may also have a problem with orthographic reading.

Transposed-Letter and Laterality Effects in Lexical Decision

ERIC Educational Resources Information Center

Perea, Manuel; Fraga, Isabel

2006-01-01

Two divided visual field lexical decision experiments were conducted to examine the role of the cerebral hemispheres in transposed-letter similarity effects. In Experiment 1, we created two types of nonwords: nonadjacent transposed-letter nonwords ("TRADEGIA"; the base word was "TRAGEDIA," the Spanish for "TRAGEDY") and two-letter different…

Measures of extents of laterality for high-frequency ``transposed'' stimuli under conditions of binaural interference

NASA Astrophysics Data System (ADS)

Bernstein, Leslie R.; Trahiotis, Constantine

2005-09-01

Our purpose in this study was to determine whether across-frequency binaural interference would occur if ITD-based extents of laterality were measured using high-frequency transposed stimuli as targets. The results of an earlier study [L. R. Bernstein and C. Trahiotis, J. Acoust. Soc. Am. 116, 3062-3069 (2004)], which focused on threshold-ITDs, rather than extents of laterality, suggested that high-frequency transposed stimuli might be ``immune'' to binaural interference effects resulting from the addition of a spectrally remote, low-frequency interferer. In contrast to the earlier findings, the data from this study indicate that high-frequency transposed targets are susceptible to binaural interference. Nevertheless, high-frequency transposed targets, even when presented along with an interferer, yielded greater extents of ITD-based laterality than did high-frequency Gaussian noise targets presented in isolation. That is, the ``enhanced potency'' of ITDs conveyed by transposed stimuli persisted, even in the presence of a low-frequency interferer. Predictions made using an extension of the model of Heller and Trahiotis [L. M. Heller and C. Trahiotis, J. Acoust. Soc. Am. 99, 3632-3637 (1996)] accounted well for across-frequency binaural interference obtained with conventional Gaussian noise targets but, in all but one case, overpredicted the amounts of interference found with the transposed targets.

A Finite Element Analysis of the Creep Response of Lumbar Intervertebral Joints in the Rhesus Monkey.

DTIC Science & Technology

1982-12-01

shown in the figure is the cartilagenous end-plate, which is comprised of a hyaline cartilage structure. It serves as a boundary region between a disk...without whose love and support this study would have been impossible. ii S’ Contents Page Preface.................... .. . ..... . .. .. . ... List of...T Vector transpose (’) Differentiation with respect to time xiv I 1.. AFIT/GAE/AA/82D-24 Abstract This study consisted of two phases. During the

An Interactive Activation Model of the Effect of Context in Perception. Part 2

DTIC Science & Technology

1980-07-15

nonword strings are often seen with letters transposed if the transposition will produce legal strings (Estes, 1975a; c.f. experiment by Stevens reported...Activation Model Rumelhart & McClelland Part II 90 References Anderson, J. A. Neural models with cognitive implications. In D. LaBerge & S. J. Samuels...Washington, DC 20372 Coe391 Dr. Gory PoockNavy Personnel R&D Center Operations Research Department LT Steven D. Harris. MSC, USN San Diego, CA 92152 Code

An analysis of polygenes affecting wing shape on chromosome 2 in Drosophila melanogaster.

PubMed Central

Weber, K; Eisman, R; Higgins, S; Morey, L; Patty, A; Tausek, M; Zeng, Z B

2001-01-01

Genetic effects on an index of wing shape on chromosome 2 of Drosophila melanogaster were mapped using isogenic recombinants with transposable element markers. At least 10 genes with small additive effects are dispersed evenly along the chromosome. Many interactions exist, with only small net effects in homozygous recombinants and little effect on phenotypic variance. Heterozygous chromosome segments show almost no dominance. Pleiotropic effects on leg shape are only minor. At first view, wing shape genes form a rather homogeneous class, but certain complexities remain unresolved. PMID:11729152

Activating distillation with an infinitesimal amount of bound entanglement.

PubMed

Vollbrecht, Karl Gerd H; Wolf, Michael M

2002-06-17

We show that bipartite quantum states of any dimension, which do not have a positive partial transpose (NPPT), become 1-distillable when one adds an infinitesimal amount of bound entanglement. To this end we investigate the activation properties of a new class of symmetric bound entangled states of full rank. It is shown that in this set there exist universal activator states capable of activating the distillation of any NPPT state. The result shows that even a small amount of bound entanglement can be useful for quantum information purposes.

Identification of miniature inverted-repeat transposable elements (MITEs) and biogenesis of their siRNAs in the Solanaceae: New functional implications for MITEs

USDA-ARS?s Scientific Manuscript database

Small RNAs regulate the genome by guiding transcriptional and post-transcriptional silencing machinery to specific target sequences, including genes and transposable elements (TEs). Although miniature inverted-repeat transposable elements (MITEs) are closely associated with euchromatic genes, the br...

Can "CANISO" Activate "CASINO"? Transposed-Letter Similarity Effects with Nonadjacent Letter Positions

ERIC Educational Resources Information Center

Perea, Manuel; Lupker, Stephen J.

2004-01-01

Nonwords created by transposing two "adjacent" letters (i.e., transposed-letter (TL) nonwords like "jugde") are very effective at activating the lexical representation of their base words. This fact poses problems for most computational models of word recognition (e.g., the interactive-activation model and its extensions), which assume that exact…

TRANSPOSABLE REGULARIZED COVARIANCE MODELS WITH AN APPLICATION TO MISSING DATA IMPUTATION

PubMed Central

Allen, Genevera I.; Tibshirani, Robert

2015-01-01

Missing data estimation is an important challenge with high-dimensional data arranged in the form of a matrix. Typically this data matrix is transposable, meaning that either the rows, columns or both can be treated as features. To model transposable data, we present a modification of the matrix-variate normal, the mean-restricted matrix-variate normal, in which the rows and columns each have a separate mean vector and covariance matrix. By placing additive penalties on the inverse covariance matrices of the rows and columns, these so called transposable regularized covariance models allow for maximum likelihood estimation of the mean and non-singular covariance matrices. Using these models, we formulate EM-type algorithms for missing data imputation in both the multivariate and transposable frameworks. We present theoretical results exploiting the structure of our transposable models that allow these models and imputation methods to be applied to high-dimensional data. Simulations and results on microarray data and the Netflix data show that these imputation techniques often outperform existing methods and offer a greater degree of flexibility. PMID:26877823

TRANSPOSABLE REGULARIZED COVARIANCE MODELS WITH AN APPLICATION TO MISSING DATA IMPUTATION.

PubMed

Allen, Genevera I; Tibshirani, Robert

2010-06-01

Missing data estimation is an important challenge with high-dimensional data arranged in the form of a matrix. Typically this data matrix is transposable , meaning that either the rows, columns or both can be treated as features. To model transposable data, we present a modification of the matrix-variate normal, the mean-restricted matrix-variate normal , in which the rows and columns each have a separate mean vector and covariance matrix. By placing additive penalties on the inverse covariance matrices of the rows and columns, these so called transposable regularized covariance models allow for maximum likelihood estimation of the mean and non-singular covariance matrices. Using these models, we formulate EM-type algorithms for missing data imputation in both the multivariate and transposable frameworks. We present theoretical results exploiting the structure of our transposable models that allow these models and imputation methods to be applied to high-dimensional data. Simulations and results on microarray data and the Netflix data show that these imputation techniques often outperform existing methods and offer a greater degree of flexibility.

The site-specific ribosomal DNA insertion element R1Bm belongs to a class of non-long-terminal-repeat retrotransposons.

PubMed Central

Xiong, Y; Eickbush, T H

1988-01-01

Two types of insertion elements, R1 and R2 (previously called type I and type II), are known to interrupt the 28S ribosomal genes of several insect species. In the silkmoth, Bombyx mori, each element occupies approximately 10% of the estimated 240 ribosomal DNA units, while at most only a few copies are located outside the ribosomal DNA units. We present here the complete nucleotide sequence of an R1 insertion from B. mori (R1Bm). This 5.1-kilobase element contains two overlapping open reading frames (ORFs) which together occupy 88% of its length. ORF1 is 461 amino acids in length and exhibits characteristics of retroviral gag genes. ORF2 is 1,051 amino acids in length and contains homology to reverse transcriptase-like enzymes. The analysis of 3' and 5' ends of independent isolates from the ribosomal locus supports the suggestion that R1 is still functioning as a transposable element. The precise location of the element within the genome implies that its transposition must occur with remarkable insertion sequence specificity. Comparison of the deduced amino acid sequences from six retrotransposons, R1 and R2 of B. mori, I factor and F element of Drosophila melanogaster, L1 of Mus domesticus, and Ingi of Trypanosoma brucei, reveals a relatively high level of sequence homology in the reverse transcriptase region. Like R1, these elements lack long terminal repeats. We have therefore named this class of related elements the non-long-terminal-repeat (non-LTR) retrotransposons. Images PMID:2447482

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

PubMed Central

Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard; Schoch, Conrad L.; Horwitz, Benjamin A.; Barry, Kerrie W.; Condon, Bradford J.; Copeland, Alex C.; Dhillon, Braham; Glaser, Fabian; Hesse, Cedar N.; Kosti, Idit; LaButti, Kurt; Lindquist, Erika A.; Lucas, Susan; Salamov, Asaf A.; Bradshaw, Rosie E.; Ciuffetti, Lynda; Hamelin, Richard C.; Kema, Gert H. J.; Lawrence, Christopher; Scott, James A.; Spatafora, Joseph W.; Turgeon, B. Gillian; de Wit, Pierre J. G. M.; Zhong, Shaobin; Goodwin, Stephen B.; Grigoriev, Igor V.

2012-01-01

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appears to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress. PMID:23236275

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ohm, Robin A.; Feau, Nicolas; Henrissat, Bernard

The class Dothideomycetes is one of the largest groups of fungi with a high level of ecological diversity including many plant pathogens infecting a broad range of hosts. Here, we compare genome features of 18 members of this class, including 6 necrotrophs, 9 (hemi)biotrophs and 3 saprotrophs, to analyze genome structure, evolution, and the diverse strategies of pathogenesis. The Dothideomycetes most likely evolved from a common ancestor more than 280 million years ago. The 18 genome sequences differ dramatically in size due to variation in repetitive content, but show much less variation in number of (core) genes. Gene order appearsmore » to have been rearranged mostly within chromosomal boundaries by multiple inversions, in extant genomes frequently demarcated by adjacent simple repeats. Several Dothideomycetes contain one or more gene-poor, transposable element (TE)-rich putatively dispensable chromosomes of unknown function. The 18 Dothideomycetes offer an extensive catalogue of genes involved in cellulose degradation, proteolysis, secondary metabolism, and cysteine-rich small secreted proteins. Ancestors of the two major orders of plant pathogens in the Dothideomycetes, the Capnodiales and Pleosporales, may have had different modes of pathogenesis, with the former having fewer of these genes than the latter. Many of these genes are enriched in proximity to transposable elements, suggesting faster evolution because of the effects of repeat induced point (RIP) mutations. A syntenic block of genes, including oxidoreductases, is conserved in most Dothideomycetes and upregulated during infection in L. maculans, suggesting a possible function in response to oxidative stress.« less

Transposable element distribution, abundance and role in genome size variation in the genus Oryza.

PubMed

Zuccolo, Andrea; Sebastian, Aswathy; Talag, Jayson; Yu, Yeisoo; Kim, HyeRan; Collura, Kristi; Kudrna, Dave; Wing, Rod A

2007-08-29

The genus Oryza is composed of 10 distinct genome types, 6 diploid and 4 polyploid, and includes the world's most important food crop - rice (Oryza sativa [AA]). Genome size variation in the Oryza is more than 3-fold and ranges from 357 Mbp in Oryza glaberrima [AA] to 1283 Mbp in the polyploid Oryza ridleyi [HHJJ]. Because repetitive elements are known to play a significant role in genome size variation, we constructed random sheared small insert genomic libraries from 12 representative Oryza species and conducted a comprehensive study of the repetitive element composition, distribution and phylogeny in this genus. Particular attention was paid to the role played by the most important classes of transposable elements (Long Terminal Repeats Retrotransposons, Long interspersed Nuclear Elements, helitrons, DNA transposable elements) in shaping these genomes and in their contributing to genome size variation. We identified the elements primarily responsible for the most strikingly genome size variation in Oryza. We demonstrated how Long Terminal Repeat retrotransposons belonging to the same families have proliferated to very different extents in various species. We also showed that the pool of Long Terminal Repeat Retrotransposons is substantially conserved and ubiquitous throughout the Oryza and so its origin is ancient and its existence predates the speciation events that originated the genus. Finally we described the peculiar behavior of repeats in the species Oryza coarctata [HHKK] whose placement in the Oryza genus is controversial. Long Terminal Repeat retrotransposons are the major component of the Oryza genomes analyzed and, along with polyploidization, are the most important contributors to the genome size variation across the Oryza genus. Two families of Ty3-gypsy elements (RIRE2 and Atlantys) account for a significant portion of the genome size variations present in the Oryza genus.

Enhancing interaural-delay-based extents of laterality at high frequencies by using ``transposed stimuli''

NASA Astrophysics Data System (ADS)

Bernstein, Leslie R.; Trahiotis, Constantine

2003-06-01

An acoustic pointing task was used to determine whether interaural temporal disparities (ITDs) conveyed by high-frequency ``transposed'' stimuli would produce larger extents of laterality than ITDs conveyed by bands of high-frequency Gaussian noise. The envelopes of transposed stimuli are designed to provide high-frequency channels with information similar to that conveyed by the waveforms of low-frequency stimuli. Lateralization was measured for low-frequency Gaussian noises, the same noises transposed to 4 kHz, and high-frequency Gaussian bands of noise centered at 4 kHz. Extents of laterality obtained with the transposed stimuli were greater than those obtained with bands of Gaussian noise centered at 4 kHz and, in some cases, were equivalent to those obtained with low-frequency stimuli. In a second experiment, the general effects on lateral position produced by imposed combinations of bandwidth, ITD, and interaural phase disparities (IPDs) on low-frequency stimuli remained when those stimuli were transposed to 4 kHz. Overall, the data were fairly well accounted for by a model that computes the cross-correlation subsequent to known stages of peripheral auditory processing augmented by low-pass filtering of the envelopes within the high-frequency channels of each ear.

Surgical transposition of the ovaries: imaging findings in 14 patients.

PubMed

Kier, R; Chambers, S K

1989-11-01

Pelvic radiation therapy for cervical or vaginal cancer often leads to ovarian failure. To remove the ovaries from the radiation portal and preserve their function, they can be transposed to the lateral abdomen. Serial imaging studies in 14 patients who had undergone ovarian transposition (five bilateral, nine unilateral) were reviewed. Images obtained included 32 CT scans, 20 sonograms, and one MR image. Most transposed ovaries were located along the paracolic gutters near the iliac crests, creating an extrinsic mass effect on adjacent bowel. Detection of surgical clips on the ovary on CT scans allowed confident recognition of all 19 transposed ovaries. Cysts in the transposed ovaries, noted on most imaging studies, did not correlate with complications of pain or hormonal dysfunction. In one case, a large physiologic cyst in a transposed ovary distorted the cecum and was mistaken for a mucocele of the appendix. In another case, a large ovarian cyst was thought to be tumor recurrence or a lymphocele. These findings indicate that although the transposed ovaries can be recognized on CT scans by the surgical clips attached to the ovaries, the appearance of the ovary does not predict reliably the development of complications.

Structure Prediction and Analysis of DNA Transposon and LINE Retrotransposon Proteins*

PubMed Central

Abrusán, György; Zhang, Yang; Szilágyi, András

2013-01-01

Despite the considerable amount of research on transposable elements, no large-scale structural analyses of the TE proteome have been performed so far. We predicted the structures of hundreds of proteins from a representative set of DNA and LINE transposable elements and used the obtained structural data to provide the first general structural characterization of TE proteins and to estimate the frequency of TE domestication and horizontal transfer events. We show that 1) ORF1 and Gag proteins of retrotransposons contain high amounts of structural disorder; thus, despite their very low conservation, the presence of disordered regions and probably their chaperone function is conserved. 2) The distribution of SCOP classes in DNA transposons and LINEs indicates that the proteins of DNA transposons are more ancient, containing folds that already existed when the first cellular organisms appeared. 3) DNA transposon proteins have lower contact order than randomly selected reference proteins, indicating rapid folding, most likely to avoid protein aggregation. 4) Structure-based searches for TE homologs indicate that the overall frequency of TE domestication events is low, whereas we found a relatively high number of cases where horizontal transfer, frequently involving parasites, is the most likely explanation for the observed homology. PMID:23530042

Cut-and-Paste Transposons in Fungi with Diverse Lifestyles

PubMed Central

Steczkiewicz, Kamil; Ginalski, Krzysztof

2017-01-01

Abstract Transposable elements (TEs) shape genomes via recombination and transposition, lead to chromosomal rearrangements, create new gene neighborhoods, and alter gene expression. They play key roles in adaptation either to symbiosis in Amanita genus or to pathogenicity in Pyrenophora tritici-repentis. Despite growing evidence of their importance, the abundance and distribution of mobile elements replicating in a “cut-and-paste” fashion is barely described so far. In order to improve our knowledge on this old and ubiquitous class of transposable elements, 1,730 fungal genomes were scanned using both de novo and homology-based approaches. DNA TEs have been identified across the whole data set and display uneven distribution from both DNA TE classification and fungal taxonomy perspectives. DNA TE content correlates with genome size, which confirms that many transposon families proliferate simultaneously. In contrast, it is independent from intron density, average gene distance and GC content. TE count is associated with species’ lifestyle and tends to be elevated in plant symbionts and decreased in animal parasites. Lastly, we found that fungi with both RIP and RNAi systems have more total DNA TE sequences but less elements retaining a functional transposase, what reflects stringent control over transposition. PMID:29228286

Mariner transposons are sailing in the genome of the blood-sucking bug Rhodnius prolixus.

PubMed

Filée, Jonathan; Rouault, Jacques-Deric; Harry, Myriam; Hua-Van, Aurélie

2015-12-15

The Triatomine bug Rhodnius prolixus is a vector of Trypanosoma cruzi, which causes the Chagas disease in Latin America. R. prolixus can also transfer transposable elements horizontally across a wide range of species. We have taken advantage of the availability of the 700 Mbp complete genome sequence of R. prolixus to study the dynamics of invasion and persistence of transposable elements in this species. Using both library-based and de novo methods of transposon detection, we found less than 6 % of transposable elements in the R. prolixus genome, a relatively low percentage compared to other insect genomes with a similar genome size. DNA transposons are surprisingly abundant and elements belonging to the mariner family are by far the most preponderant components of the mobile part of this genome with 11,015 mariner transposons that could be clustered in 89 groups (75 % of the mobilome). Our analysis allowed the detection of a new mariner clade in the R. prolixus genome, that we called nosferatis. We demonstrated that a large diversity of mariner elements invaded the genome and expanded successfully over time via three main processes. (i) several families experienced recent and massive expansion, for example an explosive burst of a single mariner family led to the generation of more than 8000 copies. These recent expansion events explain the unusual prevalence of mariner transposons in the R. prolixus genome. Other families expanded via older bursts of transposition demonstrating the long lasting permissibility of mariner transposons in the R. prolixus genome. (ii) Many non-autonomous families generated by internal deletions were also identified. Interestingly, two non autonomous families were generated by atypical recombinations (5' part replacement with 3' part). (iii) at least 10 cases of horizontal transfers were found, supporting the idea that host/vector relationships played a pivotal role in the transmission and subsequent persistence of transposable elements in this genome. These data provide a new insight into the evolution of transposons in the genomes of hematophagous insects and bring additional evidences that lateral exchanges of mobile genetics elements occur frequently in the R. prolixus genome.

Challenges at Petascale for Pseudo-Spectral Methods on Spheres (A Last Hurrah?)

NASA Technical Reports Server (NTRS)

Clune, Thomas

2011-01-01

Conclusions: a) Proper software abstractions should enable rapid-exploration of platform-specific optimizations/ tradeoffs. b) Pseudo-spectra! methods are marginally viable for at least some classes of petascaie problems. i.e., GPU based machine with good bisection would be best. c) Scalability at exascale is possible, but the necessary resolution will make algorithm prohibitively expensive. Efficient implementations of realistic global transposes are mtricate and tedious in MPI. PS at petascaie requires exploration of a variety of strategies for spreading local and remote communic3tions. PGAS allows far simpler implementation and thus rapid exploration of variants.

The Tolypocladium inflatum CPA element encodes a RecQ helicase-like gene.

PubMed

Kempken, Frank

2008-12-01

Previously, a repetitive CPA element was discovered in the genome of the filamentous fungus Tolypocladium inflatum; however, no further characterization was technically possible at that time. In this study, PCR amplification was used to detect a 4 kb conserved portion of the CPA element that appeared to be present in most, if not all, genomic CPA elements. The amplicons included a large open reading frame that was most similar to a RecQ helicase-like gene from Metarhizium anisopliae. The repetitive nature of the CPA element suggests that it is related to the eukaryotic Helitron class of transposable elements.

Orthodontic correction of a transposed maxillary canine and first premolar in the permanent dentition.

PubMed

Nishimura, Kazuaki; Nakao, Kimihisa; Aoki, Taijyu; Fuyamada, Mariko; Saito, Keisuke; Goto, Shigemi

2012-10-01

The patient was a 16-year-old Japanese girl whose chief complaints were crowding and transposition of the maxillary canine and first premolar. A setup model was used to preoperatively align the teeth in their transposed positions. The amount of postoperative reshaping was estimated for the occlusal surfaces of the teeth. However, the patient did not wish to have her teeth reduced by reshaping or to have composite materials for restorative camouflage. Because she strongly expected alignment of her teeth in the correct intra-arch position, her transposed teeth were corrected without extraction of the transposed teeth. Cone-beam computed tomography was used to obtain more detailed information about the transposition, and the direction of tooth movement was examined. Although the duration of the treatment was long, both the crowns and the roots of the transposed teeth were aligned correctly. Copyright © 2012 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

[The role of external letter positions in visual word recognition].

PubMed

Perea, Manuel; Lupker, Sthephen J

2007-11-01

A key issue for any computational model of visual word recognition is the choice of an input coding schema, which is responsible for assigning letter positions. Such a schema must reflect the fact that, according to recent research, nonwords created by transposing letters (e.g., caniso for CASINO ), typically, appear to be more similar to the word than nonwords created by replacing letters (e.g., caviro ). In the present research, we initially carried out a computational analysis examining the degree to which the position of the transposition influences transposed-letter similarity effects. We next conducted a masked priming experiment with the lexical decision task to determine whether a transposed-letter priming advantage occurs when the first letter position is involved. Primes were created by either transposing the first and third letters (démula-MEDULA ) or replacing the first and third letters (bérula-MEDULA). Results showed that there was no transposed-letter priming advantage in this situation. We discuss the implications of these results for models of visual word recognition.

MHC class II expression in lung cancer.

PubMed

He, Yayi; Rozeboom, Leslie; Rivard, Christopher J; Ellison, Kim; Dziadziuszko, Rafal; Yu, Hui; Zhou, Caicun; Hirsch, Fred R

2017-10-01

Immunotherapy is an exciting development in lung cancer research. In this study we described major histocompatibility complex (MHC) Class II protein expression in lung cancer cell lines and patient tissues. We studied MHC Class II (DP, DQ, DR) (CR3/43, Abcam) protein expression in 55 non-small cell lung cancer (NSCLC) cell lines, 42 small cell lung cancer (SCLC) cell lines and 278 lung cancer patient tissues by immunohistochemistry (IHC). Seven (12.7%) NSCLC cell lines were positive for MHC Class II. No SCLC cell lines were found to be MHC Class II positive. We assessed 139 lung cancer samples available in the Hirsch Lab for MHC Class II. There was no positive MHC Class II staining on SCLC tumor cells. MHC Class II expression on TILs in SCLC was significantly lower than that on TILs in NSCLC (P＜0.001). MHC Class II was also assessed in an additional 139 NSCLC tumor tissues from Medical University of Gdansk, Poland. Patients with positive staining of MHC Class II on TILs had longer regression-free survival (RFS) and overall survival (OS) than those whose TILs were MHC Class II negative (2.980 years, 95% CI 1.628-4.332 vs. 1.050 years, 95% CI 0.556-1.554, P=0.028) (3.230 years, 95% CI 2.617-3.843 vs. 1.390 years, 95% CI 0.629-2.151, P=0.014). MHC Class II was expressed both in NSCLC cell lines and tissues. However, MHC Class II was not detected in SCLC cell lines or tissue tumor cells. MHC Class II expression was lower on SCLC TILs than on NSCLC TILs. Loss of expression of MHC Class II on SCLC tumor cells and reduced expression on SCLC TILs may be a means of escaping anti-cancer immunity. Higher MHC Class II expression on TILs was correlated with better prognosis in patients with NSCLC. Copyright © 2017. Published by Elsevier B.V.

The relative immunity of high-frequency transposed stimuli to low-frequency binaural interference

NASA Astrophysics Data System (ADS)

Bernstein, Leslie R.; Trahiotis, Constantine

2004-05-01

We have recently demonstrated that high-frequency transposed stimuli, having envelopes designed to provide high-frequency channels with information similar to that normally available in only low-frequency channels, yield threshold-ITDs and extents of laterality comparable to those obtained with conventional low-frequency stimuli. This enhanced potency of ITDs conveyed by high-frequency transposed stimuli, as compared to conventional high-frequency stimuli, suggested to us that ITDs conveyed by transposed stimuli might be relatively immune to the presence of low-frequency binaural interferers. To investigate this issue, threshold-ITDs and extents of laterality were measured with a variety of conventional and transposed targets centered at 4 kHz. The targets were presented either in the presence or absence of a simultaneously gated diotic noise centered at 500 Hz, the interferer. As expected, the presence of the low-frequency interferer resulted in substantially elevated threshold-ITDs and reduced extents of laterality for the conventional high-frequency stimuli. In contrast, these interference effects were either greatly attenuated or absent for ITDs conveyed by the high-frequency transposed targets. The results will be discussed in the context of current models of binaural interference. [Work supported by NIH DC 04147, NIH DC04073, NIH DC 002304.

25 CFR 522.10 - Individually owned class II and class III gaming operations other than those operating on...

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false Individually owned class II and class III gaming... GAMING COMMISSION, DEPARTMENT OF THE INTERIOR APPROVAL OF CLASS II AND CLASS III ORDINANCES AND RESOLUTIONS SUBMISSION OF GAMING ORDINANCE OR RESOLUTION § 522.10 Individually owned class II and class III...

Contrasting evolutionary histories of MHC class I and class II loci in grouse—Effects of selection and gene conversion

USGS Publications Warehouse

Minias, Piotr; Bateson, Zachary W.; Whittingham, Linda A.; Johnson, Jeff A.; Oyler-McCance, Sara J.; Dunn, Peter O.

2016-01-01

Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens.

Contrasting evolutionary histories of MHC class I and class II loci in grouse—effects of selection and gene conversion

PubMed Central

Minias, P; Bateson, Z W; Whittingham, L A; Johnson, J A; Oyler-McCance, S; Dunn, P O

2016-01-01

Genes of the major histocompatibility complex (MHC) encode receptor molecules that are responsible for recognition of intracellular and extracellular pathogens (class I and class II genes, respectively) in vertebrates. Given the different roles of class I and II MHC genes, one might expect the strength of selection to differ between these two classes. Different selective pressures may also promote different rates of gene conversion at each class. Despite these predictions, surprisingly few studies have looked at differences between class I and II genes in terms of both selection and gene conversion. Here, we investigated the molecular evolution of MHC class I and II genes in five closely related species of prairie grouse (Centrocercus and Tympanuchus) that possess one class I and two class II loci. We found striking differences in the strength of balancing selection acting on MHC class I versus class II genes. More than half of the putative antigen-binding sites (ABS) of class II were under positive or episodic diversifying selection, compared with only 10% at class I. We also found that gene conversion had a stronger role in shaping the evolution of MHC class II than class I. Overall, the combination of strong positive (balancing) selection and frequent gene conversion has maintained higher diversity of MHC class II than class I in prairie grouse. This is one of the first studies clearly demonstrating that macroevolutionary mechanisms can act differently on genes involved in the immune response against intracellular and extracellular pathogens. PMID:26860199

Evaluation of four microbial Class II fructose 1,6-bisphosphate aldolase enzymes for use as biocatalysts.

PubMed

Labbé, Geneviève; de Groot, Sarah; Rasmusson, Timothy; Milojevic, Gorica; Dmitrienko, Gary I; Guillemette, J Guy

2011-12-01

Fructose 1,6-bisphosphate (FBP) aldolase has been used as biocatalyst in the synthesis of several pharmaceutical compounds such as monosaccharides and analogs. Is has been suggested that microbial metal-dependant Class II aldolases could be better industrial catalysts than mammalian Class I enzyme because of their greater stability. The Class II aldolases from four microbes were subcloned into the Escherichia coli vector pT7-7, expressed and purified to near homogeneity. The kinetic parameters, temperature stability, pH profile, and tolerance to organic solvents of the Class II enzymes were determined, and compared with the properties of the Class I aldolase from rabbit muscle. Contrary to results obtained previously with the E. coli Class II aldolase, which was reported to be more stable than the mammalian enzyme, other recombinant Class II aldolases were found to be generally less stable than the Class I enzyme, especially in the presence of organic solvents. Class II aldolase from Bacillus cereus showed higher temperature stability than the other enzymes tested, but only the Mycobacterium tuberculosis Class II aldolase had a stability comparable to the Class I mammalian enzyme under assay conditions. The turnover number of the recombinant M. tuberculosis and Magnaporthe grisea Class II type A aldolases was comparable or higher than that of the Class I enzyme. The recombinant B. cereus and Pseudomonas aeruginosa Class II type B aldolases had very low turnover numbers and low metal content, indicating that the E. coli overexpression system may not be suitable for the Class II type B aldolases from these microorganisms. Copyright © 2011 Elsevier Inc. All rights reserved.

25 CFR 547.3 - What are the definitions for this part?

Code of Federal Regulations, 2011 CFR

2011-04-01

... TECHNICAL STANDARDS FOR GAMING EQUIPMENT USED WITH THE PLAY OF CLASS II GAMES § 547.3 What are the... Commission. Class II game. The same as “class II gaming” in 25 U.S.C. 2703(7)(A). Class II gaming system. All..., that function together to aid the play of one or more Class II games, including accounting functions...

25 CFR 547.3 - What are the definitions for this part?

Code of Federal Regulations, 2012 CFR

2012-04-01

... TECHNICAL STANDARDS FOR GAMING EQUIPMENT USED WITH THE PLAY OF CLASS II GAMES § 547.3 What are the... Commission. Class II game. The same as “class II gaming” in 25 U.S.C. 2703(7)(A). Class II gaming system. All..., that function together to aid the play of one or more Class II games, including accounting functions...

25 CFR 547.3 - What are the definitions for this part?

Code of Federal Regulations, 2010 CFR

2010-04-01

... TECHNICAL STANDARDS FOR GAMING EQUIPMENT USED WITH THE PLAY OF CLASS II GAMES § 547.3 What are the... Commission. Class II game. The same as “class II gaming” in 25 U.S.C. 2703(7)(A). Class II gaming system. All..., that function together to aid the play of one or more Class II games, including accounting functions...

Transposable elements in cancer.

PubMed

Burns, Kathleen H

2017-07-01

Transposable elements give rise to interspersed repeats, sequences that comprise most of our genomes. These mobile DNAs have been historically underappreciated - both because they have been presumed to be unimportant, and because their high copy number and variability pose unique technical challenges. Neither impediment now seems steadfast. Interest in the human mobilome has never been greater, and methods enabling its study are maturing at a fast pace. This Review describes the activity of transposable elements in human cancers, particularly long interspersed element-1 (LINE-1). LINE-1 sequences are self-propagating, protein-coding retrotransposons, and their activity results in somatically acquired insertions in cancer genomes. Altered expression of transposable elements and animation of genomic LINE-1 sequences appear to be hallmarks of cancer, and can be responsible for driving mutations in tumorigenesis.

Alveolar bone thickness and lower incisor position in skeletal Class I and Class II malocclusions assessed with cone-beam computed tomography

PubMed Central

Ucar, Faruk Izzet; Buyuk, Suleyman Kutalmis; Ozer, Torun; Uysal, Tancan

2013-01-01

Objective To evaluate lower incisor position and bony support between patients with Class II average- and high-angle malocclusions and compare with the patients presenting Class I malocclusions. Methods CBCT records of 79 patients were divided into 2 groups according to sagittal jaw relationships: Class I and II. Each group was further divided into average- and high-angle subgroups. Six angular and 6 linear measurements were performed. Independent samples t-test, Kruskal-Wallis, and Dunn post-hoc tests were performed for statistical comparisons. Results Labial alveolar bone thickness was significantly higher in Class I group compared to Class II group (p = 0.003). Lingual alveolar bone angle (p = 0.004), lower incisor protrusion (p = 0.007) and proclination (p = 0.046) were greatest in Class II average-angle patients. Spongious bone was thinner (p = 0.016) and root apex was closer to the labial cortex in high-angle subgroups when compared to the Class II average-angle subgroup (p = 0.004). Conclusions Mandibular anterior bony support and lower incisor position were different between average- and high-angle Class II patients. Clinicians should be aware that the range of lower incisor movement in high-angle Class II patients is limited compared to average- angle Class II patients. PMID:23814708

Alveolar bone thickness and lower incisor position in skeletal Class I and Class II malocclusions assessed with cone-beam computed tomography.

PubMed

Baysal, Asli; Ucar, Faruk Izzet; Buyuk, Suleyman Kutalmis; Ozer, Torun; Uysal, Tancan

2013-06-01

To evaluate lower incisor position and bony support between patients with Class II average- and high-angle malocclusions and compare with the patients presenting Class I malocclusions. CBCT records of 79 patients were divided into 2 groups according to sagittal jaw relationships: Class I and II. Each group was further divided into average- and high-angle subgroups. Six angular and 6 linear measurements were performed. Independent samples t-test, Kruskal-Wallis, and Dunn post-hoc tests were performed for statistical comparisons. Labial alveolar bone thickness was significantly higher in Class I group compared to Class II group (p = 0.003). Lingual alveolar bone angle (p = 0.004), lower incisor protrusion (p = 0.007) and proclination (p = 0.046) were greatest in Class II average-angle patients. Spongious bone was thinner (p = 0.016) and root apex was closer to the labial cortex in high-angle subgroups when compared to the Class II average-angle subgroup (p = 0.004). Mandibular anterior bony support and lower incisor position were different between average- and high-angle Class II patients. Clinicians should be aware that the range of lower incisor movement in high-angle Class II patients is limited compared to average- angle Class II patients.

Effect of monoclonal antibodies (MoAb) to class I and class II HLA antigens on lectin- and MoAb OKT3-induced lymphocyte proliferation.

PubMed

Akiyama, Y; Zicht, R; Ferrone, S; Bonnard, G D; Herberman, R B

1985-04-01

We have examined the effect of several monoclonal antibodies (MoAb) to monomorphic determinants of class II HLA antigens, and MoAb to monomorphic determinants of class I HLA antigens and to beta-2-microglobulin (beta 2-mu) on lectin- and MoAb OKT3-induced proliferation of human peripheral blood mononuclear cells (PBMNC) and cultured T cells (CTC). Some, but not all, anti-class II HLA MoAb inhibited the proliferative response of PBMNC to MoAb OKT3 and pokeweed mitogen (PWM). The degree of inhibitory effect varied considerably. This effect was not limited to anti-class II HLA MoAb since anti-class I HLA MoAb and anti-beta 2-mu MoAb also inhibited MoAb OKT3- or PWM-induced proliferative responses. In contrast, the response of PBMNC to phytohemagglutinin (PHA) and concanavalin A (Con A) was not blocked by any anti-class II HLA MoAb. However, some anti-class II HLA MoAb also inhibited the proliferative response of CTC plus allogeneic peripheral blood adherent accessory cells (AC) to PHA or Con A as well as to MoAb OKT3 or PWM. This may be attributable to the substantially greater class II HLA antigen expression by CTC than by fresh lymphocytes. Pretreatment of either CTC or AC with anti-class II HLA MoAb inhibited OKT3-induced proliferation. In contrast, pretreatment of CTC, but not AC, with anti-class I HLA MoAb inhibited the proliferative response of CTC to OKT3. Pretreatment of CTC with anti-class I HLA MoAb inhibited PHA-, Con A and PWM-induced proliferation, to a greater degree than the anti-class II HLA MoAb. It appears as if lymphocyte activation by different mitogens exhibits variable requirements for the presence of cells expressing major histocompatibility determinants. Binding of Ab to membrane markers may interfere with lymphocyte-AC cooperation, perhaps by inhibiting binding of mitogens to their receptors or by interfering with lymphocyte and AC function. We also have examined the role of class II HLA antigens on CTC by depleting class II HLA-positive cells. As expected, elimination of class II HLA-positive AC with anti-class II HLA MoAb plus complement caused a decrease in proliferation of CTC in response to all the mitogens tested. In contrast, elimination of class II HLA-positive CTC was shown to clearly increase proliferation of CTC, perhaps because this may deplete class II HLA-positive suppressor cells.

Immunological Functions of the Membrane Proximal Region of MHC Class II Molecules

PubMed Central

Harton, Jonathan; Jin, Lei; Hahn, Amy; Drake, Jim

2016-01-01

Major histocompatibility complex (MHC) class II molecules present exogenously derived antigen peptides to CD4 T cells, driving activation of naïve T cells and supporting CD4-driven immune functions. However, MHC class II molecules are not inert protein pedestals that simply bind and present peptides. These molecules also serve as multi-functional signaling molecules delivering activation, differentiation, or death signals (or a combination of these) to B cells, macrophages, as well as MHC class II-expressing T cells and tumor cells. Although multiple proteins are known to associate with MHC class II, interaction with STING (stimulator of interferon genes) and CD79 is essential for signaling. In addition, alternative transmembrane domain pairing between class II α and β chains influences association with membrane lipid sub-domains, impacting both signaling and antigen presentation. In contrast to the membrane-distal region of the class II molecule responsible for peptide binding and T-cell receptor engagement, the membrane-proximal region (composed of the connecting peptide, transmembrane domain, and cytoplasmic tail) mediates these “non-traditional” class II functions. Here, we review the literature on the function of the membrane-proximal region of the MHC class II molecule and discuss the impact of this aspect of class II immunobiology on immune regulation and human disease. PMID:27006762

Ovarian metastasis in a transposed ovary 10 years after primary cervical cancer: the importance of histologic examination and review of literature.

PubMed

Janse, Julienne A; Sie-Go, Daisy M D S; Schreuder, Henk W R

2011-06-17

Cases of cervical carcinoma metastasing to the transposed ovary are rarely reported in the literature. In this report, the authors present the case of a 53-year-old woman with a persisting, unsuspected cyst in the right transposed ovary, 10 years after treatment for adenosquamous carcinoma of the cervix. It is the first report describing a secondary ovarian malignancy originating from a cervical adenosquamous carcinoma in a transposed ovary. In addition, this is the first account of an ovarian metastasis 10 years after primary treatment for cervical cancer. Furthermore, pathologic examination with immunohistochemistry and human papillomavirus genotyping played a key role in the diagnostic process, as the case did not raise suspicion by ultrasound findings neither by cytological examination after cytological aspiration or by appearance during surgery.

Structural physical approximation for the realization of the optimal singlet fraction with two measurements

NASA Astrophysics Data System (ADS)

Adhikari, Satyabrata

2018-04-01

Structural physical approximation (SPA) has been exploited to approximate nonphysical operation such as partial transpose. It has already been studied in the context of detection of entanglement and found that if the minimum eigenvalue of SPA to partial transpose is less than 2/9 then the two-qubit state is entangled. We find application of SPA to partial transpose in the estimation of the optimal singlet fraction. We show that the optimal singlet fraction can be expressed in terms of the minimum eigenvalue of SPA to partial transpose. We also show that the optimal singlet fraction can be realized using Hong-Ou-Mandel interferometry with only two detectors. Further we have shown that the generated hybrid entangled state between a qubit and a binary coherent state can be used as a resource state in quantum teleportation.

25 CFR 522.5 - Disapproval of a class II ordinance.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false Disapproval of a class II ordinance. 522.5 Section 522.5 Indians NATIONAL INDIAN GAMING COMMISSION, DEPARTMENT OF THE INTERIOR APPROVAL OF CLASS II AND CLASS III ORDINANCES AND RESOLUTIONS SUBMISSION OF GAMING ORDINANCE OR RESOLUTION § 522.5 Disapproval of a class II...

Comprehensive analysis of MHC class II genes in teleost fish genomes reveals dispensability of the peptide-loading DM system in a large part of vertebrates

PubMed Central

2013-01-01

Background Classical major histocompatibility complex (MHC) class II molecules play an essential role in presenting peptide antigens to CD4+ T lymphocytes in the acquired immune system. The non-classical class II DM molecule, HLA-DM in the case of humans, possesses critical function in assisting the classical MHC class II molecules for proper peptide loading and is highly conserved in tetrapod species. Although the absence of DM-like genes in teleost fish has been speculated based on the results of homology searches, it has not been definitively clear whether the DM system is truly specific for tetrapods or not. To obtain a clear answer, we comprehensively searched class II genes in representative teleost fish genomes and analyzed those genes regarding the critical functional features required for the DM system. Results We discovered a novel ancient class II group (DE) in teleost fish and classified teleost fish class II genes into three major groups (DA, DB and DE). Based on several criteria, we investigated the classical/non-classical nature of various class II genes and showed that only one of three groups (DA) exhibits classical-type characteristics. Analyses of predicted class II molecules revealed that the critical tryptophan residue required for a classical class II molecule in the DM system could be found only in some non-classical but not in classical-type class II molecules of teleost fish. Conclusions Teleost fish, a major group of vertebrates, do not possess the DM system for the classical class II peptide-loading and this sophisticated system has specially evolved in the tetrapod lineage. PMID:24279922

The impact of dissociation on transposon-mediated disease control strategies.

PubMed

Marshall, John M

2008-03-01

Vector-borne diseases such as malaria and dengue fever continue to be a major health concern through much of the world. The emergence of chloroquine-resistant strains of malaria and insecticide-resistant mosquitoes emphasize the need for novel methods of disease control. Recently, there has been much interest in the use of transposable elements to drive resistance genes into vector populations as a means of disease control. One concern that must be addressed before a release is performed is the potential loss of linkage between a transposable element and a resistance gene. Transposable elements such as P and hobo have been shown to produce internal deletion derivatives at a significant rate, and there is concern that a similar process could lead to loss of the resistance gene from the drive system following a transgenic release. Additionally, transposable elements such as Himar1 have been shown to transpose significantly more frequently when free of exogenous DNA. Here, we show that any transposon-mediated gene drive strategy must have an exceptionally low rate of dissociation if it is to be effective. Additionally, the resistance gene must confer a large selective advantage to the vector to surmount the effects of a moderate dissociation rate and transpositional handicap.

Does letter position coding depend on consonant/vowel status? Evidence with the masked priming technique.

PubMed

Perea, Manuel; Acha, Joana

2009-02-01

Recently, a number of input coding schemes (e.g., SOLAR model, SERIOL model, open-bigram model, overlap model) have been proposed that capture the transposed-letter priming effect (i.e., faster response times for jugde-JUDGE than for jupte-JUDGE). In their current version, these coding schemes do not assume any processing differences between vowels and consonants. However, in a lexical decision task, Perea and Lupker (2004, JML; Lupker, Perea, & Davis, 2008, L&CP) reported that transposed-letter priming effects occurred for consonant transpositions but not for vowel transpositions. This finding poses a challenge for these recently proposed coding schemes. Here, we report four masked priming experiments that examine whether this consonant/vowel dissociation in transposed-letter priming is task-specific. In Experiment 1, we used a lexical decision task and found a transposed-letter priming effect only for consonant transpositions. In Experiments 2-4, we employed a same-different task - a task which taps early perceptual processes - and found a robust transposed-letter priming effect that did not interact with consonant/vowel status. We examine the implications of these findings for the front-end of the models of visual word recognition.

Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates.

PubMed

Warren, Ian A; Naville, Magali; Chalopin, Domitille; Levin, Perrine; Berger, Chloé Suzanne; Galiana, Delphine; Volff, Jean-Nicolas

2015-09-01

Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.

Applying transpose matrix on advanced encryption standard (AES) for database content

NASA Astrophysics Data System (ADS)

Manurung, E. B. P.; Sitompul, O. S.; Suherman

2018-03-01

Advanced Encryption Standard (AES) is a specification for the encryption of electronic data established by the U.S. National Institute of Standards and Technology (NIST) and has been adopted by the U.S. government and is now used worldwide. This paper reports the impact of transpose matrix integration to AES. Transpose matrix implementation on AES is aimed at first stage of chypertext modifications for text based database security so that the confidentiality improves. The matrix is also able to increase the avalanche effect of the cryptography algorithm 4% in average.

The overlooked "nonclassical" functions of major histocompatibility complex (MHC) class II antigens in immune and nonimmune cells.

PubMed

Altomonte, M; Pucillo, C; Maio, M

1999-06-01

Besides their "classical" antigenic peptide-presenting activity, major histocompatibility complex (MHC) class II antigens can activate different cellular functions in immune and nonimmune cells. However, this "nonclassical" role and its functional consequences are still substantially overlooked. In this review, we will focus on these alternative functional properties of MHC class II antigens, to reawaken attention to their present and foreseeable immunobiologic and pathogenetic implications. The main issues that will be addressed concern 1) the role of MHC class II molecules as basic components of exchangeable oligomeric protein complexes with intracellular signaling ability; 2) the nonclassical functions of MHC class II antigens in immune cells; 3) the pathogenetic role of MHC class II antigens in inflammatory/autoimmune and infectious disease; and 4) the functional role of MHC class II antigens in solid malignancies.

Assessment: transcranial Doppler ultrasonography: report of the Therapeutics and Technology Assessment Subcommittee of the American Academy of Neurology.

PubMed

Sloan, M A; Alexandrov, A V; Tegeler, C H; Spencer, M P; Caplan, L R; Feldmann, E; Wechsler, L R; Newell, D W; Gomez, C R; Babikian, V L; Lefkowitz, D; Goldman, R S; Armon, C; Hsu, C Y; Goodin, D S

2004-05-11

To review the use of transcranial Doppler ultrasonography (TCD) and transcranial color-coded sonography (TCCS) for diagnosis. The authors searched the literature for evidence of 1) if TCD provides useful information in specific clinical settings; 2) if using this information improves clinical decision making, as reflected by improved patient outcomes; and 3) if TCD is preferable to other diagnostic tests in these clinical situations. TCD is of established value in the screening of children aged 2 to 16 years with sickle cell disease for stroke risk (Type A, Class I) and the detection and monitoring of angiographic vasospasm after spontaneous subarachnoid hemorrhage (Type A, Class I to II). TCD and TCCS provide important information and may have value for detection of intracranial steno-occlusive disease (Type B, Class II to III), vasomotor reactivity testing (Type B, Class II to III), detection of cerebral circulatory arrest/brain death (Type A, Class II), monitoring carotid endarterectomy (Type B, Class II to III), monitoring cerebral thrombolysis (Type B, Class II to III), and monitoring coronary artery bypass graft operations (Type B to C, Class II to III). Contrast-enhanced TCD/TCCS can also provide useful information in right-to-left cardiac/extracardiac shunts (Type A, Class II), intracranial occlusive disease (Type B, Class II to IV), and hemorrhagic cerebrovascular disease (Type B, Class II to IV), although other techniques may be preferable in these settings.

25 CFR 547.8 - What are the minimum technical software standards applicable to Class II gaming systems?

Code of Federal Regulations, 2012 CFR

2012-04-01

... OF CLASS II GAMES § 547.8 What are the minimum technical software standards applicable to Class II... of Class II games. (a) Player interface displays. (1) If not otherwise provided to the player, the player interface shall display the following: (i) The purchase or wager amount; (ii) Game results; and...

25 CFR 547.8 - What are the minimum technical software standards applicable to Class II gaming systems?

Code of Federal Regulations, 2011 CFR

2011-04-01

... OF CLASS II GAMES § 547.8 What are the minimum technical software standards applicable to Class II... of Class II games. (a) Player interface displays. (1) If not otherwise provided to the player, the player interface shall display the following: (i) The purchase or wager amount; (ii) Game results; and...

25 CFR 547.8 - What are the minimum technical software standards applicable to Class II gaming systems?

Code of Federal Regulations, 2010 CFR

2010-04-01

... OF CLASS II GAMES § 547.8 What are the minimum technical software standards applicable to Class II... of Class II games. (a) Player interface displays. (1) If not otherwise provided to the player, the player interface shall display the following: (i) The purchase or wager amount; (ii) Game results; and...

Mucin gene expression in human urothelium and in intestinal segments transposed into the urinary tract.

PubMed

N'Dow, J; Pearson, J P; Bennett, M K; Neal, D E; Robson, C N

2000-10-01

The repertoire of mucin (MUC) gene expression in the normal human urothelium is poorly defined and the alterations in MUC gene expression following transposition of intestinal segments into the urinary tract has not previously been studied. The aims of this study were to define MUC gene expression in the normal human urothelium; and in transposed intestinal segments. Non-isotopic in-situ hybridization was carried out using eight digoxigenin labeled oligonucleotide mucin gene probes (MUC 1 - 7). Immunohistochemistry using NCL-MUC1 and NCL-MUC2 monoclonal antibodies was performed on sections of paraffin-embedded tissues. Twenty-seven patients were investigated (normal human urothelium, n = 6; transposed ileal segments, n = 14 and normal ileal controls, n = 7). MUC1 and MUC4 were the predominant mucin genes expressed in the normal urothelium with MUC3 being expressed in a third of cases studied; MUC2, 5AC, 5B, 6 and 7 were not expressed. Despite the morphological changes seen in transposed ileal segments, MUC2 and MUC3 continued to be expressed in these segments albeit in a disorganised fashion. Both MUC1 and MUC4 were up-regulated in transposed ileal segments, genes expressed by the normal human urothelium. All eight mucin genes were expressed in an area of pyloric-type metaplasia found in one transposed ileal segment. In patients with clam enterocystoplasty there was evidence of increasing up-regulation of MUC2, 3, 4 and 5AC expression in the urothelium toward the anastomotic site. Transposition of ileal segments into the urinary tract results in up-regulation of MUC1 and MUC4, the predominant MUC genes expressed in the human bladder. The clinical implication of the up-regulation of some MUC genes toward the anastomotic site in patients with an enteroplasty and the aberrant expression of MUC5AC - MUC7 by transposed segments is at present unclear.

Associative priming effects with visible, transposed-letter nonwords: JUGDE facilitates COURT.

PubMed

Perea, Manuel; Palti, Dafna; Gomez, Pablo

2012-04-01

Associative priming effects can be obtained with masked nonword primes or with masked pseudohomophone primes (e.g., judpe-COURT, tode-FROG), but not with visible primes. The usual explanation is that when the prime is visible, these stimuli no longer activate the semantic representations of their base words. Given the important role of transposed-letter stimuli (e.g., jugde) in visual word recognition, here we examined whether or not an associative priming effect could be obtained with visible transposed-letter nonword primes (e.g., jugde-COURT) in a series of lexical decision experiments. Results showed a sizable associative priming effect with visible transposed-letter nonword primes (i.e., jugde-COURT faster than neevr-COURT) in Experiments 1-3 that was close to that with word primes. In contrast, we failed to find a parallel effect with replacement-letter nonword primes (Experiment 2). These findings pose some constraints to models of visual word recognition.

Transposable Elements and Genetic Instabilities in Crop Plants

DOE R&D Accomplishments Database

Burr, B.; Burr, F.

1981-04-10

Transposable elements have long been associated with certain unstable loci in maize and have been intensively studied by McClintock and others. It is known that a transposable element can control the expression of the structural genes at the locus where it resides. These controlling elements in maize are now beginning to be studied at the molecular level. Using recombinant molecular probes we have been able to describe the changes induced by the controlling element Ds at the shrunken locus. Ds elements appear to be large and dissimilar insertions into the wild-type locus - two elements actually map within the transcribed region of the gene. Genetic instabilities have been described in other economically important plants but the bases for these phenomena have not been understood. We believe that it is likely that some of these instabilities are the result of transposable element activity much as in the case of maize.

The Initiation of Epigenetic Silencing of Active Transposable Elements Is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs1[W][OA

PubMed Central

Nuthikattu, Saivageethi; McCue, Andrea D.; Panda, Kaushik; Fultz, Dalen; DeFraia, Christopher; Thomas, Erica N.; Slotkin, R. Keith

2013-01-01

Transposable elements (TEs) are mobile fragments of DNA that are repressed in both plant and animal genomes through the epigenetic inheritance of repressed chromatin and expression states. The epigenetic silencing of TEs in plants is mediated by a process of RNA-directed DNA methylation (RdDM). Two pathways of RdDM have been identified: RNA Polymerase IV (Pol IV)-RdDM, which has been shown to be responsible for the de novo initiation, corrective reestablishment, and epigenetic maintenance of TE and/or transgene silencing; and RNA-dependent RNA Polymerase6 (RDR6)-RdDM, which was recently identified as necessary for maintaining repression for a few TEs. We have further characterized RDR6-RdDM using a genome-wide search to identify TEs that generate RDR6-dependent small interfering RNAs. We have determined that TEs only produce RDR6-dependent small interfering RNAs when transcriptionally active, and we have experimentally identified two TE subfamilies as direct targets of RDR6-RdDM. We used these TEs to test the function of RDR6-RdDM in assays for the de novo initiation, corrective reestablishment, and maintenance of TE silencing. We found that RDR6-RdDM plays no role in maintaining TE silencing. Rather, we found that RDR6 and Pol IV are two independent entry points into RdDM and epigenetic silencing that perform distinct functions in the silencing of TEs: Pol IV-RdDM functions to maintain TE silencing and to initiate silencing in an RNA Polymerase II expression-independent manner, while RDR6-RdDM functions to recognize active Polymerase II-derived TE mRNA transcripts to both trigger and correctively reestablish TE methylation and epigenetic silencing. PMID:23542151

The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs.

PubMed

Nuthikattu, Saivageethi; McCue, Andrea D; Panda, Kaushik; Fultz, Dalen; DeFraia, Christopher; Thomas, Erica N; Slotkin, R Keith

2013-05-01

Transposable elements (TEs) are mobile fragments of DNA that are repressed in both plant and animal genomes through the epigenetic inheritance of repressed chromatin and expression states. The epigenetic silencing of TEs in plants is mediated by a process of RNA-directed DNA methylation (RdDM). Two pathways of RdDM have been identified: RNA Polymerase IV (Pol IV)-RdDM, which has been shown to be responsible for the de novo initiation, corrective reestablishment, and epigenetic maintenance of TE and/or transgene silencing; and RNA-dependent RNA Polymerase6 (RDR6)-RdDM, which was recently identified as necessary for maintaining repression for a few TEs. We have further characterized RDR6-RdDM using a genome-wide search to identify TEs that generate RDR6-dependent small interfering RNAs. We have determined that TEs only produce RDR6-dependent small interfering RNAs when transcriptionally active, and we have experimentally identified two TE subfamilies as direct targets of RDR6-RdDM. We used these TEs to test the function of RDR6-RdDM in assays for the de novo initiation, corrective reestablishment, and maintenance of TE silencing. We found that RDR6-RdDM plays no role in maintaining TE silencing. Rather, we found that RDR6 and Pol IV are two independent entry points into RdDM and epigenetic silencing that perform distinct functions in the silencing of TEs: Pol IV-RdDM functions to maintain TE silencing and to initiate silencing in an RNA Polymerase II expression-independent manner, while RDR6-RdDM functions to recognize active Polymerase II-derived TE mRNA transcripts to both trigger and correctively reestablish TE methylation and epigenetic silencing.

40 CFR 147.3200 - Fort Peck Indian Reservation: Assiniboine & Sioux Tribes-Class II wells.

Code of Federal Regulations, 2014 CFR

2014-07-01

...: Assiniboine & Sioux Tribes-Class II wells. 147.3200 Section 147.3200 Protection of Environment ENVIRONMENTAL... INJECTION CONTROL PROGRAMS Assiniboine and Sioux Tribes § 147.3200 Fort Peck Indian Reservation: Assiniboine & Sioux Tribes—Class II wells. The UIC program for Class II injection wells on all lands within the...

40 CFR 147.3200 - Fort Peck Indian Reservation: Assiniboine & Sioux Tribes-Class II wells.

Code of Federal Regulations, 2012 CFR

2012-07-01

...: Assiniboine & Sioux Tribes-Class II wells. 147.3200 Section 147.3200 Protection of Environment ENVIRONMENTAL... INJECTION CONTROL PROGRAMS Assiniboine and Sioux Tribes § 147.3200 Fort Peck Indian Reservation: Assiniboine & Sioux Tribes—Class II wells. The UIC program for Class II injection wells on all lands within the...

40 CFR 147.3200 - Fort Peck Indian Reservation: Assiniboine & Sioux Tribes-Class II wells.

Code of Federal Regulations, 2013 CFR

2013-07-01

...: Assiniboine & Sioux Tribes-Class II wells. 147.3200 Section 147.3200 Protection of Environment ENVIRONMENTAL... INJECTION CONTROL PROGRAMS Assiniboine and Sioux Tribes § 147.3200 Fort Peck Indian Reservation: Assiniboine & Sioux Tribes—Class II wells. The UIC program for Class II injection wells on all lands within the...

78 FR 24061 - Minimum Technical Standards for Class II Gaming Systems and Equipment

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-24

... Register that established technical standards for ensuring the integrity of electronic Class II games and aids. 73 FR 60508, Oct. 10, 2008. The technical standards were designed to assist tribal gaming... Class II gaming systems. The standards did not classify which games were Class II games and which games...

40 CFR 147.3400 - Navajo Indian lands-Class II wells.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 23 2014-07-01 2014-07-01 false Navajo Indian lands-Class II wells... Indian Lands § 147.3400 Navajo Indian lands—Class II wells. The UIC program for Class II injection wells... outside those exterior boundaries (collectively referred to as “Navajo Indian lands for which EPA has...

77 FR 37058 - Draft Guidance for Industry and Food and Drug Administration Staff; Class II Special Controls...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-20

...] Draft Guidance for Industry and Food and Drug Administration Staff; Class II Special Controls Guidance... availability of the draft guidance entitled ``Class II Special Controls Guidance Document: Implanted Blood... blood access devices may comply with the requirement of special controls for class II devices. This...

Differential Transmembrane Domain GXXXG Motif Pairing Impacts Major Histocompatibility Complex (MHC) Class II Structure*

PubMed Central

Dixon, Ann M.; Drake, Lisa; Hughes, Kelly T.; Sargent, Elizabeth; Hunt, Danielle; Harton, Jonathan A.; Drake, James R.

2014-01-01

Major histocompatibility complex (MHC) class II molecules exhibit conformational heterogeneity, which influences their ability to stimulate CD4 T cells and drive immune responses. Previous studies suggest a role for the transmembrane domain of the class II αβ heterodimer in determining molecular structure and function. Our previous studies identified an MHC class II conformer that is marked by the Ia.2 epitope. These Ia.2+ class II conformers are lipid raft-associated and able to drive both tyrosine kinase signaling and efficient antigen presentation to CD4 T cells. Here, we establish that the Ia.2+ I-Ak conformer is formed early in the class II biosynthetic pathway and that differential pairing of highly conserved transmembrane domain GXXXG dimerization motifs is responsible for formation of Ia.2+ versus Ia.2− I-Ak class II conformers and controlling lipid raft partitioning. These findings provide a molecular explanation for the formation of two distinct MHC class II conformers that differ in their inherent ability to signal and drive robust T cell activation, providing new insight into the role of MHC class II in regulating antigen-presenting cell-T cell interactions critical to the initiation and control of multiple aspects of the immune response. PMID:24619409

40 CFR 144.19 - Transitioning from Class II to Class VI.

Code of Federal Regulations, 2011 CFR

2011-07-01

... primary purpose of long-term storage into an oil and gas reservoir must apply for and obtain a Class VI geologic sequestration permit when there is an increased risk to USDWs compared to Class II operations. In... Class II operations and a Class VI permit is required. In order to make this determination the Director...

A Triad of Molecular Regions Contribute to the Formation of Two Distinct MHC Class II Conformers

PubMed Central

Drake, Lisa A.; Drake, James R.

2016-01-01

MHC class II molecules present antigen-derived peptides to CD4 T cells to drive the adaptive immune response. Previous work has established that class II αβ dimers can adopt two distinct conformations, driven by the differential pairing of transmembrane domain GxxxG dimerization motifs. These class II conformers differ in their ability to be loaded with antigen-derived peptide and to effectively engage CD4 T cells. Motif 1 (M1) paired I-Ak class II molecules are efficiently loaded with peptides derived from the processing of B cell receptor-bound antigen, have unique B cell signaling properties and high T cell stimulation activity. The 11-5.2 mAb selectively binds M1 paired I-Ak class II molecules. However, the molecular determinants of 11-5.2 binding are currently unclear. Here, we report the ability of a human class II transmembrane domain to drive both M1 and M2 class II conformer formation. Protease sensitivity analysis further strengthens the idea that there are conformational differences between the extracellular domains of M1 and M2 paired class II. Finally, MHC class II chain alignments and site directed mutagenesis reveals a triad of molecular regions that contributes to 11-5.2 mAb binding. In addition to transmembrane GxxxG motif domain pairing, 11-5.2 binding is influenced directly by α chain residue Glu-71 and indirectly by the region around the inter-chain salt bridge formed by α chain Arg-52 and β chain Glu-86. These findings provide insight into the complexity of 11-5.2 mAb recognition of the M1 paired I-Ak class II conformer and further highlight the molecular heterogeneity of peptide-MHC class II complexes that drive T cell antigen recognition. PMID:27148821

Maxillary and mandibular contribution to the establishment of class II malocclusion in an adult Lebanese population.

PubMed

El Hajj, Nadine; Bassil-Nassif, Nayla; Tauk, Alain; Mouhanna-Fattal, Carole; Bouserhal, Joseph P

2017-12-01

The main aim of this study was to describe the contribution of the maxilla and the mandible to the establishment of a Class II skeletal malocclusion in an adult Lebanese population. Secondary aims were to detect the presence of sex-based dimorphism and to study the influence of the vertical dimension on the Class II skeletal pattern. A sample of 90 adults in skeletal Class II was recruited and equally distributed according to sex and vertical typology. The study describes the skeletal and dentoalveolar cephalometric characteristics of the Class II sample, essentially according to Coben's cephalometric analysis. The total effective depth of the cranial base and the anterior cranial base angle (SN-BaH) were both greater in the Class II sample. In females, the effective depth of the maxilla (Ptm-A) was larger than normal while SNB was smaller. The parameters describing the size and shape of the body of the mandible were significantly different from those of normal subjects. The upper incisors were in a retrusive position, while the axis of the lower incisors was located normally. The mandibular molars had a more distal sagittal position. Hyperdivergent subjects had more significant posterior alveolar growth, a more retrusive mandibular position and smaller mandibular dimensions than the other two vertical sub-groups. The cranial base contributes to the establishment of a Class II malocclusion, and mandibular retrusion cannot be considered as a characteristic shared by all skeletal Class II subjects. Lessening of the absolute length of the mandibular body is the second most frequent etiological factor noted in the Class II sample studied. Most individuals in skeletal Class II have an associated dental Class II malocclusion, and the vertical dimension has an influence on the Class II skeletal pattern. Copyright © 2017 CEO. Published by Elsevier Masson SAS. All rights reserved.

Dual MAPK inhibition is an effective therapeutic strategy for a subset of class II BRAF mutant melanoma.

PubMed

Dankner, Matthew; Lajoie, Mathieu; Moldoveanu, Dan; Nguyen, Tan-Trieu; Savage, Paul; Rajkumar, Shivshankari; Huang, Xiu; Lvova, Maria; Protopopov, Alexei; Vuzman, Dana; Hogg, David; Park, Morag; Guiot, Marie-Christine; Petrecca, Kevin; Mihalcioiu, Catalin; Watson, Ian R; Siegel, Peter M; Rose, April A N

2018-06-14

Dual MAPK pathway inhibition (dMAPKi) with BRAF and MEK inhibitors improves survival in BRAF V600E/K mutant melanoma, but the efficacy of dMAPKi in non-V600 BRAF mutant tumors is poorly understood. We sought to characterize the responsiveness of class II (enhanced kinase activity, dimerization dependent) BRAF mutant melanoma to dMAPKi. Tumors from patients with BRAF WT, V600E (class I) and L597S (class II) metastatic melanoma were used to generate patient-derived-xenografts (PDX). We assembled a panel of melanoma cell lines with class IIa (activation segment) or IIb (p-loop) mutations and compared these to wild-type or V600E/K BRAF mutant cells. Cell lines and PDXs were treated with BRAFi (vemurafenib, dabrafenib, encorafenib, LY3009120), MEKi (cobimetinib, trametinib, binimetinib) or the combination. We identified two patients with BRAF L597S metastatic melanoma who were treated with dMAPKi. BRAFi impaired MAPK signalling and cell growth in class I and II BRAF mutant cells. dMAPKi was more effective than either single MAPKi at inhibiting cell growth in all class II BRAF mutant cells tested. dMAPKi caused tumor regression in two melanoma PDXs with class II BRAF mutations, and prolonged survival of mice with class II BRAF mutant melanoma brain metastases. Two patients with BRAF L597S mutant melanoma clinically responded to dMAPKi. Class II BRAF mutant melanoma are growth inhibited by dMAPKi. Responses to dMAPKi have been observed in two patients with class II BRAF mutant melanoma. This data provides rationale for clinical investigation of dMAPKi in patients with class II BRAF mutant metastatic melanoma. Copyright ©2018, American Association for Cancer Research.

Equine bone marrow-derived mesenchymal stromal cells are heterogeneous in MHC class II expression and capable of inciting an immune response in vitro

PubMed Central

2014-01-01

Introduction The horse is a valuable species to assess the effect of allogeneic mesenchymal stromal cells (MSCs) in regenerative treatments. No studies to date have examined recipient response to major histocompatibility complex (MHC)-mismatched equine MSCs. The purposes of this study were to immunophenotype MSCs from horses of known MHC haplotype and to compare the immunogenicity of MSCs with differing MHC class II expression. Methods MSCs and peripheral blood leukocytes (PBLs) were obtained from Thoroughbred horses (n = 10) of known MHC haplotype (ELA-A2, -A3, and -A9 homozygotes). MSCs were cultured through P8; cells from each passage (P2 to P8) were cryopreserved until used. Immunophenotyping of MHC class I and II, CD44, CD29, CD90, LFA-1, and CD45RB was performed by using flow cytometry. Tri-lineage differentiation assays were performed to confirm MSC multipotency. Recombinant equine IFN-γ was used to stimulate MHC class II negative MSCs in culture, after which expression of MHC class II was re-examined. To assess the ability of MHC class II negative or positive MSCs to stimulate an immune response, modified one-way mixed leukocyte reactions (MLRs) were performed by using MHC-matched and mismatched responder PBLs and stimulator PBLs or MSCs. Proliferation of gated CFSE-labeled CD3+ responder T cells was evaluated via CFSE attenuation by using flow cytometry and reported as the number of cells in the proliferating T-cell gate. Results MSCs varied widely in MHC class II expression despite being homogenous in terms of “stemness” marker expression and ability to undergo trilineage differentiation. Stimulation of MHC class II negative MSCs with IFN-γ resulted in markedly increased expression of MHC class II. MLR results revealed that MHC-mismatched MHC class II-positive MSCs caused significantly increased responder T-cell proliferation compared with MHC-mismatched MHC class II-negative and MHC-matched MSCs, and equivalent to that of the positive control of MHC-mismatched leukocytes. Conclusions The results of this study suggest that MSCs should be confirmed as MHC class II negative before allogeneic application. Additionally, it must be considered that even MHC class II-negative MSCs could upregulate MHC class II expression if implanted into an area of active inflammation, as demonstrated with in vitro stimulation with IFN-γ. PMID:24461709

Jumping Genes: The Transposable DNAs of Bacteria.

ERIC Educational Resources Information Center

Berg, Claire M.; Berg, Douglas E.

1984-01-01

Transposons are transposable elements that carry genes for antibiotic resistance. Provides background information on the structure and organization of these "jumping genes" in bacteria. Also describes the use of transposons in tagging genes and lists pertinent references and resource materials. (DH)

Orthodontic Intervention to Impacted and Transposed Lower Canines

PubMed Central

Kılıç, Nihat

2017-01-01

Impacted and transposed teeth cause serious difficulties in tooth eruption and movement as well as esthetic and functional outcomes. Proper treatment planning including good biomechanical control is essential in order to avoid side effects during traction and aligning of the impacted and/or transposed teeth. The purpose of the present study was to present a successfully treated female patient having transposed and impacted lower canines by means of a modified lingual arch and fixed orthodontic appliance. A female patient aged 13 years and 9 months presented to the orthodontic department with a chief compliant of bilateral spacing and missing teeth in mandibular dentition. After leveling and creating sufficient space in the mandibular arch for the canines, a modified lingual arch was cemented to the mandibular first molars. The lingual arch had two hooks extending to the distobuccal areas of the canine spaces. Elastic chains were applied between the hooks on the lingual arch and the ligatures tied to the attachments on the canine crowns. The light forces generated by elastic materials caused impacted canines to erupt and tend towards their own spaces in the dental arch. As a result, impacted and transposed lower canines were properly positioned in their spaces, and the treatment results were stable during the retention period. PMID:28540090

49 CFR 1150.35 - Procedures and relevant dates-transactions that involve creation of Class I or Class II carriers.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 8 2014-10-01 2014-10-01 false Procedures and relevant dates-transactions that involve creation of Class I or Class II carriers. 1150.35 Section 1150.35 Transportation Other Regulations.... 10901 § 1150.35 Procedures and relevant dates—transactions that involve creation of Class I or Class II...

49 CFR 1150.35 - Procedures and relevant dates-transactions that involve creation of Class I or Class II carriers.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 8 2013-10-01 2013-10-01 false Procedures and relevant dates-transactions that involve creation of Class I or Class II carriers. 1150.35 Section 1150.35 Transportation Other Regulations.... 10901 § 1150.35 Procedures and relevant dates—transactions that involve creation of Class I or Class II...

49 CFR 1150.35 - Procedures and relevant dates-transactions that involve creation of Class I or Class II carriers.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 8 2012-10-01 2012-10-01 false Procedures and relevant dates-transactions that involve creation of Class I or Class II carriers. 1150.35 Section 1150.35 Transportation Other Regulations.... 10901 § 1150.35 Procedures and relevant dates—transactions that involve creation of Class I or Class II...

49 CFR 1150.35 - Procedures and relevant dates-transactions that involve creation of Class I or Class II carriers.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 8 2011-10-01 2011-10-01 false Procedures and relevant dates-transactions that involve creation of Class I or Class II carriers. 1150.35 Section 1150.35 Transportation Other Regulations.... 10901 § 1150.35 Procedures and relevant dates—transactions that involve creation of Class I or Class II...

49 CFR 1150.35 - Procedures and relevant dates-transactions that involve creation of Class I or Class II carriers.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 8 2010-10-01 2010-10-01 false Procedures and relevant dates-transactions that involve creation of Class I or Class II carriers. 1150.35 Section 1150.35 Transportation Other Regulations.... 10901 § 1150.35 Procedures and relevant dates—transactions that involve creation of Class I or Class II...

49 CFR 572.127 - Test conditions and instrumentation.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Forces—Class 1000; (ii) Moments—Class 600; (iii) Pendulum acceleration—Class 180; (iv) Rotation—Class 60 (if used). (3) Thorax: (i) Rib acceleration—Class 1000; (ii) Spine and pendulum accelerations—Class...

49 CFR 572.127 - Test conditions and instrumentation.

Code of Federal Regulations, 2014 CFR

2014-10-01

...) Forces—Class 1000; (ii) Moments—Class 600; (iii) Pendulum acceleration—Class 180; (iv) Rotation—Class 60 (if used). (3) Thorax: (i) Rib acceleration—Class 1000; (ii) Spine and pendulum accelerations—Class...

49 CFR 572.127 - Test conditions and instrumentation.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) Forces—Class 1000; (ii) Moments—Class 600; (iii) Pendulum acceleration—Class 180; (iv) Rotation—Class 60 (if used). (3) Thorax: (i) Rib acceleration—Class 1000; (ii) Spine and pendulum accelerations—Class...

49 CFR 572.127 - Test conditions and instrumentation.

Code of Federal Regulations, 2013 CFR

2013-10-01

...) Forces—Class 1000; (ii) Moments—Class 600; (iii) Pendulum acceleration—Class 180; (iv) Rotation—Class 60 (if used). (3) Thorax: (i) Rib acceleration—Class 1000; (ii) Spine and pendulum accelerations—Class...

49 CFR 572.127 - Test conditions and instrumentation.

Code of Federal Regulations, 2012 CFR

2012-10-01

...) Forces—Class 1000; (ii) Moments—Class 600; (iii) Pendulum acceleration—Class 180; (iv) Rotation—Class 60 (if used). (3) Thorax: (i) Rib acceleration—Class 1000; (ii) Spine and pendulum accelerations—Class...

Postoperative surgical complications of lymphadenohysterocolpectomy

PubMed Central

Marin, F; Pleşca, M; Bordea, CI; Voinea, SC; Burlănescu, I; Ichim, E; Jianu, CG; Nicolăescu, RR; Teodosie, MP; Maher, K; Blidaru, A

2014-01-01

Rationale The current standard surgical treatment for the cervix and uterine cancer is the radical hysterectomy (lymphadenohysterocolpectomy). This has the risk of intraoperative accidents and postoperative associated morbidity. Objective The purpose of this article is the evaluation and quantification of the associated complications in comparison to the postoperative morbidity which resulted after different types of radical hysterectomy. Methods and results Patients were divided according to the type of surgery performed as follows: for cervical cancer – group A- 37 classic radical hysterectomies Class III Piver - Rutledge -Smith ( PRS ), group B -208 modified radical hysterectomies Class II PRS and for uterine cancer- group C -79 extended hysterectomies with pelvic lymphadenectomy from which 17 patients with paraaortic lymphnode biopsy . All patients performed preoperative radiotherapy and 88 of them associated radiosensitization. Discussion Early complications were intra-abdominal bleeding ( 2.7% Class III PRS vs 0.48% Class II PRS), supra-aponeurotic hematoma ( 5.4% III vs 2.4% II) , dynamic ileus (2.7% III vs 0.96% II) and uro - genital fistulas (5.4% III vs 0.96% II).The late complications were the bladder dysfunction (21.6% III vs 16.35% II) , lower limb lymphedema (13.5% III vs 11.5% II), urethral strictures (10.8% III vs 4.8% II) , incisional hernias ( 8.1% III vs 7.2% II), persistent pelvic pain (18.91% III vs 7.7% II), bowel obstruction (5.4% III vs 1.4% II) and deterioration of sexual function (83.3% III vs 53.8% II). PRS class II radical hysterectomy is associated with fewer complications than PRS class III radical hysterectomy , except for the complications of lymphadenectomy . A new method that might reduce these complications is a selective lymphadenectomy represented by sentinel node biopsy . In conclusion PRS class II radical hysterectomy associated with neoadjuvant radiotherapy is a therapeutic option for the incipient stages of cervical cancer. Abbreviations: PRS- Piver Rutledge-Smith, II- class II, III- class III PMID:24653760

49 CFR 572.146 - Test conditions and instrumentation.

Code of Federal Regulations, 2013 CFR

2013-10-01

...) Head acceleration—Class 1000 (2) Neck (i) Force—Class 1000 (ii) Moments—Class 600 (iii) Pendulum... acceleration—Class 1000 (ii) Spine and pendulum accelerations—Class 180 (iii) Sternum deflection—Class 600 (iv...

49 CFR 572.146 - Test conditions and instrumentation.

Code of Federal Regulations, 2012 CFR

2012-10-01

...) Head acceleration—Class 1000 (2) Neck (i) Force—Class 1000 (ii) Moments—Class 600 (iii) Pendulum... acceleration—Class 1000 (ii) Spine and pendulum accelerations—Class 180 (iii) Sternum deflection—Class 600 (iv...

49 CFR 572.146 - Test conditions and instrumentation.

Code of Federal Regulations, 2014 CFR

2014-10-01

...) Head acceleration—Class 1000 (2) Neck (i) Force—Class 1000 (ii) Moments—Class 600 (iii) Pendulum... acceleration—Class 1000 (ii) Spine and pendulum accelerations—Class 180 (iii) Sternum deflection—Class 600 (iv...

49 CFR 572.146 - Test conditions and instrumentation.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Head acceleration—Class 1000 (2) Neck (i) Force—Class 1000 (ii) Moments—Class 600 (iii) Pendulum... acceleration—Class 1000 (ii) Spine and pendulum accelerations—Class 180 (iii) Sternum deflection—Class 600 (iv...

49 CFR 572.146 - Test conditions and instrumentation.

Code of Federal Regulations, 2011 CFR

2011-10-01

...) Head acceleration—Class 1000 (2) Neck (i) Force—Class 1000 (ii) Moments—Class 600 (iii) Pendulum... acceleration—Class 1000 (ii) Spine and pendulum accelerations—Class 180 (iii) Sternum deflection—Class 600 (iv...

Families of vector-like deformations of relativistic quantum phase spaces, twists and symmetries

NASA Astrophysics Data System (ADS)

Meljanac, Daniel; Meljanac, Stjepan; Pikutić, Danijel

2017-12-01

Families of vector-like deformed relativistic quantum phase spaces and corresponding realizations are analyzed. A method for a general construction of the star product is presented. The corresponding twist, expressed in terms of phase space coordinates, in the Hopf algebroid sense is presented. General linear realizations are considered and corresponding twists, in terms of momenta and Poincaré-Weyl generators or gl(n) generators are constructed and R-matrix is discussed. A classification of linear realizations leading to vector-like deformed phase spaces is given. There are three types of spaces: (i) commutative spaces, (ii) κ -Minkowski spaces and (iii) κ -Snyder spaces. The corresponding star products are (i) associative and commutative (but non-local), (ii) associative and non-commutative and (iii) non-associative and non-commutative, respectively. Twisted symmetry algebras are considered. Transposed twists and left-right dual algebras are presented. Finally, some physical applications are discussed.

The Tc1/mariner transposable element family shapes genetic variation and gene expression in the protist Trichomonas vaginalis

PubMed Central

2014-01-01

Background Trichomonas vaginalis is the most prevalent non-viral sexually transmitted parasite. Although the protist is presumed to reproduce asexually, 60% of its haploid genome contains transposable elements (TEs), known contributors to genome variability. The availability of a draft genome sequence and our collection of >200 global isolates of T. vaginalis facilitate the study and analysis of TE population dynamics and their contribution to genomic variability in this protist. Results We present here a pilot study of a subset of class II Tc1/mariner TEs that belong to the T. vaginalis Tvmar1 family. We report the genetic structure of 19 Tvmar1 loci, their ability to encode a full-length transposase protein, and their insertion frequencies in 94 global isolates from seven regions of the world. While most of the Tvmar1 elements studied exhibited low insertion frequencies, two of the 19 loci (locus 1 and locus 9) show high insertion frequencies of 1.00 and 0.96, respectively. The genetic structuring of the global populations identified by principal component analysis (PCA) of the Tvmar1 loci is in general agreement with published data based on genotyping, showing that Tvmar1 polymorphisms are a robust indicator of T. vaginalis genetic history. Analysis of expression of 22 genes flanking 13 Tvmar1 loci indicated significantly altered expression of six of the genes next to five Tvmar1 insertions, suggesting that the insertions have functional implications for T. vaginalis gene expression. Conclusions Our study is the first in T. vaginalis to describe Tvmar1 population dynamics and its contribution to genetic variability of the parasite. We show that a majority of our studied Tvmar1 insertion loci exist at very low frequencies in the global population, and insertions are variable between geographical isolates. In addition, we observe that low frequency insertion is related to reduced or abolished expression of flanking genes. While low insertion frequencies might be expected, we identified two Tvmar1 insertion loci that are fixed across global populations. This observation indicates that Tvmar1 insertion may have differing impacts and fitness costs in the host genome and may play varying roles in the adaptive evolution of T. vaginalis. PMID:24834134

Diversity and structure of PIF/Harbinger-like elements in the genome of Medicago truncatula

PubMed Central

Grzebelus, Dariusz; Lasota, Slawomir; Gambin, Tomasz; Kucherov, Gregory; Gambin, Anna

2007-01-01

Background Transposable elements constitute a significant fraction of plant genomes. The PIF/Harbinger superfamily includes DNA transposons (class II elements) carrying terminal inverted repeats and producing a 3 bp target site duplication upon insertion. The presence of an ORF coding for the DDE/DDD transposase, required for transposition, is characteristic for the autonomous PIF/Harbinger-like elements. Based on the above features, PIF/Harbinger-like elements were identified in several plant genomes and divided into several evolutionary lineages. Availability of a significant portion of Medicago truncatula genomic sequence allowed for mining PIF/Harbinger-like elements, starting from a single previously described element MtMaster. Results Twenty two putative autonomous, i.e. carrying an ORF coding for TPase and complete terminal inverted repeats, and 67 non-autonomous PIF/Harbinger-like elements were found in the genome of M. truncatula. They were divided into five families, MtPH-A5, MtPH-A6, MtPH-D,MtPH-E, and MtPH-M, corresponding to three previously identified and two new lineages. The largest families, MtPH-A6 and MtPH-M were further divided into four and three subfamilies, respectively. Non-autonomous elements were usually direct deletion derivatives of the putative autonomous element, however other types of rearrangements, including inversions and nested insertions were also observed. An interesting structural characteristic – the presence of 60 bp tandem repeats – was observed in a group of elements of subfamily MtPH-A6-4. Some families could be related to miniature inverted repeat elements (MITEs). The presence of empty loci (RESites), paralogous to those flanking the identified transposable elements, both autonomous and non-autonomous, as well as the presence of transposon insertion related size polymorphisms, confirmed that some of the mined elements were capable for transposition. Conclusion The population of PIF/Harbinger-like elements in the genome of M. truncatula is diverse. A detailed intra-family comparison of the elements' structure proved that they proliferated in the genome generally following the model of abortive gap repair. However, the presence of tandem repeats facilitated more pronounced rearrangements of the element internal regions. The insertion polymorphism of the MtPH elements and related MITE families in different populations of M. truncatula, if further confirmed experimentally, could be used as a source of molecular markers complementary to other marker systems. PMID:17996080

Major histocompatibility complex class II molecule expression on muscle cells is regulated by differentiation: implications for the immunopathogenesis of muscle autoimmune diseases.

PubMed

Mantegazza, R; Gebbia, M; Mora, M; Barresi, R; Bernasconi, P; Baggi, F; Cornelio, F

1996-08-01

Major histocompatibility complex (MHC) class II molecules are expressed on myoblasts after interferon-gamma (IFN-gamma) treatment, suggesting a muscle cell involvement in antigen presentation in inflammatory myopathies. However, they were not observed on normal or pathological myofibers. This discrepancy might be related to different responsiveness of developmentally differentiated muscle cells to IFN-gamma. Myoblasts expressed class II transcripts and proteins after IFN-gamma, while myotubes and innervated contracting muscle cells did not show staining for class II molecules. At all cell stages no loss of IFN-gamma receptor was detected indicating that myofiber maturation blocks their capacity to express MHC class II molecules. This suggests that completely differentiated myofibers cannot participate in class II restricted immunological reactions.

Correlation between location of transposed ovary and function in cervical cancer patients who underwent radical hysterectomy.

PubMed

Yoon, Aera; Lee, Yoo-Young; Park, Won; Huh, Seung Jae; Choi, Chel Hun; Kim, Tae-Joong; Lee, Jeong-Won; Kim, Byoung-Gie; Bae, Duk-Soo

2015-05-01

The study investigated the association between the location of transposed ovaries and posttreatment ovarian function in patients with early cervical cancer (IB1-IIA) who underwent radical hysterectomy and ovarian transposition with or without adjuvant therapies. Retrospective medical records were reviewed to enroll the patients with early cervical cancer who underwent ovarian transposition during radical hysterectomy at Samsung Medical Center between July 1995 and July 2012. Serum follicle-stimulating hormone (FSH) level was used as a surrogate marker for ovarian function. Twenty-one patients were enrolled. The median age and body mass index (BMI) were 31 years (range, 24-39 years) and 21.3 kg/m² (range, 17.7-31.2 kg/m²), respectively. The median serum FSH level after treatment was 7.9 mIU/mL (range, 2.4-143.4 mIU/mL). The median distance from the iliac crest to transposed ovaries on erect plain abdominal x-ray was 0.5 cm (range, -2.7 to 5.2 cm). In multivariate analysis, posttreatment serum FSH levels were significantly associated with the location of transposed ovaries (β = -8.1, P = 0.032), concurrent chemoradiation (CCRT) as an adjuvant therapy (β = 71.08, P = 0.006), and BMI before treatment (underweight: β = -59.93, P = 0.05; overweight: β = -40.62, P = 0.041). Location of transposed ovaries, adjuvant CCRT, and BMI before treatment may be associated with ovarian function after treatment. We suggest that ovaries should be transposed as highly as possible during radical hysterectomy to preserve ovarian function in young patients with early cervical cancer who might be a candidate for adjuvant CCRT and who have low BMI before treatment.

Adjustable Augmented Rectus Muscle Transposition Surgery with or Without Ciliary Vessel Sparing for Abduction Deficiencies

PubMed Central

Hendler, Karen; Pineles, Stacy L.; Demer, Joseph L.; Yang, Dawn; Velez, Federico G.

2014-01-01

Background Vertical rectus transposition (VRT) is useful in abduction deficiencies. Posterior fixation sutures enhance the effect of VRT, but usually preclude the use of adjustable sutures. Augmentation of VRT by resection of the transposed muscles allows for an adjustable technique that can reduce induced vertical deviations and overcorrections. Methods We retrospectively reviewed the records of all patients undergoing adjustable partial or full tendon VRT augmented by resection of the transposed muscles. Ciliary vessels were preserved in most of the patients by either splitting the transposed muscle or by dragging the transposed muscle without disrupting the muscle insertion. Results Seven patients with abducens palsy and one with esotropic Duane syndrome were included. Both vertical rectus muscles were symmetrically resected by 3–5 mm. Preoperative central gaze esotropia of 30.6 ± 12.9Δ (range, 17–50Δ) decreased to 10.6 ± 8.8Δ (range, 0–25Δ) at the final visit (p = 0.003). Three patients required postoperative adjustment by recession of one of the transposed muscles due to an induced vertical deviation (mean 9.3Δ reduced to 0Δ), coupled with overcorrection (mean exotropia 11.3Δ reduced to 0 in two patients and exophoria 2Δ in one patient). At the final follow-up visit 3.8 ± 2.6 months postoperatively, one patient had a vertical deviation <4Δ, and none had overcorrection or anterior segment ischemia. Three patients required further surgery for recurrent esotropia. Conclusions Augmentation of VRT by resection of the transposed muscles can be performed with adjustable sutures and vessel-sparing technique. This allows for postoperative control of overcorrections and induced vertical deviations as well as less risk of anterior segment ischemia. PMID:24738948

Adjustable augmented rectus muscle transposition surgery with or without ciliary vessel sparing for abduction deficiencies.

PubMed

Hendler, Karen; Pineles, Stacy L; Demer, Joseph L; Yang, Dawn; Velez, Federico G

2014-06-01

Vertical rectus transposition (VRT) is useful in abduction deficiencies. Posterior fixation sutures enhance the effect of VRT, but usually preclude the use of adjustable sutures. Augmentation of VRT by resection of the transposed muscles allows for an adjustable technique that can reduce induced vertical deviations and overcorrections. We retrospectively reviewed the records of all patients undergoing adjustable partial or full tendon VRT augmented by resection of the transposed muscles. Ciliary vessels were preserved in most of the patients by either splitting the transposed muscle or by dragging the transposed muscle without disrupting the muscle insertion. Seven patients with abducens palsy and one with esotropic Duane syndrome were included. Both vertical rectus muscles were symmetrically resected by 3-5 mm. Preoperative central gaze esotropia of 30.6 ± 12.9Δ (range, 17-50Δ) decreased to 10.6 ± 8.8Δ (range, 0-25Δ) at the final visit (p = 0.003). Three patients required postoperative adjustment by recession of one of the transposed muscles due to an induced vertical deviation (mean 9.3Δ reduced to 0Δ), coupled with overcorrection (mean exotropia 11.3Δ reduced to 0 in two patients and exophoria 2Δ in one patient). At the final follow-up visit 3.8 ± 2.6 months postoperatively, one patient had a vertical deviation <4Δ, and none had overcorrection or anterior segment ischemia. Three patients required further surgery for recurrent esotropia. Augmentation of VRT by resection of the transposed muscles can be performed with adjustable sutures and vessel-sparing technique. This allows for postoperative control of overcorrections and induced vertical deviations as well as less risk of anterior segment ischemia.

Self-esteem in adolescents with Angle Class I, II and III malocclusion in a Peruvian sample.

PubMed

Florián-Vargas, Karla; Honores, Marcos J Carruitero; Bernabé, Eduardo; Flores-Mir, Carlos

2016-01-01

To compare self-esteem scores in 12 to 16-year-old adolescents with different Angle malocclusion types in a Peruvian sample. A cross-sectional study was conducted in a sample of 276 adolescents (159, 52 and 65 with Angle Class I, II and III malocclusions, respectively) from Trujillo, Peru. Participants were asked to complete the Rosenberg Self-Esteem Scale (RSES) and were also clinically examined, so as to have Angle malocclusion classification determined. Analysis of covariance (ANCOVA) was used to compare RSES scores among adolescents with Class I, II and III malocclusions, with participants' demographic factors being controlled. Mean RSES scores for adolescents with Class I, II and III malocclusions were 20.47 ± 3.96, 21.96 ± 3.27 and 21.26 ± 4.81, respectively. The ANCOVA test showed that adolescents with Class II malocclusion had a significantly higher RSES score than those with Class I malocclusion, but there were no differences between other malocclusion groups. Supplemental analysis suggested that only those with Class II, Division 2 malocclusion might have greater self-esteem when compared to adolescents with Class I malocclusion. This study shows that, in general, self-esteem did not vary according to adolescents' malocclusion in the sample studied. Surprisingly, only adolescents with Class II malocclusion, particularly Class II, Division 2, reported better self-esteem than those with Class I malocclusion. A more detailed analysis assessing the impact of anterior occlusal features should be conducted.

Occlusal status in Asian male adults: prevalence and ethnic variation.

PubMed

Soh, Jen; Sandham, Andrew; Chan, Yiong Huak

2005-09-01

The purpose of this study was to determine the occlusal status in young Asian male adults of three ethnic groups. Study models of a sample of male army recruits (N = 339, age 17-22 years) with no history of orthodontic treatment were assessed. The ethnic proportions of the sample were Chinese 76.1% (n = 258), Malay 17.7% (n = 60), and Indian 6.2% (n = 21). British Standard Institute (BSI) and Angle's classification were used to determine incisor and molar relationships, respectively. Chi-square test or Fisher's Exact test was performed to compare the occlusal traits between ethnic groups. The distribution of incisor relationships of the total sample consisted of Class I = 48.1%, Class II/1 = 26.3%, Class II/2 = 3.2%, and Class III = 22.4%. Right Angle's molar relationships were 49.9%, 24.5%, and 24.2% whereas left Angle's molar relationships were 53.1%, 25.1%, and 21.2% for Class I, II, and III, respectively. Comparison between ethnic groups found that Indian subjects were more likely to have Class II/1 malocclusions and clinically missing permanent teeth (P < .05). The study found that the overall prevalence of malocclusion (BSI) was Class I, Class II/1, Class III, and Class II/2 in descending order of proportions. Angle's Class I molar was most prevalent followed by Class II and Class III relations. A significant difference in occlusal status between the ethnic groups was found regarding incisor relationship and missing permanent teeth (P < .05).

RNA-Interference Pathways Display High Rates of Adaptive Protein Evolution in Multiple Invertebrates

PubMed Central

Palmer, William H.; Hadfield, Jarrod D.; Obbard, Darren J.

2018-01-01

Conflict between organisms can lead to a reciprocal adaptation that manifests as an increased evolutionary rate in genes mediating the conflict. This adaptive signature has been observed in RNA-interference (RNAi) pathway genes involved in the suppression of viruses and transposable elements in Drosophila melanogaster, suggesting that a subset of Drosophila RNAi genes may be locked in an arms race with these parasites. However, it is not known whether rapid evolution of RNAi genes is a general phenomenon across invertebrates, or which RNAi genes generally evolve adaptively. Here we use population genomic data from eight invertebrate species to infer rates of adaptive sequence evolution, and to test for past and ongoing selective sweeps in RNAi genes. We assess rates of adaptive protein evolution across species using a formal meta-analytic framework to combine data across species and by implementing a multispecies generalized linear mixed model of mutation counts. Across species, we find that RNAi genes display a greater rate of adaptive protein substitution than other genes, and that this is primarily mediated by positive selection acting on the genes most likely to defend against viruses and transposable elements. In contrast, evidence for recent selective sweeps is broadly spread across functional classes of RNAi genes and differs substantially among species. Finally, we identify genes that exhibit elevated adaptive evolution across the analyzed insect species, perhaps due to concurrent parasite-mediated arms races. PMID:29437826

Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata.

PubMed

Krishna, Srikar; Nair, Aparna; Cheedipudi, Sirisha; Poduval, Deepak; Dhawan, Jyotsna; Palakodeti, Dasaradhi; Ghanekar, Yashoda

2013-01-07

Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem-loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping-pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration.

Deep sequencing reveals unique small RNA repertoire that is regulated during head regeneration in Hydra magnipapillata

PubMed Central

Krishna, Srikar; Nair, Aparna; Cheedipudi, Sirisha; Poduval, Deepak; Dhawan, Jyotsna; Palakodeti, Dasaradhi; Ghanekar, Yashoda

2013-01-01

Small non-coding RNAs such as miRNAs, piRNAs and endo-siRNAs fine-tune gene expression through post-transcriptional regulation, modulating important processes in development, differentiation, homeostasis and regeneration. Using deep sequencing, we have profiled small non-coding RNAs in Hydra magnipapillata and investigated changes in small RNA expression pattern during head regeneration. Our results reveal a unique repertoire of small RNAs in hydra. We have identified 126 miRNA loci; 123 of these miRNAs are unique to hydra. Less than 50% are conserved across two different strains of Hydra vulgaris tested in this study, indicating a highly diverse nature of hydra miRNAs in contrast to bilaterian miRNAs. We also identified siRNAs derived from precursors with perfect stem–loop structure and that arise from inverted repeats. piRNAs were the most abundant small RNAs in hydra, mapping to transposable elements, the annotated transcriptome and unique non-coding regions on the genome. piRNAs that map to transposable elements and the annotated transcriptome display a ping–pong signature. Further, we have identified several miRNAs and piRNAs whose expression is regulated during hydra head regeneration. Our study defines different classes of small RNAs in this cnidarian model system, which may play a role in orchestrating gene expression essential for hydra regeneration. PMID:23166307

Sequence, distribution and chromosomal context of class I and class II pilin genes of Neisseria meningitidis identified in whole genome sequences

PubMed Central

2014-01-01

Background Neisseria meningitidis expresses type four pili (Tfp) which are important for colonisation and virulence. Tfp have been considered as one of the most variable structures on the bacterial surface due to high frequency gene conversion, resulting in amino acid sequence variation of the major pilin subunit (PilE). Meningococci express either a class I or a class II pilE gene and recent work has indicated that class II pilins do not undergo antigenic variation, as class II pilE genes encode conserved pilin subunits. The purpose of this work was to use whole genome sequences to further investigate the frequency and variability of the class II pilE genes in meningococcal isolate collections. Results We analysed over 600 publically available whole genome sequences of N. meningitidis isolates to determine the sequence and genomic organization of pilE. We confirmed that meningococcal strains belonging to a limited number of clonal complexes (ccs, namely cc1, cc5, cc8, cc11 and cc174) harbour a class II pilE gene which is conserved in terms of sequence and chromosomal context. We also identified pilS cassettes in all isolates with class II pilE, however, our analysis indicates that these do not serve as donor sequences for pilE/pilS recombination. Furthermore, our work reveals that the class II pilE locus lacks the DNA sequence motifs that enable (G4) or enhance (Sma/Cla repeat) pilin antigenic variation. Finally, through analysis of pilin genes in commensal Neisseria species we found that meningococcal class II pilE genes are closely related to pilE from Neisseria lactamica and Neisseria polysaccharea, suggesting horizontal transfer among these species. Conclusions Class II pilins can be defined by their amino acid sequence and genomic context and are present in meningococcal isolates which have persisted and spread globally. The absence of G4 and Sma/Cla sequences adjacent to the class II pilE genes is consistent with the lack of pilin subunit variation in these isolates, although horizontal transfer may generate class II pilin diversity. This study supports the suggestion that high frequency antigenic variation of pilin is not universal in pathogenic Neisseria. PMID:24690385

A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

PubMed Central

Biémont, Christian

2010-01-01

The idea that some genetic factors are able to move around chromosomes emerged more than 60 years ago when Barbara McClintock first suggested that such elements existed and had a major role in controlling gene expression and that they also have had a major influence in reshaping genomes in evolution. It was many years, however, before the accumulation of data and theories showed that this latter revolutionary idea was correct although, understandably, it fell far short of our present view of the significant influence of what are now known as “transposable elements” in evolution. In this article, I summarize the main events that influenced my thinking about transposable elements as a young scientist and the influence and role of these specific genomic elements in evolution over subsequent years. Today, we recognize that the findings about genomic changes affected by transposable elements have considerably altered our view of the ways in which genomes evolve and work. PMID:21156958

An efficient parallel-processing method for transposing large matrices in place.

PubMed

Portnoff, M R

1999-01-01

We have developed an efficient algorithm for transposing large matrices in place. The algorithm is efficient because data are accessed either sequentially in blocks or randomly within blocks small enough to fit in cache, and because the same indexing calculations are shared among identical procedures operating on independent subsets of the data. This inherent parallelism makes the method well suited for a multiprocessor computing environment. The algorithm is easy to implement because the same two procedures are applied to the data in various groupings to carry out the complete transpose operation. Using only a single processor, we have demonstrated nearly an order of magnitude increase in speed over the previously published algorithm by Gate and Twigg for transposing a large rectangular matrix in place. With multiple processors operating in parallel, the processing speed increases almost linearly with the number of processors. A simplified version of the algorithm for square matrices is presented as well as an extension for matrices large enough to require virtual memory.

Comparison of second molar eruption patterns in patients with skeletal Class II and skeletal Class I malocclusions.

PubMed

Brin, Ilana; Camasuvi, Semin; Dali, Nasser; Aizenbud, Dror

2006-12-01

The eruptive positions of the second molars in Class I and Class II malocclusions were studied. Pretreatment records of 221 patients with a mean age of 11.3 years were evaluated. About 19% of them had skeletal Class I, 31% had skeletal maxillary Class II, and 50% had skeletal mandibular Class II malocclusions. The mean values of the dental and chronologic ages of the subjects were similar. The eruptive positions in relation to a reference line, the developmental stages of the patients' second molars and dental ages were recorded from the panoramic roentgenograms. The distribution of the various developmental stages in each malocclusion group was similar, and no association between skeletal malocclusion and dental developmental stage of the second molars was encountered. The eruptive position of the maxillary second molars was more occlusal only in the oldest maxillary Class II group, above 12 years of age (P = .02). These results support, in part, previous reports suggesting that the maxillary second molars may erupt earlier in patients with skeletal maxillary Class II malocclusions.

Antigen-B Cell Receptor Complexes Associate with Intracellular major histocompatibility complex (MHC) Class II Molecules*

PubMed Central

Barroso, Margarida; Tucker, Heidi; Drake, Lisa; Nichol, Kathleen; Drake, James R.

2015-01-01

Antigen processing and MHC class II-restricted antigen presentation by antigen-presenting cells such as dendritic cells and B cells allows the activation of naïve CD4+ T cells and cognate interactions between B cells and effector CD4+ T cells, respectively. B cells are unique among class II-restricted antigen-presenting cells in that they have a clonally restricted antigen-specific receptor, the B cell receptor (BCR), which allows the cell to recognize and respond to trace amounts of foreign antigen present in a sea of self-antigens. Moreover, engagement of peptide-class II complexes formed via BCR-mediated processing of cognate antigen has been shown to result in a unique pattern of B cell activation. Using a combined biochemical and imaging/FRET approach, we establish that internalized antigen-BCR complexes associate with intracellular class II molecules. We demonstrate that the M1-paired MHC class II conformer, shown previously to be critical for CD4 T cell activation, is incorporated selectively into these complexes and loaded selectively with peptide derived from BCR-internalized cognate antigen. These results demonstrate that, in B cells, internalized antigen-BCR complexes associate with intracellular MHC class II molecules, potentially defining a site of class II peptide acquisition, and reveal a selective role for the M1-paired class II conformer in the presentation of cognate antigen. These findings provide key insights into the molecular mechanisms used by B cells to control the source of peptides charged onto class II molecules, allowing the immune system to mount an antibody response focused on BCR-reactive cognate antigen. PMID:26400081

The Ia.2 Epitope Defines a Subset of Lipid Raft Resident MHC Class II Molecules Crucial to Effective Antigen Presentation1

PubMed Central

Busman-Sahay, Kathleen; Sargent, Elizabeth; Harton, Jonathan A.; Drake, James R.

2016-01-01

Previous work has established that binding of the 11-5.2 anti-I-Ak mAb, which recognizes the Ia.2 epitope on I-Ak class II molecules, elicits MHC class II signaling, whereas binding of two other anti-I-Ak mAb that recognize the Ia.17 epitope fail to elicit signaling. Using a biochemical approach, we establish that the Ia.2 epitope recognized by the widely used 11-5.2 mAb defines a subset of cell surface I-Ak molecules predominantly found within membrane lipid rafts. Functional studies demonstrate that the Ia.2 bearing subset of I-Ak class II molecules is critically necessary for effective B cell–T cell interactions especially at low antigen doses, a finding consistent with published studies on the role of raft-resident class II molecules in CD4 T cell activation. Interestingly, B cells expressing recombinant I-Ak class II molecules possessing a β chain-tethered HEL peptide lack the Ia.2 epitope and fail to partition into lipid rafts. Moreover, cells expressing Ia.2 negative tethered peptide-class II molecules are severely impaired in their ability to present both tethered peptide or peptide derived from exogenous antigen to CD4 T cells. These results establish the Ia.2 epitope as defining a lipid raft-resident MHC class II confomer vital to the initiation of MHC class II restricted B cell–T cell interactions. PMID:21543648

40 CFR 82.70 - Nonessential Class II products and exceptions.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Nonessential Class II products and... PROGRAMS (CONTINUED) PROTECTION OF STRATOSPHERIC OZONE Ban on Nonessential Products Containing Class I Substances and Ban on Nonessential Products Containing or Manufactured With Class II Substances § 82.70...

40 CFR 82.70 - Nonessential Class II products and exceptions.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Nonessential Class II products and... PROGRAMS (CONTINUED) PROTECTION OF STRATOSPHERIC OZONE Ban on Nonessential Products Containing Class I Substances and Ban on Nonessential Products Containing or Manufactured With Class II Substances § 82.70...

40 CFR 82.70 - Nonessential Class II products and exceptions.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 18 2014-07-01 2014-07-01 false Nonessential Class II products and... PROGRAMS (CONTINUED) PROTECTION OF STRATOSPHERIC OZONE Ban on Nonessential Products Containing Class I Substances and Ban on Nonessential Products Containing or Manufactured With Class II Substances § 82.70...

40 CFR 82.70 - Nonessential Class II products and exceptions.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 18 2013-07-01 2013-07-01 false Nonessential Class II products and... PROGRAMS (CONTINUED) PROTECTION OF STRATOSPHERIC OZONE Ban on Nonessential Products Containing Class I Substances and Ban on Nonessential Products Containing or Manufactured With Class II Substances § 82.70...

14 CFR 61.5 - Certificates and ratings issued under this part.

Code of Federal Regulations, 2013 CFR

2013-01-01

...-control aircraft. (2) Airplane class ratings— (i) Single-engine land. (ii) Multiengine land. (iii) Single-engine sea. (iv) Multiengine sea. (3) Rotorcraft class ratings— (i) Helicopter. (ii) Gyroplane. (4) Lighter-than-air class ratings— (i) Airship. (ii) Balloon. (5) Weight-shift-control aircraft class ratings...

14 CFR 61.5 - Certificates and ratings issued under this part.

Code of Federal Regulations, 2014 CFR

2014-01-01

...-control aircraft. (2) Airplane class ratings— (i) Single-engine land. (ii) Multiengine land. (iii) Single-engine sea. (iv) Multiengine sea. (3) Rotorcraft class ratings— (i) Helicopter. (ii) Gyroplane. (4) Lighter-than-air class ratings— (i) Airship. (ii) Balloon. (5) Weight-shift-control aircraft class ratings...

14 CFR 61.5 - Certificates and ratings issued under this part.

Code of Federal Regulations, 2012 CFR

2012-01-01

...-control aircraft. (2) Airplane class ratings— (i) Single-engine land. (ii) Multiengine land. (iii) Single-engine sea. (iv) Multiengine sea. (3) Rotorcraft class ratings— (i) Helicopter. (ii) Gyroplane. (4) Lighter-than-air class ratings— (i) Airship. (ii) Balloon. (5) Weight-shift-control aircraft class ratings...

On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models.

PubMed

Fischer, Carlos N; Campos, Victor De A; Barella, Victor H

2018-05-01

Profile hidden Markov models (pHMMs) have been used to search for transposable elements (TEs) in genomes. For the learning of pHMMs aimed to search for TEs of the retrotransposon class, the conventional protocol is to use the whole internal nucleotide portions of these elements as representative sequences. To further explore the potential of pHMMs in such a search, we propose five alternative ways to obtain the sets of representative sequences of TEs other than the conventional protocol. In this study, we are interested in Bel-PAO, Copia, Gypsy, and DIRS superfamilies from the retrotransposon class. We compared the pHMMs of all six protocols. The test results show that, for each TE superfamily, the pHMMs of at least two of the proposed protocols performed better than the conventional one and that the number of correct predictions provided by the latter can be improved by considering together the results of one or more of the alternative protocols.

Ectomycorrhizal ecology is imprinted in the genome of the dominant symbiotic fungus Cenococcum geophilum

PubMed Central

Peter, Martina; Kohler, Annegret; Ohm, Robin A.; Kuo, Alan; Krützmann, Jennifer; Morin, Emmanuelle; Arend, Matthias; Barry, Kerrie W.; Binder, Manfred; Choi, Cindy; Clum, Alicia; Copeland, Alex; Grisel, Nadine; Haridas, Sajeet; Kipfer, Tabea; LaButti, Kurt; Lindquist, Erika; Lipzen, Anna; Maire, Renaud; Meier, Barbara; Mihaltcheva, Sirma; Molinier, Virginie; Murat, Claude; Pöggeler, Stefanie; Quandt, C. Alisha; Sperisen, Christoph; Tritt, Andrew; Tisserant, Emilie; Crous, Pedro W.; Henrissat, Bernard; Nehls, Uwe; Egli, Simon; Spatafora, Joseph W.; Grigoriev, Igor V.; Martin, Francis M.

2016-01-01

The most frequently encountered symbiont on tree roots is the ascomycete Cenococcum geophilum, the only mycorrhizal species within the largest fungal class Dothideomycetes, a class known for devastating plant pathogens. Here we show that the symbiotic genomic idiosyncrasies of ectomycorrhizal basidiomycetes are also present in C. geophilum with symbiosis-induced, taxon-specific genes of unknown function and reduced numbers of plant cell wall-degrading enzymes. C. geophilum still holds a significant set of genes in categories known to be involved in pathogenesis and shows an increased genome size due to transposable elements proliferation. Transcript profiling revealed a striking upregulation of membrane transporters, including aquaporin water channels and sugar transporters, and mycorrhiza-induced small secreted proteins (MiSSPs) in ectomycorrhiza compared with free-living mycelium. The frequency with which this symbiont is found on tree roots and its possible role in water and nutrient transport in symbiosis calls for further studies on mechanisms of host and environmental adaptation. PMID:27601008

Evolutionary trajectory of Pack-MULEs is determined by their epigenetic status

USDA-ARS?s Scientific Manuscript database

Acquisition and rearrangement of host genes by transposable elements is one mechanism to increase gene diversity. The rice genome is replete in such sequences and while ~3,000 Pack- Mutator-like transposable elements containing gene sequences (Pack-MULEs) have been identified, their function remains...

Detection and characterization of miniature inverted-repeat transposable elements in “Candidatus Liberibacter asiaticus”

USDA-ARS?s Scientific Manuscript database

Miniature inverted-repeat transposable elements (MITEs) are non-autonomous transposons (devoid a transposase gene, tps) involving insertion/deletion of genomic DNA in bacterial genomes influencing gene functions. No transposon has yet been reported in “Candidatus Liberibacter asiaticus”, an alpha-pr...

Transposed-Letter Priming across Inflectional Morpheme Boundaries

ERIC Educational Resources Information Center

Zargar, Ehsan Shafiee; Witzel, Naoko

2017-01-01

This study reports findings from two experiments testing whether a transposed-letter (TL) priming effect can be obtained when the transposition occurs across morphological boundaries. Previous studies have primarily tested derivationally complex words or compound words, but have not examined a more rule-based and productive morphological…

HLA Class II Defects in Burkitt Lymphoma: Bryostatin-1-Induced 17 kDa Protein Restores CD4+ T-Cell Recognition

PubMed Central

Hossain, Azim; God, Jason M.; Radwan, Faisal F. Y.; Amria, Shereen; Zhao, Dan; Bethard, Jennifer R.; Haque, Azizul

2011-01-01

While the defects in HLA class I-mediated Ag presentation by Burkitt lymphoma (BL) have been well documented, CD4+ T-cells are also poorly stimulated by HLA class II Ag presentation, and the reasons underlying this defect(s) have not yet been fully resolved. Here, we show that BL cells are deficient in their ability to optimally stimulate CD4+ T cells via the HLA class II pathway. The observed defect was not associated with low levels of BL-expressed costimulatory molecules, as addition of external co-stimulation failed to result in BL-mediated CD4+ T-cell activation. We further demonstrate that BL cells express the components of the class II pathway, and the defect was not caused by faulty Ag/class II interaction, because antigenic peptides bound with measurable affinity to BL-associated class II molecules. Treatment of BL with broystatin-1, a potent modulator of protein kinase C, led to significant improvement of functional class II Ag presentation in BL. The restoration of immune recognition appeared to be linked with an increased expression of a 17 kDa peptidylprolyl-like protein. These results demonstrate the presence of a specific defect in HLA class II-mediated Ag presentation in BL and reveal that treatment with bryostatin-1 could lead to enhanced immunogenicity. PMID:22162713

Mechanisms regulating enhanced HLA class II-mediated CD4+ T cell recognition of human B-cell lymphoma by resveratrol

PubMed Central

RADWAN, FAISAL F. Y.; ZHANG, LIXIA; HOSSAIN, AZIM; DOONAN, BENTLY P.; GOD, JASON; HAQUE, AZIZUL

2015-01-01

Malignant B-cells express measurable levels of HLA class II proteins, but often escape immune recognition by CD4+ T cells. Resveratrol (Resv) has been the focus of numerous investigations due to its potential chemopreventive and anti-cancer effects, but it has never been tested in the regulation of immune components in B-cell tumors. Here, we show for the first time that Resv treatment enhances HLA class II-mediated immune detection of B-cell lymphomas by altering immune components and class II presentation in tumor cells. Resv treatment induced an upregulation of both classical and non-classical HLA class II proteins (DR and DM) in B-lymphoma cells. Resv also altered endolysosomal cathepsins (Cat S, B and D) and a thiol reductase (GILT), increasing HLA class II-mediated antigen (Ag) processing in B-cell lymphomas and their subsequent recognition by CD4+ T cells. Mechanistic study demonstrated that Resv treatment activated the recycling class II pathway of Ag presentation through upregulation of Rab 4B protein expression in B-lymphoma cells. These findings suggest that HLA class II-mediated immune recognition of malignant B-cells can be improved by Resv treatment, thus encouraging its potential use in chemoimmunotherapy of B-cell lymphoma. PMID:21854084

Shark class II invariant chain reveals ancient conserved relationships with cathepsins and MHC class II.

PubMed

Criscitiello, Michael F; Ohta, Yuko; Graham, Matthew D; Eubanks, Jeannine O; Chen, Patricia L; Flajnik, Martin F

2012-03-01

The invariant chain (Ii) is the critical third chain required for the MHC class II heterodimer to be properly guided through the cell, loaded with peptide, and expressed on the surface of antigen presenting cells. Here, we report the isolation of the nurse shark Ii gene, and the comparative analysis of Ii splice variants, expression, genomic organization, predicted structure, and function throughout vertebrate evolution. Alternative splicing to yield Ii with and without the putative protease-protective, thyroglobulin-like domain is as ancient as the MHC-based adaptive immune system, as our analyses in shark and lizard further show conservation of this mechanism in all vertebrate classes except bony fish. Remarkable coordinate expression of Ii and class II was found in shark tissues. Conserved Ii residues and cathepsin L orthologs suggest their long co-evolution in the antigen presentation pathway, and genomic analyses suggest 450 million years of conserved Ii exon/intron structure. Other than an extended linker preceding the thyroglobulin-like domain in cartilaginous fish, the Ii gene and protein are predicted to have largely similar physiology from shark to man. Duplicated Ii genes found only in teleosts appear to have become sub-functionalized, as one form is predicted to play the same role as that mediated by Ii mRNA alternative splicing in all other vertebrate classes. No Ii homologs or potential ancestors of any of the functional Ii domains were found in the jawless fish or lower chordates. Copyright © 2011 Elsevier Ltd. All rights reserved.

Acculturation levels and personalizing orthognathic surgery for the Asian American patient.

PubMed

Sy, A A; Kim, W S; Chen, J; Shen, Y; Tao, C; Lee, J S

2016-10-01

This study was performed to investigate whether the level of acculturation among Asians living in the USA plays a significant role in their opinion of facial profiles. One hundred and ninety-eight Asian American subjects were asked to complete a pre-validated survey to measure their level of acculturation and to evaluate four sets of pictures that displayed a class II male, class II female, class III male, and class III female. Each set consisted of three lateral profile pictures: an initial unaltered photo, a picture simulating a flatter profile (orthodontic camouflage in class II; mandibular setback in class III), and a picture simulating a fuller profile (mandibular advancement in class II; maxillary advancement in class III). For the class II male, subjects who were more acculturated indicated that a flatter profile (orthodontic camouflage) was less attractive. For the class II female, higher acculturated subjects chose expansive treatment (mandibular advancement) as more aesthetic compared to the less acculturated subjects. Each of these scenarios had statistically significant odds ratios. In general, highly acculturated subjects preferred a fuller facial profile, while low acculturated subjects preferred a flatter facial profile appearance, except for the class III female profile, which did not follow this trend. Copyright © 2016 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome.

PubMed

Baucom, Regina S; Estill, James C; Chaparro, Cristian; Upshaw, Naadira; Jogi, Ansuya; Deragon, Jean-Marc; Westerman, Richard P; Sanmiguel, Phillip J; Bennetzen, Jeffrey L

2009-11-01

Recent comprehensive sequence analysis of the maize genome now permits detailed discovery and description of all transposable elements (TEs) in this complex nuclear environment. Reiteratively optimized structural and homology criteria were used in the computer-assisted search for retroelements, TEs that transpose by reverse transcription of an RNA intermediate, with the final results verified by manual inspection. Retroelements were found to occupy the majority (>75%) of the nuclear genome in maize inbred B73. Unprecedented genetic diversity was discovered in the long terminal repeat (LTR) retrotransposon class of retroelements, with >400 families (>350 newly discovered) contributing >31,000 intact elements. The two other classes of retroelements, SINEs (four families) and LINEs (at least 30 families), were observed to contribute 1,991 and approximately 35,000 copies, respectively, or a combined approximately 1% of the B73 nuclear genome. With regard to fully intact elements, median copy numbers for all retroelement families in maize was 2 because >250 LTR retrotransposon families contained only one or two intact members that could be detected in the B73 draft sequence. The majority, perhaps all, of the investigated retroelement families exhibited non-random dispersal across the maize genome, with LINEs, SINEs, and many low-copy-number LTR retrotransposons exhibiting a bias for accumulation in gene-rich regions. In contrast, most (but not all) medium- and high-copy-number LTR retrotransposons were found to preferentially accumulate in gene-poor regions like pericentromeric heterochromatin, while a few high-copy-number families exhibited the opposite bias. Regions of the genome with the highest LTR retrotransposon density contained the lowest LTR retrotransposon diversity. These results indicate that the maize genome provides a great number of different niches for the survival and procreation of a great variety of retroelements that have evolved to differentially occupy and exploit this genomic diversity.

Evaluation of skeletal and dental asymmetries in Angle Class II subdivision malocclusions with cone-beam computed tomography.

PubMed

Minich, Craig M; Araújo, Eustáquio A; Behrents, Rolf G; Buschang, Peter H; Tanaka, Orlando M; Kim, Ki Beom

2013-07-01

The purpose of this study was to determine whether Angle Class II subdivision malocclusions have skeletal or dental asymmetries between the Class II and Class I sides. A sample of 54 untreated Angle Class II subdivision patients with pretreatment photos and cone-beam computed tomography (CBCT) scans was used. The photos were used to identify the Class II subdivision malocclusion and to record the amount of crowding per quadrant. Landmarks were plotted on each CBCT volume so that direct 3-dimensional measurements could be made to compare the positions and dimensions of the skeletal and dental structures on the Class II side vs the Class I side. Significant differences were found for 2 skeletal measurements: the position of the maxilla relative to the cranial base, and the mandibular dimension from the mandibular foramen to the mental foramen. Statistically significant dental differences were found for the position of the mandibular first molars and canines in relation to the maxilla and the mandible. Statistically significant differences were found for the maxillary first molars and canines in relation to the mandible. There were significant skeletal and dental differences between the Class I and Class II sides. The dental asymmetries accounted for about two thirds of the total asymmetry. Copyright © 2013 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

TEs or not TEs? That is the evolutionary question.

PubMed

Vaknin, Keren; Goren, Amir; Ast, Gil

2009-10-23

Transposable elements (TEs) have contributed a wide range of functional sequences to their host genomes. A recent paper in BMC Molecular Biology discusses the creation of new transcripts by transposable element insertion upstream of retrocopies and the involvement of such insertions in tissue-specific post-transcriptional regulation.

A non-autonomous insect piggyBac trasposable element is mobile in tobacco

USDA-ARS?s Scientific Manuscript database

The piggyBac transposable element, originally isolated from a virus in an insect cell line, is a valuable molecular tool for transgenesis and mutagenesis of invertebrates. For heterologous transgenesis in a variety of mammals, transfer of the piggyBac transposable element from an ectopic plasmid onl...

The hobo transposable element has transposase-dependent and -independent excision activity in drosophilid species

USDA-ARS?s Scientific Manuscript database

Mobility of the hobo transposable element was determined for several strains of Drosophila melanogaster and several Drosophila species. Mobility was assessed by use of an in vivo transient assay in the soma of developing embryos, which monitored hobo excision from injected indicator plasmids. Excisi...

25 CFR 522.11 - Individually owned class II gaming operations operating on September 1, 1986.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 2 2010-04-01 2010-04-01 false Individually owned class II gaming operations operating on September 1, 1986. 522.11 Section 522.11 Indians NATIONAL INDIAN GAMING COMMISSION, DEPARTMENT OF THE INTERIOR APPROVAL OF CLASS II AND CLASS III ORDINANCES AND RESOLUTIONS SUBMISSION OF GAMING...

MORC Proteins: Novel Players in Plant and Animal Health

PubMed Central

Koch, Aline; Kang, Hong-Gu; Steinbrenner, Jens; Dempsey, D'Maris A.; Klessig, Daniel F.; Kogel, Karl-Heinz

2017-01-01

Microrchidia (MORC) proteins comprise a family of proteins that have been identified in prokaryotes and eukaryotes. They are defined by two hallmark domains: a GHKL-type ATPase and an S5 fold. MORC proteins in plants were first discovered via a genetic screen for Arabidopsis mutants compromised for resistance to a viral pathogen. Subsequent studies expanded their role in plant immunity and revealed their involvement in gene silencing and transposable element repression. Emerging data suggest that MORC proteins also participate in pathogen-induced chromatin remodeling and epigenetic gene regulation. In addition, biochemical analyses recently demonstrated that plant MORCs have topoisomerase II (topo II)-like DNA modifying activities that may be important for their function. Interestingly, animal MORC proteins exhibit many parallels with their plant counterparts, as they have been implicated in disease development and gene silencing. In addition, human MORCs, like plant MORCs, bind salicylic acid and this inhibits some of their topo II-like activities. In this review, we will focus primarily on plant MORCs, although relevant comparisons with animal MORCs will be provided. PMID:29093720

MORC Proteins: Novel Players in Plant and Animal Health.

PubMed

Koch, Aline; Kang, Hong-Gu; Steinbrenner, Jens; Dempsey, D'Maris A; Klessig, Daniel F; Kogel, Karl-Heinz

2017-01-01

Microrchidia (MORC) proteins comprise a family of proteins that have been identified in prokaryotes and eukaryotes. They are defined by two hallmark domains: a GHKL-type ATPase and an S5 fold. MORC proteins in plants were first discovered via a genetic screen for Arabidopsis mutants compromised for resistance to a viral pathogen. Subsequent studies expanded their role in plant immunity and revealed their involvement in gene silencing and transposable element repression. Emerging data suggest that MORC proteins also participate in pathogen-induced chromatin remodeling and epigenetic gene regulation. In addition, biochemical analyses recently demonstrated that plant MORCs have topoisomerase II (topo II)-like DNA modifying activities that may be important for their function. Interestingly, animal MORC proteins exhibit many parallels with their plant counterparts, as they have been implicated in disease development and gene silencing. In addition, human MORCs, like plant MORCs, bind salicylic acid and this inhibits some of their topo II-like activities. In this review, we will focus primarily on plant MORCs, although relevant comparisons with animal MORCs will be provided.

Quality of life, disability, and body mass index are related in obese patients.

PubMed

Sirtori, Anna; Brunani, Amelia; Liuzzi, Antonio; Pasqualinotto, Lucia; Villa, Valentina; Leonardi, Matilde; Raggi, Alberto

2011-09-01

The aim of this study is to analyze the relationship between health-related quality of life (QoL), disability, and degree of obesity. Adult obese patients (BMI>30) were consecutively enrolled in this cross-sectional observational study. The WHO Disability Assessment Schedule (WHO-DAS II) and the short version of the impact of weight on QoL (IWQoL-Lite) were administered. Spearman's rank correlation analysis was performed. A P value of less than 0.01 was used to set the statistical significance. A total of 117 patients (mean age: 47.4 years, mean BMI: 43.7) were enrolled. Correlations between WHO-DAS II and IWQoL-Lite were between 0.21 and 0.78. BMI between 0.19 and 0.26 correlated with WHO-DAS II and BMI between 0.23 and 0.49 correlated with IWQoL-Lite. In conclusion, low/moderate correlations between BMI index, disability, and health-related QoL measures, and a low association between the two outcome measures are reported, supporting the idea that they underline different and not transposable dimensions.

Glass ionomer-silver cermet Class II tunnel-restorations for primary molars.

PubMed

Croll, T P

1988-01-01

Tunnel preparations preserve the anatomical marginal ridge and minimize the loss of healthy tooth structure adjacent to the carious lesion. When the practitioner has developed proficiency in restoring class II carious lesions with tunnel restorations, less treatment time is required than with traditional class II preparations. The technique for restoring a primary first molar with a class II carious lesion, using a tunnel preparation and Ketac-Silver restorative material is described.

Diversity and evolutionary patterns of immune genes in free-ranging Namibian leopards (Panthera pardus pardus).

PubMed

Castro-Prieto, Aines; Wachter, Bettina; Melzheimer, Joerg; Thalwitzer, Susanne; Sommer, Simone

2011-01-01

The genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for fitness-related genetic variation in wildlife populations. Currently, no information about the MHC sequence variation and constitution in African leopards exists. In this study, we isolated and characterized genetic variation at the adaptively most important region of MHC class I and MHC class II-DRB genes in 25 free-ranging African leopards from Namibia and investigated the mechanisms that generate and maintain MHC polymorphism in the species. Using single-stranded conformation polymorphism analysis and direct sequencing, we detected 6 MHC class I and 6 MHC class II-DRB sequences, which likely correspond to at least 3 MHC class I and 3 MHC class II-DRB loci. Amino acid sequence variation in both MHC classes was higher or similar in comparison to other reported felids. We found signatures of positive selection shaping the diversity of MHC class I and MHC class II-DRB loci during the evolutionary history of the species. A comparison of MHC class I and MHC class II-DRB sequences of the leopard to those of other felids revealed a trans-species mode of evolution. In addition, the evolutionary relationships of MHC class II-DRB sequences between African and Asian leopard subspecies are discussed.

Genome wide analysis of the transition to pathogenic lifestyles in Magnaporthales fungi.

PubMed

Zhang, Ning; Cai, Guohong; Price, Dana C; Crouch, Jo Anne; Gladieux, Pierre; Hillman, Bradley; Khang, Chang Hyun; LeBrun, Marc-Henri; Lee, Yong-Hwan; Luo, Jing; Qiu, Huan; Veltri, Daniel; Wisecaver, Jennifer H; Zhu, Jie; Bhattacharya, Debashish

2018-04-12

The rice blast fungus Pyricularia oryzae (syn. Magnaporthe oryzae, Magnaporthe grisea), a member of the order Magnaporthales in the class Sordariomycetes, is an important plant pathogen and a model species for studying pathogen infection and plant-fungal interaction. In this study, we generated genome sequence data from five additional Magnaporthales fungi including non-pathogenic species, and performed comparative genome analysis of a total of 13 fungal species in the class Sordariomycetes to understand the evolutionary history of the Magnaporthales and of fungal pathogenesis. Our results suggest that the Magnaporthales diverged ca. 31 millon years ago from other Sordariomycetes, with the phytopathogenic blast clade diverging ca. 21 million years ago. Little evidence of inter-phylum horizontal gene transfer (HGT) was detected in Magnaporthales. In contrast, many genes underwent positive selection in this order and the majority of these sequences are clade-specific. The blast clade genomes contain more secretome and avirulence effector genes, which likely play key roles in the interaction between Pyricularia species and their plant hosts. Finally, analysis of transposable elements (TE) showed differing proportions of TE classes among Magnaporthales genomes, suggesting that species-specific patterns may hold clues to the history of host/environmental adaptation in these fungi.

77 FR 16123 - Draft Guidance for Industry and Food and Drug Administration Staff; Class II Special Controls...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-19

...; Class II Special Controls Guidance Document: Nucleic Acid-Based In Vitro Diagnostic Devices for the... Guidance for Industry and Food and Drug Administration Staff; Class II Special Controls Guidance Document... II Special Controls Guidance Document: Nucleic Acid-Based In Vitro Diagnostic Devices for the...

Comparison of temporomandibular joint and ramus morphology between class II and class III cases before and after bi-maxillary osteotomy.

PubMed

Iguchi, Ran; Yoshizawa, Kunio; Moroi, Akinori; Tsutsui, Takamitsu; Hotta, Asami; Hiraide, Ryota; Takayama, Akihiro; Tsunoda, Tatsuya; Saito, Yuki; Sato, Momoko; Baba, Nana; Ueki, Koichiro

2017-12-01

The purpose of this study was to compare changes in temporomandibular joint (TMJ) and ramus morphology between class II and III cases before and after sagittal split ramus osteotomy (SSRO) and Le Fort I osteotomy. The subjects were 39 patients (78 sides) who underwent bi-maxillary surgery. They consisted of 2 groups (18 class II cases and 21 class III cases), and were selected randomly from among patients who underwent surgery between 2012 and 2016. The TMJ disc tissue and joint effusion were assessed by magnetic resonance imaging (MRI) and the TMJ space, condylar height, ramus height, ramus inclination and condylar square were assessed by computed tomography (CT), pre- and post-operatively. The number of joints with anterior disc displacement in class II was significantly higher than that in class III (p < 0.0001). However, there were no significant differences between the two classes regarding ratio of joint symptoms and ratio of joint effusion pre- and post-operatively. Class II was significantly better than class III regarding reduction ratio of condylar height (p < 0.0001) and square (p = 0.0005). The study findings suggest that condylar morphology could change in both class II and III after bi-maxillary surgery. The findings of the numerical analysis also demonstrated that reduction of condylar volume occurred frequently in class II, although TMJ disc position classification did not change significantly, as previously reported. Copyright © 2017 European Association for Cranio-Maxillo-Facial Surgery. Published by Elsevier Ltd. All rights reserved.

Resonance Properties of Class I and Class II Neurons Differentially Modulated by Channel Noise

NASA Astrophysics Data System (ADS)

Wang, Lei

2018-01-01

Resonance properties of two different neuron types (Class I and Class II) induced by channel noise are investigated in this study. It is found that for Class I neuron, spiking activity is enhanced when certain noise intensity is presented, especially under weak current stimuli -- a typical phenomenon of stochastic resonance (SR); while for Class II neuron, in addition to perform the SR, certain noise intensity would inhibit neuronal activity under some current stimuli -- a typical phenomenon of inverse stochastic resonance (ISR). Moreover, we show that only sodium channel noise or potassium channel noise variation can achieve the similar phenomena. Consequently, the model results suggest that channel noise may exert differential roles in modulating the resonance properties of Class I and Class II neurons.

Thin-plate spline analysis of craniofacial growth in Class I and Class II subjects.

PubMed

Franchi, Lorenzo; Baccetti, Tiziano; Stahl, Franka; McNamara, James A

2007-07-01

To compare the craniofacial growth characteristics of untreated subjects with Class II division 1 malocclusion with those of subjects with normal (Class I) occlusion from the prepubertal through the postpubertal stages of development. The Class II division 1 sample consisted of 17 subjects (11 boys and six girls). The Class I sample also consisted of 17 subjects (13 boys and four girls). Three craniofacial regions (cranial base, maxilla, and mandible) were analyzed on the lateral cephalograms of the subjects in both groups by means of thin-plate spline analysis at T1 (prepubertal) and T2 (postpubertal). Both cross-sectional and longitudinal comparisons were performed on both size and shape differences between the two groups. The results showed an increased cranial base angulation as a morphological feature of Class II malocclusion at the prepubertal developmental phase. Maxillary changes in either shape or size were not significant. Subjects with Class II malocclusion exhibited a significant deficiency in the size of the mandible at the completion of active craniofacial growth as compared with Class I subjects. A significant deficiency in the size of the mandible became apparent in Class II subjects during the circumpubertal period and it was still present at the completion of active craniofacial growth.

Influence of pharyngeal airway respiration pressure on Class II mandibular retrusion in children: A computational fluid dynamics study of inspiration and expiration.

PubMed

Iwasaki, T; Sato, H; Suga, H; Takemoto, Y; Inada, E; Saitoh, I; Kakuno, K; Kanomi, R; Yamasaki, Y

2017-05-01

To examine the influence of negative pressure of the pharyngeal airway on mandibular retraction during inspiration in children with nasal obstruction using the computational fluid dynamics (CFD) method. Sixty-two children were divided into Classes I, II (mandibular retrusion) and III (mandibular protrusion) malocclusion groups. Cone-beam computed tomography data were used to reconstruct three-dimensional shapes of the nasal and pharyngeal airways. Airflow pressure was simulated using CFD to calculate nasal resistance and pharyngeal airway pressure during inspiration and expiration. Nasal resistance of the Class II group was significantly higher than that of the other two groups, and oropharyngeal airway inspiration pressure in the Class II (-247.64 Pa) group was larger than that in the Class I (-43.51 Pa) and Class III (-31.81 Pa) groups (P<.001). The oropharyngeal airway inspiration-expiration pressure difference in the Class II (-27.38 Pa) group was larger than that in the Class I (-5.17 Pa) and Class III (0.68 Pa) groups (P=.006). Large negative inspiratory pharyngeal airway pressure due to nasal obstruction in children with Class II malocclusion may be related to their retrognathia. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Disruption of HLA class II antigen presentation in Burkitt lymphoma: implication of a 47 000 MW acid labile protein in CD4+ T-cell recognition

PubMed Central

God, Jason M; Zhao, Dan; Cameron, Christine A; Amria, Shereen; Bethard, Jennifer R; Haque, Azizul

2014-01-01

While Burkitt lymphoma (BL) has a well-known defect in HLA class I-mediated antigen presentation, the exact role of BL-associated HLA class II in generating a poor CD4+ T-cell response remains unresolved. Here, we found that BL cells are deficient in their ability to optimally stimulate CD4+ T cells via the HLA class II pathway. This defect in CD4+ T-cell recognition was not associated with low levels of co-stimulatory molecules on BL cells, as addition of external co-stimulation failed to elicit CD4+ T-cell activation by BL. Further, the defect was not caused by faulty antigen/class II interaction, because antigenic peptides bound with measurable affinity to BL-associated class II molecules. Interestingly, functional class II–peptide complexes were formed at acidic pH 5·5, which restored immune recognition. Acidic buffer (pH 5·5) eluate from BL cells contained molecules that impaired class II-mediated antigen presentation and CD4+ T-cell recognition. Biochemical analysis showed that these molecules were greater than 30 000 molecular weight in size, and proteinaceous in nature. In addition, BL was found to have decreased expression of a 47 000 molecular weight enolase-like molecule that enhances class II-mediated antigen presentation in B cells, macrophages and dendritic cells, but not in BL cells. These findings demonstrate that BL likely has multiple defects in HLA class II-mediated antigen presentation and immune recognition, which may be exploited for future immunotherapies. PMID:24628049

Sibling rivalry: competition between MHC class II family members inhibits immunity.

PubMed

Denzin, Lisa K; Cresswell, Peter

2013-01-01

Peptide loading of major histocompatibility complex (MHC) class II molecules in the endosomes and lysosomes of antigen-presenting cells is catalyzed by human leukocyte antigen-DM (HLA-DM) and modulated by HLA-DO. In a structural study in this issue, Guce et al. show that HLA-DO is an MHC class II mimic and functions as a competitive and essentially irreversible inhibitor of HLA-DM activity, thereby inhibiting MHC class II antigen presentation.

25 CFR 547.9 - What are the minimum technical standards for Class II gaming system accounting functions?

Code of Federal Regulations, 2011 CFR

2011-04-01

... OF CLASS II GAMES § 547.9 What are the minimum technical standards for Class II gaming system... digits to accommodate the design of the game. (3) Accounting data displayed to the player may be... audit, configuration, recall and test modes; or (ii) Temporarily, during entertaining displays of game...

25 CFR 547.9 - What are the minimum technical standards for Class II gaming system accounting functions?

Code of Federal Regulations, 2010 CFR

2010-04-01

... OF CLASS II GAMES § 547.9 What are the minimum technical standards for Class II gaming system... digits to accommodate the design of the game. (3) Accounting data displayed to the player may be... audit, configuration, recall and test modes; or (ii) Temporarily, during entertaining displays of game...

25 CFR 547.9 - What are the minimum technical standards for Class II gaming system accounting functions?

Code of Federal Regulations, 2012 CFR

2012-04-01

... OF CLASS II GAMES § 547.9 What are the minimum technical standards for Class II gaming system... digits to accommodate the design of the game. (3) Accounting data displayed to the player may be... audit, configuration, recall and test modes; or (ii) Temporarily, during entertaining displays of game...

Do Transposed-Letter Similarity Effects Occur at a Morpheme Level? Evidence for Morpho-Orthographic Decomposition

ERIC Educational Resources Information Center

Dunabeitia, Jon Andoni; Peream, Manuel; Carreiras, Manuel

2007-01-01

When does morphological decomposition occur in visual word recognition? An increasing body of evidence suggests the presence of early morphological processing. The present work investigates this issue via an orthographic similarity manipulation. Three masked priming lexical decision experiments were conducted to examine the transposed-letter…

A Stimulus Sampling Theory of Letter Identity and Order

ERIC Educational Resources Information Center

Norris, Dennis; Kinoshita, Sachiko; van Casteren, Maarten

2010-01-01

Early on during word recognition, letter positions are not accurately coded. Evidence for this comes from transposed-letter (TL) priming effects, in which letter strings generated by transposing two adjacent letters (e.g., "jugde") produce large priming effects, more than primes with the letters replaced in the corresponding position (e.g.,…

[Plant transposable elements and their application in genetics and biotechnology].

PubMed

Ovcharenko, O O; Rudas, V A; Kuchuk, M V

2006-01-01

Data concerning plant transposable elements and their contribution to plant genome evolution are reviewed. Much attention is focused on utilization of transgenic plants as heterologous hosts of transposons for investigation of transposition mechanisms and gene cloning. Probable ways of the use of plant transposons as genetic tools in biotechnology are discussed.

Does Kaniso activate CASINO?: input coding schemes and phonology in visual-word recognition.

PubMed

Acha, Joana; Perea, Manuel

2010-01-01

Most recent input coding schemes in visual-word recognition assume that letter position coding is orthographic rather than phonological in nature (e.g., SOLAR, open-bigram, SERIOL, and overlap). This assumption has been drawn - in part - by the fact that the transposed-letter effect (e.g., caniso activates CASINO) seems to be (mostly) insensitive to phonological manipulations (e.g., Perea & Carreiras, 2006, 2008; Perea & Pérez, 2009). However, one could argue that the lack of a phonological effect in prior research was due to the fact that the manipulation always occurred in internal letter positions - note that phonological effects tend to be stronger for the initial syllable (Carreiras, Ferrand, Grainger, & Perea, 2005). To reexamine this issue, we conducted a masked priming lexical decision experiment in which we compared the priming effect for transposed-letter pairs (e.g., caniso-CASINO vs. caviro-CASINO) and for pseudohomophone transposed-letter pairs (kaniso-CASINO vs. kaviro-CASINO). Results showed a transposed-letter priming effect for the correctly spelled pairs, but not for the pseudohomophone pairs. This is consistent with the view that letter position coding is (primarily) orthographic in nature.

The struggle for life of the genome's selfish architects

PubMed Central

2011-01-01

Transposable elements (TEs) were first discovered more than 50 years ago, but were totally ignored for a long time. Over the last few decades they have gradually attracted increasing interest from research scientists. Initially they were viewed as totally marginal and anecdotic, but TEs have been revealed as potentially harmful parasitic entities, ubiquitous in genomes, and finally as unavoidable actors in the diversity, structure, and evolution of the genome. Since Darwin's theory of evolution, and the progress of molecular biology, transposable elements may be the discovery that has most influenced our vision of (genome) evolution. In this review, we provide a synopsis of what is known about the complex interactions that exist between transposable elements and the host genome. Numerous examples of these interactions are provided, first from the standpoint of the genome, and then from that of the transposable elements. We also explore the evolutionary aspects of TEs in the light of post-Darwinian theories of evolution. Reviewers This article was reviewed by Jerzy Jurka, Jürgen Brosius and I. King Jordan. For complete reports, see the Reviewers' reports section. PMID:21414203

Letter position coding across modalities: the case of Braille readers.

PubMed

Perea, Manuel; García-Chamorro, Cristina; Martín-Suesta, Miguel; Gómez, Pablo

2012-01-01

The question of how the brain encodes letter position in written words has attracted increasing attention in recent years. A number of models have recently been proposed to accommodate the fact that transposed-letter stimuli like jugde or caniso are perceptually very close to their base words. Here we examined how letter position coding is attained in the tactile modality via Braille reading. The idea is that Braille word recognition may provide more serial processing than the visual modality, and this may produce differences in the input coding schemes employed to encode letters in written words. To that end, we conducted a lexical decision experiment with adult Braille readers in which the pseudowords were created by transposing/replacing two letters. We found a word-frequency effect for words. In addition, unlike parallel experiments in the visual modality, we failed to find any clear signs of transposed-letter confusability effects. This dissociation highlights the differences between modalities. The present data argue against models of letter position coding that assume that transposed-letter effects (in the visual modality) occur at a relatively late, abstract locus.

Functional Anatomy of Recognition of Chinese Multi-Character Words: Convergent Evidence from Effects of Transposable Nonwords, Lexicality, and Word Frequency.

PubMed

Lin, Nan; Yu, Xi; Zhao, Ying; Zhang, Mingxia

2016-01-01

This fMRI study aimed to identify the neural mechanisms underlying the recognition of Chinese multi-character words by partialling out the confounding effect of reaction time (RT). For this purpose, a special type of nonword-transposable nonword-was created by reversing the character orders of real words. These nonwords were included in a lexical decision task along with regular (non-transposable) nonwords and real words. Through conjunction analysis on the contrasts of transposable nonwords versus regular nonwords and words versus regular nonwords, the confounding effect of RT was eliminated, and the regions involved in word recognition were reliably identified. The word-frequency effect was also examined in emerged regions to further assess their functional roles in word processing. Results showed significant conjunctional effect and positive word-frequency effect in the bilateral inferior parietal lobules and posterior cingulate cortex, whereas only conjunctional effect was found in the anterior cingulate cortex. The roles of these brain regions in recognition of Chinese multi-character words were discussed.

Functional Anatomy of Recognition of Chinese Multi-Character Words: Convergent Evidence from Effects of Transposable Nonwords, Lexicality, and Word Frequency

PubMed Central

Lin, Nan; Yu, Xi; Zhao, Ying; Zhang, Mingxia

2016-01-01

This fMRI study aimed to identify the neural mechanisms underlying the recognition of Chinese multi-character words by partialling out the confounding effect of reaction time (RT). For this purpose, a special type of nonword—transposable nonword—was created by reversing the character orders of real words. These nonwords were included in a lexical decision task along with regular (non-transposable) nonwords and real words. Through conjunction analysis on the contrasts of transposable nonwords versus regular nonwords and words versus regular nonwords, the confounding effect of RT was eliminated, and the regions involved in word recognition were reliably identified. The word-frequency effect was also examined in emerged regions to further assess their functional roles in word processing. Results showed significant conjunctional effect and positive word-frequency effect in the bilateral inferior parietal lobules and posterior cingulate cortex, whereas only conjunctional effect was found in the anterior cingulate cortex. The roles of these brain regions in recognition of Chinese multi-character words were discussed. PMID:26901644

Finishing occlusion in Class II or Class III molar relation: therapeutic Class II and III.

PubMed

Nangia, A; Darendeliler, M A

2001-11-01

The most frequent extraction regime consists of the removal of upper and lower premolars. Depending on anchorage requirements, camouflage treatment options, surgical intervention, or the absence of teeth in only one arch, it may become necessary to finalize the occlusion with a one-dental-unit discrepancy between the upper and lower dental arches. Guidelines are presented for finishing occlusions in Class II or Class III molar relation.

Evolution and Distribution of Class II-Related Endogenous Retroviruses†

PubMed Central

Gifford, Robert; Kabat, Peter; Martin, Joanne; Lynch, Clare; Tristem, Michael

2005-01-01

Endogenous retroviruses (ERVs) are widespread in vertebrate genomes and have been loosely grouped into “classes” on the basis of their phylogenetic relatedness to the established genera of exogenous retroviruses. Four of these genera—the lentiviruses, alpharetroviruses, betaretroviruses, and deltaretroviruses—form a well-supported clade in retroviral phylogenies, and ERVs that group with these genera have been termed class II ERVs. We used PCR amplification and sequencing of retroviral fragments from more than 130 vertebrate taxa to investigate the evolution of the class II retroviruses in detail. We confirm that class II retroviruses are largely confined to mammalian and avian hosts and provide evidence for a major novel group of avian retroviruses, and we identify additional members of both the alpha- and the betaretrovirus genera. Phylogenetic analyses demonstrated that the avian and mammalian viruses form distinct monophyletic groups, implying that interclass transmission has occurred only rarely during the evolution of the class II retroviruses. In contrast to previous reports, the lentiviruses clustered as sister taxa to several endogenous retroviruses derived from rodents and insectivores. This topology was further supported by the shared loss of both the class II PR-Pol frameshift site and the class II retrovirus G-patch domain. PMID:15858031

Rapid inactivation of the maize transposable element En/Spm in Medicago truncatula.

PubMed

d'Erfurth, I; Cosson, V; Eschstruth, A; Rippa, S; Messinese, E; Durand, P; Trinh, H; Kondorosi, A; Ratet, P

2003-09-01

Transposable elements have been widely used as mutagens in many organisms. Among them, the maize transposable element En/Spm has been shown to transpose efficiently in several plant species including the model plant Arabidopsis, where it has been used for large-scale mutagenesis. To determine whether we could use this transposon as a mutagen in the model legume plant Medicago truncatula, we tested the activity of the autonomous element, as well as two defective elements, in this plant, and in Arabidopsis as a positive control. In agreement with previous reports, we observed efficient excision of the autonomous En/Spm element in A. thaliana. This element was also active in M. truncatula, but the transposition activity was low and was apparently restricted to the tissue culture step necessary for the production of transgenic plants. The activity of one of the defective transposable elements, dSpm, was very low in A. thaliana and even lower in M. truncatula. The use of different sources of transposases suggested that this defect in transposition was associated with the dSpm element itself. Transposition of the other defective element, I6078, was also detected in M. truncatula, but, as observed with the autonomous element, transposition events were very rare and occurred during tissue culture. These results suggest that the En/Spm element is rapidly inactivated in the regenerated plants and their progeny, and therefore is not suitable for routine insertion mutagenesis in M. truncatula.

RAVEL: retrieval and visualization in ELectronic health records.

PubMed

Thiessard, Frantz; Mougin, Fleur; Diallo, Gayo; Jouhet, Vianney; Cossin, Sébastien; Garcelon, Nicolas; Campillo, Boris; Jouini, Wassim; Grosjean, Julien; Massari, Philippe; Griffon, Nicolas; Dupuch, Marie; Tayalati, Fayssal; Dugas, Edwige; Balvet, Antonio; Grabar, Natalia; Pereira, Suzanne; Frandji, Bruno; Darmoni, Stefan; Cuggia, Marc

2012-01-01

Because of the ever-increasing amount of information in patients' EHRs, healthcare professionals may face difficulties for making diagnoses and/or therapeutic decisions. Moreover, patients may misunderstand their health status. These medical practitioners need effective tools to locate in real time relevant elements within the patients' EHR and visualize them according to synthetic and intuitive presentation models. The RAVEL project aims at achieving this goal by performing a high profile industrial research and development program on the EHR considering the following areas: (i) semantic indexing, (ii) information retrieval, and (iii) data visualization. The RAVEL project is expected to implement a generic, loosely coupled to data sources prototype so that it can be transposed into different university hospitals information systems.

Antiviral CD8+ T Cells Restricted by Human Leukocyte Antigen Class II Exist during Natural HIV Infection and Exhibit Clonal Expansion.

PubMed

Ranasinghe, Srinika; Lamothe, Pedro A; Soghoian, Damien Z; Kazer, Samuel W; Cole, Michael B; Shalek, Alex K; Yosef, Nir; Jones, R Brad; Donaghey, Faith; Nwonu, Chioma; Jani, Priya; Clayton, Gina M; Crawford, Frances; White, Janice; Montoya, Alana; Power, Karen; Allen, Todd M; Streeck, Hendrik; Kaufmann, Daniel E; Picker, Louis J; Kappler, John W; Walker, Bruce D

2016-10-18

CD8 + T cell recognition of virus-infected cells is characteristically restricted by major histocompatibility complex (MHC) class I, although rare examples of MHC class II restriction have been reported in Cd4-deficient mice and a macaque SIV vaccine trial using a recombinant cytomegalovirus vector. Here, we demonstrate the presence of human leukocyte antigen (HLA) class II-restricted CD8 + T cell responses with antiviral properties in a small subset of HIV-infected individuals. In these individuals, T cell receptor β (TCRβ) analysis revealed that class II-restricted CD8 + T cells underwent clonal expansion and mediated killing of HIV-infected cells. In one case, these cells comprised 12% of circulating CD8 + T cells, and TCRα analysis revealed two distinct co-expressed TCRα chains, with only one contributing to binding of the class II HLA-peptide complex. These data indicate that class II-restricted CD8 + T cell responses can exist in a chronic human viral infection, and may contribute to immune control. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Variations in tooth size and arch dimensions in Malay schoolchildren.

PubMed

Hussein, Khalid W; Rajion, Zainul A; Hassan, Rozita; Noor, Siti Noor Fazliah Mohd

2009-11-01

To compare the mesio-distal tooth sizes and dental arch dimensions in Malay boys and girls with Class I, Class II and Class III malocclusions. The dental casts of 150 subjects (78 boys, 72 girls), between 12 and 16 years of age, with Class I, Class II and Class III malocclusions were used. Each group consisted of 50 subjects. An electronic digital caliper was used to measure the mesio-distal tooth sizes of the upper and lower permanent teeth (first molar to first molar), the intercanine and intermolar widths. The arch lengths and arch perimeters were measured with AutoCAD software (Autodesk Inc., San Rafael, CA, U.S.A.). The mesio-distal dimensions of the upper lateral incisors and canines in the Class I malocclusion group were significantly smaller than the corresponding teeth in the Class III and Class II groups, respectively. The lower canines and first molars were significantly smaller in the Class I group than the corresponding teeth in the Class II group. The lower intercanine width was significantly smaller in the Class II group as compared with the Class I group, and the upper intermolar width was significantly larger in Class III group as compared with the Class II group. There were no significant differences in the arch perimeters or arch lengths. The boys had significantly wider teeth than the girls, except for the left lower second premolar. The boys also had larger upper and lower intermolar widths and lower intercanine width than the girls. Small, but statistically significant, differences in tooth sizes are not necessarily accompanied by significant arch width, arch length or arch perimeter differences. Generally, boys have wider teeth, larger lower intercanine width and upper and lower intermolar widths than girls.

Transposable element-associated microRNA hairpins produce 21-nt sRNAs integrated into typical microRNA pathways in rice

PubMed Central

Ou-Yang, Fangqian; Luo, Qing-Jun; Zhang, Yue; Richardson, Casey R.; Jiang, Yingwen; Rock, Christopher D.

2013-01-01

microRNAs (miRNAs) are a class of small RNAs (sRNAs) of ~21 nucleotides (nt) in length processed from foldback hairpins by DICER-LIKE1 (DCL1) or DCL4. They regulate the expression of target mRNAs by base pairing through RNA-Induced Silencing Complex (RISC). In the RISC, ARGONAUTE1 (AGO1) is the key protein that cleaves miRNA targets at position ten of a miRNA:target duplex. The authenticity of many annotated rice miRNA hairpins is under debate because of their homology to repeat sequences. Some of them, like miR1884b, have been removed from the current release of miRBase based on incomplete information. In this study, we investigated the association of transposable element (TE)-derived miRNAs with typical miRNA pathways (DCL1/4- and AGO1-dependent) using publicly available deep sequencing datasets. Seven miRNA hairpins with 13 unique sRNAs were specifically enriched in AGO1 immunoprecipitation samples and relatively reduced in DCL1/4 knockdown genotypes. Interestingly, these species are ~21-nt long, instead of 24-nt as annotated in miRBase and the literature. Their expression profiles meet current criteria for functional annotation of miRNAs. In addition, diagnostic cleavage tags were found in degradome datasets for predicted target mRNAs. Most of these miRNA hairpins share significant homology with miniature inverted-repeat transposable elements (MITEs), one type of abundant DNA transposons in rice. Finally, the root-specific production of a 24 nt miRNA-like sRNA was confirmed by RNA blot for a novel EST that maps to the 3'-UTR of a candidate pseudogene showing extensive sequence homology to miR1884b hairpin. Our data are consistent with the hypothesis that TEs can serve as a driving force for the evolution of some MIRNAs, where co-opting of DICER-LIKE1/4 processing and integration into AGO1 could exapt transcribed TE-associated hairpins into typical miRNA pathways. PMID:23420033

77 FR 50760 - Notice and request for comments

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-22

... rehabilitation to Class II and Class III railroad infrastructure damaged by hurricanes, floods, and natural... issued by the President ( http://www.fema.gov/news/disasters.fema#sev1 ). Class II and Class III railroad...

Polymorphism at Expressed DQ and DR Loci in Five Common Equine MHC Haplotypes

PubMed Central

Miller, Donald; Tallmadge, Rebecca L.; Binns, Matthew; Zhu, Baoli; Mohamoud, Yasmin Ali; Ahmed, Ayeda; Brooks, Samantha A.; Antczak, Douglas F.

2016-01-01

The polymorphism of Major Histocompatibility Complex (MHC) class II DQ and DR genes in five common Equine Leukocyte Antigen (ELA) haplotypes was determined through sequencing of mRNA transcripts isolated from lymphocytes of eight ELA homozygous horses. Ten expressed MHC class II genes were detected in horses of the ELA-A3 haplotype carried by the donor horses of the equine Bacterial Artificial Chromosome (BAC) library and the reference genome sequence: four DR genes and six DQ genes. The other four ELA haplotypes contained at least eight expressed polymorphic MHC class II loci. Next Generation Sequencing (NGS) of genomic DNA of these four MHC haplotypes revealed stop codons in the DQA3 gene in the ELA-A2, ELA-A5, and ELA-A9 haplotypes. Few NGS reads were obtained for the other MHC class II genes that were not amplified in these horses. The amino acid sequences across haplotypes contained locus-specific residues, and the locus clusters produced by phylogenetic analysis were well supported. The MHC class II alleles within the five tested haplotypes were largely non-overlapping between haplotypes. The complement of equine MHC class II DQ and DR genes appears to be well conserved between haplotypes, in contrast to the recently described variation in class I gene loci between equine MHC haplotypes. The identification of allelic series of equine MHC class II loci will aid comparative studies of mammalian MHC conservation and evolution and may also help to interpret associations between the equine MHC class II region and diseases of the horse. PMID:27889800

40 CFR 82.23 - Transfers of allowances of class II controlled substances.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., any production, and allowable imports and exports of class II controlled substances reported by the... quantity of the transferor's class II consumption allowances, production allowances, export production... EPA; and (G) For trades of consumption allowances, production allowances, export production allowances...

Interaction of Mycobacterium avium-containing phagosomes with the antigen presentation pathway.

PubMed

Ullrich, H J; Beatty, W L; Russell, D G

2000-12-01

Pathogenic mycobacteria infect macrophages where they replicate in phagosomes that minimize contact with late endosomal/lysosomal compartments. Loading of Ags to MHC class II molecules occurs in specialized compartments with late endosomal characteristics. This points to a sequestration of mycobacteria-containing phagosomes from the sites where Ags meet MHC class II molecules. Indeed, in resting macrophages MHC class II levels decreased strongly in phagosomes containing M. avium during a 4-day infection. Phagosomal MHC class II of early (4 h) infections was partly surface-derived and associated with peptide. Activation of host macrophages led to the appearance of H2-M, a chaperon of Ag loading, and to a strong increase in MHC class II molecules in phagosomes of acute (1 day) infections. Comparison with the kinetics of MHC class II acquisition by IgG-coated bead-containing phagosomes suggests that the arrest in phagosome maturation by mycobacteria limits the intersection of mycobacteria-containing phagosomes with the intracellular trafficking pathways of Ag-presenting molecules.

Bone-anchored intermaxillary elastics in an asymmetric Class II malocclusion: A case report.

PubMed

Manni, Antonio; Lupini, Daniela; Cozzani, Mauro

2017-06-01

A 13-year-old male patient, presenting a Class II, division 1 malocclusion and crowding was treated by an innovative technique. After rapid palatal expansion by a Hyrax appliance, the teeth were bonded with straightwire brackets. Two miniscrews were inserted, one per side, in the mandibular buccal bone between the roots of the mandibular first molar and the second premolar. On the right side, the miniscrew implant was connected to the hook clamped on a 0.021×0.028″ SS wire with a twisted SS ligature in order to maintain the inclination of the frontal incisors during the Class II mechanics. On the left side, where the Class II relationship was more marked, intermaxillary elastics were applied from the upper left hook clamped on the archwire to the lower first molar and a power chain (100g) was stretched from the lower left hook to the miniscrew implant. Class II correction was accomplished using sequential Class II elastics of progressive strength coupled with rectangular stainless steel wires. After 22 months of active treatment, the results were balanced facial esthetics and a good occlusion. This dual anchorage set-up of Class II elastics reinforced with TADs produced protrusive action on the mandible with minimal side effects and with no significant change in the vertical dimension during the sagittal correction of the Class II malocclusion. Copyright © 2017 CEO. Published by Elsevier Masson SAS. All rights reserved.

Anteroposterior condylar position: a comparative study between subjects with normal occlusion and patients with Class I, Class II Division 1, and Class III malocclusions.

PubMed

Fraga, Marcelo Reis; Rodrigues, Andréia Fialho; Ribeiro, Luiz Claudio; Campos, Marcio José da Silva; Vitral, Robert Willer Farinazzo

2013-10-29

The present study aimed to determine and compare the anteroposterior position of the condyle in the mandibular fossa between groups of asymptomatic subjects with normal occlusion and asymptomatic subjects with Class I, Class II Division 1, and Class III malocclusions. Thirty persons with normal occlusion, 30 with Class I malocclusion, 30 with Class II Division 1, and 30 with Class III had computed tomography scans of their temporomandibular joints. The anterior joint space/posterior joint space (AJS/PJS) ratio was determined for the right and left joints. The paired t test was used to analyze the AJS/PJS ratio between both sides for each group. The ANOVA test was applied to verify the differences between the groups for the measurements of the right and left sides. In case the ANOVA test confirmed significance, the Dunnett's t test was performed to compare the groups of malocclusion with that of normal occlusion. The paired t test between the AJS/PJS relationships in the right and left sides showed the following p values: Class I (0.168), Class II Division 1 (0.662), Class III (0.991), and normal occlusion (0.390). The ANOVA test showed a p value of 0.445 for the comparisons of the right side and 0.040 for the left side. The Dunnett's t test demonstrated a statistically significant difference between the Class II group and the normal occlusion group (p value of 0.026) in the joints of the left side. Bilateral symmetry and lack of condyle centralization were common characteristics among all groups. The greatest condylar decentralization was observed in the Class II group, whereas the least condylar decentralization was found in the normal occlusion group.

The Quiet Clam Is Quite Calm: Transposed-Letter Neighborhood Effects on Eye Movements during Reading

ERIC Educational Resources Information Center

Johnson, Rebecca L.

2009-01-01

In responses time tasks, inhibitory neighborhood effects have been found for word pairs that differ in a transposition of two adjacent letters (e.g., "clam/calm"). Here, the author describes two eye-tracking experiments conducted to explore transposed-letter (TL) neighborhood effects within the context of normal silent reading. In…

The diversity of sequence and chromosomal distribution of new transposable element-related segments in the rye genome revealed by FISH and lineage annotation

USDA-ARS?s Scientific Manuscript database

The rye genome features a high percentage of repetitive elements, especially transposable elements (TEs). However, studies about the constitution and organization of TEs on rye chromosomes are limited. In this study, 97 unique TE segments were isolated and characterized; 50 TE segmemts showed varyin...

Transposed Letter Priming with Horizontal and Vertical Text in Japanese and English Readers

ERIC Educational Resources Information Center

Witzel, Naoko; Qiao, Xiaomei; Forster, Kenneth

2011-01-01

It is well established that in masked priming, a target word (e.g., "JUDGE") is primed more effectively by a transposed letter (TL) prime (e.g., "jugde") than by an orthographic control prime (e.g., "junpe"). This is inconsistent with the slot coding schemes used in many models of visual word recognition. Several…

Genotype dependent burst of transposable element expression in crowns of hexaploid wheat (Triticum aestivum L.) during cold acclimation

USDA-ARS?s Scientific Manuscript database

The expression of 1,613 transposable elements (TEs) represented in the Affymetix Wheat Genome Chip was examined during cold treatment in crowns of 4 hexaploid wheat genotypes that vary in tolerance to cold and in flowering time. The TE expression profiles showed a constant level of expression throug...

Differential effects of donor-specific HLA antibodies in living versus deceased donor transplant.

PubMed

Kamburova, E G; Wisse, B W; Joosten, I; Allebes, W A; van der Meer, A; Hilbrands, L B; Baas, M C; Spierings, E; Hack, C E; van Reekum, F E; van Zuilen, A D; Verhaar, M C; Bots, M L; Drop, A C A D; Plaisier, L; Seelen, M A J; Sanders, J S F; Hepkema, B G; Lambeck, A J A; Bungener, L B; Roozendaal, C; Tilanus, M G J; Voorter, C E; Wieten, L; van Duijnhoven, E M; Gelens, M; Christiaans, M H L; van Ittersum, F J; Nurmohamed, S A; Lardy, N M; Swelsen, W; van der Pant, K A; van der Weerd, N C; Ten Berge, I J M; Bemelman, F J; Hoitsma, A; van der Boog, P J M; de Fijter, J W; Betjes, M G H; Heidt, S; Roelen, D L; Claas, F H; Otten, H G

2018-02-21

The presence of donor-specific anti-HLA antibodies (DSAs) is associated with increased risk of graft failure after kidney transplant. We hypothesized that DSAs against HLA class I, class II, or both classes indicate a different risk for graft loss between deceased and living donor transplant. In this study, we investigated the impact of pretransplant DSAs, by using single antigen bead assays, on long-term graft survival in 3237 deceased and 1487 living donor kidney transplants with a negative complement-dependent crossmatch. In living donor transplants, we found a limited effect on graft survival of DSAs against class I or II antigens after transplant. Class I and II DSAs combined resulted in decreased 10-year graft survival (84% to 75%). In contrast, after deceased donor transplant, patients with class I or class II DSAs had a 10-year graft survival of 59% and 60%, respectively, both significantly lower than the survival for patients without DSAs (76%). The combination of class I and II DSAs resulted in a 10-year survival of 54% in deceased donor transplants. In conclusion, class I and II DSAs are a clear risk factor for graft loss in deceased donor transplants, while in living donor transplants, class I and II DSAs seem to be associated with an increased risk for graft failure, but this could not be assessed due to their low prevalence. © 2018 The Authors. American Journal of Transplantation published by Wiley Periodicals, Inc. on behalf of The American Society of Transplantation and the American Society of Transplant Surgeons.

7 CFR 1000.53 - Announcement of class prices, component prices, and advanced pricing factors.

Code of Federal Regulations, 2010 CFR

2010-01-01

... order) for the preceding month: (1) The Class II price; (2) The Class II butterfat price; (3) The Class... the following month: (1) The Class I price; (2) The Class I skim milk price; (3) The Class I butterfat...; (7) The butterfat price; (8) The nonfat solids price; (9) The protein price; (10) The other solids...

7 CFR 1000.53 - Announcement of class prices, component prices, and advanced pricing factors.

Code of Federal Regulations, 2014 CFR

2014-01-01

... order) for the preceding month: (1) The Class II price; (2) The Class II butterfat price; (3) The Class... the following month: (1) The Class I price; (2) The Class I skim milk price; (3) The Class I butterfat...; (7) The butterfat price; (8) The nonfat solids price; (9) The protein price; (10) The other solids...

7 CFR 1000.53 - Announcement of class prices, component prices, and advanced pricing factors.

Code of Federal Regulations, 2013 CFR

2013-01-01

... order) for the preceding month: (1) The Class II price; (2) The Class II butterfat price; (3) The Class... the following month: (1) The Class I price; (2) The Class I skim milk price; (3) The Class I butterfat...; (7) The butterfat price; (8) The nonfat solids price; (9) The protein price; (10) The other solids...

7 CFR 1000.53 - Announcement of class prices, component prices, and advanced pricing factors.

Code of Federal Regulations, 2012 CFR

2012-01-01

... order) for the preceding month: (1) The Class II price; (2) The Class II butterfat price; (3) The Class... the following month: (1) The Class I price; (2) The Class I skim milk price; (3) The Class I butterfat...; (7) The butterfat price; (8) The nonfat solids price; (9) The protein price; (10) The other solids...

7 CFR 1000.53 - Announcement of class prices, component prices, and advanced pricing factors.

Code of Federal Regulations, 2011 CFR

2011-01-01

... order) for the preceding month: (1) The Class II price; (2) The Class II butterfat price; (3) The Class... the following month: (1) The Class I price; (2) The Class I skim milk price; (3) The Class I butterfat...; (7) The butterfat price; (8) The nonfat solids price; (9) The protein price; (10) The other solids...

Comparison of BMI, AHI, and apolipoprotein E ε4 (APOE-ε4) alleles among sleep apnea patients with different skeletal classifications.

PubMed

Roedig, Jason J; Phillips, Barbara A; Morford, Lorri A; Van Sickels, Joseph E; Falcao-Alencar, Gabriel; Fardo, David W; Hartsfield, James K; Ding, Xiuhua; Kluemper, G Thomas

2014-04-15

This case-control study investigated whether variations within the APOE-ε gene were associated with having a convex facial profile (skeletal Class II) compared to exhibiting a straight or concave facial profile (Class I or Class III) among patients with obstructive sleep apnea (OSA). Associations between the apnea-hypopnea index (AHI) and body mass index (BMI) scores for these OSA patients were also examined in the context of facial profile. OSA patients with an AHI ≥ 15 were recruited from a sleep clinic and classified by facial and dental occlusal relationships based on a profile facial analysis, lateral photographs, and dental examination. Saliva was collected as a source of DNA. The APOE-ε1-4 allele-defining single nucleotide polymorphisms (SNPs) rs429358 and rs7412 were genotyped. A χ(2) analysis was used to assess Hardy-Weinberg equilibrium and for association analysis (significance at p < 0.05). ANOVA and Fisher exact test were also used. Seventy-six Caucasian OSA patients participated in the study-25 Class II cases and 51 non-Class II cases. There was no association of the APOE-ε4 allele with facial profile among these OSA patients. Class II OSA patients had significantly lower BMIs (30.7 ± 5.78) than Class I (37.3 ± 6.14) or Class III (37.8 ± 6.17) patients (p < 0.001), although there was no statistical difference in AHI for Class II patients compared with other groups. OSA patients with Class II convex profile were more likely to have a lower BMI than those in other skeletal groups. In fact 20% of them were not obese, suggesting that a Class II convex profile may influence or be associated with OSA development independent of BMI.

A cephalometric analysis of Class II dentate subjects to establish a formula to determine the occlusal plane in Class II edentate subjects: A neo adjunct.

PubMed

Sinha, Nikita; Reddy, K Mahendranadh; Gupta, Nidhi; Shastry, Y M

2017-01-01

Occlusal plane (OP) differs considerably in participants with skeletal Class I and Class II participants. In this study, cephalometrics has been used to help in the determination of orientation of the OP utilizing the nonresorbable bony anatomic landmarks in skeletal Class II participants and an attempt has been made to predict and examine the OP in individuals with skeletal class II jaw relationship. One hundred dentulous participants with skeletal Class II malocclusion who came to the hospital for correcting their jaw relationship participated in the study. Their right lateral cephalogram was taken using standardized procedures, and all the tracings were manually done by a single trained examiner. The cephalograms which were taken for the diagnostic purpose were utilized for the study, and the patient was not exposed to any unnecessary radiation. The numerical values obtained from the cephalograms were subjected to statistical analysis. Pearson's correlation of <0.001 was considered significant, and a linear regression analysis was performed to determine a formula which would help in the determination of orientation of the OP in Class II edentulous participants. Pearson's correlation coefficient and linear regression analysis were performed, and a high correlation was found between A2 and (A2 + B2)/(B2 + C2) with " r " value of 0.5. A medium correlation was found between D2 and (D2 + E2)/(E2 + F2) with " r " value of 0.42. The formula obtained for posterior reference frame through linear regression equation was y = 0.018* × +0.459 and the formula obtained for anterior reference frame was y1 = 0.011* × 1 + 0.497. It was hypothesized that by substituting these formulae in the cephalogram obtained from the Class II edentate individual, the OP can be obtained and verified. It was concluded that cephalometrics can be useful in examining the orientation of OP in skeletal Class II participants.

Paramecium tetraurelia chromatin assembly factor-1-like protein PtCAF-1 is involved in RNA-mediated control of DNA elimination.

PubMed

Ignarski, Michael; Singh, Aditi; Swart, Estienne C; Arambasic, Miroslav; Sandoval, Pamela Y; Nowacki, Mariusz

2014-10-29

Genome-wide DNA remodelling in the ciliate Paramecium is ensured by RNA-mediated trans-nuclear crosstalk between the germline and the somatic genomes during sexual development. The rearrangements include elimination of transposable elements, minisatellites and tens of thousands non-coding elements called internally eliminated sequences (IESs). The trans-nuclear genome comparison process employs a distinct class of germline small RNAs (scnRNAs) that are compared against the parental somatic genome to select the germline-specific subset of scnRNAs that subsequently target DNA elimination in the progeny genome. Only a handful of proteins involved in this process have been identified so far and the mechanism of DNA targeting is unknown. Here we describe chromatin assembly factor-1-like protein (PtCAF-1), which we show is required for the survival of sexual progeny and localizes first in the parental and later in the newly developing macronucleus. Gene silencing shows that PtCAF-1 is required for the elimination of transposable elements and a subset of IESs. PTCAF-1 depletion also impairs the selection of germline-specific scnRNAs during development. We identify specific histone modifications appearing during Paramecium development which are strongly reduced in PTCAF-1 depleted cells. Our results demonstrate the importance of PtCAF-1 for the epigenetic trans-nuclear cross-talk mechanism. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements

PubMed Central

Brunet, Tyler D.P.; Doolittle, W. Ford

2015-01-01

One of several issues at play in the renewed debate over “junk DNA” is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to “speed evolution” or as an “evolutionary repository” could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs). In many species, not least our own, TEs comprise a large fraction of all nuclear DNA, and whether they individually or collectively contribute to fitness—or are instead junk— is a subject of ongoing contestation. Even if TEs generally owe their origin to selfish selection at the lowest level (that of genomes), their prevalence in extant organisms and the prevalence of extant organisms bearing them must also respond to selection within species (on organismal fitness) and between species (on rates of speciation and extinction). At an even higher level, the persistence of clades may be affected (positively or negatively) by TE carriage. If indeed TEs speed evolution, it is at these higher levels of selection that such a function might best be attributed to them as a class. PMID:26253318

Genomic organization of the 260 kb surrounding the waxy locus in a Japonica rice

PubMed

Nagano; Wu; Kawasaki; Kishima; Sano

1999-12-01

The present study was carried out to characterize the molecular organization in the vicinity of the waxy locus in rice. To determine the structural organization of the region surrounding waxy, contiguous clones covering a total of 260 kb were constructed using a bacterial artificial chromosome (BAC) library from the Shimokita variety of Japonica rice. This map also contains 200 overlapping subclones, which allowed construction of a fine physical map with a total of 64 HindIII sites. During the course of constructing the map, we noticed the presence of some repeated regions which might be related to transposable elements. We divided the 260-kb region into 60 segments (average size of 5.7 kb) to use as probes to determine their genomic organization. Hybridization patterns obtained by probing with these segments were classified into four types: class 1, a single or a few bands without a smeared background; class 2, a single or a few bands with a smeared background; class 3, multiple discrete bands without a smeared background; and class 4, only a smeared background. These classes constituted 6.5%, 20.9%, 3.7%, and 68.9% of the 260-kb region, respectively. The distribution of each class revealed that repetitive sequences are a major component in this region, as expected, and that unique sequence regions were mostly no longer than 6 kb due to interruption by repetitive sequences. We discuss how the map constructed here might be a powerful tool for characterization and comparison of the genome structures and the genes around the waxy locus in the Oryza species.

77 FR 32465 - Technical Standards

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-01

... minimum odds for Class II games; amend standards for test labs; remove references to the Federal... the Play of Class II Games. 73 FR 60508. The rule added a new part to the Commission's regulations establishing a process for ensuring the integrity of electronic Class II games and aids. The standards were...

40 CFR 147.1600 - State-administered program-Class II wells.

Code of Federal Regulations, 2010 CFR

2010-07-01

...) WATER PROGRAMS (CONTINUED) STATE, TRIBAL, AND EPA-ADMINISTERED UNDERGROUND INJECTION CONTROL PROGRAMS New Mexico § 147.1600 State-administered program—Class II wells. The UIC program for Class II wells in the State of New Mexico, except for those on Indian lands, is the program administered by the New...

40 CFR 144.22 - Existing Class II enhanced recovery and hydrocarbon storage wells.

Code of Federal Regulations, 2010 CFR

2010-07-01

... and hydrocarbon storage wells. 144.22 Section 144.22 Protection of Environment ENVIRONMENTAL... of Underground Injection by Rule § 144.22 Existing Class II enhanced recovery and hydrocarbon storage wells. (a) An existing Class II enhanced recovery or hydrocarbon storage injection well is authorized by...

40 CFR 144.22 - Existing Class II enhanced recovery and hydrocarbon storage wells.

Code of Federal Regulations, 2011 CFR

2011-07-01

... and hydrocarbon storage wells. 144.22 Section 144.22 Protection of Environment ENVIRONMENTAL... of Underground Injection by Rule § 144.22 Existing Class II enhanced recovery and hydrocarbon storage wells. (a) An existing Class II enhanced recovery or hydrocarbon storage injection well is authorized by...

40 CFR 82.24 - Recordkeeping and reporting requirements for class II controlled substances.

Code of Federal Regulations, 2010 CFR

2010-07-01

... kilograms) of production of each class II controlled substance used in processes resulting in their...) The quantity (in kilograms) of production of each class II controlled substance used in processes... processes resulting in their transformation or eventual destruction; (vi) A list of the quantities and names...

Effect of immunodepletion of MHC class II-positive cells from pancreatic islets on generation of cytotoxic T-lymphocytes in mixed islet-lymphocyte coculture.

PubMed

Stock, P G; Ascher, N L; Platt, J L; Kaufman, D B; Chen, S; Field, M J; Sutherland, D E

1989-01-01

In vitro manipulation of pancreatic islets to decrease islet immunogenicity before transplantation has largely been directed at eliminating the major histocompatibility complex (MHC) class II-positive passenger leukocytes from the islets. The mixed islet-lymphocyte coculture (MILC) system was used to quantitate the efficacy of immunodepletion of MHC class II-positive cells from pancreatic islets in terms of reducing immunogenicity. With these experiments we compared the in vitro immunogenicity of MHC class II-depleted islets with untreated islets. B10.BR (H-2k) islets were treated with anti-Iak alloserum followed by complement. This treatment successfully eliminated MHC class II-positive cells from the islets, as demonstrated by indirect immunofluorescence techniques. Depleted islets generated slightly lower amounts of allospecific cytotoxic T-lymphocyte (CTL) activity when exposed to C57BL/6 (H-2b) splenocytes in the MILC than untreated control islets. Although the amount of CTL generated by the depleted islets was slightly less than that generated by untreated islets, there was significant stimulation of CTL by the MHC class II-depleted islets. Therefore, the presence or absence of MHC class II cells within the islet is unlikely to be the decisive factor contributing to islet immunogenicity.

Skeletal effects in Angle Class II/1 patients treated with the functional regulator type II : Cephalometric and tensor analysis.

PubMed

Schulz, Simone; Koos, Bernd; Duske, Kathrin; Stahl, Franka

2016-11-01

The purpose of this work was to employ both cephalometric and tensor analysis in characterizing the skeletal changes experienced by patients with Angle Class II/1 malocclusion during functional orthodontic treatment with the functional regulator type II. A total of 23 patients with Class II/1 malocclusion based on lateral cephalograms obtained before and after treatment with the functional regulator type II were analyzed. Another 23 patients with Angle Class II/1 malocclusion who had not undergone treatment were included as controls. Our cephalometric data attest to significant therapeutic effects of the functional regulator type II on the skeletal mandibular system, including significant advancement of the mandible, increases in effective mandibular length with enhancement of the chin profile, and reduction of growth-related bite deepening. No treatment-related effects were observed at the cranial-base and midface levels. In addition, tensor analysis revealed significant stimulation of mandibular growth in sagittal directions, without indications of growth effects on the maxilla. Its growth-pattern findings differed from those of cephalometric analysis by indicating that the appliance did promote horizontal development, which supports the functional orthodontic treatment effect in Angle Class II/1 cases. Tensor analysis yielded additional insights into sagittal and vertical growth changes not identifiable by strictly cephalometric means. The functional regulator type II was an effective treatment modality for Angle Class II/1 malocclusion and influenced the skeletal development of these patients in favorable ways.

Haemophilus ducreyi Cutaneous Ulcer Strains Diverged from Both Class I and Class II Genital Ulcer Strains: Implications for Epidemiological Studies.

PubMed

Gangaiah, Dharanesh; Spinola, Stanley M

2016-12-01

Haemophilus ducreyi has emerged as a major cause of cutaneous ulcers (CU) in yaws-endemic regions of the tropics in the South Pacific, South East Asia and Africa. H. ducreyi was once thought only to cause the genital ulcer (GU) disease chancroid; GU strains belong to 2 distinct classes, class I and class II. Using whole-genome sequencing of 4 CU strains from Samoa, 1 from Vanuatu and 1 from Papua New Guinea, we showed that CU strains diverged from the class I strain 35000HP and that one CU strain expressed β-lactamase. Recently, the Center for Disease Control and Prevention released the genomes of 11 additional CU strains from Vanuatu and Ghana; however, the evolutionary relationship of these CU strains to previously-characterized CU and GU strains is unknown. We performed phylogenetic analysis of 17 CU and 10 GU strains. Class I and class II GU strains formed two distinct clades. The class I strains formed two subclades, one containing 35000HP and HD183 and the other containing the remainder of the class I strains. Twelve of the CU strains formed a subclone under the class I 35000HP subclade, while 2 CU strains formed a subclone under the other class I subclade. Unexpectedly, 3 of the CU strains formed a subclone under the class II clade. Phylogenetic analysis of dsrA-hgbA-ncaA sequences yielded a tree similar to that of whole-genome phylogenetic tree. CU strains diverged from multiple lineages within both class I and class II GU strains. Multilocus sequence typing of dsrA-hgbA-ncaA could be reliably used for epidemiological investigation of CU and GU strains. As class II strains grow relatively poorly and are relatively more susceptible to vancomycin than class I strains, these findings have implications for methods to recover CU strains. Comparison of contemporary CU and GU isolates would help clarify the relationship between these entities.

Effectiveness of laparoscopic Roux-en-Y gastric bypass on obese class I type 2 diabetes mellitus patients.

PubMed

Xu, Lu; Yin, Jun; Mikami, Dean J; Portenier, Dana D; Zhou, Xiaojun; Mao, Zhongqi

2015-01-01

Laparoscopic Roux-en-Y gastric bypass (LRYGB) can dramatically improve type 2 diabetes mellitus (T2D) in obese class II and III patients. There is increasing evidence that shows bariatric surgery can also ameliorate T2D in patients with BMI between 30 kg/m(2) and 35 kg/m(2) (obese class I). To compare the effectiveness of LRYGB on T2D in obese class I patients with that of obese class II and III T2D patients. University Hospital, China A prospective study was performed in the authors' center from March 2010 to July 2011. Forty-two consecutive obese patients were included in the study. Anthropometric and metabolism parameters were compared between obese class II and III patients and obese class I patients before and after LRYGB. No patients were lost to follow up. After 36 months, metabolic parameters significantly improved in both groups. Partial remission rates between the 2 groups at each time point (12 months, 24 months, and 36 months) were comparable. Obese class II and III patients had higher complete remission rates at 12 months and 24 months, but no difference was observed at 36 months. Both obese class II and III patients and obese class I T2D patients showed significant improvement in multiple parameters after LRYGB. Obese class II and III patients had a higher complete remission rate than obese class I patients. Standardized remission criteria are needed to make outcomes form different centers comparable. Large prospective studies are needed and long-term outcomes have to be observed to better evaluate effectiveness of LRYGB on obese class I T2D patients. Copyright © 2015 American Society for Bariatric Surgery. All rights reserved.

Pathognomonic features of Angle's Class II division 2 malocclusion: A comparative cephalometric and arch width study

PubMed Central

Prasad, Singamsetty E.R.V.; Indukuri, Ravikishore Reddy; Singh, Rupesh; Nooney, Anitha; Palagiri, Firoz Babu; Narayana, Veera

2014-01-01

Background: A thorough knowledge of the salient features of malocclusion helps the clinician in arriving at a proper diagnosis and treatment plan, and also to predict the prognosis, prior to the onset of treatment process. Among the four classes of Angle's classification of malocclusion, Class II division 2 occurs with the least frequency. There is still continuing debate in the literature whether the Class II division 2 patients ascribe the pathognomonic skeletal and dental features. Aim of the study: The aim of this study is to describe the unique features of Angle's Class II division 2 malocclusion to differentiate it from Angle's Class II division 1 malocclusion. Materials and Methods: A total of 582 pre-treatment records (study models and cephalograms), with the age of patients ranging from 15 to 22 years, were obtained from the hospital records of Vishnu Dental College, Bhimavaram and Geetam's Dental College, Visakhapatnam. Out of these, 11 pre-treatment records were excluded because of lack of clarity. In the rest of the sample, 283 were Class II division 1 and 288 were Class II division 2. The lateral cephalograms were analyzed by using digiceph and the arch width analysis was done based on the anatomical points described by Staley et al. and Sergl et al. Results: An intergroup evaluation was done by using unpaired Student's “t” test. The skeletal vertical parameters, dental parameters, and the maxillary arch width parameters revealed a statistically significant difference between the two groups of malocclusion. Conclusion: Angle's Class II division 2 malocclusion has a pronounced horizontal growth pattern with decreased lower anterior facial height, retroclined upper anteriors, and significantly increased maxillary arch width parameters. PMID:25558449

Analysis of class II (hydrolytic) and class I (beta-lyase) apurinic/apyrimidinic endonucleases with a synthetic DNA substrate.

PubMed Central

Levin, J D; Demple, B

1990-01-01

We have developed simple and sensitive assays that distinguish the main classes of apurinic/apyrimidinic (AP) endonucleases: Class I enzymes that cleave on the 3' side of AP sites by beta-elimination, and Class II enzymes that cleave by hydrolysis on the 5' side. The distinction of the two types depends on the use of a synthetic DNA polymer that contains AP sites with 5'-[32P]phosphate residues. Using this approach, we now show directly that Escherichia coli endonuclease IV and human AP endonuclease are Class II enzymes, as inferred previously on the basis of indirect assays. The assay method does not exhibit significant interference by nonspecific nucleases or primary amines, which allows the ready determination of different AP endonuclease activities in crude cell extracts. In this way, we show that virtually all of the Class II AP endonuclease activity in E. coli can be accounted for by two enzymes: exonuclease III and endonuclease IV. In the yeast Saccharomyces cerevisiae, the Class II AP endonuclease activity is totally dependent on a single enzyme, the Apn1 protein, but there are probably multiple Class I enzymes. The versatility and ease of our approach should be useful for characterizing this important class of DNA repair enzymes in diverse systems. PMID:1698278

Tn4556, a 6.8-kilobase-pair transposable element of Streptomyces fradiae.

PubMed Central

Chung, S T

1987-01-01

A 6.8-kilobase-pair (kbp) transposable element (Tn4556) was found in a neomycin-producing strain of Streptomyces fradiae. This element was first observed in two 30.3-kbp plasmids (pUC1123 and pUC1124) which arose when a thiostrepton resistance gene (1 kbp) was ligated with the BclI-2 fragment (22.5 kbp) that contains the origin of replication of phage SF1. The Tn4556 segment was deleted when these plasmids were transduced into another S. fradiae host with phage SF1. These deletion plasmids (pUC1210 and pUC1211) had copy numbers of less than 1 per chromosome and were unstable. In contrast, pUC1123 and pUC1124, with copy numbers of 12 to 15 per chromosome, respectively, were relatively stable. When pUC1210 and pUC1211 were reintroduced into S. fradiae by protoplast transformation, the Tn4556 element transposed again to the plasmids at numerous new locations in either of two orientations. A copy of Tn4556 was found in the S. fradiae chromosome by hybridization studies. It appears that Tn4556 originated from the chromosome, transposed into unstable pUC1210 and pUC1211, and made stable plasmids. A temperature-sensitive hybrid plasmid carrying a viomycin resistance derivative of Tn4556 (pMT660::Tn4556::vph) was constructed. When Streptomyces lividans UC8390 containing the hybrid plasmid was grown at 39 degrees C, Tn4556::vph (Tn4560) transposed to random positions in the host chromosome. Images PMID:2820925

Association between the location of transposed ovary and ovarian function in patients with uterine cervical cancer treated with (postoperative or primary) pelvic radiotherapy.

PubMed

Hwang, Jong Ha; Yoo, Heon Jong; Park, Sae Hyun; Lim, Myong Cheol; Seo, Sang-Soo; Kang, Sokbom; Kim, Joo-Young; Park, Sang-Yoon

2012-06-01

To evaluate the effectiveness of ovarian transposition procedures in preserving ovarian function in relation to the location of the transposed ovaries in patients who underwent surgery with or without pelvic radiotherapy. Retrospective. Uterine cancer center. A total of 53 patients with cervical cancer who underwent ovarian transposition between November 2002 and November 2010. Ovarian transposition to the paracolic gutters with or without radical hysterectomy and lymph node dissection. Preservation of ovarian function, which was assessed by patient's symptoms and serum FSH level. Lateral ovarian transposition was performed in 53 patients. Based on receiver operator characteristic curve analysis, optimum cutoff value of location more than 1.5 cm above the iliac crest was significantly associated with preservation of ovarian function after treatment (area under receiver operator characteristic curve: 0.757, 95% confidence interval [CI]: 0.572-0.943). In univariate analysis, higher location of transposed ovary more than 1.5 cm from the iliac crest was the only independent factor for intact ovarian function (odds ratio 9.91, 95% CI: 1.75-56.3). Multivariate analysis confirmed that the location of transposed ovary (odds ratio 11.72, 95% CI 1.64-83.39) was the most important factor for intact ovarian function. Location of transposed ovary higher than 1.5 cm above the iliac crest is recommended to avoid ovarian failure after lateral ovarian transposition after primary or adjuvant pelvic radiotherapy in cervical cancer. Copyright © 2012 American Society for Reproductive Medicine. Published by Elsevier Inc. All rights reserved.

Identification and characterization of the first active endogenous transposable element in soybean

USDA-ARS?s Scientific Manuscript database

In soybean [Glycine max (L.) Merr.], W4 is one of the loci that control anthocyanin biosynthesis in flowers and hypocotyls. A putative transposable element was suggested to reside within or adjacent to this locus in the mutable T322 line resulting in the w4-m allele. We have shown that the W4 locu...

Moving from Science to Service: Transposing and Sustaining the Early Risers Prevention Program in a Community Service System

ERIC Educational Resources Information Center

Bloomquist, Michael L.; August, Gerald J.; Horowitz, Jason L.; Lee, Susanne S.; Jensen, Cheryl

2008-01-01

This paper summarizes an effort to transpose and sustain the evidence-based Early Risers "Skills for Success" conduct problems prevention program in a real world community service system. The Early Risers program had previously been implemented by a local agency within the context of research-based operations. In the current initiative,…

A Helitron-like Transposon Superfamily from Lepidoptera Disrupts (GAAA)n Microsatellites and is Responsible for Flanking Sequence Similarity within a Microsatellite Family

USDA-ARS?s Scientific Manuscript database

Transposable elements (TEs) are mobile DNA regions that alter host genome structure and gene expression. A novel 588 bp non-autonomous high copy number TE in the Ostrinia nubilalis genome has features in common with miniature inverted-repeat transposable elements (MITEs): high A+T content (62.3%),...

Distributional Analysis of the Transposed-Letter Neighborhood Effect on Naming Latency

ERIC Educational Resources Information Center

Johnson, Rebecca L.; Staub, Adrian; Fleri, Amanda M.

2012-01-01

Printed words that have a transposed-letter (TL) neighbor (e.g., angel has the TL neighbor angle) have been shown to be more difficult to process, in a range of paradigms, than words that do not have a TL neighbor. However, eye movement evidence suggests that this processing difficulty may occur on only a subset of trials. To investigate this…

Albinism due to transposable element insertion in fish.

PubMed

Koga, A; Hori, H

1997-12-01

The i locus of the medaka fish, Oryzias latipes, is responsible for tyrosinase expression, and several mutant alleles have been identified. The genotype i1/i1 exhibits a complete albino phenotype, having pale orange-red skin and red eyes. This mutant lacks in vivo tyrosinase activity. The genotype i4/i4, on the other hand, shows a quasi-albino phenotype with skin as bright as that of i1/i1 but with red-wine-colored eyes. At the light microscope level, reduced pigmentation is observed both in the skin and eyes of this mutant. The tyrosinase genes for the i1 and the i4 alleles were cloned and sequenced, and compared with that of the wild-type tyrosinase gene. The i1 allele was found to contain a 1.9-kb transposable element in the 1st exon, and the i4 allele was found to contain a 4.7-kb transposable element in the 5th exon. Both i1 and i4 are alleles that were found in a commercial breeding population. The insertion of a transposable element thus appears to constitute a natural cause of mutations that cause albinism in this organism.

Letter Position Coding Across Modalities: The Case of Braille Readers

PubMed Central

Perea, Manuel; García-Chamorro, Cristina; Martín-Suesta, Miguel; Gómez, Pablo

2012-01-01

Background The question of how the brain encodes letter position in written words has attracted increasing attention in recent years. A number of models have recently been proposed to accommodate the fact that transposed-letter stimuli like jugde or caniso are perceptually very close to their base words. Methodology Here we examined how letter position coding is attained in the tactile modality via Braille reading. The idea is that Braille word recognition may provide more serial processing than the visual modality, and this may produce differences in the input coding schemes employed to encode letters in written words. To that end, we conducted a lexical decision experiment with adult Braille readers in which the pseudowords were created by transposing/replacing two letters. Principal Findings We found a word-frequency effect for words. In addition, unlike parallel experiments in the visual modality, we failed to find any clear signs of transposed-letter confusability effects. This dissociation highlights the differences between modalities. Conclusions The present data argue against models of letter position coding that assume that transposed-letter effects (in the visual modality) occur at a relatively late, abstract locus. PMID:23071522

40 CFR 147.2201 - State-administered program-Class II wells

Code of Federal Regulations, 2011 CFR

2011-07-01

... Application to Oil, Gas, and Geothermal Resource Operations, sections .051.02.02.000 to .051.02.02.080... wells 147.2201 Section 147.2201 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Texas § 147.2201 State-administered program—Class II wells The UIC program for Class II wells in the...

38 CFR 17.162 - Eligibility for Class II dental treatment without rating action.

Code of Federal Regulations, 2011 CFR

2011-07-01

... dental treatment without rating action. 17.162 Section 17.162 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Dental Services § 17.162 Eligibility for Class II dental treatment without rating action. When an application has been made for class II dental treatment under § 17.161(b...

38 CFR 17.162 - Eligibility for Class II dental treatment without rating action.

Code of Federal Regulations, 2014 CFR

2014-07-01

... dental treatment without rating action. 17.162 Section 17.162 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Dental Services § 17.162 Eligibility for Class II dental treatment without rating action. When an application has been made for class II dental treatment under § 17.161(b...

38 CFR 17.162 - Eligibility for Class II dental treatment without rating action.

Code of Federal Regulations, 2013 CFR

2013-07-01

... dental treatment without rating action. 17.162 Section 17.162 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Dental Services § 17.162 Eligibility for Class II dental treatment without rating action. When an application has been made for class II dental treatment under § 17.161(b...

38 CFR 17.162 - Eligibility for Class II dental treatment without rating action.

Code of Federal Regulations, 2010 CFR

2010-07-01

... dental treatment without rating action. 17.162 Section 17.162 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Dental Services § 17.162 Eligibility for Class II dental treatment without rating action. When an application has been made for class II dental treatment under § 17.161(b...

38 CFR 17.162 - Eligibility for Class II dental treatment without rating action.

Code of Federal Regulations, 2012 CFR

2012-07-01

... dental treatment without rating action. 17.162 Section 17.162 Pensions, Bonuses, and Veterans' Relief DEPARTMENT OF VETERANS AFFAIRS MEDICAL Dental Services § 17.162 Eligibility for Class II dental treatment without rating action. When an application has been made for class II dental treatment under § 17.161(b...

40 CFR 147.2201 - State-administered program-Class II wells

Code of Federal Regulations, 2010 CFR

2010-07-01

... Application to Oil, Gas, and Geothermal Resource Operations, sections .051.02.02.000 to .051.02.02.080... wells 147.2201 Section 147.2201 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED... Texas § 147.2201 State-administered program—Class II wells The UIC program for Class II wells in the...

The Effect of MHC Class II Transactivator on the Growth and Metastasis of Breast Tumors

DTIC Science & Technology

1999-06-01

F. Manca, and R. S. Accolla. 1998. HLA class II expression in uninducible hepatocarcinoma cells after transfection of AIR-1 gene product CIITA...Cestari, A. D’Agostino, ’ A M Megiovanni, F. Manca, and R. S. Accolla. 1998. HLA class II expression in uninducible hepatocarcinoma cells after

40 CFR 82.23 - Transfers of allowances of class II controlled substances.

Code of Federal Regulations, 2011 CFR

2011-07-01

... section. (2) Inter-pollutant transfers will be permitted at any time during the control period and during... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Transfers of allowances of class II... § 82.23 Transfers of allowances of class II controlled substances. (a) Inter-company transfers...

40 CFR 82.23 - Transfers of allowances of class II controlled substances.

Code of Federal Regulations, 2014 CFR

2014-07-01

... section. (2) Inter-pollutant transfers will be permitted at any time during the control period and during... 40 Protection of Environment 18 2014-07-01 2014-07-01 false Transfers of allowances of class II... § 82.23 Transfers of allowances of class II controlled substances. (a) Inter-company transfers...

76 FR 16292 - Medical Devices; Immunology and Microbiology Devices; Classification of Ovarian Adnexal Mass...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-23

... test system into class II (special controls). The special control that will apply to these devices is the guidance document entitled ``Guidance for Industry and FDA Staff; Class II Special Controls... devices into class II (special controls) because special controls, in addition to general controls, will...

Major histocompatibility complex (MHC) class I and II alleles which confer susceptibility or protection in the Morphea in Adults and Children (MAC) cohort

PubMed Central

Jacobe, Heidi; Ahn, Chul; Arnett, Frank; Reveille, John D.

2014-01-01

Objective To determine human leukocyte antigen class I (HLA-class I) and II (HLA-class II) alleles associated with morphea (localized scleroderma) in the Morphea in Adults and Children (MAC) cohort by a nested case–control association study. Methods Morphea patients were included from MAC cohort and matched controls from the NIH/NIAMS Scleroderma Family Registry and DNA Repository and Division of Rheumatology at the University of Texas Health Science Center at Houston. HLA- Class II genotyping and SSCP typing was performed of HLA-A, -B, -C alleles. Associations between HLA-Class I and II alleles and morphea as well as its subphenotypes were determined. Results There were 211 cases available for HLA-class I typing with 726 matched controls and 158 cases available for HLA Class-II typing with 1108 matched controls. The strongest associations were found with DRB1*04:04 (OR 2.3, 95% CI 1.4–4.0 P=0.002) and HLA-B*37 conferred the highest OR among Class I alleles (3.3, 95% CI 1.6–6.9, P= 0.0016). Comparison with risk alleles in systemic sclerosis determined using the same methods and control population revealed one common allele (DRB*04:04). Conclusion Results of the present study demonstrate specific HLA Class I and II alleles are associated with morphea and likely generalized and linear subtypes. The associated morphea alleles are different than in scleroderma, implicating morphea is also immunogenetically distinct. Risk alleles in morphea are also associated with conditions such as rheumatoid arthritis (RA) and other autoimmune conditions. Population based studies indicate patients with RA have increased risk of morphea, implicating a common susceptibility allele. PMID:25223600

Evolution of major histocompatibility complex class I and class II genes in the brown bear

PubMed Central

2012-01-01

Background Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation and evolution of MHC class I and class II DRB, DQA and DQB genes in the brown bear Ursus arctos to characterise the level of polymorphism, estimate the strength of positive selection acting on them, and assess the extent of gene orthology and trans-species polymorphism in Ursidae. Results We found 37 MHC class I, 16 MHC class II DRB, four DQB and two DQA alleles. We confirmed the expression of several loci: three MHC class I, two DRB, two DQB and one DQA. MHC class I also contained two clusters of non-expressed sequences. MHC class I and DRB allele frequencies differed between northern and southern populations of the Scandinavian brown bear. The rate of nonsynonymous substitutions (dN) exceeded the rate of synonymous substitutions (dS) at putative antigen binding sites of DRB and DQB loci and, marginally significantly, at MHC class I loci. Models of codon evolution supported positive selection at DRB and MHC class I loci. Both MHC class I and MHC class II sequences showed orthology to gene clusters found in the giant panda Ailuropoda melanoleuca. Conclusions Historical positive selection has acted on MHC class I, class II DRB and DQB, but not on the DQA locus. The signal of historical positive selection on the DRB locus was particularly strong, which may be a general feature of caniforms. The presence of MHC class I pseudogenes may indicate faster gene turnover in this class through the birth-and-death process. South–north population structure at MHC loci probably reflects origin of the populations from separate glacial refugia. PMID:23031405

Evolution of major histocompatibility complex class I and class II genes in the brown bear.

PubMed

Kuduk, Katarzyna; Babik, Wiesław; Bojarska, Katarzyna; Sliwińska, Ewa B; Kindberg, Jonas; Taberlet, Pierre; Swenson, Jon E; Radwan, Jacek

2012-10-02

Major histocompatibility complex (MHC) proteins constitute an essential component of the vertebrate immune response, and are coded by the most polymorphic of the vertebrate genes. Here, we investigated sequence variation and evolution of MHC class I and class II DRB, DQA and DQB genes in the brown bear Ursus arctos to characterise the level of polymorphism, estimate the strength of positive selection acting on them, and assess the extent of gene orthology and trans-species polymorphism in Ursidae. We found 37 MHC class I, 16 MHC class II DRB, four DQB and two DQA alleles. We confirmed the expression of several loci: three MHC class I, two DRB, two DQB and one DQA. MHC class I also contained two clusters of non-expressed sequences. MHC class I and DRB allele frequencies differed between northern and southern populations of the Scandinavian brown bear. The rate of nonsynonymous substitutions (dN) exceeded the rate of synonymous substitutions (dS) at putative antigen binding sites of DRB and DQB loci and, marginally significantly, at MHC class I loci. Models of codon evolution supported positive selection at DRB and MHC class I loci. Both MHC class I and MHC class II sequences showed orthology to gene clusters found in the giant panda Ailuropoda melanoleuca. Historical positive selection has acted on MHC class I, class II DRB and DQB, but not on the DQA locus. The signal of historical positive selection on the DRB locus was particularly strong, which may be a general feature of caniforms. The presence of MHC class I pseudogenes may indicate faster gene turnover in this class through the birth-and-death process. South-north population structure at MHC loci probably reflects origin of the populations from separate glacial refugia.

LINE-1 Elements in Structural Variation and Disease

PubMed Central

Beck, Christine R.; Garcia-Perez, José Luis; Badge, Richard M.; Moran, John V.

2014-01-01

The completion of the human genome reference sequence ushered in a new era for the study and discovery of human transposable elements. It now is undeniable that transposable elements, historically dismissed as junk DNA, have had an instrumental role in sculpting the structure and function of our genomes. In particular, long interspersed element-1 (LINE-1 or L1) and short interspersed elements (SINEs) continue to affect our genome, and their movement can lead to sporadic cases of disease. Here, we briefly review the types of transposable elements present in the human genome and their mechanisms of mobility. We next highlight how advances in DNA sequencing and genomic technologies have enabled the discovery of novel retrotransposons in individual genomes. Finally, we discuss how L1-mediated retrotransposition events impact human genomes. PMID:21801021

A Navier-Strokes Chimera Code on the Connection Machine CM-5: Design and Performance

NASA Technical Reports Server (NTRS)

Jespersen, Dennis C.; Levit, Creon; Kwak, Dochan (Technical Monitor)

1994-01-01

We have implemented a three-dimensional compressible Navier-Stokes code on the Connection Machine CM-5. The code is set up for implicit time-stepping on single or multiple structured grids. For multiple grids and geometrically complex problems, we follow the 'chimera' approach, where flow data on one zone is interpolated onto another in the region of overlap. We will describe our design philosophy and give some timing results for the current code. A parallel machine like the CM-5 is well-suited for finite-difference methods on structured grids. The regular pattern of connections of a structured mesh maps well onto the architecture of the machine. So the first design choice, finite differences on a structured mesh, is natural. We use centered differences in space, with added artificial dissipation terms. When numerically solving the Navier-Stokes equations, there are liable to be some mesh cells near a solid body that are small in at least one direction. This mesh cell geometry can impose a very severe CFL (Courant-Friedrichs-Lewy) condition on the time step for explicit time-stepping methods. Thus, though explicit time-stepping is well-suited to the architecture of the machine, we have adopted implicit time-stepping. We have further taken the approximate factorization approach. This creates the need to solve large banded linear systems and creates the first possible barrier to an efficient algorithm. To overcome this first possible barrier we have considered two options. The first is just to solve the banded linear systems with data spread over the whole machine, using whatever fast method is available. This option is adequate for solving scalar tridiagonal systems, but for scalar pentadiagonal or block tridiagonal systems it is somewhat slower than desired. The second option is to 'transpose' the flow and geometry variables as part of the time-stepping process: Start with x-lines of data in-processor. Form explicit terms in x, then transpose so y-lines of data are in-processor. Form explicit terms in y, then transpose so z-lines are in processor. Form explicit terms in z, then solve linear systems in the z-direction. Transpose to the y-direction, then solve linear systems in the y-direction. Finally transpose to the x direction and solve linear systems in the x-direction. This strategy avoids inter-processor communication when differencing and solving linear systems, but requires a large amount of communication when doing the transposes. The transpose method is more efficient than the non-transpose strategy when dealing with scalar pentadiagonal or block tridiagonal systems. For handling geometrically complex problems the chimera strategy was adopted. For multiple zone cases we compute on each zone sequentially (using the whole parallel machine), then send the chimera interpolation data to a distributed data structure (array) laid out over the whole machine. This information transfer implies an irregular communication pattern, and is the second possible barrier to an efficient algorithm. We have implemented these ideas on the CM-5 using CMF (Connection Machine Fortran), a data parallel language which combines elements of Fortran 90 and certain extensions, and which bears a strong similarity to High Performance Fortran. We make use of the Connection Machine Scientific Software Library (CMSSL) for the linear solver and array transpose operations.

Maxillary molar distalization with first class appliance

PubMed Central

Ramesh, Namitha; Palukunnu, Biswas; Ravindran, Nidhi; Nair, Preeti P

2014-01-01

Non-extraction treatment has gained popularity for corrections of mild-to-moderate class II malocclusion over the past few decades. The distalization of maxillary molars is of significant value for treatment of cases with minimal arch discrepancy and mild class II molar relation associated with a normal mandibular arch and acceptable profile. This paper describes our experience with a 16-year-old female patient who reported with irregularly placed upper front teeth and unpleasant smile. The patient was diagnosed to have angles class II malocclusion with moderate maxillary anterior crowding, deep bite of 4 mm on a skeletal class II base with an orthognathic maxilla and retrognathic mandible and normal growth pattern. She presented an ideal profile and so molar distalization was planned with the first-class appliance. Molars were distalised by 8 mm on the right and left quadrants and class I molar relation achieved within 4 months. The space gained was utilised effectively to align the arch and establish a class I molar and canine relation. PMID:24577171

Distalization of maxillary arch and correction of Class II with mini-implants: A report of two cases

PubMed Central

Tekale, Pawankumar Dnyandeo; Vakil, Ketan K.; Vakil, Jeegar K.; Gore, Ketan A.

2015-01-01

This article reports the successful use of mini-screws in the maxilla to treat two patients of age 21-year and 17-year-old girls. Both the patients had a skeletal Class II malocclusion with protrusive maxillary teeth and angels Class II mal-occlusion. Temporary anchorage devices (TADs) in the posterior dental region between maxillary second premolar and maxillary first molar teeth on both sides were used as anchorage for the retraction and intrusion of her maxillary anterior teeth. Those appliances, combined with a compensatory curved maxillary archwire, eliminated spacing, deep bite, forwardly placed and proclined upper front teeth and the protrusive profile, corrected the molar relationship from Class II to Class I. With no extra TADs in the anterior region for intrusion, the treatment was workable and simple. The patient received a satisfactory occlusion and an attractive smile. This technique requires minimal compliance and is particularly useful for correcting Class II patients with protrusive maxillary front teeth and dental deep bite. PMID:26097360

25 CFR 547.7 - What are the minimum technical hardware standards applicable to Class II gaming systems?

Code of Federal Regulations, 2011 CFR

2011-04-01

... OF CLASS II GAMES § 547.7 What are the minimum technical hardware standards applicable to Class II... the game, and are specially manufactured or proprietary and not off-the-shelf, shall display a unique... outcome or integrity of any game, progressive award, financial instrument, cashless transaction, voucher...

25 CFR 547.7 - What are the minimum technical hardware standards applicable to Class II gaming systems?

Code of Federal Regulations, 2012 CFR

2012-04-01

... OF CLASS II GAMES § 547.7 What are the minimum technical hardware standards applicable to Class II... the game, and are specially manufactured or proprietary and not off-the-shelf, shall display a unique... outcome or integrity of any game, progressive award, financial instrument, cashless transaction, voucher...

25 CFR 547.7 - What are the minimum technical hardware standards applicable to Class II gaming systems?

Code of Federal Regulations, 2010 CFR

2010-04-01

... OF CLASS II GAMES § 547.7 What are the minimum technical hardware standards applicable to Class II... the game, and are specially manufactured or proprietary and not off-the-shelf, shall display a unique... outcome or integrity of any game, progressive award, financial instrument, cashless transaction, voucher...

40 CFR 82.24 - Recordkeeping and reporting requirements for class II controlled substances.

Code of Federal Regulations, 2011 CFR

2011-07-01

... transformation; (v) The date on which the class II controlled substances were imported; (vi) The port of entry.... Customs entry form; (xiv) Dated records documenting the sale or transfer of class II controlled substances... source facility; (vii) The U.S. port of entry for the import, the expected date of shipment and the...

40 CFR 82.24 - Recordkeeping and reporting requirements for class II controlled substances.

Code of Federal Regulations, 2014 CFR

2014-07-01

... transformation; (v) The date on which the class II controlled substances were imported; (vi) The port of entry.... Customs entry form; (xiv) Dated records documenting the sale or transfer of class II controlled substances... source facility; (vii) The U.S. port of entry for the import, the expected date of shipment and the...

25 CFR 547.6 - What are the minimum technical standards for enrolling and enabling Class II gaming system...

Code of Federal Regulations, 2010 CFR

2010-04-01

... and enabling Class II gaming system components? 547.6 Section 547.6 Indians NATIONAL INDIAN GAMING COMMISSION, DEPARTMENT OF THE INTERIOR HUMAN SERVICES MINIMUM TECHNICAL STANDARDS FOR GAMING EQUIPMENT USED WITH THE PLAY OF CLASS II GAMES § 547.6 What are the minimum technical standards for enrolling and...

40 CFR Appendix B to Subpart A of... - Class II Controlled Substances a

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 18 2014-07-01 2014-07-01 false Class II Controlled Substances a B Appendix B to Subpart A of Part 82 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED..., Subpt. A, App. B Appendix B to Subpart A of Part 82—Class II Controlled Substances a Controlled...

40 CFR 82.17 - Apportionment of baseline production allowances for class II controlled substances.

Code of Federal Regulations, 2010 CFR

2010-07-01

... allowances for class II controlled substances. 82.17 Section 82.17 Protection of Environment ENVIRONMENTAL... Consumption Controls § 82.17 Apportionment of baseline production allowances for class II controlled... 1,759,681 MDA Manufacturing HCFC-22 2,383,835 Solvay Solexis HCFC-142b 6,541,764 [ 74 FR 66446, Dec...

40 CFR 144.21 - Existing Class I, II (except enhanced recovery and hydrocarbon storage) and III wells.

Code of Federal Regulations, 2011 CFR

2011-07-01

... recovery and hydrocarbon storage) and III wells. 144.21 Section 144.21 Protection of Environment... hydrocarbon storage) and III wells. (a) An existing Class I, II (except enhanced recovery and hydrocarbon... decision; or (9) For Class II wells (except enhanced recovery and hydrocarbon storage), five years after...

40 CFR 144.21 - Existing Class I, II (except enhanced recovery and hydrocarbon storage) and III wells.

Code of Federal Regulations, 2010 CFR

2010-07-01

... recovery and hydrocarbon storage) and III wells. 144.21 Section 144.21 Protection of Environment... hydrocarbon storage) and III wells. (a) An existing Class I, II (except enhanced recovery and hydrocarbon... decision; or (9) For Class II wells (except enhanced recovery and hydrocarbon storage), five years after...

77 FR 24978 - Notice of Proposed Class II Reinstatement of Terminated Oil and Gas Leases, Utah.

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-26

... Proposed Class II Reinstatement of Terminated Oil and Gas Leases, Utah. AGENCY: Bureau of Land Management, Interior. ACTION: Notice of Proposed Class II Reinstatement of Terminated Oil and Gas Leases, Utah. SUMMARY: In accordance with Title IV of the Federal Oil and Gas Royalty Management Act (Pub. L. 97-451...

76 FR 14686 - Notice of Proposed Class II Reinstatement of Terminated Oil and Gas Lease, Utah

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-17

... Proposed Class II Reinstatement of Terminated Oil and Gas Lease, Utah AGENCY: Bureau of Land Management, Interior. ACTION: Notice of Proposed Class II Reinstatement of Terminated Oil and Gas Lease, Utah. SUMMARY: In accordance with Title IV of the Federal Oil and Gas Royalty Management Act (Pub. L. 97-451...

76 FR 20840 - Medical Devices; General and Plastic Surgery Devices; Classification of the Low Level Laser...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-14

... into class II (special controls). The special control(s) that will apply to the device is entitled ``Class II Special Controls Guidance Document: Low Level Laser System for Aesthetic Use.'' The Agency is classifying the device into class II (special controls) in order to provide a reasonable assurance of safety...

Assessment of the changes in quality of life of patients with class II and III deformities during and after orthodontic-surgical treatment.

PubMed

Baherimoghaddam, T; Tabrizi, R; Naseri, N; Pouzesh, A; Oshagh, M; Torkan, S

2016-04-01

The aim of this longitudinal study was to assess and compare the oral health-related quality of life (OHRQoL) of patients with class II and III deformities during and after orthodontic-surgical treatment. Thirty class III and 28 class II patients were evaluated at baseline (T0), just prior to surgery (T1), at 6 months after surgery (T2), and at 12 months after debonding (T3). OHRQoL was assessed using the Oral Health Impact Profile (OHIP-14). Friedman two-way analysis of variance and the Wilcoxon signed-rank test were performed to compare the relative changes in OHRQoL during treatment. Significant changes in the overall OHIP-14 scores were observed during and after orthodontic-surgical treatment in both groups. During the pre-surgical stage, psychological discomfort and psychological disability decreased in class III patients, and class II patients experienced a significant deterioration in psychological discomfort during the same period. Six months after surgery, patients in both groups showed improvements in psychological discomfort, social disability, and handicap. Physical disability and functional limitation showed further improvement at 12 months after debonding in class II patients. This study reaffirms that orthodontic-surgical treatment has a significant effect on the OHRQoL of class III and class II patients. Copyright © 2015 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Th-1 polarization is regulated by dendritic-cell comparison of MHC class I and class II antigens

PubMed Central

Xing, Dongxia; Li, Sufang; Robinson, Simon N.; Yang, Hong; Steiner, David; Komanduri, Krishna V.; Shpall, Elizabeth J.

2009-01-01

In the control of T-helper type I (Th-1) polarization, dendritic cells (DCs) must interpret a complex array of stimuli, many of which are poorly understood. Here we demonstrate that Th-1 polarization is heavily influenced by DC-autonomous phenomena triggered by the loading of DCs with antigenically matched major histocompatibility complex (MHC) class I and class II determinants, that is, class I and II peptide epitopes exhibiting significant amino acid sequence overlap (such as would be physiologically present during infectious processes requiring Th-1 immunity for clearance). Data were derived from 13 independent antigenic models including whole-cell systems, single-protein systems, and 3 different pairs of overlapping class I and II binding epitopes. Once loaded with matched class I and II antigens, these “Th-1 DCs” exhibited differential cytokine secretion and surface marker expression, a distinct transcriptional signature, and acquired the ability to enhance generation of CD8+ T lymphocytes. Mechanistically, tRNA-synthetases were implicated as components of a putative sensor complex involved in the comparison of class I and II epitopes. These data provide rigorous conceptual explanations for the process of Th-1 polarization and the antigenic specificity of cognate T-cell help, enhance the understanding of Th-1 responses, and should contribute to the formulation of more effective vaccination strategies. PMID:19171878

Finite-time scaling at the Anderson transition for vibrations in solids

NASA Astrophysics Data System (ADS)

Beltukov, Y. M.; Skipetrov, S. E.

2017-11-01

A model in which a three-dimensional elastic medium is represented by a network of identical masses connected by springs of random strengths and allowed to vibrate only along a selected axis of the reference frame exhibits an Anderson localization transition. To study this transition, we assume that the dynamical matrix of the network is given by a product of a sparse random matrix with real, independent, Gaussian-distributed nonzero entries and its transpose. A finite-time scaling analysis of the system's response to an initial excitation allows us to estimate the critical parameters of the localization transition. The critical exponent is found to be ν =1.57 ±0.02 , in agreement with previous studies of the Anderson transition belonging to the three-dimensional orthogonal universality class.

DMA and DMB are the only genes in the class II region of the human MHC needed for class II-associated antigen processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ceman, S.; Rudersdorf, R.A.; Petersen, J.M.

1995-03-15

Previous studies have shown that homozygous mutations between the LMP2 and DNA loci in the human MHC cause class II molecules to be abnormally conformed and unstable in the presence of SDS at low temperature, and impede class II-associated Ag processing and presentation. These abnormalities result from impaired ability to form intracellular class II/peptide complexes that predominate in normal cells. We show in this work that this defect results from deficient expression of either the DMA or the DMB gene. Human B-LCL.174 (DR3) cells, which have a deletion of all known expressible genes in the class II region, express transgene-encodedmore » HLA-DR3, but have the abnormalities. Transfer of cosmid HA14, which contains the DMA and DMB genes, into .174 (DR3) cells restored normal DR3 conformation, stability in 0.4% SDS at 0{degrees}, and ability to process and present tetanus toxoid, but only when both DMA and DMB mRNAs were present. The requirement for both genetic expressions in engendering normal phenotypes was confirmed by transferring the cloned genes into .174 (DR3) cells separately or together. Because normal phenotypes were fully restored in transferent cells expressing DMA plus DMB, other genes in the {approximately} 1-mb homozygous class II region deletion in .174 (DR3) cells either do not participate in or are dispensable for apparently normal production of intracellular class II/peptide complexes. The properties of DM-deficient EBV-transformed B lymphoblastoid cell lines (LCLs) suggest ways of identifying humans in whom DM deficiency contributes to congenital immunodeficiency and malignancy. 67 refs., 5 figs., 1 tab.« less

A retrospective study of Class II mixed-dentition treatment.

PubMed

Oh, Heesoo; Baumrind, Sheldon; Korn, Edward L; Dugoni, Steven; Boero, Roger; Aubert, Maryse; Boyd, Robert

2017-01-01

To consider the effectiveness of early treatment using one mixed-dentition approach to the correction of moderate and severe Class II malocclusions. Three groups of Class II subjects were included in this retrospective study: an early treatment (EarlyTx) group that first presented at age 7 to 9.5 years (n = 54), a late treatment (LateTx) group whose first orthodontic visit occurred between ages 12 and 15 (n = 58), and an untreated Class II (UnTx) group to assess the pretreatment comparability of the two treated groups (n = 51). Thirteen conventional cephalometric measurements were reported for each group and Class II molar severity was measured on the study casts of the EarlyTx and LateTx groups. Successful Class II correction was observed in approximately three quarters of both the EarlyTx group and the LateTx group at the end of treatment. EarlyTx patients had fewer permanent teeth extracted than did the LateTx patients (5.6% vs 37.9%, P < .001) and spent less time in full-bonded appliance therapy in the permanent dentition than did LateTx patients (1.7 ± 0.8 vs 2.6 ± 0.7years, P < .001). When supervision time is included, the EarlyTx group had longer total treatment time and averaged more visits than did the LateTx group (53.1 ± 18. 8 vs 33.7 ± 8.3, P < .0001). Fifty-five percent of the LateTx extraction cases involved removal of the maxillary first premolars only and were finished in a Class II molar relationship. EarlyTx comprehensive mixed-dentition treatment was an effective modality for early correction of Class II malocclusions.

HLA-G and MHC Class II Protein Expression in Diffuse Large B-Cell Lymphoma.

PubMed

Jesionek-Kupnicka, Dorota; Bojo, Marcin; Prochorec-Sobieszek, Monika; Szumera-Ciećkiewicz, Anna; Jabłońska, Joanna; Kalinka-Warzocha, Ewa; Kordek, Radzisław; Młynarski, Wojciech; Robak, Tadeusz; Warzocha, Krzysztof; Lech-Maranda, Ewa

2016-06-01

The expression of human leukocyte antigen-G (HLA-G) and HLA class II protein was studied by immunohistochemical staining of lymph nodes from 148 patients with diffuse large B-cell lymphoma (DLBCL) and related to the clinical course of the disease. Negative HLA-G expression was associated with a lower probability of achieving a complete remission (p = 0.04). Patients with negative HLA-G expression tended towards a lower 3-year overall survival (OS) rate compared to those with positive expression of HLA-G (p = 0.08). When restricting the analysis to patients receiving chemotherapy with rituximab, the estimated 3-year OS rate of patients with positive HLA-G expression was 73.3 % compared with 47.5 % (p = 0.03) in those with negative expression. Patients with negative HLA class II expression presented a lower 3-year OS rate compared to subjects with positive expression (p = 0.04). The loss of HLA class II expression (p = 0.05) and belonging to the intermediate high/high IPI risk group (p = 0.001) independently increased the risk of death. HLA class II expression also retained its prognostic value in patients receiving rituximab; the 3-year OS rate was 65.3 % in patients with positive HLA class II expression versus 29.6 % (p = 0.04) in subjects that had loss of HLA class II expression. To our knowledge, for the first time, the expression of HLA-G protein in DLBCL and its association with the clinical course of the disease was demonstrated. Moreover, the link between losing HLA class II protein expression and poor survival of patients treated with immunochemotherapy was confirmed.

Selection and Trans-Species Polymorphism of Major Histocompatibility Complex Class II Genes in the Order Crocodylia

PubMed Central

Jaratlerdsiri, Weerachai; Isberg, Sally R.; Higgins, Damien P.; Miles, Lee G.; Gongora, Jaime

2014-01-01

Major Histocompatibility Complex (MHC) class II genes encode for molecules that aid in the presentation of antigens to helper T cells. MHC characterisation within and between major vertebrate taxa has shed light on the evolutionary mechanisms shaping the diversity within this genomic region, though little characterisation has been performed within the Order Crocodylia. Here we investigate the extent and effect of selective pressures and trans-species polymorphism on MHC class II α and β evolution among 20 extant species of Crocodylia. Selection detection analyses showed that diversifying selection influenced MHC class II β diversity, whilst diversity within MHC class II α is the result of strong purifying selection. Comparison of translated sequences between species revealed the presence of twelve trans-species polymorphisms, some of which appear to be specific to the genera Crocodylus and Caiman. Phylogenetic reconstruction clustered MHC class II α sequences into two major clades representing the families Crocodilidae and Alligatoridae. However, no further subdivision within these clades was evident and, based on the observation that most MHC class II α sequences shared the same trans-species polymorphisms, it is possible that they correspond to the same gene lineage across species. In contrast, phylogenetic analyses of MHC class II β sequences showed a mixture of subclades containing sequences from Crocodilidae and/or Alligatoridae, illustrating orthologous relationships among those genes. Interestingly, two of the subclades containing sequences from both Crocodilidae and Alligatoridae shared specific trans-species polymorphisms, suggesting that they may belong to ancient lineages pre-dating the divergence of these two families from the common ancestor 85–90 million years ago. The results presented herein provide an immunogenetic resource that may be used to further assess MHC diversity and functionality in Crocodylia. PMID:24503938

Preview Effects of Plausibility and Character Order in Reading Chinese Transposed Words: Evidence from Eye Movements

ERIC Educational Resources Information Center

Yang, Jinmian

2013-01-01

The current paper examined the role of plausibility information in the parafovea for Chinese readers by using two-character transposed words (in which the order of the component characters is reversed but are still words). In two eye-tracking experiments, readers received a preview of a target word that was (1) identical to the target word, (2) a…

The endogenous transposable element Tgm9 is suitable for functional analyses of soybean genes and generating novel mutants for genetic improvement of soybean

USDA-ARS?s Scientific Manuscript database

In soybean, variegated flowers can be caused by somatic excision of the CACTA-type transposable element Tgm9 from intron 2 of the DFR2 gene encoding dihydroflavonol-4-reductase in the anthocyanin pigment biosynthetic pathway. DFR2 has been mapped to the W4 locus where the allele containing the elem...

Changes in Cranial Base Morphology in Class I and Class II Division 1 Malocclusions

PubMed Central

Agarwal, Anirudh; Pandey, Harsh; Bajaj, Kamal; Pandey, Lavesh

2013-01-01

Introduction: The cranial base plays a key role in craniofacial growth; it helps to integrate spatially and functionally different patterns of growth in various adjoining regions of the skull such as components of the brain, the nasal and oral cavity and the pharynx. The aim of this study was to evaluate the difference in cranial base flexure between skeletal and dental Class I and Class II division 1. Materials & Methods: Lateral cephalometric radiograph, of Class I and Class II with an average growth pattern were analyzed and compared. A total of 103 patients having class I (n=52) and class II (n=51) malocclusion, were taken from Department of Orthodontics, Rajasthan Dental College & Hospital, Jaipur. Cranial base angle (N-S-Ar) and ANB were measured on pre treatment lateral cephalograms. Results: In this study cranial base angle did not show statistically significant difference between the two groups studied. Conclusion: In the assessment of orthodontic problems involving anteroposterior malrelationships of the jaws, the problem is usually the result of size, form and position of the jaw. The present study failed to find any differences in cranial base angle between sagittal malocclusions. How to cite this article: Agarwal A, Pandey H, Bajaj K, Pandey L. Changes in Cranial Base Morphology in Class I and Class II Division 1 Malocclusion. J Int Oral Health 2013; 5(1):39-42. PMID:24155576

Investigation into the Emerging Role of the Basic Amino Acid L-Lysine in Enhancing Solubility and Permeability of BCS Class II and BCS Class IV Drugs.

PubMed

Abdelkader, Hamdy; Fathalla, Zeinab

2018-06-18

The search for a simple and scalable approach that can improve the two key biopharmaceutical processes (solubility and permeability) for BCS Class II and BCS Class IV has still been unmet need. In this study, L-lysine was investigated as a potential excipient to tackle problems with solubility and permeability. Bendazac (Class II); quercetin and rutin (Class IV) were employed. Drugs-lysine complexes in 1:1 M ratios were prepared by co-precipitation and co-grinding; characterized for solubility, partition coefficient, DSC, FTIR, SEM, dissolution rate and permeability. Chemical stability of quercetin-lysine and rutin-lysine was studied by assessing antioxidant capacity using Trolox and CUPRAC assays. Drugs-lysine salt/complexes were confirmed. Solubility enhancement factors ranged from 68- to 433-fold increases and dissolution rates were also significantly enhanced by up to 6-times, compared with drugs alone. With the exception of rutin-lysine, P app for bendazac-lysine and quercetin-lysine enhanced by 2.3- to 4-fold. P app for quercetin (Class IV) benefited more than bendazac (Class II) when complexed with lysine. This study warrants the use of L-lysine as a promising excipient for enhanced solubility and permeability of Class II and Class IV, providing that the solubility of the drug is ensured at 'the door step' of absorption sites.

MHC class II is an important genetic risk factor for canine systemic lupus erythematosus (SLE)-related disease: implications for reproductive success.

PubMed

Wilbe, M; Andersson, G

2012-01-01

Major histocompatibility complex (MHC) class II genes are important genetic risk factors for development of immune-mediated diseases in mammals. Recently, the dog (Canis lupus familiaris) has emerged as a useful model organism to identify critical MHC class II genotypes that contribute to development of these diseases. Therefore, a study aimed to evaluate a potential genetic association between the dog leukocyte antigen (DLA) class II region and an immune-mediated disease complex in dogs of the Nova Scotia duck tolling retriever breed was performed. We show that DLA is one of several genetic risk factors for this disease complex and that homozygosity of the risk haplotype is disadvantageous. Importantly, the disease is complex and has many genetic risk factors and therefore we cannot provide recommendations for breeders exclusively on the basis of genetic testing for DLA class II genotype. © 2012 Blackwell Verlag GmbH.

In silico prediction of drug dissolution and absorption with variation in intestinal pH for BCS class II weak acid drugs: ibuprofen and ketoprofen.

PubMed

Tsume, Yasuhiro; Langguth, Peter; Garcia-Arieta, Alfredo; Amidon, Gordon L

2012-10-01

The FDA Biopharmaceutical Classification System guidance allows waivers for in vivo bioavailability and bioequivalence studies for immediate-release solid oral dosage forms only for BCS class I. Extensions of the in vivo biowaiver for a number of drugs in BCS class III and BCS class II have been proposed, in particular, BCS class II weak acids. However, a discrepancy between the in vivo BE results and in vitro dissolution results for BCS class II acids was recently observed. The objectives of this study were to determine the oral absorption of BCS class II weak acids via simulation software and to determine if the in vitro dissolution test with various dissolution media could be sufficient for in vitro bioequivalence studies of ibuprofen and ketoprofen as models of carboxylic acid drugs. The oral absorption of these BCS class II acids from the gastrointestinal tract was predicted by GastroPlus™. Ibuprofen did not satisfy the bioequivalence criteria at lower settings of intestinal pH of 6.0. Further the experimental dissolution of ibuprofen tablets in a low concentration phosphate buffer at pH 6.0 (the average buffer capacity 2.2 mmol l (-1) /pH) was dramatically reduced compared with the dissolution in SIF (the average buffer capacity 12.6 mmol l (-1) /pH). Thus these predictions for the oral absorption of BCS class II acids indicate that the absorption patterns depend largely on the intestinal pH and buffer strength and must be considered carefully for a bioequivalence test. Simulation software may be a very useful tool to aid the selection of dissolution media that may be useful in setting an in vitro bioequivalence dissolution standard. Copyright © 2012 John Wiley & Sons, Ltd.

In Silico Prediction of Drug Dissolution and Absorption with variation in Intestinal pH for BCS Class II Weak Acid Drugs: Ibuprofen and Ketoprofen§

PubMed Central

Tsume, Yasuhiro; Langguth, Peter; Garcia-Arieta, Alfredo; Amidon, Gordon L.

2012-01-01

The FDA Biopharmaceutical Classification System guidance allows waivers for in vivo bioavailability and bioequivalence studies for immediate-release solid oral dosage forms only for BCS class I. Extensions of the in vivo biowaiver for a number of drugs in BCS Class III and BCS class II have been proposed, particularly, BCS class II weak acids. However, a discrepancy between the in vivo- BE results and in vitro- dissolution results for a BCS class II acids was recently observed. The objectives of this study were to determine the oral absorption of BCS class II weak acids via simulation software and to determine if the in vitro dissolution test with various dissolution media could be sufficient for in vitro bioequivalence studies of ibuprofen and ketoprofen as models of carboxylic acid drugs. The oral absorption of these BCS class II acids from the gastrointestinal tract was predicted by GastroPlus™. Ibuprofen did not satisfy the bioequivalence criteria at lower settings of intestinal pH=6.0. Further the experimental dissolution of ibuprofen tablets in the low concentration phosphate buffer at pH 6.0 (the average buffer capacity 2.2 mmol L-1/pH) was dramatically reduced compared to the dissolution in SIF (the average buffer capacity 12.6 mmol L -1/pH). Thus these predictions for oral absorption of BCS class II acids indicate that the absorption patterns largely depend on the intestinal pH and buffer strength and must be carefully considered for a bioequivalence test. Simulation software may be very useful tool to aid the selection of dissolution media that may be useful in setting an in vitro bioequivalence dissolution standard. PMID:22815122

Haemophilus ducreyi Cutaneous Ulcer Strains Diverged from Both Class I and Class II Genital Ulcer Strains: Implications for Epidemiological Studies

PubMed Central

Gangaiah, Dharanesh

2016-01-01

Background Haemophilus ducreyi has emerged as a major cause of cutaneous ulcers (CU) in yaws-endemic regions of the tropics in the South Pacific, South East Asia and Africa. H. ducreyi was once thought only to cause the genital ulcer (GU) disease chancroid; GU strains belong to 2 distinct classes, class I and class II. Using whole-genome sequencing of 4 CU strains from Samoa, 1 from Vanuatu and 1 from Papua New Guinea, we showed that CU strains diverged from the class I strain 35000HP and that one CU strain expressed β-lactamase. Recently, the Center for Disease Control and Prevention released the genomes of 11 additional CU strains from Vanuatu and Ghana; however, the evolutionary relationship of these CU strains to previously-characterized CU and GU strains is unknown. Methodology/Principal Findings We performed phylogenetic analysis of 17 CU and 10 GU strains. Class I and class II GU strains formed two distinct clades. The class I strains formed two subclades, one containing 35000HP and HD183 and the other containing the remainder of the class I strains. Twelve of the CU strains formed a subclone under the class I 35000HP subclade, while 2 CU strains formed a subclone under the other class I subclade. Unexpectedly, 3 of the CU strains formed a subclone under the class II clade. Phylogenetic analysis of dsrA-hgbA-ncaA sequences yielded a tree similar to that of whole-genome phylogenetic tree. Conclusions/Significance CU strains diverged from multiple lineages within both class I and class II GU strains. Multilocus sequence typing of dsrA-hgbA-ncaA could be reliably used for epidemiological investigation of CU and GU strains. As class II strains grow relatively poorly and are relatively more susceptible to vancomycin than class I strains, these findings have implications for methods to recover CU strains. Comparison of contemporary CU and GU isolates would help clarify the relationship between these entities. PMID:28027326

77 FR 36951 - Gastroenterology-Urology Devices; Reclassification of Implanted Blood Access Devices

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-20

... into class II (special controls). FDA is proposing this reclassification on its own initiative based on... categories (classes) of devices, reflecting the regulatory controls needed to provide reasonable assurance of their safety and effectiveness. The three categories of devices are class I (general controls), class II...

78 FR 5327 - Medical Devices; Ophthalmic Devices; Classification of the Scleral Plug

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-25

... Agency) is proposing to classify the scleral plug into class II (special controls), and proposing to... controls needed to provide reasonable assurance of their safety and effectiveness. The three categories of devices are class I (general controls), class II (special controls), and class III (premarket approval...

Nontoxic strains of cyanobacteria are the result of major gene deletion events induced by a transposable element.

PubMed

Christiansen, Guntram; Molitor, Carole; Philmus, Benjamin; Kurmayer, Rainer

2008-08-01

Blooms that are formed by cyanobacteria consist of toxic and nontoxic strains. The mechanisms that result in the occurrence of nontoxic strains are enigmatic. All the nontoxic strains of the filamentous cyanobacterium Planktothrix that were isolated from 9 European countries were found to have lost 90% of a large microcystin synthetase (mcy) gene cluster that encoded the synthesis of the toxic peptide microcystin (MC). Those strains still contain the flanking regions of the mcy gene cluster along with remnants of the transposable elements that are found in between. The majority of the strains still contain a gene coding for a distinct thioesterase type II (mcyT), which is putatively involved in MC synthesis. The insertional inactivation of mcyT in an MC-producing strain resulted in the reduction of MC synthesis by 94 +/- 2% (1 standard deviation). Nontoxic strains that occur in shallow lakes throughout Europe form a monophyletic lineage. A second lineage consists of strains that contain the mcy gene cluster but differ in their photosynthetic pigment composition, which is due to the occurrence of strains that contain phycocyanin or large amounts of phycoerythrin in addition to phycocyanin. Strains containing phycoerythrin typically occur in deep-stratified lakes. The rare occurrence of gene cluster deletion, paired with the evolutionary diversification of the lineages of strains that lost or still contain the mcy gene cluster, needs to be invoked in order to explain the absence or dominance of toxic cyanobacteria in various habitats.

Association of maternal anti-HLA class II antibodies with protection from allergy in offspring.

PubMed

Jones, M; Jeal, H; Harris, J M; Smith, J D; Rose, M L; Taylor, A N; Cullinan, P

2013-09-01

Recent studies have suggested that the birth order effect in allergy may be established during the prenatal period and that the protective effect may originate in the mother. HLA class II disparity between mother and foetus has been associated with significantly increased Th1 production. In this study, we investigated whether production of HLA antibodies 4 years after pregnancy with index child is associated with allergic outcomes in offspring at 8 years. Anti-HLA class I and II antibodies were measured in maternal serum (n = 284) and levels correlated to numbers of pregnancies and birth order, and allergic outcomes in offspring at 8 years of age. Maternal anti-HLA class I and II antibodies were significantly higher when birth order, and the number of pregnancies were larger. Anti-HLA class II, but not class I antibodies were associated with significantly less atopy and seasonal rhinitis in the offspring at age 8 years. Mothers with nonatopic (but not atopic) offspring had a significant increase in anti-HLA class I and II antibodies with birth order. This study suggests that the 'birth order' effect in children may be due to parity-related changes in the maternal immune response to foetal antigens. We have observed for the first time an association between maternal anti-HLA class II antibodies and protection from allergy in the offspring. Further work is required to determine immunologically how HLA disparity between mother and father can protect against allergy. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

25 CFR 547.12 - What are the minimum technical standards for downloading on a Class II gaming system?

Code of Federal Regulations, 2010 CFR

2010-04-01

... OF CLASS II GAMES § 547.12 What are the minimum technical standards for downloading on a Class II... software, files, data, and prize schedules. (2) Downloads of software, games, prize schedules, or other... performed in a manner that will not affect game play. (5) Downloads shall not affect the integrity of...

25 CFR 547.12 - What are the minimum technical standards for downloading on a Class II gaming system?

Code of Federal Regulations, 2011 CFR

2011-04-01

... OF CLASS II GAMES § 547.12 What are the minimum technical standards for downloading on a Class II... software, files, data, and prize schedules. (2) Downloads of software, games, prize schedules, or other... performed in a manner that will not affect game play. (5) Downloads shall not affect the integrity of...

25 CFR 547.12 - What are the minimum technical standards for downloading on a Class II gaming system?

Code of Federal Regulations, 2012 CFR

2012-04-01

... OF CLASS II GAMES § 547.12 What are the minimum technical standards for downloading on a Class II... software, files, data, and prize schedules. (2) Downloads of software, games, prize schedules, or other... performed in a manner that will not affect game play. (5) Downloads shall not affect the integrity of...

40 CFR 147.650 - State-administrative program-Class I, II, III, IV, and V wells.

Code of Federal Regulations, 2010 CFR

2010-07-01

... CONTROL PROGRAMS Idaho § 147.650 State-administrative program—Class I, II, III, IV, and V wells. The UIC program for Class I, II, III, IV, and V wells in the State of Idaho, other than those on Indian lands, is the program administered by the Idaho Department of Water Resources, approved by EPA pursuant to...

40 CFR Appendix B to Subpart A of... - Class II Controlled Substances a

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Class II Controlled Substances a B..., Subpt. A, App. B Appendix B to Subpart A of Part 82—Class II Controlled Substances a Controlled... the highest ODP, and the lower value is the estimate of the ODP of the isomer with the lowest ODP...

Poster - Thur Eve - 07: CNSC Update: "What's New in Class II".

PubMed

Heimann, M

2012-07-01

The Accelerators and Class II Facilities Division (ACFD) of the Canadian Nuclear Safety Commission (CNSC), is responsible for the oversight of radiotherapy facilities containing Class II prescribed equipment in Canada. This poster will highlight a number of new initiatives that the CNSC has implemented recently that have an impact on radiotherapy facility licensees. The presentation will discuss the recent policy decision to regulate particle accelerators of above 1 MeV. Challenges and progress with respect to the implementation of the policy will be presented. Other initiatives which will be described include: • The new ACFD webspace on the CNSC website, with direct links to relevant information on licensing, compliance and Class II prescribed equipment • The improved structure of the Appendix of Licence Documents that is part of every Class II licence • Updated licence application guides • Changes to Annual Compliance reporting requirements and progress on the ACR-Online initiative • Changes to some regulatory expectations related to medical accelerator facilities • Consolidation of Class II facility licences The poster will also include other initiatives that may be of particular interest to COMP membership. © 2012 American Association of Physicists in Medicine.

Class II G Protein-Coupled Receptors and Their Ligands in Neuronal Function and Protection

PubMed Central

Martin, Bronwen; de Maturana, Rakel Lopez; Brenneman, Randall; Walent, Tom; Mattson, Mark P.; Maudsley, Stuart

2008-01-01

G protein-coupled receptors (GPCRs) play pivotal roles in regulating the function and plasticity of neuronal circuits in the nervous system. Among the myriad of GPCRs expressed in neural cells, class II GPCRs which couples predominantly to the Gs–adenylate cyclase–cAMP signaling pathway, have recently received considerable attention for their involvement in regulating neuronal survival. Neuropeptides that activate class II GPCRs include secretin, glucagon-like peptides (GLP-1 and GLP-2), growth hormone-releasing hormone (GHRH), pituitary adenylate cyclase activating peptide (PACAP), corticotropin-releasing hormone (CRH), vasoactive intestinal peptide (VIP), parathyroid hormone (PTH), and calcitonin-related peptides. Studies of patients and animal and cell culture models, have revealed possible roles for class II GPCRs signaling in the pathogenesis of several prominent neurodegenerative conditions including stroke, Alzheimer's, Parkinson's, and Huntington's diseases. Many of the peptides that activate class II GPCRs promote neuron survival by increasing the resistance of the cells to oxidative, metabolic, and excitotoxic injury. A better understanding of the cellular and molecular mechanisms by which class II GPCRs signaling modulates neuronal survival and plasticity will likely lead to novel therapeutic interventions for neurodegenerative disorders. PMID:16052036

49 CFR 1150.45 - Procedures and relevant dates-transactions under section 10902 that involve creation of Class I...

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 8 2010-10-01 2010-10-01 false Procedures and relevant dates-transactions under section 10902 that involve creation of Class I or Class II rail carriers. 1150.45 Section 1150.45... dates—transactions under section 10902 that involve creation of Class I or Class II rail carriers. (a...

49 CFR 1150.45 - Procedures and relevant dates-transactions under section 10902 that involve creation of Class I...

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 8 2014-10-01 2014-10-01 false Procedures and relevant dates-transactions under section 10902 that involve creation of Class I or Class II rail carriers. 1150.45 Section 1150.45... dates—transactions under section 10902 that involve creation of Class I or Class II rail carriers. (a...

49 CFR 1150.45 - Procedures and relevant dates-transactions under section 10902 that involve creation of Class I...

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 8 2011-10-01 2011-10-01 false Procedures and relevant dates-transactions under section 10902 that involve creation of Class I or Class II rail carriers. 1150.45 Section 1150.45... dates—transactions under section 10902 that involve creation of Class I or Class II rail carriers. (a...

49 CFR 1150.45 - Procedures and relevant dates-transactions under section 10902 that involve creation of Class I...

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 8 2013-10-01 2013-10-01 false Procedures and relevant dates-transactions under section 10902 that involve creation of Class I or Class II rail carriers. 1150.45 Section 1150.45... dates—transactions under section 10902 that involve creation of Class I or Class II rail carriers. (a...

49 CFR 1150.45 - Procedures and relevant dates-transactions under section 10902 that involve creation of Class I...

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 8 2012-10-01 2012-10-01 false Procedures and relevant dates-transactions under section 10902 that involve creation of Class I or Class II rail carriers. 1150.45 Section 1150.45... dates—transactions under section 10902 that involve creation of Class I or Class II rail carriers. (a...

Prevalence of class-I, class-II and class-III obesity in Australian adults between 1995 and 2011-12.

PubMed

Keating, Catherine; Backholer, Kathryn; Gearon, Emma; Stevenson, Christopher; Swinburn, Boyd; Moodie, Marj; Carter, Rob; Peeters, Anna

2015-01-01

To compare the prevalence of class-I, II and III obesity in Australian adults between 1995, 2007-08 and 2011-12. Prevalence data for adults (aged 18+ years) were sourced from customised data from the nationally representative National Nutrition Survey (1995), the National Health Survey (2007-08), and the Australian Health Survey (2011-12) conducted by the Australian Bureau of Statistics. Obesity classifications were based on measured height and weight (class-I body mass index: 30.0-34.9 kg/m(2), class-II: 35.0-39.9 kg/m(2) and class-III: ≥ 40.0 kg/m(2)). Severe obesity was defined as class-II or class-III obesity. Between 1995 and 2011-12, the prevalence of obesity (all classes combined) increased from 19.1% to 27.2%. During this 17 year period, relative increases in class I, II and III obesity were 1.3, 1.7 and 2.2-fold respectively. In 2011-12, the prevalence of class I, II and III obesity was 19.4, 5.9 and 2.0 per cent respectively in men, and 16.1, 6.9 and 4.2 per cent respectively in women. One in every ten people was severely obese, increasing from one in twenty in 1995, and women were disproportionally represented in this population. Obesity prevalence increased with increasing levels of area-level socioeconomic disadvantage, particularly for the more severely obese classes. Severe obesity affected 6.2% and 13.4% in the least and most disadvantaged quintiles respectively. Over the last two decades, there have been substantial increases in the prevalence of obesity, particularly the more severe levels of obesity. This study highlights high risk groups who warrant targeted weight gain prevention interventions. Copyright © 2015 Asia Oceania Association for the Study of Obesity. Published by Elsevier Ltd. All rights reserved.

Predominant typologies of psychopathology in the United States: a latent class analysis.

PubMed

El-Gabalawy, Renée; Tsai, Jack; Harpaz-Rotem, Ilan; Hoff, Rani; Sareen, Jitender; Pietrzak, Robert H

2013-11-01

Latent class analysis (LCA) offers a parsimonious way of classifying common typologies of psychiatric comorbidity. We used LCA to identify the nature and correlates of predominant typologies of Axis I and II disorders in a large and comprehensive population-based sample of U.S. adults. We analyzed data from Wave 2 of the National Epidemiologic Survey on Alcohol and Related Conditions (2004-2005; n = 34,653), a population-based sample of U.S. adults. We derived latent classes based on all assessed Axis I and II disorders and examined the relationship between the identified Axis I classes and lifetime psychiatric disorders and suicide attempts, and physical and mental health-related quality of life. A four-class solution was optimal in characterizing predominant typologies of both Axis I and II disorders. For Axis I disorders, these included low psychopathology (n = 28,935, 84.0%), internalizing (n = 3693, 9.9%), externalizing (n = 1426, 4.5%), and high psychopathology (n = 599, 1.6%) classes. For Axis II disorders, these included no/low personality disorders (n = 31,265, 90.9%), obsessive/paranoid (n = 1635, 4.6%), borderline/dysregulated (n = 1319, 3.4%), and highly comorbid (n = 434, 1.1%) classes. Compared to the low psychopathology class, all other Axis I classes had significantly increased odds of mental disorders, elevated Axis II classes, suicide attempts and poorer quality of life, with the high psychopathology class having the overall highest rates of these correlates, with the exception of substance use disorders. Compared to the low psychopathology class, the internalizing and externalizing classes had increased rates of mood and anxiety disorders, and substance use disorders, respectively. Axis I and II psychopathology among U.S. adults may be best represented by four predominant typologies. Characterizing co-occurring patterns of psychopathology using person-based typologies represents a higher-order classification system that may be useful in clinical and research settings. Published by Elsevier Ltd.

Development of Bone-Conducted Ultrasonic Hearing Aid for the Profoundly Deaf: Assessments of the Modulation Type with Regard to Intelligibility and Sound Quality

NASA Astrophysics Data System (ADS)

Nakagawa, Seiji; Fujiyuki, Chika; Kagomiya, Takayuki

2012-07-01

Bone-conducted ultrasound (BCU) is perceived even by the profoundly sensorineural deaf. A novel hearing aid using the perception of amplitude-modulated BCU (BCU hearing aid: BCUHA) has been developed; however, further improvements are needed, especially in terms of articulation and sound quality. In this study, the intelligibility and sound quality of BCU speech with several types of amplitude modulation [double-sideband with transmitted carrier (DSB-TC), double-sideband with suppressed carrier (DSB-SC), and transposed modulation] were evaluated. The results showed that DSB-TC and transposed speech were more intelligible than DSB-SC speech, and transposed speech was closer than the other types of BCU speech to air-conducted speech in terms of sound quality. These results provide useful information for further development of the BCUHA.

Human umbilical cord mesenchymal stromal cells suppress MHC class II expression on rat vascular endothelium and prolong survival time of cardiac allograft

PubMed Central

Qiu, Ying; Yun, Mark M; Han, Xia; Zhao, Ruidong; Zhou, Erxia; Yun, Sheng

2014-01-01

Background: Human umbilical cord mesenchymal stromal cells (UC-MSCs) have low immunogenicity and immune regulation. To investigate immunomodulatory effects of human UC-MSCs on MHC class II expression and allograft, we transplanted heart of transgenic rats with MHC class II expression on vascular endothelium. Methods: UC-MSCs were obtained from human umbilical cords and confirmed with flow cytometry analysis. Transgenic rat line was established using the construct of human MHC class II transactivator gene (CIITA) under mouse ICAM-2 promoter control. The induced MHC class II expression on transgenic rat vascular endothelial cells (VECs) was assessed with immunohistological staining. And the survival time of cardiac allograft was compared between the recipients with and without UC-MSC transfusion. Results: Flow cytometry confirmed that the human UC-MSCs were positive for CD29, CD44, CD73, CD90, CD105, CD271, and negative for CD34 and HLA-DR. Repeated infusion of human UC-MSCs reduced MHC class II expression on vascular endothelia of transplanted hearts, and increased survival time of allograft. The UC-MSCs increased regulatory cytokines IL10, transforming growth factor (TGF)-β1 and suppressed proinflammatory cytokines IL2 and IFN-γ in vivo. The UC-MSC culture supernatant had similar effects on cytokine expression, and decreased lymphocyte proliferation in vitro. Conclusions: Repeated transfusion of the human UC-MSCs reduced MHC class II expression on vascular endothelia and prolonged the survival time of rat cardiac allograft. PMID:25126177

Class II ADP-ribosylation factors are required for efficient secretion of dengue viruses.

PubMed

Kudelko, Mateusz; Brault, Jean-Baptiste; Kwok, Kevin; Li, Ming Yuan; Pardigon, Nathalie; Peiris, J S Malik; Bruzzone, Roberto; Desprès, Philippe; Nal, Béatrice; Wang, Pei Gang

2012-01-02

Identification and characterization of virus-host interactions are very important steps toward a better understanding of the molecular mechanisms responsible for disease progression and pathogenesis. To date, very few cellular factors involved in the life cycle of flaviviruses, which are important human pathogens, have been described. In this study, we demonstrate a crucial role for class II Arf proteins (Arf4 and Arf5) in the dengue flavivirus life cycle. We show that simultaneous depletion of Arf4 and Arf5 blocks recombinant subviral particle secretion for all four dengue serotypes. Immunostaining analysis suggests that class II Arf proteins are required at an early pre-Golgi step for dengue virus secretion. Using a horseradish peroxidase protein fused to a signal peptide, we show that class II Arfs act specifically on dengue virus secretion without altering the secretion of proteins through the constitutive secretory pathway. Co-immunoprecipitation data demonstrate that the dengue prM glycoprotein interacts with class II Arf proteins but not through its C-terminal VXPX motif. Finally, experiments performed with replication-competent dengue and yellow fever viruses demonstrate that the depletion of class II Arfs inhibits virus secretion, thus confirming their implication in the virus life cycle, although data obtained with West Nile virus pointed out the differences in virus-host interactions among flaviviruses. Our findings shed new light on a molecular mechanism used by dengue viruses during the late stages of the life cycle and demonstrate a novel function for class II Arf proteins.

Class II ADP-ribosylation Factors Are Required for Efficient Secretion of Dengue Viruses*

PubMed Central

Kudelko, Mateusz; Brault, Jean-Baptiste; Kwok, Kevin; Li, Ming Yuan; Pardigon, Nathalie; Peiris, J. S. Malik; Bruzzone, Roberto; Desprès, Philippe; Nal, Béatrice; Wang, Pei Gang

2012-01-01

Identification and characterization of virus-host interactions are very important steps toward a better understanding of the molecular mechanisms responsible for disease progression and pathogenesis. To date, very few cellular factors involved in the life cycle of flaviviruses, which are important human pathogens, have been described. In this study, we demonstrate a crucial role for class II Arf proteins (Arf4 and Arf5) in the dengue flavivirus life cycle. We show that simultaneous depletion of Arf4 and Arf5 blocks recombinant subviral particle secretion for all four dengue serotypes. Immunostaining analysis suggests that class II Arf proteins are required at an early pre-Golgi step for dengue virus secretion. Using a horseradish peroxidase protein fused to a signal peptide, we show that class II Arfs act specifically on dengue virus secretion without altering the secretion of proteins through the constitutive secretory pathway. Co-immunoprecipitation data demonstrate that the dengue prM glycoprotein interacts with class II Arf proteins but not through its C-terminal VXPX motif. Finally, experiments performed with replication-competent dengue and yellow fever viruses demonstrate that the depletion of class II Arfs inhibits virus secretion, thus confirming their implication in the virus life cycle, although data obtained with West Nile virus pointed out the differences in virus-host interactions among flaviviruses. Our findings shed new light on a molecular mechanism used by dengue viruses during the late stages of the life cycle and demonstrate a novel function for class II Arf proteins. PMID:22105072

Morphometric analysis of long-term dentoskeletal effects induced by treatment with Balters bionator.

PubMed

Bigliazzi, Renato; Franchi, Lorenzo; Bertoz, André Pinheiro de Magalhães; McNamara, James A; Faltin, Kurt; Bertoz, Francisco Antonio

2015-09-01

To evaluate the long-term effects of the standard (Class II) Balters bionator in growing patients with Class II malocclusion with mandibular retrusion by using morphometrics (thin-plate spline [TPS] analysis). Twenty-three Class II patients (8 male, 15 female) were treated consecutively with the Balters bionator (bionator group). The sample was evaluated at T0, start of treatment; T1, end of bionator therapy; and T2, long-term observation (including fixed appliances). Mean age at the start of treatment was 10 years 2 months (T0); at posttreatment, 12 years 3 months (T1); and at long-term follow-up, 18 years 2 months (T2). The control group consisted of 22 subjects (11 male, 11 female) with untreated Class II malocclusion. Lateral cephalograms were analyzed at the three time points for all groups. TPS analysis evaluated statistical differences (permutation tests) in the craniofacial shape and size between the bionator and control groups. TPS analysis showed that treatment with the bionator is able to produce favorable mandibular shape changes (forward and downward displacement) that contribute significantly to the correction of the Class II dentoskeletal imbalance. These results are maintained at a long-term observation after completion of growth. The control group showed no statistically significant differences in the correction of Class II malocclusion. This study suggests that bionator treatment of Class II malocclusion produces favorable results over the long term with a combination of skeletal and dentoalveolar shape changes.

Genome-wide identification, splicing, and expression analysis of the myosin gene family in maize (Zea mays)

PubMed Central

Wang, Guifeng; Zhong, Mingyu; Wang, Gang; Song, Rentao

2014-01-01

The actin-based myosin system is essential for the organization and dynamics of the endomembrane system and transport network in plant cells. Plants harbour two unique myosin groups, class VIII and class XI, and the latter is structurally and functionally analogous to the animal and fungal class V myosin. Little is known about myosins in grass, even though grass includes several agronomically important cereal crops. Here, we identified 14 myosin genes from the genome of maize (Zea mays). The relatively larger sizes of maize myosin genes are due to their much longer introns, which are abundant in transposable elements. Phylogenetic analysis indicated that maize myosin genes could be classified into class VIII and class XI, with three and 11 members, respectively. Apart from subgroup XI-F, the remaining subgroups were duplicated at least in one analysed lineage, and the duplication events occurred more extensively in Arabidopsis than in maize. Only two pairs of maize myosins were generated from segmental duplication. Expression analysis revealed that most maize myosin genes were expressed universally, whereas a few members (XI-1, -6, and -11) showed an anther-specific pattern, and many underwent extensive alternative splicing. We also found a short transcript at the O1 locus, which conceptually encoded a headless myosin that most likely functions at the transcriptional level rather than via a dominant-negative mechanism at the translational level. Together, these data provide significant insights into the evolutionary and functional characterization of maize myosin genes that could transfer to the identification and application of homologous myosins of other grasses. PMID:24363426

Modified Angle's Classification for Primary Dentition.

PubMed

Chandranee, Kaushik Narendra; Chandranee, Narendra Jayantilal; Nagpal, Devendra; Lamba, Gagandeep; Choudhari, Purva; Hotwani, Kavita

2017-01-01

This study aims to propose a modification of Angle's classification for primary dentition and to assess its applicability in children from Central India, Nagpur. Modification in Angle's classification has been proposed for application in primary dentition. Small roman numbers i/ii/iii are used for primary dentition notation to represent Angle's Class I/II/III molar relationships as in permanent dentition, respectively. To assess applicability of modified Angle's classification a cross-sectional preschool 2000 children population from central India; 3-6 years of age residing in Nagpur metropolitan city of Maharashtra state were selected randomly as per the inclusion and exclusion criteria. Majority 93.35% children were found to have bilateral Class i followed by 2.5% bilateral Class ii and 0.2% bilateral half cusp Class iii molar relationships as per the modified Angle's classification for primary dentition. About 3.75% children had various combinations of Class ii relationships and 0.2% children were having Class iii subdivision relationship. Modification of Angle's classification for application in primary dentition has been proposed. A cross-sectional investigation using new classification revealed various 6.25% Class ii and 0.4% Class iii molar relationships cases in preschool children population in a metropolitan city of Nagpur. Application of the modified Angle's classification to other population groups is warranted to validate its routine application in clinical pediatric dentistry.

Analysis of metal tolerance in Rhizobium leguminosarum strains isolated from an ultramafic soil.

PubMed

Rubio-Sanz, Laura; Brito, Belén; Palacios, Jose

2018-02-01

Natural habitats containing high amounts of heavy metals provide a valuable source of bacteria adapted to deal with metal toxicity. A functional analysis of the population of legume endosymbiotic bacteria in an ultramafic soil was undertaken by studying a collection of Rhizobium leguminosarum bv viciae (Rlv) isolates obtained using pea as trap plant. One of the isolates, Rlv UPM1137, was selected on the basis of its higher tolerance to nickel and cobalt and presence of inducible mechanisms for such tolerance. A random transposon mutagenesis of Rlv UPM1137 allowed the generation of 14 transposant derivatives with increased nickel sensitivity; five of these transposants were also more sensitive to cobalt. Sequencing of the insertion sites revealed that one of the transposants (D2250) was affected in a gene homologous to the cation diffusion facilitator gene dmeF first identified in the metal-resistant bacterium Cupriavidus metallidurans CH34. The symbiotic performance of D2250 and two other transposants bearing single transposon insertions was unaffected under high-metal conditions, suggesting that, in contrast to previous observations in other Rlv strain, metal tolerance in UPM1137 under symbiotic conditions might be supported by functional redundancy between several mechanisms. © FEMS 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes

PubMed Central

Puterova, Janka; Razumova, Olga; Martinek, Tomas; Alexandrov, Oleg; Divashuk, Mikhail; Kubat, Zdenek; Hobza, Roman; Karlov, Gennady

2017-01-01

Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites but most satellites were found on autosomes. Transposable elements were located mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes. PMID:28057732

Substituted-letter and transposed-letter effects in a masked priming paradigm with French developing readers and dyslexics.

PubMed

Lété, Bernard; Fayol, Michel

2013-01-01

The aim of the study was to undertake a behavioral investigation of the development of automatic orthographic processing during reading acquisition in French. Following Castles and colleagues' 2007 study (Journal of Experimental Child Psychology, 97, 165-182) and their lexical tuning hypothesis framework, substituted-letter and transposed-letter primes were used in a masked priming paradigm with third graders, fifth graders, adults, and phonological dyslexics matched on reading level with the third graders. No priming effect was found in third graders. In adults, only a transposed-letter priming effect was found; there was no substituted-letter priming effect. Finally, fifth graders and dyslexics showed both substituted-letter and transposed-letter priming effects. Priming effects between the two groups were of the same magnitude after response time (RT) z-score transformation. Taken together, our results show that the pattern of priming effects found by Castles and colleagues in English normal readers emerges later in French normal readers. In other words, language orthographies seem to constrain the tuning of the orthographic system, with an opaque orthography producing faster tuning of orthographic processing than more transparent orthographies because of the high level of reliance on phonological decoding while learning to read. Copyright © 2012 Elsevier Inc. All rights reserved.

Letter-transposition effects are not universal: The impact of transposing letters in Hebrew

PubMed Central

Velan, Hadas; Frost, Ram

2009-01-01

We examined the effects of letter transposition in Hebrew in three masked-priming experiments. Hebrew, like English has an alphabetic orthography where sequential and contiguous letter strings represent phonemes. However, being a Semitic language it has a non-concatenated morphology that is based on root derivations. Experiment 1 showed that transposed-letter (TL) root primes inhibited responses to targets derived from the non-transposed root letters, and that this inhibition was unrelated to relative root frequency. Experiment 2 replicated this result and showed that if the transposed letters of the root created a nonsense-root that had no lexical representation, then no inhibition and no facilitation were obtained. Finally, Experiment 3 demonstrated that in contrast to English, French, or Spanish, TL nonword primes did not facilitate recognition of targets, and when the root letters embedded in them consisted of a legal root morpheme, they produced inhibition. These results suggest that lexical space in alphabetic orthographies may be structured very differently in different languages if their morphological structure diverges qualitatively. In Hebrew, lexical space is organized according to root families rather than simple orthographic structure, so that all words derived from the same root are interconnected or clustered together, independent of overall orthographic similarity. PMID:20161017

Riboregulation of bacterial and archaeal transposition.

PubMed

Ellis, Michael J; Haniford, David B

2016-05-01

The coexistence of transposons with their hosts depends largely on transposition levels being tightly regulated to limit the mutagenic burden associated with frequent transposition. For 'DNA-based' (class II) bacterial transposons there is growing evidence that regulation through small noncoding RNAs and/or the RNA-binding protein Hfq are prominent mechanisms of defense against transposition. Recent transcriptomics analyses have identified many new cases of antisense RNAs (asRNA) that potentially could regulate the expression of transposon-encoded genes giving the impression that asRNA regulation of DNA-based transposons is much more frequent than previously thought. Hfq is a highly conserved bacterial protein that plays a central role in posttranscriptional gene regulation and stress response pathways in many bacteria. Three different mechanisms for Hfq-directed control of bacterial transposons have been identified to date highlighting the versatility of this protein as a regulator of bacterial transposons. There is also evidence emerging that some DNA-based transposons encode RNAs that could regulate expression of host genes. In the case of IS200, which appears to have lost its ability to transpose, contributing a regulatory RNA to its host could account for the persistence of this mobile element in a wide range of bacterial species. It remains to be seen how prevalent these transposon-encoded RNA regulators are, but given the relatively large amount of intragenic transcription in bacterial genomes, it would not be surprising if new examples are forthcoming. WIREs RNA 2016, 7:382-398. doi: 10.1002/wrna.1341 For further resources related to this article, please visit the WIREs website. © 2016 Wiley Periodicals, Inc.

Functional condition of masseters muscles of patients with class ?? subdivision.

PubMed

Kuroyedova, Vera D; Makarova, Alexandra N; Chicor, Tatyana A

Main functional characteristics of masticator muscles in patients with class ?? malocclusions is activity dominance of m. temporalis in comparison with m. ?asseter. We have not found datum about functional status of the masticators in patients with class II subdivision. The purpose of our study was to investigate the functional characteristics of m. ?asseter, m. temporalis in adult patients with class II subdivision malocclusion. There have been carried out the surface electromyographic study of m. masseter, m. temporalis in 17 adult patients with class II subdivision. It was realized quantitative analysis of 271 electromyogram, it was determined the average bioelectric activity, index activity, symmetry and torsion index. It was observed predominance of the bioelectrical activity of m. temporales on m. masseter for all persons with class II subdivision. Bioelectrical activity for m. masseter was bigger on side of distal ratio and for m. temporales on side of neutral ratio. In class ?? subdivision right, the mandible was deviated to the left side and in class ?? subdivision left is deviated to the right side. Thus, rotational moment generated during compression of the jaws, causes deviation of the lower jaw to the side, with a neutral molar ratio. During voluntary chewing bioelectrical activity of m. masseter and m. temporalis was higher in the right side. In accordance with the functional condition of the masticatory muscles of class II subdivision is characterized with functional features of distal occlusion.

78 FR 37998 - Electronic One Touch Bingo System

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-25

... decision regarding the classification of server based electronic bingo system games that can be played... Class II or Class III game. DATES: The agency must receive comments on or before August 26, 2013... from the regulated community regarding the status of one touch bingo as a Class II or a Class III game...

77 FR 52109 - Agency Information Collection Activities; Revision of Currently-Approved Information Collection...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-28

... Request: Annual Report of Class I and Class II Motor Carriers of Property AGENCY: Federal Motor Carrier.... FMCSA requests approval to revise an ICR entitled, ``Annual Report of Class I and Class II Motor... be addressed to the attention of the Desk Officer, Department of Transportation/Federal Motor Carrier...

HLA Class I and Genetic Susceptibility to Type 1 Diabetes

PubMed Central

Noble, Janelle A.; Valdes, Ana Maria; Varney, Michael D.; Carlson, Joyce A.; Moonsamy, Priscilla; Fear, Anna Lisa; Lane, Julie A.; Lavant, Eva; Rappner, Rebecca; Louey, Anthony; Concannon, Patrick; Mychaleckyj, Josyf C.; Erlich, Henry A.

2010-01-01

OBJECTIVE We report here genotyping data and type 1 diabetes association analyses for HLA class I loci (A, B, and C) on 1,753 multiplex pedigrees from the Type 1 Diabetes Genetics Consortium (T1DGC), a large international collaborative study. RESEARCH DESIGN AND METHODS Complete eight-locus HLA genotyping data were generated. Expected patient class I (HLA-A, -B, and -C) allele frequencies were calculated, based on linkage disequilibrium (LD) patterns with observed HLA class II DRB1-DQA1-DQB1 haplotype frequencies. Expected frequencies were compared to observed allele frequencies in patients. RESULTS Significant type 1 diabetes associations were observed at all class I HLA loci. After accounting for LD with HLA class II, the most significantly type 1 diabetes–associated alleles were B*5701 (odds ratio 0.19; P = 4 × 10−11) and B*3906 (10.31; P = 4 × 10−10). Other significantly type 1 diabetes–associated alleles included A*2402, A*0201, B*1801, and C*0501 (predisposing) and A*1101, A*3201, A*6601, B*0702, B*4403, B*3502, C*1601, and C*0401 (protective). Some alleles, notably B*3906, appear to modulate the risk of all DRB1-DQA1-DQB1 haplotypes on which they reside, suggesting a class I effect that is independent of class II. Other class I type 1 diabetes associations appear to be specific to individual class II haplotypes. Some apparent associations (e.g., C*1601) could be attributed to strong LD to another class I susceptibility locus (B*4403). CONCLUSIONS These data indicate that HLA class I alleles, in addition to and independently from HLA class II alleles, are associated with type 1 diabetes. PMID:20798335

Class II malocclusion with accentuated occlusal plane inclination corrected with miniplate: a case report

PubMed Central

Farret, Marcel Marchiori; Farret, Milton M. Benitez

2016-01-01

ABSTRACT Introduction: A canted occlusal plane presents an unesthetic element of the smile. The correction of this asymmetry has been typically considered difficult by orthodontists, as it requires complex mechanics and may sometimes even require orthognathic surgery. Objective: This paper outlines the case of a 29-year-old woman with Class II malocclusion, pronounced midline deviation and accentuated occlusal plane inclination caused by mandibular deciduous molar ankylosis. Methods: The patient was treated with a miniplate used to provide anchorage in order to intrude maxillary teeth and extrude mandibular teeth on one side, thus eliminating asymmetry. Class II was corrected on the left side by means of distalization, anchored in the miniplate as well. On the right side, maxillary first premolar was extracted and molar relationship was kept in Class II, while canines were moved to Class I relationship. The patient received implant-prosthetic rehabilitation for maxillary left lateral incisor and mandibular left second premolar. Results: At the end of treatment, Class II was corrected, midlines were matched and the canted occlusal plane was totally corrected, thereby improving smile function and esthetics. PMID:27409658

Unbiased quantitative testing of conventional orthodontic beliefs.

PubMed

Baumrind, S

1998-03-01

This study used a preexisting database to test in hypothesis from the appropriateness of some common orthodontic beliefs concerning upper first molar displacement and changes in facial morphology associated with conventional full bonded/banded treatment in growing subjects. In an initial pass, the author used data from a stratified random sample of 48 subjects drawn retrospectively from the practice of a single, experienced orthodontist. This sample consisted of 4 subgroups of 12 subjects each: Class I nonextraction, Class I extraction, Class II nonextraction, and Class II extraction. The findings indicate that, relative to the facial profile, chin point did not, on average, displace anteriorly during treatment, either overall or in any subgroup. Relative to the facial profile, Point A became significantly less prominent during treatment, both overall and in each subgroup. The best estimate of the mean displacement of the upper molar cusp relative to superimposition on Anterior Cranial Base was in the mesial direction in each of the four subgroups. In only one extraction subject out of 24 did the cusp appear to be displaced distally. Mesial molar cusp displacement was significantly greater in the Class II extraction subgroup than in the Class II nonextraction subgroup. Relative to superimposition on anatomical "best fit" of maxillary structures, the findings for molar cusp displacement were similar, but even more dramatic. Mean mesial migration was highly significant in both the Class II nonextraction and Class II extraction subgroups. In no subject in the entire sample was distal displacement noted relative to this superimposition. Mean increase in anterior Total Face Height was significantly greater in the Class II extraction subgroup than in the Class II nonextraction subgroup. (This finding was contrary to the author's original expectation.) The generalizability of the findings from the initial pass to other treated growing subjects was then assessed by retesting modified hypotheses against a second database stored sample that earlier had been drawn randomly from two other orthodontic practices. The implications of the author's study strategy to the design of future shared digital databases is discussed briefly.

The genomic landscape shaped by selection on transposable elements across 18 mouse strains.

PubMed

Nellåker, Christoffer; Keane, Thomas M; Yalcin, Binnaz; Wong, Kim; Agam, Avigail; Belgard, T Grant; Flint, Jonathan; Adams, David J; Frankel, Wayne N; Ponting, Chris P

2012-06-15

Transposable element (TE)-derived sequence dominates the landscape of mammalian genomes and can modulate gene function by dysregulating transcription and translation. Our current knowledge of TEs in laboratory mouse strains is limited primarily to those present in the C57BL/6J reference genome, with most mouse TEs being drawn from three distinct classes, namely short interspersed nuclear elements (SINEs), long interspersed nuclear elements (LINEs) and the endogenous retrovirus (ERV) superfamily. Despite their high prevalence, the different genomic and gene properties controlling whether TEs are preferentially purged from, or are retained by, genetic drift or positive selection in mammalian genomes remain poorly defined. Using whole genome sequencing data from 13 classical laboratory and 4 wild-derived mouse inbred strains, we developed a comprehensive catalogue of 103,798 polymorphic TE variants. We employ this extensive data set to characterize TE variants across the Mus lineage, and to infer neutral and selective processes that have acted over 2 million years. Our results indicate that the majority of TE variants are introduced though the male germline and that only a minority of TE variants exert detectable changes in gene expression. However, among genes with differential expression across the strains there are twice as many TE variants identified as being putative causal variants as expected. Most TE variants that cause gene expression changes appear to be purged rapidly by purifying selection. Our findings demonstrate that past TE insertions have often been highly deleterious, and help to prioritize TE variants according to their likely contribution to gene expression or phenotype variation.

Low diversity, activity, and density of transposable elements in five avian genomes.

PubMed

Gao, Bo; Wang, Saisai; Wang, Yali; Shen, Dan; Xue, Songlei; Chen, Cai; Cui, Hengmi; Song, Chengyi

2017-07-01

In this study, we conducted the activity, diversity, and density analysis of transposable elements (TEs) across five avian genomes (budgerigar, chicken, turkey, medium ground finch, and zebra finch) to explore the potential reason of small genome sizes of birds. We found that these avian genomes exhibited low density of TEs by about 10% of genome coverages and low diversity of TEs with the TE landscapes dominated by CR1 and ERV elements, and contrasting proliferation dynamics both between TE types and between species were observed across the five avian genomes. Phylogenetic analysis revealed that CR1 clade was more diverse in the family structure compared with R2 clade in birds; avian ERVs were classified into four clades (alpha, beta, gamma, and ERV-L) and belonged to three classes of ERV with an uneven distributed in these lineages. The activities of DNA and SINE TEs were very low in the evolution history of avian genomes; most LINEs and LTRs were ancient copies with a substantial decrease of activity in recent, with only LTRs and LINEs in chicken and zebra finch exhibiting weak activity in very recent, and very few TEs were intact; however, the recent activity may be underestimated due to the sequencing/assembly technologies in some species. Overall, this study demonstrates low diversity, activity, and density of TEs in the five avian species; highlights the differences of TEs in these lineages; and suggests that the current and recent activity of TEs in avian genomes is very limited, which may be one of the reasons of small genome sizes in birds.

The predominantly selfing plant Arabidopsis thaliana experienced a recent reduction in transposable element abundance compared to its outcrossing relative Arabidopsis lyrata

PubMed Central

2012-01-01

Background Transposable elements (TEs) are major contributors to genome evolution. One factor that influences their evolutionary dynamics is whether their host reproduces through selfing or through outcrossing. According to the recombinational spreading hypothesis, for instance, TEs can spread more easily in outcrossing species through recombination, and should thus be less abundant in selfing species. We here studied the distribution and evolutionary dynamics of TE families in the predominantly selfing plant Arabidopsis thaliana and its close outcrossing relative Arabidopsis lyrata on a genome-wide scale. We characterized differences in TE abundance between them and asked which, if any, existing hypotheses about TE abundances may explain these differences. Results We identified 1,819 TE families representing all known classes of TEs in both species, and found three times more copies in the outcrossing A. lyrata than in the predominantly selfing A. thaliana, as well as ten times more TE families unique to A. lyrata. On average, elements in A. lyrata are younger than elements in A. thaliana. In particular, A. thaliana shows a marked decrease in element number that occurred during the most recent 10% of the time interval since A. thaliana split from A. lyrata. This most recent period in the evolution of A. thaliana started approximately 500,000 years ago, assuming a splitting time of 5 million years ago, and coincides with the time at which predominant selfing originated. Conclusions Our results indicate that the mating system may be important for determining TE copy number, and that selfing species are likely to have fewer TEs. PMID:22313744

Multilevel Selection Theory and the Evolutionary Functions of Transposable Elements.

PubMed

Brunet, Tyler D P; Doolittle, W Ford

2015-08-06

One of several issues at play in the renewed debate over "junk DNA" is the organizational level at which genomic features might be seen as selected, and thus to exhibit function, as etiologically defined. The intuition frequently expressed by molecular geneticists that junk DNA is functional because it serves to "speed evolution" or as an "evolutionary repository" could be recast as a claim about selection between species (or clades) rather than within them, but this is not often done. Here, we review general arguments for the importance of selection at levels above that of organisms in evolution, and develop them further for a common genomic feature: the carriage of transposable elements (TEs). In many species, not least our own, TEs comprise a large fraction of all nuclear DNA, and whether they individually or collectively contribute to fitness--or are instead junk--is a subject of ongoing contestation. Even if TEs generally owe their origin to selfish selection at the lowest level (that of genomes), their prevalence in extant organisms and the prevalence of extant organisms bearing them must also respond to selection within species (on organismal fitness) and between species (on rates of speciation and extinction). At an even higher level, the persistence of clades may be affected (positively or negatively) by TE carriage. If indeed TEs speed evolution, it is at these higher levels of selection that such a function might best be attributed to them as a class. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Transcriptional activation of transposable elements in mouse zygotes is independent of Tet3-mediated 5-methylcytosine oxidation.

PubMed

Inoue, Azusa; Matoba, Shogo; Zhang, Yi

2012-12-01

The methylation state of the paternal genome is rapidly reprogrammed shortly after fertilization. Recent studies have revealed that loss of 5-methylcytosine (5mC) in zygotes correlates with appearance of 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). This process is mediated by Tet3 and the 5mC oxidation products generated in zygotes are gradually lost during preimplantation development through a replication-dependent dilution process. Despite these findings, the biological significance of Tet3-mediated oxidation of 5mC to 5hmC/5fC/5caC in zygotes is unknown. DNA methylation plays an important role in silencing gene expression including the repression of transposable elements (TEs). Given that the activation of TEs during preimplantation development correlates with loss of DNA methylation, it is believed that paternal DNA demethylation may have an important role in TE activation. Here we examined this hypothesis and found that Tet3-mediated 5mC oxidation does not have a significant contribution to TE activation. We show that the expression of LINE-1 (long interspersed nucleotide element 1) and ERVL (endogenous retroviruses class III) are activated from both paternal and maternal genomes in zygotes. Inhibition of 5mC oxidation by siRNA-mediated depletion of Tet3 affected neither TE activation, nor global transcription in zygotes. Thus, our study provides the first evidence demonstrating that activation of both TEs and global transcription in zygotes are independent of Tet3-mediated 5mC oxidation.

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lang, Daniel; Ullrich, Kristian K.; Murat, Florent

Here, the draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome–scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene– and TE–rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono–centric with peaks of a class of Copia elements potentially coinciding with centromeres. Genemore » body methylation is evident in 5.7% of the protein–coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure–based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant–specific cell growth and tissue organization. The P. patens genome lacks the TE–rich pericentromeric and gene–rich distal regions typical for most flowering plant genomes. More non–seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.« less

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

DOE PAGES

Lang, Daniel; Ullrich, Kristian K.; Murat, Florent; ...

2017-12-13

Here, the draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome–scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene– and TE–rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono–centric with peaks of a class of Copia elements potentially coinciding with centromeres. Genemore » body methylation is evident in 5.7% of the protein–coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure–based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant–specific cell growth and tissue organization. The P. patens genome lacks the TE–rich pericentromeric and gene–rich distal regions typical for most flowering plant genomes. More non–seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.« less

Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies

PubMed Central

Talla, Venkat; Suh, Alexander; Kalsoom, Faheema; Dincă, Vlad; Vila, Roger; Friberg, Magne; Wiklund, Christer

2017-01-01

Abstract Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643 Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72 Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths. PMID:28981642

Mating system shifts and transposable element evolution in the plant genus Capsella.

PubMed

Agren, J Ågren; Wang, Wei; Koenig, Daniel; Neuffer, Barbara; Weigel, Detlef; Wright, Stephen I

2014-07-16

Despite having predominately deleterious fitness effects, transposable elements (TEs) are major constituents of eukaryote genomes in general and of plant genomes in particular. Although the proportion of the genome made up of TEs varies at least four-fold across plants, the relative importance of the evolutionary forces shaping variation in TE abundance and distributions across taxa remains unclear. Under several theoretical models, mating system plays an important role in governing the evolutionary dynamics of TEs. Here, we use the recently sequenced Capsella rubella reference genome and short-read whole genome sequencing of multiple individuals to quantify abundance, genome distributions, and population frequencies of TEs in three recently diverged species of differing mating system, two self-compatible species (C. rubella and C. orientalis) and their self-incompatible outcrossing relative, C. grandiflora. We detect different dynamics of TE evolution in our two self-compatible species; C. rubella shows a small increase in transposon copy number, while C. orientalis shows a substantial decrease relative to C. grandiflora. The direction of this change in copy number is genome wide and consistent across transposon classes. For insertions near genes, however, we detect the highest abundances in C. grandiflora. Finally, we also find differences in the population frequency distributions across the three species. Overall, our results suggest that the evolution of selfing may have different effects on TE evolution on a short and on a long timescale. Moreover, cross-species comparisons of transposon abundance are sensitive to reference genome bias, and efforts to control for this bias are key when making comparisons across species.

Cone-beam computed tomographic evaluation of the temporomandibular joint and dental characteristics of patients with Class II subdivision malocclusion and asymmetry

PubMed Central

Huang, Mingna; Hu, Yun; Yu, Jinfeng; Sun, Jicheng; Ming, Ye

2017-01-01

Objective Treating Class II subdivision malocclusion with asymmetry has been a challenge for orthodontists because of the complicated characteristics of asymmetry. This study aimed to explore the characteristics of dental and skeletal asymmetry in Class II subdivision malocclusion, and to assess the relationship between the condyle-glenoid fossa and first molar. Methods Cone-beam computed tomographic images of 32 patients with Class II subdivision malocclusion were three-dimensionally reconstructed using the Mimics software. Forty-five anatomic landmarks on the reconstructed structures were selected and 27 linear and angular measurements were performed. Paired-samples t-tests were used to compare the average differences between the Class I and Class II sides; Pearson correlation coefficient (r) was used for analyzing the linear association. Results The faciolingual crown angulation of the mandibular first molar (p < 0.05), sagittal position of the maxillary and mandibular first molars (p < 0.01), condylar head height (p < 0.01), condylar process height (p < 0.05), and angle of the posterior wall of the articular tubercle and coronal position of the glenoid fossa (p < 0.01) were significantly different between the two sides. The morphology and position of the condyle-glenoid fossa significantly correlated with the three-dimensional changes in the first molar. Conclusions Asymmetry in the sagittal position of the maxillary and mandibular first molars between the two sides and significant lingual inclination of the mandibular first molar on the Class II side were the dental characteristics of Class II subdivision malocclusion. Condylar morphology and glenoid fossa position asymmetries were the major components of skeletal asymmetry and were well correlated with the three-dimensional position of the first molar. PMID:28861389

DNA double-strand break in vivo at the 3' extremity of exons located upstream of group II introns. Senescence and circular DNA introns in Podospora mitochondria.

PubMed

Sainsard-Chanet, A; Begel, O; Belcour, L

1994-10-07

In the filamentous fungus Podospora anserina, the unavoidable phenomenon of senescence is associated with the amplification of the first intron of the mitochondrial cox1 that accumulates as circular DNA molecules consisting of tandem repeats. This group II intron (cox1-i1 or alpha) is able to transpose and contains an open reading frame with significant amino acid similarity with reverse transcriptases. The generation of these intronic circular DNA molecules, their amplification and their involvement in the senescence process are unresolved questions. We demonstrate here that: (1) another group II intron, the fourth intron of gene cox1, cox1-i4, is also able to give precise DNA end to end junctions; (2) this intronic sequence can be found amplified during senescence, although to a lesser extent than cox1-i1; (3) the amplification of the DNA multimeric cox1-i1 molecules likely does not proceed by autonomous replication; (4) the generation of the DNA intronic circles does not require efficient intron splicing; (5) a DNA double-strand break occurs in vivo at the 3' extremity of the cox1-e1 and cox1-e4 exons preceding the group II introns that form circular DNAs. On the whole, these results show that the ability to form DNA circular molecules is a property of some group II introns and they demonstrate the occurrence of a specific DNA cleavage at or near the integration site of these group II introns. The results strongly suggest that this cleavage is involved in the formation of the group II intronic DNA circles and could also be involved in the phenomenon of group II intron homing.

Characterization of the molecular chaperone calnexin in the channel catfish, Ictalurus punctatus, and its association with MHC class II molecules.

PubMed

Fuller, James R; Pitzer, Joshua E; Godwin, Ulla; Albertino, Mark; Machon, Benjamin D; Kearse, Kelly P; McConnell, Thomas J

2004-05-17

Folding and assembly of MHC molecules in mammals occurs in the endoplasmic reticulum (ER), but has not been studied in teleosts. Calnexin (CNX) is an ER chaperone that associates with glycoproteins bearing a monoglucosylated N-linked oligosaccharide side chain. Here we report the first identification and characterization of a full-length CNX cDNA clone in a teleost, and the association of the CNX chaperone with MHC class II in a channel catfish T cell line. The 1.8 kb CNX clone encodes a protein of 607 amino acids that is 72% identical to the consensus sequence of mammalian CNXs. The association of CNX with class II is of particular interest because the native MHC class II alpha chain of Ictalurus punctatus does not bear any N-linked oligosaccharide consensus glycosylation sequences. Thus the assembly of class II molecules in the catfish probably proceeds via different steps than occurs in mammals. Copyright 2003 Elsevier Ltd.

Binding and activation of major histocompatibility complex class II-deficient macrophages by staphylococcal exotoxins

NASA Technical Reports Server (NTRS)

Beharka, A. A.; Armstrong, J. W.; Iandolo, J. J.; Chapes, S. K.; Spooner, B. S. (Principal Investigator)

1994-01-01

Macrophages from C2D transgenic mice deficient in the expression of major histocompatibility complex (MHC) class II proteins were used to identify binding sites for superantigens distinct from the MHC class II molecule. Iodinated staphylococcal enterotoxins A and B (SEA and SEB) and exfoliative toxins A and B (ETA and ETB) bound to C2D macrophages in a concentration-dependent and competitive manner. All four toxins increased F-actin concentration within 30 s of their addition to C2D macrophages, indicating that signal transduction occurred in response to toxin in the absence of class II MHC. Furthermore, ETA, ETB, SEA, and, to a lesser extent, SEB induced C2D macrophages to produce interleukin 6. Several molecular species on C2D macrophages with molecular masses of 140, 97, 61, 52, 43, and 37 kDa bound SEA in immunoprecipitation experiments. These data indicate the presence of novel, functionally active toxin binding sites on murine macrophages distinct from MHC class II molecules.

Tolerance to MHC class II disparate allografts through genetic modification of bone marrow

PubMed Central

Jindra, Peter T.; Tripathi, Sudipta; Tian, Chaorui; Iacomini, John; Bagley, Jessamyn

2012-01-01

Induction of molecular chimerism through genetic modification of bone marrow is a powerful tool for the induction of tolerance. Here we demonstrate for the first time that expression of an allogeneic MHC class II gene in autologous bone marrow cells, resulting in a state of molecular chimerism, induces tolerance to MHC class II mismatched skin grafts, a stringent test of transplant tolerance. Reconstitution of recipients with syngeneic bone marrow transduced with retrovirus encoding H-2I-Ab (I-Ab) resulted the long-term expression of the retroviral gene product on the surface of MHC class II-expressing bone marrow derived cell types. Mechanistically, tolerance was maintained by the presence of regulatory T cells, which prevented proliferation and cytokine production by alloreactive host T cells. Thus, the introduction of MHC class II genes into bone marrow derived cells through genetic engineering results in tolerance. These results have the potential to extend the clinical applicability of molecular chimerism for tolerance induction. PMID:22833118

Clinical assessment of class II resin-based composites versus preformed metal crowns performed on primary molars in patients at high risk of caries.

PubMed

Alyahya, A; Khanum, A; Qudeimat, M

2018-02-01

To compare class II resin composite with preformed metal crowns (PMC) in the treatment of proximal dentinal caries in high caries-risk patients. The charts (270) of paediatric patients with proximal caries of their primary molars were reviewed. Success or failure of a procedure was assessed using the dental notes. Survival analysis was used to calculate the mean survival time (MST) for both procedures. The influence of variables on the mean survival time was investigated. A total of 593 class II resin composites and 243 PMCs were placed in patients ranging between 4-13 years of age. The failure percentage of class II resin composites was 22.6% with the majority having been due to recurrent caries, while the failure percentage of PMCs was 15.2% with the majority due to loss of the crown. There was no significant difference between the MST of class II resin composites and PMCs, 41.3 and 45.6 months respectively (p value = 0.06). In class II resin composites, mesial restorations were associated with lower MST compared to distal restorations (p-value < 0.001). The MST of resin composites and PMCs were comparable when performed on high caries-risk patients.

Spec Rekindled-A Simple Torque Correction Mechanics for Transposed Teeth in Conjunction with Pre-adjusted Edgewise Appliance System.

PubMed

Singh, Harpreet; Maurya, Raj Kumar; Thakkar, Surbhi

2016-12-01

Complete transposition of teeth is a rather rare phenomenon. After correction of transposed and malaligned lateral incisor and canine, attainment of appropriate individual antagonistic tooth torque is indispensable, which many orthodontists consider to be a herculean task. Here, a novel method is proposed which demonstrates the use of Spec reverse torquing auxillary as an effective adjunctive aid in conjunction with pre-adjusted edgewise brackets.

Active site nanospace of aminoacyl tRNA synthetase: difference between the class I and class II synthetases.

PubMed

Dutta, Saheb; Choudhury, Kaberi; Banik, Sindrila Dutta; Nandi, Nilashis

2014-03-01

The present work is aimed at understanding the origin of the difference in the molecular organization of the active site nanospaces of the class I and class II aminoacyl tRNA synthetases (aaRSs) which are tunnel-like structures. The active site encloses the cognate amino acid (AA) and the adenosine triphosphate (ATP) to carry out aminoacylation reaction. Comparison of the structures of the active site of the class I and class II (aaRSs) shows that the nanodimensional tunnels are curved in opposite directions in the two classes. We investigated the origin of this difference using quantum mechanical computation of electrostatic potential (ESP) of substrates, surrounding residues and ions, using Atoms in Molecule (AIM) Theory and charge population analysis. We show that the difference is principally due to the variation in the spatial charge distribution of ATP in the two classes which correspond to extended and bent conformations of ATP. The present computation shows that the most feasible pathway for nucleophilic attack to alphaP is oppositely directed for class I and class II aaRSs. The available crystal structures show that the cognate AA is indeed located along the channel favorable for nucleophilic attack as predicted by the ESP analysis. It is also shown that the direction of the channel changes its orientation when the orientation of ATP is changed from extended to a bent like structure. We further used the AIM theory to confirm the direction of the approach of AA in each case and the results corroborate the results from the ESP analysis. The opposite curvatures of the active site nanospaces in class I and class II aaRSs are related with the influence of the charge distributions of the extended and bent conformations of ATP, respectively. The results of the computation of electrostatic potential by successive addition of active site residues show that their roles on the reaction are similar in both classes despite the difference in the organization of the active sites of class I and class II aaRSs. The difference in mechanism in two classes as pointed out in recent study (S. Dutta Banik and N. Nandi, J. Biomol. Struct. Dyn. 30, 701 (2012)) is related with the fact that the relative arrangement of the ATP with respect to the AA is opposite in class I and class II aaRSs as explained in the present work. The charge population difference between the reacting centers (which are the alphaP atom of ATP (q(p)) and the attacking oxygen atom of carboxylic acid group (q(o)), respectively) denoted by delta(q), is a measure of the propensity of nucleophilic attack. The population analysis of the substrate AA shows that a non-negligible difference exists between the attacking oxygens of AA in class I (syn) and in class II (anti) which is one reason for the lower value of delta(q) in class II relative to class I. The population analysis of the AA, ATP, Mg+2 ions and active site residues shows that the difference in delta(q) values of the two classes is substantially reduced. When ions and residues are considered. Thus, the bent state of ATP, Mg+2 ions and active site residues complements it cognate AA to carry out the nucleophilic reaction in class I as efficiently as occurs in class I (with the extended state of ATP, single Mg+2 ion and active site residues). This could be one reason for the two different conformations of ATP in the two classes. The mutual arrangements of AA and ATP in each aaRS are guided by the spatial charge distribution of ATP (extended and bent). The present work shows that the construction of nanospace complements the arrangement of the substrate (AA and ATP).

Colonization of heterochromatic genes by transposable elements in Drosophila.

PubMed

Dimitri, Patrizio; Junakovic, Nikolaj; Arcà, Bruno

2003-04-01

As a further step toward understanding transposable element-host genome interactions, we investigated the molecular anatomy of introns from five heterochromatic and 22 euchromatic protein-coding genes of Drosophila melanogaster. A total of 79 kb of intronic sequences from heterochromatic genes and 355 kb of intronic sequences from euchromatic genes have been used in Blast searches against Drosophila transposable elements (TEs). The results show that TE-homologous sequences belonging to 19 different families represent about 50% of intronic DNA from heterochromatic genes. In contrast, only 0.1% of the euchromatic intron DNA exhibits homology to known TEs. Intraspecific and interspecific size polymorphisms of introns were found, which are likely to be associated with changes in TE-related sequences. Together, the enrichment in TEs and the apparent dynamic state of heterochromatic introns suggest that TEs contribute significantly to the evolution of genes located in heterochromatin.

[Active miniature inverted-repeat transposable elements transposon in plants: a review].

PubMed

Hu, Bingjie; Zhou, Mingbing

2018-02-25

Miniature inverted-repeat transposable elements transposon is a special transposon that could transpose by "cut-paste" mechanism, which is one of characteristics of DNA transposons. Otherwise, the copy number of MITEs is very high, which is one of characteristics of RNA transposons. Many MITE families have been reported, but little about active MITEs. We summarize recent advances in studying active MITEs. Most the MITEs belong to the Tourist-like family, such as mPing, mGing, PhTourist1, Tmi1 and PhTst-3. Additionally, DTstu1 and MITE-39 belong to Stowaway-like family, and AhMITEs1 belongs to Mutator-like family. Moreover, we summarize the structure (terminal inverse repeats and target site duplications), copy number, evolution pattern and transposition characteristics of these active MITEs, to provide the foundation for the identification of other active MITEs and subsequent research on MITE transposition and amplification mechanism.

Partial transpose of random quantum states: Exact formulas and meanders

NASA Astrophysics Data System (ADS)

Fukuda, Motohisa; Śniady, Piotr

2013-04-01

We investigate the asymptotic behavior of the empirical eigenvalues distribution of the partial transpose of a random quantum state. The limiting distribution was previously investigated via Wishart random matrices indirectly (by approximating the matrix of trace 1 by the Wishart matrix of random trace) and shown to be the semicircular distribution or the free difference of two free Poisson distributions, depending on how dimensions of the concerned spaces grow. Our use of Wishart matrices gives exact combinatorial formulas for the moments of the partial transpose of the random state. We find three natural asymptotic regimes in terms of geodesics on the permutation groups. Two of them correspond to the above two cases; the third one turns out to be a new matrix model for the meander polynomials. Moreover, we prove the convergence to the semicircular distribution together with its extreme eigenvalues under weaker assumptions, and show large deviation bound for the latter.

Read count-based method for high-throughput allelic genotyping of transposable elements and structural variants.

PubMed

Kuhn, Alexandre; Ong, Yao Min; Quake, Stephen R; Burkholder, William F

2015-07-08

Like other structural variants, transposable element insertions can be highly polymorphic across individuals. Their functional impact, however, remains poorly understood. Current genome-wide approaches for genotyping insertion-site polymorphisms based on targeted or whole-genome sequencing remain very expensive and can lack accuracy, hence new large-scale genotyping methods are needed. We describe a high-throughput method for genotyping transposable element insertions and other types of structural variants that can be assayed by breakpoint PCR. The method relies on next-generation sequencing of multiplex, site-specific PCR amplification products and read count-based genotype calls. We show that this method is flexible, efficient (it does not require rounds of optimization), cost-effective and highly accurate. This method can benefit a wide range of applications from the routine genotyping of animal and plant populations to the functional study of structural variants in humans.

Transposition of the maize transposable element Ac in barley (Hordeum vulgare L.).

PubMed

Scholz, S; Lörz, H; Lütticke, S

2001-01-01

Transposition of the maize autonomous element Ac (Activator) was investigated in barley (Hordeum vulgare L.) with the aim of developing a transposon tagging system for the latter. The Ac element was introduced into meristematic tissue of barley by microprojectile bombardment. Transposon activity was then examined in the resulting transgenic plants. Multiple excision events were detected in leaf tissue of all plant lines. The mobile elements generated empty donor sites with small DNA sequence alterations, similar to those found in maize. Reintegration of Ac at independent genomic loci in somatic tissue was demonstrated by isolation of new element-flanking regions by AIMS-PCR (amplification of insertion-mutagenized sites). In addition, transmission of transposed Ac elements to progeny plants was confirmed. The results indicate that the introduced Ac element is able to transpose in barley. This is a first step towards the establishment of a transposon tagging system in this economically important crop.

A WISE CENSUS OF YOUNG STELLAR OBJECTS IN CANIS MAJOR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fischer, William J.; Padgett, Deborah L.; Sewiło, Marta

With the Wide-field Infrared Survey Explorer (WISE), we searched for young stellar objects (YSOs) in a 100 deg{sup 2} region centered on the lightly studied Canis Major star-forming region. Applying stringent magnitude cuts to exclude the majority of extragalactic contaminants, we find 144 Class I candidates and 335 Class II candidates. The sensitivity to Class II candidates is limited by their faintness at the distance to Canis Major (assumed as 1000 pc). More than half the candidates (53%) are found in 16 groups of more than four members, including four groups with more than 25 members each. The ratio ofmore » Class II to Class I objects, N {sub II}/ N {sub I}, varies from 0.4 to 8.3 in just the largest four groups. We compare our results to those obtainable with combined Two Micron All Sky Survey and post-cryogenic Spitzer Space Telescope data; the latter approach recovers missing Class II sources. Via a comparison to protostars characterized with the Herschel Space Observatory , we propose new WISE color criteria for flat-spectrum and Class 0 protostars, finding 80 and 7 of these, respectively. The distribution of YSOs in CMa OB1 is consistent with supernova-induced star formation, although the diverse N {sub II}/ N {sub I} ratios are unexpected if this parameter traces age and the YSOs are due to the same supernova. Less massive clouds feature larger N {sub II}/ N {sub I} ratios, suggesting that initial conditions play a role in determining this quantity.« less

Star Formation and Young Population of the H II Complex Sh2-294

NASA Astrophysics Data System (ADS)

Samal, M. R.; Pandey, A. K.; Ojha, D. K.; Chauhan, N.; Jose, J.; Pandey, B.

2012-08-01

The Sh2-294 H II region ionized by a single B0V star features several infrared excess sources, a photodissociation region, and also a group of reddened stars at its border. The star formation scenario in this region seems to be quite complex. In this paper, we present follow-up results of Sh2-294 H II region at 3.6, 4.5, 5.8, and 8.0 μm observed with the Spitzer Space Telescope Infrared Array Camera (IRAC), coupled with H2 (2.12 μm) observation, to characterize the young population of the region and to understand its star formation history. We identified 36 young stellar object (YSO, Class I, Class II, and Class I/II) candidates using IRAC color-color diagrams. It is found that Class I sources are preferentially located at the outskirts of the H II region and associated with enhanced H2 emission; none of them are located near the central cluster. Combining the optical to mid-infrared (MIR) photometry of the YSO candidates and using the spectral energy distribution fitting models, we constrained stellar parameters and the evolutionary status of 33 YSO candidates. Most of them are interpreted by the model as low-mass (<4 M ⊙) YSOs; however, we also detected a massive YSO (~9 M ⊙) of Class I nature, embedded in a cloud of visual extinction of ~24 mag. Present analysis suggests that the Class I sources are indeed a younger population of the region relative to Class II sources (age ~ 4.5 × 106 yr). We suggest that the majority of the Class I sources, including the massive YSOs, are second-generation stars of the region whose formation is possibly induced by the expansion of the H II region powered by a ~4 × 106 yr B0 main-sequence star.

Hyperhidrosis: Anatomy, Pathophysiology and Treatment with Emphasis on the Role of Botulinum Toxins

PubMed Central

Lakraj, Amanda-Amrita D.; Moghimi, Narges; Jabbari, Bahman

2013-01-01

Clinical features, anatomy and physiology of hyperhidrosis are presented with a review of the world literature on treatment. Level of drug efficacy is defined according to the guidelines of the American Academy of Neurology. Topical agents (glycopyrrolate and methylsulfate) are evidence level B (probably effective). Oral agents (oxybutynin and methantheline bromide) are also level B. In a total of 831 patients, 1 class I and 2 class II blinded studies showed level B efficacy of OnabotulinumtoxinA (A/Ona), while 1 class I and 1 class II study also demonstrated level B efficacy of AbobotulinumtoxinA (A/Abo) in axillary hyperhidrosis (AH), collectively depicting Level A evidence (established) for botulinumtoxinA (BoNT-A). In a comparator study, A/Ona and A/Inco toxins demonstrated comparable efficacy in AH. For IncobotulinumtoxinA (A/Inco) no placebo controlled studies exist; thus, efficacy is Level C (possibly effective) based solely on the aforementioned class II comparator study. For RimabotulinumtoxinB (B/Rima), one class III study has suggested Level U efficacy (insufficient data). In palmar hyperhidrosis (PH), there are 3 class II studies for A/Ona and 2 for A/Abo (individually and collectively level B for BoNT-A) and no blinded study for A/Inco (level U). For B/Rima the level of evidence is C (possibly effective) based on 1 class II study. Botulinum toxins (BoNT) provide a long lasting effect of 3–9 months after one injection session. Studies on BoNT-A iontophoresis are emerging (2 class II studies; level B); however, data on duration and frequency of application is inconsistent. PMID:23612753

HLA-typing analysis following allogeneic bone grafting for sinus lifting.

PubMed

Piaia, Marcelo; Bub, Carolina Bonet; Succi, Guilherme de Menezes; Torres, Margareth; Costa, Thiago Henrique; Pinheiro, Fabricio Costa; Napimoga, Marcelo Henrique

2017-03-01

According to the Brazilian Association of Organ Transplants, in 2015, 19,408 bone transplants were performed in Brazil, over 90% by Dental Surgeons. The surgical technique itself has a respectable number of reports regarding its clinical efficacy, as measured by long-term survival of dental implants in grafted areas. Uncertainty remains, however, as to whether fresh frozen grafts from human bone donors remain immunologically innocuous in the body of the host. Six male with no previous medical history of note, including systemic diseases, surgery or blood transfusion were selected. These patients underwent reconstructive procedures (sinus lifting) using fresh frozen human bone from a tissue bank. All patients had venous blood samples collected prior to surgery and 6 months after the procedure. Anti-HLA analysis for the detection of HLA (human leukocyte antigen) antibodies was performed using methods such as the LABScreen PRA Class I and Class II, LABScreen Single Antigen Class I and Class II, Luminex Platform. Reactive individuals to the screening tests (LABScreen PRA) were further investigated to determine the specificity of the antibodies detected (LABScreen Single Antigen) with a cutoff value of median fluorescence intensity ≥500. As a result, it was observed that two patients (33%) were positive in screening tests, one presenting with anti-HLA Class I and II sensitization and the other with anti-HLA class II. The specificity analysis showed that the patients sensitized to HLA class II presented 4 specificities, 3 of which immunologically relevant. In the second individual, 23 specificities were identified, 6 of which immunologically important for HLA class I and 4 specificities for HLA class II, 3 of these were immunologically important. All specificities detected had average fluorescence. These findings are suggestive that sinus-lifting procedures with allogeneic bone can induce immunological sensitization.

Modified Angle's Classification for Primary Dentition

PubMed Central

Chandranee, Kaushik Narendra; Chandranee, Narendra Jayantilal; Nagpal, Devendra; Lamba, Gagandeep; Choudhari, Purva; Hotwani, Kavita

2017-01-01

Aim: This study aims to propose a modification of Angle's classification for primary dentition and to assess its applicability in children from Central India, Nagpur. Methods: Modification in Angle's classification has been proposed for application in primary dentition. Small roman numbers i/ii/iii are used for primary dentition notation to represent Angle's Class I/II/III molar relationships as in permanent dentition, respectively. To assess applicability of modified Angle's classification a cross-sectional preschool 2000 children population from central India; 3–6 years of age residing in Nagpur metropolitan city of Maharashtra state were selected randomly as per the inclusion and exclusion criteria. Results: Majority 93.35% children were found to have bilateral Class i followed by 2.5% bilateral Class ii and 0.2% bilateral half cusp Class iii molar relationships as per the modified Angle's classification for primary dentition. About 3.75% children had various combinations of Class ii relationships and 0.2% children were having Class iii subdivision relationship. Conclusions: Modification of Angle's classification for application in primary dentition has been proposed. A cross-sectional investigation using new classification revealed various 6.25% Class ii and 0.4% Class iii molar relationships cases in preschool children population in a metropolitan city of Nagpur. Application of the modified Angle's classification to other population groups is warranted to validate its routine application in clinical pediatric dentistry. PMID:29326514

MHC class II-assortative mate choice in European badgers (Meles meles).

PubMed

Sin, Yung Wa; Annavi, Geetha; Newman, Chris; Buesching, Christina; Burke, Terry; Macdonald, David W; Dugdale, Hannah L

2015-06-01

The major histocompatibility complex (MHC) plays a crucial role in the immune system, and in some species, it is a target by which individuals choose mates to optimize the fitness of their offspring, potentially mediated by olfactory cues. Under the genetic compatibility hypothesis, individuals are predicted to choose mates with compatible MHC alleles, to increase the fitness of their offspring. Studies of MHC-based mate choice in wild mammals are under-represented currently, and few investigate more than one class of MHC genes. We investigated mate choice based on the compatibility of MHC class I and II genes in a wild population of European badgers (Meles meles). We also investigated mate choice based on microsatellite-derived pairwise relatedness, to attempt to distinguish MHC-specific effects from genomewide effects. We found MHC-assortative mating, based on MHC class II, but not class I genes. Parent pairs had smaller MHC class II DRB amino acid distances and smaller functional distances than expected from random pairings. When we separated the analyses into within-group and neighbouring-group parent pairs, only neighbouring-group pairs showed MHC-assortative mating, due to similarity at MHC class II loci. Our randomizations showed no evidence of genomewide-based inbreeding, based on 35 microsatellite loci; MHC class II similarity was therefore the apparent target of mate choice. We propose that MHC-assortative mate choice may be a local adaptation to endemic pathogens, and this assortative mate choice may have contributed to the low MHC genetic diversity in this population. © 2015 The Authors. Molecular Ecology published by John Wiley & Sons Ltd.

Characterization of MHC class I and II genes in a subantarctic seabird, the blue petrel, Halobaena caerulea (Procellariiformes).

PubMed

Strandh, Maria; Lannefors, Mimi; Bonadonna, Francesco; Westerdahl, Helena

2011-10-01

The great polymorphism observed in the major histocompatibility complex (MHC) genes is thought to be maintained by pathogen-mediated selection possibly combined with MHC-disassortative mating, guided by MHC-determined olfactory cues. Here, we partly characterize the MHC class I and II B of the blue petrel, Halobaena caerulea (Procellariiformes), a bird with significant olfactory abilities that lives under presumably low pathogen burdens in Subantarctica. Blue petrels are long-lived, monogamous birds which suggest the necessity of an accurate mate choice process. The species is ancestral to songbirds (Passeriformes; many MHC loci), although not to gamefowls (Galliformes; few MHC loci). Considering the phylogenetic relationships and the low subantarctic pathogen burden, we expected few rather than many MHC loci in the blue petrel. However, when we analysed partial MHC class I and class II B cDNA and gDNA sequences we found evidence for as many as at least eight MHC class I loci and at least two class II B loci. These class I and II B sequences showed classical MHC characteristics, e.g. high nucleotide diversity, especially in putative peptide-binding regions where signatures of positive selection was detected. Trans-species polymorphism was found between MHC class II B sequences of the blue petrel and those of thin-billed prion, Pachyptila belcheri, two species that diverged ∼25 MYA. The observed MHC allele richness in the blue petrel may well serve as a basis for mate choice, especially since olfactory discrimination of MHC types may be possible in this species.

77 FR 43861 - Importer of Controlled Substances; Notice Of Application; Cody Laboratories, Inc.

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-26

... basic class of any controlled substance in schedule I or II are, and will continue to be, required to... importer of the following basic classes of controlled substances: Drug Schedule Opium, Raw (9600) II Concentrate Poppy Straw (9670) II Tapentadol (9780) II The company plans to import narcotic raw materials for...

The effects of forehead and neck position on esthetics of class I, II and III profiles.

PubMed

Salehi, Parisa; Oshagh, Morteza; Aleyasin, Zeinab S; Pakshir, Hamid Reza

2014-01-01

All parts of the face, other than jaw relationships, should be considered in orthodontic treatment planning. The role of forehead and neck in facial esthetics is well known; however, the majority of conventional facial analysis methods have not considered them. Neck and forehead may confer mutual effects on equilibrium and on esthetics of other facial components, and may change the overall convexity/concavity view of the profile. Therefore, the aim of this study was to assess the effect of anteroposterior position of the forehead and neck on the esthetics of skeletal class I, II and III jaw relationships using profile silhouettes. Class II and III jaw relationships were constructed on the silhouette of a class I normal profile by altering the mandibular position. Retruded, normal and protruded positions were also applied for the forehead and neck. Three hundred Iranian laypeople (150 men, 150 women) scored the esthetics of profile silhouettes from 1 to 7. Half of the participants were told to consider the profiles as a man, and the other half were told to consider them as a woman. Data were analyzed using non-parametric methods. Class I jaw relation was found to be the most beautiful profile followed by class II and III respectively. Esthetics of different positions of the neck and forehead were significantly different (P < 0.05). In subjects with a normal neck and forehead position, and those with a retruded neck, the best esthetic relationship was class I, and the worst was class III. For protruded foreheads, the best jaw relationship was class II for females and class I for males, and the worst was class III for both. In a retruded forehead position, the most preferred jaw relationship was class I, and the worst was class II. For profiles with a protruded neck, the best esthetics was found to be in class III jaw relationship, and the worst was in class II. There was a small difference in scoring for male and female profiles (P < 0.05); there were also small differences in scoring trends of men and women (P < 0.05). This study showed that the anteroposterior position of the forehead and neck affects the esthetics of jaw relationships in profile view. In laypeople's opinions, in a normal profile, the overall appearance is more important compared to the independent position of the neck and forehead; however, having jaw abnormalities, the neck plays an important independent role. The preferred jaw relation for profiles with each forehead or neck position was introduced.

NLRC5: a key regulator of MHC class I-dependent immune responses.

PubMed

Kobayashi, Koichi S; van den Elsen, Peter J

2012-12-01

The expression of MHC class I molecules is crucial for the initiation and regulation of adaptive immune responses against pathogens. NOD-, LRR- and CARD-containing 5 (NLRC5) was recently identified as a specific transactivator of MHC class I genes (CITA). NLRC5 and the master regulator for MHC class II genes, class II transactivator (CIITA), interact with similar MHC promoter-bound factors. Here, we provide a broad overview of the molecular mechanisms behind MHC class I transcription and the role of the class I transactivator NLRC5 in MHC class I-dependent immune responses.

[Study on the difference of corresponding age at cervical vertebral maturation stages among different skeletal malocclusions].

PubMed

Zuo, Changyan; Cong, Chao; Wang, Shihui; Gu, Yan

2015-10-01

To compare the difference of corresponding age at cervical vertebral maturation (CVM) stages among different skeletal malocclusions and provide clinic guideline on optimal treatment timing for skeletal malocclusion. Based on ANB angle, 2 575 cephalograms collected from Department of Orthodontics, Peking University School and Hospital of Stomatology from May, 2006 to November, 2014 were classified into skeletal Class I (ANB 0°~5°, 1 317 subjects), Class II (ANB > 5°, 685 subjects) and Class III (ANB < 0°, 573 subjects) groups. CVM stages were evaluated with the modified version of CVM method. Independent sample t test was performed to analyze the difference of age at different CVM stages among various skeletal groups. Significant gender difference of age was found at CS3 to CS6 for skeletal Class I group (P < 0.05), at CS5 and CS6 for skeletal Class II group (P < 0.05), and at CS3 and CS5 for skeletal Class III group (P < 0.05). At CS3 stage, the average age of male in skeletal Class II and skeletal Class III groups was (11.6 ± 1.5) years old and (10.3 ± 1.9) years old, respectively; the average age of females in those two groups was (11.7 ± 1.3) years old and (9.3 ± 1.5) years old, respectively, and significant difference was found in both comparisons (P < 0.05). Compared average age at CS5 and CS6 between skeletal Class II and skeletal Class III groups [the ages of male was (15.1 ± 1.7) and (16.8 ± 1.6) years old, the ages of male was (14.6 ± 1.2) and (15.7 ± 2.5) years old], significant difference was also found (P < 0.05). Significant gender differences were found when evaluated CVM stage and age in skeletal Class I, II and III groups. Significant differences of age at different CVM stage was noted when skeletal Class II was compared with skeletal Class III groups.

[Morphological analysis of alveolar bone of anterior mandible in high-angle skeletal class II and class III malocclusions assessed with cone-beam computed tomography].

PubMed

Ma, J; Jiang, J H

2018-02-18

To evaluate the difference of features of alveolar bone support under lower anterior teeth between high-angle adults with skeletal class II malocclusions and high-angle adults presenting skeletal class III malocclusions by using cone-beam computed tomography (CBCT). Patients who had taken the images of CBCT were selected from the Peking University School and Hospital of Stomatology between October 2015 and August 2017. The CBCT archives from 62 high-angle adult cases without orthodontic treatment were divided into two groups based on their sagittal jaw relationships: skeletal class II and skeletal class III. vertical bone level (VBL), alveolar bone area (ABA), and the width of alveolar bone were measured respectively at the 2 mm, 4 mm, 6 mm below the cemento-enamel junction (CEJ) level and at the apical level. After that, independent samples t-tests were conducted for statistical comparisons. The ABA of the mandibular alveolar bone in the area of lower anterior teeth was significantly thinner in the patients of skeletal class III than those of skeletal class II, especially in terms of the apical ABA, total ABA on the labial and lingual sides and the ABA at 6 mm below CEJ level on the lingual side (P<0.05). The thickness of the alveolar bone of mandibular anterior teeth was significantly thinner in the subjects of skeletal class III than those of skeletal class II, especially regarding the apical level on the labial and lingual side and at the level of 4 mm, 6 mm below CEJ level on the lingual side (P<0.05). The ABA and the thickness of the alveolar bone of mandibular anterior teeth were significantly thinner in the group of skeletal class III adult patients with high-angle when compared with the sample of high-angle skeletal class II adult cases. We recommend orthodontists to be more cautious in treatment of high-angle skeletal class III patients, especially pay attention to control the torque of lower anterior teeth during forward and backward movement, in case that the apical root might be absorbed or fenestration happen in the area of lower anterior teeth.

40 CFR 147.3106 - Area of review.

Code of Federal Regulations, 2014 CFR

2014-07-01

... chapter, the fixed radius shall be no less than one mile for Class I wells and one-half mile for Class II... under § 146.6(b) shall be a fixed width of not less than one mile for the circumscribing area of Class I projects and one-half mile for the circumscribing area of Class II and III projects. (b) However, in lieu...

40 CFR 147.3106 - Area of review.

Code of Federal Regulations, 2012 CFR

2012-07-01

... chapter, the fixed radius shall be no less than one mile for Class I wells and one-half mile for Class II... under § 146.6(b) shall be a fixed width of not less than one mile for the circumscribing area of Class I projects and one-half mile for the circumscribing area of Class II and III projects. (b) However, in lieu...

40 CFR 147.3106 - Area of review.

Code of Federal Regulations, 2013 CFR

2013-07-01

... chapter, the fixed radius shall be no less than one mile for Class I wells and one-half mile for Class II... under § 146.6(b) shall be a fixed width of not less than one mile for the circumscribing area of Class I projects and one-half mile for the circumscribing area of Class II and III projects. (b) However, in lieu...

25 CFR 290.11 - May an Indian tribe distribute per capita payments from net gaming revenues derived from either...

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false May an Indian tribe distribute per capita payments from net gaming revenues derived from either Class II or Class III gaming without a tribal revenue... net gaming revenues derived from either Class II or Class III gaming without a tribal revenue...

Arabidopsis Class I and Class II TCP Transcription Factors Regulate Jasmonic Acid Metabolism and Leaf Development Antagonistically1[C][W

PubMed Central

Danisman, Selahattin; van der Wal, Froukje; Dhondt, Stijn; Waites, Richard; de Folter, Stefan; Bimbo, Andrea; van Dijk, Aalt DJ; Muino, Jose M.; Cutri, Lucas; Dornelas, Marcelo C.; Angenent, Gerco C.; Immink, Richard G.H.

2012-01-01

TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) transcription factors control developmental processes in plants. The 24 TCP transcription factors encoded in the Arabidopsis (Arabidopsis thaliana) genome are divided into two classes, class I and class II TCPs, which are proposed to act antagonistically. We performed a detailed phenotypic analysis of the class I tcp20 mutant, showing an increase in leaf pavement cell sizes in 10-d-old seedlings. Subsequently, a glucocorticoid receptor induction assay was performed, aiming to identify potential target genes of the TCP20 protein during leaf development. The LIPOXYGENASE2 (LOX2) and class I TCP9 genes were identified as TCP20 targets, and binding of TCP20 to their regulatory sequences could be confirmed by chromatin immunoprecipitation analyses. LOX2 encodes for a jasmonate biosynthesis gene, which is also targeted by class II TCP proteins that are under the control of the microRNA JAGGED AND WAVY (JAW), although in an antagonistic manner. Mutation of TCP9, the second identified TCP20 target, resulted in increased pavement cell sizes during early leaf developmental stages. Analysis of senescence in the single tcp9 and tcp20 mutants and the tcp9tcp20 double mutants showed an earlier onset of this process in comparison with wild-type control plants in the double mutant only. Both the cell size and senescence phenotypes are opposite to the known class II TCP mutant phenotype in JAW plants. Altogether, these results point to an antagonistic function of class I and class II TCP proteins in the control of leaf development via the jasmonate signaling pathway. PMID:22718775

Genomic relationship between SINE retrotransposons, Pol III–Pol II transcription, and chromatin organization: the journey from junk to jewel

PubMed Central

Lunyak, Victoria V.; Atallah, Michelle

2013-01-01

A typical eukaryotic genome harbors a rich variety of repetitive elements. The most abundant are retrotransposons, mobile retroelements that utilize reverse transcriptase and an RNA intermediate to relocate to a new location within the cellular genomes. A vast majority of the repetitive mammalian genome content has originated from the retrotransposition of SINE (100–300 bp short interspersed nuclear elements that are derived from the structural 7SL RNA or tRNA), LINE (7kb long interspersed nuclear element), and LTR (2–3 kb long terminal repeats) transposable element superfamilies. Broadly labeled as “evolutionary junkyard” or “fossils”, this enigmatic “dark matter” of the genome possesses many yet to be discovered properties. PMID:21916613

Rational Design Synthesis and Evaluation of New Selective Inhibitors of Microbial Class II (Zinc Dependent) Fructose Bis-phosphate Aldolases

DOE Office of Scientific and Technical Information (OSTI.GOV)

R Daher; M Coincon; M Fonvielle

2011-12-31

We report the synthesis and biochemical evaluation of several selective inhibitors of class II (zinc dependent) fructose bis-phosphate aldolases (Fba). The products were designed as transition-state analogues of the catalyzed reaction, structurally related to the substrate fructose bis-phosphate (or sedoheptulose bis-phosphate) and based on an N-substituted hydroxamic acid, as a chelator of the zinc ion present in active site. The compounds synthesized were tested on class II Fbas from various pathogenic microorganisms and, by comparison, on a mammalian class I Fba. The best inhibitor shows Ki against class II Fbas from various pathogens in the nM range, with very highmore » selectivity (up to 105). Structural analyses of inhibitors in complex with aldolases rationalize and corroborate the enzymatic kinetics results. These inhibitors represent lead compounds for the preparation of new synthetic antibiotics, notably for tuberculosis prophylaxis.« less

Comparison of Maxilla Mandibular Transverse Ratios With Class II Anteroposterior Discrepancies

DTIC Science & Technology

2014-03-20

the structure points has shown to be at best unreliable (Jacobson 1995). “2D landmarks may be hindered by rotational, geometric , and head positioning...deficiency in Class II and Class III malocclusions: a cephalometric and morphometric study on postero‐ anterior films. Orthodontics & Craniofacial

Spec Rekindled-A Simple Torque Correction Mechanics for Transposed Teeth in Conjunction with Pre-adjusted Edgewise Appliance System

PubMed Central

Singh, Harpreet; Thakkar, Surbhi

2016-01-01

Complete transposition of teeth is a rather rare phenomenon. After correction of transposed and malaligned lateral incisor and canine, attainment of appropriate individual antagonistic tooth torque is indispensable, which many orthodontists consider to be a herculean task. Here, a novel method is proposed which demonstrates the use of Spec reverse torquing auxillary as an effective adjunctive aid in conjunction with pre-adjusted edgewise brackets. PMID:28209017

Satellite DNA and Transposable Elements in Seabuckthorn (Hippophae rhamnoides), a Dioecious Plant with Small Y and Large X Chromosomes.

PubMed

Puterova, Janka; Razumova, Olga; Martinek, Tomas; Alexandrov, Oleg; Divashuk, Mikhail; Kubat, Zdenek; Hobza, Roman; Karlov, Gennady; Kejnovsky, Eduard

2017-01-01

Seabuckthorn (Hippophae rhamnoides) is a dioecious shrub commonly used in the pharmaceutical, cosmetic, and environmental industry as a source of oil, minerals and vitamins. In this study, we analyzed the transposable elements and satellites in its genome. We carried out Illumina DNA sequencing and reconstructed the main repetitive DNA sequences. For data analysis, we developed a new bioinformatics approach for advanced satellite DNA analysis and showed that about 25% of the genome consists of satellite DNA and about 24% is formed of transposable elements, dominated by Ty3/Gypsy and Ty1/Copia LTR retrotransposons. FISH mapping revealed X chromosome-accumulated, Y chromosome-specific or both sex chromosomes-accumulated satellites but most satellites were found on autosomes. Transposable elements were located mostly in the subtelomeres of all chromosomes. The 5S rDNA and 45S rDNA were localized on one autosomal locus each. Although we demonstrated the small size of the Y chromosome of the seabuckthorn and accumulated satellite DNA there, we were unable to estimate the age and extent of the Y chromosome degeneration. Analysis of dioecious relatives such as Shepherdia would shed more light on the evolution of these sex chromosomes. © The Author(s) 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

DNA methylation dynamics during early plant life.

PubMed

Bouyer, Daniel; Kramdi, Amira; Kassam, Mohamed; Heese, Maren; Schnittger, Arp; Roudier, François; Colot, Vincent

2017-09-25

Cytosine methylation is crucial for gene regulation and silencing of transposable elements in mammals and plants. While this epigenetic mark is extensively reprogrammed in the germline and early embryos of mammals, the extent to which DNA methylation is reset between generations in plants remains largely unknown. Using Arabidopsis as a model, we uncovered distinct DNA methylation dynamics over transposable element sequences during the early stages of plant development. Specifically, transposable elements and their relics show invariably high methylation at CG sites but increasing methylation at CHG and CHH sites. This non-CG methylation culminates in mature embryos, where it reaches saturation for a large fraction of methylated CHH sites, compared to the typical 10-20% methylation level observed in seedlings or adult plants. Moreover, the increase in CHH methylation during embryogenesis matches the hypomethylated state in the early endosperm. Finally, we show that interfering with the embryo-to-seedling transition results in the persistence of high CHH methylation levels after germination, specifically over sequences that are targeted by the RNA-directed DNA methylation (RdDM) machinery. Our findings indicate the absence of extensive resetting of DNA methylation patterns during early plant life and point instead to an important role of RdDM in reinforcing DNA methylation of transposable element sequences in every cell of the mature embryo. Furthermore, we provide evidence that this elevated RdDM activity is a specific property of embryogenesis.

Prevalence of vulvovaginitis and relation to physical findings in girls assessed for suspected child sexual abuse.

PubMed

Rahman, Gisel; Ocampo, Dolores; Rubinstein, Anahí; Risso, Paula

2015-10-01

The presence of sexually transmitted infections (STIs) in patients with suspected sexual abuse is uncommon in the field of pediatrics. To establish the prevalence of anogenital findings and their relation to the presence of STIs in girls referred for suspected child sexual abuse. Retrospective study conducted between January 1st, 2003 and December 31st, 2013. Physical findings and detection of STIs in girls with suspected child sexual abuse were analyzed. One thousand thirty-four patients were included. Their median age was 7.9 years old. Anogenital findings were classified as class I (normal):38.4%, class II (nonspecific):38.1%, class III (specific):19.9% and class IV (definitive):3.6%. STIs were observed in 42 patients (4.1%). A relation was established between STIs and the classification of physical findings: 10 (class II: 9; class III: 1) Neisseria gonorrhoeae, 17 (class I: 2; class II: 8; class III: 7) Chlamydia trachomatis, 15 (class I: 2; class II: 10; class III: 3) Trichomonas vaginalis. Statistically significant differences for Trichomonas vaginalis (p= 0.01) and Neisseria gonorrhoeae (p < 0.0001) were observed, with predominance of nonspecific clinical signs. Both nonspecific and specific findings were similarly observed for Chlamydia trachomatis (p= 0.03). Most cases of girls with suspected child sexual abuse had normal or nonspecific anogenital findings. The prevalence of STIs in these girls is low. Trichomonas vaginalis and Neisseria gonorrhoeae were related to nonspecific findings, while both nonspecific and specific findings were observed for Chlamydia trachomatis.

Expression of major histocompatibility complex class II and costimulatory molecules in oral carcinomas in vitro.

PubMed

Villarroel-Dorrego, Mariana; Speight, Paul M; Barrett, A William

2005-01-01

Recognition in the 1980 s that keratinocytes can express class II molecules of the Major Histocompatibility Complex (MHC) first raised the possibility that these cells might have an immunological function, and may even act as antigen presenting cells (APC). For effective T lymphocyte activation, APC require, in addition to MHC II, appropriate costimulatory signals. The aim of this study was to determine the expression of MHC class II and the co-stimulatory molecules CD40, CD80 and CD86 in keratinocytes derived from healthy oral mucosa and oral carcinomas. Using flow cytometry, it was confirmed that oral keratinocytes, switch on, expression of MHC class II molecules after stimulation with IFNgamma in vitro. All keratinocyte lines expressed CD40 constitutively; by contrast, CD80 and CD86 were universally absent. Loss of CD80 and CD86 may be one means whereby tumours escape immunological surveillance.

14 CFR 61.107 - Flight proficiency.

Code of Federal Regulations, 2010 CFR

2010-01-01

...-engine class rating: (i) Preflight preparation; (ii) Preflight procedures; (iii) Airport and seaplane... lighter-than-air category rating with an airship class rating: (i) Preflight preparation; (ii) Preflight...

14 CFR 61.107 - Flight proficiency.

Code of Federal Regulations, 2013 CFR

2013-01-01

...-engine class rating: (i) Preflight preparation; (ii) Preflight procedures; (iii) Airport and seaplane... lighter-than-air category rating with an airship class rating: (i) Preflight preparation; (ii) Preflight...

14 CFR 61.107 - Flight proficiency.

Code of Federal Regulations, 2012 CFR

2012-01-01

...-engine class rating: (i) Preflight preparation; (ii) Preflight procedures; (iii) Airport and seaplane... lighter-than-air category rating with an airship class rating: (i) Preflight preparation; (ii) Preflight...

14 CFR 61.107 - Flight proficiency.

Code of Federal Regulations, 2011 CFR

2011-01-01

...-engine class rating: (i) Preflight preparation; (ii) Preflight procedures; (iii) Airport and seaplane... lighter-than-air category rating with an airship class rating: (i) Preflight preparation; (ii) Preflight...

14 CFR 61.107 - Flight proficiency.

Code of Federal Regulations, 2014 CFR

2014-01-01

...-engine class rating: (i) Preflight preparation; (ii) Preflight procedures; (iii) Airport and seaplane... lighter-than-air category rating with an airship class rating: (i) Preflight preparation; (ii) Preflight...

The major histocompatibility complex of tassel-eared squirrels. II. Genetic diversity associated with Abert squirrels.

PubMed

Wettstein, P J; States, J S

1986-01-01

The extent of polymorphism and the rate of divergence of class I and class II sequences mapping to the mammalian major histocompatibility complex (MHC) have been the subject of experimentation and speculation. To provide further insight into the evolution of the MHC we have initiated the analysis of two geographically isolated subspecies of tassel-eared squirrels. In the preceding communication we described the number and polymorphism of TSLA class I and class II sequences in Kaibab squirrels (S. aberti kaibabensis), which live north of the Grand Canyon. In this report we present a parallel analysis of Abert squirrels (S. aberti aberti), which live south of the Grand Canyon in northern Arizona. Genomic DNA from 12 Abert squirrels was digested with restriction enzymes, electrophoresed, blotted, and hybridized with DR alpha, DR beta, DQ alpha, DQ beta, and HLA-B7 probes. The results of these hybridizations were remarkably similar to those obtained in Kaibab squirrels. The majority of class I and class II bands were identical in size and number, suggesting that Abert and Kaibab squirrels have not significantly diverged in the TSLA complex despite their geographical separation. Relative polymorphism of class II sequences was similar to that observed with Kaibab squirrels: beta sequences exhibited higher polymorphism than alpha sequences. As in Kaibab squirrels, a number of alpha and beta sequences were apparently carried on the same fragments. In comparison to class II beta sequences, there was limited polymorphism in class I sequences, although a diverse number of class I genotypes were observed. Attempts to identify segregating TSLA haplotypes were futile in that the only families of sequences with concordant distributions were DQ alpha and DQ beta. These observations and those obtained with Kaibab squirrels suggest that the present-day TSLA haplotypes of both subspecies are derived from a limited number of common, progenitor haplotypes through repeated intra-TSLA recombination.

Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from M. tuberculosis

PubMed Central

Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

2014-01-01

Class II fructose 1,6-bisphosphate aldolases (FBA; E.C. 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff-base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs has been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies on class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation/deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI/DHAP bound form of the enzyme and determined the X-ray structure of MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information plus site-directed mutagenesis and kinetic studies conducted on a series of residues within the active-site loop revealed that E169 facilitates a water mediated deprotonation/protonation step of the MtFBA reaction mechanism. Also, secondary isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form. PMID:23298222

Antigenicity of mesenchymal stem cells in an inflamed joint environment.

PubMed

Hill, Jacqueline A; Cassano, Jennifer M; Goodale, Margaret B; Fortier, Lisa A

2017-07-01

OBJECTIVE To determine whether major histocompatability complex (MHC) class II expression in equine mesenchymal stem cells (MSCs) changes with exposure to a proinflammatory environment reflective of an inflamed joint. SAMPLE Cryopreserved bone marrow-derived MSCs from 12 horses and cartilage and synovium samples from 1 horse euthanized for reasons other than lameness. PROCEDURES In part 1 of a 3-part study, the suitability of a quantitative reverse transcriptase PCR (qRT-PCR) assay for measurement of MHC class II expression in MSCs following stimulation with interferon (IFN)-γ was assessed. In part 2, synoviocyte-cartilage cocultures were or were not stimulated with interleukin (IL)-1β (10 ng/mL) to generate conditioned media that did and did not (control) mimic an inflamed joint environment. In part 3, a qRT-PCR assay was used to measure MSC MHC class II expression after 96 hours of incubation with 1 of 6 treatments (control-conditioned medium, IL-1β-conditioned medium, and MSC medium alone [untreated control] or with IL-1β [10 ng/mL], tumor necrosis factor-α [10 ng/mL], or IFN-γ [100 ng/mL]). RESULTS The qRT-PCR assay accurately measured MHC class II expression. Compared with MHC class II expression for MSCs exposed to the untreated control medium, that for MSCs exposed to IL-1β was decreased, whereas that for MSCs exposed to IFN-γ was increased. Neither the control-conditioned nor tumor necrosis factor-α medium altered MHC class II expression. CONCLUSIONS AND CLINICAL RELEVANCE Results indicated that MSC exposure to proinflammatory cytokine IL-1β decreased MHC class II expression and antigenicity. Treatment of inflamed joints with allogeneic MSCs might not be contraindicated, but further investigation is warranted.

IL-10-dependent down-regulation of MHC class II expression level on monocytes by peritoneal fluid from endometriosis patients.

PubMed

Lee, Kyu-Sup; Baek, Dae-Won; Kim, Ki-Hyung; Shin, Byoung-Sub; Lee, Dong-Hyung; Kim, Ja-Woong; Hong, Young-Seoub; Bae, Yoe-Sik; Kwak, Jong-Young

2005-11-01

Endometriosis is a gynecologic disorder characterized by the ectopic growth of misplaced endometrial cells. Moreover, immunological abnormalities of cell-mediated and humoral immunity may be associated with the pathogenesis of endometriosis. The effects of peritoneal fluid (PF) from endometriosis patients on the expression levels of MHC class II and costimulatory molecules on the cell surfaces of monocytes were investigated. Compared to the PF of controls, the addition of 10% PF (n=10) from patients with endometriosis to culture medium significantly reduced the percentage of MHC class II-positive cells in cultures of a THP-1, monocytic cell line at 48 h. The effect of endometriosis patient PF (EPF) was dose-dependent, and similar effect was observed in peripheral blood monocytes. An inverse correlation was found between MHC class II expression level and IL-10 concentration in EPF (r=-0.518; p=0.019) and in the supernatant of peripheral blood monocyte cultured in EPF (r=-0.459; p=0.042) (n=20). The expression levels of costimulatory molecules (CD80 and CD86), but not of CD54 and B7-H1, were down-regulated by EPF. The mRNA level of HLA-DR was unaffected by EPF but protein level was reduced by EPF. Neutralizing IL-10 antibody abrogated MHC class II down-regulation on monocytes, which had been induced by EPF. However, in a functional assay, monocytes treated with EPF failed to stimulate T cell in mixed leukocyte reaction, although T cell proliferation was increased with EPF-treated monocytes and Staphylococcus enterotoxin B. These results suggest that MHC class II expression level on monocytes is down-regulated by EPF, but the cell stimulatory ability of monocytes does not coincide with MHC class II expression level.

Active site loop dynamics of a class IIa fructose 1,6-bisphosphate aldolase from Mycobacterium tuberculosis.

PubMed

Pegan, Scott D; Rukseree, Kamolchanok; Capodagli, Glenn C; Baker, Erica A; Krasnykh, Olga; Franzblau, Scott G; Mesecar, Andrew D

2013-02-05

Class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprise one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported, the structure of the active site loop responsible for catalyzing the protonation-deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA-PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation-protonation step of the MtFBA reaction mechanism. Also, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.

MHC Class II Activation and Interferon-γ Mediate the Inhibition of Neutrophils and Eosinophils by Staphylococcal Enterotoxin Type A (SEA).

PubMed

Ferreira-Duarte, Ana P; Pinheiro-Torres, Anelize S; Anhê, Gabriel F; Condino-Neto, Antônio; Antunes, Edson; DeSouza, Ivani A

2017-01-01

Staphylococcal enterotoxins are classified as superantigens that act by linking T-cell receptor with MHC class II molecules, which are expressed on classical antigen-presenting cells (APC). Evidence shows that MHC class II is also expressed in neutrophils and eosinophils. This study aimed to investigate the role of MHC class II and IFN-γ on chemotactic and adhesion properties of neutrophils and eosinophils after incubation with SEA. Bone marrow (BM) cells obtained from BALB/c mice were resuspended in culture medium, and incubated with SEA (3-30 ng/ml; 1-4 h), after which chemotaxis and adhesion were evaluated. Incubation with SEA significantly reduced the chemotactic and adhesive responses in BM neutrophils activated with IL-8 (200 ng/ml). Likewise, SEA significantly reduced the chemotactic and adhesive responses of BM eosinophils activated with eotaxin (300 ng/ml). The inhibitory effects of SEA on cell chemotaxis and adhesion were fully prevented by prior incubation with an anti-MHC class II blocking antibody (2 μg/ml). SEA also significantly reduced the intracellular Ca 2+ levels in IL-8- and eotaxin-activated BM cells. No alterations of MAC-1, VLA4, and LFA-1α expressions were observed after SEA incubation. In addition, SEA elevated by 3.5-fold ( P < 0.05) the INF-γ levels in BM cells. Incubation of BM leukocytes with IFN-γ (10 ng/ml, 2 h) reduced both neutrophil and eosinophil chemotaxis and adhesion, which were prevented by prior incubation with anti-MHC class II antibody (2 μg/ml). In conclusion, SEA inhibits neutrophil and eosinophil by MHC class II-dependent mechanism, which may be modulated by concomitant release of IFN-γ.

Active Site Loop Dynamics of a Class IIa Fructose 1,6-Bisphosphate Aldolase from Mycobacterium tuberculosis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pegan, Scott D.; Rukseree, Kamolchanok; Capodagli, Glenn C.

The class II fructose 1,6-bisphosphate aldolases (FBAs, EC 4.1.2.13) comprises one of two families of aldolases. Instead of forming a Schiff base intermediate using an ε-amino group of a lysine side chain, class II FBAs utilize Zn(II) to stabilize a proposed hydroxyenolate intermediate (HEI) in the reversible cleavage of fructose 1,6-bisphosphate, forming glyceraldehyde 3-phosphate and dihydroxyacetone phosphate (DHAP). As class II FBAs have been shown to be essential in pathogenic bacteria, focus has been placed on these enzymes as potential antibacterial targets. Although structural studies of class II FBAs from Mycobacterium tuberculosis (MtFBA), other bacteria, and protozoa have been reported,more » the structure of the active site loop responsible for catalyzing the protonation–deprotonation steps of the reaction for class II FBAs has not yet been observed. We therefore utilized the potent class II FBA inhibitor phosphoglycolohydroxamate (PGH) as a mimic of the HEI- and DHAP-bound form of the enzyme and determined the X-ray structure of the MtFBA–PGH complex to 1.58 Å. Remarkably, we are able to observe well-defined electron density for the previously elusive active site loop of MtFBA trapped in a catalytically competent orientation. Utilization of this structural information and site-directed mutagenesis and kinetic studies conducted on a series of residues within the active site loop revealed that E169 facilitates a water-mediated deprotonation–protonation step of the MtFBA reaction mechanism. Furthermore, solvent isotope effects on MtFBA and catalytically relevant mutants were used to probe the effect of loop flexibility on catalytic efficiency. Additionally, we also reveal the structure of MtFBA in its holoenzyme form.« less

Intercellular Transfer of a Soluble Viral Superantigen

PubMed Central

Reilly, Melissa; Mix, Denise; Reilly, Andrew A.; Yang Ye, Xiang; Winslow, Gary M.

2000-01-01

Mouse mammary tumor virus (MMTV) superantigens (vSAgs) can undergo intercellular transfer in vivo and in vitro such that a vSAg can be presented to T cells by major histocompatibility complex (MHC) class II proteins on antigen-presenting cells (APCs) that do not express the superantigen. This process may allow T-cell activation to occur prior to viral infection. Consistent with these findings, vSAg produced by Chinese hamster ovary (CHO) cells was readily transferred to class II IE and IA (H-2k and H-2d) proteins on a B-cell lymphoma or mouse splenocytes. Fixed class II-expressing acceptor cells were used to demonstrate that the vSAg, but not the class II proteins, underwent intercellular transfer, indicating that vSAg binding to class II MHC could occur directly at the cell surface. Intercellular transfer also occurred efficiently to splenocytes from endogenous retrovirus-free mice, indicating that other proviral proteins were not involved. Presentation of vSAg7 produced by a class II-negative, furin protease-deficient CHO variant (FD11) was unsuccessful, indicating that proteolytic processing was a requisite event and that proteolytic activity could not be provided by an endoprotease on the acceptor APC. Furthermore, vSAg presentation was effected using cell-free supernatant from class II-negative, vSAg-positive cells, indicating that a soluble molecule, most likely produced by proteolytic processing, was sufficient to stimulate T cells. Because the membrane-proximal endoproteolytic cleavage site in the vSAg (residues 68 to 71) was not necessary for intercellular transfer, the data support the notion that the carboxy-terminal endoproteolytic cleavage product is an active vSAg moiety. PMID:10954523

Dentoskeletal modifications in Class II deep bite malocclusion treatment with anterior bite plane functional appliance

PubMed Central

Ciavarella, Domenico; Laurenziello, Michele; Guida, Laura; Montaruli, Graziano; Gallo, Crescenzio; Lo Muzio, Lorenzo

2017-01-01

Background A treatment modality for Class II division 1 malocclusion is discussed. Orthodontic treatment of patients with deep bite and Class II malocclusion is an important challenge in clinical practice. The aim of this work is to compare the efficacy of anterior bite plane functional appliance (ABPFA) by assessing the changes in different times with untreated patients by literature. Material and Methods The study group comprised 22 subjects with Class II division 1 malocclusion and hypo-divergent. Eligibility criteria for this study were: dental Class II division 1 malocclusion, hypo-divergent skeletal pattern, late mixed or permanent dentition. We analyzed with the use of stable bone structure (ASCB) at two different times: pre-treatment (T0) and post-treatment (T1) after 24 months. Inter-group differences were evaluated with paired samples t-test at the P<0.05 level. Results No statistical significant differences were found in cephalometric skeletal measurements, whereas dental parameters showed a significant different overjet, which was significantly reduced (6 mm at T0 vs. 5 mm at T1) in our series. Conclusions In ABPFA group, the treatment effects were reduce mainly Class II malocclusion, overjet and overbite alteration. This appliance seems to suggest a significant beneficial effect in mandible displacement by reducing the counter clockwise rotation of the mandible, which is further confirmed by the almost absence of modifications of ArGoMe and SNGoMe angles. The ABPFA is particularly suitable to reduce the non-desirable dental effects represented by lower incisors pro inclination, and upper incisors retro-inclination. Key words:Orthodontics, Functional orthodontics, Class II malocclusion, Anterior bite plane functional appliance. PMID:28936295

18 CFR 415.21 - Class II projects.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 18 Conservation of Power and Water Resources 2 2011-04-01 2011-04-01 false Class II projects. 415.21 Section 415.21 Conservation of Power and Water Resources DELAWARE RIVER BASIN COMMISSION ADMINISTRATIVE MANUAL BASIN REGULATIONS-FLOOD PLAIN REGULATIONS Types of Projects and Jurisdiction § 415.21 Class...

78 FR 36698 - Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium tuberculosis

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-19

... specimens from class III (premarket approval) into class II (special controls). FDA is also issuing the draft special controls guideline entitled ``Class II Special Controls Guideline: Nucleic Acid-Based In... regulatory controls needed to provide reasonable assurance of their safety and effectiveness. The three...

Role of major histocompatibility complex class II in the development of autoimmune type 1 diabetes and thyroiditis in rats

PubMed Central

Yokoi, N; Hidaka, S; Tanabe, S; Ohya, M; Ishima, M; Takagi, Y; Masui, N; Seino, S

2012-01-01

Although the MHC class II ‘u' haplotype is strongly associated with type 1 diabetes (T1D) in rats, the role of MHC class II in the development of tissue-specific autoimmune diseases including T1D and autoimmune thyroiditis remains unclear. To clarify this, we produced a congenic strain carrying MHC class II ‘a' and ‘u' haplotypes on the Komeda diabetes-prone (KDP) genetic background. The u/u homozygous animals developed T1D similar to the original KDP rat; a/u heterozygous animals did develop T1D but with delayed onset and low frequency. In contrast, none of the a/a homozygous animals developed T1D; about half of the animals with a/u heterozygous or a/a homozygous genotypes showed autoimmune thyroiditis. To investigate the role of genetic background in the development of thyroiditis, we also produced a congenic strain carrying Cblb mutation of the KDP rat on the PVG.R23 genetic background (MHC class II ‘a' haplotype). The congenic rats with homozygous Cblb mutation showed autoimmune thyroiditis without T1D and slight to severe alopecia, a clinical symptom of hypothyroidism such as Hashimoto's thyroiditis. These data indicate that MHC class II is involved in the tissue-specific development of autoimmune diseases, including T1D and thyroiditis. PMID:21918539

The Bacillus subtilis ywjI (glpX) gene encodes a class II fructose-1,6-bisphosphatase, functionally equivalent to the class III Fbp enzyme.

PubMed

Jules, Matthieu; Le Chat, Ludovic; Aymerich, Stéphane; Le Coq, Dominique

2009-05-01

We present here experimental evidence that the Bacillus subtilis ywjI gene encodes a class II fructose-1,6-bisphosphatase, functionally equivalent to the fbp-encoded class III enzyme, and constitutes with the upstream gene, murAB, an operon transcribed at the same level under glycolytic or gluconeogenic conditions.

The Bacillus subtilis ywjI (glpX) Gene Encodes a Class II Fructose-1,6-Bisphosphatase, Functionally Equivalent to the Class III Fbp Enzyme▿

PubMed Central

Jules, Matthieu; Le Chat, Ludovic; Aymerich, Stéphane; Le Coq, Dominique

2009-01-01

We present here experimental evidence that the Bacillus subtilis ywjI gene encodes a class II fructose-1,6-bisphosphatase, functionally equivalent to the fbp-encoded class III enzyme, and constitutes with the upstream gene, murAB, an operon transcribed at the same level under glycolytic or gluconeogenic conditions. PMID:19270101

Curve of Spee and its relationship to vertical eruption of teeth among different malocclusion groups.

PubMed

Veli, Ilknur; Ozturk, Mehmet Ali; Uysal, Tancan

2015-03-01

Our objectives were to assess the depth of the curve of Spee (COS) in different malocclusion groups, to relate this to the eruption of anterior or posterior teeth quantitatively, and to determine whether the depth of the COS is affected by the vertical eruption of anterior or posterior teeth. Two hundred conventional lateral cephalograms and 3-dimensional models of untreated patients (70 boys, mean age: 16.4 ± 1.4 years; 130 young women, mean age: 18.1 ± 1.8 years) were included and assigned to 4 malocclusion groups as Class I, Class II Division 1, Class II Division 2, and Class III. The depth of the COS, overjet, and overbite were measured on 3-dimensional models. The perpendicular distance between the incisal tip of the mandibular central incisor (L1-MP), the deepest point of the COS (S-MP), and the distobuccal cusp tip of the mandibular second molar (L7-MP) to the mandibular plane were calculated and proportioned with each other. The Pearson correlation coefficient was calculated, and multiple linear regression analysis was carried out. Also, multivariate analysis of variance was performed at the P <0.05 level. The mesiobuccal cusp of the first molar was the deepest part of the COS in all groups, with a maximum depth of 2.44 ± 0.73 mm in the Class II Division 1 subjects and a minimum depth of 1.76 ± 0.94 in the Class III subjects. The depth of the COS changed as follows: Class II Division 1 > Class II Division 2 > Class I > Class III malocclusion groups. Statistically significant positive correlations were found between the depth of the COS and L1-MP/S-MP (r = 0.541) and L7-MP/S-MP (r = 0.269) in the Class I and Class III subjects, and between the depth of the COS and overjet (r = 0.483) and L7-MP/S-MP (r = 0.289) in the Class II Division 1 subjects. All variables except overjet had positive correlations with the depth of the COS in Class II Division 2 subjects. The multivariate analysis of variance showed statistically significant differences in overjet, overbite, L1-MP/S-MP, L7-MP/S-MP, and the depth of the COS (P <0.001) among the groups. Although the overjet differed, vertical eruption of the anterior teeth did not differ among the different malocclusion groups and had a significant contribution to the depth of the COS in subjects with Class I and Class III malocclusions. Copyright © 2015 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Biowaiver extension potential and IVIVC for BCS Class II drugs by formulation design: Case study for cyclosporine self-microemulsifying formulation.

PubMed

Yang, Su-Geun

2010-11-01

The objective of this work was to suggest the biowaiver potential of biopharmaceutical classification system (BCS) Class II drugs in self-microemulsifying drug delivery systems (SMEDDS) which are known to increase the solubility, dissolution and oral absorption of water-insoluble drugs. Cyclosporine was selected as a representative BCS Class II drug. New generic candidate of cyclosporine SMEDDS (test) was applied for the study with brand SMEDDS (reference I) and cyclosporine self-emulsifying drug delivery systems (SEDDS, reference II). Solubility and dissolution of cyclosporine from SMEDDS were critically enhanced, which were the similar behaviors with BCS class I drug. The test showed the identical dissolution rate and the equivalent bioavailability (0.34, 0.42 and 0.68 of p values for AUC₀(→)₂₄(h), C(max) and T(max), respectively) with the reference I. Based on the results, level A in vitro-in vivo correlation (IVIVC) was established from these two SMEDDS formulations. This study serves as a good example for speculating the biowaiver extension potential of BCS Class II drugs specifically in solubilizing formulation such as SMEDDS.

A Cephalometric Comparison of Twin Block and Bionator Appliances in Treatment of Class II Malocclusion

PubMed Central

Ahmadian-Babaki, Fatemeh; Araghbidi-Kashani, S. Mehdi

2017-01-01

Background Class II malocclusion is one of the most common orthodontic problems. In cases of class II malocclusion with mandibular deficiency, functional appliances often are used with the intent of stimulating mandibular growth. Bionator and twin block are two of the more popular functional appliances. The aim of this study was to compare the treatment outcomes of these two appliances using cephalometric radiographs. Material and Methods Cephalometric radiographs of 33 patients who had class II division I malocclusion, before and after treatment were digitalized. The mean changes in twin block and bionator groups were compared using independent t test. Results Twin block and bionator showed no statistically significant differences in cephalometric parameters except for ANB, NA-Pog, Basal and Ar-Go-Me angles. Conclusions There were no statistically significant differences in dentoalveolar and mandibular position between twin block and bionator (p>0.1). Twin block was more efficient in inhibition of forward movement of maxilla (p<0.1). Key words:Functional, Class II malocclusion, Cephalometrics, Twin block, Bionator, Treatment. PMID:28149473

37 GHz Methanol Masers : Horsemen of the Apocalypse for the Class II Methanol Maser Phase?

NASA Astrophysics Data System (ADS)

Ellingsen, S. P.; Breen, S. L.; Sobolev, A. M.; Voronkov, M. A.; Caswell, J. L.; Lo, N.

2011-12-01

We report the results of a search for class II methanol masers at 37.7, 38.3, and 38.5 GHz toward a sample of 70 high-mass star formation regions. We primarily searched toward regions known to show emission either from the 107 GHz class II methanol maser transition, or from the 6.035 GHz excited OH transition. We detected maser emission from 13 sources in the 37.7 GHz transition, eight of these being new detections. We detected maser emission from three sources in the 38 GHz transitions, one of which is a new detection. We find that 37.7 GHz methanol masers are only associated with the most luminous 6.7 and 12.2 GHz methanol maser sources, which in turn are hypothesized to be the oldest class II methanol sources. We suggest that the 37.7 GHz methanol masers are associated with a brief evolutionary phase (of 1000-4000 years) prior to the cessation of class II methanol maser activity in the associated high-mass star formation region.

A research for Class II defect Bored Pile’s Accept Criteria: A case of Penang Second Marine bridge

NASA Astrophysics Data System (ADS)

Huang, Kang

2018-03-01

The aim of this preliminary research is to study the accept criteria of class II bored pile with subtle defect. According to a detailed comparison of the existed different standards, Chinese ones are more applicable especially for the large diameter bored piles. Through the concrete coring at pile No P25-03 of this case and the comparison to the actual calculation, the Class II pile’s defects were very minor. Comparison was also made for the effects on pile structural capacities before and after repair of the defects. the feasible repair proposal may bring forward to more defects to the piles. The Class II piles don’t need any further repairation when piles have typical of similar character and sonic logging test result with P25-03‘s one. For other Class II piles with some differences in characters, verification is needed through further concrete coring on the pile. The recommendation of this research could be adopted for the similar huge marine structures which installed large diameter bored piles.

Cache and energy efficient algorithms for Nussinov's RNA Folding.

PubMed

Zhao, Chunchun; Sahni, Sartaj

2017-12-06

An RNA folding/RNA secondary structure prediction algorithm determines the non-nested/pseudoknot-free structure by maximizing the number of complementary base pairs and minimizing the energy. Several implementations of Nussinov's classical RNA folding algorithm have been proposed. Our focus is to obtain run time and energy efficiency by reducing the number of cache misses. Three cache-efficient algorithms, ByRow, ByRowSegment and ByBox, for Nussinov's RNA folding are developed. Using a simple LRU cache model, we show that the Classical algorithm of Nussinov has the highest number of cache misses followed by the algorithms Transpose (Li et al.), ByRow, ByRowSegment, and ByBox (in this order). Extensive experiments conducted on four computational platforms-Xeon E5, AMD Athlon 64 X2, Intel I7 and PowerPC A2-using two programming languages-C and Java-show that our cache efficient algorithms are also efficient in terms of run time and energy. Our benchmarking shows that, depending on the computational platform and programming language, either ByRow or ByBox give best run time and energy performance. The C version of these algorithms reduce run time by as much as 97.2% and energy consumption by as much as 88.8% relative to Classical and by as much as 56.3% and 57.8% relative to Transpose. The Java versions reduce run time by as much as 98.3% relative to Classical and by as much as 75.2% relative to Transpose. Transpose achieves run time and energy efficiency at the expense of memory as it takes twice the memory required by Classical. The memory required by ByRow, ByRowSegment, and ByBox is the same as that of Classical. As a result, using the same amount of memory, the algorithms proposed by us can solve problems up to 40% larger than those solvable by Transpose.

A specific insertion of a solo-LTR characterizes the Y-chromosome of Bryonia dioica (Cucurbitaceae).

PubMed

Oyama, Ryan K; Silber, Martina V; Renner, Susanne S

2010-06-14

Relatively few species of flowering plants are dioecious and even fewer are known to have sex chromosomes. Current theory posits that homomorphic sex chromosomes, such as found in Bryonia dioica (Cucurbitaceae), offer insight into the early stages in the evolution of sex chromosomes from autosomes. Little is known about these early steps, but an accumulation of transposable element sequences has been observed on the Y-chromosomes of some species with heteromorphic sex chromosomes. Recombination, by which transposable elements are removed, is suppressed on at least part of the emerging Y-chromosome, and this may explain the correlation between the emergence of sex chromosomes and transposable element enrichment. We sequenced 2321 bp of the Y-chromosome in Bryonia dioica that flank a male-linked marker, BdY1, reported previously. Within this region, which should be suppressed for recombination, we observed a solo-LTR nested in a Copia-like transposable element. We also found other, presumably paralogous, solo-LTRs in a consensus sequence of the underlying Copia-like transposable element. Given that solo-LTRs arise via recombination events, it is noteworthy that we find one in a genomic region where recombination should be suppressed. Although the solo-LTR could have arisen before recombination was suppressed, creating the male-linked marker BdY1, our previous study on B. dioica suggested that BdY1 may not lie in the recombination-suppressed region of the Y-chromosome in all populations. Presence of a solo-LTR near BdY1 therefore fits with the observed correlation between retrotransposon accumulation and the suppression of recombination early in the evolution of sex chromosomes. These findings further suggest that the homomorphic sex chromosomes of B. dioica, the first organism for which genetic XY sex-determination was inferred, are evolutionarily young and offer reference information for comparative studies of other plant sex chromosomes.

Functional Interaction between Class II Histone Deacetylases and ICP0 of Herpes Simplex Virus Type 1

PubMed Central

Lomonte, Patrick; Thomas, Joëlle; Texier, Pascale; Caron, Cécile; Khochbin, Saadi; Epstein, Alberto L.

2004-01-01

This study describes the physical and functional interactions between ICP0 of herpes simplex virus type 1 and class II histone deacetylases (HDACs) 4, 5, and 7. Class II HDACs are mainly known for their participation in the control of cell differentiation through the regulation of the activity of the transcription factor MEF2 (myocyte enhancer factor 2), implicated in muscle development and neuronal survival. Immunofluorescence experiments performed on transfected cells showed that ICP0 colocalizes with and reorganizes the nuclear distribution of ectopically expressed class I and II HDACs. In addition, endogenous HDAC4 and at least one of its binding partners, the corepressor protein SMRT (for silencing mediator of retinoid and thyroid receptor), undergo changes in their nuclear distribution in ICP0-transfected cells. As a result, during infection endogenous HDAC4 colocalizes with ICP0. Coimmunoprecipitation and glutathione S-transferase pull-down assays confirmed that class II but not class I HDACs specifically interacted with ICP0 through their amino-terminal regions. This region, which is not conserved in class I HDACs but homologous to the MITR (MEF2-interacting transcription repressor) protein, is responsible for the repression, in a deacetylase-independent manner, of MEF2 by sequestering it under an inactive form in the nucleus. Consequently, we show that ICP0 is able to overcome the HDAC5 amino-terminal- and MITR-induced MEF2A repression in gene reporter assays. This is the first report of a viral protein interacting with and controlling the repressor activity of class II HDACs. We discuss the putative consequences of such an interaction for the biology of the virus both during lytic infection and reactivation from latency. PMID:15194749

Transposon-like properties of the major, long repetitive sequence family in the genome of Physarum polycephalum

PubMed Central

Pearston, Douglas H.; Gordon, Mairi; Hardman, Norman

1985-01-01

A family of long, highly-repetitive sequences, referred to previously as `HpaII-repeats', dominates the genome of the eukaryotic slime mould Physarum polycephalum. These sequences are found exclusively in scrambled clusters. They account for about one-half of the total complement of repetitive DNA in Physarum, and represent the major sequence component found in hypermethylated, 20-50 kb segments of Physarum genomic DNA that fail to be cleaved using the restriction endonuclease HpaII. The structure of this abundant repetitive element was investigated by analysing cloned segments derived from the hypermethylated genomic DNA compartment. We show that the `HpaII-repeat' forms part of a larger repetitive DNA structure, ∼8.6 kb in length, with several structural features in common with recognised eukaryotic transposable genetic elements. Scrambled clusters of the sequence probably arise as a result of transposition-like events, during which the element preferentially recombines in either orientation with target sites located in other copies of the same repeated sequence. The target sites for transposition/recombination are not related in sequence but in all cases studied they are potentially capable of promoting the formation of small `cruciforms' or `Z-DNA' structures which might be recognised during the recombination process. ImagesFig. 3.Fig. 4. PMID:16453652

40 CFR 82.70 - Nonessential Class II products and exceptions.

Code of Federal Regulations, 2010 CFR

2010-07-01

... provide for motor vehicle safety in accordance with Federal Motor Vehicle Safety Standards until January 1... 21 CFR 2.125(e); (ii) Lubricants, coatings or cleaning fluids for electrical or electronic equipment...; (iii) Lubricants, coatings or cleaning fluids used for aircraft maintenance, which contain class II...

Differences in antigen presentation to MHC class I-and class II- restricted influenza virus-specific cytolytic T lymphocyte clones

PubMed Central

1986-01-01

We have examined requirements for antigen presentation to a panel of MHC class I-and class II-restricted, influenza virus-specific CTL clones by controlling the form of virus presented on the target cell surface. Both H-2K/D- and I region-restricted CTL recognize target cells exposed to infectious virus, but only the I region-restricted clones efficiently lysed histocompatible target cells pulsed with inactivated virus preparations. The isolated influenza hemagglutinin (HA) polypeptide also could sensitize target cells for recognition by class II-restricted, HA-specific CTL, but not by class I-restricted, HA- specific CTL. Inhibition of nascent viral protein synthesis abrogated the ability of target cells to present viral antigen relevant for class I-restricted CTL recognition. Significantly, presentation for class II- restricted recognition was unaffected in target cells exposed to preparations of either inactivated or infectious virus. This differential sensitivity suggested that these H-2I region-restricted CTL recognized viral polypeptides derived from the exogenously introduced virions, rather than viral polypeptides newly synthesized in the infected cell. In support of this contention, treatment of the target cells with the lysosomotropic agent chloroquine abolished recognition of infected target cells by class II-restricted CTL without diminishing class I-restricted recognition of infected target cells. Furthermore, when the influenza HA gene was introduced into target cells without exogenous HA polypeptide, the target cells that expressed the newly synthesized protein product of the HA gene were recognized only by H-2K/D-restricted CTL. These observations suggest that important differences may exist in requirements for antigen presentation between H-2K/D and H-2I region-restricted CTL. These differences may reflect the nature of the antigenic epitopes recognized by these two CTL subsets. PMID:3485173

Cheetah paradigm revisited: MHC diversity in the world's largest free-ranging population.

PubMed

Castro-Prieto, Aines; Wachter, Bettina; Sommer, Simone

2011-04-01

For more than two decades, the cheetah (Acinonyx jubatus) has been considered a paradigm of disease vulnerability associated with low genetic diversity, particularly at the immune genes of the major histocompatibility complex (MHC). Cheetahs have been used as a classic example in numerous conservation genetics textbooks as well as in many related scientific publications. However, earlier studies used methods with low resolution to quantify MHC diversity and/or small sample sizes. Furthermore, high disease susceptibility was reported only for captive cheetahs, whereas free-ranging cheetahs show no signs of infectious diseases and a good general health status. We examined whether the diversity at MHC class I and class II-DRB loci in 149 Namibian cheetahs was higher than previously reported using single-strand conformation polymorphism analysis, cloning, and sequencing. MHC genes were examined at the genomic and transcriptomic levels. We detected ten MHC class I and four class II-DRB alleles, of which nine MHC class I and all class II-DRB alleles were expressed. Phylogenetic analyses and individual genotypes suggested that the alleles belong to four MHC class I and three class II-DRB putative loci. Evidence of positive selection was detected in both MHC loci. Our study indicated that the low number of MHC class I alleles previously observed in cheetahs was due to a smaller sample size examined. On the other hand, the low number of MHC class II-DRB alleles previously observed in cheetahs was further confirmed. Compared with other mammalian species including felids, cheetahs showed low levels of MHC diversity, but this does not seem to influence the immunocompetence of free-ranging cheetahs in Namibia and contradicts the previous conclusion that the cheetah is a paradigm species of disease vulnerability.

Lateral-access Class II restoration using resin-modified glass-ionomer or silver-cermet cement.

PubMed

Croll, T P

1995-02-01

Direct-access preparation of a carious proximal surface is perhaps the most conservative approach to restoration. Physical properties and handling characteristics of silver amalgam and of resin composite and lack of fluoride ion release make these materials unsuitable for direct buccal- or lingual-access proximal restoration. Insufficient strengths and radiolucency of self-hardening glass-ionomer cements preclude their use for Class II restorations. However, glass-ionomer silver-cermet cement and some resin-modified glass-ionomer materials are proving useful for non-stress-bearing Class II restorations and may have applications in preventive dentistry. This article describes lateral-access Class II restoration with modified glass-ionomer cements. Emphasis is placed on careful handling of materials, maintenance of an ideal operative field, and conservation of tooth structure.

Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques.

PubMed

Creager, Hannah M; Becker, Ericka A; Sandman, Kelly K; Karl, Julie A; Lank, Simon M; Bimber, Benjamin N; Wiseman, Roger W; Hughes, Austin L; O'Connor, Shelby L; O'Connor, David H

2011-09-01

In recent years, the use of cynomolgus macaques in biomedical research has increased greatly. However, with the exception of the Mauritian population, knowledge of the MHC class II genetics of the species remains limited. Here, using cDNA cloning and Sanger sequencing, we identified 127 full-length MHC class II alleles in a group of 12 Indonesian and 12 Vietnamese cynomolgus macaques. Forty two of these were completely novel to cynomolgus macaques while 61 extended the sequence of previously identified alleles from partial to full length. This more than doubles the number of full-length cynomolgus macaque MHC class II alleles available in GenBank, significantly expanding the allele library for the species and laying the groundwork for future evolutionary and functional studies.

The relationship between Class I and Class II methanol masers at high angular resolution

NASA Astrophysics Data System (ADS)

McCarthy, T. P.; Ellingsen, S. P.; Voronkov, M. A.; Cimò, G.

2018-06-01

We have used the Australia Telescope Compact Array (ATCA) to make the first high-resolution observations of a large sample of class I methanol masers in the 95-GHz (80-71A+) transition. The target sources consist of a statistically complete sample of 6.7-GHz class II methanol masers with an associated 95-GHz class I methanol maser, enabling a detailed study of the relationship between the two methanol maser classes at arcsecond angular resolution. These sources have been previously observed at high resolution in the 36- and 44-GHz transitions, allowing comparison between all three class I maser transitions. In total, 172 95-GHz maser components were detected across the 32 target sources. We find that at high resolution, when considering matched maser components, a 3:1 flux density ratio is observed between the 95- and 44-GHz components, consistent with a number of previous lower angular resolution studies. The 95-GHz maser components appear to be preferentially located closer to the driving sources and this may indicate that this transition is more strongly inverted nearby to background continuum sources. We do not observe an elevated association rate between 95-GHz maser emission and more evolved sources, as indicated by the presence of 12.2-GHz class II masers. We find that in the majority of cases where both class I and class II methanol emission is observed, some component of the class I emission is associated with a likely outflow candidate.

Interstitial telomere-like repeats in the Arabidopsis thaliana genome.

PubMed

Uchida, Wakana; Matsunaga, Sachihiro; Sugiyama, Ryuji; Kawano, Shigeyuki

2002-02-01

Eukaryotic chromosomal ends are protected by telomeres, which are thought to play an important role in ensuring the complete replication of chromosomes. On the other hand, non-functional telomere-like repeats in the interchromosomal regions (interstitial telomeric repeats; ITRs) have been reported in several eukaryotes. In this study, we identified eight ITRs in the Arabidopsis thaliana genome, each consisting of complete and degenerate 300- to 1200-bp sequences. The ITRs were grouped into three classes (class IA-B, class II, and class IIIA-E) based on the degeneracy of the telomeric repeats in ITRs. The telomeric repeats of the two ITRs in class I were conserved for the most part, whereas the single ITR in class II, and the five ITRs in class III were relatively degenerated. In addition, degenerate ITRs were surrounded by common sequences that shared 70-100% homology to each other; these are named ITR-adjacent sequences (IAS). Although the genomic regions around ITRs in class I lacked IAS, those around ITRs in class II contained IAS (IASa), and those around five ITRs in class III had nine types of IAS (IASb, c, d, e, f, g, h, i, and j). Ten IAS types in classes II and III showed no significant homology to each other. The chromosomal locations of ITRs and IAS were not category-related, but most of them were adjacent to, or part of, a centromere. These results show that the A. thaliana genome has undergone chromosomal rearrangements, such as end-fusions and segmental duplications.

Treatment burden in patients with at least one class IV or V CFTR mutation.

PubMed

Dewulf, Jonas; Vermeulen, François; Wanyama, Simeon; Thomas, Muriel; Proesmans, Marijke; Dupont, Lieven; De Boeck, Kris

2015-12-01

CFTR mutations are grouped according to disease-causing mechanism. Several studies demonstrated that patients having at least one mutation of class IV/V, present with a milder phenotype, but little is known about their relative treatment burden. We compared treatment burden between patients with two class I, II, or III mutations and patients with at least one mutation of class IV/V in the 2010 database of the Belgian CF Registry. We calculated a "Treatment Burden Index" (TBI) by assigning long term therapies to categories low, medium and high intensity, for differential weighing in the total score. There were 779 patients with two known class I/II/III mutations and 94 patients with at least one class IV/V mutation. Compared to class I/II/III, class IV/V patients had a lower median number of clinic visits (4 vs. 5; P < 0.001), a lower risk of hospitalization (24.7% vs. 50.8%; P < 0.001) and intravenous antibiotic treatment (23.5% vs. 46.0%; P < 0.001) and a lower median TBI (6 vs. 9; P < 0.001). These differences remained significant when only class IV/V patients with pancreatic insufficiency (n = 31) were considered. This study clearly demonstrates the significantly lower treatment burden in patients with CF and at least one class IV/V mutation compared to patients with two class I/II/III mutations and contributes to providing better individual counseling at time of diagnosis. © 2015 Wiley Periodicals, Inc.

Treatment outcome of bimaxillary surgery for asymmetric skeletal class II deformity.

PubMed

Chen, Yun-Fang; Liao, Yu-Fang; Chen, Yin-An; Chen, Yu-Ray

2018-05-04

Facial asymmetry is one of the main concerns in patients with a dentofacial deformity. The aims of the study were to (1) evaluate the changes in facial asymmetry after bimaxillary surgery for asymmetric skeletal class II deformity and (2) compare preoperative and postoperative facial asymmetry of class II patients with normal controls. The facial asymmetry was assessed for 30 adults (21 women and 9 men, mean age: 29.3 years) who consecutively underwent bimaxillary surgery for asymmetric skeletal class II deformity using cone-beam computed tomography before and at least 6 months after surgery. Thirty soft tissue and two dental landmarks were identified on each three-dimensional facial image, and the asymmetry index of each landmark was calculated. Results were compared with those of 30 normal control subjects (21 women and 9 men, mean age: 26.2 years) with skeletal class I structure. Six months after surgery, the asymmetric index of the lower face and total face decreased significantly (17.8 ± 29.4 and 16.6 ± 29.5 mm, respectively, both p < 0.01), whereas the asymmetric index of the middle face increased significantly (1.2 ± 2.2 mm, p < 0.01). Postoperatively, 53% of the class II patients had residual chin asymmetry. The postoperative total face asymmetric index was positively correlated with the preoperative asymmetric index (r = 0.37, p < 0.05). Bimaxillary surgery for patients with asymmetric class II deformity resulted in a significant improvement in lower face asymmetry. However, approximately 50% of the patients still had residual chin asymmetry. The total face postoperative asymmetry was moderately related to the initial severity of asymmetry. These findings could help clinicians better understand orthognathic outcomes on different facial regions for patients with asymmetric class II deformity.

Feminist theorizing as 'transposed autobiography'.

PubMed

Hoogland, Renée C

2007-01-01

This piece considers personal investments endemic in academic writing, more specifically, in Lesbian Studies. Taking Elizabeth Bowen's phrase, "transposed autobiography," as a starting-point, the author briefly discusses the development of lesbian/straight feminist debates, and continues to explore the relative absence of lesbianism in current feminist and queer theorizing. Three 'moments' serve to explain the casting aside of lesbian desire: the subsidence of lesbian/straight feminist debates, the prevalence of 'race'/ethnicity in critical theorizing and the emergence of post-theoretical trends of thought.

Transposable elements as a molecular evolutionary force

NASA Technical Reports Server (NTRS)

Fedoroff, N. V.

1999-01-01

This essay addresses the paradoxes of the complex and highly redundant genomes. The central theses developed are that: (1) the distinctive feature of complex genomes is the existence of epigenetic mechanisms that permit extremely high levels of both tandem and dispersed redundancy; (2) the special contribution of transposable elements is to modularize the genome; and (3) the labilizing forces of recombination and transposition are just barely contained, giving a dynamic genetic system of ever increasing complexity that verges on the chaotic.

Epigenetic regulation of transcription and possible functions of mammalian short interspersed elements, SINEs.

PubMed

Ichiyanagi, Kenji

2013-01-01

Short interspersed elements (SINEs) are a class of retrotransposons, which amplify their copy numbers in their host genomes by retrotransposition. More than a million copies of SINEs are present in a mammalian genome, constituting over 10% of the total genomic sequence. In contrast to the other two classes of retrotransposons, long interspersed elements (LINEs) and long terminal repeat (LTR) elements, SINEs are transcribed by RNA polymerase III. However, like LINEs and LTR elements, the SINE transcription is likely regulated by epigenetic mechanisms such as DNA methylation, at least for human Alu and mouse B1. Whereas SINEs and other transposable elements have long been thought as selfish or junk DNA, recent studies have revealed that they play functional roles at their genomic locations, for example, as distal enhancers, chromatin boundaries and binding sites of many transcription factors. These activities imply that SINE retrotransposition has shaped the regulatory network and chromatin landscape of their hosts. Whereas it is thought that the epigenetic mechanisms were originated as a host defense system against proliferation of parasitic elements, this review discusses a possibility that the same mechanisms are also used to regulate the SINE-derived functions.

HIV Controllers Exhibit Enhanced Frequencies of Major Histocompatibility Complex Class II Tetramer+ Gag-Specific CD4+ T Cells in Chronic Clade C HIV-1 Infection

PubMed Central

Laher, Faatima; Ranasinghe, Srinika; Porichis, Filippos; Mewalal, Nikoshia; Pretorius, Karyn; Ismail, Nasreen; Buus, Søren; Stryhn, Anette; Carrington, Mary; Walker, Bruce D.; Ndung'u, Thumbi

2017-01-01

ABSTRACT Immune control of viral infections is heavily dependent on helper CD4+ T cell function. However, the understanding of the contribution of HIV-specific CD4+ T cell responses to immune protection against HIV-1, particularly in clade C infection, remains incomplete. Recently, major histocompatibility complex (MHC) class II tetramers have emerged as a powerful tool for interrogating antigen-specific CD4+ T cells without relying on effector functions. Here, we defined the MHC class II alleles for immunodominant Gag CD4+ T cell epitopes in clade C virus infection, constructed MHC class II tetramers, and then used these to define the magnitude, function, and relation to the viral load of HIV-specific CD4+ T cell responses in a cohort of untreated HIV clade C-infected persons. We observed significantly higher frequencies of MHC class II tetramer-positive CD4+ T cells in HIV controllers than progressors (P = 0.0001), and these expanded Gag-specific CD4+ T cells in HIV controllers showed higher levels of expression of the cytolytic proteins granzymes A and B. Importantly, targeting of the immunodominant Gag41 peptide in the context of HLA class II DRB1*1101 was associated with HIV control (r = −0.5, P = 0.02). These data identify an association between HIV-specific CD4+ T cell targeting of immunodominant Gag epitopes and immune control, particularly the contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infection. Furthermore, these results highlight the advantage of the use of class II tetramers in evaluating HIV-specific CD4+ T cell responses in natural infections. IMPORTANCE Increasing evidence suggests that virus-specific CD4+ T cells contribute to the immune-mediated control of clade B HIV-1 infection, yet there remains a relative paucity of data regarding the role of HIV-specific CD4+ T cells in shaping adaptive immune responses in individuals infected with clade C, which is responsible for the majority of HIV infections worldwide. Understanding the contribution of HIV-specific CD4+ T cell responses in clade C infection is particularly important for developing vaccines that would be efficacious in sub-Saharan Africa, where clade C infection is dominant. Here, we employed MHC class II tetramers designed to immunodominant Gag epitopes and used them to characterize CD4+ T cell responses in HIV-1 clade C infection. Our results demonstrate an association between the frequency of HIV-specific CD4+ T cell responses targeting an immunodominant DRB1*11-Gag41 complex and HIV control, highlighting the important contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infections. PMID:28077659

STAR FORMATION AND YOUNG POPULATION OF THE H II COMPLEX Sh2-294

DOE Office of Scientific and Technical Information (OSTI.GOV)

Samal, M. R.; Pandey, A. K.; Chauhan, N.

The Sh2-294 H II region ionized by a single B0V star features several infrared excess sources, a photodissociation region, and also a group of reddened stars at its border. The star formation scenario in this region seems to be quite complex. In this paper, we present follow-up results of Sh2-294 H II region at 3.6, 4.5, 5.8, and 8.0 {mu}m observed with the Spitzer Space Telescope Infrared Array Camera (IRAC), coupled with H{sub 2} (2.12 {mu}m) observation, to characterize the young population of the region and to understand its star formation history. We identified 36 young stellar object (YSO, Classmore » I, Class II, and Class I/II) candidates using IRAC color-color diagrams. It is found that Class I sources are preferentially located at the outskirts of the H II region and associated with enhanced H{sub 2} emission; none of them are located near the central cluster. Combining the optical to mid-infrared (MIR) photometry of the YSO candidates and using the spectral energy distribution fitting models, we constrained stellar parameters and the evolutionary status of 33 YSO candidates. Most of them are interpreted by the model as low-mass (<4 M{sub Sun }) YSOs; however, we also detected a massive YSO ({approx}9 M{sub Sun }) of Class I nature, embedded in a cloud of visual extinction of {approx}24 mag. Present analysis suggests that the Class I sources are indeed a younger population of the region relative to Class II sources (age {approx} 4.5 Multiplication-Sign 10{sup 6} yr). We suggest that the majority of the Class I sources, including the massive YSOs, are second-generation stars of the region whose formation is possibly induced by the expansion of the H II region powered by a {approx}4 Multiplication-Sign 10{sup 6} yr B0 main-sequence star.« less

High Genetic Diversity of Newcastle Disease Virus in Wild and Domestic Birds in Northeastern China from 2013 to 2015 Reveals Potential Epidemic Trends

PubMed Central

Zhang, Pingze; Xie, Guangyao; Liu, Xinxin; Ai, Lili; Chen, Yanyu; Meng, Xin; Bi, Yuhai; Chen, Jianjun; Sun, Yuzhang; Stoeger, Tobias; Ding, Zhuang

2015-01-01

Newcastle disease (ND), caused by the virulent Newcastle disease virus (NDV), is one of the most important viral diseases of birds globally, but little is currently known regarding enzootic trends of NDV in northeastern China, especially for class I viruses. Thus, we performed a surveillance study for NDV in northeastern China from 2013 to 2015. A total 755 samples from wild and domestic birds in wetlands and live bird markets (LBMs) were collected, and 10 isolates of NDV were identified. Genetic and phylogenetic analyses showed that five isolates from LBMs belong to class I subgenotype 1b, two (one from wild birds and one from LBMs) belong to the vaccine-like class II genotype II, and three (all from wild birds) belong to class II subgenotype Ib. Interestingly, the five class I isolates had epidemiological connections with viruses from southern, eastern, and southeastern China. Our findings, together with recent prevalence trends of class I and virulent class II NDV in China, suggest possible virus transmission between wild and domestic birds and the potential for an NDV epidemic in the future. PMID:26712543

High Genetic Diversity of Newcastle Disease Virus in Wild and Domestic Birds in Northeastern China from 2013 to 2015 Reveals Potential Epidemic Trends.

PubMed

Zhang, Pingze; Xie, Guangyao; Liu, Xinxin; Ai, Lili; Chen, Yanyu; Meng, Xin; Bi, Yuhai; Chen, Jianjun; Sun, Yuzhang; Stoeger, Tobias; Ding, Zhuang; Yin, Renfu

2015-12-28

Newcastle disease (ND), caused by the virulent Newcastle disease virus (NDV), is one of the most important viral diseases of birds globally, but little is currently known regarding enzootic trends of NDV in northeastern China, especially for class I viruses. Thus, we performed a surveillance study for NDV in northeastern China from 2013 to 2015. A total 755 samples from wild and domestic birds in wetlands and live bird markets (LBMs) were collected, and 10 isolates of NDV were identified. Genetic and phylogenetic analyses showed that five isolates from LBMs belong to class I subgenotype 1b, two (one from wild birds and one from LBMs) belong to the vaccine-like class II genotype II, and three (all from wild birds) belong to class II subgenotype Ib. Interestingly, the five class I isolates had epidemiological connections with viruses from southern, eastern, and southeastern China. Our findings, together with recent prevalence trends of class I and virulent class II NDV in China, suggest possible virus transmission between wild and domestic birds and the potential for an NDV epidemic in the future. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Staphylococcus-mediated T-cell activation and spontaneous natural killer cell activity in the absence of major histocompatibility complex class II molecules

NASA Technical Reports Server (NTRS)

Chapes, S. K.; Hoynowski, S. M.; Woods, K. M.; Armstrong, J. W.; Beharka, A. A.; Iandolo, J. J.; Spooner, B. S. (Principal Investigator)

1993-01-01

We used major histocompatibility complex class II antigen-deficient transgenic mice to show that in vitro natural killer cell cytotoxicity and T-cell activation by staphylococcal exotoxins (superantigens) are not dependent upon the presence of major histocompatibility complex class II molecules. T cells can be activated by exotoxins in the presence of exogenously added interleukin 1 or 2 or in the presence of specific antibody without exogenously added cytokines.

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens

PubMed Central

Glinsky, Gennadi V.

2016-01-01

Abstract Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8–10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P < 0.0001 in all instances). Present analysis supports the idea that phenotypic divergence of Homo sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of divergent sequences of regulatory DNA: (i) recombination-associated exaptation of the highly conserved ancestral regulatory DNA segments; (ii) human-specific insertions of transposable elements. PMID:27503290

25 CFR 535.1 - Amendments.

Code of Federal Regulations, 2010 CFR

2010-04-01

... GAMING COMMISSION, DEPARTMENT OF THE INTERIOR MANAGEMENT CONTRACT PROVISIONS POST-APPROVAL PROCEDURES... management contract for the operation of a class II or class III gaming activity. (b) A tribe shall submit an... information required under § 537.1(b)(1) of this chapter for class II gaming contracts or § 537.1(b)(1)(i) of...

40 CFR 144.26 - Inventory requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... “Inventory of Injection Wells,” OMB No. 158-R0170. (b) Additional contents. For EPA administered programs...) Class II enhanced recovery wells; (ii) Class IV wells; (iii) The following Class V wells: (A) Sand or... (40 CFR 146.5 (e)(11)) (C) Geothermal energy recovery wells [§ 146.5(e)(12)]; (D) Brine return flow...

Effects of Newcastle disease virus vaccine antibodies on the shedding and transmission of challenge viruses

USDA-ARS?s Scientific Manuscript database

Different genotypes of avian paramyxovirus serotype-1 virus (APMV-1) circulate in many parts of the world. Traditionally, Newcastle disease virus (NDV) is recognized as having two major divisions represented by class I and class II, with class II being further divided into eighteen genotypes. Alth...

Effects of Newcastle disease virus vaccine antibodies on the shedding and transmission of challenge viruses

USDA-ARS?s Scientific Manuscript database

Different genotypes of avian paramyxovirus serotype-1 virus (APMV-1) circulate in many parts of the world. Traditionally, Newcastle disease virus (NDV) is recognized as having two major divisions represented by class I and class II, with class II being further divided into sixteen genotypes. Althoug...

41 CFR 301-10.123 - When may I use other than coach-class airline accommodations?

Code of Federal Regulations, 2011 CFR

2011-07-01

... to: (i) Use of coach-class accommodations would endanger your life or Government property; (ii) You... coach-class accommodations would endanger your life or Government property; (ii) You are an agent on... sanitation or health standards; (4) Regularly scheduled flights between origin/destination points (including...

Cognitive Performance in Older Adults with Stable Heart Failure: Longitudinal Evidence for Stability and Improvement

PubMed Central

Alosco, Michael L.; Garcia, Sarah; Spitznagel, Mary Beth; van Dulmen, Manfred; Cohen, Ronald; Sweet, Lawrence H.; Josephson, Richard; Hughes, Joel; Rosneck, Jim; Gunstad, John

2013-01-01

Cognitive impairment is prevalent in heart failure (HF), though substantial variability in the pattern of cognitive impairment is found across studies. To clarify the nature of cognitive impairment in HF, we examined longitudinal trajectories across multiple domains of cognition in HF patients using latent growth class modeling. 115 HF patients completed a neuropsychological battery at baseline, 3-months and 12-months. Participants also completed the Beck Depression Inventory-II (BDI-II). Latent class growth analyses revealed a three-class model for attention/executive function, four-class model for memory, and a three-class model for language. The slope for attention/executive function and language remained stable, while improvements were noted in memory performance. Education and BDI-II significantly predicted the intercept for attention/executive function and language abilities. The BDI-II also predicted baseline memory. The current findings suggest that multiple performance-based classes of neuropsychological test performance exist within cognitive domains, though case-controlled prospective studies with extended follow-ups are needed to fully elucidate changes and predictors of cognitive function in HF. PMID:23906182

A Novel HURRAH Protocol Reveals High Numbers of Monomorphic MHC Class II Loci and Two Asymmetric Multi-Locus Haplotypes in the Père David's Deer

PubMed Central

Wan, Qiu-Hong; Zhang, Pei; Ni, Xiao-Wei; Wu, Hai-Long; Chen, Yi-Yan; Kuang, Ye-Ye; Ge, Yun-Fa; Fang, Sheng-Guo

2011-01-01

The Père David's deer is a highly inbred, but recovered, species, making it interesting to consider their adaptive molecular evolution from an immunological perspective. Prior to this study, genomic sequencing was the only method for isolating all functional MHC genes within a certain species. Here, we report a novel protocol for isolating MHC class II loci from a species, and its use to investigate the adaptive evolution of this endangered deer at the level of multi-locus haplotypes. This protocol was designated “HURRAH” based on its various steps and used to estimate the total number of MHC class II loci. We confirmed the validity of this novel protocol in the giant panda and then used it to examine the Père David's deer. Our results revealed that the Père David's deer possesses nine MHC class II loci and therefore has more functional MHC class II loci than the eight genome-sequenced mammals for which full MHC data are currently available. This could potentially account at least in part for the strong survival ability of this species in the face of severe bottlenecking. The results from the HURRAH protocol also revealed that: (1) All of the identified MHC class II loci were monomorphic at their antigen-binding regions, although DRA was dimorphic at its cytoplasmic tail; and (2) these genes constituted two asymmetric functional MHC class II multi-locus haplotypes: DRA1*01 ∼ DRB1 ∼ DRB3 ∼ DQA1 ∼ DQB2 (H1) and DRA1*02 ∼ DRB2 ∼ DRB4 ∼ DQA2 ∼ DQB1 (H2). The latter finding indicates that the current members of the deer species have lost the powerful ancestral MHC class II haplotypes of nine or more loci, and have instead fixed two relatively weak haplotypes containing five genes. As a result, the Père David's deer are currently at risk for increased susceptibility to infectious pathogens. PMID:21267075

Evaluation of the appropriateness and outcome of in-hospital telemetry monitoring.

PubMed

Fålun, Nina; Nordrehaug, Jan Erik; Hoff, Per Ivar; Langørgen, Jørund; Moons, Philip; Norekvål, Tone M

2013-10-15

The American Heart Association classifies monitored patients into 3 categories. The aims of this study were to (1) investigate how patients are assigned according to the American Heart Association classification, (2) determine the number and type of arrhythmic events experienced by these patients, and (3) describe subsequent changes in management. A prospective observational study design was used. All patients assigned to telemetry during a 3-month period were consecutively enrolled in our study. Data were collected 24/7. Only arrhythmias that might require a change in management were recorded. Monitor watchers at the central monitoring station completed a standard data sheet assessing 64 variables. These data, as well as medical records, were reviewed by the investigator. Overall, 1,194 patients were included. Eighteen percent of the patients were assigned to American Heart Association class I (monitoring indicated), 71% to class II (monitoring may be of benefit), and 11% to class III (monitoring not indicated). The overall arrhythmia event rate was 33%. Forty-three percent of class I patients, 28% of class II patients, and 47% of class III patients experienced arrhythmia events. Change in management occurred in 25% of class I patients, 14% of class II patients, and 29% of class III patients. Although the number of class III indications should have been reduced, nearly 1/2 of class III patients experienced arrhythmia events and 1/3 of them received management changes. This outcome challenges existing guidelines. In conclusion, most patients in this study were monitored appropriately, according to class I and II indications. Copyright © 2013 Elsevier Inc. All rights reserved.

Asymmetric severe skeletal Class II division 1 patient with temporomandibular joint disorder treated with zygomatic anchorage devices and Ni-Ti alloy wires.

PubMed

Ishida, Takayoshi; Ono, Takashi

2014-09-01

To describe the orthodontic treatment of a nongrowing 30-year-old woman with asymmetric severe skeletal Class II malocclusions (asymmetric Angle Class II), large overjet (16 mm), large overbite (8 mm), two congenitally missing mandibular incisors (presenting a deciduous anterior tooth), and signs and symptoms of temporomandibular joint disorder (TMD). We used novel improved super-elastic Ni-Ti alloy wires (ISWs) combined with Ni-Ti alloy coil springs, power hooks, and a zygomatic implant as reinforced anchorage to provide a constant and continuous mild force to the dentition. We successfully distalized maxillary molars, premolars, and retracted anterior teeth and corrected the asymmetric Angle Class II molar relationship using this system of zygomatic anchorage in conjunction with ISWs, Ni-Ti alloy open-coil springs, and crimpable power hook. The maxillary molars were distalized, and postero-occlusal relationships were improved to achieve Class I canine and molar relationships on both sides. Intrusion of the upper molars made the mandibular plane close. Ideal overbite and overjet relationships were established. Facial esthetics were improved with decreased upper and lower lip protrusion, and no symptoms of TMD were observed after treatment. The orthodontic treatment described here is a promising anchorage technique alternative to traditional techniques to improve severe skeletal Class II with TMD.

Long-term effects of Class II orthodontic treatment on oral health.

PubMed

Bock, N C; Saffar, M; Hudel, H; Evälahti, M; Heikinheimo, K; Rice, D P C; Ruf, S

2018-03-01

To investigate the long-term (≥15 years) benefit of orthodontic Class II treatment (Tx) on oral health (OH). All patients (Department of Orthodontics, University of Giessen, Giessen, Germany) who underwent Class II correction (Herbst-multibracket Tx, end of active Tx ≥ 15 years ago) and agreed to participate in a recall (clinical examination, interview, impressions, and photographs) were included. Records after active Tx were used to assess the long-term OH effects. Data were compared to corresponding population-representative age-cohorts as well as to untreated Class I controls without orthodontic Tx need during adolescence. Of 152 treated Class II patients, 75 could be located and agreed to participate at 33.7 ± 3.0 years of age (pre-Tx age: 14.0 ± 2.7 years). The majority (70.8%) were fully satisfied with their teeth and with their masticatory system. The Decayed, Missing, Filled Teeth Index (DMFT) was 7.1 ± 4.8 and, thus, almost identical to that of the untreated Class I controls (7.9 ± 3.6). In contrast, the DMFT in the population-representative age-cohort was 56% higher. The determined mean Community Periodontal Index (CPI) maximum score (1.6 ± 0.6) was also comparable to the untreated Class I controls (1.7 ± 0.9) but in the corresponding population-representative age-cohort it was 19-44% higher. The extent of lower incisor gingival recessions did not differ significantly between the treated Class II participants and the untreated Class I controls (0.1 ± 0.2 vs. 0.0 ± 0.1 mm). Patients with orthodontically treated severe Class II malocclusions had a lower risk for oral health impairment than the general population. The risk corresponded to that of untreated Class I controls (without orthodontic Tx need during adolescence).

Di-codon Usage for Gene Classification

NASA Astrophysics Data System (ADS)

Nguyen, Minh N.; Ma, Jianmin; Fogel, Gary B.; Rajapakse, Jagath C.

Classification of genes into biologically related groups facilitates inference of their functions. Codon usage bias has been described previously as a potential feature for gene classification. In this paper, we demonstrate that di-codon usage can further improve classification of genes. By using both codon and di-codon features, we achieve near perfect accuracies for the classification of HLA molecules into major classes and sub-classes. The method is illustrated on 1,841 HLA sequences which are classified into two major classes, HLA-I and HLA-II. Major classes are further classified into sub-groups. A binary SVM using di-codon usage patterns achieved 99.95% accuracy in the classification of HLA genes into major HLA classes; and multi-class SVM achieved accuracy rates of 99.82% and 99.03% for sub-class classification of HLA-I and HLA-II genes, respectively. Furthermore, by combining codon and di-codon usages, the prediction accuracies reached 100%, 99.82%, and 99.84% for HLA major class classification, and for sub-class classification of HLA-I and HLA-II genes, respectively.

Male Germline Control of Transposable Elements1

PubMed Central

Bao, Jianqiang; Yan, Wei

2012-01-01

ABSTRACT Repetitive sequences, especially transposon-derived interspersed repetitive elements, account for a large fraction of the genome in most eukaryotes. Despite the repetitive nature, these transposable elements display quantitative and qualitative differences even among species of the same lineage. Although transposable elements contribute greatly as a driving force to the biological diversity during evolution, they can induce embryonic lethality and genetic disorders as a result of insertional mutagenesis and genomic rearrangement. Temporary relaxation of the epigenetic control of retrotransposons during early germline development opens a risky window that can allow retrotransposons to escape from host constraints and to propagate abundantly in the host genome. Because germline mutations caused by retrotransposon activation are heritable and thus can be deleterious to the offspring, an adaptive strategy has evolved in host cells, especially in the germline. In this review, we will attempt to summarize general defense mechanisms deployed by the eukaryotic genome, with an emphasis on pathways utilized by the male germline to confer retrotransposon silencing. PMID:22357546

Does letter rotation slow down orthographic processing in word recognition?

PubMed

Perea, Manuel; Marcet, Ana; Fernández-López, María

2018-02-01

Leading neural models of visual word recognition assume that letter rotation slows down the conversion of the visual input to a stable orthographic representation (e.g., local detectors combination model; Dehaene, Cohen, Sigman, & Vinckier, 2005, Trends in Cognitive Sciences, 9, 335-341). If this premise is true, briefly presented rotated primes should be less effective at activating word representations than those primes with upright letters. To test this question, we conducted a masked priming lexical decision experiment with vertically presented words either rotated 90° or in marquee format (i.e., vertically but with upright letters). We examined the impact of the format on both letter identity (masked identity priming: identity vs. unrelated) and letter position (masked transposed-letter priming: transposed-letter prime vs. replacement-letter prime). Results revealed sizeable masked identity and transposed-letter priming effects that were similar in magnitude for rotated and marquee words. Therefore, the reading cost from letter rotation does not arise in the initial access to orthographic/lexical representations.

Evolutionary interaction between W/Y chromosome and transposable elements.

PubMed

Śliwińska, Ewa B; Martyka, Rafał; Tryjanowski, Piotr

2016-06-01

The W/Y chromosome is unique among chromosomes as it does not recombine in its mature form. The main side effect of cessation of recombination is evolutionary instability and degeneration of the W/Y chromosome, or frequent W/Y chromosome turnovers. Another important feature of W/Y chromosome degeneration is transposable element (TEs) accumulation. Transposon accumulation has been confirmed for all W/Y chromosomes that have been sequenced so far. Models of W/Y chromosome instability include the assemblage of deleterious mutations in protein coding genes, but do not include the influence of transposable elements that are accumulated gradually in the non-recombining genome. The multiple roles of genomic TEs, and the interactions between retrotransposons and genome defense proteins are currently being studied intensively. Small RNAs originating from retrotransposon transcripts appear to be, in some cases, the only mediators of W/Y chromosome function. Based on the review of the most recent publications, we present knowledge on W/Y evolution in relation to retrotransposable element accumulation.

The application of the high throughput sequencing technology in the transposable elements.

PubMed

Liu, Zhen; Xu, Jian-hong

2015-09-01

High throughput sequencing technology has dramatically improved the efficiency of DNA sequencing, and decreased the costs to a great extent. Meanwhile, this technology usually has advantages of better specificity, higher sensitivity and accuracy. Therefore, it has been applied to the research on genetic variations, transcriptomics and epigenomics. Recently, this technology has been widely employed in the studies of transposable elements and has achieved fruitful results. In this review, we summarize the application of high throughput sequencing technology in the fields of transposable elements, including the estimation of transposon content, preference of target sites and distribution, insertion polymorphism and population frequency, identification of rare copies, transposon horizontal transfers as well as transposon tagging. We also briefly introduce the major common sequencing strategies and algorithms, their advantages and disadvantages, and the corresponding solutions. Finally, we envision the developing trends of high throughput sequencing technology, especially the third generation sequencing technology, and its application in transposon studies in the future, hopefully providing a comprehensive understanding and reference for related scientific researchers.

Transposed-letter priming effects in reading aloud words and nonwords.

PubMed

Mousikou, Petroula; Kinoshita, Sachiko; Wu, Simon; Norris, Dennis

2015-10-01

A masked nonword prime generated by transposing adjacent inner letters in a word (e.g., jugde) facilitates the recognition of the target word (JUDGE) more than a prime in which the relevant letters are replaced by different letters (e.g., junpe). This transposed-letter (TL) priming effect has been widely interpreted as evidence that the coding of letter position is flexible, rather than precise. Although the TL priming effect has been extensively investigated in the domain of visual word recognition using the lexical decision task, very few studies have investigated this empirical phenomenon in reading aloud. In the present study, we investigated TL priming effects in reading aloud words and nonwords and found that these effects are of equal magnitude for the two types of items. We take this result as support for the view that the TL priming effect arises from noisy perception of letter order within the prime prior to the mapping of orthography to phonology.

World War II: A Technology Lesson Plan.

ERIC Educational Resources Information Center

Hagar, Suzy

1990-01-01

Presents a class activity on the history, causes, and consequences of World War II. Focuses on the development and deployment of the atomic bomb. Utilizes a Video Encyclopedia Program for historical background. Divides the class into groups that are responsible for researching and preparing a videotape on a World War II topic. (RW)

75 FR 36134 - Self-Regulatory Organizations; International Securities Exchange, LLC; Notice of Filing and...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-24

... categories of market participants: (i) Market Maker; (ii) Market Maker Plus; \\4\\ (iii) Non-ISE Market Maker... removing liquidity to the following class of market participants: (i) Customer, (ii) Directed Participant... provides a rebate for adding liquidity to the following class of market participants: (i) Customer, (ii...

Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

PubMed Central

Diez, Concepcion M.; Meca, Esteban; Tenaillon, Maud I.; Gaut, Brandon S.

2014-01-01

Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remain poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24∶22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome. PMID:24743518

Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga.

PubMed

Rodriguez, Fernando; Arkhipova, Irina R

2016-05-01

RNA-mediated silencing processes play a key role in silencing of transposable elements, especially in the germ line, where piwi-interacting RNAs (piRNAs) are responsible for suppressing transposon mobility and maintaining genome integrity. We previously reported that the genome of Adineta vaga, the first sequenced representative of the phylum Rotifera (class Bdelloidea), is characterized by massive levels of horizontal gene transfer, by unusually low transposon content, and by highly diversified RNA-mediated silencing machinery. Here, we investigate genome-wide distribution of pi-like small RNAs, which in A. vaga are 25-31 nucleotides in length and have a strong 5'-uridine bias, while lacking ping-pong amplification signatures. In agreement with expectations, 71% of mapped reads corresponded to annotated transposons, with 93% of these reads being in the antisense orientation. Unexpectedly, a significant fraction of piRNAs originate from predicted coding regions corresponding to genes of putatively foreign origin. The distribution of piRNAs across foreign genes is not biased toward 3'-UTRs, instead resembling transposons in uniform distribution pattern throughout the gene body, and in predominantly antisense orientation. We also find that genes with small RNA coverage, including a number of genes of metazoan origin, are characterized by higher occurrence of telomeric repeats in the surrounding genomic regions, and by higher density of transposons in the vicinity, which have the potential to promote antisense transcription. Our findings highlight the complex interplay between RNA-based silencing processes and acquisition of genes at the genome periphery, which can result either in their loss or eventual domestication and integration into the host genome. Copyright © 2016 by the Genetics Society of America.

Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.

PubMed

Talla, Venkat; Suh, Alexander; Kalsoom, Faheema; Dinca, Vlad; Vila, Roger; Friberg, Magne; Wiklund, Christer; Backström, Niclas

2017-10-01

Characterizing and quantifying genome size variation among organisms and understanding if genome size evolves as a consequence of adaptive or stochastic processes have been long-standing goals in evolutionary biology. Here, we investigate genome size variation and association with transposable elements (TEs) across lepidopteran lineages using a novel genome assembly of the common wood-white (Leptidea sinapis) and population re-sequencing data from both L. sinapis and the closely related L. reali and L. juvernica together with 12 previously available lepidopteran genome assemblies. A phylogenetic analysis confirms established relationships among species, but identifies previously unknown intraspecific structure within Leptidea lineages. The genome assembly of L. sinapis is one of the largest of any lepidopteran taxon so far (643 Mb) and genome size is correlated with abundance of TEs, both in Lepidoptera in general and within Leptidea where L. juvernica from Kazakhstan has considerably larger genome size than any other Leptidea population. Specific TE subclasses have been active in different Lepidoptera lineages with a pronounced expansion of predominantly LINEs, DNA elements, and unclassified TEs in the Leptidea lineage after the split from other Pieridae. The rate of genome expansion in Leptidea in general has been in the range of four Mb/Million year (My), with an increase in a particular L. juvernica population to 72 Mb/My. The considerable differences in accumulation rates of specific TE classes in different lineages indicate that TE activity plays a major role in genome size evolution in butterflies and moths. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Multitasking of the piRNA Silencing Machinery: Targeting Transposable Elements and Foreign Genes in the Bdelloid Rotifer Adineta vaga

PubMed Central

Rodriguez, Fernando; Arkhipova, Irina R.

2016-01-01

RNA-mediated silencing processes play a key role in silencing of transposable elements, especially in the germ line, where piwi-interacting RNAs (piRNAs) are responsible for suppressing transposon mobility and maintaining genome integrity. We previously reported that the genome of Adineta vaga, the first sequenced representative of the phylum Rotifera (class Bdelloidea), is characterized by massive levels of horizontal gene transfer, by unusually low transposon content, and by highly diversified RNA-mediated silencing machinery. Here, we investigate genome-wide distribution of pi-like small RNAs, which in A. vaga are 25–31 nucleotides in length and have a strong 5′-uridine bias, while lacking ping-pong amplification signatures. In agreement with expectations, 71% of mapped reads corresponded to annotated transposons, with 93% of these reads being in the antisense orientation. Unexpectedly, a significant fraction of piRNAs originate from predicted coding regions corresponding to genes of putatively foreign origin. The distribution of piRNAs across foreign genes is not biased toward 3′-UTRs, instead resembling transposons in uniform distribution pattern throughout the gene body, and in predominantly antisense orientation. We also find that genes with small RNA coverage, including a number of genes of metazoan origin, are characterized by higher occurrence of telomeric repeats in the surrounding genomic regions, and by higher density of transposons in the vicinity, which have the potential to promote antisense transcription. Our findings highlight the complex interplay between RNA-based silencing processes and acquisition of genes at the genome periphery, which can result either in their loss or eventual domestication and integration into the host genome. PMID:27017627

Evolution of Linked Avirulence Effectors in Leptosphaeria maculans Is Affected by Genomic Environment and Exposure to Resistance Genes in Host Plants

PubMed Central

Van de Wouw, Angela P.; Cozijnsen, Anton J.; Hane, James K.; Brunner, Patrick C.; McDonald, Bruce A.; Oliver, Richard P.; Howlett, Barbara J.

2010-01-01

Brassica napus (canola) cultivars and isolates of the blackleg fungus, Leptosphaeria maculans interact in a ‘gene for gene’ manner whereby plant resistance (R) genes are complementary to pathogen avirulence (Avr) genes. Avirulence genes encode proteins that belong to a class of pathogen molecules known as effectors, which includes small secreted proteins that play a role in disease. In Australia in 2003 canola cultivars with the Rlm1 resistance gene suffered a breakdown of disease resistance, resulting in severe yield losses. This was associated with a large increase in the frequency of virulence alleles of the complementary avirulence gene, AvrLm1, in fungal populations. Surprisingly, the frequency of virulence alleles of AvrLm6 (complementary to Rlm6) also increased dramatically, even though the cultivars did not contain Rlm6. In the L. maculans genome, AvrLm1 and AvrLm6 are linked along with five other genes in a region interspersed with transposable elements that have been degenerated by Repeat-Induced Point (RIP) mutations. Analyses of 295 Australian isolates showed deletions, RIP mutations and/or non-RIP derived amino acid substitutions in the predicted proteins encoded by these seven genes. The degree of RIP mutations within single copy sequences in this region was proportional to their proximity to the degenerated transposable elements. The RIP alleles were monophyletic and were present only in isolates collected after resistance conferred by Rlm1 broke down, whereas deletion alleles belonged to several polyphyletic lineages and were present before and after the resistance breakdown. Thus, genomic environment and exposure to resistance genes in B. napus has affected the evolution of these linked avirulence genes in L. maculans. PMID:21079787

Regional Dissemination of a Trimethoprim-Resistance Gene Cassette via a Successful Transposable Element

PubMed Central

Opintan, Japheth A.; Bishar, Rima A.; Aboderin, A. Oladipo; Newman, Mercy J.; Lamikanra, Adebayo; Okeke, Iruka N.

2012-01-01

Background Antimicrobial resistance is a growing international problem. We observed a 50% increase in the prevalence of trimethoprim resistance among fecal Escherichia coli from healthy Nigerian students between 1998 and 2005, a trend to increase that continued in 2009. Methods and Findings A PCR-based screen revealed that 131 (43.1%) of isolates obtained in Nigeria in 2005 and 2009 carried integron-borne dfrA cassettes. In the case of 67 (51.1%) of these isolates, the cassette was a class 1-integron-borne dfrA7 gene, which has been reported at high prevalence from E. coli isolates from other parts of Africa. Complete sequencing of a 27 Kb dfrA7-bearing plasmid from one isolate located the dfrA7 gene within a Tn21-type transposon. The transposon also contained an IS26-derived bla/sul/str element, encoding resistance to β-lactams, sulphonamides and streptomycin, and mercury resistance genes. Although the plasmid backbone was only found in 12 (5.8%) of trimethoprim-resistant isolates, dfrA7 and other transposon-borne genes were detected in 14 (16.3%) and 32 (26.3%) of trimethoprim resistant isolates collected in Nigeria in 2005 and 2009, respectively. Additionally, 37 (19.3%) of trimethoprim-resistant E. coli isolates collected between 2006 and 2008 from Ghana were positive for the dfrA7 and a transposon marker, but only 4 (2.1%) harbored the plasmid backbone. Conclusions Our data point to transposition as a principal mechanism for disseminating dfrA7 among E. coli from Nigeria and Ghana. On-going intensive use of the affordable broad-spectrum antibacterials is likely to promote selective success of a highly prevalent transposable element in West Africa. PMID:22666464

Kidney graft recipients with pretransplantation HLA CLASS I antibodies and high soluble CD30 are at high risk for graft loss.

PubMed

Rodríguez, Libia M; París, Sara C; Arbeláez, Mario; Cotes, José M; Süsal, Caner; Torres, Yolanda; García, Luís F

2007-08-01

In the present study, we investigated whether pretransplantation HLA class I and class II antibodies and pretransplantation levels of soluble CD30 (sCD30) and IgA anti-Fab autoantibodies are predictive of kidney allograft survival. Pretransplantation sera of 504 deceased-donor kidney recipients were tested for IgG HLA class I and class II antibodies, sCD30, and IgA anti-Fab levels using the CTS 4 ELISA kit. Kidney graft survival was estimated by Kaplan-Meier method and multivariate Cox regression. Regardless of the presence of HLA class II antibodies, recipients with high HLA class I reactivity had lower 1-year graft survival than recipients with low reactivity (p < 0.01). Recipients with high sCD30 had lower 5-year graft survival rate than those with low sCD30 (p < 0.01). The sCD30 effect was observed in presensitized and nonsensitized recipients, demonstrated a synergistic effect with HLA class I antibodies (p < 0.001), and appeared to be neutralized in recipients with no HLA class II mismatches. IgA anti-Fab did not influence kidney graft survival. Our results indicate that high pretransplantation sCD30 levels and HLA class I positivity increase the risk of kidney graft loss regardless of other factors. Consequently, such determinations should be routinely performed to estimate recipients' risks of graft rejection before transplantation.

Characterization of swine leucocyte antigen alleles in a crossbred pig to be used in xenotransplant studies.

PubMed

Reyes, L M; Blosser, R J; Smith, R F; Miner, A C; Paris, L L; Blankenship, R L; Tector, M F; Tector, A J

2014-11-01

We have characterized swine leucocyte antigen (SLA) classes I and II molecules of a domestic pig as a model for use in our xenotransplant program. Molecular characterization of the SLA classes I and II genes is critical to understanding the adaptive immune responses between swine and humans in the event of xenotransplantation. Seven swine leucocyte antigen genes (SLA-1, SLA-2, SLA-3, DQB1, DRB1, DQA and DRA) were analyzed and 15 alleles were identified. A novel DRA*w04re01 is reported for this limited polymorphic class II gene. The heterozygous haplotypes, Hp-32.0/35.0 and Hp-0.13/0.23 were deduced for our IU-pig model, for SLA classes I and II regions, respectively. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Identification, characterization, and quantitation of soluble HLA antigens in the circulation and peritoneal dialysate of renal patients.

PubMed Central

Gelder, F B; McDonald, J C; Landreneau, M D; McMillan, R M; Aultman, D F

1991-01-01

Human lymphocyte antigen (HLA) class I and class II antigens and beta 2 microglobulin (B2M) were identified in peritoneal dialysate (PD) and serum from patients with end-stage renal disease (ESRD) using monoclonal antibodies in an enzyme-linked immunoassay. The HLA class I and class II antigens each exhibited approximate molecular weights of 50,000 to 60,000 daltons by chromatography on Sepharose CL 6B. Class I antigens in serum and PD fluid were associated with B2M. Free B2M (Mr 11,500) also was detected in both sera and PD fluids. Unlike class I antigens, class II antigens were not found to have attached B2M. Class I and class II antigens eluted from 2-diethylaminoethanol ion exchange gradient columns at 0.07 mol/L (molar) phosphate buffer pH 7.2 and migrated with alpha 2-beta 1 mobility in agarose electrophoresis. Class I antigens were purified from ESRD patients' PD fluid by solid-phase immunoaffinity chromatography. Enzyme-linked immunoassay demonstrated that this purified protein was composed of a class I heavy chain and B2M. Class I allospecificity was confirmed by neutralization on known HLA typing antisera in a microcytotoxicity assay. Soluble HLA class I antigen preparations specifically inhibited blast transformation of responder lymphocytes in mixed lymphocyte culture reactions. Inhibition was dose dependent and ranged from 0% to 95%. The presence of soluble HLA antigens in body fluids may play an important part in the immunologic tolerance to self. This study demonstrates a ready source of large quantities of soluble HLA for detailed analysis. Images Fig. 1. PMID:2039290

Analysis of Class II patients, successfully treated with the straight-wire and Forsus appliances, based on cervical vertebral maturation status.

PubMed

Servello, David F; Fallis, Drew W; Alvetro, Lisa

2015-01-01

To assess skeletal and dental changes in patients successfully treated with the Forsus appliance based on cervical vertebral maturation status. Forty-seven Class II patients, successfully treated with the Forsus appliance, were divided into peak and postpeak growth groups determined immediately prior to Forsus placement. The mean (SD) ages of the peak and postpeak groups were 13.4 (1.0) and 14.1 (1.3) years, respectively. Superimpositions of initial, Forsus placement, Forsus removal, and final cephalometric radiographs were completed, allowing the measurement of changes during three treatment phases. There were no significant differences between groups during treatment phase 1 (alignment/leveling), with both groups demonstrating a worsening of the Class II molar relationship. However, during treatment phase 2 (Class II correction), patients within the peak group demonstrated significantly higher mean apical base, mandibular and molar changes, and an increased rate of change compared with those in the postpeak group. No significant differences were observed during treatment phase 3 (detail/finishing). Following an initial worsening of the Class II molar relationship as a result of straight-wire appliance effects, Forsus appliance treatment initiated during cervical vertebral maturation status (CS) 3-4 elicits more effective and efficient correction of Class II molar relationships than when initiated during CS 5-6. Data support that these effects are due mainly to maxillary skeletal and dentoalveolar restraint during a period of more rapid mandibular growth.

Nonsurgical treatment of an adult with a skeletal Class II gummy smile using zygomatic temporary anchorage devices and improved superelastic nickel-titanium alloy wires.

PubMed

Ishida, Yuji; Ono, Takashi

2017-11-01

Patients with a severe gummy smile and a skeletal Class II profile are difficult to treat. This case report describes an effective treatment alternative for improving a gummy smile in a patient with a severe Class II molar relationship, severe crowding, and lip protrusion using zygomatic anchorage devices and improved superelastic nickel-titanium wires. A 36-year-old woman had an excessive overjet and a deep overbite with a bilateral Angle Class II molar relationship. The cephalometric analysis demonstrated a Class II skeletal relationship (ANB, 9.5°), retroclination of the mandible (FMA, 38.4°), and severe labial inclination of the mandibular incisors (IMPA, 101.9°). The main treatment objectives included normalizing the overjet and overbite, improving the gummy smile, and establishing a satisfactory occlusion. During treatment with fixed appliances, intrusion of the total maxillary dentition using skeletal anchorage and elimination of the bimaxillary protrusion were achieved. Improvement of the lateral profile and gummy smile enhanced facial esthetics. Intrusion and distalization of the maxillary dentition with skeletal anchorage and improved superelastic nickel-titanium wires provided a satisfactory dental occlusion, esthetic improvement, and adequate function. This approach should be considered as an alternative treatment option to orthognathic surgery for adults with high-angle skeletal Class II malocclusion and a gummy smile. Copyright © 2017 American Association of Orthodontists. Published by Elsevier Inc. All rights reserved.

Probing the Evolution of Massive Young Stellar Objects using Weak Class II 6.7GHz Methanol Maser Emission

NASA Astrophysics Data System (ADS)

Ludwig, Bethany Ann; Cunningham, Nichol

2017-01-01

We present results from an investigation of class II 6.7GHz methanol masers towards four Massive Young Stellar Objects (MYSOs). The sources, selected from the Red MSX Source (RMS) Survey (Lumsden et al. 2013), were previously understood to be non-detections for class II methanol maser emission in the methanol multi-beam (MMB) Survey (Caswell et al. 2010.) Class II methanol masers are a well-known sign post of massive star forming regions and may be utilized to probe their relatively poorly understood formation. It is possible that these non-detections are simply weak masers that are potentially associated with a younger evolutionary phase of MYSOs as hypothesized by Olmi et al. (2014). The sources were chosen to sample various stages of evolution, having similar 21 to 8 micron flux ratios and bolometric luminosities as other MYSOs with previous class II methanol maser detections. We observed all 4 MYSOs with ATCA (~2" resolution) at 10 times deeper sensitivity than previously obtained with the MMB survey and have a spectral resolution of 0.087kms^-1 . The raw data is reduced using the program Miriad (Sault, R. J., et al., 1995) and deconvolutioned using the program CASA (McMullin, J. P., et al. 2007.) We determine one of the four observed MYSOs is harboring a weak class II methanol maser. We discuss the possibility of sensitivity limitations on the remaining sources as well as environmental and evolutionary differences between the sources.

The activation threshold of CD4+ T cells is defined by TCR/peptide-MHC class II interactions in the thymic medulla.

PubMed

Stephen, Tom Li; Tikhonova, Anastasia; Riberdy, Janice M; Laufer, Terri M

2009-11-01

Immature thymocytes that are positively selected based upon their response to self-peptide-MHC complexes develop into mature T cells that are not overtly reactive to those same complexes. Developmental tuning is the active process through which TCR-associated signaling pathways of single-positive thymocytes are attenuated to respond appropriately to the peptide-MHC molecules that will be encountered in the periphery. In this study, we explore the mechanisms that regulate the tuning of CD4(+) single-positive T cells to MHC class II encountered in the thymic medulla. Experiments with murine BM chimeras demonstrate that tuning can be mediated by MHC class II expressed by either thymic medullary epithelial cells or thymic dendritic cells. Tuning does not require the engagement of CD4 by MHC class II on stromal cells. Rather, it is mediated by interactions between MHC class II and the TCR. To understand the molecular changes that distinguish immature hyperactive T cells from tuned mature CD4(+) T cells, we compared their responses to TCR stimulation. The altered response of mature CD4 single-positive thymocytes is characterized by the inhibition of ERK activation by low-affinity self-ligands and increased expression of the inhibitory tyrosine phosphatase SHP-1. Thus, persistent TCR engagement by peptide-MHC class II on thymic medullary stroma inhibits reactivity to self-Ags and prevents autoreactivity in the mature repertoire.

Usefulness of the brain natriuretic peptide to atrial natriuretic peptide ratio in determining the severity of mitral regurgitation.

PubMed

Shimamoto, Ken; Kusumoto, Miyako; Sakai, Rieko; Watanabe, Hirota; Ihara, Syunichi; Koike, Natsuka; Kawana, Masatoshi

2007-03-15

Atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) levels were characterized in subjects with mitral regurgitation (MR). Sixty-two cases of moderate or severe chronic MR were studied. The blood levels of neurohormonal factors were stratified by the known MR prognostic factors of New York Heart Association (NYHA) functional class, left ventricular end-diastolic diameters, left ventricular end-systolic diameter (LVDs), ejection fraction (EF), left atrial diameter and presence of atrial fibrillation (AF). ANP levels were higher in NYHA class II and lower in classes I and III/IV (P=0.0206). BNP levels were higher in NYHA class II than class I (P=0.0355). The BNP/ANP ratio was significantly higher in NYHA classes II and III/IV than in class I (P=0.0007). To differentiate between NYHA classes I/II and III/IV, a cut-off BNP/ANP ratio of 2.97 produced a sensitivity of 78% and specificity of 87%. Compared with subjects in sinus rhythm, patients with AF had an enlarged left atrium and lower ANP levels. The BNP/ANP ratio correlated significantly with left atrial diameter, LVDs and EF (r=0.429, P=0.0017; r=0.351, P=0.0117; and r=-0.349, P=0.0122; respectively), and was significantly higher among all the known operative indications for MR tested (LVDs 45 mm or more, EF 60% or less, NYHA class II or greater and AF; P=0.0073, P=0.003, P=0.0102 and P=0.0149, respectively). In chronic MR, levels of ANP and BNP, and the BNP/ANP ratio are potential indicators of disease severity.

The Influence of Class II Division 2 Malocclusions on the Harmony of the Human Face Profile.

PubMed

Perović, Tatjana

2017-11-24

BACKGROUND Persons with class II division 2 malocclusion are characterized by a very specific dento-skeletal and soft-tissue profile (a profile in which a protruding nose and chin, retruding lips, concave and shortened lower third of the face, and gummy smile are dominant), which is the opposite of the currently modern profiles (convex profile of protruding lips and small chin). The aim of this research was to determine the differences in parameters of harmonies of facial profiles between persons with class II division 2 malocclusions and class I, and to establish the significance of those differences. MATERIAL AND METHODS For this study, 50 patients with class II division 2 malocclusions and 50 patients with class I were selected; profile photos were recorded and a photometric analysis was done: a type of profile according to Schwarz, the shape of a nose, the prominence of chin, biometrical field, the position of lips in relation to the tangent Sn-Pg, S-line (Steiner), E-line (Riketts) and a facial angle according to Arnett. RESULTS The significant differences in profiles of persons with class II division 2 compared to class I were: position and prominence of the chin, the position of the lower and upper lip in relation to the S-line, and smaller value of a facial angle in relation to persons with class I. CONCLUSIONS The differences seen in skeletal profiles were not associated with significant differences in the profiled facial contours of the examined groups. The compensatory role of the fullness of soft tissues of the lips is probably the reason why there were not significant deviations in all the examined parameters.

Isolation and molecular characterization of dTnp1, a mobile and defective transposable element of Nicotiana plumbaginifolia.

PubMed

Meyer, C; Pouteau, S; Rouzé, P; Caboche, M

1994-01-01

By Northern blot analysis of nitrate reductase-deficient mutants of Nicotiana plumbaginifolia, we identified a mutant (mutant D65), obtained after gamma-ray irradiation of protoplasts, which contained an insertion sequence in the nitrate reductase (NR) mRNA. This insertion sequence was localized by polymerase chain reaction (PCR) in the first exon of NR and was also shown to be present in the NR gene. The mutant gene contained a 565 bp insertion sequence that exhibits the sequence characteristics of a transposable element, which was thus named dTnp1. The dTnp1 element has 14 bp terminal inverted repeats and is flanked by an 8-bp target site duplication generated upon transposition. These inverted repeats have significant sequence homology with those of other transposable elements. Judging by its size and the absence of a long open reading frame, dTnp1 appears to represent a defective, although mobile, transposable element. The octamer motif TTTAGGCC was found several times in direct orientation near the 5' and 3' ends of dTnp1 together with a perfect palindrome located after the 5' inverted repeat. Southern blot analysis using an internal probe of dTnp1 suggested that this element occurs as a single copy in the genome of N. plumbaginifolia. It is also present in N. tabacum, but absent in tomato or petunia. The dTnp1 element is therefore of potential use for gene tagging in Nicotiana species.

Nuclear congression and membrane fusion: two distinct events in the yeast karyogamy pathway

PubMed Central

1994-01-01

Karyogamy is the process where haploid nuclei fuse to form a diploid nucleus during yeast mating. We devised a novel genetic screen that identified five new karyogamy (KAR) genes and three new cell fusion (FUS) genes. The kar mutants fell into two classes that represent distinct events in the yeast karyogamy pathway. Class I mutations blocked congression of the nuclei due to cytoplasmic microtubule defects. In Class II mutants, nuclear congression proceeded and the membranes of apposed nuclei were closely aligned but unfused. In vitro, Class II mutant membranes were defective in a homotypic ER/nuclear membrane fusion assay. We propose that Class II mutants define components of a novel membrane fusion complex which functions during vegetative growth and is recruited for karyogamy. PMID:8051211

Comparison of psychosocial status in treatment-seeking women with class III vs. class I-II obesity.

PubMed

Wadden, Thomas A; Butryn, Meghan L; Sarwer, David B; Fabricatore, Anthony N; Crerand, Canice E; Lipschutz, Patti E; Faulconbridge, Lucy; Raper, Steven; Williams, Noel N

2006-01-01

This study compared the psychosocial status and weight loss expectations of women with extreme (class III) obesity who sought bariatric surgery with those of women with class I-II obesity who enrolled in a research study on behavioral weight control. Before treatment, all participants completed the Beck Depression Inventory-II and the Weight and Lifestyle Inventory. This latter questionnaire assesses several domains including symptoms of depression and low self-esteem, history of psychiatric complications, current stressors, and weight loss expectations. Women with class III obesity, as compared with class I-II, reported significantly more symptoms of depression. Fully 25% of women in the former group appeared to have a significant mood disorder that would benefit from treatment. As compared with women with class I-II obesity, significantly more women with class III obesity also reported a history of psychiatric complications, which included physical and sexual abuse and greater stress related to their physical health and financial/legal matters. Both groups of women had unrealistic weight loss expectations. Those who sought surgery expected to lose 47.6 +/- 9.3% of initial weight, compared with 24.8 +/- 8.7% for those who enrolled in behavioral weight control. These findings suggest that women with extreme obesity who seek bariatric surgery should be screened for psychosocial complications. Those determined to have significant psychiatric distress should be referred for behavioral or pharmacological treatment to alleviate their suffering. Long-term studies are needed to provide definitive guidance concerning the relationship between preoperative psychopathology and the outcome of bariatric surgery.

40 CFR 147.2650 - State-administered program-Class I, II, III, IV, and V wells.

Code of Federal Regulations, 2010 CFR

2010-07-01

... CONTROL PROGRAMS Puerto Rico § 147.2650 State-administered program—Class I, II, III, IV, and V wells. The Underground Injection Control Program for all classes of wells in the Commonwealth of Puerto Rico, other than those on Indian lands, is the program administered by Puerto Rico's Environmental Quality Board (EQB...

40 CFR 147.2650 - State-administered program-Class I, II, III, IV, and V wells.

Code of Federal Regulations, 2011 CFR

2011-07-01

... CONTROL PROGRAMS Puerto Rico § 147.2650 State-administered program—Class I, II, III, IV, and V wells. The Underground Injection Control Program for all classes of wells in the Commonwealth of Puerto Rico, other than those on Indian lands, is the program administered by Puerto Rico's Environmental Quality Board (EQB...

40 CFR 147.2650 - State-administered program-Class I, II, III, IV, and V wells.

Code of Federal Regulations, 2013 CFR

2013-07-01

... CONTROL PROGRAMS Puerto Rico § 147.2650 State-administered program—Class I, II, III, IV, and V wells. The Underground Injection Control Program for all classes of wells in the Commonwealth of Puerto Rico, other than those on Indian lands, is the program administered by Puerto Rico's Environmental Quality Board (EQB...

Reliability of Growth Indicators and Efficiency of Functional Treatment for Skeletal Class II Malocclusion: Current Evidence and Controversies.

PubMed

Perinetti, Giuseppe; Contardo, Luca

2017-01-01

Current evidence on the reliability of growth indicators in the identification of the pubertal growth spurt and efficiency of functional treatment for skeletal Class II malocclusion, the timing of which relies on such indicators, is highly controversial. Regarding growth indicators, the hand and wrist (including the sole middle phalanx of the third finger) maturation method and the standing height recording appear to be most reliable. Other methods are subjected to controversies or were showed to be unreliable. Main sources of controversies include use of single stages instead of ossification events and diagnostic reliability conjecturally based on correlation analyses. Regarding evidence on the efficiency of functional treatment, when treated during the pubertal growth spurt, more favorable response is seen in skeletal Class II patients even though large individual responsiveness remains. Main sources of controversies include design of clinical trials, definition of Class II malocclusion, and lack of inclusion of skeletal maturity among the prognostic factors. While no growth indicator may be considered to have a full diagnostic reliability in the identification of the pubertal growth spurt, their use may still be recommended for increasing efficiency of functional treatment for skeletal Class II malocclusion.

Treatment of class ii in adulthood by forsus frd device.

PubMed

DE Nuccio, F; D'Emidio, M M; DE Nuccio, F

2016-01-01

Scientific research data show that the Forsus FRD seems to have a great potential in the correction of Class II in childhood. The conclusions reached by the various Authors seem to support the hypothesis of an exclusively or mainly dentoalveolar correction, as the skeletal correction seems to have no - or little - appreciable results. In the light of such provided by different Authors, the potential of dentoalveolar compensation in adult patients with mild skeletal class II was investigated. At the UOC (Complex Operative Unit) of Orthodontics at "G. Eastman" Hospital Rome, 3 cases of skeletal class II mild (ANB <5 °) in adult patients were selected. They were treated with fixed multibracket appliance and Forsus EZ2 module. Cephalometric tracings were compared at the beginning and at the end of the treatment in order to assess the skeletal and dentoalveolar changes. The occlusal correction was achieved through a dentoalveolar compensation characterized by the flaring of the lower teeth. Forsus FRD equipment is an excellent compromise for the correction of mild Class II, even during the post development age. The resulting correction is appreciated at dental alveolar level with a mesial movement of the incisors and molars.

Reliability of Growth Indicators and Efficiency of Functional Treatment for Skeletal Class II Malocclusion: Current Evidence and Controversies

PubMed Central

2017-01-01

Current evidence on the reliability of growth indicators in the identification of the pubertal growth spurt and efficiency of functional treatment for skeletal Class II malocclusion, the timing of which relies on such indicators, is highly controversial. Regarding growth indicators, the hand and wrist (including the sole middle phalanx of the third finger) maturation method and the standing height recording appear to be most reliable. Other methods are subjected to controversies or were showed to be unreliable. Main sources of controversies include use of single stages instead of ossification events and diagnostic reliability conjecturally based on correlation analyses. Regarding evidence on the efficiency of functional treatment, when treated during the pubertal growth spurt, more favorable response is seen in skeletal Class II patients even though large individual responsiveness remains. Main sources of controversies include design of clinical trials, definition of Class II malocclusion, and lack of inclusion of skeletal maturity among the prognostic factors. While no growth indicator may be considered to have a full diagnostic reliability in the identification of the pubertal growth spurt, their use may still be recommended for increasing efficiency of functional treatment for skeletal Class II malocclusion. PMID:28168195

Mind the gap: Neural coding of species identity in birdsong prosody.

PubMed

Araki, Makoto; Bandi, M M; Yazaki-Sugiyama, Yoko

2016-12-09

Juvenile songbirds learn vocal communication from adult tutors of the same species but not from adults of other species. How species-specific learning emerges from the basic features of song prosody remains unknown. In the zebra finch auditory cortex, we discovered a class of neurons that register the silent temporal gaps between song syllables and are distinct from neurons encoding syllable morphology. Behavioral learning and neuronal coding of temporal gap structure resisted song tutoring from other species: Zebra finches fostered by Bengalese finch parents learned Bengalese finch song morphology transposed onto zebra finch temporal gaps. During the vocal learning period, temporal gap neurons fired selectively to zebra finch song. The innate temporal coding of intersyllable silent gaps suggests a neuronal barcode for conspecific vocal learning and social communication in acoustically diverse environments. Copyright © 2016, American Association for the Advancement of Science.

Parasitism and the retrotransposon life cycle in plants: a hitchhiker's guide to the genome.

PubMed

Sabot, F; Schulman, A H

2006-12-01

LTR (long terminal repeat) retrotransposons are the main components of higher plant genomic DNA. They have shaped their host genomes through insertional mutagenesis and by effects on genome size, gene expression and recombination. These Class I transposable elements are closely related to retroviruses such as the HIV by their structure and presumptive life cycle. However, the retrotransposon life cycle has been closely investigated in few systems. For retroviruses and retrotransposons, individual defective copies can parasitize the activity of functional ones. However, some LTR retrotransposon groups as a whole, such as large retrotransposon derivatives and terminal repeats in miniature, are non-autonomous even though their genomic insertion patterns remain polymorphic between organismal accessions. Here, we examine what is known of the retrotransposon life cycle in plants, and in that context discuss the role of parasitism and complementation between and within retrotransposon groups.

A fast time-difference inverse solver for 3D EIT with application to lung imaging.

PubMed

Javaherian, Ashkan; Soleimani, Manuchehr; Moeller, Knut

2016-08-01

A class of sparse optimization techniques that require solely matrix-vector products, rather than an explicit access to the forward matrix and its transpose, has been paid much attention in the recent decade for dealing with large-scale inverse problems. This study tailors application of the so-called Gradient Projection for Sparse Reconstruction (GPSR) to large-scale time-difference three-dimensional electrical impedance tomography (3D EIT). 3D EIT typically suffers from the need for a large number of voxels to cover the whole domain, so its application to real-time imaging, for example monitoring of lung function, remains scarce since the large number of degrees of freedom of the problem extremely increases storage space and reconstruction time. This study shows the great potential of the GPSR for large-size time-difference 3D EIT. Further studies are needed to improve its accuracy for imaging small-size anomalies.

46 CFR 128.210 - Class II vital systems-materials.

Code of Federal Regulations, 2013 CFR

2013-10-01

... ENGINEERING: EQUIPMENT AND SYSTEMS Materials and Pressure Design § 128.210 Class II vital systems—materials... Commanding Officer, Marine Safety Center, if shown to provide a level of safety equivalent to materials in...

46 CFR 128.210 - Class II vital systems-materials.

Code of Federal Regulations, 2011 CFR

2011-10-01

... ENGINEERING: EQUIPMENT AND SYSTEMS Materials and Pressure Design § 128.210 Class II vital systems—materials... Commanding Officer, Marine Safety Center, if shown to provide a level of safety equivalent to materials in...

46 CFR 128.210 - Class II vital systems-materials.

Code of Federal Regulations, 2010 CFR

2010-10-01

... ENGINEERING: EQUIPMENT AND SYSTEMS Materials and Pressure Design § 128.210 Class II vital systems—materials... Commanding Officer, Marine Safety Center, if shown to provide a level of safety equivalent to materials in...

46 CFR 128.210 - Class II vital systems-materials.

Code of Federal Regulations, 2012 CFR

2012-10-01

... ENGINEERING: EQUIPMENT AND SYSTEMS Materials and Pressure Design § 128.210 Class II vital systems—materials... Commanding Officer, Marine Safety Center, if shown to provide a level of safety equivalent to materials in...

46 CFR 128.210 - Class II vital systems-materials.

Code of Federal Regulations, 2014 CFR

2014-10-01

... ENGINEERING: EQUIPMENT AND SYSTEMS Materials and Pressure Design § 128.210 Class II vital systems—materials... Commanding Officer, Marine Safety Center, if shown to provide a level of safety equivalent to materials in...

HLA antibodies and soluble CD30 are associated with poor renal graft outcome: updated results of a single-center cross-sectional study.

PubMed

Langan, Leanne L; D'Orsogna, Lloyd; Park, Lawrence P; Hughes, Tiffany L; Irish, Ashley; Luxton, Grant; Witt, Campbell S; Christiansen, Frank T

2006-01-01

In a previous study, we have shown that HLA class II antibodies and a high soluble CD30 (sCD30) measured at least 1 year post-transplant predict subsequent graft failure. We have now updated the results of this same cohort of 208 patients 15 months later. HLA-specific antibodies (class I and class II) were detected by ELISA LAT-M and Luminex LabScreen assays. Data on graft outcome was collected with a median follow-up of 4.7 years. By Kaplan-Meier analysis, class II antibody was again associated with a poorer outcome, with an estimated 6-year graft survival of 67% and 71% when detected by ELISA and Luminex, respectively, compared with 92% for those without class II antibody (p < or = 0.0001). A soluble CD30 level of > or = 100 U/ml was also associated with a poorer estimated 6-year graft survival (p = 0.02). HLA antibodies and high sCD30 (> or = 100 U/ml) had an additive effect such that those with both high sCD30 and class II antibodies had a hazard ratio for subsequent graft failure of 18.1 (p = 0.0008) and 8.6 (p = 0.007) when detected by ELISA and Luminex, respectively. These data show that detection of HLA class II antibodies and serum sCD30 measured at least 1 year post-transplant continues to predict a subsequent outcome up to 6 years after the initial measurement; they also show that such measures provide important information that may allow for modification of ongoing therapy.

Relationship between crown-root angulation (collum angle) of maxillary central incisors in Class II, division 2 malocclusion and lower lip line.

PubMed

Srinivasan, Bhadrinath; Kailasam, Vignesh; Chitharanjan, Arun; Ramalingam, Arthi

2013-01-01

The present study aimed to measure the magnitude of the collum angle (crown-root angulation) of maxillary central incisors present in Class II, division 2 malocclusion and to relate the changes in its magnitude with variations in the lower lip line. A set of 120 conventional lateral cephalograms were selected and divided into three groups of 40 each based on the type of malocclusion presented: Class II, division 2 (group 1); Class II, division 1 (group 2); and Class I (group 3). The collum angle of the maxillary central incisor was measured, and the lower lip line was recorded. Analysis of variance (ANOVA) revealed that the mean collum angle was statistically significantly different in the three groups. The mean collum angle was greatest in Class II, division 2 malocclusion (group 1). The mean collum angles were 3.24 ± 4.69 degrees, 0.95 ± 1.06 degrees, and 1.05 ± 1.50 degrees in groups 1, 2, and 3 respectively. In χ ² test comparison of the location of the lower lip line (incisal, middle, or apical third of the central incisor) among the three groups, the lower lip line was found to contact the middle third of the central incisor most frequently in Class II, division 2 malocclusion. ANOVA followed by Tukey honestly significant difference (HSD) test showed that the mean collum angle is significantly increased when the lower lip is in the middle third (P < .05) of the central incisor. Variations in magnitude of the collum angle with the change in the lower lip line suggest a probable etiologic role of the lower lip line in the development of the collum angle.

Molecular Characterization, Gene Evolution, and Expression Analysis of the Fructose-1, 6-bisphosphate Aldolase (FBA) Gene Family in Wheat (Triticum aestivum L.)

PubMed Central

Lv, Geng-Yin; Guo, Xiao-Guang; Xie, Li-Ping; Xie, Chang-Gen; Zhang, Xiao-Hong; Yang, Yuan; Xiao, Lei; Tang, Yu-Ying; Pan, Xing-Lai; Guo, Ai-Guang; Xu, Hong

2017-01-01

Fructose-1, 6-bisphosphate aldolase (FBA) is a key plant enzyme that is involved in glycolysis, gluconeogenesis, and the Calvin cycle. It plays significant roles in biotic and abiotic stress responses, as well as in regulating growth and development processes. In the present paper, 21 genes encoding TaFBA isoenzymes were identified, characterized, and categorized into three groups: class I chloroplast/plastid FBA (CpFBA), class I cytosol FBA (cFBA), and class II chloroplast/plastid FBA. By using a prediction online database and genomic PCR analysis of Chinese Spring nulli-tetrasomic lines, we have confirmed the chromosomal location of these genes in 12 chromosomes of four homologous groups. Sequence and genomic structure analysis revealed the high identity of the allelic TaFBA genes and the origin of different TaFBA genes. Numerous putative environment stimulus-responsive cis-elements have been identified in 1,500-bp regions of TaFBA gene promoters, of which the most abundant are the light-regulated elements (LREs). Phylogenetic reconstruction using the deduced protein sequence of 245 FBA genes indicated an independent evolutionary pathway for the class I and class II groups. Although, earlier studies have indicated that class II FBA only occurs in prokaryote and fungi, our results have demonstrated that a few class II CpFBAs exist in wheat and other closely related species. Class I TaFBA was predicted to be tetramers and class II to be dimers. Gene expression analysis based on microarray and transcriptome databases suggested the distinct role of TaFBAs in different tissues and developmental stages. The TaFBA 4–9 genes were highly expressed in leaves and might play important roles in wheat development. The differential expression patterns of the TaFBA genes in light/dark and a few abiotic stress conditions were also analyzed. The results suggested that LRE cis-elements of TaFBA gene promoters were not directly related to light responses. Most TaFBA genes had higher expression levels in the roots than in the shoots when under various stresses. Class I cytosol TaFBA genes, particularly TaFBA10/12/18 and TaFBA13/16, and three class II TaFBA genes are involved in responses to various abiotic stresses. Class I CpFBA genes in wheat are apparently sensitive to different stress conditions. PMID:28659962

Tooth size discrepancies in Class II division 1 and Class III malocclusion requiring surgical-orthodontic or orthodontic treatment.

PubMed

McSwiney, Timothy P; Millett, Declan T; McIntyre, Grant T; Barry, Mark K; Cronin, Michael S

2014-06-01

To compare mean anterior (AR) and mean overall (OR) tooth size ratios, prevalence of clinically significant tooth size discrepancies (TSDs) and correlation between AR and OR in subjects with Class II division 1 and Class III malocclusion treated by surgical-orthodontic or orthodontic means. Retrospective, cross-sectional. State-funded and private clinics. From pre-treatment cohorts of 770 surgical and 610 non-surgical subjects, Class II division 1 and Class III malocclusion groups were identified with 60 surgical and 60 non-surgical subjects, comprising 30 males and 30 females, in each. AR and OR were calculated by landmarking digital models. Differences in AR and OR and their relationship were analysed using two-way analysis of variance (ANOVA) and a correlation coefficient, respectively. The proportions of the surgical and non-surgical groups with a TSD were assessed using logistic regression. Intra-examiner reproducibility involved re-landmarking 30 randomly selected image sets and differences in ARs and ORs were compared using a paired t-test. Random error was assessed using the intraclass correlation coefficient (ICC). Analyses were performed using SAS (SAS Institute Inc., Cary, NC, USA) at the 5% level of significance. There were no statistically significant differences associated with the measurement of either the mean AR (P = 0·913) or the mean OR (P = 0·874). ICC values were very high (AR = 0·95; OR = 0·90). Differences existed between both Class II and Class III surgical (AR: P<0·001; OR: P<0·001) and non-surgical groups (AR: P = 0·012; OR: P = 0·003). The AR and OR relationship was strong (correlation coefficient = 0·72). The highest percentage of clinically significant TSDs was seen in the AR of both Class II and Class III surgical groups (23·3%). In the cohort examined: AR and OR differed significantly for malocclusion groups. The prevalence of clinically significant TSDs did not differ significantly between surgical and non-surgical groups although the highest percentage of clinically significant TSDs was recorded for AR in Class II and Class III surgical cases. AR and OR were closely related. © 2014 British Orthodontic Society.

Dynamic range of Nef-mediated evasion of HLA class II-restricted immune responses in early HIV-1 infection.

PubMed

Mahiti, Macdonald; Brumme, Zabrina L; Jessen, Heiko; Brockman, Mark A; Ueno, Takamasa

2015-07-31

HLA class II-restricted CD4(+) T lymphocytes play an important role in controlling HIV-1 replication, especially in the acute/early infection stage. But, HIV-1 Nef counteracts this immune response by down-regulating HLA-DR and up-regulating the invariant chain associated with immature HLA-II (Ii). Although functional heterogeneity of various Nef activities, including down-regulation of HLA class I (HLA-I), is well documented, our understanding of Nef-mediated evasion of HLA-II-restricted immune responses during acute/early infection remains limited. Here, we examined the ability of Nef clones from 47 subjects with acute/early progressive infection and 46 subjects with chronic progressive infection to up-regulate Ii and down-regulate HLA-DR and HLA-I from the surface of HIV-infected cells. HLA-I down-regulation function was preserved among acute/early Nef clones, whereas both HLA-DR down-regulation and Ii up-regulation functions displayed relatively broad dynamic ranges. Nef's ability to down-regulate HLA-DR and up-regulate Ii correlated positively at this stage, suggesting they are functionally linked in vivo. Acute/early Nef clones also exhibited higher HLA-DR down-regulation and lower Ii up-regulation functions compared to chronic Nef clones. Taken together, our results support enhanced Nef-mediated HLA class II immune evasion activities in acute/early compared to chronic infection, highlighting the potential importance of these functions following transmission. Copyright © 2015 Elsevier Inc. All rights reserved.

Mouse HLA-DPA homologue H2-Pa: A pseudogene that maps between H2-Pb and H2-Oa

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arimura, Y.; Koda, T.; Kishi, M.

1996-12-31

The major histocompatibility complex (MHC) class II subregion contains several subclasses of genes. The classical class II genes, HLA-DP, DQ, and DR homologues, present antigens directly to CD4{sup +} T cells. HLA-DM homologues facilitate the efficacy and transport of antigens to the cell surface by removing the CLIP peptides from the classical class II molecules. HLA-DNA/DOB homologues show unusual expression patterns and limited polymorphism, but their function is yet to be elucidated. 15 refs., 2 figs.

Evaluating the protein coding potential of exonized transposable element sequences

PubMed Central

Piriyapongsa, Jittima; Rutledge, Mark T; Patel, Sanil; Borodovsky, Mark; Jordan, I King

2007-01-01

Background Transposable element (TE) sequences, once thought to be merely selfish or parasitic members of the genomic community, have been shown to contribute a wide variety of functional sequences to their host genomes. Analysis of complete genome sequences have turned up numerous cases where TE sequences have been incorporated as exons into mRNAs, and it is widely assumed that such 'exonized' TEs encode protein sequences. However, the extent to which TE-derived sequences actually encode proteins is unknown and a matter of some controversy. We have tried to address this outstanding issue from two perspectives: i-by evaluating ascertainment biases related to the search methods used to uncover TE-derived protein coding sequences (CDS) and ii-through a probabilistic codon-frequency based analysis of the protein coding potential of TE-derived exons. Results We compared the ability of three classes of sequence similarity search methods to detect TE-derived sequences among data sets of experimentally characterized proteins: 1-a profile-based hidden Markov model (HMM) approach, 2-BLAST methods and 3-RepeatMasker. Profile based methods are more sensitive and more selective than the other methods evaluated. However, the application of profile-based search methods to the detection of TE-derived sequences among well-curated experimentally characterized protein data sets did not turn up many more cases than had been previously detected and nowhere near as many cases as recent genome-wide searches have. We observed that the different search methods used were complementary in the sense that they yielded largely non-overlapping sets of hits and differed in their ability to recover known cases of TE-derived CDS. The probabilistic analysis of TE-derived exon sequences indicates that these sequences have low protein coding potential on average. In particular, non-autonomous TEs that do not encode protein sequences, such as Alu elements, are frequently exonized but unlikely to encode protein sequences. Conclusion The exaptation of the numerous TE sequences found in exons as bona fide protein coding sequences may prove to be far less common than has been suggested by the analysis of complete genomes. We hypothesize that many exonized TE sequences actually function as post-transcriptional regulators of gene expression, rather than coding sequences, which may act through a variety of double stranded RNA related regulatory pathways. Indeed, their relatively high copy numbers and similarity to sequences dispersed throughout the genome suggests that exonized TE sequences could serve as master regulators with a wide scope of regulatory influence. Reviewers: This article was reviewed by Itai Yanai, Kateryna D. Makova, Melissa Wilson (nominated by Kateryna D. Makova) and Cedric Feschotte (nominated by John M. Logsdon Jr.). PMID:18036258

MRP (materiel requirements planning) II implementation: a case study.

PubMed

Sheldon, D

1994-05-01

Manufacturing resource planning (MRP II) is a powerful and effective business planning template on which to build a continuous improvement culture. MRP II, when successfully implemented, encourages a disciplined yet nonthreatening environment centered on measurement and accountability. From the education that accompanies an MRP II implementation, the employees can better understand the vision and mission of the organization. This common goal keeps everyone's energy directed toward the same final objective. The Raymond Corporation is a major materiels handling equipment manufacturer headquartered in Greene, New York, with class "A" MRP II manufacturing facilities in Greene and Brantford, Ontario and an aftermark distribution facility in East Syracuse, New York. Prior to the implementation of MRP II in its Greene plant (from 1988 through 1990) good intentions and hard work were proving to be less than necessary to compete in the global market. Certified class "A" in February 1990. The Raymond Corporation has built a world-class organization from these foundations.

Genomic localization of the human gene encoding Dr1, a negative modulator of transcription of class II and class III genes.

PubMed

Purrello, M; Di Pietro, C; Rapisarda, A; Viola, A; Corsaro, C; Motta, S; Grzeschik, K H; Sichel, G

1996-01-01

Dr1 is a nuclear protein of 19 kDa that exists in the nucleoplasm as a homotetramer. By binding to TBP (the DNA-binding subunit of TFIID, and also a subunit of SL1 and TFIIIB), the protein blocks class II and class III preinitiation complex assembly, thus repressing the activity of the corresponding promoters. Since transcription of class I genes is unaffected by Dr1. it has been proposed that the protein may coordinate the expression of class I, class II and class III genes. By somatic cell genetics and fluorescence in situ hybridization, we have localized the gene (DR1), present in the genome of higher eukaryotes as a single copy, to human chromosome region 1p21-->p13. The nucleotide sequence conservation of the coding segment of the gene, as determined by Noah's ark blot analysis, and its ubiquitous transcription suggest that Dr1 has an important biological role, which could be related to the negative control of cell proliferation.

HIV Controllers Exhibit Enhanced Frequencies of Major Histocompatibility Complex Class II Tetramer+ Gag-Specific CD4+ T Cells in Chronic Clade C HIV-1 Infection.

PubMed

Laher, Faatima; Ranasinghe, Srinika; Porichis, Filippos; Mewalal, Nikoshia; Pretorius, Karyn; Ismail, Nasreen; Buus, Søren; Stryhn, Anette; Carrington, Mary; Walker, Bruce D; Ndung'u, Thumbi; Ndhlovu, Zaza M

2017-04-01

Immune control of viral infections is heavily dependent on helper CD4 + T cell function. However, the understanding of the contribution of HIV-specific CD4 + T cell responses to immune protection against HIV-1, particularly in clade C infection, remains incomplete. Recently, major histocompatibility complex (MHC) class II tetramers have emerged as a powerful tool for interrogating antigen-specific CD4 + T cells without relying on effector functions. Here, we defined the MHC class II alleles for immunodominant Gag CD4 + T cell epitopes in clade C virus infection, constructed MHC class II tetramers, and then used these to define the magnitude, function, and relation to the viral load of HIV-specific CD4 + T cell responses in a cohort of untreated HIV clade C-infected persons. We observed significantly higher frequencies of MHC class II tetramer-positive CD4 + T cells in HIV controllers than progressors ( P = 0.0001), and these expanded Gag-specific CD4 + T cells in HIV controllers showed higher levels of expression of the cytolytic proteins granzymes A and B. Importantly, targeting of the immunodominant Gag41 peptide in the context of HLA class II DRB1*1101 was associated with HIV control ( r = -0.5, P = 0.02). These data identify an association between HIV-specific CD4 + T cell targeting of immunodominant Gag epitopes and immune control, particularly the contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infection. Furthermore, these results highlight the advantage of the use of class II tetramers in evaluating HIV-specific CD4 + T cell responses in natural infections. IMPORTANCE Increasing evidence suggests that virus-specific CD4 + T cells contribute to the immune-mediated control of clade B HIV-1 infection, yet there remains a relative paucity of data regarding the role of HIV-specific CD4 + T cells in shaping adaptive immune responses in individuals infected with clade C, which is responsible for the majority of HIV infections worldwide. Understanding the contribution of HIV-specific CD4 + T cell responses in clade C infection is particularly important for developing vaccines that would be efficacious in sub-Saharan Africa, where clade C infection is dominant. Here, we employed MHC class II tetramers designed to immunodominant Gag epitopes and used them to characterize CD4 + T cell responses in HIV-1 clade C infection. Our results demonstrate an association between the frequency of HIV-specific CD4 + T cell responses targeting an immunodominant DRB1*11-Gag41 complex and HIV control, highlighting the important contribution of a single class II MHC-peptide complex to the immune response against HIV-1 infections. Copyright © 2017 American Society for Microbiology.

Class I and class II major histocompatibility molecules play a role in bone marrow-derived macrophage development

NASA Technical Reports Server (NTRS)

Armstrong, J. W.; Simske, S. J.; Beharka, A. A.; Balch, S.; Luttges, M. W.; Chapes, S. K.; Spooner, B. S. (Principal Investigator)

1994-01-01

Class I and class II major histocompatibility complex (MHC) molecules play significant roles in T cell development and immune function. We show that MHCI- and MHCII-deficient mice have low numbers of macrophage precursors and circulating monocytes, as well as abnormal bone marrow cell colony-stimulating factor type 1 secretion and bone composition. We suggest that MHCI and MHCII molecules play a significant role in macrophage development.

40 CFR Figure C-2 to Subpart C of... - Illustration of the Slope and Intercept Limits for Class II and Class III PM 2.5 Candidate...

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 6 2014-07-01 2014-07-01 false Illustration of the Slope and Intercept Limits for Class II and Class III PM 2.5 Candidate Equivalent Methods C Figure C-2 to Subpart C of Part... Candidate Methods and Reference Methods Pt. 53, Subpt. C, Fig. C-2 Figure C-2 to Subpart C of Part 53...

40 CFR Figure C-2 to Subpart C of... - Illustration of the Slope and Intercept Limits for Class II and Class III PM 2.5 Candidate...

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 6 2013-07-01 2013-07-01 false Illustration of the Slope and Intercept Limits for Class II and Class III PM 2.5 Candidate Equivalent Methods C Figure C-2 to Subpart C of Part... Candidate Methods and Reference Methods Pt. 53, Subpt. C, Fig. C-2 Figure C-2 to Subpart C of Part 53...

Congenital Stapes Ankylosis in Children: Surgical Findings and Results in 35 Cases.

PubMed

Vincent, Robert; Wegner, Inge; Kamalski, Digna M A; Bittermann, Arnold J N; Grolman, Wilko

2016-04-01

To evaluate surgical findings and hearing results in children undergoing middle ear surgery for congenital stapes ankylosis with or without other ossicular malformations (Teunissen and Cremers class I and class II malformations). A nonrandomized, nonblinded case series of prospectively collected data. A tertiary referral center. Twenty-eight consecutive pediatric patients who underwent 35 surgical procedures for congenital stapes ankylosis with or without other ossicular malformations and had available postoperative pure-tone audiometry. Primary stapedotomy with vein graft interposition and reconstruction with a Teflon piston, bucket handle prosthesis or total ossicular replacement prosthesis. Pre- and postoperative audiometric evaluation using four-frequency (0.5, 1, 2, and 4 kHz) audiometry. Air-conduction thresholds, bone-conduction thresholds, and air-bone gaps (ABGs) were measured. Postoperative audiometry was performed at 3, 6, 9, 12, 18, and 24 months after surgery and at a yearly interval thereafter. Overall, a postoperative ABG closure of 10 dB or less was achieved in 73% of class I cases and in 50% of class II cases. A postoperative ABG closure of 20 dB or less was achieved in 77% of class I cases and 67% of class II cases. Postoperative sensorineural hearing loss occurred in one class I case (4%) and none of the class II cases. Stapedotomy is a safe and feasible treatment option in children with congenital stapes ankylosis.

Machine Learning-Assisted Network Inference Approach to Identify a New Class of Genes that Coordinate the Functionality of Cancer Networks.

PubMed

Ghanat Bari, Mehrab; Ung, Choong Yong; Zhang, Cheng; Zhu, Shizhen; Li, Hu

2017-08-01

Emerging evidence indicates the existence of a new class of cancer genes that act as "signal linkers" coordinating oncogenic signals between mutated and differentially expressed genes. While frequently mutated oncogenes and differentially expressed genes, which we term Class I cancer genes, are readily detected by most analytical tools, the new class of cancer-related genes, i.e., Class II, escape detection because they are neither mutated nor differentially expressed. Given this hypothesis, we developed a Machine Learning-Assisted Network Inference (MALANI) algorithm, which assesses all genes regardless of expression or mutational status in the context of cancer etiology. We used 8807 expression arrays, corresponding to 9 cancer types, to build more than 2 × 10 8 Support Vector Machine (SVM) models for reconstructing a cancer network. We found that ~3% of ~19,000 not differentially expressed genes are Class II cancer gene candidates. Some Class II genes that we found, such as SLC19A1 and ATAD3B, have been recently reported to associate with cancer outcomes. To our knowledge, this is the first study that utilizes both machine learning and network biology approaches to uncover Class II cancer genes in coordinating functionality in cancer networks and will illuminate our understanding of how genes are modulated in a tissue-specific network contribute to tumorigenesis and therapy development.

Entanglement cost under positive-partial-transpose-preserving operations.

PubMed

Audenaert, K; Plenio, M B; Eisert, J

2003-01-17

We study the entanglement cost under quantum operations preserving the positivity of the partial transpose (PPT operations). We demonstrate that this cost is directly related to the logarithmic negativity, thereby providing the operational interpretation for this entanglement measure. As examples we discuss general Werner states and arbitrary bipartite Gaussian states. Then we prove that for the antisymmetric Werner state PPT cost and PPT entanglement of distillation coincide. This is the first example of a truly mixed state for which entanglement manipulation is asymptotically reversible, which points towards a unique entanglement measure under PPT operations.

Sequence of retrovirus provirus resembles that of bacterial transposable elements

NASA Astrophysics Data System (ADS)

Shimotohno, Kunitada; Mizutani, Satoshi; Temin, Howard M.

1980-06-01

The nucleotide sequences of the terminal regions of an infectious integrated retrovirus cloned in the modified λ phage cloning vector Charon 4A have been elucidated. There is a 569-base pair direct repeat at both ends of the viral DNA. The cell-virus junctions at each end consist of a 5-base pair direct repeat of cell DNA next to a 3-base pair inverted repeat of viral DNA. This structure resembles that of a transposable element and is consistent with the protovirus hypothesis that retroviruses evolved from the cell genome.

Therapeutic approach to Class II, Division 1 malocclusion with maxillary functional orthopedics

PubMed Central

de Bittencourt, Aristeu Corrêa; Saga, Armando Yukio; Pacheco, Ariel Adriano Reyes; Tanaka, Orlando

2015-01-01

INTRODUCTION: Interceptive treatment of Class II, Division 1 malocclusion is a challenge orthodontists commonly face due to the different growth patterns they come across and the different treatment strategies they have available. OBJECTIVE: To report five cases of interceptive orthodontics performed with the aid of Klammt's elastic open activator (KEOA) to treat Class II, Division 1 malocclusion. METHODS: Treatment comprehends one or two phases; and the use of functional orthopedic appliances, whenever properly recommended, is able to minimize dentoskeletal discrepancies with consequent improvement in facial esthetics during the first stage of mixed dentition. The triad of diagnosis, correct appliance manufacture and patient's compliance is imperative to allow KEOA to contribute to Class II malocclusion treatment. RESULTS: Cases reported herein showed significant improvement in skeletal, dental and profile aspects, as evinced by cephalometric analysis and clinical photographs taken before, during and after interceptive orthodontics. PMID:26352852

Orthodontic Camouflage Treatment in an Adult Patient with a Class II, Division 1 Malocclusion – A Case Report

PubMed Central

Naragond, Appasaheb; Kenganal, Smitha; Sagarkar, Roshan; Sugaradday

2013-01-01

Since so many decades, various treatment modalities have been presented for the treatment for the class II, div 1 malocclusions. In recent times, we have seen enormously increasing numbers of young adults who desire the shortest, cost effective and a non surgical correction of Class II malocclusions and they accept dental camouflage as a treatment option to mask the skeletal discrepancy. This case report presents one such case of a 22 year old non-growing female who had a skeletal Class II, division 1 malocclusion with an orthognathic maxilla, a retrognathic mandible, a negative VTO and an overjet of 12mm, who did not want a surgical treatment. We considered the camouflage treatment by extracting the upper first premolars. Following the treatment, a satisfactory result was achieved with an ideal, static and a functional occlusion, facial profile, smile and lip competence and stability of the treatment results. PMID:23543878

Duration of the peak of adolescent growth spurt in class i and ii malocclusion subjects using a cervical vertebrae maturation analysis.

PubMed

Salazar-Lazo, Rodrigo; Arriola-Guillén, Luis E; Flores-Mir, Carlos

2014-01-01

The aim of the present work was to determine the duration of the adolescent peak growth spurt using cervical vertebral maturation analysis in class I and II malocclusion subjects. The study was conducted on a sample which consisted of 154 lateral cephalograms of children and adolescents aged 9-15 years (84 females and 70 males). The evaluation of skeletal maturation stage was performed using a visual morphological analysis of CS3 and CS4 cervical vertebrae. The sagittal skeletal relation was evaluated according to Steiner analysis. Descriptive statistics were used to summarize chronological age in each malocclusion group and for each CS3 and CS4 skeletal maturation stage. Due to a lack of normal distribution, comparisons of CS3 and CS4 age intervals on class I and II subjects were compared using the Mann-Whitney U test for independent samples. The results show that the mean duration of the adolescent peak growth spurt was 10 months between CS3 and CS4 stages in class I malocclusion subjects, whereas in class II malocclusion patients the duration was 6 months. This difference of 4 months was statistically significant (p<0.001). Finally, a clinically significant difference of 4 months in the duration of the adolescent peak growth spurt for class I and II malocclusion subjects was identified.