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Sample records for acid repeat region

  1. Understanding and identifying amino acid repeats.

    PubMed

    Luo, Hong; Nijveen, Harm

    2014-07-01

    Amino acid repeats (AARs) are abundant in protein sequences. They have particular roles in protein function and evolution. Simple repeat patterns generated by DNA slippage tend to introduce length variations and point mutations in repeat regions. Loss of normal and gain of abnormal function owing to their variable length are potential risks leading to diseases. Repeats with complex patterns mostly refer to the functional domain repeats, such as the well-known leucine-rich repeat and WD repeat, which are frequently involved in protein–protein interaction. They are mainly derived from internal gene duplication events and stabilized by ‘gate-keeper’ residues, which play crucial roles in preventing inter-domain aggregation. AARs are widely distributed in different proteomes across a variety of taxonomic ranges, and especially abundant in eukaryotic proteins. However, their specific evolutionary and functional scenarios are still poorly understood. Identifying AARs in protein sequences is the first step for the further investigation of their biological function and evolutionary mechanism. In principle, this is an NP-hard problem, as most of the repeat fragments are shaped by a series of sophisticated evolutionary events and become latent periodical patterns. It is not possible to define a uniform criterion for detecting and verifying various repeat patterns. Instead, different algorithms based on different strategies have been developed to cope with different repeat patterns. In this review, we attempt to describe the amino acid repeat-detection algorithms currently available and compare their strategies based on an in-depth analysis of the biological significance of protein repeats. PMID:23418055

  2. Activating frataxin expression by repeat-targeted nucleic acids.

    PubMed

    Li, Liande; Matsui, Masayuki; Corey, David R

    2016-02-04

    Friedreich's ataxia is an incurable genetic disorder caused by a mutant expansion of the trinucleotide GAA within an intronic FXN RNA. This expansion leads to reduced expression of frataxin (FXN) protein and evidence suggests that transcriptional repression is caused by an R-loop that forms between the expanded repeat RNA and complementary genomic DNA. Synthetic agents that increase levels of FXN protein might alleviate the disease. We demonstrate that introducing anti-GAA duplex RNAs or single-stranded locked nucleic acids into patient-derived cells increases FXN protein expression to levels similar to analogous wild-type cells. Our data are significant because synthetic nucleic acids that target GAA repeats can be lead compounds for restoring curative FXN levels. More broadly, our results demonstrate that interfering with R-loop formation can trigger gene activation and reveal a new strategy for upregulating gene expression.

  3. Repeating Earthquakes in the Darfield Region, New Zealand

    NASA Astrophysics Data System (ADS)

    Armstrong, R. S.; Syracuse, E. M.; Thurber, C. H.; Anderson, M. L.

    2012-12-01

    The M 7.1 3 September 2010 Darfield, New Zealand, earthquake ruptured a previously unknown fault system. Fault-slip models (e.g., Beavan et al. 2010; Holden et al. 2011; Eliott et al. 2012) have been calculated using InSAR, GPS, and seismic data. They show that although the rupture initiated on a SW-dipping thrust fault, the majority of fault motion was right-lateral strike slip from the surface to 10 km depth. The InSAR data used in the geodetic model provide the cumulative ground motion due to the Darfield earthquake and some early aftershocks, while the seismic model utilizes waveforms for the mainshock, limiting the solution to slip during the initial rupture. This study utilizes cross-correlation methods to identify repeating earthquakes within continuous seismic waveforms from the Canterbury Region, New Zealand between September 2010 and January 2011. Understanding the extent of repeating earthquakes, which have similar magnitudes, locations, and source mechanisms, on different fault segments with respect to the geodetic and seismic models of the initial September 2010 rupture will provide insight into post-seismic fault motion along individual segments over a 4-month period. Fault afterslip can be estimated from the cumulative moment of the repeating earthquakes within that fault segment. The most consistent groups of repeaters identified by our method tended to be located on two E-W strike-slip fault segments associated with the surface rupture of the Darfield earthquake, as well as a ~20 km long band of seismicity along a N-S fault segment that may have not been active during the Darfield mainshock.

  4. Polymorphism of Repeated Regions of Pertactin in Bordetella pertussis, Bordetella parapertussis, and Bordetella bronchiseptica

    PubMed Central

    Boursaux-Eude, Caroline; Guiso, Nicole

    2000-01-01

    Pertactin is an outer membrane protein expressed by Bordetella pertussis, Bordetella parapertussis, and Bordetella bronchiseptica that induces protective immunity to Bordetella infections. The immunodominant and immunoprotective epitopes of pertactin include two repeated regions, I and II. Comparison of these two repeated regions showed that B. parapertussis pertactin is invariant, whereas B. pertussis pertactin varies mostly in region I and B. bronchiseptica pertactin varies in both repeated regions I and II, but mostly in region II. These differences may result from specific characteristics of these Bordetella species. PMID:10899896

  5. Tandem repeats and heteroplasmy in the mitochondrial DNA control region of the loggerhead shrike (Lanius ludovicianus).

    PubMed

    Mundy, N I; Winchell, C S; Woodruff, D S

    1996-01-01

    We report the presence of a 128 bp tandem repeat in the mitochondrial control region of the loggerhead shrike (Aves: Lanius ludovicianus). All individuals examined had either two or three copies of the repeat or were heteroplasmic for two and three copies. This is the first direct demonstration of a tandem repeat associated with heteroplasmy in the control region of a bird. A novel model for repeat duplication, which involves an inverted repeat located adjacent to the tandemly repeated sequence, is presented. Individuals with three repeats are absent from the endangered population of San Clemente loggerhead shrike in southern California, suggesting that the island endemic has a small effective population size and that there is insignificant gene flow from the adjacent mainland.

  6. The Conversion of Carboxylic Acids to Ketones: A Repeated Discovery

    ERIC Educational Resources Information Center

    Nicholson, John W.; Wilson, Alan D.

    2004-01-01

    The conversion of carboxylic acids to ketones is a useful chemical transformation with a long history. Several chemists have claimed that they discovered the conversion of carboxylic acids to ketones yet in fact the reaction is actually known for centuries.

  7. Effects of repeated doses of aspartame on serotonin and its metabolite in various regions of the mouse brain.

    PubMed

    Sharma, R P; Coulombe, R A

    1987-08-01

    Following a finding that single doses (approximating to average intakes and to potential 'over-use') of aspartame administered orally to mice caused significant increases in norepinephrine and dopamine concentrations in various brain regions, the effect of repeated exposure to aspartame was studied. Male CD-1 mice were given a daily oral dose of 0, 13, 133 or 650 mg/kg for 30 days and 1 day after the last dose the animals were decapitated and their brain regions were quickly isolated. Analyses of the different regions for catecholamine and indoleamine neurotransmitters and their major metabolites indicated that the increases in adrenergic chemicals observed shortly after a single exposure were not apparent after repeated dosing. In contrast, concentrations of serotonin and its metabolite, 5-hydroxyindoleacetic acid, were decreased in several regions. An increased supply of phenylalanine may be responsible for a decrease in tryptophan uptake by the brain tissue or for a depression in tryptophan conversion to serotonin.

  8. Amino acid repeats cause extraordinary coding sequence variation in the social amoeba Dictyostelium discoideum.

    PubMed

    Scala, Clea; Tian, Xiangjun; Mehdiabadi, Natasha J; Smith, Margaret H; Saxer, Gerda; Stephens, Katie; Buzombo, Prince; Strassmann, Joan E; Queller, David C

    2012-01-01

    Protein sequences are normally the most conserved elements of genomes owing to purifying selection to maintain their functions. We document an extraordinary amount of within-species protein sequence variation in the model eukaryote Dictyostelium discoideum stemming from triplet DNA repeats coding for long strings of single amino acids. D. discoideum has a very large number of such strings, many of which are polyglutamine repeats, the same sequence that causes various human neurological disorders in humans, like Huntington's disease. We show here that D. discoideum coding repeat loci are highly variable among individuals, making D. discoideum a candidate for the most variable proteome. The coding repeat loci are not significantly less variable than similar non-coding triplet repeats. This pattern is consistent with these amino-acid repeats being largely non-functional sequences evolving primarily by mutation and drift. PMID:23029418

  9. Phenylbutyric acid protects against spatial memory deficits in a model of repeated electroconvulsive therapy.

    PubMed

    Yao, Zhao-Hui; Kang, Xiang; Yang, Liu; Niu, Yi; Lu, Ye; Gong, Cheng-Xin; Tian, Qing; Wang, Jian-Zhi

    2014-05-01

    Repeated electroconvulsive therapy (rECT) is widely applied in the treatment of refractory depression. Among the side effects of rECT, memory impairment is noticeable and needs effective protection. In this study, by employing a recognized repeated electroconvulsive shock (rECS) rat model, we found that rECS induced the significant spatial memory retention deficits with the simultaneous decreases in long-term potential (LTP), enhanced excitable postsynaptic potentials (EPSP), population spike (PS) and input/output curve in perforant pathway-dentate gyrus (PP-DG), but had no obvious neuron loss or dentritic spine loss in the brain by Nissle or Golgi stainings. Furthermore, the increased synaptic proteins of NR2A/B, PSD93, PSD95, the immediate early gene c-Fos and CREB protein were detected in hippocampus of rECS rats. rECS was also found to cause enhanced axon reorganization in DG region of hippocampus by Timm staining. Intraperitoneal injection of phenylbutyric acid (PBA), an aromatic short chain fatty acid acting as a molecule chaperon, could prevent rats from the rECS-induced memory deficits and synaptic potential enhancement by decreasing the levels of the abnormally increased memory-associated proteins and enhanced axon reorganization in hippocampus. Our data suggested that PBA might be potentially used to attenuate the rECS-induced memory impairment. PMID:24712645

  10. Variation and Evolution in the Glutamine-Rich Repeat Region of Drosophila Argonaute-2.

    PubMed

    Palmer, William H; Obbard, Darren J

    2016-01-01

    RNA interference pathways mediate biological processes through Argonaute-family proteins, which bind small RNAs as guides to silence complementary target nucleic acids . In insects and crustaceans Argonaute-2 silences viral nucleic acids, and therefore acts as a primary effector of innate antiviral immunity. Although the function of the major Argonaute-2 domains, which are conserved across most Argonaute-family proteins, are known, many invertebrate Argonaute-2 homologs contain a glutamine-rich repeat (GRR) region of unknown function at the N-terminus . Here we combine long-read amplicon sequencing of Drosophila Genetic Reference Panel (DGRP) lines with publicly available sequence data from many insect species to show that this region evolves extremely rapidly and is hyper-variable within species. We identify distinct GRR haplotype groups in Drosophila melanogaster, and suggest that one of these haplotype groups has recently risen to high frequency in a North American population. Finally, we use published data from genome-wide association studies of viral resistance in D. melanogaster to test whether GRR haplotypes are associated with survival after virus challenge. We find a marginally significant association with survival after challenge with Drosophila C Virus in the DGRP, but we were unable to replicate this finding using lines from the Drosophila Synthetic Population Resource panel.

  11. Variation and Evolution in the Glutamine-Rich Repeat Region of Drosophila Argonaute-2

    PubMed Central

    Palmer, William H.; Obbard, Darren J.

    2016-01-01

    RNA interference pathways mediate biological processes through Argonaute-family proteins, which bind small RNAs as guides to silence complementary target nucleic acids . In insects and crustaceans Argonaute-2 silences viral nucleic acids, and therefore acts as a primary effector of innate antiviral immunity. Although the function of the major Argonaute-2 domains, which are conserved across most Argonaute-family proteins, are known, many invertebrate Argonaute-2 homologs contain a glutamine-rich repeat (GRR) region of unknown function at the N-terminus . Here we combine long-read amplicon sequencing of Drosophila Genetic Reference Panel (DGRP) lines with publicly available sequence data from many insect species to show that this region evolves extremely rapidly and is hyper-variable within species. We identify distinct GRR haplotype groups in Drosophila melanogaster, and suggest that one of these haplotype groups has recently risen to high frequency in a North American population. Finally, we use published data from genome-wide association studies of viral resistance in D. melanogaster to test whether GRR haplotypes are associated with survival after virus challenge. We find a marginally significant association with survival after challenge with Drosophila C Virus in the DGRP, but we were unable to replicate this finding using lines from the Drosophila Synthetic Population Resource panel. PMID:27317784

  12. Fatty Acid Profile and Unigene-Derived Simple Sequence Repeat Markers in Tung Tree (Vernicia fordii)

    PubMed Central

    Zhang, Lin; Jia, Baoguang; Tan, Xiaofeng; Thammina, Chandra S.; Long, Hongxu; Liu, Min; Wen, Shanna; Song, Xianliang; Cao, Heping

    2014-01-01

    Tung tree (Vernicia fordii) provides the sole source of tung oil widely used in industry. Lack of fatty acid composition and molecular markers hinders biochemical, genetic and breeding research. The objectives of this study were to determine fatty acid profiles and develop unigene-derived simple sequence repeat (SSR) markers in tung tree. Fatty acid profiles of 41 accessions showed that the ratio of α-eleostearic acid was increasing continuously with a parallel trend to the amount of tung oil accumulation while the ratios of other fatty acids were decreasing in different stages of the seeds and that α-eleostearic acid (18∶3) consisted of 77% of the total fatty acids in tung oil. Transcriptome sequencing identified 81,805 unigenes from tung cDNA library constructed using seed mRNA and discovered 6,366 SSRs in 5,404 unigenes. The di- and tri-nucleotide microsatellites accounted for 92% of the SSRs with AG/CT and AAG/CTT being the most abundant SSR motifs. Fifteen polymorphic genic-SSR markers were developed from 98 unigene loci tested in 41 cultivated tung accessions by agarose gel and capillary electrophoresis. Genbank database search identified 10 of them putatively coding for functional proteins. Quantitative PCR demonstrated that all 15 polymorphic SSR-associated unigenes were expressed in tung seeds and some of them were highly correlated with oil composition in the seeds. Dendrogram revealed that most of the 41 accessions were clustered according to the geographic region. These new polymorphic genic-SSR markers will facilitate future studies on genetic diversity, molecular fingerprinting, comparative genomics and genetic mapping in tung tree. The lipid profiles in the seeds of 41 tung accessions will be valuable for biochemical and breeding studies. PMID:25167054

  13. The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes

    PubMed Central

    2009-01-01

    Background The expansion of amino acid repeats is determined by a high mutation rate and can be increased or limited by selection. It has been suggested that recent expansions could be associated with the potential of adaptation to new environments. In this work, we quantify the strength of this association, as well as the contribution of potential confounding factors. Results Mammalian positively selected genes have accumulated more recent amino acid repeats than other mammalian genes. However, we found little support for an accelerated evolutionary rate as the main driver for the expansion of amino acid repeats. The most significant predictors of amino acid repeats are gene function and GC content. There is no correlation with expression level. Conclusions Our analyses show that amino acid repeat expansions are causally independent from protein adaptive evolution in mammalian genomes. Relaxed purifying selection or positive selection do not associate with more or more recent amino acid repeats. Their occurrence is slightly favoured by the sequence context but mainly determined by the molecular function of the gene. PMID:20021652

  14. The Rhodomonas salina mitochondrial genome: bacteria-like operons, compact gene arrangement and complex repeat region.

    PubMed

    Hauth, Amy M; Maier, Uwe G; Lang, B Franz; Burger, Gertraud

    2005-01-01

    To gain insight into the mitochondrial genome structure and gene content of a putatively ancestral group of eukaryotes, the cryptophytes, we sequenced the complete mitochondrial DNA of Rhodomonas salina. The 48 063 bp circular-mapping molecule codes for 2 rRNAs, 27 tRNAs and 40 proteins including 23 components of oxidative phosphorylation, 15 ribosomal proteins and two subunits of tat translocase. One potential protein (ORF161) is without assigned function. Only two introns occur in the genome; both are present within cox1 belong to group II and contain RT open reading frames. Primitive genome features include bacteria-like rRNAs and tRNAs, ribosomal protein genes organized in large clusters resembling bacterial operons and the presence of the otherwise rare genes such as rps1 and tatA. The highly compact gene organization contrasts with the presence of a 4.7 kb long, repeat-containing intergenic region. Repeat motifs approximately 40-700 bp long occur up to 31 times, forming a complex repeat structure. Tandem repeats are the major arrangement but the region also includes a large, approximately 3 kb, inverted repeat and several potentially stable approximately 40-80 bp long hairpin structures. We provide evidence that the large repeat region is involved in replication and transcription initiation, predict a promoter motif that occurs in three locations and discuss two likely scenarios of how this highly structured repeat region might have evolved.

  15. Distribution of trinucleotide repeat sequences across a 2 Mbp region containing the Huntington's disease gene.

    PubMed

    Hummerich, H; Baxendale, S; Mott, R; Kirby, S F; MacDonald, M E; Gusella, J; Lehrach, H; Bates, G P

    1994-01-01

    The recent observation that the mutation underlying a number of genetic diseases including fragile sites, FRAXA and FRAXE (associated with mental retardation), myotonic dystrophy, spinal and bulbar muscular atrophy (Kennedy's disease), Huntington's disease and spinocerebellar ataxia type 1 are caused by the expansion of a trinucleotide repeat sequence will lead to interest in the identification of such sequences in regions related to other diseases. We report here the identification of all ten classes of trinucleotide repeats within a 2 Mbp region of 4p16.3 containing the Huntington's disease (HD) gene. Fifty one triplet repeats were identified and localised on a high resolution restriction map of a cosmid contig covering this region. This included the triplet repeat (CAG)n, which has subsequently been shown to be expanded in Huntington's disease patients.

  16. Identification of centromeric regions on the linkage map of cotton using centromere-related repeats.

    PubMed

    Zhang, Wenpan; Cao, Yujie; Wang, Kai; Zhao, Ting; Chen, Jiedan; Pan, Mengqiao; Wang, Qiong; Feng, Shouli; Guo, Wangzhen; Zhou, Baoliang; Zhang, Tianzhen

    2014-12-01

    Centromere usually contains high-copy-number retrotransposons and satellite repeats, which are difficult to map, clone and sequence. Currently, very little is known about the centromere in cotton. Here, we sequenced a bacterial artificial chromosome (BAC) mapping to the centromeric region and predicted four long-terminal-repeat (LTR) retrotransposons. They were located in the heterochromatic centromeric regions of all 52 pachytene chromosomes in Gossypium hirsutum. Fiber-FISH mapping revealed that these retrotransposons span an area of at least 1.8Mb in the centromeric region. Comparative analysis showed that these retrotransposons generated similar, strong fluorescent signals in the D progenitor Gossypium raimondii but not in the A progenitor Gossypium herbaceum, suggesting that the centromere sequence of tetraploid cotton might be derived from the D progenitor. Centromeric regions were anchored on 13 chromosomes of D-genome sequence. Characterization of these centromere-related repeats and regions will enhance cotton centromere mapping, sequencing and evolutionary studies. PMID:25238895

  17. Characterization of conservative somatic instability of the CAG repeat region in Huntington`s disease

    SciTech Connect

    Schaefer, F.V.; Calikoglu, A.S.; Whetsell, L.H.

    1994-09-01

    Instability and enlargement of a CAG repeat region at the beginning of the huntingtin gene (IT-15) has been linked with Huntington`s disease. The CAG repeat size shows a highly significant correlation with age-of-onset of clinicial features in individuals with 40 or more repeats who have Huntington disease. The clinical status of nonsymptomatic individuals with 30 to 39 CAG repeats is considered ambiguous. In order to define more carefully the nature of the HD expansion instability, we examined patients in our HD population using a discriminating fluorescence-based PCR approach. The degree of somatic mutation increases with both earlier age of onset and the size of the inherited allele. A single prominent band one repeat larger than the index peak was typical in individuals with 40-41 CAG repeats. Three to four larger bands are typically discerned in individuals with 50 or more repeats. In an extreme example, an individual with approximately 95 repeats had at least 8 prominent bands. Plotting the degree of somatic mutation relative to the size of the HD allele shows somatic mutation activity increases with size. By this approach 40-60% of the alleles in a 40-41 CAG repeat HD loci is represented in the primary allele. In contrast, the primary allele represents a relatively minor proportion of the total alleles for expansions greater than 50 CAG repeats (10-20%). The limited range of somatic mutation suggest that the instability is restricted to very early stages of embryogenesis before tissue development diverges or that persistent somatic instability occurs at a slow rate. Therefore, the properties of somatic instability in Huntington`s disease have aspects that are both in common but also different from that found in other trinucleotide repeat expanding diseases such as myotonic muscular dystrophy and fragile X syndrome.

  18. Distinct Roles of the Repeat-Containing Regions and Effector Domains of the Vibrio vulnificus Multifunctional-Autoprocessing Repeats-in-Toxin (MARTX) Toxin

    PubMed Central

    Kim, Byoung Sik; Gavin, Hannah E.

    2015-01-01

    ABSTRACT Vibrio vulnificus is a seafood-borne pathogen that destroys the intestinal epithelium, leading to rapid bacterial dissemination and death. The most important virulence factor is the multifunctional-autoprocessing repeats-in-toxin (MARTX) toxin comprised of effector domains in the center region flanked by long repeat-containing regions which are well conserved among MARTX toxins and predicted to translocate effector domains. Here, we examined the role of the repeat-containing regions using a modified V. vulnificus MARTX (MARTXVv) toxin generated by replacing all the internal effector domains with β-lactamase (Bla). Bla activity was detected in secretions from the bacterium and also in the cytosol of intoxicated epithelial cells. The modified MARTXVv toxin without effector domains retained its necrotic activity but lost its cell-rounding activity. Further, deletion of the carboxyl-terminal repeat-containing region blocked toxin secretion from the bacterium. Deletion of the amino-terminal repeat-containing region had no effect on secretion but completely abolished translocation and necrosis. Neither secretion nor translocation was affected by enzymatically inactivating the cysteine protease domain of the toxin. These data demonstrate that the amino-terminal and carboxyl-terminal repeat-containing regions of the MARTXVv toxin are necessary and sufficient for the delivery of effector domains and epithelial cell lysis in vitro but that effector domains are required for other cytopathic functions. Furthermore, Ca2+-dependent secretion of the modified MARTXVv toxin suggests that nonclassical RTX-like repeats found in the carboxyl-terminal repeat-containing region are functionally similar to classical RTX repeats found in other RTX proteins. PMID:25827415

  19. AT-rich region and repeated sequences - the essential elements of replication origins of bacterial replicons.

    PubMed

    Rajewska, Magdalena; Wegrzyn, Katarzyna; Konieczny, Igor

    2012-03-01

    Repeated sequences are commonly present in the sites for DNA replication initiation in bacterial, archaeal, and eukaryotic replicons. Those motifs are usually the binding places for replication initiation proteins or replication regulatory factors. In prokaryotic replication origins, the most abundant repeated sequences are DnaA boxes which are the binding sites for chromosomal replication initiation protein DnaA, iterons which bind plasmid or phage DNA replication initiators, defined motifs for site-specific DNA methylation, and 13-nucleotide-long motifs of a not too well-characterized function, which are present within a specific region of replication origin containing higher than average content of adenine and thymine residues. In this review, we specify methods allowing identification of a replication origin, basing on the localization of an AT-rich region and the arrangement of the origin's structural elements. We describe the regularity of the position and structure of the AT-rich regions in bacterial chromosomes and plasmids. The importance of 13-nucleotide-long repeats present at the AT-rich region, as well as other motifs overlapping them, was pointed out to be essential for DNA replication initiation including origin opening, helicase loading and replication complex assembly. We also summarize the role of AT-rich region repeated sequences for DNA replication regulation.

  20. Structural features in the HIV-1 repeat region facilitate strand transfer during reverse transcription.

    PubMed Central

    Berkhout, B; Vastenhouw, N L; Klasens, B I; Huthoff, H

    2001-01-01

    Two obligatory DNA strand transfers take place during reverse transcription of a retroviral RNA genome. The first strand transfer is facilitated by terminal repeat (R) elements in the viral genome. This strand-transfer reaction depends on base pairing between the cDNA of the 5'R and the 3'R. There is accumulating evidence that retroviral R regions contain features other than sequence complementarity that stimulate this critical nucleic acid hybridization step. The R region of the human immunodeficiency virus type 1 (HIV-1) is relatively extended (97 nt) and encodes two well-conserved stem-loop structures, the TAR and poly(A) hairpins. The role of these motifs was studied in an in vitro strand-transfer assay with two separate templates, the 5'R donor and the 3'R acceptor, and mutants thereof. The results indicate that the upper part of the TAR hairpin structure in the 5'R donor is critical for efficient strand transfer. This seems to pose a paradox, as the 5'R template is degraded by RNase H before strand transfer occurs. We propose that it is not the RNA hairpin motif in the 5'R donor, but rather the antisense motif in the ssDNA copy, which can also fold a hairpin structure, that is critical for strand transfer. Mutation of the loop sequence in the TAR hairpin of the donor RNA, which is copied in the loop of the cDNA hairpin, reduces the transfer efficiency more than fivefold. It is proposed that the natural strand-transfer reaction is enhanced by interaction of the anti-TAR ssDNA hairpin with the TAR hairpin in the 3'R acceptor. Base pairing can occur between the complementary loops ("loop-loop kissing"), and strand transfer is completed by the subsequent formation of an extended RNA-cDNA duplex. PMID:11497429

  1. STaRRRT: a table of short tandem repeats in regulatory regions of the human genome

    PubMed Central

    2013-01-01

    Background Tandem repeats (TRs) are unstable regions commonly found within genomes that have consequences for evolution and disease. In humans, polymorphic TRs are known to cause neurodegenerative and neuromuscular disorders as well as being associated with complex diseases such as diabetes and cancer. If present in upstream regulatory regions, TRs can modify chromatin structure and affect transcription; resulting in altered gene expression and protein abundance. The most common TRs are short tandem repeats (STRs), or microsatellites. Promoter located STRs are considerably more polymorphic than coding region STRs. As such, they may be a common driver of phenotypic variation. To study STRs located in regulatory regions, we have performed genome-wide analysis to identify all STRs present in a region that is 2 kilobases upstream and 1 kilobase downstream of the transcription start sites of genes. Results The Short Tandem Repeats in Regulatory Regions Table, STaRRRT, contains the results of the genome-wide analysis, outlining the characteristics of 5,264 STRs present in the upstream regulatory region of 4,441 human genes. Gene set enrichment analysis has revealed significant enrichment for STRs in cellular, transcriptional and neurological system gene promoters and genes important in ion and calcium homeostasis. The set of enriched terms has broad similarity to that seen in coding regions, suggesting that regulatory region STRs are subject to similar evolutionary pressures as STRs in coding regions and may, like coding region STRs, have an important role in controlling gene expression. Conclusions STaRRRT is a readily-searchable resource for investigating potentially polymorphic STRs that could influence the expression of any gene of interest. The processes and genes enriched for regulatory region STRs provide potential novel targets for diagnosing and treating disease, and support a role for these STRs in the evolution of the human genome. PMID:24228761

  2. Diversity of transposable elements and repeats in a 600 kb region of the fly Calliphora vicina

    PubMed Central

    2013-01-01

    Background Transposable elements (TEs) are a very dynamic component of eukaryotic genomes with important implications (e.g., in evolution) and applications (e.g., as transgenic tools). They also represent a major challenge for the assembly and annotation of genomic sequences. However, they are still largely unknown in non-model species. Results Here, we have annotated the repeats and transposable elements present in a 600 kb genomic region of the blowfly Calliphora vicina (Diptera: Calliphoridae) which contains most of the achaete-scute gene complex of this species. This is the largest genomic region to be sequenced and analyzed in higher flies outside the Drosophila genus. We find that the repeat content spans at least 24% of the sequence. It includes 318 insertions classified as 3 LTR retrotransposons, 21 LINEs, 14 cut-and-paste DNA transposons, 4 helitrons and 33 unclassified repeats. Conclusions This is the most detailed description of TEs and repeats in the Calliphoridae to date. This contribution not only adds to our knowledge about TE evolution but will also help in the annotation of repeats on Dipteran whole genome sequences. PMID:23552491

  3. Expansion of a (CAG)n repeat region in a sporadic case of HD.

    PubMed

    Bozza, A; Malagù, S; Calzolari, E; Novelletto, A; Pavoni, M; del Senno, L

    1995-08-01

    The genetic mutation underlying Huntington's disease (HD) has been identified as an expansion and instability of a specific CAG repeat sequence in a gene on chromosome 4. A simple polymerase chain reaction assay has been used for the assessment of the (CAG)n expansion in a 72-year-old woman with typical HD symptoms, but no family history of the disorder. The DNA analysis showed that the patient had an allele with 41 repeat units, in the size range seen in HD chromosomes. Therefore, HD diagnosis is confirmed in this seemingly sporadic case and the disease is newly diagnosed in a large family. The risk of inheriting this unstable expanded allele is discussed. INTRODUCTION--The discovery of an expansion of a trinucleotide (CAG) repeat region in the IT15 gene on the short arm of chromosome 4 has identified the mutational mechanism causing Huntington's disease (HD) and enables the direct diagnosis of affected subjects based on DNA analysis alone. Here a 72-year-old woman with typical HD symptoms, but no family history of the disorder, has been unambiguously diagnosed by using a quick DNA analysis. This is relevant because the disease is newly diagnosed in a large family. MATERIAL AND METHODS--A labelled polymerase chain reaction (PCR) test has been used to amplify the repeat region of the IT15 gene and DNA fragments were analyzed by Polyacrylamide gel electrophoresis. RESULTS--The number the CAG repeats in the proband displayed two alleles of 23 and 41 repeats, respectively. Since normal chromosomes are reported to contain 11-34 repeats, the clinical appearance of HD in the proband is explained by the presence of the repeat expansion. DISCUSSION--The parents of the proposita both died aged over 80 y apparently without neurological signs referable to HD. Hence, this is presumably a sporadic case of the disease. Because of the length of 41 repeats of this HD chromosome, offspring of this proband could inherit the expanded allele with 37 repeats, as expected for the

  4. Tandem repeat regions within the Burkholderia pseudomallei genome and their application for high resolution genotyping

    PubMed Central

    U'Ren, Jana M; Schupp, James M; Pearson, Talima; Hornstra, Heidie; Friedman, Christine L Clark; Smith, Kimothy L; Daugherty, Rebecca R Leadem; Rhoton, Shane D; Leadem, Ben; Georgia, Shalamar; Cardon, Michelle; Huynh, Lynn Y; DeShazer, David; Harvey, Steven P; Robison, Richard; Gal, Daniel; Mayo, Mark J; Wagner, David; Currie, Bart J; Keim, Paul

    2007-01-01

    Background The facultative, intracellular bacterium Burkholderia pseudomallei is the causative agent of melioidosis, a serious infectious disease of humans and animals. We identified and categorized tandem repeat arrays and their distribution throughout the genome of B. pseudomallei strain K96243 in order to develop a genetic typing method for B. pseudomallei. We then screened 104 of the potentially polymorphic loci across a diverse panel of 31 isolates including B. pseudomallei, B. mallei and B. thailandensis in order to identify loci with varying degrees of polymorphism. A subset of these tandem repeat arrays were subsequently developed into a multiple-locus VNTR analysis to examine 66 B. pseudomallei and 21 B. mallei isolates from around the world, as well as 95 lineages from a serial transfer experiment encompassing ~18,000 generations. Results B. pseudomallei contains a preponderance of tandem repeat loci throughout its genome, many of which are duplicated elsewhere in the genome. The majority of these loci are composed of repeat motif lengths of 6 to 9 bp with 4 to 10 repeat units and are predominately located in intergenic regions of the genome. Across geographically diverse B. pseudomallei and B.mallei isolates, the 32 VNTR loci displayed between 7 and 28 alleles, with Nei's diversity values ranging from 0.47 and 0.94. Mutation rates for these loci are comparable (>10-5 per locus per generation) to that of the most diverse tandemly repeated regions found in other less diverse bacteria. Conclusion The frequency, location and duplicate nature of tandemly repeated regions within the B. pseudomallei genome indicate that these tandem repeat regions may play a role in generating and maintaining adaptive genomic variation. Multiple-locus VNTR analysis revealed extensive diversity within the global isolate set containing B. pseudomallei and B. mallei, and it detected genotypic differences within clonal lineages of both species that were identical using previous

  5. Effects of Repeated Fires in the Forest Ecosystems of the Zabaikalye Region, Southern Siberia

    NASA Astrophysics Data System (ADS)

    Kukavskaya, E.; Buryak, L. V.; Conard, S. G.; Petkov, A.; Barrett, K.; Kalenskaya, O. P.; Ivanova, G.

    2014-12-01

    Fire is the main ecological disturbance controlling forest development in the boreal forests of Siberia and contributing substantially to the global carbon cycle. The warmer and dryer climate observed recently in the boreal forests is considered to be responsible for extreme fire weather, resulting in higher fire frequency, larger areas burned, and an increase of fire severity. Because of the increase of fire activity, boreal forests in some regions may not be able to reach maturity before they re-burn, which means less carbon will be stored in the ecosystem and more will remain in the atmosphere. Moreover, if one fire occurs within a few years of another, some stands will not re-grow at all, and even more carbon will accumulate in the atmosphere. Zabaikalye region located in the south of Siberia is characterized by the highest fire activity in Russia. With a use of the satellite-based fire product we found that there are about 7.0 million hectares in the region burned repeatedly during the last decade. We have investigated a number of sites in-situ in light-coniferous (Scots pine and larch) forests and evaluated the impacts of repeated fires on fuel loads, carbon emissions, and tree regeneration. Substantial decrease of carbon stocks, change of the vegetation structure and composition, and soil erosion were observed in many areas disturbed by repeated fires. At drier sites located in the southern regions repeated fires prohibited successful regeneration and resulted in forest conversion to grassland. Detection and monitoring of changes in the areas of Siberia where repeated fires have caused a major shift in ecosystem structure and function is required for the development of sustainable forest management strategies to mitigate climate change. The research was supported by NASA LCLUC Program.

  6. A region of human BRCA2 containing multiple BRC repeats promotes RAD51-mediated strand exchange.

    PubMed

    Shivji, Mahmud K K; Davies, Owen R; Savill, Jane M; Bates, Debbie L; Pellegrini, Luca; Venkitaraman, Ashok R

    2006-01-01

    Human BRCA2, a breast and ovarian cancer suppressor, binds to the DNA recombinase RAD51 through eight conserved BRC repeats, motifs of approximately 30 residues, dispersed across a large region of the protein. BRCA2 is essential for homologous recombination in vivo, but isolated BRC repeat peptides can prevent the assembly of RAD51 into active nucleoprotein filaments in vitro, suggesting a model in which BRCA2 sequesters RAD51 in undamaged cells, and promotes recombinase function after DNA damage. How BRCA2 might fulfill these dual functions is unclear. We have purified a fragment of human BRCA2 (BRCA2(BRC1-8)) with 1127 residues spanning all 8 BRC repeats but excluding the C-terminal DNA-binding domain (BRCA2(CTD)). BRCA2(BRC1-8) binds RAD51 nucleoprotein filaments in a ternary complex, indicating it may organize RAD51 on DNA. Human RAD51 is relatively ineffective in vitro at strand exchange between homologous DNA molecules unless non-physiological ions like NH4+ are present. In an ionic milieu more typical of the mammalian nucleus, BRCA2(BRCI-8) stimulates RAD51-mediated strand exchange, suggesting it may be an essential co-factor in vivo. Thus, the human BRC repeats, embedded within their surronding sequences as an eight-repeat unit, mediate homologous recombination independent of the BRCA2(CTD) through a previously unrecognized role in control of RAD51 activity.

  7. Predicted Coverage and Immuno-Safety of a Recombinant C-Repeat Region Based Streptococcus pyogenes Vaccine Candidate.

    PubMed

    McNeilly, Celia; Cosh, Samantha; Vu, Therese; Nichols, Jemma; Henningham, Anna; Hofmann, Andreas; Fane, Anne; Smeesters, Pierre R; Rush, Catherine M; Hafner, Louise M; Ketheesan, Natkuman; Sriprakash, Kadaba S; McMillan, David J

    2016-01-01

    The C-terminal region of the M-protein of Streptococcus pyogenes is a major target for vaccine development. The major feature is the C-repeat region, consisting of 35-42 amino acid repeat units that display high but not perfect identity. SV1 is a S. pyogenes vaccine candidate that incorporates five 14mer amino acid sequences (called J14i variants) from differing C-repeat units in a single recombinant construct. Here we show that the J14i variants chosen for inclusion in SV1 are the most common variants in a dataset of 176 unique M-proteins. Murine antibodies raised against SV1 were shown to bind to each of the J14i variants present in SV1, as well as variants not present in the vaccine. Antibodies raised to the individual J14i variants were also shown to bind to multiple but different combinations of J14i variants, supporting the underlying rationale for the design of SV1. A Lewis Rat Model of valvulitis was then used to assess the capacity of SV1 to induce deleterious immune response associated with rheumatic heart disease. In this model, both SV1 and the M5 positive control protein were immunogenic. Neither of these antibodies were cross-reactive with cardiac myosin or collagen. Splenic T cells from SV1/CFA and SV1/alum immunized rats did not proliferate in response to cardiac myosin or collagen. Subsequent histological examination of heart tissue showed that 4 of 5 mice from the M5/CFA group had valvulitis and inflammatory cell infiltration into valvular tissue, whereas mice immunised with SV1/CFA, SV1/alum showed no sign of valvulitis. These results suggest that SV1 is a safe vaccine candidate that will elicit antibodies that recognise the vast majority of circulating GAS M-types. PMID:27310707

  8. Predicted Coverage and Immuno-Safety of a Recombinant C-Repeat Region Based Streptococcus pyogenes Vaccine Candidate

    PubMed Central

    McNeilly, Celia; Cosh, Samantha; Vu, Therese; Nichols, Jemma; Henningham, Anna; Hofmann, Andreas; Fane, Anne; Smeesters, Pierre R.; Rush, Catherine M.; Hafner, Louise M.; Ketheesan, Natkuman; Sriprakash, Kadaba S.; McMillan, David J.

    2016-01-01

    The C-terminal region of the M-protein of Streptococcus pyogenes is a major target for vaccine development. The major feature is the C-repeat region, consisting of 35–42 amino acid repeat units that display high but not perfect identity. SV1 is a S. pyogenes vaccine candidate that incorporates five 14mer amino acid sequences (called J14i variants) from differing C-repeat units in a single recombinant construct. Here we show that the J14i variants chosen for inclusion in SV1 are the most common variants in a dataset of 176 unique M-proteins. Murine antibodies raised against SV1 were shown to bind to each of the J14i variants present in SV1, as well as variants not present in the vaccine. Antibodies raised to the individual J14i variants were also shown to bind to multiple but different combinations of J14i variants, supporting the underlying rationale for the design of SV1. A Lewis Rat Model of valvulitis was then used to assess the capacity of SV1 to induce deleterious immune response associated with rheumatic heart disease. In this model, both SV1 and the M5 positive control protein were immunogenic. Neither of these antibodies were cross-reactive with cardiac myosin or collagen. Splenic T cells from SV1/CFA and SV1/alum immunized rats did not proliferate in response to cardiac myosin or collagen. Subsequent histological examination of heart tissue showed that 4 of 5 mice from the M5/CFA group had valvulitis and inflammatory cell infiltration into valvular tissue, whereas mice immunised with SV1/CFA, SV1/alum showed no sign of valvulitis. These results suggest that SV1 is a safe vaccine candidate that will elicit antibodies that recognise the vast majority of circulating GAS M-types. PMID:27310707

  9. Effect of repeated harvesting on the content of caffeic acid and seven species of caffeoylquinic acids in sweet potato leaves.

    PubMed

    Sasaki, Kazunori; Oki, Tomoyuki; Kai, Yumi; Nishiba, Yoichi; Okuno, Shigenori

    2015-01-01

    The purpose of this study was to investigate the effect of repeated harvesting on the content of caffeic acid (CA) and seven species of caffeoylquinic acids (CQAs) in sweet potato leaves using a newly developed high-performance liquid chromatography method. Six cultivars and two breeding lines were used in this study. Leaves were collected at monthly intervals from 1st harvest (May) to 4th harvest (August) in 2011 and 2012. ANOVA analysis revealed that the contents of CQAs were significantly different among all cultivars and breeding lines, but no significant differences were found for CA. No annual variation was confirmed in CA and CQAs. Repeated harvest of sweet potato leaves affected the content of only 4-CQA and 5-CQA. Post-hoc comparisons using Tukey's method indicated that the contents of 4-CQA and 5-CQA in sweet potato leaves harvested at first time were significantly higher compared to those at the other harvest times.

  10. The majority of human genes have regions repeated in other human genes.

    PubMed

    Britten, Roy J

    2005-04-12

    Amino acid sequence comparisons have been made between all of 25,193 human proteins with each of the others by using blast software (National Center for Biotechnology Information) and recording the results for regions that are significantly related in sequence, that is, have an expectation of <1 x 10(-3). The results are presented for each amino acid as the number of identical or similar amino acids matched in these aligned regions. This approach avoids summing or dealing directly with the different regions of any one protein that are often related to different numbers and types of other proteins. The results are presented graphically for a sample of 140 proteins. Relationships are not observed for 26.5% of the 12,728,866 amino acids. The average number of related amino acids is 36.5 for the majority (73.5%) that show relationships. The median number of recognized relationships is approximately 3 for all of the amino acids, and the maximum number is 718. The results demonstrate the overwhelming importance of gene regional duplication forming families of proteins with related domains and show the variety of the resulting patterns of relationship. The magnitude of the set of relationships leads to the conclusion that the principal process by which new gene functions arise has been by making use of preexisting genes. PMID:15802472

  11. Variability of the tandem repeat region of the Escherichia coli tolA gene.

    PubMed

    Zhou, Kai; Vanoirbeek, Kristof; Aertsen, Abram; Michiels, Chris W

    2012-06-01

    An intragenic tandem repeat (TR) region has been previously reported in the tolA gene of Escherichia coli. In silico analysis of 123 E. coli tolA sequences from Genbank and PCR analysis of the tolA TR region from 111 additional E. coli strains revealed that this TR region is highly variable. Nine different TR sizes with 8 up to 16 repeat units were found in in silico analysis and 6 of these were also found by PCR analysis. The 13-unit TR emerged as the predominant type using both approaches (47.2% and 86.5%, respectively). Remarkably, TRs in pathogenic strains appeared to be more variable than those in non-pathogens. To demonstrate the occurrence of TR variation in a clonal population, a selection system for TR deletion events was constructed by inserting the 13-unit TR region of MG1655 in frame into a plasmid-borne chloramphenicol acetyltransferase (cat) gene. The resulting cat gene no longer conferred chloramphenicol resistance unless the insert size was reduced by TR contraction. Using this system, Cm-resistant revertants with a TR contraction were recovered at a frequency of 1.1 × 10(-7), and contraction was shown to be recA-dependent and enhanced in a DNA repair-deficient mutS background. PMID:22659144

  12. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOEpatents

    Weier, Heinz-Ulrich G.; Gray, Joe W.

    1995-01-01

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers ard probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity.

  13. Repeat sequence chromosome specific nucleic acid probes and methods of preparing and using

    DOEpatents

    Weier, H.U.G.; Gray, J.W.

    1995-06-27

    A primer directed DNA amplification method to isolate efficiently chromosome-specific repeated DNA wherein degenerate oligonucleotide primers are used is disclosed. The probes produced are a heterogeneous mixture that can be used with blocking DNA as a chromosome-specific staining reagent, and/or the elements of the mixture can be screened for high specificity, size and/or high degree of repetition among other parameters. The degenerate primers are sets of primers that vary in sequence but are substantially complementary to highly repeated nucleic acid sequences, preferably clustered within the template DNA, for example, pericentromeric alpha satellite repeat sequences. The template DNA is preferably chromosome-specific. Exemplary primers and probes are disclosed. The probes of this invention can be used to determine the number of chromosomes of a specific type in metaphase spreads, in germ line and/or somatic cell interphase nuclei, micronuclei and/or in tissue sections. Also provided is a method to select arbitrarily repeat sequence probes that can be screened for chromosome-specificity. 18 figs.

  14. Acid rain: a serious regional environmental problem.

    PubMed

    Likens, G E; Bormann, F H

    1974-06-14

    At present, acid rain or snow is falling on most of the northeastern United States. The annual acidity value averages about pH 4, but values between pH 2.1 and 5 have been recorded for individual storms. The acidity of precipitation in this region apparently increased about 20 years ago, and the increase may have been associated with the augmented use of natural gas and with the installation of particle-removal devices in tall smokestacks. Only some of the ecological and economic effects of this widespread introduction of strong acids into natural systems are known at present, but clearly they must be considered in proposals for new energy sources and in the development of air quality emission standards.

  15. Repeated verum but not placebo acupuncture normalizes connectivity in brain regions dysregulated in chronic pain.

    PubMed

    Egorova, Natalia; Gollub, Randy L; Kong, Jian

    2015-01-01

    Acupuncture, an ancient East Asian therapy, is aimed at rectifying the imbalance within the body caused by disease. Studies evaluating the efficacy of acupuncture with neuroimaging tend to concentrate on brain regions within the pain matrix, associated with acute pain. We, however, focused on the effect of repeated acupuncture treatment specifically on brain regions known to support functions dysregulated in chronic pain disorders. Transition to chronic pain is associated with increased attention to pain, emotional rumination, nociceptive memory and avoidance learning, resulting in brain connectivity changes, specifically affecting the periaqueductal gray (PAG), medial frontal cortex (MFC) and bilateral hippocampus (Hpc). We demonstrate that the PAG-MFC and PAG-Hpc connectivity in patients with chronic pain due to knee osteoarthritis indeed correlates with clinical severity scores and further show that verum acupuncture-induced improvement in pain scores (compared to sham) is related to the modulation of PAG-MFC and PAG-Hpc connectivity in the predicted direction. This study shows that repeated verum acupuncture might act by restoring the balance in the connectivity of the key pain brain regions, altering pain-related attention and memory. PMID:26594625

  16. Differential Occurrence of Interactions and Interaction Domains in Proteins Containing Homopolymeric Amino Acid Repeats.

    PubMed

    Pelassa, Ilaria; Fiumara, Ferdinando

    2015-01-01

    Homopolymeric amino acids repeats (AARs), which are widespread in proteomes, have often been viewed simply as spacers between protein domains, or even as "junk" sequences with no obvious function but with a potential to cause harm upon expansion as in genetic diseases associated with polyglutamine or polyalanine expansions, including Huntington disease and cleidocranial dysplasia. A growing body of evidence indicates however that at least some AARs can form organized, functional protein structures, and can regulate protein function. In particular, certain AARs can mediate protein-protein interactions, either through homotypic AAR-AAR contacts or through heterotypic contacts with other protein domains. It is still unclear however, whether AARs may have a generalized, proteome-wide role in shaping protein-protein interaction networks. Therefore, we have undertaken here a bioinformatics screening of the human proteome and interactome in search of quantitative evidence of such a role. We first identified the sets of proteins that contain repeats of any one of the 20 amino acids, as well as control sets of proteins chosen at random in the proteome. We then analyzed the connectivity between the proteins of the AAR-containing protein sets and we compared it with that observed in the corresponding control networks. We find evidence for different degrees of connectivity in the different AAR-containing protein networks. Indeed, networks of proteins containing polyglutamine, polyglutamate, polyproline, and other AARs show significantly increased levels of connectivity, whereas networks containing polyleucine and other hydrophobic repeats show lower degrees of connectivity. Furthermore, we observed that numerous protein-protein, -nucleic acid, and -lipid interaction domains are significantly enriched in specific AAR protein groups. These findings support the notion of a generalized, combinatorial role of AARs, together with conventional protein interaction domains, in shaping

  17. The coding region of the human c-mos pseudogene contains Alu repeat insertions.

    PubMed

    Zabarovsky, E R; Chumakov, I M; Prassolov, V S; Kisselev, L L

    1984-10-01

    We have determined the nucleotide sequence of an 841-bp fragment derived from a segment of the human genome previously cloned by Chumakov et al. [Gene 17 (1982) 19-26] and Zabarovsky et al. [Gene 23 (1983) 379-384] and containing regions homologous to the viral mos gene probe. This sequence displays homology with part of the coding region of the human and murine c-mos genes, contains several termination codons, and is interrupted by two Alu-family elements flanked by short direct repeats. Probably, the progenitor of the human c-mos gene was duplicated approximately at the time of mammalian divergence, was converted to a pseudogene, and acquired insertions of two Alu elements.

  18. The Prebiotic Synthesis of Ethylenediamine Monoacetic Acid, The Repeating Unit of Peptide Nucleic Acids

    NASA Technical Reports Server (NTRS)

    Nelson, Kevin E.; Miller, Stanley L.

    1992-01-01

    The polymerization of ribonucleic acids or their precursors constitutes an important event in prebiotic chemistry. The various problems using ribonucleotides to make RNA suggest that there may have been a precursor. An attractive possibility are the peptide nucleic acids (PNA). PNAs are nucleotide analogs that make use of a polymer of ethylenediamine monoacetic acid (EDMA or 2-amninoethyl glycine) with the bases attached by an acetic acid. EDMA is an especially attractive alternative to the ribose phosphate or deoxyribose phosphate backbone because it contains no chiral centers and is potentially prebiotic, but there is no reported prebiotic synthesis. We have synthesized both EDMA and ethylenediamine diacetic acid (EDDA) from the prebiotic compounds ethylenediamine, formaldehyde, and hydrogen cyanide. The yields of EDMA range from 11 to 79% along with some sEDDA and uEDDA. These reactions work with concentrations of 10(exp -1)M and as low as 10(exp -4)M, and the reaction is likely to be effective at even lower concentrations. Ethylenediamine is a likely prebiotic compound, but it has not yet been demonstrated, although compounds such as ethanolamine and cysteamine have been proven to be prebiotic. Under neutral pH and heating at l00 C, EDMA is converted to the lactam, monoketopiperazine (MKP). The cyclization occurs and has an approximate ratio of MKP/EDMA = 3 at equilibrium. We have measured the solubilities of EDMA center dot H20 as 6.4 m, EDMA center dot HCl center dot H20 as 13.7 m, and EDMA center dot 2HCl center dot H20 as 3.4 m. These syntheses together with the high solubility of EDMA suggest that EDMA would concentrate in drying lagoons and might efficiently form polymers. Given the instability of ribose and the poor polymerizability of nucleotides, the prebiotic presence of EDMA and the possibility of its polymerization raises the possibility that PNAs are the progenitors of present day nucleic acids. A pre-RNA world may have existed in which PNAs or

  19. Serine-scanning mutagenesis studies of the C-terminal heptad repeats in the SARS coronavirus S glycoprotein highlight the important role of the short helical region

    SciTech Connect

    Follis, Kathryn E.; York, Joanne; Nunberg, Jack H. . E-mail: jack.nunberg@umontana.edu

    2005-10-10

    The fusion subunit of the SARS-CoV S glycoprotein contains two regions of hydrophobic heptad-repeat amino acid sequences that have been shown in biophysical studies to form a six-helix bundle structure typical of the fusion-active core found in Class I viral fusion proteins. Here, we have applied serine-scanning mutagenesis to the C-terminal-most heptad-repeat region in the SARS-CoV S glycoprotein to investigate the functional role of this region in membrane fusion. We show that hydrophobic sidechains at a and d positions only within the short helical segment of the C-terminal heptad-repeat region (I1161, I1165, L1168, A1172, and L1175) are critical for cell-cell fusion. Serine mutations at outlying heptad-repeat residues that form an extended chain in the core structure (V1158, L1179, and L1182) do not affect fusogenicity. Our study provides genetic evidence for the important role of {alpha}-helical packing in promoting S glycoprotein-mediated membrane fusion.

  20. Repeated piezoelectric lithotripsy for gallstones with and without ursodeoxycholic acid dissolution: a multicenter study.

    PubMed

    Tsuchiya, Y; Ishihara, F; Kajiyama, G; Nakazawa, S; Otho, M; Tanimura, H; Akura, Y; Harada, M; Hihara, M; Kawai, Y

    1995-12-01

    The use of bile acid dissolution therapy in extracorporeal shockwave lithotripsy of gallstones, remains controversial. Our study examined whether chemolitholysis after sufficient disintegration enhanced stone clearance within 6 months of the first lithotripsy. A total of 143 patients who developed one to three radiolucent stones measuring < or = 30 mm in diameter were randomly separated into two treatment groups: 47% were given lithotripsy alone, and 53% lithotripsy plus ursodeoxycholic acid (UDCA). Repeated piezoelectric lithotripsy was given, with no limit on the total number of treatment sessions, to pulverize or disintegrate stones into fragments < 3 mm. Stones were disintegrated in 97% of all patients, and the fragments were < or = 2 mm in 50% of these patients. According to an intention-to-treat analysis, 52% in the lithotripsy alone group and 58% in the UDCA group were free of stones 6 months after the first lithotripsy (P = 0.61). Of the patients with fragments < or = 2 mm, 71% in the former and 86% in the latter group were free of stones 6 months after the first lithotripsy, with no significant difference between the groups. Biliary pain occurred in 25% of all patients, including 3 with acute cholecystitis. We concluded that the sufficient disintegration of gallstones achieved with repeated lithotripsy enhanced the early clearance of fragments, regardless of whether chemolitholysis was employed.

  1. Repeated exposure of acidic beverages on esthetic restorative materials: An in-vitro surface microhardness study

    PubMed Central

    Sunny, Steffy M.; Rai, Kavita; Hegde, Amitha M.

    2016-01-01

    Background A manifold increase in the consumption of aerated beverages has witnessed a twin increase in tooth wear and raised demand for esthetic restorative materials. This study aimed to evaluate the surface microhardness changes of esthetic restorative materials following treatment with aerated beverages in an in-vitro situation. Material and Methods The initial surface microhardness of the restorative materials GC Fuji II LC, GC Fuji IX, Nano Glass ionomer, Resin and Nano composite was recorded. These materials were studied under 3 groups that included those exposed to the acidic beverages daily, weekly once in a month and those that had no exposures at all. The final surface microhardness of the materials was recorded following experimentation and was subjected to statistical comparisons. Results The restorative materials were compared for their surface microhardness changes following respective treatments using the T-test and One-way ANOVA analysis. Inter-comparisons between the groups showed statistical significance (p<.05), when treated with both the beverages. The five restorative materials revealed surface microhardness loss; the maximum reduction noticed with the Nano glass ionomer cement tested (p<.0005). Conclusions The surface microhardness of restorative materials markedly reduced upon repeated exposures with acidic beverages; the product with phosphoric acid producing the maximum surface microhardness loss. Key words:Restorative materials, acidic beverages, surface microhardness, resin composites, glass ionomers. PMID:27398183

  2. Low numbers of repeat units in variable number of tandem repeats (VNTR) regions of white spot syndrome virus are correlated with disease outbreaks.

    PubMed

    Hoa, T T T; Zwart, M P; Phuong, N T; de Jong, M C M; Vlak, J M

    2012-11-01

    White spot syndrome virus (WSSV) is the most important pathogen in shrimp farming systems worldwide including the Mekong Delta, Vietnam. The genome of WSSV is characterized by the presence of two major 'indel regions' found at ORF14/15 and ORF23/24 (WSSV-Thailand) and three regions with variable number tandem repeats (VNTR) located in ORF75, ORF94 and ORF125. In the current study, we investigated whether or not the number of repeat units in the VNTRs correlates with virus outbreak status and/or shrimp farming practice. We analysed 662 WSSV samples from individual WSSV-infected Penaeus monodon shrimp from 104 ponds collected from two important shrimp farming regions of the Mekong Delta: Ca Mau and Bac Lieu. Using this large data set and statistical analysis, we found that for ORF94 and ORF125, the mean number of repeat units (RUs) in VNTRs was significantly lower in disease outbreak ponds than in non-outbreak ponds. Although a higher mean RU number was observed in the improved-extensive system than in the rice-shrimp or semi-intensive systems, these differences were not significant. VNTR sequences are thus not only useful markers for studying WSSV genotypes and populations, but specific VNTR variants also correlate with disease outbreaks in shrimp farming systems.

  3. Submegabase Clusters of Unstable Tandem Repeats Unique to the Tla Region of Mouse T Haplotypes

    PubMed Central

    Uehara, H.; Ebersole, T.; Bennett, D.; Artzt, K.

    1990-01-01

    We describe here the identification and genomic organization of mouse t haplotype-specific elements (TSEs) 7.8 and 5.8 kb in length. The TSEs exist as submegabase-long clusters of tandem repeats localized in the Tla region of the major histocompatibility complex of all t haplotype chromosomes examined. In contrast, no such clusters were detected among 12 inbred strains of Mus musculus and other Mus species; thus, clusters of TSEs represent the first absolutely qualitative difference between t haplotypes and wild-type chromosomes. Pulsed field gel electrophoresis shows that the number of clusters, and the number of repeats in each cluster are extremely variable. Dramatic quantitative differences of TSEs uniquely distinguish every independent t haplotype from any other. The complete nucleotide sequence of one 7.8-kb TSE reveals significant homology to the ETn (a major transcript in the early embryo of the mouse), and some homologies to intracisternal A-particles and the mammary tumor virus env gene. Apart from the diagnostic relevance to t haplotypes, evolutionary and functional significances are discussed with respect to chromosome structure and genetic recombination. PMID:2076812

  4. Structure and variable numbers of tandem repeats (VNTRs) of the mitochondrial control region in mitten crab Eriocheir (Crustacean: Brachyura).

    PubMed

    Zhang, Daizhen; Ding, Ge; Wang, Guangyue; Tang, Boping; Sun, Hongying

    2011-11-01

    Mitochondrial control region was called "A + T-rich" region in invertebrate. In the study, the general organization of control region in mitten crab was divided into two major domains: high variable segment and conserved segment. Four conserved blocks (CSB1, CSB2, CSB3 and CSB4) and two tandem repeat sequences (RT1 and RT2) were defined in control region. There were 116 polymorphic sites and 84 parsimony information sites in 571 aligned sites of the high variable segment adjacent "tRNA-Gln", in which 58 stable variable sites were defined between E. j. sinensis and E. j. hepuensis. Conserved domain contained more than two similar repeat units, and length polymorphism of control region was due to the number difference between the two repeat units (RT1 and RT2). And length polymorphism was a common phenomenon for tandem repeat in control region in the study. Furthermore, a novel result showed the core nucleotide of RT2 in control region tandem repeat was C in E. j. hepuensis, but G in E. j. sinensis. It might be a rapid and cost-effective measure of seedlings differentiation in aquaculture.

  5. Extreme variation in patterns of tandem repeats in mitochondrial control region of yellow-browed tits (Sylviparus modestus, Paridae)

    PubMed Central

    Wang, Xiaoyang; Liu, Nian; Zhang, Hongli; Yang, Xiao-Jun; Huang, Yuan; Lei, Fumin

    2015-01-01

    To investigate the evolutionary pattern and origins of tandem repeats in the mitochondrial control region of the yellow-browed tit (Sylviparus modestus), the control region and another four mitochondrial loci from fifteen individuals were analyzed. A 117-bp tandem repeat unit that repeated once, twice or three times in different individuals was found, and a rarely reported arrangement for this tandem repeats region that a 5′ imperfect copy at its downstream and a 3′ imperfect copy at its upstream was observed. The haplotype network, phylogenetic trees, and ancestral state reconstruction of the combined dataset of five loci suggested multiple origins of the same repeat number. The turnover model via slipped-strand mispairing was introduced to interpret the results, because mispairing occurred so frequently that multiple origins of certain repeat number were observed. Insertion via recombination should be a better explanation for the origin of this tandem repeat unit, considering characteristics of the combined sequence of the 3′ and 5′ imperfect copy, including identification of its homolog in other passerines and its predicted secondary structure. PMID:26288099

  6. Assessing the Genome-Wide Effect of Promoter Region Tandem Repeat Natural Variation on Gene Expression

    PubMed Central

    Elmore, Martha H.; Gibbons, John G.; Rokas, Antonis

    2012-01-01

    Copy number polymorphisms of nucleotide tandem repeat (TR) regions, such as microsatellites and minisatellites, are mutationally reversible and highly abundant in eukaryotic genomes. Studies linking TR polymorphism to phenotypic variation have led some to suggest that TR variation modulates and majorly contributes to phenotypic variation; however, studies in which the authors assess the genome-wide impact of TR variation on phenotype are lacking. To address this question, we quantified relationships between polymorphism levels in 143 genome-wide promoter region TRs across 16 isolates of the filamentous fungus Aspergillus flavus and its ecotype Aspergillus oryzae with expression levels of their downstream genes. We found that only 4.3% of relationships tested were significant; these findings were consistent with models in which TRs act as “tuning,” “volume,” or “optimality” “knobs” of phenotype but not with “switch” models. Furthermore, the promoter regions of differentially expressed genes between A. oryzae and A. flavus did not show TR enrichment, suggesting that genome-wide differences in molecular phenotype between the two species are not significantly associated with TRs. Although in some cases TR polymorphisms do contribute to transcript abundance variation, these results argue that at least in this case, TRs might not be major modulators of variation in phenotype. PMID:23275886

  7. An Unstable Trinucleotide-Repeat Region on Chromosome 13 Implicated in Spinocerebellar Ataxia: A Common Expansion Locus

    PubMed Central

    Vincent, John B; Neves-Pereira, Maria L.; Paterson, Andrew D.; Yamamoto, Etsuko; Parikh, Sagar V.; Macciardi, Fabio; Gurling, Hugh M.D.; Potkin, Steve G.; Pato, Carlos N.; Macedo, Antonio; Kovacs, Maria; Davies, Marilyn; Lieberman, Jeffrey A.; Meltzer, Herbert Y.; Petronis, Arturas; Kennedy, James L.

    2000-01-01

    Larger CAG/CTG trinucleotide-repeat tracts in individuals affected with schizophrenia (SCZ) and bipolar affective disorder (BPAD) in comparison with control individuals have previously been reported, implying a possible etiological role for trinucleotide repeats in these diseases. Two unstable CAG/CTG repeats, SEF2-1B and ERDA1, have recently been cloned, and studies indicate that the majority of individuals with large repeats as detected by repeat-expansion detection (RED) have large repeat alleles at these loci. These repeats do not show association of large alleles with either BPAD or SCZ. Using RED, we have identified a BPAD individual with a very large CAG/CTG repeat that is not due to expansion at SEF2-1B or ERDA1. From this individual’s DNA, we have cloned a highly polymorphic trinucleotide repeat consisting of (CTA)n (CTG)n, which is very long (∼1,800 bp) in this patient. The repeat region localizes to chromosome 13q21, within 1.2 cM of fragile site FRA13C. Repeat alleles in our sample were unstable in 13 (5.6%) of 231 meioses. Large alleles (>100 repeats) were observed in 14 (1.25%) of 1,120 patients with psychosis, borderline personality disorder, or juvenile-onset depression and in 5 (.7%) of 710 healthy controls. Very large alleles were also detected for Centre d’Etude Polymorphisme Humaine (CEPH) reference family 1334. This triplet expansion has recently been reported to be the cause of spinocerebellar ataxia type 8 (SCA8); however, none of our large alleles above the disease threshold occurred in individuals either affected by SCA or with known family history of SCA. The high frequency of large alleles at this locus is inconsistent with the much rarer occurrence of SCA8. Thus, it seems unlikely that expansion alone causes SCA8; other genetic mechanisms may be necessary to explain SCA8 etiology. PMID:10712198

  8. Efficient and repeated production of succinic acid by turning sugarcane bagasse into sugar and support.

    PubMed

    Chen, Pengcheng; Tao, Shengtao; Zheng, Pu

    2016-07-01

    Here we reported an endeavor in making full use of sugarcane bagasse for biological production of succinic acid. Through NaOH pre-treatment and multi-enzyme hydrolysis, a reducing sugar solution mainly composed of glucose and xylose was obtained from the sugarcane bagasse. By optimizing portions of cellulase, xylanase, β-glucanase and pectinase in the multi-enzyme "cocktail", the hydrolysis percentage of the total cellulose in pre-treated sugarcane bagasse can be as high as 88.5%. A. succinogenes CCTCC M2012036 was used for converting reducing sugars into succinic acid in a 3-L bioreactor with a sugar-fed strategy to prevent cell growth limitation. Importantly, cells were found to be adaptive on the sugarcane bagasse residue, offering possibilities of repeated batch fermentation and replacement for MgCO3 with soluble NaHCO3 in pH modulation. Three cycles of fermentation without activity loss were realized with the average succinic acid yield and productivity to be 80.5% and 1.65g·L(-1)·h(-1). PMID:27035471

  9. Comparison of the carboxy-terminal DP-repeat region in the co-chaperones Hop and Hip.

    PubMed

    Nelson, Gregory M; Huffman, Holly; Smith, David F

    2003-01-01

    Functional steroid receptor complexes are assembled and maintained by an ordered pathway of interactions involving multiple components of the cellular chaperone machinery. Two of these components, Hop and Hip, serve as co-chaperones to the major heat shock proteins (Hsps), Hsp70 and Hsp90, and participate in intermediate stages of receptor assembly. In an effort to better understand the functions of Hop and Hip in the assembly process, we focused on a region of similarity located near the C-terminus of each co-chaperone. Contained within this region is a repeated sequence motif we have termed the DP repeat. Earlier mutagenesis studies implicated the DP repeat of either Hop or Hip in Hsp70 binding and in normal assembly of the co-chaperones with progesterone receptor (PR) complexes. We report here that the DP repeat lies within a protease-resistant domain that extends to or is near the C-terminus of both co-chaperones. Point mutations in the DP repeats render the C-terminal regions hypersensitive to proteolysis. In addition, a Hop DP mutant displays altered proteolytic digestion patterns, which suggest that the DP-repeat region influences the folding of other Hop domains. Although the respective DP regions of Hop and Hip share sequence and structural similarities, they are not functionally interchangeable. Moreover, a double-point mutation within the second DP-repeat unit of Hop that converts this to the sequence found in Hip disrupts Hop function; however, the corresponding mutation in Hip does not alter its function. We conclude that the DP repeats are important structural elements within a C-terminal domain, which is important for Hop and Hip function.

  10. Arabidopsis pentatricopeptide repeat protein SOAR1 plays a critical role in abscisic acid signalling

    PubMed Central

    Mei, Chao; Jiang, Shang-Chuan; Lu, Yan-Fen; Wu, Fu-Qing; Yu, Yong-Tao; Liang, Shan; Feng, Xiu-Jing; Portoles Comeras, Sergi; Lu, Kai; Wu, Zhen; Wang, Xiao-Fang; Zhang, Da-Peng

    2014-01-01

    A dominant suppressor of the ABAR overexpressor, soar1-1D, from CHLH/ABAR [coding for Mg-chelatase H subunit/putative abscisic acid (ABA) receptor (ABAR)] overexpression lines was screened to explore the mechanism of the ABAR-mediated ABA signalling. The SOAR1 gene encodes a pentatricopeptide repeat (PPR) protein which localizes to both the cytosol and nucleus. Down-regulation of SOAR1 strongly enhances, but up-regulation of SOAR1 almost completely impairs, ABA responses, revealing that SOAR1 is a critical, negative, regulator of ABA signalling. Further genetic evidence supports that SOAR1 functions downstream of ABAR and probably upstream of an ABA-responsive transcription factor ABI5. Changes in the SOAR1 expression alter expression of a subset of ABA-responsive genes including ABI5. These findings provide important information to elucidate further the functional mechanism of PPR proteins and the complicated ABA signalling network. PMID:25005137

  11. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome.

    PubMed

    Kumar, Ashutosh; Singh, Himanshu N; Pareek, Vikas; Raza, Khursheed; Dantham, Subrahamanyam; Kumar, Pavan; Mochan, Sankat; Faiq, Muneeb A

    2016-01-01

    Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)-microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIKV genome and the response element of an early neural tube developmental marker "retinoic acid" in human DNA and (2) comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE) consensus sequence (5'-AGGTCA-3') in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly) and other viruses available in National Institute of Health genetic sequence database (GenBank) for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause fetal brain defects (for which maternal-fetal transmission during developing stage may be required). The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although, bioinformatic evidence and embryological

  12. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome.

    PubMed

    Kumar, Ashutosh; Singh, Himanshu N; Pareek, Vikas; Raza, Khursheed; Dantham, Subrahamanyam; Kumar, Pavan; Mochan, Sankat; Faiq, Muneeb A

    2016-01-01

    Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)-microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIKV genome and the response element of an early neural tube developmental marker "retinoic acid" in human DNA and (2) comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE) consensus sequence (5'-AGGTCA-3') in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly) and other viruses available in National Institute of Health genetic sequence database (GenBank) for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause fetal brain defects (for which maternal-fetal transmission during developing stage may be required). The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although, bioinformatic evidence and embryological

  13. Genetic diversity of Saccharum spontaneum from geographical regions of China assessed by simple sequence repeats.

    PubMed

    Fan, L N; Deng, H H; Luo, Q W; He, H Y; Li, Y; Wang, Q N; Huang, Z X; Wu, J T; Li, Q W; Liu, S M; Qi, Y W

    2013-11-26

    Saccharum spontaneum is the most variable wild relative of sugarcane with potential for use in sugarcane improvement programs. In order to help preserve and exploit this species, 152 accessions from eight major geographical regions in China, including Hainan, Guangdong, Guangxi, Yunnan, Sichuan, Guizhou, Fujian, and Jiangxi provinces, were investigated by analyzing 20 simple sequence repeats (SSRs), including 11 genomic SSRs (gSSRs) and nine SSRs developed from expressed sequence tags (EST-SSRs). A total of 454 alleles were generated by the 20 SSRs, with 295 and 159 alleles detected by gSSRs and EST-SSRs respectively. The Mantel test showed significant correlation between genetic matrixes among the studied accessions revealed by gSSRs versus EST-SSRs, although the average polymorphism of EST-SSRs (17.7) was much lower than that of gSSRs (26.8). Among the eight provinces, collections from Guizhou were the most diverse and those from Guangdong were the most distinct. Clustering analysis and principal component analysis accordantly classified the accessions into four groups, which were "Southwest group", "Hainan group", "Guangdong group", and "Guangxi group", based on the geographical origin of the major accessions in each group, demonstrating that geographical factors play an important role in the pattern of genetic structure of Chinese S. spontaneum. As two (Guizhou and Yunnan) of the three provinces with highest genetic diversity are located in southwest China, we concluded that southwest China is the region with the highest genetic diversity of S. spontaneum.

  14. Telomerase activity in the various regions of mouse brain: non-radioactive telomerase repeat amplification protocol (TRAP) assay.

    PubMed

    Grin, Yossi; Admoni, Tamar; Priel, Esther

    2014-01-01

    Telomerase, a ribonucleoprotein, is responsible for maintaining the telomere length and therefore promoting genomic integrity, proliferation, and lifespan. In addition, telomerase protects the mitochondria from oxidative stress and confers resistance to apoptosis, suggesting its possible importance for the surviving of non-mitotic, highly active cells such as neurons. We previously demonstrated the ability of novel telomerase activators to increase telomerase activity and expression in the various mouse brain regions and to protect motor neurons cells from oxidative stress. These results strengthen the notion that telomerase is involved in the protection of neurons from various lesions. To underline the role of telomerase in the brain, we here compare the activity of telomerase in male and female mouse brain and its dependence on age. TRAP assay is a standard method for detecting telomerase activity in various tissues or cell lines. Here we demonstrate the analysis of telomerase activity in three regions of the mouse brain by non-denaturing protein extraction using CHAPS lysis buffer followed by modification of the standard TRAP assay. In this 2-step assay, endogenous telomerase elongates a specific telomerase substrate (TS primer) by adding TTAGGG 6 bp repeats (telomerase reaction). The telomerase reaction products are amplified by PCR reaction creating a DNA ladder of 6 bp increments. The analysis of the DNA ladder is made by 4.5% high resolution agarose gel electrophoresis followed by staining with highly sensitive nucleic acid stain. Compared to the traditional TRAP assay that utilize (32)P labeled radioactive dCTP's for DNA detection and polyacrylamide gel electrophoresis for resolving the DNA ladder, this protocol offers a non-toxic time saving TRAP assay for evaluating telomerase activity in the mouse brain, demonstrating the ability to detect differences in telomerase activity in the various female and male mouse brain region. PMID:25225832

  15. Mitogenomics reveals phylogeny and repeated motifs in control regions of the deep-sea family Siboglinidae (Annelida).

    PubMed

    Li, Yuanning; Kocot, Kevin M; Schander, Christoffer; Santos, Scott R; Thornhill, Daniel J; Halanych, Kenneth M

    2015-04-01

    Deep-sea tubeworms in the annelid family Siboglinidae have drawn considerable interest regarding their ecology and evolutionary biology. As adults, they lack a digestive tract and rely on endosymbionts for nutrition. Moreover, they are important members of chemosynthetic environments including hydrothermal vents, cold seeps, muddy sediments, and whale bones. Evolution and diversification of siboglinids has been associated with host-symbiont relationships and reducing habitats. Despite their importance, the taxonomy and phylogenetics of this clade are debated due to conflicting results. In this study, 10 complete and 2 partial mitochondrial genomes and one transcriptome were sequenced and analyzed to address siboglinid evolution. Notably, repeated nucleotide motifs were found in control regions of these mt genomes, which may explain previous challenges of sequencing siboglinid mt genomes. Phylogenetic analyses of amino acid and nucleotide datasets were conducted in order to infer evolutionary history. Both analyses generally had strong nodal support and suggest Osedax is most closely related to the Vestimentifera+Sclerolinum clade, rather than Frenulata, as recently reported. These results imply Osedax, the only siboglinid lineage with heterotrophic endosymbionts, evolved from a lineage utilizing chemoautotrophic symbionts.

  16. Characterization of Protective Epitopes in a Highly Conserved Plasmodium falciparum Antigenic Protein Containing Repeats of Acidic and Basic Residues

    PubMed Central

    Sharma, Pawan; Kumar, Anil; Singh, Balwan; Bharadwaj, Ashima; Sailaja, V. Naga; Adak, T.; Kushwaha, Ashima; Malhotra, Pawan; Chauhan, V. S.

    1998-01-01

    The delineation of putatively protective and immunogenic epitopes in vaccine candidate proteins constitutes a major research effort towards the development of an effective malaria vaccine. By virtue of its role in the formation of the immune clusters of merozoites, its location on the surface of merozoites, and its highly conserved nature both at the nucleotide sequence level and the amino acid sequence level, the antigen which contains repeats of acidic and basic residues (ABRA) of the human malaria parasite Plasmodium falciparum represents such an antigen. Based upon the predicted amino acid sequence of ABRA, we synthesized eight peptides, with six of these (AB-1 to AB-6) ranging from 12 to 18 residues covering the most hydrophilic regions of the protein, and two more peptides (AB-7 and AB-8) representing its repetitive sequences. We found that all eight constructs bound an appreciable amount of antibody in sera from a large proportion of P. falciparum malaria patients; two of these peptides (AB-1 and AB-3) also elicited a strong proliferation response in peripheral blood mononuclear cells from all 11 human subjects recovering from malaria. When used as carrier-free immunogens, six peptides induced a strong, boostable, immunoglobulin G-type antibody response in rabbits, indicating the presence of both B-cell determinants and T-helper-cell epitopes in these six constructs. These antibodies specifically cross-reacted with the parasite protein(s) in an immunoblot and in an immunofluorescence assay. In another immunoblot, rabbit antipeptide sera also recognized recombinant fragments of ABRA expressed in bacteria. More significantly, rabbit antibodies against two constructs (AB-1 and AB-5) inhibited the merozoite reinvasion of human erythrocytes in vitro up to ∼90%. These results favor further studies so as to determine possible inclusion of these two constructs in a multicomponent subunit vaccine against asexual blood stages of P. falciparum. PMID:9596765

  17. The anteroventral third ventricle region is critical for the behavioral desensitization caused by repeated injections of angiotensin II.

    PubMed

    Vento, Peter J; Daniels, Derek

    2014-01-01

    A single central injection of angiotensin II (AngII) potently increases water intake; however, a growing body of research suggests that repeated, acute intracerebroventricular injections of AngII cause a reduction in the dipsogenic response to subsequent AngII. This AngII-induced behavioral desensitization is specific to the effects of angiotensin and mediated by the angiotensin type-1 (AT1) receptor. The neuroanatomical substrate for this phenomenon, however, remains unknown. The anteroventral third ventricle (AV3V) region is an important site for the behavioral and physiological actions of AngII. Therefore, we hypothesized that this region also mediates the effects of repeated central AngII administration. In support of this hypothesis, we found that repeated injections of AngII into the AV3V reduced water intake stimulated by a test injection of AngII given into this region. Moreover, repeated AngII injections in the AV3V reduced water intake after AngII was injected into the lateral ventricle. These studies also demonstrate that activation of the AT1 receptor within the AV3V is required for AngII-induced behavioral desensitization because direct injection of the AT1 receptor antagonist, losartan, into the AV3V blocked the desensitizing effect of repeated AngII injections into the lateral ventricle. These findings provide additional support for a role of the AV3V in the dipsogenic actions of AngII, and suggest that this region is critical for the desensitization that occurs after acute repeated central injections of AngII.

  18. Non-essential repeats in the promoter region of a Brassica rapa acyl carrier protein gene expressed in developing embryos.

    PubMed

    Scherer, D; Sato, A; McCarter, D W; Radke, S E; Kridl, J C; Knauf, V C

    1992-02-01

    A genomic clone of an acyl carrier protein gene (Bcg4-4) which is highly expressed in developing embryos of Brassica rapa was isolated and sequenced. The promoter and transcription terminator regions of Bcg4-4 were used to express a beta-glucuronidase reporter gene in transgenic rapeseed. Deletion of repeated domains in the promoter region did not lower beta-glucuronidase expression in seeds.

  19. Effect of acetic acid repeated treatments on post-harvest quality of "Taloppo" table grape.

    PubMed

    Venditti, T; Dore, A; Molinu, M G; D'Hallewin, G

    2012-01-01

    The most important pathogen for table grapes is Botrytis cinerea which causes a rapid deterioration of fruit. Postharvest losses are controlled with SO2 fumigations carried out every 7 or 10 days, but the use of this gas is becoming more difficult to justify because of undesirable effects on the fruit and the increasing concern for human health. Acetic acid, classified as a GRAS compound, can be employed with no restriction as preservative and represents a possible substitute to sulphur dioxide. The aims of the present work were: (1) to evaluate if repeated treatments with AAC during storage preserve table grapes fruit quality; (2) to verify the effectiveness of 3 different concentrations and time intervals between each treatment and compare the effects with SO2 treatment; The amounts of AAC used in each fumigation, performed for 15 minutes, were 30, 50 and 75 microL/L, and treatments were carried out 5, 3 and 2 times respectively during storage, in order to have the same final concentration (150 microL/L). Table grapes were also fumigated with SO2. Fruit was stored for 8 weeks at 5 degrees C and 95% of RH, followed by 4 days of a simulated shelf-life (SSL) at 20 degrees C and 85% RH. At the end of experiment decay, weight loss and visual assessment were evaluated. After eight weeks of storage the incidence of grey mould, with respect to untreated fruit, was reduced in all treatments. The comparison among the different treatments did not show significant differences between the fumigations performed 3 and 2 times, with 24.9% and 27.2% of rots respectively. A better decay control was achieved with 5 fumigations carried out every 2 weeks, (18.1% of rots), while decay in fruit treated with SO2 was 26.2%. During the SSL period no particular differences were observed among all treatments. None of the treatments affected weight loss, as well as no differences were found in the score attributed for the external quality (rachis browning and berries appearance). The results

  20. Effect of acetic acid repeated treatments on post-harvest quality of "Taloppo" table grape.

    PubMed

    Venditti, T; Dore, A; Molinu, M G; D'Hallewin, G

    2012-01-01

    The most important pathogen for table grapes is Botrytis cinerea which causes a rapid deterioration of fruit. Postharvest losses are controlled with SO2 fumigations carried out every 7 or 10 days, but the use of this gas is becoming more difficult to justify because of undesirable effects on the fruit and the increasing concern for human health. Acetic acid, classified as a GRAS compound, can be employed with no restriction as preservative and represents a possible substitute to sulphur dioxide. The aims of the present work were: (1) to evaluate if repeated treatments with AAC during storage preserve table grapes fruit quality; (2) to verify the effectiveness of 3 different concentrations and time intervals between each treatment and compare the effects with SO2 treatment; The amounts of AAC used in each fumigation, performed for 15 minutes, were 30, 50 and 75 microL/L, and treatments were carried out 5, 3 and 2 times respectively during storage, in order to have the same final concentration (150 microL/L). Table grapes were also fumigated with SO2. Fruit was stored for 8 weeks at 5 degrees C and 95% of RH, followed by 4 days of a simulated shelf-life (SSL) at 20 degrees C and 85% RH. At the end of experiment decay, weight loss and visual assessment were evaluated. After eight weeks of storage the incidence of grey mould, with respect to untreated fruit, was reduced in all treatments. The comparison among the different treatments did not show significant differences between the fumigations performed 3 and 2 times, with 24.9% and 27.2% of rots respectively. A better decay control was achieved with 5 fumigations carried out every 2 weeks, (18.1% of rots), while decay in fruit treated with SO2 was 26.2%. During the SSL period no particular differences were observed among all treatments. None of the treatments affected weight loss, as well as no differences were found in the score attributed for the external quality (rachis browning and berries appearance). The results

  1. Surface antigens and potential virulence factors from parasites detected by comparative genomics of perfect amino acid repeats

    PubMed Central

    Fankhauser, Niklaus; Nguyen-Ha, Tien-Minh; Adler, Joël; Mäser, Pascal

    2007-01-01

    Background Many parasitic organisms, eukaryotes as well as bacteria, possess surface antigens with amino acid repeats. Making up the interface between host and pathogen such repetitive proteins may be virulence factors involved in immune evasion or cytoadherence. They find immunological applications in serodiagnostics and vaccine development. Here we use proteins which contain perfect repeats as a basis for comparative genomics between parasitic and free-living organisms. Results We have developed Reptile , a program for proteome-wide probabilistic description of perfect repeats in proteins. Parasite proteomes exhibited a large variance regarding the proportion of repeat-containing proteins. Interestingly, there was a good correlation between the percentage of highly repetitive proteins and mean protein length in parasite proteomes, but not at all in the proteomes of free-living eukaryotes. Reptile combined with programs for the prediction of transmembrane domains and GPI-anchoring resulted in an effective tool for in silico identification of potential surface antigens and virulence factors from parasites. Conclusion Systemic surveys for perfect amino acid repeats allowed basic comparisons between free-living and parasitic organisms that were directly applicable to predict proteins of serological and parasitological importance. An on-line tool is available at . PMID:18096064

  2. Analysis of the renin gene intron A tandem repeat region of Milan and Lyon hypertensive rat strains.

    PubMed

    Samani, N J; Vincent, M; Sassard, J; Henderson, I W; Kaiser, M A; Brammar, W J; Swales, J D

    1990-09-01

    The region of intron A of the rat renin gene containing a unique tandemly repeated sequence was analysed in the Milan and Lyon hypertensive rat strains and their controls, and in several Sprague-Dawley rats, using an oligonucleotide probe complementary to the tandemly repeated sequence and a renin complementary DNA probe. In the Milan rats, the size of the Bgl II DNA fragment encompassing the tandem repeat region was the same in the hypertensive (MHS) and normotensive (MNS) strains. In the Lyon model, a difference of 1.1 kilobase (equivalent to about 28 copies of the 38 basepair tandem repeat sequence) was observed in the size of the Bgl II fragment of the hypertensive (LH) and normotensive (LN) strains. However, the finding that the size of the fragment in the Lyon low-blood-pressure (LL) strain was the same as that in the LH strain rather than the LN strain suggests that the difference between the two latter strains is not by itself a major cause of the blood pressure difference between them in the intron A tandem region. An analysis of Sprague-Dawley rats, from which the Lyon strains are derived, showed that at least three different renin gene alleles, two with Bgl II fragments of the same size as those seen in the Lyon strains, are randomly segregating in this population.

  3. Sequence-based definition of eight short tandem repeat loci located within the HLA-region in an Austrian population.

    PubMed

    Dauber, Eva-Maria; Wenda, Sabine; Schwartz-Jungl, Elisabeth Maria; Glock, Barbara; Mayr, Wolfgang R

    2015-01-01

    Sequenced allelic ladders are a prerequisite for reliable genotyping of short tandem repeat (STR) polymorphisms and consistent results across instrument platforms. For eight STR-loci located on the short arm of chromosome 6 (6p21.3), a sequenced based nomenclature was established according to international recommendations. Publicly available reference DNA samples were sequenced enabling interested laboratories to construct their own allelic ladders. Three tetrameric (D6S2691, D6S2678, DQIV), one trimeric (D6S2906) and four dimeric repeat loci (D6S2972, D6S2792, D6S2789, D6S273) were investigated. Apart from the very complex sequence structure at the DQIV locus, three loci showed a compound and four loci a simple repeat pattern. In the flanking regions of some loci additional single nucleotide and insertion/deletion polymorphisms occurred as well as sequence polymorphisms within the repeat region of alleles with the same length. In an Austrian Caucasoid population sample (n=293) between eight and 22 alleles were found. No significant deviation from Hardy-Weinberg expectations was observed, the power of discrimination ranged from 0.826 to 0.978. The loci cover the HLA-coding region from HLA-A to HLA-DQB1 and can be used for a better definition of HLA haplotypes for population and disease association studies, recombination point mapping, haematopoietic stem cell transplantation as well as for identity and relationship testing. PMID:25450788

  4. Sequence-based definition of eight short tandem repeat loci located within the HLA-region in an Austrian population.

    PubMed

    Dauber, Eva-Maria; Wenda, Sabine; Schwartz-Jungl, Elisabeth Maria; Glock, Barbara; Mayr, Wolfgang R

    2015-01-01

    Sequenced allelic ladders are a prerequisite for reliable genotyping of short tandem repeat (STR) polymorphisms and consistent results across instrument platforms. For eight STR-loci located on the short arm of chromosome 6 (6p21.3), a sequenced based nomenclature was established according to international recommendations. Publicly available reference DNA samples were sequenced enabling interested laboratories to construct their own allelic ladders. Three tetrameric (D6S2691, D6S2678, DQIV), one trimeric (D6S2906) and four dimeric repeat loci (D6S2972, D6S2792, D6S2789, D6S273) were investigated. Apart from the very complex sequence structure at the DQIV locus, three loci showed a compound and four loci a simple repeat pattern. In the flanking regions of some loci additional single nucleotide and insertion/deletion polymorphisms occurred as well as sequence polymorphisms within the repeat region of alleles with the same length. In an Austrian Caucasoid population sample (n=293) between eight and 22 alleles were found. No significant deviation from Hardy-Weinberg expectations was observed, the power of discrimination ranged from 0.826 to 0.978. The loci cover the HLA-coding region from HLA-A to HLA-DQB1 and can be used for a better definition of HLA haplotypes for population and disease association studies, recombination point mapping, haematopoietic stem cell transplantation as well as for identity and relationship testing.

  5. Repeated electrical stimulation of reward-related brain regions affects cocaine but not "natural" reinforcement.

    PubMed

    Levy, Dino; Shabat-Simon, Maytal; Shalev, Uri; Barnea-Ygael, Noam; Cooper, Ayelet; Zangen, Abraham

    2007-12-19

    Drug addiction is associated with long-lasting neuronal adaptations including alterations in dopamine and glutamate receptors in the brain reward system. Treatment strategies for cocaine addiction and especially the prevention of craving and relapse are limited, and their effectiveness is still questionable. We hypothesized that repeated stimulation of the brain reward system can induce localized neuronal adaptations that may either potentiate or reduce addictive behaviors. The present study was designed to test how repeated interference with the brain reward system using localized electrical stimulation of the medial forebrain bundle at the lateral hypothalamus (LH) or the prefrontal cortex (PFC) affects cocaine addiction-associated behaviors and some of the neuronal adaptations induced by repeated exposure to cocaine. Repeated high-frequency stimulation in either site influenced cocaine, but not sucrose reward-related behaviors. Stimulation of the LH reduced cue-induced seeking behavior, whereas stimulation of the PFC reduced both cocaine-seeking behavior and the motivation for its consumption. The behavioral findings were accompanied by glutamate receptor subtype alterations in the nucleus accumbens and the ventral tegmental area, both key structures of the reward system. It is therefore suggested that repeated electrical stimulation of the PFC can become a novel strategy for treating addiction. PMID:18094257

  6. Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: Evolutionary footprints of RNA silencing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Pyknons are non-random sequence patterns significantly repeated throughout non-coding genomic DNA that also appear at least once among genes. They are interesting because they portend an unforeseen connection between coding and non-coding DNA. Pyknons have only been discovered in the human genome,...

  7. Repeat-Associated Fission Yeast-Like Regional Centromeres in the Ascomycetous Budding Yeast Candida tropicalis

    PubMed Central

    Chatterjee, Gautam; Sankaranarayanan, Sundar Ram; Guin, Krishnendu; Thattikota, Yogitha; Padmanabhan, Sreedevi; Siddharthan, Rahul; Sanyal, Kaustuv

    2016-01-01

    The centromere, on which kinetochore proteins assemble, ensures precise chromosome segregation. Centromeres are largely specified by the histone H3 variant CENP-A (also known as Cse4 in yeasts). Structurally, centromere DNA sequences are highly diverse in nature. However, the evolutionary consequence of these structural diversities on de novo CENP-A chromatin formation remains elusive. Here, we report the identification of centromeres, as the binding sites of four evolutionarily conserved kinetochore proteins, in the human pathogenic budding yeast Candida tropicalis. Each of the seven centromeres comprises a 2 to 5 kb non-repetitive mid core flanked by 2 to 5 kb inverted repeats. The repeat-associated centromeres of C. tropicalis all share a high degree of sequence conservation with each other and are strikingly diverged from the unique and mostly non-repetitive centromeres of related Candida species—Candida albicans, Candida dubliniensis, and Candida lusitaniae. Using a plasmid-based assay, we further demonstrate that pericentric inverted repeats and the underlying DNA sequence provide a structural determinant in CENP-A recruitment in C. tropicalis, as opposed to epigenetically regulated CENP-A loading at centromeres in C. albicans. Thus, the centromere structure and its influence on de novo CENP-A recruitment has been significantly rewired in closely related Candida species. Strikingly, the centromere structural properties along with role of pericentric repeats in de novo CENP-A loading in C. tropicalis are more reminiscent to those of the distantly related fission yeast Schizosaccharomyces pombe. Taken together, we demonstrate, for the first time, fission yeast-like repeat-associated centromeres in an ascomycetous budding yeast. PMID:26845548

  8. Genome-wide evidence for selection acting on single amino acid repeats.

    PubMed

    Haerty, Wilfried; Golding, G Brian

    2010-06-01

    Low complexity and homopolymer sequences within coding regions are known to evolve rapidly. While their expansion may be deleterious, there is increasing evidence for a functional role associated with these amino acid sequences. Homopolymer sequences are thought to evolve mostly through replication slippage and, therefore, they may be expected to be longer in regions with relaxed selective constraint. Within the coding sequences of eukaryotes, alternatively spliced exons are known to evolve under relaxed constraints in comparison to those exons that are constitutively spliced because they are not included in all of the mature mRNA of a gene. This relaxed exposure to selection leads to faster rates of evolution for alternatively spliced exons in comparison to constitutively spliced exons. Here, we have tested the effect of splicing on the structure (composition, length) of homopolymer sequences in relation to the splicing pattern in which they are found. We observed a significant relationship between alternative splicing and homopolymer sequences with alternatively spliced genes being enriched in number and length of homopolymer sequences. We also observed lower codon diversity and longer homocodons, suggesting a balance between slippage and point mutations linked to the constraints imposed by selection.

  9. Genetic variations of human herpesvirus 7 by analysis of glycoproteins B and H, and R2-repeat regions.

    PubMed

    Thawaranantha, Duanthanorm; Chimabutra, Kanittha; Balachandra, Kruavon; Warachit, Paijit; Pantuwatana, Somsak; Tanaka-Taya, Keiko; Inagi, Reiko; Kurata, Takeshi; Yamanishi, Koichi

    2002-03-01

    Clinical isolates of human herpesvirus 7 (HHV-7) from the saliva of healthy individual were investigated for genetic variations in the regions of two immediate-early (IE) genes, the glycoprotein B (gB) and glycoprotein H (gH) genes, and in R2-repeat. The genomic DNA of 24 isolates from citizens of Thailand, Japan, and the United States was amplified to detect size variations in the IE-1 and IE-2 loci, but none was observed, suggesting that there was no deletion or insertion in these genes, in contrast with an IE gene of human herpesvirus 6 (HHV-6). The sequences of the gB gene from isolates acquired from 5 Japanese and 8 Thai subject were then compared with those of American strains JI and RK with respect to codons that are known to differentiate gB alleles. All the isolates were found to have gB allele C except for the JI strain, which has allele F. Variability was also observed in five specific gH codons, resulting in 6 different groups. The HHV-7 isolates might be classified into two major genetic variants by combining their gB and gH allelic groupings. In the present study, only JI belonged to variant 1, while the rest of the isolates appeared to belong to variant 2. In the R2-repeat region, size heterogeneities were observed among the 24 isolates, due to different repeat numbers (17, 15, 14, 13, or 12 repeats). Therefore, we used the R2-repeat to identify the origins of isolates in a study of HHV-7 transmission, and found HHV-7 to be transmitted within a family from both mothers and fathers to their children.

  10. Improvement of l-lactic acid productivity from sweet sorghum juice by repeated batch fermentation coupled with membrane separation.

    PubMed

    Wang, Yong; Meng, Hongyu; Cai, Di; Wang, Bin; Qin, Peiyong; Wang, Zheng; Tan, Tianwei

    2016-07-01

    In order to efficiently produce l-lactic acid from non-food feedstocks, sweet sorghum juice (SSJ), which is rich of fermentable sugars, was directly used for l-lactic acid fermentation by Lactobacillus rhamnosus LA-04-1. A membrane integrated repeated batch fermentation (MIRB) was developed for productivity improvement. High-cell-density fermentation was achieved with a final cell density (OD620) of 42.3, and the CCR effect was overcomed. When SSJ (6.77gL(-1) glucose, 4.51gL(-1) fructose and 50.46gL(-1) sucrose) was used as carbon source in MIRB process, l-lactic acid productivity was increased significantly from 1.45gL(-1)h(-1) (batch 1) to 17.55gL(-1)h(-1) (batch 6). This process introduces an effective way to produce l-lactic acid from SSJ.

  11. An examination of the origin and evolution of additional tandem repeats in the mitochondrial DNA control region of Japanese sika deer (Cervus Nippon).

    PubMed

    Ba, Hengxing; Wu, Lang; Liu, Zongyue; Li, Chunyi

    2016-01-01

    Tandem repeat units are only detected in the left domain of the mitochondrial DNA control region in sika deer. Previous studies showed that Japanese sika deer have more tandem repeat units than its cousins from the Asian continent and Taiwan, which often have only three repeat units. To determine the origin and evolution of these additional repeat units in Japanese sika deer, we obtained the sequence of repeat units from an expanded dataset of the control region from all sika deer lineages. The functional constraint is inferred to act on the first repeat unit because this repeat has the least sequence divergence in comparison to the other units. Based on slipped-strand mispairing mechanisms, the illegitimate elongation model could account for the addition or deletion of these additional repeat units in the Japanese sika deer population. We also report that these additional repeat units could be occurring in the internal positions of tandem repeat regions, possibly via coupling with a homogenization mechanism within and among these lineages. Moreover, the increased number of repeat units in the Japanese sika deer population could reflect a balance between mutation and selection, as well as genetic drift.

  12. SHANK3 Gene Mutations Associated with Autism Facilitate Ligand Binding to the Shank3 Ankyrin Repeat Region*

    PubMed Central

    Mameza, Marie Germaine; Dvoretskova, Elena; Bamann, Margarete; Hönck, Hans-Hinrich; Güler, Türkan; Boeckers, Tobias M.; Schoen, Michael; Verpelli, Chiara; Sala, Carlo; Barsukov, Igor; Dityatev, Alexander; Kreienkamp, Hans-Jürgen

    2013-01-01

    Shank/ProSAP proteins are major scaffold proteins of the postsynaptic density; mutations in the human SHANK3 gene are associated with intellectual disability or autism spectrum disorders. We have analyzed the functional relevance of several SHANK3 missense mutations affecting the N-terminal portion of the protein by expression of wild-type and mutant Shank3 in cultured neurons and by binding assays in heterologous cells. Postsynaptic targeting of recombinant Shank3 was unaltered. In electrophysiological experiments, both wild-type and L68P mutant forms of Shank3 were equally effective in restoring synaptic function after knockdown of endogenous Shank3. We observed that several mutations affected binding to interaction partners of the Shank3 ankyrin repeat region. One of these mutations, L68P, improved binding to both ligands. Leu-68 is located N-terminal to the ankyrin repeats, in a highly conserved region that we identify here as a novel domain termed the Shank/ProSAP N-terminal (SPN) domain. We show that the SPN domain interacts with the ankyrin repeats in an intramolecular manner, thereby restricting access of either Sharpin or α-fodrin. The L68P mutation disrupts this blockade, thus exposing the Shank3 ankyrin repeat region to its ligands. Our data identify a new type of regulation of Shank proteins and suggest that mutations in the SHANK3 gene do not necessarily induce a loss of function, but may represent a gain of function with respect to specific interaction partners. PMID:23897824

  13. Retroviral sequence located in border region of short unique region and short terminal repeat of Md5 strain of Marek's disease virus type 1.

    PubMed

    Endoh, D; Ito, M; Cho, K O; Kon, Y; Morimura, T; Hayashi, M; Kuwabara, M

    1998-02-01

    A 246-base pair (bp) retroviral sequence, which was homologous to a long terminal repeat of avian erythroblastosis virus (AEV), was detected and cloned from Md5 strain (Md5) of Marek's disease virus type 1 (MDV1) by representational difference analysis (RDA). The retroviral sequence was thought to be located in the border region of short unique region (U(s) and short terminal repeat (TRs), but did not exist in the border region of U(s) and the inverted short repeat (IRs) of the Md5 genome. A cloned fragment of the US/TRs border region of the Md5 genome showed a construction of U-E'-R-U'-E-TRs with the regions designated as follows: E, expanded TRs reported by Jones et al. [Proc. Natl. Acad. Sci. U.S.A. 90, 3855, 1993]; E', a partial copy of the expanded TRs; R, the retroviral sequence detected in Md5 genome; U, TRs-end sequence of U(s); U', a partial copy of TRs-end sequence of U(s). The sequence unit indicated as E'-R-U' was thought to be heterogeneously repeated in the Md5 genome. Since this retroviral sequence reportedly did not exist in the original stock of Md5, the retroviral sequence is thought to be inserted in the Md5 genome without experimental co-infection of avian cells with retrovirus and MDV1. These results suggest that RDA could be useful for the detection of retroviral sequences in the herpesvirus genome.

  14. A Possible Mechanism of Zika Virus Associated Microcephaly: Imperative Role of Retinoic Acid Response Element (RARE) Consensus Sequence Repeats in the Viral Genome

    PubMed Central

    Kumar, Ashutosh; Singh, Himanshu N.; Pareek, Vikas; Raza, Khursheed; Dantham, Subrahamanyam; Kumar, Pavan; Mochan, Sankat; Faiq, Muneeb A.

    2016-01-01

    Owing to the reports of microcephaly as a consistent outcome in the fetuses of pregnant women infected with ZIKV in Brazil, Zika virus (ZIKV)—microcephaly etiomechanistic relationship has recently been implicated. Researchers, however, are still struggling to establish an embryological basis for this interesting causal handcuff. The present study reveals robust evidence in favor of a plausible ZIKV-microcephaly cause-effect liaison. The rationale is based on: (1) sequence homology between ZIKV genome and the response element of an early neural tube developmental marker “retinoic acid” in human DNA and (2) comprehensive similarities between the details of brain defects in ZIKV-microcephaly and retinoic acid embryopathy. Retinoic acid is considered as the earliest factor for regulating anteroposterior axis of neural tube and positioning of structures in developing brain through retinoic acid response elements (RARE) consensus sequence (5′–AGGTCA–3′) in promoter regions of retinoic acid-dependent genes. We screened genomic sequences of already reported virulent ZIKV strains (including those linked to microcephaly) and other viruses available in National Institute of Health genetic sequence database (GenBank) for the RARE consensus repeats and obtained results strongly bolstering our hypothesis that ZIKV strains associated with microcephaly may act through precipitation of dysregulation in retinoic acid-dependent genes by introducing extra stretches of RARE consensus sequence repeats in the genome of developing brain cells. Additional support to our hypothesis comes from our findings that screening of other viruses for RARE consensus sequence repeats is positive only for those known to display neurotropism and cause fetal brain defects (for which maternal-fetal transmission during developing stage may be required). The numbers of RARE sequence repeats appeared to match with the virulence of screened positive viruses. Although, bioinformatic evidence and

  15. The Ccr4 Protein from Saccharomyces Cerevisiae Contains a Leucine-Rich Repeat Region Which Is Required for Its Control of Adh2 Gene Expression

    PubMed Central

    Malvar, T.; Biron, R. W.; Kaback, D. B.; Denis, C. L.

    1992-01-01

    The CCR4 gene from Saccharomyces cerevisiae is required for the transcription of the glucose-repressible alcohol dehydrogenase (ADH2). Mutations in CCR4 also suppress the transcription at the ADH2 and his4-912delta loci caused by defects in the SPT10 (CRE1) and SPT6 (CRE2) genes. The CCR4 gene was mapped to the left arm of chromosome I and cloned by complementation of function using previously isolated segments of chromosome I. DNA sequence analysis of the cloned gene defined CCR4 as a 2511 bp open reading frame that would encode a polypeptide of 837 amino acids. The CCR4 mRNA was found to be 2.8 kb in size and Western analysis identified CCR4 as a 95,000 D protein. Disruption of the CCR4 gene resulted in reduced levels of ADH2 expression under both glucose and ethanol growth conditions and in temperature sensitive growth on nonfermentative medium, phenotypes essentially indistinguishable from previously identified mutations in CCR4. The amino terminus of the CCR4 protein was found to be rich in glutamine residues similar to a number of genes which are required for transcription. More importantly, CCR4 showed similarity to a diverse set of proteins sharing a leucine-rich tandem repeat motif, the presence of which has been implicated in mediating protein-protein interactions. Deletions of several of the five leucine-rich repeats in CCR4 were shown to produce nonfunctional proteins indicating the importance of the repeats to CCR4 activity. This leucine-rich repeat region may mediate the contact CCR4 makes with another factor. PMID:1459446

  16. Identification and mapping of expressed genes, simple sequence repeats and transposable elements in centromeric regions of rice chromosomes.

    PubMed

    Mizuno, Hiroshi; Ito, Kazue; Wu, Jianzhong; Tanaka, Tsuyoshi; Kanamori, Hiroyuki; Katayose, Yuichi; Sasaki, Takuji; Matsumoto, Takashi

    2006-12-31

    The genomic sequences derived from rice centromeric regions were analyzed to facilitate the comprehensive understanding of the rice genome. A rice centromere-specific satellite sequence, RCS2/TrsD/CentO, was used to screen P1-derived artificial chromosome (PAC) and bacterial artificial chromosome (BAC) genomic libraries derived from Oryza sativa L. ssp. japonica cultivar Nipponbare. Physical maps of the centromeric regions were constructed by DNA fingerprinting methods and the aligned clones were analyzed by end sequencing. BLAST analysis revealed the composition of genes, centromeric satellites and other repetitive elements, such as RIRE7/CRR, RIRE8, Squiq, Anaconda, CACTA and miniature inverted-repeat transposable elements. Fiber-fluorescent in situ hybridization analysis also indicated the presence of distinct clusters of RCS2/TrsD/CentO satellite interspersed with other elements, instead of a long homogeneous region. Several expressed genes, sequences representative of ancestral organellar insertions, relatively long simple sequence repeats (SSRs), and sequences corresponding to 5S and 45S ribosomal RNA genes were also identified. Thirty-one gene sequences showed high-similarity to rice full-length cDNA sequences that had not been matched to the published rice genome sequence in silico. These results suggest the presence of expressed genes within and around the clusters of RCS2/TrsD/CentO satellites in unsequenced centromeric regions of the rice chromosomes.

  17. Genetic analysis of heptad-repeat regions in the G2 fusion subunit of the Junin arenavirus envelope glycoprotein

    SciTech Connect

    York, Joanne . E-mail: joanne.york@umontana.edu; Agnihothram, Sudhakar S. . E-mail: sudhakar.agnihothram@umontana.edu; Romanowski, Victor . E-mail: victor@biol.unlp.edu.ar; Nunberg, Jack H. . E-mail: jack.nunberg@umontana.edu

    2005-12-20

    The G2 fusion subunit of the Junin virus envelope glycoprotein GP-C contains two hydrophobic heptad-repeat regions that are postulated to form a six-helix bundle structure required for the membrane fusion activity of Class I viral fusion proteins. We have investigated the role of these heptad-repeat regions and, specifically, the importance of the putative interhelical a and d position sidechains by using alanine-scanning mutagenesis. All the mutant glycoproteins were expressed and transported to the cell surface. Proteolytic maturation at the subtilisin kexin isozyme-1/site-1-protease (SKI-1/S1P) cleavage site was observed in all but two of the mutants. Among the adequately cleaved mutant glycoproteins, four positions in the N-terminal region (I333, L336, L347 and L350) and two positions in the C-terminal region (R392 and W395) were shown to be important determinants of cell-cell fusion. Taken together, our results indicate that {alpha}-helical coiled-coil structures are likely critical in promoting arenavirus membrane fusion. These findings support the inclusion of the arenavirus GP-C among the Class I viral fusion proteins and suggest pharmacologic and immunologic strategies for targeting arenavirus infection and hemorrhagic fever.

  18. Bagasse hydrolyzates from Agave tequilana as substrates for succinic acid production by Actinobacillus succinogenes in batch and repeated batch reactor.

    PubMed

    Corona-González, Rosa Isela; Varela-Almanza, Karla María; Arriola-Guevara, Enrique; Martínez-Gómez, Álvaro de Jesús; Pelayo-Ortiz, Carlos; Toriz, Guillermo

    2016-04-01

    The aim of this work was to obtain fermentable sugars by enzymatic or acid hydrolyses of Agave tequilana Weber bagasse in order to produce succinic acid with Actinobacillus succinogenes. Hydrolyses were carried out with mineral acids (sulfuric and hydrochloric acids) or a commercial cellulolytic enzyme, and were optimized statistically by a response surface methodology, having as factors the concentration of acid/enzyme and time of hydrolysis. The concentration of sugars obtained at optimal conditions for each hydrolysis were 21.7, 22.4y 19.8g/L for H2SO4, HCl and the enzymatic preparation respectively. Concerning succinic acid production, the enzymatic hydrolyzates resulted in the highest yield (0.446g/g) and productivity (0.57g/Lh) using A. succinogenes in a batch reactor system. Repeated batch fermentation with immobilized A. succinogenes in agar and with the enzymatic hydrolyzates resulted in a maximum concentration of succinic acid of 33.6g/L from 87.2g/L monosaccharides after 5 cycles in 40h, obtaining a productivity of 1.32g/Lh.

  19. Bagasse hydrolyzates from Agave tequilana as substrates for succinic acid production by Actinobacillus succinogenes in batch and repeated batch reactor.

    PubMed

    Corona-González, Rosa Isela; Varela-Almanza, Karla María; Arriola-Guevara, Enrique; Martínez-Gómez, Álvaro de Jesús; Pelayo-Ortiz, Carlos; Toriz, Guillermo

    2016-04-01

    The aim of this work was to obtain fermentable sugars by enzymatic or acid hydrolyses of Agave tequilana Weber bagasse in order to produce succinic acid with Actinobacillus succinogenes. Hydrolyses were carried out with mineral acids (sulfuric and hydrochloric acids) or a commercial cellulolytic enzyme, and were optimized statistically by a response surface methodology, having as factors the concentration of acid/enzyme and time of hydrolysis. The concentration of sugars obtained at optimal conditions for each hydrolysis were 21.7, 22.4y 19.8g/L for H2SO4, HCl and the enzymatic preparation respectively. Concerning succinic acid production, the enzymatic hydrolyzates resulted in the highest yield (0.446g/g) and productivity (0.57g/Lh) using A. succinogenes in a batch reactor system. Repeated batch fermentation with immobilized A. succinogenes in agar and with the enzymatic hydrolyzates resulted in a maximum concentration of succinic acid of 33.6g/L from 87.2g/L monosaccharides after 5 cycles in 40h, obtaining a productivity of 1.32g/Lh. PMID:26802183

  20. Regional Neurodegeneration and Gliosis Are Amplified by Mild Traumatic Brain Injury Repeated at 24-Hour Intervals

    PubMed Central

    Bolton, Amanda Nicholle; Saatman, Kathryn Eileen

    2014-01-01

    Most traumatic brain injuries (TBIs) that occur every year are classified as ‘mild’. Individuals involved in high-risk activities may sustain multiple mild TBIs. We evaluated the acute physiological and histopathological consequences of mild TBI in a mouse model, comparing sham injury, single impact, or 5 impacts at a 24- or 48-hour inter-injury interval. A single closed skull impact resulted in bilateral gliosis in the hippocampus and entorhinal cortex that was proportional to impact depth. Midline impact, at a depth just above the threshold to induce transient unconsciousness, produced occasional axonal injury and degenerating neurons accompanied by astrogliosis in the entorhinal cortex and cerebellum. Mild TBI repeated every 24 hours resulted in bilateral hemorrhagic lesions in the entorhinal cortex along with significantly increased neurodegeneration and microglial activation despite diminished durations of apnea and unconsciousness with subsequent impacts. Astrogliosis and diffusely distributed axonal injury were also observed bilaterally in the cerebellum and the brainstem. When the interval between mild TBIs was increased to 48 hours, the pathological consequences were comparable to a single TBI. Together, these data suggest that in mice the brain remains at increased risk for damage for 24 hours after mild TBI despite reduced acute physiological responses to subsequent mild impacts. PMID:25232942

  1. Biological and biochemical characterization of mice expressing prion protein devoid of the octapeptide repeat region after infection with prions.

    PubMed

    Yamaguchi, Yoshitaka; Miyata, Hironori; Uchiyama, Keiji; Ootsuyama, Akira; Inubushi, Sachiko; Mori, Tsuyoshi; Muramatsu, Naomi; Katamine, Shigeru; Sakaguchi, Suehiro

    2012-01-01

    Accumulating lines of evidence indicate that the N-terminal domain of prion protein (PrP) is involved in prion susceptibility in mice. In this study, to investigate the role of the octapeptide repeat (OR) region alone in the N-terminal domain for the susceptibility and pathogenesis of prion disease, we intracerebrally inoculated RML scrapie prions into tg(PrPΔOR)/Prnp(0/0) mice, which express mouse PrP missing only the OR region on the PrP-null background. Incubation times of these mice were not extended. Protease-resistant PrPΔOR, or PrP(Sc)ΔOR, was easily detectable but lower in the brains of these mice, compared to that in control wild-type mice. Consistently, prion titers were slightly lower and astrogliosis was milder in their brains. However, in their spinal cords, PrP(Sc)ΔOR and prion titers were abundant and astrogliosis was as strong as in control wild-type mice. These results indicate that the role of the OR region in prion susceptibility and pathogenesis of the disease is limited. We also found that the PrP(Sc)ΔOR, including the pre-OR residues 23-50, was unusually protease-resistant, indicating that deletion of the OR region could cause structural changes to the pre-OR region upon prion infection, leading to formation of a protease-resistant structure for the pre-OR region.

  2. Recombination Analysis of Herpes Simplex Virus 1 Reveals a Bias toward GC Content and the Inverted Repeat Regions

    PubMed Central

    Lee, Kyubin; Kolb, Aaron W.; Sverchkov, Yuriy; Cuellar, Jacqueline A.; Craven, Mark

    2015-01-01

    ABSTRACT Herpes simplex virus 1 (HSV-1) causes recurrent mucocutaneous ulcers and is the leading cause of infectious blindness and sporadic encephalitis in the United States. HSV-1 has been shown to be highly recombinogenic; however, to date, there has been no genome-wide analysis of recombination. To address this, we generated 40 HSV-1 recombinants derived from two parental strains, OD4 and CJ994. The 40 OD4-CJ994 HSV-1 recombinants were sequenced using the Illumina sequencing system, and recombination breakpoints were determined for each of the recombinants using the Bootscan program. Breakpoints occurring in the terminal inverted repeats were excluded from analysis to prevent double counting, resulting in a total of 272 breakpoints in the data set. By placing windows around the 272 breakpoints followed by Monte Carlo analysis comparing actual data to simulated data, we identified a recombination bias toward both high GC content and intergenic regions. A Monte Carlo analysis also suggested that recombination did not appear to be responsible for the generation of the spontaneous nucleotide mutations detected following sequencing. Additionally, kernel density estimation analysis across the genome found that the large, inverted repeats comprise a recombination hot spot. IMPORTANCE Herpes simplex virus 1 (HSV-1) virus is the leading cause of sporadic encephalitis and blinding keratitis in developed countries. HSV-1 has been shown to be highly recombinogenic, and recombination itself appears to be a significant component of genome replication. To date, there has been no genome-wide analysis of recombination. Here we present the findings of the first genome-wide study of recombination performed by generating and sequencing 40 HSV-1 recombinants derived from the OD4 and CJ994 parental strains, followed by bioinformatics analysis. Recombination breakpoints were determined, yielding 272 breakpoints in the full data set. Kernel density analysis determined that the large

  3. The regional costs and benefits of acid rain control

    SciTech Connect

    Berkman, M.P.

    1991-01-01

    Congress recently enacted acid rain control legislation as part of the 1990 Clean Air Act Amendments following a decade-long debate among disparate regional interests. Although Congress succeeded in drafting a law acceptable to all regions, the regional costs and benefits of the legislation remain uncertain. The research presented here attempts to estimate the regional costs and benefits and the economic impacts of acid rain controls. These estimates are made using a modeling system composed of econometric, linear programming and input-output models. The econometric and linear programming components describe markets for electricity and coal. The outputs of these components including capital investment, electricity demand, and coal production are taken as exogenous inputs by a multiregional input-output model. The input-output model produces estimates of changes in final demand, gross output, and employment. The utility linear programming model also predicts sulfur dioxide emissions (an acid-rain precursor). According to model simulations, the costs of acid rain control exceed the benefits for many regions including several regions customarily thought to be the major beneficiaries of acid rain control such as New England.

  4. Paraglacial rock mass damage during repeat glacial cycles in preparing slope instabilities (Aletsch region, Switzerland)

    NASA Astrophysics Data System (ADS)

    Grämiger, Lorenz; Moore, Jeffrey R.; Gischig, Valentin S.; Loew, Simon

    2016-04-01

    Glacier advance and retreat imposes mechanical stress cycles on underlying bedrock. Stress changes propagate rock mass damage and act as preparatory factors for slope instabilities, however, the mechanics of paraglacial rock slope damage remains poorly understood. In this study, we present results of detailed, conceptual numerical models, based on extensive field mapping and characterization at our Aletsch valley study site, Switzerland. We illustrate how simple stress changes associated with repeat glacial cycles can propagate fractures, enhance slip along discontinuities, and lead to failure of intact rock bridges, conditioning adjacent valley slopes for failure. We describe the timing and location of induced damage, stress redistribution, and displacement associated with Late Pleistocene and Holocene glacial cycles, and compare numerical predictions with the spatial and temporal distribution of landslides around the Great Aletsch Glacier. Our results help clarify mechanical linkages between glacial cycles and damage propagation in alpine valley rock slopes. In our simulations, most damage occurs during first deglaciation. This is in good agreement with the relative initiation timing (post-LGM / post-Egesen) for the majority of identified landslides at Aletsch. Large Holocene glacial cycles with high amplitude ice elevation changes in our models have a significant impact on displacement patterns in adjacent slopes. This correlates with a concentrated area of landslides located around the present-day glacier terminus, where the Great Aletsch Glacier fluctuated most during the Holocene. The kinematics and dimensions of an unstable rock slope produced in our models also generally resembles field observations of toppling-mode landslides on the eastern slope. No substantial displacement was generated on the western slope, although compound rock slides are observed on the western flank in the Aletsch.

  5. Double hairpin elements and tandem repeats in the non-coding region of Adenoides eludens chloroplast gene minicircles.

    PubMed

    Nelson, Martha J; Green, Beverley R

    2005-09-26

    Dinoflagellate plastid genomes are unique in having a reduced number of genes, most of which are found on unigenic minicircles of 2-3 kb. Although the dinoflagellate Adenoides eludens has larger minicircles of about 5 kb, they still carry only one gene. In addition, digenic circles of about 10 kb were detected and mapped by PCR. The non-coding regions of both unigenic and digenic circles share a number of common features including a pair of conserved cores in opposite orientation, four large families of tandem repeats and a number of double hairpin elements (DHEs). They most closely resemble the non-coding regions of the Symbiodinium psbA minicircles, but are much longer, less conserved and have an even greater variety of DHEs and tandem repeats. The presence of so many recombinogenic elements suggests models for the origin of minicircles from a multigenic ancestral chloroplast genome, and raises the possibility of recombination-directed replication rather than defined replication origins in the minicircles.

  6. Absence of association between a polymorphic GGC repeat in the 5' untranslated region of the reelin gene and autism.

    PubMed

    Krebs, M O; Betancur, C; Leroy, S; Bourdel, M C; Gillberg, C; Leboyer, M

    2002-01-01

    Autism is a complex neurodevelopmental disorder with severe cognitive and communication disabilities, that has a strong genetic predisposition. Reelin, a protein involved in neuronal migration during development, is encoded by a gene located on 7q22, within the candidate region on 7q showing increased allele sharing in previous genome scans. A case/control and family-based association study recently reported a positive association between a trinucleotide repeat polymorphism (GGC) located in the 5' untranslated region (UTR) of the reelin gene and autism. We performed a transmission disequilibrium test (TDT) analysis of the 5'UTR polymorphism in 167 families including 218 affected subjects (117 trios and 50 affected sib pairs) and found no evidence of linkage/association. Our results do not support previous findings and suggest that this GGC polymorphism of the reelin gene is unlikely to be a major susceptibility factor in autism and/or genetic heterogeneity.

  7. Thrombospondin Type-1 Repeat Domain-Containing Proteins Are Strongly Expressed in the Head Region of Hydra

    PubMed Central

    Hamaguchi-Hamada, Kayoko; Kurumata-Shigeto, Mami; Minobe, Sumiko; Fukuoka, Nozomi; Sato, Manami; Matsufuji, Miyuki; Koizumi, Osamu; Hamada, Shun

    2016-01-01

    The head region of Hydra, the hypostome, is a key body part for developmental control and the nervous system. We herein examined genes specifically expressed in the head region of Hydra oligactis using suppression subtractive hybridization (SSH) cloning. A total of 1414 subtracted clones were sequenced and found to be derived from at least 540 different genes by BLASTN analyses. Approximately 25% of the subtracted clones had sequences encoding thrombospondin type-1 repeat (TSR) domains, and were derived from 17 genes. We identified 11 TSR domain-containing genes among the top 36 genes that were the most frequently detected in our SSH library. Whole-mount in situ hybridization analyses confirmed that at least 13 out of 17 TSR domain-containing genes were expressed in the hypostome of Hydra oligactis. The prominent expression of TSR domain-containing genes suggests that these genes play significant roles in the hypostome of Hydra oligactis. PMID:27043211

  8. Structures and Polymorphic Interactions of Two Heptad-Repeat Regions of the SARS Virus S2 Protein

    SciTech Connect

    Deng,Y.; Liu, J.; Zheng, Q.; Yong, W.; Lu, M.

    2006-01-01

    Entry of SARS coronavirus into its target cell requires large-scale structural transitions in the viral spike (S) glycoprotein in order to induce fusion of the virus and cell membranes. Here we describe the identification and crystal structures of four distinct a-helical domains derived from the highly conserved heptad-repeat (HR) regions of the S2 fusion subunit. The four domains are an antiparallel four-stranded coiled coil, a parallel trimeric coiled coil, a four-helix bundle, and a six-helix bundle that is likely the final fusogenic form of the protein. When considered together, the structural and thermodynamic features of the four domains suggest a possible mechanism whereby the HR regions, initially sequestered in the native S glycoprotein spike, are released and refold sequentially to promote membrane fusion. Our results provide a structural framework for understanding the control of membrane fusion and should guide efforts to intervene in the SARS coronavirus entry process.

  9. Thrombospondin Type-1 Repeat Domain-Containing Proteins Are Strongly Expressed in the Head Region of Hydra.

    PubMed

    Hamaguchi-Hamada, Kayoko; Kurumata-Shigeto, Mami; Minobe, Sumiko; Fukuoka, Nozomi; Sato, Manami; Matsufuji, Miyuki; Koizumi, Osamu; Hamada, Shun

    2016-01-01

    The head region of Hydra, the hypostome, is a key body part for developmental control and the nervous system. We herein examined genes specifically expressed in the head region of Hydra oligactis using suppression subtractive hybridization (SSH) cloning. A total of 1414 subtracted clones were sequenced and found to be derived from at least 540 different genes by BLASTN analyses. Approximately 25% of the subtracted clones had sequences encoding thrombospondin type-1 repeat (TSR) domains, and were derived from 17 genes. We identified 11 TSR domain-containing genes among the top 36 genes that were the most frequently detected in our SSH library. Whole-mount in situ hybridization analyses confirmed that at least 13 out of 17 TSR domain-containing genes were expressed in the hypostome of Hydra oligactis. The prominent expression of TSR domain-containing genes suggests that these genes play significant roles in the hypostome of Hydra oligactis. PMID:27043211

  10. The role of G-density in switch region repeats for immunoglobulin class switch recombination

    PubMed Central

    Zhang, Zheng Z.; Pannunzio, Nicholas R.; Hsieh, Chih-Lin; Yu, Kefei; Lieber, Michael R.

    2014-01-01

    The boundaries of R-loops are well-documented at immunoglobulin heavy chain loci in mammalian B cells. Within primary B cells or B cell lines, the upstream boundaries of R-loops typically begin early in the repetitive portion of the switch regions. Most R-loops terminate within the switch repetitive zone, but the remainder can extend a few hundred base pairs further, where G-density on the non-template DNA strand gradually drops to the genome average. Whether the G-density determines how far the R-loops extend is an important question. We previously studied the role of G-clusters in initiating R-loop formation, but we did not examine the role of G-density in permitting the elongation of the R-loop, after it had initiated. Here, we vary the G-density of different portions of the switch region in a murine B cell line. We find that both class switch recombination (CSR) and R-loop formation decrease significantly when the overall G-density is reduced from 46% to 29%. Short 50 bp insertions with low G-density within switch regions do not appear to affect either CSR or R-loop elongation, whereas a longer (150 bp) insertion impairs both. These results demonstrate that G-density is an important determinant of the length over which mammalian genomic R-loops extend. PMID:25378327

  11. Diversity, evolution, and functionality of clustered regularly interspaced short palindromic repeat (CRISPR) regions in the fire blight pathogen Erwinia amylovora.

    PubMed

    Rezzonico, Fabio; Smits, Theo H M; Duffy, Brion

    2011-06-01

    The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system confers acquired heritable immunity against mobile nucleic acid elements in prokaryotes, limiting phage infection and horizontal gene transfer of plasmids. In CRISPR arrays, characteristic repeats are interspersed with similarly sized nonrepetitive spacers derived from transmissible genetic elements and acquired when the cell is challenged with foreign DNA. New spacers are added sequentially and the number and type of CRISPR units can differ among strains, providing a record of phage/plasmid exposure within a species and giving a valuable typing tool. The aim of this work was to investigate CRISPR diversity in the highly homogeneous species Erwinia amylovora, the causal agent of fire blight. A total of 18 CRISPR genotypes were defined within a collection of 37 cosmopolitan strains. Strains from Spiraeoideae plants clustered in three major groups: groups II and III were composed exclusively of bacteria originating from the United States, whereas group I generally contained strains of more recent dissemination obtained in Europe, New Zealand, and the Middle East. Strains from Rosoideae and Indian hawthorn (Rhaphiolepis indica) clustered separately and displayed a higher intrinsic diversity than that of isolates from Spiraeoideae plants. Reciprocal exclusion was generally observed between plasmid content and cognate spacer sequences, supporting the role of the CRISPR/Cas system in protecting against foreign DNA elements. However, in several group III strains, retention of plasmid pEU30 is inconsistent with a functional CRISPR/Cas system.

  12. Repeated salicylic acid peels for the treatment of hyperplastic sebaceous glands in hypohidrotic ectodermal dysplasia.

    PubMed

    Sgontzou, Themis; Armyra, Kalliopi; Kouris, Anargyros; Bokotas, Charalampos; Kontochristopoulos, George

    2014-12-01

    Hypohidrotic ectodermal dysplasia (Christ-Siemens-Touraine syndrome) is the most common type of ectodermal dysplasia. Hypertrophic sebaceous glands (HSGs) are rarely present but they cause an aesthetic problem. We report a case of a patient suffering from hypohidrotic ectodermal dysplasia, treated with salicylic acid peels for the hyperplastic sebaceous glands.

  13. Novel microsatellite repeats (MSRs) and linkage disequilibrium analysis in the SMA region of 5q13.1

    SciTech Connect

    Yaraghi, Z.; Roy, N.; MacKenzie, A.E.

    1994-09-01

    The spinal muscular atrophies (SMA) are characterized by degeneration of the anterior horn cells of the spinal cord, leading to muscular atrophy associated with progressive paralysis. The gene involved in SMA has been mapped by linkage analysis to a region of 5q13.1 flanked centromerically by D5S435 and telomerically by D5S557. We are in the process of identifying new microsatellite repeats to further define the genetic map of the SMA region. A contiguous array of YAC clones covering the SMA containing D5S435-D56S112 interval of 5q13.1 was established. From this contig, a 700 kb clone 76C1, which contains the 200 kb CMS-1/CATT-1 critical region, was used to generate a partial Sau3A1 phage library. We have previously shown that 2 CATT-1 subloci are in linkage disequilibrium with type I SMA. The 76C1 subloci are in linkage disequilibrium with type I SMA. The 76C1 phage library has been screened for human MSRs. To date we have identified two novel polymorphic microsatellites and four further candidates are being characterized. Results of linkage disequilibrium studies currently underway will be presented. The identification of a linkage disequilibrium maximum will be helpful in the further narrowing of the SMA region.

  14. Association between simple sequence repeat-rich chromosome regions and intergenomic translocation breakpoints in natural populations of allopolyploid wild wheats

    PubMed Central

    Molnár, István; Cifuentes, Marta; Schneider, Annamária; Benavente, Elena; Molnár-Láng, Márta

    2011-01-01

    Background and Aims Repetitive DNA sequences are thought to be involved in the formation of chromosomal rearrangements. The aim of this study was to analyse the distribution of microsatellite clusters in Aegilops biuncialis and Aegilops geniculata, and its relationship with the intergenomic translocations in these allotetraploid species, wild genetic resources for wheat improvement. Methods The chromosomal localization of (ACG)n and (GAA)n microsatellite sequences in Ae. biuncialis and Ae. geniculata and in their diploid progenitors Aegilops comosa and Aegilops umbellulata was investigated by sequential in situ hybridization with simple sequence repeat (SSR) probes and repeated DNA probes (pSc119·2, Afa family and pTa71) and by dual-colour genomic in situ hybridization (GISH). Thirty-two Ae. biuncialis and 19 Ae. geniculata accessions were screened by GISH for intergenomic translocations, which were further characterized by fluorescence in situ hybridization and GISH. Key Results Single pericentromeric (ACG)n signals were localized on most U and on some M genome chromosomes, whereas strong pericentromeric and several intercalary and telomeric (GAA)n sites were observed on the Aegilops chromosomes. Three Ae. biuncialis accessions carried 7Ub–7Mb reciprocal translocations and one had a 7Ub–1Mb rearrangement, while two Ae. geniculata accessions carried 7Ug–1Mg or 5Ug–5Mg translocations. Conspicuous (ACG)n and/or (GAA)n clusters were located near the translocation breakpoints in eight of the ten translocated chromosomes analysed, SSR bands and breakpoints being statistically located at the same chromosomal site in six of them. Conclusions Intergenomic translocation breakpoints are frequently mapped to SSR-rich chromosomal regions in the allopolyploid species examined, suggesting that microsatellite repeated DNA sequences might facilitate the formation of those chromosomal rearrangements. The (ACG)n and (GAA)n SSR motifs serve as additional chromosome markers

  15. Characterisation and evaluation of antiviral recombinant peptides based on the heptad repeat regions of NDV and IBV fusion glycoproteins

    SciTech Connect

    Wang Xiaojia Li Chuangen; Chi Xiaojing; Wang Ming

    2011-06-20

    Mixed virus infections can cause livestock losses that are more devastating than those caused by single virus infections. Newcastle disease virus (NDV) and infectious bronchitis virus (IBV), serious threats to the poultry industry, can give rise to complex mixed infections that hinder diagnosis and prevention. In this study, we show that newly designed peptides, which are based on the heptad repeat (HR) region of the fusion glycoproteins from NDV and IBV, have more potent antiviral activity than the mother HR peptides. Plaque formation and chicken embryo infectivity assays confirmed these results. The novel peptides completely inhibited single virus infections and mixed infections caused by NDV and IBV. Furthermore, we assessed cell toxicity and possible targets for the peptides, thereby strengthening the notion that HR2 is an attractive site for therapeutic intervention. These results suggest the possibility of designing a relatively broad-spectrum class of antiviral peptides that can reduce the effects of mixed-infections.

  16. Brain regional acetylcholinesterase activity and muscarinic acetylcholine receptors in rats after repeated administration of cholinesterase inhibitors and its withdrawal

    SciTech Connect

    Kobayashi, Haruo . E-mail: hk1664@iwate-u.ac.jp; Suzuki, Tadahiko; Sakamoto, Maki; Hashimoto, Wataru; Kashiwada, Keiko; Sato, Itaru; Akahori, Fumiaki; Satoh, Tetsuo

    2007-03-15

    Activity of acetylcholinesterase (AChE) and specific binding of [{sup 3}H]quinuclidinyl benzilate (QNB), [{sup 3}H]pirenzepine (PZP) and [{sup 3}H]AF-DX 384 to muscarinic acetylcholine receptor (mAChR) preparations in the striatum, hippocampus and cortex of rats were determined 1, 6 and 11 days after the last treatment with an organophosphate DDVP, a carbamate propoxur or a muscarinic agonist oxotremorine as a reference for 7 and 14 days. AChE activity was markedly decreased in the three regions 1 day after the treatment with DDVP for 7 and 14 days with a gradual recovery 6 to 11 days, and much less decreased 1, 6 and 11 days after the treatment with propoxur for 7 days but not for 14 days in the hippocampus and cortex. The binding of [{sup 3}H]-QNB, PZP and AF-DX 384 in the three regions was generally decreased by the treatment with DDVP for 7 and 14 days. Such down-regulations were generally restored 6 or 11 days after the treatment for 7 but not for 14 days. The down-regulation or up-regulation as measured by [{sup 3}H]-QNB, PZP and AF-DX 384 was observed 1, 6 or 11 days after treatment with propoxur for 7 days and/or 14 days. Repeated treatment with oxotremorine produced similar effects except AChE activity to DDVP. These results suggest that repeated inhibition of AChE activity may usually cause down-regulation of mAChRs with some exception in the hippocampus when a reversible antiChE propoxur is injected.

  17. Structure-function studies of HIV-1: influence of long terminal repeat U3 region sequences on virus production.

    PubMed

    Velpandi, A; Nagashunmugam, T; Otsuka, T; Cartas, M; Srinivasan, A

    1992-06-01

    DNA sequence analyses of several human immunodeficiency virus (HIV) isolates revealed extensive genetic diversity in the env gene and, to a lesser extent, in other regions of the viral genome, including the long terminal repeat (LTR) sequences. Since the LTRs contain elements responsible for the control of transcription, the difference in the LTR region may play a crucial role in the overall replication rate of HIV. To evaluate the role of the LTR, we have constructed a number of infectious hybrid HIV molecular clones containing LTRs from different proviral DNAs linked to the body of the viral genome, and analyzed them in a transient expression system. Both parental and hybrid proviral DNAs were transfected into human rhabdomyosarcoma cells for monitoring virus production. Proviral DNA designate pZ6 (HIVZr6) showed a high level of virus in the medium of the transfected culture in comparison to the pHXB2 (HIVHTLV-III) and pARV (HIVSF-2) DNAs. Hybrid proviral DNAs containing viral genes from pZ6, linked to LTR U3 sequences of pHXB2 and pARV at the 5' end, showed virus production similar to the levels observed with pZ6. These results indicate that the extent of virus production does not correlate with the LTR U3 sequences, and may involve other regions of the viral genome.

  18. Repeated ingestion of aspartame-sweetened beverage: effect on plasma amino acid concentrations in normal adults.

    PubMed

    Stegink, L D; Filer, L J; Baker, G L

    1988-03-01

    Aspartame (APM) is a dipeptide sweetener (L-aspartyl-L-phenylalanine methyl ester). It has been suggested that excessive use of the product might elevate plasma aspartate and phenylalanine concentrations. Eight normal adults (four male, four female) ingested three successive 12-oz servings of APM-sweetened beverage at two-hour intervals. The study was carried out in two parts in a randomized cross-over design. In one study the beverage was not sweetened. In the other, the beverage provided 10 mg APM/kg body weight per serving. Plasma amino acid concentrations were measured throughout the six-hour study period. The addition of APM to the beverage had no significant effect on plasma aspartate concentration. APM addition did increase plasma phenylalanine levels 1.64 to 2.05 mumol/dL above baseline values (5.09 +/- 0.82 mumol/dL) 30 to 45 minutes after each dose. However, plasma phenylalanine levels did not exceed normal postprandial values at any time. The data indicate ready metabolism of APM's amino acid content when administered at levels likely to be ingested by individuals who are heavy users of such beverages.

  19. Effect of Intraperitoneal Administered Ginseng Total Saponins on Hyperalgesia Induced by Repeated Intramuscular Injection of Acidic Saline in Rats

    PubMed Central

    Kim, Won Joong; Kim, Jung Eun; Choi, Geun Joo; Shin, Hwa Yong; Baek, Chong Wha; Jung, Yong Hun; Woo, Young Choel; Kim, Su Hyun; Lee, Jeong Hyuk

    2014-01-01

    Abstract The aim of this study was to assess the antinociceptive activity of ginseng total saponins (GTS) on hyperalgesia induced by repeated intramuscular injections of acidic saline in rats and to examine the mechanisms involved. Rats were injected intraperitoneally with a 0.9% saline vehicle or various doses of GTS after the development of hyperalgesia. Rats were then injected with N-methyl-D-aspartate (NMDA) or naloxone 10 min before GTS injection. The mechanical withdrawal threshold (MWT) was assessed with von Frey filaments. The MWT was significantly increased after intraperitoneal injection of 100 mg/kg and 200 mg/kg of GTS when compared with the MWT after the development of hyperalgesia. Injection of GTS with NMDA showed a significant decrease in the MWT when compared with GTS injection. GTS showed an antinociceptive activity against chronic muscle-induced pain, and the effect of GTS may be mediated by NMDA. PMID:24853193

  20. Tandem repeat sequences evolutionarily related to SVA-type retrotransposons are expanded in the centromere region of the western hoolock gibbon, a small ape.

    PubMed

    Hara, Toru; Hirai, Yuriko; Jahan, Israt; Hirai, Hirohisa; Koga, Akihiko

    2012-12-01

    Hoolock hoolock (the western hoolock gibbon) is a species of the family Hylobatidae (small apes), which constitutes the superfamily Hominoidea (hominoids) together with Hominidae (great apes and human). Here, we report that centromeres or their vicinities in this gibbon species contain tandem repeat sequences that consist of 35-50-bp repeat units, and exhibit a sequence similarity with the variable number of tandem repeat (VNTR) region of the SVA, LAVA and PVA transposons. SVA is a composite retrotransposon thought to have been formed by fusion of three solo elements in the common ancestor of hominoids. LAVA and PVA are recently identified retrotransposons that have the same basic structure as SVA. Thus, the large-scale tandem repeats in the centromere region may have been derived from one or more of SVA-type transposons, including the three mentioned above and other yet unknown elements, or the repeat sequences could have served as a source for such elements. Amplification of VNTR-related sequences in another gibbon species, Hoolock leuconedys (eastern hoolock gibbon), has recently been reported, but it is yet to be examined whether the large-scale tandem repeats observed in the two species originated from a single event that occurred in their common ancestor. The repeat sequences in the western hoolock gibbon are mostly 40 kb or more in length, are present in 28 of the 38 chromosomes of the somatic cells, and are homozygous for chromosomal presence/absence.

  1. Design and analysis of post-fusion 6-helix bundle of heptad repeat regions from Newcastle disease virus F protein.

    PubMed

    Zhu, Jieqing; Li, Pengyun; Wu, Tinghe; Gao, Feng; Ding, Yi; Zhang, Catherine W-H; Rao, Zihe; Gao, George F; Tien, Po

    2003-05-01

    Fusion of paramyxovirus to the cell involves receptor binding of the HN glycoprotein and a number of conformational changes of F glycoprotein. The F protein is expressed as a homotrimer on the virus surface. In the present model, there are at least three conformations of F protein, i.e. native form, pre-hairpin intermediate and the post-fusion state. In the post-fusion state, the two highly conserved heptad repeat (HR) regions of F protein form a stable 6-helix coiled-coil bundle. However, no crystal structure is known for this state for the Newcastle disease virus, although the crystal structure of the F protein native form has been solved recently. Here we deployed an Escherichia coli in vitro expression system to engineer this 6-helix bundle by fusion of either the two HR regions (HR1, linker and HR2) or linking the 6-helix [3 x (HR1, linker and HR2)] together as a single chain. Subsequently, both of them form a stable 6-helix bundle in vitro judging by gel filtration and chemical cross-linking and the proteins show salient features of an alpha-helix structure. Crystals diffracting X-rays have been obtained from both protein preparations and the structure determination is under way. This method could be used for crystallization of the post-fusion state HR structures of other viruses.

  2. Copper complex species within a fragment of the N-terminal repeat region in opossum PrP protein.

    PubMed

    Vagliasindi, Laura I; Arena, Giuseppe; Bonomo, Raffaele P; Pappalardo, Giuseppe; Tabbì, Giovanni

    2011-03-21

    A spectroscopic (UV-Vis, CD and EPR), thermodynamic and voltammetric study of the copper(ii) complexes with the Ac-PHPGGSNWGQ-NH(2) polypeptide (L), a fragment of the opossum PrP protein N-terminal four-repeat region, was carried out in aqueous solution. It suggests the formation of a highly distorted [Cu(L)H(-2)] complex species in the neutral region, the stereochemistry of which is ascribable to a square base pyramid and a CuN(3)O(2) chromophore, resulting from the coordination of a histidine imidazole and two peptide nitrogen atoms and probably oxygen atoms from water molecules. At basic pH values a [Cu(L)H(-3)](-) species with a pseudo-octahedral geometry was also obtained, with four nitrogen donor atoms in its equatorial plane, coming from the histidine residue and from peptidic nitrogen atoms. Interestingly, at pH values relatively higher than the neutrality, the coordination sphere of the copper complex in the [Cu(L)H(-2)] species changes its stereochemistry towards a pseudo-octahedron, as suggested by the change in the parallel copper hyperfine coupling constant of the EPR spectra at low temperature. A slight difference in the redox potentials between this two-faced [Cu(L)H(-2)] complex species seems to confirm this behaviour. Both potentiometric and spectroscopic data were compared with the analogous species obtained with the Ac-PHGGGWGQ-NH(2) peptide, belonging to the octarepeat domain of the human prion protein (hPrP) N-terminal region. The [Cu(L)H(-2)] species formed by the Ac-PHPGGSNWGQ-NH(2) decapeptide, having a slightly lower stability, turned out to be less abundant and to exist within a narrow pH range.

  3. Copper complex species within a fragment of the N-terminal repeat region in opossum PrP protein.

    PubMed

    Vagliasindi, Laura I; Arena, Giuseppe; Bonomo, Raffaele P; Pappalardo, Giuseppe; Tabbì, Giovanni

    2011-03-21

    A spectroscopic (UV-Vis, CD and EPR), thermodynamic and voltammetric study of the copper(ii) complexes with the Ac-PHPGGSNWGQ-NH(2) polypeptide (L), a fragment of the opossum PrP protein N-terminal four-repeat region, was carried out in aqueous solution. It suggests the formation of a highly distorted [Cu(L)H(-2)] complex species in the neutral region, the stereochemistry of which is ascribable to a square base pyramid and a CuN(3)O(2) chromophore, resulting from the coordination of a histidine imidazole and two peptide nitrogen atoms and probably oxygen atoms from water molecules. At basic pH values a [Cu(L)H(-3)](-) species with a pseudo-octahedral geometry was also obtained, with four nitrogen donor atoms in its equatorial plane, coming from the histidine residue and from peptidic nitrogen atoms. Interestingly, at pH values relatively higher than the neutrality, the coordination sphere of the copper complex in the [Cu(L)H(-2)] species changes its stereochemistry towards a pseudo-octahedron, as suggested by the change in the parallel copper hyperfine coupling constant of the EPR spectra at low temperature. A slight difference in the redox potentials between this two-faced [Cu(L)H(-2)] complex species seems to confirm this behaviour. Both potentiometric and spectroscopic data were compared with the analogous species obtained with the Ac-PHGGGWGQ-NH(2) peptide, belonging to the octarepeat domain of the human prion protein (hPrP) N-terminal region. The [Cu(L)H(-2)] species formed by the Ac-PHPGGSNWGQ-NH(2) decapeptide, having a slightly lower stability, turned out to be less abundant and to exist within a narrow pH range. PMID:21283898

  4. Comprehensive Treatment of Periorbital Region with Hyaluronic Acid

    PubMed Central

    Rocha, Camila Roos Mariano Da; Bastos, Julien Toni De; Silva, Priscila Mara Chaves e

    2015-01-01

    The periorbital subunit is one of the first facial regions to show signs of aging, primarily due to volume depletion of the soft tissue and bony resorption. Surgical and office-based nonsurgical procedures form an important basis for periorbital rejuvenation. It is important to make a detailed clinical evaluation of the patient to indicate the most appropriate procedure to be performed. With the objective of showing a nonsurgical procedure for the rejuvenation of the periorbital area, the authors describe a technique of applying fillers in the upper and lower periorbital regions, paying attention to the anatomy of this facial region and the type of product to be used besides the expected results of the procedure and its possible adverse effects and complications. The nonsurgical rejuvenation of the periorbicular region with hyaluronic acid is a new and innovative technique. In the opinion of the authors, it is a great aesthetic impact area and consequently brings high satisfaction to patients. PMID:26155325

  5. Determination of polyfluoroalkyl phosphoric acid diesters, perfluoroalkyl phosphonic acids, perfluoroalkyl phosphinic acids, perfluoroalkyl carboxylic acids, and perfluoroalkane sulfonic acids in lake trout from the Great Lakes region.

    PubMed

    Guo, Rui; Reiner, Eric J; Bhavsar, Satyendra P; Helm, Paul A; Mabury, Scott A; Braekevelt, Eric; Tittlemier, Sheryl A

    2012-11-01

    A comprehensive method to extract perfluoroalkyl carboxylic acids, perfluoroalkane sulfonic acids, perfluoroalkyl phosphonic acids, perfluoroalkyl phosphinic acids, and polyfluoroalkyl phosphoric acid diesters simultaneously from fish samples has been developed. The recoveries of target compounds ranged from 78 % to 121 %. The new method was used to analyze lake trout (Salvelinus namaycush) from the Great Lakes region. The results showed that the total perfluoroalkane sulfonate concentrations ranged from 0.1 to 145 ng/g (wet weight) with perfluorooctane sulfonate (PFOS) as the dominant contaminant. Concentrations in fish between lakes were in the order of Lakes Ontario ≈ Erie > Huron > Superior ≈ Nipigon. The total perfluoroalkyl carboxylic acid concentrations ranged from 0.2 to 18.2 ng/g wet weight. The aggregate mean perfluorooctanoic acid (PFOA) concentration in fish across all lakes was 0.045 ± 0.023 ng/g. Mean concentrations of PFOA were not significantly different (p > 0.1) among the five lakes. Perfluoroalkyl phosphinic acids were detected in lake trout from Lake Ontario, Lake Erie, and Lake Huron with concentration ranging from non-detect (ND) to 0.032 ng/g. Polyfluoroalkyl phosphoric acid diesters were detected only in lake trout from Lake Huron, at levels similar to perfluorooctanoic acid.

  6. Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea.

    PubMed

    Pyenson, Nicholas D; Gutstein, Carolina S; Parham, James F; Le Roux, Jacobus P; Chavarría, Catalina Carreño; Little, Holly; Metallo, Adam; Rossi, Vincent; Valenzuela-Toro, Ana M; Velez-Juarbe, Jorge; Santelli, Cara M; Rogers, David Rubilar; Cozzuol, Mario A; Suárez, Mario E

    2014-04-22

    Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities. PMID:24573855

  7. Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4.

    PubMed

    Nicoludis, John M; Vogt, Bennett E; Green, Anna G; Schärfe, Charlotta Pi; Marks, Debora S; Gaudet, Rachelle

    2016-01-01

    Protocadherins (Pcdhs) are cell adhesion and signaling proteins used by neurons to develop and maintain neuronal networks, relying on trans homophilic interactions between their extracellular cadherin (EC) repeat domains. We present the structure of the antiparallel EC1-4 homodimer of human PcdhγB3, a member of the γ subfamily of clustered Pcdhs. Structure and sequence comparisons of α, β, and γ clustered Pcdh isoforms illustrate that subfamilies encode specificity in distinct ways through diversification of loop region structure and composition in EC2 and EC3, which contains isoform-specific conservation of primarily polar residues. In contrast, the EC1/EC4 interface comprises hydrophobic interactions that provide non-selective dimerization affinity. Using sequence coevolution analysis, we found evidence for a similar antiparallel EC1-4 interaction in non-clustered Pcdh families. We thus deduce that the EC1-4 antiparallel homodimer is a general interaction strategy that evolved before the divergence of these distinct protocadherin families. PMID:27472898

  8. Antiparallel protocadherin homodimers use distinct affinity- and specificity-mediating regions in cadherin repeats 1-4

    PubMed Central

    Nicoludis, John M; Vogt, Bennett E; Green, Anna G; Schärfe, Charlotta PI; Marks, Debora S; Gaudet, Rachelle

    2016-01-01

    Protocadherins (Pcdhs) are cell adhesion and signaling proteins used by neurons to develop and maintain neuronal networks, relying on trans homophilic interactions between their extracellular cadherin (EC) repeat domains. We present the structure of the antiparallel EC1-4 homodimer of human PcdhγB3, a member of the γ subfamily of clustered Pcdhs. Structure and sequence comparisons of α, β, and γ clustered Pcdh isoforms illustrate that subfamilies encode specificity in distinct ways through diversification of loop region structure and composition in EC2 and EC3, which contains isoform-specific conservation of primarily polar residues. In contrast, the EC1/EC4 interface comprises hydrophobic interactions that provide non-selective dimerization affinity. Using sequence coevolution analysis, we found evidence for a similar antiparallel EC1-4 interaction in non-clustered Pcdh families. We thus deduce that the EC1-4 antiparallel homodimer is a general interaction strategy that evolved before the divergence of these distinct protocadherin families. DOI: http://dx.doi.org/10.7554/eLife.18449.001 PMID:27472898

  9. Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea

    PubMed Central

    Pyenson, Nicholas D.; Gutstein, Carolina S.; Parham, James F.; Le Roux, Jacobus P.; Chavarría, Catalina Carreño; Little, Holly; Metallo, Adam; Rossi, Vincent; Valenzuela-Toro, Ana M.; Velez-Juarbe, Jorge; Santelli, Cara M.; Rogers, David Rubilar; Cozzuol, Mario A.; Suárez, Mario E.

    2014-01-01

    Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities. PMID:24573855

  10. Repeated mass strandings of Miocene marine mammals from Atacama Region of Chile point to sudden death at sea.

    PubMed

    Pyenson, Nicholas D; Gutstein, Carolina S; Parham, James F; Le Roux, Jacobus P; Chavarría, Catalina Carreño; Little, Holly; Metallo, Adam; Rossi, Vincent; Valenzuela-Toro, Ana M; Velez-Juarbe, Jorge; Santelli, Cara M; Rogers, David Rubilar; Cozzuol, Mario A; Suárez, Mario E

    2014-04-22

    Marine mammal mass strandings have occurred for millions of years, but their origins defy singular explanations. Beyond human causes, mass strandings have been attributed to herding behaviour, large-scale oceanographic fronts and harmful algal blooms (HABs). Because algal toxins cause organ failure in marine mammals, HABs are the most common mass stranding agent with broad geographical and widespread taxonomic impact. Toxin-mediated mortalities in marine food webs have the potential to occur over geological timescales, but direct evidence for their antiquity has been lacking. Here, we describe an unusually dense accumulation of fossil marine vertebrates from Cerro Ballena, a Late Miocene locality in Atacama Region of Chile, preserving over 40 skeletons of rorqual whales, sperm whales, seals, aquatic sloths, walrus-whales and predatory bony fish. Marine mammal skeletons are distributed in four discrete horizons at the site, representing a recurring accumulation mechanism. Taphonomic analysis points to strong spatial focusing with a rapid death mechanism at sea, before being buried on a barrier-protected supratidal flat. In modern settings, HABs are the only known natural cause for such repeated, multispecies accumulations. This proposed agent suggests that upwelling zones elsewhere in the world should preserve fossil marine vertebrate accumulations in similar modes and densities.

  11. Examples of regional environmental assessment using acid deposition data

    SciTech Connect

    Olson, R.J.; Turner, R.S.; Allison, L.J.

    1985-01-01

    Integrated assessments of acid deposition impacts require data on pollutant emissions, pollutant deposition, air quality, aquatic resources, crops, forests, and manmade materials. These data must have common spatial and temporal attributes that can be readily accessed for statistical analysis, modeling, and display purposes. The Acid Deposition Assessment Staff of Task Group I established the Acid Deposition Data Network (ADDNET) at Oak Ridge National Laboratory to provide accurate and reliable data to conduct assessment and policy analysis for the National Acid Precipitation Assessment Program (NAPAP). Although specific projects and task groups within NAPAP collect and analyze individual data files, ADDNET assembles selected files, verifies their contents, conducts quality assurance, maintains documentation, and makes data available to the NAPAP community. The ADDNET data base contains over 65 'certified' data sets that have been screened to ensure consistency across all areas of the assessment. Two applications of the ADDNET Data Base to assessment activities are described: estimation of the extent of sensitive lakes at risk to high atmospheric deposition and the mapping of regional soil properties according to hypothesized sensitivity criteria. Both examples cover New York and the New England states and show the integration of data from diverse sources for analyses. The data resources and the regional environmental assessment approach described here can be applied directly to other hazardous materials discussed at this symposium. 13 refs., 6 figs.

  12. Effects of Homology Length in the Repeat Region on Minus-Strand DNA Transfer and Retroviral Replication

    PubMed Central

    Dang, Que; Hu, Wei-Shau

    2001-01-01

    Homology between the two repeat (R) regions in the retroviral genome mediates minus-strand DNA transfer during reverse transcription. We sought to define the effects of R homology lengths on minus-strand DNA transfer. We generated five murine leukemia virus (MLV)-based vectors that contained identical sequences but different lengths of the 3′ R (3, 6, 12, 24 and 69 nucleotides [nt]); 69 nt is the full-length MLV R. After one round of replication, viral titers from the vector with a full-length downstream R were compared with viral titers generated from the other four vectors with reduced R lengths. Viral titers generated from vectors with R lengths reduced to one-third (24 nt) or one-sixth (12 nt) that of the wild type were not significantly affected; however, viral titers generated from vectors with only 3- or 6-nt homology in the R region were significantly lower. Because expression and packaging of the RNA were similar among all the vectors, the differences in the viral titers most likely reflected the impact of the homology lengths on the efficiency of minus-strand DNA transfer. The molecular nature of minus-strand DNA transfer was characterized in 63 proviruses. Precise R-to-R transfer was observed in most proviruses generated from vectors with 12-, 24-, or 69-nt homology in R, whereas aberrant transfers were predominantly used to generate proviruses from vectors with 3- or 6-nt homology. Reverse transcription using RNA transcribed from an upstream promoter, termed read-in RNA transcripts, resulted in most of the aberrant transfers. These data demonstrate that minus-strand DNA transfer is homology driven and a minimum homology length is required for accurate and efficient minus-strand DNA transfer. PMID:11134294

  13. R Region Sequences in the Long Terminal Repeat of a Murine Retrovirus Specifically Increase Expression of Unspliced RNAs

    PubMed Central

    Trubetskoy, Alla M.; Okenquist, Sharon A.; Lenz, Jack

    1999-01-01

    A stem-loop structure at the 5′ end of the R region of the long terminal repeat (LTR) of the murine leukemia virus SL3 and other type C mammalian retroviruses is important for maximum levels of expression of a reporter gene under the control of the viral LTR. This element, termed the R region stem-loop (RSL), has a small effect on transcriptional initiation and no effect on RNA polymerase processivity. Its major effect is on posttranscriptional processing of LTR-driven transcripts. Here we tested whether the RSL affected the production of RNAs from a full-length SL3 genome. Mutation of the RSL in the 5′ LTR of SL3 reduced the cytoplasmic levels of full-length viral transcripts but not those of spliced, env mRNA transcripts. Thus, the RSL specifically affected the cytoplasmic levels of the unspliced viral RNA. To test further whether the effect was specific for unspliced transcripts, a system was devised in which the expression of a reporter gene under the control of the viral LTR was tested in the presence or absence of an intron. Mutation of the RSL resulted in only about a twofold decline in the level of reporter gene expression when the transcripts contained an intron. However, when the intron was removed, mutation of the RSL reduced expression of the reporter gene about 10- to 60-fold in various cell lines. The secondary structure of the RSL was essential for its activity on the intronless transcript. Thus, the RSL appears to be important for the cytoplasmic accumulation of unspliced viral RNA and unspliced RNA from chimeric transcription units under the control of the viral LTR. PMID:10074206

  14. R region sequences in the long terminal repeat of a murine retrovirus specifically increase expression of unspliced RNAs.

    PubMed

    Trubetskoy, A M; Okenquist, S A; Lenz, J

    1999-04-01

    A stem-loop structure at the 5' end of the R region of the long terminal repeat (LTR) of the murine leukemia virus SL3 and other type C mammalian retroviruses is important for maximum levels of expression of a reporter gene under the control of the viral LTR. This element, termed the R region stem-loop (RSL), has a small effect on transcriptional initiation and no effect on RNA polymerase processivity. Its major effect is on posttranscriptional processing of LTR-driven transcripts. Here we tested whether the RSL affected the production of RNAs from a full-length SL3 genome. Mutation of the RSL in the 5' LTR of SL3 reduced the cytoplasmic levels of full-length viral transcripts but not those of spliced, env mRNA transcripts. Thus, the RSL specifically affected the cytoplasmic levels of the unspliced viral RNA. To test further whether the effect was specific for unspliced transcripts, a system was devised in which the expression of a reporter gene under the control of the viral LTR was tested in the presence or absence of an intron. Mutation of the RSL resulted in only about a twofold decline in the level of reporter gene expression when the transcripts contained an intron. However, when the intron was removed, mutation of the RSL reduced expression of the reporter gene about 10- to 60-fold in various cell lines. The secondary structure of the RSL was essential for its activity on the intronless transcript. Thus, the RSL appears to be important for the cytoplasmic accumulation of unspliced viral RNA and unspliced RNA from chimeric transcription units under the control of the viral LTR.

  15. Effects of docosahexaenoic acid on learning and memory impairment induced by repeated propofol anesthesia in young rats

    PubMed Central

    TIAN, MING; LI, ZHI; WANG, GAO; PAN, WEIZHONG; LI, KEZHONG

    2016-01-01

    The aim of the present study was to investigate the effects of docosahexaenoic acid (DHA) on the learning and memory ability of young rats exposed to propofol, and its underlying mechanisms. Sprague Dawley rats (n=60) were randomly divided into six groups: Control group (group A); solvent control group (group B); propofol group (group C); low-dose DHA + propofol group (group D); medium dose DHA + propofol group (group E); and high-dose DHA + propofol group (group F). The Morris water maze (MWM) test was performed to evaluate the rats' learning and memory ability, and tissue samples from the hippocampi of the rats were obtained for biochemical analysis. The results of the MWM test revealed that DHA supplementation administered to young rats led to an evident decrease in the latency to find the maze platform, and a significant increase in the number of platform crossings in groups E and F compared with group C (P<0.05). High-performance liquid chromatography indicated that glutamate concentration levels were significantly lower and γ-aminobutyric acid concentration levels were significantly higher in the hippocampi of group E and F rats treated with DHA compared with group C rats (P<0.05). Furthermore, DHA treatment alleviated the decrease in brain-derived neurotrophic factor levels (P<0.05), and superoxide dismutase (P<0.05) and glutathione peroxidase (P<0.05) activities induced by the administration of propofol. Additionally, DHA treatment decreased malondialdehyde levels in the hippocampi of rats (P<0.05). The aforementioned findings demonstrate that DHA was able to effectively improve learning and memory dysfunction induced by repeated propofol-induced anesthesia in young rats. This data suggests that DHA may be a potential candidate for further preclinical studies aimed at treating postoperative cognitive dysfunction. PMID:27073471

  16. Haplotype frequencies of 17 Y-chromosomal short tandem repeat loci from the Cukurova region of Turkey

    PubMed Central

    Serin, Ayse; Canan, Husniye; Alper, Behnan; Sertdemir, Yasar

    2011-01-01

    Aim To investigate the distribution of 17 Y-short tandem repeat (STR) loci in the population of the Cukurova region of Turkey. Methods In the period between 2009 and 2010, we investigated the distribution of 17 Y-STRs in a sample of 249 unrelated healthy men from the Cukurova region of Turkey. Genomic DNA was extracted with InstaGene matrix and Y-STRs were determined using the AmpFISTR Yfiler PCR amplification kit. Gene and haplotype diversity values were estimated using the Arlequin software. To compare our data to other populations, population pairwise genetic distances and associated probability values were calculated using the Y Chromosome Haplotype Reference Database Web site software. Results At 17 Y-STR loci we detected 148 alleles. The lowest gene diversity in this region was 0.51 for DYS391 and the highest 0.95 for DYS385a/b. Haplotype diversity was 0.9997 ± 0.0004. We compared our data with haplotype data of other Turkish populations and no significant differences were found, except with Ankara population (Φst = 0.025, P = 0.018). Comparisons were also made with the neighboring populations using analysis of molecular variance of the Y-STR loci genetic structure and our population was nearest to Lenkoran-Azerbaijani (Φst = 0.012, P = 0.068) and Iranian Ahvaz population (Φst = 0.007, P = 0.173), followed by Greek (Φst = 0.026, P = 0.000) and Russian (Φst = 0.048, P = 0.000) population. Other countries like Portugal, Spain, Italy, Egypt, Israel (Palestinian Authority Area), and Taiwan showed a high genetic distance from our population. Conclusion Our study showed that Y-STR polymorphisms were a powerful discrimination tool for routine forensic applications and could be used in genealogical investigations. PMID:22180269

  17. Repeated ingestion of aspartame-sweetened beverage: effect on plasma amino acid concentrations in individuals heterozygous for phenylketonuria.

    PubMed

    Stegink, L D; Filer, L J; Baker, G L; Bell, E F; Ziegler, E E; Brummel, M C; Krause, W L

    1989-01-01

    It has been suggested that excessive use of aspartame (APM) (N-L-alpha-aspartyl-L-phenylalanine methyl ester) might grossly elevate plasma aspartate and phenylalanine concentrations in individuals heterozygous for phenylketonuria (PKUH). In study 1 six adult PKUH (three males; three females) ingested three successive 12-oz servings of beverage at 2-h intervals. The study was carried out in two parts in a randomized crossover design. In one arm the beverage was not sweetened. In the other the beverage provided 10 mg APM/kg body weight per serving. The addition of APM to the beverage did not significantly increase plasma aspartate concentration but did increase plasma phenylalanine levels 2.3 to 4.1 mumol/dL above baseline values 30 to 45 min after each dose. The high mean plasma phenylalanine level after repeated APM dosing (13.9 +/- 2.15 mumol/dL) was slightly, but not significantly, above the normal postprandial range for PKUH (12.6 +/- 2.11 mumol/dL). In study 2 six different adult PKUH ingested beverage providing 30 mg APM/kg body weight as a single bolus. The high mean plasma phenylalanine concentration and the phenylalanine to large neutral amino acid ratio were significantly higher when APM was ingested as a single bolus than when ingested as a divided dose.

  18. Plasma Amino Acids Changes in Complex Regional Pain Syndrome

    PubMed Central

    Alexander, Guillermo M.; Reichenberger, Erin; Peterlin, B. Lee; Perreault, Marielle J.; Grothusen, John R.; Schwartzman, Robert J.

    2013-01-01

    Complex regional pain syndrome (CRPS) is a severe chronic pain condition that most often develops following trauma. Blood samples were collected from 220 individuals, 160 CRPS subjects, and 60 healthy pain-free controls. Plasma amino acid levels were compared and contrasted between groups. L-Aspartate, L-glutamate, and L-ornithine were significantly increased, whereas L-tryptophan and L-arginine were significantly decreased in CRPS subjects as compared to controls. In addition, the L-kynurenine to L-tryptophan ratio demonstrated a significant increase, whereas the global arginine bioavailability ratio (GABR) was significantly decreased in the CRPS subjects. The CRPS subjects demonstrated a significant correlation between overall pain and the plasma levels of L-glutamate and the L-kynurenine to L-tryptophan ratio. CRPS subjects also showed a correlation between the decrease in plasma L-tryptophan and disease duration. This study shows that CRPS subjects exhibit significant changes in plasma levels of amino acids involved in glutamate receptor activation and in amino acids associated with immune function as compared to healthy pain-free controls. A better understanding of the role plasma amino acids play in the pathophysiology of CRPS may lead to novel treatments for this crippling condition. PMID:24303215

  19. In situ optical sequencing and structure analysis of a trinucleotide repeat genome region by localization microscopy after specific COMBO-FISH nano-probing

    NASA Astrophysics Data System (ADS)

    Stuhlmüller, M.; Schwarz-Finsterle, J.; Fey, E.; Lux, J.; Bach, M.; Cremer, C.; Hinderhofer, K.; Hausmann, M.; Hildenbrand, G.

    2015-10-01

    Trinucleotide repeat expansions (like (CGG)n) of chromatin in the genome of cell nuclei can cause neurological disorders such as for example the Fragile-X syndrome. Until now the mechanisms are not clearly understood as to how these expansions develop during cell proliferation. Therefore in situ investigations of chromatin structures on the nanoscale are required to better understand supra-molecular mechanisms on the single cell level. By super-resolution localization microscopy (Spectral Position Determination Microscopy; SPDM) in combination with nano-probing using COMBO-FISH (COMBinatorial Oligonucleotide FISH), novel insights into the nano-architecture of the genome will become possible. The native spatial structure of trinucleotide repeat expansion genome regions was analysed and optical sequencing of repetitive units was performed within 3D-conserved nuclei using SPDM after COMBO-FISH. We analysed a (CGG)n-expansion region inside the 5' untranslated region of the FMR1 gene. The number of CGG repeats for a full mutation causing the Fragile-X syndrome was found and also verified by Southern blot. The FMR1 promotor region was similarly condensed like a centromeric region whereas the arrangement of the probes labelling the expansion region seemed to indicate a loop-like nano-structure. These results for the first time demonstrate that in situ chromatin structure measurements on the nanoscale are feasible. Due to further methodological progress it will become possible to estimate the state of trinucleotide repeat mutations in detail and to determine the associated chromatin strand structural changes on the single cell level. In general, the application of the described approach to any genome region will lead to new insights into genome nano-architecture and open new avenues for understanding mechanisms and their relevance in the development of heredity diseases.

  20. Micro-sized erosions in a nanofilled composite after repeated acidic beverage exposures: consequences of clusters dislodgments

    PubMed Central

    SVIZERO, Nádia da Rocha; de GÓES, Adriana Regina Cruz Grando; BUENO, Tamires de Luccas; DI HIPÓLITO, Vinicius; WANG, Linda; D'ALPINO, Paulo Henrique Perlatti

    2014-01-01

    Objective To evaluate the hardness (KHN), color stability (DE), and superficial micromorphology of two categories of composites after immersion in either distilled water or grape juice for up to 45 days. Material and Methods Cylindrical specimens (6 mm diameter x 2 mm thick) were obtained according to the factors: composite [Opallis (FGM) and Filtek Z350XT (3M ESPE)]; immersion solution (distilled water and grape juice); and evaluation time: 24 h and 7, 14, 21, 28, and 45 days. After photoactivation, the specimens were stored at 37ºC for 24 h. KHN (50 g/15 s) and ΔE were then repeatedly assessed according to the immersion solutions. Data were analyzed (three-way ANOVA/Tukey's test). Scanning electron microscopy (SEM) topographic analysis was also performed. Results In general, KHN of both composites reduced after 24 h, irrespective of the immersion solution and time. A significantly lower KHN was noted for Opallis compared with Filtek Z350XT in all parameters. An increase in ΔE over time was noted for both composites, irrespective of the immersion solution. Significantly higher ΔE was noted for Filtek Z350XT immersed in grape juice compared with Opallis, regardless of the evaluation time. The grape juice caused significantly higher DE compared with water in all periods. SEM analysis showed eroded areas for Filtek Z350XT but not for Opallis. Conclusions The compositions and immersion solutions influence the composite hardness and the color stability. In spite of the higher hardness, the nanofilled composite is more susceptible to color change than the microhybrid when immersed in an acidic dyed solution. PMID:25004054

  1. Variation in repeat length and heteroplasmy of the mitochondrial DNA control region along a core-edge gradient in the eastern spadefoot toad (Pelobates syriacus).

    PubMed

    Munwes, Inbar; Geffen, Eli; Friedmann, Adam; Tikochinski, Yaron; Gafny, Sarig

    2011-07-01

    Peripheral populations are those situated at the distribution margins of a species and are often subjected to more extreme abiotic and biotic conditions than those at the core. Here, we hypothesized that shorter repeat length and fewer heteroplasmic mitochondrial DNA (mtDNA) copies, which are associated with more efficient mitochondrial function, may be related to improved survival under extreme environmental conditions. We sampled eastern spadefoot toads (mostly as tadpoles) from 43 rain pools distributed along a 300-km gradient from core to edge of the species' distribution. We show that mean pool tandem repeat length and heteroplasmy increase from edge to core, even after controlling for body size. We evaluate several alternative hypotheses and propose the Fisher hypothesis as the most likely explanation. However, additional sequential sampling and experimental studies are required to determine whether selection under extreme conditions, or alternative mechanisms, could account for the gradient in heteroplasmy and repeat length in the mtDNA control region.

  2. A variable number of tandem repeats in the 3'-untranslated region of the dopamine transporter modulates striatal function during working memory updating across the adult age span.

    PubMed

    Sambataro, Fabio; Podell, Jamie E; Murty, Vishnu P; Das, Saumitra; Kolachana, Bhaskar; Goldberg, Terry E; Weinberger, Daniel R; Mattay, Venkata S

    2015-08-01

    Dopamine modulation of striatal function is critical for executive functions such as working memory (WM) updating. The dopamine transporter (DAT) regulates striatal dopamine signaling via synaptic reuptake. A variable number of tandem repeats in the 3'-untranslated region of SLC6A3 (DAT1-3'-UTR-VNTR) is associated with DAT expression, such that 9-repeat allele carriers tend to express lower levels (associated with higher extracellular dopamine concentrations) than 10-repeat homozygotes. Aging is also associated with decline of the dopamine system. The goal of the present study was to investigate the effects of aging and DAT1-3'-UTR-VNTR on the neural activity and functional connectivity of the striatum during WM updating. Our results showed both an age-related decrease in striatal activity and an effect of DAT1-3'-UTR-VNTR. Ten-repeat homozygotes showed reduced striatal activity and increased striatal-hippocampal connectivity during WM updating relative to the 9-repeat carriers. There was no age by DAT1-3'-UTR-VNTR interaction. These results suggest that, whereas striatal function during WM updating is modulated by both age and genetically determined DAT levels, the rate of the age-related decline in striatal function is similar across both DAT1-3'-UTR-VNTR genotype groups. They further suggest that, because of the baseline difference in striatal function based on DAT1-3'-UTR-VNTR polymorphism, 10-repeat homozygotes, who have lower levels of striatal function throughout the adult life span, may reach a threshold of decreased striatal function and manifest impairments in cognitive processes mediated by the striatum earlier in life than the 9-repeat carriers. Our data suggest that age and DAT1-3'-UTR-VNTR polymorphism independently modulate striatal function. PMID:25997640

  3. L-Lactic acid production by combined utilization of agricultural bioresources as renewable and economical substrates through batch and repeated-batch fermentation of Enterococcus faecalis RKY1.

    PubMed

    Reddy, Lebaka Veeranjaneya; Kim, Young-Min; Yun, Jong-Sun; Ryu, Hwa-Won; Wee, Young-Jung

    2016-06-01

    Enterococcus faecalis RKY1 was used to produce l-lactic acid from hydrol, soybean curd residues (SCR), and malt. Hydrol was efficiently metabolized to l-lactic acid with optical purity of >97.5%, though hydrol contained mixed sugars such as glucose, maltose, maltotriose, and maltodextrin. Combined utilization of hydrol, SCR, and malt was enough to sustain lactic acid fermentation by E. faecalis RKY1. In order to reduce the amount of nitrogen sources and product inhibition, cell-recycle repeated-batch fermentation was employed, where a high cell mass (26.3g/L) was obtained. Lactic acid productivity was improved by removal of lactic acid from fermentation broth by membrane filtration and by linearly increased cell density. When the total of 10 repeated-batch fermentations were carried out using 100g/L hydrol, 150g/L SCR hydrolyzate, and 20g/L malt hydrolyzate as the main nutrients, lactic acid productivity was increased significantly from 3.20g/L/h to 6.37g/L/h.

  4. Construction of libraries enriched for sequence repeats and jumping clones, and hybridization selection for region-specific markers

    SciTech Connect

    Kandpal, R.P.; Kandpal, G.; Weissman, S.M. )

    1994-01-04

    The authors describe a simple and rapid method for constructing small-insert genomic libraries highly enriched for dimeric, trimeric, and tetrameric nucleotide repeat motifs. The approach involves use of DNA inserts recovered by PCR amplification of a small-insert sonicated genomic phage library or by a single-primer PCR amplification of Mbo I-digested and adaptor-ligated genomic DNA. The genomic DNA inserts are heat denatured and hybridized to a biotinylated oligonucleotde. The biotinylated hybrids are retained on a Vectrex-avidin matrix and eluted specifically. The eluate is PCR amplified and cloned. More than 90% of the clones in a library enriched for (CA)[sub n] microsatellites with this approach contained clones with inserts containing CA repeats. They have also used this protocol for enrichment of (CAG)[sub n] and (AGAT)[sub n] sequence repeats and for Not I jumping clones. They have used the enriched libraries with an adaptation of the cDNA selection method to enrich for repeat motifs encoded in yeast artificial chromosomes.

  5. The human [gamma]-aminobutyric acid receptor subunit [beta]3 and [alpha]5 gene cluster in chromosome 15q11-q13 is rich in highly polymorphic (CA)[sub n] repeats

    SciTech Connect

    Glatt, K.; Lalande, M. ); Sinnett, D. )

    1994-01-01

    The [gamma]-aminobutyric acid (GABA[sub A]) receptor [beta]33 (GABRB3) and [alpha]5 (GABRA5) subunit genes have been localized to the Angelman and Prader-Willi syndrome region of chromosome 15q11-q13. GABRB3, which encompasses 250 kb, is located 100 kb proximal of GABRA5, with the two genes arranged in head-to-head transcriptional orientation. In screening 135 kb of cloned DNA within a 260-kb interval extending from within GABRB3 to the 5[prime] end of GABRA5, 10 new (CA), repeats have been identified. Five of these have been analyzed in detail and found to be highly polymorphic, with the polymorphism information content (PIC) ranging from 0.7 to 0.85 and with heterozygosities of 67 to 94%. In the clones from GABRB3/GABRA5 region, therefore, the frequency of (CA)[sub n] with PICs [ge] 0.7 is 1 per 27 kb. Previous estimates of the density of (CA)[sub n] with PICs [ge] 0.7 in the human genome have been approximately 10-fold lower. The GABRB3/GABRA5 region appears, therefore, to be enriched for highly informative (CA)[sub n]. This set of closely spaced, short tandem repeat polymorphisms will be useful in the molecular analyses of Prader-Willi and Angelman syndromes and in high-resolution studies of genetic recombination within this region. 21 refs., 2 figs., 1 tab.

  6. Repeated pseudotachylytes generation events along regional scale faults: the Orobic and Porcile thrusts (Southern Alps, N Italy)

    NASA Astrophysics Data System (ADS)

    Zanchetta, Stefano; D'Adda, Paolo; Barberini, Valentina; Villa, Igor Maria; Zanchi, Andrea

    2010-05-01

    many cases re-melting phenomena of pre-existing pseudotachylytes were observed at the micro-scale. Old pseudotachylyte fragments with evident resorption features are present within new veins, and "intrusive" contact were locally observed between different vein generations. Different melt pulses along the same vein are differentiated on the base of clast/matrix ratios and chemical composition of both matrix and crystallites. Brittle deformation producing brecciation of old pseudotachylytes seems to be contemporaneous with new melt injection and flow, resulting in the coexistence, within the same vein, of old fractured pseudotachylyte layers and new, undeformed, ones. Structural data relative to fault veins point out that both old and young pseudotachylytes formed along reverse fault planes with similar geometric features. This suggest that no significant changes occurred in the main stress axes orientations and resulting deformation structures correlated to the Late Cretaceous and the Eocene compressive deformation events along the Orobic and Porcile fault zones. Field data, 40Ar/39Ar ages, microstructural and mineralogical data on pseudotachylytes along the Orobic and Porcile thrusts reveal that repeated coseismic friction-induced melting occurred along same faults with a time interval in excess of 15 Ma. This implies that the seismic history of regional scale faults could be very complex and polyphasic, with successive long time range re-activations that can be individuated exploring the geological record associated to fault zones.

  7. Citric acid production from glycerol-containing waste of biodiesel industry by Yarrowia lipolytica in batch, repeated batch, and cell recycle regimes.

    PubMed

    Rymowicz, Waldemar; Fatykhova, Alina R; Kamzolova, Svetlana V; Rywińska, Anita; Morgunov, Igor G

    2010-07-01

    Yarrowia lipolytica A-101-1.22 produces high citric acid (112 g l(-1)) with a yield of 0.6 g g(-1) and a productivity of 0.71 g l(-1) h(-1) during batch cultivation in the medium with glycerol-containing waste of biodiesel industry. However, it was observed that the specific citric acid production rate, which was maximal at the beginning of the biosynthesis, gradually decreases in the late production phase and it makes continuation of the process over 100 h pointless. The cell recycle and the repeated batch regimes were performed as ways for prolongation of citric acid synthesis by yeast. Using cell recycle, the active citric acid biosynthesis (96-107 g l(-1)) with a yield of 0.64 g g(-1) and a productivity of 1.42 g l(-1) h(-1) was prolongated up to 300 h. Repeated batch culture remained stable for over 1000 h; the RB variant of 30% feed every 3 days showed the best results: 124.2 g l(-1) citric acid with a yield of 0.77 g g(-1) and a productivity of 0.85 g l(-1) h(-1).

  8. Characterization of a novel dimorphism in the 5' flanking region of the short tandem repeat (STR) locus, c-fes/fps (FES).

    PubMed

    Bieschke, Erik T; Wallace, Margaret M; De Forest, Peter R; Shaler, Robert C; Prinz, Mechthild

    2003-01-01

    The FES short tandem repeat (STR) locus contains seven to 14 repeats of the tetranucleotide sequence ATTT. A novel 10 base pair dimorphism in the 5' flanking region of the FES locus was characterized in four broad populations: African-American, Hispanic, Caucasian, and Asian. The absence of the 10 base pair sequence, or (-) allele, was closely linked to FES STR alleles with 10 or fewer repeats. The presence of the 10 base pair sequence, or (+) allele, was closely linked to FES STR alleles with 12 or more repeats. The (-) and (+) alleles occurred equally often in FES STR allele 11. The nucleotide sequence (5'-GGCTGTTTTG-3') of the (+) allele, located 179 base pairs upstream of the FES STR, was determined to be consistent within and among the four populations. Statistical and sequence analysis confirmed the linkage between the two polymorphic sites. The results indicate that the exclusion rate of the FES locus is increased, above that for the STR alone, when both polymorphic characteristics are considered.

  9. Persistent heteroplasmy of a mutation in the human mtDNA control region: hypermutation as an apparent consequence of simple-repeat expansion/contraction.

    PubMed Central

    Howell, N; Smejkal, C B

    2000-01-01

    In the genealogical and phylogenetic analyses that are reported here, we obtained evidence for an unusual pattern of mutation/reversion in the human mitochondrial genome. The cumulative results indicate that, when there is a T-->C polymorphism at nt 16189 and a C-->T substitution at nt 16192, there is an extremely high rate of reversion (hypermutation) at the latter site. The apparent reversion rate is sufficiently high that there is persistent heteroplasmy at nt 16192 in maternal lineages and at the phylogenetic level, a situation that is similar to that observed for the rapid expansion/contraction of simple repeats within the control region. This is the first specific instance in which the mutation frequency at one site in the D-loop is markedly influenced by the local sequence "context." The 16189 T-->C polymorphism lengthens a (C:G)n simple repeat, which then undergoes expansion and contraction, probably through replication slippage. This proclivity toward expansion/contraction is more pronounced when there is a C residue, rather than a T, at nt 16192. The high T-->C reversion frequency at nt 16192 apparently is the result of polymerase misincorporation or slippage during replication, the same mechanism that also causes the expansion/contraction of this simple-repeat sequence. In addition to the first analysis of this mitochondrial hypermutation process, these results also yield mechanistic insights into the expansion/contraction of simple-repeat sequences in mtDNA. PMID:10762545

  10. PM2, a group 3 LEA protein from soybean, and its 22-mer repeating region confer salt tolerance in Escherichia coli

    SciTech Connect

    Yun Liu; Zheng Yizhi . E-mail: yzzheng@szu.edu.cn

    2005-05-27

    To have knowledge of the effect of soybean PM2 protein in protecting dehydrated cells and its functional region, PM2 cDNA was isolated from soybean immature seeds. The recombinants expressing full-length PM2, truncated polypeptides of PM2A (aa 1-262) or PM2B (aa 129-262, 22-mer repeating region), or artificial polypeptide PM2C (duplication of 22-mer repeating region) were constructed. By using SDS-PAGE and mass spectrometry approaches, these fusion polypeptides were identified and proved to be hydrophilic and heat-stable. Spot assays of BL/PM2 and BL/pET28 (as control) showed that protein PM2 increased salt tolerance (500 mM NaCl or 500 mM KCl) of Escherichia coli, rather than osmotic tolerance (1100 mM sorbitol). In addition, comparing the survival ratios of the transformants under 500 mM NaCl or 500 mM KCl stresses, the results showed that: (1) the survival ratios of BL/PM2 and BL/PM2B were quite similar, both showing much higher values than those of BL/pET28. (2) The survival ratios of BL/PM2C were much higher than those of BL/PM2, BL/PM2A, and BL/PM2B. This provides the first experimental evidence that PM2 polypeptide enhances salt tolerance of E. coli cells, and the 22-mer repeat region is an important functional region.

  11. PM2, a group 3 LEA protein from soybean, and its 22-mer repeating region confer salt tolerance in Escherichia coli.

    PubMed

    Liu, Yun; Zheng, Yizhi

    2005-05-27

    To have knowledge of the effect of soybean PM2 protein in protecting dehydrated cells and its functional region, PM2 cDNA was isolated from soybean immature seeds. The recombinants expressing full-length PM2, truncated polypeptides of PM2A (aa 1-262) or PM2B (aa 129-262, 22-mer repeating region), or artificial polypeptide PM2C (duplication of 22-mer repeating region) were constructed. By using SDS-PAGE and mass spectrometry approaches, these fusion polypeptides were identified and proved to be hydrophilic and heat-stable. Spot assays of BL/PM2 and BL/pET28 (as control) showed that protein PM2 increased salt tolerance (500 mM NaCl or 500 mM KCl) of Escherichia coli, rather than osmotic tolerance (1100 mM sorbitol). In addition, comparing the survival ratios of the transformants under 500 mM NaCl or 500 mM KCl stresses, the results showed that: (1) the survival ratios of BL/PM2 and BL/PM2B were quite similar, both showing much higher values than those of BL/pET28. (2) The survival ratios of BL/PM2C were much higher than those of BL/PM2, BL/PM2A, and BL/PM2B. This provides the first experimental evidence that PM2 polypeptide enhances salt tolerance of E. coli cells, and the 22-mer repeat region is an important functional region.

  12. Molecular cloning of the breakpoints of a complex Philadelphia chromosome translocation: identification of a repeated region on chromosome 17.

    PubMed Central

    McKeithan, T W; Warshawsky, L; Espinosa, R; LeBeau, M M

    1992-01-01

    Complex translocations in chronic myelogenous leukemia involve various chromosomes, in addition to chromosomes 9 and 22, in a nonrandom fashion. We have analyzed the DNA from leukemia cells characterized by a complex translocation, t(9;22;10;17)(q34;q11;p13;q21), by using the techniques of Southern blot hybridization, in situ hybridization, and molecular cloning; one of the breakpoints is at 17q21, a band that is frequently involved in complex 9;22 translocations. All of the breakpoint junctions and the corresponding normal sequences from the four involved chromosomes have been molecularly cloned. Restriction mapping is consistent with a simple concerted exchange of chromosomal material among the four chromosomes, except that additional changes appeared to have occurred within the chromosome 17 sequences. The cloned sequences on chromosome 17 at band q21 were found to be repeated in normal cells. By fluorescence in situ hybridization, a strong signal is seen at 17q21, but a weaker signal is also present at 17q23. By comparison with other primate species, an inversion in chromosome 17 during evolution appears to be responsible for the splitting of the cluster of repeat units in normal human cells. Images PMID:1594595

  13. New Insights into Poly(Lactic-co-glycolic acid) Microstructure: Using Repeating Sequence Copolymers to Decipher Complex NMR and Thermal Behavior

    PubMed Central

    Stayshich, Ryan M.; Meyer, Tara Y.

    2012-01-01

    Sequence, which Nature uses to spectacular advantage, has not been fully exploited in synthetic copolymers. To investigate the effect of sequence and stereosequence on the physical properties of copolymers a family of complex isotactic, syndiotactic and atactic repeating sequence poly(lactic-co-glycolic acid) copolymers (RSC PLGAs) were prepared and their NMR and thermal behavior was studied. The unique suitability of polymers prepared from the bioassimilable lactic and glycolic acid monomers for biomedical applications makes them ideal candidates for this type of sequence engineering. Polymers with repeating units of LG, GLG and LLG (L = lactic, G = glycolic) with controlled and varied tacticities were synthesized by assembly of sequence specific, stereopure dimeric, trimeric and hexameric segmer units. Specifically labeled deuterated lactic and glycolic acid segmers were likewise prepared and polymerized. Molecular weights for the copolymers ranged from Mn = 12-40 kDa by size exclusion chromatography in THF. Although the effects of sequence-influenced solution conformation were visible in all resonances of the 1H and 13C NMR spectra, the diastereotopic methylene resonances in the 1H NMR (CDCl3) for the glycolic units of the copolymers proved most sensitive. An octad level of resolution, which corresponds to an astounding 31-atom distance between the most separated stereocenters, was observed in some mixed sequence polymers. Importantly, the level of sensitivity of a particular NMR resonance to small differences in sequence was found to depend on the sequence itself. Thermal properties were also correlated with sequence. PMID:20681726

  14. An alternative conformation of the gp41 heptad repeat 1 region coiled coil exists in the human immunodeficiency virus (HIV-1) envelope glycoprotein precursor

    SciTech Connect

    Mische, Claudia C.; Yuan Wen; Strack, Bettina; Craig, Stewart; Farzan, Michael; Sodroski, Joseph . E-mail: joseph_sodroski@dfci.harvard.edu

    2005-07-20

    The human immunodeficiency virus (HIV-1) transmembrane envelope glycoprotein, gp41, which mediates virus-cell fusion, exists in at least three different conformations within the trimeric envelope glycoprotein complex. The structures of the prefusogenic and intermediate states are unknown; structures representing the postfusion state have been solved. In the postfusion conformation, three helical heptad repeat 2 (HR2) regions pack in an antiparallel fashion into the hydrophobic grooves on the surface of a triple-helical coiled coil formed by the heptad repeat 1 (HR1) regions. We studied the prefusogenic conformation of gp41 by mutagenic alteration of membrane-anchored and soluble forms of the HIV-1 envelope glycoproteins. Our results indicate that, in the HIV-1 envelope glycoprotein precursor, the gp41 HR1 region is in a conformation distinct from that of a trimeric coiled coil. Thus, the central gp41 coiled coil is formed during the transition of the HIV-1 envelope glycoproteins from the precursor state to the receptor-bound intermediate.

  15. Revisiting the TALE repeat.

    PubMed

    Deng, Dong; Yan, Chuangye; Wu, Jianping; Pan, Xiaojing; Yan, Nieng

    2014-04-01

    Transcription activator-like (TAL) effectors specifically bind to double stranded (ds) DNA through a central domain of tandem repeats. Each TAL effector (TALE) repeat comprises 33-35 amino acids and recognizes one specific DNA base through a highly variable residue at a fixed position in the repeat. Structural studies have revealed the molecular basis of DNA recognition by TALE repeats. Examination of the overall structure reveals that the basic building block of TALE protein, namely a helical hairpin, is one-helix shifted from the previously defined TALE motif. Here we wish to suggest a structure-based re-demarcation of the TALE repeat which starts with the residues that bind to the DNA backbone phosphate and concludes with the base-recognition hyper-variable residue. This new numbering system is consistent with the α-solenoid superfamily to which TALE belongs, and reflects the structural integrity of TAL effectors. In addition, it confers integral number of TALE repeats that matches the number of bound DNA bases. We then present fifteen crystal structures of engineered dHax3 variants in complex with target DNA molecules, which elucidate the structural basis for the recognition of bases adenine (A) and guanine (G) by reported or uncharacterized TALE codes. Finally, we analyzed the sequence-structure correlation of the amino acid residues within a TALE repeat. The structural analyses reported here may advance the mechanistic understanding of TALE proteins and facilitate the design of TALEN with improved affinity and specificity.

  16. Repeated functional convergent effects of NaV1.7 on acid insensitivity in hibernating mammals.

    PubMed

    Liu, Zhen; Wang, Wei; Zhang, Tong-Zuo; Li, Gong-Hua; He, Kai; Huang, Jing-Fei; Jiang, Xue-Long; Murphy, Robert W; Shi, Peng

    2014-02-01

    Hibernating mammals need to be insensitive to acid in order to cope with conditions of high CO2; however, the molecular basis of acid tolerance remains largely unknown. The African naked mole-rat (Heterocephalus glaber) and hibernating mammals share similar environments and physiological features. In the naked mole-rat, acid insensitivity has been shown to be conferred by the functional motif of the sodium ion channel NaV1.7. There is now an opportunity to evaluate acid insensitivity in other taxa. In this study, we tested for functional convergence of NaV1.7 in 71 species of mammals, including 22 species that hibernate. Our analyses revealed a functional convergence of amino acid sequences, which occurred at least six times independently in mammals that hibernate. Evolutionary analyses determined that the convergence results from both parallel and divergent evolution of residues in the functional motif. Our findings not only identify the functional molecules responsible for acid insensitivity in hibernating mammals, but also open new avenues to elucidate the molecular underpinnings of acid insensitivity in mammals.

  17. The Internal Region Leucine-rich Repeat 6 of Decorin Interacts with Low Density Lipoprotein Receptor-related Protein-1, Modulates Transforming Growth Factor (TGF)-β-dependent Signaling, and Inhibits TGF-β-dependent Fibrotic Response in Skeletal Muscles*

    PubMed Central

    Cabello-Verrugio, Claudio; Santander, Cristian; Cofré, Catalina; Acuña, Maria José; Melo, Francisco; Brandan, Enrique

    2012-01-01

    Decorin is a small proteoglycan, composed of 12 leucine-rich repeats (LRRs) that modulates the activity of transforming growth factor type β (TGF-β) and other growth factors, and thereby influences proliferation and differentiation in a wide array of physiological and pathological processes, such as fibrosis, in several tissues and organs. Previously we described two novel modulators of the TGF-β-dependent signaling pathway: LDL receptor-related protein (LRP-1) and decorin. Here we have determined the regions in decorin that are responsible for interaction with LRP-1 and are involved in TGF-β-dependent binding and signaling. Specifically, we used decorin deletion mutants, as well as peptides derived from internal LRR regions, to determine the LRRs responsible for these decorin functions. Our results indicate that LRR6 and LRR5 participate in the interaction with LRP-1 and TGF-β as well as in its dependent signaling. Furthermore, the internal region (LRR6i), composed of 11 amino acids, is responsible for decorin binding to LRP-1 and subsequent TGF-β-dependent signaling. Furthermore, using an in vivo approach, we also demonstrate that the LRR6 region of decorin can inhibit TGF-β mediated action in response to skeletal muscle injury. PMID:22203668

  18. Computational modeling of Repeat1 region of INI1/hSNF5: An evolutionary link with ubiquitin.

    PubMed

    Bhutoria, Savita; Kalpana, Ganjam V; Acharya, Seetharama A

    2016-09-01

    The structure of a protein can be very informative of its function. However, determining protein structures experimentally can often be very challenging. Computational methods have been used successfully in modeling structures with sufficient accuracy. Here we have used computational tools to predict the structure of an evolutionarily conserved and functionally significant domain of Integrase interactor (INI)1/hSNF5 protein. INI1 is a component of the chromatin remodeling SWI/SNF complex, a tumor suppressor and is involved in many protein-protein interactions. It belongs to SNF5 family of proteins that contain two conserved repeat (Rpt) domains. Rpt1 domain of INI1 binds to HIV-1 Integrase, and acts as a dominant negative mutant to inhibit viral replication. Rpt1 domain also interacts with oncogene c-MYC and modulates its transcriptional activity. We carried out an ab initio modeling of a segment of INI1 protein containing the Rpt1 domain. The structural model suggested the presence of a compact and well defined ββαα topology as core structure in the Rpt1 domain of INI1. This topology in Rpt1 was similar to PFU domain of Phospholipase A2 Activating Protein, PLAA. Interestingly, PFU domain shares similarity with Ubiquitin and has ubiquitin binding activity. Because of the structural similarity between Rpt1 domain of INI1 and PFU domain of PLAA, we propose that Rpt1 domain of INI1 may participate in ubiquitin recognition or binding with ubiquitin or ubiquitin related proteins. This modeling study may shed light on the mode of interactions of Rpt1 domain of INI1 and is likely to facilitate future functional studies of INI1. PMID:27261671

  19. Computational modeling of Repeat1 region of INI1/hSNF5: An evolutionary link with ubiquitin.

    PubMed

    Bhutoria, Savita; Kalpana, Ganjam V; Acharya, Seetharama A

    2016-09-01

    The structure of a protein can be very informative of its function. However, determining protein structures experimentally can often be very challenging. Computational methods have been used successfully in modeling structures with sufficient accuracy. Here we have used computational tools to predict the structure of an evolutionarily conserved and functionally significant domain of Integrase interactor (INI)1/hSNF5 protein. INI1 is a component of the chromatin remodeling SWI/SNF complex, a tumor suppressor and is involved in many protein-protein interactions. It belongs to SNF5 family of proteins that contain two conserved repeat (Rpt) domains. Rpt1 domain of INI1 binds to HIV-1 Integrase, and acts as a dominant negative mutant to inhibit viral replication. Rpt1 domain also interacts with oncogene c-MYC and modulates its transcriptional activity. We carried out an ab initio modeling of a segment of INI1 protein containing the Rpt1 domain. The structural model suggested the presence of a compact and well defined ββαα topology as core structure in the Rpt1 domain of INI1. This topology in Rpt1 was similar to PFU domain of Phospholipase A2 Activating Protein, PLAA. Interestingly, PFU domain shares similarity with Ubiquitin and has ubiquitin binding activity. Because of the structural similarity between Rpt1 domain of INI1 and PFU domain of PLAA, we propose that Rpt1 domain of INI1 may participate in ubiquitin recognition or binding with ubiquitin or ubiquitin related proteins. This modeling study may shed light on the mode of interactions of Rpt1 domain of INI1 and is likely to facilitate future functional studies of INI1.

  20. The Ancestral Gene for Transcribed, Low-Copy Repeats in the Prader-Willi/Angleman Region Encodes a Large Protein Implicated in Protein Trafficking that is Deficient in Mice with Neuromuscular and

    SciTech Connect

    Ji, Y.

    1999-01-01

    Transcribed, low-copy repeat elements are associated with the breakpoint regions of common deletions in Prader-Willi and Angelman syndromes. We report here the identification of the ancestral gene ( HERC2 ) and a family of duplicated, truncated copies that comprise these low-copy repeats. This gene encodes a highly conserved giant protein, HERC2, that is distantly related to p532 (HERC1), a guanine nucleotide exchange factor (GEF) implicated in vesicular trafficking. The mouse genome contains a single Herc2 locus, located in the jdf2 (juvenile development and fertility-2) interval of chromosome 7C. We have identified single nucleotide splice junction mutations in Herc2 in three independent N-ethyl-N-nitrosourea-induced jdf2 mutant alleles, each leading to exon skipping with premature termination of translation and/or deletion of conserved amino acids. Therefore, mutations in Herc2 lead to the neuromuscular secretory vesicle and sperm acrosome defects, other developmental abnormalities and juvenile lethality of jdf2 mice. Combined, these findings suggest that HERC2 is an important gene encoding a GEF involved in protein trafficking and degradation pathways in the cell.

  1. Repeated lysergic acid diethylamide in an animal model of depression: Normalisation of learning behaviour and hippocampal serotonin 5-HT2 signalling.

    PubMed

    Buchborn, Tobias; Schröder, Helmut; Höllt, Volker; Grecksch, Gisela

    2014-06-01

    A re-balance of postsynaptic serotonin (5-HT) receptor signalling, with an increase in 5-HT1A and a decrease in 5-HT2A signalling, is a final common pathway multiple antidepressants share. Given that the 5-HT1A/2A agonist lysergic acid diethylamide (LSD), when repeatedly applied, selectively downregulates 5-HT2A, but not 5-HT1A receptors, one might expect LSD to similarly re-balance the postsynaptic 5-HT signalling. Challenging this idea, we use an animal model of depression specifically responding to repeated antidepressant treatment (olfactory bulbectomy), and test the antidepressant-like properties of repeated LSD treatment (0.13 mg/kg/d, 11 d). In line with former findings, we observe that bulbectomised rats show marked deficits in active avoidance learning. These deficits, similarly as we earlier noted with imipramine, are largely reversed by repeated LSD administration. Additionally, bulbectomised rats exhibit distinct anomalies of monoamine receptor signalling in hippocampus and/or frontal cortex; from these, only the hippocampal decrease in 5-HT2 related [(35)S]-GTP-gamma-S binding is normalised by LSD. Importantly, the sham-operated rats do not profit from LSD, and exhibit reduced hippocampal 5-HT2 signalling. As behavioural deficits after bulbectomy respond to agents classified as antidepressants only, we conclude that the effect of LSD in this model can be considered antidepressant-like, and discuss it in terms of a re-balance of hippocampal 5-HT2/5-HT1A signalling. PMID:24785760

  2. Repeated lysergic acid diethylamide in an animal model of depression: Normalisation of learning behaviour and hippocampal serotonin 5-HT2 signalling.

    PubMed

    Buchborn, Tobias; Schröder, Helmut; Höllt, Volker; Grecksch, Gisela

    2014-06-01

    A re-balance of postsynaptic serotonin (5-HT) receptor signalling, with an increase in 5-HT1A and a decrease in 5-HT2A signalling, is a final common pathway multiple antidepressants share. Given that the 5-HT1A/2A agonist lysergic acid diethylamide (LSD), when repeatedly applied, selectively downregulates 5-HT2A, but not 5-HT1A receptors, one might expect LSD to similarly re-balance the postsynaptic 5-HT signalling. Challenging this idea, we use an animal model of depression specifically responding to repeated antidepressant treatment (olfactory bulbectomy), and test the antidepressant-like properties of repeated LSD treatment (0.13 mg/kg/d, 11 d). In line with former findings, we observe that bulbectomised rats show marked deficits in active avoidance learning. These deficits, similarly as we earlier noted with imipramine, are largely reversed by repeated LSD administration. Additionally, bulbectomised rats exhibit distinct anomalies of monoamine receptor signalling in hippocampus and/or frontal cortex; from these, only the hippocampal decrease in 5-HT2 related [(35)S]-GTP-gamma-S binding is normalised by LSD. Importantly, the sham-operated rats do not profit from LSD, and exhibit reduced hippocampal 5-HT2 signalling. As behavioural deficits after bulbectomy respond to agents classified as antidepressants only, we conclude that the effect of LSD in this model can be considered antidepressant-like, and discuss it in terms of a re-balance of hippocampal 5-HT2/5-HT1A signalling.

  3. A Recombinationally Repressed Region between Mat2 and Mat3 Loci Shares Homology to Centromeric Repeats and Regulates Directionality of Mating-Type Switching in Fission Yeast

    PubMed Central

    Grewal, SIS.; Klar, AJS.

    1997-01-01

    Cells of the fission yeast Schizosaccharomyces pombe switch mating type by replacing genetic information at the transcriptionally active mat1 locus with sequences copied from one of two closely linked silent loci, mat2-P or mat3-M. By a process referred to as directionality of switching, cells predominantly switch to the opposite mat1 allele; the mat1-P allele preferentially recombines with mat3, while mat1-M selects the mat2. In contrast to efficient recombination at mat1, recombination within the adjoining mat2-mat3 interval is undetectable. We defined the role of sequences between mat2 and mat3, designated the K-region, in directionality as well as recombinational suppression. Cloning and sequencing analysis revealed that a part of the K-region is homologous to repeat sequences present at centromeres, which also display transcriptional and recombinational suppression. Replacement of 7.5 kb of the K-region with the ura4(+) gene affected directionality in a variegated manner. Analysis of the swi6-mod locus, which was previously shown to affect directionality, in KΔ::ura4(+) strains suggested the existence of at least two overlapping directionality mechanisms. Our work furthers the model that directionality is regulated by cell-type-specific organization of the heterochromatin-like structure in the mating-type region and provides evidence that the K-region contributes to silencing of the mat2-mat3 interval. PMID:9258669

  4. The R Region Found in the Human Foamy Virus Long Terminal Repeat Is Critical for both Gag and Pol Protein Expression

    PubMed Central

    Russell, Rebecca A.; Zeng, Yan; Erlwein, Otto; Cullen, Bryan R.; McClure, Myra O.

    2001-01-01

    It has been suggested that sequences located within the 5′ noncoding region of human foamy virus (HFV) are critical for expression of the viral Gag and Pol structural proteins. Here, we identify a discrete ∼151-nucleotide sequence, located within the R region of the HFV long terminal repeat, that activates HFV Gag and Pol expression when present in the 5′ noncoding region but that is inactive when inverted or when placed in the 3′ noncoding region. Sequences that are critical for the expression of both Gag and Pol include not only the 5′ splice site positioned at +51 in the R region, which is used to generate the spliced pol mRNA, but also intronic R sequences located well 3′ to this splice site. Analysis of total cellular gag and pol mRNA expression demonstrates that deletion of the R region has little effect on gag mRNA levels but that R deletions that would be predicted to leave the pol 5′ splice site intact nevertheless inhibit the production of the spliced pol mRNA. Gag expression can be largely rescued by the introduction of an intron into the 5′ noncoding sequence in place of the R region but not by an intron or any one of several distinct retroviral nuclear RNA export sequences inserted into the mRNA 3′ noncoding sequence. Neither the R element nor the introduced 5′ intron markedly affects the cytoplasmic level of HFV gag mRNA. The poor translational utilization of these cytoplasmic mRNAs when the R region is not present in cis also extended to a cat indicator gene linked to an internal ribosome entry site introduced into the 3′ noncoding region. Together these data imply that the HFV R region acts in the nucleus to modify the cytoplasmic fate of target HFV mRNA. The close similarity between the role of the HFV R region revealed in this study and previous data (M. Butsch, S. Hull, Y. Wang, T. M. Roberts, and K. Boris-Lawrie, J. Virol. 73:4847–4855, 1999) demonstrating a critical role for the R region in activating gene expression in

  5. Molecular instability in the COII-tRNA(Lys) intergenic region of the human mitochondrial genome: multiple origins of the 9-bp deletion and heteroplasmy for expanded repeats.

    PubMed Central

    Thomas, M G; Cook, C E; Miller, K W; Waring, M J; Hagelberg, E

    1998-01-01

    We have identified two individuals from Glasgow in Scotland who have a deletion of one of two copies of the intergenic 9-bp sequence motif CCCCCTCTA, located between the cytochrome oxidase II (COII) and lysine tRNA (tRNA(Lys)) genes of the human mitochondrial genome. Although this polymorphism is common in Africa and Asia, it has not been reported in Northern Europe. Analysis of the mitochondrial DNA control region sequences of these two individuals suggests that they belong to a lineage that originated independently of the previously characterized African and Asian 9-bp deleted lineages. Among the Scottish population we have also identified a maternal lineage of three generations exhibiting heteroplasmy for two, three and four copies of the CCCCCTCTA motif. Polymerase chain reaction amplification across the COII-tRNA(Lys) intergenic region of these individuals gives different ratios of the three product lengths that are dependent on the concentration of the DNA-binding dye crystal violet. To investigate whether changes in repeat number were generated de novo, we constructed clones containing known numbers of the CCCCCTCTA motif. In the presence of high concentrations of crystal violet we obtained two, three and four copies of this motif when the amplification template contained only four copies. Various DNA-binding drugs are known to stabilize bulged structures in DNA and contribute to the process of slipped-strand mispairing during DNA replication. These results suggest that the COII-tRNA(Lys) intergenic region is unstable owing to slipped-strand mispairing. Although sequences containing four copies of the CCCCCTCTA motif are less stable in vitro, we observed an increase in the proportion of mitochondrial genomes with four repeats between-a mother and a daughter in the heteroplasmic lineage. From this we conclude that drift in the germ-line lineage is a main factor in the maintenance or loss of heteroplasmy. PMID:9684291

  6. Upstream regions of the human cardiac actin gene that modulate its transcription in muscle cells: presence of an evolutionarily conserved repeated motif.

    PubMed Central

    Minty, A; Kedes, L

    1986-01-01

    Transfection into cultured cell lines was used to investigate the transcriptional regulation of the human cardiac actin gene. We first demonstrated that in both human heart and human skeletal muscle, cardiac actin mRNAs initiate at the identical site and contain the same first exon, which is separated from the first coding exon by an intron of 700 base pairs. A region of 485 base pairs upstream from the transcription initiation site of the human cardiac actin gene directs high-level transient expression of the bacterial chloramphenicol acetyltransferase gene in differentiated myotubes of the mouse C2C12 muscle cell line, but not in mouse L fibroblast or rat PC-G2 pheochromocytoma cells. Deletion analysis of this region showed that at least two physically separated sequence elements are involved, a distal one starting between -443 and -395 and a proximal one starting between -177 and -118, and suggested that these sequences interact with positively acting transcriptional factors in muscle cells. When these two sequence elements are inserted separately upstream of a heterologous (simian virus 40) promoter, they do not affect transcription but do give a small (four- to fivefold) stimulation when tested together. Overall, these regulatory regions upstream of the cap site of the human cardiac actin gene show remarkably high sequence conservation with the equivalent regions of the mouse and chick genes. Furthermore, there is an evolutionarily conserved repeated motif that may be important in the transcriptional regulation of actin and other contractile protein genes. Images PMID:3785189

  7. Region-specific effects of isoflurane anesthesia on Fos immunoreactivity in response to intravenous cocaine challenge in rats with a history of repeated cocaine administration

    PubMed Central

    Kufahl, Peter R.; Peartree, Natalie A.; Heintzelman, Krista L.; Chung, Maggie; Neisewander, Janet L.

    2016-01-01

    We have previously shown that acute intravenous (i.v.) administration of cocaine increases Fos immunoreactivity in rats under isoflurane anesthesia. Given that Fos expression is a marker of neural activation, the results suggested that isoflurane is appropriate for imaging cocaine effects under anesthesia. However, most imaging research in this area utilizes subjects with a history of repeated cocaine exposure and this drug history may interact with anesthetic use differently from acute cocaine exposure. Thus, this study further examined Fos expression under isoflurane in rats with a history of repeated i.v. cocaine administration. Rats received daily injections of either saline or cocaine (2 mg/kg, i.v.) across 7 consecutive days, followed by 5 days of no drug exposure. On the test day, rats were either nonanesthetized or anesthetized under isoflurane and were given an acute challenge of cocaine (2 mg/kg, i.v.). Additional saline-exposed controls received a saline challenge. Ninety min after the drug challenge, the rats were perfused under isoflurane anesthesia and their brains were processed for Fos protein immunohistochemistry. We found that challenge injections of cocaine following a regimen of repeated cocaine exposure resulted in Fos expression in the prefrontal cortex and striatum roughly equivalent to that found in rats who had received the cocaine challenge after a history of vehicle injections. Additionally, isoflurane anesthesia resulted in a heterogeneous attenuation of cocaine-induced Fos expression, with the most robust effect in the orbital cortex but no effect in the nucleus accumbens core (NAcC). These results indicate that cocaine-induced Fos is preserved in the NAcC under isoflurane, suggesting that isoflurane can be used in imaging studies involving cocaine effects in this region. PMID:25451087

  8. Single-chain protein mimetics of the N-terminal heptad-repeat region of gp41 with potential as anti–HIV-1 drugs

    PubMed Central

    Crespillo, Sara; Cámara-Artigas, Ana; Casares, Salvador; Morel, Bertrand; Cobos, Eva S.; Mateo, Pedro L.; Mouz, Nicolas; Martin, Christophe E.; Roger, Marie G.; El Habib, Raphaelle; Su, Bin; Moog, Christiane; Conejero-Lara, Francisco

    2014-01-01

    During HIV-1 fusion to the host cell membrane, the N-terminal heptad repeat (NHR) and the C-terminal heptad repeat (CHR) of the envelope subunit gp41 become transiently exposed and accessible to fusion inhibitors or Abs. In this process, the NHR region adopts a trimeric coiled-coil conformation that can be a target for therapeutic intervention. Here, we present an approach to rationally design single-chain protein constructs that mimic the NHR coiled-coil surface. The proteins were built by connecting with short loops two parallel NHR helices and an antiparallel one with the inverse sequence followed by engineering of stabilizing interactions. The constructs were expressed in Escherichia coli, purified with high yield, and folded as highly stable helical coiled coils. The crystal structure of one of the constructs confirmed the predicted fold and its ability to accurately mimic an exposed gp41 NHR surface. These single-chain proteins bound to synthetic CHR peptides with very high affinity, and furthermore, they showed broad inhibitory activity of HIV-1 fusion on various pseudoviruses and primary isolates. PMID:25489108

  9. Evaluation of novel Streptococcus pyogenes vaccine candidates incorporating multiple conserved sequences from the C-repeat region of the M-protein.

    PubMed

    Bauer, Michelle J; Georgousakis, Melina M; Vu, Therese; Henningham, Anna; Hofmann, Andreas; Rettel, Mandy; Hafner, Louise M; Sriprakash, Kadaba S; McMillan, David J

    2012-03-01

    A major challenge for Streptococcus pyogenes vaccine development is the identification of epitopes that confer protection from infection by multiple S. pyogenes M-types. Here we have identified and characterised the distribution of common variant sequences from individual repeat units of the C-repeat region (CRR) of M-proteins representing 77 different M-types. Three polyvalent fusion vaccine candidates (SV1, SV2 and SV3) incorporating the most common variants were subsequently expressed and purified, and demonstrated to be alpha-helical by Circular Dichroism (CD), a secondary conformational characteristic of the CRR in the M-protein. Antibodies raised against each of these constructs recognise M-proteins that vary in their CRR, and bind to the surface of multiple S. pyogenes isolates. Antibodies raised against SV1, containing five variant sequences, also kill heterologous S. pyogenes isolates in in vitro bactericidal assays. Further structural characterisation of this construct demonstrated the conformation of SV1 was stable at different pHs, and thermal unfolding of SV1 is a reversible process. Our findings demonstrate that linkage of multiple variant sequences into a single recombinant construct overcomes the need to embed the variant sequences in foreign helix promoting flanking sequences for conformational stability, and demonstrates the viability of the polyvalent candidates as global S. pyogenes vaccine candidates. PMID:22265945

  10. Long terminal repeat (LTR) sequences, env, and a region near the 5' LTR influence the pathogenic potential of recombinants between Rous-associated virus types 0 and 1.

    PubMed Central

    Brown, D W; Blais, B P; Robinson, H L

    1988-01-01

    A series of recombinants between Rous-associated virus type 0 (RAV-0), RAV-1, and a replication-competent avian leukosis virus vector (RCAN) have been tested for disease potential in day-old inoculated K28 chicks. RAV-0 is a benign virus, whereas RAV-1 and RCAN induce lymphoma and a low incidence of a variety of other neoplasms. The results of the oncogenicity tests indicate that (i) the long terminal repeat regions of RAV-1 and RCAN play a major role in disease potential, (ii) subgroup A envelope glycoproteins are associated with a two- to fourfold higher incidence of lymphoma than subgroup E glycoproteins, and (iii) certain combinations of 5' viral and env sequences cause osteopetrosis in a highly context-dependent manner. Long terminal repeat and env sequences appeared to influence lymphomogenic potential by determining the extent of bursal infection within the first 2 to 3 weeks of life. This would suggest that bursal but not postbursal stem cells are targets for avian leukosis virus-induced lymphomogenesis. The induction of neutralizing antibody had no obvious influence on the incidence of lymphoma. PMID:2841495

  11. Eclipse Mapping of the Chromopsheric and Transition Region Structure of HR2554 (G6 Ii) -- Repeat - Hopr 0247

    NASA Astrophysics Data System (ADS)

    Brown, Alexander

    1994-01-01

    We propose to observe an eclipse of the Zeta Aurigae-type binary HR2554 using the GHRS. Every 195 days the A1 dwarf secondary passes behind the outer atmosphere of the G6 II primary and can be used as light source to observe absorption lines from plasma in the G star atmopshere. The G star has a hybrid-chromosphere structure with hot transition region plasma and a cool stellar wind. THESE OBSERVATIONS WOULD BE THE FIRST ECLIPSE OBSRRVATIONS OF THIS TYPE OF ATMOSPHERE WITH GHRS AND COMPARED WITH OUR RESULTS FOR THE K4 SUPERGIANT Zeta Aur, which shows only the typical red supergiant wind. We shall model the observed line profiles and determine the temperature structure, density stratification, wind acceleration/turbulence/ionization as a function of distance above the G star photosphere. The hot and cool plasma are intermixed in this outer atmosphere and we will quantify this "thermal bifurcation". Both the static and outflowing components of the atmopshere will be modelled. The mass loss rate and the wind velocity and density laws as a function of radius will be determined. The vast majority of the needed modelling code will have been developed already for our Zeta Aur analysis. This project represents an opportunity to significantly advance knowledge about the spatial structuring of cool star outer atmospheres and the physical process operating within them.

  12. Activation of cell division and nucleic acid synthesis in the corneal epithelium of albino rats by repeated stress

    SciTech Connect

    Berezhnova, N.I.; Timoshin, S.S.

    1985-05-01

    Adaption to unfavorable factors is accompanied by activation of nucleic acid and protein synthesis in systems responsible for adaption. The authors investigate the possibility of similar changes taking place in structures not actively participating in adaptation. The corneas of the dead male albin rats were preincubated with tritium-uridine for 1.5 hours. The mitotic index, the index of tritium-thymidine-labeled nuclei and the intensity of thymidine labeling were determined. The results indicate that after a single exposure to hypoxia, hyperthermia, and immobilization, mitotic index in the corneal epithelium decreased and DNA synthesis under these circumstances remained stable.

  13. The Secondary Structure of the R Region of a Murine Leukemia Virus Is Important for Stimulation of Long Terminal Repeat-Driven Gene Expression

    PubMed Central

    Cupelli, Lisa; Okenquist, Sharon A.; Trubetskoy, Alla; Lenz, Jack

    1998-01-01

    In addition to their role in reverse transcription, the R-region sequences of some retroviruses affect viral transcription. The first 28 nucleotides of the R region within the long terminal repeat (LTR) of the murine type C retrovirus SL3 were predicted to form a stem-loop structure. We tested whether this structure affected the transcriptional activity of the viral LTR. Mutations that altered either side of the stem and thus disrupted base pairing were generated. These decreased the level of expression of a reporter gene under the control of viral LTR sequences about 5-fold in transient expression assays and 10-fold in cells stably transformed with the LTR-reporter plasmids. We also generated a compensatory mutant in which both the ascending and descending sides of the stem were mutated such that the nucleotide sequence was different but the predicted secondary structure was maintained. Most of the activity of the wild-type SL3 element was restored in this mutant. Thus, the stem-loop structure was important for the maximum activity of the SL3 LTR. Primer extension analysis indicated that the stem-loop structure affected the levels of cytoplasmic RNA. Nuclear run-on assays indicated that deletion of the R region had a small effect on transcriptional initiation and no effect on RNA polymerase processivity. Thus, the main effect of the R-region element was on one or more steps that occurred after the template was transcribed by RNA polymerase. This finding implied that the main function of the R-region element involved RNA processing. R-region sequences of human immunodeficiency virus type 1 or mouse mammary tumor virus could not replace the SL3 element. R-region sequences from an avian reticuloendotheliosis virus partially substituted for the SL3 sequences. R-region sequences from Moloney murine leukemia virus or feline leukemia virus did function in place of the SL3 element. Thus, the R region element appears to be a general feature of the mammalian type C genus of

  14. The secondary structure of the R region of a murine leukemia virus is important for stimulation of long terminal repeat-driven gene expression.

    PubMed

    Cupelli, L; Okenquist, S A; Trubetskoy, A; Lenz, J

    1998-10-01

    In addition to their role in reverse transcription, the R-region sequences of some retroviruses affect viral transcription. The first 28 nucleotides of the R region within the long terminal repeat (LTR) of the murine type C retrovirus SL3 were predicted to form a stem-loop structure. We tested whether this structure affected the transcriptional activity of the viral LTR. Mutations that altered either side of the stem and thus disrupted base pairing were generated. These decreased the level of expression of a reporter gene under the control of viral LTR sequences about 5-fold in transient expression assays and 10-fold in cells stably transformed with the LTR-reporter plasmids. We also generated a compensatory mutant in which both the ascending and descending sides of the stem were mutated such that the nucleotide sequence was different but the predicted secondary structure was maintained. Most of the activity of the wild-type SL3 element was restored in this mutant. Thus, the stem-loop structure was important for the maximum activity of the SL3 LTR. Primer extension analysis indicated that the stem-loop structure affected the levels of cytoplasmic RNA. Nuclear run-on assays indicated that deletion of the R region had a small effect on transcriptional initiation and no effect on RNA polymerase processivity. Thus, the main effect of the R-region element was on one or more steps that occurred after the template was transcribed by RNA polymerase. This finding implied that the main function of the R-region element involved RNA processing. R-region sequences of human immunodeficiency virus type 1 or mouse mammary tumor virus could not replace the SL3 element. R-region sequences from an avian reticuloendotheliosis virus partially substituted for the SL3 sequences. R-region sequences from Moloney murine leukemia virus or feline leukemia virus did function in place of the SL3 element. Thus, the R region element appears to be a general feature of the mammalian type C genus of

  15. Optical properties in the UV and visible spectral region of organic acids relevant to tropospheric aerosols

    NASA Astrophysics Data System (ADS)

    Lund Myhre, C. E.; Nielsen, C. J.

    2004-09-01

    Refractive and absorption indices in the UV and visible region of selected aqueous organic acids relevant to tropospheric aerosols are reported. The acids investigated are the aliphatic dicarboxylic acids oxalic, malonic, tartronic, succinic and glutaric acid. In addition we report data for pyruvic, pinonic, benzoic and phthalic acid. To cover a wide range of conditions we have investigated the aqueous organic acids at different concentrations spanning from highly diluted samples to concentrations close to saturation. The density of the investigated samples is reported and a parameterisation of the absorption and refractive index that allows the calculation of the optical constants of mixed aqueous organic acids at different concentrations is presented. The single scattering albedo is calculated for two size distributions using measured and a synthetic set of optical constants. The results show that tropospheric aerosols consisting of only these organic acids and water have a pure scattering effect.

  16. Optical properties in the UV and visible spectral region of organic acids relevant to tropospheric aerosols

    NASA Astrophysics Data System (ADS)

    Lund Myhre, C. E.; Nielsen, C. J.

    2004-06-01

    Refractive and absorption indices in the UV and visible region of selected aqueous organic acids relevant to tropospheric aerosols are reported. The acids investigated are the aliphatic dicarboxylic acids oxalic, malonic, tartronic, succinic and glutaric acid. In addition we report data for pyruvic, pinonic, benzoic and phthalic acid. To cover a wide range of conditions we have investigated the aqueous organic acids at different concentrations spanning from highly diluted samples to concentrations close to saturation. The density of the investigated samples is reported and a parameterisation of the absorption and refractive index that allows the calculation of the optical constants of mixed aqueous organic acids at different concentrations is presented. The single scattering albedo is calculated for two size distributions using measured and a synthetic set of optical constants. The results show that tropospheric aerosols consisting of only these organic acids and water have a pure scattering effect.

  17. Functional insights from the distribution and role of homopeptide repeat-containing proteins.

    PubMed

    Faux, Noel G; Bottomley, Stephen P; Lesk, Arthur M; Irving, James A; Morrison, John R; de la Banda, Maria Garcia; Whisstock, James C

    2005-04-01

    Expansion of "low complex" repeats of amino acids such as glutamine (Poly-Q) is associated with protein misfolding and the development of degenerative diseases such as Huntington's disease. The mechanism by which such regions promote misfolding remains controversial, the function of many repeat-containing proteins (RCPs) remains obscure, and the role (if any) of repeat regions remains to be determined. Here, a Web-accessible database of RCPs is presented. The distribution and evolution of RCPs that contain homopeptide repeats tracts are considered, and the existence of functional patterns investigated. Generally, it is found that while polyamino acid repeats are extremely rare in prokaryotes, several eukaryote putative homologs of prokaryote RCP-involved in important housekeeping processes-retain the repetitive region, suggesting an ancient origin for certain repeats. Within eukarya, the most common uninterrupted amino acid repeats are glutamine, asparagines, and alanine. Interestingly, while poly-Q repeats are found in vertebrates and nonvertebrates, poly-N repeats are only common in more primitive nonvertebrate organisms, such as insects and nematodes. We have assigned function to eukaryote RCPs using Online Mendelian Inheritance in Man (OMIM), the Human Reference Protein Database (HRPD), FlyBase, and Wormpep. Prokaryote RCPs were annotated using BLASTp searches and Gene Ontology. These data reveal that the majority of RCPs are involved in processes that require the assembly of large, multiprotein complexes, such as transcription and signaling.

  18. Modeling wet deposition of acid substances over the PRD region in China

    NASA Astrophysics Data System (ADS)

    Lu, Xingcheng; Fung, Jimmy Chi Hung; Wu, Dongwei

    2015-12-01

    The Pearl River Delta (PRD) region in southern China has suffered heavily from acid rain in the last 10 years due to the anthropogenic emission of sulfur dioxide and nitrogen dioxide. Several measurement-based studies about this issue have been conducted to analyze the chemical composition of precipitation in this area. However, no detailed, high resolution numerical simulation regarding this topic has ever been done in this region. In this study, the WRF-SMOKE-CMAQ system was applied to simulate the wet deposition of acid substances (SO42- and NO3-) in the PRD region from 2009 to 2011 with a resolution of 3 km. The simulation output agreed well with the observation data. Our results showed that Guangzhou was the city most affected by acid rain in this region. The ratio of non-sea-salt sulfate to nitrate indicated that the acid rain in this region belonged to the sulfate-nitrate mixed type. The source apportionment result suggests that point source and super regional source are the ones that contribute the pollutants most in the rain water over PRD Region. The sulfate and nitrate input to some reservoirs via wet deposition was also estimated based on the model simulation. Our results suggest that further cross-city cooperation and emission reduction are needed to further curb acid rain in this region.

  19. Evaluating the trans fatty acid, CLA, PUFA and erucic acid diversity in human milk from five regions in China.

    PubMed

    Li, Jing; Fan, Yawei; Zhang, Zhiwu; Yu, Hai; An, Yin; Kramer, John K G; Deng, Zeyuan

    2009-03-01

    Human milk was obtained from 97 healthy lactating women from five different regions in China. Twenty-four hour dietary questionnaire identified the foods consumed that showed distinct differences in food types between cities. The southern and central regions had higher levels of total trans fatty acids (TFA) and conjugated linoleic acids (CLA) in human milk than the northern region. The major isomers in human milk from the northern region were vaccenic and rumenic acids, whereas the other regions had a random distribution of these isomers. This was consistent with the isomer distribution in the refined vegetable oils used and their increased formation during high temperature stir-frying. The human milk composition showed little evidence that partially hydrogenated fats were consumed, except eight mothers in Guangzhou who reported eating crackers, plus four other mothers. The TFA concentration in these human milk samples was higher (2.06-3.96%). The amount of n-6 (1.70-2.24%) and n-3 (0.60-1.47%) highly unsaturated fatty acids (HUFA) in human milk and the resultant ratio (1.43-2.95) showed all mothers in China had an adequate supply of HUFA in their diet. Rapeseed oil was consumed evidenced by erucic acids in human milk. The levels of erucic acid were below internationally accepted limits for human consumption. The levels of undesirable TFA and CLA isomers in human milk are a concern. Efforts to decrease the practice of high temperature stir-frying using unsaturated oils, and a promotion to increase consumption of dairy and ruminant products should be considered in China.

  20. Genetic and physical mapping of 2q35 in the region of NRAMP and IL8R genes: Identification of a polymorphic repeat in exon 2 of NRAMP

    SciTech Connect

    White, J.K.; Shaw, M.A.; Barton, C.H.

    1994-11-15

    Recent interest has focused on the region of conserved synteny between mouse chromosome 1 and human 2q33-q37, particularly over the region encoding the murine macrophage resistance gene Ity/Lsh/Bcg (candidate Nramp) and members of the Il8r interleukin-8 (IL8) receptor gene cluster. In this paper, identification of a restriction fragment length polymorphism in the Il8RB gene in 35 pedigrees previously typed for markers in the 2q33-37 interval provided evidence (lod scores > 3) for linkage between Il8RB and the 2q34-135 markers FN1, TNP1, VIL1, and DES. Physical mapping, using yeast artificial chromosomes isolated with VIL1, confirmed that IL8RA, IL8RB and the IL8RB pseudogene map within the NRAMP-VIL1 interval, with the physical distance (155 kb) from 5{prime} LSH to 3{prime} VIL1 representing {approx}3-fold that observed in the mouse. Partial sequencing of NRAMP confirmed the presence of the N-terminal proline/serine-rich putative SH3 binding domain in exon 2 of the human gene. Further analysis of Brazilian leprosy and visceral leishmaniasis pedigrees identified a rare second allele varying in a 9-nucleotide repeat motif of the exon 2 sequence but segregating independently of the disease phenotype. 38 refs., 4 figs., 3 tabs.

  1. Structure of the O-specific, sialic acid containing polysaccharide chain and its linkage to the core region in lipopolysaccharide from Hafnia alvei strain 2 as elucidated by chemical methods, gas-liquid chromatography/mass spectrometry, and sup 1 H NMR spectroscopy

    SciTech Connect

    Gamian, A.; Romanowska, E. ); Dabrowski, U.; Dabrowski, J. )

    1991-05-21

    Mild acid hydrolysis of Hafnia alvei strain 2 lipopolysaccharide released no O-specific polysaccharide but instead gave a monomeric octasaccharide repeating unit with N-acetylneuraminic acid as the reducing terminus. In addition, a dimer of the octasaccharide repeating unit, and also a decasaccharide composed of a fragment of the O-specific polysaccharide chain and the core region, were obtained in minute amounts. On the basis of the sugar and methylation analyses, periodate oxidation, and {sup 1}H NMR spectroscopy of the lipopolysaccharide hydrolytic products, the biological repeating unit of the O-specific polysaccharide was shown to be a branched octasaccharide. The linkage between the O-specific polysaccharide chain and core region has also been determined and has yielded strong evidence that N-acetylneuraminic acid is an inherent lipopolysaccharide component. The lipopolysaccharide of H. alvei strain 2 is the first lipopolysaccharide reported to contain 4-substituted neuraminic acid in its O-specific polysaccharide region.

  2. Repeated systemic administration of the nutraceutical alpha-linolenic acid exerts neuroprotective efficacy, an antidepressant effect and improves cognitive performance when given after soman exposure.

    PubMed

    Pan, Hongna; Piermartiri, Tetsade C B; Chen, Jun; McDonough, John; Oppel, Craig; Driwech, Wafae; Winter, Kristin; McFarland, Emylee; Black, Katelyn; Figueiredo, Taiza; Grunberg, Neil; Marini, Ann M

    2015-12-01

    Exposure to nerve agents results in severe seizures or status epilepticus caused by the inhibition of acetylcholinesterase, a critical enzyme that breaks down acetylcholine to terminate neurotransmission. Prolonged seizures cause brain damage and can lead to long-term consequences. Current countermeasures are only modestly effective against the brain damage supporting interest in the evaluation of new and efficacious therapies. The nutraceutical alpha-linolenic acid (LIN) is an essential omega-3 polyunsaturated fatty acid that has a wide safety margin. Previous work showed that a single intravenous injection of alpha-linolenic acid (500 nmol/kg) administered before or after soman significantly protected against soman-induced brain damage when analyzed 24h after exposure. Here, we show that administration of three intravenous injections of alpha-linolenic acid over a 7 day period after soman significantly improved motor performance on the rotarod, enhanced memory retention, exerted an anti-depressant-like activity and increased animal survival. This dosing schedule significantly reduced soman-induced neuronal degeneration in four major vulnerable brain regions up to 21 days. Taken together, alpha-linolenic acid reduces the profound behavioral deficits induced by soman possibly by decreasing neuronal cell death, and increases animal survival.

  3. Molecular analysis of a U3 RNA gene locus in tomato: transcription signals, the coding region, expression in transgenic tobacco plants and tandemly repeated pseudogenes.

    PubMed

    Kiss, T; Solymosy, F

    1990-04-25

    By screening a tomato genomic library with a tomato U3 RNA probe, we detected a U3 genomic locus whose coding region was determined by primer extension (5' end) and direct RNA sequencing of purified U3 RNA from tomato (3' end). Tomato U3 RNA is 216 nucleotides long, contains all the four evolutionarily highly conserved sequence blocks (Boxes A to D), has at its 5' end a cap not precipitable with anti-m3G antibodies and can be folded into a peculiar secondary structure with two stem-loops at its 5' end. A tagged derivative of the U3 gene was faithfully expressed in transgenic tobacco plants. In the 5' flanking region both plant-specific UsnRNA transcription signals [the TATA-like sequence and the upstream sequence element (USE)] were present, but were positioned closer to each other and also to the cap site in the U3 gene than in the genes for the plant spliceosomal UsnRNAs studied so far. The 3' flanking region of the tomato U3 gene lacked the consensus sequence of the putative termination signal established for the plant spliceosomal UsnRNA genes and contained a pyrimidine-rich tract (R1) followed by four tandemly repeated U3 pseudogenes (U3.1 ps to U3.4 ps) flanked by slightly altered forms (R2 to R5) of R1 and most probably generated by DNA-mediated events. Our results are in line with the conjecture that the enzyme transcribing the tomato U3 gene has different structural requirements for transcriptional activity than the enzyme transcribing plant U1, U2 and U5 genes.

  4. Comparative analysis of the 5'-end regions of two repressible acid phosphatase genes in Saccharomyces cerevisiae.

    PubMed Central

    Thill, G P; Kramer, R A; Turner, K J; Bostian, K A

    1983-01-01

    The nucleotide sequence of 5'-noncoding and N-terminal coding regions of two coordinately regulated, repressible acid phosphatase genes from Saccharomyces cerevisiae were determined. These unlinked genes encode different, but structurally related polypeptides of molecular weights 60,000 and 56,000. The DNA sequences of their 5'-flanking regions show stretches of extensive homology upstream of, and surrounding, a "TATA" sequence and in a region in which heterogeneous 5' ends of the p60 mRNA were mapped. The predicted amino acid sequences encoded by the N-terminal regions of both genes were confirmed by determination of the amino acid sequence of the native exocellular acid phosphatase and the partial sequence of the presecretory polypeptide synthesized in a cell-free protein synthesizing system. The N-terminal region of the p60 polypeptide was shown to be characterized by a hydrophobic 17-amino acid signal polypeptide which is absent in the native exocellular protein and thought to be necessary for acid phosphatase secretion. Images PMID:6343840

  5. Phenolic Acid Composition, Antiatherogenic and Anticancer Potential of Honeys Derived from Various Regions in Greece

    PubMed Central

    Spilioti, Eliana; Jaakkola, Mari; Tolonen, Tiina; Lipponen, Maija; Virtanen, Vesa; Chinou, Ioanna; Kassi, Eva; Karabournioti, Sofia; Moutsatsou, Paraskevi

    2014-01-01

    The phenolic acid profile of honey depends greatly on its botanical and geographical origin. In this study, we carried out a quantitative analysis of phenolic acids in the ethyl acetate extract of 12 honeys collected from various regions in Greece. Our findings indicate that protocatechuic acid, p-hydroxybenzoic acid, vanillic acid, caffeic acid and p-coumaric acid are the major phenolic acids of the honeys examined. Conifer tree honey (from pine and fir) contained significantly higher concentrations of protocatechuic and caffeic acid (mean: 6640 and 397 µg/kg honey respectively) than thyme and citrus honey (mean of protocatechuic and caffeic acid: 437.6 and 116 µg/kg honey respectively). p-Hydroxybenzoic acid was the dominant compound in thyme honeys (mean: 1252.5 µg/kg honey). We further examined the antioxidant potential (ORAC assay) of the extracts, their ability to influence viability of prostate cancer (PC-3) and breast cancer (MCF-7) cells as well as their lowering effect on TNF- α-induced adhesion molecule expression in endothelial cells (HAEC). ORAC values of Greek honeys ranged from 415 to 2129 µmol Trolox equivalent/kg honey and correlated significantly with their content in protocatechuic acid (p<0.001), p-hydroxybenzoic acid (p<0.01), vanillic acid (p<0.05), caffeic acid (p<0.01), p-coumaric acid (p<0.001) and their total phenolic content (p<0.001). Honey extracts reduced significantly the viability of PC-3 and MCF-7 cells as well as the expression of adhesion molecules in HAEC. Importantly, vanillic acid content correlated significantly with anticancer activity in PC-3 and MCF-7 cells (p<0.01, p<0.05 respectively). Protocatechuic acid, vanillic acid and total phenolic content correlated significantly with the inhibition of VCAM-1 expression (p<0.05, p<0.05 and p<0.01 respectively). In conclusion, Greek honeys are rich in phenolic acids, in particular protocatechuic and p-hydroxybenzoic acid and exhibit significant antioxidant, anticancer and

  6. Phenolic acid composition, antiatherogenic and anticancer potential of honeys derived from various regions in Greece.

    PubMed

    Spilioti, Eliana; Jaakkola, Mari; Tolonen, Tiina; Lipponen, Maija; Virtanen, Vesa; Chinou, Ioanna; Kassi, Eva; Karabournioti, Sofia; Moutsatsou, Paraskevi

    2014-01-01

    The phenolic acid profile of honey depends greatly on its botanical and geographical origin. In this study, we carried out a quantitative analysis of phenolic acids in the ethyl acetate extract of 12 honeys collected from various regions in Greece. Our findings indicate that protocatechuic acid, p-hydroxybenzoic acid, vanillic acid, caffeic acid and p-coumaric acid are the major phenolic acids of the honeys examined. Conifer tree honey (from pine and fir) contained significantly higher concentrations of protocatechuic and caffeic acid (mean: 6640 and 397 µg/kg honey respectively) than thyme and citrus honey (mean of protocatechuic and caffeic acid: 437.6 and 116 µg/kg honey respectively). p-Hydroxybenzoic acid was the dominant compound in thyme honeys (mean: 1252.5 µg/kg honey). We further examined the antioxidant potential (ORAC assay) of the extracts, their ability to influence viability of prostate cancer (PC-3) and breast cancer (MCF-7) cells as well as their lowering effect on TNF- α-induced adhesion molecule expression in endothelial cells (HAEC). ORAC values of Greek honeys ranged from 415 to 2129 µmol Trolox equivalent/kg honey and correlated significantly with their content in protocatechuic acid (p<0.001), p-hydroxybenzoic acid (p<0.01), vanillic acid (p<0.05), caffeic acid (p<0.01), p-coumaric acid (p<0.001) and their total phenolic content (p<0.001). Honey extracts reduced significantly the viability of PC-3 and MCF-7 cells as well as the expression of adhesion molecules in HAEC. Importantly, vanillic acid content correlated significantly with anticancer activity in PC-3 and MCF-7 cells (p<0.01, p<0.05 respectively). Protocatechuic acid, vanillic acid and total phenolic content correlated significantly with the inhibition of VCAM-1 expression (p<0.05, p<0.05 and p<0.01 respectively). In conclusion, Greek honeys are rich in phenolic acids, in particular protocatechuic and p-hydroxybenzoic acid and exhibit significant antioxidant, anticancer and

  7. The trans-inhibitory Rep78 protein of adeno-associated virus binds to TAR region DNA of the human immunodeficiency virus type 1 long terminal repeat.

    PubMed

    Batchu, R B; Hermonat, P L

    1995-07-01

    The large rep gene products, Rep78 and Rep68, of adeno-associated virus (AAV) are pleiotropic effector proteins which are required for AAV DNA replication and the trans-regulation of AAV gene expression. Apart from these essential functions prerequisite for the life cycle of AAV, these rep products are able to inhibit the replication and gene expression of human immunodeficiency virus type 1 (HIV-1) and a number of DNA viruses. Here, it is demonstrated that Rep78, as a chimeric with the maltose binding protein, directly binds the full-length HIV-1 long terminal repeat (LTR), and to a subset of these sequences containing the trans-activation response (TAR) sequence as DNA. These interactions, an effector protein physically binding a target promoter, suggest a direct mechanism of action for Rep78 inhibition. Furthermore, competitive binding studies between the TAR region and the full-length HIV-LTR, strongly suggested that another site(s) within the LTR was also bound by Rep78. Finally, as Rep78 binding is also believed to be affected by secondary structure within the DNA, it was found that Rep78 preferentially binds with HIV-LTR sequences with promoted secondary structure generated by heat denaturation and rapid cooling.

  8. A unique nuclear receptor direct repeat 17 (DR17) is present within the upstream region of Schistosoma mansoni female-specific p14 gene

    SciTech Connect

    Fantappie, Marcelo Rosado Furtado, Daniel Rodrigues; Rumjanek, Franklin David; LoVerde, Philip T.

    2008-07-11

    The eggs produced by sexually mature female Schistosma mansoni are responsible for the pathogenesis of the disease. The eggshell precursor gene p14 is expressed only in the vitelline cells of sexually mature female worms in response to a yet unidentified male stimulus. Herein, we report the identification of a novel nuclear receptor response element in the upstream region of the p14 gene. This element contains the canonical hexameric DNA core motif, 5'-PuGGTCA, composed of an atypically spaced direct repeat (DR17). Schistosome nuclear receptors SmRXR1 and SmNR1 specifically bound to the p14-DR17 element as a heterodimer. SmRXR1, but not SmNR1, bound to the motif as a monomer. Introduction of mutations in the TCA core sequence completely abolished the binding by SmRXR1/SmNR1 heterodimer. This finding supports our hypothesis that the expression of Schistosoma mansonip14 gene is regulated through the nuclear receptor signaling pathway.

  9. Linkage disequilibrium in the insulin gene region is related to the exact number of repeat units present at the 5{prime} flanking polymorphism

    SciTech Connect

    McGinnis, R.E.; Spielman, R.S.

    1994-09-01

    Tandem DNA repeat units (RUs) located 5{prime} to the insulin (INS) gene give rise to a {open_quotes}5{prime} flanking polymorphism{close_quotes} (5{prime}FP) with minisatellite alleles belonging to 3 size classes. The shortest or {open_quotes}class 1{close_quotes} alleles (mean length of {approximately}40 RUs) are associated with insulin-dependent diabetes mellitus (IDDM), and the 5{prime}FP is one of several INS region loci in strong linkage disequilibrium with IDDM. We have amplified class 1 alleles and have determined the exact number of RUs in individual class 1 alleles found in parents of 50 IDDM families. We also obtained INS region haplotypes by typing two loci near tyrosine hydroxylase (TH) and two loci near insulin-like growth factor II (IGF2). We obtained these results: (1) Class 1 alleles (n=101) were found at every integer length from 30 to 44 RUs, the lengths of smallest and largest class 1 alleles observed. The allele frequency distribution was trimodal with peaks at 31, 40 and 42 RUs; 18%, 34% and 48% of the alleles belonged to the three components, respectively. (2) Allelic variation at each flanking locus was highly associated with the exact number of RUs present at the 5{prime}FP. Our results suggest that creation of new 5{prime}FP or other minisatellite haplotypes may be {open_quotes}constrained{close_quotes} in that flanking alleles usually become associated with a new minisatellite length different by only one or two RUs. Furthermore, since many flanking alleles were associated with a single narrow range of class 1 integer lengths, determining exact RU length may aid in visualizing linkage disequilibrium and allelic associations involving other minisatellite loci.

  10. High molecular weight β-poly(L-malic acid) produced by A. pullulans with Ca²⁺ added repeated batch culture.

    PubMed

    Cao, Weifeng; Chen, Xiangrong; Luo, Jianquan; Yin, Junxiang; Qiao, Changsheng; Wan, Yinhua

    2016-04-01

    β-Poly(malic acid) (PMLA) has attracted increasing attentions because of its potential application in medicine and other industries. In this study, the variation of PMLA molecular weight (Mw) in the batch culture and the strategies to enhance PMLA Mw were studied. Adding exogenous Ca(2+) (0.1g/L CaCl2) to the medium caused a significant increase in both PMLA concentration and Mw (11.38% and 26.3%, respectively) when Na2CO3 was used as the neutralizer. The Mw of PMLA during the process of batch culture, which associated with the specific PMLA production per unit cell mass (Yp/x) before glucose was depleted, increased from 12.522 KDa to its maximum 18.693 KDa and then kept decreasing until the end of the culture. Compared with the results in batch culture, Mw increased by 84.4% (up to 19.51 kDa) with a productivity of 1.1 gh(-1)L(-1) when the cells were maintained in exponential growth phase during Ca(2+) added repeated batch culture. The present work provides an efficient approach to obtain superior quality PMLA product with high Mw.

  11. Repeated ketamine administration alters N-methyl-D-aspartic acid receptor subunit gene expression: implication of genetic vulnerability for ketamine abuse and ketamine psychosis in humans.

    PubMed

    Xu, Ke; Lipsky, Robert H

    2015-02-01

    For more than 40 years following its approval by the Food and Drug Administration (FDA) as an anesthetic, ketamine, a non-competitive N-methyl-D-aspartic acid (NMDA) receptor antagonist, has been used as a tool of psychiatric research. As a psychedelic drug, ketamine induces psychotic symptoms, cognitive impairment, and mood elevation, which resemble some symptoms of schizophrenia. Recreational use of ketamine has been increasing in recent years. However, little is known of the underlying molecular mechanisms responsible for ketamine-associated psychosis. Recent animal studies have shown that repeated ketamine administration significantly increases NMDA receptor subunit gene expression, in particular subunit 1 (NR1 or GluN1) levels. This results in neurodegeneration, supporting a potential mechanism where up-regulation of NMDA receptors could produce cognitive deficits in chronic ketamine abuse patients. In other studies, NMDA receptor gene variants are associated with addictive behavior. Here, we focus on the roles of NMDA receptor gene subunits in ketamine abuse and ketamine psychosis and propose that full sequencing of NMDA receptor genes may help explain individual vulnerability to ketamine abuse and ketamine-associated psychosis.

  12. Monitoring the regional ocean circulation around New Caledonia from a combination of repeated glider measurements and other in situ observing systems

    NASA Astrophysics Data System (ADS)

    Marin, Frédéric; Fuda, Jean-Luc; Durand, Fabien; Terre, Thierry; Panché, Jean-Yves; Mahiouz, Karim; Béguery, Laurent

    2013-04-01

    The South-West Pacific basin is a key region for the ocean circulation and the climate system of the tropical Pacific. First it is the region where a broad westward-flowing current - the South Equatorial Current - encounters a large number of islands and subdivides into multiple intense zonal jets. Second it is the region where thermocline waters of subtropical origin transit in their route towards the equator, giving to this area a potential role for the low-frequency modulation of El Niño - Southern Oscillation (ENSO). The main objective of the present poster is to describe a multi-observational program (AltiGlidEx) to monitor two major currents of the South-West Pacific ocean - the East Caledonian Current and the South Caledonian Jet - that flow respectively along the East coast of New Caledonia (167°E-168°E, 22°S-17°S) and South of New Caledonia (27°S-23°S). One expected achievement of the AltiGlidEx program is to provide a platform of multiple in situ observations, including repeated sections with SLOCUM and SPRAY gliders, a long-term subsurface current mooring and dedicated cruises, to ultimately assess the performance of the new AltiKa altimeter - that will be embarked on the SARAL satellite in 2013 - to observe swift boundary currents near the coast of New Caledonia in 2013-2014. This program takes full advantage of the potential of gliders to estimate (i) the geostrophic component of the velocity from the surface down to 1000 meters from hydrological measurements and (ii) the depth-averaged currents during each dive through the GPS-derived dead-reckoning of the vehicle (based on the comparison of the total horizontal distance during each dive that can be computed from the GPS positions of the diving/surfacing points with the one that would be expected in the absence of ocean currents from a flight model, once an adequate flight model is known for the glider). In this presentation, the preliminary results of the first 3 glider experiments (2010, 2011

  13. RepeatsDB: a database of tandem repeat protein structures

    PubMed Central

    Di Domenico, Tomás; Potenza, Emilio; Walsh, Ian; Gonzalo Parra, R.; Giollo, Manuel; Minervini, Giovanni; Piovesan, Damiano; Ihsan, Awais; Ferrari, Carlo; Kajava, Andrey V.; Tosatto, Silvio C.E.

    2014-01-01

    RepeatsDB (http://repeatsdb.bio.unipd.it/) is a database of annotated tandem repeat protein structures. Tandem repeats pose a difficult problem for the analysis of protein structures, as the underlying sequence can be highly degenerate. Several repeat types haven been studied over the years, but their annotation was done in a case-by-case basis, thus making large-scale analysis difficult. We developed RepeatsDB to fill this gap. Using state-of-the-art repeat detection methods and manual curation, we systematically annotated the Protein Data Bank, predicting 10 745 repeat structures. In all, 2797 structures were classified according to a recently proposed classification schema, which was expanded to accommodate new findings. In addition, detailed annotations were performed in a subset of 321 proteins. These annotations feature information on start and end positions for the repeat regions and units. RepeatsDB is an ongoing effort to systematically classify and annotate structural protein repeats in a consistent way. It provides users with the possibility to access and download high-quality datasets either interactively or programmatically through web services. PMID:24311564

  14. Yin Yang 1, Oct1, and NFAT-4 form repeating, cyclosporin-sensitive regulatory modules within the murine CD21 intronic control region.

    PubMed

    Zabel, Mark D; Wheeler, Wells; Weis, Janis J; Weis, John H

    2002-04-01

    The murine complement receptor type 2 gene (Cr2/CD21) is expressed by murine B and follicular dendritic cells, but not murine T cells. We have previously shown that appropriate transcriptional control of the CD21 gene requires the CD21 promoter as well as intronic sequences. We have also demonstrated that altering chromatin structure by inhibiting histone deacetylases induces CD21 expression in murine T cells by increasing the accessibility of promoter and intronic regulatory elements. In this report, we identify seven distinct regulatory areas within the first intron of the murine CD21 gene that are conserved between mouse and human CD21 intronic sequences. EMSA competition and supershift analyses reveal the formation of multiple DNA-protein complexes at these sites that include Yin Yang 1, Oct1, and NFAT-4. NFAT-containing complexes were altered in B cells treated with the NFAT inhibitor cyclosporin A and correlated with a repression of CD21 gene transcription implicating NFAT transcriptional control. Functional data revealed that no single region conferred cell-specific reporter gene expression, but rather the entire CD21 regulatory element was required to confer cell-specific gene expression. Taken together, these data demonstrate the formation of repeating, overlapping regulatory modules, all of which are required to coordinately control the cell-specific expression of the murine CD21 gene. We propose a model in which Yin Yang 1 and Oct1 may recruit histone deacetylase to multiple sites in the CD21 intronic regulatory element in nonexpressing cells and NFAT either displaces this histone deacetylase or recruits a histone acetylase to allow the formation of a functional transcriptional complex in expressing cells.

  15. HIV-1 Induced Nuclear Factor I-B (NF-IB) Expression Negatively Regulates HIV-1 Replication through Interaction with the Long Terminal Repeat Region

    PubMed Central

    Vemula, Sai Vikram; Veerasamy, Ravichandran; Ragupathy, Viswanath; Biswas, Santanu; Devadas, Krishnakumar; Hewlett, Indira

    2015-01-01

    Background: Retroviruses rely on host factors for cell entry, replication, transcription, and other major steps during their life cycle. Human Immunodeficiency Virus-1 (HIV-1) is well known for utilizing a plethora of strategies to evade the host immune response, including the establishment of latent infection within a subpopulation of susceptible cells. HIV-1 also manipulates cellular factors in latently infected cells and persists for long periods of time, despite the presence of successful highly active antiretroviral therapy (HAART). Results: In this study we demonstrate that Nuclear Factor-IB (NF-IB) is induced during HIV-1 infection and its expression negatively impacts viral replication. During HIV-1 infection in peripheral blood mononuclear cells (PBMCs), and the T cell line, Jurkat or during induction of virus replication in latently infected cells, ACH2 and J1.1, we observed a time-dependent alteration in NF-IB expression pattern that correlated with HIV-1 viral expression. Using the Chip assay, we observed an association of NF-IB with the long terminal repeat region of HIV-1 (LTR) (-386 to -453 nt), and this association negatively correlated with HIV-1 transcription. Furthermore, knock-down of NF-IB levels in J1.1 cells resulted in an increase of HIV-1 levels. Knock-down of NF-IB levels in J-Lat-Tat-GFP (A1), (a Jurkat cell GFP reporter model for latent HIV-1 infection) resulted in an increase in GFP levels, indicating a potential negative regulatory role of NF-IB in HIV-1 replication. Conclusion: Overall, our results suggest that NF-IB may play a role in intrinsic antiretroviral defenses against HIV-1. These observations may offer new insights into the correlation of the latently infected host cell types and HIV-1, and help to define new therapeutic approaches for triggering the switch from latency to active replication thereby eliminating HIV-1 latent infection. PMID:25664610

  16. Regional trends in soil acidification and exchangeable metal concentrations in relation to acid deposition rates.

    PubMed

    Stevens, Carly J; Dise, Nancy B; Gowing, David J

    2009-01-01

    The deposition of high levels of reactive nitrogen (N) and sulphur (S), or the legacy of that deposition, remain among the world's most important environmental problems. Although regional impacts of acid deposition in aquatic ecosystems have been well documented, quantitative evidence of wide-scale impacts on terrestrial ecosystems is not common. In this study we analysed surface and subsoil chemistry of 68 acid grassland sites across the UK along a gradient of acid deposition, and statistically related the concentrations of exchangeable soil metals (1 M KCl extraction) to a range of potential drivers. The deposition of N, S or acid deposition was the primary correlate for 8 of 13 exchangeable metals measured in the topsoil and 5 of 14 exchangeable metals in the subsoil. In particular, exchangeable aluminium and lead both show increased levels above a soil pH threshold of about 4.5, strongly related to the deposition flux of acid compounds.

  17. Repeat length variation in the 5'UTR of myo-inositol monophosphatase gene is related to phytic acid content and contributes to drought tolerance in chickpea (Cicer arietinum L.).

    PubMed

    Joshi-Saha, Archana; Reddy, Kandali S

    2015-09-01

    Myo-inositol metabolism plays a significant role in plant growth and development, and is also used as a precursor for many important metabolites, such as ascorbate, pinitol, and phytate. Phytate (inositol hexakisphosphate) is the major storage pool for phosphate in the seeds. It is utilized during seed germination and growth of the developing embryo. In addition, it is implicated in protection against oxidative stress. In the present study, a panel of chickpea accessions was used for an association analysis. Association analysis accounting for population structure and relative kinship identified alleles of a simple sequence repeat marker, NCPGR90, that are associated with both phytic acid content and drought tolerance. These alleles varied with respect to the dinucleotide CT repeats present within the marker. NCPGR90 located to the 5'UTR of chickpea myo-inositol monophosphatase gene (CaIMP) and showed transcript length variation in drought-tolerant and drought-susceptible accessions. CaIMP from a drought-tolerant accession with a smaller repeat was almost 2-fold upregulated as compared to a susceptible accession having a longer repeat, even under control non-stressed conditions. This study suggests an evolution of simple sequence repeat length variation in CaIMP, which might be regulating phytic acid levels to confer drought tolerance in natural populations of chickpea.

  18. Acid rain: neutralization within the hubbard brook ecosystem and regional implications.

    PubMed

    Johnson, N M

    1979-05-01

    The neutralization of strong acids from precipitation is largely accomplished (75 percent) in the soil zone by rapid reaction with basic aluminum salts and biologic matter. On a regional basis, acidified and aluminum-rich lakes and streams in New England are confined mainly to low-order watersheds.

  19. The complete chloroplast genome sequence of Taxus chinensis var. mairei (Taxaceae): loss of an inverted repeat region and comparative analysis with related species.

    PubMed

    Zhang, Yanzhen; Ma, Ji; Yang, Bingxian; Li, Ruyi; Zhu, Wei; Sun, Lianli; Tian, Jingkui; Zhang, Lin

    2014-05-01

    Taxus chinensis var. mairei (Taxaceae) is a domestic variety of yew species in local China. This plant is one of the sources for paclitaxel, which is a promising antineoplastic chemotherapy drugs during the last decade. We have sequenced the complete nucleotide sequence of the chloroplast (cp) genome of T. chinensis var. mairei. The T. chinensis var. mairei cp genome is 129,513 bp in length, with 113 single copy genes and two duplicated genes (trnI-CAU, trnQ-UUG). Among the 113 single copy genes, 9 are intron-containing. Compared to other land plant cp genomes, the T. chinensis var. mairei cp genome has lost one of the large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperm such as Cycas revoluta and Ginkgo biloba L. Compared to related species, the gene order of T. chinensis var. mairei has a large inversion of ~110kb including 91 genes (from rps18 to accD) with gene contents unarranged. Repeat analysis identified 48 direct and 2 inverted repeats 30 bp long or longer with a sequence identity greater than 90%. Repeated short segments were found in genes rps18, rps19 and clpP. Analysis also revealed 22 simple sequence repeat (SSR) loci and almost all are composed of A or T.

  20. Transgenic retinoic acid sensor lines in zebrafish indicate regions of available embryonic retinoic acid

    PubMed Central

    Mandal, Amrita; Rydeen, Ariel; Anderson, Jane; Sorrell, Mollie R.J.; Zygmunt, Tomas; Torres-Vázquez, Jesús; Waxman, Joshua S.

    2013-01-01

    Background Retinoic acid (RA) signaling plays a critical role in vertebrate development. Transcriptional reporters of RA signaling in zebrafish, thus far, have not reflected the broader availability of embryonic RA, necessitating additional tools to enhance our understanding of the spatial and temporal activity of RA signaling in vivo. Results We have generated novel transgenic RA sensors in which a RA receptor (RAR) ligand-binding domain (RLBD) is fused to the Gal4 DNA binding domain (GDBD) or a VP16-GDBD (VPBD) construct. Stable transgenic lines expressing these proteins when crossed with UAS reporter lines are responsive to RA. Interestingly, the VPBD RA sensor is significantly more sensitive than the GDBD sensor and demonstrates there may be almost ubiquitous availability of RA within the early embryo. Using confocal microscopy to compare the expression of the GDBD RA sensor to our previously established RA signaling transcriptional reporter line, Tg(12XRARE:EGFP), illustrates these reporters have significant overlap, but that expression from the RA sensor is much broader. We also identify previously unreported domains of expression for the Tg(12XRARE:EGFP) line. Conclusions Our novel RA sensor lines will be useful and complementary tools for studying RA signaling during development and anatomical structures independent of RA signaling. PMID:23703807

  1. Investigation of secondary formation of formic acid: urban environment vs. oil and gas producing region

    NASA Astrophysics Data System (ADS)

    Yuan, B.; Veres, P. R.; Warneke, C.; Roberts, J. M.; Gilman, J. B.; Koss, A.; Edwards, P. M.; Graus, M.; Kuster, W. C.; Li, S.-M.; Wild, R. J.; Brown, S. S.; Dubé, W. P.; Lerner, B. M.; Williams, E. J.; Johnson, J. E.; Quinn, P. K.; Bates, T. S.; Lefer, B.; Hayes, P. L.; Jimenez, J. L.; Weber, R. J.; Zamora, R.; Ervens, B.; Millet, D. B.; Rappenglück, B.; de Gouw, J. A.

    2015-02-01

    Formic acid (HCOOH) is one of the most abundant carboxylic acids in the atmosphere. However, current photochemical models cannot fully explain observed concentrations and in particular secondary formation of formic acid across various environments. In this work, formic acid measurements made at an urban receptor site (Pasadena) in June-July 2010 during CalNex (California Research at the Nexus of Air Quality and Climate Change) and a site in an oil and gas producing region (Uintah Basin) in January-February 2013 during UBWOS 2013 (Uintah Basin Winter Ozone Studies) will be discussed. Although the VOC (volatile organic compounds) compositions differed dramatically at the two sites, measured formic acid concentrations were comparable: 2.3 ± 1.3 in UBWOS 2013 and 2.0 ± 1.0 ppb in CalNex. We determine that concentrations of formic acid at both sites were dominated by secondary formation (> 99%). A constrained box model using the Master Chemical Mechanism (MCM v3.2) underestimates the measured formic acid concentrations drastically at both sites (by a factor of > 10). Compared to the original MCM model that includes only ozonolysis of unsaturated organic compounds and OH oxidation of acetylene, when we updated yields of ozonolysis of alkenes and included OH oxidation of isoprene, vinyl alcohol chemistry, reaction of formaldehyde with HO2, oxidation of aromatics, and reaction of CH3O2 with OH, the model predictions for formic acid were improved by a factor of 6.4 in UBWOS 2013 and 4.5 in CalNex, respectively. A comparison of measured and modeled HCOOH/acetone ratios is used to evaluate the model performance for formic acid. We conclude that the modified chemical mechanism can explain 19 and 45% of secondary formation of formic acid in UBWOS 2013 and CalNex, respectively. The contributions from aqueous reactions in aerosol and heterogeneous reactions on aerosol surface to formic acid are estimated to be 0-6 and 0-5% in UBWOS 2013 and CalNex, respectively. We observe that

  2. Acid rain phenomenon in niger delta region of Nigeria: economic, biodiversity, and public health concern.

    PubMed

    Nduka, J K C; Orisakwe, O E; Ezenweke, L O; Ezenwa, T E; Chendo, M N; Ezeabasili, N G

    2008-01-01

    Rain samples were collected from Warri and Port Harcourt, two major oil-producing cities of Nigeria in April-June, July-August, and September-October 2005 and 2006. Awka, a "non-oil" city was used as control. Samples were collected from three points, using clean plastic basins fastened to a table, 2 m above ground level and 115 m away from tall buildings and trees. Water samples were filtered and acidity determined using digital pH meter. The results show that the rain samples were acidic. The pH values for the 2 years under study show that the rainfall in Warri was more acidic than that of Port Harcourt. Oil exploration and other anthropogenic sources may be responsible for the acid rain in the Niger Delta region of Nigeria.

  3. Use of Soil-Streamwater Relationships to Assess Regional Patterns of Recovery from Acidic Deposition Effects

    NASA Astrophysics Data System (ADS)

    Siemion, J.; Lawrence, G. B.; Murdoch, P. S.

    2012-12-01

    Declines of acidic deposition levels by as much as 50% since 1990 have led to partial recovery of surface waters in the Northeastern United States, but continued depletion of soil calcium through this same period suggests a disconnection between soil and surface water chemistry. To investigate the role of soil-surface water interactions in recovery from acidification, the first regional survey to directly relate soil chemistry to stream chemistry during high flow was implemented in the Catskill region of New York, where acidic deposition levels are among the highest in the East. More than 40% of streams sampled in the southwestern Catskill Mountains were determined to be acidified with inorganic monomeric aluminum concentrations that exceeded a threshold that is toxic to aquatic biota and more than 80% likely to exceed this threshold during the highest flows, but less than 10% were acidified in the northwestern portion of the region. Median Oa horizon soil base saturation ranged from 50-80% across the region, but median base saturation in the upper 10cm of the B horizon was less than 20% across the region and was only 2% in the southwestern area. Therefore, aluminum is likely to be interfering with calcium uptake in the mineral horizon by trees in half the watersheds where soils were collected. These results indicate stream chemistry over the Catskill region does not reflect the calcuim depletion of the B horizon that our sampling suggests is ubiquitous throughout the region.

  4. The central leucine-rich repeat region of chicken TLR16 dictates unique ligand specificity and species-specific interaction with TLR2.

    PubMed

    Keestra, A Marijke; de Zoete, Marcel R; van Aubel, Rémon A M H; van Putten, Jos P M

    2007-06-01

    The ligand specificity of human TLR (hTLR) 2 is determined through the formation of functional heterodimers with either hTLR1 or hTLR6. The chicken carries two TLR (chTLR) 2 isoforms, type 1 and type 2 (chTLR2t1 and chTLR2t2), and one putative TLR1/6/10 homologue (chTLR16) of unknown function. In this study, we report that transfection of HeLa cells with the various chicken receptors yields potent NF-kappaB activation for the receptor combination of chTLR2t2 and chTLR16 only. The sensitivity of this complex was strongly enhanced by human CD14. The functional chTLR16/chTLR2t2 complex responded toward both the hTLR2/6-specific diacylated peptide S-(2,3-bispalmitoyloxypropyl)-Cys-Gly-Asp-Pro-Lys-His-Pro-Lys-Ser-Phe (FSL-1) and the hTLR2/1 specific triacylated peptide tripalmitoyl-S-(bis(palmitoyloxy)propyl)-Cys-Ser-(Lys)(3)-Lys (Pam(3)CSK(4)), indicating that chTLR16 covers the functions of both mammalian TLR1 and TLR6. Dissection of the species specificity of TLR2 and its coreceptors showed functional chTLR16 complex formation with chTLR2t2 but not hTLR2. Conversely, chTLR2t2 did not function in combination with hTLR1 or hTLR6. The use of constructed chimeric receptors in which the defined domains of chTLR16 and hTLR1 or hTLR6 had been exchanged revealed that the transfer of leucine-rich repeats (LRR) 6-16 of chTLR16 into hTLR6 was sufficient to confer dual ligand specificity to the human receptor and to establish species-specific interaction with chTLR2t2. Collectively, our data indicate that diversification of the central LRR region of the TLR2 coreceptors during evolution has put constraints on both their ligand specificity and their ability to form functional complexes with TLR2. PMID:17513760

  5. Molecular characterization of an acidic region deletion mutant of Cockayne syndrome group B protein.

    PubMed

    Sunesen, M; Selzer, R R; Brosh, R M; Balajee, A S; Stevnsner, T; Bohr, V A

    2000-08-15

    Cockayne syndrome (CS) is a human genetic disorder characterized by post-natal growth failure, neurological abnormalities and premature aging. CS cells exhibit high sensitivity to UV light, delayed RNA synthesis recovery after UV irradiation and defective transcription-coupled repair (TCR). Two genetic complementation groups of CS have been identified, designated CS-A and CS-B. The CSB gene encodes a helicase domain and a highly acidic region N-terminal to the helicase domain. This study describes the genetic characterization of a CSB mutant allele encoding a full deletion of the acidic region. We have tested its ability to complement the sensitivity of UV61, the hamster homolog of human CS-B cells, to UV and the genotoxic agent N-acetoxy-2-acetylaminofluorene (NA-AAF). Deleting 39 consecutive amino acids, of which approximately 60% are negatively charged, did not impact on the ability of the protein to complement the sensitive phenotype of UV61 cells to either UV or NA-AAF. Our data indicate that the highly acidic region of CSB is not essential for the TCR and general genome repair pathways of UV- and NA-AAF-induced DNA lesions. PMID:10931931

  6. The minimal transactivation region of Saccharomyces cerevisiae Gln3p is localized to 13 amino acids.

    PubMed Central

    Svetlov, V; Cooper, T G

    1997-01-01

    Regulated nitrogen catabolic gene transcription in Saccharomyces cerevisiae is mediated by four positive (Gln3p and Gat1p/Nil1p) and negative (Dal80p/Uga43p and Deh1p/Nil2p/GZF3p) regulators which function in opposition to one another. All four proteins contain GATA-type zinc finger domains, and three of them (Gln3p, Dal80p, and Deh1p) have been shown to bind to GATA sequences situated upstream of genes whose expression is sensitive to nitrogen catabolite repression (NCR). The positive regulators, Gln3p and Gat1p, are able to support transcriptional activation when tethered by LexAp to the promoter of a reporter gene whose upstream activation sequences have been replaced with one or more lexA operator sites. Existing data suggest that these four proteins regulate transcription by competing with one another for binding to the GATA sequences which mediate NCR-sensitive gene expression. We show that the minimal Gln3p domain mediating transcriptional activation consists of 13 amino acids with a predicted propensity to form an alpha-helix. Genetic analysis of this region (Gln3p residues 126 to 138, QQNGEIAQLWDFN) demonstrated that alanine may be substituted for the aromatic and acidic amino acids without destroying transcriptional activation potential. Similar substitution of alanine for the two hydrophobic amino acids, isoleucine and leucine, however, destroys activation, as does introduction of basic amino acids in place of the acidic residues or introduction of proline into the center of the sequence. A point mutation in the Gln3p activation region destroys its in vivo ability to support NCR-sensitive DAL5 expression. We find no convincing evidence that NCR regulates Gln3p function by modulating the functioning of its activation region. PMID:9401021

  7. Regional anomalies in chronic obstructive pulmonary disease; comparison with acid air pollution particulate characteristics.

    PubMed

    Winchester, J W

    1989-01-01

    Mortality rates due to chronic obstructive pulmonary disease (COPD) for males and females in standard metropolitan statistical areas are highest in two broad regions of the U.S. One is the southeast, with age-adjusted rates high in Georgia and north Florida but decreasing toward south Florida; the other is the western plains, with rates high in Colorado and north Texas but decreasing toward south Texas. Rates are generally low in the northeast, upper midwest, and far west, as well as in the largest cities of these regions. These geographic patterns suggest that atmospheric environmental conditions may contribute to the risk of COPD. Based on measured aerosol characteristics and atmospheric chemical reasoning, it is argued that ambient air in the high COPD regions may be especially irritating to the respiratory tract because of fine particles that contain the reaction products of acid air pollutants. In the southeast, sulfuric acid aerosol concentrations are high, apparently because of a sunny warm humid climate that favors rapid oxidation of sulfur dioxide as well as the region's proximity to large primary air pollution sources further north. Particulate sulfur is also associated with soil mineral constituents. In the western plains, concentrations of alkaline dust are high because of soil erosion during windy dry conditions. Acid air pollutants can be scavenged to mineral particle surfaces and form chemical reaction products that may include solubilized mineral aluminum. These may be inhaled and deposited in the respiratory tract so as to contribute to COPD mortality risk.

  8. Characterization of DNA sequences that mediate nuclear protein binding to the regulatory region of the Pisum sativum (pea) chlorophyl a/b binding protein gene AB80: identification of a repeated heptamer motif.

    PubMed

    Argüello, G; García-Hernández, E; Sánchez, M; Gariglio, P; Herrera-Estrella, L; Simpson, J

    1992-05-01

    Two protein factors binding to the regulatory region of the pea chlorophyl a/b binding protein gene AB80 have been identified. One of these factors is found only in green tissue but not in etiolated or root tissue. The second factor (denominated ABF-2) binds to a DNA sequence element that contains a direct heptamer repeat TCTCAAA. It was found that presence of both of the repeats is essential for binding. ABF-2 is present in both green and etiolated tissue and in roots and factors analogous to ABF-2 are present in several plant species. Computer analysis showed that the TCTCAAA motif is present in the regulatory region of several plant genes. PMID:1303797

  9. NONLINEARITIES IN THE SULFATE SECONDARY FINE PARTICULATE RESPONSE TO NOX EMISSIONS REDUCTIONS AS MODELED BY THE REGIONAL ACID DEPOSITION MODEL

    EPA Science Inventory

    Attention is increasingly being devoted to the health effects of fine particulates. In regions that have a large production of sulfate, sulfuric acid and nitric acid compete for the available ammonia to form aerosols. In addition, the available nitric acid is the result of ur...

  10. Protein Repeats from First Principles.

    PubMed

    Turjanski, Pablo; Parra, R Gonzalo; Espada, Rocío; Becher, Verónica; Ferreiro, Diego U

    2016-01-01

    Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family. PMID:27044676

  11. Protein Repeats from First Principles.

    PubMed

    Turjanski, Pablo; Parra, R Gonzalo; Espada, Rocío; Becher, Verónica; Ferreiro, Diego U

    2016-04-05

    Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family.

  12. Protein Repeats from First Principles

    PubMed Central

    Turjanski, Pablo; Parra, R. Gonzalo; Espada, Rocío; Becher, Verónica; Ferreiro, Diego U.

    2016-01-01

    Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repeating patterns within a single repeat protein can be extremely variable at the sequence level. We use a mathematical definition of a repetition and investigate the occurrences of these in sequences of different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness. We show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast quantification of the likelihood of a protein to belong to a family. PMID:27044676

  13. Use of stream chemistry for monitoring acidic deposition effects in the Adirondack region of New York

    USGS Publications Warehouse

    Lawrence, G.B.; Momen, B.; Roy, K.M.

    2004-01-01

    Acid-neutralizing capacity (ANC) and pH were measured weekly from October 1991 through September 2001 in three streams in the western Adirondack Mountain region of New York to identify trends in stream chemistry that might be related to changes in acidic deposition. A decreasing trend in atmospheric deposition of SO42- was observed within the region over the 10-yr period, although most of the decrease occurred between 1991 and 1995. Both ANC and pH were inversely related to flow in all streams; therefore, a trend analysis was conducted on (i) the measured values of ANC and pH and (ii) the residuals of the concentration-discharge relations. In Buck Creek, ANC increased significantly (p 0.10). In Bald Mountain Brook, ANC and residuals of ANC increased significantly (p < 0.01), although the trend was diatonic-a distinct decrease from 1991 to 1996 was followed by a distinct increase from 1996 to 2001. In Fly Pond outlet, ANC and residuals of ANC increased over the study period (p < 0.01), although the trend of the residuals resulted largely from an abrupt increase in 1997. In general, the trends observed in the three streams are similar to results presented for Adirondack lakes in a previous study, and are consistent with the declining trend in atmospheric deposition for this region, although the observed trends in ANC and pH in streams could not be directly attributed to the trends in acidic deposition.

  14. Bovine chromosomal regions affecting rheological traits in acid-induced skim milk gels.

    PubMed

    Glantz, M; Gustavsson, F; Bertelsen, H P; Stålhammar, H; Lindmark-Månsson, H; Paulsson, M; Bendixen, C; Gregersen, V R

    2015-02-01

    The production of fermented milk products has increased worldwide during the last decade and is expected to continue to increase during the coming decade. The quality of these products may be optimized through breeding practices; however, the relations between cow genetics and technological properties of acid milk gels are not fully known. Therefore, the aim of this study was to identify chromosomal regions affecting acid-induced coagulation properties and possible candidate genes. Skim milk samples from 377 Swedish Red cows were rheologically analyzed for acid-induced coagulation properties using low-amplitude oscillation measurements. The resulting traits, including gel strength, coagulation time, and yield stress, were used to conduct a genome-wide association study. Single nucleotide polymorphisms (SNP) were identified using the BovineHD SNPChip (Illumina Inc., San Diego, CA), resulting in almost 621,000 segregating markers. The genome was scanned for putative quantitative trait loci (QTL) regions, haplotypes based on highly associated SNP were inferred, and the additive genetic effects of haplotypes within each QTL region were analyzed using mixed models. A total of 8 genomic regions were identified, with large effects of the significant haplotype explaining between 4.8 and 9.8% of the phenotypic variance of the studied traits. One major QTL was identified to overlap between gel strength and yield stress, the QTL identified with the most significant SNP closest to the gene coding for κ-casein (CSN3). In addition, a chromosome-wide significant region affecting yield stress on BTA 11 was identified to be colocated with PAEP, coding for β-lactoglobulin. Furthermore, the coagulation properties of the genetic variants within the 2 genes were compared with the coagulation properties identified by the patterns of the haplotypes within the regions, and it was discovered that the haplotypes were more diverse and in one case slightly better at explaining the

  15. Repeat-until-success quantum repeaters

    NASA Astrophysics Data System (ADS)

    Bruschi, David Edward; Barlow, Thomas M.; Razavi, Mohsen; Beige, Almut

    2014-09-01

    We propose a repeat-until-success protocol to improve the performance of probabilistic quantum repeaters. Conventionally, these rely on passive static linear-optics elements and photodetectors to perform Bell-state measurements (BSMs) with a maximum success rate of 50%. This is a strong impediment for entanglement swapping between distant quantum memories. Every time a BSM fails, entanglement needs to be redistributed between the corresponding memories in the repeater link. The key ingredients of our scheme are repeatable BSMs. Under ideal conditions, these turn probabilistic quantum repeaters into deterministic ones. Under realistic conditions, our protocol too might fail. However, using additional threshold detectors now allows us to improve the entanglement generation rate by almost orders of magnitude, at a nominal distance of 1000 km, compared to schemes that rely on conventional BSMs. This improvement is sufficient to make the performance of our scheme comparable to the expected performance of some deterministic quantum repeaters.

  16. Amino acid residues 201-205 in C-terminal acidic tail region plays a crucial role in antibacterial activity of HMGB1

    PubMed Central

    2009-01-01

    Background Antibacterial activity is a novel function of high-mobility group box 1 (HMGB1). However, the functional site for this new effect is presently unknown. Methods and Results In this study, recombinant human HMGB1 A box and B box (rHMGB1 A box, rHMGB1 B box), recombinant human HMGB1 (rHMGB1) and the truncated C-terminal acidic tail mutant (tHMGB1) were prepared by the prokaryotic expression system. The C-terminal acidic tail (C peptide) was synthesized, which was composed of 30 amino acid residues. Antibacterial assays showed that both the full length rHMGB1 and the synthetic C peptide alone could efficiently inhibit bacteria proliferation, but rHMGB1 A box and B box, and tHMGB1 lacking the C-terminal acidic tail had no antibacterial function. These results suggest that C-terminal acidic tail is the key region for the antibacterial activity of HMGB1. Furthermore, we prepared eleven different deleted mutants lacking several amino acid residues in C-terminal acidic tail of HMGB1. Antibacterial assays of these mutants demonstrate that the amino acid residues 201-205 in C-terminal acidic tail region is the core functional site for the antibacterial activity of the molecule. Conclusion In sum, these results define the key region and the crucial site in HMGB1 for its antibacterial function, which is helpful to illustrating the antibacterial mechanisms of HMGB1. PMID:19751520

  17. Fibronectin Binding to the Salmonella enterica Serotype Typhimurium ShdA Autotransporter Protein Is Inhibited by a Monoclonal Antibody Recognizing the A3 Repeat

    PubMed Central

    Kingsley, Robert A.; Abi Ghanem, Daad; Puebla-Osorio, Nahum; Keestra, A. Marijke; Berghman, Luc; Bäumler, Andreas J.

    2004-01-01

    ShdA is a large outer membrane protein of the autotransporter family whose passenger domain binds the extracellular matrix proteins fibronectin and collagen I, possibly by mimicking the host ligand heparin. The ShdA passenger domain consists of ∼1,500 amino acid residues that can be divided into two regions based on features of the primary amino acid sequence: an N-terminal nonrepeat region followed by a repeat region composed of two types of imperfect direct amino acid repeats, called type A and type B. The repeat region bound bovine fibronectin with an affinity similar to that for the complete ShdA passenger domain, while the nonrepeat region exhibited comparatively low fibronectin-binding activity. A number of fusion proteins containing truncated fragments of the repeat region did not bind bovine fibronectin. However, binding of the passenger domain to fibronectin was inhibited in the presence of immune serum raised to one truncated fragment of the repeat region that contained repeats A2, B8, A3, and B9. Furthermore, a monoclonal antibody that specifically recognized an epitope in a recombinant protein containing the A3 repeat inhibited binding of ShdA to fibronectin. PMID:15262930

  18. Fibronectin binding to the Salmonella enterica serotype Typhimurium ShdA autotransporter protein is inhibited by a monoclonal antibody recognizing the A3 repeat.

    PubMed

    Kingsley, Robert A; Abi Ghanem, Daad; Puebla-Osorio, Nahum; Keestra, A Marijke; Berghman, Luc; Bäumler, Andreas J

    2004-08-01

    ShdA is a large outer membrane protein of the autotransporter family whose passenger domain binds the extracellular matrix proteins fibronectin and collagen I, possibly by mimicking the host ligand heparin. The ShdA passenger domain consists of approximately 1,500 amino acid residues that can be divided into two regions based on features of the primary amino acid sequence: an N-terminal nonrepeat region followed by a repeat region composed of two types of imperfect direct amino acid repeats, called type A and type B. The repeat region bound bovine fibronectin with an affinity similar to that for the complete ShdA passenger domain, while the nonrepeat region exhibited comparatively low fibronectin-binding activity. A number of fusion proteins containing truncated fragments of the repeat region did not bind bovine fibronectin. However, binding of the passenger domain to fibronectin was inhibited in the presence of immune serum raised to one truncated fragment of the repeat region that contained repeats A2, B8, A3, and B9. Furthermore, a monoclonal antibody that specifically recognized an epitope in a recombinant protein containing the A3 repeat inhibited binding of ShdA to fibronectin. PMID:15262930

  19. A human sleep homeostasis phenotype in mice expressing a primate-specific PER3 variable-number tandem-repeat coding-region polymorphism.

    PubMed

    Hasan, Sibah; van der Veen, Daan R; Winsky-Sommerer, Raphaelle; Hogben, Alexandra; Laing, Emma E; Koentgen, Frank; Dijk, Derk-Jan; Archer, Simon N

    2014-06-01

    In humans, a primate-specific variable-number tandem-repeat (VNTR) polymorphism (4 or 5 repeats 54 nt in length) in the circadian gene PER3 is associated with differences in sleep timing and homeostatic responses to sleep loss. We investigated the effects of this polymorphism on circadian rhythmicity and sleep homeostasis by introducing the polymorphism into mice and assessing circadian and sleep parameters at baseline and during and after 12 h of sleep deprivation (SD). Microarray analysis was used to measure hypothalamic and cortical gene expression. Circadian behavior and sleep were normal at baseline. The response to SD of 2 electrophysiological markers of sleep homeostasis, electroencephalography (EEG) θ power during wakefulness and δ power during sleep, were greater in the Per3(5/5) mice. During recovery, the Per3(5/5) mice fully compensated for the SD-induced deficit in δ power, but the Per3(4/4) and wild-type mice did not. Sleep homeostasis-related transcripts (e.g., Homer1, Ptgs2, and Kcna2) were differentially expressed between the humanized mice, but circadian clock genes were not. These data are in accordance with the hypothesis derived from human data that the PER3 VNTR polymorphism modifies the sleep homeostatic response without significantly influencing circadian parameters.

  20. Regional Differentiation of Retinoic Acid-Induced Human Pluripotent Embryonic Carcinoma Stem Cell Neurons

    PubMed Central

    Coyle, Dennis E.; Li, Jie; Baccei, Mark

    2011-01-01

    The NTERA2 cl D1 (NT2) cell line, derived from human teratocarcinoma, exhibits similar properties as embryonic stem (ES) cells or very early neuroepitheial progenitors. NT2 cells can be induced to become postmitotic central nervous system neurons (NT2N) with retinoic acid. Although neurons derived from pluripotent cells, such as NT2N, have been characterized for their neurotransmitter phenotypes, their potential suitability as a donor source for neural transplantation also depends on their ability to respond to localized environmental cues from a specific region of the CNS. Therefore, our study aimed to characterize the regional transcription factors that define the rostocaudal and dorsoventral identity of NT2N derived from a monolayer differentiation paradigm using quantitative PCR (qPCR). Purified NT2N mainly expressed both GABAergic and glutamatergic phenotypes and were electrically active but did not form functional synapses. The presence of immature astrocytes and possible radial glial cells was noted. The NT2N expressed a regional transcription factor code consistent with forebrain, hindbrain and spinal cord neural progenitors but showed minimal expression of midbrain phenotypes. In the dorsoventral plane NT2N expressed both dorsal and ventral neural progenitors. Of major interest was that even under the influence of retinoic acid, a known caudalization factor, the NT2N population maintained a rostral phenotype subpopulation which expressed cortical regional transcription factors. It is proposed that understanding the regional differentiation bias of neurons derived from pluripotent stem cells will facilitate their successful integration into existing neuronal networks within the CNS. PMID:21283767

  1. Use of stream chemistry for monitoring acidic deposition effects in the Adirondack region of New York.

    PubMed

    Lawrence, Gregory B; Momen, Bahram; Roy, Karen M

    2004-01-01

    Acid-neutralizing capacity (ANC) and pH were measured weekly from October 1991 through September 2001 in three streams in the western Adirondack Mountain region of New York to identify trends in stream chemistry that might be related to changes in acidic deposition. A decreasing trend in atmospheric deposition of SO4/2- was observed within the region over the 10-yr period, although most of the decrease occurred between 1991 and 1995. Both ANC and pH were inversely related to flow in all streams; therefore, a trend analysis was conducted on (i) the measured values of ANC and pH and (ii) the residuals of the concentration-discharge relations. In Buck Creek, ANC increased significantly (p < 0.05) over the 10 yr, but the residuals of ANC showed no trend (p > 0.10). In Bald Mountain Brook, ANC and residuals of ANC increased significantly (p < 0.01), although the trend was diatonic-a distinct decrease from 1991 to 1996 was followed by a distinct increase from 1996 to 2001. In Fly Pond outlet, ANC and residuals of ANC increased over the study period (p < 0.01), although the trend of the residuals resulted largely from an abrupt increase in 1997. In general, the trends observed in the three streams are similar to results presented for Adirondack lakes in a previous study, and are consistent with the declining trend in atmospheric deposition for this region, although the observed trends in ANC and pH in streams could not be directly attributed to the trends in acidic deposition.

  2. Use of stream chemistry for monitoring acidic deposition effects in the Adirondack region of New York.

    PubMed

    Lawrence, Gregory B; Momen, Bahram; Roy, Karen M

    2004-01-01

    Acid-neutralizing capacity (ANC) and pH were measured weekly from October 1991 through September 2001 in three streams in the western Adirondack Mountain region of New York to identify trends in stream chemistry that might be related to changes in acidic deposition. A decreasing trend in atmospheric deposition of SO4/2- was observed within the region over the 10-yr period, although most of the decrease occurred between 1991 and 1995. Both ANC and pH were inversely related to flow in all streams; therefore, a trend analysis was conducted on (i) the measured values of ANC and pH and (ii) the residuals of the concentration-discharge relations. In Buck Creek, ANC increased significantly (p < 0.05) over the 10 yr, but the residuals of ANC showed no trend (p > 0.10). In Bald Mountain Brook, ANC and residuals of ANC increased significantly (p < 0.01), although the trend was diatonic-a distinct decrease from 1991 to 1996 was followed by a distinct increase from 1996 to 2001. In Fly Pond outlet, ANC and residuals of ANC increased over the study period (p < 0.01), although the trend of the residuals resulted largely from an abrupt increase in 1997. In general, the trends observed in the three streams are similar to results presented for Adirondack lakes in a previous study, and are consistent with the declining trend in atmospheric deposition for this region, although the observed trends in ANC and pH in streams could not be directly attributed to the trends in acidic deposition. PMID:15224937

  3. A Repeat Look at Repeating Patterns

    ERIC Educational Resources Information Center

    Markworth, Kimberly A.

    2016-01-01

    A "repeating pattern" is a cyclical repetition of an identifiable core. Children in the primary grades usually begin pattern work with fairly simple patterns, such as AB, ABC, or ABB patterns. The unique letters represent unique elements, whereas the sequence of letters represents the core that is repeated. Based on color, shape,…

  4. Repeating regional acute pancreatitis in the head of the pancreas caused by intraductal papillary mucinous neoplasms in the tail: report of a case.

    PubMed

    Asari, Sadaki; Matsumoto, Ippei; Toyama, Hirochika; Shinzeki, Makoto; Goto, Tadahiro; Shirakawa, Sachiyo; Yamada, Isamu; Ajiki, Tetsuo; Fukumoto, Takumi; Ito, Tomoo; Ku, Yonson

    2012-04-01

    Intraductal papillary mucinous neoplasm (IPMN) of the pancreas is a distinct entity characterized by papillary proliferations of mucin-producing epithelial cells with excessive mucin production and cystic dilatation of the pancreatic ducts. The clinical presentation often involves recurrent episodes of pancreatitis associated with the temporal obstruction of the main pancreatic duct caused by the hypersecretion of mucin. We herein describe a case in which the patient repeatedly experienced the occurrence of idiopathic acute pancreatitis in the head of the pancreas over a 9-year period, and who was ultimately was cured by distal pancreatectomy for IPMNs in the pancreatic tail. This case illustrates the potential pitfalls in the diagnosis of IPMNs owing to a discrepancy between the site of pancreatitis and that of the IPMN. The possible mechanisms linking acute pancreatitis with the formation of IPMNs are also reviewed.

  5. Sinapinic acid clusters distribution from monomer to mega Dalton's region in MALDI process

    NASA Astrophysics Data System (ADS)

    Lai, Szu-Hsueh; Chang, Kuang-Hua; Lin, Jung-Lee; Wu, Chia-Lin; Chen, Chung-Hsuan

    2013-03-01

    In this work, we report the first complete sinapinic acid clusters distribution from monomer to mega Dalton's region by matrix-assisted laser desorption/ionization (MALDI). A decrease of eight orders in intensity was observed from monomer ion to 10 000-mer ion. The results fit to the model of laser ablation induced desorption process with bimodal power-law dependence. In addition, the detailed measurements on the populations of different sizes of clusters can provide some insight of different models of the mechanism for MALDI.

  6. Characterization of Regional Left Ventricular Function in Nonhuman Primates Using Magnetic Resonance Imaging Biomarkers: A Test-Retest Repeatability and Inter-Subject Variability Study

    PubMed Central

    Sampath, Smita; Klimas, Michael; Feng, Dai; Baumgartner, Richard; Manigbas, Elaine; Liang, Ai-Leng; Evelhoch, Jeffrey L.; Chin, Chih-Liang

    2015-01-01

    Pre-clinical animal models are important to study the fundamental biological and functional mechanisms involved in the longitudinal evolution of heart failure (HF). Particularly, large animal models, like nonhuman primates (NHPs), that possess greater physiological, biochemical, and phylogenetic similarity to humans are gaining interest. To assess the translatability of these models into human diseases, imaging biomarkers play a significant role in non-invasive phenotyping, prediction of downstream remodeling, and evaluation of novel experimental therapeutics. This paper sheds insight into NHP cardiac function through the quantification of magnetic resonance (MR) imaging biomarkers that comprehensively characterize the spatiotemporal dynamics of left ventricular (LV) systolic pumping and LV diastolic relaxation. MR tagging and phase contrast (PC) imaging were used to quantify NHP cardiac strain and flow. Temporal inter-relationships between rotational mechanics, myocardial strain and LV chamber flow are presented, and functional biomarkers are evaluated through test-retest repeatability and inter subject variability analyses. The temporal trends observed in strain and flow was similar to published data in humans. Our results indicate a dominant dimension based pumping during early systole, followed by a torsion dominant pumping action during late systole. Early diastole is characterized by close to 65% of untwist, the remainder of which likely contributes to efficient filling during atrial kick. Our data reveal that moderate to good intra-subject repeatability was observed for peak strain, strain-rates, E/circumferential strain-rate (CSR) ratio, E/longitudinal strain-rate (LSR) ratio, and deceleration time. The inter-subject variability was high for strain dyssynchrony, diastolic strain-rates, peak torsion and peak untwist rate. We have successfully characterized cardiac function in NHPs using MR imaging. Peak strain, average systolic strain-rate, diastolic E

  7. Characterizing the interaction between uranyl ion and fulvic acid using regional integration analysis (RIA) and fluorescence quenching.

    PubMed

    Zhu, Bingqi; Ryan, David K

    2016-03-01

    The development of chemometric methods has substantially improved the quantitative usefulness of the fluorescence excitation-emission matrix (EEM) in the analysis of dissolved organic matter (DOM). In this study, Regional Integration Analysis (RIA) was used to quantitatively interpret EEMs and assess fluorescence quenching behavior in order to study the binding between uranyl ion and fulvic acid. Three fulvic acids including soil fulvic acid (SFA), Oyster River fulvic acid (ORFA) and Suwannee River fulvic acid (SRFA) were used and investigated by the spectroscopic techniques. The EEM spectra obtained were divided into five regions according to fluorescence structural features and two distinct peaks were observed in region III and region V. Fluorescence quenching analysis was conducted for these two regions with the stability constants, ligand concentrations and residual fluorescence values calculated using the Ryan-Weber model. Results indicated a relatively strong binding ability between uranyl ion and fulvic acid samples at low pH (log K value varies from 4.11 to 4.67 at pH 3.50). Fluorophores in region III showed a higher binding ability with fewer binding sites than in region V. Stability constants followed the order, SFA > ORFA > SRFA, while ligand concentrations followed the reverse order, SRFA > ORFA > SFA. A comparison between RIA and Parallel Factor Analysis (PARAFAC) data treatment methods was also performed and good agreement between these two methods (less than 4% difference in log K values) demonstrates the reliability of the RIA method in this study. PMID:26736183

  8. [Analysis of acid rain characteristics of Lin'an Regional Background Station using long-term observation data].

    PubMed

    Li, Zheng-Quan; Ma, Hao; Mao, Yu-Ding; Feng, Tao

    2014-02-01

    Using long-term observation data of acid rain at Lin'an Regional Background Station (Lin'an RBS), this paper studied the interannual and monthly variations of acid rain, the reasons for the variations, and the relationships between acid rain and meteorological factors. The results showed that interannual variation of acid rain at Lin'an RBS had a general increasing trend in which there were two obvious intensifying processes and two distinct weakening processes, during the period ranging from 1985 to 2012. In last two decades, the monthly variation of acid rain at Lin'an RBS indicated that rain acidity and frequency of severe acid rain were increasing but the frequency of weak acid rain was decreasing when moving towards bilateral side months of July. Acid rain occurrence was affected by rainfall intensity, wind speed and wind direction. High frequency of severe acid rain and low frequency of weak acid rain were on days with drizzle, but high frequency of weak acid rain and low frequency of severe acid rain occurred on rainstorm days. With wind speed upgrading, the frequency of acid rain and the proportion of severe acid rain were declining, the pH value of precipitation was reducing too. Another character is that daily dominant wind direction of weak acid rain majorly converged in S-W section ,however that of severe acid rain was more likely distributed in N-E section. The monthly variation of acid rain at Lin'an RBS was mainly attributed to precipitation variation, the increasing and decreasing of monthly incoming wind from SSE-WSW and NWN-ENE sections of wind direction. The interannual variation of acid rain could be due to the effects of energy consumption raising and significant green policies conducted in Zhejiang, Jiangsu and Shanghai.

  9. [Analysis of acid rain characteristics of Lin'an Regional Background Station using long-term observation data].

    PubMed

    Li, Zheng-Quan; Ma, Hao; Mao, Yu-Ding; Feng, Tao

    2014-02-01

    Using long-term observation data of acid rain at Lin'an Regional Background Station (Lin'an RBS), this paper studied the interannual and monthly variations of acid rain, the reasons for the variations, and the relationships between acid rain and meteorological factors. The results showed that interannual variation of acid rain at Lin'an RBS had a general increasing trend in which there were two obvious intensifying processes and two distinct weakening processes, during the period ranging from 1985 to 2012. In last two decades, the monthly variation of acid rain at Lin'an RBS indicated that rain acidity and frequency of severe acid rain were increasing but the frequency of weak acid rain was decreasing when moving towards bilateral side months of July. Acid rain occurrence was affected by rainfall intensity, wind speed and wind direction. High frequency of severe acid rain and low frequency of weak acid rain were on days with drizzle, but high frequency of weak acid rain and low frequency of severe acid rain occurred on rainstorm days. With wind speed upgrading, the frequency of acid rain and the proportion of severe acid rain were declining, the pH value of precipitation was reducing too. Another character is that daily dominant wind direction of weak acid rain majorly converged in S-W section ,however that of severe acid rain was more likely distributed in N-E section. The monthly variation of acid rain at Lin'an RBS was mainly attributed to precipitation variation, the increasing and decreasing of monthly incoming wind from SSE-WSW and NWN-ENE sections of wind direction. The interannual variation of acid rain could be due to the effects of energy consumption raising and significant green policies conducted in Zhejiang, Jiangsu and Shanghai. PMID:24812937

  10. Regional pulmonary distribution of iodine-125-labeled oleic acid. Its relationship to the pattern of oleic acid edema and pulmonary blood flow

    SciTech Connect

    Tarver, R.D.; Tsai, J.; Hedlund, L.W.; Sullivan, D.C.; Lischko, M.M.; Harris, C.C.; Effmann, E.L.; Putman, C.E.

    1986-02-01

    Oleic acid infusion in dogs produces a patchy, predominantly peripheral lesion on CT scans. This study correlates the pattern of oleic acid injury with the distribution of infused oleic acid and pulmonary blood flow. Radiolabeled oleic acid (I-125, 0.05 ml/kg) and radiolabeled 15-micron microspheres (Co-57) were infused into the right atria of 11 dogs. Oleic acid was given after the microspheres in six dogs and before microspheres in five dogs. Ten minutes after infusion, the lungs were removed. Four transverse slices (0.5 cm thick) of the lower lobes were taken from each dog and cubed. Samples were grouped into three regions of the transverse slice: outer, middle, and inner concentric rings. In both groups, I-125 (oleic acid) activity was greater in the outer than the middle and inner concentric layers (P less than 0.001). When Cobalt-57 microspheres were given before oleic acid, Cobalt-57 activity was marginally lower in the outer layer compared with the middle and inner layers. However, when oleic acid was given first, microsphere activity in the outer layer was significantly lower (P less than 0.001) than the middle layer. Thus, oleic acid was preferentially distributed to the peripheral regions of the lung, similar to the regions of injury on CT. This distribution did not correspond to the pattern of pulmonary blood flow as indicated by the microspheres. Immediately after oleic acid infusion, pulmonary blood flow to the periphery was reduced, reflecting a response to the predominantly peripheral injury by oleic acid.

  11. Differences in the Pathological Diagnosis and Repeat Craniotomy Rates in Cerebral Tumors Undergoing Biopsy or Resection in an Urban Versus Regional Center

    PubMed Central

    Vonhoff, Craig R.; Lochhead, Alistair; Koustais, Stavros; Watson, Nicole; Andrici, Juliana; Brewer, Janice; Gill, Anthony J.

    2015-01-01

    Abstract Primary intracranial tumors occur with an incidence of between 2.5 and 6 per 100,000 individuals. They require specialist expertise for investigation and management including input from radiology, pathology, neurosurgery, and oncology. Therefore, most patients with intracranial neoplasia are investigated and managed in larger hospitals. The geographically dispersed population of Australia has facilitated the development of neurosurgical units in regional areas. However, major metropolitan hospitals are over-represented compared with regional centers in most research cohorts. We therefore sought to investigate the spectrum of intracranial neoplasms undergoing biopsy and surgery at a major regional center in Australia and to compare the demographic and pathological features to similar cohorts treated in major metropolitan hospitals. We searched the pathological databases of both a major regional pathology provider and a major metropolitan pathology practice, which provides surgical pathology services for both a large private and a large public neurosurgical hospital, to identify all cerebral tumors undergoing biopsy or resection over a 14-year period (calendar years 2001 and 2014). In all, 3717 cerebral tumors were identified. Among them, 51% were from an urban private hospital, 33% from an urban public hospital, and 16% from a regional public hospital. Overall, one-third of them were neuroepithelial in origin, a quarter metastatic disease, a fifth meningeal, and one-tenth were pituitary adenomas. The regional center treated a higher proportion of metastatic tumors and less meningeal tumors compared with the urban center. Additionally, patients were less likely to undergo a second operation in the regional center (P < 0.001). The differences give an important insight into the burden of neurosurgical disease in regional Australia, and how it differs from that encountered in large metropolitan centers. PMID:26632735

  12. Construction of a genomic library of the human cytomegalovirus genome and analysis of late transcription of its inverted internal repeat region

    SciTech Connect

    Silva, K.F.S.T.

    1989-01-01

    The investigations described in this dissertation were designed to determine the transcriptionally active DNA sequences of IIR region and to identify the viral mRNA transcribed from the transcriptionally most active DNA sequences of that region during late phase of HCMV Towne infection. Preliminary transcriptional studies which included the hybridization of a southern blot of XbaI digested entire HCMV genome to {sup 32}P-labelled late phase infected cell A{sup +} RNA, indicated that late viral transcripts homologous to XbaI Q fragment of IIR region were very highly abundant while XbaI Q fragment showed a very low transcriptional activity. To facilitate further analysis of late transcription of IIR region, the entire DNA sequences of IIR region were molecularly cloned as U, S, and H BamHI fragments in pACYC-184 plasmid vector. In addition, to be used in future studies on other regions of the genome, except for y and c{prime} smaller fragments the entire 240 kb HCMV genome was cloned as BamHI fragments in the same vector. Furthermore, the U, S, and H BamHI fragments were mapped with six other restriction enzymes in order to use that mapping data in subsequent transcriptional analysis of the IIR region. Further localization of transcriptionally active DNA sequences within IIR region was achieved by hybridization of southern blots of restricted U, S, and H BamHI fragments with 3{prime} {sup 32}P-labelled infected cell late A{sup +} RNA. The 1.5 kb EcooRI subfragments of S BamHI fragment and the adjoining 0.72 kb XhoI subfragment of H BamHI fragment revealed the highest level of transcription, although the remainder of the S fragment was also transcribed at a substantial level. The U fragment and the remainder of the H fragment was transcribed at a very low level.

  13. Specific effects of punishment on amino acids turnover in discrete rat brain regions.

    PubMed

    Miyauchi, T; Dworkin, S I; Co, C; Smith, J E

    1988-11-01

    Specific effects of punishment on the turnover rates of aspartate (Asp), glutamate (Glu) and gamma-aminobutyric acid (GABA) in 14 brain regions were investigated in rats exposed to punishment. Two yoked controls were also used in an attempt to separate the nonspecific effects of response rate, reinforcement density and direct effects of punisher (foot shock). Punished and unpunished littermate rats had similar response rates, and the reinforcement density was almost identical for both groups. A third group (yoked-shock rats) received food and shock independent of responding whenever these were given to the punished rats. When compared to the unpunished rats, the punishment increased the turnover rates of the three amino acids in all brain regions examined except GABA turnover in the caudate-putamen and preoptic-diagonal band. The majority of these changes by the punishment were similar to the effects of the yoked-shock (yoked-shock versus unpunished), although the magnitude of increase by the punishment was mostly larger than that by the yoked-shock. Six changes by the punishment (increase in the turnover rates of Asp in the thalamus, Glu in the hypothalamus and GABA in the cingulate cortex, entorhinal-subicular cortex, dentate gyrus and hypothalamus) appeared to be the specific effects of punishment since the yoked-shock did not affect these parameters. These results suggest that the punishment caused a hyperexcitation of the amino acidergic neurons in the limbic systems, particularly those in Papez's circuit. PMID:3251236

  14. Acid deposition in the Athabasca Oil Sands Region: a policy perspective.

    PubMed

    Whitfield, Colin J; Watmough, Shaun A

    2015-12-01

    Industrial emissions of sulphur (S) and nitrogen (N) to the atmosphere associated with the oil sands industry in north-eastern Alberta are of interest as they represent the largest localized source in Canada (with potential for future growth) and the region features acid-sensitive upland terrain. Existing emission management policy for the Regional Municipality of Wood Buffalo, where the industry is located, is based on a time-to-effect approach that relies on dynamic model simulations of temporal changes in chemistry and features highly protective chemical criteria. In practice, the policy is difficult to implement and it is unlikely that a scientifically defensible estimate of acidification risk can be put forward due to the limitations primarily associated with issues of scale, chemical endpoint designation (selection of chemical limit for ecosystem protection from acidification) and data availability. A more implementable approach would use a steady-state critical load (CL) assessment approach to identify at-risk areas. The CL assessment would consider areas of elevated acid deposition associated with oil sands emissions rather than targeted political jurisdictions. Dynamic models should only be (strategically) used where acidification risk is identified via CL analysis, in order to characterize the potential for acidification-induced changes that can be detrimental to sensitive biota within the lifespan of the industry. PMID:26607154

  15. Acid deposition in the Athabasca Oil Sands Region: a policy perspective.

    PubMed

    Whitfield, Colin J; Watmough, Shaun A

    2015-12-01

    Industrial emissions of sulphur (S) and nitrogen (N) to the atmosphere associated with the oil sands industry in north-eastern Alberta are of interest as they represent the largest localized source in Canada (with potential for future growth) and the region features acid-sensitive upland terrain. Existing emission management policy for the Regional Municipality of Wood Buffalo, where the industry is located, is based on a time-to-effect approach that relies on dynamic model simulations of temporal changes in chemistry and features highly protective chemical criteria. In practice, the policy is difficult to implement and it is unlikely that a scientifically defensible estimate of acidification risk can be put forward due to the limitations primarily associated with issues of scale, chemical endpoint designation (selection of chemical limit for ecosystem protection from acidification) and data availability. A more implementable approach would use a steady-state critical load (CL) assessment approach to identify at-risk areas. The CL assessment would consider areas of elevated acid deposition associated with oil sands emissions rather than targeted political jurisdictions. Dynamic models should only be (strategically) used where acidification risk is identified via CL analysis, in order to characterize the potential for acidification-induced changes that can be detrimental to sensitive biota within the lifespan of the industry.

  16. Runoff changes in Czech headwater regions after deforestation induced by acid rains

    NASA Astrophysics Data System (ADS)

    Buchtele, J.; Buchtelova, M.; Hrkal, Z.; Koskova, R.

    2003-04-01

    Tendencies in water regime resulting from land-use change represent an important subject for research and in the region of so called Black Triangle at the borders of Czech Republic, Germany and Poland urgent practical problem. Namely extensive deforestation in Czech hilly basins induced by acid rains, which appeared in seventies and eighties, requires attention. Discussions among professionals and public, sometimes having emotional character, took place after large floods on the rivers Odra and Morava in 1997 and in Vltava and Elbe river basins in August 2002. The influence of deforestation induced by acid rains in the Central Europe has been considered as important contribution to disastrous character of floods. Simulations of rainfall-runoff process in several catchments and experimental basins in two distinct headwater regions along German borders, with different extent of deforestation have been carried out using daily time series up to 40 years long. The outputs of two hydrological models of different structure have been compared in these investigations: - the conceptual model SAC-SMA - Sacramento soil moisture accounting - physically based 1- D model BROOK´90 The differences between observed and simulated discharge, which could show the tendencies in the runoff have been followed. They indicate increase of runoff after deforestation.

  17. Tissue and regional distribution of cysteic acid decarboxylase. A new assay method.

    PubMed

    Wu, J Y; Moss, L G; Chen, M S

    1979-04-01

    A sensitive and rapid assay method method for cysteic acid decarboxylase was develped which combined the selectivity of ion exchange resin (a complete retention of the substrate, cysteic acid, and exclusion of the product, taurine) with the speed of a vacuum filtration. The synthesis and purification of 35S-labeled cysteic acid were described. The validity of the assay was established by the identification of the reaction product as taurine. With this new method, the decarboxylase activity was measured in discrete regions of bovine brain. Putamen had the highest activity, 172 pmol taurine formed/min/mg protein (100%), followed by caudate nucleus, 90%; cerebral cortex, 82%; hypothalamus, 81%; cerebellar cortex, 79%; cerebellar peduncle, 59%; thalamus, 42%; brain stem, 25%; pons, 10%; and corpus callosum, 3%. The decarboxylase activity in various mouse tissues was also determined as follows: liver, 403; brain, 145; kidney, 143; spinal cord, 59; lung, 21; and spleen, 10 pmol taurine formed/min/mg. No activity could be detected in skeleton muscle and heart, suggesting a different biosynthetic pathway for taurine synthesis in these tissues. The advantages and disadvantages of the new assay method are also discussed.

  18. Analysis of cytosine-adenine repeats in P1 promoter region of IGF-1 gene in peripheral blood cells and cervical tissue samples of females with cervical intraepithelial lesions and squamous cervical cancer

    PubMed Central

    KWASNIEWSKI, WOJCIECH; GOZDZICKA-JOZEFIAK, ANNA; KOTARSKA, MARIA; POLAK, GRZEGORZ; BARCZYNSKI, BARTLOMIEJ; BRONIARCZYK, JUSTYNA; NOWAK, WITOLD; WOLUN-CHOLEWA, MARIA; KWASNIEWSKA, ANNA; KOTARSKI, JAN

    2015-01-01

    High oncogenic risk human papillomaviruses (HPVs) are closely associated with cancer of the cervix. However, HPV infection alone may not be sufficient to cause cervical cancer, and other factors or cofactors may have a cumulative effect on the risk of progression from cervical HPV infection to cancer. The present study investigates the cytosine-adenine (CA) repeat polymorphism in the P1 promoter region of the insulin-like growth factor-1 (IGF-1) gene among cervical precancerous and cancer patients and healthy control females. The association between these polymorphisms, tissue and blood serum levels of IGF-1, and cervical cancer risk and progression is evaluated. The material for analysis consisted of blood cells and postoperative tissues from patients diagnosed with low-grade squamous intraepithelial lesions (L-SILs), high-grade squamous intraepithelial lesions (H-SILs) and invasive cervical cancer (ICC). A polymerase chain reaction amplification and the sequencing of DNA were used for the identification of (CA)n repeats in the IGF-1 P1 region and detection of HPV DNA. The blood serum concentration of IGF was determined by enzyme-linked immunosorbent assay. The identification of the IGF-1 protein in the cervical tissues was performed by immunohistochemical analysis. The range of the length of the CA repeats in the study DNA was 11 to 21. However, the most common allele length and genotype in the control and study patients from serum and tissues was 19 CA repeats and a homozygous genotype of CA19/19. Statistically significant differences in the concentration of IGF-1 in the blood serum were observed between H-SILs and controls, only (p=0.047). However, the concentration of IGF-1 in the group of females with CA19/19, CA19<19 and CA19>19 was significantly higher in the group of patients with H-SIL (P=0.041) and ICC (P=0.048) in comparison with the control group. An association was detected between CA repeat length <19 and/or >19, IGF concentration in blood serum and

  19. A further analysis of the relationship between yellow ripe-fruit color and the capsanthin-capsorubin synthase gene in pepper (Capsicum sp.) indicated a new mutant variant in C. annuum and a tandem repeat structure in promoter region.

    PubMed

    Li, Zheng; Wang, Shu; Gui, Xiao-Ling; Chang, Xiao-Bei; Gong, Zhen-Hui

    2013-01-01

    Mature pepper (Capsicum sp.) fruits come in a variety of colors, including red, orange, yellow, brown, and white. To better understand the genetic and regulatory relationships between the yellow fruit phenotype and the capsanthin-capsorubin synthase gene (Ccs), we examined 156 Capsicum varieties, most of which were collected from Northwest Chinese landraces. A new ccs variant was identified in the yellow fruit cultivar CK7. Cluster analysis revealed that CK7, which belongs to the C. annuum species, has low genetic similarity to other yellow C. annuum varieties. In the coding sequence of this ccs allele, we detected a premature stop codon derived from a C to G change, as well as a downstream frame-shift caused by a 1-bp nucleotide deletion. In addition, the expression of the gene was detected in mature CK7 fruit. Furthermore, the promoter sequences of Ccs from some pepper varieties were examined, and we detected a 176-bp tandem repeat sequence in the promoter region. In all C. annuum varieties examined in this study, the repeat number was three, compared with four in two C. chinense accessions. The sequence similarity ranged from 84.8% to 97.7% among the four types of repeats, and some putative cis-elements were also found in every repeat. This suggests that the transcriptional regulation of Ccs expression is complex. Based on the analysis of the novel C. annuum mutation reported here, along with the studies of three mutation types in yellow C. annuum and C. chinense accessions, we suggest that the mechanism leading to the production of yellow color fruit may be not as complex as that leading to orange fruit production.

  20. Amino acid preservation in saline halite core samples: Analogs for Martian dry evaporitic regions

    NASA Astrophysics Data System (ADS)

    Bada, J.; Aubrey, A.; Lowenstein, T.; Timofeeff, M.

    2008-12-01

    in the deepest core section. This may indicate some recent amino acid contribution to the pool of certain amino acids. Racemization rates can be calculated from the equation: ln[(1+D/L)/(1-D/L)] - ln [(1+D/L)/(1-D/L)]t=0 = 2ki(time) where ki is the first-order rate constant for the interconversion of the enantiomers. Using the D/L ratios at the top of the core for the t = 0 term gives kasp = 3.5x10exp-5 y-1 and 1.3x10exp-5 y-1 for the 18 and 70 ka samples, respectively. For valine, the values are kval = 5.6x10exp-6 y-1 and 7.3x10exp-6 y-1. Extrapolating these values to the average surface temperatures on Mars indicates that the chirality of these amino acids would be preserved for billions of years. Thus, closed basin lacustrine and dry desert valley regions with evaporite-rich deposits are suitable environments in the search for preserved biosignatures on Mars. References [1] Bibring, J.P., et al., Science 307, 1576 (2005) [2] Klinghofer, G., et al., Science 306, 1740 (2004) [3] Osterloo, M.M., et al., Science 319, 1651 (2008) [4] Squyres, S.W., et al., Nature 443, E1 (2006) [5] Lowenstein, T.K., et al., Geology 27, 3 (1999) [6] Glavin, D., et al., Earth Planet. Sci. Lett. 185,1 (2001) [7] Aubrey, A. D., et al., in preparation, Nature Geo. Sci.

  1. Design and evaluation of antiretroviral peptides corresponding to the C-terminal heptad repeat region (C-HR) of human immunodeficiency virus type 1 envelope glycoprotein gp41

    SciTech Connect

    Soonthornsata, Bongkot; Tian, Yu-Shi; Utachee, Piraporn; Sapsutthipas, Sompong; Isarangkura-na-ayuthaya, Panasda; Auwanit, Wattana; Takagi, Tatsuya; Ikuta, Kazuyoshi; Sawanpanyalert, Pathom; Kawashita, Norihito; Kameoka, Masanori

    2010-09-15

    Two {alpha}-helical heptad repeats, N-HR and C-HR, located in the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp41, play an important role in membrane fusion by forming a 6-helix bundle. C34, a peptide mimicking C-HR, inhibits the formation of the 6-helix bundle; thus, it has potential as a novel antiretroviral compound. In order to improve the inhibitory effect of C34 on HIV-1 replication, we designed new C34-derived peptides based on computational analysis of the stable conformation of the 6-helix bundle. Newly designed peptides showed a stronger inhibitory effect on the replication of recombinant viruses containing CRF01{sub A}E, subtype B or subtype C Env than C34 or a fusion inhibitor, T-20. In addition, these peptides inhibited the replication of a T-20-resistant virus. We propose that these peptides could be applied to develop novel antiretroviral compounds to inhibit the replication of various subtypes of HIV-1 as well as of T-20-resistant variants.

  2. A Deep Near-Infrared Survey of the N 49 Region around the Soft Gamma-Ray Repeater 0526-66

    NASA Technical Reports Server (NTRS)

    Klose, S.; Henden, A. A.; Geppert, U.; Greiner, J.; Guetter, H. H.; Hartmann, D. H.; Kouveliotou, C.; Luginbuhl, C. B.; Stecklurn, B.; Vrba, F. J.

    2004-01-01

    We report the results of a deep near-infrared survey of the vicinity of supernova remnant N49 in the Large Magellanic Cloud (LMC), which contains the soft gamma-ray repeater (SGR) 0526-66. Two of the four confirmed SGRs are potentially associated with compact stellar clusters. We thus searched for a similar association of SGR0526-66, and find the unexplored young stellar cluster SL 463 at a projected distance of approx. 30 pc from the SGR. This constitutes the third cluster-SGR link, and lends support to scenarios in which SGR progenitors originate in young, embedded clusters. If real, the cluster-SGR association constrains the age and thus the initial mass of these stars. In addition, our high-resolution images of the super- nova remnant N49 reveal an area of excess K-band flux in the southeastern part of the SNR. This feature coincides with the maximum flux area at 8.28 microns as detected by the Midcourse Space Experiment (MSX satellite), which we identify with IRAS 052594607.

  3. Microscopic evaluation of trace metals in cloud droplets in an acid precipitation region.

    PubMed

    Li, Weijun; Wang, Yan; Collett, Jeffrey L; Chen, Jianmin; Zhang, Xiaoye; Wang, Zifa; Wang, Wenxing

    2013-05-01

    Mass concentrations of soluble trace metals and size, number, and mixing properties of nanometal particles in clouds determine their toxicity to ecosystems. Cloud water was found to be acidic, with a pH of 3.52, at Mt. Lu (elevation 1,165 m) in an acid precipitation region in South China. A combination of Inductively Coupled Plasma Mass Spectrometry (ICPMS) and Transmission Electron Microscopy (TEM) for the first time demonstrates that the soluble metal concentrations and solid metal particle number are surprisingly high in acid clouds at Mt. Lu, where daily concentrations of SO2, NO2, and PM10 are 18 μg m(-3), 7 μg m(-3), and 22 μg m(-3). The soluble metals in cloudwater with the highest concentrations were zinc (Zn, 200 μg L(-1)), iron (Fe, 88 μg L(-1)), and lead (Pb, 77 μg L(-1)). TEM reveals that 76% of cloud residues include metal particles that range from 50 nm to 1 μm diameter with a median diameter of 250 nm. Four major metal-associated particle types are Pb-rich (35%), fly ash (27%), Fe-rich (23%), and Zn-rich (15%). Elemental mapping shows that minor soluble metals are distributed within sulfates of cloud residues. Emissions of fine metal particles from large, nonferrous industries and coal-fired power plants with tall stacks were transported upward to this high elevation. Our results suggest that the abundant trace metals in clouds aggravate the impacts of acid clouds or associated precipitation on the ecosystem and human health.

  4. Repeated administration of phytocannabinoid Δ(9)-THC or synthetic cannabinoids JWH-018 and JWH-073 induces tolerance to hypothermia but not locomotor suppression in mice, and reduces CB1 receptor expression and function in a brain region-specific manner.

    PubMed

    Tai, S; Hyatt, W S; Gu, C; Franks, L N; Vasiljevik, T; Brents, L K; Prather, P L; Fantegrossi, W E

    2015-12-01

    These studies probed the relationship between intrinsic efficacy and tolerance/cross-tolerance between ∆(9)-THC and synthetic cannabinoid drugs of abuse (SCBs) by examining in vivo effects and cellular changes concomitant with their repeated administration in mice. Dose-effect relationships for hypothermic effects were determined in order to confirm that SCBs JWH-018 and JWH-073 are higher efficacy agonists than ∆(9)-THC in mice. Separate groups of mice were treated with saline, sub-maximal hypothermic doses of JWH-018 or JWH-073 (3.0mg/kg or 10.0mg/kg, respectively) or a maximally hypothermic dose of 30.0mg/kg ∆(9)-THC once per day for 5 consecutive days while core temperature and locomotor activity were monitored via biotelemetry. Repeated administration of all drugs resulted in tolerance to hypothermic effects, but not locomotor effects, and this tolerance was still evident 14 days after the last drug administration. Further studies treated mice with 30.0mg/kg ∆(9)-THC once per day for 4 days, then tested with SCBs on day 5. Mice with a ∆(9)-THC history were cross-tolerant to both SCBs, and this cross-tolerance also persisted 14 days after testing. Select brain regions from chronically treated mice were examined for changes in CB1 receptor expression and function. Expression and function of hypothalamic CB1Rs were reduced in mice receiving chronic drugs, but cortical CB1R expression and function were not altered. Collectively, these data demonstrate that repeated ∆(9)-THC, JWH-018 and JWH-073 can induce long-lasting tolerance to some in vivo effects, which is likely mediated by region-specific downregulation and desensitization of CB1Rs.

  5. Examining the Impact of Nitrous Acid Chemistry on Ozone and PM over the Pearl River Delta Region

    EPA Science Inventory

    The impact of nitrous acid (HONO) chemistry on regional ozone and particulate matter in Pearl River Delta region was investigated using the community multiscale air quality (CMAQ) modeling system and the CB05 mechanism. Model simulations were conducted for a ten-day period in Oct...

  6. Identification of a nucleic acid-binding region within the largest subunit of Drosophila melanogaster RNA polymerase II.

    PubMed Central

    Kontermann, R. E.; Kobor, M.; Bautz, E. K.

    1993-01-01

    The largest and the second-largest subunit of the multisubunit eukaryotic RNA polymerases are involved in interaction with the DNA template and the nascent RNA chain. Using Southwestern DNA-binding techniques and nitrocellulose filter binding assays of bacterially expressed fusion proteins, we have identified a region of the largest, 215-kDa, subunit of Drosophila RNA polymerase II that has the potential to bind nucleic acids nonspecifically. This nucleic acid-binding region is located between amino acid residues 309-384 and is highly conserved within the largest subunits of eukaryotic and bacterial RNA polymerases. A homology to a region of the DNA-binding cleft of Escherichia coli DNA polymerase I involved in binding of the newly synthesized DNA duplex provides indirect evidence that the nucleic acid-binding region of the largest subunit participates in interaction with double-stranded nucleic acids during transcription. The nonspecific DNA-binding behavior of the region is similar to that observed for the native enzyme in nitrocellulose filter binding assays and that of the separated largest subunit in Southwestern assays. A high content of basic amino acid residues is consistent with the electrostatic nature of nonspecific DNA binding by RNA polymerases. PMID:8443600

  7. Development of a SCAR (sequence-characterised amplified region) marker for acid resistance-related gene in Lactobacillus plantarum.

    PubMed

    Liu, Shu-Wen; Li, Kai; Yang, Shi-Ling; Tian, Shu-Fen; He, Ling

    2015-03-01

    A sequence characterised amplified region marker was developed to determine an acid resistance-related gene in Lactobacillus plantarum. A random amplified polymorphic DNA marker named S116-680 was reported to be closely related to the acid resistance of the strains. The DNA band corresponding to this marker was cloned and sequenced with the induction of specific designed PCR primers. The results of PCR test helped to amplify a clear specific band of 680 bp in the tested acid-resistant strains. S116-680 marker would be useful to explore the acid-resistant mechanism of L. plantarum and to screen desirable malolactic fermentation strains.

  8. Recent crustal deformation of İzmir, Western Anatolia and surrounding regions as deduced from repeated GPS measurements and strain field

    NASA Astrophysics Data System (ADS)

    Aktuğ, Bahadır; Kılıçoğlu, Ali

    2006-07-01

    To investigate contemporary neotectonic deformation in İzmir, Western Anatolia and in its neighborhood, a relatively dense Global Positioning System (GPS) monitoring network was established in 2001. Combination of three spatially dense GPS campaigns in 2001, 2003 and 2004 with temporally dense campaigns between 1992 and 2004 resulted in a combined velocity field representing active deformation rate in the region. We computed horizontal and vertical velocity fields with respect to Earth-centered, Earth-fixed ITRF2000, to Eurasia and to Anatolia as well. The rates of principal and shear strains along with rigid-body rotation rates were derived from velocity field. Results show east-west shortening between Karaburun Peninsula and northern part of İzmir Bay together with the extension of İzmir Bay in accordance with general extension regime of Western Anatolia and Eastern Agea. East-west shortening and north-south extension of Karaburun Peninsula are closely related to right-lateral faulting and a clockwise rotation. There exists a block in the middle of the peninsula with a differential motion at a rate of 3-5 ± 1 mm/year and 5-6 ± 1 mm/year to the east and south, respectively. As is in Western Anatolia, north-south extension is dominant in almost all parts of the region despite the fact that they exhibit significantly higher rates in the middle of the peninsula. Extensional rates along Tuzla Fault lying nearly perpendicular to İzmir Bay and in its west are maximum in the region with an extension rate of 300-500 ± 80-100 nanostrain/year and confirm its active state. Extensional rates in other parts of the region are at level of 50-150 nanostrain/year as expected in the other parts of Western Anatolia.

  9. Rediscovery of historical Vitis vinifera varieties from the South Anatolia region by using amplified fragment length polymorphism and simple sequence repeat DNA fingerprinting methods.

    PubMed

    Yilancioglu, Kaan; Cetiner, Selim

    2013-05-01

    Anatolia played an important role in the diversification and spread of economically important Vitis vinifera varieties. Although several biodiversity studies have been conducted with local cultivars in different regions of Anatolia, our aim is to gain a better knowledge on the biodiversity of endangered historical V. vinifera varieties in the northern Adana region of southern Anatolia, particularly those potentially displaying viticulture characteristics. We also demonstrate the genetic relatedness in a selected subset of widely cultivated and commercialized V. vinifera collection cultivars, which were obtained from the National Grapevine Germplasm located at the Institute of Viticulture, Turkey. In the present study, microsatellites were used in narrowing the sample size from 72 accessions down to a collection of 27 varieties. Amplified fragment length polymorphisms were then employed to determine genetic relatedness among this collection and local V. vinifera cultivars. The unweighted pair group method with arithmetic mean cluster and principal component analyses revealed that Saimbeyli local cultivars form a distinct group, which is distantly related to a selected subset of V. vinifera collection varieties from all over Turkey. To our knowledge, this is the first study conducted with these cultivars. Further preservation and use of these potential viticultural varieties will be helpful to avoid genetic erosion and to promote continued agriculture in the region.

  10. Rediscovery of historical Vitis vinifera varieties from the South Anatolia region by using amplified fragment length polymorphism and simple sequence repeat DNA fingerprinting methods.

    PubMed

    Yilancioglu, Kaan; Cetiner, Selim

    2013-05-01

    Anatolia played an important role in the diversification and spread of economically important Vitis vinifera varieties. Although several biodiversity studies have been conducted with local cultivars in different regions of Anatolia, our aim is to gain a better knowledge on the biodiversity of endangered historical V. vinifera varieties in the northern Adana region of southern Anatolia, particularly those potentially displaying viticulture characteristics. We also demonstrate the genetic relatedness in a selected subset of widely cultivated and commercialized V. vinifera collection cultivars, which were obtained from the National Grapevine Germplasm located at the Institute of Viticulture, Turkey. In the present study, microsatellites were used in narrowing the sample size from 72 accessions down to a collection of 27 varieties. Amplified fragment length polymorphisms were then employed to determine genetic relatedness among this collection and local V. vinifera cultivars. The unweighted pair group method with arithmetic mean cluster and principal component analyses revealed that Saimbeyli local cultivars form a distinct group, which is distantly related to a selected subset of V. vinifera collection varieties from all over Turkey. To our knowledge, this is the first study conducted with these cultivars. Further preservation and use of these potential viticultural varieties will be helpful to avoid genetic erosion and to promote continued agriculture in the region. PMID:23789998

  11. Fish-friendly prophylaxis/disinfection in aquaculture: Low concentration of peracetic acid is stress-free to the carp (Cyprinus carpio) after repeated applications

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Application of peracetic acid (PAA) at low concentrations has been proved to be a broad functional and eco-friendly prophylaxis/disinfection method against various fish pathogens. Therefore, regular applications of low concentration PAA is sufficient to control (potential) pathogens in recirculatin...

  12. Comparison of sulfur measurements from a regional fine particle network with concurrent acid modes network results

    SciTech Connect

    Bennett, R.L.; Stockburger, L.; Barnes, H.M.

    1994-01-01

    The Fine Particle Network (FPN), a system of fine particle (less than 2.5 micrometers) samplers, was operated at 41 sites selected from the Enviromental Protection Agency Acid MODES program during the two year period in 1988-90. The 24-hour sample results included fine particle mass and the most predominant chemical element concentrations determined by wavelength dispersive x-ray fluorescence analysis. Statistical summaries of the fine mass and sulfur concentrations by site and season were prepared. The availability of simultaneous particulate sulfate measurements from independent collection and analytical procedures provided an opportunity to examine their agreement and provide a more reliable data base for evaluation of regional particulate models and estimation of contribution to urban aerosol concentration.

  13. Evidence for Acid-Sulfate Alteration in the Pahrump Hills Region, Gale Crater, Mars

    NASA Astrophysics Data System (ADS)

    Rampe, E. B.; Ming, D. W.; Vaniman, D. T.; Blake, D. F.; Chipera, S.; Morris, R. V.; Bish, D. L.; Cavanagh, P.; Achilles, C.; Bristow, T.; Fairen, A.; Morrison, S. M.; Treiman, A. H.; Crisp, J. A.; Downs, R. T.; Farmer, J. D.; Fendrich, K.; Morookian, J.

    2015-12-01

    The Pahrump Hills region of Gale crater is a ~12 m thick section of sedimentary rock in the Murray formation, interpreted as the basal geological unit of Mount Sharp. The Mars Science Laboratory, Curiosity, arrived at the Pahrump Hills in September 2014 and performed a detailed six-month investigation of the sedimentary structures, geochemistry, and mineralogy of the area. During the campaign, Curiosity drilled and delivered three mudstone samples (targets Confidence Hills, Mojave 2, and Telegraph Peak) to its internal instruments, including the CheMin XRD/XRF. Results from CheMin show that these samples have variable amounts of plagioclase, pyroxene, iron oxides, jarosite, phyllosilicates, cristobalite, and X-ray amorphous material. The presence of jarosite in all samples indicates these rocks were affected by acid-sulfate alteration, and the mineralogical and geochemical trends observed through the section may give more insight into this process. Geochemical data measured by APXS show enrichment in Si and depletion in Mg moving up section. CheMin data show that cristobalite is more abundant up section, whereas pyroxene and phyllosilicates are more abundant at the bottom of the section. Based on mineralogical and geochemical trends and diagenetic features observed in the Pahrump Hills, we hypothesize that the sediments were altered in-situ by acid-sulfate fluids moving down from the top of the section to leach mobile elements, dissolve the minerals most susceptible to acidic alteration, and precipitate secondary silica at the top of the section. Alternative interpretations of the observed mineralogical and geochemical data are possible, including the hypothesis that the redox conditions of the body of water in which the sediments were deposited changed over time.

  14. Structural and functional characterization of the acidic region from the RIZ tumor suppressor.

    PubMed

    Sun, Yizhi; Stine, Jessica M; Atwater, Daniel Z; Sharmin, Ayesha; Ross, J B Alexander; Briknarová, Klára

    2015-02-17

    RIZ (retinoblastoma protein-interacting zinc finger protein), also denoted PRDM2, is a transcriptional regulator and tumor suppressor. It was initially identified because of its ability to interact with another well-established tumor suppressor, the retinoblastoma protein (Rb). A short motif, IRCDE, in the acidic region (AR) of RIZ was reported to play an important role in the interaction with the pocket domain of Rb. The IRCDE motif is similar to a consensus Rb-binding sequence LXCXE (where X denotes any amino acid) that is found in several viral Rb-inactivating oncoproteins. To improve our understanding of the molecular basis of binding of Rb to RIZ, we investigated the interaction between purified recombinant AR and the pocket domain of Rb using nuclear magnetic resonance spectroscopy, isothermal titration calorimetry, and fluorescence anisotropy experiments. We show that AR is intrinsically disordered and that it binds the pocket domain with submicromolar affinity. We also demonstrate that the interaction between AR and the pocket domain is mediated primarily by the short stretch of residues containing the IRCDE motif and that the contribution of other parts of AR to the interaction with the pocket domain is minimal. Overall, our data provide clear evidence that RIZ is one of the few cellular proteins that can interact directly with the LXCXE-binding cleft on Rb.

  15. Chemical response of lakes in the Adirondack Region of New York to declines in acidic deposition.

    PubMed

    Driscoll, Charles T; Driscoll, Kimberley M; Roy, Karen M; Mitchell, Myron J

    2003-05-15

    Long-term changes in the chemistry of wet deposition and lake water were investigated in the Adirondack Region of New York. Marked decreases in concentrations of SO4(2-) and H+ in wet deposition have occurred at two sites since the late 1970s. These decreases are consistent with long-term declines in emissions of sulfur dioxide (SO2) in the eastern United States. Changes in wet NO3- deposition and nitrogen oxides (NOx) emissions have been minor over the same interval. Virtually all Adirondack Lakes have shown marked decreases in concentrations of SO4(2-), which coincide with decreases in atmospheric S deposition. Concentrations of NO3- have also decreased in several Adirondack lakes. As atmospheric N deposition has not changed over this period, the mechanism contributing to this apparent increase in lake/watershed N retention is not evident. Decreases in concentrations of SO4(2-) + NO3- have resulted in increases in acid-neutralizing capacity (ANC) and pH and resulted in a shift in the speciation of monomeric Al from toxic inorganic species toward less toxic organic forms in some lakes. Nevertheless, many lakes continue to exhibit pH values and concentrations of inorganic monomeric Al that are critical to aquatic biota. Extrapolation of rates of ANC increase suggests that the time frame of chemical recovery of Adirondack Lakes will be several decades if current decreases in acidic deposition are maintained.

  16. Structural and Functional Characterization of the Acidic Region from the RIZ Tumor Suppressor

    PubMed Central

    Sun, Yizhi; Stine, Jessica M.; Atwater, Daniel Z.; Sharmin, Ayesha; Ross, J. B. Alexander; Briknarová, Klára

    2015-01-01

    RIZ (retinoblastoma protein-interacting zinc finger protein), also denoted PRDM2, is a transcriptional regulator and tumor suppressor. It was initially identified because of its ability to interact with another well-established tumor suppressor, the retinoblastoma protein (Rb). A short motif, IRCDE, in the acidic region (AR) of RIZ was reported to play an important role in the interaction with the pocket domain of Rb. The IRCDE motif is similar to a consensus Rb-binding sequence LXCXE (where X denotes any amino acid) that is found in several viral Rb-inactivating oncoproteins. To improve our understanding of the molecular basis of binding of Rb to RIZ, we investigated the interaction between purified recombinant AR and the pocket domain of Rb using nuclear magnetic resonance spectroscopy, isothermal titration calorimetry, and fluorescence anisotropy experiments. We show that AR is intrinsically disordered and that it binds the pocket domain with submicromolar affinity. We also demonstrate that the interaction between AR and the pocket domain is mediated primarily by the short stretch of residues containing the IRCDE motif and that the contribution of other parts of AR to the interaction with the pocket domain is minimal. Overall, our data provide clear evidence that RIZ is one of the few cellular proteins that can interact directly with the LXCXE-binding cleft on Rb. PMID:25640033

  17. Generation of a chickenized catalytic anti-nucleic acid antibody by complementarity-determining region grafting.

    PubMed

    Roh, Jooho; Byun, Sung June; Seo, Youngsil; KIm, Minjae; Lee, Jae-Ho; Kim, Songmi; Lee, Yuno; Lee, Keun Woo; Kim, Jin-Kyoo; Kwon, Myung-Hee

    2015-02-01

    In contrast to a number of studies on the humanization of non-human antibodies, the reshaping of a non-human antibody into a chicken antibody has never been attempted. Therefore, nothing is known about the animal species-dependent compatibility of the framework regions (FRs) that sustain the appropriate conformation of the complementarity-determining regions (CDRs). In this study, we attempted the reshaping of the variable domains of the mouse catalytic anti-nucleic acid antibody 3D8 (m3D8) into the FRs of a chicken antibody (“chickenization”) by CDR grafting, which is a common method for the humanization of antibodies. CDRs of the acceptor chicken antibody that showed a high homology to the FRs of m3D8 were replaced with those of m3D8, resulting in the chickenized antibody (ck3D8). ck3D8 retained the biochemical properties (DNA binding, DNA hydrolysis, and cellular internalizing activities) and three-dimensional structure of m3D8 and showed reduced immunogenicity in chickens. Our study demonstrates that CDR grafting can be applied to the chickenization of a mouse antibody, probably due to the interspecies compatibility of the FRs.

  18. INTERSTITIAL PLASMIN ACTIVITY WITH EPSILON AMINOCAPROIC ACID: TEMPORAL AND REGIONAL HETEROGENEITY

    PubMed Central

    Reust, Daryl L.; Reeves, Scott T.; Abernathy, James H.; Dixon, Jennifer A.; Gaillard, William F.; Mukherjee, Rupak; Koval, Christine N.; Stroud, Robert E.; Spinale, Francis G.

    2010-01-01

    Background Epsilon aminocaproic acid (EACA) is used in cardiac surgery to modulate plasmin activity (PLact). The present study developed a fluorogenic-microdialysis system to measure in-vivo region specific temporal changes in PLact following EACA administration. Methods Pigs (25-35kg) received EACA (75mg/kg, n=7) or saline in which microdialysis probes were placed in the liver, myocardium, kidney and quadricep muscle. The microdialysate contained a plasmin specific fluorogenic peptide and fluorescence emission, which directly reflected PLact, determined at baseline, 30, 60, 90 and 120 minutes following EACA/vehicle infusion. Results EACA caused significant decreases in liver and quadricep PLact at 60, 90, 120 minutes and at 30, 60, 120 minutes respectively (p<0.05). In contrast, EACA induced significant biphasic changes in heart and kidney PLact profiles with initial increases followed by decreases at 90 and 120 minutes (p<0.05). The peak EACA interstitial concentrations for all compartments occurred at 30 minutes post infusion, and were 5-fold higher in the renal compartment and 4-fold higher in the myocardium, when compared to the liver or muscle (p<0.05). Conclusions Using a large animal model and in-vivo microdialysis measurements of plasmin activity, the unique findings from this study were 2-fold. First, EACA induced temporally distinct plasmin activity profiles within the plasma and interstitial compartments. Second, EACA caused region specific changes in plasmin activity profiles. These temporal and regional heterogeneic effects of EACA may have important therapeutic considerations when managing fibrinolysis in the perioperative period. PMID:20417774

  19. Emissions of the natural acidic substance in the acid rain region: Dimethyl sulfide and hydrogen sulfide in the region of Xiamen, China

    SciTech Connect

    Yubao Wang; Miaoqin Lu

    1996-12-31

    The global anthropogenic emissions of sulfur, mainly SO2, are relatively well studied for most of the industrialized world, and relatively little is known to date about natural sulfur emission sources, such as, coastal waters and wetland. The most important atmospheric sulfur compounds originating from biogeochemical sources are DMS and H{sub 2}S. Previous studies suggest that biogenic DMS is mainly emitted from oceanic phytoplankton species. The global emission of sulfur by this process was estimated to be 40 Tg S/year. Major sources of biogenic H{sub 2}S in the atmosphere are believed to be bacterial sulfate reduction in anoxic soils and degradation of organic matter. The mentioned reduced sulfur compounds are partially oxidation in the troposphere to SO{sub 2} and further to sulfur acid, another strong acid produced from DMS oxidation is methane sulphonic acid (CH{sub 3}S(O{sub 2})OH). These compounds are strong acid and will influence the pH of precipitation and will be the important impact in acid rain phenomena.

  20. Randomised clinical trial: safety, tolerability, pharmacokinetics and pharmacodynamics of repeated doses of TAK-438 (vonoprazan), a novel potassium-competitive acid blocker, in healthy male subjects

    PubMed Central

    Jenkins, H; Sakurai, Y; Nishimura, A; Okamoto, H; Hibberd, M; Jenkins, R; Yoneyama, T; Ashida, K; Ogama, Y; Warrington, S

    2015-01-01

    Background TAK-438 (vonoprazan) is a potassium-competitive acid blocker that reversibly inhibits gastric H+, K+-ATPase. Aim To evaluate the safety, tolerability, pharmacokinetics and pharmacodynamics of TAK-438 in healthy Japanese and non-Japanese men. Methods In two Phase I, randomised, double-blind, placebo-controlled studies, healthy men (Japan N = 60; UK N = 48) received TAK-438 10–40 mg once daily at a fixed dose level for 7 consecutive days. Assessments included safety, tolerability, pharmacokinetics and pharmacodynamics (intragastric pH). Results Plasma concentration–time profiles of TAK-438 at all dose levels showed rapid absorption (median Tmax ≤2 h). Mean elimination half-life was up to 9 h. Exposure was slightly greater than dose proportional, with no apparent time-dependent inhibition of metabolism. There was no important difference between the two studies in AUC0-tau on Day 7. TAK-438 caused dose-dependent acid suppression. On Day 7, mean 24-h intragastric pH>4 holding time ratio (HTR) with 40 mg TAK-438 was 100% (Japan) and 93.2% (UK), and mean night-time pH>4 HTR was 100% (Japan) and 90.4% (UK). TAK-438 was well tolerated. The frequency of adverse events was similar at all dose levels and there were no serious adverse events. There were no important increases in serum alanine transaminase activity. Serum gastrin and pepsinogen I and II concentrations increased with TAK-438 dose. Conclusions TAK-438 in multiple rising oral dose levels of 10–40 mg once daily for 7 days was safe and well tolerated in healthy men and caused rapid, profound and sustained suppression of gastric acid secretion throughout each 24-h dosing interval. Clinicaltrials.gov identifiers: NCT02123953 and NCT02141711. PMID:25707624

  1. Simple sequence repeat variations expedite phage divergence: Mechanisms of indels and gene mutations.

    PubMed

    Lin, Tiao-Yin

    2016-07-01

    Phages are the most abundant biological entities and influence prokaryotic communities on Earth. Comparing closely related genomes sheds light on molecular events shaping phage evolution. Simple sequence repeat (SSR) variations impart over half of the genomic changes between T7M and T3, indicating an important role of SSRs in accelerating phage genetic divergence. Differences in coding and noncoding regions of phages infecting different hosts, coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2, frequently arise from SSR variations. Such variations modify noncoding and coding regions; the latter efficiently changes multiple amino acids, thereby hastening protein evolution. Four classes of events are found to drive SSR variations: insertion/deletion of SSR units, expansion/contraction of SSRs without alteration of genome length, changes of repeat motifs, and generation/loss of repeats. The categorization demonstrates the ways SSRs mutate in genomes during phage evolution. Indels are common constituents of genome variations and human diseases, yet, how they occur without preexisting repeat sequence is less understood. Non-repeat-unit-based misalignment-elongation (NRUBME) is proposed to be one mechanism for indels without adjacent repeats. NRUBME or consecutive NRUBME may also change repeat motifs or generate new repeats. NRUBME invoking a non-Watson-Crick base pair explains insertions that initiate mononucleotide repeats. Furthermore, NRUBME successfully interprets many inexplicable human di- to tetranucleotide repeat generations. This study provides the first evidence of SSR variations expediting phage divergence, and enables insights into the events and mechanisms of genome evolution. NRUBME allows us to emulate natural evolution to design indels for various applications.

  2. Active upper plate thrust faulting in regions of low plate interface coupling, repeated slow slip events, and coastal uplift: Example from the Hikurangi Margin, New Zealand

    NASA Astrophysics Data System (ADS)

    Mountjoy, Joshu J.; Barnes, Philip M.

    2011-01-01

    Contractional fore-arc faulting and deformation is a characteristic feature of many subduction systems. Definition of the three-dimensional geometry and displacement rates of active, upper plate, out-of-sequence thrust faults along ˜250 km of the upper Hikurangi Margin enables us to examine the relationship between fore-arc deformation and the subduction interface in light of interseismic coupling estimates and distribution of slow slip events, both modeled from GPS measurements. These mid-fore-arc structures include the seaward vergent, outer shelf Lachlan and Ariel faults, with vertical separation rates up to 5 mm/yr, and several other major inner shelf faults with rates that are up to 3.8 mm/yr and comparable with Holocene coastal uplift rates. Seismic reflection imaging and geometric projection of these faults at depth indicate that they splay from the region of the plate interface where geodetic inversions for interseismic coupling and slow slip events suggest that the plate boundary undergoes aseismic slip. This observation may indicate either (1) that frictional properties and interseismic coupling on the plate interface are independent and unrelated to the active splay fault deformation in the inner-middle fore arc or (2) that the active splay faulting reflects long-term mechanical coupling related to higher shear stress, or the relative yield strength of the plate interface to the overriding plate, and that the current pattern of interseismic coupling may not be persistent over geological time scales of 20 ka. We compare structure and processes on the northern Hikurangi and Costa Rican margins and find similarities and significant differences astride these subduction systems.

  3. Mapping of the human dentin matrix acidic phosphoprotein gene (DMP1) to the dentinogenesis imperfecta type II critical region at chromosome 4q21

    SciTech Connect

    Aplin, H.M.; Hirst, K.L.; Crosby, A.H.; Dixon, M.J.

    1995-11-20

    Dentinogenesis imperfecta type II (DGI1) is an autosomal dominant disorder of dentin formation, which has been mapped to human chromosome 4q12-q21. The region most likely to contain the DGI1 locus is a 3.2-cM region surrounding the osteopontin (SPP1) locus. Recently, a novel dentin-specific acidic phosphoprotein (dmp1) has been cloned in the rat and mapped to mouse chromosome 5q21. In the current investigation, we have isolated a cosmid containing the human DMP1 gene. The isolation of a short tandem repeat polymorphism at this locus has allowed us to map the DMP1 locus to human chromosome 4q21 and demonstrate that it is tightly linked to DGI1 in two families (Z{sub max} = 11.01, {theta} = 0.001). The creation of a yeast artificial chromosome contig around SPP1 has further allowed us to demonstrate that DMP1 is located within 150 kb of the bone sialoprotein and 490 kb of the SPP1 loci, respectively. DMP1 is therefore a strong candidate for the DGI1 locus. 12 refs., 2 figs., 1 tab.

  4. Survey of SSC12 Regions Affecting Fatty Acid Composition of Intramuscular Fat Using High-Density SNP Data

    PubMed Central

    Muñoz, María; Alves, Estefânia; Corominas, Jordi; Folch, Josep María; Casellas, Joaquim; Noguera, Jose Luis; Silió, Luis; Fernández, Ana Isabel

    2012-01-01

    Fatty acid composition is a critical aspect of pork because it affects sensorial and technological aspects of meat quality and it is relevant for human health. Previous studies identified significant QTLs in porcine chromosome 12 for fatty acid profile of back fat (BF) and intramuscular fat (IMF). In the present study, 374 SNPs mapped in SSC12 from the 60K Porcine SNP Beadchip were used. We have combined linkage and association analyses with expression data analysis in order to identify regions of SSC12 that could affect fatty acid composition of IMF in longissimus muscle. The QTL scan showed a region around the 60-cM position that significantly affects palmitic fatty acid and two related fatty acid indexes. The Iberian QTL allele increased the palmitic content (+2.6% of mean trait). This QTL does not match any of those reported in the previous study on fatty acid composition of BF, suggesting different genetic control acting at both tissues. The SNP association analyses showed significant associations with linolenic and palmitic acids besides several indexes. Among the polymorphisms that affect palmitic fatty acid and match the QTL region at 60 cM, there were three that mapped in the Phosphatidylcholine transfer protein (PCTP) gene and one in the Acetyl-CoA Carboxylase ∝ gene (ACACA). Interestingly one of the PCTP SNPs also affected significantly unsaturated and double bound indexes and the ratio between polyunsaturated/monounsaturated fatty acids. Differential expression was assessed on longissimus muscle conditional on the genotype of the QTL and on the most significant SNPs, according to the results obtained in the former analyses. Results from the microarray expression analyses, validated by RT-qPCR, showed that PCTP expression levels significantly vary depending on the QTL as well as on the own PCTP genotype. The results obtained with the different approaches point out the PCTP gene as a powerful candidate underlying the QTL for palmitic content. PMID

  5. Amino Acid Residues in the ω-Minus Region Participate in Cellular Localization of Yeast Glycosylphosphatidylinositol-Attached Proteins

    PubMed Central

    Hamada, Kenji; Terashima, Hiromichi; Arisawa, Mikio; Yabuki, Nami; Kitada, Kunio

    1999-01-01

    The final destination of glycosylphosphatidylinositol (GPI)-attached proteins in Saccharomyces cerevisiae is the plasma membrane or the cell wall. Two kinds of signals have been proposed for their cellular localization: (i) the specific amino acid residues V, I, or L at the site 4 or 5 amino acids upstream of the GPI attachment site (the ω site) and Y or N at the site 2 amino acids upstream of the ω site for cell wall localization and (ii) dibasic residues in the region upstream of the ω site (the ω-minus region) for plasma membrane localization. The relationships between these amino acid residues and efficiencies of cell wall incorporation were examined by constructing fusion reporter proteins from open reading frames encoding putative GPI-attached proteins. The levels of incorporation were high in the constructs containing the specific amino acid residues and quite low in those containing two basic amino acid residues in the ω-minus region. With constructs that contained neither specific residues nor two basic residues, levels of incorporation were moderate. These correlations clearly suggest that GPI-attached proteins have two different signals which act positively or negatively in cell wall incorporation for their cellular localization. PMID:10383953

  6. Stream chemistry in the eastern United States. 1. Synoptic survey design, acid-base status, and regional patterns

    SciTech Connect

    Kaufmann, P.R.; Herlihy, A.T.; Mitch, M.E.; Messer, J.J. ); Overton, W.S. )

    1991-04-01

    To assess the regional acid-base status of streams in the mid-Atlantic and southern US, spring base flow chemistry was surveyed in a probability sample of 500 stream reaches representing a population of 64,300 reaches (224,000 km). Approximately half of the streams had acid-neutralizing capacity (ANC) {le} 200 {mu}eq L{sup {minus}1}. Acidic (ANC {le} 0) streams were located in the highlands of the Mid-Atlantic region (southern New York to southern Virginia, 2,330 km), in coastal lowlands of the Mid-Atlantic (2,600 km), and in Florida (462 km). Acidic streams were rare (less than 1%) in the highlands of the Southeast. Inorganic monomeric aluminum (Al{sub im}) concentrations were highest in acidic streams of the Mid-Atlantic Highlands where over 70% of the acidic streams had Al{sub im} greater than 100 {mu}g L{sup {minus}1}, a concentration above which deleterious biological effects have frequently been reported. Dissolved organic carbon concentrations were much higher in lowland coastal streams, compared with inland streams. The authors data supports a hypothesis that atmospheric sources and watershed retention control regional patterns in streamwater sulfate concentrations. Most stream watersheds retain the vast majority of the total nitrogen loading from wet deposition. The data suggest, however, that some deposition nitrogen may be reaching streams in the Northern Appalachians.

  7. Contamination with retinoic acid receptor agonists in two rivers in the Kinki region of Japan.

    PubMed

    Inoue, Daisuke; Nakama, Koki; Sawada, Kazuko; Watanabe, Taro; Takagi, Mai; Sei, Kazunari; Yang, Min; Hirotsuji, Junji; Hu, Jianying; Nishikawa, Jun-ichi; Nakanishi, Tsuyoshi; Ike, Michihiko

    2010-04-01

    This study was conducted to investigate the agonistic activity against human retinoic acid receptor (RAR) alpha in the Lake Biwa-Yodo River and the Ina River in the Kinki region of Japan. To accomplish this, a yeast two-hybrid assay was used to elucidate the spatial and temporal variations and potential sources of RARalpha agonist contamination in the river basins. RARalpha agonistic activity was commonly detected in the surface water samples collected along two rivers at different periods, with maximum all-trans retinoic acid (atRA) equivalents of 47.6 ng-atRA/L and 23.5 ng-atRA/L being observed in Lake Biwa-Yodo River and Ina River, respectively. The results indicated that RARalpha agonists are always present and widespread in the rivers. Comparative investigation of RARalpha and estrogen receptor alpha agonistic activities at 20 stations along each river revealed that the spatial variation pattern of RARalpha agonist contamination was entirely different from that of the estrogenic compound contamination. This suggests that the effluent from municipal wastewater treatment plants, a primary source of estrogenic compounds, seemed not to be the cause of RARalpha agonist contamination in the rivers. Fractionation using high performance liquid chromatography (HPLC) directed by the bioassay found two bioactive fractions from river water samples, suggesting the presence of at least two RARalpha agonists in the rivers. Although a trial conducted to identify RARalpha agonists in the major bioactive fraction was not completed as part of this study, comparison of retention times in HPLC analysis and quantification with liquid chromatography-mass spectrometry analysis revealed that the major causative contaminants responsible for the RARalpha agonistic activity were not RAs (natural RAR ligands) and 4-oxo-RAs, while 4-oxo-RAs were identified as the major RAR agonists in sewage in Beijing, China. These findings suggest that there are unknown RARalpha agonists with high

  8. Tandem repeats derived from centromeric retrotransposons

    PubMed Central

    2013-01-01

    Background Tandem repeats are ubiquitous and abundant in higher eukaryotic genomes and constitute, along with transposable elements, much of DNA underlying centromeres and other heterochromatic domains. In maize, centromeric satellite repeat (CentC) and centromeric retrotransposons (CR), a class of Ty3/gypsy retrotransposons, are enriched at centromeres. Some satellite repeats have homology to retrotransposons and several mechanisms have been proposed to explain the expansion, contraction as well as homogenization of tandem repeats. However, the origin and evolution of tandem repeat loci remain largely unknown. Results CRM1TR and CRM4TR are novel tandem repeats that we show to be entirely derived from CR elements belonging to two different subfamilies, CRM1 and CRM4. Although these tandem repeats clearly originated in at least two separate events, they are derived from similar regions of their respective parent element, namely the long terminal repeat (LTR) and untranslated region (UTR). The 5′ ends of the monomer repeat units of CRM1TR and CRM4TR map to different locations within their respective LTRs, while their 3′ ends map to the same relative position within a conserved region of their UTRs. Based on the insertion times of heterologous retrotransposons that have inserted into these tandem repeats, amplification of the repeats is estimated to have begun at least ~4 (CRM1TR) and ~1 (CRM4TR) million years ago. Distinct CRM1TR sequence variants occupy the two CRM1TR loci, indicating that there is little or no movement of repeats between loci, even though they are separated by only ~1.4 Mb. Conclusions The discovery of two novel retrotransposon derived tandem repeats supports the conclusions from earlier studies that retrotransposons can give rise to tandem repeats in eukaryotic genomes. Analysis of monomers from two different CRM1TR loci shows that gene conversion is the major cause of sequence variation. We propose that successive intrastrand deletions

  9. Fatty acid profile of the milk of cows reared in the mountain region of Poland.

    PubMed

    Rutkowska, Jarosława; Adamska, Agata; Bialek, Malgorzata

    2012-11-01

    An appropriate composition of milk fatty acids (FA) improves the nutritional value of milk and milk products, and improves milk processing. Polish dairy farms in the mountainous region are rather small, animal nutrition there is based on locally produced forages and this, together with the transitional climate zone brings about seasonal changes in FA composition of milk. The aim of the study was to evaluate the composition of FA in bovine milk fat in relation to fat intake in forages and their FA profiles. The study involved 5 herds reared in low-input mountain farms located at an altitude of 670-780 m above sea level (Beskid Mountains). The cows were fed forages produced locally. FAs in forages and milk samples were subjected to gas chromatography. Highest fat intake observed in grazing season (4·2-4·7%) and high amounts of polyunsaturated FA in forages from that period (51·8-64·1 g/100 g FA) resulted in a markedly high content of valuable FAs: t-11 C18:1 (3·22 g/100 g FA), c-9, t-11 C18:2 (CLA; 1·20 g/100 g FA) in milk. Lower fat intake of forages containing high amount of SFA (32·42-38·83 g/100 g FA) in the indoor period resulted in changes in milk composition. The content of total short-chain saturated FA (SCFA) was highest in winter and early spring samples (14·10 and 13·44 g/100 g FA, respectively), like the amounts of myristic C14:0 and palmitic C16:0 acids (11·80 and 37·92 g/100 g FA). Total odd- and branched-chain fatty acids (OBCFA; 6·58 g/100 g FA) content was highest at the beginning of the grazing period. Fresh grass consumed by cows promoted the activity of Δ(9)-desaturase in mammary gland as evidenced by higher C14:1 : C14:0 (0·054) and C16:1 : C16:0 (0·026) ratios in grazing than in the indoor periods.

  10. Wetlands serve as natural sources for improvement of stream ecosystem health in regions affected by acid deposition.

    PubMed

    Pound, Katrina L; Lawrence, Gregory B; Passy, Sophia I

    2013-09-01

    For over 40 years, acid deposition has been recognized as a serious international environmental problem, but efforts to restore acidified streams and biota have had limited success. The need to better understand the effects of different sources of acidity on streams has become more pressing with the recent increases in surface water organic acids, or 'brownification,' associated with climate change and decreased inorganic acid deposition. Here, we carried out a large scale multi-seasonal investigation in the Adirondacks, one of the most acid-impacted regions in the United States, to assess how acid stream producers respond to local and watershed influences and whether these influences can be used in acidification remediation. We explored the pathways of wetland control on aluminum chemistry and diatom taxonomic and functional composition. We demonstrate that streams with larger watershed wetlands have higher organic content, lower concentrations of acidic anions, and lower ratios of inorganic to organic monomeric aluminum, all beneficial for diatom biodiversity and guilds producing high biomass. Although brownification has been viewed as a form of pollution, our results indicate that it may be a stimulating force for biofilm producers with potentially positive consequences for higher trophic levels. Our research also reveals that the mechanism of watershed control of local stream diatom biodiversity through wetland export of organic matter is universal in running waters, operating not only in hard streams, as previously reported, but also in acid streams. Our findings that the negative impacts of acid deposition on Adirondack stream chemistry and biota can be mitigated by wetlands have important implications for biodiversity conservation and stream ecosystem management. Future acidification research should focus on the potential for wetlands to improve stream ecosystem health in acid-impacted regions and their direct use in stream restoration, for example, through

  11. Wetlands serve as natural sources for improvement of stream ecosystem health in regions affected by acid deposition

    USGS Publications Warehouse

    Pound, Katrina L; Lawrence, Gregory B.; Passy, Sophia I.

    2013-01-01

    For over 40 years, acid deposition has been recognized as a serious international environmental problem, but efforts to restore acidified streams and biota have had limited success. The need to better understand the effects of different sources of acidity on streams has become more pressing with the recent increases in surface water organic acids, or 'brownification' associated with climate change and decreased inorganic acid deposition. Here, we carried out a large scale multi-seasonal investigation in the Adirondacks, one of the most acid-impacted regions in the United States, to assess how acid stream producers respond to local and watershed influences and whether these influences can be used in acidification remediation. We explored the pathways of wetland control on aluminum chemistry and diatom taxonomic and functional composition. We demonstrate that streams with larger watershed wetlands have higher organic content, lower concentrations of acidic anions, and lower ratios of inorganic to organic monomeric aluminum, all beneficial for diatom biodiversity and guilds producing high biomass. Although brownification has been viewed as a form of pollution, our results indicate that it may be a stimulating force for biofilm producers with potentially positive consequences for higher trophic levels. Our research also reveals that the mechanism of watershed control of local stream diatom biodiversity through wetland export of organic matter is universal in running waters, operating not only in hard streams, as previously reported, but also in acid streams. Our findings that the negative impacts of acid deposition on Adirondack stream chemistry and biota can be mitigated by wetlands have important implications for biodiversity conservation and stream ecosystem management. Future acidification research should focus on the potential for wetlands to improve stream ecosystem health in acid-impacted regions and their direct use in stream restoration, for example, through

  12. Wetlands serve as natural sources for improvement of stream ecosystem health in regions affected by acid deposition.

    PubMed

    Pound, Katrina L; Lawrence, Gregory B; Passy, Sophia I

    2013-09-01

    For over 40 years, acid deposition has been recognized as a serious international environmental problem, but efforts to restore acidified streams and biota have had limited success. The need to better understand the effects of different sources of acidity on streams has become more pressing with the recent increases in surface water organic acids, or 'brownification,' associated with climate change and decreased inorganic acid deposition. Here, we carried out a large scale multi-seasonal investigation in the Adirondacks, one of the most acid-impacted regions in the United States, to assess how acid stream producers respond to local and watershed influences and whether these influences can be used in acidification remediation. We explored the pathways of wetland control on aluminum chemistry and diatom taxonomic and functional composition. We demonstrate that streams with larger watershed wetlands have higher organic content, lower concentrations of acidic anions, and lower ratios of inorganic to organic monomeric aluminum, all beneficial for diatom biodiversity and guilds producing high biomass. Although brownification has been viewed as a form of pollution, our results indicate that it may be a stimulating force for biofilm producers with potentially positive consequences for higher trophic levels. Our research also reveals that the mechanism of watershed control of local stream diatom biodiversity through wetland export of organic matter is universal in running waters, operating not only in hard streams, as previously reported, but also in acid streams. Our findings that the negative impacts of acid deposition on Adirondack stream chemistry and biota can be mitigated by wetlands have important implications for biodiversity conservation and stream ecosystem management. Future acidification research should focus on the potential for wetlands to improve stream ecosystem health in acid-impacted regions and their direct use in stream restoration, for example, through

  13. Ambient concentrations of atmospheric ammonia, nitrogen dioxide and nitric acid in an intensive agricultural region

    NASA Astrophysics Data System (ADS)

    Zbieranowski, Antoni L.; Aherne, Julian

    2013-05-01

    The spatial and temporal distribution of ambient atmospheric gaseous reactive nitrogen (Nr) species concentrations (ammonia [NH3], nitrogen dioxide [NO2] and nitric acid [HNO3]) were measured at the field scale in an intensive agricultural region in southern Ontario, Canada. Atmospheric concentrations were measured with the Willems badge diffusive passive sampler (18 sites for NH3, 9 sites for NO2 and HNO3) for one year (April 2010-March 2011; under a two week measurement frequency) within a 15 km × 15 km area. Dry deposition was calculated using the inferential method and estimated across the entire study area. The spatial distribution of emission sources associated with agricultural activity resulted in high spatial variability in annual average ambient NH3 concentrations (<3->8 μg m-3 within a 2 km distance, coefficient of variation ˜50%) and estimated dry deposition (4-13 kg N ha-1 yr-1) between sample sites. In contrast, ambient concentrations and deposition of both NO2 (˜5.2->6.5 μg m-3; 1.0-1.5 kg N ha-1 yr-1) and HNO3 (0.6-0.7 μg m-3; 0.5-1 kg N ha-1 yr-1) had low variability (coefficient of variation <10%). The observed NH3 concentrations accounted for ˜70% of gaseous Nr dry deposition. High NH3 concentrations suggest that reduced nitrogen species (NHx) will continue to make up an increasing fraction of Nr deposition within intensive agricultural regions in southern Ontario under legislated nitrogen oxide emission reductions. Further, estimated total inorganic Nr deposition (15-28 kg N ha-1 yr-1) may lead to potential changes in soil processes, nutrient imbalance and altered composition of mycorrhiza and ground vegetation within adjacent semi-natural ecosystems (estimated at ˜10% of the study area).

  14. Temperature dependence of amino acid side chain IR absorptions in the amide I' region.

    PubMed

    Anderson, Benjamin A; Literati, Alex; Ball, Borden; Kubelka, Jan

    2014-05-01

    Amide I' IR spectra are widely used for studies of structural changes in peptides and proteins as a function of temperature. Temperature dependent absorptions of amino acid side-chains that overlap the amide I' may significantly complicate the structural analyses. While the side-chain IR spectra have been investigated previously, thus far their dependence on temperature has not been reported. Here we present the study of the changes in the IR spectra with temperature for side-chain groups of aspartate, glutamate, asparagine, glutamine, arginine, and tyrosine in the amide I' region (in D2O). Band fitting analysis was employed to extract the temperature dependence of the individual spectral parameters, such as peak frequency, integrated intensity, band width, and shape. As expected, the side-chain IR bands exhibit significant changes with temperature. The majority of the spectral parameters, particularly the frequency and intensity, show linear dependence on temperature, but the direction and magnitude vary depending on the particular side-chain group. The exception is arginine, which exhibits a distinctly nonlinear frequency shift with temperature for its asymmetric CN3H5(+) bending signal, although a linear fit can account for this change to within ~1/3 cm(-1). The applicability of the determined spectral parameters for estimations of temperature-dependent side-chain absorptions in peptides and proteins are discussed.

  15. Hyaluronic acid-based hydrogel for regional delivery of paclitaxel to intraperitoneal tumors

    PubMed Central

    Bajaj, Gaurav; Kim, Mi Ran; Mohammed, Sulma I.; Yeo, Yoon

    2012-01-01

    Intraperitoneal (IP) chemotherapy is an effective way of treating local and regional malignancies confined in the peritoneal cavity such as ovarian cancer. However, a persistent major challenge in IP chemotherapy is the need to provide effective drug concentrations in the peritoneal cavity for an extended period of time. We hypothesized that hyaluronic acid (HA)-based in-situ crosslinkable hydrogel would serve as a carrier of paclitaxel (PTX) particles to improve their IP retention and therapeutic effects. In-vitro gel degradation and release kinetics studies demonstrated that HA gels could entrap microparticulate PTX (>100 μm) and release the drug over 10 days, gradually degraded by hyaluronidase, but had limited effect on retention of Taxol, a 14-nm micelle form of PTX. When administered IP to tumor-bearing nude mice, PTX was best retained in the peritoneal cavity as PTX-gel (microparticulate PTX entrapped in the HA gel), whereas Taxol-gel and other Taxol-based formulations left negligible amount of PTX in the cavity after 14 days. Despite the increase in IP retention of PTX, PTX-gel did not further decrease the tumor burdens than Taxol-based formulations, presumably due to the limited dissolution of PTX. This result indicates that spatial availability of a drug does not necessarily translate to the enhanced anti-tumor effect unless it is accompanied by the temporal availability. PMID:22178261

  16. Immunohistochemical characterization of glial fibrillary acidic protein (GFAP)-expressing cells in a rat liver cirrhosis model induced by repeated injections of thioacetamide (TAA).

    PubMed

    Tennakoon, Anusha Hemamali; Izawa, Takeshi; Wijesundera, Kavindra Kumara; Murakami, Hiroshi; Katou-Ichikawa, Chisa; Tanaka, Miyuu; Golbar, Hossain M; Kuwamura, Mitsuru; Yamate, Jyoji

    2015-01-01

    Hepatic stellate cells, the principal fibrogenic cell type in the liver, are known to express the astrocyte marker glial fibrillary acidic protein (GFAP). However, the exact role of GFAP-expressing cells in liver fibrosis remains to be elucidated. In this study, cellular properties of GFAP-expressing cells were investigated in a rat model of liver cirrhosis. Six-week-old male F344 rats were injected intraperitoneally with thioacetamide (100 mg/kg BW, twice a week) and examined at post first injection weeks 5, 10, 15, 20 and 25. Appearance of GFAP-expressing myofibroblasts peaked at week 15, associated with fibrosis progression. The majority of GFAP-expressing myofibroblasts co-expressed vimentin, desmin and alpha-smooth muscle actin. Some GFAP-positive myofibroblasts co-expressed nestin (neural stem cell marker), while a few co-expressed A3 (mesenchymal stem cell marker) and Thy-1 (immature mesenchymal cell marker). A few GFAP expressing cells underwent both mitosis and apoptosis. These results indicate that there is a dynamic participation of GFAP-expressing myofibroblasts in rat liver cirrhosis, and that they are mainly derived from hepatic stellate cells, and partly from cells in the stem cell lineage. These findings, which were shown for the first time in detail, would be useful to understand the role of GFAP-expressing myofibroblasts in the pathogenesis of chemically induced liver cirrhosis.

  17. A 90-day repeated dose oral (gavage) toxicity study of perfluorohexanoic acid (PFHxA) in rats (with functional observational battery and motor activity determinations).

    PubMed

    Chengelis, Christopher P; Kirkpatrick, Jeannie B; Radovsky, Ann; Shinohara, Motoki

    2009-06-01

    Possible toxic effects of perfluorohexanoic acid (PFHxA) were evaluated when administered orally by gavage to rats at levels up to 200mg/kg/day for 90 days. Lower body weight gains were noted in the 10, 50 and 200mg/kg/day group males (not dose-responsive) throughout dosing. Other changes included lower red blood cell parameters, higher reticulocyte counts and lower globulin in the 200mg/kg/day group males and females, higher liver enzymes in males at 50 and 200mg/kg/day, lower total protein and higher albumin/globulin ratio, and lower cholesterol, calcium in males at 200mg/kg/day. Minimal centrilobular hepatocellular hypertrophy was present in 200mg/kg/day group males and correlated with higher liver weights and slightly higher peroxisome beta oxidation activity at the end of the dosing period. Based on liver histopathology and liver weight changes, the no-observed-adverse-effect level (NOAEL) for oral administration was 50mg/kg/day for males and 200mg/kg/day for females.

  18. Short and long range functions of amino acids in the transmembrane region of the sarcoplasmic reticulum ATPase. A mutational study.

    PubMed

    Chen, L; Sumbilla, C; Lewis, D; Zhong, L; Strock, C; Kirtley, M E; Inesi, G

    1996-05-01

    Mutational analysis of several amino acids in the transmembrane region of the sarcoplasmic reticulum ATPase was performed by expressing wild type ATPase and 32 site-directed mutants in COS-1 cells followed by functional characterization of the microsomal fraction. Four different phenotype characteristics were observed in the mutants: (a) functions similar to those sustained by the wild type ATPase; (b) Ca2+ transport inhibited to a greater extent than ATPase hydrolytic activity; (c) inhibition of transport and hydrolytic activity in the presence of high levels of phosphorylated enzyme intermediate; and (d) total inhibition of ATP utilization by the enzyme while retaining the ability to form phosphoenzyme by utilization of P(i). Analysis of experimental observations and molecular models revealed short and long range functions of several amino acids within the transmembrane region. Short range functions include: (a) direct involvement of five amino acids in Ca2+ binding within a channel formed by clustered transmembrane helices M4, M5, M6, and M8; (b) roles of several amino acids in structural stabilization of the helical cluster for optimal channel function; and (c) a specific role of Lys297 in sealing the distal end of the channel, suggesting that the M4 helix rotates to allow vectorial flux of Ca2+ upon enzyme phosphorylation. Long range functions are related to the influence of several transmembrane amino acids on phosphorylation reactions with ATP or P(i), transmitted to the extramembranous region of the ATPase in the presence or in the absence of Ca2+.

  19. Analysis of glial fibrillary acidic protein (GFAP)-expressing ductular cells in a rat liver cirrhosis model induced by repeated injections of thioacetamide (TAA).

    PubMed

    Tennakoon, Anusha H; Izawa, Takeshi; Wijesundera, Kavindra K; Katou-Ichikawa, Chisa; Tanaka, Miyuu; Golbar, Hossain M; Kuwamura, Mitsuru; Yamate, Jyoji

    2015-06-01

    Glial fibrillary acidic protein (GFAP), a type III intermediate filament protein, is expressed in hepatic stellate cells (HSCs), the principal fibrogenic cell type in the liver. Further, GFAP could be a marker for hepatic progenitor cells (HPCs). In this study, the participation of GFAP-expressing cells in HPC expansion/ductular reaction was investigated in a rat model of liver cirrhosis. Six-week-old male F344 rats were injected intraperitoneally with thioacetamide (100mg/kg BW, twice a week) and examined at post-first injection weeks 5, 10, 15, 20 and 25. Fibrosis-related proliferation of ductular cells was observed as demonstrated by CK19 immunostaining. Some of these cells were stained with GFAP. No co-staining was observed between CK19 and α-smooth muscle actin (α-SMA; myofibroblast marker). There were proliferating ductular cells stained with α-fetoprotein or β-catenin; the ductular reaction was related to increased expression of hepatocarcinogenesis-related factors (Wnt2, Wnt4 and glypican-3). These results for the first time show the participation of GFAP-positive HPCs in ductular reaction in a chemically induced rodent model. Though the ductular cells were chaperoned by myofibroblasts, they show no direct evidence for epithelial to mesenchymal transition. These findings shed new light in understanding the roles of GFAP-expressing HPCs in liver cirrhosis and provide further evidence of interaction between newly-formed bile ductules and HSCs, suggesting that both cells could be in the common lineage of HPCs.

  20. An acute dose of gamma-hydroxybutyric acid alters gene expression in multiple mouse brain regions.

    PubMed

    Schnackenberg, B J; Saini, U T; Robinson, B L; Ali, S F; Patterson, T A

    2010-10-13

    Gamma-hydroxybutyric acid (GHB) is normally found in the brain in low concentrations and may function as a neurotransmitter, although the mechanism of action has not been completely elucidated. GHB has been used as a general anesthetic and is currently used to treat narcolepsy and alcoholism. Recreational use of GHB is primarily as a "club drug" and a "date rape drug," due to its amnesic effects. For this study, the hypothesis was that behavioral and neurochemical alterations may parallel gene expression changes in the brain after GHB administration. Adult male C57/B6N mice (n=5/group) were administered a single dose of 500 mg/kg GHB (i.p.) and were sacrificed 1, 2 and 4 h after treatment. Control mice were administered saline. Brains were removed and regionally dissected on ice. Total RNA from the hippocampus, cortex and striatum was extracted, amplified and labeled. Gene expression was evaluated using Agilent whole mouse genome 4x44K oligonucleotide microarrays. Microarray data were analyzed by ArrayTrack and differentially expressed genes (DEGs) were identified using P < or = 0.01 and a fold change > or = 1.7 as the criteria for significance. Principal component analysis (PCA) and Hierarchical Cluster Analysis (HCA) showed that samples from each time point clustered into distinct treatment groups with respect to sacrifice time. Ingenuity pathways analysis (IPA) was used to identify involved pathways. The results show that GHB induces gene expression alterations in hundreds of genes in the hippocampus, cortex and striatum, and the number of affected genes increases throughout a 4-h time course. Many of these DEGs are involved in neurological disease, apoptosis, and oxidative stress.

  1. A 40-month multicentre, randomised placebo-controlled study to assess the efficacy and carry-over effect of repeated intra-articular injections of hyaluronic acid in knee osteoarthritis: the AMELIA project

    PubMed Central

    Navarro-Sarabia, F; Coronel, P; Collantes, E; Navarro, F J; de la Serna, A Rodriguez; Naranjo, A; Gimeno, M; Herrero-Beaumont, G

    2011-01-01

    Objective AMELIA (OsteoArthritis Modifying Effects of Long-term Intra-articular Adant) was designed to compare against placebo the efficacy and safety of repeated injections of hyaluronic acid (HA) and its effect on disease progression over 40 months. Methods A multicentre, randomised, patient and evaluator-blinded, controlled study in 306 patients fulfilling American College of Rheumatology criteria for knee osteoarthritis, radiological grades II–III (Kellgren–Lawrence) and joint space width ≥2 mm. Patients received four cycles of five intra-articular HA or placebo injections with a follow-up of 6 months after the first and second cycles, and 1 year after the third and fourth cycles. Osteoarthritis Research Society International (OARSI) 2004 responder criteria were used to assess efficacy. The consumption of rescue medication was a secondary outcome. Adverse events were recorded for safety purposes. Results At the 40-month visit significantly more patients responded to HA compared with placebo (OARSI 2004, p=0.004). The number of responders to HA increased through the study, whereas those to placebo did not change. Significant differences were also found in favour of HA for each individual component of the OARSI 2004. No safety problems were recorded. Conclusions The results of AMELIA offer pioneer evidence that repeated cycles of intra-articular injections of HA not only improve knee osteoarthritis symptoms during the in-between cycle period but also exert a marked carry-over effect for at least 1 year after the last cycle. In this respect, it is not possible to establish if this carry-over effect reflects true osteoarthritis remission or just a modification of the disease's natural course. ClinicalTrials.gov number, NCT00669032 PMID:21852252

  2. Oligomerization of the hydrophobic heptad repeat of gp41.

    PubMed Central

    Bernstein, H B; Tucker, S P; Kar, S R; McPherson, S A; McPherson, D T; Dubay, J W; Lebowitz, J; Compans, R W; Hunter, E

    1995-01-01

    The transmembrane protein of human immunodeficiency virus type 1 (HIV-1) contains a leucine zipper-like (hydrophobic heptad) repeat which has been predicted to form an amphipathic alpha helix. To evaluate the potential of the hydrophobic heptad repeat to induce protein oligomerization, this region of gp41 has been cloned into the bacterial expression vector pRIT2T. The resulting plasmid, pRIT3, expresses a fusion protein consisting of the Fc binding domain of monomeric protein A, a bacterial protein, and amino acids 538 to 593 of HIV-1 gp41. Gel filtration chromatography demonstrated the presence of oligomeric forms of the fusion protein, and analytical centrifugation studies confirmed that the chimeric protein formed a higher-order multimer that was greater than a dimer. Thus, we have identified a region of HIV-1 gp41 which is capable of directing the oligomerization of a fusion protein containing monomeric protein A. Point mutations, previously shown to inhibit the biological activity of the HIV-1 envelope glycoprotein, have been engineered into the segment of gp41 contained in the fusion protein, and expressed mutant proteins were purified and analyzed via fast protein liquid chromatography. A point mutation in the heptad repeat, which changed the central isoleucine to an alanine, caused a significant (> 60%) decrease in oligomerization, whereas changing the central isoleucine to aspartate or proline resulted in almost a complete loss of oligomerization. Deletions of one, two, or three amino acids following the first isoleucine also resulted in a profound decrease in oligomerization. The inhibitory effects of the mutations on oligomer formation correlated with the effects of the same mutations on envelope glycoprotein-mediated fusion. A possible role of the leucine zipper-like region in the fusion process and in an oligomerization event distinct from assembly of the envelope glycoprotein complex is discussed. PMID:7707497

  3. Responses of streams in central Appalachian Mountain region to reduced acidic deposition--comparisons with other regions in North America and Europe.

    PubMed

    Chen, Yushun; Lin, Lian-Shin

    2009-03-15

    Data from 5 wet deposition stations and 21 streams during 1980-2006 were analyzed to investigate chemical responses of streams to reduced acidic deposition in the central Appalachian Mountain region of West Virginia, USA. Wet deposition of acidic anions (i.e., sulfate, nitrate, and chloride) and hydrogen ions decreased significantly during the studied time period. Stream sulfate showed a delayed response to the reduced acidic deposition, and showed a decrease in the 2000s (-5.54 microeq L(-1) yr(-1)) and the whole period (-0.49 microeq L(-1) yr(-1)). No significant trend of stream nitrate+nitrite and chloride was observed. Stream alkalinity increased in the 1990s (+23.33 microeq L(-1) yr(-1)) and the whole period (+7.26 microeq L(-1) yr(-1)). Stream hydrogen ions decreased in the 1990s (-0.002 microeq L(-1) yr(-1)), 2000s (-0.001 microeq L(-1) yr(-1)), and the whole period (-0.001 microeq L(-1) yr(-1)). Compared with most acidic streams and lakes in the United States and Europe, a lower decreasing rate of hydrogen ions and higher increasing rate of alkalinity were observed in the alkaline West Virginian streams in the 1990s. However, due to their initial negative or zero alkalinity values, those acidic streams showed a higher percent increase in alkalinity than that in the alkaline West Virginian streams (from 800 microeq L(-1) yr(-1) to 1200 microeq L(-1) yr(-1)). Total aluminum in the West Virginian streams decreased in the 1990s (-0.67 micromol L(-1) yr(-1)) and the whole period (-0.22 micromol L(-1) yr(-1)). The current study advanced our understanding of streams' responses to the reduced acidic deposition in the Mid-Appalachians since the passage of the 1970 and 1990 Amendments to the United States Clean Air Act (US CAAA).

  4. Voltage-dependent motion of the catalytic region of voltage-sensing phosphatase monitored by a fluorescent amino acid

    PubMed Central

    Sakata, Souhei; Jinno, Yuka; Kawanabe, Akira; Okamura, Yasushi

    2016-01-01

    The cytoplasmic region of voltage-sensing phosphatase (VSP) derives the voltage dependence of its catalytic activity from coupling to a voltage sensor homologous to that of voltage-gated ion channels. To assess the conformational changes in the cytoplasmic region upon activation of the voltage sensor, we genetically incorporated a fluorescent unnatural amino acid, 3-(6-acetylnaphthalen-2-ylamino)-2-aminopropanoic acid (Anap), into the catalytic region of Ciona intestinalis VSP (Ci-VSP). Measurements of Anap fluorescence under voltage clamp in Xenopus oocytes revealed that the catalytic region assumes distinct conformations dependent on the degree of voltage-sensor activation. FRET analysis showed that the catalytic region remains situated beneath the plasma membrane, irrespective of the voltage level. Moreover, Anap fluorescence from a membrane-facing loop in the C2 domain showed a pattern reflecting substrate turnover. These results indicate that the voltage sensor regulates Ci-VSP catalytic activity by causing conformational changes in the entire catalytic region, without changing their distance from the plasma membrane. PMID:27330112

  5. Using the regional acid deposition model to determine the nitrogen deposition airshed of the Chesapeake Bay watershed. Book chapter

    SciTech Connect

    Dennis, R.L.

    1995-08-25

    The Regional Acid Deposition Model, RADM, an advanced Eulerian model, is used to develop an estimate of the primary airshed of nitrogen oxide (NOx) emissions that is contributing nitrogen deposition to the Chesapeake Bay watershed. A brief description of RADM together with a summary of the aggregation method used to develop annual average deposition is given. The evaluation background of RADM is summarized. The transport range of the nitrogen affecting deposition, principally the termination product nitric acid, is first established in the model. This range is compared to that determined for sulfur.

  6. Effectiveness of Folic Acid Fortified Flour for Prevention of Neural Tube Defects in a High Risk Region

    PubMed Central

    Wang, Haochen; De Steur, Hans; Chen, Gong; Zhang, Xiaotian; Pei, Lijun; Gellynck, Xavier; Zheng, Xiaoying

    2016-01-01

    Despite efforts to tackle folate deficiency and Neural Tube Defects (NTDs) through folic acid fortification, its implementation is still lacking where it is needed most, highlighting the need for studies that evaluate the effectiveness of folic acid fortified wheat flour in a poor, rural, high-risk, NTD region of China. One of the most affected regions, Shanxi Province, was selected as a case study. A community intervention was carried out in which 16,648 women of child-bearing age received fortified flour (eight villages) and a control group received ordinary flour (three villages). NTD birth prevalence and biological indicators were measured two years after program initiation at endline only. The effect on the NTD burden was calculated using the disability-adjusted life years (DALYs) method. In the intervention group, serum folate level was higher than in the control group. NTDs in the intervention group were 68.2% lower than in the control group (OR = 0.313, 95% CI = 0.207–0473, p < 0.001). In terms of DALYs, burden in intervention group was approximately 58.5% lower than in the control group. Flour fortification was associated with lower birth prevalence and burden of NTDs in economically developing regions with a high risk of NTDs. The positive findings confirm the potential of fortification when selecting an appropriate food vehicle and target region. As such, this study provides support for decision makers aiming for the implementation of (mandatory) folic acid fortification in China. PMID:27005659

  7. Altered development and function of the placental regions in preeclampsia and its association with long-chain polyunsaturated fatty acids.

    PubMed

    Rani, Alka; Wadhwani, Nisha; Chavan-Gautam, Preeti; Joshi, Sadhana

    2016-09-01

    The placenta is an essential organ formed during pregnancy that mainly transfers nutrients from the mother to the fetus. Nutrients taken up by the placenta are required for its own growth and development and to optimize fetal growth. Hence, placental function is an important determinant of pregnancy outcome. Among various nutrients, fatty acids, especially long-chain polyunsaturated fatty acids (LCPUFAs), including omega 3 and omega 6 fatty acids, are essential for placental development from the time of implantation. Studies have associated these LCPUFAs with placental development through their roles in regulating oxidative stress, angiogenesis, and inflammation, which may in turn influence their transfer to the fetus. The placenta has a heterogeneous morphology with variable regional vasculature, oxidative stress, and LCPUFA levels in healthy pregnancies depending upon the location within the placenta. However, these regional structural and functional parameters are found to be disturbed in pathological conditions, such as preeclampsia (PE), thereby affecting pregnancy outcome. Hence, the alterations in LCPUFA metabolism and transport in different regions of the PE placenta as compared with normal placenta could potentially be contributing to the pathological features of PE. The regional variations in development and function of the placenta and its possible association with placental LCPUFA metabolism and transport in normal and PE pregnancies are discussed in this review. WIREs Dev Biol 2016, 5:582-597. doi: 10.1002/wdev.238 For further resources related to this article, please visit the WIREs website. PMID:27239793

  8. Differentiation of Positional Isomers of Hybrid Peptides Containing Repeats of β-Nucleoside Derived Amino Acid (β-Nda-) and L-Amino Acids by Positive and Negative Ion Electrospray Ionization Tandem Mass Spectrometry (ESI-MS n )

    NASA Astrophysics Data System (ADS)

    Raju, B.; Ramesh, M.; Srinivas, R.; Chandrasekhar, S.; Kiranmai, N.; Sarma, V. U. M.

    2011-04-01

    A new class of positional isomeric pairs of -Boc protected oligopeptides comprised of alternating nucleoside derived β-amino acid (β-Nda-) and L-amino acid residues (alanine, valine, and phenylalanine) have been differentiated by both positive and negative ion electrospray ionization ion-trap tandem mass spectrometry (ESI-MS n ). The protonated dipeptide positional isomers with β-Nda- at the N-terminus lose CH3OH, NH3, and C2H4O2, whereas these processes are absent for the peptides with L-amino acids at the N-terminus. Instead, the presence of L-amino acids at the N-terminus results in characteristic retro-Mannich reaction involving elimination of imine. A good correlation has been observed between the conformational structure of the peptides and the abundance of y{n/+} and b{n/+} ions in MS n spectra. In the case of tetrapeptide isomers that are reported to form helical structures in solution phase, no y{n/+} and b{n/+} ions are observed when the corresponding amide -NH- participates in the helical structures. In contrast, significant y{n/+} and b{n/+} ions are formed when the amide -NH- is not involved in the H-bonding. In the case of tetra- and hexapeptides, it is observed that abundant b{n/+} ions are formed, presumably with stable oxazolone structures when the C-terminus of the b{n/+} ions possessed L-amino acid and the β-Nda- at the C-terminus appears to prevent the cyclization process leading to the absence of corresponding b{n/+} ions.

  9. Perfluorinated carboxylic and sulphonic acids in surface water media from the regions of Tibetan Plateau: Indirect evidence on photochemical degradation?

    PubMed

    Yamazaki, Eriko; Falandysz, Jerzy; Taniyasu, Sachi; Hui, Ge; Jurkiewicz, Gabriela; Yamashita, Nobuyoshi; Yang, Yong-Liang; Lam, Paul K S

    2016-01-01

    Perfluorinated surfactants and repellents are synthetic substances that have found numerous industrial and customer applications. Due to their persistence, at least two groups of these substances-perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonic acids (PFSAs)-are diffused widely in the environment. It is hypothesized that the Tibetan Plateau, is one of few unique places on the Earth, due to its topography, specifically the vast space and high elevation above sea level, geographic location, climate, high solar radiation, lack of industry, little urbanization and general lack of significant direct sources of pollution. There it is believed possible to gain an insight into atmospheric fate (possible photochemical degradation of higher molecular mass and formation of lower molecular mass PFCAs and PFSAs) of PFASs under un-disturbed environmental conditions. Ultratrace analytical method for PFCAs and PFSAs and use of transportation and field blanks, laboratory blanks and isotopically labelled surrogates for recovery control has allowed the determination of nine perfluorinated carboxylic acids and six perfluorinated sulfonic acids at ultra-trace levels in water based samples from the alpine dimension regions of the Tibetan Plateau, the eastern slope of Minya Konka peak at the eastern edge of the Tibetan Plateau, and also from the city of Chengdu from the lowland of the Sichuan Province in China. The specific compositional pattern of PFCAs and PFSAs and low levels of pollution with those compounds were observed in the central region of the Tibetan Plateau and in the region adjacent to the peaks of Minya Konka in the Eastern Tibetan Plateau. The fingerprint of the compositional pattern of PFCAs and PFSAs in water samples in the central region of the Tibetan Plateau and in the alpine region adjacent to the peaks of Minya Konka in the Eastern Tibetan Plateau may be explained by the result of photochemical degradation with dealkylation of longer chain

  10. Comparative evaluation of essential fatty acid composition of mothers' milk of some urban and suburban regions of West Bengal, India.

    PubMed

    Roy, Susmita; Dhar, Pubali; Ghosh, Santinath

    2012-12-01

    This study investigated the fatty acid composition of lipid present in breast milk of mothers residing in urban and suburban regions of West Bengal with special emphasis on n-6 and n-3 polyunsaturated fatty acids, which played a crucial role in the growth and development of neonates. Milk samples collected from 135 mothers of middle income group (average monthly income around 'Rs 10,000/-') were analysed by gas liquid chromatography after extraction and transmethylation to determine fatty acid composition. Information about the dietary intake of individual mothers was obtained through food frequency questionnaire. The fractions of n-6 and n-3 polyunsaturated fatty acids available in milk of urban mothers were 13.59 ± 0.94 and 3.65 ± 0.49, respectively, and in suburban mothers 12.74 ± 0.89 and 4.36 ± 0.39, respectively. The green leafy vegetables, fishes and vegetable oils were the major sources of essential fatty acids in the diet of the experimental groups of Bengali mothers. This study revealed a relationship between the alimentary habits of mothers and the concentration of essential fatty acids in breast milk of Bengali mothers.

  11. Acylation of keratinocyte transglutaminase by palmitic and myristic acids in the membrane anchorage region

    SciTech Connect

    Chakravarty, R.; Rice, R.H.

    1989-01-05

    The membrane-bound form of keratinocyte transglutaminase was found to be labeled by addition of (/sup 3/H) acetic, (/sup 3/H)myristic, or (/sup 3/H)palmitic acids to the culture medium of human epidermal cells. Acid methanolysis and high performance liquid chromatography analysis of palmitate-labeled transglutaminase yielded only methyl palmitate. In contrast, analysis of the myristate-labeled protein yielded approximately 40% methyl myristate and 60% methyl palmitate. Incorporation of neither label was significantly affected by cycloheximide inhibition of protein synthesis. The importance of the fatty acid moiety for membrane anchorage was demonstrated in three ways. First, the enzyme was solubilized from the particulate fraction of cell extracts by treatment with neutral 1 M hydroxylamine, which was sufficient to release the fatty acid label. Second, solubilization of active enzyme from the particulate fraction upon mild trypsin treatment resulted in a reduction in size by approximately 10 kDa and removal of the fatty acid radiolabels. Third, the small fraction of soluble transglutaminase in cell extracts was found almost completely to lack fatty acid labeling. Keratinocyte transglutaminase translated from poly(A+) RNA in a reticulocyte cell-free system was indistinguishable in size from the native enzyme, suggesting anchorage requires only minor post-translational processing. Thus, the data are highly compatible with membrane anchorage by means of fatty acid acylation within 10 kDa of the NH/sub 2/ or COOH terminus.

  12. Effects of ethylene and gibberellic Acid on cellular growth and development in apical and subapical regions of etiolated pea seedling.

    PubMed

    Stewart, R N; Lieberman, M; Kunishi, A T

    1974-07-01

    Subhook swelling of 4-day-old etiolated pea seedlings (var. Alaska), caused by 0.5 microliter per liter ethylene, was prevented by preincubation and continued growth in 0.1 mm gibberellic acid (GA). The subhook region exhibited normal elongation and cell size and volume. However, inhibition of elongation and cessation of cell division caused by 0.5 microliter per liter ethylene in the apical hook region of the etiolated pea stem were not overcome by GA. Most of the arrested cells were in G(2). These data suggest a possible interaction of GA and ethylene in cell enlargement in the subhook region of the etiolated pea seedlings. They also suggest a different mode of action by ethylene in the apical hook region where the ethylene effect was not counteracted by GA. PMID:16658821

  13. Seven New Complete Plastome Sequences Reveal Rampant Independent Loss of the ndh Gene Family across Orchids and Associated Instability of the Inverted Repeat/Small Single-Copy Region Boundaries

    PubMed Central

    Moore, Michael J.; Neubig, Kurt M.; Williams, Norris H.; Whitten, W. Mark; Kim, Joo-Hwan

    2015-01-01

    Earlier research has revealed that the ndh loci have been pseudogenized, truncated, or deleted from most orchid plastomes sequenced to date, including in all available plastomes of the two most species-rich subfamilies, Orchidoideae and Epidendroideae. This study sought to resolve deeper-level phylogenetic relationships among major orchid groups and to refine the history of gene loss in the ndh loci across orchids. The complete plastomes of seven orchids, Oncidium sphacelatum (Epidendroideae), Masdevallia coccinea (Epidendroideae), Sobralia callosa (Epidendroideae), Sobralia aff. bouchei (Epidendroideae), Elleanthus sodiroi (Epidendroideae), Paphiopedilum armeniacum (Cypripedioideae), and Phragmipedium longifolium (Cypripedioideae) were sequenced and analyzed in conjunction with all other available orchid and monocot plastomes. Most ndh loci were found to be pseudogenized or lost in Oncidium, Paphiopedilum and Phragmipedium, but surprisingly, all ndh loci were found to retain full, intact reading frames in Sobralia, Elleanthus and Masdevallia. Character mapping suggests that the ndh genes were present in the common ancestor of orchids but have experienced independent, significant losses at least eight times across four subfamilies. In addition, ndhF gene loss was correlated with shifts in the position of the junction of the inverted repeat (IR) and small single-copy (SSC) regions. The Orchidaceae have unprecedented levels of homoplasy in ndh gene presence/absence, which may be correlated in part with the unusual life history of orchids. These results also suggest that ndhF plays a role in IR/SSC junction stability. PMID:26558895

  14. Factors affecting acid neutralizing capacity in the Adirondack region of New York: a solute mass balance approach.

    PubMed

    Ito, Mari; Mitchell, Myron J; Driscoll, Charles T; Roy, Karen M

    2005-06-01

    High rates of acidic deposition in the Adirondack region of New York have accelerated acidification of soils and surface waters. Annual input-output budgets for major solutes and acid-neutralizing capacity (ANC) were estimated for 43 drainage lake-watersheds in the Adirondacks from 1998 to 2000. Sulfate was the predominant anion on an equivalent basis in both precipitation and drainage export. Calcium ion had the largest cation drainage export, followed by Mg2+. While these watersheds showed net nitrogen (N) retention, the drainage losses of SO4(2-), Cl-, base cations, and ANC exceeded their respective inputs from precipitation. Land cover (forest type and wetlands) affected the export of SO4(2-), N solutes, and dissolved organic carbon (DOC). The relationships of solute export with elevation (negative for base cations and Cl-, positive for NO3- and H+) suggest the importance of the concomitant changes of biotic and abiotic watershed characteristics associated with elevational gradients. The surface water ANC increased with the sum of base cations and was greatest in the lakes with watersheds characterized by thick deposits of glacial till. The surface water ANC was also higher in the lake-watersheds with lower DOC export. Some variation in lake ANC was associated with variability in acidic deposition. Using a classification system previously developed for Adirondack lakes on the basis primarily of surficial geology, lake-watersheds were grouped into five classes. The calculated ANC fluxes based on the major sinks and sources of ANC were comparable with measured ANC for the thick-till (I) and the medium-till lake-watersheds with low DOC (II). The calculated ANC was overestimated for the medium-till with high DOC (III) and the thin-till with high DOC (V) lake-watersheds, suggesting the importance of naturally occurring organic acids as an ANC sink, which was not included in the calculations. The lower calculated estimates than the measured ANC for the thin-till lake

  15. A Tat-conjugated Peptide Nucleic Acid Tat-PNA-DR Inhibits Hepatitis B Virus Replication In Vitro and In Vivo by Targeting LTR Direct Repeats of HBV RNA

    PubMed Central

    Zeng, Zhengyang; Han, Shisong; Hong, Wei; Lang, Yange; Li, Fangfang; Liu, Yongxiang; Li, Zeyong; Wu, Yingliang; Li, Wenxin; Zhang, Xianzheng; Cao, Zhijian

    2016-01-01

    Hepatitis B virus (HBV) infection is a major cause of chronic active hepatitis, cirrhosis, and primary hepatocellular carcinoma, all of which are severe threats to human health. However, current clinical therapies for HBV are limited by potential side effects, toxicity, and drug-resistance. In this study, a cell-penetrating peptide-conjugated peptide nucleic acid (PNA), Tat-PNA-DR, was designed to target the direct repeat (DR) sequences of HBV. Tat-PNA-DR effectively inhibited HBV replication in HepG2.2.15 cells. Its anti-HBV effect relied on the binding of Tat-PNA-DR to the DR, whereby it suppressed the translation of hepatitis B e antigen (HBeAg), HBsAg, HBV core, hepatitis B virus x protein, and HBV reverse transcriptase (RT) and the reverse transcription of the HBV genome. Furthermore, Tat-PNA-DR administered by intravenous injection efficiently cleared HBeAg and HBsAg in an acute hepatitis B mouse model. Importantly, it induced an 80% decline in HBV DNA in mouse serum, which was similar to the effect of the widely used clinical drug Lamivudine (3TC). Additionally, a long-term hydrodynamics HBV mouse model also demonstrated Tat-PNA-DR's antiviral effect. Interestingly, Tat-PNA-DR displayed low cytotoxicity, low mouse acute toxicity, low immunogenicity, and high serum stability. These data indicate that Tat-PNA-DR is a unique PNA and a promising drug candidate against HBV. PMID:26978579

  16. Enhanced Extracorporeal CO2 Removal by Regional Blood Acidification: Effect of Infusion of Three Metabolizable Acids.

    PubMed

    Scaravilli, Vittorio; Kreyer, Stefan; Linden, Katharina; Belenkiy, Slava; Pesenti, Antonio; Zanella, Alberto; Cancio, Leopoldo C; Batchinsky, Andriy I

    2015-01-01

    Acidification of blood entering a membrane lung (ML) with lactic acid enhances CO2 removal (VCO2ML). We compared the effects of infusion of acetic, citric, and lactic acids on VCO2ML. Three sheep were connected to a custom-made circuit, consisting of a Hemolung device (Alung Technologies, Pittsburgh, PA), a hemofilter (NxStage, NxStage Medical, Lawrence, MA), and a peristaltic pump recirculating ultrafiltrate before the ML. Blood flow was set at 250 ml/min, gas flow (GF) at 10 L/min, and recirculating ultrafiltrate flow at 100 ml/min. Acetic (4.4 M), citric (0.4 M), or lactic (4.4 M) acids were infused in the ultrafiltrate at 1.5 mEq/min, for 2 hours each, in randomized fashion. VCO2ML was measured by the Hemolung built-in capnometer. Circuit and arterial blood gas samples were collected at baseline and during acid infusion. Hemodynamics and ventilation were monitored. Acetic, citric, or lactic acids similarly enhanced VCO2ML (+35%), from 37.4 ± 3.6 to 50.6 ± 7.4, 49.8 ± 5.6, and 52.0 ± 8.2 ml/min, respectively. Acids similarly decreased pH, increased pCO2, and reduced HCO3 of the post-acid extracorporeal blood sample. No significant effects on arterial gas values, ventilation, or hemodynamics were observed. In conclusion, it is possible to increase VCO2ML by more than one-third using any one of the three metabolizable acids.

  17. Stereo and region-selective biosynthesis of two new dihydroartemisinic acid glycosides by suspension-cultured cells of Artemisia annua

    PubMed Central

    Zhu, Jianhua; Zeng, Zihan; Song, Liyan; Hu, Yanshan; Wen, Wei; Yu, Rongming

    2014-01-01

    Background: The system of plant-cultured cells is one of the optimal systems to investigate biosynthesis pathway and their bioactive intermediates. Objective: To study the biosynthesis of dihydroartemisinic acid (1) by suspension-cultured cells of Artemisia annua. Materials and Methods: Substrate (compound 1) was administered into the suspension-cultured cells of A. annua and co-cultured for 2 days. The methanol extract was separated on various column chromatography methods and the structures of two biosynthesis products were elucidated based on the analysis of 1H NMR, 13C NMR, 2D NMR, and ESI-MS. Time-course curve was also established. Furthermore, in vitro antitumor activities of compounds 1-3 against HepG2, K562, and A549 cell lines were evaluated by MTT assay. Results: Two new compounds were obtained, namely 3α-hydroxy-dihydroartemisinic acid-α-D-glucopyranosyl ester (2) and 15-hydroxy-cadin-4-en-12-oic acid-β-d-glucopyranosyl ester (3). The results demonstrated that the cultured cells of A. annua possessed the abilities to stereo-selective hydroxylate and region-selective glycosylate sesquiterpene compounds in a highly efficient manner. Inhibitory effects of compounds 1-3 on proliferation of HepG2, K562, and A549 cell lines in vitro were also investigated. Conclusion: Two new dihydroartemisinic acid glycosides were obtained by stereo- and region-selective biosynthesis with cultured cells of A. annua. PMID:24914289

  18. Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization

    SciTech Connect

    Shiheido, Hirokazu Shimizu, Jun

    2015-02-20

    BEN domain-containing protein 3 (BEND3) has recently been reported to function as a heterochromatin-associated protein in transcriptional repression in the nucleus. BEND3 should have nuclear localization signals (NLSs) to localize to the nucleus in light of its molecular weight, which is higher than that allowed to pass through nuclear pore complexes. We here analyzed the subcellular localization of deletion/site-directed mutants of human BEND3 by an immunofluorescence assay in an attempt to identify the amino acids essential for its nuclear localization. We found that three basic amino acid residues located in the N-terminal region of BEND3 (BEND3{sub 56–58}, KRK) are essential, suggesting that these residues play a role as a functional NLS. These results provide valuable information for progressing research on BEND3. - Highlights: • BEND3 localizes to the nucleus. • The N-terminal 60 amino acids region of BEND3 contains NLS. • Amino acids located between 56 and 58 of BEND3 (KRK) are part of NLS. • KRK motif is highly conserved among BEND3 homologs.

  19. Honesty through repeated interactions.

    PubMed

    Rich, Patricia; Zollman, Kevin J S

    2016-04-21

    In the study of signaling, it is well known that the cost of deception is an essential element for stable honest signaling in nature. In this paper, we show how costs for deception can arise endogenously from repeated interactions between individuals. Utilizing the Sir Philip Sidney game as an illustrative case, we show that repeated interactions can sustain honesty with no observable signal costs, even when deception cannot be directly observed. We provide a number of potential experimental tests for this theory which distinguish it from the available alternatives.

  20. A highly conserved region between amino acids 221 and 266 of dengue virus non-structural protein 1 is a major epitope region in infected patients.

    PubMed

    Omokoko, Magot Diata; Pambudi, Sabar; Phanthanawiboon, Supranee; Masrinoul, Promsin; Setthapramote, Chayanee; Sasaki, Tadahiro; Kuhara, Motoki; Ramasoota, Pongrama; Yamashita, Akifumi; Hirai, Itaru; Ikuta, Kazuyoshi; Kurosu, Takeshi

    2014-07-01

    The immune response to dengue virus (DENV) infection generates high levels of antibodies (Abs) against the DENV non-structural protein 1 (NS1), particularly in cases of secondary infection. Therefore, anti-NS1 Abs may play a role in severe dengue infections, possibly by interacting (directly or indirectly) with host factors or regulating virus production. If it does play a role, NS1 may contain epitopes that mimic those epitopes of host molecules. Previous attempts to map immunogenic regions within DENV-NS1 were undertaken using mouse monoclonal Abs (MAbs). The aim of this study was to characterize the epitope regions of nine anti-NS1 human monoclonal Abs (HuMAbs) derived from six patients secondarily infected with DENV-2. These anti-NS1 HuMAbs were cross-reactive with DENV-1, -2, and -3 but not DENV-4. All HuMAbs bound a common epitope region located between amino acids 221 and 266 of NS1. This study is the first report to map a DENV-NS1 epitope region using anti-DENV MAbs derived from patients. PMID:24778195

  1. A Semiparametric Bayesian Model for Repeatedly Repeated Binary Outcomes

    PubMed Central

    Quintana, Fernando A.; Müller, Peter; Rosner, Gary L.; Relling, Mary V.

    2009-01-01

    Summary We discuss the analysis of data from single nucleotide polymorphism (SNP) arrays comparing tumor and normal tissues. The data consist of sequences of indicators for loss of heterozygosity (LOH) and involve three nested levels of repetition: chromosomes for a given patient, regions within chromosomes, and SNPs nested within regions. We propose to analyze these data using a semiparametric model for multi-level repeated binary data. At the top level of the hierarchy we assume a sampling model for the observed binary LOH sequences that arises from a partial exchangeability argument. This implies a mixture of Markov chains model. The mixture is defined with respect to the Markov transition probabilities. We assume a nonparametric prior for the random mixing measure. The resulting model takes the form of a semiparametric random effects model with the matrix of transition probabilities being the random effects. The model includes appropriate dependence assumptions for the two remaining levels of the hierarchy, i.e., for regions within chromosomes and for chromosomes within patient. We use the model to identify regions of increased LOH in a dataset coming from a study of treatment-related leukemia in children with an initial cancer diagnostic. The model successfully identifies the desired regions and performs well compared to other available alternatives. PMID:19746193

  2. Use of soil-streamwater relationships to assess regional patterns of acidic deposition effects in the northeastern USA

    USGS Publications Warehouse

    Siemion, Jason; Lawrence, Gregory B.; Murdoch, Peter S.

    2013-01-01

    Declines of acidic deposition levels by as much as 50% since 1990 have led to partial recovery of surface waters in the northeastern USA but continued depletion of soil calcium through this same period suggests a disconnection between soil and surface water chemistry. To investigate the role of soil-surface water interactions in recovery from acidification, the first regional survey to directly relate soil chemistry to stream chemistry during high flow was implemented in a 4144-km2 area of the Catskill region of New York, where acidic deposition levels are among the highest in the East. More than 40% of 95 streams sampled in the southern Catskill Mountains were determined to be acidified and had inorganic monomeric aluminum concentrations that exceeded a threshold that is toxic to aquatic biota. More than 80% likely exceeded this threshold during the highest flows, but less than 10% of more than 100 streams sampled were acidified in the northwestern portion of the region. Median Oa horizon soil base saturation ranged from 50% to 80% at 200 sites across the region, but median base saturation in the upper 10 cm of the B horizon was less than 20% across the region and was only 2% in the southern area. Aluminum is likely to be interfering with root uptake of calcium in the mineral horizon in approximately half the sampled watersheds. Stream chemistry was highly variable over the Catskill region and, therefore, did not always reflect the calcium depletion of the B horizon that our sampling suggested was nearly ubiquitous throughout the region.

  3. Development of a total maximum daily load (TMDL) for acid-impaired lakes in the Adirondack region of New York

    NASA Astrophysics Data System (ADS)

    Fakhraei, Habibollah; Driscoll, Charles T.; Selvendiran, Pranesh; DePinto, Joseph V.; Bloomfield, Jay; Quinn, Scott; Rowell, H. Chandler

    2014-10-01

    Acidic deposition has impaired acid-sensitive surface waters in the Adirondack region of New York by decreasing pH and acid neutralizing capacity (ANC). In spite of air quality programs over past decades, 128 lakes in the Adirondacks were classified as “impaired” under Section 303(d) of the Clean Water Act in 2010 due to elevated acidity. The biogeochemical model, PnET-BGC, was used to relate decreases in atmospheric sulfur (S) and nitrogen (N) deposition to changes in lake water chemistry. The model was calibrated and confirmed using observed soil and lake water chemistry data and then was applied to calculate the maximum atmospheric deposition that the impaired lakes can receive while still achieving ANC targets. Two targets of ANC were used to characterize the recovery of acid-impaired lakes: 11 and 20 μeq L-1. Of the 128 acid-impaired lakes, 97 currently have ANC values below the target value of 20 μeq L-1 and 83 are below 11 μeq L-1. This study indicates that a moderate control scenario (i.e., 60% decrease from the current atmospheric S load) is projected to recover the ANC of lakes at a mean rate of 0.18 and 0.05 μeq L-1 yr-1 during the periods 2022-2050 and 2050-2200, respectively. The total maximum daily load (TMDL) of acidity corresponding to this moderate control scenario was estimated to be 7.9 meq S m-2 yr-1 which includes a 10% margin of safety.

  4. Formic and acetic acid over the central Amazon region, Brazil. I - Dry season

    NASA Technical Reports Server (NTRS)

    Andreae, M. O.; Andreae, T. W.; Talbot, R. W.; Harriss, R. C.

    1988-01-01

    The concentrations of formic and acetic acids in the gas phase, atmospheric aerosol, and rainwater samples collected in Amazonia at ground level and in the atmosphere during the Amazon Boundary Layer Experiment in July/August 1985 were analyzed by ion exchange chromatography. The diurnal behavior of both acids at ground level and their vertical distribution in the forest canopy point to the existence of vegetative sources as well as to production by chemical reactions in the atmosphere. The concentrations of formic and acetic acids in the gas phase were about 2 orders of magnitude higher than the corresponding concentrations in the atmospheric aerosol. In rainwater, the total formate and acetate represented about one half of the anion equivalents, in contrast to less than 10 percent of the soluble anionic equivalents contributed by these acids in the atmospheric aerosol. The observed levels of these ions in rainwater are considered to be the result of a combination of chemical reactions in hydrometeors and the scavenging of the gaseous acids by cloud droplets.

  5. Slit Wheel Repeatability

    NASA Astrophysics Data System (ADS)

    DiFelice, Audrey

    2012-10-01

    Test the repeatibility of the slit wheel by taking a sequence of comparison lamp spectra with grating G230MB {2697} and the three smallest long slits {52X0.2, 52X0.1, and 52X0.05}. This is a clone of Cycle 19 Program 12771.

  6. Slit Wheel Repeatability

    NASA Astrophysics Data System (ADS)

    Long, Chris

    2011-10-01

    Test the repeatibility of the slit wheel by taking a sequence of comparison lamp spectra with grating G230MB {2697} and the three smallest long slits {52X0.2, 52X0.1, and 52X0.05}. This is a clone of Cycle 18 Program 12410.

  7. Slit Wheel Repeatability

    NASA Astrophysics Data System (ADS)

    DiFelice, Audrey

    2013-10-01

    Test the repeatibility of the slit wheel by taking a sequence of comparison lamp spectra with grating G230MB {2697} and the three smallest long slits {52X0.2, 52X0.1, and 52X0.05}. This is a clone of Cycle 20 Program 13140.

  8. Slit Wheel Repeatability

    NASA Astrophysics Data System (ADS)

    Zheng, Wei

    2010-09-01

    Test the repeatibility of the slit wheel by taking a sequence of comparison lamp spectra with grating G230MB {2697} and the three smallest long slits {52X0.2, 52X0.1, and 52X0.05}. This is a clone of Cycle 17 Program 11851.

  9. Repeated Causal Decision Making

    ERIC Educational Resources Information Center

    Hagmayer, York; Meder, Bjorn

    2013-01-01

    Many of our decisions refer to actions that have a causal impact on the external environment. Such actions may not only allow for the mere learning of expected values or utilities but also for acquiring knowledge about the causal structure of our world. We used a repeated decision-making paradigm to examine what kind of knowledge people acquire in…

  10. All-optical repeater.

    PubMed

    Silberberg, Y

    1986-06-01

    An all-optical device containing saturable gain, saturable loss, and unsaturable loss is shown to transform weak, distorted optical pulses into uniform standard-shape pulses. The proposed device performs thresholding, amplification, and pulse shaping as required from an optical repeater. It is shown that such a device could be realized by existing semiconductor technology.

  11. Bidirectional Manchester repeater

    NASA Technical Reports Server (NTRS)

    Ferguson, J.

    1980-01-01

    Bidirectional Manchester repeater is inserted at periodic intervals along single bidirectional twisted pair transmission line to detect, amplify, and transmit bidirectional Manchester 11 code signals. Requiring only 18 TTL 7400 series IC's, some line receivers and drivers, and handful of passive components, circuit is simple and relatively inexpensive to build.

  12. Long-term recovery of lakes in the Adirondack region of New York to decreases in acidic deposition

    NASA Astrophysics Data System (ADS)

    Waller, Kristin; Driscoll, Charles; Lynch, Jason; Newcomb, Dani; Roy, Karen

    2012-01-01

    After years of adverse impacts to the acid-sensitive ecosystems of the eastern United States, the Acid Rain Program and Nitrogen Budget Program were developed to control sulfur dioxide (SO 2) and nitrogen oxide (NO x) emissions through market-based cap and trade systems. We used data from the National Atmospheric Deposition Program's National Trends Network (NTN) and the U.S. EPA Temporally Integrated Monitoring of Ecosystems (TIME) program to evaluate the response of lake-watersheds in the Adirondack region of New York to changes in emissions of sulfur dioxide and nitrogen oxides resulting from the Acid Rain Program and the Nitrogen Budget Program. TIME is a long-term monitoring program designed to sample statistically selected subpopulations of lakes and streams across the eastern U.S. to quantify regional trends in surface water chemistry due to changes in atmospheric deposition. Decreases in wet sulfate deposition for the TIME lake-watersheds from 1991 to 2007 (-1.04 meq m -2-yr) generally corresponded with decreases in estimated lake sulfate flux (-1.46 ± 0.72 meq m -2-yr), suggesting declines in lake sulfate were largely driven by decreases in atmospheric deposition. Decreases in lake sulfate and to a lesser extent nitrate have generally coincided with increases in acid neutralizing capacity (ANC) resulting in shifts in lakes among ANC sensitivity classes. The percentage of acidic Adirondack lakes (ANC <0 μeq L -1) decreased from 15.5% (284 lakes) to 8.3% (152 lakes) since the implementation of the Acid Rain Program and the Nitrogen Budget Program. Two measures of ANC were considered in our analysis: ANC determined directly by Gran plot analysis (ANC G) and ANC calculated by major ion chemistry (ANC calc = CB - CA). While these two metrics should theoretically show similar responses, ANC calc (+2.03 μeq L -1-yr) increased at more than twice the rate as ANC G (+0.76 μeq L -1-yr). This discrepancy has important implications for assessments of lake recovery

  13. Amino acid racemization dating of Upper Pleistocene - Holocene terrestrial gastropods from a Mediterranean region (Murcia, SE Spain)

    NASA Astrophysics Data System (ADS)

    Garcia-Mayordomo, Julian; Ortiz, Jose E.; Torres, Trinidad; Insua-Arevalo, Juan M.; Martinez-Diaz, Jose J.; Altolaguirre, Yul; Canales-Fernandez, Maria L.; Martin-Banda, Raquel

    2014-05-01

    The amino acid racemization method has become a widely used geochronological tool for dating Quaternary deposits. The method is based on the fact that living organisms contain only L-amino acids which gradually racemize into D-amino acids after death. Thus, the D/L ratio increases with time after death until it is equal to 1, that is, when equilibrium is reached. Gastropod shells are particularly useful for amino acid racemization dating. Because the amino acid racemization method is not a numerical dating method in isolation, it needs to be calibrated, mainly with radiometric dating methods. The racemization process is genus- and temperature-dependent. In this work we present a preliminary analysis that compares the radiometric age estimated from different dating methods of a number of gastropods recovered in localities from Murcia (Southeastern Spain), with the age obtained through the amino acid racemization method. Taking advantage of recent paleoseismological research in the Murcia region (SE Spain), 28 gastropods specimens were collected from different trenches dug in young Quaternary alluvial deposits. The specimens were subsequently classified and then analyzed according to the standards protocols of the Biomolecular Stratigraphy Laboratory (UPM, Madrid School of Mines). The species found were Otala lactea, Iberus gualterianus, Sphincterochila candidissima and Theba pisana. The D/L ratios of aspartic acid, leucine, phenylalanine and glutamic acid were determined, and the corresponding average age of each specimen was calculated introducing the D/L values in the age calculation algorithm of Torres et al. (1997) for gastropods of central and southern Spain. The racemization age for each locality was then compared to the radiometric age of the deposit where the specimens were collected. To this respect, the samples were classified in different groups considering the reliability on the age control method. The most reliable sample consists only on dates obtained

  14. Assembly of Repeat Content Using Next Generation Sequencing Data

    SciTech Connect

    labutti, Kurt; Kuo, Alan; Grigoriev, Igor; Copeland, Alex

    2014-03-17

    Repetitive organisms pose a challenge for short read assembly, and typically only unique regions and repeat regions shorter than the read length, can be accurately assembled. Recently, we have been investigating the use of Pacific Biosciences reads for de novo fungal assembly. We will present an assessment of the quality and degree of repeat reconstruction possible in a fungal genome using long read technology. We will also compare differences in assembly of repeat content using short read and long read technology.

  15. The ATPase domain but not the acidic region of Cockayne syndrome group B gene product is essential for DNA repair.

    PubMed

    Brosh, R M; Balajee, A S; Selzer, R R; Sunesen, M; Proietti De Santis, L; Bohr, V A

    1999-11-01

    Cockayne syndrome (CS) is a human genetic disorder characterized by UV sensitivity, developmental abnormalities, and premature aging. Two of the genes involved, CSA and CSB, are required for transcription-coupled repair (TCR), a subpathway of nucleotide excision repair that removes certain lesions rapidly and efficiently from the transcribed strand of active genes. CS proteins have also been implicated in the recovery of transcription after certain types of DNA damage such as those lesions induced by UV light. In this study, site-directed mutations have been introduced to the human CSB gene to investigate the functional significance of the conserved ATPase domain and of a highly acidic region of the protein. The CSB mutant alleles were tested for genetic complementation of UV-sensitive phenotypes in the human CS-B homologue of hamster UV61. In addition, the CSB mutant alleles were tested for their ability to complement the sensitivity of UV61 cells to the carcinogen 4-nitroquinoline-1-oxide (4-NQO), which introduces bulky DNA adducts repaired by global genome repair. Point mutation of a highly conserved glutamic acid residue in ATPase motif II abolished the ability of CSB protein to complement the UV-sensitive phenotypes of survival, RNA synthesis recovery, and gene-specific repair. These data indicate that the integrity of the ATPase domain is critical for CSB function in vivo. Likewise, the CSB ATPase point mutant failed to confer cellular resistance to 4-NQO, suggesting that ATP hydrolysis is required for CSB function in a TCR-independent pathway. On the contrary, a large deletion of the acidic region of CSB protein did not impair the genetic function in the processing of either UV- or 4-NQO-induced DNA damage. Thus the acidic region of CSB is likely to be dispensable for DNA repair, whereas the ATPase domain is essential for CSB function in both TCR-dependent and -independent pathways. PMID:10564257

  16. Deletions and Mutations in the Acidic Lipid-binding Region of the Plasma Membrane Ca2+ Pump

    PubMed Central

    Brini, Marisa; Di Leva, Francesca; Ortega, Claudia K.; Domi, Teuta; Ottolini, Denis; Leonardi, Emanuela; Tosatto, Silvio C. E.; Carafoli, Ernesto

    2010-01-01

    Acidic phospholipids increase the affinity of the plasma membrane Ca2+-ATPase pump for Ca2+. They interact with the C-terminal region of the pump and with a domain in the loop connecting transmembrane domains 2 and 3 (AL region) next to site A of alternative splicing. The contribution of the two phospholipid-binding sites and the possible interference of splicing inserts at site A with the regulation of the ATPase activity of isoform 2 of the pump by phospholipids have been analyzed. The activity of the full-length z/b variant (no insert at site A), the w/b (with insert at site A), and the w/a variant, containing both the 45-amino acid A-site insert and a C-site insert that truncates the pump in the calmodulin binding domain, has been analyzed in microsomal membranes of overexpressing CHO cells. The A-site insertion did not modify the phospholipid sensitivity of the pump, but the doubly inserted w/a variant became insensitive to acidic phospholipids, even if containing the intact AL phospholipid binding domain. Pump mutants in which 12 amino acids had been deleted, or single lysine mutations introduced, in the AL region were studied by monitoring agonist-induced Ca2+ transients in overexpressing CHO cells. The 12-residue deletion completely abolished the ATPase activity of the w/a variant but only reduced that of the z/b variant, which was also affected by the single lysine substitutions in the same domain. A structural interpretation of the interplay of the pump with phospholipids, and of the mechanism of their activation, is proposed on the basis of molecular modeling studies. PMID:20643655

  17. TPR repeats and ELTR pattern: length variation as a function evolution mechanism.

    PubMed

    Yang, Ke-Qian

    2007-12-01

    TPR repeat was originally defined as a 34 amino acid structural repeat (TPR-34). Equal length tandem repeats (ELTR) was proposed to represent the ancestral repeat pattern. Length polymorphism of TPR repeats was analyzed using PATTINPROT, two new versions of TPR repeat of 40 and 42 amino acids were identified. These 'long' TPRs endow new functional capacities to the resulting proteins. A strong correlation between varied lengths and new functions supports the hypothesis that length variation is an underlying mechanism for the function evolution of repeat containing proteins.

  18. The human mid-size neurofilament subunit: a repeated protein sequence and the relationship of its gene to the intermediate filament gene family.

    PubMed Central

    Myers, M W; Lazzarini, R A; Lee, V M; Schlaepfer, W W; Nelson, D L

    1987-01-01

    We report the isolation and sequence of cDNA and genomic clones for one of the two large subunits of human neurofilament, NF-M. Analysis of the sequence has allowed us to investigate the structure of the carboxy-terminal tail of this protein, and to compare it to that of the small neurofilament as well as to other intermediate filaments. The carboxy-terminal region of the protein contains a 13 amino acid proline- and serine-rich sequence repeated six times in succession. Within each repeat unit are two smaller repeats of the sequence Lys-Ser-Pro-Val. The four amino acid repeat may represent a kinase recognition site in a region of the protein that is known to be highly phosphorylated. We also note the presence of an additional heptad repeat at the extreme carboxy terminus of the protein. This region of 60 amino acids may be involved in coiled-coil interactions similar to those that facilitate the filament formation in the rod region. The human gene contains only two introns. Their positions correspond to two of the three introns found in the small neurofilament of the mouse. Thus, two of the three neurofilament genes of mammals have similar structures which are quite different from those of the other intermediate filaments. This finding suggests a common origin of the neurofilament subunits, whose evolutionary relationship to other intermediate filament genes is uncertain. Images Fig. 1. PMID:3608989

  19. Mutational analysis reveals that all tailoring region genes are required for production of polyketide antibiotic mupirocin by pseudomonas fluorescens: pseudomonic acid B biosynthesis precedes pseudomonic acid A.

    PubMed

    Hothersall, Joanne; Wu, Ji'en; Rahman, Ayesha S; Shields, Jennifer A; Haddock, James; Johnson, Nicola; Cooper, Sian M; Stephens, Elton R; Cox, Russell J; Crosby, John; Willis, Christine L; Simpson, Thomas J; Thomas, Christopher M

    2007-05-25

    The Pseudomonas fluorescens mupirocin biosynthetic cluster encodes six proteins involved in polyketide biosynthesis and 26 single polypeptides proposed to perform largely tailoring functions. In-frame deletions in the tailoring open reading frames demonstrated that all are required for mupirocin production. A bidirectional promoter region was identified between mupF, which runs counter to other open reading frames and its immediate neighbor macpC, implying the 74-kb cluster consists of two transcriptional units. mupD/E and mupJ/K must be cotranscribed as pairs for normal function implying co-assembly during translation. MupJ and K belong to a widely distributed enzyme pair implicated, with MupH, in methyl addition. Deletion of mupF, a putative ketoreductase, produced a mupirocin analogue with a C-7 ketone. Deletion of mupC, a putative dienoyl CoA reductase, generated an analogue whose structure indicated that MupC is also implicated in control of the oxidation state around the tetrahydropyran ring of monic acid. Double mutants with DeltamupC and DeltamupO, DeltamupU, DeltamupV, or DeltamacpE produced pseudomonic acid B but not pseudomonic acid A, as do the mupO, U, V, and macpE mutants, indicating that MupC must work after MupO, U, and V.

  20. Two-step identification of taro (Colocasia esculenta cv. Xinmaoyu) using specific psbE-petL and simple sequence repeat-sequence characterized amplified regions (SSR-SCAR) markers.

    PubMed

    Dai, H J; Zhang, Y M; Sun, X Q; Xue, J Y; Li, M M; Cao, M X; Shen, X L; Hang, Y Y

    2016-01-01

    Colocasia esculenta cv. Xinmaoyu is an eddoe-type taro cultivar local to Taicang, Jiangsu Province, China; it is characterized by its pure flavor, glutinous texture, and high nutritional value. Due to its excellent qualities, the Trademark Office of the State Administration for Industry and Commerce of the People's Republic of China awarded Xinmaoyu, a geographical indication certification in 2014. Therefore, there is an urgent need to develop an efficient molecular marker for the specific identification of this cultivar, which would greatly facilitate the conservation and utilization of this unique germplasm resource. In the present study, amplifying the psbE-petL fragment from two dasheen-type and seven eddoe-type taro cultivars revealed three conserved insertions/deletions among sequences from the two taro types. Based on these sequence differences, a pair of site-specific primers was designed targeting the psbE-petL sequence from the dasheen-type taro, which specifically amplified a DNA band in all individuals from cultivars of this type, but not in those from the seven eddoe-type cultivars. To discriminate Xinmaoyu from the other eddoe-type taro cultivars, a pair of simple sequence repeat-sequence characterized amplified region (SSR-SCAR) primers was further developed to specifically amplify a DNA band from all Xinmaoyu individuals, but not from individuals of other eddoe-type taro cultivars. In conclusion, through a two-step-screening procedure using psbE-petL and SSR-SCAR markers, we developed a pair of primers that could specifically discriminate Xinmaoyu from nine taro cultivars commonly cultivated in Jiangsu Province and Fujian Province.

  1. Two-step identification of taro (Colocasia esculenta cv. Xinmaoyu) using specific psbE-petL and simple sequence repeat-sequence characterized amplified regions (SSR-SCAR) markers.

    PubMed

    Dai, H J; Zhang, Y M; Sun, X Q; Xue, J Y; Li, M M; Cao, M X; Shen, X L; Hang, Y Y

    2016-01-01

    Colocasia esculenta cv. Xinmaoyu is an eddoe-type taro cultivar local to Taicang, Jiangsu Province, China; it is characterized by its pure flavor, glutinous texture, and high nutritional value. Due to its excellent qualities, the Trademark Office of the State Administration for Industry and Commerce of the People's Republic of China awarded Xinmaoyu, a geographical indication certification in 2014. Therefore, there is an urgent need to develop an efficient molecular marker for the specific identification of this cultivar, which would greatly facilitate the conservation and utilization of this unique germplasm resource. In the present study, amplifying the psbE-petL fragment from two dasheen-type and seven eddoe-type taro cultivars revealed three conserved insertions/deletions among sequences from the two taro types. Based on these sequence differences, a pair of site-specific primers was designed targeting the psbE-petL sequence from the dasheen-type taro, which specifically amplified a DNA band in all individuals from cultivars of this type, but not in those from the seven eddoe-type cultivars. To discriminate Xinmaoyu from the other eddoe-type taro cultivars, a pair of simple sequence repeat-sequence characterized amplified region (SSR-SCAR) primers was further developed to specifically amplify a DNA band from all Xinmaoyu individuals, but not from individuals of other eddoe-type taro cultivars. In conclusion, through a two-step-screening procedure using psbE-petL and SSR-SCAR markers, we developed a pair of primers that could specifically discriminate Xinmaoyu from nine taro cultivars commonly cultivated in Jiangsu Province and Fujian Province. PMID:27525909

  2. [Relationships between soil moisture and needle-fall in Masson pine forests in acid rain region of Chongqing, Southwest China].

    PubMed

    Wang, Yi-Hao; Wang, Yan-Hui; Li, Zhen-Hua; Yu, Peng-Tao; Xiong, Wei; Hao, Jia; Duan, Jian

    2012-10-01

    From March 2009 to November 2011, an investigation was conducted on the spatiotemporal variation of soil moisture and its effects on the needle-fall in Masson pine (Pinus massoniana) forests in acid rain region of Chongqing, Southeast China, with the corresponding soil moisture thresholds determined. No matter the annual precipitation was abundant, normal or less than average, the seasonal variation of soil moisture in the forests could be obviously divided into four periods, i.e., sufficient (before May), descending (from June to July), drought (from August to September), and recovering (from October to November). With increasing soil depth, the soil moisture content increased after an initial decrease, but the difference of the soil moisture content among different soil layers decreased with decreasing annual precipitation. The amount of monthly needle-fall in the forests in growth season was significantly correlated with the water storage in root zone (0-60 cm soil layer), especially in the main root zone (20-50 cm soil layer). Soil field capacity (or capillary porosity) and 82% of field capacity (or 80% of capillary porosity) were the main soil moisture thresholds affecting the litter-fall. It was suggested that in acid rain region, Masson pine forest was easily to suffer from water deficit stress, especially in dry-summer period. The water deficit stress, together with already existed acid rain stress, would further threaten the health of the Masson forest.

  3. [Relationships between soil moisture and needle-fall in Masson pine forests in acid rain region of Chongqing, Southwest China].

    PubMed

    Wang, Yi-Hao; Wang, Yan-Hui; Li, Zhen-Hua; Yu, Peng-Tao; Xiong, Wei; Hao, Jia; Duan, Jian

    2012-10-01

    From March 2009 to November 2011, an investigation was conducted on the spatiotemporal variation of soil moisture and its effects on the needle-fall in Masson pine (Pinus massoniana) forests in acid rain region of Chongqing, Southeast China, with the corresponding soil moisture thresholds determined. No matter the annual precipitation was abundant, normal or less than average, the seasonal variation of soil moisture in the forests could be obviously divided into four periods, i.e., sufficient (before May), descending (from June to July), drought (from August to September), and recovering (from October to November). With increasing soil depth, the soil moisture content increased after an initial decrease, but the difference of the soil moisture content among different soil layers decreased with decreasing annual precipitation. The amount of monthly needle-fall in the forests in growth season was significantly correlated with the water storage in root zone (0-60 cm soil layer), especially in the main root zone (20-50 cm soil layer). Soil field capacity (or capillary porosity) and 82% of field capacity (or 80% of capillary porosity) were the main soil moisture thresholds affecting the litter-fall. It was suggested that in acid rain region, Masson pine forest was easily to suffer from water deficit stress, especially in dry-summer period. The water deficit stress, together with already existed acid rain stress, would further threaten the health of the Masson forest. PMID:23359920

  4. Responses of 20 lake-watersheds in the Adirondack region of New York to historical and potential future acidic deposition.

    PubMed

    Zhou, Qingtao; Driscoll, Charles T; Sullivan, Timothy J

    2015-04-01

    Critical loads (CLs) and dynamic critical loads (DCLs) are important tools to guide the protection of ecosystems from air pollution. In order to quantify decreases in acidic deposition necessary to protect sensitive aquatic species, we calculated CLs and DCLs of sulfate (SO4(2-))+nitrate (NO3-) for 20 lake-watersheds from the Adirondack region of New York using the dynamic model, PnET-BGC. We evaluated lake water chemistry and fish and total zooplankton species richness in response to historical acidic deposition and under future deposition scenarios. The model performed well in simulating measured chemistry of Adirondack lakes. Current deposition of SO4(2-)+NO3-, calcium (Ca2+) weathering rate and lake acid neutralizing capacity (ANC) in 1850 were related to the extent of historical acidification (1850-2008). Changes in lake Al3+ concentrations since the onset of acidic deposition were also related to Ca2+ weathering rate and ANC in 1850. Lake ANC and fish and total zooplankton species richness were projected to increase under hypothetical decreases in future deposition. However, model projections suggest that lake ecosystems will not achieve complete chemical and biological recovery in the future.

  5. Identification of repeat structure in large genomes using repeat probability clouds.

    PubMed

    Gu, Wanjun; Castoe, Todd A; Hedges, Dale J; Batzer, Mark A; Pollock, David D

    2008-09-01

    The identification of repeat structure in eukaryotic genomes can be time-consuming and difficult because of the large amount of information ( approximately 3 x 10(9) bp) that needs to be processed and compared. We introduce a new approach based on exact word counts to evaluate, de novo, the repeat structure present within large eukaryotic genomes. This approach avoids sequence alignment and similarity search, two of the most time-consuming components of traditional methods for repeat identification. Algorithms were implemented to efficiently calculate exact counts for any length oligonucleotide in large genomes. Based on these oligonucleotide counts, oligonucleotide excess probability clouds, or "P-clouds," were constructed. P-clouds are composed of clusters of related oligonucleotides that occur, as a group, more often than expected by chance. After construction, P-clouds were mapped back onto the genome, and regions of high P-cloud density were identified as repetitive regions based on a sliding window approach. This efficient method is capable of analyzing the repeat content of the entire human genome on a single desktop computer in less than half a day, at least 10-fold faster than current approaches. The predicted repetitive regions strongly overlap with known repeat elements as well as other repetitive regions such as gene families, pseudogenes, and segmental duplicons. This method should be extremely useful as a tool for use in de novo identification of repeat structure in large newly sequenced genomes.

  6. Duct Leakage Repeatability Testing

    SciTech Connect

    Walker, Iain; Sherman, Max

    2014-01-01

    Duct leakage often needs to be measured to demonstrate compliance with requirements or to determine energy or Indoor Air Quality (IAQ) impacts. Testing is often done using standards such as ASTM E1554 (ASTM 2013) or California Title 24 (California Energy Commission 2013 & 2013b), but there are several choices of methods available within the accepted standards. Determining which method to use or not use requires an evaluation of those methods in the context of the particular needs. Three factors that are important considerations are the cost of the measurement, the accuracy of the measurement and the repeatability of the measurement. The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards.

  7. Accumulate repeat accumulate codes

    NASA Technical Reports Server (NTRS)

    Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

    2004-01-01

    In this paper we propose an innovative channel coding scheme called 'Accumulate Repeat Accumulate codes' (ARA). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes, thus belief propagation can be used for iterative decoding of ARA codes on a graph. The structure of encoder for this class can be viewed as precoded Repeat Accumulate (RA) code or as precoded Irregular Repeat Accumulate (IRA) code, where simply an accumulator is chosen as a precoder. Thus ARA codes have simple, and very fast encoder structure when they representing LDPC codes. Based on density evolution for LDPC codes through some examples for ARA codes, we show that for maximum variable node degree 5 a minimum bit SNR as low as 0.08 dB from channel capacity for rate 1/2 can be achieved as the block size goes to infinity. Thus based on fixed low maximum variable node degree, its threshold outperforms not only the RA and IRA codes but also the best known LDPC codes with the dame maximum node degree. Furthermore by puncturing the accumulators any desired high rate codes close to code rate 1 can be obtained with thresholds that stay close to the channel capacity thresholds uniformly. Iterative decoding simulation results are provided. The ARA codes also have projected graph or protograph representation that allows for high speed decoder implementation.

  8. Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization.

    PubMed

    Shiheido, Hirokazu; Shimizu, Jun

    2015-02-20

    BEN domain-containing protein 3 (BEND3) has recently been reported to function as a heterochromatin-associated protein in transcriptional repression in the nucleus. BEND3 should have nuclear localization signals (NLSs) to localize to the nucleus in light of its molecular weight, which is higher than that allowed to pass through nuclear pore complexes. We here analyzed the subcellular localization of deletion/site-directed mutants of human BEND3 by an immunofluorescence assay in an attempt to identify the amino acids essential for its nuclear localization. We found that three basic amino acid residues located in the N-terminal region of BEND3 (BEND356-58, KRK) are essential, suggesting that these residues play a role as a functional NLS. These results provide valuable information for progressing research on BEND3.

  9. Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization.

    PubMed

    Shiheido, Hirokazu; Shimizu, Jun

    2015-02-20

    BEN domain-containing protein 3 (BEND3) has recently been reported to function as a heterochromatin-associated protein in transcriptional repression in the nucleus. BEND3 should have nuclear localization signals (NLSs) to localize to the nucleus in light of its molecular weight, which is higher than that allowed to pass through nuclear pore complexes. We here analyzed the subcellular localization of deletion/site-directed mutants of human BEND3 by an immunofluorescence assay in an attempt to identify the amino acids essential for its nuclear localization. We found that three basic amino acid residues located in the N-terminal region of BEND3 (BEND356-58, KRK) are essential, suggesting that these residues play a role as a functional NLS. These results provide valuable information for progressing research on BEND3. PMID:25600804

  10. An amino acid outside the pore region influences apamin sensitivity in small conductance Ca2+-activated K+ channels.

    PubMed

    Nolting, Andreas; Ferraro, Teresa; D'hoedt, Dieter; Stocker, Martin

    2007-02-01

    Small conductance calcium-activated potassium channels (SK, K(Ca)) are a family of voltage-independent K+ channels with a distinct physiology and pharmacology. The bee venom toxin apamin inhibits exclusively the three cloned SK channel subtypes (SK1, SK2, and SK3) with different affinity, highest for SK2, lowest for SK1, and intermediate for SK3 channels. The high selectivity of apamin made it a valuable tool to study the molecular makeup and function of native SK channels. Three amino acids located in the outer vestibule of the pore are of particular importance for the different apamin sensitivities of SK channels. Chimeric SK1 channels, enabling the homomeric expression of the rat SK1 (rSK1) subunit and containing the core domain (S1-S6) of rSK1, are apamin-insensitive. By contrast, channels formed by the human orthologue human SK1 (hSK1) are sensitive to apamin. This finding hinted at the involvement of regions beyond the pore as determinants of apamin sensitivity, because hSK1 and rSK1 have an identical amino acid sequence in the pore region. Here we investigated which parts of the channels outside the pore region are important for apamin sensitivity by constructing chimeras between apamin-insensitive and -sensitive SK channel subunits and by introducing point mutations. We demonstrate that a single amino acid situated in the extracellular loop between the transmembrane segments S3 and S4 has a major impact on apamin sensitivity. Our findings enabled us to convert the hSK1 channel into a channel that was as sensitive for apamin as SK2, the SK channel with the highest sensitivity.

  11. Responses of grape berry anthocyanin and titratable acidity to the projected climate change across the Western Australian wine regions

    NASA Astrophysics Data System (ADS)

    Barnuud, Nyamdorj N.; Zerihun, Ayalsew; Mpelasoka, Freddie; Gibberd, Mark; Bates, Bryson

    2014-08-01

    More than a century of observations has established that climate influences grape berry composition. Accordingly, the projected global climate change is expected to impact on grape berry composition although the magnitude and direction of impact at regional and subregional scales are not fully known. The aim of this study was to assess potential impacts of climate change on levels of berry anthocyanin and titratable acidity (TA) of the major grapevine varieties grown across all of the Western Australian (WA) wine regions. Grape berry anthocyanin and TA responses across all WA wine regions were projected for 2030, 2050 and 2070 by utilising empirical models that link these berry attributes and climate data downscaled (to ˜5 km resolution) from the csiro_mk3_5 and miroc3_2_medres global climate model outputs under IPCC SRES A2 emissions scenario. Due to the dependence of berry composition on maturity, climate impacts on anthocyanin and TA levels were assessed at a common maturity of 22 °Brix total soluble solids (TSS), which necessitated the determination of when this maturity will be reached for each variety, region and warming scenario, and future period. The results indicate that both anthocyanin and TA levels will be affected negatively by a warming climate, but the magnitude of the impacts will differ between varieties and wine regions. Compared to 1990 levels, median anthocyanins concentrations are projected to decrease, depending on global climate model, by up to 3-12 % and 9-33 % for the northern wine regions by 2030 and 2070, respectively while 2-18 % reductions are projected in the southern wine regions for the same time periods. Patterns of reductions in the median Shiraz berry anthocyanin concentrations are similar to that of Cabernet Sauvignon; however, the magnitude is lower (up to 9-18 % in southern and northern wine regions respectively by 2070). Similarly, uneven declines in TA levels are projected across the study regions. The largest reductions

  12. Responses of grape berry anthocyanin and titratable acidity to the projected climate change across the Western Australian wine regions.

    PubMed

    Barnuud, Nyamdorj N; Zerihun, Ayalsew; Mpelasoka, Freddie; Gibberd, Mark; Bates, Bryson

    2014-08-01

    More than a century of observations has established that climate influences grape berry composition. Accordingly, the projected global climate change is expected to impact on grape berry composition although the magnitude and direction of impact at regional and subregional scales are not fully known. The aim of this study was to assess potential impacts of climate change on levels of berry anthocyanin and titratable acidity (TA) of the major grapevine varieties grown across all of the Western Australian (WA) wine regions. Grape berry anthocyanin and TA responses across all WA wine regions were projected for 2030, 2050 and 2070 by utilising empirical models that link these berry attributes and climate data downscaled (to ∼5 km resolution) from the csiro_mk3_5 and miroc3_2_medres global climate model outputs under IPCC SRES A2 emissions scenario. Due to the dependence of berry composition on maturity, climate impacts on anthocyanin and TA levels were assessed at a common maturity of 22 °Brix total soluble solids (TSS), which necessitated the determination of when this maturity will be reached for each variety, region and warming scenario, and future period. The results indicate that both anthocyanin and TA levels will be affected negatively by a warming climate, but the magnitude of the impacts will differ between varieties and wine regions. Compared to 1990 levels, median anthocyanins concentrations are projected to decrease, depending on global climate model, by up to 3-12 % and 9-33 % for the northern wine regions by 2030 and 2070, respectively while 2-18 % reductions are projected in the southern wine regions for the same time periods. Patterns of reductions in the median Shiraz berry anthocyanin concentrations are similar to that of Cabernet Sauvignon; however, the magnitude is lower (up to 9-18 % in southern and northern wine regions respectively by 2070). Similarly, uneven declines in TA levels are projected across the study regions. The largest reductions

  13. Spectroscopic and Computational Study of Acetic Acid and Its Cyclic Dimer in the Near-Infrared Region.

    PubMed

    Beć, Krzysztof B; Futami, Yoshisuke; Wójcik, Marek J; Nakajima, Takahito; Ozaki, Yukihiro

    2016-08-11

    Anharmonic vibrational analysis of near-infrared (NIR) spectra of acetic acid was carried out by anharmonic quantum chemical calculation in a wide concentration range of its CCl4 solution. By predicting vibrational spectra of acetic acid for the first time over a wide NIR region, it was possible to elucidate the influence of the formation of acetic acid cyclic dimer on its NIR spectrum. Quantum chemical simulations were based on coupled cluster and density functional theory quantum methods. Additionally, Møller-Plesset perturbation theory was employed for the additional calculation of hydrogen bonding stabilization energies. An anharmonic vibrational analysis was performed with the use of generalized second-order vibrational perturbation theory (GVPT2). A hybrid approach was assumed, in which monomeric species was treated by CCSD(T)/aug-cc-pVDZ (harmonic approximation) and B3LYP/SNSD (anharmonic approximation) methods. For the cyclic dimer, B3LYP and B2PLYP single and double hybrid functionals, paired with an SNSD basis set, were employed. DFT calculations were augmented with additional empirical dispersion correction. It was found that quantum chemically calculated vibrational modes in the NIR region are in a good agreement with experimental data. The results of anharmonic vibrational analysis were supported by a harmonic shift analysis, for elucidating the very strong anharmonic coupling observed between stretching modes of hydrogen bonded bridge in the cyclic dimer. However, the calculated wavenumbers for combination modes of double hydrogen bonded bridge in the cyclic dimer, which are very sensitive to the formation of hydrogen bonding, were found to be underestimated by quantum chemical methods. Therefore, by band fitting, the wavenumbers and shape parameters for these bands were found, and the modeled spectra were adjusted accordingly. A high accuracy of simulated spectra was achieved, and a detailed analysis of the experimental NIR spectra of acetic acid

  14. Spectroscopic and Computational Study of Acetic Acid and Its Cyclic Dimer in the Near-Infrared Region.

    PubMed

    Beć, Krzysztof B; Futami, Yoshisuke; Wójcik, Marek J; Nakajima, Takahito; Ozaki, Yukihiro

    2016-08-11

    Anharmonic vibrational analysis of near-infrared (NIR) spectra of acetic acid was carried out by anharmonic quantum chemical calculation in a wide concentration range of its CCl4 solution. By predicting vibrational spectra of acetic acid for the first time over a wide NIR region, it was possible to elucidate the influence of the formation of acetic acid cyclic dimer on its NIR spectrum. Quantum chemical simulations were based on coupled cluster and density functional theory quantum methods. Additionally, Møller-Plesset perturbation theory was employed for the additional calculation of hydrogen bonding stabilization energies. An anharmonic vibrational analysis was performed with the use of generalized second-order vibrational perturbation theory (GVPT2). A hybrid approach was assumed, in which monomeric species was treated by CCSD(T)/aug-cc-pVDZ (harmonic approximation) and B3LYP/SNSD (anharmonic approximation) methods. For the cyclic dimer, B3LYP and B2PLYP single and double hybrid functionals, paired with an SNSD basis set, were employed. DFT calculations were augmented with additional empirical dispersion correction. It was found that quantum chemically calculated vibrational modes in the NIR region are in a good agreement with experimental data. The results of anharmonic vibrational analysis were supported by a harmonic shift analysis, for elucidating the very strong anharmonic coupling observed between stretching modes of hydrogen bonded bridge in the cyclic dimer. However, the calculated wavenumbers for combination modes of double hydrogen bonded bridge in the cyclic dimer, which are very sensitive to the formation of hydrogen bonding, were found to be underestimated by quantum chemical methods. Therefore, by band fitting, the wavenumbers and shape parameters for these bands were found, and the modeled spectra were adjusted accordingly. A high accuracy of simulated spectra was achieved, and a detailed analysis of the experimental NIR spectra of acetic acid

  15. Sources of atmospheric acidity in an agricultural-industrial region of São Paulo State, Brazil

    NASA Astrophysics Data System (ADS)

    Da Rocha, G. O.; Franco, A.; Allen, A. G.; Cardoso, A. A.

    2003-04-01

    Surface-based measurements of atmospheric formic acid (HCOOH), acetic acid (CH3COOH), sulfur dioxide (SO2), hydrogen chloride (HCl), and nitric acid (HNO3) were made in central São Paulo State, Brazil, between April 1999 and March 2000. Mean concentrations were 9.0 ppb (HCOOH), 1.3 ppb (CH3COOH), 4.9 ppb (SO2), 0.3 ppb (HCl), and 0.5 ppb (HNO3). Concentrations in sugar cane burning plumes were 1160-4230 ppb (HCOOH), 360-1750 ppb (CH3COOH), 10-630 ppb (SO2), 4-210 ppb (HCl), and 14-90 ppb (HNO3). Higher ambient concentrations of SO2, HCl and HNO3 were measured during the burning season (May-November). Concentrations of SO2 and HCl increased during the evening, and of HCOOH and CH3COOH were lowest in the morning, with peak levels in the afternoon. Ratios obtained between different species showed either nighttime maxima (SO2/HCOOH, SO2/CH3COOH, SO2/HNO3, CH3COOH/HNO3, SO2/HCl and HCOOH/HNO3), daytime maxima (HCOOH/HCl, CH3COOH/HCl and HNO3/HCl), or no clear trends (HCOOH/CH3COOH). Correlation analysis showed that SO2 and HCl were primary emissions from biomass burning and road transport; HCOOH, HNO3 and CH3COOH were products of photochemistry; HCOOH and CH3COOH were emitted directly during combustion as well as from biogenic sources. Biomass burning affected atmospheric acidity on a regional scale, while vehicular emissions had greater impact in urban and adjacent areas. Atmospheric ammonia levels were insufficient to neutralize atmospheric acidity, which was mainly removed by deposition to the surface.

  16. Copy number of tandem direct repeats within the inverted repeats of Marek's disease virus DNA.

    PubMed

    Kanamori, A; Nakajima, K; Ikuta, K; Ueda, S; Kato, S; Hirai, K

    1986-12-01

    We previously reported that DNA of the oncogenic strain BC-1 of Marek's disease virus serotype 1 (MDV1) contains three units of tandem direct repeats with 132 base pair (bp) repeats within the inverted repeats of the long regions of the MDV1 genome, whereas the attenuated, nononcogenic viral DNA contains multiple units of tandem direct repeats (Maotani et al., 1986). In the present study, the difference in the copy numbers of 132 bp repeats of oncogenic and nononcogenic MDV1 DNAs in other strains of MDV1 was investigated by Southern blot hybridization. The main copy numbers in different oncogenic MDV1 strains differed: those of BC-1, JM and highly oncogenic Md5 were 3, 5 to 12 and 2, respectively. The viral DNA population with two units of repeats was small, but detectable, in cells infected with either the oncogenic BC-1 or JM strain. The MDV1 DNA in various MD cell lines contained either two units or both two and three units of repeats. The significance of the copy number of repeats in oncogenicity of MDV1 is discussed.

  17. Epigenetics and Triplet-Repeat Neurological Diseases

    PubMed Central

    Nageshwaran, Sathiji; Festenstein, Richard

    2015-01-01

    The term “junk DNA” has been reconsidered following the delineation of the functional significance of repetitive DNA regions. Typically associated with centromeres and telomeres, DNA repeats are found in nearly all organisms throughout their genomes. Repetitive regions are frequently heterochromatinized resulting in silencing of intrinsic and nearby genes. However, this is not a uniform rule, with several genes known to require such an environment to permit transcription. Repetitive regions frequently exist as dinucleotide, trinucleotide, and tetranucleotide repeats. The association between repetitive regions and disease was emphasized following the discovery of abnormal trinucleotide repeats underlying spinal and bulbar muscular atrophy (Kennedy’s disease) and fragile X syndrome of mental retardation (FRAXA) in 1991. In this review, we provide a brief overview of epigenetic mechanisms and then focus on several diseases caused by DNA triplet-repeat expansions, which exhibit diverse epigenetic effects. It is clear that the emerging field of epigenetics is already generating novel potential therapeutic avenues for this group of largely incurable diseases. PMID:26733936

  18. Epigenetics and Triplet-Repeat Neurological Diseases.

    PubMed

    Nageshwaran, Sathiji; Festenstein, Richard

    2015-01-01

    The term "junk DNA" has been reconsidered following the delineation of the functional significance of repetitive DNA regions. Typically associated with centromeres and telomeres, DNA repeats are found in nearly all organisms throughout their genomes. Repetitive regions are frequently heterochromatinized resulting in silencing of intrinsic and nearby genes. However, this is not a uniform rule, with several genes known to require such an environment to permit transcription. Repetitive regions frequently exist as dinucleotide, trinucleotide, and tetranucleotide repeats. The association between repetitive regions and disease was emphasized following the discovery of abnormal trinucleotide repeats underlying spinal and bulbar muscular atrophy (Kennedy's disease) and fragile X syndrome of mental retardation (FRAXA) in 1991. In this review, we provide a brief overview of epigenetic mechanisms and then focus on several diseases caused by DNA triplet-repeat expansions, which exhibit diverse epigenetic effects. It is clear that the emerging field of epigenetics is already generating novel potential therapeutic avenues for this group of largely incurable diseases. PMID:26733936

  19. The existence region and composition of a polymer-induced liquid precursor phase for DL-glutamic acid crystals.

    PubMed

    Jiang, Yuan; Gower, Laurie; Volkmer, Dirk; Cölfen, Helmut

    2012-01-14

    The existence region of a polymer-induced liquid precursor (PILP) phase for crystals of an organic compound (DL-glutamic acid, Glu) was determined for the first time in the phase diagram of the Glu-polyethyleneimine-water-ethanol system. The existence region and the amount of PILP phase relative to the thermodynamically stable crystal phase were very small. Other phases detected in the phase diagram were coacervates, homogenous mixtures, and crystals obtained via a clear solution. The PILP phase is rich in the polymeric additive, which helps to explain the long induction period of PILP before crystallization occurs. Volume measurements indicated that its amount is <1 vol%, showing that this precursor phase is only a minor component.

  20. The C34 Peptide Fusion Inhibitor Binds to the Six-Helix Bundle Core Domain of HIV-1 gp41 by Displacement of the C-Terminal Helical Repeat Region.

    PubMed

    Louis, John M; Baber, James L; Clore, G Marius

    2015-11-17

    The conformational transition of the core domain of HIV-1 gp41 from a prehairpin intermediate to a six-helix bundle is responsible for virus-cell fusion. Several inhibitors which target the N-heptad repeat helical coiled-coil trimer that is fully accessible in the prehairpin intermediate have been designed. One such inhibitor is the peptide C34 derived from the C-heptad repeat of gp41 that forms the exterior of the six-helix bundle. Here, using a variety of biophysical techniques, including dye tagging, size-exclusion chromatography combined with multiangle light scattering, double electron-electron resonance EPR spectroscopy, and circular dichroism, we investigate the binding of C34 to two six-helix bundle mimetics comprising N- and C-heptad repeats either without (core(SP)) or with (core(S)) a short spacer connecting the two. In the case of core(SP), C34 directly exchanges with the C-heptad repeat. For core(S), up to two molecules of C34 bind the six-helix bundle via displacement of the C-heptad repeat. These results suggest that fusion inhibitors such as C34 can target a continuum of transitioning conformational states from the prehairpin intermediate to the six-helix bundle prior to the occurrence of irreversible fusion of viral and target cell membranes.

  1. Folate analogues altered in the C9-N10 bridge region: 11-thiohomofolic acid.

    PubMed

    Nair, M G; Chen, S Y; Kisliuk, R L; Gaumont, Y; Strumpf, D

    1979-07-01

    The synthesis of 11-thiohomofolic acid (2) has been accomplished by an unambiguous procedure. Reaction of 1-chloro-4-[p-(carbomethoxy)thiophenoxy]-2-butanone (10) with hydroxylamine under carefully controlled conditions gave the corresponding oxime 33. Conversion of this oxime to 1-phthalimido-4-[p-(carbomethoxy)thiophenoxy]-2-butanone oxime (4) was carried out by its reaction with potassium phthalimide using crown 18 ether as a catalyst. Hydrazinolysis of compound 4 gave 1-amino-4-[p-(carbomethoxy)thiophenoxy]-2-butanone oxime (5), which was used for the construction of the title compound 2 by modification of the Boon and Leigh procedure. An alternate synthesis utilizing 1-hydroxy-4-[p-(carbomethoxy)thiophenoxy]-2-butanone (11) and 4-hydroxy-2,5,6-triaminopyrimidine has also been carried out. Compound 2 did not exhibit any antifolate activity against Lactobacillus casei or Streptococcus faecium. The dithionite reduction product, 7,8-dihydro-11-thiohomofolic acid, was able to function as a substrate of L. casei dihydrofolate reductase. The catalytic reduction product of 2, consisting of a mixture of diastereomers, exhibited powerful antifolate activity against both these organisms.

  2. Insertions of up to 17 amino acids into a region of alpha-tubulin do not disrupt function in vivo.

    PubMed

    Schatz, P J; Georges, G E; Solomon, F; Botstein, D

    1987-10-01

    Microtubules in yeasts are essential components of the mitotic and meiotic spindle and are necessary for nuclear movement during cell division and mating. The yeast Saccharomyces cerevisiae has two alpha-tubulin genes, TUB1 and TUB3, either of which alone is sufficient for these processes when present in a high enough copy number. Comparisons of sequences from several species reveals the presence of a variable region near the amino terminus of alpha-tubulin proteins. We perturbed the structure of this region in TUB3 by inserting into it 3, 9, or 17 amino acids and tested the ability of these altered proteins to function as the only alpha-tubulin protein in yeast cells. We found that each of these altered proteins was sufficient on its own for mitotic growth, mating, and methods of yeast. We conclude that this region can tolerate considerable variation without losing any of the highly conserved functions of alpha-tubulin. Our results suggest that variability in this region occurs because it can be tolerated, not because it specifies an important function for the protein. PMID:3316988

  3. Duct Leakage Repeatability Testing

    SciTech Connect

    Walker, Iain; Sherman, Max

    2014-08-01

    The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques for duct leakage using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards. The three duct leak measurement methods assessed in this report are the two duct pressurization methods that are commonly used by many practitioners and the DeltaQ technique. These are methods B, C and A, respectively of the ASTM E1554 standard. Although it would be useful to evaluate other duct leak test methods, this study focused on those test methods that are commonly used and are required in various test standards, such as BPI (2010), RESNET (2014), ASHRAE 62.2 (2013), California Title 24 (CEC 2012), DOE Weatherization and many other energy efficiency programs.

  4. Repeated measures with zeros.

    PubMed

    Berk, K N; Lachenbruch, P A

    2002-08-01

    Consider repeated measures data with many zeros. For the case with one grouping factor and one repeated measure, we examine several models, assuming that the nonzero data are roughly lognormal. One of the simplest approaches is to model the zeros as left-censored observations from the lognormal distribution. A random effect is assumed for subjects. The censored model makes a strong assumption about the relationship between the zeros and the nonzero values. To check on this, you can instead assume that some of the zeros are 'true' zeros and model them as Bernoulli. Then the other values are modeled with a censored lognormal. A logistic model is used for the Bernoulli p, the probability of a true nonzero. The fit of the pure left-censored lognormal can be assessed by testing the hypothesis that p is 1, as described by Moulton and Halsey. The model can also be simplified by omitting the censoring, leaving a logistic model for the zeros and a lognormal model for the nonzero values. This is approximately equivalent to modeling the zero and nonzero values separately, a two-part model. In contrast to the censored model, this model assumes only a slight relationship (a covariance component) between the occurrence of zeros and the size of the nonzero values. The models are compared in terms of an example with data from children's private speech. PMID:12197298

  5. Evidence for Acid-Sulfate Alteration in the Pahrump Hills Region, Gale Crater, Mars

    NASA Technical Reports Server (NTRS)

    Rampe, E. B.; Ming, D. W.; Blake, D. F.; Morris, R. V.; Bish, D. L.; Bristow, T. F.; Crisp, J. A.; Morookian, J. M.; Vaniman. D. T.; Chipera, S. J.; Cavanagh, P. D.; Achilles, C. N.; Fairen, A. G.; Morrison, S. M.; Treiman, A. H.; Downs, R. T.; Farmer, J. D.; Fendrich, K. V.

    2015-01-01

    The Pahrump Hills region of Gale crater is a approximately 12 millimeter thick section of sedimentary rock in the Murray formation, interpreted as the basal geological unit of Mount Sharp. The Mars Science Laboratory, Curiosity, arrived at the Pahrump Hills in September 2014 and performed a detailed six-month investigation of the sedimentary structures, geochemistry, and mineralogy of the area. During the campaign, Curiosity drilled and delivered three mudstone samples (targets Confidence Hills, Mojave 2, and Telegraph Peak) to its internal instruments, including the CheMin XRD/XRF.

  6. Analysis of separate isolates of Bordetella pertussis repeated DNA sequences.

    PubMed

    McPheat, W L; Hanson, J H; Livey, I; Robertson, J S

    1989-06-01

    Two independent isolates of a Bordetella pertussis repeated DNA unit were sequenced and shown to be an insertion sequence element with five nucleotide differences between the two copies. The sequences were 1053 bp in length with near-perfect terminal inverted repeats of 28 bp, had three open reading frames, and were each flanked by short direct repeats. The two insertion sequences showed considerable homology to two other B. pertussis repeated DNA sequences reported recently: IS481 and a 530 bp repeated DNA unit. The B. pertussis insertion sequence would appear to comprise a group of closely related sequences differing mainly in flanking direct repeats and the terminal inverted repeats. The two isolates reported here, which were from the adenylate cyclase and agglutinogen 2 regions of the genome, were numbered IS48lvl and IS48lv2 respectively. PMID:2559151

  7. Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

    PubMed Central

    Parra, R. Gonzalo; Espada, Rocío; Verstraete, Nina; Ferreiro, Diego U.

    2015-01-01

    Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins. PMID:26691182

  8. Repeat Customer Success in Extension

    ERIC Educational Resources Information Center

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

    Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

  9. Characterization of transcriptional regulatory domains of ankyrin repeat cofactor-1

    SciTech Connect

    Zhang, Aihua; Li, Chia-Wei; Chen, J. Don . E-mail: chenjd@umdnj.edu

    2007-07-13

    The ankyrin repeats cofactor-1 (ANCO-1) was recently identified as a p160 coactivator-interacting protein that may inhibit transcriptional activity of nuclear receptors. Here, we have characterized the transcriptional regulatory domains of ANCO-1. Two intrinsic repression domains (RD) were identified: an N-terminal RD1 at residues 318-611 and a C-terminal RD2 at 2369-2663. ANCO-1 also contains an activation domain (AD) capable of stimulating transcription in both mammalian and yeast cells. The minimal AD was delimited to a 70-amino acid region at residues 2076-2145. Overall, full-length ANCO-1 exhibited transcriptional repressor activity, suggesting that RD domains may suppress the AD activity. We further demonstrated that ANCO-1 silencing by siRNA enhanced progesterone receptor-mediated transcription. Together, these results indicate that the transcriptional potential of ANCO-1 may be modulated by a combination of repression and activation signals.

  10. Body regional distribution and stratification of fatty acids in the blubber of New Zealand sea lions: implications for diet predictions.

    PubMed

    Lambert, Antoine; Meynier, Laureline; Donaldson, Laura C; Roe, Wendi D; Morel, Patrick C H

    2013-01-01

    Fatty acids (FAs) from blubber are often analysed to assess the diet of marine mammals. However, distribution of blubber FAs is not necessarily uniform along the body. It is therefore important to understand the deposition of dietary fat to be able to estimate the diet. We analysed the FA compositions of the thoracic ventral (T region) blubber of 28 New Zealand (NZ) sea lions Phocarctos hookeri by-caught by the southern arrow squid Nototodarus sloani fishery. Each blubber sample was divided into an inner and an outer layer. For 16 of these 28 animals, the pelvic dorsal (P) region was also sampled. The influence of body region and layer was statistically tested on the distribution of blubber FAs. We found minimal differences between the P and T regions (3 out of 29 FAs). The outer blubber layer was more concentrated in short-chain monounsaturated FAs, and less concentrated in saturated FAs, but the degree of stratification was small. Diet predictions from quantitative FA signature analysis (QFASA) applied on different body regions were similar. When applied to different blubber layers, QFASA gave some variation in the contribution of rattails (~25 % in outer blubber vs. ~12 % in inner blubber). Nonetheless, diet predicted from both layers was dominated by similar prey species: octopus, hoki and rattails. Hoki and rattails shared a similar ecological niche. Therefore, feeding ecology of NZ sea lions inferred from the inner or the outer blubber would lead to the same conclusions. In the case of NZ sea lions, the outer layer of blubber, if the only sample accessible, could be a useful tissue for diet inference from FAs.

  11. Radical formation of amino acid precursors in interstellar regions? Ser, Cys and Asp.

    PubMed

    Knowles, Daniel J; Wang, Tianfang; Bowie, John H

    2010-11-01

    It is proposed that the glycine precursor NH(2)CH(2)CN may be synthesised in interstellar dust clouds by the radical combination reactions NH(2)˙ + ˙CH(2)CN → NH(2)CH(2)CN (ΔG = -302 kJ mol(-1)) and/or NH(2)CH(2)˙ + ˙CN → NH(2)CH(2)CN (ΔG = -414 kJ mol(-1)). All calculations at the CCSD(T)/aug-cc-pVDZ//B3LYP/6-31+G(d) level of theory. This paper extends that concept to radical/radical coupling reactions to form Ser, Cys and Asp precursor nitriles. The hydrogen abstraction process NH(2)CH(2)CN + HO˙→ NH(2)˙CHCN + H(2)O (ΔG = -130 kJ mol(-1)) is suggested to precede the radical coupling reactions NH(2)˙CHCN + R˙→ NH(2)CHRCN (R˙ = ˙CH(2)OH, ˙CH(2)SH and ˙CH(2)CN) to form nitrile precursors of the amino acids Ser, Cys and Asp. These three reactions are all favourable (ΔG = -240, -227 and -223 kJ mol(-1)). The radical species ˙CH(2)NH(2), ˙CH(2)OH, ˙CH(2)SH and ˙CH(2)CN are shown to be stable for the microsecond timeframe by a combination of theoretical calculations and the experimental mass spectrometric neutralization/reionization procedure.

  12. The influence of different land management practices on the transformation of humic acids in heavy loamy soddy-podzolic soils of the Cis-Urals region

    NASA Astrophysics Data System (ADS)

    Zavyalova, N. E.; Konchits, V. A.

    2011-01-01

    The elemental composition and structure of humic acids were studied in heavy loamy soddy-podzolic soils of the Cis-Urals region under different land management practices. The humic acids in the soil of the long-term clean fallow, overgrown fallow (abandoned plot), and crop rotation plots differed in their composition and properties. The humic acids in the soils of the crop rotation with the regular application of manure and of the overgrown fallow were enriched in the components of both their central (nuclear) and peripheral parts. Such a structure ensured the active participation of humic acids in the carbon cycle with the simultaneous preservation of the soil's fertility.

  13. Human immunoglobulin subclasses. Partial amino acid sequence of the constant region of a γ4 chain

    PubMed Central

    Pink, J. R. L.; Buttery, S. H.; De Vries, G. M.; Milstein, C.

    1970-01-01

    The heavy chain of a human myeloma protein (Vin) belonging to the γ4 subclass was subjected to tryptic digestion after reduction and carboxymethylation. Cyanogen bromide fragments were also prepared and all 19 tryptic peptides that account for one of them (the Fc-like fragment) were studied. Selected peptic peptides were isolated and provided evidence for the order of 15 of the tryptic peptides. In addition the sequence of two large peptic peptides derived from two sections of the molecule including all the interchain bridges is presented. Comparison with published data on other chains allows us to propose a sequence of γ4 chains that extends from just before the presumed starting point of the invariable region (at about residue 113) to the C-terminal end of the chain (approx. residue 446), except for a section of about 50 residues. The results of the comparison suggest that the immunoglobulin subclasses have a recent independent evolutionary origin in different species. Implications for complement fixation and for the evolutionary origin of antibody diversity are also discussed. PMID:4192699

  14. Vibration-Rotation Spectrum of Formic Acid Dimer in the 7.3μm Region

    NASA Astrophysics Data System (ADS)

    Duan, Chuanxi

    2016-06-01

    The vibration-rotation-tunneling spectrum of formic acid dimer, (HCOOH)2, in the spectral region 1369-1375 wn has been measured by a multi-step rapid-can method in a slit jet expansion using a distributed-feedback quantum cascade laser. The observed spectrum is assigned to the O-C-H bending fundamental band. The tunneling splitting in the vibrational excited state is determined to be about 0.005 wn, which is much smaller than that in the ground state, 0.0165 wn (Goroya et al.,J. Chem. Phys. 140, 164311 (2014)). Strong local perturbations involving transitions with J > 9, K = 0 and 1 are identified in the observed spectrum. The deperturbation analysis will be presented.

  15. The Cipher Code of Simple Sequence Repeats in "Vampire Pathogens".

    PubMed

    Zou, Geng; Bello-Orti, Bernardo; Aragon, Virginia; Tucker, Alexander W; Luo, Rui; Ren, Pinxing; Bi, Dingren; Zhou, Rui; Jin, Hui

    2015-07-28

    Blood inside mammals is a forbidden area for the majority of prokaryotic microbes; however, red blood cells tropism microbes, like "vampire pathogens" (VP), succeed in matching scarce nutrients and surviving strong immunity reactions. Here, we found VP of Mycoplasma, Rhizobiales, and Rickettsiales showed significantly higher counts of (AG)n dimeric simple sequence repeats (Di-SSRs) in the genomes, coding and non-coding regions than non Vampire Pathogens (N_VP). Regression analysis indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation. Gene Ontology (GO) terms with abundance of (AG)3-Di-SSRs shared by the VP strains were associated with purine nucleotide metabolism (FDR < 0.01), indicating an adaptation to the limited availability of purine and nucleotide precursors in blood. Di-amino acids coded by (AG)n-Di-SSRs included all three six-fold code amino acids (Arg, Leu and Ser) and significantly higher counts of Di-amino acids coded by (AG)3, (GA)3, and (TC)3 in VP than N_VP. Furthermore, significant differences (P < 0.001) on the numbers of triplexes formed from (AG)n-Di-SSRs between VP and N_VP in Mycoplasma suggested the potential role of (AG)n-Di-SSRs in gene regulation.

  16. Detection of retinoic acid receptor antagonist contamination in the aquatic environment of the Kinki region of Japan.

    PubMed

    Inoue, Daisuke; Sawada, Kazuko; Sei, Kazunari; Ike, Michihiko

    2016-10-15

    Retinoic acid receptor (RAR) antagonists are potential toxic compounds that can cause teratogenesis in vertebrates. This study was conducted to evaluate the occurrence of RAR antagonist contamination in aquatic environments and identify its potential sources in detail. To accomplish this, the RAR antagonistic activities of surface waters of two rivers (the Yodo River and the Ina River) and influents and effluents of municipal wastewater treatment plants (WWTPs) in the Kinki region of Japan were investigated using a yeast two-hybrid assay. In the investigated rivers, remarkable RAR antagonistic activities were detected relatively consistently in specific regions, although the levels varied with time, and tended to increase downstream of municipal WWTPs. Investigations of WWTPs also revealed that RAR antagonists were present at remarkably high levels in municipal wastewater, and that RAR antagonist contamination remained in effluent after activated sludge treatments. Comparison of the concentration factors that reduced 50% of the RAR agonistic activity of 10(-7) M all-trans retinoic acid (IC50) for selected river water and WWTP effluent samples revealed that the contamination levels were greater in effluent (IC50: concentration factors of 92-313) than river water (IC50: concentration factors of 10.2-68.9). These results indicate that municipal WWTPs could be an important source of RAR antagonist contamination in the receiving rivers. Fractionations with high-performance liquid chromatography directed by the bioassay indicated that there were multiple RAR antagonists in municipal wastewater. Although a trial to identify the causative compounds in municipal wastewater was not completed, multiple bioactive peaks that should be studied further were isolated. This study clarified the occurrence of novel endocrine disrupting chemicals (i.e., RAR antagonists) in the aquatic environment at the watershed level and identified their possible source for the first time, which

  17. Detection of retinoic acid receptor antagonist contamination in the aquatic environment of the Kinki region of Japan.

    PubMed

    Inoue, Daisuke; Sawada, Kazuko; Sei, Kazunari; Ike, Michihiko

    2016-10-15

    Retinoic acid receptor (RAR) antagonists are potential toxic compounds that can cause teratogenesis in vertebrates. This study was conducted to evaluate the occurrence of RAR antagonist contamination in aquatic environments and identify its potential sources in detail. To accomplish this, the RAR antagonistic activities of surface waters of two rivers (the Yodo River and the Ina River) and influents and effluents of municipal wastewater treatment plants (WWTPs) in the Kinki region of Japan were investigated using a yeast two-hybrid assay. In the investigated rivers, remarkable RAR antagonistic activities were detected relatively consistently in specific regions, although the levels varied with time, and tended to increase downstream of municipal WWTPs. Investigations of WWTPs also revealed that RAR antagonists were present at remarkably high levels in municipal wastewater, and that RAR antagonist contamination remained in effluent after activated sludge treatments. Comparison of the concentration factors that reduced 50% of the RAR agonistic activity of 10(-7) M all-trans retinoic acid (IC50) for selected river water and WWTP effluent samples revealed that the contamination levels were greater in effluent (IC50: concentration factors of 92-313) than river water (IC50: concentration factors of 10.2-68.9). These results indicate that municipal WWTPs could be an important source of RAR antagonist contamination in the receiving rivers. Fractionations with high-performance liquid chromatography directed by the bioassay indicated that there were multiple RAR antagonists in municipal wastewater. Although a trial to identify the causative compounds in municipal wastewater was not completed, multiple bioactive peaks that should be studied further were isolated. This study clarified the occurrence of novel endocrine disrupting chemicals (i.e., RAR antagonists) in the aquatic environment at the watershed level and identified their possible source for the first time, which

  18. Photophysical properties of praseodymium complexes with aromatic carboxylic acids: double light conversion both in ultraviolet and visible region.

    PubMed

    Yan, Bing; Wang, Weijing; Song, Yishan

    2007-04-01

    A series of luminescent praseodymium complexes with different aromatic carboxylic acids have been synthesized and characterized. The photophysical properties of these complexes have been studied with ultraviolet spectra, phosphorescence spectra and fluorescence spectra. Ultraviolet absorption spectra show that the praseodymium complexes systems with aromatic carboxylate form the more extensive conjugated systems to be suitable for the distribution of electron in the whole coordination environment, resulting in the energy decrease and red-shifts of ultraviolet spectral bands. Phosphorescence spectra suggest that excited triplet state of aromatic carboxylic acids, which can indicate the energy match and intermolecular energy transfer process between the excited triplet state of ligands and the resonant emissive energy level of Pr ions. The emission spectra of all praseodymium complexes show two emission peaks under the excitation band of 245 nm at about 395 and 595 nm, respectively, while one peak at about 595 nm under 415 nm excitation, which attributed to be 1S0-->1I6 (395 nm) transition and the characteristic emission 1D2-->3H4 (595 nm) transition of Pr3+ ion. The 1S0-->1I6 transition can be speculated to belong to the transition of charge transfer state, and the 1D2-->3H4 can be further proved that there exists an antenna effect in the luminescence of praseodymium with aromatic carboxylic acids. In conclusion, the praseodymium complexes systems can realize the double proton light conversion both in the ultraviolet and visible region, which can be further studied to have potential application.

  19. Early region 1B of adenovirus 2 encodes two coterminal proteins of 495 and 155 amino acid residues.

    PubMed Central

    Anderson, C W; Schmitt, R C; Smart, J E; Lewis, J B

    1984-01-01

    Partial sequence analysis of tryptic peptides has identified the E1B-495R (E1b-57K) (early transcription region 1B of 495 amino acid residues, with an approximate molecular weight of 57,000) protein of adenovirus 2 as encoded by the 495 amino acid open reading frame located in the adenovirus 2 DNA sequence between nucleotides 2016 and 3500. Additional proteins of 16,000 Mr and 18,000 Mr that are related to the E1B-495R protein were identified by cell-free translation of hybridization-selected mRNA. Analysis of [35S]methionine-containing amino terminal tryptic peptides by thin-layer chromatography showed that the E1B-495R, E1B-18K, and E1B-16K proteins all begin at the same initiation codon. The E1B-495R protein from 293 cells also has the same initial tryptic peptide, acetyl-methionyl-glutamyl-arginine. Sequence analysis of E1B-18K tryptic peptides indicated that this protein also has the same carboxy terminus as the E1B-495R protein and that it is derived from an mRNA that is spliced to remove sequences between nucleotides 2250 and 3269, resulting in a protein product of 155 amino acid residues. Analysis of E1B-16K tryptic peptides has not yet revealed the carboxy terminal structure of this protein. Both the E1B-495R and the E1B-155R (E1B-18K) proteins, as well as the E1B-16K protein, were precipitated from cell-free translations and from extracts of infected cells by antiserum against an amino terminal nonapeptide common to these proteins. Images PMID:6323739

  20. A time-series analysis of acidic particulate matter and daily mortality and morbidity in the Buffalo, New York, region.

    PubMed Central

    Gwynn, R C; Burnett, R T; Thurston, G D

    2000-01-01

    A component of particulate matter (PM) air pollution that may provide one biologically plausible pathway for the observed PM air pollution-health effect associations is aerosol acidity (H(+)). An increasing number of observational studies have demonstrated associations between H(+) and increased adverse health effects in the United States and abroad. Although studies have shown significant H(+) associations with increased morbidity in the United States, similar associations have yet to be shown with daily mortality. We considered a 2.5-year record of daily H(+) and sulfate measurements (May 1988-October 1990) collected in the Buffalo, New York, region in a time-series analysis of respiratory, circulatory, and total daily mortality and hospital admissions. Other copollutants considered included particulate matter [less than/equal to] 10 microm in aerodynamic diameter, coefficient of haze, ozone, carbon monoxide, sulfur dioxide, and nitrogen dioxide. Various modeling techniques were applied to control for confounding of effect estimates due to seasonality, weather, and day-of-week effects. We found multiple significant pollutant-health effect associations--most strongly between SO(4)(2-) and respiratory hospital admissions (as indicated by its t-statistic). Additionally, H(+) and SO(4)(2-) demonstrated the most coherent associations with both respiratory hospital admissions [H(+): relative risk (RR) = 1. 31; 95% confidence interval (CI), 1.14-1.51; and SO(4)(2-): RR = 1. 18, CI, 1.09-1.28] and respiratory mortality (H(+): RR = 1.55, CI, 1. 09-2.20; and SO(4)(2-): RR = 1.24, CI, 1.01-1.52). Thus, acidic sulfate aerosols represent a component of PM air pollution that may contribute to the previously noted adverse effects of PM mass on human health, and the associations demonstrated in this study support the need for further investigations into the potential health effects of acidic aerosols. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 PMID:10656852

  1. Reversing and nonreversing heat capacity of poly(lactic acid) in the glass transition region by TMDSC

    SciTech Connect

    Pyda, Marek {nmn}; Wunderlich, Bernhard {nmn}

    2005-11-01

    A study of the glass transition of an amorphous and a semicrystalline poly(lactic acid) (PLA) is performed with adiabatic calorimetry, differential scanning calorimetry (DSC), and temperature-modulated DSC (TMDSC). The reversing, total, and nonreversing apparent heat capacities of samples with different contents of L- and D-lactic acid and with various thermal histories were evaluated. Different modes of TMDSC analyses of amorphous and semicrystalline PLA were compared to the total heat capacity from standard DSC. The enthalpy relaxation and the cold crystallization in the glass transition region are largely irreversible. The melting is largely irreversible, but a 100% reversing fraction is observed at low temperatures from 375 to 420 K, which becomes small inside the major melting peak at about 440 K. From the TMDSC of amorphous PLA, the combined information on endothermic and exothermic enthalpy relaxation and glass transition were deconvoluted into the reversing and nonreversing components. The glass transition temperature from the reversing heat capacity and the enthalpy relaxation peaks from the nonreversing component shift to higher temperature for increasingly annealed PLA. The relaxation times for aging decrease on cooling until the glass transition is reached and then increase. This behavior is linked to cooperativity. All quantitative thermal analyses are based on the heat capacity of the solid and liquid, evaluated earlier with the advanced thermal analysis system (ATHAS).

  2. Factors contributing to decreased protein stability when aspartic acid residues are in {beta}-sheet regions.

    SciTech Connect

    Pokkuluri, P. R.; Cai, X.; Raffen, R.; Gu, M.; Stevens, F. J.; Schiffer, M.

    2002-07-01

    Asp residues are significantly under represented in {beta}-sheet regions of proteins, especially in the middle of {beta}-strands, as found by a number of studies using statistical, modeling, or experimental methods. To further understand the reasons for this under representation of Asp, we prepared and analyzed mutants of a {beta}-domain. Two Gln residues of the immunoglobulin light-chain variable domain (V{sub L}) of protein Len were replaced with Asp, and then the effects of these changes on protein stability and protein structure were studied. The replacement of Q38D, located at the end of a {beta}-strand, and that of Q89D, located in the middle of a {beta}-strand, reduced the stability of the parent immunoglobulin VL domain by 2.0 kcal/mol and 5.3 kcal/mol, respectively. Because the Q89D mutant of the wild-type V{sub L}-Len domain was too unstable to be expressed as a soluble protein, we prepared the Q89D mutant in a triple mutant background, V{sub L}-Len M4L/Y27dD/T94H, which was 4.2 kcal/mol more stable than the wild-type V{sub L}-Len domain. The structures of mutants V{sub L}-Len Q38D and V{sub L}-Len Q89D/M4L/Y27dD/T94H were determined by X-ray diffraction at 1.6 A resolution. We found no major perturbances in the structures of these QD mutant proteins relative to structures of the parent proteins. The observed stability changes have to be accounted for by cumulative effects of the following several factors: (1) by changes in main-chain dihedral angles and in side-chain rotomers, (2) by close contacts between some atoms, and, most significantly, (3) by the unfavorable electrostatic interactions between the Asp side chain and the carbonyls of the main chain. We show that the Asn side chain, which is of similar size but neutral, is less destabilizing. The detrimental effect of Asp within a {beta}-sheet of an immunoglobulin-type domain can have very serious consequences. A somatic mutation of a {beta}-strand residue to Asp could prevent the expression of the

  3. Amino acid region 1000-1008 of factor V is a dynamic regulator for the emergence of procoagulant activity.

    PubMed

    Wiencek, Joesph R; Na, Mahesheema; Hirbawi, Jamila; Kalafatis, Michael

    2013-12-27

    Single chain factor V (fV) circulates as an Mr 330,000 quiescent pro-cofactor. Removal of the B domain and generation of factor Va (fVa) are vital for procoagulant activity. We investigated the role of the basic amino acid region 1000-1008 within the B domain of fV by constructing a recombinant mutant fV molecule with all activation cleavage sites (Arg(709)/Arg(1018)/Arg(1545)) mutated to glutamine (fV(Q3)), a mutant fV molecule with region 1000-1008 deleted (fV(ΔB9)), and a mutant fV molecule containing the same deletion with activation cleavage sites changed to glutamine (fV(ΔB9/Q3)). The recombinant molecules along with wild type fV (fV(WT)) were transiently expressed in COS-7L cells, purified, and assessed for their ability to bind factor Xa (fXa) prior to and following incubation with thrombin. The data showed that fV(Q3) was severely impaired in its interaction with fXa before and after incubation with thrombin. In contrast, KD(app) values for fV(ΔB9) (0.9 nM), fVa(ΔB9) (0.4 nM), and fV(ΔB9/Q3) (0.7 nM) were similar to the affinity of fVa(WT) for fXa (0.3 nM). Two-stage clotting assays revealed that although fV(Q3) was deficient in its clotting activity, fV(ΔB9/Q3) had clotting activity comparable with fVa(WT). The kcat value of prothrombinase assembled with fV(ΔB9/Q3) was minimally affected, whereas the Km value of the reaction was increased 57-fold compared with the Km value obtained with prothrombinase assembled with fVa(WT). These findings strongly suggest that amino acid region 1000-1008 of fV is a regulatory sequence protecting the organisms from spontaneous binding to fXa and unnecessary prothrombinase complex formation, which in turn results in catastrophic physiological consequences. PMID:24178294

  4. Saturation of repeated quantum measurements

    NASA Astrophysics Data System (ADS)

    Haapasalo, Erkka; Heinosaari, Teiko; Kuramochi, Yui

    2016-08-01

    We study sequential measurement scenarios where the system is repeatedly subjected to the same measurement process. We first provide examples of such repeated measurements where further repetitions of the measurement do not increase our knowledge on the system after some finite number of measurement steps. We also prove, however, that repeating the Lüders measurement of an unsharp two-outcome observable never saturates in this sense, and we characterize the observable measured in the limit of infinitely many repetitions. Our result implies that a repeated measurement can be used to correct the inherent noise of an unsharp observable.

  5. Evolution of subterminal satellite (StSat) repeats in hominids.

    PubMed

    Koga, Akihiko; Notohara, Morihiro; Hirai, Hirohisa

    2011-02-01

    Subterminal satellite (StSat) repeats, consisting of 32-bp-long AT-rich units (GATATTTCCATGTT(T/C)ATACAGATAGCGGTGTA), were first found in chimpanzee and gorilla (African great apes) as one of the major components of heterochromatic regions located proximal to telomeres of chromosomes. StSat repeats have not been found in orangutan (Asian great ape) or human. This patchy distribution among species suggested that the StSat repeats were present in the common ancestor of African great apes and subsequently lost in the lineage leading to human. An alternative explanation is that the StSat repeats in chimpanzee and gorilla have different origins and the repeats did not occur in human. The purpose of the present study was quantitative evaluation of the above alternative possibilities by analyzing the nucleotide variation contained in the repeats. We collected large numbers of sequences of repeat units from genome sequence databases of chimpanzee and gorilla, and also bonobo (an African great ape phylogenetically closer to chimpanzee). We then compared the base composition of the repeat units among the 3 species, and found statistically significant similarities in the base composition. These results support the view that the StSat repeats had already formed multiple arrays in the common ancestor of African great apes. It is thus suggested that humans lost StSat repeats which had once grown to multiple arrays.

  6. Comparison of simple sequence repeats in 19 Archaea.

    PubMed

    Trivedi, S

    2006-01-01

    All organisms that have been studied until now have been found to have differential distribution of simple sequence repeats (SSRs), with more SSRs in intergenic than in coding sequences. SSR distribution was investigated in Archaea genomes where complete chromosome sequences of 19 Archaea were analyzed with the program SPUTNIK to find di- to penta-nucleotide repeats. The number of repeats was determined for the complete chromosome sequences and for the coding and non-coding sequences. Different from what has been found for other groups of organisms, there is an abundance of SSRs in coding regions of the genome of some Archaea. Dinucleotide repeats were rare and CG repeats were found in only two Archaea. In general, trinucleotide repeats are the most abundant SSR motifs; however, pentanucleotide repeats are abundant in some Archaea. Some of the tetranucleotide and pentanucleotide repeat motifs are organism specific. In general, repeats are short and CG-rich repeats are present in Archaea having a CG-rich genome. Among the 19 Archaea, SSR density was not correlated with genome size or with optimum growth temperature. Pentanucleotide density had an inverse correlation with the CG content of the genome. PMID:17183484

  7. REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads

    PubMed Central

    Chu, Chong; Nielsen, Rasmus; Wu, Yufeng

    2016-01-01

    Repeat elements are important components of eukaryotic genomes. One limitation in our understanding of repeat elements is that most analyses rely on reference genomes that are incomplete and often contain missing data in highly repetitive regions that are difficult to assemble. To overcome this problem we develop a new method, REPdenovo, which assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo can construct various types of repeats that are highly repetitive and have low sequence divergence within copies. We show that REPdenovo is substantially better than existing methods both in terms of the number and the completeness of the repeat sequences that it recovers. The key advantage of REPdenovo is that it can reconstruct long repeats from sequence reads. We apply the method to human data and discover a number of potentially new repeats sequences that have been missed by previous repeat annotations. Many of these sequences are incorporated into various parasite genomes, possibly because the filtering process for host DNA involved in the sequencing of the parasite genomes failed to exclude the host derived repeat sequences. REPdenovo is a new powerful computational tool for annotating genomes and for addressing questions regarding the evolution of repeat families. The software tool, REPdenovo, is available for download at https://github.com/Reedwarbler/REPdenovo. PMID:26977803

  8. To Repeat or Not to Repeat a Course

    ERIC Educational Resources Information Center

    Armstrong, Michael J.; Biktimirov, Ernest N.

    2013-01-01

    The difficult transition from high school to university means that many students need to repeat (retake) 1 or more of their university courses. The authors examine the performance of students repeating first-year core courses in an undergraduate business program. They used data from university records for 116 students who took a total of 232…

  9. DWI Repeaters and Non-Repeaters: A Comparison.

    ERIC Educational Resources Information Center

    Weeber, Stan

    1981-01-01

    Discussed how driving-while-intoxicated (DWI) repeaters differed signigicantly from nonrepeaters on 4 of 23 variables tested. Repeaters were more likely to have zero or two dependent children, attend church frequently, drink occasionally and have one or more arrests for public intoxication. (Author)

  10. Characterization of Arbequina virgin olive oils produced in different regions of Brazil and Spain: Physicochemical properties, oxidative stability and fatty acid profile.

    PubMed

    Borges, Thays H; Pereira, José Alberto; Cabrera-Vique, Carmen; Lara, Luis; Oliveira, Adelson F; Seiquer, Isabel

    2017-01-15

    Production of virgin olive oil is beginning in Brazil. This paper analyzes the characteristics of the EVOO Arbequina from Brazil in comparison with Spanish Arbequina from different regions. Quality parameters, oxidative stability, pigments, colour and fatty acid profile were assessed, and relationships with geographic and climatic conditions were studied. All the samples presented good quality and met EU standards for extra-virgin olive oil, but there were significant differences between regions and countries for many of the parameters evaluated. Major differences between Brazilian and Spanish samples were observed for free acidity and colour of the oils, as well as minor variations in the fatty acid profile. The colour differences were related to rainfall, whereas the fatty acid content was strongly influenced by altitude and temperature. These results highlight the fact that geographic area and environmental factors influence the characteristics of Arbequina oil and play an important role in newly introduced cultivars. PMID:27542498

  11. Characterization of Arbequina virgin olive oils produced in different regions of Brazil and Spain: Physicochemical properties, oxidative stability and fatty acid profile.

    PubMed

    Borges, Thays H; Pereira, José Alberto; Cabrera-Vique, Carmen; Lara, Luis; Oliveira, Adelson F; Seiquer, Isabel

    2017-01-15

    Production of virgin olive oil is beginning in Brazil. This paper analyzes the characteristics of the EVOO Arbequina from Brazil in comparison with Spanish Arbequina from different regions. Quality parameters, oxidative stability, pigments, colour and fatty acid profile were assessed, and relationships with geographic and climatic conditions were studied. All the samples presented good quality and met EU standards for extra-virgin olive oil, but there were significant differences between regions and countries for many of the parameters evaluated. Major differences between Brazilian and Spanish samples were observed for free acidity and colour of the oils, as well as minor variations in the fatty acid profile. The colour differences were related to rainfall, whereas the fatty acid content was strongly influenced by altitude and temperature. These results highlight the fact that geographic area and environmental factors influence the characteristics of Arbequina oil and play an important role in newly introduced cultivars.

  12. Repeated exposure to low doses of kainic acid activates nuclear factor kappa B (NF-κB) prior to seizure in transgenic NF-κB/EGFP reporter mice.

    PubMed

    Miller, James A; Kirkley, Kelly A; Padmanabhan, Rachel; Liang, Li-Ping; Raol, Yogendra H; Patel, Manisha; Bialecki, Russell A; Tjalkens, Ronald B

    2014-09-01

    Predicting seizurogenic properties of pharmacologically active compounds is difficult due to the complex nature of the mechanisms involved and because of the low sensitivity and high variability associated with current behavioral-based methods. To identify early neuronal signaling events predictive of seizure, we exposed transgenic NF-κB/EGFP reporter mice to multiple low doses of kainic acid (KA), postulating that activation of the stress-responsive NF-κB pathway could be a sensitive indicator of seizurogenic potential. The sub-threshold dose level proximal to the induction of seizure was determined as 2.5mg/kg KA, using video EEG monitoring. Subsequent analysis of reporter expression demonstrated significant increases in NF-κB activation in the CA3 and CA1 regions of the hippocampus 24h after a single dose of 2.5mg/kg KA. This response was primarily observed in pyramidal neurons with little non-neuronal expression. Neuronal NF-κB/EGFP expression was observed in the absence of glial activation, indicating a lack of neurodegeneration-induced neuroinflammation. Protein expression of the immediate-early gene, Nurr1, increased in neurons in parallel to NF-κB activation, supporting that the sub-threshold doses of KA employed directly caused neuronal stress. Lastly, KA also stimulated NF-κB activation in organotypic hippocampal slice cultures established from NF-κB/EGFP reporter mice. Collectively, these data demonstrate the potential advantages of using genetically encoded stress pathway reporter models in the screening of seizurogenic properties of new pharamacologically active compounds.

  13. Modeling Repeatedly Flaring δ Sunspots.

    PubMed

    Chatterjee, Piyali; Hansteen, Viggo; Carlsson, Mats

    2016-03-11

    Active regions (ARs) appearing on the surface of the Sun are classified into α, β, γ, and δ by the rules of the Mount Wilson Observatory, California on the basis of their topological complexity. Amongst these, the δ sunspots are known to be superactive and produce the most x-ray flares. Here, we present results from a simulation of the Sun by mimicking the upper layers and the corona, but starting at a more primitive stage than any earlier treatment. We find that this initial state consisting of only a thin subphotospheric magnetic sheet breaks into multiple flux tubes which evolve into a colliding-merging system of spots of opposite polarity upon surface emergence, similar to those often seen on the Sun. The simulation goes on to produce many exotic δ sunspot associated phenomena: repeated flaring in the range of typical solar flare energy release and ejective helical flux ropes with embedded cool-dense plasma filaments resembling solar coronal mass ejections.

  14. Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates

    SciTech Connect

    Jackson, P.J.; Walthers, E.A.; Richmond, K.L.

    1997-04-01

    PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five Polymorphisms differed by the presence Of two to six copies of the 12-bp tandem repeat 5{prime}-CAATATCAACAA-3{prime}. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats are generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations. 22 refs., 4 figs., 3 tabs.

  15. Regional differences in production of aflatoxin B1 and cyclopiazonic acid by soil isolates of aspergillus flavus along a transect within the United States.

    PubMed

    Horn, B W; Dorner, J W

    1999-04-01

    Soil isolates of Aspergillus flavus from a transect extending from eastern New Mexico through Georgia to eastern Virginia were examined for production of aflatoxin B1 and cyclopiazonic acid in a liquid medium. Peanut fields from major peanut-growing regions (western Texas; central Texas; Georgia and Alabama; and Virginia and North Carolina) were sampled, and fields with other crops were sampled in regions where peanuts are not commonly grown. The A. flavus isolates were identified as members of either the L strain (n = 774), which produces sclerotia that are >400 micrometer in diameter, or the S strain (n = 309), which produces numerous small sclerotia that are <400 micrometer in diameter. The S-strain isolates generally produced high levels of aflatoxin B1, whereas the L-strain isolates were more variable in aflatoxin production; variation in cyclopiazonic acid production also was greater in the L strain than in the S strain. There was a positive correlation between aflatoxin B1 production and cyclopiazonic acid production in both strains, although 12% of the L-strain isolates produced only cyclopiazonic acid. Significant differences in production of aflatoxin B1 and cyclopiazonic acid by the L-strain isolates were detected among regions. In the western half of Texas and the peanut-growing region of Georgia and Alabama, 62 to 94% of the isolates produced >10 microgram of aflatoxin B1 per ml. The percentages of isolates producing >10 microgram of aflatoxin B1 per ml ranged from 0 to 52% in the remaining regions of the transect; other isolates were often nonaflatoxigenic. A total of 53 of the 126 L-strain isolates that did not produce aflatoxin B1 or cyclopiazonic acid were placed in 17 vegetative compatibility groups. Several of these groups contained isolates from widely separated regions of the transect.

  16. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1998-01-01

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

  17. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1998-03-24

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. 14 figs.

  18. Trinucleotide repeat expansion and DRPLA (Smith`s disease): Molecular characterization of atrophin-1

    SciTech Connect

    Margolis, R.L.; Li, S.H.; Li, X.J.; Ross, C.A.

    1994-09-01

    Smith`s disease (also known as dentatorubral pallidoluysian atrophy or DRPLA) is a rare, progressive, fatal neuropsychiatric disorder similar to Huntington`s disease (HD). Smith`s disease is characterized by ataxia, choreoathetosis, myoclonic epilepsy, dementia, and genetic anticipation. Neuropathological findings include prominent cell loss in the dentate nucleus of the cerebellum, the globus pallidus, the red nucleus, and the subthalamic nucleus. An expansion of a CAG trinucleotide repeat encoding polyglutamine in a gene originally identified in our laboratory as part of a program to clone candidate genes for disorders with anticipation has recently been found to cause this disorder. We have identified two families that demonstrate the pathological and genetic features (expanded CAG repeat and anticipation) of this disease. Northern analysis indicates that the gene, which we have termed atrophin-1, is widely expressed as a 5 kb mRNA in normal human brain and peripheral tissues. Brain expression is highest in the cerebellum. The developmental expression of the rat homologues of IT-15 (the gene in which a CAG expansion causes HD) and atrophin-1 were compared. Atrophin-1 was most highly expressed in early rat embryo brain (E16), whereas the greatest expression of IT-15 was in the adult rat brain. Cloning and sequencing of the open reading frame from inserts contained in brain cDNA libraries is in progress. In addition to the CAG repeat, the ORF contains an unusual region of alternating acidic and basic amino acids. Further characterization of atrophin-1, and comparison of it to other genes in which trinucleotide repeat expansion leads to neuropsychiatric disorders, should lead to a better understanding of the pathophysiology by which CAG repeat expansion causes human disease.

  19. Upper limits for stereoselective photodissociation of free amino acids in the vacuum ultraviolet region and at the C 1s edge

    SciTech Connect

    Pruemper, Georg; Viefhaus, Jens; Cvejanovic, Slobodan; Rolles, Daniel; Gessner, Oliver; Lischke, Toralf; Hentges, Rainer; Wienberg, Christian; Mahler, Willy; Becker, Uwe; Langer, Burkhard; Prosperi, Tommaso; Zema, Nicola; Turchini, Stefano; Zada, Birgitt; Senf, Fred

    2004-06-01

    We measured the total and partial ion yields of the two chiral amino acids alanine and serine in the gas phase both in the vacuum ultraviolet region and at the C(1s) edge using circularly polarized light. We did not detect any circular dichroism asymmetry larger than 1x10{sup -3}. A similar measurement of fixed-in-space amino acids yielded an upper limit of 1x10{sup -2} for the stereoselective effect of circularly polarized light. The results obtained are relevant for quantitative models of stereoselective photodecomposition of amino acids that try to explain the homochirality of life.

  20. Nifty Nines and Repeating Decimals

    ERIC Educational Resources Information Center

    Brown, Scott A.

    2016-01-01

    The traditional technique for converting repeating decimals to common fractions can be found in nearly every algebra textbook that has been published, as well as in many precalculus texts. However, students generally encounter repeating decimal numerals earlier than high school when they study rational numbers in prealgebra classes. Therefore, how…

  1. Estimating repeatability of egg size

    USGS Publications Warehouse

    Flint, P.L.; Rockwell, R.F.; Sedinger, J.S.

    2001-01-01

    Measures of repeatability have long been used to assess patterns of variation in egg size within and among females. We compared different analytical approaches for estimating repeatability of egg size of Black Brant. Separate estimates of repeatability for eggs of each clutch size and laying sequence number varied from 0.49 to 0.64. We suggest that using the averaging egg size within clutches results in underestimation of variation within females and thereby overestimates repeatability. We recommend a nested design that partitions egg-size variation within clutches, among clutches within females, and among females. We demonstrate little variation in estimates of repeatability resulting from a nested model controlling for egg laying sequence and a nested model in which we assumed laying sequence was unknown.

  2. All-photonic quantum repeaters.

    PubMed

    Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong

    2015-01-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories.

  3. All-photonic quantum repeaters

    PubMed Central

    Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong

    2015-01-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories. PMID:25873153

  4. Triggering of repeating earthquakes in central California

    USGS Publications Warehouse

    Wu, Chunquan; Gomberg, Joan; Ben-Naim, Eli; Johnson, Paul

    2014-01-01

    Dynamic stresses carried by transient seismic waves have been found capable of triggering earthquakes instantly in various tectonic settings. Delayed triggering may be even more common, but the mechanisms are not well understood. Catalogs of repeating earthquakes, earthquakes that recur repeatedly at the same location, provide ideal data sets to test the effects of transient dynamic perturbations on the timing of earthquake occurrence. Here we employ a catalog of 165 families containing ~2500 total repeating earthquakes to test whether dynamic perturbations from local, regional, and teleseismic earthquakes change recurrence intervals. The distance to the earthquake generating the perturbing waves is a proxy for the relative potential contributions of static and dynamic deformations, because static deformations decay more rapidly with distance. Clear changes followed the nearby 2004 Mw6 Parkfield earthquake, so we study only repeaters prior to its origin time. We apply a Monte Carlo approach to compare the observed number of shortened recurrence intervals following dynamic perturbations with the distribution of this number estimated for randomized perturbation times. We examine the comparison for a series of dynamic stress peak amplitude and distance thresholds. The results suggest a weak correlation between dynamic perturbations in excess of ~20 kPa and shortened recurrence intervals, for both nearby and remote perturbations.

  5. Methylation variation at IGF2 differentially methylated regions and maternal folic acid use before and during pregnancy.

    PubMed

    Hoyo, Cathrine; Murtha, Amy P; Schildkraut, Joellen M; Jirtle, Randy L; Demark-Wahnefried, Wendy; Forman, Michele R; Iversen, Edwin S; Kurtzberg, Joanne; Overcash, Francine; Huang, Zhiqing; Murphy, Susan K

    2011-07-01

    Folic acid (FA) supplementation before and during pregnancy has been associated with decreased risk of neural tube defects although recent reports suggest it may also increase the risk of other chronic diseases. We evaluated exposure to maternal FA supplementation before and during pregnancy in relation to aberrant DNA methylation at two differentially methylated regions (DMRs) regulating Insulin-like Growth Factor 2 (IGF2) expression in infants. Aberrant methylation at these regions has been associated with IGF2 deregulation and increased susceptibility to several chronic diseases. Using a self-administered questionnaire, we assessed FA intake before and during pregnancy in 438 pregnant women. Pyrosequencing was used to measure methylation at two IGF2 DMRs in umbilical cord blood leukocytes. Mixed models were used to determine relationships between maternal FA supplementation before or during pregnancy and DNA methylation levels at birth. Average methylation at the H19 DMR was 61.2%. Compared to infants born to women reporting no FA intake before or during pregnancy, methylation levels at the H19 DMR decreased with increasing FA intake (2.8%, p=0.03, and 4.9%, p=0.04, for intake before and during pregnancy, respectively). This methylation decrease was most pronounced in male infants (p=0.01). Methylation alterations at the H19 DMR are likely an important mechanism by which FA risks and/or benefits are conferred in utero. Because stable methylation marks at DMRs regulating imprinted genes are acquired before gastrulation, they may serve as archives of early exposures with the potential to improve our understanding of developmental origins of adult disease.

  6. The repeat domain of the type III effector protein PthA shows a TPR-like structure and undergoes conformational changes upon DNA interaction.

    PubMed

    Murakami, Mário Tyago; Sforça, Mauricio Luis; Neves, Jorge Luiz; Paiva, Joice Helena; Domingues, Mariane Noronha; Pereira, André Luiz Araujo; Zeri, Ana Carolina de Mattos; Benedetti, Celso Eduardo

    2010-12-01

    Many plant pathogenic bacteria rely on effector proteins to suppress defense and manipulate host cell mechanisms to cause disease. The effector protein PthA modulates the host transcriptome to promote citrus canker. PthA possesses unusual protein architecture with an internal region encompassing variable numbers of near-identical tandem repeats of 34 amino acids termed the repeat domain. This domain mediates protein-protein and protein-DNA interactions, and two polymorphic residues in each repeat unit determine DNA specificity. To gain insights into how the repeat domain promotes protein-protein and protein-DNA contacts, we have solved the structure of a peptide corresponding to 1.5 units of the PthA repeat domain by nuclear magnetic resonance (NMR) and carried out small-angle X-ray scattering (SAXS) and spectroscopic studies on the entire 15.5-repeat domain of PthA2 (RD2). Consistent with secondary structure predictions and circular dichroism data, the NMR structure of the 1.5-repeat peptide reveals three α-helices connected by two turns that fold into a tetratricopeptide repeat (TPR)-like domain. The NMR structure corroborates the theoretical TPR superhelix predicted for RD2, which is also in agreement with the elongated shape of RD2 determined by SAXS. Furthermore, RD2 undergoes conformational changes in a pH-dependent manner and upon DNA interaction, and shows sequence similarities to pentatricopeptide repeat (PPR), a nucleic acid-binding motif structurally related to TPR. The results point to a model in which the RD2 structure changes its compactness as it embraces the DNA with the polymorphic diresidues facing the interior of the superhelix oriented toward the nucleotide bases.

  7. The effects of acidic deposition on streams in the Appalachian Mountain and Piedmont region of the mid-Atlantic United States

    SciTech Connect

    Herlihy, A.T.; Kaufman, P.R. ); Church, M.R.; Wigington, P.J. Jr. ); Webb, J.R. ); Sale, M.J. )

    1993-08-01

    Streams in the Appalachian Mountain area of the mid-Atlantic receive some of the largest acidic deposition loadings of any region of the US. A synthesis of the survey data from the mid-Appalachians yields a consistent picture of the acid base status of streams. Acidic streams, and streams with very low acid neutralizing capacity (ANC), are almost all located in small (<20 km[sup 2]), upland, forested catchments in areas of base-poor bedrock. In the subpopulation in the mid-Appalachian area, data from various local surveys show that 6-27% of the streams are acidic, and about 25-50% have ANC less than 50 [mu]eq L[sup [minus]1]. After excluding streams with acid mine drainage, National Stream Survey estimates for the whole region show that there are 2330 km of acidic streams and 7500 km of streams with ANC less than 50 [mu]eq L[sup [minus]1]. Many of the streams with base flow ANC less than 50 [mu]eq L[sup [minus]1] become acidic during storm or snowmelt episodes. Sulfate from atmospheric deposition is the dominant source of strong acid anions in acid mid-Appalachian streams. Their low pH (median, 4.9) and high levels of inorganic monomeric aluminum (median, 129 [mu]g L[sup [minus]1]) leached through soils by acidic deposition are causing damage to aquatic biota. Quantification of the extent of biological effects, however, is not possible with available data. Localized studies have shown that stream water ANC is closely related to bedrock mineralogy. Attempts to quantify this relationship across the mid-Appalachians, however, were frustrated by the lack of adequate scale geologic mapping throughout the region. Sulfate mass balance analyses indicate that soils and surface waters of the region have not yet realized the full effects of elevated sulfur deposition due to watershed sulfate retention. Sulfur retention is likely to decrease in the future, resulting in further losses of stream ANC. 70 refs., 5 figs., 4 tabs.

  8. The effects of acidic deposition on streams in the Appalachian Mountain and Piedmont Region of the Mid-Atlantic United States

    NASA Astrophysics Data System (ADS)

    Herlihy, A. T.; Kaufmann, P. R.; Church, M. R.; Wigington, P. J.; Webb, J. R.; Sale, M. J.

    1993-08-01

    Streams in the Appalachian Mountain area of the mid-Atlantic receive some of the largest acidic deposition loadings of any region of the United States. A synthesis of the survey data from the mid-Appalachians yields a consistent picture of the acid base status of streams. Acidic streams, and streams with very low acid neutralizing capacity (ANC), are almost all located in small (<20 km2), upland, forested catchments in areas of base-poor bedrock. In the subpopulation of upland forested systems, which comprises about half the total stream population in the mid-Appalachian area, data from various local surveys show that 6-27% of the streams are acidic, and about 25-50% have ANC less than 50 μeq L-1. After excluding streams with acid mine drainage, National Stream Survey estimates for the whole region show that there are 2330 km of acidic streams and 7500 km of streams with ANC less than 50 μeq L-1. Many of the streams with base flow ANC less than 50 μeq L-1 become acidic during storm or snowmelt episodes. Sulfate from atmospheric deposition is the dominant source of strong acid anions in acidic mid-Appalachian streams. Their low pH (median, 4.9) and high levels of inorganic monomeric aluminum (median, 129 μg L-1) leached through soils by acidic deposition are causing damage to aquatic biota. Quantification of the extent of biological effects, however, is not possible with available data. Localized studies have shown that stream water ANC is closely related to bedrock mineralogy. Attempts to quantify this relationship across the mid-Appalachians, however, were frustrated by the lack of adequate scale geologic mapping throughout the region. Sulfate mass balance analyses indicate that soils and surface waters of the region have not yet realized the full effects of elevated sulfur deposition due to watershed sulfate retention. Sulfur retention is likely to decrease in the future, resulting in further losses of stream ANC.

  9. Two single amino acid substitutions in the intervening region of Newcastle disease virus HN protein attenuate viral replication and pathogenicity

    PubMed Central

    Liu, Bin; Ji, Yanhong; Lin, Zhongqing; Fu, Yuguang; Muhammad Dafallah, Rihab; Zhu, Qiyun

    2015-01-01

    Among the proteins encoded by Newcastle disease virus (NDV), the attachment protein (HN) is an important determinant of virulence and pathogenicity. HN has been molecularly characterized at the protein level; however, the relationship between the molecular character of HN and the animal pathotype it causes has not been well explored. Here, we revisited the intervening region (IR) of the HN stalk and extended the known biological functions of HN. Three distinct substitutions (A89Q, P93A, and L94A) in the IR of genotype VII NDV (G7 strain) HN protein were analyzed. The A89Q and L94A mutations weakened the fusion promotion activity of HN to 44% and 41% of that of wild type, respectively, whereas P93A decreased the neuraminidase activity to 21% of the parental level. At the virus level, P93A and L94A-bearing viruses displayed impaired receptor recognition ability, neuraminidase activity, and fusion-promoting activity, all of which led to virus attenuation. In addition, the L94A-mutated virus showed a dramatic decline in replication and was attenuated in cells and in chickens. Our data demonstrate that the HN biological activities and functions modulated by these specific amino acids in the IR are associated with NDV replication and pathogenicity. PMID:26267791

  10. Integrated defence reaction elicited by excitatory amino acid microinjection in the midbrain periaqueductal grey region of the unrestrained cat.

    PubMed

    Bandler, R; Carrive, P

    1988-01-26

    Unilateral microinjections (0.20 microliter) of the excitatory amino acids (EAA), L-aspartate (ASP), D,L-homocysteate (DLH) or kainate (KA) were made into the midbrain of freely moving cats. Injections of DLH (20 nmol) or ASP (200 nmol) made within the midbrain periaqueductal grey matter (PAG) consistently elicited a threat display characteristic of defensive behaviour (i.e., pupillary dilatation, piloerection, retraction of the ears, sideways backing, arching of the back, hissing, howling, growling), whereas injections of DLH or ASP made in the tegmentum bordering the PAG did not elicit such behaviour. Injections of KA (940 pmol) made within the PAG, but not the tegmentum, elicited not only a threat display but also directed attack (striking with unsheathed claws and biting). As injections of EAA depolarize cell bodies, but not axons, the results suggest that a population of neurones whose excitation elicits all of the behavioural signs of defence, including directed attack, is found within the PAG. Histology indicated that the region of the PAG from which the defence reaction was elicited was not confined to any PAG subnucleus. Rather, the 'defence region' of the PAG formed a cylindrical column lateral to the midbrain aqueduct, approximately 1.5 mm in diameter and 5.0 mm in length, the rostral end of which lay dorsal to the caudal end. Further, it was found that EAA microinjections made in different portions of the defence region of the PAG elicited defence reactions characterised by different patterns of vocalization and differing intensities of display. It was also observed following unilateral injection of KA into the PAG that defence reactions, including attack, were elicited by approach in the visual hemifield or touch of the body contralateral, but not ipsilateral, to the injection site. The asymmetry of the defence reaction was not due to any obvious ipsilateral motor impairment and thus suggests that the PAG mediation of the defence reaction, in addition

  11. The impact of mineral fertilizers and lime on the transformation of humic acids in a soddy-podzolic heavy loamy soil of the Cis-Ural region

    NASA Astrophysics Data System (ADS)

    Zav'yalova, N. E.

    2015-06-01

    The composition and structure of humic acids in a soddy-podzolic heavy loamy soil (Retisol) of the Cis-Ural region after the long-term application of mineral fertilizers and lime was studied by the methods of elemental analysis, infrared spectroscopy, and thermogravimetry. It was found that mineral fertilizers and lime did not change the ranges of C, H, O, and N contents and general structure typical of humic acids in soddy-podzolic soils. The long-term anthropogenic impact on the soil resulted in some transformation of the composition and properties of humic acids. Clear absorption bands in the area of 1700 cm-1 (C=O of carbonyl group) and 1620 cm-1 (C=C of aromatic rings), which characterize the benzenoid structures of molecules, were found in the infrared spectra of humic acids from the soil treated with lime at the rate to compensate for the total acidity. Soil liming favored the accumulation of thermodynamically stable fragments of the central part of humic acid molecules and the destruction of peripheral radicals. The application of mineral fertilizers resulted in the enrichment of humic acids with aliphatic fragments. The combined application of mineral fertilizers and lime increased the portion of aromatic structures and, at the same time, enriched humic acids in aliphatic fragments less resistant to pyrolysis. These fragments are biologically and chemically active and can be readily involved in the element turnover processes, thus protecting the stable part of humus from the biological destruction.

  12. Bovine gall-bladder mucin contains two distinct tandem repeating sequences: evidence for scavenger receptor cysteine-rich repeats.

    PubMed

    Nunes, D P; Keates, A C; Afdhal, N H; Offner, G D

    1995-08-15

    Gall-bladder mucin is a densely glycosylated macromolecule which is the primary secretory product of the gall-bladder epithelium. It has been shown to bind cholesterol and other biliary lipids and to promote cholesterol crystal nucleation in vitro. In order to understand the molecular basis for mucin-lipid interactions, bovine gall-bladder mucin cDNAs were identified by expression cloning and were isolated and sequenced. The nucleotide sequences of these cDNAs revealed two distinct tandem repeating domains. One of these domains contained a 20-amino acid tandem repeating sequence enriched in threonine, serine and proline. This sequence was similar to, but not identical with, the short tandem repeating sequences identified previously in other mammalian mucins. The other domain contained a 127-amino acid tandem repeating sequence enriched in cysteine and glycine. This repeat displayed considerable sequence similarity to a family of receptor- and ligand-binding proteins containing scavenger receptor cysteine-rich repeats. By analogy with other proteins containing these cysteine-rich repeats, it is possible that, in gall-bladder mucin, this domain serves as a binding site for hydrophobic ligands such as bilirubin, cholesterol and other biliary lipids.

  13. Variation in seed fatty acid composition and sequence divergence in the FAD2 gene coding region between wild and cultivated sesame.

    PubMed

    Chen, Zhenbang; Tonnis, Brandon; Morris, Brad; Wang, Richard B; Zhang, Amy L; Pinnow, David; Wang, Ming Li

    2014-12-01

    Sesame germplasm harbors genetic diversity which can be useful for sesame improvement in breeding programs. Seven accessions with different levels of oleic acid were selected from the entire USDA sesame germplasm collection (1232 accessions) and planted for morphological observation and re-examination of fatty acid composition. The coding region of the FAD2 gene for fatty acid desaturase (FAD) in these accessions was also sequenced. Cultivated sesame accessions flowered and matured earlier than the wild species. The cultivated sesame seeds contained a significantly higher percentage of oleic acid (40.4%) than the seeds of the wild species (26.1%). Nucleotide polymorphisms were identified in the FAD2 gene coding region between wild and cultivated species. Some nucleotide polymorphisms led to amino acid changes, one of which was located in the enzyme active site and may contribute to the altered fatty acid composition. Based on the morphology observation, chemical analysis, and sequence analysis, it was determined that two accessions were misnamed and need to be reclassified. The results obtained from this study are useful for sesame improvement in molecular breeding programs.

  14. Development of simple sequence repeat markers in cymbopogon species.

    PubMed

    Kumar, Jitendra; Verma, Vijeshwar; Shahi, Ashok Kumar; Qazi, Gulam Nab; Balyan, Harindra Singh

    2007-03-01

    The genus Cymbopogon comprises about 140 species, which produce characteristic aromatic essential oils. However, the phenotypic identification of species of Cymbopogon has been difficult as a result of widespread occurrence of natural variants, which differ in ploidy levels and chemotaxonomic complexities. Therefore, we have developed a set of simple sequence repeat markers from a genomic library of Cymbopogon jwarancusa to help in the precise identification of the species (including accessions) of Cymbopogon. For this purpose, we isolated 16 simple sequence repeat containing genomic deoxyribonucleic acid clones of C. jwarancusa, which contained a total of 32 simple sequence repeats with a range of 1 to 3 simple sequence repeats per clone. The majority (68.8%) of the 32 simple sequence repeats comprised dinucleotide repeat motifs followed by simple sequence repeats with trinucleotide (21.8%) and other higher order repeat motifs. Eighteen (81.8%) of the 22 designed primers for the above simple sequence repeats amplified products of expected sizes, when tried with genomic DNA of C. jwarancusa, the source species. Thirteen (72.2%) of the 18 functional primers detected polymorphism among the three species of Cymbopogon (C. flexuosus, C. pendulus and C. jwarancusa) and amplified a total of 95 alleles (range 1-18 alleles) with a PIC value of 0.44 to 0.96 per simple sequence repeat. Thus, the higher allelic range and high level of polymorphism demonstrated by the newly developed simple sequence repeat markers are likely to have many applications such as in improvement of essential oil quality by authentication of Cymbopogon species and varieties and mapping or tagging the genes controlling agronomically important traits of essential oils, which can further be utilized in marker assisted breeding.

  15. Approaching improved adhesive bonding repeatability

    NASA Astrophysics Data System (ADS)

    Schlette, Christian; Müller, Tobias; Roβmann, Jürgen; Brecher, Christian

    2016-03-01

    Today, the precision of micro-optics assembly is mostly limited by the accuracy of the bonding process ― and in the case of adhesive bonding by the prediction and compensation of adhesive shrinkage during curing. In this contribution, we present a novel approach to address adhesive bonding based on hybrid control system theory. In hybrid control, dynamic systems are described as "plants" which produce discrete and/or continuous outputs from given discrete and/or continuous inputs, thus yielding a hybrid state space description of the system. The task of hybrid controllers is to observe the plant and to generate a discrete and/or continuous input sequence that guides or holds the plant in a desired target state region while avoiding invalid or unwanted intermediate states. Our approach is based on a series of experiments carried out in order to analyze, define and decouple the dependencies of adhesive shrinkage on multiple parameters, such as application geometries, fixture forces and UV intensities. As some of the dependencies describe continuous effects (e.g. shrinkage from UV intensity) and other dependencies describe discrete state transitions (e.g. fixture removal during curing), the resulting model of the overall bonding process is a hybrid dynamic system in the general case. For this plant model, we then propose a concept of sampling-based parameter search as a basis to design suitable hybrid controllers, which have the potential to optimize process control for a selection of assembly steps, thus improving the repeatability of related production steps like beam-shaping optics or mounting of turning mirrors for fiber coupling.

  16. Regional and global impacts of Criegee intermediates on atmospheric sulphuric acid concentrations and first steps of aerosol formation.

    PubMed

    Percival, Carl J; Welz, Oliver; Eskola, Arkke J; Savee, John D; Osborn, David L; Topping, David O; Lowe, Douglas; Utembe, Steven R; Bacak, Asan; McFiggans, Gordon; Cooke, Michael C; Xiao, Ping; Archibald, Alexander T; Jenkin, Michael E; Derwent, Richard G; Riipinen, Ilona; Mok, Daniel W K; Lee, Edmond P F; Dyke, John M; Taatjes, Craig A; Shallcross, Dudley E

    2013-01-01

    Carbonyl oxides ("Criegee intermediates"), formed in the ozonolysis of alkenes, are key species in tropospheric oxidation of organic molecules and their decomposition provides a non-photolytic source of OH in the atmosphere (Johnson and Marston, Chem. Soc. Rev., 2008, 37, 699, Harrison et al, Sci, Total Environ., 2006, 360, 5, Gäb et al., Nature, 1985, 316, 535, ref. 1-3). Recently it was shown that small Criegee intermediates, C.I.'s, react far more rapidly with SO2 than typically represented in tropospheric models, (Welz, Science, 2012, 335, 204, ref. 4) which suggested that carbonyl oxides could have a substantial influence on the atmospheric oxidation of SO2. Oxidation of 502 is the main atmospheric source of sulphuric acid (H2SO4), which is a critical contributor to aerosol formation, although questions remain about the fundamental nucleation mechanism (Sipilä et al., Science, 2010, 327, 1243, Metzger et al., Proc. Natl. Acad. Sci. U. S. A., 2010 107, 6646, Kirkby et al., Nature, 2011, 476, 429, ref. 5-7). Non-absorbing atmospheric aerosols, by scattering incoming solar radiation and acting as cloud condensation nuclei, have a cooling effect on climate (Intergovernmental Panel on Climate Change (IPCC), Climate Change 2007: The Physical Science Basis, Cambridge University Press, 2007, ref. 8). Here we explore the effect of the Criegees on atmospheric chemistry, and demonstrate that ozonolysis of alkenes via the reaction of Criegee intermediates potentially has a large impact on atmospheric sulphuric acid concentrations and consequently the first steps in aerosol production. Reactions of Criegee intermediates with SO2 will compete with and in places dominate over the reaction of OH with SO2 (the only other known gas-phase source of H2SO4) in many areas of the Earth's surface. In the case that the products of Criegee intermediate reactions predominantly result in H2SO4 formation, modelled particle nucleation rates can be substantially increased by the improved

  17. Trends in summer chemistry linked to productivity in lakes recovering from acid deposition in the Adirondack region of New York

    USGS Publications Warehouse

    Momen, B.; Lawrence, G.B.; Nierzwicki-Bauer, S. A.; Sutherland, J.W.; Eichler, L.W.; Harrison, J.P.; Boylen, C.W.

    2006-01-01

    The US Environmental Protection Agency established the Adirondack Effects Assessment Program (AEAP) to evaluate and monitor the status of biological communities in lakes in the Adirondack region of New York that have been adversely affected by acid deposition. This program includes chemical analysis of 30 lakes, sampled two to three times each summer. Results of trends analysis for lake chemistry and chlorophyll a (chlor a) are presented for 1994 to 2003, and a general comparison is made with recent results of the Adirondack Long-Term Monitoring (ALTM) Program, which included chemical analysis of all but two of these lakes (plus an additional 24 lakes) monthly, year-round for 1992-2004. Increases in pH were found in 25 of the 30 AEAP lakes (P < 0.05) and increases in acid-neutralizing capacity (ANC) were found in 12 of the 30 lakes (P < 0.05). Concentrations of both SO 42- and Mg 2+ decreased in 11 lakes (P < 0.05), whereas concentrations of NO 3- decreased in 20 lakes (P < 0.05). Concentrations of NH 4+ decreased in 10 lakes at a significance level of P < 0.05 and in three other lakes based on P < 0.1. Concentrations of inorganic and organic monomeric aluminum generally were below the reporting limit of 1.5 ??mol L-1, but decreases were detected in four and five lakes, respectively (P < 0.1). Concentrations of chlor a increased in seven lakes at a significance level of P < 0.05 and two lakes at a significance level of P < 0.1. A significant inverse correlation was also found between chlor a and NO 3- concentrations in nine lakes at a significance level of P < 0.05 and two lakes at a significance level of P < 0.1. Results of AEAP analysis of lake chemistry were similar to those of the ALTM Program, although decreases in SO 42- concentrations were more evident in the year-round ALTM record. Overall, the results suggest (a) a degree of chemical recovery from acidification during the summer, (b) an increase in phytoplankton productivity, and (c) a decreasing trend in

  18. Regional and global impacts of Criegee intermediates on atmospheric sulphuric acid concentrations and first steps of aerosol formation.

    PubMed

    Percival, Carl J; Welz, Oliver; Eskola, Arkke J; Savee, John D; Osborn, David L; Topping, David O; Lowe, Douglas; Utembe, Steven R; Bacak, Asan; McFiggans, Gordon; Cooke, Michael C; Xiao, Ping; Archibald, Alexander T; Jenkin, Michael E; Derwent, Richard G; Riipinen, Ilona; Mok, Daniel W K; Lee, Edmond P F; Dyke, John M; Taatjes, Craig A; Shallcross, Dudley E

    2013-01-01

    Carbonyl oxides ("Criegee intermediates"), formed in the ozonolysis of alkenes, are key species in tropospheric oxidation of organic molecules and their decomposition provides a non-photolytic source of OH in the atmosphere (Johnson and Marston, Chem. Soc. Rev., 2008, 37, 699, Harrison et al, Sci, Total Environ., 2006, 360, 5, Gäb et al., Nature, 1985, 316, 535, ref. 1-3). Recently it was shown that small Criegee intermediates, C.I.'s, react far more rapidly with SO2 than typically represented in tropospheric models, (Welz, Science, 2012, 335, 204, ref. 4) which suggested that carbonyl oxides could have a substantial influence on the atmospheric oxidation of SO2. Oxidation of 502 is the main atmospheric source of sulphuric acid (H2SO4), which is a critical contributor to aerosol formation, although questions remain about the fundamental nucleation mechanism (Sipilä et al., Science, 2010, 327, 1243, Metzger et al., Proc. Natl. Acad. Sci. U. S. A., 2010 107, 6646, Kirkby et al., Nature, 2011, 476, 429, ref. 5-7). Non-absorbing atmospheric aerosols, by scattering incoming solar radiation and acting as cloud condensation nuclei, have a cooling effect on climate (Intergovernmental Panel on Climate Change (IPCC), Climate Change 2007: The Physical Science Basis, Cambridge University Press, 2007, ref. 8). Here we explore the effect of the Criegees on atmospheric chemistry, and demonstrate that ozonolysis of alkenes via the reaction of Criegee intermediates potentially has a large impact on atmospheric sulphuric acid concentrations and consequently the first steps in aerosol production. Reactions of Criegee intermediates with SO2 will compete with and in places dominate over the reaction of OH with SO2 (the only other known gas-phase source of H2SO4) in many areas of the Earth's surface. In the case that the products of Criegee intermediate reactions predominantly result in H2SO4 formation, modelled particle nucleation rates can be substantially increased by the improved

  19. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants

    PubMed Central

    Sharma, Manisha; Pandey, Girdhar K.

    2016-01-01

    The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein–protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants. PMID:26793205

  20. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants.

    PubMed

    Sharma, Manisha; Pandey, Girdhar K

    2015-01-01

    The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein-protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants. PMID:26793205

  1. Long terminal repeat of murine retroviral DNAs: sequence analysis, host-proviral junctions, and preintegration site.

    PubMed Central

    Van Beveren, C; Rands, E; Chattopadhyay, S K; Lowy, D R; Verma, I M

    1982-01-01

    The nucleotide sequence of the long terminal repeat (LTR) of three murine retroviral DNAs has been determined. The data indicate that the U5 region (sequences originating from the 5' end of the genome) of various LTRs is more conserved than the U3 region (sequences from the 3' end of the genome). The location and sequence of the control elements such as the 5' cap, "TATA-like" sequences, "CCAAT-box," and presumptive polyadenylic acid addition signal AATAAA in the various LTRs are nearly identical. Some murine retroviral DNAs contain a duplication of sequences within the LTR ranging in size from 58 to 100 base pairs. A variant of molecularly cloned Moloney murine sarcoma virus DNA in which one of the two LTRs integrated into the viral DNA was also analyzed. A 4-base-pair duplication was generated at the site of integration of LTR in the viral DNA. The host-viral junction of two molecularly cloned AKR-murine leukemia virus DNAs (clones 623 and 614) was determined. In the case of AKR-623 DNA, a 3- or 4-base-pair direct repeat of cellular sequences flanking the viral DNA was observed. However, AKR-614 DNA contained a 5-base-pair repeat of cellular sequences. The nucleotide sequence of the preintegration site of AKR-623 DNA revealed that the cellular sequences duplicated during integration are present only once. Finally, a striking homology between the sequences flanking the preintegration site and viral LTRs was observed. Images PMID:6281466

  2. Trace element uptake by Eleocharis equisetina (spike rush) in an abandoned acid mine tailings pond, northeastern Australia: implications for land and water reclamation in tropical regions.

    PubMed

    Lottermoser, Bernd G; Ashley, Paul M

    2011-10-01

    This study was conducted to determine the uptake of trace elements by the emergent wetland plant species Eleocharis equisetina at the historic Jumna tin processing plant, tropical Australia. The perennial emergent sedge was found growing in acid waters (pH 2.45) and metal-rich tailings (SnAsCuPbZn). E. equisetina displayed a pronounced acid tolerance and tendency to exclude environmentally significant elements (Al, As, Cd, Ce, Co, Cu, Fe, La, Ni, Pb, Se, Th, U, Y, Zn) from its above-substrate biomass. This study demonstrates that geobotanical and biogeochemical examinations of wetland plants at abandoned mined lands of tropical areas can reveal pioneering, metal-excluding macrophytes. Such aquatic macrophytes are of potential use in the remediation of acid mine waters and sulfidic tailings and the reclamation of disturbed acid sulfate soils in subtropical and tropical regions.

  3. Trace element uptake by Eleocharis equisetina (spike rush) in an abandoned acid mine tailings pond, northeastern Australia: implications for land and water reclamation in tropical regions.

    PubMed

    Lottermoser, Bernd G; Ashley, Paul M

    2011-10-01

    This study was conducted to determine the uptake of trace elements by the emergent wetland plant species Eleocharis equisetina at the historic Jumna tin processing plant, tropical Australia. The perennial emergent sedge was found growing in acid waters (pH 2.45) and metal-rich tailings (SnAsCuPbZn). E. equisetina displayed a pronounced acid tolerance and tendency to exclude environmentally significant elements (Al, As, Cd, Ce, Co, Cu, Fe, La, Ni, Pb, Se, Th, U, Y, Zn) from its above-substrate biomass. This study demonstrates that geobotanical and biogeochemical examinations of wetland plants at abandoned mined lands of tropical areas can reveal pioneering, metal-excluding macrophytes. Such aquatic macrophytes are of potential use in the remediation of acid mine waters and sulfidic tailings and the reclamation of disturbed acid sulfate soils in subtropical and tropical regions. PMID:21550704

  4. Characterization of 10 new polymorphic dinucleotide repeats and generation of a high-density microsatellite-based physical map of the BRCA1 region of chromosome 17q21

    SciTech Connect

    Couch, F.J.; Xu, J.; Weber, B.L.

    1994-12-01

    A familial early onset breast cancer gene (BRCA1) has been localized to chromosome 17q21. To aid in the identification of this gene a number of new microsatellite markers from the D17S857 to D17S78 region were isolated and characterized. These markers, along with previously published markers from the region, were localized on a physical map by STS content mapping of cosmids from the BRCA1 interval. This high-density STS map of the BRCA1 region will be useful for linkage studies of families with apparent inherited breast cancer and for loss of heterozygosity analysis of breast tumor DNAs. 19 refs., 2 figs., 2 tabs.

  5. Ventricular zone gene-1 (vzg-1) encodes a lysophosphatidic acid receptor expressed in neurogenic regions of the developing cerebral cortex

    PubMed Central

    1996-01-01

    Neocortical neuroblast cell lines were used to clone G-protein-coupled receptor (GPCR) genes to study signaling mechanisms regulating cortical neurogenesis. One putative GPCR gene displayed an in situ expression pattern enriched in cortical neurogenic regions and was therefore named ventricular zone gene-1 (vzg-1). The vzg-1 cDNA hybridized to a 3.8-kb mRNA transcript and encoded a protein with a predicted molecular mass of 41-42 kD, confirmed by Western blot analysis. To assess its function, vzg-1 was overexpressed in a cell line from which it was cloned, inducing serum-dependent "cell rounding." Lysophosphatidic acid (LPA), a bioactive lipid present in high concentrations in serum, reproduced the effect seen with serum alone. Morphological responses to other related phospholipids or to thrombin, another agent that induces cell rounding through a GPCR, were not observed in vzg-1 overexpressing cells. Vzg-1 overexpression decreased the EC50 of both cell rounding and Gi activation in response to LPA. Pertussis toxin treatment inhibited vzg-1-dependent LPA-mediated Gi activation, but had no effect on cell rounding. Membrane binding studies indicated that vzg-1 overexpression increased specific LPA binding. These analyses identify the vzg-1 gene product as a receptor for LPA, suggesting the operation of LPA signaling mechanisms in cortical neurogenesis. Vzg-1 therefore provides a link between extracellular LPA and the activation of LPA- mediated signaling pathways through a single receptor and will allow new investigations into LPA signaling both in neural and nonneural systems. PMID:8922387

  6. Acid-sensing ion channels in trigeminal ganglion neurons innervating the orofacial region contribute to orofacial inflammatory pain.

    PubMed

    Fu, Hui; Fang, Peng; Zhou, Hai-Yun; Zhou, Jun; Yu, Xiao-Wei; Ni, Ming; Zheng, Jie-Yan; Jin, You; Chen, Jian-Guo; Wang, Fang; Hu, Zhuang-Li

    2016-02-01

    Orofacial pain is a common clinical symptom that is accompanied by tooth pain, migraine and gingivitis. Accumulating evidence suggests that acid-sensing ion channels (ASICs), especially ASIC3, can profoundly affect the physiological properties of nociception in peripheral sensory neurons. The aim of this study is to examine the contribution of ASICs in trigeminal ganglion (TG) neurons to orofacial inflammatory pain. A Western blot (WB), immunofluorescence assay of labelled trigeminal ganglion neurons, orofacial formalin test, cell preparation and electrophysiological experiments are performed. This study demonstrated that ASIC1, ASIC2a and ASIC3 are highly expressed in TG neurons innervating the orofacial region of rats. The amplitude of ASIC currents in these neurons increased 119.72% (for ASIC1-like current) and 230.59% (for ASIC3-like current) in the formalin-induced orofacial inflammatory pain model. In addition, WB and immunofluorescence assay demonstrated a significantly augmented expression of ASICs in orofacial TG neurons during orofacial inflammation compared with the control group. The relative protein density of ASIC1, ASIC2a and ASIC3 also increased 58.82 ± 8.92%, 45.30 ± 11.42% and 55.32 ± 14.71%, respectively, compared with the control group. Furthermore, pharmacological blockade of ASICs and genetic deletion of ASIC1 attenuated the inflammation response. These findings indicate that peripheral inflammation can induce the upregulation of ASICs in TG neurons, causing orofacial inflammatory pain. Additionally, the specific inhibitor of ASICs may have a significant analgesic effect on orofacial inflammatory pain.

  7. DNA sequence of the serum opacity factor of group A streptococci: identification of a fibronectin-binding repeat domain.

    PubMed Central

    Rakonjac, J V; Robbins, J C; Fischetti, V A

    1995-01-01

    The serum opacity factor (SOF) is a group A streptococcal protein that induces opacity of mammalian serum. The serum opacity factor 22 gene (sof22) from an M type 22 strain was cloned from an EMBL4 library by screening for plaques exhibiting serum opacity activity. DNA sequencing yielded an open reading frame of 3,075 bp. Its deduced amino acid sequence predicts a protein of 1,025 residues with a molecular weight of 112,735, a size that approximates that of the SOF22 protein isolated from both the original streptococcal strain and Escherichia coli harboring the cloned sof22 gene. The molecule is composed of three domains: an N-terminal domain responsible for the opacity reaction (opacity domain), a repeat domain with fibronectin-binding (Fn-binding) activity, and a C-terminal cell attachment domain. The C-terminal end of SOF22 is characterized by a hexameric LPXTGX motif, an adjacent hydrophobic region, and a charged C terminus, which are the hallmarks of cell-bound surface proteins found on nearly all gram-positive bacteria. Immediately upstream of this cell anchor region, SOF22 contains four tandem repeat sequence blocks, flanked by prolinerich segments. The repeats share up to 50% identity with a repeated motif found in other group A streptococcal Fn-binding proteins and exhibit Fn-binding activity, as shown by subcloning experiments. According to deletion analysis, the opacity domain is confined to the region N terminal to the repeat segment. Thus, SOF22 is unique among the known Fn-binding proteins from gram-positive bacteria in containing an independent module with a defined function in its N-terminal portion. Southern blot analysis with a probe from this N-terminal region indicates that the opacity domain of SOF varies extensively among different SOF-producing M types. PMID:7822031

  8. Phenolic compounds, organic acids and antioxidant activity of grape juices produced from new Brazilian varieties planted in the Northeast Region of Brazil.

    PubMed

    Lima, Marcos Dos Santos; Silani, Igor de Souza Veras; Toaldo, Isabela Maia; Corrêa, Luiz Claudio; Biasoto, Aline Camarão Telles; Pereira, Giuliano Elias; Bordignon-Luiz, Marilde T; Ninow, Jorge Luiz

    2014-10-15

    The phenolic compounds, organic acids and the antioxidant activity were determined for grape juice samples from new Brazilian varieties grown in the Sub-middle São Francisco Valley in the Northeast Region of Brazil. The results showed that the Brazilian grape juices have high antioxidant activity, which was significantly correlated with the phenolic compounds catechin, epicatechin gallate, procyanidin B1, rutin, gallic acid, caffeic acid, p-coumaric acid, pelargonidin-3-glucoside, cyanidin-3-glucoside, cyaniding-3,5-diglucoside and delphinidin-3-glucoside. The produced juice samples showed higher concentrations of trans-resveratrol than those observed in juices made from different varieties of grapes from traditional growing regions. Organic acids concentrations were similar to those of juices produced from other classical varieties. It was demonstrated that it is possible to prepare juices from grapes of new varieties grown in the Northeast of Brazil containing a high content of bioactive compounds and typical characteristics of the tropical viticulture practised in the Sub-middle São Francisco Valley.

  9. Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution

    PubMed Central

    Rocha, Eduardo P. C.; Blanchard, Alain

    2002-01-01

    Mycoplasmas evolved by a drastic reduction in genome size, but their genomes contain numerous repeated sequences with important roles in their evolution. We have established a bioinformatic strategy to detect the major recombination hot-spots in the genomes of Mycoplasma pneumoniae, Mycoplasma genitalium, Ureaplasma urealyticum and Mycoplasma pulmonis. This allowed the identification of large numbers of potentially variable regions, as well as a comparison of the relative recombination potentials of different genomic regions. Different trends are perceptible among mycoplasmas, probably due to different functional and structural constraints. The largest potential for illegitimate recombination in M.pulmonis is found at the vsa locus and its comparison in two different strains reveals numerous changes since divergence. On the other hand, the main M.pneumoniae and M.genitalium adhesins rely on large distant repeats and, hence, homologous recombination for variation. However, the relation between the existence of repeats and antigenic variation is not necessarily straightforward, since repeats of P1 adhesin were found to be anti-correlated with epitopes recognized by patient antibodies. These different strategies have important consequences for the structures of genomes, since large distant repeats correlate well with the major chromosomal rearrangements. Probably to avoid such events, mycoplasmas strongly avoid inverse repeats, in comparison to co-oriented repeats. PMID:11972343

  10. Reprint of The improvement of the energy resolution in epi-thermal neutron region of Bonner sphere using boric acid water solution moderator.

    PubMed

    Ueda, H; Tanaka, H; Sakurai, Y

    2015-12-01

    Bonner sphere is useful to evaluate the neutron spectrum in detail. We are improving the energy resolution in epi-thermal neutron region of Bonner sphere, using boric acid water solution as a moderator. Its response function peak is narrower than that for polyethylene moderator and the improvement of the resolution is expected. The resolutions between polyethylene moderator and boric acid water solution moderator were compared by simulation calculation. Also the influence in the uncertainty of Bonner sphere configuration to spectrum estimation was simulated. PMID:26508275

  11. The improvement of the energy resolution in epi-thermal neutron region of Bonner sphere using boric acid water solution moderator.

    PubMed

    Ueda, H; Tanaka, H; Sakurai, Y

    2015-10-01

    Bonner sphere is useful to evaluate the neutron spectrum in detail. We are improving the energy resolution in epi-thermal neutron region of Bonner sphere, using boric acid water solution as a moderator. Its response function peak is narrower than that for polyethylene moderator and the improvement of the resolution is expected. The resolutions between polyethylene moderator and boric acid water solution moderator were compared by simulation calculation. Also the influence in the uncertainty of Bonner sphere configuration to spectrum estimation was simulated.

  12. Reprint of The improvement of the energy resolution in epi-thermal neutron region of Bonner sphere using boric acid water solution moderator.

    PubMed

    Ueda, H; Tanaka, H; Sakurai, Y

    2015-12-01

    Bonner sphere is useful to evaluate the neutron spectrum in detail. We are improving the energy resolution in epi-thermal neutron region of Bonner sphere, using boric acid water solution as a moderator. Its response function peak is narrower than that for polyethylene moderator and the improvement of the resolution is expected. The resolutions between polyethylene moderator and boric acid water solution moderator were compared by simulation calculation. Also the influence in the uncertainty of Bonner sphere configuration to spectrum estimation was simulated.

  13. CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

    PubMed Central

    Alkhnbashi, Omer S.; Costa, Fabrizio; Shah, Shiraz A.; Garrett, Roger A.; Saunders, Sita J.; Backofen, Rolf

    2014-01-01

    Motivation: The discovery of CRISPR-Cas systems almost 20 years ago rapidly changed our perception of the bacterial and archaeal immune systems. CRISPR loci consist of several repetitive DNA sequences called repeats, inter-spaced by stretches of variable length sequences called spacers. This CRISPR array is transcribed and processed into multiple mature RNA species (crRNAs). A single crRNA is integrated into an interference complex, together with CRISPR-associated (Cas) proteins, to bind and degrade invading nucleic acids. Although existing bioinformatics tools can recognize CRISPR loci by their characteristic repeat-spacer architecture, they generally output CRISPR arrays of ambiguous orientation and thus do not determine the strand from which crRNAs are processed. Knowledge of the correct orientation is crucial for many tasks, including the classification of CRISPR conservation, the detection of leader regions, the identification of target sites (protospacers) on invading genetic elements and the characterization of protospacer-adjacent motifs. Results: We present a fast and accurate tool to determine the crRNA-encoding strand at CRISPR loci by predicting the correct orientation of repeats based on an advanced machine learning approach. Both the repeat sequence and mutation information were encoded and processed by an efficient graph kernel to learn higher-order correlations. The model was trained and tested on curated data comprising >4500 CRISPRs and yielded a remarkable performance of 0.95 AUC ROC (area under the curve of the receiver operator characteristic). In addition, we show that accurate orientation information greatly improved detection of conserved repeat sequence families and structure motifs. We integrated CRISPRstrand predictions into our CRISPRmap web server of CRISPR conservation and updated the latter to version 2.0. Availability: CRISPRmap and CRISPRstrand are available at http://rna.informatik.uni-freiburg.de/CRISPRmap. Contact: backofen

  14. Effects of different cooking methods on fatty acid profiles in four freshwater fishes from the Laurentian Great Lakes region.

    PubMed

    Neff, Margaret R; Bhavsar, Satyendra P; Braekevelt, Eric; Arts, Michael T

    2014-12-01

    Fish is often promoted as a healthy part of the human diet due its high content of long chain n-3 polyunsaturated fatty acids (LC-PUFA). Previous studies have shown that cooked fish can have different fatty acid profiles than raw fillets, depending on the cooking method and fish species. In this study, the fatty acid content of broiled, baked or fried skinless, boneless fillets of four fish species from the tributaries of the Great Lakes, or connecting rivers, was compared to fatty acid profiles in raw sections from the same fillet. Cooking treatments had little effect on n-3 fatty acid content; however, fried treatments generally had higher n-6 and MUFA content, which is likely a result of the cooking oil used (canola). Broiling or baking is generally the most healthy option presented in this study, as these methods result in lower levels of less-favourable fatty acids; however, the choice of cooking oil may also influence the overall fatty acid content in cooked fish.

  15. Limitations on quantum key repeaters.

    PubMed

    Bäuml, Stefan; Christandl, Matthias; Horodecki, Karol; Winter, Andreas

    2015-04-23

    A major application of quantum communication is the distribution of entangled particles for use in quantum key distribution. Owing to noise in the communication line, quantum key distribution is, in practice, limited to a distance of a few hundred kilometres, and can only be extended to longer distances by use of a quantum repeater, a device that performs entanglement distillation and quantum teleportation. The existence of noisy entangled states that are undistillable but nevertheless useful for quantum key distribution raises the question of the feasibility of a quantum key repeater, which would work beyond the limits of entanglement distillation, hence possibly tolerating higher noise levels than existing protocols. Here we exhibit fundamental limits on such a device in the form of bounds on the rate at which it may extract secure key. As a consequence, we give examples of states suitable for quantum key distribution but unsuitable for the most general quantum key repeater protocol.

  16. Limitations on quantum key repeaters.

    PubMed

    Bäuml, Stefan; Christandl, Matthias; Horodecki, Karol; Winter, Andreas

    2015-01-01

    A major application of quantum communication is the distribution of entangled particles for use in quantum key distribution. Owing to noise in the communication line, quantum key distribution is, in practice, limited to a distance of a few hundred kilometres, and can only be extended to longer distances by use of a quantum repeater, a device that performs entanglement distillation and quantum teleportation. The existence of noisy entangled states that are undistillable but nevertheless useful for quantum key distribution raises the question of the feasibility of a quantum key repeater, which would work beyond the limits of entanglement distillation, hence possibly tolerating higher noise levels than existing protocols. Here we exhibit fundamental limits on such a device in the form of bounds on the rate at which it may extract secure key. As a consequence, we give examples of states suitable for quantum key distribution but unsuitable for the most general quantum key repeater protocol. PMID:25903096

  17. Modeling the Seasonal Ice Zone from the Air: use of repeat aerial hydrographic surveys to constrain a regional ice-ocean model in an area of rapidly evolving ice cover

    NASA Astrophysics Data System (ADS)

    Dewey, S.; Morison, J.; Zhang, J.

    2015-12-01

    The Seasonal Ice Zone of the Beaufort Sea is the area of ocean north of Alaska over which sea ice melts and reforms annually. It contains the more narrow, near-edge marginal ice zone (MIZ). Seasonal Ice Zone Reconnaissance Surveys (SIZRS) measure hydrography along two meridional sections using Air eXpendable CTDs (AXCTDs) and Air eXpendable Current Profilers (AXCPs). These surveys take place aboard U.S. Coast Guard Arctic Domain Awareness flights of opportunity during each melt season (June-October) starting in 2012. The Marginal Ice Zone Modeling and Assimilation System (MIZMAS) is a high-resolution regional ice-ocean model with daily, three-dimensional output encompassing the SIZRS survey area. Direct comparison of the SIZRS data with MIZMAS output as well as with several regional climatologies can constrain the ice-ocean model and help to explain recent changes in subsurface heat content and salinity. For example, observed freshening relative to climatology has been used as a reference to which MIZMAS surface salinity values can be relaxed. MIZMAS may in turn shed light on the physical mechanisms driving the observed freshening. In addition, use of MIZMAS surface fluxes to drive a one-dimensional mixed layer model gives results close to observations when the model is initialized with SIZRS profiles. Because SIZRS observations range in time from the onset of melt to the onset of Fall freeze-up, the comparison of the one-dimensional model with MIZMAS illustrates the relative roles of local and regional processes in forming near-surface temperature maxima and salinity minima. The SIZRS observations and one-dimensional model are used to constrain MIZMAS estimations of stored subsurface heat while establishing the physical drivers of these temperature and salinity changes.

  18. System using tandem repeats of the cA peptidoglycan-binding domain from Lactococcus lactis for display of both N- and C-terminal fusions on cell surfaces of lactic acid bacteria.

    PubMed

    Okano, Kenji; Zhang, Qiao; Kimura, Sakurako; Narita, Junya; Tanaka, Tsutomu; Fukuda, Hideki; Kondo, Akihiko

    2008-02-01

    Here, we established a system for displaying heterologous protein to the C terminus of the peptidoglycan-binding domain (cA domain) of AcmA (a major autolysin from Lactococcus lactis). Western blot and flow cytometric analyses revealed that the fusion proteins (cA-AmyA) of the cA domain and alpha-amylase from Streptococcus bovis 148 (AmyA) are efficiently expressed and successfully displayed on the surfaces of L. lactis cells. AmyA was also displayed on the cell surface while retaining its activity. Moreover, with an increase in the number of cA domains, the quantity of cA-AmyA fusion proteins displayed on the cell surface increased. When three repeats of the cA domain were used as an anchor protein, 82% of alpha-amylase activity was detected on the cells. The raw starch-degrading activity of AmyA was significantly higher when AmyA was fused to the C terminus of the cA domain than when it was fused to the N terminus. In addition, cA-AmyA fusion proteins were successfully displayed on the cell surfaces of Lactobacillus plantarum and Lactobacillus casei. PMID:18156338

  19. Sequence of human tryptophan 2,3-dioxygenase (TDO2): Presence of a glucocorticoid response-like element composed of a GTT repeat and an intronic CCCCT repeat

    SciTech Connect

    Comings, D.E.; Muhleman, D.; Dietz, G.

    1995-09-20

    Abnormalities in serotonin levels have been implicated in a wide range of psychiatric disorders. Tryptophan 2,3-dioxygenase is the rate-limiting enzyme in the catabolism of tryptophan, the precursor of serotonin. As such it is a potential major candidate gene in psychiatric genetics. The regulatory, intron, and exon regions of the human TDO2 gene have been sequenced. Twelve exons were identified. The amino acid sequence of the enzyme was 88% homologous to that of the rat. Compared to the rat, the regulatory region of the human TDO2 gene had an insertion of approximately 1064 bp of random DNA beginning at -293 bp and extending to -1357 bp. This displaced the glucocorticoid response element (GRE) occurring at -1174 bp in the rat to -1500 in the human. The proximal GRE at -419 in the rat was missing in the human. However, within the DNA insert there was a GRE-like microsatellite region containing multiple GTT repeats plus additional GT(n) sequences. This could produce several staggered regions of the sequence TGTTGTnnnTGTTGT similiar to a GRE consensus sequence of TGTTCAnnnTGTTCT. The intron regions 5` and 3` to each exon were sequenced. This allowed each exon to be screened for mutations. This showed a His{r_arrow}Val mutation polymorphism in exon 7. Three introns, 1, 5, and 6, were completely sequenced and examined for polymorphisms. This identified two polymorphisms consisting of G{r_arrow}T and G{r_arrow}A mutations 2 bp apart in intron 6. The 3` end of intron 5` showed an extensive CCCCT pentanucleotide repeat that was markedly polymorphic. These polymorphisms allow the TDO2 gene to be examined for a possible role in psychiatric disorders. 35 refs., 4 figs., 1 tab.

  20. [Folic acid and cobalamine intake in daily food rations of women from the region of Lower Silesia].

    PubMed

    Bronkowska, Monika; Biernat, Jadwiga

    2008-01-01

    The aim of paper was to assess the folic acid and cobalamine women (n = 960). The information about vitamins intake were collected using 24-hour recall and diet history questionnaire. The intake of vitamins folic acid and cobalamine was too low. The mean folic acid content in the diets of 100 women from Lower Silesia was 221.5 mcg and complied in 79% recommended level. The mean cobalamine content in the diets of 100 women from Lower Silesia was 2.9 mcg and complied in 97% recommended level. In examined group low knowledge about importance role of folic acid and cobalamine in health was noticed. Educational interventions are required to inform women and to increase its intake among them.

  1. CAG trinucleotide RNA repeats interact with RNA-binding proteins.

    PubMed Central

    McLaughlin, B. A.; Spencer, C.; Eberwine, J.

    1996-01-01

    Genes associated with several neurological diseases are characterized by the presence of an abnormally long trinucleotide repeat sequence. By way of example, Huntington's disease (HD), is characterized by selective neuronal degeneration associated with the expansion of a polyglutamine-encoding CAG tract. Normally, this CAG tract is comprised of 11-34 repeats, but in HD it is expanded to > 37 repeats in affected individuals. The mechanism by which CAG repeats cause neuronal degeneration is unknown, but it has been speculated that the expansion primarily causes abnormal protein functioning, which in turn causes HD pathology. Other mechanisms, however, have not been ruled out. Interactions between RNA and RNA-binding proteins have previously been shown to play a role in the expression of several eukaryotic genes. Herein, we report the association of cytoplasmic proteins with normal length and extended CAG repeats, using gel shift and UV crosslinking assays. Cytoplasmic protein extracts from several rat brain regions, including the striatum and cortex, sites of neuronal degeneration in HD, contain a 63-kD RNA-binding protein that specifically interacts with these CAG-repeat sequences. These protein-RNA interactions are dependent on the length of the CAG repeat, with longer repeats binding substantially more protein. Two CAG repeat-binding proteins are present in human cortex and striatum; one comigrates with the rat protein at 63 kD, while the other migrates at 49 kD. These data suggest mechanisms by which RNA-binding proteins may be involved in the pathological course of trinucleotide repeat-associated neurological diseases. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 PMID:8751857

  2. Inhibition of the mutagenicity of bay-region diol epoxides of polycyclic aromatic hydrocarbons by naturally occurring plant phenols: Exceptional activity of ellagic acid

    PubMed Central

    Wood, Alexander W.; Huang, Mou-Tuan; Chang, Richard L.; Newmark, Harold L.; Lehr, Roland E.; Yagi, Haruhiko; Sayer, Jane M.; Jerina, Donald M.; Conney, Allan H.

    1982-01-01

    Ferulic, caffeic, chlorogenic, and ellagic acids, four naturally occurring plant phenols, inhibit the mutagenicity and cytotoxicity of (±)-7β,8α-dihydroxy-9α, 10α-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (B[a]P 7,8-diol-9,10-epoxide-2), the only known ultimate carcinogenic metabolite of benzo[a]pyrene. The mutagenicity of 0.05 nmol of B[a]P 7,8-diol-9,10-epoxide-2 in strain TA100 of Salmonella typhimurium is inhibited 50% by incubation of the bacteria and the diol epoxide with 150 nmol of ferulic acid, 75 nmol of caffeic acid, 50 nmol of chlorogenic acid or, most strikingly, 1 nmol of ellagic acid in the 0.5-ml incubation mixture. A 3-nmol dose of ellagic acid inhibits mutation induction by 90%. Ellagic acid is also a potent antagonist of B[a]P 7,8-diol-9,10-epoxide-2 in Chinese hamster V79 cells. Mutations to 8-azaguanine resistance induced by 0.2 μM diol epoxide are reduced by 50% when tissue culture media also contains 2 μM ellagic acid. Similar to results obtained with the bacteria, ferulic, caffeic, and chlorogenic acids are approximately two orders of magnitude less active than ellagic acid in the mammalian cell assay. The antimutagenic effects of the plant phenols result from their direct interaction with B[a]P 7,8-diol-9,10-epoxide-2, because a concentration-dependent increase in the rate of diol epoxide disappearance in cell-free solutions of 1:9 dioxane/water, pH 7.0, is observed with all four phenols. In parallel with the mutagenicity studies, ellagic acid is 80-300 times more effective than the other phenols in accelerating the disappearance of B[a]P 7,8-diol-9,10-epoxide-2. Ellagic acid at 10 μM increases the disappearance of B[a]P 7,8-diol-9,10-epoxide-2 by approximately 20-fold relative to the spontaneous and hydronium ion-catalyzed hydrolysis of the diol epoxide at pH 7.0. Ellagic acid is a highly potent inhibitor of the mutagenic activity of bay-region diol epoxides of benzo[a]pyrene, dibenzo[a,h]pyrene, and dibenzo[a,i]pyrene, but higher

  3. Repeated exposure to moderate doses of ethanol augments hippocampal glutamate neurotransmission by increasing release

    PubMed Central

    Chefer, Vladimir; Meis, Jennifer; Wang, Grace; Kuzmin, Alexander; Bakalkin, Georgy; Shippenberg, Toni

    2013-01-01

    The present study used conventional and quantitative microdialysis to assess glutamatergic and GABAergic neurotransmission in the hippocampal CA3 area of the rat following a moderate-dose ethanol treatment regimen. Male Wistar rats received 3.4 g/kg of ethanol or water for 6 days via gastric gavage. Microdialysis experiments commenced 2 days later. Basal and depolarization-induced glutamate overflow were significantly elevated in ethanol-treated animals. Basal and depolarization-induced gamma-aminobutyric acid (GABA) overflow were unaltered. Quantitative no-net-flux microdialysis was used to determine if changes in dialysate glutamate levels following ethanol administration are due to an increase in release or a decrease in uptake.To confirm the validity of this method for quantifying basal glutamate dynamics, extracellular concentrations of glutamate and the extraction fraction, which reflects changes in analyte clearance, were quantified in response to retro-dialysis of the glutamate uptake blocker trans-pyrrolidine-2,4-dicarboxylic acid (tPDC). tPDC significantly decreased the extraction fraction for glutamate, resulting in augmented extracellular glutamate concentrations. Repeated ethanol administration did not alter the glutamate extraction fraction. However, extracellular glutamate concentrations were significantly elevated, indicating that glutamate release is increased as a consequence of repeated ethanol administration. These data demonstrate that repeated bouts of moderate ethanol consumption alter basal glutamate dynamics in the CA3 region of the dorsal hippocampus. Basal glutamate release is augmented, whereas glutamate uptake is unchanged. Furthermore, they suggest that dysregulation of glutamate transmission in this region may contribute to the previously documented deficits in cognitive function associated with moderate dose ethanol use. PMID:21182572

  4. Tandem-repeat protein domains across the tree of life

    PubMed Central

    Jernigan, Kristin K.

    2015-01-01

    Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species. PMID:25653910

  5. Do Twelfths Terminate or Repeat?

    ERIC Educational Resources Information Center

    Ambrose, Rebecca; Burnison, Erica

    2015-01-01

    When finding the decimal equivalent of a fraction with 12 in the denominator, will it terminate or repeat? This question came from a seventh grader in author Erica Burnison's class as the student was pondering a poster generated by one of her classmates. Not only was the question intriguing, but it also affirmed the belief in the power of…

  6. 78 FR 65594 - Vehicular Repeaters

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-01

    ... mobile repeaters by public safety licensees on certain frequencies in the VHF band. DATES: Submit..., CART, etc.) by email: FCC504@fcc.gov or phone: 202-418- 0530 or TTY: 202-418-0432. For detailed... Proceedings, 63 FR 24121 (May 1, 1998). Electronic Filers: Comments may be filed electronically using...

  7. Repeat Pregnancies among Adolescent Mothers.

    ERIC Educational Resources Information Center

    Gillmore, Mary Rogers; Lewis, Steven M.; Lohr, Mary Jane; Spencer, Michael S.; White, Rachelle D.

    1997-01-01

    Reports the results of an event history analysis of rapidly repeated pregnancies among a sample of 170 adolescents. Results show that the best fitting model for these girls included two proximate determinants of pregnancy, contraceptive use, and other factors. Findings indicate that such pregnancies among teenagers are somewhat predictable. (RJM)

  8. The last half-repeat of transcription activator-like effector (TALE) is dispensable and thereby TALE-based technology can be simplified.

    PubMed

    Zheng, Chong-Ke; Wang, Chun-Lian; Zhang, Xiao-Ping; Wang, Fu-Jun; Qin, Teng-Fei; Zhao, Kai-Jun

    2014-09-01

    To activate the expression of host genes that contribute to pathogen growth, pathogenic Xanthomonas bacteria inject their transcription activator-like effectors (TALEs) into plant cells and the TALEs bind to target gene promoters by the central repeat region consisting of near-perfect 34-amino-acid repeats (34-aa repeats). Based on the recognition codes between the 34-aa repeats and the targeted nucleotides, TALE-based technologies, such as designer TALEs (dTALEs) and TALE nucleases (TALENs), have been developed. Amazingly, every natural TALE invariantly has a truncated last half-repeat (LHR) at the end of the 34-aa repeats. Consequently, all the reported dTALEs and TALENs also harbour their LHRs. Here, we show that the LHRs in dTALEs are dispensable for the function of gene activation by both transient expression assays in Nicotiana benthamiana and gene-specific targeting in the rice genome, indicating that TALEs might originate from a single progenitor. In the light of this finding, we demonstrate that dTALEs can be constructed through two simple steps. Moreover, the activation strengths of dTALEs lacking the LHR are comparable with those of dTALEs harbouring the LHR. Our results provide new insights into the origin of natural TALEs, and will facilitate the simplification of the design and assembly of TALE-based tools, such as dTALEs and TALENs, in the near future.

  9. Pentapeptide Repeat Proteins and Cyanobacteria

    SciTech Connect

    Buchko, Garry W.

    2009-10-16

    Cyanobacteria are unique in many ways and one unusual feature is the presence of a suite of proteins that contain at least one domain with a minimum of eight tandem repeated five-residues (Rfr) of the general consensus sequence A[N/D]LXX. The function of such pentapeptide repeat proteins (PRPs) are still unknown, however, their prevalence in cyanobacteria suggests that they may play some role in the unique biological activities of cyanobacteria. As part of an inter-disciplinary Membrane Biology Grand Challenge at the Environmental Molecular Sciences Laboratory (Pacific Northwest National Laboratory) and Washington University in St. Louis, the genome of Cyanothece 51142 was sequenced and its molecular biology studied with relation to circadian rhythms. The genome of Cyanothece encodes for 35 proteins that contain at least one PRP domain. These proteins range in size from 105 (Cce_3102) to 930 (Cce_2929) kDa with the PRP domains ranging in predicted size from 12 (Cce_1545) to 62 (cce_3979) tandem pentapeptide repeats. Transcriptomic studies with 29 out of the 35 genes showed that at least three of the PRPs in Cyanothece 51142 (cce_0029, cce_3083, and cce_3272) oscillated with repeated periods of light and dark, further supporting a biological function for PRPs. Using X-ray diffraction crystallography, the structure for two pentapeptide repeat proteins from Cyanothece 51142 were determined, cce_1272 (aka Rfr32) and cce_4529 (aka Rfr23). Analysis of their molecular structures suggests that all PRP may share the same structural motif, a novel type of right-handed quadrilateral β-helix, or Rfr-fold, reminiscent of a square tower with four distinct faces. Each pentapeptide repeat occupies one face of the Rfr-fold with four consecutive pentapeptide repeats completing a coil that, in turn, stack upon each other to form “protein skyscrapers”. Details of the structural features of the Rfr-fold are reviewed here together with a discussion for the possible role of end

  10. Statistical Approaches to Detecting and Analyzing Tandem Repeats in Genomic Sequences

    PubMed Central

    Anisimova, Maria; Pečerska, Julija; Schaper, Elke

    2015-01-01

    Tandem repeats (TRs) are frequently observed in genomes across all domains of life. Evidence suggests that some TRs are crucial for proteins with fundamental biological functions and can be associated with virulence, resistance, and infectious/neurodegenerative diseases. Genome-scale systematic studies of TRs have the potential to unveil core mechanisms governing TR evolution and TR roles in shaping genomes. However, TR-related studies are often non-trivial due to heterogeneous and sometimes fast evolving TR regions. In this review, we discuss these intricacies and their consequences. We present our recent contributions to computational and statistical approaches for TR significance testing, sequence profile-based TR annotation, TR-aware sequence alignment, phylogenetic analyses of TR unit number and order, and TR benchmarks. Importantly, all these methods explicitly rely on the evolutionary definition of a tandem repeat as a sequence of adjacent repeat units stemming from a common ancestor. The discussed work has a focus on protein TRs, yet is generally applicable to nucleic acid TRs, sharing similar features. PMID:25853125

  11. Evaluation of safety and pharmacokinetics of sodium 2,2 dimethylbutyrate, a novel short chain fatty acid derivative, in a phase 1, double-blind, placebo-controlled, single-dose, and repeat-dose studies in healthy volunteers.

    PubMed

    Perrine, Susan P; Wargin, William A; Boosalis, Michael S; Wallis, Wayne J; Case, Sally; Keefer, Jeffrey R; Faller, Douglas V; Welch, William C; Berenson, Ronald J

    2011-08-01

    Pharmacologic induction of fetal globin synthesis is an accepted therapeutic strategy for treatment of the beta hemoglobinopathies and thalassemias, as even small increases in hemoglobin F (HbF) levels reduce clinical severity in sickle cell disease (SCD) and reduce anemia in beta thalassemia. Prior generation short chain fatty acid therapeutics, arginine butyrate (AB), and phenylbutyrate, increased fetal and total hemoglobin levels in patients, but were limited by high doses or intravenous (IV) infusion. A fetal globin-inducing therapeutic with convenient oral dosing would be an advance for these classic molecular diseases. Healthy adult human subjects were treated with a novel short chain fatty acids (SCFA) derivative, sodium 2,2 dimethylbutyrate (SDMB), or placebo, with 1 of 4 single dose levels (2, 5, 10, and 20 mg/kg) or daily doses (5, 10, or 15 mg/kg) over 14 days, and monitored for adverse clinical and laboratory events, drug levels, reticulocytes, and HbF assays. SDMB was well-tolerated with no clinically significant adverse events related to study medication. The terminal half-life ranged from 9 to 15 hours. Increases in mean absolute reticulocytes were observed at all dose levels in the 14-day study. The favorable pharmacokinetics (PK) profiles and safety findings indicate that SDMB warrants further investigation for treatment of anemic subjects with beta hemoglobinopathies.

  12. Characterization and amino acid sequence of a fatty acid-binding protein from human heart.

    PubMed Central

    Offner, G D; Brecher, P; Sawlivich, W B; Costello, C E; Troxler, R F

    1988-01-01

    The complete amino acid sequence of a fatty acid-binding protein from human heart was determined by automated Edman degradation of CNBr, BNPS-skatole [3'-bromo-3-methyl-2-(2-nitrobenzenesulphenyl)indolenine], hydroxylamine, Staphylococcus aureus V8 proteinase, tryptic and chymotryptic peptides, and by digestion of the protein with carboxypeptidase A. The sequence of the blocked N-terminal tryptic peptide from citraconylated protein was determined by collisionally induced decomposition mass spectrometry. The protein contains 132 amino acid residues, is enriched with respect to threonine and lysine, lacks cysteine, has an acetylated valine residue at the N-terminus, and has an Mr of 14768 and an isoelectric point of 5.25. This protein contains two short internal repeated sequences from residues 48-54 and from residues 114-119 located within regions of predicted beta-structure and decreasing hydrophobicity. These short repeats are contained within two longer repeated regions from residues 48-60 and residues 114-125, which display 62% sequence similarity. These regions could accommodate the charged and uncharged moieties of long-chain fatty acids and may represent fatty acid-binding domains consistent with the finding that human heart fatty acid-binding protein binds 2 mol of oleate or palmitate/mol of protein. Detailed evidence for the amino acid sequences of the peptides has been deposited as Supplementary Publication SUP 50143 (23 pages) at the British Library Lending Division, Boston Spa, Yorkshire LS23 7BQ, U.K., from whom copies may be obtained as indicated in Biochem. J. (1988) 249, 5. PMID:3421901

  13. Chromosome-specific DNA Repeat Probes

    SciTech Connect

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

    2006-03-16

    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

  14. Characterization of Japanese polished rice by stable hydrogen isotope analysis of total fatty acids for tracing regional origin.

    PubMed

    Suzuki, Yaeko; Akamatsu, Fumikazu; Nakashita, Rumiko; Korenaga, Takashi

    2013-01-01

    We determined the δD values of the total fatty acids of Japanese rice to test the hypothesis that there is a wide variation in the hydrogen isotopic composition (δD) of the total fatty acids of Japanese rice sourced from different growth areas in Japan and to distinguish the minor differences among these growth areas. The δD values showed a wide variation ranging from -216‰ (Hokkaido) to -183‰ (Okinawa), indicating a good correlation with the corresponding variations for ambient water (r = 0.63) and mean temperature (r = 0.84). These results suggest that the δD values for the total fatty acids can be representative of the growth environments in Japan. PMID:23303100

  15. The repeat domain of the melanosome fibril protein Pmel17 forms the amyloid core promoting melanin synthesis

    PubMed Central

    McGlinchey, Ryan P.; Shewmaker, Frank; McPhie, Peter; Monterroso, Begoña; Thurber, Kent; Wickner, Reed B.

    2009-01-01

    Pmel17 is a melanocyte protein necessary for eumelanin deposition 1 in mammals and found in melanosomes in a filamentous form. The luminal part of human Pmel17 includes a region (RPT) with 10 copies of a partial repeat sequence, pt.e.gttp.qv., known to be essential in vivo for filament formation. We show that this RPT region readily forms amyloid in vitro, but only under the mildly acidic conditions typical of the lysosome-like melanosome lumen, and the filaments quickly become soluble at neutral pH. Under the same mildly acidic conditions, the Pmel filaments promote eumelanin formation. Electron diffraction, circular dichroism, and solid-state NMR studies of Pmel17 filaments show that the structure is rich in beta sheet. We suggest that RPT is the amyloid core domain of the Pmel17 filaments so critical for melanin formation. PMID:19666488

  16. The mouse and human excitatory amino acid transporter gene (EAAT1) maps to mouse chromosome 15 and a region of syntenic homology on human chromosome 5

    SciTech Connect

    Kirschner, M.A.; Arriza, J.L.; Amara, S.G.

    1994-08-01

    The gene for human excitatory amino acid transporter (EAAT1) was localized to the distal region of human chromosome 5p13 by in situ hybridization of metaphase chromosome spreads. Interspecific backcross analysis identified the mouse Eaat1 locus in a region of 5p13 homology on mouse chromosome 15. Markers that are linked with EAAT1 on both human and mouse chromosomes include the receptors for leukemia inhibitory factor, interleukin-7, and prolactin. The Eaat1 locus appears not be linked to the epilepsy mutant stg locus, which is also on chromosome 15. The EAAT1 locus is located in a region of 5p deletions that have been associated with mental retardation and microcephaly. 22 refs., 2 figs.

  17. Behavior of variable V3 region from 16S rDNA of lactic acid bacteria in denaturing gradient gel electrophoresis.

    PubMed

    Ercolini, D; Moschetti, G; Blaiotta, G; Coppola, S

    2001-03-01

    Separation of amplified V3 region from 16S rDNA by denaturing gradient gel electrophoresis (DGGE) was tested as a tool for differentiation of lactic acid bacteria commonly isolated from food. Variable V3 regions of 21 reference strains and 34 wild strains referred to species belonging to the genera Pediococcus, Enterococcus, Lactococcus, Lactobacillus, Leuconostoc, Weissella, and Streptococcus were analyzed. DGGE profiles obtained were species-specific for most of the cultures tested. Moreover, it was possible to group the remaining LAB reference strains according to the migration of their 16S V3 region in the denaturing gel. The results are discussed with reference to their potential in the analysis of LAB communities in food, besides shedding light on taxonomic aspects.

  18. Directionality switchable gain stabilized linear repeater

    NASA Astrophysics Data System (ADS)

    Ota, Takayuki; Ohmachi, Tadashi; Aida, Kazuo

    2004-10-01

    We propose a new approach to realize a bidirectional linear repeater suitable for future optical internet networks and fault location in repeater chain with OTDR. The proposed approach is the linear repeater of simple configuration whose directionality is rearranged dynamically by electrical control signal. The repeater is composed of a magneto-optical switch, a circulator, a dynamically gain stabilized unidirectional EDFA, and control circuits. The repeater directionality is rearranged as fast as 0.1ms by an electrical control pulse. It is experimentally confirmed that OTDR with the directionality switchable repeater is feasible for repeater chain. The detailed design and performance of the repeater are also discussed, including the multi-pass interference (MPI) which may arise in the proposed repeater, the effect of the MPI on SNR degradation of the repeater chain and the feed-forward EDFA gain control circuit.

  19. Response of surface water chemistry to reduced levels of acid precipitation: comparison of trends in two regions of New York, USA

    NASA Astrophysics Data System (ADS)

    Burns, Douglas A.; McHale, Michael R.; Driscoll, Charles T.; Roy, Karen M.

    2006-04-01

    In light of recent reductions in sulphur (S) and nitrogen (N) emissions mandated by Title IV of the Clean Air Act Amendments of 1990, temporal trends and trend coherence in precipitation (1984-2001 and 1992-2001) and surface water chemistry (1992-2001) were determined in two of the most acid-sensitive regions of North America, i.e. the Catskill and Adirondack Mountains of New York. Precipitation chemistry data from six sites located near these regions showed decreasing sulphate (SO42-), nitrate (NO3-), and base cation (CB) concentrations and increasing pH during 1984-2001, but few significant trends during 1992-2001. Data from five Catskill streams and 12 Adirondack lakes showed decreasing trends in SO42- concentrations at all sites, and decreasing trends in NO3-, CB, and H+ concentrations and increasing trends in dissolved organic carbon at most sites. In contrast, acid-neutralizing capacity (ANC) increased significantly at only about half the Adirondack lakes and in one of the Catskill streams. Flow correction prior to trend analysis did not change any trend directions and had little effect on SO42- trends, but it caused several significant non-flow-corrected trends in NO3- and ANC to become non-significant, suggesting that trend results for flow-sensitive constituents are affected by flow-related climate variation. SO42- concentrations showed high temporal coherence in precipitation, surface waters, and in precipitation-surface water comparisons, reflecting a strong link between S emissions, precipitation SO42- concentrations, and the processes that affect S cycling within these regions. NO3- and H+ concentrations and ANC generally showed weak coherence, especially in surface waters and in precipitation-surface water comparisons, indicating that variation in local-scale processes driven by factors such as climate are affecting trends in acid-base chemistry in these two regions.

  20. Response of surface water chemistry to reduced levels of acid precipitation: Comparison of trends in two regions of New York, USA

    USGS Publications Warehouse

    Burns, Douglas A.; McHale, M.R.; Driscoll, C.T.; Roy, K.M.

    2006-01-01

    In light of recent reductions in sulphur (S) and nitrogen (N) emissions mandated by Title IV of the Clean Air Act Amendments of 1990, temporal trends and trend coherence in precipitation (1984-2001 and 1992-2001) and surface water chemistry (1992-2001) were determined in two of the most acid-sensitive regions of North America, i.e. the Catskill and Adirondack Mountains of New York. Precipitation chemistry data from six sites located near these regions showed decreasing sulphate (SO42-), nitrate (NO3-), and base cation (CB) concentrations and increasing pH during 1984-2001, but few significant trends during 1992-2001. Data from five Catskill streams and 12 Adirondack lakes showed decreasing trends in SO42- concentrations at all sites, and decreasing trends in NO3-, CB, and H+ concentrations and increasing trends in dissolved organic carbon at most sites. In contrast, acid-neutralizing capacity (ANC increased significantly at only about half the Adirondack lakes and in one of the Catskill streams. Flow correction prior to trend analysis did not change any trend directions and had little effect on SO42- trends, but it caused several significant non-flow-corrected trends in NO3- and ANC to become non-significant, suggesting that trend results for flow-sensitive constituents are affected by flow-related climate variation. SO42- concentrations showed high temporal coherence in precipitation, surface waters, and in precipitation-surface water comparisons, reflecting a strong link between S emissions, precipitation SO42- concentrations, and the processes that affect S cycling within these regions. NO3- and H+ concentrations and ANC generally showed weak coherence, especially in surface waters and in precipitation-surface water comparisons, indicating that variation in local-scale processes driven by factors such as climate are affecting trends in acid-base chemistry in these two regions. Copyright ?? 2005 John Wiley & Sons, Ltd.

  1. Observations of Soft Gamma Repeaters

    NASA Technical Reports Server (NTRS)

    Kouveliotou, Chryssa

    2004-01-01

    Magnetars (Soft Gamma Repeaters and Anomalous X-ray Pulsars) are a subclass of neutron stars characterized by their recurrent X-ray bursts. While in an active (bursting) state (lasting anywhere between days and years), they are emit&ng hundreds of predominantly soft (kT=30 kev), short (0.1-100 ms long) events. Their quiescent source x-ray light ewes exhibit puhlions rotational period rate changes (spin-down) indicate that their magnetic fields are extremely high, of the order of 10^14- 10^l5 G. Such high B-field objects, dubbed "magnetars", had been predicted to exist in 1992, but the first concrete observational evidence were obtained in 1998 for two of these sources. I will discuss here the history of Soft Gamma Repeaters, and their spectral, timing and flux characteristics both in the persistent and their burst emission.

  2. An integrative approach for codon repeats evolutionary analyses.

    PubMed

    Lousado, José Paulo; Oliveira, José Luis; Moura, Gabriela; Santos, Manuel A S

    2012-01-01

    The relationship between genome characteristics and several human diseases has been a central research goal in genomics. Many studies have shown that specific gene patterns, such as amino acid repetitions, are associated with human diseases. However, several open questions still remain, such as, how these tandem repeats appeared in the evolutionary path or how they have evolved in orthologous genes of related organisms. In this paper, we present a computational solution that facilitates comparative studies of orthologous genes from various organisms. The application uses various web services to gather gene sequence information, local algorithms for tandem repeats identification and similarity measures for gene clustering.

  3. Mapping of a gene for epidermolytic palmoplantar keratoderma to the region of the acidic keratin gene cluster at 17q12-q21.

    PubMed

    Reis, A; Küster, W; Eckardt, R; Sperling, K

    1992-01-01

    Epidermolytic palmoplantar keratoderma (EPPK) (Vörner-Unna-Thost) is an autosomal dominantly inherited skin disease of unknown etiology characterized by diffuse severe hyperkeratosis of the palms and soles and, histologically, by cellular degeneration. We have mapped a gene for EPPK to chromosome 17q11-q23, with linkage analysis using microsatellite DNA-polymorphisms, in a single large family of 7 generations. A maximum lod score of z = 6.66 was obtained with the probe D17S579 at a recombination fraction of theta = 0.00. This locus maps to the same region as the type I (acidic) keratin gene cluster. Keratins, members of the intermediate filament family, the major proteins of the cytoskeleton in epidermis, are differentially expressed in a tissue-specific manner. One acidic keratin, keratin 9 (KRT9), is expressed only in the terminally differentiated epidermis of palms and soles. The KRT9 gene has not yet been cloned; however, since the genes for most acidic keratins are clustered, it is highly probable that it too will map to this region. We therefore propose KRT9 as the candidate gene for EPPK.

  4. Prostaglandin E2-Mediated Attenuation of Mesocortical Dopaminergic Pathway Is Critical for Susceptibility to Repeated Social Defeat Stress in Mice

    PubMed Central

    Tanaka, Kohei; Furuyashiki, Tomoyuki; Kitaoka, Shiho; Senzai, Yuta; Imoto, Yuki; Segi-Nishida, Eri; Deguchi, Yuichi; Breyer, Richard M.; Breyer, Matthew D.; Narumiya, Shuh

    2013-01-01

    Various kinds of stress are thought to precipitate psychiatric disorders, such as major depression. Whereas studies in rodents have suggested a critical role of medial prefrontal cortex (mPFC) in stress susceptibility, the mechanism of how stress susceptibility is determined through mPFC remains unknown. Here we show a critical role of prostaglandin E2 (PGE2), a bioactive lipid derived from arachidonic acid, in repeated social defeat stress in mice. Repeated social defeat increased the PGE2 level in the subcortical region of the brain, and mice lacking either COX-1, a prostaglandin synthase, or EP1, a PGE receptor, were impaired in induction of social avoidance by repeated social defeat. Given the reported action of EP1 that augments GABAergic inputs to midbrain dopamine neurons, we analyzed dopaminergic response upon social defeat. Analyses of c-Fos expression of VTA dopamine neurons and dopamine turnover in mPFC showed that mesocortical dopaminergic pathway is activated upon social defeat and attenuated with repetition of social defeat in wild-type mice. EP1 deficiency abolished such repeated stress-induced attenuation of mesocortical dopaminergic pathway. Blockade of dopamine D1-like receptor during social defeat restored social avoidance in EP1-deficient mice, suggesting that disinhibited dopaminergic response during social defeat blocks induction of social avoidance. Furthermore, mPFC dopaminergic lesion by local injection of 6-hydroxydopamine, which mimicked the action of EP1 during repeated stress, facilitated induction of social avoidance upon social defeat. Taken together, our data suggest that PGE2-EP1 signaling is critical for susceptibility to repeated social defeat stress in mice through attenuation of mesocortical dopaminergic pathway. PMID:22442093

  5. Utilization of folic acid and iron supplementation services by pregnant women attending an antenatal clinic at a regional referral hospital in Kenya.

    PubMed

    Maina-Gathigi, L; Omolo, J; Wanzala, P; Lindan, C; Makokha, A

    2013-09-01

    To determine utilization of iron and folic acid supplementation services among pregnant women in Kenya. A cross sectional study was conducted at Nyeri Hospital, a regional referral hospital in central Kenya. Women attending the antenatal clinic were selected through systematic sampling. A semi-structured questionnaire was administered to collect information on utilization of folic acid and iron supplementation services. Women who ingested folic acid or iron supplements for >4 days in a week were considered "highly compliant". The health worker in-charge of the antenatal clinic was interviewed about the frequency of supplement stock-outs during the past year. Haemoglobin concentration was measured directly from one drop of capillary blood and measured using portable HEMOCUE B-Hb photometer. Of the 381 women interviewed, only 23.6 % obtained antenatal care in the first trimester; 69.3 and 51.2 % received folic acid and iron supplements, respectively. However, only half (45-58 %) received any information about supplementation. Most women were initiated on folic acid (80.7 %) or iron (67.7 %) after 12 and 16 weeks of gestation, respectively, well after the recommended time period. However, more than 80 % of those who received folic acid and iron were highly compliant. Stock-outs were common at the facility. Of 361 women tested for Hb level, the prevalence of anaemia (Hb levels < 11 g/dl) was 7.8 %. Health workers need to better explain the importance of supplements to pregnant women. Women who come late to antenatal clinic miss opportunities to start supplementation early in pregnancy. Problems with supply chain management exacerbate the problem.

  6. A repeating fast radio burst.

    PubMed

    Spitler, L G; Scholz, P; Hessels, J W T; Bogdanov, S; Brazier, A; Camilo, F; Chatterjee, S; Cordes, J M; Crawford, F; Deneva, J; Ferdman, R D; Freire, P C C; Kaspi, V M; Lazarus, P; Lynch, R; Madsen, E C; McLaughlin, M A; Patel, C; Ransom, S M; Seymour, A; Stairs, I H; Stappers, B W; van Leeuwen, J; Zhu, W W

    2016-03-10

    Fast radio bursts are millisecond-duration astronomical radio pulses of unknown physical origin that appear to come from extragalactic distances. Previous follow-up observations have failed to find additional bursts at the same dispersion measure (that is, the integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of these bursts has led to the suggestion that they originate in cataclysmic events. Here we report observations of ten additional bursts from the direction of the fast radio burst FRB 121102. These bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB 121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB 121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and which vary on timescales of minutes or less. Although there may be multiple physical origins for the population of fast radio bursts, these repeat bursts with high dispersion measure and variable spectra specifically seen from the direction of FRB 121102 support an origin in a young, highly magnetized, extragalactic neutron star. PMID:26934226

  7. A repeating fast radio burst.

    PubMed

    Spitler, L G; Scholz, P; Hessels, J W T; Bogdanov, S; Brazier, A; Camilo, F; Chatterjee, S; Cordes, J M; Crawford, F; Deneva, J; Ferdman, R D; Freire, P C C; Kaspi, V M; Lazarus, P; Lynch, R; Madsen, E C; McLaughlin, M A; Patel, C; Ransom, S M; Seymour, A; Stairs, I H; Stappers, B W; van Leeuwen, J; Zhu, W W

    2016-03-10

    Fast radio bursts are millisecond-duration astronomical radio pulses of unknown physical origin that appear to come from extragalactic distances. Previous follow-up observations have failed to find additional bursts at the same dispersion measure (that is, the integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of these bursts has led to the suggestion that they originate in cataclysmic events. Here we report observations of ten additional bursts from the direction of the fast radio burst FRB 121102. These bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB 121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB 121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and which vary on timescales of minutes or less. Although there may be multiple physical origins for the population of fast radio bursts, these repeat bursts with high dispersion measure and variable spectra specifically seen from the direction of FRB 121102 support an origin in a young, highly magnetized, extragalactic neutron star.

  8. Repeat Size Determination by Two Molecular Rulers in the Type I-E CRISPR Array.

    PubMed

    Goren, Moran G; Doron, Shany; Globus, Rea; Amitai, Gil; Sorek, Rotem; Qimron, Udi

    2016-09-13

    Prokaryotic adaptive immune systems are composed of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins. These systems adapt to new threats by integrating short nucleic acids, termed spacers, into the CRISPR array. The functional motifs in the repeat and the mechanism by which a constant repeat size is maintained are still elusive. Here, through a series of mutations within the repeat of the CRISPR-Cas type I-E, we identify motifs that are crucial for adaptation and show that they serve as anchor sites for two molecular rulers determining the size of the new repeat. Adaptation products from various repeat mutants support a model in which two motifs in the repeat bind to two different sites in the adaptation complex that are 8 and 16 bp away from the active site. This model significantly extends our understanding of the adaptation process and broadens the scope of its applications. PMID:27626652

  9. Comparative genome analysis of cortactin and HS1: the significance of the F-actin binding repeat domain

    PubMed Central

    van Rossum, Agnes GSH; Schuuring-Scholtes, Ellen; Seggelen, Vera van Buuren-van; Kluin, Philip M; Schuuring, Ed

    2005-01-01

    Background In human carcinomas, overexpression of cortactin correlates with poor prognosis. Cortactin is an F-actin-binding protein involved in cytoskeletal rearrangements and cell migration by promoting actin-related protein (Arp)2/3 mediated actin polymerization. It shares a high amino acid sequence and structural similarity to hematopoietic lineage cell-specific protein 1 (HS1) although their functions differ considerable. In this manuscript we describe the genomic organization of these two genes in a variety of species by a combination of cloning and database searches. Based on our analysis, we predict the genesis of the actin-binding repeat domain during evolution. Results Cortactin homologues exist in sponges, worms, shrimps, insects, urochordates, fishes, amphibians, birds and mammalians, whereas HS1 exists in vertebrates only, suggesting that both genes have been derived from an ancestor cortactin gene by duplication. In agreement with this, comparative genome analysis revealed very similar exon-intron structures and sequence homologies, especially over the regions that encode the characteristic highly conserved F-actin-binding repeat domain. Cortactin splice variants affecting this F-actin-binding domain were identified not only in mammalians, but also in amphibians, fishes and birds. In mammalians, cortactin is ubiquitously expressed except in hematopoietic cells, whereas HS1 is mainly expressed in hematopoietic cells. In accordance with their distinct tissue specificity, the putative promoter region of cortactin is different from HS1. Conclusions Comparative analysis of the genomic organization and amino acid sequences of cortactin and HS1 provides inside into their origin and evolution. Our analysis shows that both genes originated from a gene duplication event and subsequently HS1 lost two repeats, whereas cortactin gained one repeat. Our analysis genetically underscores the significance of the F-actin binding domain in cytoskeletal remodeling, which

  10. Monitoring of quality and stability characteristics and fatty acid compositions of refined olive and seed oils during repeated pan- and deep-frying using GC, FT-NIRS, and chemometrics.

    PubMed

    Zribi, Akram; Jabeur, Hazem; Aladedunye, Felix; Rebai, Ahmed; Matthäus, Bertrand; Bouaziz, Mohamed

    2014-10-22

    Refined olive, corn, soybean, and sunflower oils were used as cooking oils for deep-frying at two different temperatures, 160 and 190 °C, and for pan-frying of potatoes at 180 °C for 10 successive sessions under the usual domestic practice. Several chemical parameters were assayed during frying operations to evaluate the status of the frying oils. Refined olive oil, as frying oil, was found to be more stable than the refined seed oils. In fact, this oil has proven the greatest resistance to oxidative deterioration, and its trans-fatty acid contents and percentages of total polar compounds were found to be lower at 160 °C during deep-frying. Finally, chemometric analysis has demonstrated that the lowest deterioration of the quality of all refined oils occurred in the refined olive oil during deep-frying at 160 °C and the highest deterioration occurred in the refined sunflower oil during pan-frying at 180 °C.

  11. Monitoring of quality and stability characteristics and fatty acid compositions of refined olive and seed oils during repeated pan- and deep-frying using GC, FT-NIRS, and chemometrics.

    PubMed

    Zribi, Akram; Jabeur, Hazem; Aladedunye, Felix; Rebai, Ahmed; Matthäus, Bertrand; Bouaziz, Mohamed

    2014-10-22

    Refined olive, corn, soybean, and sunflower oils were used as cooking oils for deep-frying at two different temperatures, 160 and 190 °C, and for pan-frying of potatoes at 180 °C for 10 successive sessions under the usual domestic practice. Several chemical parameters were assayed during frying operations to evaluate the status of the frying oils. Refined olive oil, as frying oil, was found to be more stable than the refined seed oils. In fact, this oil has proven the greatest resistance to oxidative deterioration, and its trans-fatty acid contents and percentages of total polar compounds were found to be lower at 160 °C during deep-frying. Finally, chemometric analysis has demonstrated that the lowest deterioration of the quality of all refined oils occurred in the refined olive oil during deep-frying at 160 °C and the highest deterioration occurred in the refined sunflower oil during pan-frying at 180 °C. PMID:25264922

  12. Evaluation of Safety and Pharmacokinetics of Sodium 2,2 Dimethylbutyrate, a Novel Short Chain Fatty Acid Derivative, in a Phase 1, Double-Blind, Placebo-Controlled, Single- and Repeat-Dose Studies in Healthy Volunteers

    PubMed Central

    Perrine, Susan P.; Wargin, William A.; Boosalis, Michael S.; Wallis, Wayne J.; Case, Sally; Keefer, Jeffrey R.; Faller, Douglas V.; Welch, William C.; Berenson, Ronald J.

    2013-01-01

    Pharmacologic induction of fetal globin synthesis is an accepted therapeutic strategy for treatment of the beta hemoglobinopathies and thalassemias, as even small increases in hemoglobin F (HbF) levels reduce clinical severity in sickle cell disease and reduce anemia in beta thalassemia. Prior generation short chain fatty acid therapeutics, arginine butyrate and phenylbutyrate, increased fetal and total hemoglobin levels in patients, but were limited by high doses or intravenous infusion. A fetal globin-inducing therapeutic with convenient oral dosing would be an advance for these classic molecular diseases. Healthy adult human subjects were treated with a novel SCFA derivative, sodium 2,2 dimethylbutyrate (SDMB), or placebo, with one of four single dose levels (2, 5, 10 and 20 mg/kg) or daily doses (5, 10, or 15 mg/kg) over 14 days, and monitored for adverse clinical and laboratory events, drug levels, reticulocytes, and HbF assays. SDMB was well-tolerated with no clinically significant adverse events related to study medication. The terminal half-life ranged from 9–15 hours. Increases in mean absolute reticulocytes were observed at all dose levels in the 14-day study. The favorable PK profiles and safety findings indicate that SDMB warrants further investigation for treatment of anemic subjects with beta hemoglobinopathies. PMID:21422239

  13. Effects of Non-Natural Amino Acid Incorporation into the Enzyme Core Region on Enzyme Structure and Function

    PubMed Central

    Wong, H. Edward; Kwon, Inchan

    2015-01-01

    Techniques to incorporate non-natural amino acids (NNAAs) have enabled biosynthesis of proteins containing new building blocks with unique structures, chemistry, and reactivity that are not found in natural amino acids. It is crucial to understand how incorporation of NNAAs affects protein function because NNAA incorporation may perturb critical function of a target protein. This study investigates how the site-specific incorporation of NNAAs affects catalytic properties of an enzyme. A NNAA with a hydrophobic and bulky sidechain, 3-(2-naphthyl)-alanine (2Nal), was site-specifically incorporated at six different positions in the hydrophobic core of a model enzyme, murine dihydrofolate reductase (mDHFR). The mDHFR variants with a greater change in van der Waals volume upon 2Nal incorporation exhibited a greater reduction in the catalytic efficiency. Similarly, the steric incompatibility calculated using RosettaDesign, a protein stability calculation program, correlated with the changes in the catalytic efficiency. PMID:26402667

  14. Communication: Protonation process of formic acid from the ionization and fragmentation of dimers induced by synchrotron radiation in the valence region

    NASA Astrophysics Data System (ADS)

    Arruda, Manuela S.; Medina, Aline; Sousa, Josenilton N.; Mendes, Luiz A. V.; Marinho, Ricardo R. T.; Prudente, Frederico V.

    2016-04-01

    The ionization and fragmentation of monomers of organic molecules have been extensively studied in the gas phase using mass spectroscopy. In the spectra of these molecules it is possible to identify the presence of protonated cations, which have a mass-to-charge ratio one unit larger than the parent ion. In this work, we investigate this protonation process as a result of dimers photofragmentation. Experimental photoionization and photofragmentation results of doubly deuterated formic acid (DCOOD) in the gas phase by photons in the vacuum ultraviolet region are presented. The experiment was performed by using a time-of-flight mass spectrometer installed at the Brazilian Synchrotron Light Laboratory and spectra for different pressure values in the experimental chamber were obtained. The coupled cluster approach with single and double substitutions was employed to assist the experimental analysis. Results indicate that protonated formic acid ions are originated from dimer dissociation, and the threshold photoionization of (DCOOD)ṡD+ is also determined.

  15. Dataset for the NMR structure of the intrinsically disordered acidic region of XPC bound to the PH domain of TFIIH p62

    PubMed Central

    Okuda, Masahiko; Nishimura, Yoshifumi

    2016-01-01

    The global genome nucleotide excision repair factor XPC firstly detects DNA lesions and then recruits a ten-subunit complex TFIIH through binding to the subunit p62 to unwind the damaged DNA for excision repair. This data article contains detailed nuclear magnetic resonance (NMR) restraints (nuclear Overhauser enhancement (NOE)-derived distance restraints, dihedral angle restraints, and hydrogen bond restraints) used for the structure determination of the complex formed between the intrinsically disordered acidic region of XPC and the pleckstrin homology (PH) domain of TFIIH p62, related to the recent work entitled “Structural insight into the mechanism of TFIIH recognition by the acidic string of the nucleotide excision repair factor XPC.” [1]. PMID:26909369

  16. [Identification of new conserved and variable regions in the 16S rRNA gene of acetic acid bacteria and acetobacteraceae family].

    PubMed

    Chakravorty, S; Sarkar, S; Gachhui, R

    2015-01-01

    The Acetobacteraceae family of the class Alpha Proteobacteria is comprised of high sugar and acid tolerant bacteria. The Acetic Acid Bacteria are the economically most significant group of this family because of its association with food products like vinegar, wine etc. Acetobacteraceae are often hard to culture in laboratory conditions and they also maintain very low abundances in their natural habitats. Thus identification of the organisms in such environments is greatly dependent on modern tools of molecular biology which require a thorough knowledge of specific conserved gene sequences that may act as primers and or probes. Moreover unconserved domains in genes also become markers for differentiating closely related genera. In bacteria, the 16S rRNA gene is an ideal candidate for such conserved and variable domains. In order to study the conserved and variable domains of the 16S rRNA gene of Acetic Acid Bacteria and the Acetobacteraceae family, sequences from publicly available databases were aligned and compared. Near complete sequences of the gene were also obtained from Kombucha tea biofilm, a known Acetobacteraceae family habitat, in order to corroborate the domains obtained from the alignment studies. The study indicated that the degree of conservation in the gene is significantly higher among the Acetic Acid Bacteria than the whole Acetobacteraceae family. Moreover it was also observed that the previously described hypervariable regions V1, V3, V5, V6 and V7 were more or less conserved in the family and the spans of the variable regions are quite distinct as well.

  17. Evolution of vertebrate IgM: complete amino acid sequence of the constant region of Ambystoma mexicanum mu chain deduced from cDNA sequence.

    PubMed

    Fellah, J S; Wiles, M V; Charlemagne, J; Schwager, J

    1992-10-01

    cDNA clones coding for the constant region of the Mexican axolotl (Ambystoma mexicanum) mu heavy immunoglobulin chain were selected from total spleen RNA, using a cDNA polymerase chain reaction technique. The specific 5'-end primer was an oligonucleotide homologous to the JH segment of Xenopus laevis mu chain. One of the clones, JHA/3, corresponded to the complete constant region of the axolotl mu chain, consisting of a 1362-nucleotide sequence coding for a polypeptide of 454 amino acids followed in 3' direction by a 179-nucleotide untranslated region and a polyA+ tail. The axolotl C mu is divided into four typical domains (C mu 1-C mu 4) and can be aligned with the Xenopus C mu with an overall identity of 56% at the nucleotide level. Percent identities were particularly high between C mu 1 (59%) and C mu 4 (71%). The C-terminal 20-amino acid segment which constitutes the secretory part of the mu chain is strongly homologous to the equivalent sequences of chondrichthyans and of other tetrapods, including a conserved N-linked oligosaccharide, the penultimate cysteine and the C-terminal lysine. The four C mu domains of 13 vertebrate species ranging from chondrichthyans to mammals were aligned and compared at the amino acid level. The significant number of mu-specific residues which are conserved into each of the four C mu domains argues for a continuous line of evolution of the vertebrate mu chain. This notion was confirmed by the ability to reconstitute a consistent vertebrate evolution tree based on the phylogenic parsimony analysis of the C mu 4 sequences. PMID:1382992

  18. CGG repeat in the FMR1 gene: size matters.

    PubMed

    Willemsen, R; Levenga, J; Oostra, B A

    2011-09-01

    The FMR1 gene contains a CGG repeat present in the 5'-untranslated region which can be unstable upon transmission to the next generation. The repeat is up to 55 CGGs long in the normal population. In patients with fragile X syndrome (FXS), a repeat length exceeding 200 CGGs (full mutation: FM) generally leads to methylation of the repeat and the promoter region, which is accompanied by silencing of the FMR1 gene. The absence of FMR1 protein, FMRP, seen in FM is the cause of the mental retardation in patients with FXS. The premutation (PM) is defined as 55-200 CGGs. Female PM carriers are at risk of developing primary ovarian insufficiency. Elderly PM carriers might develop a progressive neurodegenerative disorder called fragile X-associated tremor/ataxia syndrome (FXTAS). Although arising from the mutations in the same gene, distinct mechanisms lead to FXS (absence of FMRP), FXTAS (toxic RNA gain-of-function) and FXPOI. The pathogenic mechanisms thought to underlie these disorders are discussed. This review gives insight on the implications of all possible repeat length categories seen in fragile X families.

  19. Amino Acid Polymorphisms Within the Entire HCV NS5A Region in Estonian Chronic HCV 1b Patients With Different Treatment Response

    PubMed Central

    Kuznetsova, Tatiana; Tallo, Tatjana; Brjalin, Vadim; Reshetnjak, Irina; Salupere, Riina; Priimagi, Ljudmilla; Katargina, Olga; Smirnova, Maria; Jansons, Juris; Tefanova, Valentina

    2013-01-01

    Background A substantial proportion of hepatitis C virus (HCV)-1b infected patients do not response to pegylated interferon-α plus ribavirin (PegIFNα/RBV) combination therapy that was partially associated with mutations in the non-structural 5A (NS5A) protein. Objectives Analysis of NS5A polymorphisms in HCV genotype 1b pre-treatment serum samples from Estonian patients and their effect on the treatment response. Patients and Methods Twenty-nine complete NS5A sequences obtained from patients with chronic HCV-1b infection who had received combined therapy with PegIFNα-2a/RBV were analyzed and compared with the prototype strain HCV-J. Twelve patients achieved a sustained virological response (SVR), 15 were non-SVR and 2 patients stopped treatment because of side effects. Results No significant difference in total number of amino acid mutations was observed between isolates from SVR and non-SVR patients in any known regions of the NS5A protein. However, specific amino acid substitutions at positions 1989 and 2283 correlated significantly with SVR, mutations at positions 1979, 2107, 2171 and 2382 were associated with non-response to treatment and amino acid substitution at position 2319 was observed in relapsers. At phylogenetic analysis, NS5A nucleotide sequences have been subdivided into four groups characterized by the different treatment response. Twenty-four novel nucleotide polymorphisms and 11 novel amino acid polymorphisms were identified based on the phylogenetic tree topology. Conclusions Specific amino acid substitutions correlating with the treatment response were found. Polymorphisms revealed by phylogenetic analysis may define the signature patterns for treatment susceptible and treatment resistant strains prevalent in Estonia. PMID:24358043

  20. Excision of plastid marker genes using directly repeated DNA sequences.

    PubMed

    Mudd, Elisabeth A; Madesis, Panagiotis; Avila, Elena Martin; Day, Anil

    2014-01-01

    Excision of marker genes using DNA direct repeats makes use of the predominant homologous recombination pathways present in the plastids of algae and plants. The method is simple, efficient, and widely applicable to plants and microalgae. Marker excision frequency is dependent on the length and number of directly repeated sequences. When two repeats are used a repeat size of greater than 600 bp promotes efficient excision of the marker gene. A wide variety of sequences can be used to make the direct repeats. Only a single round of transformation is required, and there is no requirement to introduce site-specific recombinases by retransformation or sexual crosses. Selection is used to maintain the marker and ensure homoplasmy of transgenic plastid genomes. Release of selection allows the accumulation of marker-free plastid genomes generated by marker excision, which is spontaneous, random, and a unidirectional process. Positive selection is provided by linking marker excision to restoration of the coding region of an herbicide resistance gene from two overlapping but incomplete coding regions. Cytoplasmic sorting allows the segregation of cells with marker-free transgenic plastids. The marker-free shoots resulting from direct repeat-mediated excision of marker genes have been isolated by vegetative propagation of shoots in the T0 generation. Alternatively, accumulation of marker-free plastid genomes during growth, development and flowering of T0 plants allows the collection of seeds that give rise to a high proportion of marker-free T1 seedlings. The simplicity and convenience of direct repeat excision facilitates its widespread use to isolate marker-free crops. PMID:24599849

  1. Accumulate Repeat Accumulate Coded Modulation

    NASA Technical Reports Server (NTRS)

    Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

    2004-01-01

    In this paper we propose an innovative coded modulation scheme called 'Accumulate Repeat Accumulate Coded Modulation' (ARA coded modulation). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes that are combined with high level modulation. Thus at the decoder belief propagation can be used for iterative decoding of ARA coded modulation on a graph, provided a demapper transforms the received in-phase and quadrature samples to reliability of the bits.

  2. The Bel1 protein of human foamy virus contains one positive and two negative control regions which regulate a distinct activation domain of 30 amino acids.

    PubMed Central

    Lee, C W; Chang, J; Lee, K J; Sung, Y C

    1994-01-01

    The Bel1 transactivator is essential for the replication of human foamy virus (HFV). To define the functional domains of HFV Bel1, we generated random missense mutations throughout the entire coding sequence of Bel1. Functional analyses of 24 missense mutations have revealed the presence of at least two functional domains in Bel1. One domain corresponds to a basic amino acid-rich motif which acts as a bipartite nuclear targeting sequence. A second, central domain corresponds to a presumed effector region which, when mutated, leads to dominant-negative mutants and/or lacks transactivating ability. In addition, deletion analyses and domain-swapping experiments further showed that Bel1 protein contains a strong carboxy-terminal activation domain. The activating region is also capable of functioning as a transcription-activating domain in yeast cells, although it does not bear any significant sequence homology to the well-characterized acidic activation domain which is known to function only in yeast and mammalian cells. We also demonstrated that the regions of Bel1 from residues 1 to 76 and from residues 153 to 225 repressed transcriptional activation exerted by the Bel1 activation domain. In contrast, the region from residues 82 to 150 appears to overcome an inhibitory effect. These results indicate that Bel1 contains one positive and two negative regulatory domains that modulate a distinct activation domain of Bel1. These regulatory domains of Bel1 cannot affect the function of the VP16 activation domain, suggesting that these domains specifically regulate the activation domain of Bel1. Furthermore, in vivo competition experiments showed that the positive regulatory domain acts in trans. Thus, our results demonstrate that Bel1-mediated transactivation appears to undergo a complex regulatory pathway which provides a novel mode of regulation for a transcriptional activation domain. Images PMID:8139046

  3. Regional vulnerability of the hippocampus to repeated motor activity deprivation.

    PubMed

    Faraji, Jamshid; Soltanpour, Nabiollah; Moeeini, Reza; Hosseini, Seyed Abedin; Pakdel, Shiva; Moharrerie, Alireza; Arjang, Kaveh; Soltanpour, Nasrin; Metz, Gerlinde A S

    2016-03-15

    Spontaneous vertical and horizontal exploratory movements are integral components of rodent behavior. Little is known, however, about the structural and functional consequences of restricted spontaneous exploration. Here, we report two experiments to probe whether restriction in vertical activity (rearing) in rats could induce neuro-hormonal and behavioral disturbances. Rearing movements in rats were deprived for 3h/day for 30 consecutive days by placing the animal into a circular tunnel task. Rats temporarily deprived of rearing behavior showed elevated plasma corticosterone levels but no detectable psychological distress and/or anxiety-related behavior within an elevated plus maze. However, rats emitted a greater number of 22-kHz ultrasonic vocalizations and spent significantly more time vocalizing than controls when deprived of their rearing behavior. Despite intact spatial performance within wet- and dry-land spatial tasks, rearing-deprived rats also exhibited a significant alteration in search strategies within both spatial tasks along with reduced volume and neuron number in the hippocampal subregion CA2. These data suggest a new approach to test the importance of free exploratory behavior in endocrine and structural manifestations. The results support a central role of the CA2 in spontaneous exploratory behavior and vulnerability to psychological stress. PMID:26723539

  4. Regional vulnerability of the hippocampus to repeated motor activity deprivation.

    PubMed

    Faraji, Jamshid; Soltanpour, Nabiollah; Moeeini, Reza; Hosseini, Seyed Abedin; Pakdel, Shiva; Moharrerie, Alireza; Arjang, Kaveh; Soltanpour, Nasrin; Metz, Gerlinde A S

    2016-03-15

    Spontaneous vertical and horizontal exploratory movements are integral components of rodent behavior. Little is known, however, about the structural and functional consequences of restricted spontaneous exploration. Here, we report two experiments to probe whether restriction in vertical activity (rearing) in rats could induce neuro-hormonal and behavioral disturbances. Rearing movements in rats were deprived for 3h/day for 30 consecutive days by placing the animal into a circular tunnel task. Rats temporarily deprived of rearing behavior showed elevated plasma corticosterone levels but no detectable psychological distress and/or anxiety-related behavior within an elevated plus maze. However, rats emitted a greater number of 22-kHz ultrasonic vocalizations and spent significantly more time vocalizing than controls when deprived of their rearing behavior. Despite intact spatial performance within wet- and dry-land spatial tasks, rearing-deprived rats also exhibited a significant alteration in search strategies within both spatial tasks along with reduced volume and neuron number in the hippocampal subregion CA2. These data suggest a new approach to test the importance of free exploratory behavior in endocrine and structural manifestations. The results support a central role of the CA2 in spontaneous exploratory behavior and vulnerability to psychological stress.

  5. New insights into atmospheric sources and sinks of isocyanic acid, HNCO, from recent urban and regional observations

    NASA Astrophysics Data System (ADS)

    Roberts, James M.; Veres, Patrick R.; VandenBoer, Trevor C.; Warneke, Carsten; Graus, Martin; Williams, Eric J.; Lefer, Barry; Brock, Charles A.; Bahreini, Roya; Öztürk, Fatma; Middlebrook, Ann M.; Wagner, Nicholas L.; Dubé, William P.; Gouw, Joost A.

    2014-01-01

    Isocyanic acid (HNCO) has only recently been measured in the ambient atmosphere, and many aspects of its atmospheric chemistry are still uncertain. HNCO was measured during three diverse field campaigns: California Nexus—Research at the Nexus of Air Quality and Climate Change (CalNex 2010) at the Pasadena ground site, Nitrogen, Aerosol Composition, and Halogens on a Tall Tower (NACHTT 2011) at the Boulder Atmospheric Observatory (BAO) in Weld County, CO, and Biofuel Crops emission of Ozone precursors intensive (BioCORN 2011), in a cornfield NW of Fort Collins, CO. Mixing ratios varied from below detection limit (~0.003 ppbv) to over 1.2 ppbv during a period when agricultural burning impacted the BAO Tower site. Urban areas, such as the CalNex 2010 Pasadena site, appear to have both primary (combustion) and secondary (photochemical) sources of HNCO, 50 ± 9%, and 33 ± 12%, respectively, while primary sources were responsible for the large mixing ratios of HNCO observed during the wintertime NACHTT study in suburban Colorado. Isocyanic acid during the BioCORN study in rural NE Colorado was closely correlated to ozone and therefore likely photochemically produced as a secondary product from amines or formamide. The removal of HNCO from the lower atmosphere is thought to be due to deposition, as common gas phase loss processes of photolysis and reactions with hydroxyl radicals, are slow. These ambient measurements are consistent with some HNCO deposition, which was evident at night at these surface sites.

  6. Acid fog Deposition of Crusts on Basaltic Tephra Deposits in the Sand Wash Region of Kilauea Volcano: A Possible Mechanism for Siliceous-Sulfatic Crusts on Mars

    NASA Astrophysics Data System (ADS)

    Schiffman, P.; Zierenberg, R.; Marks, N.; Bishop, J. L.

    2004-12-01

    Although the presence of sulfate minerals in martian outcrops may imply the prior existence of standing bodies of surface water, in terrestrial volcanic settings, sulfatic alteration may also occur above the water table within the vadose zone. On the summit of Kilauea volcano, sulfur dioxide, which is continuously emitted from Halemaumau crater and rapidly sequestered into sulfuric acid-rich aerosol entrained in the prevailing trade winds, is subsequently precipitated as acid-fog immediately downwind from the caldera in the Kau Desert. The characteristic pH of surface tephra deposits is < 4.0 in Sand Wash, a region of continuous, acidic aerosol fall-out immediately SW of the caldera. The upper portion of the Keanakakoi Ash tephra in Sand Wash, deposited in the late 18th century, has a ubiquitous, 0.1-0.2 mm-thick coating of amorphous silica. Conversely, vertical walls of unconsolidated tephra, exposed within small, dry gullies eroded into the ca. 3-4 m-thick Keanakakoi section at Sand Wash, are coated with ca. 0.5-1.0 mm-thick, mixed amorphous silica and jarosite-bearing crusts. Since these crusts are denuded from their outcrops during ephemeral, but probably annual flooding events in Sand Wash, we believe that they must accumulate rapidly. These crusts are apparently formed via an evaporative mechanism whereby acidic pore fluids, circulating in the upper few m's within the highly porous tephra, are wicked towards the walls of the gullies. Geochemical modeling of the crust-forming process implies that the sulfate formation via evaporation occurs subsequent to minimal interaction of acidic pore fluids with the basaltic tephra. This also suggests that the cycle from acid-fog fall-out to precipitation of the siliceous-sulfatic crusts must occur quite rapidly. Production of siliceous-sulfatic crusts via acid-fog alteration may also be occurring on Mars. The occurrence of evaporitic sulfate and silica at Sand Wash in Kilauea may serve as an example of how the jarosite

  7. Crowding by a repeating pattern.

    PubMed

    Rosen, Sarah; Pelli, Denis G

    2015-01-01

    Theinability to recognize a peripheral target among flankers is called crowding. For a foveal target, crowding can be distinguished from overlap masking by its sparing of detection, linear scaling with eccentricity, and invariance with target size.Crowding depends on the proximity and similarity of the flankers to the target. Flankers that are far from or dissimilar to the target do not crowd it. On a gray page, text whose neighboring letters have different colors, alternately black and white, has enough dissimilarity that it might escape crowding. Since reading speed is normally limited by crowding, escape from crowding should allow faster reading. Yet reading speed is unchanged (Chung & Mansfield, 2009). Why? A recent vernier study found that using alternating-color flankers produces strong crowding (Manassi, Sayim, & Herzog, 2012). Might that effect occur with letters and reading? Critical spacing is the minimum center-to-center target-flanker spacing needed to correctly identify the target. We measure it for a target letter surrounded by several equidistant flanker letters of the same polarity, opposite polarity, or mixed polarity: alternately white and black. We find strong crowding in the alternating condition, even though each flanker letter is beyond its own critical spacing (as measured in a separate condition). Thus a periodic repeating pattern can produce crowding even when the individual elements do not. Further, in all conditions we find that, once a periodic pattern repeats (two cycles), further repetition does not affect critical spacing of the innermost flanker.

  8. Glial fibrillary acidic protein is differentially expressed across cortical and subcortical regions in healthy brains and downregulated in the thalamus and caudate nucleus of depressed suicides.

    PubMed

    Torres-Platas, S G; Nagy, C; Wakid, M; Turecki, G; Mechawar, N

    2016-04-01

    There is mounting evidence to suggest aberrant astrocytic function in depression and suicide. Independent studies have reported astrocytic abnormalities in certain brain regions, but it remains unclear whether this is a brain-wide phenomenon. The present study examined this question by measuring glial fibrillary acidic protein (GFAP) expression in postmortem brain samples from suicide completers and matched non-psychiatric controls. Suicide completers were selected based on their recent characterization as low GFAP expressors in the prefrontal cortex, (Brodmann areas 8/9 and 10). Real-time PCR and immunoblotting were used to measure GFAP gene expression and protein levels in BA4 (primary motor cortex), BA17 (primary visual cortex), cerebellar cortex, mediodorsal thalamus and caudate nucleus. We found downregulation of GFAP mRNA and protein in the mediodorsal thalamus and caudate nucleus of depressed suicides compared with controls, whereas GFAP expression in other brain regions was similar between groups. Furthermore, a regional comparison including all samples revealed that GFAP expression in both subcortical regions was, on average, between 11- and 15-fold greater than in cerebellum and neocortex. Examining astrocyte morphology by immunohistochemistry showed that astrocytes in both thalamus and caudate displayed larger cell bodies and extended more ramified processes across larger domains than the previously described cortical astrocytes. This study reveals that astrocytic abnormalities are not brain wide and suggests that they are restricted to cortical and subcortical networks known to be affected in mood disorders. Additionally, our results show a greater diversity in human astrocytic phenotypes than previously thought.

  9. Evidence of Recombinant Citrus tristeza virus Isolate Occurring in Acid Lime cv. Pant Lemon Orchard in Uttarakhand Terai Region of Northern Himalaya in India.

    PubMed

    Singh, Jaywant Kumar; Tarafdar, Avijit; Sharma, Susheel Kumar; Biswas, Kajal Kumar

    2013-06-01

    The present study for the first time describes biological and molecular characterization of Citrus tristeza virus (CTV) occurring in the Terai area of Uttarakhand State in Northern Himalaya region of India. Direct antigen coated-ELISA and reverse transcriptase-polymerase chain reaction (RT-PCR) detected the CTV infection in Acid lime cv. Pant lemon (Citrus aurantifolia) orchards of Pantnagar with an estimated disease incidence of 16.6-20.5 %. To know the biological and genetic properties, an isolate, CTV Pant 4 was characterized. Isolate Pant 4 could be graft transmitted to Kinnow, Nagpur and Darjeeling mandarins, Mosambi sweet orange, Kagzi lime, Sweet lime, Sour orange but not to Rough lemon. The sequence analyses of the 5'ORF1a (3038 nucleotides) of LPro domain and 3'end (2058 nt) covering ORF7-ORF10 regions of the CTV genome revealed that Pant 4 was closely related to the previously reported Indian CTV isolate, Kpg3 from Northeastern Himalaya region with 97 and 98 % sequence identity, respectively. Whereas, it differed from the previously reported CTV isolate B165 from Southern India with 79 and 92 % identity, respectively for 5'ORF1a and 3' end regions. Recombination and SplitsTree decomposition analyses indicated that CTV isolate Pant 4 was a recombinant isolate originating from Kpg3 as a major and B165 as a minor donor. PMID:24426255

  10. Combination of nucleic acid and protein isolation with tissue array construction: using defined histologic regions in single frozen tissue blocks for multiple research purposes.

    PubMed

    Li, Hong; Sun, Yuan; Kong, Qing-You; Zhang, Kai-Li; Wang, Xiao-Wei; Chen, Xiao-Yan; Wang, Qian; Liu, Jia

    2003-09-01

    Precise dissection of defined histological regions for nucleic acid and protein isolation is a precedent step in finding out cancer-related alterations, and high quality tissue microarrays are demanded in the validation of screened genetic alterations by multiple in situ approaches. In this study, a combined technique was developed by which sample isolation and tissue array construction could be performed on the defined morphological region(s) in single tissue block. The RNA and protein samples generated from the selected portions were of good quality and sufficient for multiple experimental purposes. The frozen tissue arrays constructed on a novel recipient are suitable for multiple in situ evaluations including immunohistochemical staining and mRNA hybridisation. In most cases, the data obtained from in situ assays coincided well with the ones revealed by RT-PCR and Western blot hybridisation. The potential experimental bias caused by cell contamination can be amended by tissue array-based retrospective examination. The combination of tissue-selective sample preparations with tissue array construction thus provide a tool by which comprehensive cancer research can be performed on defined histological regions in a series of single frozen tissue blocks.

  11. Evidence of Recombinant Citrus tristeza virus Isolate Occurring in Acid Lime cv. Pant Lemon Orchard in Uttarakhand Terai Region of Northern Himalaya in India.

    PubMed

    Singh, Jaywant Kumar; Tarafdar, Avijit; Sharma, Susheel Kumar; Biswas, Kajal Kumar

    2013-06-01

    The present study for the first time describes biological and molecular characterization of Citrus tristeza virus (CTV) occurring in the Terai area of Uttarakhand State in Northern Himalaya region of India. Direct antigen coated-ELISA and reverse transcriptase-polymerase chain reaction (RT-PCR) detected the CTV infection in Acid lime cv. Pant lemon (Citrus aurantifolia) orchards of Pantnagar with an estimated disease incidence of 16.6-20.5 %. To know the biological and genetic properties, an isolate, CTV Pant 4 was characterized. Isolate Pant 4 could be graft transmitted to Kinnow, Nagpur and Darjeeling mandarins, Mosambi sweet orange, Kagzi lime, Sweet lime, Sour orange but not to Rough lemon. The sequence analyses of the 5'ORF1a (3038 nucleotides) of LPro domain and 3'end (2058 nt) covering ORF7-ORF10 regions of the CTV genome revealed that Pant 4 was closely related to the previously reported Indian CTV isolate, Kpg3 from Northeastern Himalaya region with 97 and 98 % sequence identity, respectively. Whereas, it differed from the previously reported CTV isolate B165 from Southern India with 79 and 92 % identity, respectively for 5'ORF1a and 3' end regions. Recombination and SplitsTree decomposition analyses indicated that CTV isolate Pant 4 was a recombinant isolate originating from Kpg3 as a major and B165 as a minor donor.

  12. Genome nucleotide composition shapes variation in simple sequence repeats.

    PubMed

    Tian, Xiangjun; Strassmann, Joan E; Queller, David C

    2011-02-01

    Simple sequence repeats (SSRs) or microsatellites are a common component of genomes but vary greatly across species in their abundance. We tested the hypothesis that this variation is due in part to AT/GC content of genomes, with genomes biased toward either high AT or high CG generating more short random repeats that are long enough to enhance expansion through slippage during replication. To test this hypothesis, we identified repeats with perfect tandem iterations of 1-6 bp from 25 protists with complete or near-complete genome sequences. As expected, the density and the frequency are highly related to genome AT content, with excellent fits to quadratic regressions with minima near a 50% AT content and rising toward both extremes. Within species, the same trends hold, except the limited variation in AT content within each species places each mainly on the descending (GC rich), middle, or ascending (AT rich) part of the curve. The base usages of repeat motifs are also significantly correlated with genome nucleotide compositions: Percentages of AT-rich motifs rise with the increase of genome AT content but vice versa for GC-rich subgroups. Amino acid homopolymer repeats also show the expected quadratic relationship, with higher abundance in species with AT content biased in either direction. Our results show that genome nucleotide composition explains up to half of the variance in the abundance and motif constitution of SSRs.

  13. Regional assessment of the response of the acid-base status of lake watersheds in the Adirondack region of New York to changes in atmospheric deposition using PnET-BGC.

    PubMed

    Chen, Limin; Driscoll, Charles T

    2005-02-01

    Understanding the response of soil and surface waters to changes in atmospheric deposition is critical for guiding future legislation on air pollution. The Adirondack region of New York experiences among the most severe ecological impacts from acidic deposition. The region is characterized by considerable variability in atmospheric deposition, surficial and bedrock geology, hydrologic flow paths, and vegetation resulting in variability in effects of acidic deposition. In this study, an integrated biogeochemical model (PnET-BGC) was applied to 37 forest lake watersheds to assess the response of soil and surface waters of the Adirondacks to changes in atmospheric deposition at a regional scale. Model-simulated surface water chemistry was validated against data from two synoptic surveys conducted in 1984 and 2001. Results indicate that the model is able to capture the observed changes in surface water chemistry during this period. The model was further used to forecast the response of soil and surface waters to three future emission control scenarios. Results indicate that under the Clean Air Act, surface water SO4(2-) concentrations will continue to decrease at a median rate of -0.38 microeq/L-yr, and surface water ANC is predicted to increase at a median rate of 0.11 microeq/L-yr. More aggressive emission reductions will accelerate the rate of recovery. Under an aggressive control scenario, which represents an additional 75% reduction in SO2 emissions beyond the implementation of the Clean Air Act, surface water SO4(2-) concentrations are predicted to decrease at a median rate of -0.88 microeq/L-yr, and surface water ANC is predicted to increase at a median rate of 0.43 microeq/L-yr. Model predictions of several biologically relevant chemical indicators are also reported.

  14. SdrI, a serine-aspartate repeat protein identified in Staphylococcus saprophyticus strain 7108, is a collagen-binding protein.

    PubMed

    Sakinc, Türkan; Kleine, Britta; Gatermann, Sören G

    2006-08-01

    A gene encoding a serine-aspartate repeat protein of Staphylococcus saprophyticus, an important cause of urinary tract infections in young women, has been cloned and sequenced. In contrast to other SD repeat proteins, SdrI carries 21 additional N-terminal repeats with a consensus sequence of (P/A)ATKE(K/E)A(A/V)(T/I)(A/T/S)EE and has the longest SD(AD)(1-5) repetitive region (854 amino acids) described so far. This highly repetitive sequence contains only the amino acids serine, asparagine, and a distinctly greater amount of alanine (37%) than all other known SD repeat proteins (2.3 to 4.4%). In addition, it is a collagen-binding protein of S. saprophyticus and the second example in this organism of a surface protein carrying the LPXTG motif. We constructed an isogenic sdrI knockout mutant that showed decreased binding to immobilized collagen compared with wild-type S. saprophyticus strain 7108. Binding could be reconstituted by complementation. Collagen binding is specifically caused by SdrI, and the recently described UafA protein, the only LPXTG-containing protein in the genome sequence of the type strain, is not involved in this trait. Our experiments suggest that, as in other staphylococci, the presence of different LPXTG-anchored cell wall proteins is common in S. saprophyticus and support the notion that the presence of matrix-binding surface proteins is common in staphylococci.

  15. Association of a truncated cytochrome c processed pseudogene with a similarly truncated member from a long interspersed repeat family of rat.

    PubMed Central

    Scarpulla, R C

    1985-01-01

    The cytochrome c multigene family of rat contains approximately 30 processed pseudogenes that represent genomic DNA copies of three alternate mRNAs. Here, the DNA sequence of an unusual processed pseudogene reveals that it has a complete 3' noncoding region including a short poly A tail but unlike the others is abruptly truncated at its 5' end, 19 amino acid codons from the translation terminator. At this position the pseudogene is fused through 17 consecutive adenylic acid residues to a 1.3 kb repetitive sequence. This repetitive element is flanked by direct repeats and represents a truncated member from a major long interspersed repeat family. The rat element is a composite of sequences observed in long interspersed repeats from both rodents and primates. Comparison to the equivalent mouse sequences shows that the 5' half of the repeat distal to the pseudogene has an open reading frame and is highly conserved whereas the half adjacent to the pseudogene is evolutionarily unstable. The proportion of cytochrome c pseudogene recombinant clones containing this repetitive DNA is 3 fold greater than observed in random isolates and may reflect a general tendency of processed pseudogenes to associate with other repetitive sequences in the genome. Images PMID:2987808

  16. Bone marrow mononuclear cells from patients with Paget's disease contain measles virus nucleocapsid messenger ribonucleic acid that has mutations in a specific region of the sequence.

    PubMed

    Reddy, S V; Singer, F R; Roodman, G D

    1995-07-01

    Ultrastructural, immunocytochemical, and in situ hybridization studies have suggested that paramyxoviruses, such as measles virus (MV), are present in Pagetic osteoclasts and may contribute to the abnormality in osteoclast function. However, little additional information is known about potential viruses present in Pagetic osteoclasts. As there are increased numbers of osteoclast precursors among the marrow mononuclear cells of Paget's patients, we used the reverse transcriptase-polymerase chain reaction to amplify the nucleocapsid sequence of MV from freshly isolated bone marrow-derived mononuclear cells to examine the potential role of these viruses in cells in the osteoclast lineage. We detected MV nucleocapsid transcripts in 5 of 6 individual Paget's patients' marrow samples. MV transcripts were not detected in marrow samples from 10 normal subjects. Sequence analysis of the PCR products revealed that 1 patient had the same sequence as the Edmonston strain of MV. The remaining 4 patients had point mutations clustered between position 1360-1371 base pairs. Two of the patients exhibited identical mutations at this region. In total, 3 different point mutations were identified that resulted in amino acid substitutions. These data show that 1) unlike those from normal subjects, marrow mononuclear cells from Paget's patients express MV nucleocapsid messenger ribonucleic acid; and 2) mutations of a specific region of the MV nucleocapsid gene were present in 4 of 5 patients and suggest a persistent MV infection in Pagetic osteoclast precursors. These data further suggest that osteoclasts are infected by fusion with infected precursors.

  17. A single amino acid in the stalk region of the H1N1pdm influenza virus HA protein affects viral fusion, stability and infectivity.

    PubMed

    Cotter, Christopher R; Jin, Hong; Chen, Zhongying

    2014-01-01

    The 2009 H1N1 pandemic (H1N1pdm) viruses have evolved to contain an E47K substitution in the HA2 subunit of the stalk region of the hemagglutinin (HA) protein. The biological significance of this single amino acid change was investigated by comparing A/California/7/2009 (HA2-E47) with a later strain, A/Brisbane/10/2010 (HA2-K47). The E47K change was found to reduce the threshold pH for membrane fusion from 5.4 to 5.0. An inter-monomer salt bridge between K47 in HA2 and E21 in HA1, a neighboring highly conserved residue, which stabilized the trimer structure, was found to be responsible for the reduced threshold pH for fusion. The higher structural and acid stability of the HA trimer caused by the E47K change also conferred higher viral thermal stability and infectivity in ferrets, suggesting a fitness advantage for the E47K evolutionary change in humans. Our study indicated that the pH of HA fusion activation is an important factor for influenza virus replication and host adaptation. The identification of this genetic signature in the HA stalk region that influences vaccine virus thermal stability also has significant implications for influenza vaccine production.

  18. Amino acid epimerization dating of Quaternary coastal deformation in SE Iberian Peninsula: The region between Aguas and Antas Rivers' mouths

    NASA Astrophysics Data System (ADS)

    Torres, Trinidad; Ortiz, José E.; Sánchez-Palencia, Yolanda

    2016-05-01

    The coastal area between the mouths of the Aguas and Antas Rivers presents a deformed system of raised marine deposits, some of which have been strongly affected by active tectonics. The use of amino acid epimerization dating of Glycymeris shells from raised coastal deposits allowed determining the age of these marine deposits, all of them linked to highstand sea levels in the Mediterranean realm, with ages between MIS 11 and MIS 1. These results allowed corroborating the age of some previously studied sites, and using new sampling sites, the general aminostratigraphy for the Quaternary raised marine deposits on the Mediterranean coast was confirmed. The main deformation event took place after MIS 11 and continued until MIS 5, and was linked to the activity of the Palomares Fault.

  19. Repeated Reading. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2014

    2014-01-01

    "Repeated reading" is an academic practice that aims to increase oral reading fluency. "Repeated reading" can be used with students who have developed initial word reading skills but demonstrate inadequate reading fluency for their grade level. During "repeated reading," a student sits in a quiet location with a…

  20. 47 CFR 22.1015 - Repeater operation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Repeater operation. 22.1015 Section 22.1015... Offshore Radiotelephone Service § 22.1015 Repeater operation. Offshore central stations may be used as repeater stations provided that the licensee is able to maintain control of the station, and in...

  1. Genomic distribution of simple sequence repeats in Brassica rapa.

    PubMed

    Hong, Chang Pyo; Piao, Zhong Yun; Kang, Tae Wook; Batley, Jacqueline; Yang, Tae-Jin; Hur, Yoon-Kang; Bhak, Jong; Park, Beom-Seok; Edwards, David; Lim, Yong Pyo

    2007-06-30

    Simple Sequence Repeats (SSRs) represent short tandem duplications found within all eukaryotic organisms. To examine the distribution of SSRs in the genome of Brassica rapa ssp. pekinensis, SSRs from different genomic regions representing 17.7 Mb of genomic sequence were surveyed. SSRs appear more abundant in non-coding regions (86.6%) than in coding regions (13.4%). Comparison of SSR densities in different genomic regions demonstrated that SSR density was greatest within the 5'-flanking regions of the predicted genes. The proportion of different repeat motifs varied between genomic regions, with trinucleotide SSRs more prevalent in predicted coding regions, reflecting the codon structure in these regions. SSRs were also preferentially associated with gene-rich regions, with peri-centromeric heterochromatin SSRs mostly associated with retrotransposons. These results indicate that the distribution of SSRs in the genome is non-random. Comparison of SSR abundance between B. rapa and the closely related species Arabidopsis thaliana suggests a greater abundance of SSRs in B. rapa, which may be due to the proposed genome triplication. Our results provide a comprehensive view of SSR genomic distribution and evolution in Brassica for comparison with the sequenced genomes of A. thaliana and Oryza sativa.

  2. [Distribution and evolution of simple repeats in the mtDNA D-loop in mammalian].

    PubMed

    Wei, Jin-Pu; Pan, Xue-Feng; Li, Hong-Quan; Duan, Fei

    2011-01-01

    Simple sequence repeats (SSR) distribute extensively in genomes of all organisms, but the molecular mechanism underlined is poorly understood. In this study, we characterized distribution and biological significance of the simple repetitive DNA sequences in the D-loop region in mitochondria DNA of 256 mammal species, and classified the mammal carriers into three groups including 53 species with hexanucleotide repeats, 104 species with other types of simple repeats (>6 bp) and 99 species without any repeat sequences, respectively. Furthermore, we found that the hexanucleotide repeats dispersed significantly in the interval space between CSB1 and CSB2, while other repeats dispersed mainly in the termination region, central conserved region and the conserve sequence block (CSB) regions. In addition, comparison on the base composition and the DNA contexts of the central conserved region, CSB1, CSB2, and CSB3 revealed a lack of significant differences in similarity among different species with or without repeat sequences. Moreover, a phylogenetic analysis with 256 mammal species using N-J method suggested loss of the repeat sequences in mammals in evolution.

  3. The cysteine-rich region and the whey acidic protein domain are essential for anosmin-1 biological functions.

    PubMed

    Esteban, Pedro F; Murcia-Belmonte, Verónica; García-González, Diego; de Castro, Fernando

    2013-03-01

    The protein anosmin-1, coded by the KAL1 gene responsible for the X-linked form of Kallmann syndrome (KS), exerts its biological effects mainly through the interaction with and signal modulation of fibroblast growth factor receptor 1 (FGFR1). We have previously shown the interaction of the third fibronectin-like type 3 (FnIII) domain and the N-terminal region of anosmin-1 with FGFR1. Here, we demonstrate that missense mutations reported in patients with KS, C172R and N267K did not alter or substantially reduce, respectively, the binding to FGFR1. These substitutions annulled the chemoattraction of the full-length protein over subventricular zone (SVZ) neuronal precursors (NPs), but they did not annul it in the N-terminal-truncated protein (A1Nt). We also show that although not essential for binding to FGFR1, the cysteine-rich (CR) region is necessary for anosmin-1 function and that FnIII.3 cannot substitute for FnIII.1 function. Truncated proteins recapitulating nonsense mutations found in KS patients did not show the chemotropic effect on SVZ NPs, suggesting that the presence behind FnIII.1 of any part of anosmin-1 produces an unstable protein incapable of action. We also identify the extracellular signal-regulated kinase 1/2 (ERK1/2) pathway as necessary for the chemotropic effect exerted by FGF2 and anosmin-1 on rat SVZ NPs.

  4. Regional characteristics of land use in Northeast and Southern Blue Ridge Province: Associations with acid rain effects on surface-water chemistry

    NASA Astrophysics Data System (ADS)

    Liegel, Leon; Cassell, David; Stevens, Donald; Shaffer, Paul; Church, Robbins

    1991-03-01

    The Direct/Delayed Response Project (DDRP) is one of several studies being conducted by the United States Environmental Protection Agency to assess risk to surface waters from acidic deposition in the eastern United States. In one phase of DDRP, land use, wetland, and forest cover data were collected for statistical samples of 145 Northeast lake and 35 Southern Blue Ridge Province stream watersheds in the United States. Land-use and other data then were extrapolated from individual to target watershed populations. Project statistical design allows summarization of results for various subsets of the target population. This article discusses results and implications of the land-use and land-cover characterization for both regions. Forest cover was the primary land use in both regions. In the Northeast, developed (agriculture and urban) land was positively associated with surface-water chemistry values for acid neutralizing capacity, Ca plus Mg, pH, and sulfate in the Pocono/Catskill subregion. Extensive wetlands and beaver activity occur in parts of the Northeast region, whereas topography limits wetland and riparian development in the Southern Blue Ridge Province. Northeast soils have low sulfate adsorption capacity, most watersheds are near sulfur steady state, and lake sulfate concentrations are controlled principally by levels of sulfur deposition. Net annual sulfur retention in Northeast watersheds is positively correlated with occurrence of wetlands and beaver impoundments. In contrast, most Southern Blue Ridge Province soils have high sulfate adsorption capacities, resulting in high net watershed sulfur retention. At the present time, stream sulfate concentrations and percent sulfur retention are controlled principally by soil chemical properties related to adsorption rather than atmospheric deposition and land use.

  5. The acidic amino-terminal region of herpes simplex virus type 1 alpha protein ICP27 is required for an essential lytic function.

    PubMed Central

    Rice, S A; Lam, V; Knipe, D M

    1993-01-01

    The herpes simplex virus type 1 (HSV-1) alpha protein ICP27 regulates the transition between the delayed-early and late phases of the viral infection. Previous genetic analyses have suggested that the important functional domains of ICP27 map to its carboxyl-terminal half. One striking feature of the primary sequence of ICP27, however, is an extremely acidic region near its amino terminus. To determine whether this region is required for ICP27 function, we deleted the sequences in the ICP27 gene which encode it (codons 12 through 63). In transien