Sample records for direct repeats flank

  1. Transposed genes in Arabidopsis are often associated with flanking repeats.

    Margaret R Woodhouse


    Full Text Available Much of the eukaryotic genome is known to be mobile, largely due to the movement of transposons and other parasitic elements. Recent work in plants and Drosophila suggests that mobility is also a feature of many nontransposon genes and gene families. Indeed, analysis of the Arabidopsis genome suggested that as many as half of all genes had moved to unlinked positions since Arabidopsis diverged from papaya roughly 72 million years ago, and that these mobile genes tend to fall into distinct gene families. However, the mechanism by which single gene transposition occurred was not deduced. By comparing two closely related species, Arabidopsis thaliana and Arabidopsis lyrata, we sought to determine the nature of gene transposition in Arabidopsis. We found that certain categories of genes are much more likely to have transposed than others, and that many of these transposed genes are flanked by direct repeat sequence that was homologous to sequence within the orthologous target site in A. lyrata and which was predominantly genic in identity. We suggest that intrachromosomal recombination between tandemly duplicated sequences, and subsequent insertion of the circular product, is the predominant mechanism of gene transposition.

  2. Germline mutations of STR-alleles include multi-step mutations as defined by sequencing of repeat and flanking regions.

    Dauber, Eva-Maria; Kratzer, Adelgunde; Neuhuber, Franz; Parson, Walther; Klintschar, Michael; Bär, Walter; Mayr, Wolfgang R


    Well defined estimates of mutation rates are a prerequisite for the use of short tandem repeat (STR-) loci in relationship testing. We investigated 65 isolated genetic inconsistencies, which were observed within 50,796 allelic transfers at 23 STR-loci (ACTBP2 (SE33), CD4, CSF1PO, F13A1, F13B, FES, FGA, vWA, TH01, TPOX, D2S1338, D3S1358, D5S818, D7S820, D8S1132, D8S1179, D12S391, D13S317, D16S539, D17S976, D18S51, D19S433, D21S11) in Caucasoid families residing in Austria and Switzerland. Sequencing data of repeat and flanking regions and the median of all theoretically possible mutational steps showed valuable information to characterise the mutational events with regard to parental origin, change of repeat number (mutational step size) and direction of mutation (losses and gains of repeats). Apart from predominant single-step mutations including one case with a double genetic inconsistency, two double-step and two apparent four-step mutations could be identified. More losses than gains of repeats and more mutations originating from the paternal than the maternal lineage were observed (31 losses, 22 gains, 12 losses or gains and 47 paternal, 11 maternal mutations and 7 unclear of parental origin). The mutation in the paternal germline was 3.3 times higher than in the maternal germline. The results of our study show, that apart from the vast majority of single-step mutations rare multi-step mutations can be observed. Therefore, the interpretation of mutational events should not rigidly be restricted to the shortest possible mutational step, because rare but true multi-step mutations can easily be overlooked, if haplotype analysis is not possible.

  3. Directionality switchable gain stabilized linear repeater

    Ota, Takayuki; Ohmachi, Tadashi; Aida, Kazuo


    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.

  4. Correlation of inter-locus polyglutamine toxicity with CAG•CTG triplet repeat expandability and flanking genomic DNA GC content.

    Colm E Nestor

    Full Text Available Dynamic expansions of toxic polyglutamine (polyQ-encoding CAG repeats in ubiquitously expressed, but otherwise unrelated, genes cause a number of late-onset progressive neurodegenerative disorders, including Huntington disease and the spinocerebellar ataxias. As polyQ toxicity in these disorders increases with repeat length, the intergenerational expansion of unstable CAG repeats leads to anticipation, an earlier age-at-onset in successive generations. Crucially, disease associated alleles are also somatically unstable and continue to expand throughout the lifetime of the individual. Interestingly, the inherited polyQ length mediating a specific age-at-onset of symptoms varies markedly between disorders. It is widely assumed that these inter-locus differences in polyQ toxicity are mediated by protein context effects. Previously, we demonstrated that the tendency of expanded CAG•CTG repeats to undergo further intergenerational expansion (their 'expandability' also differs between disorders and these effects are strongly correlated with the GC content of the genomic flanking DNA. Here we show that the inter-locus toxicity of the expanded polyQ tracts of these disorders also correlates with both the expandability of the underlying CAG repeat and the GC content of the genomic DNA flanking sequences. Inter-locus polyQ toxicity does not correlate with properties of the mRNA or protein sequences, with polyQ location within the gene or protein, or steady state transcript levels in the brain. These data suggest that the observed inter-locus differences in polyQ toxicity are not mediated solely by protein context effects, but that genomic context is also important, an effect that may be mediated by modifying the rate at which somatic expansion of the DNA delivers proteins to their cytotoxic state.

  5. DNA profiling of extended tracts of primitive DNA repeats: Direct identification of unstable simple repeat loci in complex genome

    Rogaeva, E.A.; Korovaitseva, G.; St. George-Hyslop, P. [Univ. of Toronto (Canada)] [and others


    The most simple DNA repetitive elements, with repetitive monomer units of only 1-10 bp in tandem tracts, are an abundant component of the human genome. The expansion of at least one type of these repeats ((CCG)n and (CTG)n) have been detected for a several neurological diseases with anticipation in successive generations. We propose here a simple method for the identification of particularly expanded repeats and for the recovery of flanking sequences. We generated DNA probes using PCR to create long concatamers (n>100) by amplification of the di-, tri-, tetra-, penta- and hexa-nucleotide repeat oligonucleotide primer pairs. To reduce the complexity of the background band pattern, the genomic DNA was restricted with a mixture of at least five different endonucleases, thereby reducing the size of restriction fragments containing short simple repeat arrays while leaving intact the large fragments containing the longer simple repeats arrays. Direct blot hybridization has shown different {open_quotes}DNA fingerprint{close_quotes} patterns with all arbitrary selected di-hexa nucleotide repeat probes. Direct hybridization of the (CTG)n and (CCG)n probes revealed simple or multiple band patterns depending upon stringency conditions. We were able to detect the presence of expanded unstable tri-nucleotide alleles by (CCG)n probe for some FRAXA subjects and by (CTG)n probe for some myotonic dystrophy subjects which were not present in the parental DNA patterns. The cloning of the unstable alleles for simple repeats can be performed by direct recover from agarose gels of the aberrant unstable bands detected above. The recovered flanking regions can be cloned, sequenced and used for PCR detection of expanded alleles or can be used to screen cDNA. This method may be used for testing of small families with diseases thought to display clinical evidence of anticipation.

  6. A Novel Variable Number of Tandem Repeat of the Natriuretic Peptide Precursor B gene's 5'-Flanking Region is Associated with Essential Hypertension among Japanese Females

    Kotoko Kosuge, Masayoshi Soma, Tomohiro Nakayama, Noriko Aoi, Mikano Sato, Yoichi Izumi, Koichi Matsumoto


    Full Text Available Background: Brain natriuretic peptide (BNP acts primarily as a cardiac hormone; it is produced by the ventricle and has both vasodilatory and natriuretic actions. Therefore, the BNP gene is thought to be a candidate gene for essential hypertension (EH. The present study identified variants in the 5'-flanking region of natriuretic peptide precursor B (NPPB gene and assessed the relationship between gene variants and EH. Methods: The polymerase chain reaction-single strand conformation polymorphism method and nucleotide sequencing were used to identify variants. Results: A novel variable number of tandem repeat (VNTR polymorphism in the 5'-flanking region (-1241 nucleotides from the major transcriptional initiation site was discovered. This VNTR polymorphism is a tandem repeat of the 4-nucleotide sequence TTTC. There were 8 alleles, ranging from 9-repeat to 19-repeat. An association study was done involving 317 EH patients and 262 age-matched normotensive (NT subjects. The 11-repeat allele was the most frequent (88.2%; the 16-repeat allele was the second most frequent (10.5% in the NT group. The observed and expected genotypes were in agreement with the predicted Hardy-Weinberg equilibrium values (P=0.972. Among females, the overall distribution of genotypes was significantly different between the EH and NT groups (p=0.039. The frequency of the 16-repeat allele was significantly lower in the female EH group (6.5% than in the female NT group (12.2%, p=0.046. Conclusions: The 16-repeat allele of the VNTR in the 5'-flanking region of NPPB appears to be a useful genetic marker of EH in females.

  7. Flank pain

    Pain - side; Side pain ... Flank pain can be a sign of a kidney problem. But, since many organs are in this area, other causes are possible. If you have flank pain and fever , chills, blood in the urine, or ...

  8. Copy number of tandem direct repeats within the inverted repeats of Marek's disease virus DNA.

    Kanamori, A; Nakajima, K; Ikuta, K; Ueda, S; Kato, S; Hirai, K


    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.

  9. Minimum length of direct repeat sequences required for efficient homologous recombination induced by zinc finger nuclease in yeast.

    Ren, ChongHua; Yan, Qiang; Zhang, ZhiYing


    Zinc finger nuclease (ZFN) technology is a powerful molecular tool for targeted genome modifications and genetic engineering. However, screening for specific ZFs and validation of ZFN activity are labor intensive and time consuming. We previously designed a yeast-based ZFN screening and validation system by inserting a ZFN binding site flanked by a 164 bp direct repeat sequence into the middle of a Gal4 transcription factor, disrupting the open reading frame of the yeast Gal4 gene. Expression of the ZFN causes a double stranded break at its binding site, which promotes the cellular DNA repair system to restore expression of a functional Gal transcriptional factor via homologous recombination. Expression of Gal4 transcription factor leads to activation of three reporter genes in an AH109 yeast two-hybrid strain. However, the 164 bp direct repeat appears to generate spontaneous homologous recombination frequently, resulting in many false positive ZFNs. To overcome this, a series of DNA fragments of various lengths from 10 to 150 bp with 10 bp increase each and 164 bp direct repeats flanking the ZFN binding site were designed and constructed. The results demonstrated that the minimum length required for ZFN-induced homologous recombination was 30 bp, which almost eliminated spontaneous recombination. Using the 30 bp direct repeat sequence, ZFN could efficiently induce homologous recombination, while false positive ZFNs resulting from spontaneous homologous recombination were minimized. Thus, this study provided a simple, fast and sensitive ZFN screening and activity validation system in yeast.

  10. Diagnosis of acute flank pain caused by ureteral stones: value of combined direct and indirect signs on IVU and unenhanced helical CT

    Wang, Li-Jen; Wong, Yon-Cheong [Department of Diagnostic Radiology, Chang Gung Memorial Hospital, Chang Gung University, 5, Fu-Hsing St., Gueishan, 33333, Taipei (Taiwan); Ng, Chip-Jin; Chen, Jih-Chang; Chiu, Te-Fa [Department of Emergency Medicine, Chang Gung Memorial Hospital, Chang Gung University, 5, Fu-Hsing St., Gueishan, 33333, Taipei (Taiwan)


    The aim of this study was to assess the usefulness of combined direct and indirect signs on intravenous urography (IVU) and unenhanced helical computed tomography (UHCT) for the diagnosis of ureteral stones in emergency patients with acute flank pain. During an 8-month period, 82 emergency patients with acute flank pain undergoing IVU and UHCT with sufficient clinical follow-up formed the study group. The presence or absence of direct sign (visualization of ureteral stones) and indirect signs on IVU and UHCT was recorded. The diagnostic accuracy of each direct/indirect sign and their combination for the diagnosis of ureteral stones on IVU and UHCT were analyzed and compared. Of the 82 patients, 66 had ureteral stones, four had passed urinary stones prior to imaging and 12 had other diseases. The diagnostic accuracies of direct signs on IVU and UHCT for the diagnosis of ureteral stones were 79.3 and 98.8%, respectively, which was more accurate than that of any single indirect sign on IVU and UHCT. However, the diagnostic accuracy of ureteral stones by IVU increased to 90.2% when using diagnostic criteria requiring the presence of a direct sign or at least three indirect signs, and by UHCT, it increased to 100% when using diagnostic criteria requiring the presence of a direct sign with at least one indirect sign. Therefore, for emergency patients with acute flank pain, the use of the above combinations of direct/indirect signs is useful as the diagnostic criterion for ureteral stones. (orig.)

  11. Repeated games and direct reciprocity under active linking.

    Pacheco, Jorge M; Traulsen, Arne; Ohtsuki, Hisashi; Nowak, Martin A


    Direct reciprocity relies on repeated encounters between the same two individuals. Here we examine the evolution of cooperation under direct reciprocity in dynamically structured populations. Individuals occupy the vertices of a graph, undergoing repeated interactions with their partners via the edges of the graph. Unlike the traditional approach to evolutionary game theory, where individuals meet at random and have no control over the frequency or duration of interactions, we consider a model in which individuals differ in the rate at which they seek new interactions. Moreover, once a link between two individuals has formed, the productivity of this link is evaluated. Links can be broken off at different rates. Whenever the active dynamics of links is sufficiently fast, population structure leads to a simple transformation of the payoff matrix, effectively changing the game under consideration, and hence paving the way for reciprocators to dominate defectors. We derive analytical conditions for evolutionary stability.

  12. Direct detection of expanded trinucleotide repeats using DNA hybridization techniques

    Petronis, A.; Tatuch, Y.; Kennedy, J.L. [Univ. of Toronto (Canada)] [and others


    Recently, unstable trinucleotide repeats have been shown to be the etiologic factor in several neuropsychiatric diseases, and they may play a similar role in other disorders. To our knowledge, a method that detects expanded trinucleotide sequences with the opportunity for direct localization and cloning has not been achieved. We have developed a set of hybridization-based methods for direct detection of unstable DNA expansion. Our analysis of myotonic dystrophy patients that possess different degrees of (CTG){sub n} expansion, versus unaffected controls, has demonstrated the identification of the trinucleotide instability site without any prior information regarding genetic map location. High stringency modified Southern blot hybridization with a PCR-generated trinucleotide repeat probe allowed us to detect the DNA fragment containing the expansion in myotonic dystrophy patients. The same probe was used for fluorescent in situ hybridization and several regions of (CTG){sub n}/(CAG){sub n} repeats in the human genome were detected, including the myotonic dystrophy locus on chromosome 19q. These strategies can be applied to directly clone genes involved in disorders caused by unstable DNA.

  13. Shadow enhancers flanking the HoxB cluster direct dynamic Hox expression in early heart and endoderm development.

    Nolte, Christof; Jinks, Tim; Wang, Xinghao; Martinez Pastor, María Teresa; Krumlauf, Robb


    The products of Hox genes function in assigning positional identity along the anterior-posterior body axis during animal development. In mouse embryos, Hox genes located at the 3' end of HoxA and HoxB complexes are expressed in nested patterns in the progenitors of the secondary heart field during early cardiogenesis and the combined activities of both of these clusters are required for proper looping of the heart. Using Hox bacterial artificial chromosomes (BACs), transposon reporters, and transgenic analyses in mice, we present the identification of several novel enhancers flanking the HoxB complex which can work over a long range to mediate dynamic reporter expression in the endoderm and embryonic heart during development. These enhancers respond to exogenously added retinoic acid and we have identified two retinoic acid response elements (RAREs) within these control modules that play a role in potentiating their regulatory activity. Deletion analysis in HoxB BAC reporters reveals that these control modules, spread throughout the flanking intergenic region, have regulatory activities that overlap with other local enhancers. This suggests that they function as shadow enhancers to modulate the expression of genes from the HoxB complex during cardiac development. Regulatory analysis of the HoxA complex reveals that it also has enhancers in the 3' flanking region which contain RAREs and have the potential to modulate expression in endoderm and heart tissues. Together, the similarities in their location, enhancer output, and dependence on retinoid signaling suggest that a conserved cis-regulatory cassette located in the 3' proximal regions adjacent to the HoxA and HoxB complexes evolved to modulate Hox gene expression during mammalian cardiac and endoderm development. This suggests a common regulatory mechanism, whereby the conserved control modules act over a long range on multiple Hox genes to generate nested patterns of HoxA and HoxB expression during

  14. Directional Cell Migration in Response to Repeated Substratum Stretching

    Okimura, Chika; Iwadate, Yoshiaki


    Crawling migration plays an essential role in a variety of biological phenomena, including development, wound healing, and immune system function. Migration properties such as anterior-posterior polarity, directionality, and velocity are regulated not only by the reception of a chemoattractant but also by sensing mechanical inputs from the external environment. In this review, we describe the mechanical response of migrating cells, particularly under repeated stretching of the elastic substratum, highlighting the fact that there appear to be two independent mechanosensing systems that generate the polarity needed for migration. Cells that have no stress fibers, such as Dictyostelium cells and neutrophil-like differentiated HL-60 cells, migrate perpendicular to the stretching direction via myosin II localization. Cells that do possess stress fibers, however, such as fish keratocytes, migrate parallel to the stretching via a stress-fiber-dependent process.

  15. Zinc-finger directed double-strand breaks within CAG repeat tracts promote repeat instability in human cells.

    Mittelman, David; Moye, Christopher; Morton, Jason; Sykoudis, Kristen; Lin, Yunfu; Carroll, Dana; Wilson, John H


    Expanded triplet repeats have been identified as the genetic basis for a growing number of neurological and skeletal disorders. To examine the contribution of double-strand break repair to CAG x CTG repeat instability in mammalian systems, we developed zinc finger nucleases (ZFNs) that recognize and cleave CAG repeat sequences. Engineered ZFNs use a tandem array of zinc fingers, fused to the FokI DNA cleavage domain, to direct double-strand breaks (DSBs) in a site-specific manner. We first determined that the ZFNs cleave CAG repeats in vitro. Then, using our previously described tissue culture assay for identifying modifiers of CAG repeat instability, we found that transfection of ZFN-expression vectors induced up to a 15-fold increase in changes to the CAG repeat in human and rodent cell lines, and that longer repeats were much more sensitive to cleavage than shorter ones. Analysis of individual colonies arising after treatment revealed a spectrum of events consistent with ZFN-induced DSBs and dominated by repeat contractions. We also found that expressing a dominant-negative form of RAD51 in combination with a ZFN, dramatically reduced the effect of the nuclease, suggesting that DSB-induced repeat instability is mediated, in part, through homology directed repair. These studies identify a ZFN as a useful reagent for characterizing the effects of DSBs on CAG repeats in cells.

  16. Direct evidence for a three-dimensional magnetic flux rope flanked by two active magnetic reconnection X lines at Earth's magnetopause.

    Øieroset, M; Phan, T D; Eastwood, J P; Fujimoto, M; Daughton, W; Shay, M A; Angelopoulos, V; Mozer, F S; McFadden, J P; Larson, D E; Glassmeier, K-H


    We report the direct detection by three THEMIS spacecraft of a magnetic flux rope flanked by two active X lines producing colliding plasma jets near the center of the flux rope. The observed density depletion and open magnetic field topology inside the flux rope reveal important three-dimensional effects. There was also evidence for nonthermal electron energization within the flux rope core where the fluxes of 1-4 keV superthermal electrons were higher than those in the converging reconnection jets. The observed ion and electron energizations differ from current theoretical predictions.

  17. Recombination frequency in plasmid DNA containing direct repeats--predictive correlation with repeat and intervening sequence length.

    Oliveira, Pedro H; Lemos, Francisco; Monteiro, Gabriel A; Prazeres, Duarte M F


    In this study, a simple non-linear mathematical function is proposed to accurately predict recombination frequencies in bacterial plasmid DNA harbouring directly repeated sequences. The mathematical function, which was developed on the basis of published data on deletion-formation in multicopy plasmids containing direct-repeats (14-856 bp) and intervening sequences (0-3872 bp), also accounts for the strain genotype in terms of its recA function. A bootstrap resampling technique was used to estimate confidence intervals for the correlation parameters. More than 92% of the predicted values were found to be within a pre-established +/-5-fold interval of deviation from experimental data. The correlation does not only provide a way to predict, with good accuracy, the recombination frequency, but also opens the way to improve insight into these processes.

  18. Repeated sprint ability in young basketball players: one vs. two changes of direction (Part 2).

    Attene, Giuseppe; Laffaye, Guillaume; Chaouachi, Anis; Pizzolato, Fabio; Migliaccio, Gian Mario; Padulo, Johnny


    The aim of this study was to compare the training effects based on repeated sprint ability (RSA) (with one change of direction) with an intensive repeated sprint ability (IRSA) (with two changes of direction) on jump performance and aerobic fitness. Eighteen male basketball players were assigned to repeated sprint ability and intensive repeated sprint ability training groups (RSAG and IRSAG). RSA, IRSA, squat jump (SJ), countermovement jump (CMJ) and Yo-Yo intermittent recovery level 1 test were assessed before and after four training weeks. The RSA and IRSA trainings consisted of three sets of six sprints (first two weeks) and eight sprints (second two weeks) with 4-min sets recovery and 20-s of sprints recovery. Four weeks of training led to an overall improvement in most of the measures of RSA, but little evidence of any differences between the two training modes. Jump performance was enhanced: CMJ of 7.5% (P repeated sprint training with one/two changes of direction promotes improvements in both RSA and IRSA respectively but the better increase on jump performance shown a few changes on sprint and endurance performances.

  19. Kearns-Sayre syndrome case presenting a mitochondrial DNA deletion with unusual direct repeats and a rudimentary RNAse mitochondria ribonucleotide processing target sequence

    Remes, A.M.; Hassinen, I.E. (Univ. of Oulu (Finland)); Peuhkurinen, K.J.; Herva, R.; Majamaa, K. (Oulu Univ. Central Hospital (Finland))


    A mitochondrial DNA deletion in a case of Kearns-Sayre syndrome is described. The deletion is bracketed by direct repeats that were unusual in that one of them was located 11--13 nucleotides from the deletion seam and both were conserved, which should not occur in slip replication or illegitimate elongation. The deleted region was demarcated on the deletion side by sequences that could be predicted to form hairpin structures. The 5[prime]-side of the deletion was flanked by a sequence homologous to a 9-nucleotide piece of the conserved sequence block II of the D-loop. This arrangement around the deletion in Kearns-Sayre syndrome bears some resemblance to the arrangement in the Pearson marrow- pancreas syndrome described by A. Rotig et al. (1991, Genomics 10: 502--504). 10 refs., 1 fig.

  20. Direct detection of expanded trinucleotide repeats using PCR and DNA hybridization techniques

    Petronis, A.; Tatuch, Y.; Klempan, T.A.; Kennedy, J.L. [Hospital for Sick Children, Toronto (Canada)] [and others


    Recently, unstable trinucleotide repeats have been shown to be the etiologic factor in seven neuropsychiatric diseases, and they may play a similar role in other genetic disorders which exhibit genetic anticipation. We have tested one polymerase chain reaction (PCR)-based and two hybridization-based methods for direct detection of unstable DNA expansion in genomic DNA. This technique employs a single primer (asymmetric) PCR using total genomic DNA as a template to efficiently screen for the presence of large trinucleotide repeat expansions. High-stringency Southern blot hybridization with a PCR-generated trinucleotide repeat probe allowed detection of the DNA fragment containing the expansion. Analysis of myotonic dystrophy patients containing different degrees of (CTG){sub n} expansion demonstrated the identification of the site of trinucleotide instability in some affected individuals without any prior information regarding genetic map location. The same probe was used for fluorescent in situ hybridization and several regions of (CTG){sub n}/(CAG){sub n} repeats in the human genome were detected, including the myotonic dystrophy locus on chromosome 19q. Although limited at present to large trinucleotide repeat expansions, these strategies can be applied to directly clone genes involved in disorders caused by large expansions of unstable DNA. 33 refs., 4 figs.

  1. Re-directing CD4+ T cell responses with the flanking residues of MHC class II-bound peptides: the core is not enough

    David Kenneth Cole


    Full Text Available Recombinant αβ T cell receptors (TCRs recognise short peptides presented at the cell surface in complex with MHC molecules. There are two main subsets of αβ T cells: CD8+ T cells that recognise mainly cytosol-derived peptides in the context of MHC class I (pMHC-I, and CD4+ T cells that recognise peptides usually derived from exogenous proteins presented by MHC class II (pMHC-II. Unlike the more uniform peptide lengths (usually 8-13mers bound in the MHC-I closed groove, MHC-II presented peptides are of a highly variable length. The bound peptides consist of a core bound 9mer (reflecting the binding motif for the particular MHC-II type but with variable peptide flanking residues (PFRs that can extend from both the N- and C-terminus of the MHC-II binding groove. Although pMHC-I and pMHC-II play a virtually identical role during T cell responses (T cell antigen presentation and are very similar in overall conformation, there exist a number of subtle but important differences that may govern the functional dichotomy observed between CD8+ and CD4+ T cells. Here, we provide an overview of the impact of structural differences between pMHC-I and pMHC-II and the molecular interactions with the TCR including the functional importance of MHC-II peptide flanking residues. We consider how factors such as anatomical location, inflammatory milieu and particular types of APC might, in theory, contribute to the quantitative (i.e. pMHC ligand frequency as well as qualitative (i.e. variable PFR nature of peptide epitopes, and hence offer a means of control and influence of a CD4+ T cell response. Lastly, we review our recent findings showing how modifications to these flanking regions modify CD4+ T cell antigen recognition. These findings may have novel applications for the development of CD4+ T cell peptide vaccines and diagnostics.

  2. Control of PHERES1 Imprinting in Arabidopsis by Direct Tandem Repeats

    Corina Belle R.Villar; Aleksandra Erilova; Grigory Makarevich; Raphael Tr(o)sch; Claudia K(o)hler


    Genomic imprinting is an epigenetic phenomenon that causes monoallelic expression of specific genes dependent on the parent-of-origin.Imprinting of the Arabiclopsis gene PHERES1 requires the function of the FERTILIZATION INDEPENDENT SEED (FIS) Polycomb group complex as well as a distally located methylated region containing a tandem triple repeat sequence.In this study,we investigated the regulation of the close PHERES1 homolog PHERES2.We found that PHERES2 is also a direct target gene of the FIS Polycomb group complex,but,in contrast to PHERES1,PHERES2 is equally expressed from maternal and paternal alleles.Thus,PHERES2 is not regulated by genomic imprinting,correlating with the lack of tandem repeats at PHERES2.Eliminating tandem repeats from the PHERES1 locus abolishes PHERES1 imprinting,demonstrating that tandem repeats are essential for PHERES1 imprinting.Taking these results together,our study shows that the recently duplicated genes PHERES1 and PHERES2 are both target genes of the FIS Polycomb group complex but only PHERES1 is regulated by genomic imprinting,which is likely caused by the presence of repeat sequences in the proximity of the PHERES1 locus.

  3. Repeated transcranial direct current stimulation prevents abnormal behaviors associated with abstinence from chronic nicotine consumption.

    Pedron, Solène; Monnin, Julie; Haffen, Emmanuel; Sechter, Daniel; Van Waes, Vincent


    Successful available treatments to quit smoking remain scarce. Recently, the potential of transcranial direct current stimulation (tDCS) as a tool to reduce craving for nicotine has gained interest. However, there is no documented animal model to assess the neurobiological mechanisms of tDCS on addiction-related behaviors. To address this topic, we have developed a model of repeated tDCS in mice and used it to validate its effectiveness in relieving nicotine addiction. Anodal repeated tDCS was applied over the frontal cortex of Swiss female mice. The stimulation electrode (anode) was fixed directly onto the cranium, and the reference electrode was placed onto the ventral thorax. A 2 × 20 min/day stimulation paradigm for five consecutive days was used (0.2 mA). In the first study, we screened for behaviors altered by the stimulation. Second, we tested whether tDCS could alleviate abnormal behaviors associated with abstinence from nicotine consumption. In naive animals, repeated tDCS had antidepressant-like properties 3 weeks after the last stimulation, improved working memory, and decreased conditioned place preference for nicotine without affecting locomotor activity and anxiety-related behavior. Importantly, abnormal behaviors associated with chronic nicotine exposure (ie, depression-like behavior, increase in nicotine-induced place preference) were normalized by repeated tDCS. Our data show for the first time in an animal model that repeated tDCS is a promising, non-expensive clinical tool that could be used to reduce smoking craving and facilitate smoking cessation. Our animal model will be useful to investigate the mechanisms underlying the effects of tDCS on addiction and other psychiatric disorders.

  4. Microsatellites grant more stable flanking genes

    Joukhadar Reem


    Full Text Available Abstract Background Microsatellites, or simple sequence repeats (SSRs, are DNA sequences that include tandem copies of specific sequences no longer than six bases. SSRs are ubiquitous in all genomes and highly mutable. Presentation of the hypothesis Results from previous studies suggest that flanking regions of SSR are exhibit high stability in a wide range of organisms. We hypothesized that the SSRs ability to discard weak DNA polymerases could be responsible for this unusual stability. . When the weak polymerases are being decayed over SSRs, the flanking sequences would have higher opportunity to be replicated by more stable DNA polymerases. We present evidence of the molecular basis of our hypothesis. Testing the hypothesis The hypothesis could be tested by examining the activity of DNA polymerase during and after a number of PCRs. The PCR reactions should be run with the same SSR locus possessing differences in the SSR length. The hypothesis could also be tested by comparing the mutational rate of a transferred gene between two transformations. The first one has a naked T-DNA (transferred DNA, while the second one has the same T-DNA flanked with two SSRs. Implications of the hypothesis In any transformation experiment, flanking the T-DNA fragment with SSR sequences would result in more stably transferred genes. This process would decrease the unpredictable risks that may occur because of the mutational pressure on this foreign segment.

  5. Large Direct Repeats Flank Genomic Rearrangements between a New Clinical Isolate of Francisella tularensis subsp. tularensis A1 and Schu S4


    Author Contributions Conceived and designed the experiments: UN KS SHH PDF. Performed the experiments: UN KS RDB GX TSB PDF. Analyzed the data: UN KS RDB...GX TSB SHH PDF. Contributed reagents/materials/analysis tools: UN MPD PCI SCF RDB GX TSB SHH PDF. Wrote the paper: UN KS SHH PDF. References 1. Farlow

  6. The P-SSP7 cyanophage has a linear genome with direct terminal repeats.

    Sabehi, Gazalah; Lindell, Debbie


    P-SSP7 is a T7-like phage that infects the cyanobacterium Prochlorococcus MED4. MED4 is a member of the high-light-adapted Prochlorococcus ecotypes that are abundant in the surface oceans and contribute significantly to primary production. P-SSP7 has become a model system for the investigation of T7-like phages that infect Prochlorococcus. It was classified as T7-like based on genome content and organization. However, because its genome assembled as a circular molecule, it was thought to be circularly permuted and to lack the direct terminal repeats found in other T7-like phages. Here we sequenced the ends of the P-SSP7 genome and found that the genome map is linear and contains a 206 bp repeat at both genome ends. Furthermore, we found that a 728 bp region of the genome originally placed downstream of the last ORF is actually located upstream of the first ORF on the genome map. These findings suggest that P-SSP7 is likely to use the direct terminal repeats for genome replication and packaging in a similar manner to other T7-like phages. Moreover, these results highlight the importance of experimentally verifying the ends of phage genomes, and will facilitate the use of P-SSP7 as a model for the correct assembly and end determination of the many T7-like phages isolated from the marine environment that are currently being sequenced.

  7. The P-SSP7 cyanophage has a linear genome with direct terminal repeats.

    Gazalah Sabehi

    Full Text Available P-SSP7 is a T7-like phage that infects the cyanobacterium Prochlorococcus MED4. MED4 is a member of the high-light-adapted Prochlorococcus ecotypes that are abundant in the surface oceans and contribute significantly to primary production. P-SSP7 has become a model system for the investigation of T7-like phages that infect Prochlorococcus. It was classified as T7-like based on genome content and organization. However, because its genome assembled as a circular molecule, it was thought to be circularly permuted and to lack the direct terminal repeats found in other T7-like phages. Here we sequenced the ends of the P-SSP7 genome and found that the genome map is linear and contains a 206 bp repeat at both genome ends. Furthermore, we found that a 728 bp region of the genome originally placed downstream of the last ORF is actually located upstream of the first ORF on the genome map. These findings suggest that P-SSP7 is likely to use the direct terminal repeats for genome replication and packaging in a similar manner to other T7-like phages. Moreover, these results highlight the importance of experimentally verifying the ends of phage genomes, and will facilitate the use of P-SSP7 as a model for the correct assembly and end determination of the many T7-like phages isolated from the marine environment that are currently being sequenced.

  8. Orientation of Sandhoppers Under Natural Conditions in Repeated Trials: an Analysis Using Longitudinal Directional Data

    D'elia, A.; Borgioli, C.; Scapini, F.


    Zonal recovery is a prompt escape towards the sea performed by sandhoppers under stressful environmental conditions. Differences in habitat features, meteorological conditions during the tests and morphological characteristics of the individuals are all factors affecting orientation. This paper deals with the temporal variation of the orientation of a sandhopper sample, taking into account the effect of some environmental and morphological variables on these changes. The directions chosen by single animals in repeated trials under natural conditions were analysed, using longitudinal circular data. The longitudinal analysis highlights several details about three different kinds of intrapopulation variation due to: sun, wind and eye left/right asymmetry. A clear link between the successive directional responses is demonstrated as well as modulation of behaviour with time: the animals stabilise orientation towards a certain direction in successive trials. The use of longitudinal sets of data in orientation studies produces a good synthesis of directional behaviour, due to several advantages of this kind of analysis. These include the fact that the association between successive behaviours and variability through repeated trials is taken into account; a progressive improvement, due to the integration of information from previous experiences, can be detected; the role of the main cues and factors affecting orientation is more accurately defined; and more parsimonious statistical models can be used to fit the data.

  9. Repeated sprint ability in young basketball players: one vs. two changes of direction (Part 1).

    Padulo, Johnny; Laffaye, Guillaume; Haddad, Monoem; Chaouachi, Anis; Attene, Giuseppe; Migliaccio, Gian Mario; Chamari, Karim; Pizzolato, Fabio


    The present study aimed to compare the changes of direction on repeated sprint ability (RSA) vs. intensive repeated sprint ability (IRSA) protocols in basketball. Eighteen young male basketball players performed on RSA [10 × 30-m (15 + 15-m, one change of direction)] and IRSA [10 × 30-m (10 + 10 + 10-m, two changes of direction)]. A correlation matrix between RSA, IRSA, "squat jump (SJ)-countermovement jump (CMJ)", footstep analysis and total distance in Yo-Yo intermittent recovery level 1 was performed. The best time, worst time, total time and the number of footsteps were significantly smaller in the RSA test compared to IRSA test (P  0.80, P  0.478, P  0.515, P  0.489, P basketball game's actions (~2 s). Besides, IRSA could be an appropriate choice for assessing both RSA and changes of direction capacities in basketball players.

  10. Repeated sprint ability in young basketball players: multi-direction vs. one-change of direction (Part 1

    Johnny ePadulo


    Full Text Available The aim of the present study was to examine the reliability of a novel multi-direction repeated sprint ability test (RSM; 10×(6×5-m compared with a repeated sprint ability test (RSA with one change of direction (10×(2×15-m, and the relationship of the RSM and RSA with Yo-Yo intermittent recovery test level 1 (Yo-Yo IR1 and jump performances [squat jump (SJ and counter-movement-jump (CMJ]. Thirty-six (male, n=14, female n=22 young basketball players (age 16.0±0.9 yrs performed the RSM, RSA, Yo-Yo IR1, SJ and CMJ, and were re-tested only for RSM and RSA after one week. The absolute error of reliability (standard error of the measurement was lower than 0.212-s and 0.617-s for the time variables of the RSA and RSM test, respectively. Performance in the RSA and RSM test significantly correlated with CMJ and SJ. The best time, worst time and total time of the RSA and RSM test were negatively correlated with Yo-Yo IR1 distance. Based on these findings, consistent with previously published studies, it was concluded that the novel RSM test was valid and reliable.

  11. Re-Directing CD4(+) T Cell Responses with the Flanking Residues of MHC Class II-Bound Peptides: The Core is Not Enough.

    Holland, Christopher J; Cole, David K; Godkin, Andrew


    Recombinant αβ T cell receptors, expressed on T cell membranes, recognize short peptides presented at the cell surface in complex with MHC molecules. There are two main subsets of αβ T cells: CD8(+) T cells that recognize mainly cytosol-derived peptides in the context of MHC class I (pMHC-I), and CD4(+) T cells that recognize peptides usually derived from exogenous proteins presented by MHC class II (pMHC-II). Unlike the more uniform peptide lengths (usually 8-13mers) bound in the MHC-I closed groove, MHC-II presented peptides are of a highly variable length. The bound peptides consist of a core bound 9mer (reflecting the binding motif for the particular MHC-II type) but with variable peptide flanking residues (PFRs) that can extend from both the N- and C-terminus of the MHC-II binding groove. Although pMHC-I and pMHC-II play a virtually identical role during T cell responses (T cell antigen presentation) and are very similar in overall conformation, there exist a number of subtle but important differences that may govern the functional dichotomy observed between CD8(+) and CD4(+) T cells. Here, we provide an overview of the impact of structural differences between pMHC-I and pMHC-II and the molecular interactions with the T cell receptor including the functional importance of MHC-II PFRs. We consider how factors such as anatomical location, inflammatory milieu, and particular types of antigen presenting cell might, in theory, contribute to the quantitative (i.e., pMHC ligand frequency) as well as qualitative (i.e., variable PFR) nature of peptide epitopes, and hence offer a means of control and influence of a CD4(+) T cell response. Lastly, we review our recent findings showing how modifications to MHC-II PFRs can modify CD4(+) T cell antigen recognition. These findings may have novel applications for the development of CD4(+) T cell peptide vaccines and diagnostics.

  12. Single-step blood direct PCR: A robust and rapid method to diagnose triplet repeat disorders.

    Singh, Inder; Swarup, Vishnu; Shakya, Sunil; Goyal, Vinay; Faruq, Mohammed; Srivastava, Achal Kumar


    DNA extraction prior to polymerase chain reaction (PCR) amplification in genetic diagnoses of triplet repeat disorders (TRDs) is tedious and labour-intensive and has the limitations of sample contamination with foreign DNA, including that from preceding samples. Therefore, we aimed to develop a rapid, robust, and cost-effective method for expeditious genetic investigation of TRDs from whole blood as a DNA template. Peripheral blood samples were collected from 70 clinically suspected patients of progressive ataxia. The conventional method using genomic DNA and single-step Blood-Direct PCR (BD-PCR) method with just 2μl of whole blood sample were tested to amplify triplet repeat expansion in genes related to spinocerebellar ataxia (SCA) types 1, 2, 3, 12 and Friedreich's ataxia (FRDA). Post-PCR, the allele sizes were mapped and repeat numbers were calculated using GeneMapper and macros run in Microsoft Excel programmes. Successful amplification of target regions was achieved in all samples by both methods. The frequency of the normal and mutated allele was concordant between both methods, diagnosing 37% positive for a mutation in either of the candidate genes. The BD-PCR resulted in higher intensities of product peaks of normal and pathogenic alleles. The nearly-accurate sizing of the normal and expanded allele was achieved in a shorter time (4-5h), without DNA extraction and any risk of cross contamination, which suggests the BD-PCR to be a reliable, inexpensive, and rapid method to confirm TRDs. This technique can be introduced in routine diagnostic procedures of other tandem repeat disorders. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Evidence of sheared sills related to flank destabilization in a basaltic volcano

    Berthod, C.; Famin, V.; Bascou, J.; Michon, L.; Ildefonse, B.; Monié, P.


    Piton des Neiges basaltic volcano (La Réunion) has been deeply dissected by erosion, exposing large volumes of debris avalanche deposits. To shed light on the factors that led to volcano flank destabilizations, we studied the structure, the crystallographic and magnetic fabrics of the substratum of a debris avalanche unit. This substratum is a complex of > 50 seaward-dipping sills that has been exposed by the avalanche. Structural observations show that the sill plane in contact with the avalanche is one of the latest intrusions in the sill complex. In this uppermost sill, the anisotropy of magnetic susceptibility (AMS) is correlated to the crystallographic preferred orientation of magmatic silicate minerals, allowing us to use AMS as a proxy to infer the magmatic flow. The AMS fabric across the intrusion is strongly asymmetric, which reveals that the contact sill was emplaced with a normal shear displacement of its hanging wall. The shear displacement and the magma flow in the intrusion are both directed toward the NNE, i.e. toward the sea, which is also the direction of the slope and of the debris avalanche runout. Because all the sills in the intrusion complex have a similar dip and dip direction, it is likely that several of them also underwent a cointrusive slip toward the NNE. We conclude that this cointrusive normal slip, repeated over many intrusions of the sill complex, increased the flank instability of the volcano. This incremental instability may have ended up into the observed debris avalanche deposit. At Piton de la Fournaise, the active volcano of La Réunion, sill intrusion and cointrusive flank displacement have been inferred from geophysical studies for the April 2007 eruption. By providing direct evidence of sheared sills, our study substantiates the idea that repeated sill intrusions may eventually trigger flank destabilizations in basaltic volcanoes.

  14. Functional and histologic changes after repeated transcranial direct current stimulation in rat stroke model.

    Kim, Sang Jun; Kim, Byeong Kwon; Ko, Young Jin; Bang, Moon Suk; Kim, Man Ho; Han, Tai Ryoon


    Transcranial direct current stimulation (tDCS) is associated with enhancement or weakening of the NMDA receptor activity and change of the cortical blood flow. Therefore, repeated tDCS of the brain with cerebrovascular injury will induce the functional and histologic changes. Sixty-one Sprague-Dawley rats with cerebrovascular injury were used. Twenty rats died during the experimental course. The 41 rats that survived were allocated to the exercise group, the anodal stimulation group, the cathodal stimulation group, or the control group according to the initial motor function. Two-week treatment schedules started from 2 days postoperatively. Garcia, modified foot fault, and rota-rod performance scores were checked at 2, 9, and 16 days postoperatively. After the experiments, rats were sacrificed for the evaluation of histologic changes (changes of the white matter axon and infarct volume). The anodal stimulation and exercise groups showed improvement of Garcia's and modified foot fault scores at 16 days postoperatively. No significant change of the infarct volume happened after exercise and tDCS. Neuronal axons at the internal capsule of infarct hemispheres showed better preserved axons in the anodal stimulation group. From these results, repeated tDCS might have a neuroprotective effect on neuronal axons in rat stroke model.

  15. A model of human nasal epithelial cells adapted for direct and repeated exposure to airborne pollutants.

    Bardet, Gaëlle; Achard, Sophie; Loret, Thomas; Desauziers, Valérie; Momas, Isabelle; Seta, Nathalie


    Airway epithelium lining the nasal cavity plays a pivotal role in respiratory tract defense and protection mechanisms. Air pollution induces alterations linked to airway diseases such as asthma. Only very few in vitro studies to date have succeeded in reproducing physiological conditions relevant to cellular type and chronic atmospheric pollution exposure. We therefore, set up an in vitro model of human Airway Epithelial Cells of Nasal origin (hAECN) close to real human cell functionality, specifically adapted to study the biological effects of exposure to indoor gaseous pollution at the environmental level. hAECN were exposed under air-liquid interface, one, two, or three-times at 24 h intervals for 1 h, to air or formaldehyde (200 μg/m(3)), an indoor air gaseous pollutant. All experiments were ended at day 4, when both cellular viability and cytokine production were assessed. Optimal adherence and confluence of cells were obtained 96 h after cell seeding onto collagen IV-precoated insert. Direct and repeated exposure to formaldehyde did not produce any cellular damage or IL-6 production change, although weak lower IL-8 production was observed only after the third exposure. Our model is significantly better than previous ones due to cell type and the repeated exposure protocol.

  16. Repeated Sprint Ability in Young Basketball Players: Multi-direction vs. One-Change of Direction (Part 1).

    Padulo, Johnny; Bragazzi, Nicola L; Nikolaidis, Pantelis T; Dello Iacono, Antonio; Attene, Giuseppe; Pizzolato, Fabio; Dal Pupo, Juliano; Zagatto, Alessandro M; Oggianu, Marcello; Migliaccio, Gian M


    The aim of the present study was to examine the reliability of a novel multi-direction repeated sprint ability (RSA) test [RSM; 10 × (6 × 5-m)] compared with a RSA with one change of direction [10 × (2 × 15-m)], and the relationship of the RSM and RSA with Yo-Yo intermittent recovery test level 1 (Yo-Yo IR1) and jump performances [squat jump (SJ) and counter-movement-jump (CMJ)]. Thirty-six (male, n = 14, female n = 22) young basketball players (age 16.0 ± 0.9 yrs) performed the RSM, RSA, Yo-Yo IR1, SJ, and CMJ, and were re-tested only for RSM and RSA after 1 week. The absolute error of reliability (standard error of the measurement) was lower than 0.212 and 0.617-s for the time variables of the RSA and RSM test, respectively. Performance in the RSA and RSM test significantly correlated with CMJ and SJ. The best time, worst time, and total time of the RSA and RSM test were negatively correlated with Yo-Yo IR1 distance. Based on these findings, consistent with previously published studies, it was concluded that the novel RSM test was valid and reliable.

  17. Role of reciprocal exchange, one-ended invasion crossover and single-strand annealing on inverted and direct repeat recombination in yeast: Different requirements for the RAD1, RAD 10, and RAD52 genes

    Prado, F.; Aguilera, A. [Universidad de Sevilla (Spain)


    We have constructed novel DNA substrates (one inverted and three direct repeats) based on the same 0.6-kb repeat sequence to study deletions and inversions in Saccharomyces cerevisiae. Spontaneous deletions occur six to eight times more frequently than inversions, irrespective of the distance between the repeats. This difference can be explained by the observation that deletion events can be mediated by a recombination mechanism that can initiate within the intervening sequence of the repeats. Spontaneous and double-strand break (DSB)-induced deletions occur as RAD52-dependent and RAD52-independent events. Those deletion events initiated through a DSB in the unique intervening sequence require the Rad1/Rad10 endonuclease only if the break is distantly located from the flanking DNA repeats. We propose that deletions can occur as three types of recombination events: the conservative RAD52-dependent reciprocal exchange and the nonconservative events, one-ended invasion crossover, and single-strand annealing (SSA). We suggest that one-ended invasion is RAD52 dependent, whereas SSA is RAD52 independent. Whereas deletions, like inversions, occur through reciprocal exchange, deletions can also occur through SSA or one-ended invasion. We propose that the contribution of reciprocal exchange and one-ended invasion crossover vs. SSA events to overall spontaneous deletions is a feature specific for each repeat system, determined by the initiation event and the availability of the Rad52 protein. We discuss the role of the Rad1/Rad10 endonuclease on the initial steps of one-ended invasion crossover and SSA as a function of the location of the initiation event relative to the repeats. We also show that the frequency of recombination between repeats is the same independent of their location (whether on circular plasmids, linear minichromosomes, or natural chromosomes) and have similar RAD52 dependence. 74 refs., 5 figs., 6 tabs.

  18. Aberrant splicing in transgenes containing introns, exons, and V5 epitopes: lessons from developing an FSHD mouse model expressing a D4Z4 repeat with flanking genomic sequences.

    Eugénie Ansseau

    Full Text Available The DUX4 gene, encoded within D4Z4 repeats on human chromosome 4q35, has recently emerged as a key factor in the pathogenic mechanisms underlying Facioscapulohumeral muscular dystrophy (FSHD. This recognition prompted development of animal models expressing the DUX4 open reading frame (ORF alone or embedded within D4Z4 repeats. In the first published model, we used adeno-associated viral vectors (AAV and strong viral control elements (CMV promoter, SV40 poly A to demonstrate that the DUX4 cDNA caused dose-dependent toxicity in mouse muscles. As a follow-up, we designed a second generation of DUX4-expressing AAV vectors to more faithfully genocopy the FSHD-permissive D4Z4 repeat region located at 4q35. This new vector (called AAV.D4Z4.V5.pLAM contained the D4Z4/DUX4 promoter region, a V5 epitope-tagged DUX4 ORF, and the natural 3' untranslated region (pLAM harboring two small introns, DUX4 exons 2 and 3, and the non-canonical poly A signal required for stabilizing DUX4 mRNA in FSHD. AAV.D4Z4.V5.pLAM failed to recapitulate the robust pathology of our first generation vectors following delivery to mouse muscle. We found that the DUX4.V5 junction sequence created an unexpected splice donor in the pre-mRNA that was preferentially utilized to remove the V5 coding sequence and DUX4 stop codon, yielding non-functional DUX4 protein with 55 additional residues on its carboxyl-terminus. Importantly, we further found that aberrant splicing could occur in any expression construct containing a functional splice acceptor and sequences resembling minimal splice donors. Our findings represent an interesting case study with respect to AAV.D4Z4.V5.pLAM, but more broadly serve as a note of caution for designing constructs containing V5 epitope tags and/or transgenes with downstream introns and exons.

  19. "Pseudo-Beijing": evidence for convergent evolution in the direct repeat region of Mycobacterium tuberculosis.

    Lukas Fenner

    Full Text Available BACKGROUND: Mycobacterium tuberculosis has a global population structure consisting of six main phylogenetic lineages associated with specific geographic regions and human populations. One particular M. tuberculosis genotype known as "Beijing" has repeatedly been associated with drug resistance and has been emerging in some parts of the world. "Beijing" strains are traditionally defined based on a characteristic spoligotyping pattern. We used three alternative genotyping techniques to revisit the phylogenetic classification of M. tuberculosis complex (MTBC strains exhibiting the typical "Beijing" spoligotyping pattern. METHODS AND FINDINGS: MTBC strains were obtained from an ongoing molecular epidemiological study in Switzerland and Nepal. MTBC genotyping was performed based on SNPs, genomic deletions, and 24-loci MIRU-VNTR. We identified three MTBC strains from patients originating from Tibet, Portugal and Nepal which exhibited a spoligotyping patterns identical to the classical Beijing signature. However, based on three alternative molecular markers, these strains were assigned to Lineage 3 (also known as Delhi/CAS rather than to Lineage 2 (also known as East-Asian lineage. Sequencing of the RD207 in one of these strains showed that the deletion responsible for this "Pseudo-Beijing" spoligotype was about 1,000 base pairs smaller than the usual deletion of RD207 in classical "Beijing" strains, which is consistent with an evolutionarily independent deletion event in the direct repeat (DR region of MTBC. CONCLUSIONS: We provide an example of convergent evolution in the DR locus of MTBC, and highlight the limitation of using spoligotypes for strain classification. Our results indicate that a proportion of "Beijing" strains may have been misclassified in the past. Markers that are more phylogenetically robust should be used when exploring strain-specific differences in experimental or clinical phenotypes.

  20. Integrated study to define the hazard of the unstable flanks of Mt. Etna: the Italian DPC-INGV FLANK Project

    Acocella, Valerio; Puglisi, Giuseppe


    Volcanoes are often characterized by unstable flanks. The eastern and south-eastern flanks of Mt. Etna (Italy) have shown repeated evidence of instability in the recent past. The extent and frequency of these processes varies widely, from nearly continuous creep-like movements of specific portions of the flank to the rarer slip of the entire eastern sector, involving also the off-shore portion. Estimated slip rates may vary enormously, from mm/yr to m/week. The most dramatic instability events are associated with major eruptions and shallow seismic activity, as during 2002-2003, posing a serious hazard to the inhabited flanks of the volcano. The Italian Department of Civil Defense (DPC), with the National Institute of Geophysics and Volcanology (INGV), as well as with the involvement of Italian Universities and other Research Institutes, has launched a 2-years project (may 2008-may 2010) devoted to minimize the hazard deriving from the instability of the Etna flanks. This multidisciplinary project embraces geological, geophysical, volcanological, modeling and hazard studies, both on the on-shore and the off-shore portions of the E and SE flanks of the volcano. Indeed, the main aims are to define: (a) the 3D geometry of the collapsing sector(s); (b) the relationships between flank movement and volcanic and seismic activity; (c) the hazard related to the flank instability. The collected data populate a GIS database implemented according the WoVo rules. This project represents the first attempt, at least in Europe, to use an integrated approach to minimize the hazard deriving from flank instability in a volcano. Here we briefly summarize the state of the art of the project at an advanced stage, highlighting the path of the different Tasks, as well as the main results.

  1. Direct Repeat Unit (dru) Typing of Methicillin-Resistant Staphylococcus pseudintermedius from Dogs and Cats.

    Kadlec, Kristina; Schwarz, Stefan; Goering, Richard V; Weese, J Scott


    Methicillin-resistant Staphylococcus pseudintermedius (MRSP) has emerged in a remarkable manner as an important problem in dogs and cats. However, limited molecular epidemiological information is available. The aims of this study were to apply direct repeat unit (dru) typing in a large collection of well-characterized MRSP isolates and to use dru typing to analyze a collection of previously uncharacterized MRSP isolates. Two collections of MRSP isolates from dogs and cats were included in this study. The first collection comprised 115 well-characterized MRSP isolates from North America and Europe. The data for these isolates included multilocus sequence typing (MLST) and staphylococcal protein A gene (spa) typing results as well as SmaI macrorestriction patterns after pulsed-field gel electrophoresis (PFGE). The second collection was a convenience sample of 360 isolates from North America. The dru region was amplified by PCR, sequenced, and analyzed. For the first collection, the discriminatory indices of the typing methods were calculated. All isolates were successfully dru typed. The discriminatory power for dru typing (D = 0.423) was comparable to that of spa typing (D = 0.445) and of MLST (D = 0.417) in the first collection. Occasionally, dru typing was able to further discriminate between isolates that shared the same spa type. Among all 475 isolates, 26 different dru types were identified, with 2 predominant types (dt9a and dt11a) among 349 (73.4%) isolates. The results of this study underline that dru typing is a useful tool for MRSP typing, being an objective, standardized, sequence-based method that is relatively cost-efficient and easy to perform.

  2. HOT1 is a mammalian direct telomere repeat-binding protein contributing to telomerase recruitment

    Kappei, D.; Butter, F.; Benda, C.; Scheibe, M.; Draskovic, Irena; Stevense, M.; Novo, C.L.; Basquin, C.; Araki, M.; Araki, K.; Krastev, D.B.; Kittler, R.; Jessberger, R.; Londono-Vallejo, J.A.; Mann, M.; Buchholz, F.


    Telomeres are repetitive DNA structures that, together with the shelterin and the CST complex, protect the ends of chromosomes. Telomere shortening is mitigated in stem and cancer cells through the de novo addition of telomeric repeats by telomerase. Telomere elongation requires the delivery of the

  3. Genome-wide stochastic adaptive DNA amplification at direct and inverted DNA repeats in the parasite Leishmania.

    Jean-Michel Ubeda


    Full Text Available Gene amplification of specific loci has been described in all kingdoms of life. In the protozoan parasite Leishmania, the product of amplification is usually part of extrachromosomal circular or linear amplicons that are formed at the level of direct or inverted repeated sequences. A bioinformatics screen revealed that repeated sequences are widely distributed in the Leishmania genome and the repeats are chromosome-specific, conserved among species, and generally present in low copy number. Using sensitive PCR assays, we provide evidence that the Leishmania genome is continuously being rearranged at the level of these repeated sequences, which serve as a functional platform for constitutive and stochastic amplification (and deletion of genomic segments in the population. This process is adaptive as the copy number of advantageous extrachromosomal circular or linear elements increases upon selective pressure and is reversible when selection is removed. We also provide mechanistic insights on the formation of circular and linear amplicons through RAD51 recombinase-dependent and -independent mechanisms, respectively. The whole genome of Leishmania is thus stochastically rearranged at the level of repeated sequences, and the selection of parasite subpopulations with changes in the copy number of specific loci is used as a strategy to respond to a changing environment.

  4. Genome-wide stochastic adaptive DNA amplification at direct and inverted DNA repeats in the parasite Leishmania.

    Ubeda, Jean-Michel; Raymond, Frédéric; Mukherjee, Angana; Plourde, Marie; Gingras, Hélène; Roy, Gaétan; Lapointe, Andréanne; Leprohon, Philippe; Papadopoulou, Barbara; Corbeil, Jacques; Ouellette, Marc


    Gene amplification of specific loci has been described in all kingdoms of life. In the protozoan parasite Leishmania, the product of amplification is usually part of extrachromosomal circular or linear amplicons that are formed at the level of direct or inverted repeated sequences. A bioinformatics screen revealed that repeated sequences are widely distributed in the Leishmania genome and the repeats are chromosome-specific, conserved among species, and generally present in low copy number. Using sensitive PCR assays, we provide evidence that the Leishmania genome is continuously being rearranged at the level of these repeated sequences, which serve as a functional platform for constitutive and stochastic amplification (and deletion) of genomic segments in the population. This process is adaptive as the copy number of advantageous extrachromosomal circular or linear elements increases upon selective pressure and is reversible when selection is removed. We also provide mechanistic insights on the formation of circular and linear amplicons through RAD51 recombinase-dependent and -independent mechanisms, respectively. The whole genome of Leishmania is thus stochastically rearranged at the level of repeated sequences, and the selection of parasite subpopulations with changes in the copy number of specific loci is used as a strategy to respond to a changing environment.

  5. Isolation of human minisatellite loci detected by synthetic tandem repeat probes: direct comparison with cloned DNA fingerprinting probes.

    Armour, J A; Vergnaud, G; Crosier, M; Jeffreys, A J


    As a direct comparison with cloned 'DNA fingerprinting' probes, we present the results of screening an ordered array Charomid library for hypervariable human loci using synthetic tandem repeat (STR) probes. By recording the coordinates of positive hybridization signals, the subset of clones within the library detected by each STR probe can be defined, and directly compared with the set of clones detected by naturally occurring (cloned) DNA fingerprinting probes. The STR probes vary in the efficiency of detection of polymorphic minisatellite loci; among the more efficient probes, there is a strong overlap with the sets of clones detected by the DNA fingerprinting probes. Four new polymorphic loci were detected by one or more of the STR probes but not by any of the naturally occurring repeats. Sequence comparisons with the probe(s) used to detect the locus suggest that a relatively poor match, for example 10 out of 14 bases in a limited region of each repeat, is sufficient for the positive detection of tandem repeats in a clone in this type of library screening by hybridization. These results not only provide a detailed evaluation of the usefulness of STR probes in the isolation of highly variable loci, but also suggest strategies for the use of these multi-locus probes in screening libraries for clones from hypervariable loci.

  6. Accuracy and repeatability of direct ciliary sulcus diameter measurements by full-scale 50-megahertz ultrasound biomicroscopy

    LI De-jiao; WANG Ning-li; CHEN Shu; LI Shu-ning; MU Da-peng; WANG Tao


    Background Phakic intraocular lens (pIOL) implantation has been a popular means for the treatment of high ametropia. Measurements of ciliary sulcus diameter is important for pIOL size determining. But till now, no perfect system can directly measure it. The present study was to evaluate the accuracy, repeatability and reproducibility of direct sulcus diameter measurements obtained by a full-scale 50-megahertz (MHz) ultrasound biomicroscopy (UBM).Methods A fresh cadaver human eye with a scale marker inserted through the posterior chamber plane from 3 o'clock to 9 o'clock meridian and 30 randomly selected eyes from 30 normal subjects were scanned by full-scale 50-MHz UBM in horizontal meridional scan plane. The distance between the scales and the whole length of the marker inside the cadaver eye were measured by the same observer using the "built-in" measurement tools and the indicating error of instrument was calculated. Reproducibility of the measurement was evaluated in 30 eyes by 2 operators using Blander and Altman plot test. Repeatability was evaluated from 10 successive eyes randomly selected from the 30 eyes by one operator.Results On a scale of 1 mm, the greatest indicating error was 40 μm; the mean largest indicating error of 1 mm scale from the 10 images was (26±14) μm; on a scale of 11 mm, the greatest indicating error was 70 μo; the error rate was 0.64%. The mean length of the needle inside the eye of the 10 images was 11.05 mm, with the mean indicating error of 47 μm, the average error rate was 0.43%. For ciliary sulcus diameter measurements in vivo, the coefficient of variation was 0.38%; the coefficients of repeatability for intra-observer and inter-observer measurements were 1.99% and 2.55%, respectively. The limits of agreement for intra-observer and inter-observer measurement were-0.41 mm to 0.48 mm and -0.59 mm to 0.58 ram, respectively.Conclusion The full-scale 50-MHz UBM can be a high accuracy and good repeatability means for direct

  7. Direct comparison of repeated soil inventory and carbon flux budget to detect soil carbon stock changes in grassland

    Ammann, C.; Leifeld, J.; Neftel, A.; Fuhrer, J.


    Experimental assessment of soil carbon (C) stock changes over time is typically based on the application of either one of two methods, namely (i) repeated soil inventory and (ii) determination of the ecosystem C budget or net biome productivity (NBP) by continuous measurement of CO2 exchange in combination with quantification of other C imports and exports. However, there exist hardly any published study hitherto that directly compared the results of both methods. Here, we applied both methods in parallel to determine C stock changes of two temperate grassland fields previously converted from long-term cropland. The grasslands differed in management intensity with either intensive management (high fertilization, frequent cutting) or extensive management (no fertilization, less frequent cutting). Soil organic C stocks (0-45 cm depth) were quantified at the beginning (2001) and the end (2006) of a 5 year observational period using the equivalent soil mass approach. For the same period and in both fields, NBP was quantified from net CO2 fluxes monitored using eddy covariance systems, and measured C import by organic fertilizer and C export by harvest. Both NBP and repeated soil inventories revealed a consistent and significant difference between management systems of 170 ± 48 and 253 ± 182 g C m-2 a-1, respectively. For both fields, the inventory method showed a tendency towards higher C loss/smaller C gain than NBP. In the extensive field, a significant C loss was observed by the inventory but not by the NBP approach. Thus both, flux measurements and repeated soil sampling, seem to be adequate and equally suited for detecting relative management effects. However, the suitability for tracking absolute changes in SOC could not be proven for neither of the two methods. Overall, our findings stress the need for more direct comparisons to evaluate whether the observed difference in the outcome of the two approaches reflects a general methodological bias, which would

  8. The development of behavioral and endocrine abnormalities in rats after repeated exposure to direct and indirect stress.

    Daniels, Willie Mark Uren; de Klerk Uys, Joachim; van Vuuren, Petra; Stein, Daniel Joseph


    The present study compared the effects of direct and indirect stress on the behavior and hypothalamic-pituitary-adrenal axis of rats. Animals were placed in a two compartment box. In one compartment the direct stressed rat was subjected to electric foot shocks randomly applied for 10 minutes (0.5 mA of 1 s duration). In the adjacent compartment, the indirect stressed rats witnessed the application of these electric foot shocks. Our data showed substantial behavioral changes in the open field test, but limited effects in the elevated plus maze. The findings suggested that single and repeated stress exposure may have different consequences, that the effects of stress exposure may develop over time and persist for an extended period, and that both direct and indirect stressed rats displayed a hyposensitive HPA axis following acute restraint stress. Overall our observations moderately indicate direct exposure to elicit behavioral changes, and both direct and indirect exposure to stress to result in aberrations within the neuroendocrine system. With additional development our stress models may be considered for studying the complex interrelationship between an external stressor, and the experience of the organism.

  9. Repeated Thermal Stress, Shading, and Directional Selection in the Florida Reef Tract

    Robert van Woesik


    Full Text Available Over the last three decades reef corals have been subjected to an unprecedented frequency and intensity of thermal-stress events, which have led to extensive coral bleaching, disease, and mortality. Over the next century, the climate is predicted to drive sea-surface temperatures to even higher levels, consequently increasing the risk of mass bleaching and disease outbreaks. Yet, there is considerable temporal and spatial variation in coral bleaching and in disease prevalence. Using data collected from 2,398 sites along the Florida reef tract from 2005 to 2015, this study examined the temporal and spatial patterns of coral bleaching and disease in relation to coral-colony size, depth, temperature, and chlorophyll-a concentrations. The results show that coral bleaching was most prevalent during the warmest years in 2014 and 2015, and disease was also most prevalent in 2010, 2014, and 2015. Although the majority of the corals surveyed were found in habitats with low chlorophyll-a concentrations, and high irradiance, these same habitats showed the highest prevalence of coral bleaching and disease outbreaks during thermal-stress events. These results suggest that directional selection in a warming ocean may favor corals able to tolerate inshore, shaded environments with high turbidity and productivity.

  10. Repeated sessions of transcranial direct current stimulation evaluation on fatigue and daytime sleepiness in Parkinson's disease.

    Forogh, Bijan; Rafiei, Maryam; Arbabi, Amin; Motamed, Mohammad Reza; Madani, Seyed Pezhman; Sajadi, Simin


    Parkinson is a common and disabling disease that affects patient's and career's quality of life. Unfortunately, medications, such as dopaminergic and sedative-hypnotic drugs, as an effective treatment have unwilling side effects. Recently, Transcranial Direct Current Stimulation (tDCS) in conjunction with medication becomes popular as a complementary safe treatment and several studies have proved its effectiveness on controlling motor and specially non-motor aspects of Parkinson's disease. In this randomized double-blind parallel study, 23 patients with Parkinson's disease divided into two groups of real tDCS plus occupational therapy and sham tDCS plus occupational therapy and the effects of therapeutic sessions (eight sessions tDCS with 0.06 mA/cm(2) current, 20 min on dorsolateral prefrontal cortex) were evaluated on fatigue and daytime sleepiness just after therapeutic course and in 3-month follow-up. tDCS had a significant effect on fatigue and no effect on daytime sleepiness reduction in patients with Parkinson's disease. tDCS is an effective and safe complementary treatment on fatigue reduction in Parkinson's disease.

  11. The Interaction of Polyglutamine Peptides with Lipid Membranes Is Regulated by Flanking Sequences Associated with Huntingtin*

    Burke, Kathleen A.; Kauffman, Karlina J.; Umbaugh, C. Samuel; Frey, Shelli L.; Legleiter, Justin


    Huntington disease (HD) is caused by an expanded polyglutamine (poly(Q)) repeat near the N terminus of the huntingtin (htt) protein. Expanded poly(Q) facilitates formation of htt aggregates, eventually leading to deposition of cytoplasmic and intranuclear inclusion bodies containing htt. Flanking sequences directly adjacent to the poly(Q) domain, such as the first 17 amino acids on the N terminus (Nt17) and the polyproline (poly(P)) domain on the C-terminal side of the poly(Q) domain, heavily influence aggregation. Additionally, htt interacts with a variety of membraneous structures within the cell, and Nt17 is implicated in lipid binding. To investigate the interaction between htt exon1 and lipid membranes, a combination of in situ atomic force microscopy, Langmuir trough techniques, and vesicle permeability assays were used to directly monitor the interaction of a variety of synthetic poly(Q) peptides with different combinations of flanking sequences (KK-Q35-KK, KK-Q35-P10-KK, Nt17-Q35-KK, and Nt17-Q35-P10-KK) on model membranes and surfaces. Each peptide aggregated on mica, predominately forming extended, fibrillar aggregates. In contrast, poly(Q) peptides that lacked the Nt17 domain did not appreciably aggregate on or insert into lipid membranes. Nt17 facilitated the interaction of peptides with lipid surfaces, whereas the poly(P) region enhanced this interaction. The aggregation of Nt17-Q35-P10-KK on the lipid bilayer closely resembled that of a htt exon1 construct containing 35 repeat glutamines. Collectively, this data suggests that the Nt17 domain plays a critical role in htt binding and aggregation on lipid membranes, and this lipid/htt interaction can be further modulated by the presence of the poly(P) domain. PMID:23572526

  12. Direct and inverted repeats elicit genetic instability by both exploiting and eluding DNA double-strand break repair systems in mycobacteria.

    Ewelina A Wojcik

    Full Text Available Repetitive DNA sequences with the potential to form alternative DNA conformations, such as slipped structures and cruciforms, can induce genetic instability by promoting replication errors and by serving as a substrate for DNA repair proteins, which may lead to DNA double-strand breaks (DSBs. However, the contribution of each of the DSB repair pathways, homologous recombination (HR, non-homologous end-joining (NHEJ and single-strand annealing (SSA, to this sort of genetic instability is not fully understood. Herein, we assessed the genome-wide distribution of repetitive DNA sequences in the Mycobacterium smegmatis, Mycobacterium tuberculosis and Escherichia coli genomes, and determined the types and frequencies of genetic instability induced by direct and inverted repeats, both in the presence and in the absence of HR, NHEJ, and SSA. All three genomes are strongly enriched in direct repeats and modestly enriched in inverted repeats. When using chromosomally integrated constructs in M. smegmatis, direct repeats induced the perfect deletion of their intervening sequences ~1,000-fold above background. Absence of HR further enhanced these perfect deletions, whereas absence of NHEJ or SSA had no influence, suggesting compromised replication fidelity. In contrast, inverted repeats induced perfect deletions only in the absence of SSA. Both direct and inverted repeats stimulated excision of the constructs from the attB integration sites independently of HR, NHEJ, or SSA. With episomal constructs, direct and inverted repeats triggered DNA instability by activating nucleolytic activity, and absence of the DSB repair pathways (in the order NHEJ>HR>SSA exacerbated this instability. Thus, direct and inverted repeats may elicit genetic instability in mycobacteria by 1 directly interfering with replication fidelity, 2 stimulating the three main DSB repair pathways, and 3 enticing L5 site-specific recombination.

  13. Role of direct repeat and stem-loop motifs in mtDNA deletions: cause or coincidence?

    Lakshmi Narayanan Lakshmanan

    Full Text Available Deletion mutations within mitochondrial DNA (mtDNA have been implicated in degenerative and aging related conditions, such as sarcopenia and neuro-degeneration. While the precise molecular mechanism of deletion formation in mtDNA is still not completely understood, genome motifs such as direct repeat (DR and stem-loop (SL have been observed in the neighborhood of deletion breakpoints and thus have been postulated to take part in mutagenesis. In this study, we have analyzed the mitochondrial genomes from four different mammals: human, rhesus monkey, mouse and rat, and compared them to randomly generated sequences to further elucidate the role of direct repeat and stem-loop motifs in aging associated mtDNA deletions. Our analysis revealed that in the four species, DR and SL structures are abundant and that their distributions in mtDNA are not statistically different from randomized sequences. However, the average distance between the reported age associated mtDNA breakpoints and their respective nearest DR motifs is significantly shorter than what is expected of random chance in human (p10 bp tend to decrease with increasing lifespan among the four mammals studied here, further suggesting an evolutionary selection against stable mtDNA misalignments associated with long DRs in long-living animals. In contrast to the results on DR, the probability of finding SL motifs near a deletion breakpoint does not differ from random in any of the four mtDNA sequences considered. Taken together, the findings in this study give support for the importance of stable mtDNA misalignments, aided by long DRs, as a major mechanism of deletion formation in long-living, but not in short-living mammals.


    Brunskog, Jonas; Lhomond, Alice; Ohlrich, Mogens


    In this paper the attenuation and flanking transmissions of impact noise in lightweight building structures is studied using a modal approach. The structural field is mainly analysed, putting the main attention to the parts being important in the modelling. The amount of attenuation produced...... by the periodically reinforcing beams used in lightweight building structures is analysed. The consequence of these factors in modelling flanking transmission is also discussed....

  15. Effects of leg contrast strength training on sprint, agility and repeated change of direction performance in male soccer players.

    Hammami, Mehréz; Negra, Yassine; Shephard, Roy J; Chelly, Mohamed-Souhaiel


    Contrast training is a popular technique among individuals who are involved in dynamic sports, having as its goal an increase in dynamic muscular performance. It is characterized by the use of high and low loads in the same strength training session. The present investigation aimed to determine the effects of adding 8 weeks of contrast strength training (CSTP) to regular soccer practice in U-17 male soccer players during the competitive season. We hypothesized that CSTP would enhance their performance. Subjects were divided randomly between a control group (CG, N.=12) and a contrast strength group (CSG, N.=19). The 2 groups trained together; controls followed the regular soccer program, which was replaced by a contrast strength training program for the experimental group. Performance was assessed before and after training, using 10 measures: 5-10-, 20- 30-, and 40-m sprints, a 4x5 m sprint (S4x5), a 9-3-6-3-9 m sprint with 180° turns (S180), a 9-3-6-3-9 m sprint with backward and forward running (SBF), a Repeated-Shuttle-Sprint Ability Test (RSSA), and a Repeated Change of Direction Test (RCOD). CSG showed gains relative to controls in 5-m (Psprints. There were also significant gains in S180°, SBF, and S4 x 5 agility tests (P<0.01), and all RCOD parameters (P<0.05) except RCOD-FI (P=0.055) but no significant change in any RSSA parameters. We conclude that biweekly contrast strength training can be commended to U-17 male soccer players as a means of improving many important components of athletic performance relative to standard in-season training.

  16. Identification of polymorphic tandem repeats by direct comparison of genome sequence from different bacterial strains : a web-based resource

    Vergnaud Gilles


    Full Text Available Abstract Background Polymorphic tandem repeat typing is a new generic technology which has been proved to be very efficient for bacterial pathogens such as B. anthracis, M. tuberculosis, P. aeruginosa, L. pneumophila, Y. pestis. The previously developed tandem repeats database takes advantage of the release of genome sequence data for a growing number of bacteria to facilitate the identification of tandem repeats. The development of an assay then requires the evaluation of tandem repeat polymorphism on well-selected sets of isolates. In the case of major human pathogens, such as S. aureus, more than one strain is being sequenced, so that tandem repeats most likely to be polymorphic can now be selected in silico based on genome sequence comparison. Results In addition to the previously described general Tandem Repeats Database, we have developed a tool to automatically identify tandem repeats of a different length in the genome sequence of two (or more closely related bacterial strains. Genome comparisons are pre-computed. The results of the comparisons are parsed in a database, which can be conveniently queried over the internet according to criteria of practical value, including repeat unit length, predicted size difference, etc. Comparisons are available for 16 bacterial species, and the orthopox viruses, including the variola virus and three of its close neighbors. Conclusions We are presenting an internet-based resource to help develop and perform tandem repeats based bacterial strain typing. The tools accessible at now comprise four parts. The Tandem Repeats Database enables the identification of tandem repeats across entire genomes. The Strain Comparison Page identifies tandem repeats differing between different genome sequences from the same species. The "Blast in the Tandem Repeats Database" facilitates the search for a known tandem repeat and the prediction of amplification product sizes. The "Bacterial

  17. Abundant intergenic TAACTGA direct repeats and putative alternate RNA polymerase β´ subunits in marine Beggiatoaceae genomes: possible regulatory roles and origins

    Barbara J. MacGregor


    Full Text Available The genome sequences of several giant marine sulfur-oxidizing bacteria present evidence of a possible post-transcriptional regulatory network that may have been transmitted to or from two distantly related bacteria lineages. The draft genome of a Cand. Maribeggiatoa filament from the Guaymas Basin (Gulf of California, Mexico seafloor contains 169 sets of TAACTGA direct repeats and one indirect repeat, with two to six copies per set. Related heptamers are rarely or never found as direct repeats. TAACTGA direct repeats are also found in some other Beggiatoaceae, Thiocystis violascens, a range of Cyanobacteria, and five Bacteroidetes. This phylogenetic distribution suggests they may have been transmitted horizontally, but no mechanism is evident. There is no correlation between total TAACTGA occurrences and repeats per genome. In most species the repeat units are relatively short, but longer arrays of up to 43 copies are found in several Bacteroidetes and Cyanobacteria. The majority of TAACTGA repeats in the Cand. Maribeggiatoa Orange Guaymas (BOGUAY genome are within several nucleotides upstream of a putative start codon, suggesting they may be binding sites for a post-transcriptional regulator. Candidates include members of the ribosomal protein S1, Csp (cold shock protein, and Csr (carbon storage regulator families. No pattern was evident in the predicted functions of the open reading frames (ORFs downstream of repeats, but some encode presumably essential products such as ribosomal proteins. Among these is an ORF encoding a possible alternate or modified RNA polymerase beta prime subunit, predicted to have the expected subunit interaction domains but lacking most catalytic residues. A similar ORF was found in the Thioploca ingrica draft genome, but in no others. In both species they are immediately upstream of putative sensor kinase genes with nearly identical domain structures. In the marine Beggiatoaceae, a role for the TAACTGA repeats in

  18. Colored neon flanks and line gap enhancement.

    Redies, C; Spillmann, L; Kunz, K


    When a colored line connects two black (or differently colored) lines across a gap, colored neon flanks are seen on either side of it. These flanks extend over gap sizes of 50 min arc foveally and are not explained by Bezold-type assimilation. They may be elicited by black lines as short as 6 min arc adjoining the colored line at each end. To maximize these flanks, the black and colored lines must appear linearly continuous. Nonaligned junctions weaken the effect and an angular tilt of more than 40 dog destroys it. In this and other respects, (local) neon flanks are similar to van Tuijl's (global) neon color spreading (1975). Both phenomena have analogs in brightness perception. We propose that neon spreading is a lateral extension of neon flanks across the empty space between them, and discuss similarities of these effects with other brightness illusions (Schumann, Prandtl, Ehrenstein). For this group of illusions the term "line gap enhancement" is introduced to imply perceptual enhancement of changes in brightness and/or color along lines. Correspondences between the psychophysical properties and structural prerequisites for line gap enhancement on one hand and neuronal response properties of end-zone inhibited (hypercomplex) cortical cells on the other are discussed.

  19. Direct repeat unit (dru) typing and antimicrobial resistance of methicillin-resistant Staphylococcus pseudintermedius isolated from dogs in Atlantic Canada.

    Saab, Matthew E; Weese, J Scott; McClure, J T


    There are few reports investigating the characterization of methicillin-resistant Staphylococcus pseudintermedius (MRSP) in dogs in Canada and none from Atlantic Canada. The objectives of this study were to strain type MRSP isolates cultured at a regional diagnostic laboratory using direct repeat unit (dru) typing and to describe their antimicrobial resistance profiles. Ninety-four isolates recovered from dogs between 2010 and 2012 had dru typing, cluster analysis, and antimicrobial susceptibility testing done. The majority of isolates belonged to type dt11a (30.9%), dt10h (24.5%), dt9a (18.1%), and dt11af (10.6%) with the remaining 15.9% of isolates distributed among 13 dru types. The predominant dru types identified were similar in Ontario; however, cluster 9a appears to be less common in Atlantic Canada. A significant difference in the distribution of clusters among Atlantic provinces was detected (P = 0.01). Resistance to ≥ 2 non-β-lactam antimicrobials was observed in 71.4% of the isolates. The MRSP isolates from this study were notably less resistant than those reported in the literature. A more comprehensive study of the MRSP dru types could help further elucidate the distribution of this pathogen in Canada.

  20. Direct and accurate measurement of CAG repeat configuration in the ataxin-1 (ATXN-1) gene by "dual-fluorescence labeled PCR-restriction fragment length analysis".

    Lin, Jiang X; Ishikawa, Kinya; Sakamoto, Masaki; Tsunemi, Taiji; Ishiguro, Taro; Amino, Takeshi; Toru, Shuta; Kondo, Ikuko; Mizusawa, Hidehiro


    Spinocerebellar ataxia type 1 (SCA1; OMIM: #164400) is an autosomal dominant cerebellar ataxia caused by an expansion of CAG repeat, which encodes polyglutamine, in the ataxin-1 (ATXN1) gene. Length of polyglutamine in the ATXN1 protein is the critical determinant of pathogenesis of this disease. Molecular diagnosis of SCA1 is usually undertaken by assessing the length of CAG repeat configuration using primers spanning this configuration. However, this conventional method may potentially lead to misdiagnosis in assessing polyglutamine-encoding CAG repeat length, since CAT interruptions may be present within the CAG repeat configuration, not only in normal controls but also in neurologically symptomatic subjects. We developed a new method for assessing actual CAG repeat numbers not interrupted by CAT sequences. Polymerase chain reaction using a primer pair labeled with two different fluorescences followed by restriction enzyme digestion with SfaNI which recognizes the sequence "GCATC(N)(5)", lengths of actual CAG repeats that encode polyglutamine were directly detected. We named this method "dual fluorescence labeled PCR-restriction fragment length analysis". We found that numbers of actual CAG repeat encoding polyglutamine do not overlap between our cohorts of normal chromosomes (n=385) and SCA1 chromosomes (n=5). We conclude that the present method is a useful way for molecular diagnosis of SCA1.

  1. A method for amplification of unknown flanking sequences based on touchdown PCR and suppression-PCR.

    Gao, Song; He, Dan; Li, Guangquan; Zhang, Yanhua; Lv, Huiying; Wang, Li


    Thermal asymmetric staggered PCR is the most widely used technique to obtain the flanking sequences. However, it has some limitations, including a low rate of positivity, and complex operation. In this study, a improved method of it was made based on suppression-PCR and touchdown PCR. The PCR fragment obtained by the amplification was used directly for sequencing after gel purification. Using this improved method, the positive rate of amplified flanking sequences of the ATMT mutants reached 99%. In addition, the time from DNA extraction to flanking sequence analysis was shortened to 2 days with about 6 dollars each sample.

  2. A Direct Interaction between Leucine-rich Repeat Kinase 2 and Specific β-Tubulin Isoforms Regulates Tubulin Acetylation*

    Law, Bernard M. H.; Spain, Victoria A.; Leinster, Veronica H. L.; Chia, Ruth; Beilina, Alexandra; Cho, Hyun J.; Taymans, Jean-Marc; Urban, Mary K.; Sancho, Rosa M.; Ramírez, Marian Blanca; Biskup, Saskia; Baekelandt, Veerle; Cai, Huaibin; Cookson, Mark R.; Berwick, Daniel C.; Harvey, Kirsten


    Mutations in LRRK2, encoding the multifunctional protein leucine-rich repeat kinase 2 (LRRK2), are a common cause of Parkinson disease. LRRK2 has been suggested to influence the cytoskeleton as LRRK2 mutants reduce neurite outgrowth and cause an accumulation of hyperphosphorylated Tau. This might cause alterations in the dynamic instability of microtubules suggested to contribute to the pathogenesis of Parkinson disease. Here, we describe a direct interaction between LRRK2 and β-tubulin. This interaction is conferred by the LRRK2 Roc domain and is disrupted by the familial R1441G mutation and artificial Roc domain mutations that mimic autophosphorylation. LRRK2 selectively interacts with three β-tubulin isoforms: TUBB, TUBB4, and TUBB6, one of which (TUBB4) is mutated in the movement disorder dystonia type 4 (DYT4). Binding specificity is determined by lysine 362 and alanine 364 of β-tubulin. Molecular modeling was used to map the interaction surface to the luminal face of microtubule protofibrils in close proximity to the lysine 40 acetylation site in α-tubulin. This location is predicted to be poorly accessible within mature stabilized microtubules, but exposed in dynamic microtubule populations. Consistent with this finding, endogenous LRRK2 displays a preferential localization to dynamic microtubules within growth cones, rather than adjacent axonal microtubule bundles. This interaction is functionally relevant to microtubule dynamics, as mouse embryonic fibroblasts derived from LRRK2 knock-out mice display increased microtubule acetylation. Taken together, our data shed light on the nature of the LRRK2-tubulin interaction, and indicate that alterations in microtubule stability caused by changes in LRRK2 might contribute to the pathogenesis of Parkinson disease. PMID:24275654

  3. Reverse time migration of prism waves for salt flank delineation

    Dai, Wei


    In this paper, we present a new reverse time migration method for imaging salt flanks with prism wave reflections. It consists of four steps: (1) migrating the seismic data with conventional RTM to give the RTM image; (2) using the RTM image as a reflectivity model to simulate source-side reflections with the Born approximation; (3) zero-lag correlation of the source-side reflection wavefields and receiver-side wavefields to produce the prism wave migration image; and (4) repeating steps 2 and 3 for the receiver-side reflections. An advantage of this method is that there is no need to pick the horizontal reflectors prior to migration of the prism waves. It also separately images the vertical structures at a different step to reduce crosstalk interference. The disadvantage of prism wave migration algorithm is that its computational cost is twice that of conventional RTM. The empirical results with a salt model suggest that prism wave migration can be an effective method for salt flank delineation in the absence of diving waves.

  4. CAG repeat polymorphism in androgen receptor gene is not directly associated with polycystic ovary syndrome but influences serum testosterone levels.

    Skrgatic, L; Baldani, D Pavicic; Cerne, J Z; Ferk, P; Gersak, K


    Hyperandrogenemia has been the most consistent feature of polycystic ovary syndrome (PCOS). Androgens exert their effects through androgen receptors (ARs). The expansion of the codon CAG trinucleotide repeat polymorphism in exon 1 of the AR gene represents a type of genetic alteration associated with changes in the AR gene function. The purpose of this study was to establish a possible association of the AR gene CAG repeat length polymorphism with PCOS, and its influence on clinical and biochemical androgen traits. Two hundred and fourteen Croatian women with PCOS and 209 healthy control women of reproductive age were enrolled. Phenotypic hyperandrogenism, BMI and waist to hip ratio were recorded. Hormonal profiles, fasting insulin and glucose levels were measured on cycle days 3-5. Genotyping of the CAG repeat polymorphism in the AR gene was performed. We found no significant difference in the mean CAG repeat number between the PCOS patients and controls (22.1±3.4 vs. 21.9±3.2, P=0.286). There was a positive correlation between the CAG repeat length and total testosterone (TT) in the PCOS group (R=0.225, P=0.015). A multiple linear regression model using mean CAG repeat length, BMI, age and HOMA-IR as predictors explained 8.5% (adjusted R²) of the variability in serum TT levels. In this model the CAG repeat polymorphism was found to be a significant predictor of serum TT levels in PCOS patients (P=0.015). The logistic regression analysis revealed that the CAG repeat length is not a significant predictor of hirsutism and acne status (P=0.921 and P=0.437, respectively). The model was adjusted for serum TT, free testosterone, androstendione and DHEAS levels as independent variables, which were also not found to be significant predictors of hirsutism (P=0.687, P=0.194, P=0.675 and P=0.938, respectively) or acne status (P=0.594, P=0.095, P=0.290 and P=0.151, respectively). In conclusion, the AR CAG repeat polymorphism is not a major determinant of PCOS in the

  5. The Hubble Deep Field South Flanking Fields

    Lucas, R A; Brown, T M; Casertano, S; Conselice, C J; De Mello, D F; Dickinson, M E; Ferguson, H C; Fruchter, A S; Gardner, J P; Gilmore, D; González-Lopezlira, R A; Heyer, I; Hook, R N; Kaiser, M E; Mack, J; Makidon, R B; Martin, C L; Mutchler, M Y; Smith, T E; Stiavelli, M; Teplitz, H I; Wiggs, M S; Williams, R E; Zurek, D R; Lucas, Ray A.; Baum, Stefi A.; Brown, Thomas M.; Casertano, Stefano; Conselice, Chris; Mello, Duilia de; Dickinson, Mark E.; Ferguson, Henry C.; Fruchter, Andrew S.; Gardner, Jonathan P.; Gilmore, Diane; Gonzalez-Lopezlira, Rosa A.; Heyer, Inge; Hook, Richard N.; Kaiser, Mary Elizabeth; Mack, Jennifer; Makidon, Russell; Martin, Crystal L.; Mutchler, Max; Stiavelli, Massimo; Teplitz, Harry I.; Wiggs, Michael S.; Williams, Robert E.; Zurek, David R.


    As part of the Hubble Deep Field South program, a set of shorter 2-orbit observations were obtained of the area adjacent to the deep fields. The WFPC2 flanking fields cover a contiguous solid angle of 48 square arcminutes. Parallel observations with the STIS and NICMOS instruments produce a patchwork of additional fields with optical and near-infrared (1.6 micron) response. Deeper parallel exposures with WFPC2 and NICMOS were obtained when STIS observed the NICMOS deep field. These deeper fields are offset from the rest, and an extended low surface brightness object is visible in the deeper WFPC2 flanking field. In this data paper, which serves as an archival record of the project, we discuss the observations and data reduction, and present SExtractor source catalogs and number counts derived from the data. Number counts are broadly consistent with previous surveys from both ground and space. Among other things, these flanking field observations are useful for defining slit masks for spectroscopic follow-up o...

  6. Understanding Etna flank instability through numerical models

    Apuani, Tiziana; Corazzato, Claudia; Merri, Andrea; Tibaldi, Alessandro


    As many active volcanoes, Mount Etna shows clear evidence of flank instability, and different mechanisms were suggested to explain this flank dynamics, based on the recorded deformation pattern and character. Shallow and deep deformations, mainly associated with both eruptive and seismic events, are concentrated along recognised fracture and fault systems, mobilising the eastern and south-eastern flank of the volcano. Several interacting causes were postulated to control the phenomenon, including gravity force, magma ascent along the feeding system, and a very complex local and/or regional tectonic activity. Nevertheless, the complexity of such dynamics is still an open subject of research and being the volcano flanks heavily urbanised, the comprehension of the gravitative dynamics is a major issue for public safety and civil protection. The present research explores the effects of the main geological features (in particular the role of the subetnean clays, interposed between the Apennine-Maghrebian flysch and the volcanic products) and the role of weakness zones, identified by fracture and fault systems, on the slope instability process. The effects of magma intrusions are also investigated. The problem is addressed by integrating field data, laboratory tests and numerical modelling. A bi- and tri-dimensional stress-strain analysis was performed by a finite difference numerical code (FLAC and FLAC3D), mainly aimed at evaluating the relationship among geological features, volcano-tectonic structures and magmatic activity in controlling the deformation processes. The analyses are well supported by dedicated structural-mechanical field surveys, which allowed to estimate the rock mass strength and deformability parameters. To take into account the uncertainties which inevitably occur in a so complicated model, many efforts were done in performing a sensitivity analysis along a WNW-ESE section crossing the volcano summit and the Valle del Bove depression. This was

  7. Dissecting the influence of the collinear and flanking bars in White's effect.

    Blakeslee, Barbara; Padmanabhan, Ganesh; McCourt, Mark E


    In White's effect equiluminant test patches placed on the black and white bars of a square-wave grating appear different in brightness. The illusion has generated intense interest because the direction of the brightness effect does not correlate with the amount of black or white border in contact with the test patch, or in its general vicinity. Therefore, unlike brightness induction effects such as simultaneous contrast, White's effect is not consistent with explanations based on contrast or assimilation that depend solely on the relative amounts of black and white surrounding the test patches. We independently manipulated the luminance of the collinear and flanking bars to investigate their influence on test patch matching luminance (brightness). The inducing grating was a 0.5c/d square-wave and test patches measured 1.0° in width and either 0.5° or 3.0° in height. Test patches measuring 0.5° in height had more extensive contact with the collinear bars and test patches measuring 3.0° in height had more extensive contact with the flanking bars. The luminance of the collinear (or flanking) bars assumed twenty values from 3.2 to 124.8cd/m(2), while the luminance of the flanking (or collinear) bars remained white (124.8cd/m(2)) or black (3.2cd/m(2)). Under these conditions the influence of the collinear and flanking bars was found to be purely in the direction of contrast. The effect was dominated by contrast from the collinear bars (which results in White's effect), however, the influence of the flanking bars was also in the contrast direction. The data elucidate the luminance relationships between the collinear and flanking bars which produce the behavior associated with White's effect as well as that associated with "the inverted White effect" which is akin to simultaneous contrast.

  8. Flanking region variation of ForenSeq™ DNA Signature Prep Kit STR and SNP loci in Yavapai Native Americans.

    Wendt, Frank R; King, Jonathan L; Novroski, Nicole M M; Churchill, Jennifer D; Ng, Jillian; Oldt, Robert F; McCulloh, Kelly L; Weise, Jessica A; Smith, David Glenn; Kanthaswamy, Sreetharan; Budowle, Bruce


    Massively parallel sequencing (MPS) offers advantages over current capillary electrophoresis-based analysis of short tandem repeat (STR) loci for human identification testing. In particular STR repeat motif sequence information can be obtained, thereby increasing the discrimination power of some loci. While sequence variation within the repeat region is observed relatively frequently in some of the commonly used STRs, there is an additional degree of variation found in the flanking regions adjacent to the repeat motif. Repeat motif and flanking region sequence variation have been described for major population groups, however, not for more isolated populations. Flanking region sequence variation in STR and single nucleotide polymorphism (SNP) loci in the Yavapai population was analyzed using the ForenSeq™ DNA Signature Prep Kit and STRait Razor v2s. Seven and 14 autosomal STRs and identity-informative single nucleotide polymorphisms (iiSNPs), respectively, had some degree of flanking region variation. Three and four of these identity-informative loci, respectively, showed ≥5% increase in expected heterozygosity. The combined length- and sequence-based random match probabilities (RMPs) for 27 autosomal STRs were 6.11×10(-26) and 2.79×10(-29), respectively. When combined with 94 iiSNPs (a subset of which became microhaplotypes) the combined RMP was 5.49×10(-63). Analysis of length-based and sequence-based autosomal STRs in STRUCTURE indicated that the Yavapai are most similar to the Hispanic population. While producing minimal increase in X- and Y-STR discrimination potential, access to flanking region data enabled identification of one novel X-STR and three Y-STR alleles relative to previous reports. Five ancestry-informative SNPs (aiSNPs) and two phenotype-informative SNPs (piSNPs) exhibited notable flanking region variation.

  9. Composition measurements in the dusk flank magnetosphere

    Fuselier, S. A.; Elphic, R. C.; Gosling, J. T.


    The dusk flank magnetosphere exhibits significant structure. Several regions have been identified, including the plasma sheet, mantle, and low latitude boundary layer. Transitions from one region to the next, for example from the mantle to the plasma sheet, can be abrupt or indistinct. In addition, the density within the flank mantle can range over several orders of magnitude. Although there is significant structure in this region of the magnetosphere, individual regions often can be distinguished by their energy spectra and ion composition. ISEE Fast Plasma Experiment and Plasma Composition Experiment data are used to examine the composition of the mantle and to study a set of transitions from the mantle to the plasma sheet where plasmas with mantle-like and plasma sheet-like energies mix. This study indicates that the variability of the mantle density is largely due to variability in the solar wind component (H+ and He2+); the ionospheric plasma (O+) density is roughly constant. Similarly, the plasma with mantle-like energy found in the mixed region is largely of solar wind origin.

  10. Influence of the number of trials and the exercise to rest ratio in repeated sprint ability, with changes of direction and orientation.

    Ruscello, Bruno; Tozzo, Nazzareno; Briotti, Gianluca; Padua, Elvira; Ponzetti, Francesco; D'Ottavio, Stefano


    The purpose of this investigation was to determine if there were different trends in physical fatigue observed in 3 different sets, of 7 trials each, in repeated sprint training, performed in 3 different modes: straight sprinting over 30 m, shuttle sprinting over 15 + 15 m, and sprinting over 30 m with changes of direction. Recovery time among trials in the sets was administered according to the 1:5 exercise to rest ratio. The sets were performed on 3 different days, with at least 48 hours between each set. The study involved 17 trained male soccer players (height, 177.33 ± 6.21 cm; body mass, 71.63 ± 9.58 kg; body mass index, 23 ± 2.39 kg·m; age, 21.94 ± 3.58 years). To compare the different values of the time recorded, an index of fatigue was used. Significant differences among trials within each set (repeated measures analysis of variance; p repeated sprint ability in nonlinear and multidirectional sprints (shuttle and change of direction), which might imply a different number of trials within the set or different exercise to rest ratios from the ones usually adopted for straight sprinting, to induce similar trends of fatigue. As practical applications, the estimated numbers of necessary trials in the different sets and the possible exercise to rest ratios, resulting from mathematical modeling, are provided for each investigated sprinting mode.

  11. Cluster observations of surface waves on the dawn flank magnetopause

    C. J. Owen


    Full Text Available On 14 June 2001 the four Cluster spacecraft recorded multiple encounters of the dawn-side flank magnetopause. The characteristics of the observed electron populations varied between a cold, dense magnetosheath population and warmer, more rarified boundary layer population on a quasi-periodic basis. The demarcation between these two populations can be readily identified by gradients in the scalar temperature of the electrons. An analysis of the differences in the observed timings of the boundary at each spacecraft indicates that these magnetopause crossings are consistent with a surface wave moving across the flank magnetopause. When compared to the orientation of the magnetopause expected from models, we find that the leading edges of these waves are approximately 45° steeper than the trailing edges, consistent with the Kelvin-Helmholtz (KH driving mechanism. A stability analysis of this interval suggests that the magnetopause is marginally stable to this mechanism during this event. Periods in which the analysis predicts that the magnetopause is unstable correspond to observations of greater wave steepening. Analysis of the pulses suggests that the waves have an average wavelength of approximately 3.4 RE and move at an average speed of ~65km s-1 in an anti-sunward and northward direction, despite the spacecraft location somewhat south of the GSE Z=0 plane. This wave propagation direction lies close to perpendicular to the average magnetic field direction in the external magnetosheath, suggesting that these waves may preferentially propagate in the direction that requires no bending of these external field lines

    Key words. Magnetospheric physics (magnetospheric configuration and dynamics; MHD waves and unstabilities; solar wind-magnetosphere interactions

  12. Large-scale flank collapse events during the activity of Montagne Pelée, Martinique, Lesser Antilles

    Le Friant, Anne; Boudon, Georges; Deplus, Christine; Villemant, Benoã®T.


    A horseshoe-shaped structure already identified on the southwestern flank of Montagne Pelée (Martinique, Lesser Antilles arc) was previously interpreted as resulting of a flank collapse event, but no debris avalanche deposits were observed at the time. New offshore high-resolution bathymetry and geophysical data (Aguadomar cruise; December 1998 to January 1999; R/V L'Atalante) lead us to identify three debris avalanche deposits on the submarine western flank of Montagne Pelée extending down to the Grenada Basin. They display morphological fronts and hummocky morphology on bathymetric data, speckled pattern on backscatter data and hyperbolic facies on 3.5 kHz and seismic profiles. New on-land geological studies lead us to identify two other horseshoe-shaped structures on the same flank of the volcano. The three submarine deposits have been traced back to the structures identified on land, which confirms the occurrence of repeated flank collapse events during the evolution of Montagne Pelée. The ages of the last two events are estimated at ˜9 ka and ˜25 ka on the basis of 14C and 238U/230Th dates. Every flank collapse produced debris avalanches which flowed down to the Caribbean Sea. We propose that the repeated instabilities are due to the large asymmetry of the island with western aerial and submarine slopes steeper than the eastern slopes. The asymmetry results from progressive loading by accumulation of volcanic products on the western slopes of the volcano and development of long-term gravitational instabilities. Meteoric and hydrothermal fluid circulation on the floor of the second flank collapse structure also creates a weakened hydrothermalized area, which favors the recurrence of flank collapses.

  13. A modal-spectral model for flanking transmissions

    Poblet-Puig, Jordi


    A model for the prediction of direct and indirect (flanking) sound transmissions is presented. It can be applied to geometries with extrusion symmetry. The structures are modelled with spectral finite elements. The acoustic domains are described by means of a modal expansion of the pressure field and must be cuboid-shaped. These reasonable simplifications in the geometry allow the use of more efficient numerical methods. Consequently the coupled vibroacoustic problem in structures such as junctions is efficiently solved. The vibration reduction index of T-junctions with acoustic excitation and with point force excitation is compared. The differences due to the excitation type obey quite general trends that could be taken into account by prediction formulas. However, they are smaller than other uncertainties not considered in practice. The model is also used to check if the sound transmissions of a fully vibroacoustic problem involving several flanking paths can be reproduced by superposition of independent paths. There exist some differences caused by the interaction between paths, which are more important at low frequencies.

  14. Comparison between Underground Cable and Overhead Line for a Low-Voltage Direct Current Distribution Network Serving Communication Repeater

    Jae-Han Kim


    Full Text Available This paper compares the differences in economic feasibility and dynamic characteristics between underground (U/G cable and overhead (O/H line for low-voltage direct current (LVDC distribution. Numerous low loaded long-distance distribution networks served by medium-voltage alternative current (MVAC distribution lines exist in the Korean distribution network. This is an unavoidable choice to compensate voltage drop, therefore, excessive cost is expended for the amount of electrical power load. The Korean Electric Power Corporation (KEPCO is consequently seeking a solution to replace the MVAC distribution line with a LVDC distribution line, reducing costs and providing better quality direct current (DC electricity. A LVDC distribution network can be installed with U/G cables or O/H lines. In this paper, a realistic MVAC distribution network in a mountainous area was selected as the target model to replace with LVDC. A 30 year net present value (NPV analysis of the economic feasibility was conducted to compare the cost of the two types of distribution line. A simulation study compared the results of the DC line fault with the power system computer aided design/electro-magnetic transient direct current (PSCAD/EMTDC. The economic feasibility evaluation and simulation study results will be used to select the applicable type of LVDC distribution network.

  15. Mitigation of Flanking Noise in Double-Plate Panel Structures by Periodic Stiffening

    Domadiya, Parthkumar Gandalal; Dickow, Kristoffer Ahrens; Andersen, Lars


    The present analysis focuses on flanking noise transmission within a two-wall structure of finite size. The walls are lightweight panel structures, each consisting of two plates with internal ribs. A finite-element model is utilized, assuming that the studs are fully fixed to the plates. Further...... is important. Hence, analyses are carried out for different positions of the load. It has been found that the ribs have a significant impact, not only on the flanking noise but also on the direct radiation of sound from the wall on which the external force has been placed. Furthermore, the response changes...

  16. The Effect of Standard Strength vs. Contrast Strength Training on the Development of Sprint, Agility, Repeated Change of Direction, and Jump in Junior Male Soccer Players.

    Hammami, Mehréz; Negra, Yassine; Shephard, Roy J; Chelly, Mohamed Souhaiel


    Hammami, M, Negra, Y, Shephard, RJ, and Chelly, MS. The effect of standard strength vs. contrast strength training on the development of sprint, agility, repeated change of direction, and jump in junior male soccer players. J Strength Cond Res 31(4): 901-912, 2017-The aim was to compare the impact of 2 differing strength training (ST) programs on the athletic performance of junior male soccer players at a critical phase during their competitive season. Participants aged 16.0 ± 0.5 years were randomly assigned between control (C, n = 12), standard ST (n = 16), and contrast strength training (CST, n = 16), each performed twice a week. Athletic performance was assessed before and after the intervention using 8 tests: 40-m sprint, 4 × 5-m sprint (S4 × 5), 9-3-6-3-9 m sprint with 180° turns (S180°), 9-3-6-3-9 m sprint with backward and forward running (SBF), repeated shuttle sprint ability (RSSA), repeated change of direction (RCOD), squat jump (SJ), and countermovement jump (CMJ). The control group's (CG) performance tended to improve in some tests and decrease in others, but these changes were not statistically significant. Both training programs enhanced all sprint performances relative to controls (p ≤ 0.05). The strength training group (SG) and the CST group (CSG) increased significantly in S180°, SBF, and S4 × 5 relative to CG, although the S4 × 5 also increased in CSG relative to SG (p ≤ 0.05). No intergroup difference of RSSA performance was observed. The RCOD parameters increased significantly in CSG relative to both SG and CG (p ≤ 0.05). The SJ and CMJ height increased significantly in both experimental groups (p < 0.000). We conclude that during the competitive season, some measures of athletic performance in male soccer players were increased more by 8 weeks of CST than by ST.

  17. Evaluation of Flanking Noise Transmission within Periodically Distributed Lightweight Beam Elements

    Domadiya, Parthkumar Gandalal; Andersen, Lars Vabbersgaard; Sorokin, Sergey


    Wooden frame structures are highly preferred as lightweight building systems nowadays. Lightweight building structures have gained more interest due to lower cost of production. However, there is a growing concern regarding noise and vibration issues within lightweight structures. Sound may pass...... from one room to another as indirect or flanking noise via joints or as direct transmission between adjacent rooms. The present analysis concerns flanking transmission within two-dimensional infinite periodic beam structures. The beam is comprised of two different materials placed in a periodic manner....... Two different theoretical methods are taken into consideration to evaluate flanking noise transmission within the beam structure: The finite-element method (FEM) and a Floquet theory approach. Research is carried out regarding the effects of periodicity in a wide range of frequencies from 0 to 300 Hz...

  18. Time course of the induction of homeostatic plasticity generated by repeated transcranial direct current stimulation of the human motor cortex.

    Fricke, K; Seeber, A A; Thirugnanasambandam, N; Paulus, W; Nitsche, M A; Rothwell, J C


    Several mechanisms have been proposed that control the amount of plasticity in neuronal circuits and guarantee dynamic stability of neuronal networks. Homeostatic plasticity suggests that the ease with which a synaptic connection is facilitated/suppressed depends on the previous amount of network activity. We describe how such homeostatic-like interactions depend on the time interval between two conditioning protocols and on the duration of the preconditioning protocol. We used transcranial direct current stimulation (tDCS) to produce short-lasting plasticity in the motor cortex of healthy humans. In the main experiment, we compared the aftereffect of a single 5-min session of anodal or cathodal tDCS with the effect of a 5-min tDCS session preceded by an identical 5-min conditioning session administered 30, 3, or 0 min beforehand. Five-minute anodal tDCS increases excitability for about 5 min. The same duration of cathodal tDCS reduces excitability. Increasing the duration of tDCS to 10 min prolongs the duration of the effects. If two 5-min periods of tDCS are applied with a 30-min break between them, the effect of the second period of tDCS is identical to that of 5-min stimulation alone. If the break is only 3 min, then the second session has the opposite effect to 5-min tDCS given alone. Control experiments show that these shifts in the direction of plasticity evolve during the 10 min after the first tDCS session and depend on the duration of the first tDCS but not on intracortical inhibition and facilitation. The results are compatible with a time-dependent "homeostatic-like" rule governing the response of the human motor cortex to plasticity probing protocols.

  19. Effects of an In-season Plyometric Training Program on Repeated Change of Direction and Sprint Performance in the Junior Soccer Player.

    Hammami, Mehréz; Negra, Yassine; Aouadi, Ridha; Shephard, Roy J; Chelly, Mohamed Souhaiel


    Hammami, M, Negra, Y, Aouadi, R, Shephard, RJ, and Chelly, MS. Effects of an in-season plyometric training program on repeated change of direction and sprint performance in the junior soccer player. J Strength Cond Res 30(12): 3312-3320, 2016-We aimed to determine the gains in explosive movements of male junior soccer players induced by incorporating an 8-week plyometric training program (PTP) into a standard soccer conditioning regimen 5 months after the beginning of the competitive season. Our hypothesis was that PTP would enhance explosive movements, and thus sprint running, repeated shuttle sprint ability (RSSA), agility and the ability to make repeated changes of direction (RCOD). A group of junior soccer players were randomly divided into 2 groups: an experimental group (E, n = 15, age 15.7 ± 0.2 years) and a control group (C, n = 13, age 15.8 ± 0.2 years). The participants in E and C performed training exercises and matches together, but for an 8-week period in the latter part of the season, the experimental group replaced a part of the normal regimen (the tactical session) by a biweekly course of PTP (hurdle and drop jumps). Two familiarization sessions were held 2 weeks before definitive testing. The ability of the players was assessed by 3 agility tests (a sprint test with 180° turns, a 9-3-6-3-9 m sprint with backward and forward running, and a four 5-m sprint test with turns); 2 repeated sprint tests (RSSA and RCOD); and running times over 5-, 10-, 20-, 30-, and 40-m distances. Participants in E showed gains relative to C in sprint times (p ≤ 0.05 for 5, 10, and 20 m), and 2 of 3 the RCOD parameters (RCOD best, p ≤ 0.001; RCOD total, p ≤ 0.05). However, with the pattern of plyometric training that we adopted, and perhaps because participants were in good initial physical condition, the agility and RSSA test scores remained unchanged. Nevertheless, we conclude that our PTP can be commended to junior soccer players as a means of improving

  20. Performance and Metabolic Demand of a New Repeated-Sprint Ability Test in Basketball Players: Does the Number of Changes of Direction Matter?

    Zagatto, Alessandro M; Ardigò, Luca P; Barbieri, Fabio A; Milioni, Fabio; Dello Iacono, Antonio; Camargo, Bruno H F; Padulo, Johnny


    Zagatto, AM, Ardigò, LP, Barbieri, FA, Milioni, F, Dello Iacono, A, Camargo, BHF, and Padulo, J. Performance and metabolic demand of a new repeated-sprint ability test in basketball players: does the number of changes of direction matter? J Strength Cond Res 31(9): 2438-2446, 2017-This study compared 2 repeated-sprint ability (RSA) tests in basketball players. Both tests included 10 × 30-m sprints, with the difference that the previously validated test (RSA2COD) featured 2 changes of direction (COD) per sprint, whereas the experimental test (RSA5COD) featured 5 CODs per sprint. Test performances and metabolic demands were specifically assessed in 20 basketball players. First, RSA5COD test-retest reliability was investigated. Then, RSA2COD, RSA5COD sprint times, peak speeds, oxygen uptake (V[Combining Dot Above]O2) and posttest blood lactate concentration [La] were measured. The RSA5COD results showed to be reliable. RSA2COD performance resulted better than the RSA5COD version (p sprint times and higher peak speeds. Over sprints, the tests did not differ from each other in terms of V[Combining Dot Above]O2 (p > 0.05). Over whole bout, the RSA2COD was more demanding than the RSA5COD, considering overall metabolic power requirement (i.e., VO2-driven + [La]-driven components). Given that RSA5COD (a) mimics real game-play as sprint distance and action change frequency/direction and (b) has the same metabolic expenditure per task completion as metabolic cost, RSA5COD is a valuable option for players and coaches for training basketball-specific agility and assessing bioenergetic demands.

  1. Effect of flanking sounds on the auditory continuity illusion.

    Maori Kobayashi

    Full Text Available BACKGROUND: The auditory continuity illusion or the perceptual restoration of a target sound briefly interrupted by an extraneous sound has been shown to depend on masking. However, little is known about factors other than masking. METHODOLOGY/PRINCIPAL FINDINGS: We examined whether a sequence of flanking transient sounds affects the apparent continuity of a target tone alternated with a bandpass noise at regular intervals. The flanking sounds significantly increased the limit of perceiving apparent continuity in terms of the maximum target level at a fixed noise level, irrespective of the frequency separation between the target and flanking sounds: the flanking sounds enhanced the continuity illusion. This effect was dependent on the temporal relationship between the flanking sounds and noise bursts. CONCLUSIONS/SIGNIFICANCE: The spectrotemporal characteristics of the enhancement effect suggest that a mechanism to compensate for exogenous attentional distraction may contribute to the continuity illusion.

  2. Experimental study of the interplay between magmatic rift intrusion and flank instability with application to the 2001 Mount Etna eruption

    Le Corvec, Nicolas


    Mount Etna volcano is subject to transient magmatic intrusions and flank movement. The east flank of the edifice, in particular, is moving eastward and is dissected by the Timpe Fault System. The relationship of this eastward motion with intrusions and tectonic fault motion, however, remains poorly constrained. Here we explore this relationship by using analogue experiments that are designed to simulate magmatic rift intrusion, flank movement, and fault activity before, during, and after a magmatic intrusion episode. Using particle image velocimetry allows for a precise temporal and spatial analysis of the development and activity of fault systems. The results show that the occurrence of rift intrusion episodes has a direct effect on fault activity. In such a situation, fault activity may occur or may be hindered, depending on the interplay of fault displacement and flank acceleration in response to dike intrusion. Our results demonstrate that a complex interplay may exist between an active tectonic fault system and magmatically induced flank instability. Episodes of magmatic intrusion change the intensity pattern of horizontal flank displacements and may hinder or activate associated faults. We further compare our results with the GPS data of the Mount Etna 2001 eruption and intrusion. We find that syneruptive displacement rates at the Timpe Fault System have differed from the preeruptive or posteruptive periods, which shows a good agreement of both the experimental and the GPS data. Therefore, understanding the flank instability and flank stability at Mount Etna requires consideration of both tectonic and magmatic forcing. Key Points Analyzing Mount Etna east flank dynamics during the 2001 eruption Good correlation between analogue models and GPS data Understanding the different behavior of faulting before/during/after an eruption © 2014. American Geophysical Union. All Rights Reserved.

  3. Rosa26-GFP direct repeat (RaDR-GFP mice reveal tissue- and age-dependence of homologous recombination in mammals in vivo.

    Michelle R Sukup-Jackson


    Full Text Available Homologous recombination (HR is critical for the repair of double strand breaks and broken replication forks. Although HR is mostly error free, inherent or environmental conditions that either suppress or induce HR cause genomic instability. Despite its importance in carcinogenesis, due to limitations in our ability to detect HR in vivo, little is known about HR in mammalian tissues. Here, we describe a mouse model in which a direct repeat HR substrate is targeted to the ubiquitously expressed Rosa26 locus. In the Rosa26 Direct Repeat-GFP (RaDR-GFP mice, HR between two truncated EGFP expression cassettes can yield a fluorescent signal. In-house image analysis software provides a rapid method for quantifying recombination events within intact tissues, and the frequency of recombinant cells can be evaluated by flow cytometry. A comparison among 11 tissues shows that the frequency of recombinant cells varies by more than two orders of magnitude among tissues, wherein HR in the brain is the lowest. Additionally, de novo recombination events accumulate with age in the colon, showing that this mouse model can be used to study the impact of chronic exposures on genomic stability. Exposure to N-methyl-N-nitrosourea, an alkylating agent similar to the cancer chemotherapeutic temozolomide, shows that the colon, liver and pancreas are susceptible to DNA damage-induced HR. Finally, histological analysis of the underlying cell types reveals that pancreatic acinar cells and liver hepatocytes undergo HR and also that HR can be specifically detected in colonic somatic stem cells. Taken together, the RaDR-GFP mouse model provides new understanding of how tissue and age impact susceptibility to HR, and enables future studies of genetic, environmental and physiological factors that modulate HR in mammals.

  4. Organization of ATPA coding and 3' flanking sequences associated with cytoplasmic male sterility in Phaseolus vulgaris L.

    Chase, C D; Ortega, V M


    A region of the mitochondrial genome associated with cytoplasmic male sterility (CMS) in Phaseolus vulgaris was flanked by two different repeated sequences designated x and y. The DNA sequence of the CMS-unique region and a portion of each flanking repeat was determined. Repeat x contained a complete coding copy of the F1 ATPase subunit A (atpA) gene, as well as an open reading frame (orf) predicting a protein of 209 amino acids. The TGA termination codon of the atpA gene and the ATG initiation codon of orf209 were overlapping. These reading frames were oriented with their 3' ends proximal to the CMS-unique region. The CMS-unique region of 3736 nucleotides contained numerous orfs. The longest of these predicted proteins being of 239, 98 and 97 amino acids. The 3' coding and 3' flanking regions of orf98 were derived from an internal region of the higher plant chloroplast tRNA alanine intron. The region of repeat y immediately adjacent to the CMS-unique region contained the 111 carboxy-terminal coding residues of the apocytochrome b (cob) gene. This segment was oriented with its 5' end proximal to the CMS-unique region, but cob gene sequences were not fused to an initiation codon within the unique region.

  5. Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs.

    Port, Fillip; Bullock, Simon L


    We present tRNA-based vectors for producing multiple clustered regularly interspaced short palindromic repeats (CRISPR) single guide RNAs (sgRNAs) from a single RNA polymerase II or III transcript in Drosophila. The system, which is based on liberation of sgRNAs by processing flanking tRNAs, permits highly efficient multiplexing of Cas9-based mutagenesis. We also demonstrate that the tRNA-sgRNA system markedly increases the efficacy of conditional gene disruption by Cas9 and can promote editing by the recently discovered RNA-guided endonuclease Cpf1.

  6. Specific binding of the replication protein of plasmid pPS10 to direct and inverted repeats is mediated by an HTH motif.

    García de Viedma, D; Serrano-López, A; Díaz-Orejas, R


    The initiator protein of the plasmid pPS10, RepA, has a putative helix-turn-helix (HTH) motif at its C-terminal end. RepA dimers bind to an inverted repeat at the repA promoter (repAP) to autoregulate RepA synthesis. [D. García de Viedma, et al. (1996) EMBO J. in press]. RepA monomers bind to four direct repeats at the origin of replication (oriV) to initiate pPS10 replication This report shows that randomly generated mutations in RepA, associated with defficiencies in autoregulation, map either at the putative HTH motif or in its vicinity. These mutant proteins do not promote pPS10 replication and are severely affected in binding to both the repAP and oriV regions in vitro. Revertants of a mutant that map in the vicinity of the HTH motif have been obtained and correspond to a second amino acid substitution far upstream of the motif. However, reversion of mutants that map in the helices of the motif occurs less frequently, at least by an order of magnitude. All these data indicate that the helices of the HTH motif play an essential role in specific RepA-DNA interactions, although additional regions also seem to be involved in DNA binding activity. Some mutations have slightly different effects in replication and autoregulation, suggesting that the role of the HTH motif in the interaction of RepA dimers or monomers with their respective DNA targets (IR or DR) is not the same. Images PMID:8559664

  7. Rapid changes of microsatellite flanking sequence in the allopolyploidization of new synthesized hexaploid wheat

    ZHANG Lianquan; LIU Dengcai; YAN Zehong; LAN Xiujin; ZHENG Youliang; ZHOU Yonghong


    It was suggested that the rapid changes of DNA sequence and gene expression occurred at the early stages of allopolyploid formation. In this study, we revealed the microsatellite (SSR) differences between newly formed allopolyploids and their donor parents by using 21 primer sets specific for D genome of wheat. It was indicated that rapid changes had occurred in the "shock" process of the allopolyploid formation between tetraploid wheat and Aegilops tauschii. The changes of SSR flanking sequence resulted in appearance of novel bands or disappearance of parental bands. The disappearance of the parental bands showed much higher frequencies in comparison with that of appearance of novel bands. Disappearance of the parental bands was not random. The frequency of disappearance in tetraploid wheat was much higher than in Ae. tauschii, i. e. the disappearance frequency in AABB genome was much higher than in D genome. Changes of SSR flanking sequence occurred at the early stage of F1 hybrid or just after chromosome doubling. From the above results, it can be inferred that SSR flanking sequence region was very active and was amenable to change in the process of polyploidization. This suggested that SSR flanking sequence probably had special biological function at the early stage of ployploidization. The rapid and directional changes at the early stage of polyploidization might contribute to the rapid evolution of the newly formed allopolyploid and allow the divergent genomes to act in harmony.

  8. Isolation of sequences flanking Ac insertion sites by Ac casting.

    Wang, Dafang; Peterson, Thomas


    Localizing Ac insertions is a fundamental task in studying Ac-induced mutation and chromosomal rearrangements involving Ac elements. Researchers may sometimes be faced with the situation in which the sequence flanking one side of an Ac/Ds element is known, but the other flank is unknown. Or, a researcher may have a small sequence surrounding the Ac/Ds insertion site and needs to obtain additional flanking genomic sequences. One way to rapidly clone unknown Ac/Ds flanking sequences is via a PCR-based method termed Ac casting. This approach utilizes the somatic transposition activity of Ac during plant development, and provides an efficient means for short-range genome walking. Here we describe the principle of Ac casting, and show how it can be applied to isolate Ac macrotransposon insertion sites.

  9. Sludge reduction by direct addition of chlorine dioxide into a sequencing batch reactor under operational mode of repeatedly alternating aeration/non-aeration.

    Peng, Hong; Liu, Weiyi; Li, Yuanmei; Xiao, Hong


    The effect of direct addition of chlorine dioxide (ClO2) into a repeatedly alternating aeration/non-aeration sequencing batch reactor (SBR) on its sludge reduction and process performance was investigated. The experimental results showed that the sludge reduction efficiency was 32.9% and the observed growth yield (Yobs) of SBR was 0.11 kg VSS (volatile suspended solids) /kg COD (chemical oxygen demand) for 80 days' operation at the optimum ClO2 dosage of 2.0 mg/g TSS (total suspended solids). It was speculated that cell lysis and cryptic growth, uncoupled metabolism and endogenous metabolism were jointly responsible for the sludge reduction in this study. COD, NH3-N, total nitrogen (TN) and total phosphorus (TP) in the effluent increased on average 29.47, 4.44, 1.97 and 0.05 mg/L, respectively. However, the effluent quality still satisfied the first-class B discharge standards for municipal wastewater treatment plants in China. In that case, the sludge maintained fine viability with the specific oxygen uptake rate (SOUR) being 14.47 mg O2/(g VSS·h) and demonstrated good settleability with the sludge volume index (SVI) being 116 mL/g. The extra cost of sludge reduction at the optimum ClO2 dosage was estimated to be 2.24 CNY (or 0.36 dollar)/kg dry sludge.

  10. Effects of a small-sided game-based training programme on repeated sprint and change of direction abilities in recreationally-trained football players.

    Bujalance-Moreno, Pascual; García-Pinillos, Felipe; Latorre-Román, Pedro Á


    To examine the effects of 6-week periodized small-sided game (SSG) training intervention on change of direction [COD], sprint and repeated sprint ability [RSA] in recreational male football players. Twenty-three young football players (age: 20.86 years) were randomized in a control group (n = 11) and an experimental group (n = 12). The SSG programme was included in the experimental group's training sessions. The players completed two variations of a SSG (i.e. 2 vs. 2 and 4 vs. 4 players) during intervention. To examine the changes in physical performance after the 6-week periodized SSG training intervention, all players were tested 6 weeks apart (i.e. pre-test and post-test) in sprint, COD ability test, and RSA shuttle test. A 2x2 ANOVA showed that 6-week SSG training intervention induced significant improvements (P0.7) in COD ability test, and variables related to both sprint test and RSA in the experimental group, whereas the control group remained unchanged (P≥0.05, ESsprint in recreationally trained football players.

  11. Direct analysis of tau from PSP brain identifies new phosphorylation sites and a major fragment of N-terminally cleaved tau containing four microtubule-binding repeats.

    Wray, Selina; Saxton, Malcolm; Anderton, Brian H; Hanger, Diane P


    Tangles containing hyperphosphorylated aggregates of insoluble tau are a pathological hallmark of progressive supranuclear palsy (PSP). Several phosphorylation sites on tau in PSP have been identified using phospho-specific antibodies, but no sites have been determined by direct sequencing due to the difficulty in enriching insoluble tau from PSP brain. We describe a new method to enrich insoluble PSP-tau and report eight phosphorylation sites [Ser46, Thr181, Ser202, Thr217, Thr231, Ser235, Ser396/Ser400 (one site) and Thr403/Ser404 (one site)] identified by mass spectrometry. We also describe a 35 kDa C-terminal tau fragment (tau35), lacking the N-terminus of tau but containing four microtubule-binding repeats (4R), that is present only in neurodegenerative disorders in which 4R tau is over-represented. Tau35 was readily detectable in PSP, corticobasal degeneration and 4R forms of fronto-temporal dementia with parkinsonism linked to chromosome 17, but was absent from control, Alzheimer's disease and Pick's disease brain. Our findings suggest the aggregatory characteristics of PSP-tau differ from those of insoluble tau in Alzheimer's disease brain and this might be related to the presence of a C-terminal cleavage product of tau.

  12. Amplification of a single-locus variable-number direct repeats with restriction fragment length polymorphism (DR-PCR/RFLP) for genetic typing of Acinetobacter baumannii strains.

    Nowak-Zaleska, Alicja; Krawczyk, Beata; Kotłowski, Roman; Mikucka, Agnieszka; Gospodarek, Eugenia


    In search of an effective DNA typing technique for Acinetobacter baumannii strains for hospital epidemiology use, the performance and convenience of a new target sequence was evaluated. Using known genomic sequences of Acinetobacter baumannii strains AR 319754 and ATCC 17978, we developed single-locus variable-number direct-repeat analysis using polymerase chain reaction-restriction fragment length polymorphism (DR-PCR/RFLP) method. A total of 90 Acinetobacter baumannii strains isolated from patients of the Clinical Hospital in Bydgoszcz, Poland, were examined. Initially, all strains were typed using macrorestriction analysis of the chromosomal DNA by pulsed-field gel electrophoresis (REA-PFGE). Digestion of the chromosomal DNA with the ApaI endonuclease and separation of the fragments by PFGE revealed 21 unique types. Application of DR-PCR/RFLP resulted in recognition of 12 clusters. The results showed that the DR-PCR/RFLP method is less discriminatory than REA-PFGE, however, the novel genotyping method can be used as an alternative technique for generating DNA profiles in epidemiological studies of intra-species genetic relatedness of Acinetobacter baumannii strains.

  13. Assess drug resistance pattern and genetic profile of Mycobacterium tuberculosis clinical isolates by molecular typing methods using direct repeats and IS6110 in pulmonary tuberculosis cases

    Kalo, Deepika; Kant, Surya; Srivastava, Kanchan; Sharma, Ajay K


    Background: Tuberculosis (TB), a highly contagious disease that sees no gender, age, or race is mainly a disease of lungs. According to World Health Organization, a TB patient can be completely cured with 6–9 months of anti-TB treatment under directly observed treatment short course. Objectives: The aim of this study was to check the mono, multi- and triple-drug resistance to first line drugs (FLDs) among TB patients and to access their genetic profile using DR 3074, DR 0270, DR 0642, DR 2068, and DR 4110 using molecular techniques. Material and Methods: To gain a better understanding of drug resistant TB, we characterized 121 clinical isolates recovered from 159 drug resistant pulmonary tuberculosis patients by IS6110 genotyping. MTB isolates recovered from HIV- negative, and smear positive cases of both genders, age varied from 18 to 70 years with drug resistant-TB that was refractory to chemotherapy given for > 12 months. Of a total of 159 sputum smear positive patients sum number of male and female patients was 121 (76.10%) and 38 (23.89%), respectively. Among these patients, number of literate and illiterate patients were 123 (77.3%) and 36 (22.6%). 25 (15.7%) patients had farming as their occupation, 80 (50.3%) had nonagricultural occupation and 54 (33.9%) women were housewives. Results: Mono drug resistant, multi-drug resistant, and totally drug resistant (TDR) cases of TB were calculated as 113.83%, 125.1%, and 67.9%. Isoniazid showed the highest percentage of resistance among the patients. Conclusion: Any noncompliance to TB medications, lack of knowledge, and poor management in health centers, etc., results in the emergence of deadly direct repeat forms of TB, which are further complicated and complex to treat. PMID:28360464

  14. Repeated Sprint Ability in Young Basketball Players (Part 2): The Chronic Effects of Multidirection and of One Change of Direction Are Comparable in Terms of Physiological and Performance Responses

    Attene, Giuseppe; Nikolaidis, Pantelis T.; Bragazzi, Nicola L.; Dello Iacono, Antonio; Pizzolato, Fabio; Zagatto, Alessandro M.; Dal Pupo, Juliano; Oggianu, Marcello; Migliaccio, Gian M.; Mannucci Pacini, Elena; Padulo, Johnny


    The aim of this study was to examine the effects of a 5-week training program, consisting of repeated 30-m sprints, on two repeated sprint ability (RSA) test formats: one with one change of direction (RSA) and the other with multiple changes of direction (RSM). Thirty-six young male and female basketball players (age 16.1 ± 0.9 years), divided into two experimental groups, were tested for RSA, RSM, squat jump, counter-movement jump, and the Yo-Yo Intermittent Recovery-Level-1 (Yo-Yo IR1) test...

  15. (TG/CAn repeats in human gene families: abundance and selective patterns of distribution according to function and gene length

    Ramachandran Srinivasan


    Full Text Available Abstract Background Creation of human gene families was facilitated significantly by gene duplication and diversification. The (TG/CAn repeats exhibit length variability, display genome-wide distribution, and are abundant in the human genome. Accumulation of evidences for their multiple functional roles including regulation of transcription and stimulation of recombination and splicing elect them as functional elements. Here, we report analysis of the distribution of (TG/CAn repeats in human gene families. Results The 1,317 human gene families were classified into six functional classes. Distribution of (TG/CAn repeats were analyzed both from a global perspective and from a stratified perspective based on their biological properties. The number of genes with repeats decreased with increasing repeat length and several genes (53% had repeats of multiple types in various combinations. Repeats were positively associated with the class of Signaling and communication whereas, they were negatively associated with the classes of Immune and related functions and of Information. The proportion of genes with (TG/CAn repeats in each class was proportional to the corresponding average gene length. The repeat distribution pattern in large gene families generally mirrored the global distribution pattern but differed particularly for Collagen gene family, which was rich in repeats. The position and flanking sequences of the repeats of Collagen genes showed high conservation in the Chimpanzee genome. However the majority of these repeats displayed length polymorphism. Conclusion Positive association of repeats with genes of Signaling and communication points to their role in modulation of transcription. Negative association of repeats in genes of Information relates to the smaller gene length, higher expression and fundamental role in cellular physiology. In genes of Immune and related functions negative association of repeats perhaps relates to the smaller gene

  16. Increasing the repeating units of ethylene glycol-based dimethacrylates directed toward reduced oxidative stress and co-stimulatory factors expression in human monocytic cells.

    Tamura, Atsushi; Fukumoto, Izumi; Yui, Nobuhiko; Matsumura, Mitsuaki; Miura, Hiroyuki


    The ethylene glycol-based dimethacrylates are commonly used in biomaterials and dental restorative materials as a cross-linking agent. In this study, toxic effect of triethylene glycol dimethacrylate (TEGDMA) and poly(ethylene glycol) dimethacrylates (PEG-DMAs) with various ethylene glycol repeating units was investigated in terms of cytotoxicity, oxidative stress, and the expression of co-stimulatory factors in human leukemia cell line (THP-1 cells) to verify the effect of ethylene glycol repeating units. Note that the 1-octanol/water partition coefficient of PEG-based dimethacrylates decreased with increasing the ethylene glycol repeating units, indicating that the hydrophilicity of PEG-DMAs increased with ethylene glycol repeating units. The toxic effect of PEG-DMAs such as cytotoxicity, oxidative stress, and the expression of CD86 in treated THP-1 cells are reduced with increasing the ethylene glycol repeating units in PEG-DMAs. However, the expression of CD54 in treated THP-1 cells was not influenced with the ethylene glycol repeating units and the maximal expression level of CD54 was observed at the concentration range of 2-4 mM for all samples. Accordingly, hydrophilic character of PEG-DMAs with long ethylene glycol chains definitely alleviates the some toxic aspect of PEG-based DMAs. This finding would provide important insight into the design of new biomaterials and dental materials with superior biocompatibility. © 2014 Wiley Periodicals, Inc.

  17. Deployment Repeatability


    controlled to great precision, but in a Cubesat , there may be no attitude determination at all. Such a Cubesat might treat sun angle and tumbling rates as...could be sensitive to small differences in motor controller timing. In these cases, the analyst might choose to model the entire deployment path, with...knowledge of the material damage model or motor controller timing precision. On the other hand, if many repeated and environmentally representative

  18. Flank solar wind interaction. Annual report, June 1991-July 1992

    Moses, S.L.; Greenstadt, E.W.


    This report summarizes the results of the first 12 months of our program to study the interaction of the Earth's magnetosphere with the solar wind on the far flanks of the bow shock. This study employs data from the ISEE-3 spacecraft during its traversals of the Earth's magnetotail and correlative data from spacecraft monitoring the solar wind upstream. Our main effort to date has involved assembling data sets and developing new plotting programs. Two talks were given at the Spring Meeting of the American Geophysical Union describing our initial results from analyzing data from the far flank foreshock and magnetosheath. The following sections summarize our results.

  19. Transducer model produces facilitation from opposite-sign flanks

    Solomon, J. A.; Watson, A. B.; Morgan, M. J.


    Small spots, lines and Gabor patterns can be easier to detect when they are superimposed upon similar spots, lines and Gabor patterns. Traditionally, such facilitation has been understood to be a consequence of nonlinear contrast transduction. Facilitation has also been reported to arise from non-overlapping patterns with opposite sign. We point out that this result does not preclude the traditional explanation for superimposed targets. Moreover, we find that facilitation from opposite-sign flanks is weaker than facilitation from same-sign flanks. Simulations with a transducer model produce opposite-sign facilitation.

  20. Acute Responses to 10×15 m Repeated Sprint Ability Exercise in Adolescent Athletes: the Role of Change of Direction and Sport Specialization.

    Nikolaidis, Pantelis Theodoros; Meletakos, Panagiotis; Tasiopoulos, Ioannis; Kostoulas, Ioannis; Ganavias, Panagiotis


    The repeated sprint ability (RSA) has been studied with protocols using distances longer than 20 m per sprint, whereas basketball players cover on average less than 20-meter distance per sprint during match. The aim of the present study was to examine the physiological impact of 10 × 15 m RSA test in straight-line (RSASL) or with change of direction (RSACOD), i.e. 10 × (7.5 + 7.5 m)) in young national level basketball players. Young basketball players (n = 11, age 17.1 (1.0) years, body mass 76 (6) kg, height 184 (4) cm, body mass index 22.6 (1.8) kgm(-2), sport experience 6.9 (2.7) years, mean (standard deviation)) and a control group consisting of high-school athletes (n = 7, 16.1 (0.7) years, 67 (6) kg, 177 (6) cm, 21.5 (1.0) kgm(-2), 7.7 (1.6) years, respectively) performed RSASL and RSACOD on a counter-balanced order. Sprints started every 30 seconds (active recovery) and there was 30 minutes break between RSA protocols; time variables were total time (TT), best time (BT) and fatigue index (FI). Countermovement jump (CMJ) was tested before and after each RSA protocol. Heart rate (HR) was continuously monitored during testing procedures. Compared with RSASL, TT and BT were worst in RSACOD (38.13 vs. 27.52 s and 3.67 vs. 2.66 s, P repeated measures ANOVA showed main effect of RSA on CMJ (pre-test vs. post-test, increase + 1.8 cm, P = 0.020, η(2) = 0.28); there was neither main effect of RSA protocols (RSASL vs. RSACOD +0.7 cm, P = 0.251, η(2) = 0.08) nor an interaction between pre-post measurements and RSA protocols (P = 0.578, η(2) = 0.02). Compared with RSASL, RSACOD induced higher mean and peak HR responses (175 vs 172 bpm, P < 0.001, and 185 vs 182 bpm, P = 0.002, respectively). No statistical difference was observed between basketball players and control group neither for TT (27.98 vs. 26.80 seconds, + 4.4%, P = 0.149) and BT (2.71 vs. 2.59 seconds, + 4.5%, P = 0.157) in RSASL nor for TT (38.55 vs. 37.47 seconds, + 2.9%, P = 0.169) and BT (3.70 vs. 3

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

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


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

  2. Long-period seismic events with strikingly regular temporal patterns on Katla volcano's south flank (Iceland)

    Sgattoni, Giulia; Jeddi, Zeinab; Gudmundsson, Ólafur; Einarsson, Páll; Tryggvason, Ari; Lund, Björn; Lucchi, Federico


    Katla is a threatening volcano in Iceland, partly covered by the Mýrdalsjökull ice cap. The volcano has a large caldera with several active geothermal areas. A peculiar cluster of long-period seismic events started on Katla's south flank in July 2011, during an unrest episode in the caldera that culminated in a glacier outburst. The seismic events were tightly clustered at shallow depth in the Gvendarfell area, 4 km south of the caldera, under a small glacier stream at the southern margin of Mýrdalsjökull. No seismic events were known to have occurred in this area before. The most striking feature of this seismic cluster is its temporal pattern, characterized by regular intervals between repeating seismic events, modulated by a seasonal variation. Remarkable is also the stability of both the time and waveform features over a long time period, around 3.5 years. We have not found any comparable examples in the literature. Both volcanic and glacial processes can produce similar waveforms and therefore have to be considered as potential seismic sources. Discerning between these two causes is critical for monitoring glacier-clad volcanoes and has been controversial at Katla. For this new seismic cluster on the south flank, we regard volcano-related processes as more likely than glacial ones for the following reasons: 1) the seismic activity started during an unrest episode involving sudden melting of the glacier and a jökulhlaup; 2) the glacier stream is small and stagnant; 3) the seismicity remains regular and stable for years; 4) there is no apparent correlation with short-term weather changes, such as rainstorms. We suggest that a small, shallow hydrothermal system was activated on Katla's south flank in 2011, either by a minor magmatic injection or by changes of permeability in a local crack system.

  3. Sequence Analysis of SSR-Flanking Regions Identifies Genome Affinities between Pasture Grass Fungal Endophyte Taxa

    Eline van Zijll de Jong


    Full Text Available Fungal species of the Neotyphodium and Epichloë genera are endophytes of pasture grasses showing complex differences of life-cycle and genetic architecture. Simple sequence repeat (SSR markers have been developed from endophyte-derived expressed sequence tag (EST collections. Although SSR array size polymorphisms are appropriate for phenetic analysis to distinguish between taxa, the capacity to resolve phylogenetic relationships is limited by both homoplasy and heteroploidy effects. In contrast, nonrepetitive sequence regions that flank SSRs have been effectively implemented in this study to demonstrate a common evolutionary origin of grass fungal endophytes. Consistent patterns of relationships between specific taxa were apparent across multiple target loci, confirming previous studies of genome evolution based on variation of individual genes. Evidence was obtained for the definition of endophyte taxa not only through genomic affinities but also by relative gene content. Results were compatible with the current view that some asexual Neotyphodium species arose following interspecific hybridisation between sexual Epichloë ancestors. Phylogenetic analysis of SSR-flanking regions, in combination with the results of previous studies with other EST-derived SSR markers, further permitted characterisation of Neotyphodium isolates that could not be assigned to known taxa on the basis of morphological characteristics.

  4. Meiotic stability of transgene expression is unaffected by flanking matrix-associated regions

    Conner, A.J.; Mlynarova, L.; Stiekema, W.J.; Nap, J.P.H.


    DNA repeats are associated with gene instability and silencing phenomena in plants. Therefore, the presence of a direct repeat of matrix-associated region (MAR) DNA, that considerably reduced position effects between independent transformants, may increase (epi)genetic instability. To investigate th

  5. Repeated Sprint Ability in Young Basketball Players (Part 2): The Chronic Effects of Multidirection and of One Change of Direction Are Comparable in Terms of Physiological and Performance Responses.

    Attene, Giuseppe; Nikolaidis, Pantelis T; Bragazzi, Nicola L; Dello Iacono, Antonio; Pizzolato, Fabio; Zagatto, Alessandro M; Dal Pupo, Juliano; Oggianu, Marcello; Migliaccio, Gian M; Mannucci Pacini, Elena; Padulo, Johnny


    The aim of this study was to examine the effects of a 5-week training program, consisting of repeated 30-m sprints, on two repeated sprint ability (RSA) test formats: one with one change of direction (RSA) and the other with multiple changes of direction (RSM). Thirty-six young male and female basketball players (age 16.1 ± 0.9 years), divided into two experimental groups, were tested for RSA, RSM, squat jump, counter-movement jump, and the Yo-Yo Intermittent Recovery-Level-1 (Yo-Yo IR1) test, before and after a 4-week training program and 1 week of tapering. One group performed 30-m sprints with one change of direction (RSA group, RSAG), whereas the other group performed multidirectional 30-m sprints (RSM group, RSMG). Both groups improved in all scores in the post-intervention measurements (P repeated 30-m sprints, either with one change of direction or multidirectional, induce similar physiological and performance responses in young basketball players, but have a different psycho-physiological impact.

  6. A general method for the detection of large CAG repeat expansions by fluorescent PCR

    Warner, J P; Barron, L H; Goudie, D; Kelly, K; Dow, D.; FitzPatrick, D.R.; Brock, D J


    The expansion of a tandemly repeated trinucleotide sequence, CAG, is the mutational mechanism for several human genetic diseases. We present a generally applicable PCR amplification method using a fluorescently labelled locus specific primer flanking the CAG repeat together with paired primers amplifying from multiple priming sites within the CAG repeat. Triplet repeat primed PCR (TP PCR) gives a characteristic ladder on the fluorescence trace enabling the rapid identification of large pathog...

  7. An unusual manifestation of acute appendicitis with left flank pain

    Roland Talanow, MD, PhD


    Full Text Available The author presents a case with an unusual presentation of early appendicitis. The patient presented initially with left sided flank pain. Workup for nephrolithiasis, including non-contrast CT of the abdomen and pelvis was negative for renal stones or hydronephrosis. After discharge, the patient presented one week later in the ED with right lower quadrant pain. Contrast enhanced CT of the abdomen revealed perforated appendicitis.

  8. [Importance of the flank line in the radiologic semiotics of abdominal pathology].

    Minutoli, A; Gaeta, M; Mantineo, G; Bosurgi, G


    The authors have analysed the flank stripe in 70 normal subjects and in patients with abdominal disease. The flank stripe has a wide variability and is very useful to detect and locate abdominal pathologic conditions.

  9. Efficient gusA Transient Expression in Porphyra yezoensis Protoplasts Mediated by Endogenous Beta-tubulin Flanking Sequences

    GONG Qianhong; YU Wengong; DAI Jixun; LIU Hongquan; XU Rifu; GUAN Huashi; PAN Kehou


    Endogenous tubulin promoter has been widely used for expressing foreign genes in green algae, but the efficiency and feasibility of endogenous tubulin promoter in the economically important Porphyra yezoensis (Rhodophyta) are tmknown. In this study, the flanking sequences of beta-tubulin gene from P. yezoensis were amplified and two transient expression vectors were constructed to determine their transcription promoting feasibility for foreign gene gusA. The testing vector pATubGUS was constructed by inserting 5'- and 3'-flanking regions (Tub5'and Tub3') up- and down-stream of β-glucuronidase (GUS) gene (gusA), respectively,into pA, a derivative of pCAT(R)3-enhancer vector. The control construct, pAGUSTub3, contains only gusA and Tub3 '. These constructs were electroporated into P. yezoensis protoplasts and the GUS activities were quantitatively analyzed by spectrometry. The results demonstrated that gusA gene was efficiently expressed in P. yezoensis protoplasts under the regulation of 5'-flanking sequence of the beta-tubulin gene. More interestingly, the pATubGUS produced stronger GUS activity in P. yezoensis protoplasts when compared to the result from pBI221, in which the gusA gene was directed by a constitutive CaMV 35 S promoter. The data suggest that the integration of P. yezoensis protoplast and its endogenous beta-tubulin flanking sequences is a potential novel system for foreign gene expression.

  10. In the Staphylococcus aureus two-component system sae, the response regulator SaeR binds to a direct repeat sequence and DNA binding requires phosphorylation by the sensor kinase SaeS.

    Sun, Fei; Li, Chunling; Jeong, Dowon; Sohn, Changmo; He, Chuan; Bae, Taeok


    Staphylococcus aureus uses the SaeRS two-component system to control the expression of many virulence factors such as alpha-hemolysin and coagulase; however, the molecular mechanism of this signaling has not yet been elucidated. Here, using the P1 promoter of the sae operon as a model target DNA, we demonstrated that the unphosphorylated response regulator SaeR does not bind to the P1 promoter DNA, while its C-terminal DNA binding domain alone does. The DNA binding activity of full-length SaeR could be restored by sensor kinase SaeS-induced phosphorylation. Phosphorylated SaeR is more resistant to digestion by trypsin, suggesting conformational changes. DNase I footprinting assays revealed that the SaeR protection region in the P1 promoter contains a direct repeat sequence (GTTAAN(6)GTTAA [where N is any nucleotide]). This sequence is critical to the binding of phosphorylated SaeR. Mutational changes in the repeat sequence greatly reduced both the in vitro binding of SaeR and the in vivo function of the P1 promoter. From these results, we concluded that SaeR recognizes the direct repeat sequence as a binding site and that binding requires phosphorylation by SaeS.

  11. File list: InP.Emb.50.AllAg.Embryonic_flank [Chip-atlas[Archive

    Full Text Available InP.Emb.50.AllAg.Embryonic_flank mm9 Input control Embryo Embryonic flank SRX804059... ...

  12. File list: ALL.Emb.20.AllAg.Embryonic_flank [Chip-atlas[Archive

    Full Text Available ALL.Emb.20.AllAg.Embryonic_flank mm9 All antigens Embryo Embryonic flank SRX804058,...SRX804059 ...

  13. File list: ALL.Emb.10.AllAg.Embryonic_flank [Chip-atlas[Archive

    Full Text Available ALL.Emb.10.AllAg.Embryonic_flank mm9 All antigens Embryo Embryonic flank SRX804058,...SRX804059 ...

  14. File list: InP.Emb.10.AllAg.Embryonic_flank [Chip-atlas[Archive

    Full Text Available InP.Emb.10.AllAg.Embryonic_flank mm9 Input control Embryo Embryonic flank SRX804059... ...

  15. STEREO and Wind observations of a fast ICME flank triggering a prolonged geomagnetic storm on 5-7 April 2010

    Möstl, Christian; Rollett, Tanja; Farrugia, Charles J; Liu, Ying; Veronig, Astrid M; Leitner, M; Galvin, Antoinette B; Biernat, Helfried K


    On 5 April 2010 an interplanetary (IP) shock was detected by the Wind spacecraft ahead of Earth, followed by a fast (average speed 650 km/s) IP coronal mass ejection (ICME). During the subsequent moderate geomagnetic storm (minimum Dst = -72 nT, maximum Kp=8-), communication with the Galaxy 15 satellite was lost. We link images from STEREO/SECCHI to the near-Earth in situ observations and show that the ICME did not decelerate much between Sun and Earth. The ICME flank was responsible for a long storm growth phase. This type of glancing collision was for the first time directly observed with the STEREO Heliospheric Imagers. The magnetic cloud (MC) inside the ICME cannot be modeled with approaches assuming an invariant direction. These observations confirm the hypotheses that parts of ICMEs classified as (1) long-duration MCs or (2) magnetic-cloud-like (MCL) structures can be a consequence of a spacecraft trajectory through the ICME flank.

  16. Measurement of surface roughness and flank wear on hard martensitic stainless steel by CBN and PCBN cutting tools

    S. Thamizhmanii


    Full Text Available Purpose: The experiments with different operating parameters using CBN and PCBN tools on hard AISI 440 C material were investigated in this paper.Design/methodology/approach: In this research AISI 440 C stainless was used under hard condition. The cutting tools are having three cutting edges and each edge repeated for 5 times. The test conducted by each cutting edge was termed as trail 1, 2, 3, 4 & 5. The length of cutting was 150 mm and each trail. The surface roughness and flank wear, crater wear and BUE were measured by SEM.Findings: The surface roughness was low by CBN at high turning cutting speed and the flank wear was high. The surface roughness was high by PCBN tool than CBN tool and flank wear recorded was low for PCBN tool than CBN tool. The chips produced were saw tooth in all operating parameters. The CBN tool was unable to withstand heat at cutting zone and hence more flank wear occurred. The PCBN tool sustained the temperature and less tool wear occurred. More crater wear formed on PCBN tools where as CBN tool produced less crater wear. The formation of crater wear on the rake face was due to rough surface of the saw tooth chips.Practical implications: The investigation results will provide useful information to applying CBN and PCBN cutting tools in hard turning stainless steels.Originality/value: Hard turning is a latest technology and possible to turn all hard materials. The hard turning produce net shaped products and reduces machining time, low cost per products, etc. The difficult to cut materials like stainless steels was turned by super hard cutting tools like CBN and PCBN to achieve good surface roughness, dimensional control and reduced tool wear.

  17. Comparative Evaluation of Midventral and Flank Laparotomy Approaches in Goat

    A. A. Abubakar


    Full Text Available The aim of the study was to compare two laparotomy approaches (flank and midventral. Ten (n=10 apparently healthy goats of different breeds and sex, average age of 12±2.1 months, and average weight of 13.4±2 kg were used for the investigation. The goats were randomly divided into flank and midventral groups, each group comprising five goats (n=5. Standard aseptic laparotomy was performed under lumbosacral epidural anaesthesia with mild sedation. Postsurgical wound score showed significant difference (P<0.05 in erythema at 18–24 hours and 10–14 days after surgery between the two approaches; significant difference of dehiscence between the two groups was also recorded at 10–14 days after surgery. Total white blood cells (WBC and lymphocytes counts were significantly different (P<0.05 at the first and second week after surgery. There was significant difference of platelets critical value and platelets dimension width at the first and second week after surgery. Significant difference of packed cells volume between the two approaches was also recorded one week after surgery. It was concluded that midventral laparotomy approach can be conveniently and safely performed under aseptic precautions without fear of intra- and postoperative clinical problems.

  18. Plasma Transport at the Magnetospheric Flank Boundary. Final report

    Otto, Antonius


    Progress is highlighted in these areas: 1. Model of magnetic reconnection induced by three-dimensional Kelvin Helmholtz (KH) modes at the magnetospheric flank boundary; 2. Quantitative evaluation of mass transport from the magnetosheath onto closed geomagnetic field for northward IMF; 3. Comparison of mass transfer by cusp reconnection and Flank Kelvin Helmholtz modes; 4. Entropy constraint and plasma transport in the magnetotail - a new mechanism for current sheet thinning; 5. Test particle model for mass transport onto closed geomagnetic field for northward IMF; 6. Influence of density asymmetry and magnetic shear on (a) the linear and nonlinear growth of 3D Kelvin Helmholtz (KH) modes, and (b) three-dimensional KH mediated mass transport; 7. Examination of entropy and plasma transport in the magnetotail; 8. Entropy change and plasma transport by KH mediated reconnection - mixing and heating of plasma; 9. Entropy and plasma transport in the magnetotail - tail reconnection; and, 10. Wave coupling at the magnetospheric boundary and generation of kinetic Alfven waves.

  19. Direct inhibition of matrix metalloproteinase-2 (MMP-2) by (-)-epigallocatechin-3-gallate: A possible role for the fibronectin type II repeats.

    Jha, Shalinee; Kanaujia, Shankar Prasad; Limaye, Anil M


    Matrix metalloproteinases (MMPs) -2 and -9, also called gelatinases, constitute a distinct subgroup within the MMP family of extracellular matrix remodeling proteases. Gelatinases are implicated in tumor cell invasion and metastasis, and are attractive therapeutic targets. Several synthetic small molecule inhibitors of MMPs developed till date have failed in clinical trials. This has prompted explorations into the gamut of dietary compounds and nutraceuticals for specific inhibitors of MMPs with desirable properties. (-)-epigallocatechin-3-gallate (EGCG), a major green tea polyphenol, is popular as a potential chemotherapeutic agent with demonstrable anti-metastatic and MMP inhibitory activities. Here, we have addressed the mechanism of EGCG-mediated inhibition of MMP-2 using in silico molecular docking approach. We show for the first time that EGCG targets the fibronectin type II repeat regions 1 and 3 of MMP-2, binds amino acids that constitute the exosite of this enzyme and hinders proper positioning of the substrate. This study offers a novel insight into the inhibition of MMP-2 by EGCG and presents a starting point for development of novel therapeutic molecules that can specifically target the gelatinases.

  20. Optimization of standard in-house 24-locus variable-number tandem-repeat typing for Mycobacterium tuberculosis and its direct application to clinical material.

    de Beer, Jessica L; Akkerman, Onno W; Schürch, Anita C; Mulder, Arnout; van der Werf, Tjip S; van der Zanden, Adri G M; van Ingen, Jakko; van Soolingen, Dick


    Variable-number tandem-repeat (VNTR) typing with a panel of 24 loci is the current gold standard in the molecular typing of Mycobacterium tuberculosis complex isolates. However, because of technical problems, a part of the loci often cannot be amplified by multiplex PCRs. Therefore, a considerable number of single-locus PCRs have to be performed for the loci with missing results, which impairs the laboratory work flow. Therefore, the original in-house method described by Supply et al. in 2006 was reevaluated. We modified seven primers and the PCR master mixture and obtained a strongly optimized in-house 24-locus VNTR typing method. The percentage of instantly complete 24-locus VNTR patterns detected in the routine flow of typing activities increased to 84.7% from the 72.3% obtained with the typing conducted with the commercially available Genoscreen MIRU-VNTR typing kit. The analytical sensitivity of the optimized in-house method was assessed by serial dilutions of M. tuberculosis in bronchoalveolar lavage fluid. A 1:10 dilution of the different strains tested was the lowest dilution for the detection of a complete 24-locus VNTR pattern. The optimized in-house 24-locus VNTR typing method will reduce the turnaround time of typing significantly and also the financial burden of these activities.

  1. Determining injuries from posterior and flank stab wounds using computed tomography tractography.

    Bansal, Vishal; Reid, Chris M; Fortlage, Dale; Lee, Jeanne; Kobayashi, Leslie; Doucet, Jay; Coimbra, Raul


    Unlike anterior stab wounds (SW), in which local exploration may direct management, posterior SW can be challenging to evaluate. Traditional triple contrast computed tomography (CT) imaging is cumbersome and technician-dependent. The present study examines the role of CT tractography as a strategy to manage select patients with back and flank SW. Hemodynamically stable patients with back and flank SW were studied. After resuscitation, Betadine- or Visipaque®-soaked sterile sponges were inserted into each SW for the estimated depth of the wound. Patients underwent abdominal helical CT scanning, including intravenous contrast, as the sole abdominal imaging study. Images were reviewed by an attending radiologist and trauma surgeon. The tractogram was evaluated to determine SW trajectory and injury to intra- or retroperitoneal organs, vascular structures, the diaphragm, and the urinary tract. Complete patient demographics including operative management and injuries were collected. Forty-one patients underwent CT tractography. In 11 patients, tractography detected violation of the intra- or retroperitoneal cavity leading to operative exploration. Injuries detected included: the spleen (two), colon (one), colonic mesentery (one), kidney (kidney), diaphragm (kidney), pneumothorax (seven), hemothorax (two), iliac artery (one), and traumatic abdominal wall hernia (two). In all patients, none had negative CT findings that failed observation. In this series, CT tractography is a safe and effective imaging strategy to evaluate posterior torso SW. It is unknown whether CT tractography is superior to traditional imaging modalities. Other uses for CT tractography may include determining trajectory from missile wounds and tangential penetrating injuries.

  2. New type of starch-binding domain: the direct repeat motif in the C-terminal region of Bacillus sp. no. 195 alpha-amylase contributes to starch binding and raw starch degrading.

    Sumitani, J; Tottori, T; Kawaguchi, T; Arai, M


    The alpha-amylase from Bacillus sp. no. 195 (BAA) consists of two domains: one is the catalytic domain similar to alpha-amylases from animals and Streptomyces in the N-terminal region; the other is the functionally unknown domain composed of an approx. 90-residue direct repeat in the C-terminal region. The gene coding for BAA was expressed in Streptomyces lividans TK24. Three active forms of the gene products were found. The pH and thermal profiles of BAAs, and their catalytic activities for p-nitrophenyl maltopentaoside and soluble starch, showed almost the same behaviours. The largest, 69 kDa, form (BAA-alpha) was of the same molecular mass as that of the mature protein estimated from the nucleotide sequence, and had raw-starch-binding and -degrading abilities. The second largest, 60 kDa, form (BAA-beta), whose molecular mass was the same as that of the natural enzyme from Bacillus sp. no. 195, was generated by proteolytic processing between the two repeat sequences in the C-terminal region, and had lower activities for raw starch binding and degrading than those of BAA-alpha. The smallest, 50 kDa, form (BAA-gamma) contained only the N-terminal catalytic domain as a result of removal of the C-terminal repeat sequence, which led to loss of binding and degradation of insoluble starches. Thus the starch adsorption capacity and raw-starch-degrading activity of BAAs depends on the existence of the repeat sequence in the C-terminal region. BAA-alpha was specifically adsorbed on starch or dextran (alpha-1,4 or alpha-1,6 glucan), and specifically desorbed with maltose or beta-cyclodextrin. These observations indicated that the repeat sequence of the enzyme was functional in the starch-binding domain (SBD). We propose the designation of the homologues to the SBD of glucoamylase from Aspergillus niger as family I SBDs, the homologues to that of glucoamylase from Rhizopus oryzae as family II, and the homologues of this repeat sequence of BAA as family III.

  3. A general method for the detection of large CAG repeat expansions by fluorescent PCR.

    Warner, J P; Barron, L H; Goudie, D; Kelly, K; Dow, D; Fitzpatrick, D R; Brock, D J


    The expansion of a tandemly repeated trinucleotide sequence, CAG, is the mutational mechanism for several human genetic diseases. We present a generally applicable PCR amplification method using a fluorescently labelled locus specific primer flanking the CAG repeat together with paired primers amplifying from multiple priming sites within the CAG repeat. Triplet repeat primed PCR (TP PCR) gives a characteristic ladder on the fluorescence trace enabling the rapid identification of large pathogenetic CAG repeats that cannot be amplified using flanking primers. We used our method to test a cohort of 183 people from myotonic dystrophy families including unaffected subjects and spouses. Eighty five clinically affected subjects with expanded alleles on Southern blot analysis were all correctly identified by TP PCR. This method is applicable for any human diseases involving CAG repeat expansions.

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

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


    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.

  5. Microsatellite flanking region similarities among different loci within insect species.

    Meglécz, E; Anderson, S J; Bourguet, D; Butcher, R; Caldas, A; Cassel-Lundhagen, A; d'Acier, A C; Dawson, D A; Faure, N; Fauvelot, C; Franck, P; Harper, G; Keyghobadi, N; Kluetsch, C; Muthulakshmi, M; Nagaraju, J; Patt, A; Péténian, F; Silvain, J-F; Wilcock, H R


    Although microsatellites are ubiquitous in eukaryota, the number of available markers varies strongly among taxa. This meta-analysis was conducted on 32 insect species. Sequences were obtained from two assembled whole genomes, whole genome shotgun (WGS) sequences from 10 species and screening partial genomic libraries for microsatellites from 23 species. We have demonstrated: (1) strong differences in the abundance of microsatellites among species; (2) that microsatellites within species are often grouped into families based on similarities in their flanking sequences; (3) that the proportion of microsatellites grouped into families varies strongly among taxa; and (4) that microsatellite families were significantly more often associated with transposable elements - or their remnants - than unique microsatellite sequences.

  6. Evidence of Multiple Flank Collapse at Volcan Baru, Panama

    Herrick, J. A.; Rose, W. I.


    Michigan Tech's Peace Corps Master's International program (PCMI) in Geological Hazards has enabled several long-term investigations of active volcanoes in Latin America. To contribute to volcanic hazard assessments in Panama and achieve the goals defined by the PCMI program, we developed this debris avalanche project to address outstanding questions regarding Volcan Baru's most devastating event - massive slope failure of the western flank. Relying on basic mapping tools as well as the 2007 USGS Open-File Report focusing on hazard assessments of Panama's youngest and potentially active volcano, identification of the debris avalanche deposits (DAD) required detailed field investigations to determine the limits of the units. Extending across an area larger than 600 km2, field strategies were developed based on outcrop exposures within drainages and road-cuts. Aerial photos and DEMs of Baru's nested craters were interpreted by earlier scientists as the remains of two collapsed flanks. The results from in-depth field traverses provide several important discoveries: paleosols and sharp contacts within the stratigraphy indicate multiple DAD, deeply weathered hummocks red-flag the deposits more than 50-km away from Baru's crater, and high-quality radiocarbon samples (up to 45-cm long fragments of entrained wood) lie in the distal reaches of the debris flow area. During the 2008-2009 field seasons, we received assistance from the University of Panama, Civil Protection, and Panama's National Institute of Geography. Support from local experts and feedback from professional scientists of the Smithsonian Institution and Costa Rica's Institute of Electricity were invaluable. The 2-year investment in volcanic hazard studies has brought together resources from several countries as well as fresh data that will benefit the residents and emergency management officials of Panama. Jigsaw fractured clasts lie within Volcan Baru's debris avalanche deposits more than 28 km south of the

  7. Repeat-until-success quantum repeaters

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


    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.

  8. Catastrophic flank collapses and slumping in Pico Island during the last 130 kyr (Pico-Faial ridge, Azores Triple Junction)

    Costa, A. C. G.; Hildenbrand, A.; Marques, F. O.; Sibrant, A. L. R.; Santos de Campos, A.


    The Pico Island constitutes the easternmost sub-aerial domain of a steep WNW-ESE volcanic ridge, which has developed within the Nubia-Eurasia diffuse plate boundary (Azores Triple Junction). The island comprises three volcanic systems, from older to younger: the Topo Volcano, the Fissural System, and the Pico Stratovolcano. From a high-resolution Digital Elevation Model (10 m), and new bathymetric, stratigraphic, structural, and high-precision K-Ar data, we reconstruct the main successive stages of growth and partial destruction of the island over the last 200 kyr. We especially concentrate on the central sector of the island, which has recorded gradual movements through slumping and catastrophic flank collapses since ca. 130 kyr. The remmants of the Topo Volcano are partly exposed on Pico's SE flank, and are here dated between 186 ± 5 and 115 ± 4 ka. Topo was significantly destroyed by N- and S-directed large-scale flank collapses between ca. 125 and 70 ka. On Pico's N flank, collapse seems to have removed all the unstable material, but in the S the collapse structure is composite, including a major flank collapse and a remnant slump complex that is still active. A first episode of deformation occurred between ca. 125 and 115 ka along the master fault of the slump. Between ca. 115 and 69 ka, most of the unstable material was removed by a major flank collapse, leaving behind a still considerable volume of unstable material that comprises the active slump. This first collapse was catastrophic and generated a large debris deposit recognized on the high-resolution bathymetry, with a minimum run-out of ca. 17 km. The scar was partially filled by volcanic products erupted from volcanic cones developed within the slump depression, and possibly also from the early WNW-ESE Fissural System. Subsequent deformation in the slump area affected in part the filling units, leading to the individualization of secondary curved faults. Younger volcanic products have gradually

  9. Effects of tool flank wear on orthogonal cutting process of aluminum alloy

    YUAN Ping; KE Ying-lin


    The tool flank begins to wear out as soon as cutting process proceeds. Cutting parameters such as cutting forces and cutting temperature will vary with increasing degree of flank wear. In order to reveal the relationship between them, the theoretical situations of cutting process were analyzed considering the tool flank wear effect. The variation rules of cutting force, residual stress and temperature distributions along with the tool flank wear were analyzed comparing with the sharp tool tip. Through FEM simulation method, affections of the tool flank wear value VB on cutting forces, residual stress and temperature distributions were analyzed. A special result in this simulation is that the thrust force is more sensitive to tool flank wear, which can be used as a recognition method of tool condition monitoring. The FEM simulation analysis result agrees well with the experimental measuring data in public literatures and some experiments made also by the authors.

  10. The flank eruption history of Etna (1610-2006 as a constraint on lava flow hazard

    Stefano Branca


    Full Text Available Data of the flank eruptions of Etna from over the last 400 years were extracted from the new geological map for the lava flow extensions and vent positions, and from the catalogs of historical eruptions for the eruption durations and lava volumes. The partially or widely hidden lava fields on the new geological map were retrieved from older geological maps. The distributions of the eruption durations and lava volumes were analyzed, with the definition of six eruptive classes for use in numerical simulations. The threshold values for the eruption durations and lava volumes were set at 45 days and at 35 × 106 m3 and 100 × 106 m3, respectively. A global analysis was performed on the whole volcano to evaluate the recurrence of the classes, and to estimate for each class the ranges, means and standard deviations of the durations, volumes and elevations of the main vent. The same analysis was repeated by subdividing the volcano into three sectors, which were defined on the basis of the distribution of the eruptive fissures over the last 15 ka. The classes have different recurrences across these various sectors, and different distributions of volumes, durations and elevations of the main vent. Finally, a lava flow resurfacing map that counts the number of lava flows on each given area of the volcano over the last 400 years was compiled and then normalized.

  11. Long-period seismic events with strikingly regular temporal patterns on Katla volcano's south flank (Iceland)

    Sgattoni, Giulia; Guðmundsson, Ólafur; Einarsson, Páll; Tryggvason, Ari; Lund, Björn; Lucchi, Federico


    Katla is a threatening volcano in Iceland, partly covered by the M\\'yrdalsj\\"okull ice cap. The volcano has a large caldera with several active geothermal areas. A peculiar cluster of long-period seismic events started on Katla's south flank in July 2011, during an unrest episode in the caldera that culminated in a glacier outburst. The seismic events were tightly clustered at shallow depth in the Gvendarfell area, 4 km south of the caldera, under a small glacier stream on the southern margin of M\\'yrdalsj\\"okull. No seismic events were known to have occurred in this area before. The most striking feature of this seismic cluster is its temporal pattern, characterized by regular intervals between repeating seismic events, modulated by a seasonal variation. Remarkable is also the stability of both the time and waveform features over a long time period, around 3.5 years. No comparable examples have been found in the literature. Both volcanic and glacial processes can produce similar waveforms and therefore have ...

  12. Flank transparency: transparent filters seen in dynamic two-color displays.

    Wollschläger, D; Rodriguez, A M; Hoffman, D D


    Flank transparency is the perception of a colored transparent filter evoked by apparent-motion displays containing as few as two colors. Displays of flank transparency contain a random array of line segments placed on a uniform background. Small flanks are added to the line segments if the segments fall in the interior of a moving virtual shape, such as a virtual disk. This leads to the perception of a colored transparent disk with well-defined boundaries moving over the array of lines. Current qualitative and quantitative models of luminance and color conditions for perceptual transparency do not account for flank transparency as they require displays containing at least three different colors.

  13. Patterns of nucleotides that flank substitutions in human orthologous genes

    Huang Zhuoran


    Full Text Available Abstract Background Sequence context is an important aspect of base mutagenesis, and three-base periodicity is an intrinsic property of coding sequences. However, how three-base periodicity is influenced in the vicinity of substitutions is still unclear. The effect of context on mutagenesis should be revealed in the usage of nucleotides that flank substitutions. Relative entropy (also known as Kullback-Leibler divergence is useful for finding unusual patterns in biological sequences. Results Using relative entropy, we visualized the periodic patterns in the context of substitutions in human orthologous genes. Neighbouring patterns differed both among substitution categories and within a category that occurred at three codon positions. Transition tended to occur in periodic sequences relative to transversion. Periodic signals were stronger in a set of flanking sequences of substitutions that occurred at the third-codon positions than in those that occurred at the first- or second-codon positions. To determine how the three-base periodicity was affected near the substitution sites, we fitted a sine model to the values of the relative entropy. A sine of period equal to 3 is a good approximation for the three-base periodicity at sites not in close vicinity to some substitutions. These periods were interrupted near the substitution site and then reappeared away from substitutions. A comparative analysis between the native and codon-shuffled datasets suggested that the codon usage frequency was not the sole origin of the three-base periodicity, implying that the native order of codons also played an important role in this periodicity. Synonymous codon shuffling revealed that synonymous codon usage bias was one of the factors responsible for the observed three-base periodicity. Conclusions Our results offer an efficient way to illustrate unusual periodic patterns in the context of substitutions and provide further insight into the origin of three

  14. Scanning mutagenesis of the amino acid sequences flanking phosphorylation site 1 of the mitochondrial pyruvate dehydrogenase complex

    Nagib eAhsan


    Full Text Available The mitochondrial pyruvate dehydrogenase complex is regulated by reversible seryl-phosphorylation of the E1α subunit by a dedicated, intrinsic kinase. The phospho-complex is reactivated when dephosphorylated by an intrinsic PP2C-type protein phosphatase. Both the position of the phosphorylated Ser-residue and the sequences of the flanking amino acids are highly conserved. We have used the synthetic peptide-based kinase client assay plus recombinant pyruvate dehydrogenase E1α and E1α-kinase to perform scanning mutagenesis of the residues flanking the site of phosphorylation. Consistent with the results from phylogenetic analysis of the flanking sequences, the direct peptide-based kinase assays tolerated very few changes. Even conservative changes such as Leu, Ile, or Val for Met, or Glu for Asp, gave very marked reductions in phosphorylation. Overall the results indicate that regulation of the mitochondrial pyruvate dehydrogenase complex by reversible phosphorylation is an extreme example of multiple, interdependent instances of co-evolution.

  15. Biogeochemical Fluxes Across the Juan de Fuca Ridge-Flank: Minor and Trace Element Systematics

    Hulme, S. M.; Wheat, C. G.; Jannasch, H. W.


    Crustal ridge-flank hydrothermal convection of seawater profoundly affects; global geochemical fluxes and cycles, plate tectonics through crustal cooling, and the deep biosphere. Comprehensive assessment of chemical fluxes from this type of hydrothermal circulation has been obscured by sampling artifacts during sample retrieval and extraction from drilling and the lack of uncontaminated in situ samples. With the development of sealed borehole observatories (CORKs) it is now possible to obtainable uncontaminated crustal formation fluids. The Endeavor Segment of the Juan de Fuca Ridge presented an ideal region for addressing the effects of ridge flank hydrothermal circulation on global processes because of direct access to basement fluids through six CORKs and the known composition of nearby spring fluids. We present data from fluids collected via osmotically-pumped continuous fluid samplers (OsmoSamplers) from within sealed boreholes. Methods using high-resolution ICP-MS were developed to allow analysis of trace elements (V, Cr, Co, Ni, Cu, Zn, Rb, Y, Mo, Cd, Cs, Ba, and U) and the entire suite of rare-earth elements in 5ml of sample. Fluids from OsmoSamplers deployed at 3 drill sites (1024, 1026, and 1027) were analyzed along with borehole fluids collected at two additional sites (1025 and 1026). Pore fluids from multiple drilling legs were also compared for sampling artifacts associated with differing sediment core collection techniques. The results of this study determined which trace elements can be accurately determined from ocean drilling and pore water extraction from sediments and borehole sampling by comparison with the time-integrated samples obtained from within the sealed boreholes. Once the accurate composition of basement fluids was determined, it was possible to examine regional trends of the hydrothermal aquifer system both along and across strike of the ridge axis. These data of crustal fluids can then be compared to pore fluids collected during

  16. Evolution of a behavior-linked microsatellite-containing element in the 5' flanking region of the primate AVPR1A gene

    Bai Yaohui


    Full Text Available Abstract Background The arginine vasopressin V1a receptor (V1aR modulates social cognition and behavior in a wide variety of species. Variation in a repetitive microsatellite element in the 5' flanking region of the V1aR gene (AVPR1A in rodents has been associated with variation in brain V1aR expression and in social behavior. In humans, the 5' flanking region of AVPR1A contains a tandem duplication of two ~350 bp, microsatellite-containing elements located approximately 3.5 kb upstream of the transcription start site. The first block, referred to as DupA, contains a polymorphic (GT25 microsatellite; the second block, DupB, has a complex (CT4-(TT-(CT8-(GT24 polymorphic motif, known as RS3. Polymorphisms in RS3 have been associated with variation in sociobehavioral traits in humans, including autism spectrum disorders. Thus, evolution of these regions may have contributed to variation in social behavior in primates. We examined the structure of these regions in six ape, six monkey, and one prosimian species. Results Both tandem repeat blocks are present upstream of the AVPR1A coding region in five of the ape species we investigated, while monkeys have only one copy of this region. As in humans, the microsatellites within DupA and DupB are polymorphic in many primate species. Furthermore, both single (lacking DupB and duplicated alleles (containing both DupA and DupB are present in chimpanzee (Pan troglodytes populations with allele frequencies of 0.795 and 0.205 for the single and duplicated alleles, respectively, based on the analysis of 47 wild-caught individuals. Finally, a phylogenetic reconstruction suggests two alternate evolutionary histories for this locus. Conclusion There is no obvious relationship between the presence of the RS3 duplication and social organization in primates. However, polymorphisms identified in some species may be useful in future genetic association studies. In particular, the presence of both single and duplicated

  17. Flank pseudohernia following posterior rib fracture: a case report.

    Butensky, Adam M; Gruss, Leah P; Gleit, Zachary L


    A pseudohernia is an abdominal wall bulge that may be mistaken for a hernia but that lacks the disruption of the abdominal wall that characterizes a hernia. Thus, the natural history and treatment of this condition differ from those of a hernia. This is the first report of a pseudohernia due to cough-associated rib fracture. A case of pseudohernia due to fractures of the 10(th) and 11(th) ribs in a 68-year-old white woman is presented. The patient suffered from a major coughing episode 1 year prior to her presentation, after which she noted a progressively enlarging bulge in her left flank. Computed tomography demonstrated a bulge in the abdominal wall containing bowel and spleen but with all muscle and fascial layers intact; in addition, lateral 10(th) rib and posterior 11(th) rib fractures were noted. As there was no defect in muscle or fascia, we diagnosed a pseudohernia, likely due to a denervation injury from the fractured ribs. Symptomatic treatment was recommended, including wearing a corset and referral to a pain management clinic. Symptomatic treatment is thought to be the mainstay of therapy for pseudohernias, as surgical intervention is unlikely to be of benefit.

  18. The study of double flank micro gear roll testing

    Liu, Yen-Chih; An, Nai-Chun; Yang, Shu-Han; Yan, Sheng-Zhan; Chen, Shih-Lu


    The recent fast development of multifunctional portable electronic devices results in the obvious requirement of micro mechanical components. Due to the popular application of the micro actuators and the micro gearboxes, micro gears become the frequently used micro mechanical component in a small device such as small intelligent robots or dental surgical devices. Metal Industries Research & Development Centre (MIRDC) has successfully developed a small speed reducer that comprises several micro planetary gear trains. The module of this micro planetary gear train is 0.12mm. Since all gears are small, no commercial instrument is available for inspection. How to evaluate the manufacturing quality of micro gears becomes an important issue. This study focuses on the double flank gear rolling test and a specialized apparatus is built referring to the testing requirements in the international standards. The center distance variation during the rolling test is recorded and two indices, the total radial composite deviation and the maximum tooth-to-tooth radial composite deviation, are calculated to evaluate the accuracy grade of the micro gears. Experimental results show that the accuracy of the micro gear made by the cold forging process conforms to grade 7 defined in the ISO 1328-2 while grade 2 is achieved if the JGMA 116-02 is specified.

  19. Asymmetric nucleosomes flank promoters in the budding yeast genome.

    Ramachandran, Srinivas; Zentner, Gabriel E; Henikoff, Steven


    Nucleosomes in active chromatin are dynamic, but whether they have distinct structural conformations is unknown. To identify nucleosomes with alternative structures genome-wide, we used H4S47C-anchored cleavage mapping, which revealed that 5% of budding yeast (Saccharomyces cerevisiae) nucleosome positions have asymmetric histone-DNA interactions. These asymmetric interactions are enriched at nucleosome positions that flank promoters. Micrococcal nuclease (MNase) sequence-based profiles of asymmetric nucleosome positions revealed a corresponding asymmetry in MNase protection near the dyad axis, suggesting that the loss of DNA contacts around H4S47 is accompanied by protection of the DNA from MNase. Chromatin immunoprecipitation mapping of selected nucleosome remodelers indicated that asymmetric nucleosomes are bound by the RSC chromatin remodeling complex, which is required for maintaining nucleosomes at asymmetric positions. These results imply that the asymmetric nucleosome-RSC complex is a metastable intermediate representing partial unwrapping and protection of nucleosomal DNA on one side of the dyad axis during chromatin remodeling.

  20. Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences.

    Stéphanie Barthe

    Full Text Available Simple sequence repeat (SSR markers are widely used tools for inferences about genetic diversity, phylogeography and spatial genetic structure. Their applications assume that variation among alleles is essentially caused by an expansion or contraction of the number of repeats and that, accessorily, mutations in the target sequences follow the stepwise mutation model (SMM. Generally speaking, PCR amplicon sizes are used as direct indicators of the number of SSR repeats composing an allele with the data analysis either ignoring the extent of allele size differences or assuming that there is a direct correlation between differences in amplicon size and evolutionary distance. However, without precisely knowing the kind and distribution of polymorphism within an allele (SSR and the associated flanking region (FR sequences, it is hard to say what kind of evolutionary message is conveyed by such a synthetic descriptor of polymorphism as DNA amplicon size. In this study, we sequenced several SSR alleles in multiple populations of three divergent tree genera and disentangled the types of polymorphisms contained in each portion of the DNA amplicon containing an SSR. The patterns of diversity provided by amplicon size variation, SSR variation itself, insertions/deletions (indels, and single nucleotide polymorphisms (SNPs observed in the FRs were compared. Amplicon size variation largely reflected SSR repeat number. The amount of variation was as large in FRs as in the SSR itself. The former contributed significantly to the phylogenetic information and sometimes was the main source of differentiation among individuals and populations contained by FR and SSR regions of SSR markers. The presence of mutations occurring at different rates within a marker's sequence offers the opportunity to analyse evolutionary events occurring on various timescales, but at the same time calls for caution in the interpretation of SSR marker data when the distribution of within

  1. mCAL: A New Approach for Versatile Multiplex Action of Cas9 Using One sgRNA and Loci Flanked by a Programmed Target Sequence.

    Finnigan, Gregory C; Thorner, Jeremy


    Genome editing exploiting CRISPR/Cas9 has been adopted widely in academia and in the biotechnology industry to manipulate DNA sequences in diverse organisms. Molecular engineering of Cas9 itself and its guide RNA, and the strategies for using them, have increased efficiency, optimized specificity, reduced inappropriate off-target effects, and introduced modifications for performing other functions (transcriptional regulation, high-resolution imaging, protein recruitment, and high-throughput screening). Moreover, Cas9 has the ability to multiplex, i.e., to act at different genomic targets within the same nucleus. Currently, however, introducing concurrent changes at multiple loci involves: (i) identification of appropriate genomic sites, especially the availability of suitable PAM sequences; (ii) the design, construction, and expression of multiple sgRNA directed against those sites; (iii) potential difficulties in altering essential genes; and (iv) lingering concerns about "off-target" effects. We have devised a new approach that circumvents these drawbacks, as we demonstrate here using the yeast Saccharomyces cerevisiae First, any gene(s) of interest are flanked upstream and downstream with a single unique target sequence that does not normally exist in the genome. Thereafter, expression of one sgRNA and cotransformation with appropriate PCR fragments permits concomitant Cas9-mediated alteration of multiple genes (both essential and nonessential). The system we developed also allows for maintenance of the integrated, inducible Cas9-expression cassette or its simultaneous scarless excision. Our scheme-dubbed mCAL for " M: ultiplexing of C: as9 at A: rtificial L: oci"-can be applied to any organism in which the CRISPR/Cas9 methodology is currently being utilized. In principle, it can be applied to install synthetic sequences into the genome, to generate genomic libraries, and to program strains or cell lines so that they can be conveniently (and repeatedly

  2. mCAL: A New Approach for Versatile Multiplex Action of Cas9 Using One sgRNA and Loci Flanked by a Programmed Target Sequence

    Gregory C. Finnigan


    Full Text Available Genome editing exploiting CRISPR/Cas9 has been adopted widely in academia and in the biotechnology industry to manipulate DNA sequences in diverse organisms. Molecular engineering of Cas9 itself and its guide RNA, and the strategies for using them, have increased efficiency, optimized specificity, reduced inappropriate off-target effects, and introduced modifications for performing other functions (transcriptional regulation, high-resolution imaging, protein recruitment, and high-throughput screening. Moreover, Cas9 has the ability to multiplex, i.e., to act at different genomic targets within the same nucleus. Currently, however, introducing concurrent changes at multiple loci involves: (i identification of appropriate genomic sites, especially the availability of suitable PAM sequences; (ii the design, construction, and expression of multiple sgRNA directed against those sites; (iii potential difficulties in altering essential genes; and (iv lingering concerns about “off-target” effects. We have devised a new approach that circumvents these drawbacks, as we demonstrate here using the yeast Saccharomyces cerevisiae. First, any gene(s of interest are flanked upstream and downstream with a single unique target sequence that does not normally exist in the genome. Thereafter, expression of one sgRNA and cotransformation with appropriate PCR fragments permits concomitant Cas9-mediated alteration of multiple genes (both essential and nonessential. The system we developed also allows for maintenance of the integrated, inducible Cas9-expression cassette or its simultaneous scarless excision. Our scheme—dubbed mCAL for “Multiplexing of Cas9 at Artificial Loci”—can be applied to any organism in which the CRISPR/Cas9 methodology is currently being utilized. In principle, it can be applied to install synthetic sequences into the genome, to generate genomic libraries, and to program strains or cell lines so that they can be conveniently (and

  3. InSAR Measurements of Flank Stability at Cumbre Vieja Volcano, La Palma (Spain)

    Holley, Rachel; Thomas, Adam; Li, Zhenhong; McGuire, Bill; Ziebart, Marek; Day, Simon


    It has been suggested that instability of the western flank of Cumbre Vieja volcano, on the island of La Palma (Canary Islands), could have the potential to result in a lateral collapse of the flank, which in turn could generate an Atlantic tsunami. InSAR measurements provide an excellent way to corroborate data from GPS and structural surveys to provide independent corroboration. This work will use maps of atmospheric phase delay to improve the accuracy of persistent scatterer interferometry results over the island, and integrate these measurements with new GPS data, to give a complete assessment of flank stability and allow better assessment of the risks posed by the volcano.

  4. A 55-Year Old Man with Acute Painful Flank Mass, a Case Report

    Aida Alavi-Moghaddam


    Full Text Available Lumbar hernias (LH accounts for less than 1.5% of total hernia incidence. It can occur in two separate triangular areas of the flank. About 300 cases have been reported in the literature. Here, we report a 55-year old man with acute painful left side flank mass and final diagnosis of LH. The mass was appeared about three hours before admission and his pain was slight at first but became more severe gradually. He had stable vital sign and the only positive finding on his physical examination was the sphere shape, firm, mobile, and mild tender mass at his left flank.

  5. 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

    Zhengyang Zeng


    Full Text Available 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.

  6. East flank of the Sibumasu block in NW Thailand and Myanmar and its possible northward continuation into Yunnan: a review and suggested tectono-stratigraphic interpretation

    Ridd, Michael F.


    The east flank of the Sibumasu block was a passive continental margin, and in NW Thailand is marked by the absence of the autochthonous Middle Permian-Triassic platform carbonates which are widespread across the rest of Sibumasu further west. Instead, the carbonates are represented by hemipelagic cherts, mudstones and sandstones including turbidites. During the northward drift of Sibumasu, following its Early Permian rifting from Gondwana, an accretionary complex was present where Palaeotethyan pelagic rocks as old as Devonian were subducted beneath the Sukhothai volcanic arc. At the time of Sibumasu's collision with the Sukhothai arc, beginning in the Middle Triassic, the accretionary complex was thrust westwards across the east flank of Sibumasu. It is suggested that in the Late Triassic the thrust pile which had been the accretionary complex underwent erosion and was the source of terrigenous clastic rocks deposited further west in a foredeep basin. The boundary of Sibumasu's east flank with the Permo-Triassic carbonate platform further west is the arcuate Mae Ping-Nam Teng Fault system. Notwithstanding later Cenozoic strike-slip displacement, those faults (as well as the Mae Yuam Fault) are interpreted to have had an earlier history of westward-directed Indosinian thrusting. Northwards in Myanmar and Yunnan the Sibumasu Permo-Triassic carbonate shelf continues as the Shan Plateau and Baoshan Block. The east flank is represented by the Changning-Menglian Belt, and the Palaeotethys 'cryptic suture' in Thailand possibly joins with the Lancangjiang Suture.

  7. Quantum repeated games revisited

    Frackiewicz, Piotr


    We present a scheme for playing quantum repeated 2x2 games based on the Marinatto and Weber's approach to quantum games. As a potential application, we study twice repeated Prisoner's Dilemma game. We show that results not available in classical game can be obtained when the game is played in the quantum way. Before we present our idea, we comment on the previous scheme of playing quantum repeated games.

  8. Geophysical and geological surveys along the northeastern flank of Mount error, Northwestern Indian Ocean

    Ramana, M.V.; Rajendraprasad, B.; Hansen, R.D.

    Bathymetry, multichannel continuous seismic reflection, magnetic and gravity surveys and sampling were carried out over Mount Error in the northwestern Indian Ocean and along the northeastern flank of the seamount, to study the nature of its...


    Xing-jian Lin; Ying-dong Zhang; Qing-shan Guan; Qing Di; Jing-ping Shi; Wei-guo Liu


    Objective To analyze the role of resistin in insulin resistance (IR) through investigating the variation of plasma resistin levels and single-nucleotide polymorphisms (SNPs) in resistin gene 5' flanking region in stroke patients.Methods In 103 atherothrombotic cerebral infarction (ACI) patients, 85 lacunar infarction (LI) patients, 70 intrac-erebral hemorrhage (ICH) patients, and 86 healthy controls, plasma resistin and insulin levels were measured by ELISA , SNPs in resistin gene 5' flanking region were detected by PCR and direct DNA sequencing. The subjects' body height and weight, the body mass index, quantitative insulin sensitivity check index (QUICKI), blood pressure, and the concentration of fasting plasma glucose, triglyceride, total cholesterol, creatinine, low-density lipoprotein, and high-density lipo-protein were also determined.Results QUICKI was significantly lower in the ACI and ICH patients (0.316±0.037 and 0.309±0.032, respectively) than that in the controls (0.342±0.043, P<0.001), while plasma resistin level was significantly higher in the ACI and ICH patients (6.36±3.79 and 7.15±4.27 ng/mL, respectively) than that in the controls (5.28±2.56ng/mL,P<0.05), but such difference was not observed in the LI patients compared with controls. There was a statistically negative correlation between plasma resistin level withQUICKI (r=-0.228,P<0.001). The distributions of allele and genotype frequencies ofresistin gene -420C>G and -537A>C SNPs were not significantly different among the different groups, and those SNPs were not correlated with other clinical and biochemical parameters. Conclusions Plasma resistin is associated with stroke by participating in the development of IR. The SNPs in resistin gene 5' flanking region has no impact on the plasma resistin level.

  10. Joint relative location of earthquakes without a predefined velocity model: an example from a peculiar seismic cluster on Katla volcano's south-flank (Iceland)

    Sgattoni, G.; Gudmundsson, Ó.; Einarsson, P.; Lucchi, F.


    Relative location methods are commonly used to precisely locate earthquake clusters consisting of similar waveforms. Repeating waveforms are often recorded at volcanoes, where, however, the crust structure is expected to contain strong heterogeneities and therefore the 1D velocity model assumption that is made in most location strategies is not likely to describe reality. A peculiar cluster of repeating low-frequency seismic events was recorded on the south flank of Katla volcano (Iceland) from 2011. As the hypocentres are located at the rim of the glacier, the seismicity may be due to volcanic or glacial processes. Information on the size and shape of the cluster may help constraining the source process. The extreme similarity of waveforms points to a very small spatial distribution of hypocentres. In order to extract meaningful information about size and shape of the cluster, we minimize uncertainty by optimizing the cross-correlation measurements and relative-location process. With a synthetic test we determine the best parameters for differential-time measurements and estimate their uncertainties, specifically for each waveform. We design a location strategy to work without a predefined velocity model, by formulating and inverting the problem to seek changes in both location and slowness, thus accounting for azimuth, take-off angles and velocity deviations from a 1D model. We solve the inversion explicitly in order to propagate data errors through the calculation. With this approach we are able to resolve a source volume few tens of meters wide in horizontal directions and around 100 meters in depth. There is no suggestion that the hypocentres lie on a single fault plane and the depth distribution indicates that their source is unlikely to be related to glacial processes as the ice thickness is not expected to exceed few tens of meters in the source area. Our method is designed for a very small source region, allowing us to assume a constant slowness for the

  11. Joint relative location of earthquakes without a pre-defined velocity model: an example from a peculiar seismic cluster on Katla volcano's south-flank (Iceland)

    Sgattoni, G.; Gudmundsson, Ó.; Einarsson, P.; Lucchi, F.


    Relative location methods are commonly used to precisely locate earthquake clusters consisting of similar waveforms. Repeating waveforms are often recorded at volcanoes, where, however, the crust structure is expected to contain strong heterogeneities and therefore the 1-D velocity model assumption that is made in most location strategies is not likely to describe reality. A peculiar cluster of repeating low-frequency seismic events was recorded on the south flank of Katla volcano (Iceland) from 2011. As the hypocentres are located at the rim of the glacier, the seismicity may be due to volcanic or glacial processes. Information on the size and shape of the cluster may help constraining the source process. The extreme similarity of waveforms points to a very small spatial distribution of hypocentres. In order to extract meaningful information about size and shape of the cluster, we minimize uncertainty by optimizing the cross-correlation measurements and relative-location process. With a synthetic test we determine the best parameters for differential-time measurements and estimate their uncertainties, specifically for each waveform. We design a location strategy to work without a pre-defined velocity model, by formulating and inverting the problem to seek changes in both location and slowness, thus accounting for azimuth, take-off angles and velocity deviations from a 1-D model. We solve the inversion explicitly in order to propagate data errors through the calculation. With this approach we are able to resolve a source volume few tens of metres wide in horizontal directions and around 100 metres in depth. There is no suggestion that the hypocentres lie on a single fault plane and the depth distribution indicates that their source is unlikely to be related to glacial processes as the ice thickness is not expected to exceed few tens of metres in the source area. Our method is designed for a very small source region, allowing us to assume a constant slowness for the

  12. Cyclic Explosivity in High Elevation Phreatomagmatic Eruptions at Ocean Island Volcanoes: Implications for Aquifer Pressurization and Volcano Flank Destabilization.

    Tarff, R.; Day, S. J.; Downes, H.; Seghedi, I.


    Groundwater heating and pressurization of aquifers trapped between dikes in ocean island volcanoes has been proposed as a mechanism for destabilizing and triggering large-volume flank collapses. Previous modelling has indicated that heat transfer from sustained magma flow through dikes during eruption has the potential to produce destabilizing levels of pressure on time scales of 4 to 400 days, if the aquifers remain confined. Here we revisit this proposal from a different perspective. We examine evidence for pressure variations in dike-confined aquifers during eruptions at high elevation vents on ocean island volcanoes. Initially magmatic, these eruptions change to mostly small-volume explosive phreatomagmatic activity. A recent example is the 1949 eruption on La Palma, Canary Islands. Some such eruptions involve sequences of larger-volume explosive phases or cycles, including production of voluminous low-temperature, pyroclastic density currents (PDC). Here we present and interpret data from the Cova de Paul crater eruption (Santo Antao, Cape Verde Islands). The phreatomagmatic part of this eruption formed two cycles, each culminating with eruption of PDCs. Compositional and textural variations in the products of both cycles indicate that the diatreme fill began as coarse-grained and permeable which allowed gas to escape. During the eruption, the fill evolved to a finer grained, poorly sorted, less permeable material, in which pore fluid pressures built up to produce violent explosive phases. This implies that aquifers adjacent to the feeder intrusion were not simply depressurized at the onset of phreatomagmatic explosivity but experienced fluctuations in pressure throughout the eruption as the vent repeatedly choked and emptied. In combination with fluctuations in magma supply rate, driving of aquifer pressurization by cyclical vent choking will further complicate the prediction of flank destabilization during comparable eruptions on ocean island volcanoes.

  13. Relative relocation of earthquakes without a predefined velocity model: an example from a peculiar seismic cluster on Katla volcano's south-flank (Iceland)

    Sgattoni, Giulia; Einarsson, Páll; Lucchi, Federico


    Relative relocation methods are commonly used to precisely relocate earthquake clusters consisting of similar waveforms. Repeating waveforms are often recorded at volcanoes, where, however, the crust structure is expected to contain strong heterogeneities and therefore the 1D velocity model assumption that is made in most location strategies is not likely to describe reality. A peculiar cluster of repeating low-frequency seismic events was recorded on the south flank of Katla volcano (Iceland) from 2011. As the hypocentres are located at the rim of the glacier, the seismicity may be due to volcanic or glacial processes. Information on the size and shape of the cluster may help constraining the source process. The extreme similarity of waveforms points to a very small spatial distribution of hypocentres. In order to extract meaningful information about size and shape of the cluster, we minimize uncertainty by optimizing the cross-correlation measurements and relative-relocation process. With a synthetic test w...

  14. Origin and spread of beta-globin gene mutations in India, Africa, and Mediterranea: analysis of the 5' flanking and intragenic sequences of beta S and beta C genes.

    Trabuchet, G; Elion, J; Baudot, G; Pagnier, J; Bouhass, R; Nigon, V M; Labie, D; Krishnamoorthy, R


    Nucleotide polymorphisms of both the 5' flanking and intragenic regions of the human beta-globin gene were investigated by directly sequencing genomic DNA after amplification by the polymerase chain reaction in 47 subjects homozygous for the beta S or the beta C mutation. The sickle-cell mutation was found in the context of five different haplotypes defined by eight nucleotide substitutions and various structures of a region of the simple repeated sequence (AT) chi Ty. All subjects from the same geographic origin bear an identical chromosomal structure, defining the Senegal-, Bantu-, Benin-, Cameroon-, and Indian-type chromosomes. These results strengthen our previous conclusions about the multiple occurrence of the sickle-cell mutation. The Benin-type chromosome was also found among Algerian and Sicilian sickle-cell patients, whereas the Indian-type chromosome was observed in two geographically distant tribes, illustrating the spread of these sickle-cell genes. We also found that the intragenic sequence polymorphisms (frameworks) are not always in linkage disequilibrium with the BamH I polymorphism downstream from the beta-globin gene, as had been previously observed. Finally, we present a tentative phylogenetic tree of the different alleles at this locus. Some polymorphisms of this sequence might be contemporary with our last common ancestor, the great apes, that is, about 4-6 millions years old.

  15. Reconfigurable multiport EPON repeater

    Oishi, Masayuki; Inohara, Ryo; Agata, Akira; Horiuchi, Yukio


    An extended reach EPON repeater is one of the solutions to effectively expand FTTH service areas. In this paper, we propose a reconfigurable multi-port EPON repeater for effective accommodation of multiple ODNs with a single OLT line card. The proposed repeater, which has multi-ports in both OLT and ODN sides, consists of TRs, BTRs with the CDR function and a reconfigurable electrical matrix switch, can accommodate multiple ODNs to a single OLT line card by controlling the connection of the matrix switch. Although conventional EPON repeaters require full OLT line cards to accommodate subscribers from the initial installation stage, the proposed repeater can dramatically reduce the number of required line cards especially when the number of subscribers is less than a half of the maximum registerable users per OLT. Numerical calculation results show that the extended reach EPON system with the proposed EPON repeater can save 17.5% of the initial installation cost compared with a conventional repeater, and can be less expensive than conventional systems up to the maximum subscribers especially when the percentage of ODNs in lightly-populated areas is higher.

  16. Revisiting the TALE repeat.

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


    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.

  17. A Repeating Fast Radio Burst

    Spitler, L G; 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


    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 measures (i.e. integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of the fast radio bursts has led several authors to hypothesise that they originate in cataclysmic astrophysical events. Here we report the detection of ten additional bursts from the direction of FRB121102, using the 305-m Arecibo telescope. These new bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and wh...

  18. Recursive quantum repeater networks

    Van Meter, Rodney; Horsman, Clare


    Internet-scale quantum repeater networks will be heterogeneous in physical technology, repeater functionality, and management. The classical control necessary to use the network will therefore face similar issues as Internet data transmission. Many scalability and management problems that arose during the development of the Internet might have been solved in a more uniform fashion, improving flexibility and reducing redundant engineering effort. Quantum repeater network development is currently at the stage where we risk similar duplication when separate systems are combined. We propose a unifying framework that can be used with all existing repeater designs. We introduce the notion of a Quantum Recursive Network Architecture, developed from the emerging classical concept of 'recursive networks', extending recursive mechanisms from a focus on data forwarding to a more general distributed computing request framework. Recursion abstracts independent transit networks as single relay nodes, unifies software layer...

  19. An ancient repeat sequence in the ATP synthase beta-subunit gene of forcipulate sea stars.

    Foltz, David W


    A novel repeat sequence with a conserved secondary structure is described from two nonadjacent introns of the ATP synthase beta-subunit gene in sea stars of the order Forcipulatida (Echinodermata: Asteroidea). The repeat is present in both introns of all forcipulate sea stars examined, which suggests that it is an ancient feature of this gene (with an approximate age of 200 Mya). Both stem and loop regions show high levels of sequence constraint when compared to flanking nonrepetitive intronic regions. The repeat was also detected in (1) the family Pterasteridae, order Velatida and (2) the family Korethrasteridae, order Velatida. The repeat was not detected in (1) the family Echinasteridae, order Spinulosida, (2) the family Astropectinidae, order Paxillosida, (3) the family Solasteridae, order Velatida, or (4) the family Goniasteridae, order Valvatida. The repeat lacks similarity to published sequences in unrestricted GenBank searches, and there are no significant open reading frames in the repeat or in the flanking intron sequences. Comparison via parametric bootstrapping to a published phylogeny based on 4.2 kb of nuclear and mitochondrial sequence for a subset of these species allowed the null hypothesis of a congruent phylogeny to be rejected for each repeat, when compared separately to the published phylogeny. In contrast, the flanking nonrepetitive sequences in each intron yielded separate phylogenies that were each congruent with the published phylogeny. In four species, the repeat in one or both introns has apparently experienced gene conversion. The two introns also show a correlated pattern of nucleotide substitutions, even after excluding the putative cases of gene conversion.

  20. Flank wear analysing of high speed end milling for hardened steel D2 using Taguchi Method

    Hazza Faizi Al-Hazza, Muataz; Ibrahim, Nur Asmawiyah bt; Adesta, Erry T. Y.; Khan, Ahsan Ali; Abdullah Sidek, Atiah Bt.


    One of the main challenges for any manufacturer is how to decrease the machining cost without affecting the final quality of the product. One of the new advanced machining processes in industry is the high speed hard end milling process that merges three advanced machining processes: high speed milling, hard milling and dry milling. However, one of the most important challenges in this process is to control the flank wear rate. Therefore a analyzing the flank wear rate during machining should be investigated in order to determine the best cutting levels that will not affect the final quality of the product. In this research Taguchi method has been used to investigate the effect of cutting speed, feed rate and depth of cut and determine the best level s to minimize the flank wear rate up to total length of 0.3mm based on the ISO standard to maintain the finishing requirements.

  1. The 5' flanking region of a barley B hordein gene controls tissue and developmental specific CAT expression in tobacco plants.

    Marris, C; Gallois, P; Copley, J; Kreis, M


    The 549 base pairs of the 5' flanking region of a barley seed storage protein (B1 hordein) gene were linked to the reporter gene encoding chloramphenicol acetyl transferase (CAT). The chimaeric gene was transferred into tobacco plants using Agrobacterium tumefaciens. CAT enzyme activity was detected in the seeds, but not in the leaves, of the transgenic plants. Furthermore, enzyme activity was found only in the endosperm, and only from fifteen days after pollination. In contrast, the constitutive 19S promoter from cauliflower mosaic virus (CaMV) directed the expression of the CAT gene in the leaves as well as in both the endosperm and embryo and at all stages in seed development.

  2. Simulation of flanking transmission in super-light structures for airborne and impact sound

    Christensen, Jacob Ellehauge; Hertz, Kristian Dahl; Brunskog, Jonas


    Super-light structures are an invention based on combining lightweight concrete with normal concrete for better structural performance and lighter structures. The overall principle is based on load carrying arches of a normal concrete stabilised and protected from fire by a light-aggregate concrete....... In the flanking transmission analysis the influence of a large array of different flanking walls, structural connection details, room size and floor constructions, all typical or desirable for common multi-storey residential constructions, have been investigated. The results form a basis for guidelines on how...

  3. 胁痛病因证治源流%Flank Pains Etiology and Pathogenesis



    Reviewing Flank pains common etiology and pathogenesis, dialectical analysis and pathogenic factor. Think of the dialectical type of Flank pains including: the exogenous attacks, depressed,blood stasis block, phlegm retention block, yin deficiency of liver and kidney, be distressed about diet,Pathogenic viruses.%回顾分析古代医家常用胁痛病因病机,辨证分析及治则治法.认为胁痛的辨证分型有:外邪侵袭,情志不遂,瘀血阻滞,痰饮留着,肝肾阴虚,饮食所伤,外感疠气.

  4. Influence of substrate tectonic heritage on the evolution of composite volcanoes: Predicting sites of flank eruption, lateral collapse, and erosion

    Tibaldi, Alessandro; Corazzato, Claudia; Kozhurin, Andrey; Lagmay, Alfredo F. M.; Pasquarè, Federico A.; Ponomareva, Vera V.; Rust, Derek; Tormey, Daniel; Vezzoli, Luigina


    This paper aims to aid understanding of the complicated interplay between construction and destruction of volcanoes, with an emphasis on the role of substrate tectonic heritage in controlling magma conduit geometry, lateral collapse, landslides, and preferential erosion pathways. The influence of basement structure on the development of six composite volcanoes located in different geodynamic/geological environments is described: Stromboli (Italy), in an island arc extensional tectonic setting, Ollagüe (Bolivia-Chile) in a cordilleran extensional setting, Kizimen (Russia) in a transtensional setting, Pinatubo (Philippines) in a transcurrent setting, Planchon (Chile) in a compressional cordilleran setting, and Mt. Etna (Italy) in a complex tectonic boundary setting. Analogue and numerical modelling results are used to enhance understanding of processes exemplified by these volcanic centres. We provide a comprehensive overview of this topic by considering a great deal of relevant, recently published studies and combine these with the presentation of new results, in order to contribute to the discussion on substrate tectonics and its control on volcano evolution. The results show that magma conduits in volcanic rift zones can be geometrically controlled by the regional tectonic stress field. Rift zones produce a lateral magma push that controls the direction of lateral collapse and can also trigger collapse. Once lateral collapse occurs, the resulting debuttressing produces a reorganization of the shallow-level magma migration pathways towards the collapse depression. Subsequent landslides and erosion tend to localize along rift zones. If a zone of weakness underlies a volcano, long-term creep can occur, deforming a large sector of the cone. This deformation can trigger landslides that propagate along the destabilized flank axis. In the absence of a rift zone, normal and transcurrent faults propagating from the substrate through the volcano can induce flank

  5. The Pentapeptide Repeat Proteins

    Vetting,M.; Hegde, S.; Fajardo, J.; Fiser, A.; Roderick, S.; Takiff, H.; Blanchard, J.


    The Pentapeptide Repeat Protein (PRP) family has over 500 members in the prokaryotic and eukaryotic kingdoms. These proteins are composed of, or contain domains composed of, tandemly repeated amino acid sequences with a consensus sequence of [S, T,A, V][D, N][L, F]-[S, T,R][G]. The biochemical function of the vast majority of PRP family members is unknown. The three-dimensional structure of the first member of the PRP family was determined for the fluoroquinolone resistance protein (MfpA) from Mycobacterium tuberculosis. The structure revealed that the pentapeptide repeats encode the folding of a novel right-handed quadrilateral {beta}-helix. MfpA binds to DNA gyrase and inhibits its activity. The rod-shaped, dimeric protein exhibits remarkable size, shape and electrostatic similarity to DNA.

  6. Repeating the Past

    Moore, John W.


    As part of the celebration of the Journal 's 75th year, we are scanning each Journal issue from 25, 50, and 74 years ago. Many of the ideas and practices described are so similar to present-day "innovations" that George Santayana's adage (1) "Those who cannot remember the past are condemned to repeat it" comes to mind. But perhaps "condemned" is too strong - sometimes it may be valuable to repeat something that was done long ago. One example comes from the earliest days of the Division of Chemical Education and of the Journal.

  7. All-optical repeater.

    Silberberg, Y


    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.

  8. Bidirectional Manchester repeater

    Ferguson, J.


    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.

  9. Finite Element Approach for Analyses of Flanking Noise Transmission within Lightweight Panel Structure

    Domadiya, Parthkumar Gandalal; Dickow, Kristoffer Ahrens; Andersen, Lars;


    This paper concerns the analysis of noise transmission in a lightweight panel structure. The analysis is based on Finite Element Analysis (FEA) employing solid elements for the structure. The analysis focuses on flanking noise transmission in panel structures of finite size. A parametric study...

  10. A New Mathematical Model for Flank Wear Prediction Using Functional Data Analysis Methodology

    Sonja Jozić


    Full Text Available This paper presents a new approach improving the reliability of flank wear prediction during the end milling process. In the present work, prediction of flank wear has been achieved by using cutting parameters and force signals as the sensitive carriers of information about the machining process. A series of experiments were conducted to establish the relationship between flank wear and cutting force components as well as the cutting parameters such as cutting speed, feed per tooth, and radial depth of cut. In order to be able to predict flank wear a new linear regression mathematical model has been developed by utilizing functional data analysis methodology. Regression coefficients of the model are in the form of time dependent functions that have been determined through the use of functional data analysis methodology. The mathematical model has been developed by means of applied cutting parameters and measured cutting forces components during the end milling of workpiece made of 42CrMo4 steel. The efficiency and flexibility of the developed model have been verified by comparing it with the separate experimental data set.

  11. Heme regulates the expression in Saccharomyces cerevisiae of chimaeric genes containing 5'-flanking soybean leghemoglobin sequences

    Jensen, E O; Marcker, K A; Villadsen, IS


    The TM1 yeast mutant was transformed with a 2 micron-derived plasmid (YEp24) which carries a chimaeric gene containing the Escherichia coli chloramphenicol acetyl transferase (CAT) gene fused to the 5'- and 3'-flanking regions of the soybean leghemoglobin (Lb) c3 gene. Expression of the chimaeric...

  12. Supported PCR : an efficient procedure to amplify sequences flanking a known DNA segment

    Rudenko, George N.; Rommens, Caius M.T.; Nijkamp, H. John J.; Hille, Jacques


    We describe a novel modification of the polymerase chain reaction for efficient in vitro amplification of genomic DNA sequences flanking short stretches of known sequence. The technique utilizes a target enrichment step, based on the selective isolation of biotinylated fragments from the bulk of gen

  13. Genomic flank-sequencing of plasposon insertion sites for rapid identification of functional genes

    Leveau, J.H.J.; Gerards, S.; Fritsche, K.; Zondag, G.; Van Veen, J.A.


    Plasposons are modified mini-Tn5 transposons for random mutagenesis of Gram-negative bacteria. Their unique design allows for the rescue cloning and sequencing of DNA that flanks insertion sites in plasposon mutants. However, this process can be laborious and time-consuming, as it involves genomic D

  14. Analysis of Roughness and Flank Wear in Turning Gray Cast Iron Using Cryogenically Treated Cutting Tools

    B.R. Ramji


    Full Text Available The purpose of this research was to examine the flank wear and surface roughness in turning gray cast iron using cryogenically treated carbide inserts. Turning experiments were conducted with cutting velocities: 53, 85, 99, 149 m/sec, feeds: 0.12, 0.16, 0.2, 0.24 mm/rev and a constant depth of cut: 1.5 mm. The specimens were turned using cryogenically treated and non-treated carbide inserts. The cryogenic treatment cycle consisted of cooling the test samples from room temperature to cryogenic temperature of -178.9 C in 3 h, soaking at cryogenic tem perature around 24 h and warming to room temperature in about 5 h. The surface roughness (Ra, R z, Rq and Rt :m of the turned specimens was measured using talysurf and flank wear of the tool was measured using toolm akers microscope. The experimental layout was designed based on the Taguchi’s Orthogonal Array technique and ANOVA was performed to identify the effect of the parameters on the response variables. Cryogenically treated inserts proved superior to the non-treated in all the test conditions in terms of lesser flank wear of the inserts and reduced surface roughness of the specimens. The after turned inserts w ere examined using Scanning Electron Microscopy for studying the flank wear mechanism.

  15. Sudden aseismic fault slip on the south flank of Kilauea volcano.

    Cervelli, Peter; Segall, Paul; Johnson, Kaj; Lisowski, Michael; Miklius, Asta


    One of the greatest hazards associated with oceanic volcanoes is not volcanic in nature, but lies with the potential for catastrophic flank failure. Such flank failure can result in devastating tsunamis and threaten not only the immediate vicinity, but coastal cities along the entire rim of an ocean basin. Kilauea volcano on the island of Hawaii, USA, is a potential source of such flank failures and has therefore been monitored by a network of continuously recording geodetic instruments, including global positioning system (GPS) receivers, tilt meters and strain meters. Here we report that, in early November 2000, this network recorded transient southeastward displacements, which we interpret as an episode of aseismic fault slip. The duration of the event was about 36 hours, it had an equivalent moment magnitude of 5.7 and a maximum slip velocity of about 6[?]cm per day. Inversion of the GPS data reveals a shallow-dipping thrust fault at a depth of 4.5[?]km that we interpret as the down-dip extension of the Hilina Pali--Holei Pali normal fault system. This demonstrates that continuously recording geodetic networks can detect accelerating slip, potentially leading to warnings of volcanic flank collapse.

  16. Forests of the tropical eastern Andean flank during the middle Pleistocene

    Cárdenas, M.L.; Gosling, W.D.; Pennington, R.T.; Poole, I.; Sherlock, S.C.; Mothes, P.


    Inter-bedded volcanic and organic sediments from Erazo (Ecuador) indicate the presence of four different forest assemblages on the eastern Andean flank during the middle Pleistocene. Radiometric dates (40Ar-39Ar) obtained from the volcanic ash indicate that deposition occurred between 620,000 and 19

  17. Tsunami deposits at high altitudes on the flanks of volcanic islands

    Paris, Raphael


    It is actually difficult to infer the mechanisms and dynamics of giant mass failures of oceanic shield volcanoes and to evaluate related tsunami hazards. Marine conglomerates and gravels found at unusually high elevations in Hawaii, Cape Verde, Mauritius and Canary Islands are often interpreted as being the result of tsunami waves generated by such massive flank failures. In the first part of this contribution, we document tsunami deposits (marine gravels with pumices) attached to the northwestern slopes of Tenerife, Canary Islands, at altitudes up to 132 m asl. Stratigraphy of the deposits and composition of the pumices allows identifying sources of the successive tsunamis and proposing a new scenario for the Icod flank failure and El Abrigo caldera-forming eruption ca. 170 ka. Then we propose a litterature review of tsunami deposits at high altitudes on the flanks of volcanic islands, and especially oceanic shield volcanoes. These deposits are discussed in terms of texture, structure, composition and particularly the juvenile volcanic material, and implications for better understanding the mechanisms controlling massive flank failures.

  18. Interphase FISH detection of BCL2 rearrangement in follicular lymphoma using breakpoint-flanking probes

    Vaandrager, J W; Schuuring, E; Raap, T; Philippo, K; Kleiverda, K; Kluin, P


    Rearrangement of the BCL2 gene is an important parameter for the differential diagnosis of non-Hodgkin lymphomas. Although a relatively large proportion of breakpoints is clustered, many are missed by standard PCR. A FISH assay is therefore desired. Up to now, a lack of probes flanking the BCL2 gene

  19. Causal link between Quaternary paleoclimatic changes and flank collapses on volcanic islands

    Hildenbrand, A.; Quidelleur, X.; Samper, A.


    Giant landslides and resulting tsunamis represent the main geologic hazards linked to volcanic island evolution. From bathymetric data and on-land geological studies, flank failures have been identified around numerous volcanic islands, in most geodynamic contexts. However, the enabling and triggering conditions are still poorly understood and several internal and external causes may act simultaneously to reach a critical threshold. We here present a compilation of well-dated flank destabilization events within the last 1 Myr from Tahiti, Hawaii, Canary Islands, Guadeloupe and Martinique (Lesser Antilles), and examine their relationships with global paleoclimatic changes evidenced by a global stack of benthic ?18O records. We show that a causal relationship between flank collapse of volcanic islands and global climatic changes has existed at least since 900 kyr. Moreover, high precision ages reported here favor the hypothesis that major flank collapse events occurred during the onset of glacial to interglacial transitions when a sudden influx of melt water from polar ice caps causes rapid sea level rise. We propose that following a sub aerial erosion interval during low sea level stands, rapid sea level rise induces enhanced coastal erosion and sudden changes of pore pressure conditions within basal layers, which favor edifice failure.

  20. Absces i højre flanke--senkomplikation til laparoskopisk kolecystektomi

    Hillingsø, Jens; Kristiansen, V B


    Laparoscopic cholecystectomy (LC) is the treatment of choice in cases of symptomatic gallstones. A 74-year-old female presented with a spontaneously perforated abscess in her right flank and passage through it of gallstones. Four years previously during LC the gallbladder perforated and 10...

  1. Implementing reverse genetics in Rosaceae: analysis of T-DNA flanking sequences of insertional mutant lines in the diploid strawberry, Fragaria vesca.

    Oosumi, Teruko; Ruiz-Rojas, Juan Jairo; Veilleux, Richard E; Dickerman, Allan; Shulaev, Vladimir


    Reverse genetics is used for functional genomics research in model plants. To establish a model system for the systematic reverse genetics research in the Rosaceae family, we analyzed genomic DNA flanking the T-DNA insertions in 191 transgenic plants of the diploid strawberry, Fragaria vesca. One hundred and seventy-six T-DNA flanking sequences were amplified from the right border (RB) and 37 from the left border (LB) by thermal asymmetric interlaced PCR. Analysis of the T-DNA nick positions revealed that T-DNA was most frequently nicked at the cleavage sites. Analysis of 11 T-DNA integration sites indicated that T-DNA was integrated into the F. vesca genome by illegitimate recombination, as reported in other model plants: Arabidopsis, rice and tobacco. First, deletion of DNA was found at T-DNA integration target sites in all transgenic plants tested. Second, microsimilarities of a few base pairs between the left and/or right ends of the T-DNA and genomic sites were found in all transgenic plants tested. Finally, filler DNA was identified in four break-points. Out of 191 transgenic plants, T-DNA flanking sequences of 79 plants (41%) showed significant similarity to genes, elements or proteins of other plant species and 67 (35%) of the sequences are still unknown strawberry gene fragments. T-DNA flanking sequences of 126 plants (66%) showed homology to plant ESTs. This is the first report of T-DNA integration in a sizeable population of a rosaceous species. We have shown in this paper that T-DNA integration in strawberry is not random but directed by sequence microsimilarities in the host genome.

  2. Marine neotectonic investigation of the San Gregorio Fault Zone on the northern flank of Monterey Canyon, offshore central California

    Maier, K. L.; Paull, C. K.; Brothers, D. S.; McGann, M.; Caress, D. W.; Lundsten, E. M.; Anderson, K.; Gwiazda, R.


    The San Gregorio Fault Zone (SGFZ) is part of the North American-Pacific plate boundary and is thought to accommodate right-lateral offset up to 10 mm/yr. Because much of the SGFZ in Monterey Bay, central California, lies offshore in steep submarine canyon bathymetry, little is known of its recent activity. We provide initial direct evidence for faulting where the SGFZ has been interpreted based on canyon morphology to cross the northern flank of Monterey Canyon. High-resolution multibeam bathymetry and chirp subbottom profiles were acquired during 13 dives with the Monterey Bay Aquarium Research Institute's (MBARI) Autonomous Underwater Vehicle (AUV) from 2009-2014 on the northern flank of Monterey Canyon, extending from the shelf edge ~15 km offshore Santa Cruz to ~1850 m water depth. Chirp profiles resolve layered sediments up to ~40 m subsurface in this region, and no fault scarps or seafloor lineaments are visible in the 1-m resolution multibeam bathymetry. At least one subsurface fault is identified within the SGFZ by offset reflections across a discrete, nearly vertical fault. However, this fault is only imaged where mass wasting has exhumed older strata to within ~25 m of the seafloor. Numerous slumps scars on the seafloor and packages of chaotic internal reflectivity in chirp profiles suggest that submarine landslide processes dominate the study area. To constrain the age of reflections offset by the fault, MBARI's Remotely Operated Vehicle (ROV) Doc Ricketts, sampled faces of slump scars where the offset reflections crop out using vibracores and horizontal push cores. Radiocarbon dating of foraminifera within these core samples is being used to constrain the last recorded movement on the fault. Application of AUV and ROV methods allows detailed neotectonic investigation of significant offshore structures, like the SGFZ, that contribute to hazard assessment.

  3. Effect of the Flanking Sequence Architecture of Translation Initiation AUG Codon on Gene Expression Level in Rice

    LIU Qing-po; TAN Jun; XUE Qing-zhong


    The relationship between the codon usage bias, gene expression level and the AUG context (from -20 to +6 positions relative to the initiator AUG codon) was examined in 541unigene sequences of rice. A significant correlation for CAI values (codon adaptation index) was observed at five nucleotide positions (-19, -18, -9, -4, +5), eight (-19, -18,-14, -9, -6, -4, -1, +5) for CPP (codon preference parameter), and seven (-18, -16, -15,-9, -7, -1, + 6) for mRNA abundance in the flanking sequence of the initiator AUG codon respectively, but a significantly positive correlation for both CAI and CPP at two positions (-4 and +5), indicating that both those positions are evolutionally under the natural selection constraint at the translational level. By site-directed mutagenesis at seven specific positions (-18, -16, -15, -9, -7, -1 and + 6) for allergenic protein that had the highest mRNA abundance in this study, its expression level decreased dramatically 63.3 and 72.5% respectively, indicating the importance of those 7 positions for gene expression. A highly positive correlation (r= 0.625, P< 0.01) between AUGCAI and GC content in the flanking sequence of the initiator AUG codon showed a more effective higher GC content on translation initiation efficiency. The strong preference for G or C at those 8 positions (-6, -5, -3, -2, -1, +4, +5 and +6) in the AUG context suggested that an important factor in modulation of the translation efficiency, as well as synonymous codon usage bias, particularly in highly expressed genes.

  4. Formation of Extrachromosomal Circular DNA from Long Terminal Repeats of Retrotransposons in Saccharomyces cerevisiae

    Henrik D. Møller


    Full Text Available Extrachromosomal circular DNA (eccDNA derived from chromosomal Ty retrotransposons in yeast can be generated in multiple ways. Ty eccDNA can arise from the circularization of extrachromosomal linear DNA during the transpositional life cycle of retrotransposons, or from circularization of genomic Ty DNA. Circularization may happen through nonhomologous end-joining (NHEJ of long terminal repeats (LTRs flanking Ty elements, by Ty autointegration, or by LTR–LTR recombination. By performing an in-depth investigation of sequence reads stemming from Ty eccDNAs obtained from populations of Saccharomyces cerevisiae S288c, we find that eccDNAs predominantly correspond to full-length Ty1 elements. Analyses of sequence junctions reveal no signs of NHEJ or autointegration events. We detect recombination junctions that are consistent with yeast Ty eccDNAs being generated through recombination events within the genome. This opens the possibility that retrotransposable elements could move around in the genome without an RNA intermediate directly through DNA circularization.

  5. Duct Leakage Repeatability Testing

    Walker, Iain [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Sherman, Max [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)


    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.

  6. Comparative genomics and molecular dynamics of DNA repeats in eukaryotes.

    Richard, Guy-Franck; Kerrest, Alix; Dujon, Bernard


    Repeated elements can be widely abundant in eukaryotic genomes, composing more than 50% of the human genome, for example. It is possible to classify repeated sequences into two large families, "tandem repeats" and "dispersed repeats." Each of these two families can be itself divided into subfamilies. Dispersed repeats contain transposons, tRNA genes, and gene paralogues, whereas tandem repeats contain gene tandems, ribosomal DNA repeat arrays, and satellite DNA, itself subdivided into satellites, minisatellites, and microsatellites. Remarkably, the molecular mechanisms that create and propagate dispersed and tandem repeats are specific to each class and usually do not overlap. In the present review, we have chosen in the first section to describe the nature and distribution of dispersed and tandem repeats in eukaryotic genomes in the light of complete (or nearly complete) available genome sequences. In the second part, we focus on the molecular mechanisms responsible for the fast evolution of two specific classes of tandem repeats: minisatellites and microsatellites. Given that a growing number of human neurological disorders involve the expansion of a particular class of microsatellites, called trinucleotide repeats, a large part of the recent experimental work on microsatellites has focused on these particular repeats, and thus we also review the current knowledge in this area. Finally, we propose a unified definition for mini- and microsatellites that takes into account their biological properties and try to point out new directions that should be explored in a near future on our road to understanding the genetics of repeated sequences.

  7. Evidence for microbial carbon and sulfur cycling in deeply buried ridge flank basalt.

    Lever, Mark A; Rouxel, Olivier; Alt, Jeffrey C; Shimizu, Nobumichi; Ono, Shuhei; Coggon, Rosalind M; Shanks, Wayne C; Lapham, Laura; Elvert, Marcus; Prieto-Mollar, Xavier; Hinrichs, Kai-Uwe; Inagaki, Fumio; Teske, Andreas


    Sediment-covered basalt on the flanks of mid-ocean ridges constitutes most of Earth's oceanic crust, but the composition and metabolic function of its microbial ecosystem are largely unknown. By drilling into 3.5-million-year-old subseafloor basalt, we demonstrated the presence of methane- and sulfur-cycling microbes on the eastern flank of the Juan de Fuca Ridge. Depth horizons with functional genes indicative of methane-cycling and sulfate-reducing microorganisms are enriched in solid-phase sulfur and total organic carbon, host δ(13)C- and δ(34)S-isotopic values with a biological imprint, and show clear signs of microbial activity when incubated in the laboratory. Downcore changes in carbon and sulfur cycling show discrete geochemical intervals with chemoautotrophic δ(13)C signatures locally attenuated by heterotrophic metabolism.

  8. The human SOX18 gene: Expression analysis and characterization of its 5’ flanking region

    Petrović Isidora


    Full Text Available The aim of this study was to establish an adequate in vitro model system for studying transcriptional regulation of the human SOX18 gene. The paper presents an analysis of expression of this gene in cultured cell lines and characterization of its 5' flanking region. Using RT-PCR, Northern and Western blot analysis, we demonstrated SOX18 expression in HeLa cells, indicating that this cell line provides a suitable model system for studying transcriptional regulation of the given gene. We also cloned, sequenced and for the first time characterized the human SOX18 5’ flanking region. It is shown that the region 892 bp in size immediately upstream from the start codone harbors regulatory elements sufficient for transcription and represents an SOX18 promoter region.

  9. Stability analysis of Western flank of Cumbre Vieja volcano (La Palma) using numerical modelling

    Bru, Guadalupe; Gonzalez, Pablo J.; Fernandez-Merodo, Jose A.; Fernandez, Jose


    La Palma volcanic island is one of the youngest of the Canary archipelago, being a composite volcano formed by three overlapping volcanic centers. There are clear onshore and offshore evidences of past giant landslides that have occurred during its evolution. Currently, the active Cumbre Vieja volcano is in an early development state (Carracedo et al., 2001). The study of flank instability processes aim to assess, among other hazards, catastrophic collapse and potential tsunami generation. Early studies of the potential instability of Cumbre Vieja volcano western flank have focused on the use of sparse geodetic networks (Moss et al. 1999), surface geological mapping techniques (Day et al. 1999) and offshore bathymetry (Urgeles et al. 1999). Recently, a dense GNSS network and satellite radar interferometry results indicate ground motion consistent with deep-seated creeping processes (Prieto et al. 2009, Gonzalez et al. 2010). In this work, we present a geomechanical advanced numerical model that captures the ongoing deformation processes at Cumbre Vieja. We choose the Finite Elements Method (FEM) which is based in continuum mechanics and is the most used for geotechnical applications. FEM has the ability of using arbitrary geometry, heterogeneities, irregular boundaries and different constitutive models representative of the geotechnical units involved. Our main contribution is the introduction of an inverse approach to constrain the geomechanical parameters using satellite radar interferometry displacements. This is the first application of such approach on a large volcano flank study. We suggest that the use of surface displacements and inverse methods to rigorously constrain the geomechanical model parameter space is a powerful tool to understand volcano flank instability. A particular important result of the studied case is the estimation of displaced rock volume, which is a parameter of critical importance for simulations of Cumbre Vieja tsunamigenic hazard

  10. A 75-Year Old Man Complaining of Flank Pain and Obstructive Urinary Symptoms: A Case Report

    Farid Kowsari


    Full Text Available "nBenign renal cystic adenoma with out malignant features is a very rare entity. A 75 year old male with obstructive Lower tract symptoms and vague flank pain was admitted and planned for nephrectomy of non functional kidney -due to long term nephrolithiasis- intra operative finding was a cystic hydronephrotic kidney filled by thick mucous secretions which turned out to be a cyst adenoma of kidney with no malignant features.

  11. Evidence for a Mega-Tsunami Generated by Giant Flank Collapse of Fogo Volcano, Cape Verde

    Ramalho, R. S.; Madeira, J.; Helffrich, G. R.; Schaefer, J. M.; Winckler, G.; Quartau, R.; Adena, K.


    Mega-tsunamis generated by ocean island flank collapses are expected to be some of the most hazardous forces of nature, yet evidence for their near-source effects and inferred high run-ups so far is scarce or hotly debated. A newly discovered deposit on the northern coast of Santiago Island (Cape Verde), however, documents the magnitude and run-up height associated with this kind of event. Additionally to chaotic conglomerates distributed from sea-level up to 100 m elevation standing on slopes as steep as 20°, the deposit comprises a number of scattered megaclasts of submarine lava flows, limestone and tuff. The megaclasts are presently located over a higher substructural slope built on younger subaerial lava flows and at elevations ranging 160-220 m a.s.l. All megaclasts correspond to lithologies that crop out exclusively in nearby cliff faces. The origin of this deposit is consequently attributed to an exceptional wave that plucked blocks from the cliff face, transported them inland and deposited them over the higher slopes of the volcanic edifice. The distribution of the megaclasts, together with the local geomorphology, is in agreement with a tsunami that approached the island edifice from the west and was refracted along its northern flank, flooding a series of northwest-oriented valleys. This suggests that the well-known flank collapse of Fogo volcano, located 55 km west of Santiago, is the most likely source, a hypothesis being tested with surface exposure dating. The inferred run-up exceeded 200 m and is consistent with numerical simulations by Paris et al. 2011, implying that the present Fogo island morphology probably developed by at least one giant flank collapse with devastating near-source effects.

  12. Supported PCR: an efficient procedure to amplify sequences flanking a known DNA segment

    Rudenko, George N.; Rommens, Caius M.T.; Nijkamp, H. John J.; Hille, Jacques


    We describe a novel modification of the polymerase chain reaction for efficient in vitro amplification of genomic DNA sequences flanking short stretches of known sequence. The technique utilizes a target enrichment step, based on the selective isolation of biotinylated fragments from the bulk of genomic DNA on streptavidin-containing support. Subsequently, following ligation with a second universal linker primer, the selected fragments can be amplified to amounts suitable for further molecula...

  13. BPTs: thiophene-flanked benzodipyrrolidone conjugated polymers for ambipolar organic transistors.

    Rumer, Joseph W; Levick, Matthew; Dai, Sheng-Yao; Rossbauer, Stephan; Huang, Zhenggang; Biniek, Laure; Anthopoulos, Thomas D; Durrant, James R; Procter, David J; McCulloch, Iain


    A series of novel thiophene-flanked benzodipyrrolidone (BPT)-based alternating copolymers are synthesised, their optical and electrical properties evaluated. The BPT unit promotes a conjugated, planar polymer backbone, with a low bandgap, primarily due to low lying LUMO energy levels. Copolymerisation with thiophene exhibits well balanced ambipolar organic field-effect transistor performance, with electron and hole mobilities 0.1 and 0.2 cm(2) V(-1) s(-1), respectively.

  14. Repeatability of Cryogenic Multilayer Insulation

    Johnson, W. L.; Vanderlaan, M.; Wood, J. J.; Rhys, N. O.; Guo, W.; Van Sciver, S.; Chato, D. J.


    Due to the variety of requirements across aerospace platforms, and one off projects, the repeatability of cryogenic multilayer insulation has never been fully established. The objective of this test program is to provide a more basic understanding of the thermal performance repeatability of MLI systems that are applicable to large scale tanks. There are several different types of repeatability that can be accounted for: these include repeatability between multiple identical blankets, repeatability of installation of the same blanket, and repeatability of a test apparatus. The focus of the work in this report is on the first two types of repeatability. Statistically, repeatability can mean many different things. In simplest form, it refers to the range of performance that a population exhibits and the average of the population. However, as more and more identical components are made (i.e. the population of concern grows), the simple range morphs into a standard deviation from an average performance. Initial repeatability testing on MLI blankets has been completed at Florida State University. Repeatability of five GRC provided coupons with 25 layers was shown to be +/- 8.4 whereas repeatability of repeatedly installing a single coupon was shown to be +/- 8.0. A second group of 10 coupons have been fabricated by Yetispace and tested by Florida State University, through the first 4 tests, the repeatability has been shown to be +/- 16. Based on detailed statistical analysis, the data has been shown to be statistically significant.

  15. New primer for specific amplification of the CAG repeat in Huntington disease alleles

    Bond, C.E.; Hodes, M.E. [Indiana Univ. School of Medicine, Indianapolis (United States)


    Huntington disease is an autosomal dominant neurodegenerative disorder caused by an expansion of a CAG trinucleotide repeat near the 5{prime} end of the gene for Huntington disease (IT15). The CAG repeat is flanked by a variable-length CCG repeat that is included in the amplification product obtained with most currently used primer sets and PCR protocols. Inclusion of this adjacent CCG repeat complicates the accurate assessment of CAG repeat length and interferes with the genotype determination of those individuals carrying alleles in the intermediate range between normal and expanded sized. Due to the GC-rich nature of this region, attempts at designing a protocol for amplification of only the CAG repeat have proved unreliable and difficult to execute. We report here the development of a compatible primer set and PCR protocol that yields consistent amplification of the CAG-repeat region. PCR products can be visualized in ethidium bromide-stained agarose gels for rapid screening or in 6% polyacrylamide gels for determination of exact repeat length. This assay produces bands that can be sized accurately, while eliminating most nonspecific products. Fifty-five specimens examined showed consistency with another well-known method, but one that amplifies the CCG repeats as well. The results we obtained also matched the known carrier status of the donors.

  16. The excess of small inverted repeats in prokaryotes.

    Ladoukakis, Emmanuel D; Eyre-Walker, Adam


    Recent analyses have shown that there is a large excess of perfect inverted repeats in many prokaryotic genomes but not in eukaryotic ones. This difference could be due to a genuine difference between prokaryotes and eukaryotes or to differences in the methods and types of data analyzed--full genome versus protein coding sequences. We used simulations to show that the method used previously tends to underestimate the expected number of inverted repeats. However, this bias is not large and cannot explain the excess of inverted repeats observed in real data. In contrast, our method is unbiased. When both methods are applied to bacterial protein coding sequences they both detect an excess of inverted repeats, which is much lower than previously reported in whole prokaryotic genomes. This suggests that the reported large excess of inverted repeats is due to repeats found in intergenic regions. These repeats could be due to transcription factor binding sites, or other types of repetitive DNA, on opposite strands of the DNA sequence. In contrast, the smaller, but significant, excess of inverted repeats that we report in protein coding sequences may be due to sequence-directed mutagenesis (SDM). SDM is a process where one copy of a small, imperfect, inverted repeat corrects the other copy via strand misalignment, resulting in a perfect repeat and a series of mutations. We show by simulation that even very low levels of SDM, relative to the rate of point mutation, can generate a substantial excess of inverted repeats.

  17. Modeling "secular" flank motion at Kilauea Volcano (Hawai'i) during 2000-2003

    Plattner, C.; Amelung, F.; Baker, S.; Govers, R. M.; Poland, M. P.; Lavallee, Y.


    Kilauea's south flank is moving seaward due to flank instabilities. The rate is influenced by magmatic events (dike intrusions) and tectonic events (earthquakes and slow-slip events at the decollement), but the general flank motion signal remains significant at any time, with rates of 6-10 cm/yr during the past decade. The surface displacements were explained by fault slip along the decollement beneath Kilauea combined with deep-rift opening in elastic halfspace dislocation models. While these models explain the kinematics well, the dynamics of the rift opening are not resolved, and the question on contribution from magmatic driving forces versus an entirely gravitationally-driven system remains. InSAR time-series analysis (Small Baseline Algorithm; SBAS) showed linear surface subsidence at Kilauea summit (maximum rate 5.5 cm/yr south of the caldera) during 2000-2003, a time-period during which the influence of distinct deformation events is small in comparison to previous and later time-periods. Here, we investigate if summit subsidence can be explained as a consequence of secular flank motion at Kilauea by ductile creep of a deep magma mush, using a numerical model with time-dependent material deformation properties to constrain velocities rather than displacements. We developed a 2D finite element model that investigates the deformation response of Kilauea to gravitational driving forces only. The model geometry includes a decollement fault beneath the volcano that can have locked and creeping fault segments. We introduce time-dependent material behavior using a viscoelastic model media. The host rock remains stable over geodetic timescales given its high viscosity value, while the deep-seated magma mush beneath Kilauea caldera is assigned a lower viscosity and spreads at significant rates. The deformation signal of the magma mush is transmitted to the surface, causing local subsidence at Kilauea summit, showing that summit subsidence can be explained by flank

  18. Topology of eukaryotic type II membrane proteins: importance of N-terminal positively charged residues flanking the hydrophobic domain.

    Parks, G D; Lamb, R A


    We have tested the role of different charged residues flanking the sides of the signal/anchor (S/A) domain of a eukaryotic type II (N(cyt)C(exo)) integral membrane protein in determining its topology. The removal of positively charged residues on the N-terminal side of the S/A yields proteins with an inverted topology, while the addition of positively charged residues to only the C-terminal side has very little effect on orientation. Expression of chimeric proteins composed of domains from a type II protein (HN) and the oppositely oriented membrane protein M2 indicates that the HN N-terminal domain is sufficient to confer a type II topology and that the M2 N-terminal ectodomain can direct a type II topology when modified by adding positively charged residues. These data suggest that eukaryotic membrane protein topology is governed by the presence or absence of an N-terminal signal for retention in the cytoplasm that is composed in part of positive charges.

  19. Replication fork progression is paused in two large chromosomal zones flanking the DNA replication origin in Escherichia coli.

    Akiyama, Masahiro Tatsumi; Oshima, Taku; Chumsakul, Onuma; Ishikawa, Shu; Maki, Hisaji


    Although the speed of nascent DNA synthesis at individual replication forks is relatively uniform in bacterial cells, the dynamics of replication fork progression on the chromosome are hampered by a variety of natural impediments. Genome replication dynamics can be directly measured from an exponentially growing cell population by sequencing newly synthesized DNA strands that were specifically pulse-labeled with the thymidine analogue 5-bromo-2'-deoxyuridine (BrdU). However, a short pulse labeling with BrdU is impracticable for bacteria because of poor incorporation of BrdU into the cells, and thus, the genomewide dynamics of bacterial DNA replication remain undetermined. Using a new thymidine-requiring Escherichia coli strain, eCOMB, and high-throughput sequencing, we succeeded in determining the genomewide replication profile in bacterial cells. We also found that fork progression is paused in two ~200-kb chromosomal zones that flank the replication origin in the growing cells. This origin-proximal obstruction to fork progression was overcome by an increased thymidine concentration in the culture medium and enhanced by inhibition of transcription. These indicate that DNA replication near the origin is sensitive to the impediments to fork progression, namely a scarcity of the DNA precursor deoxythymidine triphosphate and probable conflicts between replication and transcription machineries.

  20. Sequence and single-base polymorphisms of the bovine alpha-lactalbumin 5'-flanking region.

    Bleck, G T; Bremel, R D


    The alpha-lactalbumin (alpha LA)-encoding gene is a potential quantitative trait locus in dairy animals. In cattle, the production of alpha LA is tightly coupled to the onset of lactation and it serves as a regulatory subunit of the enzyme responsible for lactose synthesis. Lactose is the major osmole controlling water movement in the mammary gland. To better understand the control of bovine alpha LA expression, the 5'-flanking region of a Holstein alpha LA gene was cloned and sequenced. The sequenced clone contains 1952 bp of 5'-flanking region and 66-bp of the protein-coding region. Three single-bp polymorphisms were identified within this region. These polymorphisms occur at positions +15, +21 and +54 relative to the mRNA transcription start point (tsp). The +15 and +21 variations occur in the region encoding the 5'-untranslated region of the mRNA-coding sequence. The +54 polymorphism is a silent mutation in the SP-coding region of the gene. A polymerase chain reaction (PCR, Cetus)-based screening method has been employed to analyze the genotype of cattle at the +15 position. A total of 501 randomly selected cattle from seven breeds were screened for this allele. Of these animals, only the Holstein breed of cattle was found to contain the +15 variation and it occurs at a gene frequency of 32%. Sequence comparisons were conducted between the 5'-flanking regions of the bovine-milk-protein encoding genes, alpha LA, beta-casein and alpha S1-casein, which are coordinately expressed. Regions of similarity extending to 350 bp in length were observed between these sequences.

  1. Role of large flank-collapse events on magma evolution of volcanoes. Insights from the Lesser Antilles Arc

    Boudon, Georges; Villemant, Benoît; Friant, Anne Le; Paterne, Martine; Cortijo, Elsa


    Flank-collapse events are now recognized as common processes of destruction of volcanoes. They may occur several times on a volcanic edifice pulling out varying volumes of material from km3 to thousands of km3. In the Lesser Antilles Arc, a large number of flank-collapse events were identified. Here, we show that some of the largest events are correlated to significant variations in erupted magma compositions and eruptive styles. On Montagne Pelée (Martinique), magma production rate has been sustained during several thousand years following a 32 ka old flank-collapse event. Basic and dense magmas were emitted through open-vent eruptions that generated abundant scoria flows while significantly more acidic magmas were produced before the flank collapse. The rapid building of a new cone increased the load on magma bodies at depth and the density threshold. Magma production rate decreased and composition of the erupted products changed to more acidic compared to the preceding period of activity. These low density magma generated plinian and dome-forming eruptions up to the Present. In contrast at Soufrière Volcanic Centre of St. Lucia and at Pitons du Carbet in Martinique, the flank-collapses have an opposite effect: in both cases, the acidic magmas erupted immediately after the flank-collapses. These magmas are highly porphyritic (up to 60% phenocrysts) and much more viscous than the magmas erupted before the flank-collapses. They have been generally emplaced as voluminous and uptight lava domes (called “the Pitons”). Such magmas could not ascent without a significant decrease of the threshold effect produced by the volcanic edifice loading before the flank-collapse.

  2. Polyglutamine Amyloid Core Boundaries and Flanking Domain Dynamics in Huntingtin Fragment Fibrils Determined by Solid-State Nuclear Magnetic Resonance

    Hoop, Cody L.; Lin, Hsiang-Kai; Kar, Karunakar; Hou, Zhipeng; Poirier, Michelle A.; Wetzel, Ronald; van der Wel, Patrick C.A.


    In Huntington’s disease, expansion of a polyglutamine (polyQ) domain in the huntingtin (htt) protein leads to misfolding and aggregation. There is much interest in the molecular features that distinguish monomeric, oligomeric, and fibrillar species that populate the aggregation pathway and likely differ in cytotoxicity. The mechanism and rate of aggregation are greatly affected by the domains flanking the polyQ segment within exon 1 of htt. A “protective” C-terminal proline-rich flanking doma...

  3. Evaluation of Various Joints between Studs and Plates on Flanking Noise Transmission within Lightweight Periodic Structures

    Domadiya, Parthkumar Gandalal; Dickow, Kristoffer Ahrens; Andersen, Lars Vabbersgaard;


    Noise propagation in lightweight building structures is an issue that needs attention in the current building trend. In this paper, a finite-element model is utilized for the analysis of flanking noise transmission in a lightweight panel structure consisting of two plates with internal ribs using...... various joints between the studs and the plates. Four different coupling configurations are considered: 1) all structural contact points are completely tied; 2) only nodes on the centre lines of the structure are tied; 3) a narrow strip of 5 mm, 10 mm or 20 mm tied elements connect the frame to the plates...

  4. Geochemistry of summit fumarole vapors and flanking thermal/mineral waters at Popocatepetl Volcano, Mexico

    Werner, C.; Goff, F. [Los Alamos National Lab., NM (United States); Janik, C.J. [Geological Survey, Menlo Park, CA (United States)] [and others


    Popocatepetl Volcano is potentially devastating to populations living in the greater Mexico City area. Systematic monitoring of fumarole gases and flanking thermal/mineral springs began in early 1994 after increased fumarolic and seismic activity were noticed in 1991. These investigations had two major objectives: (1) to determine if changes in magmatic conditions beneath Popocatepetl might be reflected by chemical changes in fumarolic discharges and (2) to determine if thermal/mineral spring waters in the vicinity of Popocatepetl are geochemically related to or influences by the magmatic system. This report summarizes results from these two discrete studies.

  5. Autism associated gene, engrailed2, and flanking gene levels are altered in post-mortem cerebellum.

    Jiyeon Choi

    Full Text Available BACKGROUND: Previous genetic studies demonstrated association between the transcription factor engrailed2 (EN2 and Autism Spectrum Disorder (ASD. Subsequent molecular analysis determined that the EN2 ASD-associated haplotype (rs1861972-rs1861973 A-C functions as a transcriptional activator to increase gene expression. EN2 is flanked by 5 genes, serotonin receptor5a (HTR5A, insulin induced gene1 (INSIG1, canopy1 homolog (CNPY1, RNA binding motif protein33 (RBM33, and sonic hedgehog (SHH. These flanking genes are co-expressed with EN2 during development and coordinate similar developmental processes. To investigate if mRNA levels for these genes are altered in individuals with autism, post-mortem analysis was performed. METHODS: qRT-PCR quantified mRNA levels for EN2 and the 5 flanking genes in 78 post-mortem cerebellar samples. mRNA levels were correlated with both affection status and rs1861972-rs1861973 genotype. Molecular analysis investigated whether EN2 regulates flanking gene expression. RESULTS: EN2 levels are increased in affected A-C/G-T individuals (p = .0077. Affected individuals also display a significant increase in SHH and a decrease in INSIG1 levels. Rs1861972-rs1861973 genotype is correlated with significant increases for SHH (A-C/G-T and CNPY1 (G-T/G-T levels. Human cell line over-expression and knock-down as well as mouse knock-out analysis are consistent with EN2 and SHH being co-regulated, which provides a possible mechanism for increased SHH post-mortem levels. CONCLUSIONS: EN2 levels are increased in affected individuals with an A-C/G-T genotype, supporting EN2 as an ASD susceptibility gene. SHH, CNPY1, and INSIG1 levels are also significantly altered depending upon affection status or rs1861972-rs1861973 genotype. Increased EN2 levels likely contribute to elevated SHH expression observed in the post-mortem samples.

  6. Postmortem Evaluation of Left Flank Laparoscopic Access in an Adult Female Giraffe (Giraffa camelopardalis

    R. Pizzi


    Full Text Available There are still few reports of laparoscopy in megavertebrates. The giraffe (Giraffa camelopardalis is the tallest land mammal, and the largest ruminant species. An 18-year-old multiparous female hybrid giraffe, weighing 650 kg, was euthanized for chronic health problems, and left flank laparoscopy was performed less than 30 minutes after death. Safe primary access was achieved under visualisation using an optical bladed trocar (Visiport Plus, Tyco healthcare UK Ltd without prior abdominal insufflation. A left paralumbar fossa approach allowed access to the spleen, rumen, left kidney, and intestines, but did not allow access to the reproductive tract which in nongravid females is intrapelvic in nature.

  7. Genetic analysis on 3'-terminal flanking region of uncoupling protein 3 in different pig breeds


    The 3′-terminal flanking region of porcine uncoupling protein 3 (UCP3) was cloned, the sequence data revealed 15 nucleotide substitutions among Landrace and three Chinese native pig breeds named Neijiang, Minpig and Erhualian. The continuous 9 polymorphic sites were checked by PCR-RFLP, the results indicatedthat Erhualian had extraordinary gene frequency, presented most significant difference by χ2 test compared with Landrace, Largewhite, Neijiang and Minpig respectively, significant level compared with Meishan; and Meishan also had significant difference compared with Landrace and Minpig respectively. These results canbe concluded that Taihu pigs have special genetic characteristics among pig breeds.

  8. Stability analysis of Hawaiian Island flanks using insight gained from strength testing of the HSDP core

    Thompson, Nick; Watters, Robert J.; Schiffman, Peter


    Hawaiian Island flank failures are recognized as the largest landslide events on Earth, reaching volumes of several thousand cubic kilometers and lengths of over 200 km and occurring on an average of once every 100 000 years. The 3.1 km deep Hawaii Scientific Drilling Project (HSDP) enabled an investigation of the rock mass strength variations on the island of Hawaii [Schiffman, P., Watters, R.J., Thompson, N., Walton, A.W., 2006. Hyaloclastites and the slope stability of Hawaiian volcanoes: insights from the Hawaiian Scientific Drilling Project's 3-km drill core. Journal of Volcanology and Geothermal Research, 151 (1-3): 217-228]. This study builds on that of Schiffman et al. [Schiffman, P., Watters, R.J., Thompson, N., Walton, A.W., 2006. Hyaloclastites and the slope stability of Hawaiian volcanoes: Insights from the Hawaiian Scientific Drilling Project's 3-km drill core. Journal of Volcanology and Geothermal Research, 151 (1-3): 217-228] by considering more in-depth rock mass classification and strength testing methods of the HSDP core. Geotechnical core logging techniques combined with laboratory strength testing methods show that rock strength differences exist within the edifice. Comparing the rock strength parameters obtained from the various volcano lithologies identified weak zones, suggesting the possible location of future slip surfaces for large flank failures. Relatively weak rock layers were recognized within poorly consolidated hyaloclastite zones, with increases in strength based on degree of alteration. Subaerial and submarine basalt flows are found to be significantly stronger. With the aid of digital elevation models, cross-sections have been developed of key flank areas on the island of Hawaii. Limit equilibrium slope stability analyses are performed on each cross-section using various failure criteria for the rock mass strength calculations. Based on the stability analyses the majority of the slopes analyzed are considered stable. In cases

  9. A romifidine and morphine combination for epidural analgesia of the flank in cattle

    Fierheller, Erin E.; Caulkett, Nigel A.; Bailey, Jeremy V.


    The objective of the study reported here was to determine the onset, duration, and degree of analgesia achieved with a combination of romifidine (50 μg/kg body weight [BW]) and morphine (0.1 mg/kg BW) administered epidurally. Ten adult Holstein Friesen cows were assigned to either a treatment group receiving the romifidine and morphine combination or a control group receiving 0.9% saline in a randomized, blinded, crossover design. Cows were assessed for degree of flank analgesia and systemic ...

  10. North Kona slump: Submarine flank failure during the early(?) tholeiitic shield stage of Hualalai Volcano

    Lipman, P.W.; Coombs, M.L.


    The North Kona slump is an elliptical region, about 20 by 60 km (1000-km2 area), of multiple, geometrically intricate benches and scarps, mostly at water depths of 2000–4500 m, on the west flank of Hualalai Volcano. Two dives up steep scarps in the slump area were made in September 2001, using the ROV Kaiko of the Japan Marine Science and Technology Center (JAMSTEC), as part of a collaborative Japan–USA project to improve understanding of the submarine flanks of Hawaiian volcanoes. Both dives, at water depths of 2700–4000 m, encountered pillow lavas draping the scarp-and-bench slopes. Intact to only slightly broken pillow lobes and cylinders that are downward elongate dominate on the steepest mid-sections of scarps, while more equant and spherical pillow shapes are common near the tops and bases of scarps and locally protrude through cover of muddy sediment on bench flats. Notably absent are subaerially erupted Hualalai lava flows, interbedded hyaloclastite pillow breccia, and/or coastal sandy sediment that might have accumulated downslope from an active coastline. The general structure of the North Kona flank is interpreted as an intricate assemblage of downdropped lenticular blocks, bounded by steeply dipping normal faults. The undisturbed pillow-lava drape indicates that slumping occurred during shield-stage tholeiitic volcanism. All analyzed samples of the pillow-lava drape are tholeiite, similar to published analyses from the submarine northwest rift zone of Hualālai. Relatively low sulfur (330–600 ppm) and water (0.18–0.47 wt.%) contents of glass rinds suggest that the eruptive sources were in shallow water, perhaps 500–1000-m depth. In contrast, saturation pressures calculated from carbon dioxide concentrations (100–190 ppm) indicate deeper equilibration, at or near sample sites at water depths of − 3900 to − 2800 m. Either vents close to the sample sites erupted mixtures of undegassed and degassed magmas, or volatiles were resorbed from

  11. “Isolated Spontaneous Renal Artery Thrombosis – A Rare Cause of Acute Flank Pain”

    M. Raghavendran


    Full Text Available Many patients present with severe abdominal pain. Renal Artery Thrombosis (RAT is rare, serious and misdiagnosed. RAT has been well described in association with various disorders, but isolated spontaneously occurring RAT is rare and only 2 cases have been described as of date. We present a case of flank pain presenting to emergency for evaluation and discuss the clinical aspects and management. We would like to stress on the important role of serum LDH levels and CT scan in RAT. Early diagnosis may result in salvage of organ by minimally invasive techniques. Late diagnosis will almost always result in nephrectomy.

  12. Simple sequence repeats in watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai).

    Jarret, R L; Merrick, L C; Holms, T; Evans, J; Aradhya, M K


    Simple sequence repeat length polymorphisms were utilized to examine genetic relatedness among accessions of watermelon (Citrullus lanatus (Thunb.) Matsum. & Nakai). A size-fractionated TaqI genomic library was screened for the occurrence of dimer and trimer simple sequence repeats (SSRs). A total of 96 (0.53%) SSR-bearing clones were identified and the inserts from 50 of these were sequenced. The dinucleotide repeats (CT)n and (GA)n accounted for 82% of the SSRs sequenced. PCR primer pairs flanking seven SSR loci were used to amplify SSRs from 32 morphologically variable watermelon genotypes from Africa, Europe, Asia, and Mexico and a single accession of Citrullus colocynthis from Chad. Cluster analysis of SSR length polymorphisms delineated 4 groups at the 25% level of genetic similarity. The largest group contained C. lanatus var. lanatus accessions. The second largest group contained only wild and cultivated "citron"-type or C. lanatus var. citroides accessions. The third group contained an accession tentatively identified as C. lanatus var. lanatus but which perhaps is a hybrid between C. lanatus var. lanatus and C. lanatus var. citroides. The fourth group consisted of a single accession identified as C. colocynthis. "Egusi"-type watermelons from Nigeria grouped with C. lanatus var. lanatus. The use of SSRs for watermelon germplasm characterization and genetic diversity studies is discussed.

  13. Alu repeats as markers for forensic DNA analyses

    Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Kass, D.H. [Louisiana State Univ., New Orleans, LA (United States)] [and others


    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 98.9% nucleotide identity with the HS subfamily consensus sequence, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 inch and 3 inch unique flanking DNA sequences from each HS Alu that allow the locus to be assayed for the presence or absence of the Alu repeat. The dimorphic HS Alu sequences probably inserted in the human genome after the radiation of modem humans (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project. HS Alu family member insertions differ from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) in that polymorphisms due to Alu insertions arise as a result of a unique event which has occurred only one time in the human population and spread through the population from that point. Therefore, individuals that share HS Alu repeats inherited these elements from a common ancestor. Most VNTR and RFLP polymorphisms may arise multiple times in parallel within a population.

  14. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats

    Vergnaud Gilles


    Full Text Available Abstract Background In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows that new motifs (one spacer and one repeated element are added in a polarised fashion. Although their principal characteristics have been described, a lot remains to be discovered on the way CRISPRs are created and evolve. As new genome sequences become available it appears necessary to develop automated scanning tools to make available CRISPRs related information and to facilitate additional investigations. Description We have produced a program, CRISPRFinder, which identifies CRISPRs and extracts the repeated and unique sequences. Using this software, a database is constructed which is automatically updated monthly from newly released genome sequences. Additional tools were created to allow the alignment of flanking sequences in search for similarities between different loci and to build dictionaries of unique sequences. To date, almost six hundred CRISPRs have been identified in 475 published genomes. Two Archeae out of thirty-seven and about half of Bacteria do not possess a CRISPR. Fine analysis of repeated sequences strongly supports the current view that new motifs are added at one end of the CRISPR adjacent to the putative promoter. Conclusion It is hoped that availability of a public database, regularly updated and which can be queried on the web will help in further dissecting and understanding CRISPR structure and flanking sequences evolution. Subsequent analyses of the intra-species CRISPR polymorphism will be facilitated by CRISPRFinder and the

  15. The unstable CCTG repeat responsible for myotonic dystrophy type 2 originates from an AluSx element insertion into an early primate genome.

    Tatsuaki Kurosaki

    Full Text Available Myotonic dystrophy type 2 (DM2 is a subtype of the myotonic dystrophies, caused by expansion of a tetranucleotide CCTG repeat in intron 1 of the zinc finger protein 9 (ZNF9 gene. The expansions are extremely unstable and variable, ranging from 75-11,000 CCTG repeats. This unprecedented repeat size and somatic heterogeneity make molecular diagnosis of DM2 difficult, and yield variable clinical phenotypes. To better understand the mutational origin and instability of the ZNF9 CCTG repeat, we analyzed the repeat configuration and flanking regions in 26 primate species. The 3'-end of an AluSx element, flanked by target site duplications (5'-ACTRCCAR-3'or 5'-ACTRCCARTTA-3', followed the CCTG repeat, suggesting that the repeat was originally derived from the Alu element insertion. In addition, our results revealed lineage-specific repetitive motifs: pyrimidine (CT-rich repeat motifs in New World monkeys, dinucleotide (TG repeat motifs in Old World monkeys and gibbons, and dinucleotide (TG and tetranucleotide (TCTG and/or CCTG repeat motifs in great apes and humans. Moreover, these di- and tetra-nucleotide repeat motifs arose from the poly (A tail of the AluSx element, and evolved into unstable CCTG repeats during primate evolution. Alu elements are known to be the source of microsatellite repeats responsible for two other repeat expansion disorders: Friedreich ataxia and spinocerebellar ataxia type 10. Taken together, these findings raise questions as to the mechanism(s by which Alu-mediated repeats developed into the large, extremely unstable expansions common to these three disorders.

  16. Expansion of protein domain repeats.

    Asa K Björklund


    Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

  17. An Expanded CAG Repeat in Huntingtin Causes +1 Frameshifting.

    Saffert, Paul; Adamla, Frauke; Schieweck, Rico; Atkins, John F; Ignatova, Zoya


    Maintenance of triplet decoding is crucial for the expression of functional protein because deviations either into the -1 or +1 reading frames are often non-functional. We report here that expression of huntingtin (Htt) exon 1 with expanded CAG repeats, implicated in Huntington pathology, undergoes a sporadic +1 frameshift to generate from the CAG repeat a trans-frame AGC repeat-encoded product. This +1 recoding is exclusively detected in pathological Htt variants, i.e. those with expanded repeats with more than 35 consecutive CAG codons. An atypical +1 shift site, UUC C at the 5' end of CAG repeats, which has some resemblance to the influenza A virus shift site, triggers the +1 frameshifting and is enhanced by the increased propensity of the expanded CAG repeats to form a stem-loop structure. The +1 trans-frame-encoded product can directly influence the aggregation of the parental Htt exon 1.

  18. Isolation of T—DNA flanking plant DNA from T—DNA insertional embryo—lethal mutants of Arabidopsis thaliana by plasmid rescue technique



    Three T-DNA insertional embryonic lethal mutants from NASC(The Nottingham Arabidopsis Stock Center) were first checked with their segregation ratio of abortive and normal seeds and the copy number of T-DNA insertion.The N4081 mutant has a segregation ratio of 1:3.04 in average and one T-DNA insertion site according to our assay.It was therefore chosen for further analysis.To isolate the joint fragment of T-DNA and plant DNA,the plasmid rescue technique was used.pEL-7,one of plasmids from left border of T-DNA,which contained pBR322 was selected from ampicillin plate.The T-DNA fragment of pEL-7 was checked by restriction enzyme analysis and Southern Blot.Restriction analysis confirmed the presence of known sites of EcoRI,PstI and PvuII on it.For confirming the presence of flanking plant DNA in this plasmid,pEL-7 DNA was labeled and hybridized with wild type and mutant plant DNA.The Southern Blot indicated the hybridization band in both of them.Furthermore,the junction of T-DNA/plant DNA was subcloned into bluescript SK+ and sequenced by Applied Biosystem 373A sequencer.The results showed the 822 bp fragment contained a 274 bp sequence,which is 99.6%homolog(273bp/274bp) to Ti plasmid pTi 15955,DNA.The bp of left 25 bp border repeat were also found in the juction of T-DNA and Plant DNA. Taken together,pEL-7 should coutain a joint fragment of T-DNA and flanking plant DNA.This plasmid DNA could be used for the isolation of plant gene,which will be helpful to elucidate the relationship between gene function and plant embryo development.

  19. DWI Repeaters and Non-Repeaters: A Comparison.

    Weeber, Stan


    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)

  20. To Repeat or Not to Repeat a Course

    Armstrong, Michael J.; Biktimirov, Ernest N.


    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…

  1. REPdenovo: Inferring De Novo Repeat Motifs from Short Sequence Reads.

    Chong Chu

    Full Text Available 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

  2. Character of shell beds flanking Herod Point shoal, southeastern Long Island Sound, New York

    Poppe, L.J.; Williams, S.J.; Babb, Ivar G.


    High biogenic productivity, strong tidal currents, shoal topography, and short transport distances combine to favor shell-bed formation along the lower flanks of a cape-associated shoal off Herod Point on Long Island, New York. This shell bed has a densely packed, clast-supported fabric composed largely of undegraded surf clam (Spisula solidissima) valves. It is widest along the central part of the western flank of the shoal where topographic gradients are steep and a stronger flood tide results in residual flow. The bed is narrower and thinner toward the landward margins where currents are too weak to transport larger valves and topographic gradients are gentle, limiting bed-load transport mechanisms by which the shells are concentrated. Reconnaissance mapping off Roanoke Point suggests that shell beds are also present at the other cape-associated shoals off northeastern Long Island, where relatively similar geomorphic and oceanographic conditions exist. These shell beds are important to the Long Island Sound ecosystem because they provide complex benthic habitats of rough and hard substrates at the boundary between the muddy basin floor and mobile sand of the shoals. ?? 2011, the Coastal Education & Research Foundation (CERF).

  3. Overview of the geology of the east flank of the Front Range

    Grose, T.L.T. [Colorado School of Mines, Golden, CO (United States). Dept. of Geology


    This paper describes the geology encountered as part of a geology field trip. This stop identifies the monocline that forms the east flank of the Front Range and the west flank of the Denver Basin. The stratigraphic section viewed in cross section to the south is composed of: (1) migmatitic quartzo-feldspathic gneiss of Early Proterozoic age; (2) red sandstone and conglomerate of the Pennsylvanian-Permian Fountain Formation, 1,700 Feet thick; (3) Lyons Sandstone of Permian age, 200 feet thick; (4) shale, siltstone, and limestone of the Lykins Formation of Permian and Triassic age, 200 Feet thick; (5) gypsum, shale, and limestone of the Ralston Creek Formation of Jurassic age, 90 feet thick; (6) sandstone, shale, and limestone of the Morrison Formation of Jurassic age, 300 feet thick, locally containing dinosaur bones; (7) Lower Cretaceous Dakota Group, including the Lytle Formation of sandstone and conglomerate, 80 feet thick, and the South Platte Formation of sandstone and shale, 220 feet thick.

  4. Microarray analyses and comparisons of upper or lower flanks of rice shoot base preceding gravitropic bending.

    Liwei Hu

    Full Text Available Gravitropism is a complex process involving a series of physiological pathways. Despite ongoing research, gravitropism sensing and response mechanisms are not well understood. To identify the key transcripts and corresponding pathways in gravitropism, a whole-genome microarray approach was used to analyze transcript abundance in the shoot base of rice (Oryza sativa sp. japonica at 0.5 h and 6 h after gravistimulation by horizontal reorientation. Between upper and lower flanks of the shoot base, 167 transcripts at 0.5 h and 1202 transcripts at 6 h were discovered to be significantly different in abundance by 2-fold. Among these transcripts, 48 were found to be changed both at 0.5 h and 6 h, while 119 transcripts were only changed at 0.5 h and 1154 transcripts were changed at 6 h in association with gravitropism. MapMan and PageMan analyses were used to identify transcripts significantly changed in abundance. The asymmetric regulation of transcripts related to phytohormones, signaling, RNA transcription, metabolism and cell wall-related categories between upper and lower flanks were demonstrated. Potential roles of the identified transcripts in gravitropism are discussed. Our results suggest that the induction of asymmetrical transcription, likely as a consequence of gravitropic reorientation, precedes gravitropic bending in the rice shoot base.

  5. Characterization of Bovine 5′-flanking Region during Differentiation of Mouse Embryonic Stem Cells

    Hye-Jeong Jang


    Full Text Available Embryonic stem cells (ESCs have been used as a powerful tool for research including gene manipulated animal models and the study of developmental gene regulation. Among the critical regulatory factors that maintain the pluripotency and self-renewal of undifferentiated ESCs, NANOG plays a very important role. Nevertheless, because pluripotency maintaining factors and specific markers for livestock ESCs have not yet been probed, few studies of the NANOG gene from domestic animals including bovine have been reported. Therefore, we chose mouse ESCs in order to understand and compare NANOG expression between bovine, human, and mouse during ESCs differentiation. We cloned a 600 bp (−420/+181 bovine NANOG 5′-flanking region, and tagged it with humanized recombinant green fluorescent protein (hrGFP as a tracing reporter. Very high GFP expression for bovine NANOG promoter was observed in the mouse ESC line. GFP expression was monitored upon ESC differentiation and was gradually reduced along with differentiation toward neurons and adipocyte cells. Activity of bovine NANOG (−420/+181 promoter was compared with already known mouse and human NANOG promoters in mouse ESC and they were likely to show a similar pattern of regulation. In conclusion, bovine NANOG 5-flanking region functions in mouse ES cells and has characteristics similar to those of mouse and human. These results suggest that bovine gene function studied in mouse ES cells should be evaluated and extrapolated for application to characterization of bovine ES cells.

  6. Performance of genotype imputation for rare variants identified in exons and flanking regions of genes.

    Li Li

    Full Text Available Genotype imputation has the potential to assess human genetic variation at a lower cost than assaying the variants using laboratory techniques. The performance of imputation for rare variants has not been comprehensively studied. We utilized 8865 human samples with high depth resequencing data for the exons and flanking regions of 202 genes and Genome-Wide Association Study (GWAS data to characterize the performance of genotype imputation for rare variants. We evaluated reference sets ranging from 100 to 3713 subjects for imputing into samples typed for the Affymetrix (500K and 6.0 and Illumina 550K GWAS panels. The proportion of variants that could be well imputed (true r(2>0.7 with a reference panel of 3713 individuals was: 31% (Illumina 550K or 25% (Affymetrix 500K with MAF (Minor Allele Frequency less than or equal 0.001, 48% or 35% with 0.0010.05. The performance for common SNPs (MAF>0.05 within exons and flanking regions is comparable to imputation of more uniformly distributed SNPs. The performance for rare SNPs (0.01

  7. Stratigraphy and Characterization of Volcanic Deposits on the Northwestern Flanks of Mt. Makiling, Laguna, Philippines

    Ybanez, R. L.; Bonus, A. A. B.; Judan, J. M.; Racoma, B. A.; Morante, K. A. M.; Balangue, M. I. R. D.


    Mt. Makiling is an inactive stratovolcano located in the province of Laguna. Semi-detailed geologic field mapping on the northwestern low-level flanks and apron of the volcano was conducted. Exposures reveal a volcanic terrain hosting a wide variety of volcanic rocks: lava flows, pyroclastic surges, pyroclastic flows, and tuff deposits. Stratigraphic logging of the volcanic deposits showed differences in occurrence of the deposit types as well as their characteristics. The pyroclastic flow deposits are found at the base of the column overlain by pyroclastic surges which were more common in the area. Capping the pyroclastic surges is a thin layer of tuffaceous units. Isolated deposits of lava flows of andesitic composition were mapped in the western flank of Mt. Makiling. These varying volcanic deposits are derived from different eruptive activities of Mt. Makiling, with at least three separate eruptive episodes indicated by the exposed deposits. Two separate explosive eruptions are marked by two different pyroclastic deposits, while an effusive episode, marked by andesitic lava flows, can also be identified. The pyroclastic surge deposit is uncharacteristically thick, around a hundred meters or more exposed, providing further questions as to the magnitude of past eruptions or the mechanism of pyroclastic material deposition around the volcano. Mt. Makiling, thus, has historically undergone different eruption types, but still releases generally the same material composition across varying deposits: intermediate or andesitic composition. This is consistent with the trend of Philippine volcanoes, and with the Macolod corridor which hosts this volcanic system.

  8. Renal infarction versus pyelonephritis in a woman presenting with fever and flank pain.

    Piccoli, Giorgina B; Priola, Adriano M; Vigotti, Federica N; Guzzo, Gabriella; Veltri, Andrea


    Patients with fever, flank pain, and dysuria frequently are encountered in the emergency department. Acute pyelonephritis is the most likely diagnosis; however, its clinical and radiologic presentation consistently overlap with that of acute renal infarction. Ultrasound is unable to distinguish early infarction from nonabscessed acute pyelonephritis. Hence, computed tomography or magnetic resonance imaging are needed. We report the case of a 68-year-old woman who presented with fever, flank pain, and dysuria, along with respiratory distress and tachycardia. Elevated values for inflammatory indexes suggested a diagnosis of acute pyelonephritis, and subsequent contrast-enhanced computed tomography showed hypodense wedge-shaped areas in both kidneys. However, the presence of a thin rim of capsular enhancement (cortical rim sign), the absence of perirenal inflammatory changes, and the location of the lesions apart from defined calyces suggested the alternative diagnosis of renal infarction. The underlying cause was not identified until an episode of acute dyspnea revealed paroxysmal arrhythmia. Our case demonstrates that a thorough knowledge of the imaging findings of renal infarction and acute pyelonephritis is essential to correctly making the diagnosis. Copyright © 2014 National Kidney Foundation, Inc. Published by Elsevier Inc. All rights reserved.

  9. A deep scar in the flank of Tenerife (Canary Islands): Geophysical contribution to tsunami hazard assessment

    Coppo, Nicolas P.; Schnegg, Pierre-André; Falco, Pierik; Costa, Roberto


    Among the high-intensity on-Earth tsunami generating events, seismicity, submarine landslides, and volcano lateral collapses are the most important [Ward, S.H., 2001. Landslide tsunami. J. Geophy. Res. 106, 11201-11215; Holcomb, R.T., Searle, R.C., 1991. Large landslides from oceanic volcanoes. Mar. Geotech. 10, 19-32; Tinti, S., Bortolucci, E., Romagnoli, C., 2000. Computer simulations of tsunamis due to the sector collapse ar Stromboli, Italy. J. Volcano. Geotherm. Res. 96, 103-128; Ward, S.N., Day, S., 2003. Ritter Island Volcano — lateral collapse and the tsunami of 1888. Geophys. J. Int. 154, 891-902; MacGuire, W.J., 2003. Volcano instability and lateral collapse. Revista 1, 33-45]. Offshore bathymetry studies highlighted huge accumulations of large mass-waste flows (up to thousands cubic kilometres) inherited from past lateral collapses or submarine landslides [ Le Friant, A., Boudon, G., Deplus, C., Villemant, B., 2003. Large-scale flank collapse events during the activity of Montagne Pelée, Martinique, Lesser Antilles. J. Geophys. Res. 108, ECV13; Moore, J.G. et al., 1989. Prodigious submarine Landslides on the Hawaiian ridge. J. Geophys. Res. 94, 17465-17484] which spread over more than 100 km off the northern Tenerife (Canary Islands) coastline [Watts, A.B., Masson, D.G., 1995. A giant landslide on the north flank of Tenerife, Canary Islands. J. Geophys. Res. 100, 24487-24498]. Although mechanics and dynamics triggering such catastrophic events follow from combined complex processes and interactions [Hürlimann, M., Garcia-Piera, J.-O., Ledesma, A., 2000. Causes and mobility of large volcanic landslides: application to Tenerife, Canary Islands. J. Volcano. Geotherm. Res. 103, 121-134; Masson, D.G. et al., 2002. Slope failures on the flanks of the western Canary Islands. Earth-Sci. Rev. 57, 1-35; Reid, M.E., Sisson, T.W., Brien, D.L., 2001. Volcano collapse promoted by hydrothermal alteration and edifice shape, Mount Rainier, Washington. Geology 29, 779

  10. Multidisciplinary geophysical study of the NE sector of the unstable flank of Etna volcano

    Bonforte, Alessandro; Cocina, Ornella; Siniscalchi, Agata; Barberi, Graziella; Guglielmino, Francesco; Romano, Gerardo; Sicali, Simona; Tripaldi, Simona


    On volcanic areas, usually characterized by complex structural environments, a lot of independent geophysical studies are usually performed. The non-uniqueness of the geophysical inverse models, the different level of resolution and sensitivity of the results spurred us to integrate independent geophysical datasets and results collected on Mt. Etna volcano, in order to obtain more accurate and reliable model interpretation. Mt. Etna volcano is located along the eastern coast of Sicily and it is characterized by a complex structural setting. In this region, the general N-S compressive regime related to the Africa - Europe collision interacts with the WNW-ESE extensional regime associated to the Malta Escarpment dynamics, observable along the eastern coast of Sicily. At Mt Etna, a great number of studies concerns the existence of instability phenomena; a general eastward motion of the eastern flank of the volcano has been measured with always increasing detail and its relationship with the eruptive and magmatic activity is being investigated. The unstable flank appears bounded to the north by the E-W-trending Provenzana - Pernicana Fault System and to the SW by the NS Ragalna Fault system. Eastwards, this area is divided by several NW-SE trending faults. Recent studies consider this area as divided into several blocks characterized by different shape and kinematics. Ground deformation studies (GPS and InSAR) define the NE portion of the unstable flank as the most mobile one. In the frame of the MEDiterranean Supersites Volcanoes (MED-SUV) project, ground deformation data (GPS and INSAR), 3D seismicity, seismic tomography and two resistivity model profiles, have been analyzed together, in order to put some constraints on the deep structure of the NE sector of the unstable flank. Seismic data come from the permanent network run by the Istituto Nazionale di Geofisica e Vulcanologia (INGV) - Sezione di Catania, Osservatorio Etneo. Ground deformation data comes from In

  11. CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats

    Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine


    Clustered regularly interspaced short palindromic repeat (CRISPR) elements are a particular family of tandem repeats present in prokaryotic genomes, in almost all archaea and in about half of bacteria, and which participate in a mechanism of acquired resistance against phages. They consist in a succession of direct repeats (DR) of 24–47 bp separated by similar sized unique sequences (spacers). In the large majority of cases, the direct repeats are highly conserved, while the number and nature...

  12. Nifty Nines and Repeating Decimals

    Brown, Scott A.


    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…

  13. Nifty Nines and Repeating Decimals

    Brown, Scott A.


    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…

  14. On balanced minimal repeated measurements designs

    Shakeel Ahmad Mir


    Full Text Available Repeated Measurements designs are concerned with scientific experiments in which each experimental unit is assigned more than once to a treatment either different or identical. This class of designs has the property that the unbiased estimators for elementary contrasts among direct and residual effects are obtainable. Afsarinejad (1983 provided a method of constructing balanced Minimal Repeated Measurements designs p < t , when t is an odd or prime power, one or more than one treatment may occur more than once in some sequences and  designs so constructed no longer remain uniform in periods. In this paper an attempt has been made to provide a new method to overcome this drawback. Specifically, two cases have been considered                RM[t,n=t(t-t/(p-1,p], λ2=1 for balanced minimal repeated measurements designs and  RM[t,n=2t(t-t/(p-1,p], λ2=2 for balanced  repeated measurements designs. In addition , a method has been provided for constructing              extra-balanced minimal designs for special case RM[t,n=t2/(p-1,p], λ2=1.

  15. All-photonic quantum repeaters

    Azuma, Koji; Tamaki, Kiyoshi; Lo, Hoi-Kwong


    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

  16. Linkage of congenital isolated adrenocorticotropic hormone deficiency to the corticotropin releasing hormone locus using simple sequence repeat polymorphisms

    Kyllo, J.H.; Collins, M.M.; Vetter, K.L. [Univ. of Iowa College of Medicine, Iowa City, IA (United States)] [and others


    Genetic screening techniques using simple sequence repeat polymorphisms were applied to investigate the molecular nature of congenital isolated adrenocorticotropic hormone (ACTH) deficiency. We hypothesize that this rare cause of hypocortisolism shared by a brother and sister with two unaffected sibs and unaffected parents is inherited as an autosomal recessive single gene mutation. Genes involved in the hypothalamic-pituitary axis controlling cortisol sufficiency were investigated for a causal role in this disorder. Southern blotting showed no detectable mutations of the gene encoding pro-opiomelanocortin (POMC), the ACTH precursor. Other candidate genes subsequently considered were those encoding neuroendocrine convertase-1, and neuroendocrine convertase-2 (NEC-1, NEC-2), and corticotropin releasing hormone (CRH). Tests for linkage were performed using polymorphic di- and tetranucleotide simple sequence repeat markers flanking the reported map locations for POMC, NEC-1, NEC-2, and CRH. The chromosomal haplotypes determined by the markers flanking the loci for POMC, NEC-1, and NEC-2 were not compatible with linkage. However, 22 individual markers defining the chromosomal haplotypes flanking CRH were compatible with linkage of the disorder to the immediate area of this gene of chromosome 8. Based on these data, we hypothesize that the ACTH deficiency in this family is due to an abnormality of CRH gene structure or expression. These results illustrate the useful application of high density genetic maps constructed with simple sequence repeat markers for inclusion/exclusion studies of candidate genes in even very small nuclear families segregating for unusual phenotypes. 25 refs., 5 figs., 2 tabs.

  17. Ecological Resilience and Resistance in the Hyper Diverse Forests on the Eastern Andean Flank (Mera, Ecuador)

    Keen, H. F.; Gosling, W. D.; Montoya, E.; Sherlock, S.; Mothes, P. A.


    Today the Neotropics contain some of the world's most biodiverse and threatened ecosystems. Sediments obtained from two radiocarbon infinite (>48,000 years) stratigraphic sections on the eastern Andean flank, provide new insight into the relationship between biodiversity and disturbance during the Pleistocene (~200,000 years). Pollen analysis of modern and fossil material indicates that hyper diverse forest vegetation has been a feature of the Andean flank landscape for 100,000 years (pollen richness: modern = 44, fossil = 48). Correlation of past vegetation with disturbance events (volcanic and fluvial) indicates the response of hyper-diverse forest to past landscape scale change. Pollen records from near Mera (01°27 S, 78°06 W; 1117 m asl) indicate two major changes in the pollen assemblage, with forest communities dominated by: i) Hedyosmum-Alnus-Ilex, and ii) Combretaceae-Melastomataceae-Myrtaceae. These two pollen assemblages most closely resemble modern vegetation cloud forest (2500-3400m asl) and lower montane rain forest (700-2499 m asl) respectively. Sedimentary evidence suggests that at least 21 volcanic events and three changes in the local fluvial regime perturbed the regional landscape during the period of deposition. However, there is no evidence for volcanic or fluvial disturbance events causing a persistent change in vegetation community. Volcanic events (tephra deposits) are associated with increased fire (charcoal particles), and changes in vegetation (pollen grains); however, within ~50cm of sediment accumulation above each tephra, pollen assemblages revert to pre-deposition compositions. Increased fluvial influence (gravel deposits) is associated with elevated input of pollen from taxa today found at higher elevations (Podocarpus-Celtis). The input of high elevation taxa concomitant with fluvial deposits is most likely indicative of an increase in long-distance transport of pollen along water courses originating in the Andes. Our data indicate

  18. Flank gland-secreted putative chemosignals pertaining to photoperiod, endocrine states, and sociosexual behavior in golden hamsters

    Ying-Juan LIU, Da-Wei WANG, Lixing SUN, Jin-Hua ZHANG, Jian-Xu ZHANG


    Full Text Available Behavioral studies have shown that flank glands are involved in chemical communication in golden hamsters Mesocricetus auratus but little chemical analysis has been conducted on volatiles arising from these glands. Using gas chromatography-mass spectrometry, we detected compounds from the flank glands of males, only eight of which were also produced in females. Based on these chemical data we performed a number of further experiments. By manipulating light we found that males exposed to short-photoperiods developed smaller flank glands than those exposed to long-photoperiods. Six flank gland volatiles reduced in relative abundance, which possibly coded for reproductive status of males of this seasonally breeding hamster species. Through dyadic encounters, we were able to induce the formation of dominant-subordinate relationships and show that two glandular compounds became high in relative abundance and may function as dominance pheromones. Castration eliminated all male-specific compounds resulting from flank glands, but bilateral ovariectomies only affected one compound in females. Once these ovariectomized females were treated with testosterone, their glandular compounds resembled those of males, suggesting these compounds are under the main control of androgen. Two female putative pheromones, tetradecanoic acid and hexadecanoic acid, were used in binary choice tests and were both found to attract males over females. Applying a solution of these pheromone compounds to adult males also suppressed their agonistic behavior [Current Zoology 56 (6: 800–812, 2010].

  19. Closed-Loop Feedback Flank Errors Correction of Topographic Modification of Helical Gears Based on Form Grinding

    Huiliang Wang


    Full Text Available To increase quality, reduce heavy-duty gear noise, and avoid edge contact in manufacturing helical gears, a closed-loop feedback correction method in topographic modification tooth flank is proposed based on the gear form grinding. Equations of grinding wheel profile and grinding wheel additional radial motion are derived according to tooth segmented profile modification and longitudinal modification. Combined with gear form grinding kinematics principles, the equations of motion for each axis of five-axis computer numerical control forming grinding machine are established. Such topographical modification is achieved in gear form grinding with on-machine measurement. Based on a sensitivity analysis of polynomial coefficients of axis motion and the topographic flank errors by on-machine measuring, the corrections are determined through an optimization process that targets minimization of the tooth flank errors. A numerical example of gear grinding, including on-machine measurement and closed-loop feedback correction completing process, is presented. The validity of this flank correction method is demonstrated for tooth flank errors that are reduced. The approach is useful to precision manufacturing of spiral bevel and hypoid gears, too.

  20. Coexistence of 3G repeaters with LTE base stations.

    Yeo, Woon-Young; Lee, Sang-Min; Hwang, Gyung-Ho; Kim, Jae-Hoon


    Repeaters have been an attractive solution for mobile operators to upgrade their wireless networks at low cost and to extend network coverage effectively. Since the first LTE commercial deployment in 2009, many mobile operators have launched LTE networks by upgrading their 3G and legacy networks. Because all 3G frequency bands are shared with the frequency bands for LTE deployment and 3G mobile operators have an enormous number of repeaters, reusing 3G repeaters in LTE networks is definitely a practical and cost-efficient solution. However, 3G repeaters usually do not support spatial multiplexing with multiple antennas, and thus it is difficult to reuse them directly in LTE networks. In order to support spatial multiplexing of LTE, the role of 3G repeaters should be replaced with small LTE base stations or MIMO-capable repeaters. In this paper, a repeater network is proposed to reuse 3G repeaters in LTE deployment while still supporting multilayer transmission of LTE. Interestingly, the proposed network has a higher cluster throughput than an LTE network with MIMO-capable repeaters.

  1. Squamous cell carcinoma in left flank due to saree: Largest reported case

    Nisha Mandhane


    Full Text Available Saree is a female costume unique for Indian ladies. This includes a superficial cloth and a skirt underneath which is fastened securely to the waist by a cord. Persistent and long term wearing of this costume has resulted in waist dermatoses. Waist dermatoses theoretically may present with malignant transformation. Here we present a case of 60 year old female who presented with left flank ulcer following chronic irritation from saree, biopsy was taken and it showed squamous cell carcinoma (SCC. We decided to do wide excision with tension free suturing. Post operatively the patient followed up for 12 week and has shown to be disease free. This turns out to be the third case being reported and the largest ever to be reported in the literature. [Int J Res Med Sci 2015; 3(7.000: 1803-1806

  2. Flank pain after minor trauma as the initial manifestation of malignant pheochromocytoma; a case report

    Niroomand Hassan


    Full Text Available Pheochromocytoma is a tumor which originates from chromaffin cells of the adrenal medulla or the sympathetic ganglia. This tumor secrets a high amount of catecholamine and metabolites, causing hypertension crisis with headache, tachycardia, sweating and flushing (classic triad of pheochromocytoma. However, in some cases the disease may cause atypical symptoms or may be asymptomatic. The presented patient is a 34-year-old man who referred to our clinic with left flank pain. He had a history of falling from height. In the primary physical examination, a large mass in the abdominal left upper quadrant was palpated. After diagnostic evaluation malignant pheochromocytoma was detected. The patient was discharged on the fourth day after surgery. Malignant pheochromocytoma can presented with atypical symptoms or can be asymptomatic.

  3. Global optimization of tool path for five-axis flank milling with a cylindrical cutter


    In this paper, optimum positioning of cylindrical cutter for five-axis flank milling of non-developable ruled surface is addressed from the perspective of surface approximation. Based on the developed interchangeability principle, global optimization of the five-axis tool path is modeled as approximation of the tool envelope surface to the data points on the design surface following the minimum zone criterion recommended by ANSI and ISO standards for tolerance evaluation. By using the signed point-to-surface distance function, tool path plannings for semi-finish and finish millings are formulated as two constrained optimization problems in a unified framework. Based on the second order Taylor approximation of the distance function, a sequential approximation algorithm along with a hierarchical algorithmic structure is developed for the optimization. Numerical examples are presented to confirm the validity of the proposed approach.

  4. Global optimization of tool path for five-axis flank milling with a cylindrical cutter

    DING Han; ZHU LiMin


    In this paper,optimum positioning of cylindrical cutter for five-axis flank milling of non-developable ruled surface is addressed from the perspective of surface approximation.Based on the developed interchangeability principle,global optimization of the five-axis tool path is modeled as approximation of the tool envelope surface to the data points on the design surface following the minimum zone criterion recommended by ANSI and ISO standards for tolerance evaluation.By using the signed point-to-surface distance function,tool path plannings for semi-finish and finish millings are formulated as two constrained optimization problems in a unified framework.Based on the second order Taylor approximation of the distance function,a sequential approximation algorithm along with a hierarchical algorithmic structure is developed for the optimization.Numerical examples are presented to confirm the validity of the proposed approach.

  5. Mitigation of Flanking Noise Transmission in Periodic Structures of Lightweight Elements

    Domadiya, Parthkumar Gandalal

    Lightweight structures becoming increasingly popular within the building industry and hence they requires immediate attention to address their vibro-acoustic behaviour. Flanking noise transmission is one of the main concerns while using lightweight panels in buildings, since sound can travel...... characteristics in periodic structures, the structure must be simplified; hence, one dimensional structures such as bars and beams are considered for further investigation. A periodic bar model comprised of systemically placed Plexiglas and steel elements is generated using two methods: an FE method and a Floquet...... transmission in periodic structures of lightweight elements by employing various numerical, analytical and experimental methods. At first, three dimensional finite-element (FE) models of a Z-shaped lightweight panel structure based on various frame designs, inclusion of air and structural coupling between...

  6. A Twenty-Four-Year-Old Woman with Left Flank Lipoma-Like Hibernoma

    R.E. Shackelford


    Full Text Available A 24-year-old woman presented with a 5-month history of a left flank mass that was painful on palpation. Magnetic resonance imaging revealed a 10.0 × 6.0 × 2.5 cm mass consistent with lipoma. A fatty lobulated mass was excised and subjected to H&E staining and immunohistochemical analyses. The specimen consisted of mature univacuolated adipocytic cells, with intermixed multivacuolated eosinophilic granular cells. No atypia or hyperchromasia was identified. Most of the cells were S100 positive and Ki-67 immunonegative. A diagnosis of a lipoma-like hibernoma was rendered. Hibernomas are rare benign lipomatous tumors that show differentiation toward brown fat. The lipoma-like hibernoma subtype is rare and can be misdiagnosed as atypical lipoma or well-differentiated liposarcoma. Here we describe an example of this rare tumor.

  7. Towards Quantum Repeaters

    Gisin, Nicolas


    The ultimate limit of direct point to point quantum key distribution is around 300-500 km. Longer distances fiber-based quantum communication will require both high-fidelity entanglement swapping and multi-mode quantum memories. A new protocol for an efficient multimode quantum memory based on atomic ensembles has been developed and demonstrated. The rare-earth ions ensemble is ``frozen'' in a crystal inside a cryostat. The protocol, named AFC (Atomic Frequency Comb) is inspired from photon echoes, but avoids any control light pulse after the single-photon(s) is (are) stored in the medium, thus avoiding any noise due to fluorescence. First results on the new protocol for quantum memories in Nd:YVO4 doped crystals demonstrate a quantum light-matter interface at the single-photon level. The coherence of the re-emitted photons is investigated in an interference experiment showing net visibilities above 95%. Further results in Nd:YSO (Geneva), Tm:YAG (Paris) and Pr:YSO (Lund) shall also be presented. Many hundreds of km long quantum communication is a long term objective. Many of the necessary building blocks have been demonstrated, but usually in independent experiments and with insufficient fidelities and specifications to meet the goal. Still, today's the roadmap is relatively clear and a lot of interesting physics shall be found along the journey.

  8. Simultaneous Double Star and Cluster FTEs observations on the dawnside flank of the magnetosphere

    A. Marchaudon


    Full Text Available We present Cluster and Double Star-1 (TC-1 observations from a close magnetic conjunction on 8 May 2004. The five spacecraft were on the dawnside flank of the magnetosphere, with TC-1 located near the equatorial plane and Cluster at higher geographic latitudes in the Southern Hemisphere. TC-1, at its apogee, skimmed the magnetopause for almost 8h (between 08:00-16:00 UT. Flux Transfer Events (FTEs, moving southward/tailward from the reconnection site, were observed by TC-1 throughout almost all of the period. Cluster, travelling on a mainly dawn-dusk trajectory, crossed the magnetopause at around 10:30 UT in the same Magnetic Local Time (MLT sector as TC-1 and remained close to the magnetopause boundary layer in the Southern Hemisphere. The four Cluster spacecraft observed FTEs for a period of 6.5h between 07:30 and 14:00 UT.

    The very clear signatures and the finite transverse sizes of the FTEs observed by TC-1 and Cluster imply that, during this event, sporadic reconnection occurred. From the properties of these FTEs, the reconnection site was located northward of both TC-1 and Cluster on the dawn flank of the magnetosphere. Reconnection occurred between draped magnetosheath and closed magnetospheric field lines. Despite variable interplanetary magnetic field (IMF conditions and IMF-Bz turnings, the IMF clock angle remained greater than 70° and the location site appeared to remain relatively stable in position during the whole period. This result is in agreement with previous studies which reported that the dayside reconnection remained active for an IMF clock angle greater than 70°. The simultaneous observation of FTEs at both Cluster and TC-1, separated by 2h in MLT, implies that the reconnection site on the magnetopause must have been extended over several hours in MLT.

  9. Expression of the human glucokinase gene: important roles of the 5' flanking and intron 1 sequences.

    Yi Wang

    Full Text Available BACKGROUND: Glucokinase plays important tissue-specific roles in human physiology, where it acts as a sensor of blood glucose levels in the pancreas, and a few other cells of the gut and brain, and as the rate-limiting step in glucose metabolism in the liver. Liver-specific expression is driven by one of the two tissue-specific promoters, and has an absolute requirement for insulin. The sequences that mediate regulation by insulin are incompletely understood. METHODOLOGY/PRINCIPAL FINDINGS: To better understand the liver-specific expression of the human glucokinase gene we compared the structures of this gene from diverse mammals. Much of the sequence located between the 5' pancreatic beta-cell-specific and downstream liver-specific promoters of the glucokinase genes is composed of repetitive DNA elements that were inserted in parallel on different mammalian lineages. The transcriptional activity of the liver-specific promoter 5' flanking sequences were tested with and without downstream intronic sequences in two human liver cells lines, HepG2 and L-02. While glucokinase liver-specific 5' flanking sequences support expression in liver cell lines, a sequence located about 2000 bases 3' to the liver-specific mRNA start site represses gene expression. Enhanced reporter gene expression was observed in both cell lines when cells were treated with fetal calf serum, but only in the L-02 cells was expression enhanced by insulin. CONCLUSIONS/SIGNIFICANCE: Our results suggest that the normal liver L-02 cell line may be a better model to understand the regulation of the liver-specific expression of the human glucokinase gene. Our results also suggest that sequences downstream of the liver-specific mRNA start site have important roles in the regulation of liver-specific glucokinase gene expression.

  10. Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences

    Zhou Kaiya


    Full Text Available Abstract Background A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales, and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. Results An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae, and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. Conclusions Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae, whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving

  11. Flanking region sequence information to refine microRNA target predictions

    Russiachand Heikham; Ravi Shankar


    The non-coding elements of a genome, with many of them considered as junk earlier, have now started gaining long due respectability, with microRNAs as the best current example. MicroRNAs bind preferentially to the 3′ untranslated regions (UTRs) of the target genes and negatively regulate their expression most of the time. Several microRNA:target prediction softwares have been developed based upon various assumptions and the majority of them consider the free energy of binding of a target to its microRNA and seed conservation. However, the average concordance between the predictions made by these softwares is limited and compounded by a large number of false-positive results. In this study, we describe a methodology developed by us to refine microRNA:target prediction by target prediction softwares through observations made from a comprehensive study. We incorporated the information obtained from dinucleotide content variation patterns recorded for flanking regions around the target sites using support vector machines (SVMs) trained over two different major sources of experimental data, besides other sources. We assessed the performance of our methodology with rigorous tests over four different dataset models and also compared it with a recently published refinement tool, MirTif. Our methodology attained a higher average accuracy of 0.88, average sensitivity and specificity of 0.81 and 0.94, respectively, and areas under the curves (AUCs) for all the four models scored above 0.9, suggesting better performance by our methodology and a possible role of flanking regions in microRNA targeting control. We used our methodology over genes of three different pathways – toll-like receptor (TLR), apoptosis and insulin – to finally predict the most probable targets. We also investigated their possible regulatory associations, and identified a hsa-miR-23a regulatory module.

  12. [Sequence characterization of the 5'-Flanking region of the GHR gene in Tibetan sheep].

    Ma, Zhi-Jie; Wei, Ya-Ping; Zhong, Jin-Cheng; Chen, Zhi-Hua; Lu, Hong; Tong, Zi-Bao


    The 5'-Flanking sequence (including the P1 promotor and exon 1A) of the GHR gene in Oura-type Tibetan sheep (O. aries) was cloned by T-A method and sequenced (GenBank accession No. EF116490). Characterization and comparison of this sequence with mouflons (O. musimon), goat (C. hircus), cattle (B. taurus) and European bison (B. bonasus) orthologues were also conducted. Results showed that: 1) The 5'-flanking region contained many potential transcriptional factor binding sites such as those for C/EBPb, C/EBP, SP1, Cap, USF, HFH-2, HNF-3b, and Oct-1, which might have an important effect on transcription activation and regulation as well as tissue-specific expression. The rate of repetitive sequences was 2.55% and no SINEs, LINEs, LTR anti-transcription elements or DNA transposon elements were found, although one (TG)11 microsatellite was found. 2) In the P1 promotor region, sequence homology between the Tibetan sheep and mouflon, goat, cattle and European bison was 99.7%, 94.2%, 85.9% and 86.5%, respectively, while that for exon 1A was 99.0%, 97.0%, 92.7% and 94.6%, respectively. 3) The molecular phylogenetic tree among these species, constructed by the neighborhood joining method based on the sequences of no-coding region of the GHR genes, placed the two Bovinae species on one branch and the three Caprinae species on the other. Tibetan sheep and mouflons were joined first, followed by the goat, and then the Bovinae species, including the cattle and European bison. This result of phylogenetic clustering was not only identical to the taxonomy, but also to the phylogenetic clustering using the mitochondrial DNA of these species.

  13. Evidence for the concerted evolution between short linear protein motifs and their flanking regions.

    Claudia Chica

    Full Text Available BACKGROUND: Linear motifs are short modules of protein sequences that play a crucial role in mediating and regulating many protein-protein interactions. The function of linear motifs strongly depends on the context, e.g. functional instances mainly occur inside flexible regions that are accessible for interaction. Sometimes linear motifs appear as isolated islands of conservation in multiple sequence alignments. However, they also occur in larger blocks of sequence conservation, suggesting an active role for the neighbouring amino acids. RESULTS: The evolution of regions flanking 116 functional linear motif instances was studied. The conservation of the amino acid sequence and order/disorder tendency of those regions was related to presence/absence of the instance. For the majority of the analysed instances, the pairs of sequences conserving the linear motif were also observed to maintain a similar local structural tendency and/or to have higher local sequence conservation when compared to pairs of sequences where one is missing the linear motif. Furthermore, those instances have a higher chance to co-evolve with the neighbouring residues in comparison to the distant ones. Those findings are supported by examples where the regulation of the linear motif-mediated interaction has been shown to depend on the modifications (e.g. phosphorylation at neighbouring positions or is thought to benefit from the binding versatility of disordered regions. CONCLUSION: The results suggest that flanking regions are relevant for linear motif-mediated interactions, both at the structural and sequence level. More interestingly, they indicate that the prediction of linear motif instances can be enriched with contextual information by performing a sequence analysis similar to the one presented here. This can facilitate the understanding of the role of these predicted instances in determining the protein function inside the broader context of the cellular network

  14. Temperature Estimates for the Slow Slip Region on the Decollement Underlying the South Flank of Kilauea

    Spinelli, G. A.


    Eleven slow slip events on the decollement beneath the south flank of Kilauea volcano have been documented geodetically since 1998 (Brooks et al., 2006; Montgomery-Brown et al., 2009; 2013). Tectonic tremor has not been observed associated with these events, in contrast to most slow slip events in subduction zones (Montgomery-Brown et al., 2013). The slow slip events occur on the decollement at ~8 km depth, and updip of the 'normal' earthquakes on the fault. Constraining temperatures on Kilauea's decollement allows comparisons between its slow slip events and those in subduction zones. Kilauea's slow slip events (~8 km depth) are significantly shallower than most subduction zone slow slip events. I estimate temperatures in a 2-D cross-section through the south flank of Kilauea by combining methods used in subduction zone thermal models (Wang et al., 1995) with elements of intrusion cooling models of volcanoes (e.g., Civetta et al., 2004). Temperatures in the cross-section are controlled by: 1) heat sources from friction on the decollement, radioactive decay, and volcanic activity, and 2) heat transport by conduction, advection of the volcanic pile to the southeast over the underlying oceanic lithosphere, and advective heat transport associated with groundwater flow. I examine the thermal effects of a range of effective friction coefficients on the fault from 0-0.2. I determine the potential effects of groundwater flow in the upper ~1-2 km of the onshore and near-offshore volcanic pile (e.g., Kauahikaua, 1993; Buttner and Huenges, 2003) on decollement temperatures. Finally, I examine how heat input from Kilauea volcano may result in higher decollement temperatures than at the same depth on plate boundary faults in subduction zones.

  15. HSDP II Drill Core: Preliminary Rock Strength Results and Implications to Flank Stability, Mauna Kea Volcano

    Thompson, N.; Watters, R. J.; Schiffman, P.


    Selected portions of the 3-km HSDP II core were tested to provide unconfined rock strength data from hyaloclastite alteration zones and pillow lavas. Though the drilling project was not originally intended for strength purpose, it is believed the core can provide unique rock strength insights into the flank stability of the Hawaiian Islands. The testing showed that very weak rock exists in the hyaloclastite abundant zones in the lower 2-km of the core with strength dependent on the degree of consolidation and type of alteration. Walton and Schiffman identified three zones of alteration, an upper incipient alteration zone (1080-1335m), a smectitic zone (1405-1573m) and a lower palagonitic zone from about 1573 m to the base of the core. These three zones were sampled and tested together with pillow lava horizons for comparison. Traditional cylindrical core was not available as a consequence of the entire core having been split lengthwise for archival purposes. Hence, point load strength testing was utilized which provides the unconfined compressive strength on irregular shaped samples. The lowest unconfined strengths were recorded from incipient alteration zones with a mean value of 9.5 MPa. Smectitic alteration zones yielded mean values of 16.4 MPa, with the highest measured alteration strengths from the palagonite zones with a mean value of 32.1 MPa. As anticipated, the highest strengths were from essentially unaltered lavas with a mean value of 173 MPa. Strength variations of between one to two orders of magnitude were identified in comparing the submarine hyaloclastite with the intercalated submarine lavas. The weakest zones within the hyaloclastites may provide horizons for assisting flank collapse by serving as potential thrust zones and landslide surfaces.

  16. Whale phylogeny and rapid radiation events revealed using novel retroposed elements and their flanking sequences.

    Chen, Zhuo; Xu, Shixia; Zhou, Kaiya; Yang, Guang


    A diversity of hypotheses have been proposed based on both morphological and molecular data to reveal phylogenetic relationships within the order Cetacea (dolphins, porpoises, and whales), and great progress has been made in the past two decades. However, there is still some controversy concerning relationships among certain cetacean taxa such as river dolphins and delphinoid species, which needs to be further addressed with more markers in an effort to address unresolved portions of the phylogeny. An analysis of additional SINE insertions and SINE-flanking sequences supported the monophyly of the order Cetacea as well as Odontocete, Delphinoidea (Delphinidae + Phocoenidae + Mondontidae), and Delphinidae. A sister relationship between Delphinidae and Phocoenidae + Mondontidae was supported, and members of classical river dolphins and the genera Tursiops and Stenella were found to be paraphyletic. Estimates of divergence times revealed rapid divergences of basal Odontocete lineages in the Oligocene and Early Miocene, and a recent rapid diversification of Delphinidae in the Middle-Late Miocene and Pliocene within a narrow time frame. Several novel SINEs were found to differentiate Delphinidae from the other two families (Monodontidae and Phocoenidae), whereas the sister grouping of the latter two families with exclusion of Delphinidae was further revealed using the SINE-flanking sequences. Interestingly, some anomalous PCR amplification patterns of SINE insertions were detected, which can be explained as the result of potential ancestral SINE polymorphisms and incomplete lineage sorting. Although a few loci were potentially anomalous, this study demonstrated that the SINE-based approach is a powerful tool in phylogenetic studies. Identifying additional SINE elements that resolve the relationships in the superfamily Delphinoidea and family Delphinidae will be important steps forward in completely resolving cetacean phylogenetic relationships in the future.

  17. Late Pleistocene flank collapse of Zempoala volcano (Central Mexico) and the role of fault reactivation

    Arce, José Luis; Macías, Rodolfo; García Palomo, Armando; Capra, Lucia; Macías, José Luis; Layer, Paul; Rueda, Hernando


    Zempoala is an extinct Pleistocene (˜ 0.7-0.8 Ma) stratovolcano that together with La Corona volcano (˜ 0.9 Ma) forms the southern end of the Sierra de las Cruces volcanic range, Central Mexico. The volcano consists of andesitic and dacitic lava flows and domes, as well as pyroclastic and epiclastic sequences, and has had a complex history with several flank collapses. One of these collapses occurred during the late Pleistocene on the S-SE flank of the volcano and produced the Zempoala debris avalanche deposit. This collapse could have been triggered by the reactivation of two normal fault systems (E-W and NE-SW), although magmatic activity cannot be absolutely excluded. The debris avalanche traveled 60 km to the south, covers an area of 600 km 2 and has a total volume of 6 km 3, with a calculated Heim coefficient (H/L) of 0.03. Based on the textural characteristics of the deposit we recognized three zones: proximal, axial, and lateral distal zone. The proximal zone consists of debris avalanche blocks that develop a hummocky topography; the axial zone corresponds with the main debris avalanche deposit made of large clasts set in a sandy matrix, which transformed to a debris flow in the lateral distal portion. The deposit is heterolithologic in composition, with dacitic and andesitic fragments from the old edifice that decrease in volume as bulking of exotic clasts from the substratum increase. Several cities (Cuernavaca, Jojutla de Juárez, Alpuyeca) with associated industrial, agricultural, and tourism activities have been built on the deposit, which pose in evidence the possible impact in case of a new event with such characteristics, since the area is still tectonically active.

  18. Both 5' and 3' flanks regulate Zebrafish brain-derived neurotrophic factor gene expression

    Heinrich Gerhard


    Full Text Available Abstract Background Precise control of developmental and cell-specific expression of the brain-derived neurotrophic factor (BDNF gene is essential for normal neuronal development and the diverse functions of BDNF in the adult organism. We previously showed that the zebrafish BDNF gene has multiple promoters. The complexity of the promoter structure and the mechanisms that mediate developmental and cell-specific expression are still incompletely understood. Results Comparison of pufferfish and zebrafish BDNF gene sequences as well as 5' RACE revealed three additional 5' exons and associated promoters. RT-PCR with exon-specific primers showed differential developmental and organ-specific expression. Two exons were detected in the embryo before transcription starts. Of the adult organs examined, the heart expressed a single 5' exon whereas the brain, liver and eyes expressed four of the seven 5' exons. Three of the seven 5' exons were not detectable by RT-PCR. Injection of promoter/GFP constructs into embryos revealed distinct expression patterns. The 3' flank profoundly affected expression in a position-dependent manner and a highly conserved sequence (HCS1 present in 5' exon 1c in a dehancer-like manner. Conclusions The zebrafish BDNF gene is as complex in its promoter structure and patterns of differential promoter expression as is its murine counterpart. The expression of two of the promoters appears to be regulated in a temporally and/or spatially highly circumscribed fashion. The 3' flank has a position-dependent effect on expression, either by affecting transcription termination or post-transcriptional steps. HCS1, a highly conserved sequence in 5' exon 1c, restricts expression to primary sensory neurons. The tools are now available for detailed genetic and molecular analyses of zebrafish BDNF gene expression.

  19. Airborne sound insulation evaluation and flanking path prediction of coupled room

    Tassia, R. D.; Asmoro, W. A.; Arifianto, D.


    One of the parameters to review the acoustic comfort is based on the value of the insulation partition in the classroom. The insulation value can be expressed by the sound transmission loss which converted into a single value as weighted sound reduction index (Rw, DnTw) and also have an additional sound correction factor in low frequency (C, Ctr) .In this study, the measurements were performed in two positions at each point using BSWA microphone and dodecahedron speaker as the sound source. The results of field measurements indicate the acoustic insulation values (DnT w + C) is 19.6 dB. It is noted that the partition wall not according to the standard which the DnTw + C> 51 dB. Hence the partition wall need to be redesign to improve acoustic insulation in the classroom. The design used gypsum board, plasterboard, cement board, and PVC as the replacement material. Based on the results, all the material is simulated in accordance with established standards. Best insulation is cement board with the insulation value is 69dB, the thickness of 12.5 mm on each side and the absorber material is 50 mm. Many factors lead to increase the value of acoustic insulation, such as the thickness of the panel, the addition of absorber material, density, and Poisson's ratio of a material. The prediction of flanking path can be estimated from noise reduction values at each measurement point in the class room. Based on data obtained, there is no significant change in noise reduction from each point so that the pathway of flanking is not affect the sound transmission in the classroom.

  20. Nonparametric additive regression for repeatedly measured data

    Carroll, R. J.


    We develop an easily computed smooth backfitting algorithm for additive model fitting in repeated measures problems. Our methodology easily copes with various settings, such as when some covariates are the same over repeated response measurements. We allow for a working covariance matrix for the regression errors, showing that our method is most efficient when the correct covariance matrix is used. The component functions achieve the known asymptotic variance lower bound for the scalar argument case. Smooth backfitting also leads directly to design-independent biases in the local linear case. Simulations show our estimator has smaller variance than the usual kernel estimator. This is also illustrated by an example from nutritional epidemiology. © 2009 Biometrika Trust.

  1. Simultaneous Optimization of Tooth Flank Form of Involute Helical Gears in Terms of Both Vibration and Load Carrying Capacity

    Komori, Masaharu; Kubo, Aizoh; Suzuki, Yoshitomo

    The alignment condition of automotive gears changes considerably during operation due to the deformation of shafts, bearings, and gear box by transmission of load. Under such conditions, the gears are required to satisfy not only reliability in strength and durability under maximum loading conditions, but also low vibrational characteristics under light loading conditions during the cruising of a car. In this report, the characteristics of the optimum tooth flank form of gears in terms of both vibration and load carrying capacity are clarified. The local optimum tooth flank form appears in each excitation valley, where the vibrational excitation is low and the actual contact ratio takes a specific value. The influence of the choice of different local optimum solutions on the vibrational performance of the optimized gears is investigated. The practical design algorithm for the optimum tooth flank form of a gear set in terms of both vibration and load carrying capacity is then proposed and its result is evaluated by field experience.

  2. Repeat Associated Non-AUG Translation (RAN Translation Dependent on Sequence Downstream of the ATXN2 CAG Repeat.

    Daniel R Scoles

    Full Text Available Spinocerebellar ataxia type 2 (SCA2 is a progressive autosomal dominant disorder caused by the expansion of a CAG tract in the ATXN2 gene. The SCA2 disease phenotype is characterized by cerebellar atrophy, gait ataxia, and slow saccades. ATXN2 mutation causes gains of toxic and normal functions of the ATXN2 gene product, ataxin-2, and abnormally slow Purkinje cell firing frequency. Previously we investigated features of ATXN2 controlling expression and noted expression differences for ATXN2 constructs with varying CAG lengths, suggestive of repeat associated non-AUG translation (RAN translation. To determine whether RAN translation occurs for ATXN2 we assembled various ATXN2 constructs with ATXN2 tagged by luciferase, HA or FLAG tags, driven by the CMV promoter or the ATXN2 promoter. Luciferase expression from ATXN2-luciferase constructs lacking the ATXN2 start codon was weak vs AUG translation, regardless of promoter type, and did not increase with longer CAG repeat lengths. RAN translation was detected on western blots by the anti-polyglutamine antibody 1C2 for constructs driven by the CMV promoter but not the ATXN2 promoter, and was weaker than AUG translation. Strong RAN translation was also observed when driving the ATXN2 sequence with the CMV promoter with ATXN2 sequence downstream of the CAG repeat truncated to 18 bp in the polyglutamine frame but not in the polyserine or polyalanine frames. Our data demonstrate that ATXN2 RAN translation is weak compared to AUG translation and is dependent on ATXN2 sequences flanking the CAG repeat.

  3. Improving repeated sprint ability in young elite soccer players: repeated shuttle sprints vs. explosive strength training.

    Buchheit, Martin; Mendez-Villanueva, Alberto; Delhomel, Gregory; Brughelli, Matt; Ahmaidi, Said


    To compare the effects of explosive strength (ExpS) vs. repeated shuttle sprint (RS) training on repeated sprint ability (RSA) in young elite soccer players, 15 elite male adolescents (14.5 ± 0.5 years) performed, in addition to their soccer training program, RS (n = 7) or ExpS (n = 8) training once a week for a total of 10 weeks. RS training consisted of 2-3 sets of 5-6 × 15- to 20-m repeated shuttle sprints interspersed with 14 seconds of passive or 23 seconds of active recovery (≈2 m·s⁻¹); ExpS training consisted of 4-6 series of 4-6 exercises (e.g., maximal unilateral countermovement jumps (CMJs), calf and squat plyometric jumps, and short sprints). Before and after training, performance was assessed by 10 and 30 m (10 and 30 m) sprint times, best (RSAbest) and mean (RSAmean) times on a repeated shuttle sprint ability test, a CMJ, and a hopping (Hop) test. After training, except for 10 m (p = 0.22), all performances were significantly improved in both groups (all p's repeated shuttle sprint test were only observed after RS training, whereas CMJ height was only increased after ExpS. Because RS and ExpS were equally efficient at enhancing maximal sprinting speed, RS training-induced improvements in RSA were likely more related to progresses in the ability to change direction.

  4. Analysis of repeated measures data

    Islam, M Ataharul


    This book presents a broad range of statistical techniques to address emerging needs in the field of repeated measures. It also provides a comprehensive overview of extensions of generalized linear models for the bivariate exponential family of distributions, which represent a new development in analysing repeated measures data. The demand for statistical models for correlated outcomes has grown rapidly recently, mainly due to presence of two types of underlying associations: associations between outcomes, and associations between explanatory variables and outcomes. The book systematically addresses key problems arising in the modelling of repeated measures data, bearing in mind those factors that play a major role in estimating the underlying relationships between covariates and outcome variables for correlated outcome data. In addition, it presents new approaches to addressing current challenges in the field of repeated measures and models based on conditional and joint probabilities. Markov models of first...

  5. Regulation of mRNA translation by MID1: a common mechanism of expanded CAG repeat RNAs

    Nadine Griesche


    Full Text Available Expansion of CAG repeats, which code for the disease-causing polyglutamine protein, is a common feature in polyglutamine diseases. RNA-mediated mechanisms that contribute to neuropathology in polyglutamine diseases are important. RNA-toxicity describes a phenomenon by which the mutant CAG repeat RNA recruits RNA-binding proteins, thereby leading to aberrant function. For example the MID1 protein binds to mutant huntingtin (HTT RNA, which is linked to Huntington’s disease (HD, at its CAG repeat region and induces protein synthesis of mutant protein. But is this mechanism specific to HD or is it a common mechanism in CAG repeat expansion disorders? To answer this question, we have analysed the interaction between MID1 and three other CAG repeat mRNAs, Ataxin2 (ATXN2, Ataxin3 (ATXN3, and Ataxin7 (ATXN7, that all differ in the sequence flanking the CAG repeat. We show that ATXN2, ATXN3 and ATXN7 bind to MID1 in a CAG repeat length-dependent manner. Furthermore, we show that functionally, in line with what we have previously observed for HTT, the binding of MID1 to ATXN2, ATXN3 and ATXN7 mRNA induces protein synthesis in a repeat length-dependent manner. Our data suggest that regulation of protein translation by the MID1 complex is a common mechanism for CAG repeat containing mRNAs.

  6. C9orf72 hexanucleotide repeat expansions in Chinese sporadic amyotrophic lateral sclerosis.

    He, Ji; Tang, Lu; Benyamin, Beben; Shah, Sonia; Hemani, Gib; Liu, Rong; Ye, Shan; Liu, Xiaolu; Ma, Yan; Zhang, Huagang; Cremin, Katie; Leo, Paul; Wray, Naomi R; Visscher, Peter M; Xu, Huji; Brown, Matthew A; Bartlett, Perry F; Mangelsdorf, Marie; Fan, Dongsheng


    A hexanucleotide repeat expansion (HRE) in the C9orf72 gene has been identified as the most common mutation in amyotrophic lateral sclerosis (ALS) among Caucasian populations. We sought to comprehensively evaluate genetic and epigenetic variants of C9orf72 and the contribution of the HRE in Chinese ALS cases. We performed fragment-length and repeat-primed polymerase chain reaction to determine GGGGCC copy number and expansion within the C9orf72 gene in 1092 sporadic ALS (sALS) and 1062 controls from China. We performed haplotype analysis of 23 single-nucleotide polymorphisms within and surrounding C9orf72. The C9orf72 HRE was found in 3 sALS patients (0.3%) but not in control subjects (p = 0.25). For 2 of the cases with the HRE, genotypes of 8 single-nucleotide polymorphisms flanking the HRE were inconsistent with the haplotype reported to be strongly associated with ALS in Caucasian populations. For these 2 individuals, we found hypermethylation of the CpG island upstream of the repeat, an observation not detected in other sALS patients (p Chinese samples provides robust evidence that may not be consistent with a single Caucasian founder event. Both the Caucasian and Chinese haplotypes associated with HRE were highly associated with repeat lengths >8 repeats implying that both haplotypes may confer instability of repeat length.

  7. Repeat prescribing: scale, problems and quality management in ambulatory care patients.

    Smet, P.A.G.M. de; Dautzenberg, M.


    The reported scale of repeat prescriptions ranges from 29% to 75% of all items prescribed, depending on the definition of repeat prescribing and other variables. It is likely that a substantial part of repeat prescribing by general practitioners (GPs) occurs without direct doctor-patient contact.

  8. PCR-free digital minisatellite tandem repeat genotyping.

    Chen, Yuchao; Seo, Tae Seok


    We demonstrated a proof-of-concept for novel minisatellite tandem repeat typing, called PCR-free digital VNTR (variable number tandem repeat) typing, which is composed of three steps: a ligation reaction instead of PCR thermal cycling, magnetic bead-based solid-phase capture for purification, and an elongated sample stacking microcapillary electrophoresis (μCE) for sensitive digital coding of repeat number. We designed a 16-bp fluorescently labeled ligation probe which is complementary to a repeat unit of a biotinylated synthetic template mimicking the human D1S80 VNTR locus and is randomly hybridized with the minisatellite tandem repeats. A quick isothermal ligation reaction was followed to link the adjacent ligation probes on the DNA templates, and then the ligated products were purified by streptavidin-coated magnetic beads. After a denaturing step, a large amount of ligated products whose size difference was equivalent to the repeat unit were released and recovered. Through the elongated sample stacking μCE separation on a microdevice, the fluorescence signal of the ligated products was generated in the electropherogram and the peak number was directly counted which was exactly matched with the repeat number of VNTR locus. We could successfully identify the minisatellite tandem repeat number with only 5 fmol of DNA template in 30 min.

  9. Repeated-sprint ability and aerobic fitness.

    Thébault, Nicolas; Léger, Luc A; Passelergue, Philippe


    The purpose of this study was to reinvestigate the relationship between aerobic fitness and fatigue indices of repeated-sprint ability (RSA), with special attention to methodological normalization. Soldiers were divided into low (n = 10) and high (n = 9) fitness groups according to a preset maximal aerobic speed (MAS) of 17 km·h(-1) (∼60 ml O2·kg(-1)·min) measured with the University of Montreal Track Test (UMTT). Subjects' assessment included the RSA test (3 sets of 5 40-m sprints with 1-minute rest between sprints and 1.5 minutes between sets), a 40-m sprint (criterion test used in the computation of fatigue indices for the RSA test), strength and power measurement of the lower limbs, and the 20-m shuttle run test (20-m SRT) and the UMTT, which are measures of maximal aerobic power. The highest correlation with the RSA fatigue indices was obtained with the 20-m SRT (r = 0.90, p = 0.0001, n = 19), a test with 180° direction changes and accelerations and decelerations. The lower correlation (r = 0.66, p repeated sprints and achieved better recovery between series. A MAS of at least 17 km·h(-1) favors constant and high speed level during repeated sprints. From a practical point of view, a high aerobic fitness is a precious asset in counteracting fatigue in sports with numerous sprint repetitions.

  10. The occurrence of Mt Barca flank eruption in the evolution of the NW periphery of Etna volcano (Italy)

    Branca, S.; Del Carlo, P.; Lo Castro, M. D.; de Beni, E.; Wijbrans, J.


    Geological surveys, tephrostratigraphic study, and 40Ar/39Ar age determinations have allowed us to chronologically constrain the geological evolution of the lower NW flank of Etna volcano and to reconstruct the eruptive style of the Mt Barca flank eruption. This peripheral sector of the Mt Etna edifice, corresponding to the upper Simeto valley, was invaded by the Ellittico volcano lava flows between 41 and 29 ka ago when the Mt Barca eruption occurred. The vent of this flank eruption is located at about 15 km away from the summit craters, close to the town of Bronte. The Mt Barca eruption was characterized by a vigorous explosive activity that produced pyroclastic deposits dispersed eastward and minor effusive activity with the emission of a 1.1-km-long lava flow. Explosive activity was characterized by a phreatomagmatic phase followed by a magmatic one. The geological setting of this peripheral sector of the volcano favors the interaction between the rising magma and the shallow groundwater hosted in the volcanic pile resting on the impermeable sedimentary basement. This process produced phreatomagmatic activity in the first phase of the eruption, forming a pyroclastic fall deposit made of high-density, poorly vesicular scoria lapilli and lithic clasts. Conversely, during the second phase, a typical strombolian fall deposit formed. In terms of hazard assessment, the possible occurrence of this type of highly explosive flank eruption, at lower elevation in the densely inhabited areas, increases the volcanic risk in the Etnean region and widens the already known hazard scenario.

  11. Contrasting neogene denudation histories of different structural regions in the transantarctic mountains rift flank constrained by cosmogenic isotope measurements

    Wateren, F.M. van der; Dunai, T.J.; Balen, R.T. van; Klas, W.; Verbers, A.L.L.M.; Passchier, S.; Herpers, U.


    Separate regions within the Transantarctic Mountains, the uplifted flank of the West Antarctic rift system, appear to have distinct Neogene histories of glaciation and valley downcutting. Incision of deep glacial outlet valleys occurred at different times throughout central and northern Victoria Lan

  12. Polymorphisms of Flanking Region of the ASB15 Gene and Their Associations with Performance Traits in Chicken.

    Wang, Y C; Han, R L; Li, Z J; Geng, J; Tian, Y D; Jiang, R R; Wu, J P; Kang, X T


    Research on the identity of genes and their relationship with traits of economic importance in chickens could assist in the selection of poultry. In this study, an F2 resource population of Gushi chickens crossed with Anka broilers was used to detect single-nucleotide polymorphisms (SNPs) in the flanking region of the ASB15 gene by DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). One SNP of -1271 C>T in 5' flanking region of the chicken ASB15 gene and two SNPs of the 10618 A>G and 10716 G>A in 3' flanking region were identified. Furthermore, the 10618 A>G and 10716 G>A in 3' flanking region were in complete linkage. Association analysis results showed that -1271 C>T was not associated with performance traits, while the 10618 A>G and 10716 G>A were significantly associated with BW2, 4, 6, 8, 10, 12, SL12, CD8, CW4, 8, 12, BSL4, 8, 12, and SEW, EW, WW, BMW, LW, CW, SFT. Our results suggest that the ASB15 gene profoundly affects chicken performance traits.

  13. Rare case of a strangulated intercostal flank hernia following open nephrectomy: A case report and review of literature.

    Akinduro, Oluwaseun O; Jones, Frank; Turner, Jacquelyn; Cason, Frederick; Clark, Clarence


    Flank incisions may be associated with incisional flank hernias, which may progress to incarceration and strangulation. Compromised integrity of the abdominal and intercostal musculature due to previous surgery may be associated with herniation of abdominal contents into the intercostal space. There have been six previously reported cases of herniation into the intercostal space after a flank incision for a surgical procedure. This case highlights the clinical picture associated with an emergent strangulated hernia and highlights the critical steps in its management. We present a case of a 79-year-old adult man with multiple comorbidities presenting with a strangulated flank hernia secondary to an intercostal incision for a right-sided open nephrectomy. The strangulated hernia required emergent intervention including right-sided hemi-colectomy with ileostomy and mucous fistula. Abdominal incisional hernias are rare and therefore easily overlooked, but may result in significant morbidity or even death in the patient.. The diagnosis can be made with a thorough clinical examination and ultrasound or computed topographical investigation. Once a hernia has become incarcerated, emergent surgical management is necessary to avoid strangulation and small bowel obstruction. Urgent diagnosis and treatment of this extremely rare hernia is paramount especially in the setting of strangulation. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. Iron oxidation state in (Mg,Fe)O: Calibration of the flank method on synthetic samples and application to natural inclusions in Lower Mantle diamonds

    Longo, M.; McCammon, C.; Bulanova, G.; Kaminsky, F.


    Ferropericlase (Mg,Fe)O and (Mg,Fe)(Si,Al)O3 perovskite are believed to form the bulk of the Lower Mantle (LM). The interval of redox conditions in the LM is still debatable. It was shown that the Fe3+ concentration in perovskite is insensitive to oxygen fugacity, therefore we have turned our attention to (Mg,Fe)O. Our work involves calibrating the so-called "flank method" for synthetic (Mg,Fe)O, and applying the results to determine Fe3+/Fetot in ferropericlase inclusions from LM diamonds, as a direct tool for investigating LM redox conditions during diamond formation. Experiments were performed in a multi anvil apparatus to obtain ferropericlase crystals with high quality surfaces, and Fe3+/Fetot in them was determined by Moessbauer spectroscopy. Samples were subsequently analyzed using the EMP. The flank method sensu strictu consists of measuring two pre-defined energy positions FeLAlfa and FeLBeta, whose ratio is sensitive to Fe2+/Fe3+. Positive correlations of LBeta/LAlfa as a function of Fetot (wt percent) and Fe2+ (wt percent) were observed for (Mg,Fe)O similar to those reported in the literature for garnets. We applied a least-squares regression model to fit the three variables Fetot, LBeta/LAlfa and Fe2+, and chose the simplest equation that fit the data. Our calibration for (Mg,Fe)O with xFe between 2 and 36.6 wt percent shows an agreement of 1 sigma with Fe3+/Fetot determined by Moessbauer spectroscopy, but with the additional advantage of a spatial resolution on the order of 10 microns (compared to no smaller than 100 microns for Moessbauer). We applied the flank method calibration to 6 ferropericlase inclusions from ultra deep diamonds (4 from Mato Grosso and 2 from Machado River, Brazil). Results show that LBeta/LAlfa ratios are consistent with the trend observed for synthetic (Mg,Fe)O, with no obvious evidence for magnesioferrite exsolution. The obtained Fe3+/Fetot values between 8 and 13 percent, and their correlations with Na, Cr and Al show that

  15. Global Design Analysis for Highly Repeatable Solid-state Klystron Modulators

    Anthony, Dal Gobbo


    This paper presents an analysis of the repeatability issue in the electrical-to-radio frequency conversion chains using pulsed klystrons. The focus is on the power electronics used in klystron modulators. Repeatability definition is presented and simulation results allow deriving important conclusions regarding the voltage repeatability harmonic content versus power electronics design directions. The trade-off between klystron modulator and low level RF controls is a key point for optimizing the global system repeatability performance.

  16. Alu repeats as markers for human population genetics

    Batzer, M.A.; Alegria-Hartman, M. [Lawrence Livermore National Lab., CA (United States); Bazan, H. [Louisiana State Univ., New Orleans, LA (United States). Medical Center] [and others


    The Human-Specific (HS) subfamily of Alu sequences is comprised of a group of 500 nearly identical members which are almost exclusively restricted to the human genome. Individual subfamily members share an average of 97.9% nucleotide identity with each other and an average of 98.9% nucleotide identity with the HS subfamily consensus sequence. HS Alu family members are thought to be derived from a single source ``master`` gene, and have an average age of 2.8 million years. We have developed a Polymerase Chain Reaction (PCR) based assay using primers complementary to the 5 in. and 3 in. unique flanking DNA sequences from each HS Alu that allows the locus to be assayed for the presence or absence of an Alu repeat. Individual HS Alu sequences were found to be either monomorphic or dimorphic for the presence or absence of each repeat. The monomorphic HS Alu family members inserted in the human genome after the human/great ape divergence (which is thought to have occurred 4--6 million years ago), but before the radiation of modem man. The dimorphic HS Alu sequences inserted in the human genome after the radiation of modem man (within the last 200,000-one million years) and represent a unique source of information for human population genetics and forensic DNA analyses. These sites can be developed into Dimorphic Alu Sequence Tagged Sites (DASTS) for the Human Genome Project as well. HS Alu family member insertion dimorphism differs from other types of polymorphism (e.g. Variable Number of Tandem Repeat [VNTR] or Restriction Fragment Length Polymorphism [RFLP]) because individuals share HS Alu family member insertions based upon identity by descent from a common ancestor as a result of a single event which occurred one time within the human population. The VNTR and RFLP polymorphisms may arise multiple times within a population and are identical by state only.

  17. Limitations on quantum key repeaters.

    Bäuml, Stefan; Christandl, Matthias; Horodecki, Karol; Winter, Andreas


    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.

  18. Hysteresis of magnetostructural transitions: Repeatable and non-repeatable processes

    Provenzano, Virgil [National Institute of Standards and Technology, Gaithersburg, MD 20899 (United States); Della Torre, Edward; Bennett, Lawrence H. [Department of Electrical and Computer Engineering, The George Washington University, Washington, DC 20052 (United States); ElBidweihy, Hatem, E-mail: [Department of Electrical and Computer Engineering, The George Washington University, Washington, DC 20052 (United States)


    The Gd{sub 5}Ge{sub 2}Si{sub 2} alloy and the off-stoichiometric Ni{sub 50}Mn{sub 35}In{sub 15} Heusler alloy belong to a special class of metallic materials that exhibit first-order magnetostructural transitions near room temperature. The magnetic properties of this class of materials have been extensively studied due to their interesting magnetic behavior and their potential for a number of technological applications such as refrigerants for near-room-temperature magnetic refrigeration. The thermally driven first-order transitions in these materials can be field-induced in the reverse order by applying a strong enough field. The field-induced transitions are typically accompanied by the presence of large magnetic hysteresis, the characteristics of which are a complicated function of temperature, field, and magneto-thermal history. In this study we show that the virgin curve, the major loop, and sequentially measured MH loops are the results of both repeatable and non-repeatable processes, in which the starting magnetostructural state, prior to the cycling of field, plays a major role. Using the Gd{sub 5}Ge{sub 2}Si{sub 2} and Ni{sub 50}Mn{sub 35}In{sub 15} alloys, as model materials, we show that a starting single phase state results in fully repeatable processes and large magnetic hysteresis, whereas a mixed phase starting state results in non-repeatable processes and smaller hysteresis.

  19. Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt.

    Jungbluth, Sean P; Bowers, Robert M; Lin, Huei-Ting; Cowen, James P; Rappé, Michael S


    Although little is known regarding microbial life within our planet's rock-hosted deep subseafloor biosphere, boreholes drilled through deep ocean sediment and into the underlying basaltic crust provide invaluable windows of access that have been used previously to document the presence of microorganisms within fluids percolating through the deep ocean crust. In this study, the analysis of 1.7 million small subunit ribosomal RNA genes amplified and sequenced from marine sediment, bottom seawater and basalt-hosted deep subseafloor fluids that span multiple years and locations on the Juan de Fuca Ridge flank was used to quantitatively delineate a subseafloor microbiome comprised of distinct bacteria and archaea. Hot, anoxic crustal fluids tapped by newly installed seafloor sampling observatories at boreholes U1362A and U1362B contained abundant bacterial lineages of phylogenetically unique Nitrospirae, Aminicenantes, Calescamantes and Chloroflexi. Although less abundant, the domain Archaea was dominated by unique, uncultivated lineages of marine benthic group E, the Terrestrial Hot Spring Crenarchaeotic Group, the Bathyarchaeota and relatives of cultivated, sulfate-reducing Archaeoglobi. Consistent with recent geochemical measurements and bioenergetic predictions, the potential importance of methane cycling and sulfate reduction were imprinted within the basalt-hosted deep subseafloor crustal fluid microbial community. This unique window of access to the deep ocean subsurface basement reveals a microbial landscape that exhibits previously undetected spatial heterogeneity.

  20. Chandra X-Ray Observations of Young Clusters. III. NGC 2264 and the Orion Flanking Fields

    Rebull, L M; Micela, G; Ramírez, S V; Sciortino, S; Stauffer, J R; Strom, S E; Wolff, S C


    Chandra observations of solar-like pre-main sequence (PMS) stars in the Orion Flanking Fields (age ~1 Myr) and NGC 2264 (~3 Myr) are compared with the results of the COUP survey of similar objects in the ONC (~0.5 Myr). The correlations between log Lx and mass found for PMS stars on convective tracks in these clusters are consistent with the relationships found for the ONC, indicating little change in the median values of either log Lx or log Lx/Lbol during the first ~3-5 Myr of evolution down convective tracks. The fraction of stars with extreme values of Lx, more than 10 times higher than the average for a given Lbol or with log Lx/Lbol greater than the canonical saturation value of -2.9, is however larger by a factor of two in the younger ONC when compared with the Orion FF and NGC 2264. PMS stars in NGC 2264 on radiative tracks have Lx/Lbol values that are systematically lower by a factor of ~10 times than those found for stars of similar mass on convective tracks. The dramatic decrease in flux from conve...

  1. The chicken vitellogenin II gene is flanked by a GATA factor-dependent estrogen response unit.

    Davis, D L; Burch, J B


    The chicken vitellogenin II (VTGII) gene is flanked by an imperfect estrogen response element (ERE) at -350 and a perfect ERE at -620. In the present study we show that this imperfect ERE lies within an estrogen response unit (ERU) that requires a GATA factor and the estrogen receptor to function as an estrogen-dependent enhancer. We infer that GATA-6 contributes to the estrogen-dependent and liver-specific regulation of the endogenous VTGII gene since this is the predominant GATA factor expressed in adult liver. Our analysis of the VTGII ERU revealed four salient points. First, this ERU is comprised of an ERE and a bank of functionally redundant GATA-binding sites. Second, the GATA-6 transactivation domain is necessary (and sufficient, when tethered near the ERE) to render this ERU functional. Third, ERU enhancer activity is dependent on GATA 6, regardless of whether the resident ERE is imperfect or perfect. Fourth, in contrast to a report that the estrogen receptor antagonizes the activity of another GATA factor (GATA-1), we show that these two factors can function in a synergistic manner within the context of the VTGII ERU.

  2. Increasing long-wavelength relief across the southeastern flank of the Sierra Nevada, California

    Bennett, R. A.; Fay, N. P.; Hreinsdóttir, S.; Chase, C.; Zandt, G.


    A high degree of correlation between present-day relative rock uplift measured using continuous GPS geodesy and spatially averaged surface elevations suggests that long-wavelength topographic relief is presently increasing along the southeastern flank of the Sierra Nevada range and within an adjacent portion of the northern Basin and Range province. Current estimates for erosion rate are an order of magnitude smaller than the relative rates determined by geodesy. Thus, although the uplift serves to enhance long-wavelength relief, it cannot be explained entirely as an isostatic response to erosion. If uplift rates have been constant through time, the duration over which the uplift could have been active (Sierra are evolving with time. According to either hypothesis, vertical surface motions may have slowly accelerated since ~mid-Pliocene time. Several possible mechanisms for progressive reduction of EET may be attributable to thermo-mechanical disequilibrium that began with the removal of an ultramafic root from the Sierran batholith during late Miocene or early Pliocene time. Specific mechanisms for ongoing enhancement of loads are less obvious. Based on these results, we suggest that dense networks of long-running continuous GPS stations around the world currently represent an underutilized resource for studies of orogenesis and upper mantle processes.

  3. Flanking magnitudes: dissociation between numerosity and numerical value in a selective attention task.

    Naparstek, Sharon; Safadi, Ziad; Lichtenstein-Vidne, Limor; Henik, Avishai


    The current research examined whether peripherally presented numerical information can affect the speed of number processing. In 2 experiments, participants were presented with a target matrix flanked by a distractor matrix and were asked to perform a comparative judgment (i.e., decide whether the target was larger or smaller than the reference 5). In Experiment 1, the target was symbolic (i.e., a single digit), and in Experiment 2, it was nonsymbolic (i.e., a random presentation of dots). In both experiments, flanker matrices had 2 dimensions-numerosity and numerical value-that were manipulated orthogonally to create stimulus congruent and stimulus incongruent conditions. Incongruent trials differed in the laterality between target and flanker (i.e., their location in relation to the reference 5). When responding to symbolic targets (Experiment 1), only the flanker's numerical value affected reaction times (RTs), whereas when responding to nonsymbolic targets (Experiment 2), only the flanker's numerosity affected RTs. In addition, the pattern of flanker interference differed between targets: For symbolic targets, laterality did not affect responses, whereas for nonsymbolic targets, laterality did affect responses. These results imply both symbolic and nonsymbolic magnitudes can be automatically activated; however, this activation is contingent upon their relevance to the task at hand. Implications of these results on the efficiency of the visual processing system and on numerical cognition are further discussed.

  4. Influence of PAS domain flanking regions on oligomerisation and redox signalling by NifL.

    Richard Little

    Full Text Available Per-ARNT-Sim (PAS domains constitute a typically dimeric, conserved α/β tertiary fold of approximately 110 amino acids that perform signalling roles in diverse proteins from all kingdoms of life. The amino terminal PAS1 domain of NifL from Azotobacter vinelandii accommodates a redox-active FAD group; elevation of cytosolic oxygen concentrations result in FAD oxidation and a concomitant conformational re-arrangement that is relayed via a short downstream linker to a second PAS domain, PAS2. At PAS2, the signal is amplified and passed on to effector domains generating the 'on' (inhibitory state of the protein. Although the crystal structure of oxidised PAS1 reveals regions that contribute to the dimerisation interface, 21 amino acids at the extreme N-terminus of NifL, are unresolved. Furthermore, the structure and function of the linker between the two PAS domains has not been determined. In this study we have investigated the importance to signalling of residues extending beyond the core PAS fold. Our results implicate the N-terminus of PAS1 and the helical linker connecting the two PAS domains in redox signal transduction and demonstrate a role for these flanking regions in controlling the oligomerisation state of PAS1 in solution.

  5. A romifidine and morphine combination for epidural analgesia of the flank in cattle.

    Fierheller, Erin E; Caulkett, Nigel A; Bailey, Jeremy V


    The objective of the study reported here was to determine the onset, duration, and degree of analgesia achieved with a combination of romifidine (50 microg/kg body weight [BW]) and morphine (0.1 mg/kg BW) administered epidurally. Ten adult Holstein Friesen cows were assigned to either a treatment group receiving the romifidine and morphine combination or a control group receiving 0.9% saline in a randomized, blinded, crossover design. Cows were assessed for degree of flank analgesia and systemic sedation at various time intervals over a period of 24 hours. The romifidine and morphine combination, compared with saline, provided significant analgesia for at least 10 minutes (P = 0.016) and up to 12 hours (P = 0.004) after epidural administration. Treated cows were sedate between 10 minutes (P = 0.016) and 6 hours (P = 0.002) after epidural administration. These results provide evidence for a potential cost-effective intra- and postoperative method of analgesia; however, the sedation seen in this study could be detrimental to patients expected return to the farm shortly after surgery. Further research into withdrawal times, systemic effects, and potential adverse effects are needed before an opiod and alpha2-adrenergic agonist combination can be used safely in a clinical setting.

  6. Spatial Distribution of Rolled up Kelvin-Helmholtz Vortices at Earth's Dayside and Flank Magnetopause

    Taylor, M. G. G. T.; Hasegawa, H.; Lavraud, B.; Phan, T.; Escoubet, C. P.; Dunlop, M. W.; Bogdanova, Y. V.; Borg, A. L.; Volwerk, M.; Berchem, J.; Constantinescu, O. D.; Eastwood, J. P.; Masson, A.; Laakso, H.; Soucek, J.; Fazakerley, A. N.; Frey, H. U.; Panov, E. V.; Shen, C.; Shi, J. K.; Sibeck, D. G.; Pu, Z. Y.; Wang, J.; Wild, J. A.


    The Kelvin-Helmholtz Instability (KHI) can drive waves at the magnetopause. These waves can grow to form rolled-up vortices and facilitate transfer of plasma into the magnetosphere. To investigate the persistence and frequency of such waves at the magnetopause we have carried out a survey of all Double Star 1 magnetopause crossings, using a combination of ion and magnetic field measurements. Using criteria originally used in a Geotail study made by Hasegawa et al. (2006) (forthwith referred to as H2006), 17 candidate events were identified from the entire TC-1 mission (covering 623 orbits where the magnetopause was sampled), a majority of which were on the dayside of the terminator. The relationship between density and shear velocity was then investigated, to identify the predicted signature of a rolled up vortex from H2006 and all 17 events exhibited some level of rolled up behavior. The location of the events had a clear dawn-dusk asymmetry, with 12 (71 %) on the post noon, dusk flank suggesting preferential growth in this region.

  7. The Radical Flank Effect and Cross-occupational Collaboration for Technology Development during a Power Shift.

    Truelove, Emily; Kellogg, Katherine C


    This 12-month ethnographic study of an early entrant into the U.S. car-sharing industry demonstrates that when an organization shifts its focus from developing radical new technology to incrementally improving this technology, the shift may spark an internal power struggle between the dominant engineering group and a challenger occupational group such as the marketing group. Analyzing 42 projects in two time periods that required collaboration between engineering and marketing during such a shift, we show how cross-occupational collaboration under these conditions can be facilitated by a radical flank threat, through which the bargaining power of moderates is strengthened by the presence of a more-radical group. In the face of a strong threat by radical members of a challenger occupational group, moderate members of the dominant engineering group may change their perceptions of their power to resist challengers' demands and begin to distinguish between the goals of radical versus more-moderate challengers. To maintain as much power as possible and prevent the more-dramatic change in engineering occupational goals demanded by radical challengers, moderate engineers may build a coalition with moderate challengers and collaborate for incremental technology development.

  8. Age of Yingfeng rapakivi granite pluton on the north flank of Qaidam and its geological significance

    XIAO Qinghui; LU Xinxiang; WANG Fei; SUN Yangui; WEI Xiangdong; XlNG Zuoyun


    The Yingfeng rapakivi granite on the north flank of Qaidam is a newly discovered Proterozoic rapakivi pluton in China, which was found after the discovery of Shachang rapakivi in Miyun County, Beijing and Kuandian rapakivi in Jilin Province. Yingfeng rapakivi pluton is exposed on the north side of the suture belt between Qinling-Kunlun orogenic belt and North China plate. U-Pb zircon isotopic dating and Ar-Ar isotopic dating of both hornblende and K-feldspar from the Yingfeng rapakivi granite have been conducted. The results show that the age of (1776±33)Ma at the upper intercept in Concorde diagram represents the age of formation of the pluton,whereas the age of (526 ± 281) Ma at the lower intercept and Ar-Ar mineral dating of hornblende and K-feldspar correspond to the age of a later event affecting the pluton, suggesting that Yingfeng pluton has ever been affected by strong regional Caledonian-Hercynian tectonic movement after its formation. The discovery of middle Proterozoic Yingfeng rapakivi granite provides a petrologic evidence for the timing of cratonization of both the continental crust basement in western China and the basement of the North China plate and for a rifting event taking place in the mid-Proterozoic, suggesting that an amalgamation of ancient China continents had ever happened during the "L(u) liang Movement" between the early Proterozoic and the mid-Proterozoic.

  9. A rhodanine flanked nonfullerene acceptor for solution-processed organic photovoltaics

    Holliday, Sarah


    A novel small molecule, FBR, bearing 3-ethylrhodanine flanking groups was synthesized as a nonfullerene electron acceptor for solution-processed bulk heterojunction organic photovoltaics (OPV). A straightforward synthesis route was employed, offering the potential for large scale preparation of this material. Inverted OPV devices employing poly(3-hexylthiophene) (P3HT) as the donor polymer and FBR as the acceptor gave power conversion efficiencies (PCE) up to 4.1%. Transient and steady state optical spectroscopies indicated efficient, ultrafast charge generation and efficient photocurrent generation from both donor and acceptor. Ultrafast transient absorption spectroscopy was used to investigate polaron generation efficiency as well as recombination dynamics. It was determined that the P3HT:FBR blend is highly intermixed, leading to increased charge generation relative to comparative devices with P3HT:PC60BM, but also faster recombination due to a nonideal morphology in which, in contrast to P3HT:PC60BM devices, the acceptor does not aggregate enough to create appropriate percolation pathways that prevent fast nongeminate recombination. Despite this nonoptimal morphology the P3HT:FBR devices exhibit better performance than P3HT:PC60BM devices, used as control, demonstrating that this acceptor shows great promise for further optimization.

  10. Geologic map of the northeast flank of Mauna Loa volcano, Island of Hawai'i, Hawaii

    Trusdell, Frank A.; Lockwood, John P.


    SummaryMauna Loa, the largest volcano on Earth, has erupted 33 times since written descriptions became available in 1832. Some eruptions were preceded by only brief seismic unrest, while others followed several months to a year of increased seismicity.The majority of the eruptions of Mauna Loa began in the summit area (>12,000-ft elevation; Lockwood and Lipman, 1987); yet the Northeast Rift Zone (NERZ) was the source of eight flank eruptions since 1843 (table 1). This zone extends from the 13,680-ft-high summit towards Hilo (population ~60,000), the second largest city in the State of Hawaii. Although most of the source vents are farther than 30 km away, the 1880 flow from one of the vents extends into Hilo, nearly reaching Hilo Bay. The city is built entirely on flows erupted from the NERZ, most older than that erupted in 1843.Once underway, Mauna Loa's eruptions can produce lava flows that reach the sea in less than 24 hours, severing roads and utilities in their path. For example, lava flows erupted from the Southwest Rift Zone (SWRZ) in 1950 advanced at an average rate of 9.3 km per hour, and all three lobes reached the ocean within approximately 24 hours (Finch and Macdonald, 1953). The flows near the eruptive vents must have traveled even faster.In terms of eruption frequency, pre-eruption warning, and rapid flow emplacement, Mauna Loa poses an enormous volcanic-hazard threat to the Island of Hawai‘i. By documenting past activity and by alerting the public and local government officials of our findings, we can anticipate the volcanic hazards and substantially mitigate the risks associated with an eruption of this massive edifice.From the geologic record, we can deduce several generalized facts about the geologic history of the NERZ. The middle to the uppermost section of the rift zone were more active in the past 4,000 years than the lower part, perhaps due to buttressing of the lower east rift zone by Mauna Kea and Kīlauea volcanoes. The historical flows

  11. Palagonitization of Basalt Glass in the Flanks of Mid-Ocean Ridges: Implications for the Bioenergetics of Oceanic Intracrustal Ecosystems.

    Türke, Andreas; Nakamura, Kentaro; Bach, Wolfgang


    When basalt is exposed to oxygenated aqueous solutions, rims of palagonite form along fractures at the expense of glass. We employed electron microprobe and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) analyses of fresh glass and adjacent palagonite crusts to determine the geochemical changes involved in palagonite formation. Samples were retrieved from drill cores taken in the North Pond Area, located on the western flank of the Mid-Atlantic Ridge at 22°45'N and 46°05'W. We also analyzed whole rock powders to determine the overall crust-seawater exchange in a young ridge flank. Radioactive elements are enriched in palagonite relative to fresh glass, reaching concentrations where radiolytic production of molecular hydrogen (H2) may be a significant energy source. Based on these results, we hypothesize that microbial ecosystems in ridge flank habitats undergo a transition in the principal energy carrier, fueling carbon fixation from Fe oxidation in very young crust to H2 consumption in older crust. Unless the H2 is swept away by rapid fluid flow (i.e., in young flanks), it may easily accumulate to levels high enough to support chemolithoautotrophic life. In older flanks, crustal sealing and sediment accumulation have slowed down seawater circulation, and the significance of radiolytically produced H2 for catalytic energy supply is expected to increase greatly. Similar habitats on other planetary surfaces are theoretically possible, as accumulation of radiolytically produced hydrogen merely requires the presence of H2O molecules and a porous medium, from which the hydrogen is not lost.

  12. The role of viscous magma mush spreading in volcanic flank motion at Kīlauea Volcano, Hawai‘i

    Plattner, C.; Amelung, F.; Baker, S.; Govers, R.; Poland, M.


    Multiple mechanisms have been suggested to explain seaward motion of the south flank of Kīlauea Volcano, Hawai‘i. The consistency of flank motion during both waxing and waning magmatic activity at Kīlauea suggests that a continuously acting force, like gravity body force, plays a substantial role. Using finite element models, we test whether gravity is the principal driver of long-term motion of Kīlauea's flank. We compare our model results to geodetic data from Global Positioning System and interferometric synthetic aperture radar during a time period with few magmatic and tectonic events (2000-2003), when deformation of Kīlauea was dominated by summit subsidence and seaward motion of the south flank. We find that gravity-only models can reproduce the horizontal surface velocities if we incorporate a regional décollement fault and a deep, low-viscosity magma mush zone. To obtain quasi steady state horizontal surface velocities that explain the long-term seaward motion of the flank, we find that an additional weak zone is needed, which is an extensional rift zone above the magma mush. The spreading rate in our model is mainly controlled by the magma mush viscosity, while its density plays a less significant role. We find that a viscosity of 2.5 × 1017–2.5 × 1019 Pa s for the magma mush provides an acceptable fit to the observed horizontal surface deformation. Using high magma mush viscosities, such as 2.5 × 1019 Pa s, the deformation rates remain more steady state over longer time scales. These models explain a significant amount of the observed subsidence at Kīlauea's summit. Some of the remaining subsidence is probably a result of magma withdrawal from subsurface reservoirs

  13. Study of surface roughness and flank wear in hard turning of AISI 4140 steel with coated ceramic inserts

    Das, Sudhansu Ranjan; Kuma, Amaresh [National Institute of Technology, Jamshedpur (India); Dhupal, Debabrata [Veer Surendra Sai University of Technology, Burla (India)


    This experimental investigation deals with dry hard turning of AISI 4140 steel using PVD-TiN coated Al{sub 2}O{sub 3}+TiCN mixed ceramic inserts. The combined effect of cutting parameters (cutting speed, feed and depth of cut) on performance characteristics such as surface roughness and flank wear is explored by Full factorial design (FFD) and analysis of variance (ANOVA). The results show that feed is the principal cutting parameter influencing surface roughness, followed by cutting speed. However, flank wear is affected by the cutting speed and interaction of feed-depth of cut, although depth of cut has not been found statistically significant, but flank wear is an increasing function of depth of cut. Observations are made on the machined surface, and worn tool by Scanning electron microscope (SEM) to establish the process. Abrasion was the major wear mechanism found during hard turning within the studied range. The effect of tool wear on surface roughness was also studied. The experimental data were analyzed to predict the optimal range of surface roughness and flank wear. Based on Response surface methodology (RSM), mathematical models were developed for surface roughness (Ra) and flank wear (VB) with 95% confidence level. Finally, under optimum cutting conditions (obtained by response optimization technique), tool life was evaluated to perform cost analysis for justifying the economic viability of coated ceramic inserts in hard turning. The estimated machining cost per part for TiN coated ceramic was found to be lower (Rs. 12.31) because of higher tool life (51 min), which results in the reduction of downtime and increase in savings.

  14. The role of viscous magma mush spreading in volcanic flank motion at Kīlauea Volcano, Hawai`i

    Plattner, C.; Amelung, F.; Baker, S.; Govers, R.; Poland, M.


    Multiple mechanisms have been suggested to explain seaward motion of the south flank of Kīlauea Volcano, Hawai`i. The consistency of flank motion during both waxing and waning magmatic activity at Kīlauea suggests that a continuously acting force, like gravity body force, plays a substantial role. Using finite element models, we test whether gravity is the principal driver of long-term motion of Kīlauea's flank. We compare our model results to geodetic data from Global Positioning System and interferometric synthetic aperture radar during a time period with few magmatic and tectonic events (2000-2003), when deformation of Kīlauea was dominated by summit subsidence and seaward motion of the south flank. We find that gravity-only models can reproduce the horizontal surface velocities if we incorporate a regional décollement fault and a deep, low-viscosity magma mush zone. To obtain quasi steady state horizontal surface velocities that explain the long-term seaward motion of the flank, we find that an additional weak zone is needed, which is an extensional rift zone above the magma mush. The spreading rate in our model is mainly controlled by the magma mush viscosity, while its density plays a less significant role. We find that a viscosity of 2.5 × 1017-2.5 × 1019 Pa s for the magma mush provides an acceptable fit to the observed horizontal surface deformation. Using high magma mush viscosities, such as 2.5 × 1019 Pa s, the deformation rates remain more steady state over longer time scales. These models explain a significant amount of the observed subsidence at Kīlauea's summit. Some of the remaining subsidence is probably a result of magma withdrawal from subsurface reservoirs.

  15. The role of viscous magma mush spreading in volcanic flank motion at Kilauea Volcano, Hawai'i

    Plattner, Christina; Amelung, Falk; Baker, Scott; Govers, Rob; Poland, Mike


    Multiple mechanisms have been suggested to explain seaward motion of the south flank of Kīlauea Volcano, Hawai'i. The consistency of flank motion during both waxing and waning magmatic activity at Kīlauea suggests that a continuously acting force, like gravity body force, plays a substantial role. Using finite element models, we test whether gravity is the principal driver of long-term motion of Kīlauea's flank. We compare our model results to geodetic data from Global Positioning System and interferometric synthetic aperture radar during a time period with few magmatic and tectonic events (2000-2003), when deformation of Kīlauea was dominated by summit subsidence and seaward motion of the south flank. We find that gravity-only models can reproduce the horizontal surface velocities if we incorporate a regional décollement fault and a deep, low-viscosity magma mush zone. To obtain quasi steady state horizontal surface velocities that explain the long-term seaward motion of the flank, we find that an additional weak zone is needed, which is an extensional rift zone above the magma mush. The spreading rate in our model is mainly controlled by the magma mush viscosity, while its density plays a less significant role.We find that a viscosity of 2.5 x 10^17 - 2.5 x 10^19 Pa s for the magma mush provides an acceptable fit to the observed horizontal surface deformation. Using high magma mush viscosities, such as 2.5 x 10^19 Pa s, the deformation rates remain more steady state over longer time scales. These models explain a significant amount of the observed subsidence at Kīlauea's summit. Some of the remaining subsidence is probably a result of magma withdrawal from subsurface reservoirs.

  16. Location and extent of recently active lava flows on the eastern flank of Idunn Mons on Venus

    D'Incecco, Piero; Mueller, Nils; Helbert, Joern; D'Amore, Mario


    The eastern flank of Idunn Mons, Imdr Regio's single large volcano, was identified in VIRTIS data as one of the regions with relatively high values of thermal emissivity at 1 μm wavelength. Our study intends to identify location and extent of the sources of such anomalies, thus the lava flows responsible for the relatively high emissivity observed by VIRTIS over the eastern flank of Idunn Mons. We perform a simulation iterating the geologic mapping made over Magellan radar images of the same area with modeling of the blurring caused by the scattering of the 1 μm radiation in the atmosphere. At every iteration, we map the lava flow units in the surroundings of Idunn Mons and we assign each unit an assumed value of emissivity. We observed a good match between the mapped flows and the clusters resulting from the consistency of the mapped lava flows through the ISO clustering analysis. We tested eight different configurations, calculating the total RMS error compared to VIRTIS observations. The best-fit configuration is that where we assigned high values of emissivity to the flank lava flows. Results also show a correlation between the ISO clustering analysis and the best-fit configuration. We reconstructed the post-eruption stratigraphy of the eastern flank of Idunn Mons, displaying the three flank lava flows units likely responsible for the relatively high 1 μm emissivity anomalies observed by VIRTIS. The average microwave emissivity provides a further evidence of the basaltic composition of the mapped lava flows.

  17. Internal structure of the western flank of the Cumbre Vieja volcano, La Palma, Canary Islands, from land magnetotelluric imaging

    Garcia, X.; Jones, A. G.


    Large-scale mass wasting is a natural part of the evolution of volcanic islands, where deformation and indications of flank instability, such as large-scale faulting and seismic and aseismic slip are common. The Cumbre Vieja volcano on the island of La Palma (Canary Islands) provides an ideal setting to address fundamental questions about the structure, evolution and stability of island volcanoes. The island of La Palma is still in a shield-building stage, and it has been postulated that the western side of the island lies over a pre-existing zone of weakness that can nucleate ruptures. We undertook an audiomagnetotelluric (AMT) survey over the proposed unstable western flank to try to image structures that may be associated with the zone of weakness. The magnetotelluric method (MT) is a geophysical technique used to map the presence of fluids or image important structural contrasts. The goals of this study were (1) to delineate the unstable flank, (2) to map the structures underneath and (3) to determine the presence and geometry of fluids. The results show a 1 km thick top resistive layer overlaying an area of reduced resistivity (enhanced conductivity), interpreted as a layer consisting of an alteration zone and also fluids. Our results confirm previous studies that suggested the existence of a western flank lying over collapse debris material and hyaloclastites, and also they allow us to map part of the subaerial southern extent of the Cumbre Nueva units that lie beneath the more recent Cumbre Vieja rocks. In addition, dimensionality analysis maps the rotation of the dike emplacement off ridge, along the western flank in an en echelon fashion.

  18. Modeling of Principal Flank Wear: An Empirical Approach Combining the Effect of Tool, Environment and Workpiece Hardness

    Mia, Mozammel; Al Bashir, Mahmood; Dhar, Nikhil Ranjan


    Hard turning is increasingly employed in machining, lately, to replace time-consuming conventional turning followed by grinding process. An excessive amount of tool wear in hard turning is one of the main hurdles to be overcome. Many researchers have developed tool wear model, but most of them developed it for a particular work-tool-environment combination. No aggregate model is developed that can be used to predict the amount of principal flank wear for specific machining time. An empirical model of principal flank wear (VB) has been developed for the different hardness of workpiece (HRC40, HRC48 and HRC56) while turning by coated carbide insert with different configurations (SNMM and SNMG) under both dry and high pressure coolant conditions. Unlike other developed model, this model includes the use of dummy variables along with the base empirical equation to entail the effect of any changes in the input conditions on the response. The base empirical equation for principal flank wear is formulated adopting the Exponential Associate Function using the experimental results. The coefficient of dummy variable reflects the shifting of the response from one set of machining condition to another set of machining condition which is determined by simple linear regression. The independent cutting parameters (speed, rate, depth of cut) are kept constant while formulating and analyzing this model. The developed model is validated with different sets of machining responses in turning hardened medium carbon steel by coated carbide inserts. For any particular set, the model can be used to predict the amount of principal flank wear for specific machining time. Since the predicted results exhibit good resemblance with experimental data and the average percentage error is <10 %, this model can be used to predict the principal flank wear for stated conditions.

  19. The association of SNPs in Hsp90β gene 5' flanking region with thermo tolerance traits and tissue mRNA expression in two chicken breeds.

    Chen, Zhuo-Yu; Gan, Jian-Kang; Xiao, Xiong; Jiang, Li-Yan; Zhang, Xi-Quan; Luo, Qing-Bin


    Thermo stress induces heat shock proteins (HSPs) expression and HSP90 family is one of them that has been reported to involve in cellular protection against heat stress. But whether there is any association of genetic variation in the Hsp90β gene in chicken with thermo tolerance is still unknown. Direct sequencing was used to detect possible SNPs in Hsp90β gene 5' flanking region in 3 chicken breeds (n = 663). Six mutations, among which 2 SNPs were chosen and genotypes were analyzed with PCR-RFLP method, were found in Hsp90β gene in these 3 chicken breeds. Association analysis indicated that SNP of C.-141G>A in the 5' flanking region of the Hsp90β gene in chicken had some effect on thermo tolerance traits, which may be a potential molecular marker of thermo tolerance, and the genotype GG was the thermo tolerance genotype. Hsp90β gene mRNA expression in different tissues detected by quantitative real-time PCR assay were demonstrated to be tissue dependent, implying that different tissues have distinct sensibilities to thermo stress. Besides, it was shown time specific and varieties differences. The expression of Hsp90β mRNA in Lingshan chickens in some tissues including heart, liver, brain and spleen were significantly higher or lower than that of White Recessive Rock (WRR). In this study, we presume that these mutations could be used in marker assisted selection for anti-heat stress chickens in our breeding program, and WRR were vulnerable to tropical thermo stress whereas Lingshan chickens were well adapted.

  20. Genotyping of simple sequence repeats--factors implicated in shadow band generation revisited.

    Olejniczak, Marta; Krzyzosiak, Wlodzimierz J


    PCR amplification of microsatellite sequences generates, besides the main product corresponding to allele size, also additional, undesired products usually shorter by multiples of the repeated unit. These extra products known as shadow bands or stutter products may complicate genotyping. The mechanism by which these artifacts are formed is not well understood and so no effective remedy has been found to cope with these spurious products. In this study, using the DNA templates containing the CAG/CTG repeats flanked by gene-specific sequences and universal priming sites, we analyzed the effects of many PCR variables on the shadow band generation. The most important result was that at the decreased temperature of the denaturation step during PCR cycling the shadow bands were either not formed or were strongly suppressed. Several possible sources of this effect are discussed.

  1. EAMJ Dec. Repeatability.indd


    Dec 12, 2008 ... Results:Kappa values for four-week repeatability for the wheeze and asthma questions were 0.61 ... for logistic, cultural and ethical reasons, to use ... individual with baseline forced expiratory volume in .... period is likely to also include the effects of true ... data, the writing of the manuscript or the decision.

  2. Distribution of contact loads over the flank-land of the cutter with a rounded cutting edge

    Kozlov, V.; Gerasimov, A.; Kim, A.


    In this paper, contact conditions between a tool and a workpiece material for wear-simulating turning by a cutter with a sharp-cornered edge and with a rounded cutting edge are analysed. The results of the experimental study of specific contact load distribution over the artificial flank wear-land of the cutter in free orthogonal turning of the disk from titanium alloy (Ti6Al2Mo2Cr), ductile (63Cu) and brittle (57Cu1Al3Mn) brasses are described. Investigations were carried out by the method of ‘split cutter’ and by the method of the artificial flank-land of variable width. The experiments with a variable feed rate and a cutting speed show that in titanium alloy machining with a sharp-cornered cutting edge the highest normal contact load (σh max = 3400…2200 MPa) is observed immediately at the cutting edge, and the curve has a horizontal region with the length of 0.2… 0.6 mm. At a distance from the cutting edge, the value of specific normal contact load is dramatically reduced to 1100…500 MPa. The character of normal contact load for a rounded cutting edge is different -it is uniform, and its value is approximately 2 times smaller compared to machining with a sharp-cornered cutting edge. In author’s opinion it is connected with generation of a seizure zone in a chip formation region and explains the capacity of highly worn-out cutting tools for titanium alloys machining. The paper analyses the distribution of tangential contact loads over the flank land, which pattern differs considerably for machining with a sharp-cornered edge and with a rounded cutting edge. Abbreviation and symbols: m/s - meter per second (cutting speed v); mm/r - millimeter per revolution (feed rate f); MPa - mega Pascal (specific contact load as a stress σ or τ) hf - the width of the flank wear land (chamfer) of the cutting tool, flank wear land can be natural or artificial like the one in this paper [mm]; xh - distance from the cutting edge on the surface of the flank-land [mm

  3. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.

    Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine


    Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at

  4. Isolation and characterization of human cerebellum cDNAs containing polymorphic CAG trinucleotide repeats

    Igarashi, S.; Onodera, O.; Tanaka, H. [Niigata Univ. (Japan)] [and others


    It has been discovered that neurologic diseases such as X linked spinal and bulbar muscular atrophy, Huntington`s disease, spinocerebellar ataxia type 1 (SCA1), and dentatorubral-pallidoluysian atrophy (DRPLA) are caused by unstable expansions of CAG repeats, which shed a light on a new mechanism of human hereditary diseases. The genetic anticipation, a common genetic feature in these diseases, can be explained by the trinucleotide repeat expansions, and an inverse correlation between the ages of onset and the numbers of trinucleotide repeats is demonstrated in these diseases. Furthermore, there have been diseases such as spinocerebellar ataxia 2 (SCA2) and Machado-Joseph disease showing similar genetic anticipation, which suggests that their causative mutations are unstable expansions of trinucleotide repeats. To identify candidate genes for neurodegenerative diseases which are expressed in human cerebellum and contain CAG repeats, we screened a human cerebellum cDNA library with an oligonucleotide (CAG){sub 10}, labelled with [{gamma}{sup 32}P]ATP. Out of 78 clones we have isolated, 43 clones were partially sequenced and 31 clones were shown to contain CAG or CTG tinucleotide repeats. From homology searches, 12 of the 59 clones were identified to contain known sequences including human MAR/SAR DNA binding protein, human glial fibrillary acidic protein, human myelin transcription factor 1, human neuronal growth protein 43 and human myocyte-specific enhancer 2. From 6 clones out of the 43 novel genes, we were able to develop primer pairs flanking CAG repeats and determined chromosomal localizations with human and rodent hybrid mapping panels. These CAG repeats were shown to be polymorphic and mapped to 1, 15, 17 and 18. These novel cDNAs will be useful as candidate genes for hereditary neurologic diseases showing genetic anticipation.

  5. Efecto de un calentamiento con estiramientos estáticos y dinámicos sobre el salto horizontal y la capacidad para repetir esprint con cambio de dirección. [Effect of warm-up with static and dynamic stretching on the horizontal jump and repeated sprint ability with changes of direction].

    Javier Sánchez-Sánchez


    Full Text Available El objetivo de este trabajo ha sido comparar el efecto de tres calentamientos diferentes (calentamiento aeróbico de baja intensidad, estiramiento estático y estiramiento dinámico sobre el salto horizontal y la capacidad de repetir esprint con cambios de dirección. Diecisiete practicantes de deportes de equipo de 20.8±1.1 años realizaron 3 tipos de calentamiento (10 min: ejercicio aeróbico sin estiramiento (CAE, con estiramiento estático (CAES y con estiramiento dinámico (CAED. Se estudió el efecto agudo de cada calentamiento sobre el rendimiento en una prueba de salto horizontal (SH y un test de repetición de esprint con cambio de dirección (RSCOD. No se obtuvieron diferencias significativas (p>0,05 en ninguna de las variables en función del calentamiento realizado. El tamaño del efecto (TE indicó que probablemente el RSCODmejor sea más sensible al CAE que al CAES (TE: 0,52 y al CAED (TE: 0,44. El escaso efecto de los estiramientos estáticos sobre el rendimiento en SH y RSCOD puede ser debido a la dosis, la intensidad y el tiempo de recuperación empleado. Los estiramientos dinámicos no mejoraron el rendimiento en SH y RSCOD. Abstract The purpose of this study was to compare the effect of three different warm-ups (low intensity aerobic warm-up, static stretching and dynamic stretching on the horizontal jump and repeated sprint ability with changes of direction. Seventeen players of team sports whose age was 20.8±1.1 years old performed three types of warm up (10 minutes: aerobic exercise without stretching (WU, with static stretching (WUSS and with dynamic stretching (WUDS. The acute effect of each warming over performance was studied in a test of horizontal jump (HJ and repeat sprint test with change of direction (RSCD. No significant differences were obtained (p>0.05 in any of the variables studied according to the warming developed. The effect size (ES indicated that probably RSCDbest was more sensitive to WU than WUDS (ES

  6. A porous flow model of flank eruptions on Mt. Etna: second-order perturbation theory

    N. Cenni


    Full Text Available A porous flow model for magma migration from a deep source within a volcanic edifice is developed. The model is based on the assumption that an isotropic and homogeneous system of fractures allows magma migration from one localized feeding dyke up to the surface of the volcano. The maximum level that magma can reach within the volcano (i.e., the «free surface» of magma, where fluid pressure equals the atmospheric pressure is reproduced through a second-order perturbation approach to the non-linear equations governing the migration of incompressible fluids through a porous medium. The perturbation parameter is found to depend on the ratio of the volumic discharge rate at the source (m3/s divided by the product of the hydraulic conductivity of the medium (m1/s times the square of the source depth. The second-order corrections for the free surface of Mt. Etna are found to be small but not negligible; from the comparison between first-order and second-order free surfaces it appears that the former is higher near the summit, slightly lower at intermediate altitudes and slightly higher far away from the axis of the volcano. Flank eruptions in the southern sector are found to be located in regions where the topography is actually lower than the theoretical free surface of magma. In this sector, modulations in the eruption site density correlate well with even minor differences between free surface and topography. In the northern and western sectors similar good fits are found, while the NE rift and the eastern sector seem to require mechanisms or structures respectively favouring and inhibiting magma migration.

  7. Temperature and redox effect on mineral colonization in Juan de Fuca Ridge flank subsurface crustal fluids

    Jean-Paul eBaquiran


    Full Text Available To examine microbe-mineral interactions in subsurface oceanic crust, we evaluated microbial colonization on crustal minerals that were incubated in borehole fluids for one year at the seafloor wellhead of a crustal borehole observatory (IODP Hole U1301A, Juan de Fuca Ridge flank as compared to an experiment that was not exposed to subsurface crustal fluids (at nearby IODP Hole U1301B. In comparison to previous studies at these same sites, this approach allowed assessment of the effects of temperature, fluid chemistry, and/or mineralogy on colonization patterns of different mineral substrates, and an opportunity to verify the approach of deploying colonization experiments at an observatory wellhead at the seafloor instead of within the borehole. The Hole U1301B deployment did not have biofilm growth, based on microscopy and DNA extraction, thereby confirming the integrity of the colonization design against bottom seawater intrusion. In contrast, the Hole U1301A deployment supported biofilms dominated by Epsilonproteobacteria (43.5% of 370 16S rRNA gene clone sequences and Gammaproteobacteria (29.3%. Sequence analysis revealed overlap in microbial communities between different minerals incubated at the Hole U1301A wellhead, indicating that mineralogy did not separate biofilm structure within the one-year colonization experiment. Differences in the Hole U1301A wellhead biofilm community composition relative to previous studies from within the borehole using similar mineral substrates suggest that temperature and the diffusion of dissolved oxygen through plastic components influenced the mineral colonization experiments positioned at the wellhead. This highlights the capacity of low abundance crustal fluid taxa to rapidly establish communities on diverse mineral substrates under changing environmental conditions such as from temperature and oxygen.

  8. Removal of ureteral calculi in two geldings via a standing flank approach.

    Frederick, Jeremy; Freeman, David E; MacKay, Robert J; Matyjaszek, Sarah; Lewis, Jordan; Sanchez, L Chris; Meyer, Stephanie


    Two geldings, aged 11 and 17 years, were examined for treatment of ureteroliths located approximately 10 cm proximal to the bladder. Ureteral obstruction was an incidental finding in 1 horse that was referred because of urinary tract obstruction and a cystic calculus. This horse did not have clinical or laboratory evidence of renal failure, although severe hydronephrosis was evident on transabdominal ultrasonography. The second patient had a serum creatinine concentration of 6.3 mg/dL (reference range, 0.8 to 2.2 mg/dL) and mild hydronephrosis of the affected left kidney. In both patients, the obstructed ureter was exteriorized through a flank incision as a standing procedure, and the calculus was crushed and removed with a uterine biopsy forceps introduced through a ureterotomy approximately 25 cm proximal to the calculus. The cystic calculus was removed through a perineal urethrostomy by lithotripsy, piecemeal extraction, and lavage. The horse without azotemia developed pyelonephritis in the affected kidney and was euthanatized because of complications of a nephrectomy 13 months later. In the horse with azotemia, the serum creatinine concentration decreased after surgery, and the horse returned to its intended use. However, it was euthanatized approximately 2 years after surgery because of progressive renal failure, and a large nephrolith was found in the previously unobstructed right kidney. The technique used for ureterolith removal was successful in both horses in this report, did not require sophisticated equipment, and could be effective in the early stages of ureteral obstruction as a means of restoring urine flow and renal function. The outcome in the horse with advanced unilateral renal disease without azotemia would suggest that nephrectomy should be considered as a treatment in such patients.

  9. Evaluation of the flanking nucleotide sequences of sarcomeric hypertrophic cardiomyopathy substitution mutations.

    Meurs, Kathryn M; Mealey, Katrina L


    Hypertrophic cardiomyopathy (HCM) is a familial myocardial disease with a prevalence of 1 in 500. More than 400 causative mutations have been identified in 13 sarcomeric and myofilament related genes, 350 of these are substitution mutations within eight sarcomeric genes. Within a population, examples of recurring identical disease causing mutations that appear to have arisen independently have been noted as well as those that appear to have been inherited from a common ancestor. The large number of novel HCM mutations could suggest a mechanism of increased mutability within the sarcomeric genes. The objective of this study was to evaluate the most commonly reported HCM genes, beta myosin heavy chain (MYH7), myosin binding protein C, troponin I, troponin T, cardiac regulatory myosin light chain, cardiac essential myosin light chain, alpha tropomyosin and cardiac alpha-actin for sequence patterns surrounding the substitution mutations that may suggest a mechanism of increased mutability. The mutations as well as the 10 flanking nucleotides were evaluated for frequency of di-, tri- and tetranucleotides containing the mutation as well as for the presence of certain tri- and tetranculeotide motifs. The most common substitutions were guanine (G) to adenine (A) and cytosine (C) to thymidine (T). The CG dinucleotide had a significantly higher relative mutability than any other dinucleotide (pmutation was calculated; none were at a statistically higher frequency than the others. The large number of G to A and C to T mutations as well as the relative mutability of CG may suggest that deamination of methylated CpG is an important mechanism for mutation development in at least some of these cardiac genes.

  10. Tool flank wear model and parametric optimization in end milling of metal matrix composite using carbide tool: Response surface methodology approach

    R. Arokiadass


    Full Text Available Highly automated CNC end milling machines in manufacturing industry requires reliable model for prediction of tool flank wear. This model later can be used to predict the tool flank wear (VBmax according to the process parameters. In this investigation an attempt was made to develop an empirical relationship to predict the tool flank wear (VBmax of carbide tools while machining LM25 Al/SiCp incorporating the process parameters such as spindle speed (N, feed rate (f, depth of cut (d and various % wt. of silicon carbide (S. Response surface methodology (RSM was applied to optimizing the end milling process parameters to attain the minimum tool flank wear. Predicted values obtained from the developed model and experimental results are compared, and error <5 percent is observed. In addition, it is concluded that the flank wear increases with the increase of SiCp percentage weight in the MMC.

  11. Promoter-bound trinucleotide repeat mRNA drives epigenetic silencing in fragile X syndrome.

    Colak, Dilek; Zaninovic, Nikica; Cohen, Michael S; Rosenwaks, Zev; Yang, Wang-Yong; Gerhardt, Jeannine; Disney, Matthew D; Jaffrey, Samie R


    Epigenetic gene silencing is seen in several repeat-expansion diseases. In fragile X syndrome, the most common genetic form of mental retardation, a CGG trinucleotide-repeat expansion adjacent to the fragile X mental retardation 1 (FMR1) gene promoter results in its epigenetic silencing. Here, we show that FMR1 silencing is mediated by the FMR1 mRNA. The FMR1 mRNA contains the transcribed CGG-repeat tract as part of the 5' untranslated region, which hybridizes to the complementary CGG-repeat portion of the FMR1 gene to form an RNA·DNA duplex. Disrupting the interaction of the mRNA with the CGG-repeat portion of the FMR1 gene prevents promoter silencing. Thus, our data link trinucleotide-repeat expansion to a form of RNA-directed gene silencing mediated by direct interactions of the trinucleotide-repeat RNA and DNA.

  12. Pathogen corruption and site-directed recombination at a plant disease resistance gene cluster

    Nagy, Ervin D.; Bennetzen, Jeffrey L.


    The Pc locus of sorghum (Sorghum bicolor) determines dominant sensitivity to a host-selective toxin produced by the fungal pathogen Periconia circinata. The Pc region was cloned by a map-based approach and found to contain three tandemly repeated genes with the structures of nucleotide binding site–leucine-rich repeat (NBS–LRR) disease resistance genes. Thirteen independent Pc-to-pc mutations were analyzed, and each was found to remove all or part of the central gene of the threesome. Hence, this central gene is Pc. Most Pc-to-pc mutations were associated with unequal recombination. Eight recombination events were localized to different sites in a 560-bp region within the ∼3.7-kb NBS–LRR genes. Because any unequal recombination located within the flanking NBS–LRR genes would have removed Pc, the clustering of cross-over events within a 560-bp segment indicates that a site-directed recombination process exists that specifically targets unequal events to generate LRR diversity in NBS–LRR loci. PMID:18719093

  13. Measurement-based quantum repeaters

    Zwerger, M; Briegel, H J


    We introduce measurement-based quantum repeaters, where small-scale measurement-based quantum processors are used to perform entanglement purification and entanglement swapping in a long-range quantum communication protocol. In the scheme, pre-prepared entangled states stored at intermediate repeater stations are coupled with incoming photons by simple Bell-measurements, without the need of performing additional quantum gates or measurements. We show how to construct the required resource states, and how to minimize their size. We analyze the performance of the scheme under noise and imperfections, with focus on small-scale implementations involving entangled states of few qubits. We find measurement-based purification protocols with significantly improved noise thresholds. Furthermore we show that already resource states of small size suffice to significantly increase the maximal communication distance. We also discuss possible advantages of our scheme for different set-ups.




    Full Text Available AISI 304 austenitic stainless steel is a popularly used grade in the various fields of manufacturing because of its high ductility, high durability and excellent corrosion resistance. High work hardening, low heat conductivity and high built up edge (BUE formation made this as difficult-to- machine material. Poor surface quality and rapid tool wear are the common problems encountered while machining it. In the present work, an attempt has been made to explore the influence of machining parameters on the performance measures, surface roughness and flank wear in turning of AISI 304 austenitic stainless steel with a two layer Chemical vapour deposition(CVD coated tool. In order to achieve this, Taguchi approach has been employed. The results revealed that the cutting speed most significantly, influences both surface roughness and flank wear. In addition to this the optimal setting of process parameters and optimal ranges of performance measures are predicted.

  15. Preliminary assessment of the state of CO2 soil degassing on the flanks of Gede volcano (West Java, Indonesia)

    Kunrat, S. L.; Schwandner, F. M.


    Gede Volcano (West Java) is part of an andesitic stratovolcano complex consisting of Pangrango in the north-west and Gede in the south-east. The last recorded eruptive activity was a phreatic subvolcanian ash eruption in 1957. Current activity is characterized by episodic swarms at 2-4 km depth, and low-temperature (~160°C) crater degassing in two distinct summit crater fumarolic areas. Hot springs occur in the saddle between the Gede and Pangrango edifice, as well as on the NE flank base. The most recent eruptive events produced pyroclastic material, their flow deposits concentrate toward the NE. A collaborative effort between the Center for Volcanology and Geological Hazard Mitigation (CVGHM), Geological Agency and the Earth Observatory of Singapore (EOS) is since 2010 aimed at upgrading the geophysical and geochemical monitoring network at Gede Volcano. To support the monitoring instrumentation upgrades under way, surveys of soil CO2 degassing have been performed on the flanks of Gede, in circular and radial traverses.The goal was to establish a spatial distribution of flank CO2 fluxes, and to allow smart siting for continuous gas monitoring stations. Crater fluxes were not surveyed, as its low-temperature hydrothermal system is likely prone to large hydraulic changes in this tropical environment, resulting in variable permeability effects that might mask signals from deeper reservoir or conduit degassing. The high precipitation intensity in the mountains of tropical Java pose challenges to this method, since soil gas permeability is largely controlled by soil moisture content. Simultaneous soil moisture measurements were undertaken. The soil CO2 surveys were carried out using a LI-8100A campaign flux chamber instrument (LICOR Biosciences, Lincoln, Nebraska). This instrument has a very precise and highly stable sensor and an atmospheric pressure equilibrator, making it highly sensitive to low fluxes. It is the far superior choice for higher precision low

  16. Can comodulation masking release occur when frequency changes could promote perceptual segregation of the on-frequency and flanking bands?

    Verhey, Jesko L; Epp, Bastian; Stasiak, Arkadiusz


    bands relative to the inhibitory areas (as seen in physiological recordings using stationary flanking bands). Preliminary physiological results in the cochlear nucleus of the Guinea pig show that a correlate of CMR can also be found at this level of the auditory pathway with sweeping flanking bands.......A common characteristic of natural sounds is that the level fluctuations in different frequency regions are coherent. The ability of the auditory system to use this comodulation is shown when a sinusoidal signal is masked by a masker centred at the signal frequency (on-frequency masker, OFM...... and comodulation could serve as cues to indicate which of the stimulus components originate from one source. If the common fate of frequency components is the stronger binding cue, the sweeping FBs and the OFM with a fixed centre frequency should no longer form one auditory object and the CMR should be abolished...

  17. A new colorful species of Pristimantis (Anura: Craugastoridae) from the eastern flank of the Cordillera Central in Colombia .

    Rivera-Prieto, Diego A; Rivera-Correa, Mauricio; Daza, Juan M


    We describe a new species of Pristimantis from the humid forests on the eastern flank of the northern Cordillera Central in Colombia (6º 23' 19.3554" N, 75º 1' 24.0594" W; ca. 1150 m.a.s.l.). Pristimantis jaguensis sp. nov. is characterized by an extraordinary variation in color and is readily distinguished from congeneric species by lacking nuptial pads, discoidal fold and conical calcar tubercles; flanks and belly white to cream without blotches as well as iris yellow ocher to copper with thick brown reticulation and cream sclera. Molecular phylogenetic analyses recovered the new species in a clade with species mostly distributed in Ecuador. Our finding suggests that new taxa can still be discovered in the Middle Magdalena River valley of Colombia despite the extensive sampling this region has received during the last decades. 

  18. [Brood parasitism and egg mimicry on Brownish-flanked Bush Warbler (Cettia fortipes) by Lesser Cuckoo (Cuculus poliocephalus)].

    Yang, Can-Chao; Cai, Yan; Liang, Wei


    Nest fate of Brownish-flanked Bush Warbler (Cettia fortipes) was conducted in breeding seasons from 1999 to 2009 in Kuankuoshui Natural Reserve, Guizhou province. Predation rate, parasitism rate, hatching success, nesting success and reproductive success were surveyed and egg color was quantified using spectrophotometer. Principal component analysis, reflectance spectrum and Robinson Project were used to analyze the egg color of bush warbler and egg mimicry of Lesser Cuckoo (Cuculus poliocephalus) in parasitized nests. Our results indicated that the Brownish-flanked Bush Warbler suffered from high predation rate and relatively high parasitism rate of 49.26% and 9.18%, respectively. Reflectance analysis showed that the hue and chroma of Lesser Cuckoo eggs were highly mimetic but the egg brightness and ultraviolet reflectance were different from the bush warbler.

  19. Proteins binding to the 5‘—flanking regualtory elements of the human β—globin gene



    The binding of nuclear proteins prepared from mouse erythroid tissue in different developmental stages to the 5'-flanking regulatory elements of human β-globin gene,two negative control regions(NCR1,-610to-490 bp;NCR2,-338,to-233bp),was identified.Two stage specific protein factors corresponding to embryonic and fetal stages were found to be capable of binding to NCR2.These data provided evidence that the cis acting elements of the 5'-flanking region might be involved in the developmental control of β-globin gene and NCR2 might be responsible in art for the silence of β-glolbin gene in the embryonic and fetal stages.

  20. Higher primates, but not New World monkeys, have a duplicate set of enhancers flanking their apoC-I genes.

    Puppione, Donald L


    Previous studies have demonstrated that the apoC-I gene and its pseudogene on human chromosome 19 are flanked by a duplicate set of enhancers. Multienhancers, ME.1 and ME.2, are located upstream from the genes and the hepatic control region enhancers, HCR.1 and HCR.2, are located downstream. The duplication of the enhancers has been thought to have occurred when the apoC-I gene was duplicated during primate evolution. Currently, the only primate data are for the human enhancers. Examining the genome of other primates (great and lesser apes, Old and New World monkeys), it was possible to locate the duplicate set of enhancers in apes and Old World monkeys. However, only a single set was found in New World monkeys. These observations provide additional evidence that the apoC-I gene and the flanking enhancers underwent duplication after the divergence of Old and New World monkeys.

  1. Repeatability of Harris Corner Detector

    HU Lili


    Interest point detectors are commonly employed to reduce the amount of data to be processed. The ideal interest point detector would robustly select those features which are most appropriate or salient for the application and data at hand. This paper shows that interest points are geometrically stable under different transformations.This property makes interest points very successful in the context of image matching. To measure this property quantatively, we introduce a evaluation criterion: repeatability rate.

  2. Qualitative and quantitative event-specific PCR detection methods for oxy-235 canola based on the 3' integration flanking sequence.

    Yang, Litao; Guo, Jinchao; Zhang, Haibo; Liu, Jia; Zhang, Dabing


    As more genetically modified plant events are approved for commercialization worldwide, the event-specific PCR method has become the key method for genetically modified organism (GMO) identification and quantification. This study reveals the 3' flanking sequence of the exogenous integration of Oxy-235 canola employing thermal asymmetric interlaced PCR (TAIL-PCR). On the basis of the revealed 3' flanking sequence, PCR primers and TaqMan probe were designed and qualitative and quantitative PCR assays were established for Oxy-235 canola. The specificity and limits of detection (LOD) and quantification (LOQ) of these two PCR assays were validated to as low as 0.1% for the relative LOD of qualitative PCR assay; the absolute LOD and LOQ were low to 10 and 20 copies of canola genomic DNA in quantitative PCR assay, respectively. Furthermore, ideal quantified results were obtained in the practical canola sample detection. All of the results indicate that the developed qualitative and quantitative PCR methods based on the revealed 3' integration flanking sequence are suitable for GM canola Oxy-235 identification and quantification.

  3. Comparison of flank margin cave development on San Salvador island, Bahamas, and Isla de Mona, Puerto Rico

    Mylroie, J.; Carew, J.L.; Frank, E.F.; Larsen, Matthew C.; Boardman, M.


    San Salvador Island, Bahamas is a 161 Km2 tectonically stable late Quaternary carbonate island located 600 km east-southeast of Miami FL. San Salvador contains numerous flank margin caves (phreatic karst features) that developed primarily in late Pleistocene eolianites. These caves developed during a short time in versy small fresh-water lenses. Cave elevations and Uranium-series ages from stalagmites indicate that all currently subaerial flank margin caves developed during the last interglacial seal-level highstand that was 6 m above current mean seal level 125,000 years ago (oxygen isotope substage 5e), which lasted no more than 14,000 years. The caves were formed by dissolution in the mixing zone at the margin of a freshwater lens that was elevated by the substage 5e highstand, and which resided within the small emergent portions of eolianite ridges. The flank margin caves have chambers with volumes greater than 1000 m3 on San Salvador; on other Bahamian islands, chambers as large as 14,000 m3 are known.

  4. Compartmentalization of the Coso East Flank Geothermal Field Imaged by 3-D Full-tensor MT Inversion

    Lindsey, Nathaniel J.; Kaven, Joern Ole; Davatzes, Nicholas; Newman, Gregory A.


    Previous magnetotelluric (MT) studies of the high-temperature Coso geothermal system in California identified a subvertical feature of low resistivity (2 - 5 Ohm-m) and appreciable lateral extent (>1 km) in the producing zone of the East Flank field. However, these models could not reproduce gross 3-D effects in the recorded data. We perform 3-D full-tensor inversion and retrieve a resistivity model that out-performs previous 2-D and 3-D off-diagonal models in terms of its fit to the complete 3-D MT dataset as well as the degree of modeling bias. Inclusion of secondary Zxx and Zyy data components leads to a robust east-dip (60o) to the previously identified conductive East Flank reservoir feature, which correlates strongly with recently mapped surface faults, downhole well temperatures, 3-D seismic reflection data, and local microseismicity. We perform synthetic forward modeling to test the best fit dip of this conductor using the response at a nearby MT station. We interpret the dipping conductor as a fractured and fluidized compartment, which is structurally-controlled by an unmapped blind East Flank fault zone.

  5. Compartmentalization of the Coso East Flank geothermal field imaged by 3-D full-tensor MT inversion

    Lindsey, Nathaniel J.; Kaven, Joern Ole; Davatzes, Nicholas; Newman, Gregory A.


    Previous magnetotelluric (MT) studies of the high-temperature Coso geothermal system in California identified a subvertical feature of low resistivity (2-5 Ohm m) and appreciable lateral extent (>1 km) in the producing zone of the East Flank field. However, these models could not reproduce gross 3-D effects in the recorded data. We perform 3-D full-tensor inversion and retrieve a resistivity model that out-performs previous 2-D and 3-D off-diagonal models in terms of its fit to the complete 3-D MT data set as well as the degree of modelling bias. Inclusion of secondary Zxx and Zyy data components leads to a robust east-dip (60†) to the previously identified conductive East Flank reservoir feature, which correlates strongly with recently mapped surface faults, downhole well temperatures, 3-D seismic reflection data, and local microseismicity. We perform synthetic forward modelling to test the best-fit dip of this conductor using the response at a nearby MT station. We interpret the dipping conductor as a fractured and fluidized compartment, which is structurally controlled by an unmapped blind East Flank fault zone.

  6. Flanking sequence determination and event-specific detection of genetically modified wheat B73-6-1

    Junyi Xu; Jijuan Cao; Dongmei Cao; Tongtong Zhao; Xin Huang; Piqiao Zhang; Fengxia Luan


    In order to establish a specific identification method for genetically modified (GM) wheat,exogenous insert DNA and flanking sequence between exogenous fragment and recombinant chromosome of GM wheat B73-6-1 were successfully acquired by means of conventional polymerase chain reaction (PCR) and thermal asymmetric interlaced (TAIL)-PCR strategies.Newly acquired exogenous fragment covered the full-length sequence of transformed genes such as transformed plasmid and corresponding functional genes including marker uidA,herbicide-resistant bar,ubiquitin promoter,and high-molecular-weight gluten subunit.The flanking sequence between insert DNA revealed high similarity with Triticum turgidum A gene (GenBank:AY494981.1).A specific PCR detection method for GM wheat B73-6-1 was established on the basis of primers designed according to the flanking sequence.This specific PCR method was validated by GM wheat,GM corn,GM soybean,GM rice,and non-GM wheat.The specifically amplified target band was observed only in GM wheat B73-6-1.This method is of high specificity,high reproducibility,rapid identification,and excellent accuracy for the identification of GM wheat B73-6-1.

  7. Cloning of Genomic DNA Flanking Transposon in the Nonpathogenic Mutant of Xanthomonas axonopodis pv. glycines M715



    Full Text Available The objective of this work is to clone flanking DNA derived from Tn-5 mutagenesis of wild type strain Xanthomonas axonopodis pv. glycines as first step to clone and to identify the gene involved in pathogenicity mechanism. We have localized the flanking DNA fragment from a nonpathogenic mutant of Xag M715. Southern hybridization analysis using 2.8 kb EcoRI from pYR103 as a probe showed that the fragment is located within 2.0 kb PstI fragment. A 0.7 kb flanking DNA was amplified using inverse PCR technique, and inserted into pGEM-T Easy vector generating a 3.7 kb recombinant plasmid (pAA01. Southern hybridization analysis of the wild type (YR32 with pAA01 as a probe indicated a hybridization signal located at approximately 3.0 kb PstI fragment. DNA sequence analysis revealed that the DNA fragment has a 64% identity to a vir gene of Bacillus anthracis.

  8. Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA.

    Zhaorong Ma

    Full Text Available Conserved plant microRNAs (miRNAs modulate important biological processes but little is known about conserved cis-regulatory elements (CREs surrounding MIRNA genes. We developed a solution-based targeted genomic enrichment methodology to capture, enrich, and sequence flanking genomic regions surrounding conserved MIRNA genes with a locked-nucleic acid (LNA-modified, biotinylated probe complementary to the mature miRNA sequence. Genomic DNA bound by the probe is captured by streptavidin-coated magnetic beads, amplified, sequenced and assembled de novo to obtain genomic DNA sequences flanking MIRNA locus of interest. We demonstrate the sensitivity and specificity of this enrichment methodology in Arabidopsis thaliana to enrich targeted regions spanning 10-20 kb surrounding known MIR166 and MIR165 loci. Assembly of the sequencing reads successfully recovered all targeted loci. While further optimization for larger, more complex genomes is needed, this method may enable determination of flanking genomic DNA sequence surrounding a known core (like a conserved mature miRNA from multiple species that currently don't have a full genome assembly available.

  9. Short 5'-flanking regions of the Amy gene of Drosophila kikkawai affect amylase gene expression and respond to food environments.

    Inomata, Nobuyuki; Nakashima, Shuichi


    Evolution of the duplicated genes and regulation in gene expression is of great interest, especially in terms of adaptation. Molecular population genetic and evolutionary studies on the duplicated amylase genes of Drosophila species have suggested that their 5'-flanking (cis-regulatory) regions play an important role in evolution of these genes. For better understanding of evolution of the duplicated amylase genes and gene expression, we studied functional significance of the Amy1 gene of Drosophila kikkawai using in vitro deletion mutagenesis followed by P-element-mediated germline transformation. We found that a 1.6-kb of the 5'-flanking region can produce strikingly higher level of larval amylase activity on starch food compared with that on glucose food. We found two cis-regulatory elements, which increase larval amylase activity on starch food. We also found a larval cis-regulatory element, which responds to the food difference. This food-response element is necessary for the function of the element increasing larval activity on starch food. A 5-bp deletion in a putative GRE caused high amylase activity, indicating a cis-regulatory element decreasing amylase activity. These cis-regulatory elements identified in the 5'-flanking region could be the targets of natural selection.

  10. The last glacial termination on the eastern flank of the central Patagonian Andes (47 ° S)

    Henríquez, William I.; Villa-Martínez, Rodrigo; Vilanova, Isabel; De Pol-Holz, Ricardo; Moreno, Patricio I.


    dispersal of hygrophilous trees and herbs from the eastern flank of the central Patagonian Andes, contributing to the afforestation of the western Andean slopes and pacific coasts of central Patagonia during T1.

  11. Investigation of Anomalous Terrains on the West Flank of Olympus Mons using CRISM Data

    Seelos, K. D.; Bridges, N. T.; Andrews-Hanna, J. C.; Seelos, F. P.; Murchie, S. L.


    The west flank of the Olympus Mons volcano hosts an anomalous linear chain of semicircular terrains. We report here analyses of these features using data from the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) and other instruments. The terrains appear bright in both daytime and nighttime data from the Thermal Emission Imaging Experiment (THEMIS) and have moderate thermal inertia, contrasting with the regional dust mantle. They have no observable topographic relief, and morphologically appear inconsistent with volcanic or sedimentary deposits. Several forms of aeolian activity are evident, including yardangs, dunes, and scour-like features. However, the yardangs and scours appear to predate the terrains, and superposed dunes, while ubiquitous, do not fully account for the spectral and morphologic properties. Targeted hyperspectral visible and near infrared data from CRISM (20-40 m/pixel, ~0.4 to 4 μm) of the terrains show distinct circumferential color zonation and internal banding. Differences in spectral slope and depth of the 3 μm water absorption are apparent within these color units. Relatively low albedo materials that comprise small dune fields are superposed on variably higher albedo areas. Both of these materials exhibit negative infrared spectral slopes, but it is most pronounced in the areas with highest albedo. Around the perimeter of the terrains are two albedo zones that appear transitional with the surrounding high albedo dust cover, progressively darkening inward. Along with the overall decrease in albedo, however, is an apparent increase in the depth of the 3 μm hydration band. Spectral features indicative of specific hydrated minerals (e.g, sulfates, phyllosilicates) have not been observed, but an enhanced 3 μm absorption could indicate that these anomalous terrains were influenced by ephemeral water at some point in the near past. Recent aqueous activity on the largest volcano on Mars may represent a unique opportunity for

  12. Adhesive and migratory effects of phosphophoryn are modulated by flanking peptides of the integrin binding motif.

    Shigeki Suzuki

    Full Text Available Phosphophoryn (PP is generated from the proteolytic cleavage of dentin sialophosphoprotein (DSPP. Gene duplications in the ancestor dentin matrix protein-1 (DMP-1 genomic sequence created the DSPP gene in toothed animals. PP and DMP-1 are phosphorylated extracellular matrix proteins that belong to the family of small integrin-binding ligand N-linked glycoproteins (SIBLINGs. Many SIBLING members have been shown to evoke various cell responses through the integrin-binding Arg-Gly-Asp (RGD domain; however, the RGD-dependent function of PP is not yet fully understood. We demonstrated that recombinant PP did not exhibit any obvious cell adhesion ability, whereas the simultaneously purified recombinant DMP-1 did. A cell adhesion inhibitory analysis was performed by pre-incubating human osteosarcoma MG63 cells with various PP peptides before seeding onto vitronectin. The results obtained revealed that the incorporation of more than one amino acid on both sides of the PP-RGD domain was unable to inhibit the adhesion of MG63 cells onto vitronectin. Furthermore, the inhibitory activity of a peptide containing the PP-RGD domain with an open carboxyl-terminal side (H-463SDESDTNSESANESGSRGDA482-OH was more potent than that of a peptide containing the RGD domain with an open amino-terminal side (H-478SRGDASYTSDESSDDDNDSDSH499-OH. This phenomenon was supported by the potent cell adhesion and migration abilities of the recombinant truncated PP, which terminated with Ala482. Furthermore, various point mutations in Ala482 and/or Ser483 converted recombinant PP into cell-adhesive proteins. Therefore, we concluded that the Ala482-Ser483 flanking sequence, which was detected in primates and mice, was the key peptide bond that allowed the PP-RGD domain to be sequestered. The differential abilities of PP and DMP-1 to act on integrin imply that DSPP was duplicated from DMP-1 to serve as a crucial extracellular protein for tooth development rather than as an integrin

  13. Structural Studies of a Four-MBT Repeat Protein MBTD1

    Eryilmaz, Jitka; Pan, Patricia; Amaya, Maria F.; Allali-Hassani, Abdellah; Dong, Aiping; Adams-Cioaba, Melanie A.; MacKenzie, Farrell; Vedadi, Masoud; Min, Jinrong; (Toronto); (Toronto)


    The Polycomb group (PcG) of proteins is a family of important developmental regulators. The respective members function as large protein complexes involved in establishment and maintenance of transcriptional repression of developmental control genes. MBTD1, Malignant Brain Tumor domain-containing protein 1, is one such PcG protein. MBTD1 contains four MBT repeats. We have determined the crystal structure of MBTD1 (residues 130-566aa covering the 4 MBT repeats) at 2.5 {angstrom} resolution by X-ray crystallography. The crystal structure of MBTD1 reveals its similarity to another four-MBT-repeat protein L3MBTL2, which binds lower methylated lysine histones. Fluorescence polarization experiments confirmed that MBTD1 preferentially binds mono- and di-methyllysine histone peptides, like L3MBTL1 and L3MBTL2. All known MBT-peptide complex structures characterized to date do not exhibit strong histone peptide sequence selectivity, and use a 'cavity insertion recognition mode' to recognize the methylated lysine with the deeply buried methyl-lysine forming extensive interactions with the protein while the peptide residues flanking methyl-lysine forming very few contacts. Nevertheless, our mutagenesis data based on L3MBTL1 suggested that the histone peptides could not bind to MBT repeats in any orientation. The four MBT repeats in MBTD1 exhibits an asymmetric rhomboid architecture. Like other MBT repeat proteins characterized so far, MBTD1 binds mono- or dimethylated lysine histones through one of its four MBT repeats utilizing a semi-aromatic cage.

  14. Airborne Radar Interferometric Repeat-Pass Processing

    Hensley, Scott; Michel, Thierry R.; Jones, Cathleen E.; Muellerschoen, Ronald J.; Chapman, Bruce D.; Fore, Alexander; Simard, Marc; Zebker, Howard A.


    Earth science research often requires crustal deformation measurements at a variety of time scales, from seconds to decades. Although satellites have been used for repeat-track interferometric (RTI) synthetic-aperture-radar (SAR) mapping for close to 20 years, RTI is much more difficult to implement from an airborne platform owing to the irregular trajectory of the aircraft compared with microwave imaging radar wavelengths. Two basic requirements for robust airborne repeat-pass radar interferometry include the ability to fly the platform to a desired trajectory within a narrow tube and the ability to have the radar beam pointed in a desired direction to a fraction of a beam width. Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) is equipped with a precision auto pilot developed by NASA Dryden that allows the platform, a Gulfstream III, to nominally fly within a 5 m diameter tube and with an electronically scanned antenna to position the radar beam to a fraction of a beam width based on INU (inertial navigation unit) attitude angle measurements.

  15. Repeated Reading Intervention Effects in Kindergartners with Partial Letter Knowledge

    van Gorp, Karly; Segers, Eliane; Verhoeven, Ludo


    The direct, transfer and retention effects of a repeated reading intervention study of single CVC (consonant in the onset and a vowel and consonant in the rime) words in kindergartners with partial letter knowledge were examined. A total of 26 second-year kindergartners participated in this study. Participants were divided over two feedback…

  16. Origin and fate of repeats in bacteria.

    Achaz, G; Rocha, E P C; Netter, P; Coissac, E


    We investigated 53 complete bacterial chromosomes for intrachromosomal repeats. In previous studies on eukaryote chromosomes, we proposed a model for the dynamics of repeats based on the continuous genesis of tandem repeats, followed by an active process of high deletion rate, counteracted by rearrangement events that may prevent the repeats from being deleted. The present study of long repeats in the genomes of Bacteria and Archaea suggests that our model of interspersed repeats dynamics may apply to them. Thus the duplication process might be a consequence of very ancient mechanisms shared by all three domains. Moreover, we show that there is a strong negative correlation between nucleotide composition bias and the repeat density of genomes. We hypothesise that in highly biased genomes, non-duplicated small repeats arise more frequently by random effects and are used as primers for duplication mechanisms, leading to a higher density of large repeats.

  17. Improving repeatability by improving quality

    Ronen, Shuki; Ackers, Mark; Schlumberger, Geco-Prakla; Brink, Mundy


    Time lapse (4-D) seismic is a promising tool for reservoir characterization and monitoring. The method is apparently simple: to acquire data repeatedly over the same reservoir, process and interpret the data sets, then changes between the data sets indicate changes in the reservoir. A problem with time lapse seismic data is that reservoirs are a relatively small part of the earth and important reservoir changes may cause very small differences to the time lapse data. The challenge is to acquire and process economical time lapse data such that reservoir changes can be detected above the noise of varying acquisition and environment. 7 refs., 9 figs.

  18. Coordinated hybrid automatic repeat request

    Makki, Behrooz


    We develop a coordinated hybrid automatic repeat request (HARQ) approach. With the proposed scheme, if a user message is correctly decoded in the first HARQ rounds, its spectrum is allocated to other users, to improve the network outage probability and the users\\' fairness. The results, which are obtained for single- and multiple-antenna setups, demonstrate the efficiency of the proposed approach in different conditions. For instance, with a maximum of M retransmissions and single transmit/receive antennas, the diversity gain of a user increases from M to (J+1)(M-1)+1 where J is the number of users helping that user.

  19. Evidence of flank failure deposit reactivation in a shield volcano. A favorable context for deep-seated landslide activation (La Réunion Island)

    Belle, Pierre; Aunay, Bertrand; Famin, Vincent; Join, Jean-Lambert


    Giant flank failures are recurrent features of shield volcanoes, and their deposits (i.e. breccia), constitute a significant volume in a volcanic edifice. On La Réunion Island, the growth and development of Piton des Neiges volcano has been punctuated by several flank failure episodes. One of these failures is a deep-seated landslide (>200 Mm3) occurring nowadays in Grand Ilet, a plateau inhabited by 1 000 people in the cirque of Salazie, on the northern flank of Piton des Neiges. Here we present the results of a multidisciplinary study (structural geology and field mapping, GNSS monitoring, borehole logging) performed to characterize the geological structure the Grand Ilet landslide, and identify the instability factors that control this category of destabilization. Basic breccia deposits, up to 160 meters thick, constitute the main geological formation of the unstable mass. This breccia are cut by the headwall scar of the landslide, and covered by lava flows, indicating a minimum age of 200 kyr for the destabilization that produced the deposits. The breccia is consolidated out of the landslide area. The NE toe of the landslide is evidenced by an important compressional deformation of the base of the breccia, and striated surfaces in this deformed volume indicate a NE-direction of transport. In this deformed bulge, a clay-rich layer at the base of the breccia has been identified as the main slip plane. Using a video inspection of drill casings on three exploration boreholes, we reconstructed the 3D geometry of the slip plane at the base of the breccia. This reconstruction shows that the landslide plane has an average dip of 6° toward the NE. The displacement monitoring network shows that the unstable mass has a 5.5 km2 extension, with a variable azimuth of movement direction (N140° for the SW sector, and N45° for the NE sector). The planimetric displacements velocities range between 2 cm/year in the inner part of the unstable mass to 52 cm/year at the

  20. Estimating volume of deposits associated with landslides on volcanic landscapes in the SW flank of the volcano Pico de Orizaba, Puebla-Veracruz

    Gabriel Legorreta Paulín


    dangerous situation for more than 360 000 people living on the southern flank of the volcano Pico de Orizaba, where landslides along the hillslopes and the river system threaten towns like Cordova, Orizaba, Rio Blanco, Nogales and Ciudad Mendoza. Today the most common and dangerous landslides are associated with unconsolidated volcanic deposits and heavy seasonal rains. In this paper, the cause, distribution, and link between landslides and the volcanic landscape relief susceptibility are analyzed. Similarly, the volume of displaced material is estimated in order to characterize the landslide instability in volcanic terrains. The Río El Estado watershed on the southwestern flank of Pico de Orizaba volcano is selected to describe and analyze susceptible areas of gravitational processes. The study area allows to show a systematic methodology for landslide mapping and volume calculation in areas with scarce information. The methodology encompasses three main stages of analysis. In the first stage, background information is collected to provide context and establish a generalized characterization of landslide processes, landsforms and volumes within the study area. Background information includes the following maps: topographic, geologic, land use, climate, slope, slope curvature, contributing area, flow direction, saturation, reclassified hypsomety, reclassified slope, and morphography. By retrieval and on-off switching of the background information in the GIS, a base map is created to assist in the digitizing of landslides. The base map and the theoretical aspects of the geomorphological mapping help to develop a conceptual base of support for mapping landslides. Landslides are digitized directly into a geographic information system (GIS, and in parallel, a spatial geodatabase of landslides attributes (eg. size, volume, activity, landslide type, etc. is constructed. Previous landslide mapping in the study area is verified and new landslides are added to the landslide

  1. Crowding by a repeating pattern.

    Rosen, Sarah; Pelli, Denis G


    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.

  2. The bi-directional transcriptional promoters for the latency-relating transcripts of the pp38/pp24 mRNAs and the 1.8 kb-mRNA in the long inverted repeats of Marek's disease virus serotype 1 DNA are regulated by common promoter-specific enhancers.

    Shigekane, H; Kawaguchi, Y; Shirakata, M; Sakaguchi, M; Hirai, K


    In cell lines established from Marek's disease tumors, several viral transcripts are expressed and among them the products of pp38/pp24 mRNA and 1.8 kb-mRNA have been suggested to be involved in viral oncogenicity. The long inverted repeats of Marek's Disease virus serotype 1 (MDV1) genome contain closely located transcriptional promoters for phosphorylated protein pp38/pp24 and 1.8 kb-mRNA. These promoters initiate transcription in opposite directions and are separated only by a short enhancer region, which is likely to regulate both promoters simultaneously. We have analyzed the transcription activity of these promoters in MDV1 (Md5 strain) infected CEF by transient expression of CAT reporter genes and found that the promoters were in fact active in infected cells and the promoter for 1.8 kb-mRNA was more active than the pp38/pp24 promoter. Deletion analysis of the short enhancer region revealed that the 30 bp region overlapping the enhancer elements for 1.8 kb-mRNA was important for promoter activity for pp38/pp24. The gel shift analysis revealed that nuclear factor(s) actually bound to the overlapping 30 bp region. In addition, the activity of these promoters in infected cells varied with MDV strains. These results suggest that pp38/pp24 and 1.8 kb-mRNA promoters share a common regulatory sequence but a viral or a cellular factor(s) induced by viral infection regulates the promoter by distinct mechanisms.

  3. Automatization and familiarity in repeated checking

    Dek, Eliane C P; van den Hout, Marcel A.; Giele, Catharina L.; Engelhard, Iris M.


    Repeated checking paradoxically increases memory uncertainty. This study investigated the underlying mechanism of this effect. We hypothesized that as a result of repeated checking, familiarity with stimuli increases, and automatization of the checking procedure occurs, which should result in decrea

  4. CDC Vital Signs: Preventing Repeat Teen Births

    ... file Error processing SSI file Preventing Repeat Teen Births Recommend on Facebook Tweet Share Compartir On this ... Too many teens, ages 15–19, have repeat births. Nearly 1 in 5 births to teens, ages ...

  5. Expanded complexity of unstable repeat diseases

    Polak, Urszula; McIvor, Elizabeth; Dent, Sharon Y.R.; Wells, Robert D.; Napierala, Marek.


    Unstable Repeat Diseases (URDs) share a common mutational phenomenon of changes in the copy number of short, tandemly repeated DNA sequences. More than 20 human neurological diseases are caused by instability, predominantly expansion, of microsatellite sequences. Changes in the repeat size initiate a cascade of pathological processes, frequently characteristic of a unique disease or a small subgroup of the URDs. Understanding of both the mechanism of repeat instability and molecular consequen...

  6. Hawaiian Volcano Flank Stability Appraised From Strength Testing the Hawaiian Scientific Drilling Project's (HSDP) 3.1-km Drill Core

    Thompson, N.; Watters, R. J.; Schiffman, P.


    the means of the basaltic flows, intrusive and pillow lava values. The test results imply that shallow rotational slumps that develop within the upper few kilometers of spreading Hawai'ian volcanoes within low strength, poorly-consolidated, smectite-rich hyaloclastites are similar to those we have found from the incipient and smectitic alteration zones of the HSDP cores. Deeper slumps might be directed through over-pressured pillow lava units as a result of the stronger pillow lava units permitting deeper failure surfaces to develop. Petrographically the Mauna Kea hyaloclastites appear similar to those from actively spreading Hawai'ian shield volcanoes. Alteration processes apparently affect the strength of these hyaloclastites. In the shallower zones of incipient and smectitic alteration, hyaloclastites generally retain their high primary porosities. In the deeper, palagonitic zone of alteration, the hyaloclastites gain both compressive and shear strength, primarily through consolidation and zeolitic cementation. The marked strength contrast between hyaloclastites, and the lavas that overlie and underlie them is significant, and may be a primary factor in localizing the destabilization of the flanks of Hawaiian volcanoes.

  7. 47 CFR 97.205 - Repeater station.


    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Repeater station. 97.205 Section 97.205... SERVICE Special Operations § 97.205 Repeater station. (a) Any amateur station licensed to a holder of a Technician, General, Advanced or Amateur Extra Class operator license may be a repeater. A holder of...

  8. 47 CFR 22.1015 - Repeater operation.


    ... 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...

  9. ProtRepeatsDB: a database of amino acid repeats in genomes

    Chauhan Virander S


    Full Text Available Abstract Background Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repeats constitute vital functional and structural regions in proteins. Repeats are of great consequence in evolution of proteins, as evident from analysis of repeats in different organisms. In the post genomic era, availability of protein sequences encoded in different genomes provides a unique opportunity to perform large scale comparative studies of amino acid repeats. ProtRepeatsDB is a relational database of perfect and mismatch repeats, access to which is designed as a resource and collection of tools for detection and cross species comparisons of different types of amino acid repeats. Description ProtRepeatsDB (v1.2 consists of perfect as well as mismatch amino acid repeats in the protein sequences of 141 organisms, the genomes of which are now available. The web interface of ProtRepeatsDB consists of different tools to perform repeat s; based on protein IDs, organism name, repeat sequences, and keywords as in FASTA headers, size, frequency, gene ontology (GO annotation IDs and regular expressions (REGEXP describing repeats. These tools also allow formulation of a variety of simple, complex and logical queries to facilitate mining and large-scale cross-species comparisons of amino acid repeats. In addition to this, the database also contains sequence analysis tools to determine repeats in user input sequences. Conclusion ProtRepeatsDB is a multi-organism database of different types of amino acid repeats present in proteins. It integrates useful tools to perform genome wide queries for rapid screening and identification of amino acid repeats and facilitates comparative and evolutionary studies of the repeats. The database is useful for identification of species or organism specific

  10. A-T linker adapter polymerase chain reaction for determining flanking sequences by rescuing inverse PCR or thermal asymmetric interlaced PCR products.

    Trinh, Quoclinh; Zhu, Pengyu; Shi, Hui; Xu, Wentao; Hao, Junran; Luo, Yunbo; Huang, Kunlun


    The polymerase chain reaction (PCR)-based genome walking method has been extensively used to isolate unknown flanking sequences, whereas nonspecific products are always inevitable. To resolve these problems, we developed a new strategy to isolate the unknown flanking sequences by combining A-T linker adapter PCR with inverse PCR (I-PCR) or thermal asymmetric interlaced PCR (TAIL-PCR). The result showed that this method can be efficiently achieved with the flanking sequence from the Arabidopsis mutant and papain gene. Our study provides researchers with an additional method for determining genomic DNA flanking sequences to identify the target band from bulk of bands and to eliminate the cloning step for sequencing.

  11. Soil salinity data from Grand Liard Bayou and flanking marshes, New Orleans, LA, 2015-12-01 to 2016-03-30 (NCEI Accession 0151634)

    National Oceanic and Atmospheric Administration, Department of Commerce — The project restored both structural and habitat functions of Grand Liard Bayou and flanking marshes. The project created and nourished marsh and restored a ridge on...

  12. Soil salinity data from Bayou Dupont and flanking marshes, New Orleans, LA, 2015-09-16 to 2016-03-30 (NCEI Accession 0151633)

    National Oceanic and Atmospheric Administration, Department of Commerce — The project restored both structural and habitat functions of Bayou Dupont and flanking marshes. The project created and nourished marsh and restored a ridge on the...

  13. Characterization of simple sequence repeats (SSRs from Phlebotomus papatasi (Diptera: Psychodidae expressed sequence tags (ESTs

    Hamarsheh Omar


    Full Text Available Abstract Background Phlebotomus papatasi is a natural vector of Leishmania major, which causes cutaneous leishmaniasis in many countries. Simple sequence repeats (SSRs, or microsatellites, are common in eukaryotic genomes and are short, repeated nucleotide sequence elements arrayed in tandem and flanked by non-repetitive regions. The enrichment methods used previously for finding new microsatellite loci in sand flies remain laborious and time consuming; in silico mining, which includes retrieval and screening of microsatellites from large amounts of sequence data from sequence data bases using microsatellite search tools can yield many new candidate markers. Results Simple sequence repeats (SSRs were characterized in P. papatasi expressed sequence tags (ESTs derived from a public database, National Center for Biotechnology Information (NCBI. A total of 42,784 sequences were mined, and 1,499 SSRs were identified with a frequency of 3.5% and an average density of 15.55 kb per SSR. Dinucleotide motifs were the most common SSRs, accounting for 67% followed by tri-, tetra-, and penta-nucleotide repeats, accounting for 31.1%, 1.5%, and 0.1%, respectively. The length of microsatellites varied from 5 to 16 repeats. Dinucleotide types; AG and CT have the highest frequency. Dinucleotide SSR-ESTs are relatively biased toward an excess of (AXn repeats and a low GC base content. Forty primer pairs were designed based on motif lengths for further experimental validation. Conclusion The first large-scale survey of SSRs derived from P. papatasi is presented; dinucleotide SSRs identified are more frequent than other types. EST data mining is an effective strategy to identify functional microsatellites in P. papatasi.

  14. Post-translational processing of surfactant protein-C proprotein: targeting motifs in the NH(2)-terminal flanking domain are cleaved in late compartments.

    Johnson, A L; Braidotti, P; Pietra, G G; Russo, S J; Kabore, A; Wang, W J; Beers, M F


    Rat surfactant protein (SP)-C is a 3.7-kD hydrophobic lung-specific protein generated from proteolytic processing of a 21-kD propeptide (SP-C(21)). We have demonstrated that initial post-translational processing of SP-C(21) involves two cleavages of the COOH-terminus (Beers and colleagues, J. Biol. Chem. 1994;269:20,318--20,328). The goal of the current study was to define processing and function of the NH(2)-terminal flanking domain. Epitope-specific antisera directed against spatially distinct regions of the NH(2) terminus, NPROSP-C(2-9) (epitope = D(2)-L(9)) and NPROSP-C(11-23) (= E(11)-Q(23)) were produced. By Western blotting, both antisera identified SP-C(21) in microsomes. A 6-kD form (SP-C(6)), enriched in lamellar bodies (LBs), was detected only by NPROSP-C(11-23) and not extractable with NaCO(3) treatment. Immunogold staining of ultrathin lung sections with NPROSP-C(11-23) identified proSP-C in both multivesicular bodies (mvb) and LBs whereas NPROSP-C(2-9) labeled only mvb. (35)S-pulse chase analysis demonstrated synthesis of SP-C(21) and three intermediate forms (SP-C(16), SP-C(7), and SP-C(6)). Complete processing involved four separate cleavages with a precursor- product relationship between the low molecular weight forms SP-C(7) and SP-C(6). Fluorescence microscopy of A549 cells expressing fusion proteins of enhanced green fluorescent protein (EGFP) and proSP-C NH(2)-terminal deletion mutants showed targeting of EGFP/SP-C(1-194) and EGFP/SP-C(10-194) to early endosomal antigen-1-negative, CD-63-positive cytoplasmic vesicles whereas EGFP/SP-C(19-194), EGFP/SP-C(Delta 10-18), and EGFP/SP-C(24-194) were restricted to the endoplasmic reticulum (ER). We conclude that synthetic processing includes a previously unrecognized cleavage of the proximal NH(2) terminus (M(1)-L(9)), which occurs after removal of COOH-flanking domains (H(59)-I(194)) but before packaging in LBs, and that the region M(10)-T(18) is required for targeting of proSP-C to post-ER vesicular

  15. IODP Expedition 327 and Atlantis Expedition AT 18-07: Observatories and Experiments on the Eastern Flank of the Juan de Fuca Ridge

    the IODP Expedition 327 and Atlantis Expedition AT18-07 Shipboard Parties


    Full Text Available Integrated Ocean Drilling Program (IODP Expedition 327 (summer 2010 was designed to resolve the nature of fluid-rock interactions in young, upper volcanic crust on the eastern flank of the Juan de Fuca Ridge. Expedition 327 drilled, cased and cored two new basement holes, conducted hydrogeologic experiments, and installed subseafloorborehole observatories (Circulation Obviation Retrofit Kits, CORKs. These CORKs were intended to allow borehole conditions to recover to a more natural state after the dissipation of disturbances caused by drilling, casing, and other operations; provide a long-term monitoring and sampling presence for determining fluid pressure, temperature, composition,and microbiology; and facilitate the completion of active experiments to resolve crustal hydrogeologic conditions and processes. Expedition 327 was followed (summer2011 by R/V Atlantis Expedition AT18-07, with the remotely-operated vehicle (ROV Jason, to service these CORKs, collect subseafloor pressure data, recover and deploy autonomous fluid and microbial samplers, collect large volumes of borehole fluids, and initiate a cross-hole hydrogeologic experiment using an electromagnetic flowmeter. In addition, Atlantis Expedition AT18-07 refurbished an old CORK that could not be replaced during IODP Expedition 327, completing a critical part of the three-dimensional observation network that is currently being used to monitor a large-scale, directional formation response to long-term fluid flow from the crust.

  16. The nexus of soil radon and hydrogen dynamics and seismicity of the northern flank of the Kuril-Kamchatka subduction zone

    O. P. Malysheva


    Full Text Available The comparison of kinematics and dynamic parameters of radon and molecular hydrogen concentration in subsoil air on the stations network at the Petropavlovsk-Kamchatsky geodynamic proving ground with seismicity of the northern flank of the Kuril-Kamchatka subduction zone was fulfilled in the period from July till August 2004. On the basis of correlation analysis of the regional seismicity and variations of radon flux density calculated using the data of gas-discharge counters of STS-6 type and SSNTDs it was shown that the radon mass transfer abnormal variations are conditioned by both regional seismicity in total and the subduction zone of proving ground. The azimuths of «geodeformation waves» coming to the registration points are calculated during clearly expressed anomaly beginnings, which coincide with directions to earthquake epicenters taking place at the same time. The geochemical anomalies recorded are presumptively deformative by nature and can be conditioned by processes of «quasi-viscous» flow of the lithosphere during rearrangement of tectonic stress fields of the subduction zone. The short-term (predicted time ? <14 days precursor of the earthquakes swarm was revealed in hydrogen dynamics on August, 4-5 (four earthquakes had M?5.3 and epicentral distance about 130 km from the Paratunka base station.

  17. Numerical modeling of tsunami waves generated by the flank collapse of the Cumbre Vieja Volcano (La Palma, Canary Islands): Tsunami source and near field effects

    Abadie, S. M.; Harris, J. C.; Grilli, S. T.; Fabre, R.


    In this work, we study waves generated by the potential collapse of the west flank of the Cumbre Vieja Volcano (CVV; La Palma, Canary Island, Spain) through numerical simulations performed in two stages: (i) the initial slide motion and resulting free surface elevation are first calculated using a 3D Navier-Stokes model; (ii) generated waves are then input into a 2D (horizontal) Boussinesq model to further simulate propagation to the nearby islands. Unlike in earlier work on CVV, besides a similar extreme slide volume scenario of 450 km3, in our simulations: (i) we consider several slide scenarios featuring different volumes (i.e., 20, 40, 80 km3), which partly result from a geotechnical slope stability analysis; (ii) we use a more accurate bathymetry; and (iii) an incompressible version of a multiple-fluid/material Navier-Stokes model. We find wave trains for each scenario share common features in terms of wave directivity, frequency, and time evolution, but maximum elevations near CVV significantly differ, ranging from 600 to 1200 m (for increasing slide volume). Additionally, our computations show that significant energy transfer from slide to waves only lasts for a short duration (order 200 s), which justifies concentrating our best modeling efforts on the early slide motion phase. The anticipated consequences of such wave trains on La Palma and other Canary Islands are assessed in detail in the paper.

  18. Molecular cloning, SNP detection and association analysis of 5' flanking region of the goat IGF1 gene with prolificacy.

    Thomas, Naicy; Venkatachalapathy, Thirupathy; Aravindakshan, Thazhathuveettil; Raghavan, K C


    The insulin-like growth factor 1 has an important role in reproduction, foetal development and growth. It regulates the secretion of gonadotrophin releasing hormone, stimulates ovarian function and steroidogenesis. The present study was conducted to characterise the 5' flanking region of goat IGF 1 gene, ascertain ovarian expression of the IGF1 gene, detect SNPs and assess the association with prolificacy in the two indigenous goat breeds of South India viz., low prolific Attappady Black and high prolific Malabari. The 5' flanking region of IGF1 gene was PCR amplified, cloned and sequenced from both breeds. Genotyping was performed in 277 goats from the two genetic groups using the PCR-Single Strand Conformational Polymorphism (SSCP) and the expression of the IGF1 gene in the ovary was analysed by quantitative real time PCR. The 5' flanking region of the IGF1 gene was 601 bp long and located at 450 bp upstream of the start codon. Sequence exhibited 97-99% similarity with that of the sheep, cattle and sika deer IGF1 genes. Three genotypes, PP, PQ and QR were observed at this locus with the frequency of 0.62, 0.30 and 0.08, respectively. Sequencing of the representative PCR products from each genotype revealed two SNPs, g.224A>G and g.227C>T. The population was found to be in Hardy-Weinberg disequilibrium at both loci. Statistical results indicated that these loci were associated with litter size (P ≤ 0.05). However, no significant difference was found in the expression of the IGF1 gene in the ovaries of the two goat breeds. These results suggest the significant influence of the IGF1 gene on prolificacy in goats and identified SNPs would benefit the selection of prolific animals in future breeding programs.


    Lisa eNigro


    Full Text Available The microbiology of subsurface, hydrothermally-influenced basaltic crust flanking mid-ocean ridges has remained understudied, due to the difficulty in accessing the subsurface environment. The instrumented boreholes resulting from scientific ocean drilling offer access to samples of the formation fluids circulating through oceanic crust. We analyzed the phylogenetic diversity of bacterial communities of fluid and microbial mat samples collected in situ from the observatory at Ocean Drilling Program Hole 896A, drilled into ~6.5-million-year-old basaltic crust on the flank of the Costa Rica Rift in the equatorial Pacific Ocean. Bacterial 16S rRNA gene sequences recovered from borehole fluid and from a microbial mat coating the outer surface of the fluid port revealed both unique and shared phylotypes. The dominant bacterial clones from both samples were related to the autotrophic, sulfur-oxidizing genus Thiomicrospira. Both samples yielded diverse gamma- and alphaproteobacterial phylotypes, as well as members of the Bacteroidetes, Planctomycetes, and Verrucomicrobia. Analysis of ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO genes (cbbL and cbbM from the sampling port mat and from the borehole fluid demonstrated autotrophic carbon assimilation potential for in-situ microbial communities; most cbbL genes were related to those of the sulfur-oxidizing genera Thioalkalivibrio and Thiomicrospira, and cbbM genes were affiliated with uncultured phyloytypes from hydrothermal vent plumes and marine sediments. Several 16S rRNA gene phylotypes from the 896A observatory grouped with phylotypes recovered from seawater-exposed basalts and sulfide deposits at inactive hydrothermal vents, but there is little overlap with hydrothermally-influenced basaltic boreholes 1026B and U1301A on the Juan de Fuca Ridge flank, suggesting that site-specific characteristics of Hole 896A (i.e. seawater mixing into borehole fluids affect the microbial community

  20. Pentatricopeptide repeat proteins in plants.

    Barkan, Alice; Small, Ian


    Pentatricopeptide repeat (PPR) proteins constitute one of the largest protein families in land plants, with more than 400 members in most species. Over the past decade, much has been learned about the molecular functions of these proteins, where they act in the cell, and what physiological roles they play during plant growth and development. A typical PPR protein is targeted to mitochondria or chloroplasts, binds one or several organellar transcripts, and influences their expression by altering RNA sequence, turnover, processing, or translation. Their combined action has profound effects on organelle biogenesis and function and, consequently, on photosynthesis, respiration, plant development, and environmental responses. Recent breakthroughs in understanding how PPR proteins recognize RNA sequences through modular base-specific contacts will help match proteins to potential binding sites and provide a pathway toward designing synthetic RNA-binding proteins aimed at desired targets.

  1. Two-dimensional quantum repeaters

    Wallnöfer, J.; Zwerger, M.; Muschik, C.; Sangouard, N.; Dür, W.


    The endeavor to develop quantum networks gave rise to a rapidly developing field with far-reaching applications such as secure communication and the realization of distributed computing tasks. This ultimately calls for the creation of flexible multiuser structures that allow for quantum communication between arbitrary pairs of parties in the network and facilitate also multiuser applications. To address this challenge, we propose a two-dimensional quantum repeater architecture to establish long-distance entanglement shared between multiple communication partners in the presence of channel noise and imperfect local control operations. The scheme is based on the creation of self-similar multiqubit entanglement structures at growing scale, where variants of entanglement swapping and multiparty entanglement purification are combined to create high-fidelity entangled states. We show how such networks can be implemented using trapped ions in cavities.

  2. General benchmarks for quantum repeaters

    Pirandola, Stefano


    Using a technique based on quantum teleportation, we simplify the most general adaptive protocols for key distribution, entanglement distillation and quantum communication over a wide class of quantum channels in arbitrary dimension. Thanks to this method, we bound the ultimate rates for secret key generation and quantum communication through single-mode Gaussian channels and several discrete-variable channels. In particular, we derive exact formulas for the two-way assisted capacities of the bosonic quantum-limited amplifier and the dephasing channel in arbitrary dimension, as well as the secret key capacity of the qubit erasure channel. Our results establish the limits of quantum communication with arbitrary systems and set the most general and precise benchmarks for testing quantum repeaters in both discrete- and continuous-variable settings.

  3. Hungarian repeat station survey, 2010

    Péter Kovács


    Full Text Available The last Hungarian repeat station survey was completed between October 2010 and February 2011. Declination, inclination and the total field were observed using one-axial DMI fluxgate magnetometer mounted on Zeiss20A theodolite and GSM 19 Overhauser magnetometer. The magnetic elements of the sites were reduced to the epoch of 2010.5 on the basis of the continuous recordings of Tihany Geophysical Observatory. In stations located far from the reference observatory, the observations were carried out in the morning and afternoon in order to decrease the effect of the distant temporal correction. To further increase the accuracy, on-site dIdD variometer has also been installed near the Aggtelek station, in the Baradla cave, during the survey of the easternmost sites. The paper presents the technical details and the results of our last campaign. The improvement of the accuracy of the temporal reduction by the use of the local variometer is also reported.

  4. Structural analysis of the 5 prime flanking region of the. beta. -globin gene in African sickle cell anemia patients: Further evidence for three origins of the sickle cell mutation in Africa

    Chebloune, Y.; Pagnier, J.; Trabuchet, G.; Faure, C.; Verdier, G.; Labie, D.; Nigon, V. (Universite Claude Bernard-Lyon, Villeurbane (France))


    Haplotype analysis of the {beta}-globin gene cluster shows two regions of DNA characterized by nonrandom association of restriction site polymorphisms. These regions are separated by a variable segment containing the repeated sequences (ATTTT){sub n} and (AT){sub x}T{sub y}, which might be involved in recombinational events. Studies of haplotypes linked to the sickle cell gene in Africa provide strong argument for three origins of the mutation: Benin, Senegal, and the Central African Republic. The structure of the variable segment in the three African populations was studied by S1 nuclease mapping of genomic DNA, which allows a comparison of several samples. A 1080-base-pair DNA segment was sequenced for one sample from each population. S1 nuclease mapping confirmed the homogeneity of each population with regard to both (ATTTT){sub n} and (AT){sub x}T{sub y} repeats. The authors found three additional structures for (AT){sub x}T{sub y} correlating with the geographic origin of the patients. Ten other nucleotide positions, 5{prime} and 3{prime} to the (AT){sub x}T{sub y} copies, were found to be variable when compared to homologous sequences from human and monkey DNAs. These results allow us to propose an evolutionary scheme for the polymorphisms in the 5{prime} flanking region of the {beta}-globin gene. The results strongly support the hypothesis of three origins for the sickle mutation in Africa.

  5. Connections between hyper-acid crater lakes and flank springs: new evidence from Rincón de la Vieja volcano (Costa Rica)

    Martínez, M.; Fernández, E.; Sáenz, W.; van Bergen, M. J.; Ayres, G.; Pacheco, J. F.; Brenes, J.; Avard, G.; Malavassi, E.


    Rincón de la Vieja, a complex andesitic stratovolcano in NW Costa Rica, shows various hydrothermal surface manifestations that comprise: (1) A hyper-acid crater lake and subaerial fumaroles receiving direct input of fluids of magmatic origin, (2) Acid thermal discharges along the northeastern slopes of the volcano that feed the headwaters of the Cucaracho river, and (3) Small lakes and a geothermal field with bubbling-boiling mud pools, acid-sulfate springs, steaming ground and fumarolic emissions in a region on the western flank. Here the streams are of relatively low flow rate and their chemical signatures correspond to that of deep fluids from an extensive geothermal reservoir mixed with shallow meteoric water. Physico-chemical properties of the sulfate-chloride hyper-acid lake (T=28-58 °C; pH between 1.2 and water body supplied by a significant input of chemical components derived from hydrolysis of magmatic volatiles and from intense rock leaching. The Cucaracho catchment receives input from warm acid brines with no free-gas phase but carrying a high load of hydrolyzed magmatic volatiles and rock-forming elements. One of these brines (Spring 4) is characterized by a sulfate-chloride chemical signature, medium temperatures of 27-38 °C, pH between 2 and 4 and TDS values between 780 and 1300 mg/L. Based on water and heat-balance considerations, chemical and stable-isotope signatures and groundwater transport modeling, it has been proposed that these acid springs represent brine water from the lake-hydrothermal system that is diluted by shallow groundwater permeating tephra layers (Kempter and Rowe, 2000). Since Rincóńs latest phreatomagmatic activity in 1983, episodes of phreatic eruptions from the crater lake have been registered in 1983-87, 1991, 1995, 1998 and 2011. Some of these eruptions (VEI 1) have expelled large quantities of lake water, triggering small to medium- sized fast-moving acidic lahars running along effluents of the Cucaracho River. They

  6. Quality control during repeated fryings

    Cuesta, C.


    Full Text Available Most of the debate ¡s about how the slow or frequent turnover of fresh fat affects the deterioration, of fat used in frying. Then, the modification of different oils used in repeated fryings of potatoes without or with turnover of fresh oil, under similar frying conditions, was evaluated by two criteria: by measuring the total polar component isolated by column chromatography and by the evaluation of the specific compounds related to thermoxidative and hydrolytic alteration by High Performance Size Exclusion Chromatography (HPSEC. The results indicate that with frequent turnover of fresh oil, the critical level of 25% of polar material is rarely reached, and there are fewer problems with fat deterioration because the frying tended to increase the level of polar material and thermoxidative compounds (polymers and dimers of triglycerides and oxidized triglycerides in the fryer oil during the first fryings, followed by minor changes and a tendency to reach a near-steady state in successive fryings. However, in repeated frying of potatoes using a null turnover the alteration rate was higher being linear the relationship found between polar material or the different thermoxidative compounds and the number of fryings. On the other hand chemical reactions produced during deep-fat frying can be minimized by using proper oils. In addition the increased level of consumers awareness toward fat composition and its impact on human health could had an impact on the selection of fats for snacks and for industry. In this way monoenic fats are the most adequate from a nutritional point of view and for its oxidative stability during frying.

  7. The hercynian compressive then extensive tectonic of the north flank of the Montagne Noire (southern French Massif Central)

    Turpaud, P.; Matte, P.


    The Montagne Noire, (southernmost edge of the Massif Central) is well known on its southern flank by low-grade spectacular hercynian nappes and southward recumbent folds. The northern flank, much less known is separated from the southern nappes by a large high grade metamorphic dome, the Axial Zone, which has been interpreted either as a purely extensive metamorphic core complex or as a compressive migmatitic antiform. The northern flank made of Lower Paleozoic epizonal sediments and granitic orthogneisses was previously interpreted as tectonic units separated by, NE-SW trending, southeastward verging thrusts. Our recent kinematic study shows a more complex structure and history: -- Some of the so-called southeastward thrusts (Brusque area) are in fact large, kilometre thick, ductile sinistral shear-zones with a southwestward thrust component (Guérangé-Lozes et Alsac, 1986), southward verging folds and slaty cleavage. That is the first major deformation in the Northern Montagne Noire and it is still undated. -- Closer to the Axial dome, in the Lacaune area, the most conspicuous structures are younger and related to large northeastward detachment with a LP/MT metamorphism. NE-SW trending lineations are here significant of a strong top to the NE shearing well expressed by fish-like biotites, synkinematic cordierites with helicitic inclusion trails, asymmetric boudinage and F2 northeastward drag folds. This spectacular detachment tectonic, which affects as well the whole northern flank of the granitic-gneissic Axial Zone, is dated by Ar39/Ar40 laser method on synkinematic micas at about 300--310 Ma. This event helped to the exhumation and denudation of the gneissic Axial Zone, just before the deposit of Stephanian limnic coal basins. The MT/BP metamophism is contemporaneous of the ductile detachment tectonic but some clues of gaps of metamorphism in the PT section indicate probably late normal faults with the same kinematics but posterior to the metamorphic climax

  8. Thermal-rheological structure of lithosphere beneath the northern flank of Tarim Basin, western China:Implications for geodynamics

    LIU; Shaowen; WANG; Liangshu; LI; Cheng; LI; Hua; HAN; Yong


    Based on the data of geo-temperature and thermophysical parameters of rocks in the Kuqa Depression and the Tabei Uplift, northern flank of the Tarim Basin, in terms of the analytical solution of 1-D heat transfer equation, the thermal structure of the lithosphere under this region is determined. Our results show that the average surface heat flow of the northern flank of the Tarim Basin is 45 mW/m2, and the mantle heat flow is between 20 and 23 mW/m2; the temperature at crust-mantle boundary (Moho) ranges from 514℃ to 603℃ and the thermal lithosphere where the heat conduction dominates is 138-182 km thick. Furthermore, in combination with the P wave velocity structure resulting from the deep seismic sounding profile across this region and rheological modeling, we have studied the local composition of the lithosphere and its rheological profile, as well as the strength distribution. We find that the rheological stratification of the lithosphere in this region is apparent. The lowermost of the lower crust is ductile; however,the uppermost of the mantle and the upper and middle parts of the crust are both brittle layers,which is typically the so-called sandwich-like structure. Lithospheric strength is also characterized by the lateral variation, and the uplift region is stronger than the depression region. The lithospheric strength of the northem flank of the Tarim Basin decreases gradually from south to north; the Kuqa Depression has the lowest strength and the south of the Tabei Uplift is strongest.The total lithospheric strength of this region is 4.77× 1012-5.03 × 1013 N/m under extension, and 6.5 × 1012-9.4× 1013 N/m under compression. The lithospheric brittle-ductile transition depth is between 20 km and 33 km. In conclusion, the lithosphere of the northern flank of the Tarim Basin is relatively cold with higher strength, so it behaves rigidly and deforms as a whole, which is also supported by the seismic activity in this region. This rigidity of the

  9. 3C3D VSP Imaging of Salt Flanks Using Converted Waves in the Gulf of Mexico

    Li, Y.; Doherty, F.; Jackson, J.


    Locating salt boundary and imaging updip sediment structures flanking the salt domes are very important tasks for exploration in the Gulf of Mexico since major petroleum reserves are often trapped underneath overhangs of diapiric salt domes. Although the top of salt and less steep structures can be well imaged using current surface seismic methods, the steep sides of a salt dome with irregularly shapes are hard to image with adequate accuracy. Thus, Vertical Seismic Profiling (VSP) surveys with three-component (3C) receivers in wells are usually requested for improving images of subsurface structures. Conventional multi-offset VSP (OVSP) and refraction salt proximity (SP) surveys are widely applied in the Gulf of Mexico to improve images of slat interfaces, sub-salt and salt flank structures using P waves. In this paper, we will focus on using converted waves to image the steep salt-sediment boundary. A VSP dataset, including multi-OVSP and a SP survey, acquired in the Gulf of Mexico was used in this study. We analyzed 3C OVSP data to identify and separate converted waves, such as PS, P-SP, P-SS, generated at a salt boundary. Then both PP wave and converted waves were 3C3D depth migrated to generate images of the steep salt-sediment interface. Both transmitted P-P and P-S converted waves from the SP survey were used to calculate 3D salt exit points which delineate the steep salt face. The VSP results derived from both methods are abundant and a suitable 3D visualization tool is required for visual integration and interpretation. The image volumes and other available geophysical and geological data were integrated using a 3D visualization tool specially designed for VSP solutions. The migrated images using PP and converted waves provides a precise and complete definition of the steep salt face and reservoir sands flanking the salt dome. This study indicates that both reflection and reflection surveys can result in a consistent location of the steep salt flank

  10. Amplification, analysis and chromosome mapping of novel homeobox-containing and homeobox-flanking sequences in rice

    刘国振; 严长杰; 翟文学; 何平; 杨江; 李小兵; 朱立煌


    Homeobox genes, widely distributed among animal and plant kingdoms, play an important role in developmental process. Several homeobox conserved fragments were amplified by PCR and the flanking regions were also obtained by an LM-PCR procedure. Sequencing and Southern analysis showed that they belong to a homeobox gene family of rice. Six homeobox-containing fragments were mapped on the molecular linkage map of rice. They were located on chromosomes 3, 4 and 7 respectively. It is noteworthy that there are 4 homeobox fragments located on rice chromosome 3 and the result is also consistent with the comparative genomics between rice and maize.

  11. Sistema Faro, Isla de Mona, Puerto Rico: speleogenesis of the worlds largest flank margin cave; Sistema Faro, Isla de Mona, Puerto Rico: espeleogenesis de la cueva del tipo flank margin mas grande del mundo

    Lace, M. J.; Kambesis, P. N.; Mylroie, J. E.


    Isla de Mona, a small, uplifted carbonate plateau jutting out of the waters of the Mona Passage, is an incredibly fragile and densely karstic environment. Expedition work was conducted by the Isla de Mona Project in cooperation with the Departamento Recursos Naturales y Ambientales de Puerto Rico (DRNA), including contributions from many researchers and cavers volunteering from across the U.S and Puerto Rico in the course of 12 separate expeditions, spanning a 14 year period (1998 to 2013). Over 200 caves have been documented on the island to date, the majority of this inventory is composed of flank margin caves but also includes sea caves, pit caves and talus caves. The most extensive example of cave development on the island is Sistema Faro - a sprawling maze-like series of chambers formed within the eastern point of the island with over 40 cliffside entrances overlooking the Caribbean Sea. Detailed cartography and analysis of the geomorphology and development of the Sistema Faro has helped form a complex model of carbonate island cave development as a function of tectonic uplift, lithology, sea level changes, karst hydrogeology and cliff retreat. This communication examines the roles these controls have played in the genesis of the world's largest flank margin cave. (Author)

  12. Sequence breakpoints in the aflatoxin biosynthesis gene cluster and flanking regions in nonaflatoxigenic Aspergillus flavus isolates.

    Chang, Perng-Kuang; Horn, Bruce W; Dorner, Joe W


    Aspergillus flavus populations are genetically diverse. Isolates that produce either, neither, or both aflatoxins and cyclopiazonic acid (CPA) are present in the field. We investigated defects in the aflatoxin gene cluster in 38 nonaflatoxigenic A. flavus isolates collected from southern United States. PCR assays using aflatoxin-gene-specific primers grouped these isolates into eight (A-H) deletion patterns. Patterns C, E, G, and H, which contain 40 kb deletions, were examined for their sequence breakpoints. Pattern C has one breakpoint in the cypA 3' untranslated region (UTR) and another in the verA coding region. Pattern E has a breakpoint in the amdA coding region and another in the ver1 5'UTR. Pattern G contains a deletion identical to the one found in pattern C and has another deletion that extends from the cypA coding region to one end of the chromosome as suggested by the presence of telomeric sequence repeats, CCCTAATGTTGA. Pattern H has a deletion of the entire aflatoxin gene cluster from the hexA coding region in the sugar utilization gene cluster to the telomeric region. Thus, deletions in the aflatoxin gene cluster among A. flavus isolates are not rare, and the patterns appear to be diverse. Genetic drift may be a driving force that is responsible for the loss of the entire aflatoxin gene cluster in nonaflatoxigenic A. flavus isolates when aflatoxins have lost their adaptive value in nature.

  13. Long tract of untranslated CAG repeats is deleterious in transgenic mice.

    Ren-Jun Hsu

    Full Text Available The most frequent trinucleotide repeat found in human disorders is the CAG sequence. Expansion of CAG repeats is mostly found in coding regions and is thought to cause diseases through a protein mechanism. Recently, expanded CAG repeats were shown to induce toxicity at the RNA level in Drosophila and C. elegans. These findings raise the possibility that CAG repeats may trigger RNA-mediated pathogenesis in mammals. Here, we demonstrate that transgenic mice expressing EGFP transcripts with long CAG repeats in the 3' untranslated region develop pathogenic features. Expression of the transgene was directed to the muscle in order to compare the resulting phenotype to that caused by the CUG expansion, as occurs in myotonic dystrophy. Transgenic mice expressing 200, but not those expressing 0 or 23 CAG repeats, showed alterations in muscle morphology, histochemistry and electrophysiology, as well as abnormal behavioral phenotypes. Expression of the expanded CAG repeats in testes resulted in reduced fertility due to defective sperm motility. The production of EGFP protein was significantly reduced by the 200 CAG repeats, and no polyglutamine-containing product was detected, which argues against a protein mechanism. Moreover, nuclear RNA foci were detected for the long CAG repeats. These data support the notion that expanded CAG repeat RNA can cause deleterious effects in mammals. They also suggest the possible involvement of an RNA mechanism in human diseases with long CAG repeats.

  14. Associations between inverted repeats and the structural evolution of bacterial genomes.

    Achaz, Guillaume; Coissac, Eric; Netter, Pierre; Rocha, Eduardo P C


    The stability of the structure of bacterial genomes is challenged by recombination events. Since major rearrangements (i.e., inversions) are thought to frequently operate by homologous recombination between inverted repeats, we analyzed the presence and distribution of such repeats in bacterial genomes and their relation to the conservation of chromosomal structure. First, we show that there is a strong under-representation of inverted repeats, relative to direct repeats, in most chromosomes, especially among the ones regarded as most stable. Second, we show that the avoidance of repeats is frequently associated with the stability of the genomes. Closely related genomes reported to differ in terms of stability are also found to differ in the number of inverted repeats. Third, when using replication strand bias as a proxy for genome stability, we find a significant negative correlation between this strand bias and the abundance of inverted repeats. Fourth, when measuring the recombining potential of inverted repeats and their eventual impact on different features of the chromosomal structure, we observe a tendency of repeats to be located in the chromosome in such a way that rearrangements produce a smaller strand switch and smaller asymmetries than expected by chance. Finally, we discuss the limitations of our analysis and the influence of factors such as the nature of repeats, e.g., transposases, or the differences in the recombination machinery among bacteria. These results shed light on the challenges imposed on the genome structure by the presence of inverted repeats.

  15. Implementation of bipartite or remote unitary gates with repeater nodes

    Yu, Li; Nemoto, Kae


    We propose some protocols to implement various classes of bipartite unitary operations on two remote parties with the help of repeater nodes in-between. We also present a protocol to implement a single-qubit unitary with parameters determined by a remote party with the help of up to three repeater nodes. It is assumed that the neighboring nodes are connected by noisy photonic channels, and the local gates can be performed quite accurately, while the decoherence of memories is significant. A unitary is often a part of a larger computation or communication task in a quantum network, and to reduce the amount of decoherence in other systems of the network, we focus on the goal of saving the total time for implementing a unitary including the time for entanglement preparation. We review some previously studied protocols that implement bipartite unitaries using local operations and classical communication and prior shared entanglement, and apply them to the situation with repeater nodes without prior entanglement. We find that the protocols using piecewise entanglement between neighboring nodes often require less total time compared to preparing entanglement between the two end nodes first and then performing the previously known protocols. For a generic bipartite unitary, as the number of repeater nodes increases, the total time could approach the time cost for direct signal transfer from one end node to the other. We also prove some lower bounds of the total time when there are a small number of repeater nodes. The application to position-based cryptography is discussed.

  16. The diversity and evolution of Wolbachia ankyrin repeat domain genes.

    Stefanos Siozios

    Full Text Available Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intra-genic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions.

  17. Enhanced detection of polymicrobic bacteremia by repeat subculture of previously positive blood cultures.

    Hansen, S.L.; Hetmanski, J


    Blood subcultures repeated 3 days after the cultures were first identified as positives increased our detection of polymicrobic bacteremia in 9.1 to 27% of clinically significant patient episodes. Reincubation and repeated subculture of previously positive blood cultures had a direct impact on the therapeutic management of patients with polymicrobic bacteremia.

  18. Methods for sequencing GC-rich and CCT repeat DNA templates

    Robinson, Donna L.


    The present invention is directed to a PCR-based method of cycle sequencing DNA and other polynucleotide sequences having high CG content and regions of high GC content, and includes for example DNA strands with a high Cytosine and/or Guanosine content and repeated motifs such as CCT repeats.

  19. Nitrogen Stimulates the Growth of Subsurface Basalt-associated Microorganisms at the Western Flank of the Mid-Atlantic Ridge.

    Zhang, Xinxu; Fang, Jing; Bach, Wolfgang; Edwards, Katrina J; Orcutt, Beth N; Wang, Fengping


    Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane) and nitrogen (nitrate and ammonium) sources revealed significant cell growth (one magnitude higher cell abundance), higher intracellular DNA content, and increased Fe(3+)/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement.

  20. TM6, a novel nuclear matrix attachment region, enhances its flanking gene expression through influencing their chromatin structure.

    Ji, Lusha; Xu, Rui; Lu, Longtao; Zhang, Jiedao; Yang, Guodong; Huang, Jinguang; Wu, Changai; Zheng, Chengchao


    Nuclear matrix attachment regions (MARs) regulate the higher-order organization of chromatin and affect the expression of their flanking genes. In this study, a tobacco MAR, TM6, was isolated and demonstrated to remarkably increase the expression of four different promoters that drive gusA gene and adjacent nptII gene. In turn, this expression enhanced the transformation frequency of transgenic tobacco. Deletion analysis of topoisomerase II-binding site, AT-rich element, and MAR recognition signature (MRS) showed that MRS has the highest contribution (61.7%) to the TM6 sequence-mediated transcription activation. Micrococcal nuclease (MNase) accessibility assay showed that 35S and NOS promoter regions with TM6 are more sensitive than those without TM6. The analysis also revealed that TM6 reduces promoter DNA methylation which can affect the gusA expression. In addition, two tobacco chromatin-associated proteins, NtMBP1 and NtHMGB, isolated using a yeast one-hybrid system, specifically bound to the TM6II-1 region (761 bp to 870 bp) and to the MRS element in the TM6II-2 (934 bp to 1,021 bp) region, respectively. We thus suggested that TM6 mediated its chromatin opening and chromatin accessibility of its flanking promoters with consequent enhancement of transcription.

  1. Three-Dimensional Passive Source Localisation using the Flank Array of an Autonomous Underwater Vehicle in Shallow Water

    Dexin Zhao


    Full Text Available Researchers have become interested in autonomous underwater vehicles equipped with various kinds of sonar systems that can perform many of underwater tasks, which is encouraged by the potential benefits of cost reduction and flexible deployment. This paper proposes an approach to three-dimensional passive source localisation with the flank array of an autonomous underwater vehicle in shallow water. The approach is developed based on matched-field processing for the likelihood of passive source localisation in the shallow water environment. Inter-position processing is also used for the improved localisation performance and the enhanced stability of the estimation process against the lack of spatial gain due to the small physical size of the flank array. The proposed approach is presented and validated through simulation and experimental data. The results illustrate the localisation performance at different signal-to-noise ratios and demonstrate the build up over time of the positional parameters of the estimated source as the autonomous underwater vehicle cruises at a low speed along a straight line at a constant depth.Defence Science Journal, 2013, 63(3, pp.323-330, DOI:

  2. Three-Dimensional Passive Source Localisation using the Flank Array of an Autonomous Underwater Vehicle in Shallow Water

    Dexin Zhao


    Full Text Available Researchers have become interested in autonomous underwater vehicles equipped with various kinds of sonar systems that can perform many of underwater tasks, which is encouraged by the potential benefits of cost reduction and flexible deployment. This paper proposes an approach to three-dimensional passive source localisation with the flank array of an autonomous underwater vehicle in shallow water. The approach is developed based on matched-field processing for the likelihood of passive source localisation in the shallow water environment. Inter-position processing is also used for the improved localisation performance and the enhanced stability of the estimation process against the lack of spatial gain due to the small physical size of the flank array. The proposed approach is presented and validated through simulation and experimental data. The results illustrate the localisation performance at different signal-to-noise ratios and demonstrate the build up over time of the positional parameters of the estimated source as the autonomous underwater vehicle cruises at a low speed along a straight line at a constant depth.

  3. Comparative analysis on the structural features of the 5' flanking region of κ-casein genes from six different species

    Whitelaw C Bruce A


    Full Text Available Abstract κ-casein plays an essential role in the formation, stabilisation and aggregation of milk micelles. Control of κ-casein expression reflects this essential role, although an understanding of the mechanisms involved lags behind that of the other milk protein genes. We determined the 5'-flanking sequences for the murine, rabbit and human κ-casein genes and compared them to the published ruminant sequences. The most conserved region was not the proximal promoter region but an approximately 400 bp long region centred 800 bp upstream of the TATA box. This region contained two highly conserved MGF/STAT5 sites with common spacing relative to each other. In this region, six conserved short stretches of similarity were also found which did not correspond to known transcription factor consensus sites. On the contrary to ruminant and human 5' regulatory sequences, the rabbit and murine 5'-flanking regions did not harbour any kind of repetitive elements. We generated a phylogenetic tree of the six species based on multiple alignment of the κ-casein sequences. This study identified conserved candidate transcriptional regulatory elements within the κ-casein gene promoter.

  4. Venting formation fluids from deep-sea boreholes in a ridge flank setting: ODP Sites 1025 and 1026

    Wheat, C. Geoffrey; Jannasch, Hans W.; Kastner, Miriam; Plant, Josh N.; Decarlo, Eric H.; Lebon, Geoff


    During ODP Leg 168, two of ten boreholes, ODP Holes 1025C and 1026B, were cased through the sediment section, penetrated basaltic crust that is overpressured, and sealed. In 1999 and 2000 the seals were removed, allowing crustal formation fluids to vent and be sampled. The composition of these fluids is compared to those of basal deep-sea pore waters, which have been the basis for estimating geochemical fluxes from low-temperature ridge flank hydrothermal systems. Estimates for the composition of the major ions in formation fluids based on basal pore waters are within 5% of the values measured in borehole fluids. Similar comparisons for minor and trace elements are not as good; some are reactive in the sediment section, resulting in large uncertainties in the pore water extrapolation, while others are influenced by a variety of contaminants, including steel, grease, drilling muds, and basal sediment. Evidence for contamination includes high dissolved and particulate concentrations of several metals (e.g., Fe, Cu, Co, Zn, and Pb) and measurable changes in concentration during the past four years in response to reaction with basal sediment. This new confidence in estimating the primary composition of formation fluids, coupled with advances in thermodynamic and kinetic models, reveals the possibility of anhydrite precipitation in ridge flank hydrothermal systems at temperatures of ˜70°C. Such new insights allow us to address the timing and conditions under which seawater-crustal reactions occur, leading to more accurate models of crustal evolution.


    Shaun Williams


    Full Text Available Ta’u, the easternmost inhabited island in the Samoan Islands archipelago, exhibits a series of down-faulted benches on its southern flank, believed to be the remnant of ~30 km3 catastrophic collapse. A historical map of Ta’u charted in 1839 during the United States Exploring Expedition, which did not show the benches, suggests that the event occurred less than 170 years ago. A collapse event of this magnitude would have generated a locally devastating tsunami, with possible impacts experienced at the regional level. However, no written or oral records of such an event exist. A number of key questions thus emerge, and formed the basis for this study. Did this event actually happen within the last 170 years, and if so, how and why could it have gone unnoticed? Or, is the event much older than the impression obtained from the literature? The catastrophic flank collapse was modeled using 100 m contour-resolution bathymetry data of the Ta’u region, coupled with rational assumptions made on the geometry of the failed mass. This enabled numerical landslide- tsunami simulation in the Cornell Multigrid Coupled Tsunami Model (COMCOT. The results indicate that if an event of this magnitude occurred in the last 170 years, it could not have gone unnoticed by local inhabitants. It thus seems likely that the initial survey conducted during the Exploring Expedition was inaccurate. Nevertheless, the well-preserved nature of the benches indicates collapse relatively recently and raises the possibility of future collapse.

  6. Nitrogen stimulates the growth of subsurface basalt-associated microorganisms at the western flank of the Mid-Atlantic Ridge

    Xinxu eZhang


    Full Text Available Oceanic crust constitutes the largest aquifer system on Earth, and microbial activity in this environment has been inferred from various geochemical analyses. However, empirical documentation of microbial activity from subsurface basalts is still lacking, particularly in the cool (<25 °C regions of the crust, where are assumed to harbor active iron-oxidizing microbial communities. To test this hypothesis, we report the enrichment and isolation of crust-associated microorganisms from North Pond, a site of relatively young and cold basaltic basement on the western flank of the Mid-Atlantic Ridge that was sampled during Expedition 336 of the Integrated Ocean Drilling Program. Enrichment experiments with different carbon (bicarbonate, acetate, methane and nitrogen (nitrate and ammonium sources revealed significant cell growth (one magnitude higher cell abundance, higher intracellular DNA content, and increased Fe3+/ΣFe ratios only when nitrogen substrates were added. Furthermore, a Marinobacter strain with neutrophilic iron-oxidizing capabilities was isolated from the basalt. This work reveals that basalt-associated microorganisms at North Pond had the potential for activity and that microbial growth could be stimulated by in vitro nitrogen addition. Furthermore, iron oxidation is supported as an important process for microbial communities in subsurface basalts from young and cool ridge flank basement.

  7. Cutting force and machine kinematics constrained cutter location planning for five-axis flank milling of ruled surfaces

    Ke Xu


    Full Text Available Five-axis flank milling has been commonly used in the manufacturing of complex workpieces because of its greater productivity than that of three-axis or five-axis end milling. The advantage of this milling operation largely depends on effective cutter location planning. The finished surface sometimes suffers from large geometrical errors induced by improper tool positioning, due to the non-developability of most ruled surfaces in industrial applications. In addition, a slender flank-milling cutter may be deflected when subjected to large cutting forces during the machining process, further degrading the surface quality or even breaking the cutter. This paper proposes a novel tool path planning scheme to address those problems. A simple but effective algorithm is developed to adaptively allocate a series of cutter locations over the design surface with each one being confined within an angular rotation range. The allocation result satisfies a given constraint of geometrical errors on the finished surface, which consists of the tool positioning errors at each cutter location and the sweeping errors between consecutive ones. In addition, a feed rate scheduling algorithm is proposed to maximize the machining efficiency subject to the cutting force constraint and the kinematical constraints of a specific machine configuration. Simulation and experimental tests are conducted to validate the effectiveness of the proposed algorithms. Both the machining efficiency and finish surface quality are greatly improved compared with conventional cutter locations.

  8. Influence of the cutting parameters on flank wear of coated inserts during turning of AISI 316L

    Yusimit Zamora Hernández


    Full Text Available (Received: 2015/01/20 - Accepted: 2015/03/25The continuous improvement of manufacturing processes is critical to achieve optimum levels of productivity, quality and cut production of components and products. This research aims to determine the cutting tool flank wearing progression, during a high speed dry turning, for AISI 316L steel parts. Experimental data were acquired using two cutting feed levels, two material levels, three cutting speeds, and four principal cutting times. A scanning electron microscope (SEM was used to measure and analyze the wear of the cutting tools. Results were compared using analysis of variance and multiple regression for describing the relation between the variables used in the study. The analysis showed that the three layers coating insert did not exceed the end of life wearing criterion, while the one layer insert suffered a catastrophic wearing at the highest cutting speed. It was found that a relation exists between the experimental data and the predicted values for flank wear with a general average error of 4.1182%.

  9. Repetitive flanking sequences challenge microsatellite marker development: a case study in the lepidopteran Melanargia galathea.

    Schmid, Max; Csencsics, Daniela; Gugerli, Felix


    Microsatellite DNA families (MDF) are stretches of DNA that share similar or identical sequences beside nuclear simple-sequence repeat (nSSR) motifs, potentially causing problems during nSSR marker development. Primers positioned within MDFs can bind several times within the genome and might result in multiple banding patterns. It is therefore common practice to exclude MDF loci in the course of marker development. Here, we propose an approach to deal with multiple primer-binding sites by purposefully positioning primers within the detected repetitive element. We developed a new protocol to determine the family type and the primer position in relation to MDFs using the software packages repark and repeatmasker together with an in-house R script. We re-evaluated newly developed nSSR markers for the lepidopteran Marbled White (Melanargia galathea) and explored the implications of our results with regard to published data sets of the butterfly Euphydryas aurinia, the grasshopper Stethophyma grossum, the conifer Pinus cembra and the crucifer Arabis alpina. For M. galathea, we show that it is not only possible to develop reliable nSSR markers for MDF loci, but even to benefit from their presence in some cases: We used one unlabelled primer, successfully binding within an MDF, for two different loci in a multiplex PCR, combining this family primer with uniquely binding and fluorescently labelled primers outside of MDFs, respectively. As MDFs are abundant in many taxa, we propose to consider these during nSSR marker development in taxa concerned. Our new approach might help in reducing the number of tested primers during nSSR marker development. © 2016 John Wiley & Sons Ltd.

  10. Structural Analyses of the Ankyrin Repeat Domain of TRPV6 and Related TRPV Ion Channels

    Phelps, C.B.; Huang, R.J.; Lishko, P.V.; Wang, R.R.; Gaudet, R. (Harvard)


    Transient receptor potential (TRP) proteins are cation channels composed of a transmembrane domain flanked by large N- and C-terminal cytoplasmic domains. All members of the vanilloid family of TRP channels (TRPV) possess an N-terminal ankyrin repeat domain (ARD). The ARD of mammalian TRPV6, an important regulator of calcium uptake and homeostasis, is essential for channel assembly and regulation. The 1.7 A crystal structure of the TRPV6-ARD reveals conserved structural elements unique to the ARDs of TRPV proteins. First, a large twist between the fourth and fifth repeats is induced by residues conserved in all TRPV ARDs. Second, the third finger loop is the most variable region in sequence, length and conformation. In TRPV6, a number of putative regulatory phosphorylation sites map to the base of this third finger. Size exclusion chromatography and crystal packing indicate that the TRPV6-ARD does not assemble as a tetramer and is monomeric in solution. Adenosine triphosphate-agarose and calmodulin-agarose pull-down assays show that the TRPV6-ARD does not interact with either ligand, indicating a different functional role for the TRPV6-ARD than in the paralogous thermosensitive TRPV1 channel. Similar biochemical findings are also presented for the highly homologous mammalian TRPV5-ARD. The implications of the structural and biochemical data on the role of the ankyrin repeats in different TRPV channels are discussed.

  11. Diversity in the androgen receptor CAG repeat has been shaped by a multistep mutational mechanism.

    Santos, Diana; Pimenta, João; Wong, Virginia C N; Amorim, António; Martins, Sandra


    The androgen receptor (AR) gene encodes a type of nuclear receptor that functions as a steroid-hormone activated transcription factor. In its coding region, AR includes a CAG repeat, which has been intensely studied due to the inverse correlation between repeat size and AR transcriptional activity. Several studies have reported different (CAG)n sizes associated with the risk of androgen-linked diseases. We aimed at clarifying the mechanisms on the origin of newly CAG sized alleles through a strategy involving the analysis of the associated haplotype diversity. We genotyped 374 control individuals of European and Asian ancestry, and reconstructed the haplotypes associated with the CAG repeat, defined by 10 SNPs and 6 flanking STRs. The most powerful SNPs to tag AR lineages are rs7061037-rs12012620 and rs34191540-rs6625187-rs2768578 in Europeans and Asians, respectively. In the most frequent AR lineage, (CAG)18 alleles seem to have been generated by a multistep mutation mechanism, most probably from longer alleles. We further noticed that the DXS1194-DXS1111 haplotype, in linkage disequilibrium with AR-(CAG)n expanded alleles responsible for spinal bulbar muscular atrophy (SBMA), is rare among our controls; however, the haplotype strategy here described may be used to clarify the origin of expansions in other populations, as in future association studies.

  12. Repeatability in Redundant Manipulator Systems


    IEEE Transactions on Robotics and Automation...34Nonholonomic Motion Planning of Space Robots via a Bi-Directional Approach", IEEE Transactions on Robotics and Automation, Vol. 7, No. 4, pp. 500-514. [12...Nakamura, Y., and Mukherjee, R., 1993, "Exploiting Nonholonomic Redundancy in Free-Flying Space Robots", IEEE Transactions on Robotics and Automation,

  13. Repeat organization and epigenetic regulation of the DH-Cmu domain of the immunoglobulin heavy-chain gene locus.

    Chakraborty, Tirtha; Chowdhury, Dipanjan; Keyes, Amanda; Jani, Anant; Subrahmanyam, Ramesh; Ivanova, Irina; Sen, Ranjan


    The first steps of murine immunoglobulin heavy-chain (IgH) gene recombination take place within a chromosomal domain that contains diversity (D(H)) and joining (J(H)) gene segments, but not variable (V(H)) gene segments. Here we show that the chromatin state of this domain is markedly heterogeneous. Specifically, only 5'- and 3'-most D(H) gene segments carry active chromatin modifications, whereas intervening D(H)s are associated with heterochromatic marks that are maintained by ongoing histone deacetylation. The intervening D(H)s form part of a tandemly repeated sequence that expresses tissue-specific, antisense oriented transcripts. We propose that the intervening D(H) genes are actively suppressed by repeat-induced epigenetic silencing, which is reflected in their infrequent representation in DJ(H) junctions compared to the flanking D(H) genes.

  14. Strengthening concept learning by repeated testing.

    Wiklund-Hörnqvist, Carola; Jonsson, Bert; Nyberg, Lars


    The aim of this study was to examine whether repeated testing with feedback benefits learning compared to rereading of introductory psychology key-concepts in an educational context. The testing effect was examined immediately after practice, after 18 days, and at a five-week delay in a sample of undergraduate students (n = 83). The results revealed that repeated testing with feedback significantly enhanced learning compared to rereading at all delays, demonstrating that repeated retrieval enhances retention compared to repeated encoding in the short- and the long-term. In addition, the effect of repeated testing was beneficial for students irrespectively of working memory capacity. It is argued that teaching methods involving repeated retrieval are important to consider by the educational system.

  15. Cloning and analysing of 5‘ flanking region of Xenopus organizer gene noggin



    Xenopus organizer specific gene noggin possesses nearly all the characterestic properties of the action of organizer to specify the embryonic body acis.To analyze how the maternal inherited factors control its expression pattern,we cloned the 5' regulatory region of noggin gene.The 1.5 kb upstream sequense could direct reporter gene to express in vivo and data from deletion analysis indicated that a 229 base pair fragmet is essential for activating noggin expression.We further demonstrated that the response elements within this regulatory region were indeed under the control of growth factor activin and Wnt signaling pathway components.

  16. Repeat concussions in the national football league.

    Casson, Ira R; Viano, David C; Powell, John W; Pellman, Elliot J


    Repeat concussion is an important issue in the National Football League (NFL). An initial description of repeat injuries was published for 6 years (1996-2001). The characteristics and frequency of repeat concussion in the NFL have not changed in the subsequent 6 years (2002-2007). Case control. From 1996 to 2007, concussions were reported using a standardized form documenting signs and symptoms, loss of consciousness and medical action taken. Data on repeat concussions were analyzed for the 12 years and compared between the 2 periods. In 2002-2007, 152 players had repeat concussions (vs 160 in 1996-2001); 44 had 3+ head injuries (vs 52). The positions most often associated with repeat concussion in 2002-2007 were the defensive secondary, kick unit, running back, and linebacker. The odds for repeat concussion were elevated for wide receivers, tight ends, and linebackers but lower than in the earlier period. During 2002-2007, over half of players with repeat concussion were removed from play, and fewer immediately returned (vs 1996-2001). The average duration between concussions was 1.25 years for 2002-2007 and 1.65 years for the 12-year period. Over 12 years, 7.6% of all repeat concussions occurred within 2 weeks of the prior concussion. The defensive secondary, kick unit, running back, and linebacker have the highest incidence of repeat concussion. During 2002-2007, more than half of players with repeat concussion were removed from play, and only a fraction immediately returned. Although concussion was managed more conservatively by team physicians in the recent 6 years, repeat concussions occurred at similar rates during both periods.

  17. Automated quality checks on repeat prescribing.

    Rogers, Jeremy E; Wroe, Christopher J; Roberts, Angus; Swallow, Angela; Stables, David; Cantrill, Judith A; Rector, Alan L.


    BACKGROUND: Good clinical practice in primary care includes periodic review of repeat prescriptions. Markers of prescriptions that may need review have been described, but manually checking all repeat prescriptions against the markers would be impractical. AIM: To investigate the feasibility of computerising the application of repeat prescribing quality checks to electronic patient records in United Kingdom (UK) primary care. DESIGN OF STUDY: Software performance test against benchmark manual...

  18. Short Tandem Repeat DNA Internet Database

    SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

  19. Cloning, sequencing, and functional analysis of the 5'-flanking region of the rat 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase gene.

    Lin, H K; Penning, T M


    Rat liver 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase (3 alpha-HSD/DD) is a member of the aldo-keto reductase gene superfamily. It displays high constitutive expression and inactivates circulating steroid hormones and suppresses the formation of polycyclic aromatic hydrocarbon anti- and syn-diol-epoxides (ultimate carcinogens). To elucidate mechanisms responsible for constitutive expression of the 3 alpha-HSD/DD gene a rat genomic library obtained from adult Sprague-Dawley female liver (HaeIII partial digest) was screened, using a probe corresponding to the 5'-end of the cDNA (-15 to +250), and a 15.8-kb genomic clone was isolated. Sequencing revealed that 6.3 kb contained exon 1 (+16 to +138 bp) plus additional introns and exons. The transcription start site (+1) was located by primer extension analysis, and the initiation codon, ATG, was located at +55 bp. The remaining 9.5 kb represented the 5'-flanking region of the rat 3 alpha-HSD/DD gene. A 1.6-kb fragment of this region was sequenced. A TATTTAA sequence (TATA box) was found at 33 bp upstream from the major transcription start site. cis-acting elements responsible for the constitutive expression of the rat 3 alpha-HSD/DD gene were located on the 5'-flanking region by transient transfection of reporter-gene (chloramphenicol acetyl transferase, CAT) constructs into human hepatoma cells (HepG2). CAT assays identified the basal promoter between (-199 and +55 bp), the presence of a proximal enhancer (-498 to -199 bp) which stimulated CAT activity 6-fold, the existence of a powerful silencer (-755 to -498 bp), and a strong distal enhancer (-4.0 to -2.0 kb) which increased CAT activity by 20-40-fold. A computer search of available consensus sequences for trans-acting factors revealed that a cluster of Oct-sites were uniquely located in the silencer region. Using the negative response element (-797 to -498 bp) as a probe and nuclear extracts from HepG2 cells, three bands were identified by gel mobility shift

  20. Geology of the western, eastern and northern flanks of the Olympus Mons volcano as seen in HRSC and MOC images

    Basilevsky, A. T.; Werner, S. C.; van Gasselt, S.; Neukum, G.; Dumke, A.; Ivanov, B. A.; Gwinner, K.

    This study is based on the analysis of images taken by MEX High Resolution Stereo Camera and in combination with MGS MOC images. 3-D imagery in the form of HRSC-based anaglyphs and DTMs were very helpful for the study. Our observation and analysis confirm the well-known interpretation of Olympus Mons as a giant shield volcano, but also show that this construct locally has probably partly been made of airborne dust (and/or ash) and ice layered deposits (Neukum et al, 2004; Basilevsky et al., 2005; this study). The deposits form mesas locally standing above the lava fields in the volcano western and eastern flanks as well as ridges locally observed at the top parts of the scarps rimming the Olympus construct on its western and northern flanks. The ridge tops stand a few hundred meters above the adjacent lava flows coming from the volcano top. Ice presence in these deposits was inferred from the presence of "collapse" features locally extending downslope as channel-like forms. The neutron-spectrometry measurements (Feldman et al., 2004) show a noticeable decrease in the neutron flux suggesting presence of up to 15-18 vol. % of equivalent water (ice) in the upper 1 m surface layer in the western part of the construct. The ice-rich deposits could have been emplaced during the epochs of high orbital inclination of Mars (Mishna et al., 2004) and could be partly preserved in the modern epoch due to protecting dust covers (Skorov et al., 2001). At the foot of the western slope of the volcano are seen flow-like features interpreted as remnants of rock glaciers (Lucchitta, 1981; Milkovich and Head, 2006). The dating by crater statistics shows that different areas of the Olympus Mons construct and lava fields at its foot have a spread of ages from >3.5 b.y. to 2 m.y. and glacier-like flows show a 0.5 b.y. to 4 m.y. age range. The eastern flank of the volcano shows a complex of morphologies caused by fluvial (channels), tectonic (wrinkle ridges) and volcanic (lava flows and

  1. Identification of Genomic Insertion and Flanking Sequence of G2-EPSPS and GAT Transgenes in Soybean Using Whole Genome Sequencing Method

    Guo, Bingfu; Guo, Yong; Hong, Huilong; Qiu, Li-Juan


    Molecular characterization of sequence flanking exogenous fragment insertion is essential for safety assessment and labeling of genetically modified organism (GMO). In this study, the T-DNA insertion sites and flanking sequences were identified in two newly developed transgenic glyphosate-tolerant soybeans GE-J16 and ZH10-6 based on whole genome sequencing (WGS) method. More than 22.4 Gb sequence data (∼21 × coverage) for each line was generated on Illumina HiSeq 2500 platform. The junction reads mapped to boundaries of T-DNA and flanking sequences in these two events were identified by comparing all sequencing reads with soybean reference genome and sequence of transgenic vector. The putative insertion loci and flanking sequences were further confirmed by PCR amplification, Sanger sequencing, and co-segregation analysis. All these analyses supported that exogenous T-DNA fragments were integrated in positions of Chr19: 50543767–50543792 and Chr17: 7980527–7980541 in these two transgenic lines. Identification of genomic insertion sites of G2-EPSPS and GAT transgenes will facilitate the utilization of their glyphosate-tolerant traits in soybean breeding program. These results also demonstrated that WGS was a cost-effective and rapid method for identifying sites of T-DNA insertions and flanking sequences in soybean. PMID:27462336

  2. Vasopressin-dependent flank marking in golden hamsters is suppressed by drugs used in the treatment of obsessive-compulsive disorder

    Messenger Tara


    Full Text Available Abstract Background Alterations in arginine vasopressin regulation and secretion have been proposed as one possible biochemical abnormality in patients with obsessive-compulsive disorder. In golden hamsters, arginine vasopressin microinjections into the anterior hypothalamus trigger robust grooming and flank marking, a stereotyped scent marking behaviors. The intensity and repetition of the behaviors induced by arginine vasopressin is somewhat reminiscent of Obsessive Compulsive Disorder in humans. The present experiments were carried out to test whether pharmacological agents used to alleviate obsessive compulsive disorder could inhibit arginine vasopressin-induced flank marking and grooming. Results Male golden hamsters were treated daily for two weeks with either vehicle, fluoxetine, clomipramine, or desipramine (an ineffective drug, before being tested for arginine vasopressin-induced flank marking and grooming. Flank marking was significantly inhibited in animals treated with fluoxetine or clomipramine but unaffected by treatment with desipramine. Grooming behavior was not affected by any treatment. Conclusion These data suggest that arginine vasopressin-induced flank marking may serve as an animal model for screening drugs used in the control of Obsessive Compulsive Disorder.

  3. Application of response surface methodology on investigating flank wear in machining hardened steel using PVD TiN coated mixed ceramic insert

    Ashok Kumar Sahoo


    Full Text Available The paper presents the development of flank wear model in turning hardened EN 24 steel with PVD TiN coated mixed ceramic insert under dry environment. The paper also investigates the effect of process parameter on flank wear (VBc. The experiments have been conducted using three level full factorial design techniques. The machinability model has been developed in terms of cutting speed (v, feed (f and machining time (t as input variable using response surface methodology. The adequacy of model has been checked using correlation coefficients. As the determination coefficient, R2 (98% is higher for the model developed; the better is the response model fits the actual data. In addition, residuals of the normal probability plot lie reasonably close to a straight line showing that the terms mentioned in the model are statistically significant. The predicted flank wear has been found to lie close to the experimental value. This indicates that the developed model can be effectively used to predict the flank wear in the hard turning. Abrasion and diffusion has been found to be the dominant wear mechanism in machining hardened steel from SEM micrographs at highest parametric range. Machining time has been found to be the most significant parameter on flank wear followed by cutting speed and feed as observed from main effect plot and ANOVA study.

  4. Identification of genomic insertion and flanking sequence of G2-EPSPS and GAT transgenes in soybean using whole genome sequencing method

    Bingfu Guo


    Full Text Available Molecular characterization of sequences flanking exogenous fragment insertions is essential for safety assessment and labeling of genetically modified organisms (GMO. In this study, the T-DNA insertion sites and flanking sequences were identified in two newly developed transgenic glyphosate-tolerant soybeans GE-J16 and ZH10-6 based on whole genome sequencing (WGS method. About 21 Gb sequence data (~21× coverage for each line was generated on Illumina HiSeq 2500 platform. The junction reads mapped to boundary of T-DNA and flanking sequences in these two events were identified by comparing all sequencing reads with soybean reference genome and sequence of transgenic vector. The putative insertion loci and flanking sequences were further confirmed by PCR amplification, Sanger sequencing, and co-segregation analysis. All these analyses supported that exogenous T-DNA fragments were integrated in positions of Chr19: 50543767-50543792 and Chr17: 7980527-7980541 in these two transgenic lines. Identification of the genomic insertion site of the G2-EPSPS and GAT transgenes will facilitate the use of their glyphosate-tolerant traits in soybean breeding program. These results also demonstrated that WGS is a cost-effective and rapid method of identifying sites of T-DNA insertions and flanking sequences in soybean.

  5. Numerical simulation of the last flank-collapse event of Montagne Pelée, Martinique, Lesser Antilles

    Le Friant, Anne; Heinrich, Philippe; Deplus, Christine; Boudon, Georges


    We model the submarine emplacement of a debris avalanche generated by the last flank-collapse event of Montagne Pelée volcano. We estimate the collapsed volume (1.7 km3) using both the volume of the missing material in the horseshoe-shaped structure and the volume of submarine deposits. This avalanche is treated as the gravitational flow of a homogeneous continuum. It is simulated by a finite-difference model, solving mass and momentum conservation equations, that are depth-averaged over the slide thickness. Numerical simulations show that the emplacement of this debris-avalanche can be suitably modeled by a Coulomb-type friction law with a variable friction angle below 10°. We propose that variations of the friction angle are mainly influenced by the thickness of the flowing mass.

  6. Long-term (17 Ma) turbidite record of the timing and frequency of large flank collapses of the Canary Islands

    Hunt, J. E.; Talling, P. J.; Clare, M. A.; Jarvis, I.; Wynn, R. B.


    turbidites on the Madeira Abyssal Plain provide a record of large-volume volcanic island flank collapses from the Canary Islands. This long-term record spans 17 Ma, and comprises 125 volcaniclastic beds. Determining the timing, provenance and volumes of these turbidites provides key information about the occurrence of mass wasting from the Canary Islands, especially the western islands of Tenerife, La Palma and El Hierro. These turbidite records demonstrate that landslides often coincide with protracted periods of volcanic edifice growth, suggesting that loading of the volcanic edifices may be a key preconditioning factor for landslide triggers. Furthermore, the last large-volume failures from Tenerife coincide with explosive volcanism at the end of eruptive cycles. Many large-volume Canary Island landslides also occurred during periods of warmer and wetter climates associated with sea-level rise and subsequent highstand. However, these turbidites are not serially dependent and any association with climate or sea level change is not statistically significant.

  7. Geomechanical parameters of intact rocks and rock masses from the Canary Islands: Implications on their flank stability

    Rodríguez-Losada, J. A.; Hernández-Gutiérrez, L. E.; Olalla, C.; Perucho, A.; Serrano, A.; Eff-Darwich, A.


    New data on the geomechanical properties of the highly cohesive volcanic rocks of the Canary Archipelago and their role in the flank stability on oceanic islands are provided in this work. On the basis of the textural and petrological features, a preliminary classification of rocks, grouped into lithotypes, was carried out. This classification includes vesicular and non vesicular basalts, trachybasalts, trachytes, phonolites, welded and non welded ignimbrites. Strength and strain-related features are summarized here for each distinctive lithotype. Taking into account the results of the uniaxial and triaxial compressive tests, the geological strength index of rock masses and their textural-structural features, an estimate of the rock mass parameters and Mohr-Coulomb fit has been carried out. A final discussion on the impact of those geomechanical parameters as factors governing the stability of steep slopes in volcanic islands is then made here as a contribution in volcanic risk.

  8. Rapid Amplification of Flanking Sequences of a Known DNA Region by Partial Restriction Digestion and Hot Start PCR

    LOU Qun-feng; LIU Qiang; YANG Yin-gui; CHEN Jin-feng


    A simple and efficient method for cloning the flanking genomic sequences of a known DNA region is reported in this study. This method combined partial restriction endonuclease digestion, adaptor ligation, and a single round polymerase chain reaction. Total genomic DNA was partially digested with the frequent-cutting restriction enzyme Mse Ⅰ. The partially digested products were ligated to an unphosphorylated adaptor. A hot start PCR amplification with Taq polymerase and dNTP was performed with a DNA-specific primer and the adaptor primer complementary to the adaptor and the Mse Ⅰ recognition site. The amplified products were fractionated, cloned and sequenced. By this method, we cloned the downstream region of a gynoecious marker TG/CAC234 from cucumber (Cucumis sativus L.).

  9. Sequence-specific flexibility organization of splicing flanking sequence and prediction of splice sites in the human genome.

    Zuo, Yongchun; Zhang, Pengfei; Liu, Li; Li, Tao; Peng, Yong; Li, Guangpeng; Li, Qianzhong


    More and more reported results of nucleosome positioning and histone modifications showed that DNA structure play a well-established role in splicing. In this study, a set of DNA geometric flexibility parameters originated from molecular dynamics (MD) simulations were introduced to discuss the structure organization around splice sites at the DNA level. The obtained profiles of specific flexibility/stiffness around splice sites indicated that the DNA physical-geometry deformation could be used as an alternative way to describe the splicing junction region. In combination with structural flexibility as discriminatory parameter, we developed a hybrid computational model for predicting potential splicing sites. And the better prediction performance was achieved when the benchmark dataset evaluated. Our results showed that the mechanical deformability character of a splice junction is closely correlated with both the splice site strength and structural information in its flanking sequences.

  10. Three-dimensional structure of the submarine flanks of La Réunion inferred from geophysical data

    Gailler, Lydie-Sarah; LéNat, Jean-FrançOis


    La Réunion (Indian Ocean) constitutes a huge volcanic oceanic system of which most of the volume is submerged. We present a study of its submarine part based on the interpretation of magnetic and gravity data compiled from old and recent surveys. A model of the submarine internal structure is derived from 3-D and 2-D models using constraints from previous geological and geophysical studies. Two large-scale, previously unknown, buried volcanic construction zones are discovered in continuation of the island's construction. To the east, the Alizés submarine zone is interpreted as the remnants of Les Alizés volcano eastward flank whose center is marked by a large hypovolcanic intrusion complex. To the southwest, the Etang Salé submarine zone is interpreted as an extension of Piton des Neiges, probably fed by a volcanic rift zone over a large extent. They were predominantly built during the Matuyama period and thus probably belong to early volcanism. A correlation exists between their top and seismic horizons recognized in previous studies and interpreted as the base of the volcanic edifice. Their morphology suggested a lithospheric bulging beneath La Réunion, not required to explain our data, since the seismic interfaces match the top of our volcanic constructions. The coastal shelf coincides with a negative Bouguer anomaly belt, often associated with magnetic anomalies, suggesting a shelf built by hyaloclastites. A detailed analysis of the offshore continuation of La Montagne Massif to the north confirms this hypothesis. The gravity analysis confirms that the bathymetric bulges, forming the northern, eastern, southern, and western submarine flanks, are predominantly built by debris avalanche deposits at the surface.

  11. Shallow seismic imaging of flank collapse structures in oceanic island volcanoes: Application to the Western Canary Islands

    Sanchez, L.; González, P.; Tiampo, K. F.


    Volcanic flank collapse counts among the many hazards associated with volcanic activity. This type of event involves the mobilization of large volumes, producing debris avalanches. It affects mostly oceanic island volcanoes, involving the potential for tsunami occurrence. Geophysical imaging can illuminate subvolcanic features such as volcano-tectonic structures, magmatic plumbing systems or differences in rock type. The most commonly used geophysical methods are gravity, electromagnetics and seismics. In particular, seismic measurements quantify anomalies in seismic waves propagation velocities and can be used to obtain information on the subsurface arrangement of different materials. In the Western Canary Islands, the Cumbre Vieja volcano in La Palma (Canary Islands) has been proposed to be near the collapse stage. Previous geophysical studies that have been carried out on the flank of the volcano comprise gravity and electromagnetic methods. These types of surveys gather information on the deep structures of the volcano (1-2 km). In this project, we complement previous studies by using seismic methods to investigate the near-surface seismic structure of the Cumbre Vieja fault system (La Palma Island) and the structure of the well-developed San Andres fault system (El Hierro Island). We aim to compare the Cumbre Vieja and San Andres fault systems to infer the degree of maturity of collapse structures. We carried out reflection and refraction seismic surveys in order to image approximately the first 10 meters of the subsurface. We used 24 low frequency (4,5 Hz) geophones as receivers and a sledge hammer as the seismic source. The survey lines were located across visible parts of the fault systems at the Cumbre Vieja volcano and the San Andres fault in El Hierro. Here, we present the survey setup and results from the preliminary analysis of the data.

  12. Mapping of a gene for familial juvenile nephronophthisis: Refining the map and defining flanking markers on chromosome 2

    Hildebrandt, F.; Singh-Sawhney, I.; Schnieders, B.; Centofante, L.; Omran, H.; Pohlmann, A.; Schmaltz, C.; Wedekind, H.; Schubotz, D.; Brandis, M. (Freiburg Univ. (Germany)); Antignac, C. (Hopital Necker-Enfants Malades, Paris (France)); Weber, J.L. (Marshfield Medical Foundation, WI (United States))


    Familial juvenile nephronophthisis (NPH) is an autosomal recessive kidney disease that leads to end-stage renal failure in adolescence and is associated with the formation of cysts at the cortico-medullary junction of the kidneys. NPH is responsible for about 15% of end-stage renal disease in children, as shown by Kleinknecht and Habib. NPH in combination with autosomal recessive retinitis pigmentosa is known as the Senior-Loken syndrome (SLS) and exhibits renal pathology that is identical to NPH. The authors had excluded 40% of the human genome from linkage with a disease locus for NH or SLS when Antignac et al. first demonstrated linkage for an NPH locus on chromosome 2. The authors present confirmation of linkage of an NPH locus to microsatellite markers on chromosome 2 in nine families with NPH. By linkage analysis with marker AFM262xb5 at locus D2S176, a maximum lod score of 5.05 at a [theta][sub max] = .03 was obtained. In a large NPH family that yielded at D2S176 a maximum lod score of 2.66 at [theta][sub max] = .0, markers AFM172xc3 and AFM016yc5, representing loci D2S135 and D2S110, respectively, were identified as flanking markers, thereby defining the interval for an NPH locus to a region of approximately 15 cM. Furthermore, the cytogenetic assignment of the NPH region was specified to 2p12-(2q13 or adjacent bands) by calculation of linkage between these flanking markers and markers with known unique cytogenic assignment. The refined map may serve as a genetic framework for additional genetic and physical mapping of the region. 26 refs., 3 figs., 1 tab.

  13. Use of the contrast-enhanced CT enema in the management of penetrating trauma to the flank and back.

    Phillips, T; Sclafani, S J; Goldstein, A; Scalea, T; Panetta, T; Shaftan, G


    There have been few innovations in the management of penetrating trauma of the flank and back since that reported by Peck and Berne in 1981. During 1984-1985 our Trauma Service treated 119 patients with injuries in these areas. In 56 patients management was based on the results of the contrast-enhanced CT enema (CECTE), a computerized tomographic technique designed to delineate all of the retroperitoneal viscera by simultaneously opacifying the small bowel, duodenum, colon, GU tract, and major vessels. Specific radiographic findings were present on 44 scans. Twelve scans were negative. Six scans were considered indications for angiography because of the proximity of the identified missile wounds or their hematomas to major vascular structures. One of these arteriograms revealed a renal artery pseudoaneurysm which would otherwise have remained undiagnosed. In 30 cases the penetrating wounds were well delineated by CECTE, and their nature and location were considered appropriate for nonoperative management. None required subsequent exploration. In eight cases CECTE demonstrated that the wounds were located so as to place specific viscera at risk for significant injury, but no definite injury was identified. Five of these patients were successfully managed by further evaluation and close observation, two were explored, and one signed out of the hospital. No scan demonstrated extravasation from a hollow viscus. Overall, 52 of our 56 patients (92%) were successfully managed nonoperatively on the basis of the interpretation of their CECTE findings. CECTE can be useful in the management of stable patients with penetrating trauma to the back and flank by identifying the nature and location of the resulting retroperitoneal injuries.(ABSTRACT TRUNCATED AT 250 WORDS)

  14. Reliability of the Brownish-flanked Bush Warbler’s soft song in male-male conflict

    Canwei; Xia; Boye; Liu; Daiping; Wang; Huw; Lloyd; Yanyun; Zhang


    Background: Soft song is a low-amplitude song produced by many birds. Recent studies have confirmed that soft song is an aggressive signal. For example, the Brownish-flanked Bush Warblers Cettia fortipes use soft song in male-male conflicts, particularly prior to attacks. Although stable signaling systems require that signals be honest on average,models predict that cheating is an acceptable strategy for some individuals or in some contexts.Methods: This study aimed to test the reliability of soft song as an aggressive signal in the brownish-flanked bush warbler. We used mounted specimens accompanied by broadcast songs or soft songs to simulate a male attempting to invade an existing territory.Results: We found the mounted specimen that coupled playback of soft songs suffered more and quicker attacks from the territory owner and that the relationship between soft song and subsequent attack in the territory owner was far from perfect. We observed territory owners that both over-signaled(i.e., produced soft song but did not attack) and under-signaled(i.e., attacked without producing soft song). Under-signaling territory owners were relatively more commonly than were over-signaling territory owners, particularly in simulated intrusion that coupled playback of soft song with a mount specimen.Conclusions: We discuss the cost of producing soft song and the potential benefit of the unreliable use of soft song and propose a new hypothesis for under-signaling with soft song; i.e., under-signaling territory owners might benefit from taking the initiative in fights.

  15. Reliability of the Brownish-flanked Bush Warbler’s soft song in male-male conflict

    Canwei Xia; Boye Liu; Daiping Wang; Huw Lloyd; Yanyun Zhang


    Background:Soft song is a low-amplitude song produced by many birds. Recent studies have confirmed that soft song is an aggressive signal. For example, the Brownish-flanked Bush Warblers Cettia fortipes use soft song in male-male conflicts, particularly prior to attacks. Although stable signaling systems require that signals be honest on average, models predict that cheating is an acceptable strategy for some individuals or in some contexts. Methods:This study aimed to test the reliability of soft song as an aggressive signal in the brownish-flanked bush warbler. We used mounted specimens accompanied by broadcast songs or soft songs to simulate a male attempting to invade an existing territory. Results:We found the mounted specimen that coupled playback of soft songs suffered more and quicker attacks from the territory owner and that the relationship between soft song and subsequent attack in the territory owner was far from perfect. We observed territory owners that both over-signaled (i.e., produced soft song but did not attack) and under-signaled (i.e., attacked without producing soft song). Under-signaling territory owners were relatively more commonly than were over-signaling territory owners, particularly in simulated intrusion that coupled playback of soft song with a mount specimen. Conclusions:We discuss the cost of producing soft song and the potential benefit of the unreliable use of soft song and propose a new hypothesis for under-signaling with soft song;i.e., under-signaling territory owners might benefit from taking the initiative in fights.

  16. Impact of bottom trawling on deep-sea sediment properties along the flanks of a submarine canyon.

    Jacobo Martín

    Full Text Available The offshore displacement of commercial bottom trawling has raised concerns about the impact of this destructive fishing practice on the deep seafloor, which is in general characterized by lower resilience than shallow water regions. This study focuses on the flanks of La Fonera (or Palamós submarine canyon in the Northwestern Mediterranean, where an intensive bottom trawl fishery has been active during several decades in the 400-800 m depth range. To explore the degree of alteration of surface sediments (0-50 cm depth caused by this industrial activity, fishing grounds and control (untrawled sites were sampled along the canyon flanks with an interface multicorer. Sediment cores were analyzed to obtain vertical profiles of sediment grain-size, dry bulk density, organic carbon content and concentration of the radionuclide 210Pb. At control sites, surface sediments presented sedimentological characteristics typical of slope depositional systems, including a topmost unit of unconsolidated and bioturbated material overlying sediments progressively compacted with depth, with consistently high 210Pb inventories and exponential decaying profiles of 210Pb concentrations. Sediment accumulation rates at these untrawled sites ranged from 0.3 to 1.0 cm y-1. Sediment properties at most trawled sites departed from control sites and the sampled cores were characterized by denser sediments with lower 210Pb surface concentrations and inventories that indicate widespread erosion of recent sediments caused by trawling gears. Other alterations of the physical sediment properties, including thorough mixing or grain-size sorting, as well as organic carbon impoverishment, were also visible at trawled sites. This work contributes to the growing realization of the capacity of bottom trawling to alter the physical properties of surface sediments and affect the seafloor integrity over large spatial scales of the deep-sea.

  17. Retroposed elements and their flanking regions resolve the evolutionary history of xenarthran mammals (armadillos, anteaters, and sloths).

    Möller-Krull, Maren; Delsuc, Frédéric; Churakov, Gennady; Marker, Claudia; Superina, Mariella; Brosius, Jürgen; Douzery, Emmanuel J P; Schmitz, Jürgen


    Armadillos, anteaters, and sloths (Order Xenarthra) comprise 1 of the 4 major clades of placental mammals. Isolated in South America from the other continental landmasses, xenarthrans diverged over a period of about 65 Myr, leaving more than 200 extinct genera and only 31 living species. The presence of both ancestral and highly derived anatomical features has made morphoanatomical analyses of the xenarthran evolutionary history difficult, and previous molecular analyses failed to resolve the relationships within armadillo subfamilies. We investigated the presence/absence patterns of retroposons from approximately 7,400 genomic loci, identifying 35 phylogenetically informative elements and an additional 39 informative rare genomic changes (RGCs). DAS-short interspersed elements (SINEs), previously described only in the Dasypus novemcinctus genome, were found in all living armadillo genera, including the previously unsampled Chlamyphorus, but were noticeably absent in sloths. The presence/absence patterns of the phylogenetically informative retroposed elements and other RGCs were then compared with data from the DNA sequences of the more than 12-kb flanking regions of these retroposons. Together, these data provide the first fully resolved genus tree of xenarthrans. Interestingly, multiple evidence supports the grouping of Chaetophractus and Zaedyus as a sister group to Euphractus within Euphractinae, an association that was not previously demonstrated. Also, flanking sequence analyses favor a close phylogenetic relationship between Cabassous and Tolypeutes within Tolypeutinae. Finally, the phylogenetic position of the subfamily Chlamyphorinae is resolved by the noncoding sequence data set as the sister group of Tolypeutinae. The data provide a stable phylogenetic framework for further evolutionary investigations of xenarthrans and important information for defining conservation priorities to save the diversity of one of the most curious groups of mammals.

  18. Repeatability & Workability Evaluation of SIGMOD 2009

    Manegold, Stefan


    SIGMOD 2008 was the first database conference that offered to test submitters\\' programs against their data to verify the repeatability of the experiments published [1]. Given the positive feedback concerning the SIGMOD 2008 repeatability initiative, SIGMOD 2009 modified and expanded the initiative with a workability assessment.

  19. Instability of the expanded (CTG){sub n} repeats in the myotonin protein kinase gene in cultured lymphoblastoid cell lines from patients with myotonic dystrophy

    Ashizawa, Tetsuo; Patel, B.J.; Monckton, D.G. [Baylor College of Medicine, Houston, TX (United States)] [and other


    The mutation associated with myotonic dystrophy (DM) is the expansion of an unstable trinucleotide repeat, (CTG){sub n}, in the 3{prime}-untranslated region of the myotonin protein kinase gene. Although expanded repeats show both germline and somatic instability, the mechanisms of the instability are poorly understood. To establish a model system in which somatic instability of the DM repeat could be studied in more detail, we established lymphoblastoid cell lines (LBCL) from DM patients. Analysis of the DNA from DM LBCL using Southern blotting showed that the (CTG). repeats were apparently stable up to 29 passages in culture. To study infrequent repeat size mutations that are undetectable due to the size heterogeneity, we established LBCL of single-cell origins by cloning using multiple steps of limiting dilution. After expansion to approximately 10{sup 6} cells (equivalent to approximately 20 cell cycles), the DNAs of these cell lines were analyzed by the small pool PCR technique using primers flanking the (CTG), repeat region. Two types of mutations of the expanded (CTG){sub n} repeat alleles were detected: (1) frequent mutations that show small changes of the (CTG){sub n} repeat size, resulting in alleles in a normal distribution around the progenitor allele, and (2) relatively rare mutations with large changes of the (CTG){sub n} repeat size, with a bias toward contraction. The former may represent the mechanism responsible for the so matic heterogeneity of the (CTG), repeat size observe in blood cells of DM patients. This in vitro experimental system will be useful for further studies on mechanisms involved in the regulation of the somatic stability of the (CTG). repeats in DM. 24 refs., 4 figs.

  20. A regional inventory of the landslide processes and the elements at risk on the Rift flanks west of Lake Kivu (DRC)

    Maki Mateso, Jean-Claude; Monsieurs, Elise; Jacobs, Liesbet; Bagalwa Mateso, Luc; Fiama Bondo, Silvanos; Delvaux, Damien; Albino, Fabien; Kervyn, François; Dewitte, Olivier


    The Rift flanks west of Lake Kivu (DRC) are one of the Congolese regions most affected by fatal landslides. However, information on the distribution of these processes and their impact on society is still lacking. Here we present a first regional landslide inventory and the associated elements at risk. The inventory was conducted in an area of 5,700 km² in three administrative territories between the cities of Bukavu and Goma. The region is one of the most densely populated area of DRC with a density of up to 200 persons/km². The approach for the inventory relies on visual analysis of Google Earth imagery and a 5 m resolution DEM that we produced from TanDEM-X interferometry. Field validation was performed in target places accounting for 5% of the study area. More than 2,000 landslides were mapped and distinction was made between deep and shallow, and slide and flow processes. Average landslide area is 6 ha (max. = 430 ha). Geomorphological analysis of landslide distribution shows topographic, lithologic, climatic and seismic controls. For 600 randomly-selected landslides, elements at risk (house, road, cultivated land, river) were inventoried in the areas affected and potentially affected by the instabilities; 10% of the landslides are inhabited and 25% do not present any risk. Numerous landslides have caused direct and indirect damage in recent years. In some places, the impact of mining activities on slope stability can be important. Google Earth was the only way to locate the recent shallow failures triggered by known extreme rainfall events. This inventory is a first step towards the understanding of the landslide processes in the region. Further studies are needed to complete and validate the information, to better infer about the triggers, and to compute susceptibility and risk maps.

  1. Structure and promoter activity of the 5' flanking region of ace-1, the gene encoding acetylcholinesterase of class A in Caenorhabditis elegans.

    Culetto, E; Combes, D; Fedon, Y; Roig, A; Toutant, J P; Arpagaus, M


    We report the structure and the functional activity of the promoter region of ace-1, the gene encoding acetylcholinesterase of class A in the nematode Caenorhabditis elegans. We found that ace-1 was trans -spliced to the SL1 spliced leader and that transcription was initiated at a cluster of multiple starts. There was neither a TATA nor a CAAT box at consensus distances from these starts. Interspecies sequence comparison of the 5' regions of ace-1 in C. elegans and in the related nematode Caenorhabditis briggsae identified four blocks of conserved sequences located within a sequence of 2.4 kilobases upstream from the initiator ATG. In vitro expression of CAT reporter genes in mammalian cells allowed the determination of a minimal promoter in the first 288 nucleotides. In phenotype rescue experiments in vivo, the ace-1 gene containing 2.4 kilobases of 5' flanking region of either C. elegans or C. briggsae was found to restore a coordinated mobility to the uncoordinated double mutants ace-1(-);ace-2(-)of C. elegans. This showed that the ace-1 promoter was contained in 2.4 kilobases of the 5' region, and indicated that cis -regulatory elements as well as coding sequences of ace-1 were functionally conserved between the two nematode species. The pattern of ace-1 expression was established through microinjection of Green Fluorescent Protein reporter gene constructs and showed a major mesodermal expression. Deletion analysis showed that two of the four blocks of conserved sequences act as tissue-specific activators. The distal block is a mesodermal enhancer responsible for the expression in body wall muscle cells, anal sphincter and vulval muscle cells. Another block of conserved sequence directs expression in pharyngeal muscle cells pm5 and three pairs of cephalic sensory neurons. Copyright 1999 Academic Press.

  2. The membrane-binding domain of an amphitropic enzyme suppresses catalysis by contact with an amphipathic helix flanking its active site.

    Huang, Harris K-H; Taneva, Svetla G; Lee, Jaeyong; Silva, Leslie P; Schriemer, David C; Cornell, Rosemary B


    CTP:phosphocholine cytidylyltransferase (CCT), the regulatory enzyme in the synthesis of phosphatidylcholine, is activated by binding membranes using a lipid-induced amphipathic helix (domain M). Domain M functions to silence catalysis when CCT is not membrane engaged. The silencing mechanism is unknown. We used photo-cross-linking and mass spectrometry to identify contacts between domain M and other CCT domains in its soluble form. Each of four sites in domain M forged cross-links to the same set of peptides that flank the active site and overlap at helix αE at the base of the active site. These cross-links were broken in the presence of activating lipid vesicles. Mutagenesis of domain M revealed that multiple hydrophobic residues within a putative auto-inhibitory (AI) motif contribute to the contact with helix αE and silencing. Helix αE was confirmed as the docking site for domain M by deuterium exchange analysis. We compared the dynamics and fold stability of CCT domains by site-directed fluorescence anisotropy and urea denaturation. The results suggest a bipartite structure for domain M: a disordered N-terminal portion and an ordered C-terminal AI motif with an unfolding transition identical with that of helix αE. Reduction in hydrophobicity of the AI motif decreased its order and fold stability, as did deletion of the catalytic domain. These results support a model in which catalytic silencing is mediated by the docking of an amphipathic AI motif onto the amphipathic helices αE. An unstructured leash linking αE with the AI motif may facilitate both the silencing contact and its membrane-triggered disruption. Copyright © 2012 Elsevier Ltd. All rights reserved.

  3. The 5'-flanking region of the RP58 coding sequence shows prominent promoter activity in multipolar cells in the subventricular zone during corticogenesis.

    Ohtaka-Maruyama, C; Hirai, S; Miwa, A; Takahashi, A; Okado, H


    Pyramidal neurons of the neocortex are produced from progenitor cells located in the neocortical ventricular zone (VZ) and subventricular zone (SVZ) during embryogenesis. RP58 is a transcriptional repressor that is strongly expressed in the developing brain and plays an essential role in corticogenesis. The expression of RP58 is strictly regulated in a time-dependent and spatially restricted manner. It is maximally expressed in E15-16 embryonic cerebral cortex, localized specifically to the cortical plate and SVZ of the neocortex, hippocampus, and parts of amygdala during brain development, and found in glutamatergic but not GABAergic neurons. Identification of the promoter activity underlying specific expression patterns provides important clues to their mechanisms of action. Here, we show that the RP58 gene promoter is activated prominently in multipolar migrating cells, the first in vivo analysis of RP58 promoter activity in the brain. The 5.3 kb 5'-flanking genomic DNA of the RP58 coding region demonstrates promoter activity in neurons both in vitro and in vivo. This promoter is highly responsive to the transcription factor neurogenin2 (Ngn2), which is a direct upstream activator of RP58 expression. Using in utero electroporation, we demonstrate that RP58 gene promoter activity is first detected in a subpopulation of pin-like VZ cells, then prominently activated in migrating multipolar cells in the multipolar cell accumulation zone (MAZ) located just above the VZ. In dissociated primary cultured cortical neurons, RP58 promoter activity mimics in vivo expression patterns from a molecular standpoint that RP58 is expressed in a fraction of Sox2-positive progenitor cells, Ngn2-positive neuronal committed cells, and Tuj1-positive young neurons, but not in Dlx2-positive GABAergic neurons. Finally, we show that Cre recombinase expression under the control of the RP58 gene promoter is a feasible tool for conditional gene switching in post-mitotic multipolar migrating

  4. Optimizing prostate biopsy for repeat transrectal prostate biopsies patients

    Xiaojun Deng; Jianwei Cao; Feng Liu; Weifeng Wang; Jidong Hao; Jiansheng Wan; Hui Liu


    Objective:Diagnosis of patients with negative prostate biopsy and persistent suspicion of prostate cancer re-mains a serious problem. In this study, we investigated the application of optimizing prostate biopsy for patients who need repeat prostate biopsy. Methods:In this prospective, non-randomized phase-I clinical trial, the prostate cancer detection rate of initial detection scheme was compared with optimizing prostate biopsy scheme. The number of punctures of initial detection scheme was the same as that of optimizing prostate biopsy scheme. The puncture direction of optimizing prostate biopsy was a 45° angle to the sagittal plane from front, middle, and back. The two cores from each lateral lobe were horizontal y inwardly inclined 45°. Results:A total of 45 patients with initial negative biopsy for cancer were received the optimizing prostate biopsy scheme. The cancer detection rate was 17.8%(8/45), and prostate intraepithelial neoplasm (PIN) was 6.7%(3/45). The pa-tients receiving repeat transrectal prostate biopsies were pathological y diagnosed as lower Gleason grade prostate cancers. Conclusion:The cancer detection rate of repeat biopsy prostate cancer is lower than that of initial biopsy. Our study showed that the optimizing prostate biopsy is important to improve the detection rate of repeat transrectal prostate biopsies patients.

  5. Shear-wave polarization alignment on the eastern flank of Mt. Etna volcano (Sicily, Italy

    G. Vilardo


    Full Text Available Recently, with the improvement of three-component seismic networks, studies revealing anisotropic characteristics in different regions have assumed great interest. In a complex volcanic area like Mt. Etna (Sicily, Italy, the existence of both iso-oriented fault systems and intrusive bodies consisting of olivine and clinopyroxene suggest the presence of anisotropic structures. In order to investigate this we analyzed the physical phenomenon of shear-wave splitting since under certain constraints, shear waves are less sensitive to local heterogeneity. The aims of this paper are: 1 to evaluate if in a structural complex situation like that at Mt. Etna the signal crossing an anisotropic volume could be enhanced in spite of effects due to undirectional properties along the source-receiver path; 2 to investigate the correlations, if any, between polarization direction of the leading shear wave and the patterns of compressive stress acting on the investigated area. Therefore we measured time-delays between the S-onsets on the horizontal components of 3D seismograms to reveal the possible seismic anisotropy in the Etnean region; moreover, we analyzed the polarization vector of shear-waves seismic data recorded during a survey carried out in the spring-summer 1988. We found clear evidence of splitting that we attributed to the presence of an anisotropic volume not homogeneously distributed on the eastern slope of Mt. Etna volcano.

  6. Grating-flanked plasmonic coaxial apertures for efficient fiber optical tweezers.

    Saleh, Amr A E; Sheikhoelislami, Sassan; Gastelum, Steven; Dionne, Jennifer A


    Subwavelength plasmonic apertures have been foundational for direct optical manipulation of nanoscale specimens including sub-100 nm polymeric beads, metallic nanoparticles and proteins. While most plasmonic traps result in two-dimensional localization, three-dimensional manipulation has been demonstrated by integrating a plasmonic aperture on an optical fiber tip. However, such 3D traps are usually inefficient since the optical mode of the fiber and the subwavelength aperture only weakly couple. In this paper we design more efficient optical-fiber-based plasmonic tweezers combining a coaxial plasmonic aperture with a plasmonic grating coupler at the fiber tip facet. Using full-field finite difference time domain analysis, we optimize the grating design for both gold and silver fiber-based coaxial tweezers such that the optical transmission through the apertures is maximized. With the optimized grating, we show that the maximum transmission efficiency increases from 2.5% to 19.6% and from 1.48% to 16.7% for the gold and silver structures respectively. To evaluate their performance as optical tweezers, we calculate the optical forces and the corresponding trapping potential on dielectric particles interacting with the apertures. We demonstrate that the enahncement in the transmission translates into an equivalent increase in the optical forces. Consequently, the optical power required to achieve stable optical trapping is significantly reduced allowing for efficient localization and 3D manipulation of sub-30 nm dielectric particles.

  7. Reward modulation of contextual cueing: Repeated context overshadows repeated target location.

    Sharifian, Fariba; Contier, Oliver; Preuschhof, Claudia; Pollmann, Stefan


    Contextual cueing can be enhanced by reward. However, there is a debate if reward is associated with the repeated target-distractor configurations or with the repeated target locations that occur in both repeated and new displays. Based on neuroimaging evidence, we hypothesized that reward becomes associated with the target location only in new displays, but not in repeated displays, where the repeated target location is overshadowed by the more salient repeated target-distractor configuration. To test this hypothesis, we varied the reward value associated with the same target location in repeated and new displays. The results confirmed the overshadowing hypothesis in that search facilitation in repeated target-distractor configurations was modulated by the variable value associated with the target location. This effect was observed mainly in early learning.

  8. High similarity between flanking regions of different microsatellites detected within each of two species of Lepidoptera: Parnassius apollo and Euphydryas aurinia.

    Meglecz, Emese; Petenian, Frederic; Danchin, Etienne; D'Acier, Armelle Coeur; Rasplus, Jean-Yves; Faure, Eric


    Microsatellite flanking regions have been compared in two butterfly species. Several microsatellite flanking regions showed high similarity to one another among different microsatellites within a same species, but very few similarities were found between species. This can be the consequence of either duplication/multiplication events involving large regions containing microsatellites or of microsatellites imbedded in minisatellite regions. The multiplication of microsatellites might also be linked to mobile elements. Furthermore, crossing over between nonhomologous microsatellites can lead to the exchange of the flanking regions between microsatellites. The same phenomenon was observed in both studied butterfly species but not in Aphis fabae (Hemiptera), which was screened at the same time using the same protocol. These findings might explain, at least partially, why microsatellite isolation in Lepidoptera has been relatively unsuccessful so far.

  9. Childhood experiences and repeated suicidal behavior

    Krarup, Gertrud; Nielsen, Bent; Rask, P


    The aim of this study was to elucidate the influence of various events in childhood on suicidal behavior in adult age. For this purpose, 99 patients admitted to the Department of Psychiatry of Odense University Hospital after making a suicide attempt were followed for 5 years, to register repeated...... suicidal behavior. The results showed that three fourths of the patients attempted suicide more than once (62% nonfatal and 14% fatal outcome). The sex distribution was about the same among the first-evers as among the repeaters. Most repeaters were younger people in their twenties and thirties......, and the first-evers on average were past the age of 40. Somewhat unexpectedly, significantly more repeaters than first-evers had grown up with both their parents. However, the results also showed that significantly more repeaters than first-evers had had an unhappy childhood. This indicates...

  10. UK 2009-2010 repeat station report

    Thomas J.G. Shanahan


    Full Text Available The British Geological Survey is responsible for conducting the UK geomagnetic repeat station programme. Measurements made at the UK repeat station sites are used in conjunction with the three UK magnetic observatories: Hartland, Eskdalemuir and Lerwick, to produce a regional model of the local field each year. The UK network of repeat stations comprises 41 stations which are occupied at approximately 3-4 year intervals. Practices for conducting repeat station measurements continue to evolve as advances are made in survey instrumentation and as the usage of the data continues to change. Here, a summary of the 2009 and 2010 UK repeat station surveys is presented, highlighting the measurement process and techniques, density of network, reduction process and recent results.

  11. Effect of Saw Palmetto Supplements on Androgen-Sensitive LNCaP Human Prostate Cancer Cell Number and Syrian Hamster Flank Organ Growth

    Alexander B. Opoku-Acheampong


    Full Text Available Saw palmetto supplements (SPS are commonly consumed by men with prostate cancer. We investigated whether SPS fatty acids and phytosterols concentrations determine their growth-inhibitory action in androgen-sensitive LNCaP cells and hamster flank organs. High long-chain fatty acids-low phytosterols (HLLP SPS ≥ 750 nM with testosterone significantly increased and ≥500 nM with dihydrotestosterone significantly decreased LNCaP cell number. High long-chain fatty acids-high phytosterols (HLHP SPS ≥ 500 nM with dihydrotestosterone and high medium-chain fatty acids-low phytosterols (HMLP SPS ≥ 750 nM or with androgens significantly decreased LNCaP cell number (n=3; p<0.05. Five- to six-week-old, castrated male Syrian hamsters were randomized to control (n=4, HLLP, HLHP, and HMLP SPS (n=6 groups. Testosterone or dihydrotestosterone was applied topically daily for 21 days to the right flank organ; the left flank organ was treated with ethanol and served as the control. Thirty minutes later, SPS or ethanol was applied to each flank organ in treatment and control groups, respectively. SPS treatments caused a notable but nonsignificant reduction in the difference between left and right flank organ growth in testosterone-treated SPS groups compared to the control. The same level of inhibition was not seen in dihydrotestosterone-treated SPS groups (p<0.05. Results may suggest that SPS inhibit 5α-reductase thereby preventing hamster flank organ growth.

  12. Directed PCR-free engineering of highly repetitive DNA sequences

    Preissler Steffen


    Full Text Available Abstract Background Highly repetitive nucleotide sequences are commonly found in nature e.g. in telomeres, microsatellite DNA, polyadenine (poly(A tails of eukaryotic messenger RNA as well as in several inherited human disorders linked to trinucleotide repeat expansions in the genome. Therefore, studying repetitive sequences is of biological, biotechnological and medical relevance. However, cloning of such repetitive DNA sequences is challenging because specific PCR-based amplification is hampered by the lack of unique primer binding sites resulting in unspecific products. Results For the PCR-free generation of repetitive DNA sequences we used antiparallel oligonucleotides flanked by restriction sites of Type IIS endonucleases. The arrangement of recognition sites allowed for stepwise and seamless elongation of repetitive sequences. This facilitated the assembly of repetitive DNA segments and open reading frames encoding polypeptides with periodic amino acid sequences of any desired length. By this strategy we cloned a series of polyglutamine encoding sequences as well as highly repetitive polyadenine tracts. Such repetitive sequences can be used for diverse biotechnological applications. As an example, the polyglutamine sequences were expressed as His6-SUMO fusion proteins in Escherichia coli cells to study their aggregation behavior in vitro. The His6-SUMO moiety enabled affinity purification of the polyglutamine proteins, increased their solubility, and allowed controlled induction of the aggregation process. We successfully purified the fusions proteins and provide an example for their applicability in filter retardation assays. Conclusion Our seamless cloning strategy is PCR-free and allows the directed and efficient generation of highly repetitive DNA sequences of defined lengths by simple standard cloning procedures.

  13. Telling the Story of Ridge Flank Research to all Ages and Audiences

    Cooper, S. K.; Brennon, R.; Hamner, K.; Kane, J.; Ringlein, J.; Strong, L. R.; Orcutt, B. N.; Fisher, A. T.; Edwards, K. J.; Cowen, J. P.; Hulme, S.; Wheat, C. G.; Scientific Team of Expedition AT18-07


    this experience directly on the team members. Special thanks to the Center for Dark Energy Biosphere Investigations and Deep Earth Academy for sponsoring this work.

  14. Periodicity and repeatability in data

    Southwood, D.

    Using magnetic data from the first two years in Saturn orbit, the basic periodicity of apparent is examined with the aim of elucidating the `cam' shaft model of Espinosa et al. (2003) identifying the nature of the `cam' and giving a definitive period for its rotation. An initial hypothesis, supported by the spectral analysis of analysis of the first 8 months in orbit Gianpieri et al. (2006), is made that the source of the period is linked to something inside the planet and therefore that the source inertia means that the period effectively does not change over the 2 years. Moreover one expects that the source phase is fixed. Using this approach, not only can the period identified by spectral analysis (647.1 + 0.6 min.) be verified but also by phase analysis between successive passes over the 2 years the period can be refined to 647.6 + 0.1 min. The signal itself is remarkably reproducible from pass to pass. It appears in all three components of the field and its polarisation is unambiguously not attributable to direct detection of an internal field. Not only does the signal not decay rapidly with distance from the planet, but although it has the m=1 symmetry of a tilted dipole, the field lines diverge from the planet indicating an exterior source. This feature led to the `cam' model. The polarisation and comparisons of passes with different latitude profiles show a surprising north-south symmetry in the azimuthal field. The absence of asymmetry with respect to the magnetic equator rules out a direct magnetospheric-ionospheric interaction source. Accordingly, it is proposed that the basic `cam' effect is generated by a single hemisphere anomaly which creates hemisphere to hemisphere field aligned currents. The existence of Saturn phase related anomaly appears to produce a basic asymmetry in the inner magnetosphere that sets the phase of both an inflowing and outflowing sector in a rotating circulation system.

  15. A simple repeat polymorphism in the MITF-M promoter is a key regulator of white spotting in dogs.

    Izabella Baranowska Körberg

    Full Text Available The white spotting locus (S in dogs is colocalized with the MITF (microphtalmia-associated transcription factor gene. The phenotypic effects of the four S alleles range from solid colour (S to extreme white spotting (s(w. We have investigated four candidate mutations associated with the s(w allele, a SINE insertion, a SNP at a conserved site and a simple repeat polymorphism all associated with the MITF-M promoter as well as a 12 base pair deletion in exon 1B. The variants associated with white spotting at all four loci were also found among wolves and we conclude that none of these could be a sole causal mutation, at least not for extreme white spotting. We propose that the three canine white spotting alleles are not caused by three independent mutations but represent haplotype effects due to different combinations of causal polymorphisms. The simple repeat polymorphism showed extensive diversity both in dogs and wolves, and allele-sharing was common between wolves and white spotted dogs but was non-existent between solid and spotted dogs as well as between wolves and solid dogs. This finding was unexpected as Solid is assumed to be the wild-type allele. The data indicate that the simple repeat polymorphism has been a target for selection during dog domestication and breed formation. We also evaluated the significance of the three MITF-M associated polymorphisms with a Luciferase assay, and found conclusive evidence that the simple repeat polymorphism affects promoter activity. Three alleles associated with white spotting gave consistently lower promoter activity compared with the allele associated with solid colour. We propose that the simple repeat polymorphism affects cooperativity between transcription factors binding on either flanking sides of the repeat. Thus, both genetic and functional evidence show that the simple repeat polymorphism is a key regulator of white spotting in dogs.

  16. MARINE CONGLOMERATE AND REEF MEGACLASTS AT MAURITUS ISLAND: Evidences of a tsunami generated by a flank collapse of the PITON DE LA Fournaise volcano, Reunion Island?

    R. Paris


    Full Text Available Tsunamis related to volcano flank collapse are typically a high-magnitude, low frequency hazard for which evaluation and mitigation are difficult to address. In this short communication, we present field evidences of a large tsunami along the southern coast of Mauritius Island ca. 4400 years ago. Tsunami deposits described include both marine conglomerates and coral boulders up to 90 m3 (> 100 tons. The most probable origin of the tsunami is a flank collapse of Piton de la Fournaise volcano, Réunion Island.

  17. Late Holocene stratigraphy of the Tetimpa archaeological sites, northeast flank of Popocatepetl volcano, central Mexico

    Panfil, M.S.; Gardner, T.W.; Hirth, K.G.


    Late Holocene (240 km2 on the east side of the volcano with >25 cm of tephra. Lavas from eruptive sequence I dammed drainage in the lowland area near the town of San Nicolas and caused local upstream deposition of as much as 30 m of lacustrine silts, clays, and sands. These lacustrine deposits record an eruptive hiatus for the Tetimpa area of about 750 14C yr: between ca. 2100 and ca. 1350 yr B.P., no major tephras were deposited in the Tetimpa area. In upland areas, this time period is represented by an unconformity and by Entisols formed in the top of pumice deposits and lavas from eruptive sequence I. Artifacts, agricultural furrows, and dwellings record human reoccupation of this surface. At the end of this hiatus, several lahars were deposited above the lacustrine sequence and locally above the Entisol in upland positions adjacent to streams. Between ca. 1350 and ca. 1200 yr B.P., tephras from eruptive sequence II buried these paleosols, occupation sites, lacustrine sediments, and lahars. Andesitic (~62% SiO2) pumice lapilli deposits in the Tetimpa area record three pumice-fall eruptions directed northeast and east of the crater. The first and smallest of these (maximum Tetimpa area thickness = 12 cm; >52 km2 covered by >25 cm) took place at ca. 1350 yr B.P. and was accompanied by pyroclastic surge events preserved in the Tetimpa area by charcoal, sand waves, and cross-stratified sand-sized tephra. At ca. 1200 yr B.P., the products of two Plinian-style events and additional pyroclastic surges reached the Tetimpa area. The largest of these tephra-fall events covered the Tetimpa area with 0.5-1 m of tephra and blanketed an area of >230 km2 with a thickness of >25 cm. The Tetimpa record confirms two of the four periods of explosive volcanism recognized by studies conducted around Popocatepetl in the past 30 yr. Eruptive sequence I corresponds to the explosive period between 2100 and 2500 yr B.P., and eruptive sequence II corresponds to the period between 900 and

  18. Replication Stalling and Heteroduplex Formation within CAG/CTG Trinucleotide Repeats by Mismatch Repair

    Viterbo, David


    Trinucleotide repeat expansions are responsible for at least two dozen neurological disorders. Mechanisms leading to these large expansions of repeated DNA are still poorly understood. It was proposed that transient stalling of the replication fork by the repeat tract might trigger slippage of the newly-synthesized strand over its template, leading to expansions or contractions of the triplet repeat. However, such mechanism was never formally proven. Here we show that replication fork pausing and CAG/CTG trinucleotide repeat instability are not linked, stable and unstable repeats exhibiting the same propensity to stall replication forks when integrated in a yeast natural chromosome. We found that replication fork stalling was dependent on the integrity of the mismatch-repair system, especially the Msh2p-Msh6p complex, suggesting that direct interaction of MMR proteins with secondary structures formed by trinucleotide repeats in vivo, triggers replication fork pauses. We also show by chromatin immunoprecipitation that Msh2p is enriched at trinucleotide repeat tracts, in both stable and unstable orientations, this enrichment being dependent on MSH3 and MSH6. Finally, we show that overexpressing MSH2 favors the formation of heteroduplex regions, leading to an increase in contractions and expansions of CAG/CTG repeat tracts during replication, these heteroduplexes being dependent on both MSH3 and MSH6. These heteroduplex regions were not detected when a mutant msh2-E768A gene in which the ATPase domain was mutated was overexpressed. Our results unravel two new roles for mismatch-repair proteins: stabilization of heteroduplex regions and transient blocking of replication forks passing through such repeats. Both roles may involve direct interactions between MMR proteins and secondary structures formed by trinucleotide repeat tracts, although indirect interactions may not be formally excluded.

  19. LRRCE: a leucine-rich repeat cysteine capping motif unique to the chordate lineage

    Bishop Paul N


    Full Text Available Abstract Background The small leucine-rich repeat proteins and proteoglycans (SLRPs form an important family of regulatory molecules that participate in many essential functions. They typically control the correct assembly of collagen fibrils, regulate mineral deposition in bone, and modulate the activity of potent cellular growth factors through many signalling cascades. SLRPs belong to the group of extracellular leucine-rich repeat proteins that are flanked at both ends by disulphide-bonded caps that protect the hydrophobic core of the terminal repeats. A capping motif specific to SLRPs has been recently described in the crystal structures of the core proteins of decorin and biglycan. This motif, designated as LRRCE, differs in both sequence and structure from other, more widespread leucine-rich capping motifs. To investigate if the LRRCE motif is a common structural feature found in other leucine-rich repeat proteins, we have defined characteristic sequence patterns and used them in genome-wide searches. Results The LRRCE motif is a structural element exclusive to the main group of SLRPs. It appears to have evolved during early chordate evolution and is not found in protein sequences from non-chordate genomes. Our search has expanded the family of SLRPs to include new predicted protein sequences, mainly in fishes but with intriguing putative orthologs in mammals. The chromosomal locations of the newly predicted SLRP genes would support the large-scale genome or gene duplications that are thought to have occurred during vertebrate evolution. From this expanded list we describe a new class of SLRP sequences that could be representative of an ancestral SLRP gene. Conclusion Given its exclusivity the LRRCE motif is a useful annotation tool for the identification and classification of new SLRP sequences in genome databases. The expanded list of members of the SLRP family offers interesting insights into early vertebrate evolution and suggests an

  20. Leakage of active crater lake brine through the north flank at Rincon de la Vieja volcano, northwest Costa Rica, and implications for crater collapse

    Kempter, K.A.; Rowe, G.L.


    The Active Crater at Rincon de la Vieja volcano, Costa Rica, reaches an elevation of 1750 m and contains a warm, hyper-acidic crater lake that probably formed soon after the eruption of the Rio Blanco tephra deposit approximately 3500 years before present. The Active Crater is buttressed by volcanic ridges and older craters on all sides except the north, which dips steeply toward the Caribbean coastal plains. Acidic, above-ambient-temperature streams are found along the Active Crater's north flank at elevations between 800 and 1000 m. A geochemical survey of thermal and non-thermal waters at Rincon de la Vieja was done in 1989 to determine whether hyper-acidic fluids are leaking from the Active Crater through the north flank, affecting the composition of north-flank streams. Results of the water-chemistry survey reveal that three distinct thermal waters are found on the flanks of Rincon de la Vieja volcano: acid chloride-sulfate (ACS), acid sulfate (AS), and neutral chloride (NC) waters. The most extreme ACS water was collected from the crater lake that fills the Active Crater. Chemical analyses of the lake water reveal a hyper-acidic (pH ~ 0) chloride-sulfate brine with elevated concentrations of calcium, magnesium, aluminum, iron, manganese, copper, zinc, fluorine, and boron. The composition of the brine reflects the combined effects of magmatic degassing from a shallow magma body beneath the Active Crater, dissolution of andesitic volcanic rock, and evaporative concentration of dissolved constituents at above-ambient temperatures. Similar cation and anion enrichments are found in the above-ambient-temperature streams draining the north flank of the Active Crater. The pH of north-flank thermal waters range from 3.6 to 4.1 and chloride:sulfate ratios (1.2-1.4) that are a factor of two greater than that of the lake brine (0.60). The waters have an ACS composition that is quite different from the AS and NC thermal waters that occur along the southern flank of Rincon

  1. Leakage of Active Crater lake brine through the north flank at Rincón de la Vieja volcano, northwest Costa Rica, and implications for crater collapse

    Kempter, K. A.; Rowe, G. L.


    The Active Crater at Rincón de la Vieja volcano, Costa Rica, reaches an elevation of 1750 m and contains a warm, hyper-acidic crater lake that probably formed soon after the eruption of the Rio Blanco tephra deposit approximately 3500 years before present. The Active Crater is buttressed by volcanic ridges and older craters on all sides except the north, which dips steeply toward the Caribbean coastal plains. Acidic, above-ambient-temperature streams are found along the Active Crater's north flank at elevations between 800 and 1000 m. A geochemical survey of thermal and non-thermal waters at Rincón de la Vieja was done in 1989 to determine whether hyper-acidic fluids are leaking from the Active Crater through the north flank, affecting the composition of north-flank streams. Results of the water-chemistry survey reveal that three distinct thermal waters are found on the flanks of Rincón de la Vieja volcano: acid chloride-sulfate (ACS), acid sulfate (AS), and neutral chloride (NC) waters. The most extreme ACS water was collected from the crater lake that fills the Active Crater. Chemical analyses of the lake water reveal a hyper-acidic (pH∼0) chloride-sulfate brine with elevated concentrations of calcium, magnesium, aluminum, iron, manganese, copper, zinc, fluorine, and boron. The composition of the brine reflects the combined effects of magmatic degassing from a shallow magma body beneath the Active Crater, dissolution of andesitic volcanic rock, and evaporative concentration of dissolved constituents at above-ambient temperatures. Similar cation and anion enrichments are found in the above-ambient-temperature streams draining the north flank of the Active Crater. The pH of north-flank thermal waters range from 3.6 to 4.1 and chloride:sulfate ratios (1.2-1.4) that are a factor of two greater than that of the lake brine (0.60). The waters have an ACS composition that is quite different from the AS and NC thermal waters that occur along the southern flank of

  2. Far-Field Tsunami Impact in the North Atlantic Basin from Large Scale Flank Collapses of the Cumbre Vieja Volcano, La Palma

    Tehranirad, Babak; Harris, Jeffrey C.; Grilli, Annette R.; Grilli, Stephan T.; Abadie, Stéphane; Kirby, James T.; Shi, Fengyan


    In their pioneering work, Ward and Day suggested that a large scale flank collapse of the Cumbre Vieja Volcano (CVV) on La Palma (Canary Islands) could trigger a mega-tsunami throughout the North Atlantic Ocean basin, causing major coastal impact in the far-field. While more recent studies indicate that near-field waves from such a collapse would be more moderate than originally predicted by Ward and Day [Løvholt et al. (J Geophy Res 113:C09026, 2008); Abadie et al. (J Geophy Res 117:C05030, 2012)], these would still be formidable and devastate the Canary Island, while causing major impact in the far-field at many locations along the western European, African, and the US east coasts. Abadie et al. (J Geophy Res 117:C05030, 2012) simulated tsunami generation and near-field tsunami impact from a few CVV subaerial slide scenarios, with volumes ranging from 20 to 450 km^3; the latter representing the most extreme scenario proposed by Ward and Day. They modeled tsunami generation, i.e., the tsunami source, using THETIS, a 3D Navier-Stokes (NS) multi-fluid VOF model, in which slide material was considered as a nearly inviscid heavy fluid. Near-field tsunami impact was then simulated for each source using FUNWAVE-TVD, a dispersive and fully nonlinear long wave Boussinesq model [ Shi et al. (Ocean Modell 43-44:36-51, 2012); Kirby et al. (Ocean Modeling, 62:39-55, 2013)]. Here, using FUNWAVE-TVD for a series of nested grids of increasingly fine resolution, we model and analyze far-field tsunami impact from two of Abadie et al.'s extreme CVV flank collapse scenarios: (i) that deemed the most "credible worst case scenario" based on a slope stability analysis, with a 80 km^3 volume; and (ii) the most extreme scenario, similar to Ward and Day's, with a 450 km^3 volume. Simulations are performed using a one-way coupling scheme in between two given levels of nested grids. Based on the simulation results, the overall tsunami impact is first assessed in terms of maximum surface

  3. The child accident repeater: a review.

    Jones, J G


    The child accident repeater is defined as one who has at least three accidents that come to medical attention within a year. The accident situation has features in common with those of the child who has a single accident through simple "bad luck", but other factors predispose him to repeated injury. In the child who has a susceptible personality, a tendency for accident repetition may be due to a breakdown in adjustment to a stressful environment. Prevention of repeat accidents should involve the usual measures considered appropriate for all children as well as an attempt to provide treatment of significant maladjustment and modification of a stressful environment.

  4. (AC)n dinucleotide repeat polymorphism in 5' beta-globin gene in native and Mestizo Mexican populations.

    Peñaloza, R; Delgado, P; Arenas, D; Barrientos, C; Buentello, L; Loeza, F; Salamanca, F


    Repeated sequences are dispersed along the human genome. These sequences are useful as markers in diagnosis of inherited diseases, in forensic medicine, and in tracking the origin and evolution of human populations. The (AC)n repeated element is the most frequent in the human genome. In this paper, the (AC)n repeated element located in the 5' flanking region of the beta-globin gene was studied by single-strand conformation polymorphism (SSCP). Four ethnic Mexican groups (Mixteca, Nahua, Otomí, Purépecha) and a Mestizo population were analyzed. We observed three alleles, A [(AC)16, B [(AC)14], and C [(AC)18], with a frequency of between 68.2% and 86.9%, 13.1% and 18.2%, and 6.7% and 13.7%, respectively. Allele C was present only in Purépecha and Mestizo groups. The absence of this allele in the other ethnic groups studied suggests that there is low genetic admixture of Purépecha and that this is a relatively isolated population. However, it could be that the C allele occurs in low frequencies in the other groups as a result of small sample sizes. The (AC)n repeat polymorphism in the beta-globin gene has not been previously studied in Amerindian populations.

  5. Quantum repeaters based on atomic ensembles and linear optics

    Sangouard, Nicolas; Simon, Christoph; de Riedmatten, Hugues; Gisin, Nicolas


    The distribution of quantum states over long distances is limited by photon loss. Straightforward amplification as in classical telecommunications is not an option in quantum communication because of the no-cloning theorem. This problem could be overcome by implementing quantum repeater protocols, which create long-distance entanglement from shorter-distance entanglement via entanglement swapping. Such protocols require the capacity to create entanglement in a heralded fashion, to store it in quantum memories, and to swap it. One attractive general strategy for realizing quantum repeaters is based on the use of atomic ensembles as quantum memories, in combination with linear optical techniques and photon counting to perform all required operations. Here the theoretical and experimental status quo of this very active field are reviewed. The potentials of different approaches are compared quantitatively, with a focus on the most immediate goal of outperforming the direct transmission of photons.

  6. Quantum repeaters based on atomic ensembles and linear optics

    Sangouard, Nicolas; de Riedmatten, Hugues; Gisin, Nicolas


    The distribution of quantum states over long distances is limited by photon loss. Straightforward amplification as in classical telecommunications is not an option in quantum communication because of the no-cloning theorem. This problem could be overcome by implementing quantum repeater protocols, which create long-distance entanglement from shorter-distance entanglement via entanglement swapping. Such protocols require the capacity to create entanglement in a heralded fashion, to store it in quantum memories, and to swap it. One attractive general strategy for realizing quantum repeaters is based on the use of atomic ensembles as quantum memories, in combination with linear optical techniques and photon counting to perform all required operations. Here we review the theoretical and experimental status quo of this very active field. We compare the potential of different approaches quantitatively, with a focus on the most immediate goal of outperforming the direct transmission of photons.

  7. Protocols and prospects for building a quantum repeater

    Loock, Peter van [Institute of Physics, Johannes Gutenberg Universitaet Mainz (Germany)


    An overview will be given of various approaches to implementing a quantum repeater for quantum communication over large distances. This includes a discussion of systems and protocols that are experimentally feasible and thus realizable in the midterm in order to go beyond the current limit of a few hundred km given by direct quantum-state transmissions. At the same time, these schemes should be, in principle, scalable to arbitrary distances. In this context, the influence of various elements and strategies in a quantum repeater protocol on the final fidelities and rates are addressed: initial entanglement distribution, Bell measurements, multiplexing, postselection, quantum memories, and quantum error detection/correction. Solely on the hardware side, the differences in using just single quanta or instead employing many quanta for the flying (photons) and the stationary (atoms) qubits are pointed out.

  8. A high stability and repeatability electrochemical scanning tunneling microscope

    Xia, Zhigang; Wang, Jihao; Lu, Qingyou, E-mail: [High Magnetic Field Laboratory, Chinese Academy of Sciences and University of Science and Technology of China, Hefei, Anhui 230026 (China); Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026 (China); Hou, Yubin [High Magnetic Field Laboratory, Chinese Academy of Sciences and University of Science and Technology of China, Hefei, Anhui 230026 (China)


    We present a home built electrochemical scanning tunneling microscope (ECSTM) with very high stability and repeatability. Its coarse approach is driven by a closely stacked piezo motor of GeckoDrive type with four rigid clamping points, which enhances the rigidity, compactness, and stability greatly. It can give high clarity atomic resolution images without sound and vibration isolations. Its drifting rates in XY and Z directions in solution are as low as 84 pm/min and 59 pm/min, respectively. In addition, repeatable coarse approaches in solution within 2 mm travel distance show a lateral deviation less than 50 nm. The gas environment can be well controlled to lower the evaporation rate of the cell, thus reducing the contamination and elongating the measurement time. Atomically resolved SO{sub 4}{sup 2−} image on Au (111) work electrode is demonstrated to show the performance of the ECSTM.

  9. Preliminary Mineralogic and Stable Isotope Studies of Altered Summit and Flank Rocks and Osceola Mudflow Deposits on Mount Rainier, Washington

    Rye, Robert O.; Breit, George N.; Zimbelman, David R.


    About 5600 years ago part of Mount Rainier?s edifice collapsed with the resultant Osceola Mudflow traveling more than 120 km and covering an area of at least 505 km2. Mineralogic and stable isotope studies were conducted on altered rocks from outcrops near the summit and east flank of the volcano and samples of clasts and matrix from the Osceola Mudflow. Results of these analyses are used to constrain processes responsible for pre-collapse alteration and provide insight into the role of alteration in edifice instability prior to the Osceola collapse event. Jarosite, pyrite, alunite, and kaolinite occur in hydrothermally altered rock exposed in summit scarps formed by edifice collapse events and in altered rock within the east-west structural zone (EWSZ) of the volcano?s east flank. Deposits of the Osceola Mudflow contain clasts of variably altered and unaltered andesite within a clay-rich matrix. Minerals detected in samples from the edifice are also present in many of the clasts. The matrix includes abundant smectite, kaolinite and variably abundant jarosite. Hydrothermal fluid compositions calculated from hydrogen and oxygen isotope data of alunite, and smectite on Mount Rainier reflect mixing of magmatic and meteoric waters. The range in the dD values of modern meteoric water on the volcano (-85 to 155?) reflect the influence of elevation on the dD of precipitation. The d34S and d18OSO4 values of alunite, gypsum and jarosite are distinct but together range from 1.7 to 17.6? and -12.3 to 15.0?, respectively; both parameters increase from jarosite to gypsum to alunite. The variations in sulfur isotope composition are attributed to the varying contributions of disproportionation of magmatic SO2, the supergene oxidation of hydrothermal pyrite and possible oxidation of H2S to the parent aqueous sulfate. The 18OSO4 values of jarosite are the lowest recorded for the mineral, consistent with a supergene origin. The mineralogy and isotope composition of alteration

  10. Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals.

    Patel, Vidushi S; Cooper, Steven J B; Deakin, Janine E; Fulton, Bob; Graves, Tina; Warren, Wesley C; Wilson, Richard K; Graves, Jennifer A M


    Vertebrate alpha (alpha)- and beta (beta)-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin locus, the alpha- and beta-globin clusters expanded, and then were separated onto different chromosomes. The previous finding of a fossil beta-globin gene (omega) in the marsupial alpha-cluster, however, suggested that duplication of the alpha-beta cluster onto two chromosomes, followed by lineage-specific gene loss and duplication, produced paralogous alpha- and beta-globin clusters in birds and mammals. Here we analyse genomic data from an egg-laying monotreme mammal, the platypus (Ornithorhynchus anatinus), to explore haemoglobin evolution at the stem of the mammalian radiation. The platypus alpha-globin cluster (chromosome 21) contains embryonic and adult alpha- globin genes, a beta-like omega-globin gene, and the GBY globin gene with homology to cytoglobin, arranged as 5'-zeta-zeta'-alphaD-alpha3-alpha2-alpha1-omega-GBY-3'. The platypus beta-globin cluster (chromosome 2) contains single embryonic and adult globin genes arranged as 5'-epsilon-beta-3'. Surprisingly, all of these globin genes were expressed in some adult tissues. Comparison of flanking sequences revealed that all jawed vertebrate alpha-globin clusters are flanked by MPG-C16orf35 and LUC7L, whereas all bird and mammal beta-globin clusters are embedded in olfactory genes. Thus, the mammalian alpha- and beta-globin clusters are orthologous to the bird alpha- and beta-globin clusters respectively. We propose that alpha- and beta-globin clusters evolved from an ancient MPG-C16orf35-alpha-beta-GBY-LUC7L arrangement 410 million years ago. A copy of the original beta (represented by omega in marsupials and monotremes) was inserted into an array of olfactory genes before the amniote radiation (>315 million years ago), then duplicated and diverged to form orthologous clusters of beta-globin genes with different expression

  11. Flank collapse at Mount Wrangell, Alaska, recorded by volcanic mass-flow deposits in the Copper River lowland

    Waythomas, C.F.; Wallace, K.L.


    An areally extensive volcanic mass-flow deposit of Pleistocene age, known as the Chetaslina volcanic mass-flow deposit, is a prominent and visually striking deposit in the southeastern Copper River lowland of south-central Alaska. The mass-flow deposit consists of a diverse mixture of colorful, variably altered volcanic rocks, lahar deposits, glaciolacustrine diamicton, and till that record a major flank collapse on the southwest flank of Mount Wrangell. The deposit is well exposed near its presumed source, and thick, continuous, stratigraphic exposures have permitted us to study its sedimentary characteristics as a means of better understanding the origin, significance, and evolution of the deposit. Deposits of the Chetaslina volcanic mass flow in the Chetaslina River drainage are primary debris-avalanche deposits and consist of two principal facies types, a near-source block facies and a distal mixed facies. The block facies is composed entirely of block-supported, shattered and fractured blocks with individual blocks up to 40 m in diameter. The mixed facies consists of block-sized particles in a matrix of poorly sorted rock rubble, sand, and silt generated by the comminution of larger blocks. Deposits of the Chetaslina volcanic mass flow exposed along the Copper, Tonsina, and Chitina rivers are debris-flow deposits that evolved from the debris-avalanche component of the flow and from erosion and entrainment of local glacial and glaciolacustrine diamicton in the Copper River lowland. The debris-flow deposits were probably generated through mixing of the distal debris avalanche with the ancestral Copper River, or through breaching of a debris-avalanche dam across the ancestral river. The distribution of facies types and major-element chemistry of clasts in the deposit indicate that its source was an ancestral volcanic edifice, informally known as the Chetaslina vent, on the southwest side of Mount Wrangell. A major sector collapse of the Chetaslina vent initiated

  12. Flank instability assessment at Kick-'em-Jenny submarine volcano (Grenada, Lesser Antilles): a multidisciplinary approach using experiments and modeling

    Dondin, F. J.-Y.; Heap, M. J.; Robertson, R. E. A.; Dorville, J.-F. M.; Carey, S.


    Kick-'em-Jenny (KeJ)—located ca. 8 km north of the island of Grenada—is the only active submarine volcano of the Lesser Antilles Volcanic Arc. Previous investigations of KeJ revealed that it lies within a collapse scar inherited from a past flank instability episode. To assess the likelihood of future collapse, we employ here a combined laboratory and modeling approach. Lavas collected using a remotely operated vehicle (ROV) provided samples to perform the first rock physical property measurements for the materials comprising the KeJ edifice. Uniaxial and triaxial deformation experiments showed that the dominant failure mode within the edifice host rock is brittle. Edifice fractures (such as those at Champagne Vent) will therefore assist the outgassing of the nearby magma-filled conduit, favoring effusive behavior. These laboratory data were then used as input parameters in models of slope stability. First, relative slope stability analysis revealed that the SW to N sector of the volcano displays a deficit of mass/volume with respect to a volcanoid (ideal 3D surface). Slope stability analysis using a limit equilibrium method (LEM) showed that KeJ is currently stable, since all values of stability factor or factor of safety (Fs) are greater than unity. The lowest values of Fs were found for the SW-NW sector of the volcano (the sector displaying a mass/volume deficit). Although currently stable, KeJ may become unstable in the future. Instability (severe reductions in Fs) could result, for example, from overpressurization due to the growth of a cryptodome. Our modeling has shown that instability-induced flank collapse will most likely initiate from the SW-NW sector of KeJ, therefore mobilizing a volume of at least ca. 0.7 km3. The mobilization of ca. 0.7 km3 of material is certainly capable of generating a tsunami that poses a significant hazard to the southern islands of the West Indies.

  13. Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals

    Warren Wesley C


    Full Text Available Abstract Background Vertebrate alpha (α- and beta (β-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin locus, the α- and β-globin clusters expanded, and then were separated onto different chromosomes. The previous finding of a fossil β-globin gene (ω in the marsupial α-cluster, however, suggested that duplication of the α-β cluster onto two chromosomes, followed by lineage-specific gene loss and duplication, produced paralogous α- and β-globin clusters in birds and mammals. Here we analyse genomic data from an egg-laying monotreme mammal, the platypus (Ornithorhynchus anatinus, to explore haemoglobin evolution at the stem of the mammalian radiation. Results The platypus α-globin cluster (chromosome 21 contains embryonic and adult α- globin genes, a β-like ω-globin gene, and the GBY globin gene with homology to cytoglobin, arranged as 5'-ζ-ζ'-αD-α3-α2-α1-ω-GBY-3'. The platypus β-globin cluster (chromosome 2 contains single embryonic and adult globin genes arranged as 5'-ε-β-3'. Surprisingly, all of these globin genes were expressed in some adult tissues. Comparison of flanking sequences revealed that all jawed vertebrate α-globin clusters are flanked by MPG-C16orf35 and LUC7L, whereas all bird and mammal β-globin clusters are embedded in olfactory genes. Thus, the mammalian α- and β-globin clusters are orthologous to the bird α- and β-globin clusters respectively. Conclusion We propose that α- and β-globin clusters evolved from an ancient MPG-C16orf35-α-β-GBY-LUC7L arrangement 410 million years ago. A copy of the original β (represented by ω in marsupials and monotremes was inserted into an array of olfactory genes before the amniote radiation (>315 million years ago, then duplicated and diverged to form orthologous clusters of β-globin genes with different expression profiles in different lineages.

  14. The Moral Maturity of Repeater Delinquents.

    Petronio, Richard J.


    Differences in moral development (as conceived by Kohlberg) were examined in a sample of delinquent teenagers. The repeater group was not found, as had been hypothesized, to be lower on moral maturity than those who engaged in less delinquency. (GC)

  15. Application of inter simple sequence repeat (ISSR) markers to plant genetics.

    Godwin, I D; Aitken, E A; Smith, L W


    Microsatellites or simple sequence repeats (SSRs) are ubiquitous in eukaryotic genomes. Single-locus SSR markers have been developed for a number of species, although there is a major bottleneck in developing SSR markers whereby flanking sequences must be known to design 5'-anchors for polymerase chain reaction (PCR) primers. Inter SSR (ISSR) fingerprinting was developed such that no sequence knowledge was required. Primers based on a repeat sequence, such as (CA)n, can be made with a degenerate 3'-anchor, such as (CA)8RG or (AGC)6TY. The resultant PCR reaction amplifies the sequence between two SSRs, yielding a multilocus marker system useful for fingerprinting, diversity analysis and genome mapping. PCR products are radiolabelled with 32P or 33P via end-labelling or PCR incorporation, and separated on a polyacrylamide sequencing gel prior to autoradiographic visualisation. A typical reaction yields 20-100 bands per lane depending on the species and primer. We have used ISSR fingerprinting in a number of plant species, and report here some results on two important tropical species, sorghum and banana. Previous investigators have demonstrated that ISSR analysis usually detects a higher level of polymorphism than that detected with restriction fragment length polymorphism (RFLP) or random amplified polymorphic DNA (RAPD) analyses. Our data indicate that this is not a result of greater polymorphism genetically, but rather technical reasons related to the detection methodology used for ISSR analysis.

  16. Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2

    Kenchappa, Chandra; Heiðarsson, Pétur Orri; Kragelund, Birthe;


    in facilitating high affinity DNA binding of Cbp2 by tethering the two domains. Structural studies on mutant proteins provide support for Cys(7) and Cys(28) enhancing high thermal stability of Cbp2(Hb) through disulphide bridge formation. Consistent with their proposed CRISPR transcriptional regulatory role, Cbp2......Clustered regularly interspaced short palindromic repeats (CRISPR) form the basis of diverse adaptive immune systems directed primarily against invading genetic elements of archaea and bacteria. Cbp1 of the crenarchaeal thermoacidophilic order Sulfolobales, carrying three imperfect repeats, binds...... specifically to CRISPR DNA repeats and has been implicated in facilitating production of long transcripts from CRISPR loci. Here, a second related class of CRISPR DNA repeat-binding protein, denoted Cbp2, is characterized that contains two imperfect repeats and is found amongst members of the crenarchaeal...

  17. Solution properties of the archaeal CRISPR DNA repeat-binding homeodomain protein Cbp2

    Kenchappa, Chandra; Heiðarsson, Pétur Orri; Kragelund, Birthe


    Clustered regularly interspaced short palindromic repeats (CRISPR) form the basis of diverse adaptive immune systems directed primarily against invading genetic elements of archaea and bacteria. Cbp1 of the crenarchaeal thermoacidophilic order Sulfolobales, carrying three imperfect repeats, binds...... specifically to CRISPR DNA repeats and has been implicated in facilitating production of long transcripts from CRISPR loci. Here, a second related class of CRISPR DNA repeat-binding protein, denoted Cbp2, is characterized that contains two imperfect repeats and is found amongst members of the crenarchaeal...... in facilitating high affinity DNA binding of Cbp2 by tethering the two domains. Structural studies on mutant proteins provide support for Cys(7) and Cys(28) enhancing high thermal stability of Cbp2(Hb) through disulphide bridge formation. Consistent with their proposed CRISPR transcriptional regulatory role, Cbp2...

  18. Star repeaters for fiber optic links.

    McMahon, D H; Gravel, R L


    A star repeater combines the functions of a passive star coupler and a signal regenerating amplifier. By more effectively utilizing the light power radiated by a light emitting diode, the star repeater can, when used with small diameter channels, couple as much power to all receivers of a multiterminal link as would be coupled to the single receiver of a simple point-to-point link.

  19. Tool Wear Analysis on Five-Axis Flank Milling for Curved Shape Part – Full Flute and Ground Shank End Mill

    Syahrul Azwan Sundi


    Full Text Available This paper is a study on full flute (extra-long tool and ground shank end mill wear analysis by utilizing five-axis CNC to implement flank milling strategy on curved shape part. Five-axis machining eases the user to implement variations of strategy such as flank milling. Flank milling is different from point milling. Point milling cuts materials by using the tip of the tool whereas the flank milling uses the cutting tool body to cut material. The type of cutting tool used was end mill 10 mm diameter with High Speed Steel (HSS material. One factor at a time was utilized to analyze the overall data. Feed rate and spindle speed were the two main factors that been set up equally for both full flute and ground shank end mill. At the end of this research, the qualitative analysis based on tool wear between full flute and ground shank end mill is observed. Generally, both types of cutting tools showed almost the same failure indication such as broken edge or chipped off edge, formation of pinned hole on the surface and serration formation or built-up edge (BUE on the primary flute. However, the results obtained from the enlarged images which were captured by Optical Microscope indicated that, the ground shank end mill is better than the full flute end mill.

  20. Pigs suffering from injurious behaviours like flank biting and tail biting are more interested to manipulate a novel rope than uninjured control animals

    Bracke, M.B.M.; Ettema, K.


    Injurious behaviours in pigs may involve persistent or forceful biting in specific body parts and may result in wounds of the pigs’ tails, ears, flanks and legs. Such behaviours, which may lead to progressive tissue damage, are difficult to counteract. On a commercial farm 22 groups of pigs with

  1. Digital repeat analysis; setup and operation.

    Nol, J; Isouard, G; Mirecki, J


    Since the emergence of digital imaging, there have been questions about the necessity of continuing reject analysis programs in imaging departments to evaluate performance and quality. As a marketing strategy, most suppliers of digital technology focus on the supremacy of the technology and its ability to reduce the number of repeats, resulting in less radiation doses given to patients and increased productivity in the department. On the other hand, quality assurance radiographers and radiologists believe that repeats are mainly related to positioning skills, and repeat analysis is the main tool to plan training needs to up-skill radiographers. A comparative study between conventional and digital imaging was undertaken to compare outcomes and evaluate the need for reject analysis. However, digital technology still being at its early development stages, setting a credible reject analysis program became the major task of the study. It took the department, with the help of the suppliers of the computed radiography reader and the picture archiving and communication system, over 2 years of software enhancement to build a reliable digital repeat analysis system. The results were supportive of both philosophies; the number of repeats as a result of exposure factors was reduced dramatically; however, the percentage of repeats as a result of positioning skills was slightly on the increase for the simple reason that some rejects in the conventional system qualifying for both exposure and positioning errors were classified as exposure error. The ability of digitally adjusting dark or light images reclassified some of those images as positioning errors.

  2. Quantum Key Distribution over Probabilistic Quantum Repeaters

    Amirloo, Jeyran; Majedi, A Hamed


    A feasible route towards implementing long-distance quantum key distribution (QKD) systems relies on probabilistic schemes for entanglement distribution and swapping as proposed in the work of Duan, Lukin, Cirac, and Zoller (DLCZ) [Nature 414, 413 (2001)]. Here, we calculate the conditional throughput and fidelity of entanglement for DLCZ quantum repeaters, by accounting for the DLCZ self-purification property, in the presence of multiple excitations in the ensemble memories as well as loss and other sources of inefficiency in the channel and measurement modules. We then use our results to find the generation rate of secure key bits for QKD systems that rely on DLCZ quantum repeaters. We compare the key generation rate per logical memory employed in the two cases of with and without a repeater node. We find the cross-over distance beyond which the repeater system outperforms the non-repeater one. That provides us with the optimum inter-node distancing in quantum repeater systems. We also find the optimal exci...

  3. Remarkable selective constraints on exonic dinucleotide repeats.

    Haasl, Ryan J; Payseur, Bret A


    Long dinucleotide repeats found in exons present a substantial mutational hazard: mutations at these loci occur often and generate frameshifts. Here, we provide clear and compelling evidence that exonic dinucleotides experience strong selective constraint. In humans, only 18 exonic dinucleotides have repeat lengths greater than six, which contrasts sharply with the genome-wide distribution of dinucleotides. We genotyped each of these dinucleotides in 200 humans from eight 1000 Genomes Project populations and found a near-absence of polymorphism. More remarkably, divergence data demonstrate that repeat lengths have been conserved across the primate phylogeny in spite of what is likely considerable mutational pressure. Coalescent simulations show that even a very low mutation rate at these loci fails to explain the anomalous patterns of polymorphism and divergence. Our data support two related selective constraints on the evolution of exonic dinucleotides: a short-term intolerance for any change to repeat length and a long-term prevention of increases to repeat length. In general, our results implicate purifying selection as the force that eliminates new, deleterious mutants at exonic dinucleotides. We briefly discuss the evolution of the longest exonic dinucleotide in the human genome--a 10 x CA repeat in fibroblast growth factor receptor-like 1 (FGFRL1)--that should possess a considerably greater mutation rate than any other exonic dinucleotide and therefore generate a large number of deleterious variants. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

  4. Dynamic combinatorial libraries of artificial repeat proteins.

    Eisenberg, Margarita; Shumacher, Inbal; Cohen-Luria, Rivka; Ashkenasy, Gonen


    Repeat proteins are found in almost all cellular systems, where they are involved in diverse molecular recognition processes. Recent studies have suggested that de novo designed repeat proteins may serve as universal binders, and might potentially be used as practical alternative to antibodies. We describe here a novel chemical methodology for producing small libraries of repeat proteins, and screening in parallel the ligand binding of library members. The first stage of this research involved the total synthesis of a consensus-based three-repeat tetratricopeptide (TPR) protein (~14 kDa), via sequential attachment of the respective peptides. Despite the effectiveness of the synthesis and ligation steps, this method was found to be too demanding for the production of proteins containing variable number of repeats. Additionally, the analysis of binding of the individual proteins was time consuming. Therefore, we designed and prepared novel dynamic combinatorial libraries (DCLs), and show that their equilibration can facilitate the formation of TPR proteins containing up to eight repeating units. Interestingly, equilibration of the library building blocks in the presence of the biologically relevant ligands, Hsp90 and Hsp70, induced their oligomerization into forming more of the proteins with large recognition surfaces. We suggest that this work presents a novel simple and rapid tool for the simultaneous screening of protein mixtures with variable binding surfaces, and for identifying new binders for ligands of interest.

  5. Fuel cell repeater unit including frame and separator plate

    Yamanis, Jean; Hawkes, Justin R; Chiapetta, Jr., Louis; Bird, Connie E; Sun, Ellen Y; Croteau, Paul F


    An example fuel cell repeater includes a separator plate and a frame establishing at least a portion of a flow path that is operative to communicate fuel to or from at least one fuel cell held by the frame relative to the separator plate. The flow path has a perimeter and any fuel within the perimeter flow across the at least one fuel cell in a first direction. The separator plate, the frame, or both establish at least one conduit positioned outside the flow path perimeter. The conduit is outside of the flow path perimeter and is configured to direct flow in a second, different direction. The conduit is fluidly coupled with the flow path.

  6. Influence of the genetic polymorphisms in the 5' flanking and exonic regions of CYP2C19 on proguanil oxidation.

    Satyanarayana, Chakradhara Rao Uppugunduri; Devendran, Anichavezhi; Jayaraman, Muthukumaran; Mannu, Jayakanthan; Mathur, Premendu P; Gopal, Shewade Deepak; Rajagopal, Krishnamoorthy; Chandrasekaran, Adithan


    CYP2C19 is a polymorphic enzyme which metabolizes several clinically important drugs including proguanil. Variation in the 5' regulatory region may influence CYP2C19 activity. This study evaluates the relationship between proguanil metabolic ratio and genetic variations of CYP2C19 in a South Indian population. Fifty unrelated healthy subjects were genotyped for CYP2C19 (*)2 and (*)3 alleles and the 5' flanking region of CYP2C19 was sequenced. Plasma concentrations of proguanil and cycloguanil were estimated by reverse phase HPLC after single oral doses (200 mg) of proguanil. In silico docking analysis of transcription factors binding to its sites in CYP2C19 5' regulatory region was performed. The mean metabolic ratios (proguanil/cycloguanil) were highest in (*)1/(*)2 or (*)1/(*)3 subjects and in (*)2/(*)2 or (*)2/(*)3 as compared to (*)1/(*)1 subjects. Subjects with promoter region variation -98T>C showed decrease in the metabolic ratios irrespective of other variation, which may explain the deviation from the genotype-phenotype association of CYP2C19. In silico analysis predicted alteration in the interaction of transcription factors to their binding sites in the presence of variant alleles. The results of this study would be useful in predicting interindividual differences in the metabolism of substrates of CYP2C19.

  7. The Kuqa late Cenozoic fold-thrust belt on the southern flank of the Tian Shan Mountains

    Li, Yue-Jun; Wen, Lei; Zhang, Hong-An; Huang, Tai-Zhu; Li, Hui-Li; Shi, Yuan-Yuan; Meng, Qing-Long; Peng, Geng-Xin; Huang, Shao-Ying; Zhang, Qiang


    The Kuqa fold-thrust belt (KFTB), a late Cenozoic fold-thrust belt on the southern flank of the Tian Shan Mountains, consists of several deformation zones trending nearly W-E. The main décollement fault of the KFTB gradually rises southwards. There are three regional main décollement faults in the Triassic dark mudstone, Paleogene gypsum salt (Kumugeliemu Formation), and Neogene gypsum salt (Jidike Formation), respectively, and possibly a fourth in the Jurassic coalbed. Laterally, thin-skinned structures are developed in the main segments of the KFTB, whereas thick-skinned structures are in the root zone. Vertically, the structural deformation above the Cenozoic gypsum-salt layers (Paleogene gypsum salt in the middle segment of the KFTB and Neogene gypsum salt in the eastern segment) is characterized by décollement folding, whereas that below is characterized by thrusting. The KFTB was resulted from the late Cenozoic intra-continental orogeny in the Tian Shan area under the far-field effect of the India-Asia collision. The deformation of KFTB began (folding and thrusting) ca. 23 Ma, when the far-field effect of the India-Asia collision reached the Tian Shan area. The deformation of KFTB accelerated ca. 10, 5-2, and 1-0 Ma. In general, the evolution of the KFTB is forward propagating, and the hinter parts of the KFTB continue to deform, while its front propagates southwards.

  8. Association analysis of urotensin II gene (UTS2 and flanking regions with biochemical parameters related to insulin resistance.

    María E Sáez

    Full Text Available BACKGROUND: Urotensin II (UII is a potent vasoconstrictor peptide, which signals through a G-protein coupled receptor (GPCR known as GPR14 or urotensin receptor (UTR. UII exerts a broad spectrum of actions in several systems such as vascular cell, heart muscle or pancreas, where it inhibits insulin release. OBJECTIVE: Given the reported role of UII in insulin secretion, we have performed a genetic association analysis of the UTS2 gene and flanking regions with biochemical parameters related to insulin resistance (fasting glucose, glucose 2 hours after a glucose overload, fasting insulin and insulin resistance estimated as HOMA. RESULTS AND CONCLUSIONS: We have identified several polymorphisms associated with the analysed clinical traits, not only at the UTS2 gene, but also in thePER3 gene, located upstream from UTS2. Our results are compatible with a role for UII in glucose homeostasis and diabetes although we cannot rule out the possibility that PER3 gene may underlie the reported associations.

  9. Quantitative analysis of the 1981 and 2001 Etna flank eruptions: a contribution for future hazard evaluation and mitigation

    Cristina Proietti


    Full Text Available Lava flows produced during Etna flank eruptions represent severe hazards for the nearby inhabited areas, which can be protected by adopting prompt mitigation actions, such as the building of diversion barriers. Lava diversion measures were attempted recently during the 1983, 1991-93, 2001 and 2002 Etna eruptions, although with different degrees of success. In addition to the complexity of barrier construction (due to the adverse physical conditions, the time available to successfully slow the advance of a lava flow depends on the lava effusion rate, which is not easily measurable. One method to estimate the average lava effusion rate over a specified period of time is based on a volumetric approach; i.e. the measurement of the volume changes of the lava flow over that period. Here, this has been compared to an approach based on thermal image processing, as applied to estimate the average effusion rates of lava flows during the 1981 and 2001 Etna eruptions. The final volumes were measured by the comparison of pre-eruption and post-eruption photogrammetric digital elevation models and orthophotographs. Lava volume growth during these eruptions was estimated by locating the flow-front positions from analyses of scientific papers and newspapers reports, as well as from helicopter photographs. The analyses of these two eruptions contribute to the understanding of the different eruptive mechanisms, highlighting the role of the peak effusion rate, which represents a critical parameter for planning of mitigation actions and for hazard evaluation.

  10. Estimates of Europa's ice shell thickness and strain rate from flanking cracks and bulge along Ridge R

    ZHAN Zhongwen; CHEN Chuxin


    Europa,the second Galilean satellite outward from Jupiter,has an outer layer of water of about 100 km thick and an outmost ice shell.The thickness of the ice shell is very important in understanding Europa's habitability and thermal history,but estimates from different studies are very inconsistent,ranging from 0.2 to 30 km.Here we obtain an estimate of the ice shell thickness from locations of flanking crack and forebulge along Ridge R.Considering the water's heating process to nearby ice shell in the crack,a flexure model is applied and it suggests the thickness of an ice shell to be 500-1500 m without a convective layer.Compared with previous studies using the same method but ignoring the water's heating process,the rationality and accuracy have been improved dramatically in our results.We also get some constraints on the strain rate ε and the characteristic temperature Tc,which defines the base of the elastic layer.

  11. HIV Tat Domain Improves Cross-correction of Human Galactocerebrosidase in a Gene- and Flanking Sequence-dependent Manner

    Xing-Li Meng


    Full Text Available Krabbe disease is a devastating neurodegenerative lysosomal storage disorder caused by a deficiency of β-galactocerebrosidase (GALC. Gene therapy is a promising therapeutic approach for Krabbe disease. As the human brain is large and it is difficult to achieve global gene transduction, the efficacy of cross-correction is a critical determinant of the outcome of gene therapy for this disease. We investigated whether HIV Tat protein transduction domain (PTD can improve the cross-correction of GALC. Tat-PTD significantly increased (~6-fold cross-correction of GALC through enhanced secretion and uptake in a cell-culture model system. The effects of Tat-PTD were gene and flanking amino acids dependent. Tat-fusion increased the secretion of α-galactosidase A (α-gal A, but this did not improve its cross-correction. Tat-fusion did not change either secretion or uptake of β-glucocerebrosidase (GC. Tat-PTD increased GALC protein synthesis, abolished reactivity of GC to the 8E4 antibody, and likely reduced mannose phosphorylation in all these lysosomal enzymes. This study demonstrated that Tat-PTD can be useful for increasing cross-correction efficiency of lysosomal enzymes. However, Tat-PTD is not a mere adhesive motif but possesses a variety of biological functions. Therefore, the potential beneficial effect of Tat-PTD should be assessed individually on each lysosomal enzyme.

  12. Natural radioactivity content in groundwater of Mt. Etna’s eastern flank and gamma background of surrounding rocks.

    Beata Kozłowska


    Full Text Available Waters of Mt. Etna are the main source of drinking water for the local population and are also distributed in municipal supply systems to neighbouring areas. Radioactivity in underground waters and surrounding rocks from the eastern flank of Mt.Etnawas investigated on the basis of 9 water and 8 rocks samples from 12 localities altogether. Three samples were from water drainage galleries and six from water wells. All water intakes are used for consumption. Activity concentration of uranium isotopes 234,238U, radium isotopes 226,228Ra and radon 222Rn were determined with the use different nuclear spectrometry techniques. The determination of uranium isotopes was carried out with the use of alpha spectrometry. The measurements of radium and radon activity concentration in water were performed with the use of a liquid scintillation technique. Additionally, rocks surrounding the intakes were examined with gamma spectrometry. All water samples showed uranium concentration above Minimum Detectable Activity (MDA, with the highest total uranium (234U + 238U activity concentration equal to 149.2±6 mBq/L. Conversely, all samples showed radium isotopes activity concentrations below MDA. Radon activity concentration was within the range from 2.91±0.36 to 21.21±1.10 Bq/L, hence these waters can be classified as low – radon waters. Gamma natural background of the rocks surrounding the water sampling sites was found on the same levels as other volcanic rocks of Italy.

  13. Shaking of pyroclastic cones and the formation of granular flows on their flanks: Results from laboratory experiments

    Cagnoli, B.; Romano, G. P.; Ventura, G.


    We have carried out laboratory experiments to study the generation of granular flows on the slopes of pyroclastic cones that are experiencing volcanic tremor or tectonic earthquakes. These experiments are inspired by the occurrence of granular flows on the flanks of Mount Vesuvius during its 1944 eruption. Our laboratory model consists of sand cones built around a vibrating tube which represents a volcanic conduit with erupting magma inside. A video camera allows the study of the granular flow inception, movement and deposition. Although the collapse of the entire cone is obtained at a specific resonance frequency, single granular flows can be generated by all the vibration frequencies (1-16 Hz) and all the vibration amplitudes (0.5-1.5 mm) that our experimental apparatus has allowed us to adopt. We believe that this is due to the fact that the energy threshold to trigger the flows is small in value. Therefore, if this is true in nature as well, shaken pyroclastic cones are always potentially dangerous because they can easily generate flows that can strike the surrounding areas.

  14. Insight from Laboratory Experiments on the Generation of Granular Flows on the Flanks of Vibrated Pyroclastic Cones

    Cagnoli, B.; Romano, G. P.; Ventura, G.


    We have carried out laboratory experiments to study the generation of granular flows on the slopes of pyroclastic cones that are experiencing volcanic tremor or tectonic earthquakes. These experiments are inspired by the occurrence of granular flows on the flanks of Mount Vesuvius during its 1944 eruption. Our laboratory model consists of sand cones built around a vibrating tube which represents a volcanic conduit with erupting magma inside. A video camera allows the study of the granular flow inception, movement and deposition. Although the collapse of the entire cone is obtained at a specific resonance frequency, individual granular flows can be generated by all the vibration frequencies and all the vibration amplitudes that our experimental apparatus has allowed us to adopt. We believe that this is due to the fact that the energy threshold to generate the flows is small in value. Therefore, if this is true in nature as well, shaken pyroclastic cones are always potentially dangerous because they can easily generate flows that can strike the surrounding areas.

  15. Characterization of the 5' flanking region of lipase gene from Penicillium expansum and its application in molecular breeding.

    Zhang, Tian; Peng, Ying; Yu, Qingsheng; Wang, Jieliang; Tang, Kexuan


    A major challenge for further promotion of lipase productivity in Penicillium expansum PE-12 is to find a suitable promoter that can function efficiently in this industrial strain. In this study, the 5' flanking region of P. expansum lipase (Ppel) containing a putative novel promoter sequence was characterized by fusing to β-glucuronidase (GUS) and subsequently introducing into P. expansum. As a result, all the transformants showed blue color quickly after incubation in GUS detection buffer, suggesting a strong promoter activity of this fragment. Glucose repression was identified for the promoter, whereas olive oil acted as a positive regulator. Facilitated by this novel promoter, P. expansum PE-12 was genetically modified, with an improved lipase yield, via a recombinant plasmid with P. expansum lipase gene (PEL) under the control of Ppel promoter and TtrpC terminator. The highest lipase yield among the modified strains could attain 2,100 U/mL, which is more than twofold of the previous industrial strain (900 U/mL). The engineered strain through molecular breeding method as well as this new promoter has great value in lipase industry.

  16. Composition, geometry, and emplacement dynamics of a large volcanic island landslide offshore Martinique: From volcano flank-collapse to seafloor sediment failure?

    Brunet, Morgane; Le Friant, Anne; Boudon, Georges; Lafuerza, Sara; Talling, Peter; Hornbach, Matthew; Ishizuka, Osamu; Lebas, Elodie; Guyard, Hervé


    Landslides are common features in the vicinity of volcanic islands. In this contribution, we investigate landslides emplacement and dynamics around the volcanic island of Martinique based on the first scientific drilling of such deposits. The evolution of the active Montagne Pelée volcano on this island has been marked by three major flank-collapses that removed much of the western flank of the volcano. Subaerial collapse volumes vary from 2 to 25 km3 and debris avalanches flowed into the Grenada Basin. High-resolution seismic data (AGUADOMAR-1999, CARAVAL-2002, and GWADASEIS-2009) is combined with new drill cores that penetrate up to 430 m through the three submarine landslide deposits previously associated to the aerial flank-collapses (Site U1399, Site U1400, Site U1401, IODP Expedition 340, Joides Resolution, March-April 2012). This combined geophysical and core data provide an improved understanding of landslide processes offshore a volcanic island. The integrated analysis shows a large submarine landslide deposit, without debris avalanche deposits coming from the volcano, comprising up to 300 km3 of remobilized seafloor sediment that extends for 70 km away from the coast and covers an area of 2100 km2. Our new data suggest that the aerial debris avalanche deposit enter the sea but stop at the base of submarine flank. We propose a new model dealing with seafloor sediment failures and landslide propagation mechanisms, triggered by volcanic flank-collapse events affecting Montagne Pelée volcano. Newly recognized landslide deposits occur deeper in the stratigraphy, suggesting the recurrence of large-scale mass-wasting processes offshore the island and thus, the necessity to better assess the associated tsunami hazards in the region.

  17. Comparative sequence analysis of leucine-rich repeats (LRRs within vertebrate toll-like receptors

    Taga Masae


    Full Text Available Abstract Background Toll-like receptors (TLRs play a central role in innate immunity. TLRs are membrane glycoproteins and contain leucine rich repeat (LRR motif in the ectodomain. TLRs recognize and respond to molecules such as lipopolysaccharide, peptidoglycan, flagellin, and RNA from bacteria or viruses. The LRR domains in TLRs have been inferred to be responsible for molecular recognition. All LRRs include the highly conserved segment, LxxLxLxxNxL, in which "L" is Leu, Ile, Val, or Phe and "N" is Asn, Thr, Ser, or Cys and "x" is any amino acid. There are seven classes of LRRs including "typical" ("T" and "bacterial" ("S". All known domain structures adopt an arc or horseshoe shape. Vertebrate TLRs form six major families. The repeat numbers of LRRs and their "phasing" in TLRs differ with isoforms and species; they are aligned differently in various databases. We identified and aligned LRRs in TLRs by a new method described here. Results The new method utilizes known LRR structures to recognize and align new LRR motifs in TLRs and incorporates multiple sequence alignments and secondary structure predictions. TLRs from thirty-four vertebrate were analyzed. The repeat numbers of the LRRs ranges from 16 to 28. The LRRs found in TLRs frequently consists of LxxLxLxxNxLxxLxxxxF/LxxLxx ("T" and sometimes short motifs including LxxLxLxxNxLxxLPx(xLPxx ("S". The TLR7 family (TLR7, TLR8, and TLR9 contain 27 LRRs. The LRRs at the N-terminal part have a super-motif of STT with about 80 residues. The super-repeat is represented by STTSTTSTT or _TTSTTSTT. The LRRs in TLRs form one or two horseshoe domains and are mostly flanked by two cysteine clusters including two or four cysteine residue. Conclusion Each of the six major TLR families is characterized by their constituent LRR motifs, their repeat numbers, and their patterns of cysteine clusters. The central parts of the TLR1 and TLR7 families and of TLR4 have more irregular or longer LRR motifs. These

  18. Clustered regularly interspaced short palindromic repeats (CRISPRs) for the genotyping of bacterial pathogens.

    Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine


    Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences composed of a succession of repeats (23- to 47-bp long) separated by unique sequences called spacers. Polymorphism can be observed in different strains of a species and may be used for genotyping. We describe protocols and bioinformatics tools that allow the identification of CRISPRs from sequenced genomes, their comparison, and their component determination (the direct repeats and the spacers). A schematic representation of the spacer organization can be produced, allowing an easy comparison between strains.

  19. Automated genotyping of dinucleotide repeat markers

    Perlin, M.W.; Hoffman, E.P. [Carnegie Mellon Univ., Pittsburgh, PA (United States)]|[Univ. of Pittsburgh, PA (United States)


    The dinucleotide repeats (i.e., microsatellites) such as CA-repeats are a highly polymorphic, highly abundant class of PCR-amplifiable markers that have greatly streamlined genetic mapping experimentation. It is expected that over 30,000 such markers (including tri- and tetranucleotide repeats) will be characterized for routine use in the next few years. Since only size determination, and not sequencing, is required to determine alleles, in principle, dinucleotide repeat genotyping is easily performed on electrophoretic gels, and can be automated using DNA sequencers. Unfortunately, PCR stuttering with these markers generates not one band for each allele, but a pattern of bands. Since closely spaced alleles must be disambiguated by human scoring, this poses a key obstacle to full automation. We have developed methods that overcome this obstacle. Our model is that the observed data is generated by arithmetic superposition (i.e., convolution) of multiple allele patterns. By quantitatively measuring the size of each component band, and exploiting the unique stutter pattern associated with each marker, closely spaced alleles can be deconvolved; this unambiguously reconstructs the {open_quotes}true{close_quotes} allele bands, with stutter artifact removed. We used this approach in a system for automated diagnosis of (X-linked) Duchenne muscular dystrophy; four multiplexed CA-repeats within the dystrophin gene were assayed on a DNA sequencer. Our method accurately detected small variations in gel migration that shifted the allele size estimate. In 167 nonmutated alleles, 89% (149/167) showed no size variation, 9% (15/167) showed 1 bp variation, and 2% (3/167) showed 2 bp variation. We are currently developing a library of dinucleotide repeat patterns; together with our deconvolution methods, this library will enable fully automated genotyping of dinucleotide repeats from sizing data.

  20. The shadow of the future promotes cooperation in a repeated prisoner’s dilemma for children

    Peter R Blake; David G Rand; Tingley, Dustin; Warneken, Felix


    Cooperation among genetically unrelated individuals can be supported by direct reciprocity. Theoretical models and experiments with adults show that the possibility of future interactions with the same partner can promote cooperation via conditionally cooperative strategies such as tit-for-tat (TFT). Here, we introduce a novel implementation of the repeated Prisoner’s Dilemma (PD) designed for children to examine whether repeated interactions can successfully promote cooperation in 10 and 11 ...

  1. Embedded real-time control of optically amplified repeaters in broadband access networks

    Stubbe, Brecht; Vaes, Peter; Gouwy, Lieven; Coene, Chris; Qiu, Xing-Zhi; Staelens, Bart; Vandewege, Jan; Slabbinck, B. Hans; Martin, Claire M.; Van de Voorde, Ingrid


    This paper presents the use of distributed, intelligent control and management in optically amplified repeaters. These optical repeater units (ORUs) are used in an optical access network. A semiconductor optical amplifier (SOA) has been used in the upstream direction because of the possibility of fast switching. The real time control platform consists of both a hard- and a software part. The software control is handled with the embedded control system FORTRESS developed by IMEC.

  2. Effects of ligand binding on the mechanical properties of ankyrin repeat protein gankyrin.

    Giovanni Settanni

    Full Text Available Ankyrin repeat proteins are elastic materials that unfold and refold sequentially, repeat by repeat, under force. Herein we use atomistic molecular dynamics to compare the mechanical properties of the 7-ankyrin-repeat oncoprotein Gankyrin in isolation and in complex with its binding partner S6-C. We show that the bound S6-C greatly increases the resistance of Gankyrin to mechanical stress. The effect is specific to those repeats of Gankyrin directly in contact with S6-C, and the mechanical 'hot spots' of the interaction map to the same repeats as the thermodynamic hot spots. A consequence of stepwise nature of unfolding and the localized nature of ligand binding is that it impacts on all aspects of the protein's mechanical behavior, including the order of repeat unfolding, the diversity of unfolding pathways accessed, the nature of partially unfolded intermediates, the forces required and the work transferred to the system to unfold the whole protein and its parts. Stepwise unfolding thus provides the means to buffer repeat proteins and their binding partners from mechanical stress in the cell. Our results illustrate how ligand binding can control the mechanical response of proteins. The data also point to a cellular mechano-switching mechanism whereby binding between two partner macromolecules is regulated by mechanical stress.

  3. Semihierarchical quantum repeaters based on moderate lifetime quantum memories

    Liu, Xiao; Zhou, Zong-Quan; Hua, Yi-Lin; Li, Chuan-Feng; Guo, Guang-Can


    The construction of large-scale quantum networks relies on the development of practical quantum repeaters. Many approaches have been proposed with the goal of outperforming the direct transmission of photons, but most of them are inefficient or difficult to implement with current technology. Here, we present a protocol that uses a semihierarchical structure to improve the entanglement distribution rate while reducing the requirement of memory time to a range of tens of milliseconds. This protocol can be implemented with a fixed distance of elementary links and fixed requirements on quantum memories, which are independent of the total distance. This configuration is especially suitable for scalable applications in large-scale quantum networks.

  4. Fast Adaptive Beamforming with Smart Antenna for Radio Frequency Repeater

    Wang Chaoqun


    Full Text Available We present a fast adaptive beamforming null algorithm with smart antenna for Radio Frequency Repeater (RFR. The smart antenna system is realized by a Direction Of Arrival (DOA Estimator, whose output is used by an adaptive beamforming algorithm to shape a suitable radiation pattern of the equivalent antenna; so that the co-channel interference due to retransmitting antenna can be reduced. The proposed adaptive beamforming algorithm, which has been proved by formulaic analysis and simulation, has a lower computation complexity yet better performance.

  5. Neuroimaging Findings and Repeat Neuroimaging Value in Pediatric Chronic Ataxia.

    Salman, Michael S; Chodirker, Bernard N; Bunge, Martin


    Chronic ataxia, greater than two months in duration, is encountered relatively commonly in clinical pediatric neurology practise and presents with diagnostic challenges. It is caused by multiple and diverse disorders. Our aims were to describe the neuroimaging features and the value of repeat neuroimaging in pediatric chronic ataxia to ascertain their contribution to the diagnosis and management. A retrospective charts and neuroimaging reports review was undertaken in 177 children with chronic ataxia. Neuroimaging in 130 of 177 patients was also reviewed. Nineteen patients had head computed tomography only, 103 brain magnetic resonance imaging only, and 55 had both. Abnormalities in the cerebellum or other brain regions were associated with ataxia. Neuroimaging was helpful in 73 patients with 30 disorders: It was diagnostic in 9 disorders, narrowed down the diagnostic possibilities in 14 disorders, and revealed important but non-diagnostic abnormalities, e.g. cerebellar atrophy in 7 disorders. Having a normal magnetic resonance imaging scan was mostly seen in genetic diseases or in the early course of ataxia telangiectasia. Repeat neuroimaging, performed in 108 patients, was generally helpful in monitoring disease evolution and in making a diagnosis. Neuroimaging was not directly helpful in 36 patients with 10 disorders or by definition the 55 patients with unknown disease etiology. Normal or abnormal neuroimaging findings and repeat neuroimaging are very valuable in the diagnosis and management of disorders associated with pediatric chronic ataxia.

  6. Combined use of repeated active shots and ambient noise to detect temporal changes in seismic velocity: application to Sakurajima volcano, Japan

    Hirose, Takashi; Nakahara, Hisashi; Nishimura, Takeshi


    Coda-wave interferometry is a technique to detect small seismic velocity changes using phase changes in similar waveforms from repeating natural or artificial sources. Seismic interferometry is another technique for detecting seismic velocity changes from cross-correlation functions of ambient seismic noise. We simultaneously use these two techniques to clarify seismic velocity changes at Sakurajima volcano, one of the most active volcanoes in Japan, examining the two methods. We apply coda-wave interferometry to the records of repeated active seismic experiments conducted once a year from 2011 to 2014, and seismic interferometry to the ambient seismic noise data. We directly compare seismic velocity changes from these two techniques. In coda-wave interferometry analyses, we detect significant seismic velocity increases between 2011 and 2013, and seismic velocity decreases between 2013 and 2014 at the northern and eastern flanks of the volcano. The absolute values are at a maximum 0.47 ± 0.06% for 2-4 Hz, 0.24 ± 0.03% for 4-8 Hz, and 0.15 ± 0.03% for 8-16 Hz, respectively. In seismic interferometry analyses, vertical-vertical cross-correlations in 1-2, 2-4, and 4-8 Hz bands indicate seismic velocity increases and decreases during 3 years of 2012-2014 with the maximum amplitudes of velocity change of ±0.3% for 1-2 Hz, ±0.4% for 2-4 Hz, and ±0.2% for 4-8 Hz, respectively. Relative velocity changes indicate the almost annual change. These periodical changes are well matched with volcano deformation detected by GNSS receivers deployed around the volcano. We compare the results from coda-wave interferometry with those from seismic interferometry on the shot days and find that most of them are consistent. This study illustrates that the combined use of coda-wave interferometry and seismic interferometry is useful to obtain accurate and continuous measurements of seismic velocity changes.[Figure not available: see fulltext.

  7. Direct reciprocity in structured populations

    C.M. van Veelen; J. García; D.G. Rand; M.A. Nowak


    Reciprocity and repeated games have been at the center of attention when studying the evolution of human cooperation. Direct reciprocity is considered to be a powerful mechanism for the evolution of cooperation, and it is generally assumed that it can lead to high levels of cooperation. Here we expl

  8. Celiac disease T-cell epitopes from gamma-gliadins: immunoreactivity depends on the genome of origin, transcript frequency, and flanking protein variation

    Salentijn Elma MJ


    Full Text Available Abstract Background Celiac disease (CD is caused by an uncontrolled immune response to gluten, a heterogeneous mixture of wheat storage proteins. The CD-toxicity of these proteins and their derived peptides is depending on the presence of specific T-cell epitopes (9-mer peptides; CD epitopes that mediate the stimulation of HLA-DQ2/8 restricted T-cells. Next to the thoroughly characterized major T-cell epitopes derived from the α-gliadin fraction of gluten, γ-gliadin peptides are also known to stimulate T-cells of celiac disease patients. To pinpoint CD-toxic γ-gliadins in hexaploid bread wheat, we examined the variation of T-cell epitopes involved in CD in γ-gliadin transcripts of developing bread wheat grains. Results A detailed analysis of the genetic variation present in γ-gliadin transcripts of bread wheat (T. aestivum, allo-hexaploid, carrying the A, B and D genome, together with genomic γ-gliadin sequences from ancestrally related diploid wheat species, enabled the assignment of sequence variants to one of the three genomic γ-gliadin loci, Gli-A1, Gli-B1 or Gli-D1. Almost half of the γ-gliadin transcripts of bread wheat (49% was assigned to locus Gli-D1. Transcripts from each locus differed in CD epitope content and composition. The Gli-D1 transcripts contained the highest frequency of canonical CD epitope cores (on average 10.1 per transcript followed by the Gli-A1 transcripts (8.6 and the Gli-B1 transcripts (5.4. The natural variants of the major CD epitope from γ-gliadins, DQ2-γ-I, showed variation in their capacity to induce in vitro proliferation of a DQ2-γ-I specific and HLA-DQ2 restricted T-cell clone. Conclusions Evaluating the CD epitopes derived from γ-gliadins in their natural context of flanking protein variation, genome specificity and transcript frequency is a significant step towards accurate quantification of the CD toxicity of bread wheat. This approach can be used to predict relative levels of CD toxicity of

  9. Human histamine N-methyltransferase pharmacogenetics: gene resequencing, promoter characterization, and functional studies of a common 5'-flanking region single nucleotide polymorphism (SNP).

    Wang, Liewei; Thomae, Bianca; Eckloff, Bruce; Wieben, Eric; Weinshilboum, Richard


    Histamine N-methyltransferase (HNMT) catalyzes one of two major metabolic pathways for histamine. The levels of HNMT activity and immunoreactive protein in human tissues are regulated primarily by inheritance. Previous studies of HNMT identified two common single nucleotide polymorphisms (SNPs), including a functionally significant nonsynonymous coding SNP (cSNP), (C314T, Thr105Ile), but that polymorphism did not explain all of the phenotypic variation. In the present study, a genotype-to-phenotype strategy was used to search for additional genetic factors that might contribute to the regulation of human HNMT activity. Specifically, we began by resequencing the human HNMT gene using 90 ethnically anonymous DNA samples from the Coriell Cell Repository and identified a total of eight SNPs, including the two that had been reported previously. No new nonsynonymous cSNPs were observed, but three of the six novel SNPs were located in the 5'-flanking region (5'-FR) of the gene-including a third common polymorphism with a frequency of 0.367 (36.7%). That observation directed our attention to possible genetic effects on HNMT transcription. As a first step in testing that possibility, we created and studied a series of reporter gene constructs for the initial 1kb of the HNMT 5'-FR. The core promoter and possible regulatory regions were identified and verified by electrophoresis mobility shift assays. We then studied the possible functional implications of the new common HNMT 5'-FR SNP. However, on the basis of reporter gene studies, that SNP appeared to have little effect on transcription. Phenotype-genotype correlation analysis performed with 112 human kidney biopsy samples that had been phenotyped for their level of HNMT activity confirmed that the common 5'-FR SNP was not associated with the level of HNMT activity in vivo. In summary, this series of experiments resulted in the identification of several novel HNMT polymorphisms, identification of the HNMT core promoter

  10. The role of feedback and differences between good and poor decoders in a repeated word reading paradigm in first grade

    Gorp, K. van; Segers, P.C.J.; Verhoeven, L.T.W.


    The direct, retention, and transfer effects of repeated word and pseudoword reading were studied in a pretest, training, posttest, retention design. First graders (48 good readers, 47 poor readers) read 25 CVC words and 25 CVC pseudowords in ten repeated word reading sessions, preceded and followed

  11. Mining of simple sequence repeats in the Genome of Gentianaceae

    R Sathishkumar


    Full Text Available Simple sequence repeats (SSRs or short tandem repeats are short repeat motifs that show high level of length polymorphism due to insertion or deletion mutations of one or more repeat types. Here, we present the detection and abundance of microsatellites or SSRs in nucleotide sequences of Gentianaceae family. A total of 545 SSRs were mined in 4698 nucleotide sequences downloaded from the National Center for Biotechnology Information (NCBI. Among the SSR sequences, the frequency of repeat type was about 429 -mono repeats, 99 -di repeats, 15 -tri repeats, and 2 --hexa repeats. Mononucleotide repeats were found to be abundant repeat types, about 78%, followed by dinucleotide repeats (18.16% among the SSR sequences. An attempt was made to design primer pairs for 545 identified SSRs but these were found only for 169 sequences.

  12. 53BP1 fosters fidelity of homology-directed DNA repair

    Ochs, Fena; Somyajit, Kumar; Altmeyer, Matthias


    Repair of DNA double-strand breaks (DSBs) in mammals is coordinated by the ubiquitin-dependent accumulation of 53BP1 at DSB-flanking chromatin. Owing to its ability to limit DNA-end processing, 53BP1 is thought to promote nonhomologous end-joining (NHEJ) and to suppress homology-directed repair...

  13. Direct Democracy

    Doerr, Nicole


    Direct democracy describes a theory of democracy and a form of collective decision-making in which sovereignty is directly exercised by the people. Democracy is direct if it is characterized by citizens making all decisions together with a maximum of equal participation. Direct democracy can...

  14. The Rock Engineering System (RES) applied to landslide susceptibility zonation of the northeastern flank of Etna: methodological approach and results

    Apuani, Tiziana; Corazzato, Claudia


    Ground deformations in the northeastern flank of Etna are well known. Despite only a few landslide events have been documented, these have significantly involved and damaged lifelines and buildings. These events are mainly related to the activity of the volcano-tectonic structures and associated seismicity, as in the case of the 2002 reactivation of the Presa landslide during an increased activity of the Pernicana fault system. In order to highlight the areal distribution of potentially unstable slopes based on a detailed, site-specific study of the factors responsible for landslide, and to ultimately contribute to risk management, a landslide susceptibility analysis of the northeastern flank of Etna in the Pernicana area was carried out, and a susceptibility map at 1:10.000 scale was produced, extending over an area of 168 km2. Different methods are proposed in the literature to obtain the regional distribution of potentially unstable slopes, depending on the problem scale, the slope dynamic evolution in the geological context, and the availability of data. Among semi-quantitative approaches, the present research combines the Rock Engineering System (RES) methodology with parameter zonation mapping in a GIS environment. The RES method represents a structured approach to manage a high number of interacting factors involved in the instability problem. A numerically coded, site-specific interaction matrix (IM) analyzes the cause-effect relationship in these factors, and calculates the degree of interactivity of each parameter, normalized by the overall interactivity of the system (weight factor). In the specific Etna case, the considered parameters are: slope attitude, lithotechnical properties (lithology, structural complexity, soil and rock mass quality), land use, tectonic structures, seismic activity (horizontal acceleration) and hydrogeological conditions (groundwater and drainage). Thematic maps are prepared at 1:10.000 scale for each of these parameters, and

  15. PolyQ repeat expansions in ATXN2 associated with ALS are CAA interrupted repeats.

    Zhenming Yu

    Full Text Available Amyotrophic lateral sclerosis (ALS is a devastating, rapidly progressive disease leading to paralysis and death. Recently, intermediate length polyglutamine (polyQ repeats of 27-33 in ATAXIN-2 (ATXN2, encoding the ATXN2 protein, were found to increase risk for ALS. In ATXN2, polyQ expansions of ≥ 34, which are pure CAG repeat expansions, cause spinocerebellar ataxia type 2. However, similar length expansions that are interrupted with other codons, can present atypically with parkinsonism, suggesting that configuration of the repeat sequence plays an important role in disease manifestation in ATXN2 polyQ expansion diseases. Here we determined whether the expansions in ATXN2 associated with ALS were pure or interrupted CAG repeats, and defined single nucleotide polymorphisms (SNPs rs695871 and rs695872 in exon 1 of the gene, to assess haplotype association. We found that the expanded repeat alleles of 40 ALS patients and 9 long-repeat length controls were all interrupted, bearing 1-3 CAA codons within the CAG repeat. 21/21 expanded ALS chromosomes with 3CAA interruptions arose from one haplotype (GT, while 18/19 expanded ALS chromosomes with <3CAA interruptions arose from a different haplotype (CC. Moreover, age of disease onset was significantly earlier in patients bearing 3 interruptions vs fewer, and was distinct between haplotypes. These results indicate that CAG repeat expansions in ATXN2 associated with ALS are uniformly interrupted repeats and that the nature of the repeat sequence and haplotype, as well as length of polyQ repeat, may play a role in the neurological effect conferred by expansions in ATXN2.

  16. Influence of Igneous Basement on Deep Sediment Microbial Diversity on the Eastern Juan de Fuca Ridge Flank

    Jessica M. Labonté


    Full Text Available Microbial communities living in deeply buried sediment may be adapted to long-term energy limitation as they are removed from new detrital energy inputs for thousands to millions of years. However, sediment layers near the underlying oceanic crust may receive inputs from below that influence microbial community structure and/or activity. As part of the Census of Deep Life, we used 16S rRNA gene tag pyrosequencing on DNA extracted from a spectrum of deep sediment-basement interface samples from the subsurface of the Juan de Fuca Ridge flank (collected on IODP Expedition 327 to examine this possible basement influence on deep sediment communities. This area experiences rapid sedimentation, with an underlying basaltic crust that hosts a dynamic flux of hydrothermal fluids that diffuse into the sediment. Chloroflexi sequences dominated tag libraries in all sediment samples, with variation in the abundance of other bacterial groups (e.g., Actinobacteria, Aerophobetes, Atribacteria, Planctomycetes, and Nitrospirae. These variations occur in relation to the type of sediment (clays versus carbonate-rich and the depth of sample origin, and show no clear connection to the distance from the discharge outcrop or to basement fluid microbial communities. Actinobacteria-related sequences dominated the basalt libraries, but these should be viewed cautiously due to possibilities for imprinting from contamination. Our results indicate that proximity to basement or areas of seawater recharge is not a primary driver of microbial community composition in basal sediment, even though fluids diffusing from basement into sediment may stimulate microbial activity.

  17. Intein-Promoted Cyclization of Aspartic Acid Flanking the Intein Leads to Atypical N-Terminal Cleavage.

    Minteer, Christopher J; Siegart, Nicolle M; Colelli, Kathryn M; Liu, Xinyue; Linhardt, Robert J; Wang, Chunyu; Gomez, Alvin V; Reitter, Julie N; Mills, Kenneth V


    Protein splicing is a post-translational reaction facilitated by an intein, or intervening protein, which involves the removal of the intein and the ligation of the flanking polypeptides, or exteins. A DNA polymerase II intein from Pyrococcus abyssi (Pab PolII intein) can promote protein splicing in vitro on incubation at high temperature. Mutation of active site residues Cys1, Gln185, and Cys+1 to Ala results in an inactive intein precursor, which cannot promote the steps of splicing, including cleavage of the peptide bond linking the N-extein and intein (N-terminal cleavage). Surprisingly, coupling the inactivating mutations to a change of the residue at the C-terminus of the N-extein (N-1 residue) from the native Asn to Asp reactivates N-terminal cleavage at pH 5. Similar "aspartic acid effects" have been observed in other proteins and peptides but usually only occur at lower pH values. In this case, however, the unusual N-terminal cleavage is abolished by mutations to catalytic active site residues and unfolding of the intein, indicating that this cleavage effect is mediated by the intein active site and the intein fold. We show via mass spectrometry that the reaction proceeds through cyclization of Asp resulting in anhydride formation coupled to peptide bond cleavage. Our results add to the richness of the understanding of the mechanism of protein splicing and provide insight into the stability of proteins at moderately low pH. The results also explain, and may help practitioners avoid, a side reaction that may complicate intein applications in biotechnology.

  18. A Receptor-Based Explanation for Tsetse Fly Catch Distribution between Coloured Cloth Panels and Flanking Nets.

    Santer, Roger D


    Tsetse flies transmit trypanosomes that cause nagana in cattle, and sleeping sickness in humans. Therefore, optimising visual baits to control tsetse is an important priority. Tsetse are intercepted at visual baits due to their initial attraction to the bait, and their subsequent contact with it due to landing or accidental collision. Attraction is proposed to be driven in part by a chromatic mechanism to which a UV-blue photoreceptor contributes positively, and a UV and a green photoreceptor contribute negatively. Landing responses are elicited by stimuli with low luminance, but many studies also find apparently strong landing responses when stimuli have high UV reflectivity, which would imply that UV wavelengths contribute negatively to attraction at a distance, but positively to landing responses at close range. The strength of landing responses is often judged using the number of tsetse sampled at a cloth panel expressed as a proportion of the combined catch of the cloth panel and a flanking net that samples circling flies. I modelled these data from two previously published field studies, using calculated fly photoreceptor excitations as predictors. I found that the proportion of tsetse caught on the cloth panel increased with an index representing the chromatic mechanism driving attraction, as would be expected if the same mechanism underlay both long- and close-range attraction. However, the proportion of tsetse caught on the cloth panel also increased with excitation of the UV-sensitive R7p photoreceptor, in an apparently separate but interacting behavioural mechanism. This R7p-driven effect resembles the fly open-space response which is believed to underlie their dispersal towards areas of open sky. As such, the proportion of tsetse that contact a cloth panel likely reflects a combination of deliberate landings by potentially host-seeking tsetse, and accidental collisions by those seeking to disperse, with a separate visual mechanism underlying each

  19. A Receptor-Based Explanation for Tsetse Fly Catch Distribution between Coloured Cloth Panels and Flanking Nets.

    Roger D Santer

    Full Text Available Tsetse flies transmit trypanosomes that cause nagana in cattle, and sleeping sickness in humans. Therefore, optimising visual baits to control tsetse is an important priority. Tsetse are intercepted at visual baits due to their initial attraction to the bait, and their subsequent contact with it due to landing or accidental collision. Attraction is proposed to be driven in part by a chromatic mechanism to which a UV-blue photoreceptor contributes positively, and a UV and a green photoreceptor contribute negatively. Landing responses are elicited by stimuli with low luminance, but many studies also find apparently strong landing responses when stimuli have high UV reflectivity, which would imply that UV wavelengths contribute negatively to attraction at a distance, but positively to landing responses at close range. The strength of landing responses is often judged using the number of tsetse sampled at a cloth panel expressed as a proportion of the combined catch of the cloth panel and a flanking net that samples circling flies. I modelled these data from two previously published field studies, using calculated fly photoreceptor excitations as predictors. I found that the proportion of tsetse caught on the cloth panel increased with an index representing the chromatic mechanism driving attraction, as would be expected if the same mechanism underlay both long- and close-range attraction. However, the proportion of tsetse caught on the cloth panel also increased with excitation of the UV-sensitive R7p photoreceptor, in an apparently separate but interacting behavioural mechanism. This R7p-driven effect resembles the fly open-space response which is believed to underlie their dispersal towards areas of open sky. As such, the proportion of tsetse that contact a cloth panel likely reflects a combination of deliberate landings by potentially host-seeking tsetse, and accidental collisions by those seeking to disperse, with a separate visual mechanism

  20. Three indel variants in chicken LPIN1 exon 6/flanking region are associated with performance and carcass traits.

    Wang, R; Wang, T; Lu, W; Zhang, W; Chen, W; Kang, X; Huang, Y


    LPIN1 is a Mg(2+)-dependent phosphatidic acid phosphatase. Variation in chicken LPIN1 exon 6 and its flanking regions were identified and three indel variants in 6 breeds and their associations with performance traits were studied. Seven variants were detected from 6 breeds, which contained a synonymous tri-allelic variant (c.924A/T/C) and three indels. The exon 6 variants detected from chicken breeds were conserved among bird species. The indel variation frequency presented clear differences among breeds. Two coding indels (c.1014-1018del3 and c.1125-1138del12) were multiples of three nucleotides and maintained the open reading frames of LPIN1 proteins. However, they were predicted to result in the clear change of the RNA secondary structure of chicken LPIN1 exon 6 and LPIN1 protein conformation. The association analysis showed that c.871-15-22del6 variation had a significant effect on body weight at hatch (BW0) and 2 weeks (BW2); c. 1014-1018del3 variation had a significant effect on BW4, BW6, caecum length and gizzard weight (GW) traits; c.1125-1138del12 variation had a significant effect on BW12, shank length at 4 weeks (SL4), carcass weight, lactate dehydrogenase traits (LDH), glucose (GLU) and albumin (ALB) traits. The genotype combination for c.1014-1018del3 and c.1125-1138del12 also presented significant effects on SL4, SL8, GW, leg muscle weight, ALB, GLU and LDH. The study demonstrated that chicken LPIN1 has an important effect on body, carcass and organ weight, serum LDH, GLU and ALB level.