Patient satisfaction with the endoscopy experience and willingness to return in a central Canadian health region.

PubMed

Loftus, Russell; Nugent, Zoann; Graff, Lesley A; Schumacher, Frederick; Bernstein, Charles N; Singh, Harminder

2013-01-01

Patient experiences with endoscopy visits within a large central Canadian health region were evaluated to determine the relationship between the visit experience and the patients' willingness to return for future endoscopy, and to identify the factors associated with patients' willingness to return. A self-report survey was distributed to 1200 consecutive individuals undergoing an upper and⁄or lower gastrointestinal endoscopy at any one of the six hospital-based endoscopy facilities in the region. The Spearman correlation coefficient was used to assess the association between the patients' overall rating of the visits and willingness to return for repeat procedures under similar medical circumstances. Logistic regression analyses were performed to identify the factors associated with willingness to return for repeat endoscopy and overall satisfaction (rating) of the visit. A total of 529 (44%) individuals returned the questionnaire, with 45% rating the visit as excellent and 56% indicating they were extremely likely to return for repeat endoscopy. There was a low moderate correlation between overall rating of the visit and patients' willingness to return for repeat endoscopy (r=0.30). The factors independently associated with patient willingness to return for repeat endoscopy included perceived technical skills of the endoscopists (OR 2.7 [95% CI 1.3 to 5.5]), absence of pain during the procedure (OR 2.2 [95% CI 1.3 to 3.6]) and history of previous endoscopy (OR 2.4 [95% CI 1.4 to 4.1]). In contrast, the independent factors associated with the overall rating of the visit included information provided pre- and postprocedure, wait time before and on the day of the visit, and the physical environment. To facilitate patient return for needed endoscopy, it is important to assess patients' willingness to return because positive behavioural intent is not simply a function of satisfaction with the visit.

Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine.

PubMed

Chureau, Corinne; Prissette, Marine; Bourdet, Agnès; Barbe, Valérie; Cattolico, Laurence; Jones, Louis; Eggen, André; Avner, Philip; Duret, Laurent

2002-06-01

We have sequenced to high levels of accuracy 714-kb and 233-kb regions of the mouse and bovine X-inactivation centers (Xic), respectively, centered on the Xist gene. This has provided the basis for a fully annotated comparative analysis of the mouse Xic with the 2.3-Mb orthologous region in human and has allowed a three-way species comparison of the core central region, including the Xist gene. These comparisons have revealed conserved genes, both coding and noncoding, conserved CpG islands and, more surprisingly, conserved pseudogenes. The distribution of repeated elements, especially LINE repeats, in the mouse Xic region when compared to the rest of the genome does not support the hypothesis of a role for these repeat elements in the spreading of X inactivation. Interestingly, an asymmetric distribution of LINE elements on the two DNA strands was observed in the three species, not only within introns but also in intergenic regions. This feature is suggestive of important transcriptional activity within these intergenic regions. In silico prediction followed by experimental analysis has allowed four new genes, Cnbp2, Ftx, Jpx, and Ppnx, to be identified and novel, widespread, complex, and apparently noncoding transcriptional activity to be characterized in a region 5' of Xist that was recently shown to attract histone modification early after the onset of X inactivation.

Surface Wave Elastometry of the Cornea in Porcine and Human Donor Eyes

PubMed Central

Dupps, William J.; Netto, Marcelo V.; Herekar, Satish; Krueger, Ronald R.

2007-01-01

PURPOSE To introduce a nondestructive technique for characterization of corneal stiffness, determine measurement precision, and investigate comparative stiffness values along central, radial, and circumferential vectors in porcine corneas. The effects of epithelial debridement, relaxing incisions, and crosslink-mediated stiffening on surface wave velocity are also studied. METHODS A handheld prototype system was used to measure ultrasound surface wave propagation time between two fixed-distance transducers along a ten-position map. Repeatability was assessed with replicate measurements in 6 porcine corneas. In 12 porcine globes with controlled intraocular pressure (IOP), serial measurements were performed before and after epithelial removal, then after 250- and 750-μm-deep relaxing incisions. In human globes with constant intravitreal pressure, central wave velocity and transcorneal IOP measurements were compared before and after collagen cross-linking. RESULTS Measurement repeatability across all regions was between 2.2% and 8.1%. Epithelial removal resulted in increases in measured stiffness in 67% of eyes, but statistical power was insufficient to detect a systematic change. Wave velocity across a central incision decreased significantly after 250-μm keratotomy (P<.001), but did not undergo a significant further decrease with deeper keratotomy. Meridional stiffness changes consistent with coupling effects were detected after keratotomy. Surface wave velocity and transcorneal IOP measurements increased markedly after collagen cross-linking despite maintenance of a constant IOP. CONCLUSIONS Handheld corneal elastometry provides a repeatable measure of regional stiffness changes after relaxing incisions and collagen cross-linking in in vitro experiments. Surface wave elastometry allows focal assessment of corneal biomechanical properties that are relevant in refractive surgery, ectatic disease, and glaucoma. PMID:17269246

Identification of repeating earthquakes and spatio-temporal variations of fault zone properties around the Parkfield section of the San Andreas fault and the central Calaveras fault

NASA Astrophysics Data System (ADS)

Zhao, P.; Peng, Z.

2008-12-01

We systemically identify repeating earthquakes and investigate spatio-temporal variations of fault zone properties associated with the 2004 Mw6.0 Parkfield earthquake along the Parkfield section of the San Andreas fault, and the 1984 Mw6.2 Morgan Hill earthquake along the central Calaveras fault. The procedure for identifying repeating earthquakes is based on overlapping of the source regions and the waveform similarity, and is briefly described as follows. First, we estimate the source radius of each event based on a circular crack model and a normal stress drop of 3 MPa. Next, we compute inter-hypocentral distance for events listed in the relocated catalog of Thurber et al. (2006) around Parkfield, and Schaff et al. (2002) along the Calaveras fault. Then, we group all events into 'initial' clusters by requiring the separation distance between each event pair to be less than the source radius of larger event, and their magnitude difference to be less than 1. Next, we calculate the correlation coefficients between every event pair within each 'initial' cluster using a 3-s time window around the direct P waves for all available stations. The median value of the correlation coefficients is used as a measure of similarity between each event pair. We drop an event if the median similarity to the rest events in that cluster is less than 0.9. After identifying repeating clusters in both regions, our next step is to apply a sliding window waveform cross-correlation technique (Niu et al., 2003; Peng and Ben-Zion, 2006) to calculate the delay time and decorrelation index for each repeating cluster. By measuring temporal changes in waveforms of repeating clusters at different locations and depth, we hope to obtain a better constraint on spatio-temporal variations of fault zone properties and near-surface layers associated with the occurrence of major earthquakes.

Brain cholinergic involvement during the rapid development of tolerance to morphine

NASA Technical Reports Server (NTRS)

Wahba, Z. Z.; Oriaku, E. T.; Soliman, S. F. A.

1987-01-01

The effect of repeated administration of morphine on the activities of the cholinergic enzymes, choline acetyltransferase (ChAT) and acetylcholinesterase (AChE), in specific brain regions were studied in rats treated with 10 mg/kg morphine for one or two days. Repeated administration of morphine was associated with a decline in the degree of analgesia produced and with a significant increase of AChE activity of the medulla oblongata. A single injection of morphine resulted in a significant decline in ChAT activity in the hypothalamus, cerebellum, and medulla oblongata regions. After two consecutive injections, no decline in ChAT was observed in these regions, while in the cerebral cortex the second administration elicited a significant decline. The results suggest that the development of tolerance to morphine may be mediated through changes in ChAT activity and lend support to the involvement of the central cholinergic system in narcotic tolerance.

Structure of the circumsporozoite protein gene in 18 strains of Plasmodium falciparum.

PubMed

Weber, J L; Hockmeyer, W T

1985-06-01

Using the cloned circumsporozoite (CS) protein gene of a Brazilian strain of Plasmodium falciparum as probe, we have analyzed the structure of the CS protein gene from 17 other Asian, African, Central and South American parasite strains by nucleic acid hybridization. Each strain appears to have one CS protein gene which hybridizes readily to the Brazilian strain probe. The 5' and 3' thirds of the genes are invariant in size in all 18 strains whereas the central third containing the 12 base pair tandem repeats varies in size over a range of about 100 base pairs. Several differences were found in the locations of Sau3A sites in the genes. The Sau3A sites are significant because each of the minority Asn-Val-Asp-Pro repeats in the cloned gene has a Sau3A site. DNA melting of hybrids revealed a high degree of homology between the sequences of the cloned gene and genes from an Asian strain and an African strain. A 14 base oligodeoxynucleotide with a sequence from the central repeat region hybridized to all strains tested. We conclude that the CS protein gene is highly conserved among strains of P. falciparum and that malaria vaccine development with the CS protein is unlikely to be complicated by strain variation.

Comparison and correlation of Simple Sequence Repeats distribution in genomes of Brucella species

PubMed Central

Kiran, Jangampalli Adi Pradeep; Chakravarthi, Veeraraghavulu Praveen; Kumar, Yellapu Nanda; Rekha, Somesula Swapna; Kruti, Srinivasan Shanthi; Bhaskar, Matcha

2011-01-01

Computational genomics is one of the important tools to understand the distribution of closely related genomes including simple sequence repeats (SSRs) in an organism, which gives valuable information regarding genetic variations. The central objective of the present study was to screen the SSRs distributed in coding and non-coding regions among different human Brucella species which are involved in a range of pathological disorders. Computational analysis of the SSRs in the Brucella indicates few deviations from expected random models. Statistical analysis also reveals that tri-nucleotide SSRs are overrepresented and tetranucleotide SSRs underrepresented in Brucella genomes. From the data, it can be suggested that over expressed tri-nucleotide SSRs in genomic and coding regions might be responsible in the generation of functional variation of proteins expressed which in turn may lead to different pathogenicity, virulence determinants, stress response genes, transcription regulators and host adaptation proteins of Brucella genomes. Abbreviations SSRs - Simple Sequence Repeats, ORFs - Open Reading Frames. PMID:21738309

Altered effect of dopamine transporter 3'UTR VNTR genotype on prefrontal and striatal function in schizophrenia.

PubMed

Prata, Diana P; Mechelli, Andrea; Picchioni, Marco M; Fu, Cynthia H Y; Toulopoulou, Timothea; Bramon, Elvira; Walshe, Muriel; Murray, Robin M; Collier, David A; McGuire, Philip

2009-11-01

The dopamine transporter plays a key role in the regulation of central dopaminergic transmission, which modulates cognitive processing. Disrupted dopamine function and impaired executive processing are robust features of schizophrenia. To examine the effect of a polymorphism in the dopamine transporter gene (the variable number of tandem repeats in the 3' untranslated region) on brain function during executive processing in healthy volunteers and patients with schizophrenia. We hypothesized that this variation would have a different effect on prefrontal and striatal activation in schizophrenia, reflecting altered dopamine function. Case-control study. Psychiatric research center. Eighty-five subjects, comprising 44 healthy volunteers (18 who were 9-repeat carriers and 26 who were 10-repeat homozygotes) and 41 patients with DSM-IV schizophrenia (18 who were 9-repeat carriers and 23 who were 10-repeat homozygotes). Regional brain activation during word generation relative to repetition in an overt verbal fluency task measured by functional magnetic resonance imaging. Main effects of genotype and diagnosis on activation and their interaction were estimated with analysis of variance in SPM5. Irrespective of diagnosis, the 10-repeat allele was associated with greater activation than the 9-repeat allele in the left anterior insula and right caudate nucleus. Trends for the same effect in the right insula and for greater deactivation in the rostral anterior cingulate cortex were also detected. There were diagnosis x genotype interactions in the left middle frontal gyrus and left nucleus accumbens, where the 9-repeat allele was associated with greater activation than the 10-repeat allele in patients but not controls. Insular, cingulate, and striatal function during an executive task is normally modulated by variation in the dopamine transporter gene. Its effect on activation in the dorsolateral prefrontal cortex and ventral striatum is altered in patients with schizophrenia. This may reflect altered dopamine function in these regions in schizophrenia.

Evolutionary dynamics of the immunodominant repeats of the Plasmodium vivax malaria-vaccine candidate circumsporozoite protein (CSP)

PubMed Central

Patil, Aarti; Orjuela-Sánchez, Pamela; da Silva-Nunes, Mônica; Ferreira, Marcelo U.

2010-01-01

The circumsporozoite protein (CSP) of Plasmodium vivax, a major target for malaria vaccine development, has immunodominant B-cell epitopes mapped to central nonapeptide repeat arrays. To determine whether rearrangements of repeat motifs during mitotic DNA replication of parasites create significant CSP diversity under conditions of low effective meiotic recombination rates, we examined csp alleles from sympatric P. vivax isolates systematically sampled from an area of low malaria endemicity in Brazil over a period of 14 months. Nine unique csp types, comprising six different nonapeptide repeats, were observed in 45 isolates analyzed. Identical or nearly identical repeats predominated in most arrays, consistent with their recent expansion. We found strong linkage disequilibrium at sites across the chromosome 8 segment flanking the csp locus, consistent with rare meiotic recombination in this region. We conclude that CSP repeat diversity may not be severely constrained by rare meiotic recombination in areas of low malaria endemicity. New repeat variants may be readily created by nonhomologous recombination even when meiotic recombination is rare, with potential implications for CSP-based vaccine development. PMID:20097310

Y-chromosome distributions among populations in Northwest China identify significant contribution from Central Asian pastoralists and lesser influence of western Eurasians.

PubMed

Shou, Wei-Hua; Qiao, En-Fa; Wei, Chuan-Yu; Dong, Yong-Li; Tan, Si-Jie; Shi, Hong; Tang, Wen-Ru; Xiao, Chun-Jie

2010-05-01

Northwest China is closely adjacent to Central Asia, an intermediate region of the Eurasian continent. Moreover, the Silk Road through the northwest of China once had a vital role in the east-west intercommunications. Nevertheless, little has been known about the genetic makeup of populations in this region. We collected 503 male samples from 14 ethnic groups in the northwest of China, and surveyed 29 Y-chromosomal biallelic markers and 8 short tandem repeats (STRs) loci to reconstruct the paternal architecture. Our results illustrated obvious genetic difference among these ethnic groups, and in general their genetic background is more similar with Central Asians than with East Asians. The ancestors of present northwestern populations were the admixture of early East Asians peopling northwestward and later Central Asians immigrating eastward. This population mixture was dated to occur within the past 10 000 years. The J2-M172 lineages likely entered China during the eastward migration of Central Asians. The influence from West Eurasia through gene flows on the extant ethnic groups in Northwest China was relatively weak.

Toxic PRn poly-dipeptides encoded by the C9orf72 repeat expansion block nuclear import and export.

PubMed

Shi, Kevin Y; Mori, Eiichiro; Nizami, Zehra F; Lin, Yi; Kato, Masato; Xiang, Siheng; Wu, Leeju C; Ding, Ming; Yu, Yonghao; Gall, Joseph G; McKnight, Steven L

2017-02-14

The toxic proline:arginine (PR n ) poly-dipeptide encoded by the (GGGGCC) n repeat expansion in the C9orf72 form of heritable amyotrophic lateral sclerosis (ALS) binds to the central channel of the nuclear pore and inhibits the movement of macromolecules into and out of the nucleus. The PR n poly-dipeptide binds to polymeric forms of the phenylalanine:glycine (FG) repeat domain, which is shared by several proteins of the nuclear pore complex, including those in the central channel. A method of chemical footprinting was used to characterize labile, cross-β polymers formed from the FG domain of the Nup54 protein. Mutations within the footprinted region of Nup54 polymers blocked both polymerization and binding by the PR n poly-dipeptide. The aliphatic alcohol 1,6-hexanediol melted FG domain polymers in vitro and reversed PR n -mediated enhancement of the nuclear pore permeability barrier. These data suggest that toxicity of the PR n poly-dipeptide results in part from its ability to lock the FG repeats of nuclear pore proteins in the polymerized state. Our study offers a mechanistic interpretation of PR n poly-dipeptide toxicity in the context of a prominent form of ALS.

Primary central nervous system lymphoma in childhood presenting as progressive panhypopituitarism.

PubMed

Silfen, M E; Garvin, J H; Hays, A P; Starkman, H S; Aranoff, G S; Levine, L S; Feldstein, N A; Wong, B; Oberfield, S E

2001-02-01

We report a 15-year-old boy who had isolated central diabetes insipidus initially diagnosed at age 11 years. A brain magnetic resonance imaging (MRI) was normal at the time. At age 12 years, growth hormone (GH) testing was performed because of a decline in linear growth rate and demonstrated GH deficiency. After a repeat normal brain MRI, GH therapy was begun. Three years later, hormonal testing revealed prepubertal gonadotropins and low testosterone levels, free thyroxine index, and morning cortisol levels. Repeat brain MRI demonstrated a 9-mm enhancing lesion in the region of the pituitary stalk. The pathologic diagnosis was that of a high-grade malignant B-cell lymphoma, suggestive of Burkitt Lymphoma. Growth hormone therapy has not been associated with an increased incidence of lymphoma. This report underscores the need for vigilance in follow-up brain imaging and hormonal evaluation in children with diabetes insipidus, especially those with evolving anterior hormone deficiencies.

Repeating Marmara Sea earthquakes: indication for fault creep

NASA Astrophysics Data System (ADS)

Bohnhoff, Marco; Wollin, Christopher; Domigall, Dorina; Küperkoch, Ludger; Martínez-Garzón, Patricia; Kwiatek, Grzegorz; Dresen, Georg; Malin, Peter E.

2017-07-01

Discriminating between a creeping and a locked status of active faults is of central relevance to characterize potential rupture scenarios of future earthquakes and the associated seismic hazard for nearby population centres. In this respect, highly similar earthquakes that repeatedly activate the same patch of an active fault portion are an important diagnostic tool to identify and possibly even quantify the amount of fault creep. Here, we present a refined hypocentre catalogue for the Marmara region in northwestern Turkey, where a magnitude M up to 7.4 earthquake is expected in the near future. Based on waveform cross-correlation for selected spatial seismicity clusters, we identify two magnitude M ∼ 2.8 repeater pairs. These repeaters were identified as being indicative of fault creep based on the selection criteria applied to the waveforms. They are located below the western part of the Marmara section of the North Anatolian Fault Zone and are the largest reported repeaters for the larger Marmara region. While the eastern portion of the Marmara seismic gap has been identified to be locked, only sparse information on the deformation status has been reported for its western part. Our findings indicate that the western Marmara section deforms aseismically to a substantial extent, which reduces the probability for this region to host a nucleation point for the pending Marmara earthquake. This is of relevance, since a nucleation of the Marmara event in the west and subsequent eastward rupture propagation towards the Istanbul metropolitan region would result in a substantially higher seismic hazard and resulting risk than if the earthquake would nucleate in the east and thus propagate westward away from the population centre Istanbul.

A Novel Peptide Derived from the Fusion Protein Heptad Repeat Inhibits Replication of Subacute Sclerosing Panencephalitis Virus In Vitro and In Vivo.

PubMed

Watanabe, Masahiro; Hashimoto, Koichi; Abe, Yusaku; Kodama, Eiichi N; Nabika, Ryota; Oishi, Shinya; Ohara, Shinichiro; Sato, Masatoki; Kawasaki, Yukihiko; Fujii, Nobutaka; Hosoya, Mitsuaki

2016-01-01

Subacute sclerosing panencephalitis (SSPE) is a persistent, progressive, and fatal degenerative disease resulting from persistent measles virus (MV) infection of the central nervous system. Most drugs used to treat SSPE have been reported to have limited effects. Therefore, novel therapeutic strategies are urgently required. The SSPE virus, a variant MV strain, differs virologically from wild-type MV strain. One characteristic of the SSPE virus is its defective production of cell-free virus, which leaves cell-to-cell infection as the major mechanism of viral dissemination. The fusion protein plays an essential role in this cell-to-cell spread. It contains two critical heptad repeat regions that form a six-helix bundle in the trimer similar to most viral fusion proteins. In the case of human immunodeficiency virus type-1 (HIV-1), a synthetic peptide derived from the heptad repeat region of the fusion protein enfuvirtide inhibits viral replication and is clinically approved as an anti-HIV-1 agent. The heptad repeat regions of HIV-1 are structurally and functionally similar to those of the MV fusion protein. We therefore designed novel peptides derived from the fusion protein heptad repeat region of the MV and examined their effects on the measles and SSPE virus replication in vitro and in vivo. Some of these synthetic novel peptides demonstrated high antiviral activity against both the measles (Edmonston strain) and SSPE (Yamagata-1 strain) viruses at nanomolar concentrations with no cytotoxicity in vitro. In particular, intracranial administration of one of the synthetic peptides increased the survival rate from 0% to 67% in an SSPE virus-infected nude mouse model.

A Novel Peptide Derived from the Fusion Protein Heptad Repeat Inhibits Replication of Subacute Sclerosing Panencephalitis Virus In Vitro and In Vivo

PubMed Central

Watanabe, Masahiro; Hashimoto, Koichi; Abe, Yusaku; Kodama, Eiichi N.; Nabika, Ryota; Oishi, Shinya; Ohara, Shinichiro; Sato, Masatoki; Kawasaki, Yukihiko; Fujii, Nobutaka; Hosoya, Mitsuaki

2016-01-01

Subacute sclerosing panencephalitis (SSPE) is a persistent, progressive, and fatal degenerative disease resulting from persistent measles virus (MV) infection of the central nervous system. Most drugs used to treat SSPE have been reported to have limited effects. Therefore, novel therapeutic strategies are urgently required. The SSPE virus, a variant MV strain, differs virologically from wild-type MV strain. One characteristic of the SSPE virus is its defective production of cell-free virus, which leaves cell-to-cell infection as the major mechanism of viral dissemination. The fusion protein plays an essential role in this cell-to-cell spread. It contains two critical heptad repeat regions that form a six-helix bundle in the trimer similar to most viral fusion proteins. In the case of human immunodeficiency virus type-1 (HIV-1), a synthetic peptide derived from the heptad repeat region of the fusion protein enfuvirtide inhibits viral replication and is clinically approved as an anti-HIV-1 agent. The heptad repeat regions of HIV-1 are structurally and functionally similar to those of the MV fusion protein. We therefore designed novel peptides derived from the fusion protein heptad repeat region of the MV and examined their effects on the measles and SSPE virus replication in vitro and in vivo. Some of these synthetic novel peptides demonstrated high antiviral activity against both the measles (Edmonston strain) and SSPE (Yamagata-1 strain) viruses at nanomolar concentrations with no cytotoxicity in vitro. In particular, intracranial administration of one of the synthetic peptides increased the survival rate from 0% to 67% in an SSPE virus-infected nude mouse model. PMID:27612283

Repeated prescribed fires alter gap-phase regeneration in mixed-oak forests

Treesearch

Todd F. Hutchinson; Robert P. Long; Joanne Rebbeck; Elaine Kennedy Sutherland; Daniel A. Yaussy

2012-01-01

Oak dominance is declining in the central hardwoods region, as canopy oaks are being replaced by shade-tolerant trees that are abundant in the understory of mature stands. Although prescribed fire can reduce understory density, oak seedlings often fail to show increased vigor after fire, as the canopy remains intact. In this study, we examine the response of tree...

Influence of a heptad repeat stutter on the pH-dependent conformational behavior of the central coiled-coil from influenza hemagglutinin HA2.

PubMed

Higgins, Chelsea D; Malashkevich, Vladimir N; Almo, Steven C; Lai, Jonathan R

2014-09-01

The coiled-coil is one of the most common protein structural motifs. Amino acid sequences of regions that participate in coiled-coils contain a heptad repeat in which every third then forth residue is occupied by a hydrophobic residue. Here we examine the consequences of a "stutter," a deviation of the idealized heptad repeat that is found in the central coiled-coil of influenza hemagluttinin HA2. Characterization of a peptide containing the native stutter-containing HA2 sequence, as well as several variants in which the stutter was engineered out to restore an idealized heptad repeat pattern, revealed that the stutter is important for allowing coiled-coil formation in the WT HA2 at both neutral and low pH (7.1 and 4.5). By contrast, all variants that contained idealized heptad repeats exhibited marked pH-dependent coiled-coil formation with structures forming much more stably at low pH. A crystal structure of one variant containing an idealized heptad repeat, and comparison to the WT HA2 structure, suggest that the stutter distorts the optimal interhelical core packing arrangement, resulting in unwinding of the coiled-coil superhelix. Interactions between acidic side chains, in particular E69 and E74 (present in all peptides studied), are suggested to play a role in mediating these pH-dependent conformational effects. This conclusion is partially supported by studies on HA2 variant peptides in which these positions were altered to aspartic acid. These results provide new insight into the structural role of the heptad repeat stutter in HA2. © 2014 Wiley Periodicals, Inc.

Vegetation impoverishment despite greening: a case study from central Senegal

USGS Publications Warehouse

Herrmann, Stefanie M.; Tappan, G. Gray

2013-01-01

Recent remote sensing studies have documented a greening trend in the semi-arid Sahel and Sudan zones of West Africa since the early 1980s, which challenges the mainstream paradigm of irreversible land degradation in this region. What the greening trend means on the ground, however, has not yet been explored. This research focuses on a region in central Senegal to examine changes in woody vegetation abundance and composition in selected sites by means of a botanical inventory of woody vegetation species, repeat photography, and perceptions of local land users. Despite the greening, an impoverishment of the woody vegetation cover was observed in the studied sites, indicated by an overall reduction in woody species richness, a loss of large trees, an increasing dominance of shrubs, and a shift towards more arid-tolerant, Sahelian species since 1983. Thus, interpretation of the satellite-derived greening trend as an improvement or recovery is not always justified. The case of central Senegal represents only one of several possible pathways of greening throughout the region, all of which result in similar satellite-derived greening signals.

GenomeLandscaper: Landscape analysis of genome-fingerprints maps assessing chromosome architecture.

PubMed

Ai, Hannan; Ai, Yuncan; Meng, Fanmei

2018-01-18

Assessing correctness of an assembled chromosome architecture is a central challenge. We create a geometric analysis method (called GenomeLandscaper) to conduct landscape analysis of genome-fingerprints maps (GFM), trace large-scale repetitive regions, and assess their impacts on the global architectures of assembled chromosomes. We develop an alignment-free method for phylogenetics analysis. The human Y chromosomes (GRCh.chrY, HuRef.chrY and YH.chrY) are analysed as a proof-of-concept study. We construct a galaxy of genome-fingerprints maps (GGFM) for them, and a landscape compatibility among relatives is observed. But a long sharp straight line on the GGFM breaks such a landscape compatibility, distinguishing GRCh38p1.chrY (and throughout GRCh38p7.chrY) from GRCh37p13.chrY, HuRef.chrY and YH.chrY. We delete a 1.30-Mbp target segment to rescue the landscape compatibility, matching the antecedent GRCh37p13.chrY. We re-locate it into the modelled centromeric and pericentromeric region of GRCh38p10.chrY, matching a gap placeholder of GRCh37p13.chrY. We decompose it into sub-constituents (such as BACs, interspersed repeats, and tandem repeats) and trace their homologues by phylogenetics analysis. We elucidate that most examined tandem repeats are of reasonable quality, but the BAC-sized repeats, 173U1020C (176.46 Kbp) and 5U41068C (205.34 Kbp), are likely over-repeated. These results offer unique insights into the centromeric and pericentromeric regions of the human Y chromosomes.

Is the Forest Healthy? (Mid-Atlantic, North Central, New England, and New York Regions)

Treesearch

Jennifer Stoyenoff; John Witter; Bruce Leutscher

1997-01-01

No single measurement can summarize forest health. Instead, we need to look at a wide set of indicators which together serve as a reflection of existing conditions. Repeated monitoring of the forest over time allows us to identify trends in forest conditions and evaluate the effectiveness of our actions. Information about forest health is obtained in a variety of ways...

Region-specific disruption of the blood-brain barrier following repeated inflammatory dural stimulation in a rat model of chronic trigeminal allodynia

PubMed Central

Fried, Nathan T; Maxwell, Christina R; Elliott, Melanie B; Oshinsky, Michael L

2017-01-01

Background The blood-brain barrier (BBB) has been hypothesized to play a role in migraine since the late 1970s. Despite this, limited investigation of the BBB in migraine has been conducted. We used the inflammatory soup rat model of trigeminal allodynia, which closely mimics chronic migraine, to determine the impact of repeated dural inflammatory stimulation on BBB permeability. Methods The sodium fluorescein BBB permeability assay was used in multiple brain regions (trigeminal nucleus caudalis (TNC), periaqueductal grey, frontal cortex, sub-cortex, and cortex directly below the area of dural activation) during the episodic and chronic stages of repeated inflammatory dural stimulation. Glial activation was assessed in the TNC via GFAP and OX42 immunoreactivity. Minocycline was tested for its ability to prevent BBB disruption and trigeminal sensitivity. Results No astrocyte or microglial activation was found during the episodic stage, but BBB permeability and trigeminal sensitivity were increased. Astrocyte and microglial activation, BBB permeability, and trigeminal sensitivity were increased during the chronic stage. These changes were only found in the TNC. Minocycline treatment prevented BBB permeability modulation and trigeminal sensitivity during the episodic and chronic stages. Discussion Modulation of BBB permeability occurs centrally within the TNC following repeated dural inflammatory stimulation and may play a role in migraine. PMID:28457145

A Fracture Decoupling Experiment

NASA Astrophysics Data System (ADS)

Stroujkova, A. F.; Bonner, J. L.; Leidig, M.; Ferris, A. N.; Kim, W.; Carnevale, M.; Rath, T.; Lewkowicz, J.

2012-12-01

Multiple observations made at the Semipalatinsk Test Site suggest that conducting nuclear tests in the fracture zones left by previous explosions results in decreased seismic amplitudes for the second nuclear tests (or "repeat shots"). Decreased seismic amplitudes reduce both the probability of detection and the seismically estimated yield of a "repeat shot". In order to define the physical mechanism responsible for the amplitude reduction and to quantify the degree of the amplitude reduction in fractured rocks, Weston Geophysical Corp., in collaboration with Columbia University's Lamont Doherty Earth Observatory, conducted a multi-phase Fracture Decoupling Experiment (FDE) in central New Hampshire. The FDE involved conducting explosions of various yields in the damage/fracture zones of previously detonated explosions. In order to quantify rock damage after the blasts we performed well logging and seismic cross-hole tomography studies of the source region. Significant seismic velocity reduction was observed around the source regions after the initial explosions. Seismic waves produced by the explosions were recorded at near-source and local seismic networks, as well as several regional stations throughout northern New England. Our analysis confirms frequency dependent seismic amplitude reduction for the repeat shots compared to the explosions in un-fractured rocks. The amplitude reduction is caused by pore closing and/or by frictional losses within the fractured media.

Comparative Sequence Analysis of the X-Inactivation Center Region in Mouse, Human, and Bovine

PubMed Central

Chureau, Corinne; Prissette, Marine; Bourdet, Agnès; Barbe, Valérie; Cattolico, Laurence; Jones, Louis; Eggen, André; Avner, Philip; Duret, Laurent

2002-01-01

We have sequenced to high levels of accuracy 714-kb and 233-kb regions of the mouse and bovine X-inactivation centers (Xic), respectively, centered on the Xist gene. This has provided the basis for a fully annotated comparative analysis of the mouse Xic with the 2.3-Mb orthologous region in human and has allowed a three-way species comparison of the core central region, including the Xist gene. These comparisons have revealed conserved genes, both coding and noncoding, conserved CpG islands and, more surprisingly, conserved pseudogenes. The distribution of repeated elements, especially LINE repeats, in the mouse Xic region when compared to the rest of the genome does not support the hypothesis of a role for these repeat elements in the spreading of X inactivation. Interestingly, an asymmetric distribution of LINE elements on the two DNA strands was observed in the three species, not only within introns but also in intergenic regions. This feature is suggestive of important transcriptional activity within these intergenic regions. In silico prediction followed by experimental analysis has allowed four new genes, Cnbp2, Ftx, Jpx, and Ppnx, to be identified and novel, widespread, complex, and apparently noncoding transcriptional activity to be characterized in a region 5′ of Xist that was recently shown to attract histone modification early after the onset of X inactivation. [The sequence data described in this paper have been submitted to the EMBL data library under accession nos. AJ421478, AJ421479, AJ421480, and AJ421481. Online supplemental data are available at http://pbil.univ-lyon1.fr/datasets/Xic2002/data.html and www.genome.org.] PMID:12045143

Lithospheric controls on crustal reactivation and intraplate mountain building in the Gobi Corridor, Central Asia

NASA Astrophysics Data System (ADS)

Cunningham, D.

2017-12-01

This talk will review the Permian-Recent tectonic history of the Gobi Corridor region which includes the actively deforming Gobi Altai-Altai, Eastern Tien Shan, Beishan and North Tibetan foreland. Since terrane amalgamation in the Permian, Gobi Corridor crust has been repeatedly reactivated by Triassic-Jurassic contraction/transpression, Late Cretaceous extension and Late Cenozoic transpression. The tectonic history of the region suggests the following basic principle for intraplate continental regions: non-cratonized continental interior terrane collages are susceptible to repeated intraplate reactivation events, driven by either post-orogenic collapse and/or compressional stresses derived from distant plate boundary convergence. Thus, important related questions are: 1) what lithospheric pre-conditions favor intraplate crustal reactivation in the Gobi Corridor (simple answer: crustal thinning, thermal weakening, strong buttressing cratons), 2) what are the controls on the kinematics of deformation and style of mountain building in the Gobi-Altai-Altai, Beishan and North Tibetan margin (simple answer: many factors, but especially angular relationship between SHmax and `crustal grain'), 3) how does knowledge of the array of Quaternary faults and the historical earthquake record influence our understanding of modern earthquake hazards in continental intraplate regions (answer: extrapolation of derived fault slip rates and recurrence interval determinations are problematic), 4) what important lessons can we learn from the Mesozoic-Cenozoic tectonic history of Central Asia that is applicable to the tectonic evolution of all intraplate continental regions (simple answer: ancient intraplate deformation events may be subtly expressed in the rock record and only revealed by low-temperature thermochronometers, preserved orogen-derived sedimentary sequences, fault zone evidence for younger brittle reactivation, and recognition of a younger class of cross-cutting tectonic structures).

Characterization of IntA, a Bidirectional Site-Specific Recombinase Required for Conjugative Transfer of the Symbiotic Plasmid of Rhizobium etli CFN42

PubMed Central

Hernández-Tamayo, Rogelio; Sohlenkamp, Christian; Puente, José Luis; Brom, Susana

2013-01-01

Site-specific recombination occurs at short specific sequences, mediated by the cognate recombinases. IntA is a recombinase from Rhizobium etli CFN42 and belongs to the tyrosine recombinase family. It allows cointegration of plasmid p42a and the symbiotic plasmid via site-specific recombination between attachment regions (attA and attD) located in each replicon. Cointegration is needed for conjugative transfer of the symbiotic plasmid. To characterize this system, two plasmids harboring the corresponding attachment sites and intA were constructed. Introduction of these plasmids into R. etli revealed IntA-dependent recombination events occurring at high frequency. Interestingly, IntA promotes not only integration, but also excision events, albeit at a lower frequency. Thus, R. etli IntA appears to be a bidirectional recombinase. IntA was purified and used to set up electrophoretic mobility shift assays with linear fragments containing attA and attD. IntA-dependent retarded complexes were observed only with fragments containing either attA or attD. Specific retarded complexes, as well as normal in vivo recombination abilities, were seen even in derivatives harboring only a minimal attachment region (comprising the 5-bp central region flanked by 9- to 11-bp inverted repeats). DNase I-footprinting assays with IntA revealed specific protection of these zones. Mutations that disrupt the integrity of the 9- to 11-bp inverted repeats abolish both specific binding and recombination ability, while mutations in the 5-bp central region severely reduce both binding and recombination. These results show that IntA is a bidirectional recombinase that binds to att regions without requiring neighboring sequences as enhancers of recombination. PMID:23935046

Genetic analysis and ethnic affinities from two Scytho-Siberian skeletons.

PubMed

Ricaut, François-Xavier; Keyser-Tracqui, Christine; Cammaert, Laurence; Crubézy, Eric; Ludes, Bertrand

2004-04-01

We extracted DNA from two skeletons belonging to the Sytho-Siberian population, which were excavated from the Sebÿstei site (dating back 2,500 years) in the Altai Republic (Central Asia). Ancient DNA was analyzed by autosomal short tandem repeats (STRs) and by the sequencing of the hypervariable region 1 (HV1) of the mitochondrial DNA (mtDNA) control region. The results showed that these two skeletons were not close relatives. Moreover, their haplogroups were characteristic of Asian populations. Comparison with the haplogroup of 3,523 Asian and American individuals linked one skeleton with a putative ancestral paleo-Asiatic population and the other with Chinese populations. It appears that the genetic study of ancient populations of Central Asia brings important elements to the understanding of human population movements in Asia. Copyright 2003 Wiley-Liss, Inc.

Changes in stand structure and tree vigor with repeated prescribed fire in an Appalachian hardwood forest

Treesearch

Mary A. Arthur; Beth A. Blankenship; Angela Schörgendorfer; David L. Loftis; Heather D. Alexander

2015-01-01

Without large scale disturbances to alter forest structure and open the canopy, historically oak-dominated forests of the central and Appalachian hardwood regions of eastern North America are shifting to dominance by shade-tolerant, ‘mesophytic’ species. In response, prescribed fire is applied with increasing frequency and spatial extent to decrease non-oak species and...

Effects of repeated exposure to white noise on central cholinergic activity in the rat.

PubMed

Lai, H

1988-03-01

Acute (45 min) exposure to noise has been shown to decrease sodium-dependent high-affinity choline uptake activity in the frontal cortex and hippocampus of the rat. In the present experiment, the effects of repeated noise exposure on choline uptake in these two brain regions were studied. Rats were exposed to 100-dB white noise in ten 45-min sessions. Tolerance developed to the effects of noise on choline uptake. In addition, the effects were found to be classically conditionable to cues in the exposure environment. These data may have important implications in understanding the health hazard of noise exposure in both the public and occupational environments.

Diversity of chloroplast genome among local clones of cocoa (Theobroma cacao, L.) from Central Sulawesi

NASA Astrophysics Data System (ADS)

Suwastika, I. Nengah; Pakawaru, Nurul Aisyah; Rifka, Rahmansyah, Muslimin, Ishizaki, Yoko; Cruz, André Freire; Basri, Zainuddin; Shiina, Takashi

2017-02-01

Chloroplast genomes typically range in size from 120 to 170 kilo base pairs (kb), which relatively conserved among plant species. Recent evaluation on several species, certain unique regions showed high variability which can be utilized in the phylogenetic analysis. Many fragments of coding regions, introns, and intergenic spacers, such as atpB-rbcL, ndhF, rbcL, rpl16, trnH-psbA, trnL-F, trnS-G, etc., have been used for phylogenetic reconstructions at various taxonomic levels. Based on that status, we would like to analysis the diversity of chloroplast genome within species of local cacao (Theobroma cacao L.) from Central Sulawesi. Our recent data showed, there were more than 20 clones from local farming in Central Sulawesi, and it can be detected based on phenotypic and nuclear-genome-based characterization (RAPD- Random Amplified Polymorphic DNA and SSR- Simple Sequences Repeat) markers. In developing DNA marker for this local cacao, here we also included analysis based on the variation of chloroplast genome. At least several regions such as rpl32-TurnL, it can be considered as chloroplast markers on our local clone of cocoa. Furthermore, we could develop phylogenetic analysis in between clones of cocoa.

Mechanisms of insulin action on sympathetic nerve activity

NASA Technical Reports Server (NTRS)

Muntzel, Martin S.; Anderson, Erling A.; Johnson, Alan Kim; Mark, Allyn L.

1996-01-01

Insulin resistance and hyperinsulinemia may contribute to the development of arterial hypertension. Although insulin may elevate arterial pressure, in part, through activation of the sympathetic nervous system, the sites and mechanisms of insulin-induced sympathetic excitation remain uncertain. While sympathoexcitation during insulin may be mediated by the baroreflex, or by modulation of norepinephrine release from sympathetic nerve endings, it has been shown repeatedly that insulin increases sympathetic outflow by actions on the central nervous system. Previous studies employing norepinephrine turnover have suggested that insulin causes sympathoexcitation by acting in the hypothalamus. Recent experiments from our laboratory involving direct measurements of regional sympathetic nerve activity have provided further evidence that insulin acts in the central nervous system. For example, administration of insulin into the third cerebralventricle increased lumbar but not renal or adrenal sympathetic nerve activity in normotensive rats. Interestingly, this pattern of regional sympathetic nerve responses to central neural administration of insulin is similar to that seen with systemic administration of insulin. Further, lesions of the anteroventral third ventricle hypothalamic (AV3V) region abolished increases in sympathetic activity to systemic administration of insulin with euglycemic clamp, suggesting that AV3V-related structures are critical for insulin-induced elevations in sympathetic outflow.

Genetic diversity of major surface protein 1a of Anaplasma marginale in beef cattle.

PubMed

Molad, T; Fleidrovich, L; Mazuz, M; Fish, L; Leibovitz, B; Krigel, Y; Shkap, V

2009-04-14

The present study was aimed to demonstrate genotypic diversity of Anaplama marginale in infected beef herds grazing within anaplasmosis endemic regions. The genotypic diversity was identified among different herds, within each herd, and also within single animals. The Israeli strains revealed unique characteristics of MSP1a repeats and, in addition to the published repeats, six new tandem repeats designated Is1-5, and Is9 were identified. The superinfections of individual Anaplama centrale vaccinated animals with two genotypically different A. marginale strains were detected. Six out of 43 vaccinated animals in the G herd were each infected with two A. marginale strains carrying two distinct genotypes; in this herd the follow-up during years 2003-2007 demonstrated that several animals carried different msp1a genotypes at different time points. Coinfection with two different genotypes of A. marginale in A. centrale vaccinated cattle was observed in another herd, as well. It appears that A. marginale is composed of a heterogeneous changing bacterial population that evolves in the host or, the genotypic diversity implies high transmission intensity by the vector, or both. Learning how this diversity is generated and identification of distinct A. marginale strains coupled with high sequence variation of MSP1a will aid in understanding Anaplasma transmission and disease development.

Monitoring network confirms land use change is a substantial component of the forest carbon sink in the eastern United States

Treesearch

Christopher W. Woodall; Brian F. Walters; John Coulston; A.W. D’Amato; Grant M. Domke; M.B. Russell; Paul Sowers

2015-01-01

Quantifying forest carbon (C) stocks and stock change within a matrix of land use (LU) and LU change is a central component of large-scale forest C monitoring and reporting practices prescribed by the Intergovernmental Panel on Climate Change (IPCC). Using a region–wide, repeated forest inventory, forest C stocks and stock change by pool were examined by LU categories...

Molecular characterization and distribution of a 145-bp tandem repeat family in the genus Populus.

PubMed

Rajagopal, J; Das, S; Khurana, D K; Srivastava, P S; Lakshmikumaran, M

1999-10-01

This report aims to describe the identification and molecular characterization of a 145-bp tandem repeat family that accounts for nearly 1.5% of the Populus genome. Three members of this repeat family were cloned and sequenced from Populus deltoides and P. ciliata. The dimers of the repeat were sequenced in order to confirm the head-to-tail organization of the repeat. Hybridization-based analysis using the 145-bp tandem repeat as a probe on genomic DNA gave rise to ladder patterns which were identified to be a result of methylation and (or) sequence heterogeneity. Analysis of the methylation pattern of the repeat family using methylation-sensitive isoschizomers revealed variable methylation of the C residues and lack of methylation of the A residues. Sequence comparisons between the monomers revealed a high degree of sequence divergence that ranged between 6% and 11% in P. deltoides and between 4.2% and 8.3% in P. ciliata. This indicated the presence of sub-families within the 145-bp tandem family of repeats. Divergence was mainly due to the accumulation of point mutations and was concentrated in the central region of the repeat. The 145-bp tandem repeat family did not show significant homology to known tandem repeats from plants. A short stretch of 36 bp was found to show homology of 66.7% to a centromeric repeat from Chironomus plumosus. Dot-blot analysis and Southern hybridization data revealed the presence of the repeat family in 13 of the 14 Populus species examined. The absence of the 145-bp repeat from P. euphratica suggested that this species is relatively distant from other members of the genus, which correlates with taxonomic classifications. The widespread occurrence of the tandem family in the genus indicated that this family may be of ancient origin.

Mitochondrial genome of the tomato clownfish Amphiprion frenatus (Pomacentridae, Amphiprioninae).

PubMed

Ye, Le; Hu, Jing; Wu, Kaichang; Wang, Yu; Li, Jianlong

2016-01-01

The complete mitochondrial (mt) genome of the tomato clownfish Amphiprion frenatus was obtained in this study. The circular mtDNA molecule was 16,774 bp in size and the overall nucleotide composition of the H-strand was 29.72% A, 25.81% T, 15.38% G and 29.09% C, with an A + T bias. The complete mitogenome encoded 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a control region (D-loop), with the gene arrangement and translation direction basically identical to other typical vertebrate mitogenomes. The D-loop included termination associated sequence (TAS), central conserved domain (CCD) and conserved sequence block (CSB), and was composed of 6 complete continuity tandem repeat units and an imperfect tandem repeat unit.

Distribution and Characteristics of Repeating Earthquakes in Northern California

NASA Astrophysics Data System (ADS)

Waldhauser, F.; Schaff, D. P.; Zechar, J. D.; Shaw, B. E.

2012-12-01

Repeating earthquakes are playing an increasingly important role in the study of fault processes and behavior, and have the potential to improve hazard assessment, earthquake forecast, and seismic monitoring capabilities. These events rupture the same fault patch repeatedly, generating virtually identical seismograms. In California, repeating earthquakes have been found predominately along the creeping section of the central San Andreas Fault, where they are believed to represent failing asperities on an otherwise creeping fault. Here, we use the northern California double-difference catalog of 450,000 precisely located events (1984-2009) and associated database of 2 billion waveform cross-correlation measurements to systematically search for repeating earthquakes across various tectonic regions. An initial search for pairs of earthquakes with high-correlation coefficients and similar magnitudes resulted in 4,610 clusters including a total of over 26,000 earthquakes. A subsequent double-difference re-analysis of these clusters resulted in 1,879 sequences (8,640 events) where a common rupture area can be resolved to the precision of a few tens of meters or less. These repeating earthquake sequences (RES) include between 3 and 24 events with magnitudes up to ML=4. We compute precise relative magnitudes between events in each sequence from differential amplitude measurements. Differences between these and standard coda-duration magnitudes have a standard deviation of 0.09. The RES occur throughout northern California, but RES with 10 or more events (6%) only occur along the central San Andreas and Calaveras faults. We are establishing baseline characteristics for each sequence, such as recurrence intervals and their coefficient of variation (CV), in order to compare them across tectonic regions. CVs for these clusters range from 0.002 to 2.6, indicating a range of behavior between periodic occurrence (CV~0), random occurrence, and temporal clustering. 10% of the RES show burst-like behavior with mean recurrence times smaller than one month. 5% of the RES have mean recurrence times greater than one year and include more than 10 earthquakes. Earthquakes in the 50 most periodic sequences (CV<0.2) do not appear to be predictable by either time- or slip-predictable models, consistent with previous findings. We demonstrate that changes in recurrence intervals of repeating earthquakes can be routinely monitored. This is especially important for sequences with CV~0, as they may indicate changes in the loading rate. We also present results from retrospective forecast experiments based on near-real time hazard functions.

High level of molecular and phenotypic biodiversity in Jatropha curcas from Central America compared to Africa, Asia and South America

PubMed Central

2014-01-01

Background The main bottleneck to elevate jatropha (Jatropha curcas L.) from a wild species to a profitable biodiesel crop is the low genetic and phenotypic variation found in different regions of the world, hampering efficient plant breeding for productivity traits. In this study, 182 accessions from Asia (91), Africa (35), South America (9) and Central America (47) were evaluated at genetic and phenotypic level to find genetic variation and important traits for oilseed production. Results Genetic variation was assessed with SSR (Simple Sequence Repeat), TRAP (Target Region Amplification Polymorphism) and AFLP (Amplified fragment length polymorphism) techniques. Phenotypic variation included seed morphological characteristics, seed oil content and fatty acid composition and early growth traits. Jaccard’s similarity and cluster analysis by UPGM (Unweighted Paired Group Method) with arithmetic mean and PCA (Principle Component Analysis) indicated higher variability in Central American accessions compared to Asian, African and South American accessions. Polymorphism Information Content (PIC) values ranged from 0 to 0.65. In the set of Central American accessions. PIC values were higher than in other regions. Accessions from the Central American population contain alleles that were not found in the accessions from other populations. Analysis of Molecular Variance (AMOVA; P < 0.0001) indicated high genetic variation within regions (81.7%) and low variation across regions (18.3%). A high level of genetic variation was found on early growth traits and on components of the relative growth rate (specific leaf area, leaf weight, leaf weight ratio and net assimilation rate) as indicated by significant differences between accessions and by the high heritability values (50–88%). The fatty acid composition of jatropha oil significantly differed (P < 0.05) between regions. Conclusions The pool of Central American accessions showed very large genetic variation as assessed by DNA-marker variation compared to accessions from other regions. Central American accessions also showed the highest phenotypic variation and should be considered as the most important source for plant breeding. Some variation in early growth traits was found within a group of accessions from Asia and Africa, while these accessions did not differ in a single DNA-marker, possibly indicating epigenetic variation. PMID:24666927

Monitoring of seafloor crustal deformation using GPS/Acoustic technique along the Nankai Trough, Japan

NASA Astrophysics Data System (ADS)

Yasuda, K.; Tadokoro, K.; Ikuta, R.; Watanabe, T.; Fujii, C.; Matsuhiro, K.; Sayanagi, K.

2014-12-01

Seafloor crustal deformation is crucial for estimating the interplate locking at the shallow subduction zone and has been carried out at subduction margins in Japan, e.g., Japan Trench and Nankai Trough [Sato et al., 2011; Tadokoro et al., 2012]. Iinuma et al. [2012] derived slip distributions during the 2011 Tohoku-Oki earthquake using GPS/Acoustic data and on-land GPS data. The result showed that maximum slip is more than 85 m near the trench axis. The focal area along the Nankai trough extended to the trough axis affected this earthquake by cabinet office, government of Japan. 　We monitored seafloor crustal deformation along the Nankai trough, Japan. Observation regions are at the eastern end of Nankai trough (named Suruga trough) and at the central Nankai trough. We established and monitored by two sites across the trough at each region. In the Suruga trough region, we repeatedly observed from 2005 to 2013. We observed 13 and 14 times at a foot wall side (SNE) and at a hanging wall side (SNW), respectively. We estimated the displacement velocities with relative to the Amurian plate from the result of repeated observation. The estimated displacement velocity vectors at SNE and SNW are 42±8 mm/y to N94±3˚W direction and 39±11 mm/y to N84±9˚W direction, respectively. The directions are the same as those measured at the on-land GPS stations. The magnitudes of velocity vector indicate significant shortening by approximately 4 mm/y between SNW and on-land GPS stations at hanging wall side of the Suruga Trough. This result shows that the plate interface at the northernmost Suruga trough is strongly locked. In the central Nankai trough region, we established new two stations across the central Nankai trough (Both stations are about 15km distance from trough) and observed only three times, August 2013, January 2014, and June 2014. We report the results of monitoring performed in this year.

Repeatability of Central Corneal Thickness Measurement Using Rotating Scheimpflug Camera in Dry and Normal Eyes.

PubMed

Lee, Jong-Hyuck; Kim, Jae Hyuck; Kim, Sun Woong

2017-02-27

To compare the repeatability of central corneal thickness (CCT) measurement using the Pentacam between dry eyes and healthy eyes, as well as to investigate the effect of artificial tears on CCT measurement. The corneal thicknesses of 34 patients with dry eye and 28 healthy subjects were measured using the Pentacam. One eye from each subject was assigned randomly to a repeatability test, wherein a single operator performed three successive CCT measurements time points-before and 5 min after instillation of one artificial teardrop. The repeatability of measurements was assessed using the coefficient of repeatability and the intraclass correlation coefficient. The coefficient of repeatability values of the CCT measurements in dry and healthy eyes were 24.36 and 10.69 μm before instillation, and 16.85 and 9.72 μm after instillation, respectively. The intraclass correlation coefficient was higher in healthy eyes than that of in dry eyes (0.987 vs. 0.891), and it had improved significantly in dry eyes (0.948) after instillation of one artificial teardrop. The CCT measurement fluctuated in dry eyes (repeated-measures analysis of variance, P<0.001), whereas no significant changes were detected in healthy eyes, either before or after artificial tear instillation. Central corneal thickness measurement is less repeatable in dry eyes than in healthy eyes. Artificial tears improve the repeatability of CCT measurements obtained using the Pentacam in dry eyes.

Chromatin tethering effects of hNopp140 are involved in the spatial organization of nucleolus and the rRNA gene transcription

PubMed Central

Tsai, Yi-Tzang; Lin, Chen-I; Chen, Hung-Kai; Lee, Kuo-Ming; Hsu, Chia-Yi; Yang, Shun-Jen

2008-01-01

The short arms of five human acrocentric chromosomes contain ribosomal gene (rDNA) clusters where numerous mini-nucleoli arise at the exit of mitosis. These small nucleoli tend to coalesce into one or a few large nucleoli during interphase by unknown mechanisms. Here, we demonstrate that the N- and C-terminal domains of a nucleolar protein, hNopp140, bound respectively to α-satellite arrays and rDNA clusters of acrocentric chromosomes for nucleolar formation. The central acidic-and-basic repeated domain of hNopp140, possessing a weak self-self interacting ability, was indispensable for hNopp140 to build up a nucleolar round-shaped structure. The N- or the C-terminally truncated hNopp140 caused nucleolar segregation and was able to alter locations of the rDNA transcription, as mediated by detaching the rDNA repeats from the acrocentric α-satellite arrays. Interestingly, an hNopp140 mutant, made by joining the N- and C-terminal domains but excluding the entire central repeated region, induced nucleolar disruption and global chromatin condensation. Furthermore, RNAi knockdown of hNopp140 resulted in dispersion of the rDNA and acrocentric α-satellite sequences away from nucleolus that was accompanied by rDNA transcriptional silence. Our findings indicate that hNopp140, a scaffold protein, is involved in the nucleolar assembly, fusion, and maintenance. PMID:18253863

Pathways and intermediates in forced unfolding of spectrin repeats.

PubMed

Altmann, Stephan M; Grünberg, Raik G; Lenne, Pierre-François; Ylänne, Jari; Raae, Arnt; Herbert, Kristina; Saraste, Matti; Nilges, Michael; Hörber, J K Heinrich

2002-08-01

Spectrin repeats are triple-helical coiled-coil domains found in many proteins that are regularly subjected to mechanical stress. We used atomic force microscopy technique and steered molecular dynamics simulations to study the behavior of a wild-type spectrin repeat and two mutants. The experiments indicate that spectrin repeats can form stable unfolding intermediates when subjected to external forces. In the simulations the unfolding proceeded via a variety of pathways. Stable intermediates were associated to kinking of the central helix close to a proline residue. A mutant stabilizing the central helix showed no intermediates in experiments, in agreement with simulation. Spectrin repeats may thus function as elastic elements, extendable to intermediate states at various lengths.

Genome of Horsepox Virus

PubMed Central

Tulman, E. R.; Delhon, G.; Afonso, C. L.; Lu, Z.; Zsak, L.; Sandybaev, N. T.; Kerembekova, U. Z.; Zaitsev, V. L.; Kutish, G. F.; Rock, D. L.

2006-01-01

Here we present the genomic sequence of horsepox virus (HSPV) isolate MNR-76, an orthopoxvirus (OPV) isolated in 1976 from diseased Mongolian horses. The 212-kbp genome contained 7.5-kbp inverted terminal repeats and lacked extensive terminal tandem repetition. HSPV contained 236 open reading frames (ORFs) with similarity to those in other OPVs, with those in the central 100-kbp region most conserved relative to other OPVs. Phylogenetic analysis of the conserved region indicated that HSPV is closely related to sequenced isolates of vaccinia virus (VACV) and rabbitpox virus, clearly grouping together these VACV-like viruses. Fifty-four HSPV ORFs likely represented fragments of 25 orthologous OPV genes, including in the central region the only known fragmented form of an OPV ribonucleotide reductase large subunit gene. In terminal genomic regions, HSPV lacked full-length homologues of genes variably fragmented in other VACV-like viruses but was unique in fragmentation of the homologue of VACV strain Copenhagen B6R, a gene intact in other known VACV-like viruses. Notably, HSPV contained in terminal genomic regions 17 kbp of OPV-like sequence absent in known VACV-like viruses, including fragments of genes intact in other OPVs and approximately 1.4 kb of sequence present only in cowpox virus (CPXV). HSPV also contained seven full-length genes fragmented or missing in other VACV-like viruses, including intact homologues of the CPXV strain GRI-90 D2L/I4R CrmB and D13L CD30-like tumor necrosis factor receptors, D3L/I3R and C1L ankyrin repeat proteins, B19R kelch-like protein, D7L BTB/POZ domain protein, and B22R variola virus B22R-like protein. These results indicated that HSPV contains unique genomic features likely contributing to a unique virulence/host range phenotype. They also indicated that while closely related to known VACV-like viruses, HSPV contains additional, potentially ancestral sequences absent in other VACV-like viruses. PMID:16940536

Induced abortion in a Southern European region: examining inequalities between native and immigrant women.

PubMed

Rodriguez-Alvarez, Elena; Borrell, Luisa N; González-Rábago, Yolanda; Martín, Unai; Lanborena, Nerea

2016-09-01

To examine induced abortion (IA) inequalities between native and immigrant women in a Southern European region and whether these inequalities depend on a 2010 Law facilitating IA. We conducted two analyses: (1) prevalence of total IAs, repeat and second trimester IA, in native and immigrant women aged 12-49 years for years 2009-2013 according to country of origin; and (2) log-binomial regression was used to quantify the association of place of origin with repeat and second trimester IAs among women with IAs. Immigrants were more likely to have an IA than Spanish women, with the highest probability in Sub-Saharan Africa (PR 8.32 95 % CI 3.66-18.92). Immigrant women with an IA from countries other than Maghreb and Asia have higher probabilities of a repeat IA than women from Spain. Women from Europe non-EU/Romania were 50 % (95 % CI 0.30-0.79) less likely to have a second trimester IA, while women from Central America/Caribbean were 45 % (95 % CI 1.11-1.89) more likely than Spanish women. The 2010 Law did not affect these associations. There is a need for parenthood planning programs and more information and access to contraception methods especially in immigrant women to help decrease IAs.

A novel Amoeba proteus 120 kDa actin-binding protein with only 1 filamin repeat and a coiled-coil region.

PubMed

Sobczak, Magdalena; Kocik, Elzbieta; Redowicz, Maria Jolanta

2007-02-01

A novel 120 kDa actin-binding protein (ApABP-F1) was found in Amoeba proteus. It was distributed throughout the cytoplasm, mainly in the subplasma membrane and perinuclear-nuclear areas, enriched in actin. The full-length cDNA of ApABP consisted of 2672 nucleotides with an open reading frame of 878 amino acids, giving a ~95 kDa protein with a theoretical pI value of 5.11. It had a novel domain organization pattern: the N terminus (residues 1-104) contained 1 calponin-homology (CH) domain, followed by only 1 region that was homologous to the filamin repeat (FR, residues 209-324), and a central region (residues 344-577) exhibiting a very high probability of coiled-coil formation, probably engaged in the observed protein dimerization. A phylogenetic tree constructed for CH domains from 25 various proteins revealed that the CH domain of ApABP was most related to that of the hypothetical mouse KIAA0903-like protein, whereas not much relationship to either filamins or the gelation factor (ABP-120) of Dictyostelium discoideum and Entamoeba histolytica was found.

Causes of model dry and warm bias over central U.S. and impact on climate projections.

PubMed

Lin, Yanluan; Dong, Wenhao; Zhang, Minghua; Xie, Yuanyu; Xue, Wei; Huang, Jianbin; Luo, Yong

2017-10-12

Climate models show a conspicuous summer warm and dry bias over the central United States. Using results from 19 climate models in the Coupled Model Intercomparison Project Phase 5 (CMIP5), we report a persistent dependence of warm bias on dry bias with the precipitation deficit leading the warm bias over this region. The precipitation deficit is associated with the widespread failure of models in capturing strong rainfall events in summer over the central U.S. A robust linear relationship between the projected warming and the present-day warm bias enables us to empirically correct future temperature projections. By the end of the 21st century under the RCP8.5 scenario, the corrections substantially narrow the intermodel spread of the projections and reduce the projected temperature by 2.5 K, resulting mainly from the removal of the warm bias. Instead of a sharp decrease, after this correction the projected precipitation is nearly neutral for all scenarios.Climate models repeatedly show a warm and dry bias over the central United States, but the origin of this bias remains unclear. Here the authors associate this bias to precipitation deficits in models and after applying a correction, projected precipitation in this region shows no significant changes.

Mid- to late Holocene climate-driven regime shifts inferred from diatom, ostracod and stable isotope records from Lake Son Kol (Central Tian Shan, Kyrgyzstan)

NASA Astrophysics Data System (ADS)

Schwarz, Anja; Turner, Falko; Lauterbach, Stefan; Plessen, Birgit; Krahn, Kim J.; Glodniok, Sven; Mischke, Steffen; Stebich, Martina; Witt, Roman; Mingram, Jens; Schwalb, Antje

2017-12-01

Arid Central Asia represents a key region for understanding climate variability and interactions in the Northern Hemisphere. Patterns and mechanisms of Holocene climate change in arid Central Asia are, however, only partially understood. Multi-proxy data combining diatom, ostracod, sedimentological, geochemical and stable isotope analyses from a ca. 6000-year-old lake sediment core from Son Kol (Central Kyrgyzstan) show distinct and repeated changes in species assemblages. Diatom- and ostracod-inferred conductivity shifts between meso-euhaline and freshwater conditions suggest water balance and regime shifts. Organism-derived data are corroborated by stable isotope, mineralogical and geochemical records, underlining that Son Kol was affected by strong lake level fluctuations of several meters. The δ13Ccarb/δ18Ocarb correlation shows repeated switchovers from a closed to an open lake system. From 6000 to 3800 and 3250 to 1950 cal. yr BP, Son Kol was a closed basin lake with higher conductivities, increased nutrient availability and a water level located below the modern outflow. Son Kol became again a hydrologically open lake at 3800 and 1950 cal. yr BP. Comparisons to other local and regional paleoclimate records indicate that these regime shifts were largely controlled by changing intensity and position of the Westerlies and the Siberian Anticyclone that triggered changes in the amount of winter precipitation. A strong influence of the Westerlies ca. 5000-4400, 3800-3250 and since 1950 cal. yr BP enhanced the amount of precipitation during spring, autumn and winter, whereas cold and dry winters prevailed during phases with a strong Siberian Anticyclone and southward shifted Westerlies at ca. 6000-5000, 4400-3800 and 3250-1950 cal. yr BP. Similarities between variations in winter precipitation at Son Kol and records of the predominant NAO-mode further suggest a teleconnection between wet (dry) winter climate in Central Asia and a positive (negative) NAO-mode. Thus, this study identifies climate fluctuations as the main driver for hydrological regime shifts in Son Kol controlling physicochemical conditions and consequently causing abrupt species assemblage changes. This emphasizes the importance of multi-proxy approaches to identify triggers, thresholds and cascades of aquatic ecosystem transformations.

THICKNESS OF THE MACULA, RETINAL NERVE FIBER LAYER, AND GANGLION CELL-INNER PLEXIFORM LAYER IN THE AGE-RELATED MACULAR DEGENERATION: The Repeatability Study of Spectral Domain Optical Coherence Tomography.

PubMed

Shin, Il-Hwan; Lee, Woo-Hyuk; Lee, Jong-Joo; Jo, Young-Joon; Kim, Jung-Yeul

2018-02-01

To determine the repeatability of measuring the thickness of the central macula, retinal nerve fiber layer, and ganglion cell-inner plexiform layer (GC-IPL) using spectral domain optical coherence tomography (Cirrus HD-OCT) in eyes with age-related macular degeneration. One hundred and thirty-four eyes were included. The measurement repeatability was assessed by an experienced examiner who performed two consecutive measurements using a 512 × 128 macular cube scan and a 200 × 200 optic disk cube scan. To assess changes in macular morphology in patients with age-related macular degeneration, the patients were divided into the following three groups according to the central macular thickness (CMT): A group, CMT < 200 μm; B group, 200 μm ≤ CMT < 300 μm; and C group, CMT > 300 μm. Measurement repeatability was assessed using test-retest variability, a coefficient of variation, and an intraclass correlation coefficient. The mean measurement repeatability for the central macular, retinal nerve fiber layer, and GC-IPL thickness was high in the B group. The mean measurement repeatability for both the central macula and retinal nerve fiber layer thickness was high in the A and C groups, but was lower for the GC-IPL thickness. The measurement repeatability for GC-IPL thickness was high in the B group, but low in the A group and in the C group. The automated measurement repeatability for GC-IPL thickness was significantly lower in patients with age-related macular degeneration with out of normal CMT range. The effect of changes in macular morphology should be considered when analyzing GC-IPL thicknesses in a variety of ocular diseases.

[Analysis of H63D mutation in hemochromatosis (HFE) gene in populations of central Eurasia].

PubMed

Khusainova, R I; Khusnutdinova, N N; Litvinov, S S; Khusnutdinova, E K

2013-02-01

An analysis of the frequency of H63D (c. 187C>G) mutations in the HFEgene in 19 populations from Central Eurasia demonstrated that the distribution of the mutation in the region of interest was not uniform and that there were the areas of H63D accumulation. The investigation of three polymorphic variants, c.340+4T>C (rs2071303, IVS2(+4)T>C), c.893-44T>C (rs1800708, IVS4(-44)T>C), and c.1007-47G>A (rs1572982, IVS5(-47)A>G), in the HFE gene in individuals homozygous for H63D mutations in the HFE gene revealed the linkage of H63D with three haplotypes, *CTA, *TG, and *TTA. These findings indicated the partial spread of the mutation in Central Eurasia from Western Europe, as well as the possible repeated appearance of the mutation on the territory on interest.

Global Positioning System offers evidence of plate motions in eastern Mediterranean

NASA Astrophysics Data System (ADS)

Burc Oral, M.; Reilinger, Robert E.; Nafi Toksöz, M.; King, Robert W.; Aykut Barka, A.; Kinik, Ibrahim; Lenk, Onur

Geophysicists are using the Global Positioning System (GPS), a highly precise satellite navigation system, to monitor the slow movements (cm/yr) of the crustal plates composing the Earth's surface and the deformations where such plates interact. We report the results of repeated GPS measurements in the complex zone of interaction between the Eurasian, Arabian, and African plates in Turkey. The GPS observations made between 1988 and 1992 indicate that western, central, and east central Turkey are decoupled from the Eurasian plate and are moving as a more or less coherent unit about an axis located north of the Sinai peninsula. Other space-based measurements of crustal motion in Greece and along the Hellenic arc [Smith et al., 1994] suggest that this coherent motion includes southern Greece and the south central Aegean Sea. We refer to this region (shaded in Figure 1) as the Anatolian plate.

MicroRNAs in CAG trinucleotide repeat expansion disorders: an integrated review of the literature.

PubMed

Dumitrescu, Laura; Popescu, Bogdan O

2015-01-01

MicroRNAs are small RNAs involved in gene silencing. They play important roles in transcriptional regulation and are selectively and abundantly expressed in the central nervous system. A considerable amount of the human genome is comprised of tandem repeating nucleotide streams. Several diseases are caused by above-threshold expansion of certain trinucleotide repeats occurring in a protein-coding or non-coding region. Though monogenic, CAG trinucleotide repeat expansion disorders have a complex pathogenesis, various combinations of multiple coexisting pathways resulting in one common final consequence: selective neurodegeneration. Mutant protein and mutant transcript gain of toxic function are considered to be the core pathogenic mechanisms. The profile of microRNAs in CAG trinucleotide repeat disorders is scarcely described, however microRNA dysregulation has been identified in these diseases and microRNA-related intereference with gene expression is considered to be involved in their pathogenesis. Better understanding of microRNAs functions and means of manipulation promises to offer further insights into the pathogenic pathways of CAG repeat expansion disorders, to point out new potential targets for drug intervention and to provide some of the much needed etiopathogenic therapeutic agents. A number of disease-modifying microRNA silencing strategies are under development, but several implementation impediments still have to be resolved. CAG targeting seems feasible and efficient in animal models and is an appealing approach for clinical practice. Preliminary human trials are just beginning.

Triggering of repeating earthquakes in central California

USGS Publications Warehouse

Wu, Chunquan; Gomberg, Joan; Ben-Naim, Eli; Johnson, Paul

2014-01-01

Dynamic stresses carried by transient seismic waves have been found capable of triggering earthquakes instantly in various tectonic settings. Delayed triggering may be even more common, but the mechanisms are not well understood. Catalogs of repeating earthquakes, earthquakes that recur repeatedly at the same location, provide ideal data sets to test the effects of transient dynamic perturbations on the timing of earthquake occurrence. Here we employ a catalog of 165 families containing ~2500 total repeating earthquakes to test whether dynamic perturbations from local, regional, and teleseismic earthquakes change recurrence intervals. The distance to the earthquake generating the perturbing waves is a proxy for the relative potential contributions of static and dynamic deformations, because static deformations decay more rapidly with distance. Clear changes followed the nearby 2004 Mw6 Parkfield earthquake, so we study only repeaters prior to its origin time. We apply a Monte Carlo approach to compare the observed number of shortened recurrence intervals following dynamic perturbations with the distribution of this number estimated for randomized perturbation times. We examine the comparison for a series of dynamic stress peak amplitude and distance thresholds. The results suggest a weak correlation between dynamic perturbations in excess of ~20 kPa and shortened recurrence intervals, for both nearby and remote perturbations.

The Drosophila melanogaster Muc68E Mucin Gene Influences Adult Size, Starvation Tolerance, and Cold Recovery.

PubMed

Reis, Micael; Silva, Ana C; Vieira, Cristina P; Vieira, Jorge

2016-07-07

Mucins have been implicated in many different biological processes, such as protection from mechanical damage, microorganisms, and toxic molecules, as well as providing a luminal scaffold during development. Nevertheless, it is conceivable that mucins have the potential to modulate food absorption as well, and thus contribute to the definition of several important phenotypic traits. Here we show that the Drosophila melanogaster Muc68E gene is 40- to 60-million-yr old, and is present in Drosophila species of the subgenus Sophophora only. The central repeat region of this gene is fast evolving, and shows evidence for repeated expansions/contractions. This and/or frequent gene conversion events lead to the homogenization of its repeats. The amino acid pattern P[ED][ED][ST][ST][ST] is found in the repeat region of Muc68E proteins from all Drosophila species studied, and can occur multiple times within a single conserved repeat block, and thus may have functional significance. Muc68E is a nonessential gene under laboratory conditions, but Muc68E mutant flies are smaller and lighter than controls at birth. However, at 4 d of age, Muc68E mutants are heavier, recover faster from chill-coma, and are more resistant to starvation than control flies, although they have the same percentage of lipids as controls. Mutant flies have enlarged abdominal size 1 d after chill-coma recovery, which is associated with higher lipid content. These results suggest that Muc68E has a role in metabolism modulation, food absorption, and/or feeding patterns in larvae and adults, and under normal and stress conditions. Such biological function is novel for mucin genes. Copyright © 2016 Reis et al.

Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1.

PubMed

Chen, Jonathan L; VanEtten, Damian M; Fountain, Matthew A; Yildirim, Ilyas; Disney, Matthew D

2017-07-11

RNA repeat expansions cause a host of incurable, genetically defined diseases. The most common class of RNA repeats consists of trinucleotide repeats. These long, repeating transcripts fold into hairpins containing 1 × 1 internal loops that can mediate disease via a variety of mechanism(s) in which RNA is the central player. Two of these disorders are Huntington's disease and myotonic dystrophy type 1, which are caused by r(CAG) and r(CUG) repeats, respectively. We report the structures of two RNA constructs containing three copies of a r(CAG) [r(3×CAG)] or r(CUG) [r(3×CUG)] motif that were modeled with nuclear magnetic resonance spectroscopy and simulated annealing with restrained molecular dynamics. The 1 × 1 internal loops of r(3×CAG) are stabilized by one-hydrogen bond (cis Watson-Crick/Watson-Crick) AA pairs, while those of r(3×CUG) prefer one- or two-hydrogen bond (cis Watson-Crick/Watson-Crick) UU pairs. Assigned chemical shifts for the residues depended on the identity of neighbors or next nearest neighbors. Additional insights into the dynamics of these RNA constructs were gained by molecular dynamics simulations and a discrete path sampling method. Results indicate that the global structures of the RNA are A-form and that the loop regions are dynamic. The results will be useful for understanding the dynamic trajectory of these RNA repeats but also may aid in the development of therapeutics.

The last half-repeat of transcription activator-like effector (TALE) is dispensable and thereby TALE-based technology can be simplified.

PubMed

Zheng, Chong-Ke; Wang, Chun-Lian; Zhang, Xiao-Ping; Wang, Fu-Jun; Qin, Teng-Fei; Zhao, Kai-Jun

2014-09-01

To activate the expression of host genes that contribute to pathogen growth, pathogenic Xanthomonas bacteria inject their transcription activator-like effectors (TALEs) into plant cells and the TALEs bind to target gene promoters by the central repeat region consisting of near-perfect 34-amino-acid repeats (34-aa repeats). Based on the recognition codes between the 34-aa repeats and the targeted nucleotides, TALE-based technologies, such as designer TALEs (dTALEs) and TALE nucleases (TALENs), have been developed. Amazingly, every natural TALE invariantly has a truncated last half-repeat (LHR) at the end of the 34-aa repeats. Consequently, all the reported dTALEs and TALENs also harbour their LHRs. Here, we show that the LHRs in dTALEs are dispensable for the function of gene activation by both transient expression assays in Nicotiana benthamiana and gene-specific targeting in the rice genome, indicating that TALEs might originate from a single progenitor. In the light of this finding, we demonstrate that dTALEs can be constructed through two simple steps. Moreover, the activation strengths of dTALEs lacking the LHR are comparable with those of dTALEs harbouring the LHR. Our results provide new insights into the origin of natural TALEs, and will facilitate the simplification of the design and assembly of TALE-based tools, such as dTALEs and TALENs, in the near future. © 2014 BSPP AND JOHN WILEY & SONS LTD.

Structural characterization of Mumps virus fusion protein core

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

Liu Yueyong; Xu Yanhui; Lou Zhiyong

2006-09-29

The fusion proteins of enveloped viruses mediating the fusion between the viral and cellular membranes comprise two discontinuous heptad repeat (HR) domains located at the ectodomain of the enveloped glycoproteins. The crystal structure of the fusion protein core of Mumps virus (MuV) was determined at 2.2 A resolution. The complex is a six-helix bundle in which three HR1 peptides form a central highly hydrophobic coiled-coil and three HR2 peptides pack against the hydrophobic grooves on the surface of central coiled-coil in an oblique antiparallel manner. Fusion core of MuV, like those of simian virus 5 and human respiratory syncytium virus,more » forms typical 3-4-4-4-3 spacing. The similar charecterization in HR1 regions, as well as the existence of O-X-O motif in extended regions of HR2 helix, suggests a basic rule for the formation of the fusion core of viral fusion proteins.« less

Evolutionary Origin of OwlRep, a Megasatellite DNA Associated with Adaptation of Owl Monkeys to Nocturnal Lifestyle

PubMed Central

Nishihara, Hidenori; Stanyon, Roscoe; Kusumi, Junko; Hirai, Hirohisa

2018-01-01

Abstract Rod cells of many nocturnal mammals have a “non-standard” nuclear architecture, which is called the inverted nuclear architecture. Heterochromatin localizes to the central region of the nucleus. This leads to an efficient light transmission to the outer segments of photoreceptors. Rod cells of diurnal mammals have the conventional nuclear architecture. Owl monkeys (genus Aotus) are the only taxon of simian primates that has a nocturnal or cathemeral lifestyle, and this adaptation is widely thought to be secondary. Their rod cells were shown to exhibit an intermediate chromatin distribution: a spherical heterochromatin block was found in the central region of the nucleus although it was less complete than that of typical nocturnal mammals. We recently demonstrated that the primary DNA component of this heterochromatin block was OwlRep, a megasatellite DNA consisting of 187-bp-long repeat units. However, the origin of OwlRep was not known. Here we show that OwlRep was derived from HSAT6, a simple repeat sequence found in the centromere regions of human chromosomes. HSAT6 occurs widely in primates, suggesting that it was already present in the last common ancestor of extant primates. Notably, Strepsirrhini and Tarsiformes apparently carry a single HSAT6 copy, whereas many species of Simiiformes contain multiple copies. Comparison of nucleotide sequences of these copies revealed the entire process of the OwlRep formation. HSAT6, with or without flanking sequences, was segmentally duplicated in New World monkeys. Then, in the owl monkey linage after its divergence from other New World monkeys, a copy of HSAT6 was tandemly amplified, eventually forming a megasatellite DNA. PMID:29294004

The evolution and phylogeography of the African elephant inferred from mitochondrial DNA sequence and nuclear microsatellite markers.

PubMed

Eggert, Lori S; Rasner, Caylor A; Woodruff, David S

2002-10-07

Recent genetic results support the recognition of two African elephant species: Loxodonta africana, the savannah elephant, and Loxodonta cyclotis, the forest elephant. The study, however, did not include the populations of West Africa, where the taxonomic affinities of elephants have been much debated. We examined mitochondrial cytochrome b control region sequences and four microsatellite loci to investigate the genetic differences between the forest and savannah elephants of West and Central Africa. We then combined our data with published control region sequences from across Africa to examine patterns at the continental level. Our analysis reveals several deeply divergent lineages that do not correspond with the currently recognized taxonomy: (i) the forest elephants of Central Africa; the forest and savannah elephants of West Africa; and (iii) the savannah elephants of eastern, southern and Central Africa. We propose that the complex phylogeographic patterns we detect in African elephants result from repeated continental-scale climatic changes over their five-to-six million year evolutionary history. Until there is consensus on the taxonomy, we suggest that the genetic and ecological distinctness of these lineages should be an important factor in conservation management planning.

TALE-Like Effectors Are an Ancestral Feature of the Ralstonia solanacearum Species Complex and Converge in DNA Targeting Specificity.

PubMed

Schandry, Niklas; de Lange, Orlando; Prior, Philippe; Lahaye, Thomas

2016-01-01

Ralstonia solanacearum, a species complex of bacterial plant pathogens divided into four monophyletic phylotypes, causes plant diseases in tropical climates around the world. Some strains exhibit a broad host range on solanaceous hosts, while others are highly host-specific as for example some banana-pathogenic strains. Previous studies showed that transcription activator-like (TAL) effectors from Ralstonia, termed RipTALs, are capable of activating reporter genes in planta, if these are preceded by a matching effector binding element (EBE). RipTALs target DNA via their central repeat domain (CRD), where one repeat pairs with one DNA-base of the given EBE. The repeat variable diresidue dictates base repeat specificity in a predictable fashion, known as the TALE code. In this work, we analyze RipTALs across all phylotypes of the Ralstonia solanacearum species complex. We find that RipTALs are prevalent in phylotypes I and IV but absent from most phylotype III and II strains (10/12, 8/14, 1/24, and 1/5 strains contained a RipTAL, respectively). RipTALs originating from strains of the same phylotype show high levels of sequence similarity (>98%) in the N-terminal and C-terminal regions, while RipTALs isolated from different phylotypes show 47-91% sequence similarity in those regions, giving rise to four RipTAL classes. We show that, despite sequence divergence, the base preference for guanine, mediated by the N-terminal region, is conserved across RipTALs of all classes. Using the number and order of repeats found in the CRD, we functionally sub-classify RipTALs, introduce a new simple nomenclature, and predict matching EBEs for all seven distinct RipTALs identified. We experimentally study RipTAL EBEs and uncover that some RipTALs are able to target the EBEs of other RipTALs, referred to as cross-reactivity. In particular, RipTALs from strains with a broad host range on solanaceous hosts cross-react on each other's EBEs. Investigation of sequence divergence between RipTAL repeats allows for a reconstruction of repeat array biogenesis, for example through slipped strand mispairing or gene conversion. Using these studies we show how RipTALs of broad host range strains evolved convergently toward a shared target sequence. Finally, we discuss the differences between TALE-likes of plant pathogens in the context of disease ecology.

Chromosomal instability in Streptomyces avermitilis: major deletion in the central region and stable circularized chromosome

PubMed Central

2010-01-01

Background The chromosome of Streptomyces has been shown to be unstable, frequently undergoing gross chromosomal rearrangements. However, the mechanisms underlying this phenomenon remain unclear, with previous studies focused on two chromosomal ends as targets for rearrangements. Here we investigated chromosomal instability of Streptomyces avermitilis, an important producer of avermectins, and characterized four gross chromosomal rearrangement events, including a major deletion in the central region. The present findings provide a valuable contribution to the mechanistic study of genetic instability in Streptomyces. Results Thirty randomly-selected "bald" mutants derived from the wild-type strain all contained gross chromosomal rearrangements of various types. One of the bald mutants, SA1-8, had the same linear chromosomal structure as the high avermectin-producing mutant 76-9. Chromosomes of both strains displayed at least three independent chromosomal rearrangements, including chromosomal arm replacement to form new 88-kb terminal inverted repeats (TIRs), and two major deletions. One of the deletions eliminated the 36-kb central region of the chromosome, but surprisingly did not affect viability of the cells. The other deletion (74-kb) was internal to the right chromosomal arm. The chromosome of another bald mutant, SA1-6, was circularized with deletions at both ends. No obvious homology was found in all fusion sequences. Generational stability analysis showed that the chromosomal structure of SA1-8 and SA1-6 was stable. Conclusions Various chromosomal rearrangements, including chromosomal arm replacement, interstitial deletions and chromosomal circularization, occurred in S. avermitilis by non-homologous recombination. The finding of an inner deletion involving in the central region of S. avermitilis chromosome suggests that the entire Streptomyces chromosome may be the target for rearrangements, which are not limited, as previously reported, to the two chromosomal ends. PMID:20653985

Polymorphism and genetic mapping of the human oxytocin receptor gene on chromosome 3

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

Michelini, S.; Urbanek, M.; Goldman, D.

1995-06-19

Centrally administered oxytocin has been reported to facilitate affiliative and social behaviors, in functional harmony with its well-known peripheral effects on uterine contraction and milk ejection. The biological effects of oxytocin could be perturbed by mutations occurring in the sequence of the oxytocin receptor gene, and it would be of interest to establish the position of this gene on the human linkage map. Therefore we identified a polymorphism at the human oxytocin receptor gene. A portion of the 3{prime} untranslated region containing a 30 bp CA repeat was amplified by polymerase chain reaction (PCR), revealing a polymorphism with two allelesmore » occurring with frequencies of 0.77 and 0.23 in a sample of Caucasian CEPH parents (n = 70). The CA repeat polymorphism we detected was used to map the human oxytocin receptor to chromosome 3p25-3p26, in a region which contains several important genes, including loci for Von Hippel-Lindau disease (VHL) and renal cell carcinoma. 53 refs., 2 figs., 1 tab.« less

Slope activity in Gale crater, Mars

USGS Publications Warehouse

Dundas, Colin M.; McEwen, Alfred S.

2015-01-01

High-resolution repeat imaging of Aeolis Mons, the central mound in Gale crater, reveals active slope processes within tens of kilometers of the Curiosity rover. At one location near the base of northeastern Aeolis Mons, dozens of transient narrow lineae were observed, resembling features (Recurring Slope Lineae) that are potentially due to liquid water. However, the lineae faded and have not recurred in subsequent Mars years. Other small-scale slope activity is common, but has different spatial and temporal characteristics. We have not identified confirmed RSL, which Rummel et al. (Rummel, J.D. et al. [2014]. Astrobiology 14, 887–968) recommended be treated as potential special regions for planetary protection. Repeat images acquired as Curiosity approaches the base of Aeolis Mons could detect changes due to active slope processes, which could enable the rover to examine recently exposed material.

Prisms to Shift Pain Away: Pathophysiological and Therapeutic Exploration of CRPS with Prism Adaptation.

PubMed

Christophe, Laure; Chabanat, Eric; Delporte, Ludovic; Revol, Patrice; Volckmann, Pierre; Jacquin-Courtois, Sophie; Rossetti, Yves

Complex Regional Pain Syndrome (CRPS) is an invalidating chronic condition subsequent to peripheral lesions. There is growing consensus for a central contribution to CRPS. However, the nature of this central body representation disorder is increasingly debated. Although it has been repeatedly argued that CRPS results in motor neglect of the affected side, visual egocentric reference frame was found to be deviated toward the pain, that is, neglect of the healthy side. Accordingly, prism adaptation has been successfully used to normalize this deviation. This study aimed at clarifying whether 7 CRPS patients exhibited neglect as well as exploring the pathophysiological mechanisms of this manifestation and of the therapeutic effects of prism adaptation. Pain and quality of life, egocentric reference frames (visual and proprioceptive straight-ahead), and neglect tests (line bisection, kinematic analyses of motor neglect and motor extinction) were repeatedly assessed prior to, during, and following a one-week intense prism adaptation intervention. First, our results provide no support for visual and motor neglect in CRPS. Second, reference frames for body representations were not systematically deviated. Third, intensive prism adaptation intervention durably ameliorated pain and quality of life. As for spatial neglect, understanding the therapeutic effects of prism adaptation deserves further investigations.

[Guitarist's cramp: management with sensory re-education].

PubMed

Chaná-Cuevas, P; Kunstmann-Rioseco, C; Rodríguez-Riquelme, T

Dystonia is defined as a sustained co-contraction of agonistic and antagonistic muscles that can cause twisting, twitching and abnormal postures. Occupational dystonias are included in a special group of pathologies that are secondary to a repeated effort related to the professional activity carried out by the sufferer, as can occur in guitarists, violinists and trumpet players, for example. Its pathophysiology includes descriptions of disorders affecting the peripheral and central nervous systems. Studies conducted in monkeys have shown that, through sensory stimulation, repeated movements can give rise to central anomalies in the somatosensory cortex, with growth of the receptive fields that are stimulated and deformation of the separations between those fields. We describe the case of a professional guitarist with a seven-year history of symptoms. A neurological examination revealed a co-contraction in the right hand that triggered the extension of the index and little fingers, which made it difficult for him to play his instrument. The patient was submitted to sensory re-education therapy with the use of a splint and a two-month routine of exercises. The response was evaluated using a subjective scale of the patient's symptoms and measurements of the maximum angles of flexion and extension of the affected fingers. Both methods reduced the patient's discomfort and allowed him to exhibit greater skill when playing the guitar. Occupational dystonias produced by repeated stimulation present alterations in the sensory region of the cortex, with the involvement of motor performance that improves with sensory re-education therapy.

Hybridization drives evolution of apomicts in Rubus subgenus Rubus: evidence from microsatellite markers.

PubMed

Šarhanová, Petra; Sharbel, Timothy F; Sochor, Michal; Vašut, Radim J; Dancák, Martin; Trávnícek, Bohumil

2017-08-01

Rubus subgenus Rubus is a group of mostly apomictic and polyploid species with a complicated taxonomy and history of ongoing hybridization. The only polyploid series with prevailing sexuality is the series Glandulosi , although the apomictic series Discolores and Radula also retain a high degree of sexuality, which is influenced by environmental conditions and/or pollen donors. The aim of this study is to detect sources of genetic variability, determine the origin of apomictic taxa and validate microsatellite markers by cloning and sequencing. A total of 206 individuals from two central European regions were genotyped for 11 nuclear microsatellite loci and the chloroplast trn L- trn F region. Microsatellite alleles were further sequenced in order to determine the exact repeat number and to detect size homoplasy due to insertions/deletions in flanking regions. The results confirm that apomictic microspecies of ser. Radula are derived from crosses between sexual series Glandulosi and apomictic series Discolores , whereby the apomict acts as pollen donor. Each apomictic microspecies is derived from a single distinct genotype differing from the parental taxa, suggesting stabilized clonal reproduction. Intraspecific variation within apomicts is considerably low compared with sexual series Glandulosi , and reflects somatic mutation accumulation. While facultative apomicts produce clonal offspring, sexual species are the conduits of origin for new genetically different apomictic lineages. One of the main driving forces of evolution and speciation in the highly apomictic subgenus Rubus in central Europe is sexuality in the series Glandulosi . Palaeovegetation data suggest that initial hybridizations took place over different time periods in the two studied regions, and that the successful origin and spread of apomictic microspecies of the series Radula took place over several millennia. Additionally, the cloning and sequencing show that standard evaluations of microsatellite repeat numbers underestimate genetic variability considering homoplasy in allele size. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Historical connectivity, contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan, Rhododendron oldhamii (Ericaceae)

PubMed Central

Hsieh, Y-C; Chung, J-D; Wang, C-N; Chang, C-T; Chen, C-Y; Hwang, S-Y

2013-01-01

Elucidation of the evolutionary processes that constrain or facilitate adaptive divergence is a central goal in evolutionary biology, especially in non-model organisms. We tested whether changes in dynamics of gene flow (historical vs contemporary) caused population isolation and examined local adaptation in response to environmental selective forces in fragmented Rhododendron oldhamii populations. Variation in 26 expressed sequence tag-simple sequence repeat loci from 18 populations in Taiwan was investigated by examining patterns of genetic diversity, inbreeding, geographic structure, recent bottlenecks, and historical and contemporary gene flow. Selection associated with environmental variables was also examined. Bayesian clustering analysis revealed four regional population groups of north, central, south and southeast with significant genetic differentiation. Historical bottlenecks beginning 9168–13,092 years ago and ending 1584–3504 years ago were revealed by estimates using approximate Bayesian computation for all four regional samples analyzed. Recent migration within and across geographic regions was limited. However, major dispersal sources were found within geographic regions. Altitudinal clines of allelic frequencies of environmentally associated positively selected outliers were found, indicating adaptive divergence. Our results point to a transition from historical population connectivity toward contemporary population isolation and divergence on a regional scale. Spatial and temporal dispersal differences may have resulted in regional population divergence and local adaptation associated with environmental variables, which may have played roles as selective forces at a regional scale. PMID:23591517

Exogenous agmatine has neuroprotective effects against restraint-induced structural changes in the rat brain

PubMed Central

Zhu, Meng-Yang; Wang, Wei-Ping; Cai, Zheng-Wei; Regunathan, Soundar; Ordway, Gregory

2009-01-01

Agmatine is an endogenous amine derived from decarboxylation of arginine catalysed by arginine decarboxylase. Agmatine is considered a novel neuromodulator and possesses neuroprotective properties in the central nervous system. The present study examined whether agmatine has neuroprotective effects against repeated restraint stress-induced morphological changes in rat medial prefrontal cortex and hippocampus. Sprague-Dawley rats were subjected to 6 h of restraint stress daily for 21 days. Immunohistochemical staining with β-tubulin III showed that repeated restraint stress caused marked morphological alterations in the medial prefrontal cortex and hippocampus. Stress-induced alterations were prevented by simultaneous treatment with agmatine (50 mg/kg/day, i.p.). Interestingly, endogenous agmatine levels, as measured by high-performance liquid chromatography, in the prefrontal cortex and hippocampus as well as in the striatum and hypothalamus of repeated restraint rats were significantly reduced as compared with the controls. Reduced endogenous agmatine levels in repeated restraint animals were accompanied by a significant increase of arginine decarboxylase protein levels in the same regions. Moreover, administration of exogenous agmatine to restrained rats abolished increases of arginine decarboxylase protein levels. Taken together, these results demonstrate that exogenously administered agmatine has neuroprotective effects against repeated restraint-induced structural changes in the medial prefrontal cortex and hippocampus. These findings indicate that stress-induced reductions in endogenous agmatine levels in the rat brain may play a permissive role in neuronal pathology induced by repeated restraint stress. PMID:18364017

Comparative Maps of Human 19p13.3 and Mouse Chromosome 10 Allow Identification of Sequences at Evolutionary Breakpoints

PubMed Central

Puttagunta, Radhika; Gordon, Laurie A.; Meyer, Gary E.; Kapfhamer, David; Lamerdin, Jane E.; Kantheti, Prameela; Portman, Kathleen M.; Chung, Wendy K.; Jenne, Dieter E.; Olsen, Anne S.; Burmeister, Margit

2000-01-01

A cosmid/bacterial artificial chromosome (BAC) contiguous (contig) map of human chromosome (HSA) 19p13.3 has been constructed, and over 50 genes have been localized to the contig. Genes and anonymous ESTs from ≈4000 kb of human 19p13.3 were placed on the central mouse chromosome 10 map by genetic mapping and pulsed-field gel electrophoresis (PFGE) analysis. A region of ∼2500 kb of HSA 19p13.3 is collinear to mouse chromosome (MMU) 10. In contrast, the adjacent ≈1200 kb are inverted. Two genes are located in a 50-kb region after the inversion on MMU 10, followed by a region of homology to mouse chromosome 17. The synteny breakpoint and one of the inversion breakpoints has been localized to sequenced regions in human <5 kb in size. Both breakpoints are rich in simple tandem repeats, including (TCTG)n, (CT)n, and (GTCTCT)n, suggesting that simple repeat sequences may be involved in chromosome breaks during evolution. The overall size of the region in mouse is smaller, although no large regions are missing. Comparing the physical maps to the genetic maps showed that in contrast to the higher-than-average rate of genetic recombination in gene-rich telomeric region on HSA 19p13.3, the average rate of recombination is lower than expected in the homologous mouse region. This might indicate that a hot spot of recombination may have been lost in mouse or gained in human during evolution, or that the position of sequences along the chromosome (telomeric compared to the middle of a chromosome) is important for recombination rates. PMID:10984455

Association of aromatase (TTTA)n repeat polymorphisms with central precocious puberty in girls.

PubMed

Lee, Hae Sang; Kim, Kyung Hee; Hwang, Jin Soon

2014-09-01

Precocious puberty is characterized by early activation of the pituitary-gonadal axis. Oestrogen is the final key factor to start the onset of puberty. The cytochrome P450 19A1 (CYP19A1) gene encodes an aromatase that is responsible for the conversion of androgens to oestrogen, which is a key step in oestrogen biosynthesis. The aim of this study was to identify CYP19A1 gene mutations or polymorphisms in girls with central precocious puberty (CPP). We evaluated the frequency of allelic variants of the CYP19A1 exons and the tetranucleotide tandem repeat (TTTA)n in intron 4 in 203 idiopathic central precocious puberty (CPP) girls and 101 normal healthy women. The genotype analysis of the CYP19A1 (TTTA)n polymorphism revealed six different alleles ranging from seven to 13 repeats. Among the six different repeat alleles detected in this study, the (TTTA)₁₃ repeat allele was only detected in the patient group and carriers of the (TTTA)₁₃ allele were significantly associated with an increased risk of CPP (OR = 1·509, 95% CI = 1·425-1·598, P = 0·033). Carriers of the (TTTA)₁₃ repeat allele were significantly younger at pubertal onset and had higher levels of oestrogen than noncarriers of the (TTTA)₁₃ repeat allele. Although nine polymorphisms were detected in exons of the CYP19A1 gene, no clinical significance was observed. In this study, carriers of a higher repeat (TTTA)₁₃ polymorphism in intron 4 of the CYP19A1 gene had higher levels of oestrogen. Those carrying the (TTTA)₁₃ repeat allele may have a higher risk of developing CPP. © 2014 John Wiley & Sons Ltd.

Experiences in Applying Earth Observing Satellite Technology in SERVIR Regions with an Emphasis on Disasters: Successes, Lessons and Paths Forward

NASA Technical Reports Server (NTRS)

Anderson, Eric

2017-01-01

Earth observing satellites offer a unique perspective of our environment from the vantage point of space. Repeated measurements of the Earths subsystems such as the biosphere, atmosphere, lithosphere, hydrosphere, and of humans interactions with their environments, allow for a better understanding of Earth system processes, and they can provide input for decision making in areas of environmental management and disaster risk reduction. SERVIR is a joint initiative of the US National Aeronautics and Space Administration (NASA) and the US Agency for International Development (USAID) that began in 2005 and has been active in applying Earth observations for sustainable development in many regions around the world, recently the Lower Mekong and West Africa regions. This talk will highlight some successes achieved and lessons learned through SERVIR in Central America, Eastern Southern Africa, and the Hindu Kush-Himalaya region, focusing on disasters. We will also present opportunities for enhanced decision making with Earth observations and geospatial technologies in the Lower Mekong region.

Effects of repeated precommercial thinnings in central hardwood sapling stands

Treesearch

Donald E. Hilt; Martin E. Dale

1982-01-01

Precommercial thinnings were repeated four times in a central hardwood sapling stand beginning at age 8 and ending at age 22. Treated plots were thinned on an area-wide basis to specified density levels of 30-, 50-, and 70-percent stocking. The species composition of all stems in the stand was altered somewhat by thinning, but similar trends occurred on control plots....

Engineering DNA Backbone Interactions Results in TALE Scaffolds with Enhanced 5-Methylcytosine Selectivity.

PubMed

Rathi, Preeti; Witte, Anna; Summerer, Daniel

2017-11-08

Transcription activator-like effectors (TALEs) are DNA major-groove binding proteins widely used for genome targeting. TALEs contain an N-terminal region (NTR) and a central repeat domain (CRD). Repeats of the CRD selectively recognize each one DNA nucleobase, offering programmability. Moreover, repeats with selectivity for 5-methylcytosine (5mC) and its oxidized derivatives can be designed for analytical applications. However, both TALE domains also nonspecifically interact with DNA phosphates via basic amino acids. To enhance the 5mC selectivity of TALEs, we aimed to decrease the nonselective binding energy of TALEs. We substituted basic amino acids with alanine in the NTR and identified TALE mutants with increased selectivity. We then analysed conserved, DNA phosphate-binding KQ diresidues in CRD repeats and identified further improved mutants. Combination of mutations in the NTR and CRD was highly synergetic and resulted in TALE scaffolds with up to 4.3-fold increased selectivity in genomic 5mC analysis via affinity enrichment. Moreover, transcriptional activation in HEK293T cells by a TALE-VP64 construct based on this scaffold design exhibited a 3.5-fold increased 5mC selectivity. This provides perspectives for improved 5mC analysis and for the 5mC-conditional control of TALE-based editing constructs in vivo.

Hysteresis in the Central African Rainforest

NASA Astrophysics Data System (ADS)

Pietsch, Stephan Alexander; Elias Bednar, Johannes; Gautam, Sishir; Petritsch, Richard; Schier, Franziska; Stanzl, Patrick

2014-05-01

Past climate change caused severe disturbances of the Central African rainforest belt, with forest fragmentation and re-expansion due to drier and wetter climate conditions. Besides climate, human induced forest degradation affected biodiversity, structure and carbon storage of Congo basin rainforests. Information on climatically stable, mature rainforest, unaffected by human induced disturbances, provides means of assessing the impact of forest degradation and may serve as benchmarks of carbon carrying capacity over regions with similar site and climate conditions. BioGeoChemical (BGC) ecosystem models explicitly consider the impacts of site and climate conditions and may assess benchmark levels over regions devoid of undisturbed conditions. We will present a BGC-model validation for the Western Congolian Lowland Rainforest (WCLRF) using field data from a recently confirmed forest refuge, show model - data comparisons for disturbed und undisturbed forests under different site and climate conditions as well as for sites with repeated assessment of biodiversity and standing biomass during recovery from intensive exploitation. We will present climatic thresholds for WCLRF stability, analyse the relationship between resilience, standing C-stocks and change in climate and finally provide evidence of hysteresis.

Molecular analysis of the glucocerebrosidase gene locus

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

Winfield, S.L.; Martin, B.M.; Fandino, A.

1994-09-01

Gaucher disease is due to a deficiency in the activity of the lysosomal enzyme glucocerebrosidase. Both the functional gene for this enzyme and a pseudogene are located in close proximity on chromosome 1q21. Analysis of the mutations present in patient samples has suggested interaction between the functional gene and the pseudogene in the origin of mutant genotypes. To investigate the involvement of regions flanking the functional gene and pseudogene in the origin of mutations found in Gaucher disease, a YAC clone containing DNA from this locus has been subcloned and characterized. The original YAC containing {approximately}360 kb was truncated withmore » the use of fragmentation plasmids to about 85 kb. A lambda library derived from this YAC was screened to obtain clones containing glucocerebrosidase sequences. PCR amplification was used to identify subclones containing 5{prime}, central, or 3{prime} sequences of the functional gene or of the pseudogene. Clones spanning the entire distance from the last exon of the functional gene to intron 1 of the pseudogene, the 5{prime} end of the functional gene and 16 kb of 5{prime} flanking region and approximately 15 kb of 3{prime} flanking region of the pseudogene were sequenced. Sequence data from 48 kb of intergenic and flanking regions of the glucocerebrosidase gene and its pseudogene has been generated. A large number of Alu sequences and several simple repeats have been found. Two of these repeats exhibit fragment length polymorphism. There is almost 100% homology between the 3{prime} flanking regions of the functional gene and the pseudogene, extending to about 4 kb past the termination codons. A much lower degree of homology is observed in the 5{prime} flanking region. Patient samples are currently being screened for polymorphisms in these flanking regions.« less

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

PubMed

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

2016-01-01

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

Structural analysis of the rDNA intergenic spacer of Brassica nigra: evolutionary divergence of the spacers of the three diploid Brassica species.

PubMed

Bhatia, S; Singh Negi, M; Lakshmikumaran, M

1996-11-01

EcoRI restriction of the B. nigra rDNA recombinants, isolated from a lambda genomic library, showed that the 3.9-kb fragment corresponded to the Intergenic Spacer (IGS), which was sequenced and found to be 3,928 bp in size. Sequence and dot-matrix analyses showed that the organization of the B. nigra rDNA IGS was typical of most rDNA spacers, consisting of a central repetitive region and flanking unique sequences on either side. The repetitive region was composed of two repeat families-RF 'A' and RF 'B.' The B. nigra RF 'A' consisted of a tandem array of three full-length copies of a 106-bp sequence element. RF 'B' was composed of 66 tandemly repeated elements. Each 'B' element was only 21-bp in size and this is the smallest repeat unit identified in plant rDNA to date. The putative transcription initiation site (TIS) was identified as nucleotide position 3,110. Based on the sequence analysis it was suggested that the present organization of the repeat families was generated by successive cycles of deletions and amplifications and was being maintained by homogenization processes such as gene conversion and crossing-over.A detailed comparison of the rDNA IGS sequences of the three diploid Brassica species-namely, B. nigra, B. campestris, and B. oleracea-was carried out. First, comparisons revealed that B. campestris and B. oleracea were close to each other as the repeat families in both showed high sequence homology between each other. Second, the repeat elements in both the species were organized in an interspersed manner. Third, a 52-bp sequence, present just downstream of the repeats in B. campestris, was found to be identical to the B. oleracea repeats, thereby suggesting a common progenitor. On the other hand, in B. nigra no interspersion pattern of organization of repeats was observed. Further, the B. nigra RF 'A' was identified as distinct from the repeat families of B. campestris and B. oleracea. Based on this analysis, it was suggested that during speciation B. campestris and B. oleracea evolved in one lineage whereas B. nigra diverged into a separate lineage. The comparative analysis of the IGS helped in identifying not only conserved ancestral sequence motifs of possible functional significance such as promoters and enhancers, but also sequences which showed variation between the three diploid species and were therefore identified as species-specific sequences.

Force Spectroscopy of the Plasmodium falciparum Vaccine Candidate Circumsporozoite Protein Suggests a Mechanically Pliable Repeat Region.

PubMed

Patra, Aditya Prasad; Sharma, Shobhona; Ainavarapu, Sri Rama Koti

2017-02-10

The most effective vaccine candidate of malaria is based on the Plasmodium falciparum circumsporozoite protein (CSP), a major surface protein implicated in the structural strength, motility, and immune evasion properties of the infective sporozoites. It is suspected that reversible conformational changes of CSP are required for infection of the mammalian host, but the detailed structure and dynamic properties of CSP remain incompletely understood, limiting our understanding of its function in the infection. Here, we report the structural and mechanical properties of the CSP studied using single-molecule force spectroscopy on several constructs, one including the central region of CSP, which is rich in NANP amino acid repeats (CSP rep ), and a second consisting of a near full-length sequence without the signal and anchor hydrophobic domains (CSP ΔHP ). Our results show that the CSP rep is heterogeneous, with 40% of molecules requiring virtually no mechanical force to unfold (<10 piconewtons (pN)), suggesting that these molecules are mechanically compliant and perhaps act as entropic springs, whereas the remaining 60% are partially structured with low mechanical resistance (∼70 pN). CSP ΔHP having multiple force peaks suggests specifically folded domains, with two major populations possibly indicating the open and collapsed forms. Our findings suggest that the overall low mechanical resistance of the repeat region, exposed on the outer surface of the sporozoites, combined with the flexible full-length conformations of CSP, may provide the sporozoites not only with immune evasion properties, but also with lubricating capacity required during its navigation through the mosquito and vertebrate host tissues. We anticipate that these findings would further assist in the design and development of future malarial vaccines. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

The Influence of Relational Knowledge and Executive Function on Preschoolers' Repeating Pattern Knowledge

ERIC Educational Resources Information Center

Miller, Michael R.; Rittle-Johnson, Bethany; Loehr, Abbey M.; Fyfe, Emily R.

2016-01-01

Children's knowledge of repeating patterns (e.g., ABBABB) is a central component of early mathematics, but the developmental mechanisms underlying this knowledge are currently unknown. We sought clarity on the importance of relational knowledge and executive function (EF) to preschoolers' understanding of repeating patterns. One hundred…

Prisms to Shift Pain Away: Pathophysiological and Therapeutic Exploration of CRPS with Prism Adaptation

PubMed Central

Volckmann, Pierre; Jacquin-Courtois, Sophie

2016-01-01

Complex Regional Pain Syndrome (CRPS) is an invalidating chronic condition subsequent to peripheral lesions. There is growing consensus for a central contribution to CRPS. However, the nature of this central body representation disorder is increasingly debated. Although it has been repeatedly argued that CRPS results in motor neglect of the affected side, visual egocentric reference frame was found to be deviated toward the pain, that is, neglect of the healthy side. Accordingly, prism adaptation has been successfully used to normalize this deviation. This study aimed at clarifying whether 7 CRPS patients exhibited neglect as well as exploring the pathophysiological mechanisms of this manifestation and of the therapeutic effects of prism adaptation. Pain and quality of life, egocentric reference frames (visual and proprioceptive straight-ahead), and neglect tests (line bisection, kinematic analyses of motor neglect and motor extinction) were repeatedly assessed prior to, during, and following a one-week intense prism adaptation intervention. First, our results provide no support for visual and motor neglect in CRPS. Second, reference frames for body representations were not systematically deviated. Third, intensive prism adaptation intervention durably ameliorated pain and quality of life. As for spatial neglect, understanding the therapeutic effects of prism adaptation deserves further investigations. PMID:27668094

Central activation, metabolites, and calcium handling during fatigue with repeated maximal isometric contractions in human muscle.

PubMed

Cairns, Simeon P; Inman, Luke A G; MacManus, Caroline P; van de Port, Ingrid G L; Ruell, Patricia A; Thom, Jeanette M; Thompson, Martin W

2017-08-01

To determine the roles of calcium (Ca 2+ ) handling by sarcoplasmic reticulum (SR) and central activation impairment (i.e., central fatigue) during fatigue with repeated maximal voluntary isometric contractions (MVC) in human muscles. Contractile performance was assessed during 3 min of repeated MVCs (7-s contraction, 3-s rest, n = 17). In ten participants, in vitro SR Ca 2+ -handling, metabolites, and fibre-type composition were quantified in biopsy samples from quadriceps muscle, along with plasma venous [K + ]. In 11 participants, central fatigue was compared using tetanic stimulation superimposed on MVC in quadriceps and adductor pollicis muscles. The decline of peak MVC force with fatigue was similar for both muscles. Fatigue resistance correlated directly with % type I fibre area in quadriceps (r = 0.77, P = 0.009). The maximal rate of ryanodine-induced Ca 2+ -release and Ca 2+ -uptake fell by 31 ± 26 and 28 ± 13%, respectively. The tetanic force depression was correlated with the combined reduction of ATP and PCr, and increase of lactate (r = 0.77, P = 0.009). Plasma venous [K + ] increased from 4.0 ± 0.3 to 5.4 ± 0.8 mM over 1-3-min exercise. Central fatigue occurred during the early contractions in the quadriceps in 7 out of 17 participants (central activation ratio fell from 0.98 ± 0.05 to 0.86 ± 0.11 at 1 min), but dwindled at exercise cessation. Central fatigue was seldom apparent in adductor pollicis. Fatigue with repeated MVC in human limb muscles mainly involves peripheral aspects which include impaired SR Ca 2+ -handling and we speculate that anaerobic metabolite changes are involved. A faster early force loss in quadriceps muscle with some participants is attributed to central fatigue.

Valles Marineris Basin Beds: a Complex Story

NASA Technical Reports Server (NTRS)

Lucchitta, B. K.

1985-01-01

High resolution stereoimages of the central Valles Marineris enabled detailed geologic mapping on Ophir and Candor Chasmata. Abundant light colored deposits, both layered and massive, fill the chasmata in this region. Units within these deposits were identified by their erosional characteristics and superposition and cross cutting relations. The Valles Marineris beds reflect a history of repeated faulting, volcanic eruptions, and deposition and erosion, resulting in stratigraphic sequences with several unconformities. Because of the preponderance of apparent volcanic deposits inside the troughs, the chasmata may not be simple grabens, but rather giant volcano tectonic depressions. Major events in chasmata development are examined.

Ground motion-simulations of 1811-1812 New Madrid earthquakes, central United States

USGS Publications Warehouse

Ramirez-Guzman, L.; Graves, Robert; Olsen, Kim B.; Boyd, Oliver; Cramer, Chris H.; Hartzell, Stephen; Ni, Sidao; Somerville, Paul G.; Williams, Robert; Zhong, Jinquan

2015-01-01

The region covered by our simulation domain encompasses a large portion of the CUS centered on the NMSZ, including several major metropolitan areas. Based on our simulations, more than eight million people living and working near the NMSZ would experience potentially damaging ground motion and modified Mercalli intensities ranging from VI to VIII if a repeat of the 1811–1812 earthquakes occurred today. Moreover, the duration of strong ground shaking in the greater Memphis metropolitan area could last from 30 to more than 60 s, depending on the magnitude and epicenter.

Region-specific effects of developmental exposure to cocaine on fibroblast growth factor-2 expression in the rat brain.

PubMed

Giannotti, Giuseppe; Caffino, Lucia; Mottarlini, Francesca; Racagni, Giorgio; Fumagalli, Fabio

2016-07-01

Adolescence is a period of high vulnerability to drugs of abuse and alterations of the proper developmental trajectory via psychostimulant exposure might change the physiological brain homeostasis. By microdissection of brain areas via punching, we investigated whether repeated exposure to cocaine during adolescence (from postnatal day 28 [PND28] to PND42) has altered fibroblast growth factor-2 (FGF-2) messenger RNA (mRNA) levels in selected brain subregions critical for the action of cocaine. We found a reduction of FGF-2 mRNA levels in ventral tegmental area (VTA), where mesocortical and mesolimbic pathways originate. The analysis of the trophic factor levels in the distal projecting regions revealed a selective reduction of FGF-2 mRNA levels in infralimbic (IL) subregion of the medial prefrontal cortex (the terminal region of the mesocortical pathway) and in the nucleus accumbens core (cNAc) (the terminal region of the mesolimbic pathway). Last, we found reduced FGF-2 mRNA levels also in brain regions which, although in a different manner, contribute to the reward system, i.e., the central nucleus of amygdala (cAmy) and the ventral portion of hippocampus (vHip). The widespread and coordinated reduction of FGF-2 mRNA levels across the brain's reward neurocircuitry might represent a defensive strategy set in motion to oppose to the psychostimulant properties of cocaine. Moreover, given the role of FGF-2 in modulating mood disorders, the reduced trophic support here observed might sustain the negative emotional state set in motion by repeated exposure to cocaine.

Events at the turn of the Eocene and Oligocene in the Central Eurasia Region (middle latitudes)

NASA Astrophysics Data System (ADS)

Akhmetiev, M. A.; Gavrilov, Yu. O.; Zaporozhets, N. I.

2017-03-01

The Eocene and Oligocene transition sections (Priabonian-Rupelian) of the Aral-Turgai, West Siberian, Volga-Don, and Crimea-Caucasus regions have been studied in detail [1], and the global biospheric crisis events have been estimated at the turn of the Eocene and Oligocene. In spite of the idea of the gradual regression in the Priabonian with drainage of the inner sea basins, it has been established that shallowing of the sea was preceded by repeated transgression that continued for 1 Ma with warming up and humidification of the climate. The final regressive phase (130-200 ka) was accompanied by frequent eustatic and climatic fluctuations, reconstruction of the isotopic and geochemical background, and also the recurrence at the boundary between layers in certain continuous sections.

Genomewide Linkage Disequilibrium Mapping of Severe Bipolar Disorder in a Population Isolate

PubMed Central

Ophoff, Roel A.; Escamilla, Michael A.; Service, Susan K.; Spesny, Mitzi; Meshi, Dar B.; Poon, Wingman; Molina, Julio; Fournier, Eduardo; Gallegos, Alvaro; Mathews, Carol; Neylan, Thomas; Batki, Steven L.; Roche, Erin; Ramirez, Margarita; Silva, Sandra; De Mille, Melissa C.; Dong, Penny; Leon, Pedro E.; Reus, Victor I.; Sandkuijl, Lodewijk A.; Freimer, Nelson B.

2002-01-01

Genomewide association studies may offer the best promise for genetic mapping of complex traits. Such studies in outbred populations require very densely spaced single-nucleotide polymorphisms. In recently founded population isolates, however, extensive linkage disequilibrium (LD) may make these studies feasible with currently available sets of short tandem repeat markers, spaced at intervals as large as a few centimorgans. We report the results of a genomewide association study of severe bipolar disorder (BP-I), using patients from the isolated population of the central valley of Costa Rica. We observed LD with BP-I on several chromosomes; the most striking results were in proximal 8p, a region that has previously shown linkage to schizophrenia. This region could be important for severe psychiatric disorders, rather than for a specific phenotype. PMID:12119601

Spatial and temporal variability in benthic invertebrate assemblages in Upper Klamath Lake, Oregon

USGS Publications Warehouse

Stauffer-Olsen, Natalie J.; Carter, James L.; Fend, Steven V.

2017-01-01

Upper Klamath Lake (UKL) in southern Oregon has experienced declines in water quality due to excessive nutrient loading. This has led to annual cyanobacterial blooms, primarily of Aphanizomenon flos-aquae (AFA). Benthic invertebrates are important food resources for benthic feeding fishes; however, they can increase autochthonous nutrient cycling in lakes and as a result might be contributing to poor water quality in UKL. This study determined the density and taxonomic richness of benthic invertebrate assemblages in three geographic regions (north, central, and south) and three habitats (littoral, open-water and trench) across UKL. Sediment composition and water quality were also characterized at each of the 21 benthic invertebrate collection sites. Three sampling trips were made from May–July 2013. Mean lake-wide invertebrate density was 12 617 ± 7506 individuals m-2 (n = 63, based on 189 Ekman grabs) with oligochaetes, chironomids, and leeches representing 97% of all individuals. Mean invertebrate richness per sample was 16 ± 4 (n = 63). Two and three-way repeated measures ANOVAs identified differences in invertebrate densities and richness among regions, habitats, and sampling periods. There were no differences in total density among sampling periods. Total density was higher in littoral compared to open-water habitats, and in the northern region, proximal to all riverine inputs to the lake, compared to the central or southern regions. Although variances were heterogeneous, the number of taxa appeared to differ between habitats and regions.

Association between the length of the MUC8-minisatellite 5 region and susceptibility to chronic obstructive pulmonary disease (COPD).

PubMed

Lee, Se-Ra; Kim, Won-Tae; Kim, Tae Nam; Nam, Jong Kil; Kim, Woo Jin; Leem, Sun-Hee

2018-01-01

In asthma and chronic obstructive pulmonary disease (COPD), mucins display disease-related alterations caused by airway mucus obstruction. MUC5AC, MUC5B and MUC8 are known as the major secretory mucins in human airway epithelial cells. Analysis of mucin genes has identified the presence of several features with a variable number of tandem repeats (VNTR; minisatellites) in the central region of each mucin. In our previous study, six minisatellites in the region of the MUC8 gene were identified, and the MUC8-MS5 minisatellite showed the highest heterozygosity among them. In this study, we evaluated the relationship between MUC8-MS5 and susceptibility to asthma and COPD. A case-control study was performed with 229 controls, 123 COPD cases and 77 asthma cases. A significant association (OR 3.96) between short alleles (2/2 repeats) and the occurrence of COPD was observed [95% confidence interval (CI) 1.32-11.88; p = 0.008]. Hence, the increased frequency of 2/2 homo-short alleles were also found in asthma cases (3.11; CI 0.88-11.05; p = 0.066), though this association was not statistically significant. These results revealed a genetic association between MUC8 and COPD, and that the specific short minisatellite alleles (2/2) of MUC8-MS5 may be a risk factor for COPD.

Encoding: the keystone to efficient functioning of verbal short-term memory.

PubMed

Barry, Johanna G; Sabisch, Beate; Friederici, Angela D; Brauer, Jens

2011-11-01

Verbal short-term memory (VSTM) is thought to play a critical role in language learning. It is indexed by the nonword repetition task where listeners are asked to repeat meaningless words like 'blonterstaping'. The present study investigated the effect on nonword repetition performance of differences in efficiency of functioning of some part of the neural architecture mediating VSTM. Hypotheses were stated within Baddeley and Hitch's (1974) multicomponent model of VSTM, with respect to regions of the brain known to be active during tasks tapping into VSTM. We were specifically interested in activations associated with the posterior planum temporale (Spt) which emerge during rehearsal since this region is hypothesized to be central to VTSM (Buchsbaum, Olsen, Koch, & Berman, 2005a). Participants performed a delayed reaction time task in the scanner which explicitly mimicked the three main stages of information-processing involved in VSTM (encoding, rehearsal, recall (here recognition)). The data for each stage were then convolved with scores from a separately measured nonword repetition task. Rather than observing a pattern of individual differences located to specific regions specialized for supporting VSTM, a dissociation in direction of correlation in overlapping regions of the brain was observed during encoding and recognition. Larger hemodynamic responses during encoding were associated with better nonword repetition, and vice versa during recognition. There was little evidence for a network of activations specialized for VSTM. Instead, the main correlations were observed in regions also known to be involved in long-term memory. It seems that individuals who are better at nonword repetition and hence at language learning, activate these regions more efficiently than poorer nonword-repeaters early after stimulus input. These observations are discussed with respect to various models proposed for explaining the phenomenon of VSTM. Crown Copyright © 2011. Published by Elsevier Ltd. All rights reserved.

Population genetic structure of traditional populations in the Peruvian Central Andes and implications for South American population history.

PubMed

Cabana, Graciela S; Lewis, Cecil M; Tito, Raúl Y; Covey, R Alan; Cáceres, Angela M; Cruz, Augusto F De La; Durand, Diana; Housman, Genevieve; Hulsey, Brannon I; Iannacone, Gian Carlo; López, Paul W; Martínez, Rolando; Medina, Ángel; Dávila, Olimpio Ortega; Pinto, Karla Paloma Osorio; Santillán, Susan I Polo; Domínguez, Percy Rojas; Rubel, Meagan; Smith, Heather F; Smith, Silvia E; Massa, Verónica Rubín de Celis; Lizárraga, Beatriz; Stone, Anne C

2014-01-01

Molecular-based characterizations of Andean peoples are traditionally conducted in the service of elucidating continent-level evolutionary processes in South America. Consequently, genetic variation among "western" Andean populations is often represented in relation to variation among "eastern" Amazon and Orinoco River Basin populations. This west-east contrast in patterns of population genetic variation is typically attributed to large-scale phenomena, such as dual founder colonization events or differing long-term microevolutionary histories. However, alternative explanations that consider the nature and causes of population genetic diversity within the Andean region remain underexplored. Here we examine population genetic diversity in the Peruvian Central Andes using data from the mtDNA first hypervariable region and Y-chromosome short tandem repeats among 17 newly sampled populations and 15 published samples. Using this geographically comprehensive data set, we first reassessed the currently accepted pattern of western versus eastern population genetic structure, which our results ultimately reject: mtDNA population diversities were lower, rather than higher, within Andean versus eastern populations, and only highland Y-chromosomes exhibited significantly higher within-population diversities compared with eastern groups. Multiple populations, including several highland samples, exhibited low genetic diversities for both genetic systems. Second, we explored whether the implementation of Inca state and Spanish colonial policies starting at about ad 1400 could have substantially restructured population genetic variation and consequently constitute a primary explanation for the extant pattern of population diversity in the Peruvian Central Andes. Our results suggest that Peruvian Central Andean population structure cannot be parsimoniously explained as the sole outcome of combined Inca and Spanish policies on the region's population demography: highland populations differed from coastal and lowland populations in mtDNA genetic structure only; highland groups also showed strong evidence of female-biased gene flow and/or effective sizes relative to other Peruvian ecozones. Taken together, these findings indicate that population genetic structure in the Peruvian Central Andes is considerably more complex than previously reported and that characterizations of and explanations for genetic variation may be best pursued within more localized regions and defined time periods.

Holocene paleoseismicity, temporal clustering, and probabilities of future large (M > 7) earthquakes on the Wasatch fault zone, Utah

USGS Publications Warehouse

McCalpin, J.P.; Nishenko, S.P.

1996-01-01

The chronology of M>7 paleoearthquakes on the central five segments of the Wasatch fault zone (WFZ) is one of the best dated in the world and contains 16 earthquakes in the past 5600 years with an average repeat time of 350 years. Repeat times for individual segments vary by a factor of 2, and range from about 1200 to 2600 years. Four of the central five segments ruptured between ??? 620??30 and 1230??60 calendar years B.P. The remaining segment (Brigham City segment) has not ruptured in the past 2120??100 years. Comparison of the WFZ space-time diagram of paleoearthquakes with synthetic paleoseismic histories indicates that the observed temporal clusters and gaps have about an equal probability (depending on model assumptions) of reflecting random coincidence as opposed to intersegment contagion. Regional seismicity suggests that for exposure times of 50 and 100 years, the probability for an earthquake of M>7 anywhere within the Wasatch Front region, based on a Poisson model, is 0.16 and 0.30, respectively. A fault-specific WFZ model predicts 50 and 100 year probabilities for a M>7 earthquake on the WFZ itself, based on a Poisson model, as 0.13 and 0.25, respectively. In contrast, segment-specific earthquake probabilities that assume quasi-periodic recurrence behavior on the Weber, Provo, and Nephi segments are less (0.01-0.07 in 100 years) than the regional or fault-specific estimates (0.25-0.30 in 100 years), due to the short elapsed times compared to average recurrence intervals on those segments. The Brigham City and Salt Lake City segments, however, have time-dependent probabilities that approach or exceed the regional and fault specific probabilities. For the Salt Lake City segment, these elevated probabilities are due to the elapsed time being approximately equal to the average late Holocene recurrence time. For the Brigham City segment, the elapsed time is significantly longer than the segment-specific late Holocene recurrence time.

Integrative structure and functional anatomy of a nuclear pore complex

NASA Astrophysics Data System (ADS)

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D.; Hogan, Joanna A.; Upla, Paula; Chemmama, Ilan E.; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S.; Wang, Junjie; Williams, Rosemary; Unruh, Jay R.; Greenberg, Charles H.; Jacobs, Erica Y.; Yu, Zhiheng; de La Cruz, M. Jason; Mironska, Roxana; Stokes, David L.; Aitchison, John D.; Jarrold, Martin F.; Gerton, Jennifer L.; Ludtke, Steven J.; Akey, Christopher W.; Chait, Brian T.; Sali, Andrej; Rout, Michael P.

2018-03-01

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Central ions and lateral asparagine/glutamine zippers stabilize the post-fusion hairpin conformation of the SARS coronavirus spike glycoprotein

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

Duquerroy, Stephane; Vigouroux, Armelle; Rottier, Peter J.M.

2005-05-10

The coronavirus spike glycoprotein is a class I membrane fusion protein with two characteristic heptad repeat regions (HR1 and HR2) in its ectodomain. Here, we report the X-ray structure of a previously characterized HR1/HR2 complex of the severe acute respiratory syndrome coronavirus spike protein. As expected, the HR1 and HR2 segments are organized in antiparallel orientations within a rod-like molecule. The HR1 helices form an exceptionally long (120 A) internal coiled coil stabilized by hydrophobic and polar interactions. A striking arrangement of conserved asparagine and glutamine residues of HR1 propagates from two central chloride ions, providing hydrogen-bonding 'zippers' that stronglymore » constrain the path of the HR2 main chain, forcing it to adopt an extended conformation at either end of a short HR2 {alpha}-helix.« less

Integrative structure and functional anatomy of a nuclear pore complex.

PubMed

Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona; Shi, Yi; Zhang, Wenzhu; Raveh, Barak; Herricks, Thurston; Slaughter, Brian D; Hogan, Joanna A; Upla, Paula; Chemmama, Ilan E; Pellarin, Riccardo; Echeverria, Ignacia; Shivaraju, Manjunatha; Chaudhury, Azraa S; Wang, Junjie; Williams, Rosemary; Unruh, Jay R; Greenberg, Charles H; Jacobs, Erica Y; Yu, Zhiheng; de la Cruz, M Jason; Mironska, Roxana; Stokes, David L; Aitchison, John D; Jarrold, Martin F; Gerton, Jennifer L; Ludtke, Steven J; Akey, Christopher W; Chait, Brian T; Sali, Andrej; Rout, Michael P

2018-03-22

Nuclear pore complexes play central roles as gatekeepers of RNA and protein transport between the cytoplasm and nucleoplasm. However, their large size and dynamic nature have impeded a full structural and functional elucidation. Here we determined the structure of the entire 552-protein nuclear pore complex of the yeast Saccharomyces cerevisiae at sub-nanometre precision by satisfying a wide range of data relating to the molecular arrangement of its constituents. The nuclear pore complex incorporates sturdy diagonal columns and connector cables attached to these columns, imbuing the structure with strength and flexibility. These cables also tie together all other elements of the nuclear pore complex, including membrane-interacting regions, outer rings and RNA-processing platforms. Inwardly directed anchors create a high density of transport factor-docking Phe-Gly repeats in the central channel, organized into distinct functional units. This integrative structure enables us to rationalize the architecture, transport mechanism and evolutionary origins of the nuclear pore complex.

Single Amino Acid Repeats in the Proteome World: Structural, Functional, and Evolutionary Insights

PubMed Central

Kumar, Amitha Sampath; Sowpati, Divya Tej; Mishra, Rakesh K.

2016-01-01

Microsatellites or simple sequence repeats (SSR) are abundant, highly diverse stretches of short DNA repeats present in all genomes. Tandem mono/tri/hexanucleotide repeats in the coding regions contribute to single amino acids repeats (SAARs) in the proteome. While SSRs in the coding region always result in amino acid repeats, a majority of SAARs arise due to a combination of various codons representing the same amino acid and not as a consequence of SSR events. Certain amino acids are abundant in repeat regions indicating a positive selection pressure behind the accumulation of SAARs. By analysing 22 proteomes including the human proteome, we explored the functional and structural relationship of amino acid repeats in an evolutionary context. Only ~15% of repeats are present in any known functional domain, while ~74% of repeats are present in the disordered regions, suggesting that SAARs add to the functionality of proteins by providing flexibility, stability and act as linker elements between domains. Comparison of SAAR containing proteins across species reveals that while shorter repeats are conserved among orthologs, proteins with longer repeats, >15 amino acids, are unique to the respective organism. Lysine repeats are well conserved among orthologs with respect to their length and number of occurrences in a protein. Other amino acids such as glutamic acid, proline, serine and alanine repeats are generally conserved among the orthologs with varying repeat lengths. These findings suggest that SAARs have accumulated in the proteome under positive selection pressure and that they provide flexibility for optimal folding of functional/structural domains of proteins. The insights gained from our observations can help in effective designing and engineering of proteins with novel features. PMID:27893794

Post-Paleogene Deformation in central Anatolia, South of Ankara (Turkey)

NASA Astrophysics Data System (ADS)

Rojay, Bora

2014-05-01

The closure of the northern Neo-Tethys took place between Eurasia in the north and northern edge of Afro- Arabian plate in the south since the Early Cretaceous is documented in central Anatolia. It is mated by Cretaceous ophiolitic mélanges thrusted over southwards on to the upper Cretaceous-Paleogene fore-arc and foreland sequences along the northern margins of Haymana and Tuzgölü basins, respectively. Two main deformation episodes are recognized in the region. These include post-Cretaceous-pre Miocene compressional regime and Miocene to mid-Pliocene transcurrent regime dominated extensional deformation. The first regime is characterize by NW-SE directed compressional and contractional deformation dominated by south vergent, large wave length, asymmetric to overturned folds and associated thrust/reverse faults. Some of these reverse faults were reactivated as strike-slip faults with reverse components as evidenced by cross-cutting relationships and overprinting slickensides observed extensively in the field. Along these reactivated faults, echelon calcite veins, fault parallel meter thick silica walls with repeated phases of deformation are very common. Following the Miocene, the region is affected by a NNE-SSW to NE-SW directed extension, possibly resulted from the interaction of Tuzgölü Fault with the northwards convex splays of dextral North Anatolian Fault extending into the region. As a conclusion, the Paleogene sequences with ophiolitic mélanges are deformed under NNE-SSW directed compression related to the development of dextral strike slip tectonics during post-Paleogene-pre-Miocene period. Keywords:fault plane slip data, transcurrent regime, post-Paleogene, central Anatolia.

High levels of diversity and population structure in the potato late blight pathogen at the Mexico centre of origin.

PubMed

Wang, Jianan; Fernández-Pavía, Sylvia P; Larsen, Meredith M; Garay-Serrano, Edith; Gregorio-Cipriano, Rosario; Rodríguez-Alvarado, Gerardo; Grünwald, Niklaus J; Goss, Erica M

2017-02-01

Globally destructive crop pathogens often emerge by migrating out of their native ranges. These pathogens are often diverse at their centre of origin and may exhibit adaptive variation in the invaded range via multiple introductions from different source populations. However, source populations are generally unidentified or poorly studied compared to invasive populations. Phytophthora infestans, the causal agent of late blight, is one of the most costly pathogens of potato and tomato worldwide. Mexico is the centre of origin and diversity of P. infestans and migration events out of Mexico have enormously impacted disease dynamics in North America and Europe. The debate over the origin of the pathogen, and population studies of P. infestans in Mexico, has focused on the Toluca Valley, whereas neighbouring regions have been little studied. We examined the population structure of P. infestans across central Mexico, including samples from Michoacán, Tlaxcala and Toluca. We found high levels of diversity consistent with sexual reproduction in Michoacán and Tlaxcala and population subdivision that was strongly associated with geographic region. We determined that population structure in central Mexico has contributed to diversity in introduced populations based on relatedness of U.S. clonal lineages to Mexican isolates from different regions. Our results suggest that P. infestans exists as a metapopulation in central Mexico, and this population structure could be contributing to the repeated re-emergence of P. infestans in the United States and elsewhere. © 2016 John Wiley & Sons Ltd.

The 2.1-kb inverted repeat DNA sequences flank the mat2,3 silent region in two species of Schizosaccharomyces and are involved in epigenetic silencing in Schizosaccharomyces pombe.

PubMed Central

Singh, Gurjeet; Klar, Amar J S

2002-01-01

The mat2,3 region of the fission yeast Schizosaccharomyces pombe exhibits a phenomenon of transcriptional silencing. This region is flanked by two identical DNA sequence elements, 2.1 kb in length, present in inverted orientation: IRL on the left and IRR on the right of the silent region. The repeats do not encode any ORF. The inverted repeat DNA region is also present in a newly identified related species, which we named S. kambucha. Interestingly, the left and right repeats share perfect identity within a species, but show approximately 2% bases interspecies variation. Deletion of IRL results in variegated expression of markers inserted in the silent region, while deletion of the IRR causes their derepression. When deletions of these repeats were genetically combined with mutations in different trans-acting genes previously shown to cause a partial defect in silencing, only mutations in clr1 and clr3 showed additive defects in silencing with the deletion of IRL. The rate of mat1 switching is also affected by deletion of repeats. The IRL or IRR deletion did not cause significant derepression of the mat2 or mat3 loci. These results implicate repeats for maintaining full repression of the mat2,3 region, for efficient mat1 switching, and further support the notion that multiple pathways cooperate to silence the mat2,3 domain. PMID:12399374

Genetic characterization of UCS region of Pneumocystis jirovecii and construction of allelic profiles of Indian isolates based on sequence typing at three regions.

PubMed

Gupta, Rashmi; Mirdha, Bijay Ranjan; Guleria, Randeep; Kumar, Lalit; Luthra, Kalpana; Agarwal, Sanjay Kumar; Sreenivas, Vishnubhatla

2013-01-01

Pneumocystis jirovecii is an opportunistic pathogen that causes severe pneumonia in immunocompromised patients. To study the genetic diversity of P. jirovecii in India the upstream conserved sequence (UCS) region of Pneumocystis genome was amplified, sequenced and genotyped from a set of respiratory specimens obtained from 50 patients with a positive result for nested mitochondrial large subunit ribosomal RNA (mtLSU rRNA) PCR during the years 2005-2008. Of these 50 cases, 45 showed a positive PCR for UCS region. Variations in the tandem repeats in UCS region were characterized by sequencing all the positive cases. Of the 45 cases, one case showed five repeats, 11 cases showed four repeats, 29 cases showed three repeats and four cases showed two repeats. By running amplified DNA from all these cases on a high-resolution gel, mixed infection was observed in 12 cases (26.7%, 12/45). Forty three of 45 cases included in this study had previously been typed at mtLSU rRNA and internal transcribed spacer (ITS) region by our group. In the present study, the genotypes at those two regions were combined with UCS repeat patterns to construct allelic profiles of 43 cases. A total of 36 allelic profiles were observed in 43 isolates indicating high genetic variability. A statistically significant association was observed between mtLSU rRNA genotype 1, ITS type Ea and UCS repeat pattern 4. Copyright © 2012 Elsevier B.V. All rights reserved.

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

PubMed Central

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

2003-01-01

Functional steroid receptor complexes are assembled and maintained by an ordered pathway of interactions involving multiple components of the cellular chaperone machinery. Two of these components, Hop and Hip, serve as co-chaperones to the major heat shock proteins (Hsps), Hsp70 and Hsp90, and participate in intermediate stages of receptor assembly. In an effort to better understand the functions of Hop and Hip in the assembly process, we focused on a region of similarity located near the C-terminus of each co-chaperone. Contained within this region is a repeated sequence motif we have termed the DP repeat. Earlier mutagenesis studies implicated the DP repeat of either Hop or Hip in Hsp70 binding and in normal assembly of the co-chaperones with progesterone receptor (PR) complexes. We report here that the DP repeat lies within a protease-resistant domain that extends to or is near the C-terminus of both co-chaperones. Point mutations in the DP repeats render the C-terminal regions hypersensitive to proteolysis. In addition, a Hop DP mutant displays altered proteolytic digestion patterns, which suggest that the DP-repeat region influences the folding of other Hop domains. Although the respective DP regions of Hop and Hip share sequence and structural similarities, they are not functionally interchangeable. Moreover, a double-point mutation within the second DP-repeat unit of Hop that converts this to the sequence found in Hip disrupts Hop function; however, the corresponding mutation in Hip does not alter its function. We conclude that the DP repeats are important structural elements within a C-terminal domain, which is important for Hop and Hip function. PMID:14627198

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

PubMed

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

2003-01-01

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

Rapid Sensitization of Physiological, Neuronal, and Locomotor Effects of Nicotine: Critical Role of Peripheral Drug Actions

PubMed Central

Lenoir, Magalie; Tang, Jeremy S.; Woods, Amina S.

2013-01-01

Repeated exposure to nicotine and other psychostimulant drugs produces persistent increases in their psychomotor and physiological effects (sensitization), a phenomenon related to the drugs' reinforcing properties and abuse potential. Here we examined the role of peripheral actions of nicotine in nicotine-induced sensitization of centrally mediated physiological parameters (brain, muscle, and skin temperatures), cortical and VTA EEG, neck EMG activity, and locomotion in freely moving rats. Repeated injections of intravenous nicotine (30 μg/kg) induced sensitization of the drug's effects on all these measures. In contrast, repeated injections of the peripherally acting analog of nicotine, nicotine pyrrolidine methiodide (nicotinePM, 30 μg/kg, i.v.) resulted in habituation (tolerance) of the same physiological, neuronal, and behavioral measures. However, after repeated nicotine exposure, acute nicotinePM injections induced nicotine-like physiological responses: powerful cortical and VTA EEG desynchronization, EMG activation, a large brain temperature increase, but weaker hyperlocomotion. Additionally, both the acute locomotor response to nicotine and nicotine-induced locomotor sensitization were attenuated by blockade of peripheral nicotinic receptors by hexamethonium (3 mg/kg, i.v.). These data suggest that the peripheral actions of nicotine, which precede its direct central actions, serve as a conditioned interoceptive cue capable of eliciting nicotine-like physiological and neural responses after repeated nicotine exposure. Thus, by providing a neural signal to the CNS that is repeatedly paired with the direct central effects of nicotine, the drug's peripheral actions play a critical role in the development of nicotine-induced physiological, neural, and behavioral sensitization. PMID:23761889

Rapid sensitization of physiological, neuronal, and locomotor effects of nicotine: critical role of peripheral drug actions.

PubMed

Lenoir, Magalie; Tang, Jeremy S; Woods, Amina S; Kiyatkin, Eugene A

2013-06-12

Repeated exposure to nicotine and other psychostimulant drugs produces persistent increases in their psychomotor and physiological effects (sensitization), a phenomenon related to the drugs' reinforcing properties and abuse potential. Here we examined the role of peripheral actions of nicotine in nicotine-induced sensitization of centrally mediated physiological parameters (brain, muscle, and skin temperatures), cortical and VTA EEG, neck EMG activity, and locomotion in freely moving rats. Repeated injections of intravenous nicotine (30 μg/kg) induced sensitization of the drug's effects on all these measures. In contrast, repeated injections of the peripherally acting analog of nicotine, nicotine pyrrolidine methiodide (nicotine(PM), 30 μg/kg, i.v.) resulted in habituation (tolerance) of the same physiological, neuronal, and behavioral measures. However, after repeated nicotine exposure, acute nicotine(PM) injections induced nicotine-like physiological responses: powerful cortical and VTA EEG desynchronization, EMG activation, a large brain temperature increase, but weaker hyperlocomotion. Additionally, both the acute locomotor response to nicotine and nicotine-induced locomotor sensitization were attenuated by blockade of peripheral nicotinic receptors by hexamethonium (3 mg/kg, i.v.). These data suggest that the peripheral actions of nicotine, which precede its direct central actions, serve as a conditioned interoceptive cue capable of eliciting nicotine-like physiological and neural responses after repeated nicotine exposure. Thus, by providing a neural signal to the CNS that is repeatedly paired with the direct central effects of nicotine, the drug's peripheral actions play a critical role in the development of nicotine-induced physiological, neural, and behavioral sensitization.

Sustainable growth in America's heartland; 3-D geologic maps as the foundation

USGS Publications Warehouse

,; ,; ,; ,; ,; ,

1999-01-01

The central Great Lakes states of Illinois, Indiana, Michigan, and Ohio constitute one of the most productive and economically important regions in the country--America's heartland. The agriculture, industry, business, recreation, and ecology of these states are based on a common geologic heritage. During the last 1.8 million years, glaciers repeatedly advanced and retreated across the region, leaving behind a thick, complex blanket of intermixed layers of mud, clay, silt, sand, and gravel. Decisionmakers need knowledge of the glacial deposits--their characteristics, three-dimensional distribution, and thickness. To provide this knowledge, a coalition of state and federal geological surveys has formed to conduct the necessary studies in these four states to depict the three-dimensional nature of these glacial deposits and to interpret these data in cooperation with the user community for specific societal needs.

How Central Exams Affect Educational Achievement: International Evidence from TIMSS and TIMSS-Repeat.

ERIC Educational Resources Information Center

Woessmann, Ludger

This study asserts that central examinations need not necessarily be those administered by the government; they can be examinations centralized at some administrative level, but in any case, they are external to the school. This study also assessed the impact of central examinations on the functioning of the education system and students academic…

Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae.

PubMed

Szczecińska, Monika; Sawicki, Jakub

2015-09-15

The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161-162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae.

Genomic Resources of Three Pulsatilla Species Reveal Evolutionary Hotspots, Species-Specific Sites and Variable Plastid Structure in the Family Ranunculaceae

PubMed Central

Szczecińska, Monika; Sawicki, Jakub

2015-01-01

Background: The European continent is presently colonized by nine species of the genus Pulsatilla, five of which are encountered only in mountainous regions of southwest and south-central Europe. The remaining four species inhabit lowlands in the north-central and eastern parts of the continent. Most plants of the genus Pulsatilla are rare and endangered, which is why most research efforts focused on their biology, ecology and hybridization. The objective of this study was to develop genomic resources, including complete plastid genomes and nuclear rRNA clusters, for three sympatric Pulsatilla species that are most commonly found in Central Europe. The results will supply valuable information about genetic variation, which can be used in the process of designing primers for population studies and conservation genetics research. The complete plastid genomes together with the nuclear rRNA cluster can serve as a useful tool in hybridization studies. Methodology/principal findings: Six complete plastid genomes and nuclear rRNA clusters were sequenced from three species of Pulsatilla using the Illumina sequencing technology. Four junctions between single copy regions and inverted repeats and junctions between the identified locally-collinear blocks (LCB) were confirmed by Sanger sequencing. Pulsatilla genomes of 120 unique genes had a total length of approximately 161–162 kb, and 21 were duplicated in the inverted repeats (IR) region. Comparative plastid genomes of newly-sequenced Pulsatilla and the previously-identified plastomes of Aconitum and Ranunculus species belonging to the family Ranunculaceae revealed several variations in the structure of the genome, but the gene content remained constant. The nuclear rRNA cluster (18S-ITS1-5.8S-ITS2-26S) of studied Pulsatilla species is 5795 bp long. Among five analyzed regions of the rRNA cluster, only Internal Transcribed Spacer 2 (ITS2) enabled the molecular delimitation of closely-related Pulsatilla patens and Pulsatilla vernalis. Conclusions/significance: The determination of complete plastid genome and nuclear rRNA cluster sequences in three species of the genus Pulsatilla is an important contribution to our knowledge of the evolution and phylogeography of those endangered taxa. The resulting data can be used to identify regions that are particularly useful for barcoding, phylogenetic and phylogeographic studies. The investigated taxa can be identified at each stage of development based on their species-specific SNPs. The nuclear and plastid genomic resources enable advanced studies on hybridization, including identification of parent species, including their roles in that process. The identified nonsynonymous mutations could play an important role in adaptations to changing environments. The results of the study will also provide valuable information about the evolution of the plastome structure in the family Ranunculaceae. PMID:26389887

Molecular Convergence of Infrared Vision in Snakes

PubMed Central

Yokoyama, Shozo; Altun, Ahmet; DeNardo, Dale F.

2011-01-01

It has been discovered that the transient receptor potential ankyrin 1 (TRPA1) proteins of Boidae (boas), Pythonidae (pythons), and Crotalinae (pit vipers) are used to detect infrared radiation, but the molecular mechanism for detecting the infrared radiation is unknown. Here, relating the amino acid substitutions in their TRPA1 proteins and the functional differentiations, we propose that three parallel amino acid changes (L330M, Q391H, and S434T) are responsible for the development of infrared vision in the three groups of snakes. Protein modeling shows that the three amino acid changes alter the structures of the central region of their ankyrin repeats. PMID:20937734

The E3 Ligase CHIP: Insights into Its Structure and Regulation

PubMed Central

Paul, Indranil; Ghosh, Mrinal K.

2014-01-01

The carboxy-terminus of Hsc70 interacting protein (CHIP) is a cochaperone E3 ligase containing three tandem repeats of tetratricopeptide (TPR) motifs and a C-terminal U-box domain separated by a charged coiled-coil region. CHIP is known to function as a central quality control E3 ligase and regulates several proteins involved in a myriad of physiological and pathological processes. Recent studies have highlighted varied regulatory mechanisms operating on the activity of CHIP which is crucial for cellular homeostasis. In this review article, we give a concise account of our current knowledge on the biochemistry and regulation of CHIP. PMID:24868554

The heptad repeats region is essential for AcMNPV P10 filament formation and not the proline-rich or the C-terminus basic regions.

PubMed

Dong, Chunsheng; Deng, Fei; Li, Dan; Wang, Hualin; Hu, Zhihong

2007-09-01

Baculovirus P10 protein is a small conserved protein and is expressed as bundles of filaments in the host cell during the late phase of virus infection. So far the published results on the domain responsible for filament structural formation have been contradictory. Electron microscopy revealed that the C-terminus basic region was involved in filament structural formation in the Autographa californica multiple nucleocapsid nucleopolyhedrovirus (AcMNPV) [van Oers, M.M., Flipsen, J.T., Reusken, C.B., Sliwinsky, E.L., Vlak, J.M., 1993. Functional domains of the p10 protein of Autographa californica nuclear polyhedorsis virus. J. Gen. Virol. 74, 563-574.]. While in the Helicoverpa armigera nucleopolyhedrovirus (HearNPV), the heptad repeats region but not the C-terminus domain was proven to be responsible for filament formation [Dong, C., Li, D., Long, G., Deng, F., Wang, H., Hu, Z., 2005. Identification of functional domains required for HearNPV P10 filament formation. Virology 338, 112-120.]. In this manuscript, fluorescence confocal microscopy was applied to study AcMNPV P10 filament formation. A set of plasmids containing different P10 structural domains fused with a fluorescent protein were constructed and transfected into Sf-9 cells. The data indicated that the heptad repeats region, but not the proline-rich region or the C-terminus basic region, is essential for AcMNPV P10 filament formation. Co-transfection of P10s tagged with different fluorescent revealed that P10s with defective heptad repeats region could not interact with intact heptad repeats region or even full-length P10s to form filament structure. Within the heptad repeats region, deletion of the three amino acids spacing of AcMNPV P10 appeared to have no significant impact on the formation of filament structures, but the content of the heptad repeats region appeared to play a role in the morphology of the filaments.

A metal-linked gapped zipper model is proposed for the 90 kDa heat shock protein-estrogen receptor interface.

PubMed

Schwartz, J A; Mizukami, H

1991-06-01

A novel arrangement is proposed for the association of the 90 kDa heat shock protein (hsp 90) dimer and the human estrogen receptor (hER) monomer. Secondary structure analyses of the hsp 90 molecule reveal the presence of a cysteine-containing, leucine-rich, heptad repeat, which we refer to as region C. Similar analyses on the hER, at its hormone binding domain (HBD), have indicated the presence of a central subdomain bordered by 2 alpha-helical flanking segments which also display the heptad substructure. Due to its predicted potential for conformational change (1) we refer to this central subdomain as the Helix Conversion Unit or HCU. It contains an HX5C peptide and shares significant homology with the metal-binding domain of a gag-encoded HIV-LAV protein (2). We predict that, by virtue of its presence in duplicate, region C may be capable of simultaneous leucine zipper-like pairing with the hER at its flanking helices, as well as the formation of a shared CCHC-box-type metal binding link with the same hER at the putative HCU which lies in between.

Contextual Processing of Abstract Concepts Reveals Neural Representations of Non-Linguistic Semantic Content

PubMed Central

Wilson-Mendenhall, Christine D.; Simmons, W. Kyle; Martin, Alex; Barsalou, Lawrence W.

2014-01-01

Concepts develop for many aspects of experience, including abstract internal states and abstract social activities that do not refer to concrete entities in the world. The current study assessed the hypothesis that, like concrete concepts, distributed neural patterns of relevant, non-linguistic semantic content represent the meanings of abstract concepts. In a novel neuroimaging paradigm, participants processed two abstract concepts (convince, arithmetic) and two concrete concepts (rolling, red) deeply and repeatedly during a concept-scene matching task that grounded each concept in typical contexts. Using a catch trial design, neural activity associated with each concept word was separated from neural activity associated with subsequent visual scenes to assess activations underlying the detailed semantics of each concept. We predicted that brain regions underlying mentalizing and social cognition (e.g., medial prefrontal cortex, superior temporal sulcus) would become active to represent semantic content central to convince, whereas brain regions underlying numerical cognition (e.g., bilateral intraparietal sulcus) would become active to represent semantic content central to arithmetic. The results supported these predictions, suggesting that the meanings of abstract concepts arise from distributed neural systems that represent concept-specific content. PMID:23363408

The Armadillo Repeat Protein PF16 Is Essential for Flagellar Structure and Function in Plasmodium Male Gametes

PubMed Central

Ferguson, David J. P.; Bunting, Karen A.; Xu, Zhengyao; Bailes, Elizabeth; Sinden, Robert E.; Holder, Anthony A.; Smith, Elizabeth F.; Coates, Juliet C.; Rita Tewari

2010-01-01

Malaria, caused by the apicomplexan parasite Plasmodium, threatens 40% of the world's population. Transmission between vertebrate and insect hosts depends on the sexual stages of the life-cycle. The male gamete of Plasmodium parasite is the only developmental stage that possesses a flagellum. Very little is known about the identity or function of proteins in the parasite's flagellar biology. Here, we characterise a Plasmodium PF16 homologue using reverse genetics in the mouse malaria parasite Plasmodium berghei. PF16 is a conserved Armadillo-repeat protein that regulates flagellar structure and motility in organisms as diverse as green algae and mice. We show that P. berghei PF16 is expressed in the male gamete flagellum, where it plays a crucial role maintaining the correct microtubule structure in the central apparatus of the axoneme as studied by electron microscopy. Disruption of the PF16 gene results in abnormal flagellar movement and reduced fertility, but does not lead to complete sterility, unlike pf16 mutations in other organisms. Using homology modelling, bioinformatics analysis and complementation studies in Chlamydomonas, we show that some regions of the PF16 protein are highly conserved across all eukaryotes, whereas other regions may have species-specific functions. PF16 is the first ARM-repeat protein characterised in the malaria parasite genus Plasmodium and this study opens up a novel model for analysis of Plasmodium flagellar biology that may provide unique insights into an ancient organelle and suggest novel intervention strategies to control the malaria parasite. PMID:20886115

The effect of image alignment on capillary blood flow measurement of the neuroretinal rim using the Heidelberg retina flowmeter

PubMed Central

Sehi, M; Flanagan, J G

2004-01-01

Aim: To examine the influence of image alignment on the repeatability of blood flow measurements of the optic nerve. Methods: 10 normal subjects were examined. Heidelberg retina tomograph imaging was performed to establish best location and focus for the temporal neuroretinal rim. Two high quality Heidelberg retina flowmeter (HRF) images were acquired for three methods of alignment: central, nasal, and temporal. A 10×10 pixel measurement window was selected and exactly reproduced on all images. The interquartile pixel values were used to calculate capillary flow. ANOVA, intraclass correlation coefficients (ICC) and the coefficient of repeatability (CoR) were used for analysis. Results: There was no difference between methods (p = 0.47) or between visits (p = 0.51). The ICCs were 0.83 for the central, 0.34 for the nasal, and 0.42 for the temporal alignment. The CoR was 31.5 for central (mean effect 235.1), 234.6 for nasal, and 256.7 for temporal alignment. Conclusion: Central alignment was the most repeatable method for the measurement of neuroretinal rim capillary blood flow using the HRF. PMID:14736775

The sequence of camelpox virus shows it is most closely related to variola virus, the cause of smallpox.

PubMed

Gubser, Caroline; Smith, Geoffrey L

2002-04-01

Camelpox virus (CMPV) and variola virus (VAR) are orthopoxviruses (OPVs) that share several biological features and cause high mortality and morbidity in their single host species. The sequence of a virulent CMPV strain was determined; it is 202182 bp long, with inverted terminal repeats (ITRs) of 6045 bp and has 206 predicted open reading frames (ORFs). As for other poxviruses, the genes are tightly packed with little non-coding sequence. Most genes within 25 kb of each terminus are transcribed outwards towards the terminus, whereas genes within the centre of the genome are transcribed from either DNA strand. The central region of the genome contains genes that are highly conserved in other OPVs and 87 of these are conserved in all sequenced chordopoxviruses. In contrast, genes towards either terminus are more variable and encode proteins involved in host range, virulence or immunomodulation. In some cases, these are broken versions of genes found in other OPVs. The relationship of CMPV to other OPVs was analysed by comparisons of DNA and predicted protein sequences, repeats within the ITRs and arrangement of ORFs within the terminal regions. Each comparison gave the same conclusion: CMPV is the closest known virus to variola virus, the cause of smallpox.

Regions of conservation and divergence in the 3' untranslated sequences of genomic RNA from Ross River virus isolates.

PubMed

Faragher, S G; Dalgarno, L

1986-07-20

The 3' untranslated (UT) sequences of the genomic RNAs of five geographic variants of the alphavirus Ross River virus (RRV) were determined and compared with the 3' UT sequence of RRV T48, the prototype strain. Part of the 3' UT region of Getah virus, a close serological relative of RRV, was also sequenced. The RRV 3' UT region varies markedly in length between variants. Large deletions or insertions, sequence rearrangements and single nucleotide substitutions are observed. A sequence tract of 49 to 58 nucleotides, which is repeated as four blocks in the RRV T48 3' UT region, occurs only once in the 3' UT region of one RRV strain (NB5092), indicating that the existence of repeat sequence blocks is not essential for RRV replication. However, the precise sequence of the 3' proximal copy of the repeat block and its position relative to the poly(A) tail were identical in all RRV isolates examined, suggesting that it has an important role in RRV replication. Nucleotide substitutions between RRV variants are distributed non-randomly along the length of the 3' UT region. The sequence of 120 to 130 nucleotides adjacent to the poly(A) tail is strongly conserved. Getah virus RNA contains three repeat sequence blocks in the 3' UT region. These are similar in sequence to those in RRV RNA but differ in their arrangement. Homology between the RRV and Getah 3' UT sequences is greatest in the 3' proximal repeat sequence block that shows three differences in 49 nucleotides. The 3' proximal repeat in Getah RNA occurs at the same position, relative to the poly(A) tail, as in all RRV variants. The RRV and Getah virus 3' UT sequences show extensive homology in the region between the 3' proximal repeat and the poly(A) tail but, apart from the repeat blocks themselves, they show no significant homology elsewhere.

An efficient repeating signal detector to investigate earthquake swarms

NASA Astrophysics Data System (ADS)

Skoumal, Robert J.; Brudzinski, Michael R.; Currie, Brian S.

2016-08-01

Repetitive earthquake swarms have been recognized as key signatures in fluid injection induced seismicity, precursors to volcanic eruptions, and slow slip events preceding megathrust earthquakes. We investigate earthquake swarms by developing a Repeating Signal Detector (RSD), a computationally efficient algorithm utilizing agglomerative clustering to identify similar waveforms buried in years of seismic recordings using a single seismometer. Instead of relying on existing earthquake catalogs of larger earthquakes, RSD identifies characteristic repetitive waveforms by rapidly identifying signals of interest above a low signal-to-noise ratio and then grouping based on spectral and time domain characteristics, resulting in dramatically shorter processing time than more exhaustive autocorrelation approaches. We investigate seismicity in four regions using RSD: (1) volcanic seismicity at Mammoth Mountain, California, (2) subduction-related seismicity in Oaxaca, Mexico, (3) induced seismicity in Central Alberta, Canada, and (4) induced seismicity in Harrison County, Ohio. In each case, RSD detects a similar or larger number of earthquakes than existing catalogs created using more time intensive methods. In Harrison County, RSD identifies 18 seismic sequences that correlate temporally and spatially to separate hydraulic fracturing operations, 15 of which were previously unreported. RSD utilizes a single seismometer for earthquake detection which enables seismicity to be quickly identified in poorly instrumented regions at the expense of relying on another method to locate the new detections. Due to the smaller computation overhead and success at distances up to ~50 km, RSD is well suited for real-time detection of low-magnitude earthquake swarms with permanent regional networks.

Structure and evolution of N-domains in AAA metalloproteases.

PubMed

Scharfenberg, Franka; Serek-Heuberger, Justyna; Coles, Murray; Hartmann, Marcus D; Habeck, Michael; Martin, Jörg; Lupas, Andrei N; Alva, Vikram

2015-02-27

Metalloproteases of the AAA (ATPases associated with various cellular activities) family play a crucial role in protein quality control within the cytoplasmic membrane of bacteria and the inner membrane of eukaryotic organelles. These membrane-anchored hexameric enzymes are composed of an N-terminal domain with one or two transmembrane helices, a central AAA ATPase module, and a C-terminal Zn(2+)-dependent protease. While the latter two domains have been well studied, so far, little is known about the N-terminal regions. Here, in an extensive bioinformatic and structural analysis, we identified three major, non-homologous groups of N-domains in AAA metalloproteases. By far, the largest one is the FtsH-like group of bacteria and eukaryotic organelles. The other two groups are specific to Yme1: one found in plants, fungi, and basal metazoans and the other one found exclusively in animals. Using NMR and crystallography, we determined the subunit structure and hexameric assembly of Escherichia coli FtsH-N, exhibiting an unusual α+β fold, and the conserved part of fungal Yme1-N from Saccharomyces cerevisiae, revealing a tetratricopeptide repeat fold. Our bioinformatic analysis showed that, uniquely among these proteins, the N-domain of Yme1 from the cnidarian Hydra vulgaris contains both the tetratricopeptide repeat region seen in basal metazoans and a region of homology to the N-domains of animals. Thus, it is a modern-day representative of an intermediate in the evolution of animal Yme1 from basal eukaryotic precursors. Copyright © 2015. Published by Elsevier Ltd.

Risk factors associated with disease progression and mortality in chronic kidney disease of uncertain etiology: a cohort study in Medawachchiya, Sri Lanka.

PubMed

Senevirathna, Lalantha; Abeysekera, Tilak; Nanayakkara, Shanika; Chandrajith, Rohana; Ratnatunga, Neelakanthi; Harada, Kouji H; Hitomi, Toshiaki; Komiya, Toshiyuki; Muso, Eri; Koizumi, Akio

2012-05-01

The alarming rise in the prevalence of chronic kidney disease of uncertain etiology (CKDu) among the low socioeconomic farming community in the North Central Province of Sri Lanka has been recognized as an emerging public health issue in the country. This study sought to determine the possible factors associated with the progression and mortality of CKDu. The study utilized a single-center cohort registered in 2003 and followed up until 2009 in a regional clinic in the endemic region, and used a Cox proportional hazards model. We repeatedly found an association between disease progression and hypertension. Men were at higher risk of CKDu than women. A significant proportion of the patients in this cohort were underweight, which emphasized the need for future studies on the nutritional status of these patients. Compared with findings in western countries and other regions of Asia, we identified hypertension as a major risk factor for progression of CKDu in this cohort.

Evolution of sfbI Encoding Streptococcal Fibronectin-Binding Protein I: Horizontal Genetic Transfer and Gene Mosaic Structure

PubMed Central

Towers, Rebecca J.; Fagan, Peter K.; Talay, Susanne R.; Currie, Bart J.; Sriprakash, Kadaba S.; Walker, Mark J.; Chhatwal, Gursharan S.

2003-01-01

Streptococcal fibronectin-binding protein is an important virulence factor involved in colonization and invasion of epithelial cells and tissues by Streptococcus pyogenes. In order to investigate the mechanisms involved in the evolution of sfbI, the sfbI genes from 54 strains were sequenced. Thirty-four distinct alleles were identified. Three principal mechanisms appear to have been involved in the evolution of sfbI. The amino-terminal aromatic amino acid-rich domain is the most variable region and is apparently generated by intergenic recombination of horizontally acquired DNA cassettes, resulting in a genetic mosaic in this region. Two distinct and divergent sequence types that shared only 61 to 70% identity were identified in the central proline-rich region, while variation at the 3′ end of the gene is due to deletion or duplication of defined repeat units. Potential antigenic and functional variabilities in SfbI imply significant selective pressure in vivo with direct implications for the microbial pathogenesis of S. pyogenes. PMID:14662917

A novel surrogate-based approach for optimal design of electromagnetic-based circuits

NASA Astrophysics Data System (ADS)

Hassan, Abdel-Karim S. O.; Mohamed, Ahmed S. A.; Rabie, Azza A.; Etman, Ahmed S.

2016-02-01

A new geometric design centring approach for optimal design of central processing unit-intensive electromagnetic (EM)-based circuits is introduced. The approach uses norms related to the probability distribution of the circuit parameters to find distances from a point to the feasible region boundaries by solving nonlinear optimization problems. Based on these normed distances, the design centring problem is formulated as a max-min optimization problem. A convergent iterative boundary search technique is exploited to find the normed distances. To alleviate the computation cost associated with the EM-based circuits design cycle, space-mapping (SM) surrogates are used to create a sequence of iteratively updated feasible region approximations. In each SM feasible region approximation, the centring process using normed distances is implemented, leading to a better centre point. The process is repeated until a final design centre is attained. Practical examples are given to show the effectiveness of the new design centring method for EM-based circuits.

[Spatiotemporal pattern analysis of event-related potentials elicited by emotional Stroop task].

PubMed

Liu, Qi; Liu, Ling; He, Hui; Zhou, Shu

2007-05-01

To investigate the spatiotemporal pattern of event-related potentials (ERPs) induced by emotional Stroop task. The ERPs of 19 channels were recorded from 13 healthy subjects while performing emotional Stroop task by pressing the buttons representing the colors in which the words denoting different emotions were displayed. A repeated-measures factorial design was adopted with three levels (word valence: positive, neutral and negative). The result of ERP analysis was presented in the form of statistical parametric mapping (SPM) of F value. No significant difference was found in either reaction time or accuracy. The SPM of ERPs suggested significant emotional valence effects in the occipital region (200-220 ms), the left and central frontal regions (270-300 ms), and the bilateral temporal and parietal cortex (560-580 and 620-630 ms, respectively). Processing of task-irrelevant emotional valence information involves the dynamic operation of extensive brain regions. The ERPs are more sensitive than the behavioral indices in emotional evaluation.

Lion (Panthera leo) populations are declining rapidly across Africa, except in intensively managed areas.

PubMed

Bauer, Hans; Chapron, Guillaume; Nowell, Kristin; Henschel, Philipp; Funston, Paul; Hunter, Luke T B; Macdonald, David W; Packer, Craig

2015-12-01

We compiled all credible repeated lion surveys and present time series data for 47 lion (Panthera leo) populations. We used a Bayesian state space model to estimate growth rate-λ for each population and summed these into three regional sets to provide conservation-relevant estimates of trends since 1990. We found a striking geographical pattern: African lion populations are declining everywhere, except in four southern countries (Botswana, Namibia, South Africa, and Zimbabwe). Population models indicate a 67% chance that lions in West and Central Africa decline by one-half, while estimating a 37% chance that lions in East Africa also decline by one-half over two decades. We recommend separate regional assessments of the lion in the World Conservation Union (IUCN) Red List of Threatened Species: already recognized as critically endangered in West Africa, our analysis supports listing as regionally endangered in Central and East Africa and least concern in southern Africa. Almost all lion populations that historically exceeded ∼ 500 individuals are declining, but lion conservation is successful in southern Africa, in part because of the proliferation of reintroduced lions in small, fenced, intensively managed, and funded reserves. If management budgets for wild lands cannot keep pace with mounting levels of threat, the species may rely increasingly on these southern African areas and may no longer be a flagship species of the once vast natural ecosystems across the rest of the continent.

Targeting accuracy of single-isocenter intensity-modulated radiosurgery for multiple lesions

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

Calvo-Ortega, J.F., E-mail: jfcdrr@yahoo.es; Pozo, M.; Moragues, S.

To investigate the targeting accuracy of intensity-modulated SRS (IMRS) plans designed to simultaneously treat multiple brain metastases with a single isocenter. A home-made acrylic phantom able to support a film (EBT3) in its coronal plane was used. The phantom was CT scanned and three coplanar small targets (a central and two peripheral) were outlined in the Eclipse system. Peripheral targets were 6 cm apart from the central one. A reference IMRS plan was designed to simultaneously treat the three targets, but only a single isocenter located at the center of the central target was used. After positioning the phantom onmore » the linac using the room lasers, a CBCT scan was acquired and the reference plan were mapped on it, by placing the planned isocenter at the intersection of the landmarks used in the film showing the linac isocenter. The mapped plan was then recalculated and delivered. The film dose distribution was derived using a cloud computing application ( (www.radiochromic.com)) that uses a triple-channel dosimetry algorithm. Comparison of dose distributions using the gamma index (5%/1 mm) were performed over a 5 × 5 cm{sup 2} region centered over each target. 2D shifts required to get the best gamma passing rates on the peripheral target regions were compared with the reported ones for the central target. The experiment was repeated ten times in different sessions. Average 2D shifts required to achieve optimal gamma passing rates (99%, 97%, 99%) were 0.7 mm (SD: 0.3 mm), 0.8 mm (SD: 0.4 mm) and 0.8 mm (SD: 0.3 mm), for the central and the two peripheral targets, respectively. No statistical differences (p > 0.05) were found for targeting accuracy between the central and the two peripheral targets. The study revealed a targeting accuracy within 1 mm for off-isocenter targets within 6 cm of the linac isocenter, when a single-isocenter IMRS plan is designed.« less

Cerebral oxygenation in the beach chair position for shoulder surgery in regional anesthesia: impact on cerebral blood flow and neurobehavioral outcome.

PubMed

Aguirre, José A; Märzendorfer, Olivia; Brada, Muriel; Saporito, Andrea; Borgeat, Alain; Bühler, Philipp

2016-12-01

Beach chair position is considered a potential risk factor for central neurological events particularly if combined with low blood pressure. The aim of this study was to assess the impact of regional anesthesia on cerebral blood flow and neurobehavioral outcome. This is a prospective, assessor-blinded observational study evaluating patients in the beach chair position undergoing shoulder surgery under regional anesthesia. University hospital operating room. Forty patients with American Society of Anesthesiologists classes I-II physical status scheduled for elective shoulder surgery. Cerebral saturation and blood flow of the middle cerebral artery were measured prior to anesthesia and continued after beach chair positioning until discharge to the postanesthesia care unit. The anesthesiologist was blinded for these values. Controlled hypotension with systolic blood pressure≤100mm Hg was maintained during surgery. Neurobehavioral tests and values of regional cerebral saturation, bispectral index, the mean maximal blood flow of the middle cerebral artery, and invasive blood pressure were measured prior to regional anesthesia, and measurements were repeated after placement of the patient on the beach chair position and every 20 minutes thereafter until discharge to postanesthesia care unit. The neurobehavioral tests were repeated the day after surgery. The incidence of cerebral desaturation events was 5%. All patients had a significant blood pressure drop 5 minutes after beach chair positioning, measured at the heart as well as the acoustic meatus levels, when compared with baseline values (P<.05). There was no decrease in either the regional cerebral saturation (P=.136) or the maximal blood flow of the middle cerebral artery (P=.212) at the same time points. Some neurocognitive tests showed an impairment 24 hours after surgery (P<.001 for 2 of 3 tests). Beach chair position in patients undergoing regional anesthesia for shoulder surgery had no major impact on cerebral blood flow and cerebral oxygenation. However, some impact on neurobehavioral outcome 24 hours after surgery was observed. Copyright © 2016 Elsevier Inc. All rights reserved.

Phylogeography of competing sexual and parthenogenetic forms of a freshwater flatworm: patterns and explanations

PubMed Central

Pongratz, Norbert; Storhas, Martin; Carranza, Salvador; Michiels, Nicolaas K

2003-01-01

Background Models of the maintenance of sex predict that one reproductive strategy, sexual or parthenogenetic, should outcompete the other. Distribution patterns may reflect the outcome of this competition as well as the effect of chance and historical events. We review the distribution data of sexual and parthenogenetic biotypes of the planarian Schmidtea polychroa. Results S. polychroa lives in allopatry or sympatry across Europe except for Central and North-Western Europe, where sexual individuals have never been reported. A phylogenetic relationship between 36 populations based on a 385 bp fragment of the mitochondrial cytochrome oxidase I gene revealed that haplotypes were often similar over large geographic distances. In North Italian lakes, however, diversity was extreme, with sequence differences of up to 5% within the same lake in both sexuals and parthenogens. Mixed populations showed "endemic" parthenogenetic lineages that presumably originated from coexisting sexuals, and distantly related ones that probably result from colonization by parthenogens independent from sexuals. Conclusions Parthenogens originated repeatedly from sexuals, mainly in Italy, but the same may apply to other Mediterranean regions (Spain, Greece). The degree of divergence between populations suggests that S. polychroa survived the ice ages in separate ice-free areas in Central, Eastern and Southern Europe and re-colonised Europe after the retreat of the major glaciers. Combining these results with those based on nuclear markers, the data suggest that repeated hybridisation between sexuals and parthenogenetic lineages in mixed populations maintains high levels of genetic diversity in parthenogens. This can explain why parthenogens persist in populations that were originally sexual. Exclusive parthenogenesis in central and western populations suggests better colonisation capacity, possibly because of inbreeding costs as well as hybridisation of sexuals with parthenogens. PMID:14622447

Dual megathrust slip behaviors of the 2014 Iquique earthquake sequence

NASA Astrophysics Data System (ADS)

Meng, Lingsen; Huang, Hui; Bürgmann, Roland; Ampuero, Jean Paul; Strader, Anne

2015-02-01

The transition between seismic rupture and aseismic creep is of central interest to better understand the mechanics of subduction processes. A Mw 8.2 earthquake occurred on April 1st, 2014 in the Iquique seismic gap of northern Chile. This event was preceded by a long foreshock sequence including a 2-week-long migration of seismicity initiated by a Mw 6.7 earthquake. Repeating earthquakes were found among the foreshock sequence that migrated towards the mainshock hypocenter, suggesting a large-scale slow-slip event on the megathrust preceding the mainshock. The variations of the recurrence times of the repeating earthquakes highlight the diverse seismic and aseismic slip behaviors on different megathrust segments. The repeaters that were active only before the mainshock recurred more often and were distributed in areas of substantial coseismic slip, while repeaters that occurred both before and after the mainshock were in the area complementary to the mainshock rupture. The spatiotemporal distribution of the repeating earthquakes illustrates the essential role of propagating aseismic slip leading up to the mainshock and illuminates the distribution of postseismic afterslip. Various finite fault models indicate that the largest coseismic slip generally occurred down-dip from the foreshock activity and the mainshock hypocenter. Source imaging by teleseismic back-projection indicates an initial down-dip propagation stage followed by a rupture-expansion stage. In the first stage, the finite fault models show an emergent onset of moment rate at low frequency (< 0.1 Hz), while back-projection shows a steady increase of high frequency power (> 0.5 Hz). This indicates frequency-dependent manifestations of seismic radiation in the low-stress foreshock region. In the second stage, the rupture expands in rich bursts along the rim of a semi-elliptical region with episodes of re-ruptures, suggesting delayed failure of asperities. The high-frequency rupture remains within an area of local high trench-parallel gravity anomaly (TPGA), suggesting the presence of subducting seamounts that promote high-frequency generation. Our results highlight the complexity of the interactions between large-scale aseismic slow-slip and dynamic ruptures of megathrust earthquakes.

Sense-encoded poly-GR dipeptide repeat proteins correlate to neurodegeneration and uniquely co-localize with TDP-43 in dendrites of repeat-expanded C9orf72 amyotrophic lateral sclerosis.

PubMed

Saberi, Shahram; Stauffer, Jennifer E; Jiang, Jie; Garcia, Sandra Diaz; Taylor, Amy E; Schulte, Derek; Ohkubo, Takuya; Schloffman, Cheyenne L; Maldonado, Marcus; Baughn, Michael; Rodriguez, Maria J; Pizzo, Don; Cleveland, Don; Ravits, John

2018-03-01

Hexanucleotide repeat expansions in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis (C9 ALS). The main hypothesized pathogenic mechanisms are C9orf72 haploinsufficiency and/or toxicity from one or more of bi-directionally transcribed repeat RNAs and their dipeptide repeat proteins (DPRs) poly-GP, poly-GA, poly-GR, poly-PR and poly-PA. Recently, nuclear import and/or export defects especially caused by arginine-containing poly-GR or poly-PR have been proposed as significant contributors to pathogenesis based on disease models. We quantitatively studied and compared DPRs, nuclear pore proteins and C9orf72 protein in clinically related and clinically unrelated regions of the central nervous system, and compared them to phosphorylated TDP-43 (pTDP-43), the hallmark protein of ALS. Of the five DPRs, only poly-GR was significantly abundant in clinically related areas compared to unrelated areas (p < 0.001), and formed dendritic-like aggregates in the motor cortex that co-localized with pTDP-43 (p < 0.0001). While most poly-GR dendritic inclusions were pTDP-43 positive, only 4% of pTDP-43 dendritic inclusions were poly-GR positive. Staining for arginine-containing poly-GR and poly-PR in nuclei of neurons produced signals that were not specific to C9 ALS. We could not detect significant differences of nuclear markers RanGap, Lamin B1, and Importin β1 in C9 ALS, although we observed subtle nuclear changes in ALS, both C9 and non-C9, compared to control. The C9orf72 protein itself was diffusely expressed in cytoplasm of large neurons and glia, and nearly 50% reduced, in both clinically related frontal cortex and unrelated occipital cortex, but not in cerebellum. In summary, sense-encoded poly-GR DPR was unique, and localized to dendrites and pTDP43 in motor regions of C9 ALS CNS. This is consistent with new emerging ideas about TDP-43 functions in dendrites.

Sense-encoded poly-GR dipeptide repeat proteins correlate to neurodegeneration and uniquely co-localize with TDP-43 in dendrites of repeat expanded C9orf72 amyotrophic lateral sclerosis

PubMed Central

Saberi, Shahram; Stauffer, Jennifer E.; Jiang, Jie; Garcia, Sandra Diaz; Taylor, Amy E; Schulte, Derek; Ohkubo, Takuya; Schloffman, Cheyenne L.; Maldonado, Marcus; Baughn, Michael; Rodriguez, Maria J; Pizzo, Don; Cleveland, Don; Ravits, John

2018-01-01

Hexanucleotide repeat expansions in C9orf72 are the most common genetic cause of amyotrophic lateral sclerosis (C9 ALS). The main hypothesized pathogenic mechanisms are C9orf72 haploinsufficiency and/or toxicity from one or more of bi-directionally transcribed repeat RNAs and their dipeptide repeat proteins (DPRs) poly-GP, poly-GA, poly-GR, poly-PR and poly-PA. Recently, nuclear import and/or export defects especially caused by arginine-containing poly-GR or poly-PR have been proposed as significant contributors to pathogenesis based on disease models. We quantitatively studied and compared DPRs, nuclear pore proteins and C9orf72 protein in clinically-related and clinically-unrelated regions of the central nervous system, and compared them to phosphorylated TDP-43 (pTDP-43), the hallmark protein of ALS. Of the five DPRs, only poly-GR was significantly abundant in clinically-related areas compared to unrelated areas (p<0.001), and formed dendritic-like aggregates in the motor cortex that co-localized with pTDP-43 (p<0.0001). While most poly-GR dendritic inclusions were pTDP-43-positive, only 4% of pTDP-43 dendritic inclusions were poly-GR-positive. Staining for arginine-containing poly-GR and poly-PR in nuclei of neurons produced signals that were not specific to C9 ALS. We could not detect significant differences of nuclear markers RanGap, Lamin B1, and Importin β1 in C9 ALS, although we observed subtle nuclear changes in ALS, both C9 and non-C9, compared to control. The C9orf72 protein itself was diffusely expressed in cytoplasm of large neurons and glia, and nearly 50% reduced, in both clinically-related frontal cortex and unrelated occipital cortex, but not in cerebellum. In summary, sense-encoded poly-GR DPR was unique, and localized to neurites and pTDP43 in motor regions of C9 ALS CNS. This is consistent with new emerging ideas about TDP-43 functions in dendrites. PMID:29196813

Reliability of Pentacam HR Thickness Maps of the Entire Cornea in Normal, Post-Laser In Situ Keratomileusis, and Keratoconus Eyes.

PubMed

Xu, Zhe; Peng, Mei; Jiang, Jun; Yang, Chun; Zhu, Weigen; Lu, Fan; Shen, Meixiao

2016-02-01

To measure the repeatability and reproducibility of Pentacam HR system thickness maps for the entire cornea in normal, post-laser in situ keratomileusis (post-LASIK), and keratoconus (KC) eyes. Reliability study. Sixty normal subjects (60 eyes), 30 post-LASIK subjects (60 eyes), and 14 KC patients (27 eyes) were imaged with the Pentacam HR system by 2 well-trained operators. For pachymetry the cornea was divided into 4 zones: a central zone (2-mm diameter) and concentric pericentral zone (2-5 mm), transitional zone (5-7 mm), and peripheral zone (7-10 mm). The 3 concentric zones were subdivided into 8 sectors. Intraobserver repeatability and interobserver reproducibility of entire corneal thickness maps were tested by the repeatability and reproducibility coefficients, intraclass correlation coefficients, coefficient of variation, and 95% limits of agreement. From central to peripheral zones, the precision of corneal thickness measurements became gradually smaller. Central zone repeatability and reproducibility were the best in the normal, post-LASIK, and KC groups. The peripheral superior sectors showed poorer repeatability and reproducibility for all subjects. The intraobserver repeatability and interobserver reproducibility for all zones were ≤19.3 μm, ≤22.1 μm, and ≤20.7 μm, in the normal, post-LASIK, and KC groups, respectively. The intraobserver and interobserver coefficients of variation for all zones were ≤1.3%, ≤1.6%, and ≤1.6% for all 3 groups. Pentacam HR system pachymetry of the entire cornea provided good precision in normal, post-LASIK, and KC corneas. Thickness measurements in the peripheral cornea should be interpreted with caution in abnormal corneas after surgery or with diseases. Copyright © 2016 Elsevier Inc. All rights reserved.

Linking Field and Satellite Observations to Reveal Differences in Single vs. Double-Cropped Soybean Yields in Central Brazil

NASA Astrophysics Data System (ADS)

Jeffries, G. R.; Cohn, A.

2016-12-01

Soy-corn double cropping (DC) has been widely adopted in Central Brazil alongside single cropped (SC) soybean production. DC involves different cropping calendars, soy varieties, and may be associated with different crop yield patterns and volatility than SC. Study of the performance of the region's agriculture in a changing climate depends on tracking differences in the productivity of SC vs. DC, but has been limited by crop yield data that conflate the two systems. We predicted SC and DC yields across Central Brazil, drawing on field observations and remotely sensed data. We first modeled field yield estimates as a function of remotely sensed DC status and vegetation index (VI) metrics, and other management and biophysical factors. We then used the statistical model estimated to predict SC and DC soybean yields at each 500 m2 grid cell of Central Brazil for harvest years 2001 - 2015. The yield estimation model was constructed using 1) a repeated cross-sectional survey of soybean yields and management factors for years 2007-2015, 2) a custom agricultural land cover classification dataset which assimilates earlier datasets for the region, and 3) 500m 8-day MODIS image composites used to calculate the wide dynamic range vegetation index (WDRVI) and derivative metrics such as area under the curve for WDRVI values in critical crop development periods. A statistical yield estimation model which primarily entails WDRVI metrics, DC status, and spatial fixed effects was developed on a subset of the yield dataset. Model validation was conducted by predicting previously withheld yield records, and then assessing error and goodness-of-fit for predicted values with metrics including root mean squared error (RMSE), mean squared error (MSE), and R2. We found a statistical yield estimation model which incorporates WDRVI and DC status to be way to estimate crop yields over the region. Statistical properties of the resulting gridded yield dataset may be valuable for understanding linkages between crop yields, farm management factors, and climate.

2-D Structure of the A Region of Xist RNA and Its Implication for PRC2 Association

PubMed Central

Maenner, Sylvain; Blaud, Magali; Fouillen, Laetitia; Savoye, Anne; Marchand, Virginie; Dubois, Agnès; Sanglier-Cianférani, Sarah; Van Dorsselaer, Alain; Clerc, Philippe; Avner, Philip; Visvikis, Athanase; Branlant, Christiane

2010-01-01

In placental mammals, inactivation of one of the X chromosomes in female cells ensures sex chromosome dosage compensation. The 17 kb non-coding Xist RNA is crucial to this process and accumulates on the future inactive X chromosome. The most conserved Xist RNA region, the A region, contains eight or nine repeats separated by U-rich spacers. It is implicated in the recruitment of late inactivated X genes to the silencing compartment and likely in the recruitment of complex PRC2. Little is known about the structure of the A region and more generally about Xist RNA structure. Knowledge of its structure is restricted to an NMR study of a single A repeat element. Our study is the first experimental analysis of the structure of the entire A region in solution. By the use of chemical and enzymatic probes and FRET experiments, using oligonucleotides carrying fluorescent dyes, we resolved problems linked to sequence redundancies and established a 2-D structure for the A region that contains two long stem-loop structures each including four repeats. Interactions formed between repeats and between repeats and spacers stabilize these structures. Conservation of the spacer terminal sequences allows formation of such structures in all sequenced Xist RNAs. By combination of RNP affinity chromatography, immunoprecipitation assays, mass spectrometry, and Western blot analysis, we demonstrate that the A region can associate with components of the PRC2 complex in mouse ES cell nuclear extracts. Whilst a single four-repeat motif is able to associate with components of this complex, recruitment of Suz12 is clearly more efficient when the entire A region is present. Our data with their emphasis on the importance of inter-repeat pairing change fundamentally our conception of the 2-D structure of the A region of Xist RNA and support its possible implication in recruitment of the PRC2 complex. PMID:20052282

Central and Peripheral Vision Loss Differentially Affects Contextual Cueing in Visual Search

ERIC Educational Resources Information Center

Geringswald, Franziska; Pollmann, Stefan

2015-01-01

Visual search for targets in repeated displays is more efficient than search for the same targets in random distractor layouts. Previous work has shown that this contextual cueing is severely impaired under central vision loss. Here, we investigated whether central vision loss, simulated with gaze-contingent displays, prevents the incidental…

New insights into prevalence, genetic diversity, and proviral load of human T-cell leukemia virus types 1 and 2 in pregnant women in Gabon in equatorial central Africa.

PubMed

Etenna, Sonia Lekana-Douki; Caron, Mélanie; Besson, Guillaume; Makuwa, Maria; Gessain, Antoine; Mahé, Antoine; Kazanji, Mirdad

2008-11-01

Human T-cell leukemia virus type 1 (HTLV-1) is highly endemic in areas of central Africa; mother-to-child transmission and sexual transmission are considered to be the predominant routes. To determine the prevalence and subtypes of HTLV-1/2 in pregnant women in Gabon, we conducted an epidemiological survey in the five main cities of the country. In 907 samples, the HTLV-1 seroprevalence was 2.1%, which is lower than that previously reported. Only one case of HTLV-2 infection was found. The HTLV-1 seroprevalence increased with age and differed between regions (P

Endovascular interventions for central vein stenosis.

PubMed

Agarwal, Anil K

2015-12-01

Central vein stenosis is common because of the placement of venous access and cardiac intravascular devices and compromises vascular access for dialysis. Endovascular intervention with angioplasty and/or stent placement is the preferred approach, but the results are suboptimal and limited. Primary patency after angioplasty alone is poor, but secondary patency can be maintained with repeated angioplasty. Stent placement is recommended for quick recurrence or elastic recoil of stenosis. Primary patency of stents is also poor, though covered stents have recently shown better patency than bare metal stents. Secondary patency requires repeated intervention. Recanalization of occluded central veins is tedious and not always successful. Placement of hybrid graft-catheter with a combined endovascular surgical approach can maintain patency in many cases. In the presence of debilitating symptoms, palliative approach with endovascular banding or occlusion of the access may be necessary. Prevention of central vein stenosis is the most desirable strategy.

Origin of the CMS gene locus in rapeseed cybrid mitochondria: active and inactive recombination produces the complex CMS gene region in the mitochondrial genomes of Brassicaceae.

PubMed

Oshima, Masao; Kikuchi, Rie; Imamura, Jun; Handa, Hirokazu

2010-01-01

CMS (cytoplasmic male sterile) rapeseed is produced by asymmetrical somatic cell fusion between the Brassica napus cv. Westar and the Raphanus sativus Kosena CMS line (Kosena radish). The CMS rapeseed contains a CMS gene, orf125, which is derived from Kosena radish. Our sequence analyses revealed that the orf125 region in CMS rapeseed originated from recombination between the orf125/orfB region and the nad1C/ccmFN1 region by way of a 63 bp repeat. A precise sequence comparison among the related sequences in CMS rapeseed, Kosena radish and normal rapeseed showed that the orf125 region in CMS rapeseed consisted of the Kosena orf125/orfB region and the rapeseed nad1C/ccmFN1 region, even though Kosena radish had both the orf125/orfB region and the nad1C/ccmFN1 region in its mitochondrial genome. We also identified three tandem repeat sequences in the regions surrounding orf125, including a 63 bp repeat, which were involved in several recombination events. Interestingly, differences in the recombination activity for each repeat sequence were observed, even though these sequences were located adjacent to each other in the mitochondrial genome. We report results indicating that recombination events within the mitochondrial genomes are regulated at the level of specific repeat sequences depending on the cellular environment.

Inside the "African cattle complex": animal burials in the holocene central Sahara.

PubMed

di Lernia, Savino; Tafuri, Mary Anne; Gallinaro, Marina; Alhaique, Francesca; Balasse, Marie; Cavorsi, Lucia; Fullagar, Paul D; Mercuri, Anna Maria; Monaco, Andrea; Perego, Alessandro; Zerboni, Andrea

2013-01-01

Cattle pastoralism is an important trait of African cultures. Ethnographic studies describe the central role played by domestic cattle within many societies, highlighting its social and ideological value well beyond its mere function as 'walking larder'. Historical depth of this African legacy has been repeatedly assessed in an archaeological perspective, mostly emphasizing a continental vision. Nevertheless, in-depth site-specific studies, with a few exceptions, are lacking. Despite the long tradition of a multi-disciplinary approach to the analysis of pastoral systems in Africa, rarely do early and middle Holocene archaeological contexts feature in the same area the combination of settlement, ceremonial and rock art features so as to be multi-dimensionally explored: the Messak plateau in the Libyan central Sahara represents an outstanding exception. Known for its rich Pleistocene occupation and abundant Holocene rock art, the region, through our research, has also shown to preserve the material evidence of a complex ritual dated to the Middle Pastoral (6080-5120 BP or 5200-3800 BC). This was centred on the frequent deposition in stone monuments of disarticulated animal remains, mostly cattle. Animal burials are known also from other African contexts, but regional extent of the phenomenon, state of preservation of monuments, and associated rock art make the Messak case unique. GIS analysis, excavation data, radiocarbon dating, zooarchaeological and isotopic (Sr, C, O) analyses of animal remains, and botanical information are used to explore this highly formalized ritual and the lifeways of a pastoral community in the Holocene Sahara.

A Dynamic Tandem Repeat in Monocotyledons Inferred from a Comparative Analysis of Chloroplast Genomes in Melanthiaceae.

PubMed

Do, Hoang Dang Khoa; Kim, Joo-Hwan

2017-01-01

Chloroplast genomes (cpDNA) are highly valuable resources for evolutionary studies of angiosperms, since they are highly conserved, are small in size, and play critical roles in plants. Slipped-strand mispairing (SSM) was assumed to be a mechanism for generating repeat units in cpDNA. However, research on the employment of different small repeated sequences through SSM events, which may induce the accumulation of distinct types of repeats within the same region in cpDNA, has not been documented. Here, we sequenced two chloroplast genomes from the endemic species Heloniopsis tubiflora (Korea) and Xerophyllum tenax (USA) to cover the gap between molecular data and explore "hot spots" for genomic events in Melanthiaceae. Comparative analysis of 23 complete cpDNA sequences revealed that there were different stages of deletion in the rps16 region across the Melanthiaceae. Based on the partial or complete loss of rps16 gene in cpDNA, we have firstly reported potential molecular markers for recognizing two sections ( Veratrum and Fuscoveratrum ) of Veratrum . Melathiaceae exhibits a significant change in the junction between large single copy and inverted repeat regions, ranging from trnH_GUG to a part of rps3 . Our results show an accumulation of tandem repeats in the rpl23-ycf2 regions of cpDNAs. Small conserved sequences exist and flank tandem repeats in further observation of this region across most of the examined taxa of Liliales. Therefore, we propose three scenarios in which different small repeated sequences were used during SSM events to generate newly distinct types of repeats. Occasionally, prior to the SSM process, point mutation event and double strand break repair occurred and induced the formation of initial repeat units which are indispensable in the SSM process. SSM may have likely occurred more frequently for short repeats than for long repeat sequences in tribe Parideae (Melanthiaceae, Liliales). Collectively, these findings add new evidence of dynamic results from SSM in chloroplast genomes which can be useful for further evolutionary studies in angiosperms. Additionally, genomics events in cpDNA are potential resources for mining molecular markers in Liliales.

GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species

PubMed Central

Chandrashekar, Darshan Shimoga; Dey, Poulami; Acharya, Kshitish K.

2015-01-01

Background Genome-wide repeat sequences, such as LINEs, SINEs and LTRs share a considerable part of the mammalian nuclear genomes. These repeat elements seem to be important for multiple functions including the regulation of transcription initiation, alternative splicing and DNA methylation. But it is not possible to study all repeats and, hence, it would help to short-list before exploring their potential functional significance via experimental studies and/or detailed in silico analyses. Result We developed the ‘Genomic Repeat Element Analyzer for Mammals’ (GREAM) for analysis, screening and selection of potentially important mammalian genomic repeats. This web-server offers many novel utilities. For example, this is the only tool that can reveal a categorized list of specific types of transposons, retro-transposons and other genome-wide repetitive elements that are statistically over-/under-represented in regions around a set of genes, such as those expressed differentially in a disease condition. The output displays the position and frequency of identified elements within the specified regions. In addition, GREAM offers two other types of analyses of genomic repeat sequences: a) enrichment within chromosomal region(s) of interest, and b) comparative distribution across the neighborhood of orthologous genes. GREAM successfully short-listed a repeat element (MER20) known to contain functional motifs. In other case studies, we could use GREAM to short-list repetitive elements in the azoospermia factor a (AZFa) region of the human Y chromosome and those around the genes associated with rat liver injury. GREAM could also identify five over-represented repeats around some of the human and mouse transcription factor coding genes that had conserved expression patterns across the two species. Conclusion GREAM has been developed to provide an impetus to research on the role of repetitive sequences in mammalian genomes by offering easy selection of more interesting repeats in various contexts/regions. GREAM is freely available at http://resource.ibab.ac.in/GREAM/. PMID:26208093

Cargo crowding at actin-rich regions along axons causes local traffic jams.

PubMed

Sood, Parul; Murthy, Kausalya; Kumar, Vinod; Nonet, Michael L; Menon, Gautam I; Koushika, Sandhya P

2018-03-01

Steady axonal cargo flow is central to the functioning of healthy neurons. However, a substantial fraction of cargo in axons remains stationary up to several minutes. We examine the transport of precursors of synaptic vesicles (pre-SVs), endosomes and mitochondria in Caenorhabditis elegans touch receptor neurons, showing that stationary cargo are predominantly present at actin-rich regions along the neuronal process. Stationary vesicles at actin-rich regions increase the propensity of moving vesicles to stall at the same location, resulting in traffic jams arising from physical crowding. Such local traffic jams at actin-rich regions are likely to be a general feature of axonal transport since they also occur in Drosophila neurons. Repeated touch stimulation of C. elegans reduces the density of stationary pre-SVs, indicating that these traffic jams can act as both sources and sinks of vesicles. This suggests that vesicles trapped in actin-rich regions are functional reservoirs that may contribute to maintaining robust cargo flow in the neuron. A video abstract of this article can be found at: Video S1; Video S2. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Genetic Characterization of Circulating African Swine Fever Viruses in Nigeria (2007-2015).

PubMed

Luka, P D; Achenbach, J E; Mwiine, F N; Lamien, C E; Shamaki, D; Unger, H; Erume, J

2017-10-01

Sequencing and analysis of three discrete genome regions of African swine fever viruses (ASFV) from archival samples collected in 2007-2011 and active and passive surveillance between 2012 and 2015 in Nigeria were carried out. Analysis was conducted by genotyping of three single-copy African swine fever (ASF) genes. The E183L and B646L genes that encode structural proteins p54 and p72, respectively, were utilized to delineate genotypes before intragenotypic resolution by characterization of the tetrameric amino acid repeat region within the hypervariable central variable region of the B602L gene. The results showed no variation in the p72 and p54 gene regions sequenced. Phylogeny of p72 sequences revealed that all the Nigerian isolates belonged to genotype I, while that of the p54 recovered the Ia genotype. Analysis of B602L gene revealed the differences in the number of tetrameric repeats. Four new variants (Tet-15, Tet-17a, Tet-17b and Tet-48) were recovered, while a fifth variant (Tet-20) was the most widely distributed in the country displacing Tet-36 reported previously in 2003-2006. The viruses responsible for ASF outbreaks in Nigeria are from very closely related but mutated variants of the virus that have been circulating since 1997. A practical implication of the genetic variability of the Nigerian viral isolates in this study is the need for continuous sampling and analysis of circulating viruses, which will provide epidemiological information on the evolution of ASFV in the field versus new incursion for informed strategic control of the disease in the country. © 2016 Blackwell Verlag GmbH.

Characterization of the gene encoding the polymorphic immunodominant molecule, a neutralizing antigen of Theileria parva

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

Toye, P.G.; Metzelaar, M.J.; Wijngaard, P.L.J.

1995-08-01

Theileria parva, a tick-transmitted protozoan parasite related to Plasmodium spp., causes the disease East Coast fever, an acute and usually fatal lymphoproliferative disorder of cattle in Africa. Previous studies using sera from cattle that have survived infection identified a polymorphic immunodominant molecule (PIM) that is expressed by both the infective sporozoite stage of the parasite and the intracellular schizont. Here we show that mAb specific for the PIM Ag can inhibit sporozoite invasion of lymphocytes in vitro. A cDNA clone encoding the PIM Ag of the T. parva (Muguga) stock was obtained by using these mAb in a novel eukaryoticmore » expression cloning system that allows isolation of cDNA encoding cytoplasmic or surface Ags. To establish the molecular basis of the polymorphism of PIM, the cDNA of the PIM Ag from a buffalo-derived T. parva stock was isolated and its sequence was compared with that of the cattle-derived Muguga PIM. The two cDNAs showed considerable identity in both the 5{prime} and 3{prime} regions, but there was substantial sequence divergence in the central regions. Several types of repeated sequences were identified in the variant regions. In the Muguga form of the molecule, there were five tandem repeats of the tetrapeptide, QPEP, that were shown, by transfection of a deleted version of the PIM gene, not to react with several anti-PIM mAbs. By isolating and sequencing the genomic version of the gene, we identified two small introns in the 3{prime} region of the gene. Finally, we showed that polyclonal rat Abs against recombinant PIM neutralize sporozoite infectivity in vitro, suggesting that the PIM Ag should be evaluated for its capacity to immunize cattle against East Coast Fever.« less

Advancement of tree species across ecotonal borders into non-forested ecosystems

NASA Astrophysics Data System (ADS)

Hanberry, Brice B.; Hansen, Mark H.

2015-10-01

Woody species are increasing in density, causing transition to more densely wooded vegetation states, and encroaching across ecotonal borders into non-forested ecosystems. We examined USDA Forest Service Forest Inventory and Analysis data to identify tree species that have expanded longitudinally in range, particularly into the central United States. We analyzed compositional differences within ecological regions (i.e., subsections) in eastern and western ranges of species using repeated measures ANOVA. We considered differences in outer ranges to indicate range expansion or contraction. We also estimated the shift in forest area and basal area relative to the center of the US and compared change in deciduous forest land cover. Out of 80 candidate species, 22 species expanded to the west, seven species expanded to the east, and five species expanded in both directions. During the survey interval, eastern tree species advanced into the predominantly non-forested ecosystems of central United States. Eastern cottonwood, eastern hophornbeam, eastern redbud, honeylocust, Osage-orange, pecan, red mulberry, and Shumard oak represent some of the species that are advancing eastern forest boundaries across forest-grassland ecotones into the central United States. Forest land has shifted towards the center of the continent, as has the center of mean tree basal area, and a simple comparison of deciduous cover change also displayed forest advancement into the central United States from eastern forests. The expanding species may spread along riparian migration corridors that provide protection from drought. Humans use the advancing tree species for windbreaks, fencerows, and ornamental landscaping, while wildlife spread fruit seeds, which results in unintentional assisted migration, or translocation, to drier sites across the region.

Repeatability of Central and Peripheral Pulse Wave Velocity Measures: The Atherosclerosis Risk in Communities (ARIC) Study

PubMed Central

Tanaka, Hirofumi; Palta, Priya; Patel, Mehul D.; Camplain, Ricky; Couper, David; Cheng, Susan; Al Qunaibet, Ada; Poon, Anna K.; Heiss, Gerardo

2016-01-01

BACKGROUND Arterial stiffness measures are emerging tools for risk assessment and stratification for hypertension and cardiovascular disease (CVD). Carotid-femoral pulse wave velocity (cfPWV) is an established measure of central arterial stiffness. Other measures of PWV include femoral-ankle (faPWV), a measure of peripheral stiffness, and brachial-ankle PWV (baPWV), a composite measure of central and peripheral stiffness. Repeatability of central, peripheral, and composite PWV measures has not been adequately examined or compared. METHODS Participants (n = 79; mean age 75.7 years; USA) from a repeatability study nested within the Atherosclerosis Risk in Communities (ARIC) Study visit 5 (2011–2013) underwent 2 standardized visits, 4–8 weeks apart. Trained technicians obtained 2 PWV measurements at each visit using the VP-1000 Plus system. We calculated the intraclass correlation coefficient (ICC), SE of measurement, and minimal detectable change (MDC95; 95% confidence interval) and difference (MDD). RESULTS The ICCs and 95% confidence intervals (95% CIs) were 0.70 (0.59, 0.81) for cfPWV, 0.84 (0.78, 0.90) for baPWV, and 0.69 (0.59, 0.79) for faPWV. The MDC95 between repeat measures within an individual was 411.0cm/s for cfPWV, 370.6cm/s for baPWV, and 301.4cm/s for faPWV. The MDD for 2 independent samples of 100 per group was 139.3cm/s for cfPWV, 172.3cm/s for baPWV, and 100.4cm/s for faPWV. CONCLUSIONS Repeatability was acceptable for all PWV measures in a multicenter, population-based study of older adults and supports its use in epidemiologic studies. Quantifying PWV measurement variation is critical for applications to risk assessment and stratification and eventual translation to clinical practice. PMID:26232036

Uncertainty, variability, and earthquake physics in ground‐motion prediction equations

USGS Publications Warehouse

Baltay, Annemarie S.; Hanks, Thomas C.; Abrahamson, Norm A.

2017-01-01

Residuals between ground‐motion data and ground‐motion prediction equations (GMPEs) can be decomposed into terms representing earthquake source, path, and site effects. These terms can be cast in terms of repeatable (epistemic) residuals and the random (aleatory) components. Identifying the repeatable residuals leads to a GMPE with reduced uncertainty for a specific source, site, or path location, which in turn can yield a lower hazard level at small probabilities of exceedance. We illustrate a schematic framework for this residual partitioning with a dataset from the ANZA network, which straddles the central San Jacinto fault in southern California. The dataset consists of more than 3200 1.15≤M≤3 earthquakes and their peak ground accelerations (PGAs), recorded at close distances (R≤20  km). We construct a small‐magnitude GMPE for these PGA data, incorporating VS30 site conditions and geometrical spreading. Identification and removal of the repeatable source, path, and site terms yield an overall reduction in the standard deviation from 0.97 (in ln units) to 0.44, for a nonergodic assumption, that is, for a single‐source location, single site, and single path. We give examples of relationships between independent seismological observables and the repeatable terms. We find a correlation between location‐based source terms and stress drops in the San Jacinto fault zone region; an explanation of the site term as a function of kappa, the near‐site attenuation parameter; and a suggestion that the path component can be related directly to elastic structure. These correlations allow the repeatable source location, site, and path terms to be determined a priori using independent geophysical relationships. Those terms could be incorporated into location‐specific GMPEs for more accurate and precise ground‐motion prediction.

Molecular epidemiology of 58 new African human T-cell leukemia virus type 1 (HTLV-1) strains: identification of a new and distinct HTLV-1 molecular subtype in Central Africa and in Pygmies.

PubMed Central

Mahieux, R; Ibrahim, F; Mauclere, P; Herve, V; Michel, P; Tekaia, F; Chappey, C; Garin, B; Van Der Ryst, E; Guillemain, B; Ledru, E; Delaporte, E; de The, G; Gessain, A

1997-01-01

To gain new insights on the origin, evolution, and modes of dissemination of human T-cell leukemia virus type I (HTLV-1), we performed a molecular analysis of 58 new African HTLV-1 strains (18 from West Africa, 36 from Central Africa, and 4 from South Africa) originating from 13 countries. Of particular interest were eight strains from Pygmies of remote areas of Cameroon and the Central African Republic (CAR), considered to be the oldest inhabitants of these regions. Eight long-term activated T-cell lines producing HTLV-1 gag and env antigens were established from peripheral blood mononuclear cell cultures of HTLV-1 seropositive individuals, including three from Pygmies. A fragment of the env gene encompassing most of the gp21 transmembrane region was sequenced for the 58 new strains, while the complete long terminal repeat (LTR) region was sequenced for 9 strains, including 4 from Pygmies. Comparative sequence analyses and phylogenetic studies performed on both the env and LTR regions by the neighbor-joining and DNA parsimony methods demonstrated that all 22 strains from West and South Africa belong to the widespread cosmopolitan subtype (also called HTLV-1 subtype A). Within or alongside the previously described Zairian cluster (HTLV-1 subtype B), we discovered a number of new HTLV-1 variants forming different subgroups corresponding mainly to the geographical origins of the infected persons, Cameroon, Gabon, and Zaire. Six of the eight Pygmy strains clustered together within this Central African subtype, suggesting a common origin. Furthermore, three new strains (two originating from Pygmies from Cameroon and the CAR, respectively, and one from a Gabonese individual) were particularly divergent and formed a distinct new phylogenetic cluster, characterized by specific mutations and occupying in most analyses a unique phylogenetic position between the large Central African genotype (HTLV-1 subtype B) and the Melanesian subtype (HTLV-1 subtype C). We have tentatively named this new HTLV-1 genotype HTLV-1 subtype D. While the HTLV-1 subtype D strains were not closely related to any known African strain of simian T-cell leukemia virus type 1 (STLV-1), other Pygmy strains and some of the new Cameroonian and Gabonese HTLV-1 strains were very similar (>98% nucleotide identity) to chimpanzee STLV-1 strains, reinforcing the hypothesis of interspecies transmission between humans and monkeys in Central Africa. PMID:8995656

19 CFR 10.619 - Repeated false or unsupported preference claims.

Code of Federal Regulations, 2010 CFR

2010-04-01

... Republic-Central America-United States Free Trade Agreement Origin Verifications and Determinations § 10... 19 Customs Duties 1 2010-04-01 2010-04-01 false Repeated false or unsupported preference claims. 10.619 Section 10.619 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND...

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

PubMed Central

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

2005-01-01

Expansion of “low complex” repeats of amino acids such as glutamine (Poly-Q) is associated with protein misfolding and the development of degenerative diseases such as Huntington's disease. The mechanism by which such regions promote misfolding remains controversial, the function of many repeat-containing proteins (RCPs) remains obscure, and the role (if any) of repeat regions remains to be determined. Here, a Web-accessible database of RCPs is presented. The distribution and evolution of RCPs that contain homopeptide repeats tracts are considered, and the existence of functional patterns investigated. Generally, it is found that while polyamino acid repeats are extremely rare in prokaryotes, several eukaryote putative homologs of prokaryote RCP—involved in important housekeeping processes—retain the repetitive region, suggesting an ancient origin for certain repeats. Within eukarya, the most common uninterrupted amino acid repeats are glutamine, asparagines, and alanine. Interestingly, while poly-Q repeats are found in vertebrates and nonvertebrates, poly-N repeats are only common in more primitive nonvertebrate organisms, such as insects and nematodes. We have assigned function to eukaryote RCPs using Online Mendelian Inheritance in Man (OMIM), the Human Reference Protein Database (HRPD), FlyBase, and Wormpep. Prokaryote RCPs were annotated using BLASTp searches and Gene Ontology. These data reveal that the majority of RCPs are involved in processes that require the assembly of large, multiprotein complexes, such as transcription and signaling. PMID:15805494

Heterochromatin characterization and ribosomal gene location in two monotypic genera of bloodsucker bugs (Cimicidae, Heteroptera) with holokinetic chromosomes and achiasmatic male meiosis.

PubMed

Poggio, M G; Di Iorio, O; Turienzo, P; Papeschi, A G; Bressa, M J

2014-12-01

Members of the family Cimicidae (Heteroptera: Cimicomorpha) are temporary bloodsuckers on birds and bats as primary hosts and humans as secondary hosts. Acanthocrios furnarii (2n=12=10+XY, male) and Psitticimex uritui (2n=31=28+X1X2Y, male) are two monotypic genera of the subfamily Haematosiphoninae, which have achiasmatic male meiosis of collochore type. Here, we examined chromatin organization and constitution of cimicid holokinetic chromosomes by determining the amount, composition and distribution of constitutive heterochromatin, and number and location of nucleolus organizer regions (NORs) in both species. Results showed that these two bloodsucker bugs possess high heterochromatin content and have an achiasmatic male meiosis, in which three regions can be differentiated in each autosomal bivalent: (i) terminal heterochromatic regions in repulsion; (ii) a central region, where the homologous chromosomes are located parallel but without contact between them; and (iii) small areas within the central region, where collochores are detected. Acanthocrios furnarii presented a single NOR on an autosomal pair, whereas P. uritui presented two NORs, one on an autosomal pair and the other on a sex chromosome. All NORs were found to be associated with CMA3 bright bands, indicating that the whole rDNA repeating unit is rich in G+C base pairs. Based on the variations in the diploid autosomal number, the presence of simple and multiple sex chromosome systems, and the number and location of 18S rDNA loci in the two Cimicidae species studied, we might infer that rDNA clusters and genome are highly dynamic among the representatives of this family.

Global Trends in Adolescent Fertility, 1990-2012, in Relation to National Wealth, Income Inequalities, and Educational Expenditures.

PubMed

Santelli, John S; Song, Xiaoyu; Garbers, Samantha; Sharma, Vinit; Viner, Russell M

2017-02-01

National wealth, income inequalities, and expenditures on education can profoundly influence the health of a nation's women, children, and adolescents. We explored the association of trends in national socioeconomic status (SES) indicators with trends in adolescent birth rates (ABRs), by nation and region. An ecologic research design was employed using national-level data from the World Bank on birth rates per 1,000 women aged 15-19 years, national wealth (per capita gross domestic product or GDP), income inequality (Gini index), and expenditures on education as a percentage of GDP (EduExp). Data were available for 142 countries and seven regions for 1990-2012. Multiple linear regression for repeated measures with generalized estimating equations was used to examine independent associations. ABRs in 2012 varied >200-fold-with the highest rates in Sub-Saharan Africa and lowest rates in the Western Europe/Central Asia region. The median national ABR fell 40% from 72.4/1,000 in 1990 to 43.6/1,000 in 2012. The largest regional declines in ABR occurred in South Asia (70%), Europe/Central Asia (63%), and the Middle East/North Africa (53%)-regions with lower income inequality. In multivariable analyses considering change over time, ABRs were negatively associated with GDP and EduExp and positively associated with greater income inequality. ABRs have declined globally since 1990. Declines closely followed rising socioeconomic status and were greater where income inequalities were lower in 1990. Reducing poverty and income inequalities and increasing investments in education should be essential components of national policies to prevent adolescent childbearing. Copyright © 2016 Society for Adolescent Health and Medicine. Published by Elsevier Inc. All rights reserved.

Unc-45 Mutations in Caenorhabditis elegans Implicate a CRO1/She4p-like Domain in Myosin Assembly

PubMed Central

Barral, José M.; Bauer, Christopher C.; Ortiz, Irving; Epstein, Henry F.

1998-01-01

The Caenorhabditis elegans unc-45 locus has been proposed to encode a protein machine for myosin assembly. The UNC-45 protein is predicted to contain an NH2-terminal domain with three tetratricopeptide repeat motifs, a unique central region, and a COOH-terminal domain homologous to CRO1 and She4p. CRO1 and She4p are fungal proteins required for the segregation of other molecules in budding, endocytosis, and septation. Three mutations that lead to temperature-sensitive (ts) alleles have been localized to conserved residues within the CRO1/She4p-like domain, and two lethal alleles were found to result from stop codon mutations in the central region that would prevent translation of the COOH-terminal domain. Electron microscopy shows that thick filament accumulation in vivo is decreased by ∼50% in the CB286 ts mutant grown at the restrictive temperature. The thick filaments that assemble have abnormal structure. Immunofluorescence and immunoelectron microscopy show that myosins A and B are scrambled, in contrast to their assembly into distinct regions at the permissive temperature and in wild type. This abnormal structure correlates with the high degree of instability of the filaments in vitro as reflected by their extremely low yields and shortened lengths upon isolation. These results implicate the UNC-45 CRO1/She4p-like region in the assembly of myosin isoforms in C. elegans and suggest a possible common mechanism for the function of this UCS (UNC-45/CRO1/She4p) protein family. PMID:9832550

Two synthetic Sp1-binding sites functionally substitute for the 21-base-pair repeat region to activate simian virus 40 growth in CV-1 cells.

PubMed Central

Lednicky, J; Folk, W R

1992-01-01

The 21-bp repeat region of simian virus 40 (SV40) activates viral transcription and DNA replication and contains binding sites for many cellular proteins, including Sp1, LSF, ETF, Ap2, Ap4, GT-1B, H16, and p53, and for the SV40 large tumor antigen. We have attempted to reduce the complexity of this region while maintaining its growth-promoting capacity. Deletion of the 21-bp repeat region from the SV40 genome delays the expression of viral early proteins and DNA replication and reduces virus production in CV-1 cells. Replacement of the 21-bp repeat region with two copies of DNA sequence motifs bound with high affinities by Sp1 promotes SV40 growth in CV-1 cells to nearly wild-type levels, but substitution by motifs bound less avidly by Sp1 or bound by other activator proteins does not restore growth. This indicates that Sp1 or a protein with similar sequence specificity is primarily responsible for the function of the 21-bp repeat region. We speculate about how Sp1 activates both SV40 transcription and DNA replication. Images PMID:1328672

The effect of tracking network configuration on Global Positioning System (GPS) baseline estimates for the CASA (Central and South America) Uno experiment

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

Wolf, S.K.; Dixon, T.H.; Freymueller, J.T.

1990-04-01

Geodetic monitoring of subduction of the Nazca and Cocos plates is a goal of the CASA (Central and South America) Global Positioning System (GPS) experiments, and requires measurement of intersite distances (baselines) in excess of 500 km. The major error source in these measurements is the uncertainty in the position of the GPS satellites at the time of observation. A key aspect of the first CASA experiment, CASA Uno, was the initiation of a global network of tracking stations minimize these errors. The authors studied the effect of using various subsets of this global tracking network on long (>100 km)more » baseline estimates in the CASA region. Best results were obtained with a global tracking network consisting of three U.S. fiducial stations, two sites in the southwest pacific and two sites in Europe. Relative to smaller subsets, this global network improved baseline repeatability, resolution of carrier phase cycle ambiguities, and formal errors of the orbit estimates. Describing baseline repeatability for horizontal components as {sigma}=(a{sup 2} + b{sup 2}L{sup 2}){sup 1/2} where L is baseline length, the authors obtained a = 4 and 9 mm and b = 2.8{times}10{sup {minus}8} and 2.3{times}10{sup {minus}8} for north and east components, respectively, on CASA baselines up to 1,000 km in length with this global network.« less

Long term monitoring of the micro-seismicity along the Main Marmara Fault, Turkey using template matching

NASA Astrophysics Data System (ADS)

Matrullo, Emanuela; Lengliné, Olivier; Schmittbuhl, Jean; Karabulut, Hayrullah; Bouchon, Michel

2017-04-01

The Main Marmara Fault (MMF) represents a 150 km un-ruptured segment of the North Anatolian Fault located below the Marmara Sea. It poses a significant hazard for the large cities surrounding the region and in particular for the megalopolis of Istanbul. The seismic activity has been continuously monitored since 2007 by various seismic networks. For this purpose it represents an extraordinary natural laboratory to study in details the whole seismicity bringing insights into the geometry of the faults systems at depth and mechanical properties at various space-time scales. Waveform similarity-based analysis is performed on the continuous recordings to construct a refined catalog of earthquakes from 2009 to 2014. High-resolution relocation was applied using the double-difference algorithm, using cross-correlation differential travel-time data. Seismic moment magnitudes (Mw) have been computed combining the inversion of earthquake S-wave displacement spectra for the larger events and the estimation of the relative size of multiplets using the singular value decomposition (SVD) thanks the highly coherent waveforms. The obtained catalog of seismicity includes more than 15,000 events. The seismicity strongly varying along the strike and depth exhibits a complex structure that confirms the segmentation of the fault with different mechanical behavior (Schmittbuhl et al., GGG, 2016). In the central part of the Marmara Sea, seismicity is poor and scattered. To the east, in the Cinarcick basin, along the MMF, the seismicity is mainly located around 8-15 km in depth, except at both ends of this basin where the seismicity extends vertically up to surface. In the Yalova and Gemlik region (to the east not on the MMF) the seismicity is distributed over a wide range of depth (from surface to 15 km deep) and is characterized by several clusters vertically elongated. The spatio-temporal evolution of earthquake sequences, which repeatedly occur in specific sub-areas, and the seismic moment release reveals mainly typically two kinds of seismicity dynamics: swarm like episodes and mainshock-aftershock sequences. Similar features in the seismicity distribution are observed to the west, in the Tekirdag and Central Basin. These preliminary evidences, combined with the recent analysis on several long-lasting strike-slip seismic repeaters occurring below the Central Basin (Schmittbuhl et al., GRL, 2016) indicate the presence of both locked and creeping portions of the MMF. In the light of the accurate and extensive observations, several open questions emerge: What are the mechanisms responsible of these repeating earthquakes and of the earthquake swarms? What is the influence and the role of fluids in the generation of seismicity.

Humpback whale song on the Southern Ocean feeding grounds: implications for cultural transmission.

PubMed

Garland, Ellen C; Gedamke, Jason; Rekdahl, Melinda L; Noad, Michael J; Garrigue, Claire; Gales, Nick

2013-01-01

Male humpback whales produce a long, complex, and stereotyped song on low-latitude breeding grounds; they also sing while migrating to and from these locations, and occasionally in high-latitude summer feeding areas. All males in a population sing the current version of the constantly evolving display and, within an ocean basin, populations sing similar songs; however, this sharing can be complex. In the western and central South Pacific region there is repeated cultural transmission of song types from eastern Australia to other populations eastward. Song sharing is hypothesized to occur through several possible mechanisms. Here, we present the first example of feeding ground song from the Southern Ocean Antarctic Area V and compare it to song from the two closest breeding populations. The early 2010 song contained at least four distinct themes; these matched four themes from the eastern Australian 2009 song, and the same four themes from the New Caledonian 2010 song recorded later in the year. This provides evidence for at least one of the hypothesized mechanisms of song transmission between these two populations, singing while on shared summer feeding grounds. In addition, the feeding grounds may provide a point of acoustic contact to allow the rapid horizontal cultural transmission of song within the western and central South Pacific region and the wider Southern Ocean.

Observations of seasonal and diurnal glacier velocities at Mount Rainier, Washington using terrestrial radar interferometry

NASA Astrophysics Data System (ADS)

Allstadt, K. E.; Shean, D. E.; Campbell, A.; Fahnestock, M.; Malone, S. D.

2015-07-01

We present spatially continuous velocity maps using repeat terrestrial radar interferometry (TRI) measurements to examine seasonal and diurnal dynamics of alpine glaciers at Mount Rainier, Washington. We show that the Nisqually and Emmons glaciers have small slope-parallel velocities near the summit (< 0.2 m day-1), high velocities over their upper and central regions (1.0-1.5 m day-1), and stagnant debris-covered regions near the terminus (< 0.05 m day-1). Velocity uncertainties are as low as ±0.02-0.08 m day-1. We document a large seasonal velocity decrease of 0.2-0.7 m day-1 (-25 to -50 %) from July to November for most of the Nisqually glacier, excluding the icefall, suggesting significant seasonal subglacial water storage under most of the glacier. We did not detect diurnal variability above the noise level. Preliminary 2-D ice flow modeling using TRI velocities suggests that sliding accounts for roughly 91 and 99 % of the July velocity field for the Emmons and Nisqually glaciers, respectively. We validate our observations against recent in situ velocity measurements and examine the long-term evolution of Nisqually glacier dynamics through comparisons with historical velocity data. This study shows that repeat TRI measurements with > 10 km range can be used to investigate spatial and temporal variability of alpine glacier dynamics over large areas, including hazardous and inaccessible areas.

Sperm Bindin Divergence under Sexual Selection and Concerted Evolution in Sea Stars.

PubMed

Patiño, Susana; Keever, Carson C; Sunday, Jennifer M; Popovic, Iva; Byrne, Maria; Hart, Michael W

2016-08-01

Selection associated with competition among males or sexual conflict between mates can create positive selection for high rates of molecular evolution of gamete recognition genes and lead to reproductive isolation between species. We analyzed coding sequence and repetitive domain variation in the gene encoding the sperm acrosomal protein bindin in 13 diverse sea star species. We found that bindin has a conserved coding sequence domain structure in all 13 species, with several repeated motifs in a large central region that is similar among all sea stars in organization but highly divergent among genera in nucleotide and predicted amino acid sequence. More bindin codons and lineages showed positive selection for high relative rates of amino acid substitution in genera with gonochoric outcrossing adults (and greater expected strength of sexual selection) than in selfing hermaphrodites. That difference is consistent with the expectation that selfing (a highly derived mating system) may moderate the strength of sexual selection and limit the accumulation of bindin amino acid differences. The results implicate both positive selection on single codons and concerted evolution within the repetitive region in bindin divergence, and suggest that both single amino acid differences and repeat differences may affect sperm-egg binding and reproductive compatibility. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

[Transcription map of the 13q14 region, frequently deleted in B-cell chronic lymphocytic leukemia patients].

PubMed

Tiazhelova, T V; Ivanov, D V; Makeeva, N V; Kapanadze, B I; Nikitin, E A; Semov, A B; Sangfeldt, O; Grander, D; Vorob'ev, A I; Einhorn, S; Iankovskiĭ, N K; Baranova, A V

2001-11-01

Deletions in the region located between the STS markers D13S1168 and D13S25 on chromosome 13 are the most frequent genomic changes in patients with B-cell chronic lymphocytic leukemia (B-CLL). After sequencing of this region, two novel candidate genes were identified: C13orf1 (chromosome 13 open reading frame 1) and PLCC (putative large CLL candidate). Analysis of the repeat distribution revealed two subregions differing in composition of repetitious DNA and gene organization. The interval D13S1168-D13S319 contains 131 Alu repeats accounting for 24.8% of its length, whereas the interval GCT16C05-D13S25, which is no more than 180 kb away from the former one is extremely poor in Alu repeats (4.1% of the total length). Both intervals contain almost the same amount of the LINE-type repeats L1 and L2 (20.3 and 21.24%, respectively). In the chromosomal region studied, 29 Alu repeats were found to belong to the evolutionary young subfamily Y, which is still capable of amplifying. A considerable proportion of repeats of this type with similar nucleotide sequences may contribute to the recombinational activity of the chromosomal region 13q14.3, which is responsible for its rearrangements in some tumors in humans.

Hypothesis: a role for EBV-induced molecular mimicry in Parkinson's disease.

PubMed

Woulfe, John M; Gray, Madison T; Gray, Douglas A; Munoz, David G; Middeldorp, Jaap M

2014-07-01

Current concepts regarding the pathogenesis of Parkinson's disease support a model whereby environmental factors conspire with a permissive genetic background to initiate the disease. The identity of the responsible environmental trigger has remained elusive. There is incontrovertible evidence that aggregation of the neuronal protein alpha-synuclein is central to disease pathogenesis. A novel hypothesis of Parkinson's pathogenesis, articulated by Braak and colleagues, implicates a pathogen acting in the olfactory mucosa and gastrointestinal tract as the inciting agent. In this point-of-view article, we hypothesize that α-synuclein aggregation in Parkinson's disease is an Epstein-Barr virus (EBV)-induced autoimmune phenomenon. Specifically, we have shown evidence for molecular mimicry between the C-terminal region of α-synuclein and a repeat region in the latent membrane protein 1 encoded by EBV. We hypothesize that, in genetically-susceptible individuals, anti-EBV latent membrane protein antibodies targeting the critical repeat region cross react with the homologous epitope on α-synuclein and induce its oligomerization. Consistent with the Braak's proposed pattern of spread, we contend that axon terminals in the lamina propria of the gut are among the initial targets, with subsequent spread of pathology to the CNS. While at this time, we can only provide evidence from the literature and preliminary findings from our own laboratory, we hope that our hypothesis will stimulate the development of tractable experimental systems that can be exploited to test it. Further support for an EBV-induced immune pathogenesis for Parkinson's disease could have profound therapeutic implications. Copyright © 2014 Elsevier Ltd. All rights reserved.

Tandemly repeated sequences in mtDNA control region of whitefish, Coregonus lavaretus.

PubMed

Brzuzan, P

2000-06-01

Length variation of the mitochondrial DNA control region was observed with PCR amplification of a sample of 138 whitefish (Coregonus lavaretus). Nucleotide sequences of representative PCR products showed that the variation was due to the presence of an approximately 100-bp motif tandemly repeated two, three, or five times in the region between the conserved sequence block-3 (CSB-3) and the gene for phenylalanine tRNA. This is the first report on the tandem array composed of long repeat units in mitochondrial DNA of salmonids.

IFRD1 Is a Candidate Gene for SMNA on Chromosome 7q22-q23

PubMed Central

Brkanac, Zoran; Spencer, David; Shendure, Jay; Robertson, Peggy D.; Matsushita, Mark; Vu, Tiffany; Bird, Thomas D.; Olson, Maynard V.; Raskind, Wendy H.

2009-01-01

We have established strong linkage evidence that supports mapping autosomal-dominant sensory/motor neuropathy with ataxia (SMNA) to chromosome 7q22-q32. SMNA is a rare neurological disorder whose phenotype encompasses both the central and the peripheral nervous system. In order to identify a gene responsible for SMNA, we have undertaken a comprehensive genomic evaluation of the region of linkage, including evaluation for repeat expansion and small deletions or duplications, capillary sequencing of candidate genes, and massively parallel sequencing of all coding exons. We excluded repeat expansion and small deletions or duplications as causative, and through microarray-based hybrid capture and massively parallel short-read sequencing, we identified a nonsynonymous variant in the human interferon-related developmental regulator gene 1 (IFRD1) as a disease-causing candidate. Sequence conservation, animal models, and protein structure evaluation support the involvement of IFRD1 in SMNA. Mutation analysis of IFRD1 in additional patients with similar phenotypes is needed for demonstration of causality and further evaluation of its importance in neurological diseases. PMID:19409521

Evolution of vulnerability of communities facing repeated hazards

PubMed Central

Guikema, Seth D.; Zhu, Laiyin; Igusa, Takeru

2017-01-01

The decisions that individuals make when recovering from and adapting to repeated hazards affect a region’s vulnerability in future hazards. As such, community vulnerability is not a static property but rather a dynamic property dependent on behavioral responses to repeated hazards and damage. This paper is the first of its kind to build a framework that addresses the complex interactions between repeated hazards, regional damage, mitigation decisions, and community vulnerability. The framework enables researchers and regional planners to visualize and quantify how a community could evolve over time in response to repeated hazards under various behavioral scenarios. An illustrative example using parcel-level data from Anne Arundel County, Maryland—a county that experiences fairly frequent hurricanes—is presented to illustrate the methodology and to demonstrate how the interplay between individual choices and regional vulnerability is affected by the region’s hurricane experience. PMID:28953893

Central Engine Memory of Gamma-Ray Bursts and Soft Gamma-Ray Repeaters

NASA Astrophysics Data System (ADS)

Zhang, Bin-Bin; Zhang, Bing; Castro-Tirado, Alberto J.

2016-04-01

Gamma-ray bursts (GRBs) are bursts of γ-rays generated from relativistic jets launched from catastrophic events such as massive star core collapse or binary compact star coalescence. Previous studies suggested that GRB emission is erratic, with no noticeable memory in the central engine. Here we report a discovery that similar light curve patterns exist within individual bursts for at least some GRBs. Applying the Dynamic Time Warping method, we show that similarity of light curve patterns between pulses of a single burst or between the light curves of a GRB and its X-ray flare can be identified. This suggests that the central engine of at least some GRBs carries “memory” of its activities. We also show that the same technique can identify memory-like emission episodes in the flaring emission in soft gamma-ray repeaters (SGRs), which are believed to be Galactic, highly magnetized neutron stars named magnetars. Such a phenomenon challenges the standard black hole central engine models for GRBs, and suggest a common physical mechanism behind GRBs and SGRs, which points toward a magnetar central engine of GRBs.

Genetic dissection of the role of cannabinoid type-1 receptors in the emotional consequences of repeated social stress in mice.

PubMed

Dubreucq, Sarah; Matias, Isabelle; Cardinal, Pierre; Häring, Martin; Lutz, Beat; Marsicano, Giovanni; Chaouloff, Francis

2012-07-01

The endocannabinoid system (ECS) tightly controls emotional responses to acute aversive stimuli. Repeated stress alters ECS activity but the role played by the ECS in the emotional consequences of repeated stress has not been investigated in detail. This study used social defeat stress, together with pharmacology and genetics to examine the role of cannabinoid type-1 (CB(1)) receptors on repeated stress-induced emotional alterations. Seven daily social defeat sessions increased water (but not food) intake, sucrose preference, anxiety, cued fear expression, and adrenal weight in C57BL/6N mice. The first and the last social stress sessions triggered immediate brain region-dependent changes in the concentrations of the principal endocannabinoids anandamide and 2-arachidonoylglycerol. Pretreatment before each of the seven stress sessions with the CB(1) receptor antagonist rimonabant prolonged freezing responses of stressed mice during cued fear recall tests. Repeated social stress abolished the increased fear expression displayed by constitutive CB(1) receptor-deficient mice. The use of mutant mice lacking CB(1) receptors from cortical glutamatergic neurons or from GABAergic neurons indicated that it is the absence of the former CB(1) receptor population that is responsible for the fear responses in socially stressed CB(1) mutant mice. In addition, stress-induced hypolocomotor reactivity was amplified by the absence of CB(1) receptors from GABAergic neurons. Mutant mice lacking CB(1) receptors from serotonergic neurons displayed a higher anxiety but decreased cued fear expression than their wild-type controls. These mutant mice failed to show social stress-elicited increased sucrose preference. This study shows that (i) release of endocannabinoids during stress exposure impedes stress-elicited amplification of cued fear behavior, (ii) social stress opposes the increased fear expression and delayed between-session extinction because of the absence of CB(1) receptors from cortical glutamatergic neurons, and (iii) CB(1) receptors on central serotonergic neurons are involved in the sweet consumption response to repeated stress.

Genetic Dissection of the Role of Cannabinoid Type-1 Receptors in the Emotional Consequences of Repeated Social Stress in Mice

PubMed Central

Dubreucq, Sarah; Matias, Isabelle; Cardinal, Pierre; Häring, Martin; Lutz, Beat; Marsicano, Giovanni; Chaouloff, Francis

2012-01-01

The endocannabinoid system (ECS) tightly controls emotional responses to acute aversive stimuli. Repeated stress alters ECS activity but the role played by the ECS in the emotional consequences of repeated stress has not been investigated in detail. This study used social defeat stress, together with pharmacology and genetics to examine the role of cannabinoid type-1 (CB1) receptors on repeated stress-induced emotional alterations. Seven daily social defeat sessions increased water (but not food) intake, sucrose preference, anxiety, cued fear expression, and adrenal weight in C57BL/6N mice. The first and the last social stress sessions triggered immediate brain region-dependent changes in the concentrations of the principal endocannabinoids anandamide and 2-arachidonoylglycerol. Pretreatment before each of the seven stress sessions with the CB1 receptor antagonist rimonabant prolonged freezing responses of stressed mice during cued fear recall tests. Repeated social stress abolished the increased fear expression displayed by constitutive CB1 receptor-deficient mice. The use of mutant mice lacking CB1 receptors from cortical glutamatergic neurons or from GABAergic neurons indicated that it is the absence of the former CB1 receptor population that is responsible for the fear responses in socially stressed CB1 mutant mice. In addition, stress-induced hypolocomotor reactivity was amplified by the absence of CB1 receptors from GABAergic neurons. Mutant mice lacking CB1 receptors from serotonergic neurons displayed a higher anxiety but decreased cued fear expression than their wild-type controls. These mutant mice failed to show social stress-elicited increased sucrose preference. This study shows that (i) release of endocannabinoids during stress exposure impedes stress-elicited amplification of cued fear behavior, (ii) social stress opposes the increased fear expression and delayed between-session extinction because of the absence of CB1 receptors from cortical glutamatergic neurons, and (iii) CB1 receptors on central serotonergic neurons are involved in the sweet consumption response to repeated stress. PMID:22434220

SSR allelic variation in almond (Prunus dulcis Mill.).

PubMed

Xie, Hua; Sui, Yi; Chang, Feng-Qi; Xu, Yong; Ma, Rong-Cai

2006-01-01

Sixteen SSR markers including eight EST-SSR and eight genomic SSRs were used for genetic diversity analysis of 23 Chinese and 15 international almond cultivars. EST- and genomic SSR markers previously reported in species of Prunus, mainly peach, proved to be useful for almond genetic analysis. DNA sequences of 117 alleles of six of the 16 SSR loci were analysed to reveal sequence variation among the 38 almond accessions. For the four SSR loci with AG/CT repeats, no insertions or deletions were observed in the flanking regions of the 98 alleles sequenced. Allelic size variation of these loci resulted exclusively from differences in the structures of repeat motifs, which involved interruptions or occurrences of new motif repeats in addition to varying number of AG/CT repeats. Some alleles had a high number of uninterrupted repeat motifs, indicating that SSR mutational patterns differ among alleles at a given SSR locus within the almond species. Allelic homoplasy was observed in the SSR loci because of base substitutions, interruptions or compound repeat motifs. Substitutions in the repeat regions were found at two SSR loci, suggesting that point mutations operate on SSRs and hinder the further SSR expansion by introducing repeat interruptions to stabilize SSR loci. Furthermore, it was shown that some potential point mutations in the flanking regions are linked with new SSR repeat motif variation in almond and peach.

A novel species-specific tandem repeat DNA family from Sinapis arvensis: detection of telomere-like sequences.

PubMed

Kapila, R; Das, S; Srivastava, P S; Lakshmikumaran, M

1996-08-01

DNA sequences representing a tandemly repeated DNA family of the Sinapis arvensis genome were cloned and characterized. The 700-bp tandem repeat family is represented by two clones, pSA35 and pSA52, which are 697 and 709 bp in length, respectively. Dot matrix analysis of the sequences indicates the presence of repeated elements within each monomeric unit. Sequence analysis of the repetitive region of clones pSA35 and pSA52 shows that there are several copies of a 7-bp repeat element organized in tandem. The consensus sequence of this repeat element is 5'-TTTAGGG-3'. These elements are highly mutated and the difference in length between the two clones is due to different copy numbers of these elements. The repetitive region of clone pSA35 has 26 copies of the element TTTAGGG, whereas clone pSA52 has 28 copies. The repetitive region in both clones is flanked on either side by inverted repeats that may be footprints of a transposition event. Sequence comparison indicates that the element TTTAGGG is identical to telomeric repeats present in Arabidopsis, maize, tomato, and other plants. However, Bal31 digestion kinetics indicates non-telomeric localization of the 700-bp tandem repeats. The clones represent a novel repeat family as (i) they contain telomere-like motifs as subrepeats within each unit; and (ii) they do not hybridize to related crucifers and are species-specific in nature.

ATM activation and its recruitment to damaged DNA require binding to the C terminus of Nbs1.

PubMed

You, Zhongsheng; Chahwan, Charly; Bailis, Julie; Hunter, Tony; Russell, Paul

2005-07-01

ATM has a central role in controlling the cellular responses to DNA damage. It and other phosphoinositide 3-kinase-related kinases (PIKKs) have giant helical HEAT repeat domains in their amino-terminal regions. The functions of these domains in PIKKs are not well understood. ATM activation in response to DNA damage appears to be regulated by the Mre11-Rad50-Nbs1 (MRN) complex, although the exact functional relationship between the MRN complex and ATM is uncertain. Here we show that two pairs of HEAT repeats in fission yeast ATM (Tel1) interact with an FXF/Y motif at the C terminus of Nbs1. This interaction resembles nucleoporin FXFG motif binding to HEAT repeats in importin-beta. Budding yeast Nbs1 (Xrs2) appears to have two FXF/Y motifs that interact with Tel1 (ATM). In Xenopus egg extracts, the C terminus of Nbs1 recruits ATM to damaged DNA, where it is subsequently autophosphorylated. This interaction is essential for ATM activation. A C-terminal 147-amino-acid fragment of Nbs1 that has the Mre11- and ATM-binding domains can restore ATM activation in an Nbs1-depleted extract. We conclude that an interaction between specific HEAT repeats in ATM and the C-terminal FXF/Y domain of Nbs1 is essential for ATM activation. We propose that conformational changes in the MRN complex that occur upon binding to damaged DNA are transmitted through the FXF/Y-HEAT interface to activate ATM. This interaction also retains active ATM at sites of DNA damage.

Repeating Earthquake and Nonvolcanic Tremor Observations of Aseismic Deep Fault Transients in Central California.

NASA Astrophysics Data System (ADS)

Nadeau, R. M.; Traer, M.; Guilhem, A.

2005-12-01

Seismic indicators of fault zone deformation can complement geodetic measurements by providing information on aseismic transient deformation: 1) from deep within the fault zone, 2) on a regional scale, 3) with intermediate temporal resolution (weeks to months) and 4) that spans over 2 decades (1984 to early 2005), including pre- GPS and INSAR coverage. Along the San Andreas Fault (SAF) in central California, two types of seismic indicators are proving to be particularly useful for providing information on deep fault zone deformation. The first, characteristically repeating microearthquakes, provide long-term coverage (decades) on the evolution of aseismic fault slip rates at seismogenic depths along a large (~175 km) stretch of the SAF between the rupture zones of the ~M8 1906 San Francisco and 1857 Fort Tejon earthquakes. In Cascadia and Japan the second type of seismic indicator, nonvolcanic tremors, have shown a remarkable correlation between their activity rates and GPS and tiltmeter measurements of transient deformation in the deep (sub-seismogenic) fault zone. This correlation suggests that tremor rate changes and deep transient deformation are intimately related and that deformation associated with the tremor activity may be stressing the seismogenic zone in both areas. Along the SAF, nonvolcanic tremors have only recently been discovered (i.e., in the Parkfield-Cholame area), and knowledge of their full spatial extent is still relatively limited. Nonetheless the observed temporal correlation between earthquake and tremor activity in this area is consistent with a model in which sub-seismogenic deformation and seismogenic zone stress changes are closely related. We present observations of deep aseismic transient deformation associated with the 28 September 2004, M6 Parkfield earthquake from both repeating earthquake and nonvolcanic tremor data. Also presented are updated deep fault slip rate estimates from prepeating quakes in the San Juan Bautista area with an assessment of their significance to previously reported quasi-periodic slip rate pulses and small to moderate magnitude (> M3.5) earthquake occurrence in the area.

Comparison of peripheral and central effects of single and repeated oral dose administrations of bilastine, a new H1 antihistamine: a dose-range study in healthy volunteers with hydroxyzine and placebo as control treatments.

PubMed

García-Gea, Consuelo; Martínez-Colomer, Joan; Antonijoan, Rosa M; Valiente, Román; Barbanoj, Manuel-José

2008-12-01

Peripheral anti-H1 and central nervous system (CNS) activities after single (day 1) and repeated (day 7) administrations of increasing doses of bilastine (BIL) were assessed in 20 healthy volunteers throughout a crossover, randomized, double-blind, placebo (PLA)-controlled study. Repeated doses of BIL 20, 40, or 80 mg and hydroxyzine 25 mg (HYD) as positive standard were administered on 7 consecutive days. Before and at several time points after drug intake, skin reactivity to the intradermal injection of histamine, objective tests of psychomotor performance, and subjective mood scales were evaluated. All active treatments led to a significant and similar reduction in the wheal reaction in relation to PLA after both the single (P < 0.001) and repeated administrations (P < 0.001). No delay was observed in the onset of its peripheral activity after the first dose of BIL as compared with HYD. No tolerance or sensitization was seen when comparing acute and repetitive assessments. Central nervous system effects showed that HYD induced the greatest psychomotor impairment (P < 0.05). Repeated HYD intake showed a lower number of significant alterations in comparison to acute administration. Bilastine 80 mg also showed some impairment (P < 0.05). Subjectively, the only active treatment that could not be differentiated from PLA was BIL 20 mg. Hydroxyzine 25 mg showed the greatest differentiation (P < 0.01). A clear dissociation between peripheral anti-H1 and CNS activity was found after BIL treatment. Significant and sustained peripheral H1-blocking effects were observed after both single and repeated administrations of the therapeutic dose of 20 mg BIL. The 40-mg dose of BIL produced subjective report of sedation, whereas unwanted objective CNS side effects were observed only with the 80-mg dose.

Fixation parameter test-retest repeatability of the worse eye in central field loss.

PubMed

Samet, Saba; Tarita-Nistor, Luminita; González, Esther G; Mandelcorn, Mark S; Mandelcorn, Efrem D; Steinbach, Martin J

2018-06-01

Patients with bilateral central field loss develop peripheral retinal loci (PRLs) in the functional eccentric retina. PRL characteristics and visual performance in the better-seeing eye (BE) of these patients have previously been reported. In this study, we determined the test-retest repeatability of fixation parameters, including fixation stability, PRL eccentricity, and PRL span in the worse-seeing eye (WE). Retrospective consecutive case series. Thirty-six patients with bilateral central field loss referred from the Toronto Western Hospital Retina Clinic, who had completed 2 consecutive fixation examinations on the same day. Fixation stability was recorded using the Nidek MP-1 microperimeter (Nidek Technologies Srl., Padova, Italy). For each fixation recording, the following parameters were retrieved: (i) 68.2% bivariate contour ellipse area (BCEA), (ii) PRL span (major and minor axes of the BCEA), (iii) PRL meridian (polar angle), and (iv) PRL eccentricity. Test-retest repeatability for each parameter was assessed using Bland-Altman plots to determine 95% limits of agreement. The mean difference between the fixation trial pairs and the 95% limits of agreement for fixation stability, PRL major axis, PRL minor axis, PRL meridian, and PRL eccentricity were 0.06 ± 0.47 log deg 2 , 0.05° ± 1.42°, 0.07° ± 0.63°, -0.44° ± 66.0°, and -0.23° ±1.56°, respectively. The fixation parameters in the WE showed robust repeatability, comparable to that of the BE as determined from previous studies. The WE's fixation repeatability should be considered in the interpretation of fixation outcome measures subsequent to treatment interventions. Crown Copyright © 2018. Published by Elsevier Inc. All rights reserved.

Slow Unlocking Processes Preceding the 2015 Mw 8.4 Illapel, Chile, Earthquake

NASA Astrophysics Data System (ADS)

Huang, Hui; Meng, Lingsen

2018-05-01

On 16 September 2015, the Mw 8.4 Illapel earthquake occurred in central Chile with no intense foreshock sequences documented in the regional earthquake catalog. Here we employ the matched-filter technique based on an enhanced template data set of previously catalogued events. We perform a continuous search over an 4-year period before the Illapel mainshock to recover the uncatalogued small events and repeating earthquakes. Repeating earthquakes are found both to the north and south of the mainshock rupture zone. To the south of the rupture zone, the seismicity and repeater-inferred aseismic slip progressively accelerate around the Illapel epicenter starting from 140 days before the mainshock. This may indicate an unlocking process involving the interplay of seismic and aseismic slip. The acceleration culminates in a M 5.3 event of low-angle thrust mechanism, which occurred 36 days before the Mw 8.4 mainshock. It is then followed by a relative quiescence in seismicity until the mainshock occurred. This quiescence might correspond to an intermediate period of stable slip before rupture initiation. In addition, to the north of the mainshock rupture area, the last aseismic-slip episode occurs within 175-95 days before the mainshock and accumulates the largest amount of slip in the observation period. The simultaneous occurrence of aseismic-slip transients over a large area is consistent with large-scale slow unlocking processes preceding the Illapel mainshock.

Inside the “African Cattle Complex”: Animal Burials in the Holocene Central Sahara

PubMed Central

di Lernia, Savino; Tafuri, Mary Anne; Gallinaro, Marina; Alhaique, Francesca; Balasse, Marie; Cavorsi, Lucia; Fullagar, Paul D.; Mercuri, Anna Maria; Monaco, Andrea; Perego, Alessandro; Zerboni, Andrea

2013-01-01

Cattle pastoralism is an important trait of African cultures. Ethnographic studies describe the central role played by domestic cattle within many societies, highlighting its social and ideological value well beyond its mere function as ‘walking larder’. Historical depth of this African legacy has been repeatedly assessed in an archaeological perspective, mostly emphasizing a continental vision. Nevertheless, in-depth site-specific studies, with a few exceptions, are lacking. Despite the long tradition of a multi-disciplinary approach to the analysis of pastoral systems in Africa, rarely do early and middle Holocene archaeological contexts feature in the same area the combination of settlement, ceremonial and rock art features so as to be multi-dimensionally explored: the Messak plateau in the Libyan central Sahara represents an outstanding exception. Known for its rich Pleistocene occupation and abundant Holocene rock art, the region, through our research, has also shown to preserve the material evidence of a complex ritual dated to the Middle Pastoral (6080–5120 BP or 5200–3800 BC). This was centred on the frequent deposition in stone monuments of disarticulated animal remains, mostly cattle. Animal burials are known also from other African contexts, but regional extent of the phenomenon, state of preservation of monuments, and associated rock art make the Messak case unique. GIS analysis, excavation data, radiocarbon dating, zooarchaeological and isotopic (Sr, C, O) analyses of animal remains, and botanical information are used to explore this highly formalized ritual and the lifeways of a pastoral community in the Holocene Sahara. PMID:23437260

Zooplankton communities and Bythotrephes longimanus in lakes of the montane region of the northern Alps

PubMed Central

Horváth, Zsófia; Vad, Csaba F.; Preiler, Christian; Birtel, Julia; Matthews, Blake; Ptáčníková, Radka; Ptáčník, Robert

2017-01-01

Abstract Lakes in the Alps represent a considerable fraction of nutrient-poor lakes in Central Europe, with unique biodiversity and ecosystem properties. Although some individual lakes are well studied, less knowledge is available on large-scale patterns essential to general understanding of their functioning. Here, we aimed to describe crustacean zooplankton communities (Cladocera, Copepoda) and identify their environmental drivers in the pelagic zone of 54 oligotrophic lakes in the montane region of the Alps (400–1200 m) in Austria, Germany, and Switzerland, covering a spatial scale of 650 km. Moreover, we aimed to provide data on the distribution and ecological requirements of the North American invader Bythotrephes longimanus in its Central European native range. Communities were mainly dominated by widespread species typical of lowland habitats, and only a few true specialists of oligotrophic alpine lakes were present. The most frequent taxa were the Daphnia longispina complex and Eudiaptomus gracilis, with 48 and 45 occurrences, respectively. Species richness decreased with altitude and increased with lake area. The main structuring factors of community composition were chlorophyll a concentration and depth, which drove an apparent separation of mesotrophic and oligotrophic communities. Bythotrephes had 13 occurrences, showing a preference for deep oligotrophic lakes. Its presence was not coupled with lower crustacean species richness, as was repeatedly observed in North America. Additionally, it frequently co-occurred with the other large predatory cladoceran, Leptodora kindtii. B. longimanus might be considered a truly montane species in Central Europe, given its absence in lowland and alpine lakes. PMID:28824797

Zooplankton communities and Bythotrephes longimanus in lakes of the montane region of the northern Alps

PubMed Central

Horváth, Zsófia; Vad, Csaba F.; Preiler, Christian; Birtel, Julia; Matthews, Blake; Ptáčníková, Radka; Ptacnik, Robert

2017-01-01

Lakes in the Alps represent a considerable fraction of nutrient-poor lakes in Central Europe, with unique biodiversity and ecosystem properties. Although some individual lakes are well-studied, less knowledge is available on large-scale patterns essential to generalise the understanding of their functioning. Here, we aimed to describe crustacean zooplankton communities (Cladocera, Copepoda) and identify their environmental drivers in the pelagic zone of 54 oligotrophic lakes in the montane region of the Alps (400–1200 m) in Austria, Germany, and Switzerland, covering a spatial scale of 650 km. Moreover, we aimed to provide data on the distribution and ecological requirements of the North American invader Bytotrephes longimanus in its Central European native range. Communities were mainly dominated by widespread species typical of lowland habitats, and only a few true specialists of oligotrophic alpine lakes were present. The most frequent taxa were the Daphnia longispina complex and Eudiaptomus gracilis, with 48 and 45 occurrences, respectively. Species richness decreased with altitude and increased with lake area. The main structuring factors of community composition were chlorophyll a concentration and depth, which drove an apparent separation of mesotrophic and oligotrophic communities. Bytotrephes had 13 occurrences, showing a preference for deep oligotrophic lakes. Its presence was not coupled with lower crustacean species richness as it was repeatedly observed in North America. Additionally, it frequently co-occurred with the other large predatory cladoceran, Leptodora kindtii. B. longimanus might be considered a truly montane species in Central Europe, given its absence in lowland and alpine lakes. PMID:28649318

Complete mitochondrial genome of the whiter-spotted flower chafer, Protaetia brevitarsis (Coleoptera: Scarabaeidae).

PubMed

Kim, Min Jee; Im, Hyun Hwak; Lee, Kwang Youll; Han, Yeon Soo; Kim, Iksoo

2014-06-01

Abstract The complete nucleotide sequences of the mitochondrial genome from the whiter-spotted flower chafer, Protaetia brevitarsis (Coleoptera: Scarabaeidae), was determined. The 20,319-bp long circular genome is the longest among completely sequenced Coleoptera. As is typical in animals, the P. brevitarsis genome consisted of two ribosomal RNAs, 22 transfer RNAs, 13 protein-coding genes and one A + T-rich region. Although the size of the coding genes was typical, the non-coding A + T-rich region was 5654 bp, which is the longest in insects. The extraordinary length of this region was composed of 28,117-bp tandem repeats and 782-bp tandem repeats. These repeat sequences were encompassed by three non-repeat sequences constituting 1804 bp.

Some tests of wet tropospheric calibration for the CASA Uno Global Positioning System experiment

NASA Technical Reports Server (NTRS)

Dixon, T. H.; Wolf, S. Kornreich

1990-01-01

Wet tropospheric path delay can be a major error source for Global Positioning System (GPS) geodetic experiments. Strategies for minimizing this error are investigted using data from CASA Uno, the first major GPS experiment in Central and South America, where wet path delays may be both high and variable. Wet path delay calibration using water vapor radiometers (WVRs) and residual delay estimation is compared with strategies where the entire wet path delay is estimated stochastically without prior calibration, using data from a 270-km test baseline in Costa Rica. Both approaches yield centimeter-level baseline repeatability and similar tropospheric estimates, suggesting that WVR calibration is not critical for obtaining high precision results with GPS in the CASA region.

Development of Extranodal NK/T-cell Lymphoma Nasal Type in Cerebrum Following Epstein-Barr Virus-positive Uveitis.

PubMed

Imai, Ayano; Takase, Hiroshi; Imadome, Ken-Ichi; Matsuda, Go; Ohnishi, Iichiro; Yamamoto, Kouhei; Kudo, Takumi; Tanaka, Yoji; Maehara, Taketoshi; Miura, Osamu; Arai, Ayako

2017-01-01

A 74-year-old woman developed bilateral uveitis with high Epstein-Barr virus (EBV) DNA load in the vitreous fluid without lymphoma cells. Four years after the onset, T2-weighted contrast-enhanced MRI revealed hyperintense lesions in the right occipital and parietal lobe. A biopsy resulted in the diagnosis of extranodal NK/T-cell lymphoma nasal type (ENKL). The repeat region of LMP1, an EBV gene, detected in the brain lesion was identical to that detected in the vitreous fluid. ENKL of the central nervous system is quite rare, and the pathogenesis has not been determined. The lymphoma in this case might have been closely associated with the EBV-positive uveitis.

Effect Sizes and their Intervals: The Two-Level Repeated Measures Case

ERIC Educational Resources Information Center

Algina, James; Keselman, H. J.; Penfield, Randall D.

2005-01-01

Probability coverage for eight different confidence intervals (CIs) of measures of effect size (ES) in a two-level repeated measures design was investigated. The CIs and measures of ES differed with regard to whether they used least squares or robust estimates of central tendency and variability, whether the end critical points of the interval…

The Impact of Increasing Fire Frequency on Forest Transformations in the Zabaikal Region, Southern Siberia

NASA Astrophysics Data System (ADS)

Conard, S. G.; Kukavskaya, E. A.; Buryak, L. V.; Shvetsov, E.; Kalenskaya, O. P.; Zhila, S.

2017-12-01

The Zabaikal region of southern Siberia is characterized by some of the highest fire activity in Russia. There has been a significant increase of fire frequency and burned area in the region over the last two decades due to a combination of high anthropogenic pressure, decreased funding to the forestry sector, and increased fire danger, which was associated with higher frequency and intensity of extreme weather events. Central and southern parts of the Zabaikal region where population density is higher and road network is relatively more developed are the most disturbed by fires. Larch stands cover the largest proportion of fire-disturbed lands in the region, while the less common pine and birch stands are characterized by higher fire frequency. About 13% (3.9 M ha) of the total forest area in the Zabaikal region was burned more than once in the 20 years from 1996 to 2015, with many sites burned multiple times. Repeat disturbances led to inadequate tree regeneration on all but the moistest sites. Pine stands on dry soils, which are common in the forest-steppe zone, were the most vulnerable. After repeat burns and over large burned sites we observed transformation of the forests to steppe ecosystems. The most likely causes of insufficient forest regeneration are soil overheating, dominance of tall grasses, and lack of nearby seed sources. Extensive tree plantations have potential to mitigate negative fire impacts; however, due to high fire hazard in the recent decade about half of the plantation area has been burned. Changes in the SWVI index were used to assess postfire reforestation based on a combination of satellite and field data. In the southwestern part of the Zabaikal region, we estimated that reforestation had been hampered over 11% of the forest land area. Regional climate models project increasing temperatures and decreasing precipitation across Siberia by the end of the 21st century, with changes in the Zabaikal region projected to be more than twice the average rate in Siberia. This would likely lead to higher fire activity in the region. Implementation of sustainable forest management strategies has the potential to mitigate effects of changing climate and fire regimes on forest ecosystems in the Zabaikal region. This research was supported by the RFBR grant (# 15-04-06567) and the NASA LCLUC Program.

Molecular characterization of the canine mitochondrial DNA control region for forensic applications.

PubMed

Eichmann, Cordula; Parson, Walther

2007-09-01

The canine mitochondrial DNA (mtDNA) control region of 133 dogs living in the area around Innsbruck, Austria was sequenced. A total of 40 polymorphic sites were observed in the first hypervariable segment and 15 in the second, which resulted in the differentiation of 40 distinct haplotypes. We observed five nucleotide positions that were highly polymorphic within different haplogroups, and they represent good candidates for mtDNA screening. We found five point heteroplasmic positions; all located in HVS-I and a polythymine region in HVS-II, the latter often being associated with length heteroplasmy. In contrast to human mtDNA, the canine control region contains a hypervariable 10 nucleotide repeat region, which is located between the two hypervariable regions. In our population sample, we observed eight different repeat types, which we characterized by direct sequencing and fragment length analysis. The discrimination power of the canine mtDNA control region was 0.93, not taking the polymorphic repeat region into consideration.

Outdoor near-roadway, community and residential pollen, carbon dioxide and particulate matter measurements in the urban core of an agricultural region in central CA

NASA Astrophysics Data System (ADS)

Shendell, Derek G.; Therkorn, Jennifer H.; Yamamoto, Naomichi; Meng, Qingyu; Kelly, Sarah W.; Foster, Christine A.

2012-04-01

We can control asthma through proper clinical and environmental management and education. The U.S. population is growing, urbanizing and aging; seniors of low-to-middle income families are working and living longer. We conducted community-based participatory research in Visalia, Tulare County, California with a prospective, cross-sectional repeated measures design and quantitative and qualitative process; home environment and health-related outcomes data were collected. In this paper, we presented results of the air quality sampling-pollen, carbon dioxide (CO2) and particulate matter (PM) outdoors away from most major sources (agricultural fields, large pollinating trees, etc)-at a community central site close to a mobile line source and participant homes in the cooling season, July, 2009. Weather was hot and dry with light winds; diurnal variation ranged between 65-107 °F (18-42 °C) and 12-76% relative humidity at the study's central site. Co-located active (reference) and passive (PAAS) samplers were used for pollen; passive monitoring for CO2 (Telaire 7001) and active sampling for PM were conducted. Overall, we observed spatial variability in CO2, fine PM (PM2.5), and pollen counts. Weekday and study week average CO2 and PM2.5 concentrations were higher near study homes compared to central site sampling points, but peak measures and overnight/pre-dawn time period averages were elevated at the central site. Pollen counts were typically lower at homes-even if grass, trees, flowers or potted plants were present-compared to the central site closer to and generally downwind from commercial agricultural tree production. Data are new; the nine-county San Joaquin Valley has one pollen count station in the national network, and two of four government outdoor air monitoring stations in the county are in national parks. We suggest-given poor air quality in large part due to PM-adding routine pollen counts to regional/state agency air monitoring sites and more CO2 and PM monitoring.

Targeting accuracy of single-isocenter intensity-modulated radiosurgery for multiple lesions.

PubMed

Calvo-Ortega, J F; Pozo, M; Moragues, S; Casals, J

2017-01-01

To investigate the targeting accuracy of intensity-modulated SRS (IMRS) plans designed to simultaneously treat multiple brain metastases with a single isocenter. A home-made acrylic phantom able to support a film (EBT3) in its coronal plane was used. The phantom was CT scanned and three coplanar small targets (a central and two peripheral) were outlined in the Eclipse system. Peripheral targets were 6 cm apart from the central one. A reference IMRS plan was designed to simultaneously treat the three targets, but only a single isocenter located at the center of the central target was used. After positioning the phantom on the linac using the room lasers, a CBCT scan was acquired and the reference plan were mapped on it, by placing the planned isocenter at the intersection of the landmarks used in the film showing the linac isocenter. The mapped plan was then recalculated and delivered. The film dose distribution was derived using a cloud computing application (www.radiochromic.com) that uses a triple-channel dosimetry algorithm. Comparison of dose distributions using the gamma index (5%/1 mm) were performed over a 5 × 5 cm 2 region centered over each target. 2D shifts required to get the best gamma passing rates on the peripheral target regions were compared with the reported ones for the central target. The experiment was repeated ten times in different sessions. Average 2D shifts required to achieve optimal gamma passing rates (99%, 97%, 99%) were 0.7 mm (SD: 0.3 mm), 0.8 mm (SD: 0.4 mm) and 0.8 mm (SD: 0.3 mm), for the central and the two peripheral targets, respectively. No statistical differences (p > 0.05) were found for targeting accuracy between the central and the two peripheral targets. The study revealed a targeting accuracy within 1 mm for off-isocenter targets within 6 cm of the linac isocenter, when a single-isocenter IMRS plan is designed. Copyright © 2017 American Association of Medical Dosimetrists. Published by Elsevier Inc. All rights reserved.

Living and Working with a Central Auditory Processing Disorder (CAPD).

ERIC Educational Resources Information Center

Paton, Judith W.

This paper describes adult symptoms of Central Auditory Processing Disorder and provides strategies for dealing with this disability. Symptoms include talking or turning on the television louder than normal, interpreting words too literally, needing remarks repeated, having difficulty sounding out words, ignoring people, being unusually sensitive…

The Collision of Athletics & Consolidation

ERIC Educational Resources Information Center

Graves, Bill

2010-01-01

For decades, people questioned the sense of having two school districts, each with its own superintendent, central office and high school, operating in the same small town of The Dalles on the banks of the Columbia River in north-central Oregon. But election campaigns to consolidate repeatedly failed because each community had strong emotional…

Pulsed coherent population trapping with repeated queries for producing single-peaked high contrast Ramsey interference

NASA Astrophysics Data System (ADS)

Warren, Z.; Shahriar, M. S.; Tripathi, R.; Pati, G. S.

2018-02-01

A repeated query technique has been demonstrated as a new interrogation method in pulsed coherent population trapping for producing single-peaked Ramsey interference with high contrast. This technique enhances the contrast of the central Ramsey fringe by nearly 1.5 times and significantly suppresses the side fringes by using more query pulses ( >10) in the pulse cycle. Theoretical models have been developed to simulate Ramsey interference and analyze the characteristics of the Ramsey spectrum produced by the repeated query technique. Experiments have also been carried out employing a repeated query technique in a prototype rubidium clock to study its frequency stability performance.

Gulf War illness: Effects of repeated stress and pyridostigmine treatment on blood-brain barrier permeability and cholinesterase activity in rat brain.

PubMed

Amourette, Christine; Lamproglou, Ioannis; Barbier, Laure; Fauquette, William; Zoppe, Amélie; Viret, Roselyne; Diserbo, Michel

2009-11-05

After the first Persian Gulf War, many soldiers have complained of a variety of symptoms designated as "Gulf War Illness". Among several factors, implication of pyridostigmine (PB) in late cognitive dysfunction is highly likely. As a hypothesis to explain these behavioural disorders is a potentiation of the operational stress effects by pyridostigmine. We have previously described that repeated stress combined to pyridostigmine treatment induces learning dysfunction linked to genomic cerebral modifications [Barbier L, Diserbo M, Lamproglou I, Amourette C, Peinnequin A, Fauquette W. Repeated stress in combination with pyridostigmine: part II-changes in selected cerebral genes expression. Behav Brain Res 2009;197:292-300; Lamproglou I, Barbier L, Diserbo M, Fauvelle F, Fauquette W, Amourette C. Repeated stress in combination with pyridostigmine: part I-long-term behavioural consequences. Behav Brain Res 2009;197:301-10]. In the present study, using the same experimental model, we attempted to determine if such modifications are linked to a central passage of pyridostigmine under stress. Indeed it is known that exposure to stress can disrupt blood-brain barrier (BBB) and thereby increase the neurotoxicity induced by chemicals in many cerebral areas. Adult rats were subjected to repeated stress based on a modification of the pole climbing avoidance technique and treated daily by PB (1.5mg/kg/day, oral in water), for two 5-day periods separated by 2-day rest. Just after the last stress session, (3)H-pyridostigmine was administered as a tracer to evaluate BBB breakdown. In brain micro-punches and brain coronal cryosections, we failed to detect any radioactivity in animals chronically stressed and treated by pyridostigmine. Accordingly, no change of ChE activity was noted in any brain area studied. It thus appears that, in our experimental model, pyridostigmine induces effects on central nervous system, but these effects do not seem to be mediated by a central passage of pyridostigmine linked to a BBB opening under stress. These results suggest that pyridostigmine may have central effects, under stress, via indirect mechanisms emerging from a peripheral pathway.

Spatially heterogeneous impact of climate change on small mammals of montane California

PubMed Central

Rowe, Kevin C.; Rowe, Karen M. C.; Tingley, Morgan W.; Koo, Michelle S.; Patton, James L.; Conroy, Chris J.; Perrine, John D.; Beissinger, Steven R.; Moritz, Craig

2015-01-01

Resurveys of historical collecting localities have revealed range shifts, primarily leading edge expansions, which have been attributed to global warming. However, there have been few spatially replicated community-scale resurveys testing whether species' responses are spatially consistent. Here we repeated early twentieth century surveys of small mammals along elevational gradients in northern, central and southern regions of montane California. Of the 34 species we analysed, 25 shifted their ranges upslope or downslope in at least one region. However, two-thirds of ranges in the three regions remained stable at one or both elevational limits and none of the 22 species found in all three regions shifted both their upper and lower limits in the same direction in all regions. When shifts occurred, high-elevation species typically contracted their lower limits upslope, whereas low-elevation species had heterogeneous responses. For high-elevation species, site-specific change in temperature better predicted the direction of shifts than change in precipitation, whereas the direction of shifts by low-elevation species was unpredictable by temperature or precipitation. While our results support previous findings of primarily upslope shifts in montane species, they also highlight the degree to which the responses of individual species vary across geographically replicated landscapes. PMID:25621330

Introduction of positron emission tomography into the Western Norwegian Health Region: Regional balance in resource utilization from 2009 to 2014.

PubMed

Stokmo, Henning Langen; Reitan, Bernt Christian; Johnsen, Boel; Gulati, Ankush; Kleven-Madsen, Nina; Adamsen, Tom Christian Holm; Biermann, Martin

2017-09-01

The aim was to compare resource utilization across the four health trusts within the Western Norway Regional Health Authority since the establishment of positron emission tomography (PET) at Haukeland University Hospital in Bergen in 2009. Metadata from all PET examinations from 2009 to 2014 were automatically imported from the PET centre's central production database into a custom-developed database system, MDCake. A PET examination was defined as a procedure based on a single injection of radioactive tracer. The patients' place of residence and tentative diagnosis were coded based on the available clinical information. The total number of PET examinations increased from 293 in 2009 to 1616 in 2014. The number of PET examinations per year increased across all diagnostic groups, but plateaued for lung cancer, gastrointestinal cancer and malignant melanoma since 2013. The number of examinations per capita was evenly distributed between the three northern health trusts with an average of 1260 PET studies per million inhabitants in 2014. However, patients residing in the most southerly health trust received between 44% (2010) and 27% (2014; P<0·001, repeated measures ANOVA) fewer examinations per capita per year. Centralized PET in the Western Norwegian health region meets the current clinical demand for patients residing in the three northern health trusts while patients from the most southern health trust receive approximately 30% fewer PET examinations. Access to specialized health care should be monitored routinely in order to identify inequalities in referral patterns and resource utilization. © 2015 The Authors. Clinical Physiology and Functional Imaging published by John Wiley & Sons Ltd on behalf of Scandinavian Society of Clinical Physiology and Nuclear Medicine.

Plasmodium vivax circumsporozoite genotypes: a limited variation or new subspecies with major biological consequences?

PubMed Central

2010-01-01

Background Plasmodium vivax circumsporozoite variants have been identified in several geographical areas. The real implication of the genetic variation in this region of the P. vivax genome has been questioned for a long time. Although previous studies have observed significant association between VK210 and the Duffy blood group, we present here that evidences of this variation are limited to the CSP central portion. Methods The phylogenetic analyses were accomplished starting from the amplification of conserved domains of 18 SSU RNAr and Cyt B. The antibodies responses against the CSP peptides, MSP-1, AMA-1 and DBP were detected by ELISA, in plasma samples of individuals infected with two P. vivax CS genotypes: VK210 and P. vivax-like. Results These analyses of the two markers demonstrate high similarity among the P. vivax CS genotypes and surprisingly showed diversity equal to zero between VK210 and P. vivax-like, positioning these CS genotypes in the same clade. A high frequency IgG antibody against the N- and C-terminal regions of the P. vivax CSP was found as compared to the immune response to the R- and V- repetitive regions (p = 0.0005, Fisher's Exact test). This difference was more pronounced when the P. vivax-like variant was present in the infection (p = 0.003, Fisher's Exact test). A high frequency of antibody response against MSP-1 and AMA-1 peptides was observed for all P. vivax CS genotypes in comparison to the same frequency for DBP. Conclusions This results target that the differences among the P. vivax CS variants are restrict to the central repeated region of the protein, mostly nucleotide variation with important serological consequences. PMID:20573199

A Mitochondrial Genome of Rhyparochromidae (Hemiptera: Heteroptera) and a Comparative Analysis of Related Mitochondrial Genomes.

PubMed

Li, Teng; Yang, Jie; Li, Yinwan; Cui, Ying; Xie, Qiang; Bu, Wenjun; Hillis, David M

2016-10-19

The Rhyparochromidae, the largest family of Lygaeoidea, encompasses more than 1,850 described species, but no mitochondrial genome has been sequenced to date. Here we describe the first mitochondrial genome for Rhyparochromidae: a complete mitochondrial genome of Panaorus albomaculatus (Scott, 1874). This mitochondrial genome is comprised of 16,345 bp, and contains the expected 37 genes and control region. The majority of the control region is made up of a large tandem-repeat region, which has a novel pattern not previously observed in other insects. The tandem-repeats region of P. albomaculatus consists of 53 tandem duplications (including one partial repeat), which is the largest number of tandem repeats among all the known insect mitochondrial genomes. Slipped-strand mispairing during replication is likely to have generated this novel pattern of tandem repeats. Comparative analysis of tRNA gene families in sequenced Pentatomomorpha and Lygaeoidea species shows that the pattern of nucleotide conservation is markedly higher on the J-strand. Phylogenetic reconstruction based on mitochondrial genomes suggests that Rhyparochromidae is not the sister group to all the remaining Lygaeoidea, and supports the monophyly of Lygaeoidea.

Similarities in the chromosomal distribution of AG and AC repeats within and between Drosophila, human and barley chromosomes.

PubMed

Cuadrado, A; Jouve, N

2007-01-01

Two simple sequence repeats (SSRs), AG and AC, were mapped directly in the metaphase chromosomes of man and barley (Hordeum vulgare L.), and in the metaphase and polytene chromosomes of Drosophila melanogaster. To this end, synthetic oligonucleotides corresponding to (AG)(12) and (AC)(8) were labelled by the random primer technique and used as probes in fluorescent in situ hybridisation (FISH) under high stringency and strict washing conditions. The distribution and intensity of the signals for the repeat sequences were found to be characteristic of the chromosomes and genomes of the three species analysed. The AC repeat sites were uniformly dispersed along the euchromatic segments of all three genomes; in fact, they were largely excluded from the heterochromatin. The Drosophila genome showed a high density of AC sequences on the X chromosome in both mitotic and polytene nuclei. In contrast, the AG repeats were associated with the euchromatic regions of the polytene chromosomes (and in high density on the X chromosome), but were only seen in specific heterochromatic regions in the mitotic chromosomes of all three species. In Drosophila, the AG repeats were exclusively distributed on the tips of the Y chromosome and near the centromere on both arms of chromosome 2. In barley and man, AG repeats were associated with the centromeres (of all chromosomes) and nucleolar organizer regions, respectively. The conserved chromosome distribution of AC within and between these three phylogenetically distant species, and the association of AG in specific chromosome regions with structural or functional properties, suggests that long clusters of these repeats may have some, as yet unknown, role. Copyright (c) 2007 S. Karger AG, Basel.

Discordant expression and variable numbers of neighboring GGA- and GAA-rich triplet repeats in the 3' untranslated regions of two groups of messenger RNAs encoded by the rat polymeric immunoglobulin receptor gene.

PubMed Central

Koch, K S; Gleiberman, A S; Aoki, T; Leffert, H L; Feren, A; Jones, A L; Fodor, E J

1995-01-01

An unusual S1-nuclease sensitive microsatellite (STMS) has been found in the single copy, rat polymeric immunoglobulin receptor gene (PIGR) terminal exon. In Fisher rats, elements within or beyond the STMS are expressed variably in the 3' untranslated regions (3'UTRs) of two 'Groups' of PIGR-encoded hepatic mRNAs (pIg-R) during liver regeneration. STMS elements include neighboring constant regions (a 60-bp d[GA]-rich tract with a chi-like octamer, followed by 15 tandem d[GGA] repeats) that merge directly with 36 or 39 tandem d[GAA] repeats (Fisher or Wistar strains, respectively) interrupted by d[AA] between their 5th-6th repeat units. The Wistar STMS is flanked upstream by two regions of nearly contiguous d[CA] or d[CT] repeats in the 3' end of intron 8; and downstream, by a 283 bp 'unit' containing several inversions at its 5' end, and two polyadenylation signals at its 3' end. The 283 nt unit is expressed in Group 1 pIg-R mRNAs; but it is absent in the Group 2 family so that their GAA repeats merge with their poly A tails. In contrast to genomic sequence, GGA triplet repeats are amplified (n > or = 24-26), whereas GAA triplet repeats are truncated variably (n < or = 9-37) and expressed uninterruptedly in both mRNA Groups. These results suggest that 3' end processing of the rat PIGR gene may involve misalignment, slippage and premature termination of RNA polymerase II. The function of this unusual processing and possible roles of chi-like octamers in quiescent or extrahepatic tissues are discussed. Images PMID:7739889

Complete mitochondrial genome of the larch hawk moth, Sphinx morio (Lepidoptera: Sphingidae).

PubMed

Kim, Min Jee; Choi, Sei-Woong; Kim, Iksoo

2013-12-01

The larch hawk moth, Sphinx morio, belongs to the lepidopteran family Sphingidae that has long been studied as a family of model insects in a diverse field. In this study, we describe the complete mitochondrial genome (mitogenome) sequences of the species in terms of general genomic features and characteristic short repetitive sequences found in the A + T-rich region. The 15,299-bp-long genome consisted of a typical set of genes (13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes) and one major non-coding A + T-rich region, with the typical arrangement found in Lepidoptera. The 316-bp-long A + T-rich region located between srRNA and tRNA(Met) harbored the conserved sequence blocks that are typically found in lepidopteran insects. Additionally, the A + T-rich region of S. morio contained three characteristic repeat sequences that are rarely found in Lepidoptera: two identical 12-bp repeat, three identical 5-bp-long tandem repeat, and six nearly identical 5-6 bp long repeat sequences.

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

Follis, Kathryn E.; York, Joanne; Nunberg, Jack H.

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

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

PubMed

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

2007-03-30

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

CENTRAL ENGINE MEMORY OF GAMMA-RAY BURSTS AND SOFT GAMMA-RAY REPEATERS

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

Zhang, Bin-Bin; Castro-Tirado, Alberto J.; Zhang, Bing, E-mail: zhang.grb@gmail.com

Gamma-ray bursts (GRBs) are bursts of γ-rays generated from relativistic jets launched from catastrophic events such as massive star core collapse or binary compact star coalescence. Previous studies suggested that GRB emission is erratic, with no noticeable memory in the central engine. Here we report a discovery that similar light curve patterns exist within individual bursts for at least some GRBs. Applying the Dynamic Time Warping method, we show that similarity of light curve patterns between pulses of a single burst or between the light curves of a GRB and its X-ray flare can be identified. This suggests that themore » central engine of at least some GRBs carries “memory” of its activities. We also show that the same technique can identify memory-like emission episodes in the flaring emission in soft gamma-ray repeaters (SGRs), which are believed to be Galactic, highly magnetized neutron stars named magnetars. Such a phenomenon challenges the standard black hole central engine models for GRBs, and suggest a common physical mechanism behind GRBs and SGRs, which points toward a magnetar central engine of GRBs.« less

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

NASA Astrophysics Data System (ADS)

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

2015-10-01

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

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

PubMed

Rehm, Charlotte; Wurmthaler, Lena A; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1-5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6-9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria.

Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp.

PubMed Central

Rehm, Charlotte; Wurmthaler, Lena A.; Li, Yuanhao; Frickey, Tancred; Hartig, Jörg S.

2015-01-01

In prokaryotes simple sequence repeats (SSRs) with unit sizes of 1–5 nucleotides (nt) are causative for phase and antigenic variation. Although an increased abundance of heptameric repeats was noticed in bacteria, reports about SSRs of 6–9 nt are rare. In particular G-rich repeat sequences with the propensity to fold into G-quadruplex (G4) structures have received little attention. In silico analysis of prokaryotic genomes show putative G4 forming sequences to be abundant. This report focuses on a surprisingly enriched G-rich repeat of the type GGGNATC in Xanthomonas and cyanobacteria such as Nostoc. We studied in detail the genomes of Xanthomonas campestris pv. campestris ATCC 33913 (Xcc), Xanthomonas axonopodis pv. citri str. 306 (Xac), and Nostoc sp. strain PCC7120 (Ana). In all three organisms repeats are spread all over the genome with an over-representation in non-coding regions. Extensive variation of the number of repetitive units was observed with repeat numbers ranging from two up to 26 units. However a clear preference for four units was detected. The strong bias for four units coincides with the requirement of four consecutive G-tracts for G4 formation. Evidence for G4 formation of the consensus repeat sequences was found in biophysical studies utilizing CD spectroscopy. The G-rich repeats are preferably located between aligned open reading frames (ORFs) and are under-represented in coding regions or between divergent ORFs. The G-rich repeats are preferentially located within a distance of 50 bp upstream of an ORF on the anti-sense strand or within 50 bp from the stop codon on the sense strand. Analysis of whole transcriptome sequence data showed that the majority of repeat sequences are transcribed. The genetic loci in the vicinity of repeat regions show increased genomic stability. In conclusion, we introduce and characterize a special class of highly abundant and wide-spread quadruplex-forming repeat sequences in bacteria. PMID:26695179

Reply to "Comment on `Penetration of Action Potentials During Collision in the Median and Lateral Giant Axons of Invertebrates"'

NASA Astrophysics Data System (ADS)

Wang, Tian; Gonzalez-Perez, Alfredo; Budvytyte, Rima; Jackson, Andrew D.; Heimburg, Thomas

2017-04-01

Berg et al. did not reproduce our results but worked on different preparations and, in one central experiment, used a significantly different electrode configuration. To clarify the situation, we have repeated their experiment on the walking leg of a lobster using an apparatus that can produce both electrode configurations. With the configuration used by Berg et al., the signal of the nerve pulse disappears when forced to pass through the region strongly perturbed by the second stimulus. In our original collision setup, pulses do not travel through perturbed regions, and pulses pass through each other without annihilation as previously reported. These results demonstrate that we handle the preparations correctly. Furthermore, they call for a reinterpretation of the so-called collision block experiment performed by Berg et al. Most likely, their results merely indicate inhibition of the nerve pulse by a strong stimulus and not annihilation upon collision as claimed.

Discriminating Characteristics of Tectonic and Human-Induced Seismicity

NASA Astrophysics Data System (ADS)

Zaliapin, I. V.; Ben-Zion, Y.

2015-12-01

We analyze statistical features of background and clustered subpopulations of earthquakes in different regions in an effort to distinguish between human-induced and natural seismicity. Analysis of "end-member" areas known to be dominated by human-induced earthquakes (the Geyser geothermal field in northern California and TauTona gold mine in South Africa) and regular tectonic activity (the San Jacinto fault zone in southern California and Coso region excluding the Coso geothermal field in eastern central California) reveals several distinguishing characteristics. Induced seismicity is shown to have (i) higher rate of background events (both absolute and relative to the total rate), (ii) faster temporal offspring decay, (iii) higher intensity of repeating events, (iv) larger proportion of small clusters, and (v) larger spatial separation between parent and offspring, compared to regular tectonic activity. These differences also successfully discriminate seismicity within the Coso and Salton Sea geothermal fields in California before and after the expansion of geothermal production during the 1980s.

Repeat region of Brugia malayi sheath protein (Shp-1) carries Dominant B epitopes recognized in filarial endemic population.

PubMed

Jawaharlal, Jeya Prita Parasurama; Madhumathi, Jayaprakasam; Prince, Rajaiah Prabhu; Kaliraj, Perumal

2014-09-01

Transmission of lymphatic filariasis is mediated through microfilariae (L1 stage of the parasite) which is encased in an eggshell called sheath. The sheath protein Shp-1 stabilizes the structure due to the unique repeat region with Met-Pro-Pro-Gln-Gly sequences. Microfilarial proteins could be used as transmission blocking vaccines. Since the repeat region of Shp-1 was predicted to carry putative B epitopes, this region was used to analyze its reactivity with clinical samples towards construction of peptide vaccine. In silico analysis of Shp-1 showed the presence of B epitopes in the region 49-107. The polypeptide epitopic region Shp-149-107 was cloned and expressed in Escherichia coli. Antibody reactivity of the Shp-149-107 construct was evaluated in filarial endemic population by ELISA. Putatively immune endemic normals (EN) showed significantly high reactivity (P < 0.05) when compared to all the other categories. Antibody reactivity of Shp-1 repeat region was similar to that of whole protein proving that this region carries B epitopes responsible for its humoral response in humans. Thus this can be employed for inducing anti-microfilarial immunity in the infected population that may lead to reduction in transmission intensity and also it could be used along with other epitopes from different stages of the parasite in order to manage the disease effectively.

Potential Active Processes in Porter Crater

NASA Image and Video Library

2015-07-15

The extended-mission status of the Mars Reconnaissance Orbiter and the HiRISE camera has greatly increased our understanding of numerous active processes occurring on Mars. By taking carefully planned repeat images of surface, we now have an important record of how the surface evolves for a maximum of 5 Mars years. This image shows the central peak in Porter Crater. Although there are no repeat images here we can infer several active geologic processes, based on morphologic evidence and lessons learned from past well-monitored sites. Shallow gullies are located on the south and east facing slopes of the central peak. These features might have been carved by volatiles, such as carbon dioxide frost, sometime in the recent geologic past. Meanwhile on the northern slopes are several smaller slope features that have a morphology hinting at recurring slope lineae (RSL). Alternatively, these features could be the remnants of past active gullies. Several more HiRISE images would be needed to characterize their behavior and confirm their status as RSL (see "Recurring Slope Lineae in Equatorial Regions of Mars"). Southward on the slopes below the peak is a large dune field. Dunes show sharp crests with prominent ripples, both signs of actively migrating dunes. Also, we can see dust devil tracks crossing the nearby dusty surfaces and clear evidence for ongoing modification by swirling winds that persistently remove surface dust. Ongoing operations by HiRISE are dedicated to studying all of the active surface and atmospheric processes operating on Mars. http://photojournal.jpl.nasa.gov/catalog/PIA19853

A multidisciplinary study in the geodynamic active western Eger rift (Central Europe): The Quaternary volcanic complex Mytina and the recent CO2-degassing zone Hartousov

NASA Astrophysics Data System (ADS)

Flechsig, C.; Heinicke, J.; Kaempf, H. W.; Nickschick, T.; Mrlina, J.

2013-12-01

The Eger rift (Central Europe) belongs to the European Cenozoic rift system and represents an approximately 50 km wide and 300 km long ENE-WSW striking continental rift that formed during the Upper Cretaceous-Tertiary transition. This rift zone is one of the most active seismic regions in Central Europe. Especially, the western part of the Eger rift area is dominated by ongoing hidden magmatic processes in the intra-continental lithospheric mantle. Besides of known quaternary volcanoes, these processes take place in absence of any presently active volcanism at the surface. However, they are expressed by a series of phenomena distributed over a relatively large area, like occurrence of repeated earthquake swarms, surface exhalation of mantle-derived and CO2-enriched fluids at mofettes and mineral springs, and enhanced heat flow. At present this is the only known intra-continental region where such deep-seated, active lithospheric processes currently occur. The aim of the project is to investigate the tectonic/geologic near surface structure and the degassing processes of the mofette field of Hartousov, where soil gas measurements (concentration and flux rate) in an area of appr. 3x2 km traced a permeable NS extended segment of a fault zone and revealed highly permeable Diffuse Degassing Structures (DDS). The second target is volcanic environment of the Quaternary volcanic complex Mytina maar and the cinder cone Zelezna hurka/Eisenbühl. The investigations are intended to clarify: a) the spatio-temporal reconstruction of the maar complex, and the palaeo volcanic scenario (geological model, tectonic settings, distribution of pyroclastica, b) the geological structure and the tectonic control of the recent degassing zone, and c) the comperative interpretation of both regions in the consideration of potential future volcanic risk assessment in sub-regions of the western Eger Rift. To investigate both regions the following methods are used: geoelectrics, geomagnetics, shallow seismics, gravity and CO2-soil gas measurements, petrographic/petrophysical and remote sensing data. The results will be serve as for better understanding of geologic, volcanic and tectonic settings of the two regions as well as for the preparation of the ICDP drilling project 'Drilling the Eger rift' with a multidisciplinary approach consisting of geophysical, geochemical and other disciplines to understand the role of crustal fluid activity for swarm earthquake generation.

Why is the central area of the Alburni Mts in southern Italy so full of caves?

NASA Astrophysics Data System (ADS)

Cafaro, Simona; Gueguen, Erwan; Parise, Mario; Schiattarella, Marcello

2016-04-01

The Alburni Mts represent one of the most important karst area of southern Italy, with about 250 registered caves. Located in the southern Apennines, they constitute an impressive carbonate massif within the Mesozoic-Cenozoic Campania-Lucania platform. The study area is located inside the National Park of Cilento, Vallo di Diano and Alburni, and is bounded by two major rivers: the Calore and Tanagro rivers. This area has been repeatedly affected during Pleistocene by the activity of a regional, partly blind, NW-SE-striking fault system responsible for several huge earthquakes. The massif is limited to the north by an important normal fault zone (Alburni Line), whereas towards the E-SE it is bounded by a complex fault system linking the Alburni Mts to the Maddalena Mts across the Auletta basin and the Vallo di Diano valley. The entire massif is structured by NW-SE trending transtensional faults delimiting half-graben basins, and offset also by NE-SW trending faults. In particular, structural and geomorphological data have shown that the central area of the calcareous ridge is characterized by a relative structural low rhombic-shaped in planimetric view. Approximately 180 karst caves of the known 250, including some of the most significant from a speleological viewpoint, are located in this area. Is this simply due to repeated exploration activity in the last 25 years in this specific sector or might it be related to geological matter? New morphometric and structural data suggest that a relevant transversal structure, consisting of a complex NE-SW fault system, responsible for the genesis of the downthrown area in the central sector of the flat-topped ridge, was able to create the tectonic framework for the development of a great number of karst caves which present peculiar features and hydrological behaviour due to such structural controls. In this contribution we present and discuss these data, aimed at contributing to increase the knowledge on an area of sure karst and speleological interest.

Structure determination of a peptide model of the repeated helical domain in Samia cynthia ricini silk fibroin before spinning by a combination of advanced solid-state NMR methods.

PubMed

Nakazawa, Yasumoto; Asakura, Tetsuo

2003-06-18

Fibrous proteins unlike globular proteins, contain repetitive amino acid sequences, giving rise to very regular secondary protein structures. Silk fibroin from a wild silkworm, Samia cynthia ricini, consists of about 100 repeats of alternating polyalanine (poly-Ala) regions of 12-13 residues in length and Gly-rich regions. In this paper, the precise structure of the model peptide, GGAGGGYGGDGG(A)(12)GGAGDGYGAG, which is a typical repeated sequence of the silk fibroin, was determined using a combination of three kinds of solid-state NMR studies; a quantitative use of (13)C CP/MAS NMR chemical shift with conformation-dependent (13)C chemical shift contour plots, 2D spin diffusion (13)C solid-state NMR under off magic angle spinning and rotational echo double resonance. The structure of the model peptide corresponding to the silk fibroin structure before spinning was determined. The torsion angles of the central Ala residue, Ala(19), in the poly-Ala region were determined to be (phi, psi) = (-59 degrees, -48 degrees ) which are values typically associated with alpha-helical structures. However, the torsion angles of the Gly(25) residue adjacent to the C-terminal side of the poly-Ala chain were determined to be (phi, psi) = (-66 degrees, -22 degrees ) and those of Gly(12) and Ala(13) residues at the N-terminal of the poly-Ala chain to be (phi, psi) = (-70 degrees, -30 degrees ). In addition, REDOR experiments indicate that the torsion angles of the two C-terminal Ala residues, Ala(23) and Ala(24), are (phi, psi) = (-66 degrees, -22 degrees ) and those of N-terminal two Ala residues, Ala(13) and Ala(14) are (phi, psi) = (-70 degrees, -30 degrees ). Thus, the local structure of N-terminal and C-terminal residues, and also the neighboring residues of alpha-helical poly-Ala chain in the model peptide is a more strongly wound structure than found in typical alpha-helix structures.

Drought-induced changes in Amazon forest structure from repeat airborne lidar

NASA Astrophysics Data System (ADS)

Morton, D. C.; Leitold, V.; Longo, M.; Keller, M.; dos-Santos, M. N.; Scaranello, M. A., Sr.

2017-12-01

Drought events in tropical forests, including the 2015-2016 El Niño, may reduce net primary productivity and increase canopy tree mortality, thereby altering the short and long-term net carbon balance of tropical forests. Given the broad extent of drought impacts, forest inventory plots or eddy flux towers may not capture regional variability in forest response to drought. Here, we analyzed repeat airborne lidar data to evaluate canopy turnover from branch and tree fall before (2013-2014) and during (2014-2016) the recent El Niño drought in the eastern and central Brazilian Amazon. Coincident field surveys for a 16-ha subset of the lidar coverage provided complementary information to classify turnover areas by mechanism (branch, multiple branch, tree fall, multiple tree fall) and estimate the total coarse woody debris volume from canopy and understory tree mortality. Annualized rates of canopy turnover increased by 50%, on average, during the drought period in both intact and fragmented forests near Santarém, Pará. Turnover increased uniformly across all size classes, and there was limited evidence that taller trees contributed a greater proportion of turnover events in any size class in 2014-2016 compared to 2013-2014. This short-term increase in canopy turnover differs from findings in multi-year rainfall exclusion experiments that large trees were more sensitive to drought impacts. Field measurements confirmed the separability of the smallest (single branch) and largest damage classes (multiple tree falls), but single tree and multiple branch fall events generated similar coarse woody debris production and lidar-derived changes in canopy volume. Large-scale sampling possible with repeat airborne lidar data also captured strong local and regional gradients in canopy turnover. Differences in slope partially explained the north-south gradient in canopy turnover dynamics near Santarém, with larger increases in turnover on flatter terrain. Regional variability in canopy turnover in response to drought conditions highlights the need for a mechanistic representation of branch and tree fall dynamics in ecosystem models to resolve changes in net carbon balance from the increase in coarse woody debris production and reorganization of canopy light environments during drought years.

Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae.

PubMed

Menconi, Giulia; Bedini, Andrea; Barale, Roberto; Sbrana, Isabella

2015-04-01

In this study we provide the first comprehensive map of DNA conformational flexibility in Saccharomyces cerevisiae complete genome. Flexibility plays a key role in DNA supercoiling and DNA/protein binding, regulating DNA transcription, replication or repair. Specific interest in flexibility analysis concerns its relationship with human genome instability. Enrichment in flexible sequences has been detected in unstable regions of human genome defined fragile sites, where genes map and carry frequent deletions and rearrangements in cancer. Flexible sequences have been suggested to be the determinants of fragile gene proneness to breakage; however, their actual role and properties remain elusive. Our in silico analysis carried out genome-wide via the StabFlex algorithm, shows the conserved presence of highly flexible regions in budding yeast genome as well as in genomes of other Saccharomyces sensu stricto species. Flexibile peaks in S. cerevisiae identify 175 ORFs mapping on their 3'UTR, a region affecting mRNA translation, localization and stability. (TA)n repeats of different extension shape the central structure of peaks and co-localize with polyadenylation efficiency element (EE) signals. ORFs with flexible peaks share common features. Transcripts are characterized by decreased half-life: this is considered peculiar of genes involved in regulatory systems with high turnover; consistently, their function affects biological processes such as cell cycle regulation or stress response. Our findings support the functional importance of flexibility peaks, suggesting that the flexible sequence may be derived by an expansion of canonical TAYRTA polyadenylation efficiency element. The flexible (TA)n repeat amplification could be the outcome of an evolutionary neofunctionalization leading to a differential 3'-end processing and expression regulation in genes with peculiar function. Our study provides a new support to the functional role of flexibility in genomes and a strategy for its characterization inside human fragile sites.

Global Mapping of DNA Conformational Flexibility on Saccharomyces cerevisiae

PubMed Central

Menconi, Giulia; Bedini, Andrea; Barale, Roberto; Sbrana, Isabella

2015-01-01

In this study we provide the first comprehensive map of DNA conformational flexibility in Saccharomyces cerevisiae complete genome. Flexibility plays a key role in DNA supercoiling and DNA/protein binding, regulating DNA transcription, replication or repair. Specific interest in flexibility analysis concerns its relationship with human genome instability. Enrichment in flexible sequences has been detected in unstable regions of human genome defined fragile sites, where genes map and carry frequent deletions and rearrangements in cancer. Flexible sequences have been suggested to be the determinants of fragile gene proneness to breakage; however, their actual role and properties remain elusive. Our in silico analysis carried out genome-wide via the StabFlex algorithm, shows the conserved presence of highly flexible regions in budding yeast genome as well as in genomes of other Saccharomyces sensu stricto species. Flexibile peaks in S. cerevisiae identify 175 ORFs mapping on their 3’UTR, a region affecting mRNA translation, localization and stability. (TA)n repeats of different extension shape the central structure of peaks and co-localize with polyadenylation efficiency element (EE) signals. ORFs with flexible peaks share common features. Transcripts are characterized by decreased half-life: this is considered peculiar of genes involved in regulatory systems with high turnover; consistently, their function affects biological processes such as cell cycle regulation or stress response. Our findings support the functional importance of flexibility peaks, suggesting that the flexible sequence may be derived by an expansion of canonical TAYRTA polyadenylation efficiency element. The flexible (TA)n repeat amplification could be the outcome of an evolutionary neofunctionalization leading to a differential 3’-end processing and expression regulation in genes with peculiar function. Our study provides a new support to the functional role of flexibility in genomes and a strategy for its characterization inside human fragile sites. PMID:25860149

Strategic Interviewing to Detect Deception: Cues to Deception across Repeated Interviews

PubMed Central

Masip, Jaume; Blandón-Gitlin, Iris; Martínez, Carmen; Herrero, Carmen; Ibabe, Izaskun

2016-01-01

Previous deception research on repeated interviews found that liars are not less consistent than truth tellers, presumably because liars use a “repeat strategy” to be consistent across interviews. The goal of this study was to design an interview procedure to overcome this strategy. Innocent participants (truth tellers) and guilty participants (liars) had to convince an interviewer that they had performed several innocent activities rather than committing a mock crime. The interview focused on the innocent activities (alibi), contained specific central and peripheral questions, and was repeated after 1 week without forewarning. Cognitive load was increased by asking participants to reply quickly. The liars’ answers in replying to both central and peripheral questions were significantly less accurate, less consistent, and more evasive than the truth tellers’ answers. Logistic regression analyses yielded classification rates ranging from around 70% (with consistency as the predictor variable), 85% (with evasive answers as the predictor variable), to over 90% (with an improved measure of consistency that incorporated evasive answers as the predictor variable, as well as with response accuracy as the predictor variable). These classification rates were higher than the interviewers’ accuracy rate (54%). PMID:27847493

Multiple bidirectional initiations and terminations of transcription in the Marek's disease virus long repeat regions.

PubMed Central

Chen, X B; Velicer, L F

1991-01-01

Marek's disease is an oncogenic disease of chickens caused by a herpesvirus, Marek's disease virus (MDV). Serial in vitro passage of pathogenic MDV results in amplification of a 132-bp direct repeat in the MDV genome's TRL and IRL repeat regions and loss of tumorigenicity. This led to the hypothesis that upon such expansion, one or more tumor-inducing genes fail to be expressed. In this report a group of cDNAs mapping in the expanded regions were isolated from a pathogenic MDV strain in which the 132-bp direct repeat number was found to range between one and seven. Partial cDNA sequencing and S1 nuclease protection analysis revealed that the corresponding transcripts are either initiated or terminated within or near the expanded regions at multiple sites in both rightward and leftward directions. Furthermore, each 132-bp repeat contains one TATA box and two polyadenylation consensus sequences in each direction. These RNAs contain a partial copy or one or more full copies of the 132-bp direct repeat at either their 5' or 3' end. Northern (RNA) blot analysis showed that the majority of transcripts are 1.8 kb in size, while the minor species range in size from 0.67 to 3.1 kb. Together, these data raise the possibility that the 132-bp direct repeat, and indirectly its copy number, may be involved in the regulation of transcriptional initiation and termination and therefore in the generation of four groups of transcripts from the TRL and IRL, although this remains to be demonstrated. Images PMID:1850022

Fluctuations in central and peripheral temperatures induced by intravenous nicotine: central and peripheral contributions

PubMed Central

Tang, Jeremy; Kiyatkin, Eugene A.

2011-01-01

Nicotine (NIC) is a highly addictive substance that interacts with different subtypes of nicotinic acetylcholine receptors widely distributed in the central and peripheral nervous systems. While the direct action of NIC on central neurons appears to be essential for its reinforcing properties, the role of peripheral actions of this drug remains a matter of controversy. In this study, we examined changes in locomotor activity and temperature fluctuations in the brain (nucleus accumbens and ventral tegmental area), temporal muscle, and skin induced by intravenous (iv) NIC at low human-relevant doses (10 and 30 μg/kg) in freely moving rats. These effects were compared to those induced by social interaction, an arousing procedure that induces behavioral activation and temperature responses via pure neural mechanism procedure, and iv injections of a peripherally acting NIC analogue, NIC pyrrolidine methiodide (NIC-PM) used at equimolar doses. We found that NIC at 30 μg/kg induces a modest locomotor activation, rapid and strong decrease in skin temperature, and weak increases in brain and muscle temperature. While these effects were qualitatively similar to those induced by social interaction, they were much weaker and showed a tendency to increase with repeated drug administrations. In contrast, NIC-PM did not affect locomotion and induced much weaker than NIC increases in brain and muscle temperatures and decreases in skin temperature; these effects showed a tendency to be weaker with repeated drug administrations. Our data indicate that NIC's actions in the brain are essential to induce locomotor activation and brain and body hyperthermic responses. However, rapid peripheral action of NIC on sensory afferents could be an important factor in triggering its central effects, contributing to neural and physiological activation following repeated drug use. PMID:21295014

Numerical simulation the pollutants transport in the Lake base on remote sensing image with Lattice Boltzmann Method

NASA Astrophysics Data System (ADS)

Qiao, Y.

2013-12-01

As China's economic development, water pollution incidents happened frequently. For example, the cyanobacterial bloom events repeatedly occur in Taihu Lake. In this research, we investigate the pollutants solute transport start at different points, such as the eutrophication substances Nitrogen and Phosphorus et al, with the Lattice Boltzmann Method (LBM) performed on real pore geometries. The LBM has emerged as a powerful tool for simulating the behaviour of multi-component fluid systems in complex pore networks. We will build a quick response simulation system, which is base on the high resolution GIS figure, using the LBM numerical method.When the start two deferent points at the Meiliang Bay nearby the Wuxi City, it is shown that the pollutants solute can't transport out of the bay to influence the Taihu Lake and the diffusion areas are similar. On the other hand, when the start point at central region of the Taihu Lake, it is found that the pollutants solute covered the almost whole area of the lake and the cyanobacterial bloom with good condition. In the same way, if the cyanobacterial bloom transport in the central area, then it will pollute the whole Taihu Lake. Therefore, when we monitor and deal with the eutrophication substances, we need to focus on the central area of lake.

Greater widespread functional connectivity of the caudate in older adults who practice kripalu yoga and vipassana meditation than in controls

PubMed Central

Gard, Tim; Taquet, Maxime; Dixit, Rohan; Hölzel, Britta K.; Dickerson, Bradford C.; Lazar, Sara W.

2015-01-01

There has been a growing interest in understanding how contemplative practices affect brain functional organization. However, most studies have restricted their exploration to predefined networks. Furthermore, scientific comparisons of different contemplative traditions are largely lacking. Here we explored differences in whole brain resting state functional connectivity between experienced yoga practitioners, experienced meditators, and matched controls. Analyses were repeated in an independent sample of experienced meditators and matched controls. Analyses utilizing Network-Based Statistics (Zalesky et al., 2010) revealed difference components for yoga practitioners > controls and meditators > controls in which the right caudate was a central node. Follow up analyses revealed that yoga practitioners and meditators had significantly greater degree centrality in the caudate than controls. This greater degree centrality was not driven by single connections but by greater connectivity between the caudate and numerous brain regions. Findings of greater caudate connectivity in meditators than in controls was replicated in an independent dataset. These findings suggest that yoga and meditation practitioners have stronger functional connectivity within basal ganglia cortico-thalamic feedback loops than non-practitioners. Although we could not provide evidence for its mechanistic role, this greater connectivity might be related to the often reported effects of meditation and yoga on behavioral flexibility, mental health, and well-being. PMID:25852521

Observations of seasonal and diurnal glacier velocities at Mount Rainier, Washington, using terrestrial radar interferometry

NASA Astrophysics Data System (ADS)

Allstadt, K. E.; Shean, D. E.; Campbell, A.; Fahnestock, M.; Malone, S. D.

2015-12-01

We present surface velocity maps derived from repeat terrestrial radar interferometry (TRI) measurements and use these time series to examine seasonal and diurnal dynamics of alpine glaciers at Mount Rainier, Washington. We show that the Nisqually and Emmons glaciers have small slope-parallel velocities near the summit (< 0.2 m day-1), high velocities over their upper and central regions (1.0-1.5 m day-1), and stagnant debris-covered regions near the terminus (< 0.05 m day-1). Velocity uncertainties are as low as ±0.02-0.08 m day-1. We document a large seasonal velocity decrease of 0.2-0.7 m day-1 (-25 to -50 %) from July to November for most of the Nisqually Glacier, excluding the icefall, suggesting significant seasonal subglacial water storage under most of the glacier. We did not detect diurnal variability above the noise level. Simple 2-D ice flow modeling using TRI velocities suggests that sliding accounts for 91 and 99 % of the July velocity field for the Emmons and Nisqually glaciers with possible ranges of 60-97 and 93-99.5 %, respectively, when considering model uncertainty. We validate our observations against recent in situ velocity measurements and examine the long-term evolution of Nisqually Glacier dynamics through comparisons with historical velocity data. This study shows that repeat TRI measurements with > 10 km range can be used to investigate spatial and temporal variability of alpine glacier dynamics over large areas, including hazardous and inaccessible areas.

Isolation and characterization of two overlapping cosmid clones from the 4q35 region, near the facioscapulohumeral muscular dystrophy locus

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

Deidda, G.; Grisanti, P.; Vigneti, E.

1994-09-01

The gene for facioscapulohumeral muscular dystrophy (FSHD) has been localized by linkage analysis to the 4q35 region. The most telomeric p13E-11 prove has been shown to detect 4q35 DNA rearrangements in both sporadic and familial cases of the disease. With the aim of constructing a detailed physical map of the 4q35 region and searching for the mutant gene, we used p13E-11 probe to isolate cosmid clones from a human genomic library in a pCos-EMBL 2 vector. Two positive clones were isolated, clones 3 and 5, which partially overlap and carry human genomic inserts of 42 and 45 kb, respectively. Themore » cosmids share a common region containing the p13E-11 region and a stretch of KpnI units consisting of 3.2 kb tandemly repeated sequences (about 10). The restriction maps were constructed using the following enzymes: Bam HI, BgIII, Eco RI, EcoRV, KpnI and Sfi I. Clone 3 extends 4 kb upstream of C5 and stops within the Kpn repeats. Clone 5 extends 4 kb downstream from the Kpn repeats and it presents an additional EcoRI site. Clone 5 contains a stretch of Kpn sequences of nearly 32 kb, corresponding to 10 Kpn repeats; clone 3 contains a stretch of 29 kb corresponding to 9 Kpn repeats, as determined by PFGE analysis of partial digestion of the clones. Clone 5 seems to contain the entire Eco RI region prone to rearrangements in FSHD patients. From clone 5 several subclones were obtained, from the Kpn region and from the region spanning from the last Kpn repeat to the cloning site. No single copy sequences were detected. Subclones from the 3{prime} end region contain beta-satellite or Sau3A-like sequences. In situ hybridization with the whole C5 cosmid shows hybridization signals at the tip of chromosome 4 (4q35) and chromosome 10 (10q26), in the pericentromeric region of chromosome 1 (1q12) and in the p12 region of the acrocentric chromosomes (chr. 21, 22, 13, 14, 15).« less

Crystallization and preliminary X-ray diffraction analysis of central structure domains from mumps virus F protein

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

Liu, Yueyong; Xu, Yanhui; Zhu, Jieqing

2005-09-01

Single crystals of the central structure domains from mumps virus F protein have been obtained by the hanging-drop vapour-diffusion method. A diffraction data set has been collected to 2.2 Å resolution. Fusion of members of the Paramyxoviridae family involves two glycoproteins: the attachment protein and the fusion protein. Changes in the fusion-protein conformation were caused by binding of the attachment protein to the cellular receptor. In the membrane-fusion process, two highly conserved heptad-repeat (HR) regions, HR1 and HR2, are believed to form a stable six-helix coiled-coil bundle. However, no crystal structure has yet been determined for this state in themore » mumps virus (MuV, a member of the Paramyxoviridae family). In this study, a single-chain protein consisting of two HR regions connected by a flexible amino-acid linker (named 2-Helix) was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. A complete X-ray data set was obtained in-house to 2.2 Å resolution from a single crystal. The crystal belongs to space group C2, with unit-cell parameters a = 161.2, b = 60.8, c = 40.1 Å, β = 98.4°. The crystal structure will help in understanding the molecular mechanism of Paramyxoviridae family membrane fusion.« less

Humpback Whale Song on the Southern Ocean Feeding Grounds: Implications for Cultural Transmission

PubMed Central

Garland, Ellen C.; Gedamke, Jason; Rekdahl, Melinda L.; Noad, Michael J.; Garrigue, Claire; Gales, Nick

2013-01-01

Male humpback whales produce a long, complex, and stereotyped song on low-latitude breeding grounds; they also sing while migrating to and from these locations, and occasionally in high-latitude summer feeding areas. All males in a population sing the current version of the constantly evolving display and, within an ocean basin, populations sing similar songs; however, this sharing can be complex. In the western and central South Pacific region there is repeated cultural transmission of song types from eastern Australia to other populations eastward. Song sharing is hypothesized to occur through several possible mechanisms. Here, we present the first example of feeding ground song from the Southern Ocean Antarctic Area V and compare it to song from the two closest breeding populations. The early 2010 song contained at least four distinct themes; these matched four themes from the eastern Australian 2009 song, and the same four themes from the New Caledonian 2010 song recorded later in the year. This provides evidence for at least one of the hypothesized mechanisms of song transmission between these two populations, singing while on shared summer feeding grounds. In addition, the feeding grounds may provide a point of acoustic contact to allow the rapid horizontal cultural transmission of song within the western and central South Pacific region and the wider Southern Ocean. PMID:24278134

Associations between respiratory health and ambient air quality in Canakkale, Turkey: a long-term cohort study.

PubMed

Mentese, Sibel; Bakar, Coskun; Mirici, Nihal Arzu; Oymak, Sibel; Otkun, Muserref Tatman

2018-05-01

Few epidemiological studies investigating the association between air pollution and health are available in Turkey. The aim of this cohort-type study is to examine the relationships between ambient air quality, respiratory diseases, and decreases in pulmonary function over a year in three different towns in Canakkale: Canakkale Central town (region I), Lapseki town center (region II), and Can town (region III). Region III had four different sub-regions, which were Can town center (region III-A), and the villages located around Can town, namely Durali (region III-B), Kulfal (region III-C), and Yuvalar (region III-D). In the first stage of the study, a detailed questionnaire was completed by the participants (n = 1152) in face-to-face interviews and pulmonary function test (PFT) was performed. In the second stage of the study, PFT measurements were repeated 1 year after the first stage. Particulate matter, SO 2 , NO 2 , and ozone were gathered from air quality monitoring stations located in the centers of the three regions. The most polluted area was region III, while region I and region II were the least polluted areas. The risk of pulmonary function decline throughout a year was 2.1 times higher in region III, 2.4 times higher both in regions III-B and III-C, and 1.6 times higher for smokers in all regions. In the present study, ambient air quality was worse in region III (industrialized region), which influenced PFT scores and the prognostics for chronic respiratory diseases. The findings of this study should be considered for future investment plans in this region related to human and environmental health needs.

Sampling of the anterior apical region results in increased cancer detection and upgrading in transrectal repeat saturation biopsy of the prostate.

PubMed

Seles, Maximilian; Gutschi, Thomas; Mayrhofer, Katrin; Fischereder, Katja; Ehrlich, Georg; Gallé, Guenter; Gutschi, Stefan; Pachernegg, Oliver; Pummer, Karl; Augustin, Herbert

2016-04-01

To evaluate whether biopsy cores taken via a transrectal approach from the anterior apical region of the prostate in a repeat-biopsy population can result in an increased overall cancer detection rate and in more accurate assessment of the Gleason score. The study was a prospective, randomised (end-fire vs side-fire ultrasound probe) evaluation of 288 men by repeat transrectal saturation biopsy with 28 cores taken from the transition zone, base, mid-lobar, anterior and the anterior apical region located ventro-laterally to the urethra of the peripheral zone. The overall prostate cancer detection rate was 44.4%. Improvement of the overall detection rate by 7.8% could be achieved with additional biopsies of the anterior apical region. Two tumours featuring a Gleason score 7 could only be detected in the anterior apical region. In three cases (2.34%) Gleason score upgrading was achieved by separate analysis of each positive core of the anterior apical region. A five-fold higher cancer detection rate in the anterior apical region compared with the transition zone could be shown. Sampling of the anterior apical region results in higher overall cancer detection rate in repeat transrectal saturation biopsies of the prostate. Specimens from this region can detect clinically significant cancer, improve accuracy of the Gleason Scoring and therefore may alter therapy. © 2015 The Authors BJU International © 2015 BJU International Published by John Wiley & Sons Ltd.

Crustal seismicity in central Chile

NASA Astrophysics Data System (ADS)

Barrientos, S.; Vera, E.; Alvarado, P.; Monfret, T.

2004-06-01

Both the genesis and rates of activity of shallow intraplate seismic activity in central Chile are poorly understood, mainly because of the lack of association of seismicity with recognizable fault features at the surface and a poor record of seismic activity. The goal of this work is to detail the characteristics of seismicity that takes place in the western flank of the Andes in central Chile. This region, located less than 100 km from Santiago, has been the site of earthquakes with magnitudes up to 6.9, including several 5+ magnitude shocks in recent years. Because most of the events lie outside the Central Chile Seismic Network, at distances up to 60 km to the east, it is essential to have adequate knowledge of the velocity structure in the Andean region to produce the highest possible quality of epicentral locations. For this, a N-S refraction line, using mining blasts of the Disputada de Las Condes open pit mine, has been acquired. These blasts were detected and recorded as far as 180 km south of the mine. Interpretation of the travel times indicates an upper crustal model consisting of three layers: 2.2-, 6.7-, and 6.1-km thick, overlying a half space; their associated P wave velocities are 4.75-5.0 (gradient), 5.8-6.0 (gradient), 6.2, and 6.6 km/s, respectively. Hypocentral relocation of earthquakes in 1986-2001, using the newly developed velocity model, reveals several regions of concentrated seismicity. One clearly delineates the fault zone and extensions of the strike-slip earthquake that took place in September 1987 at the source of the Cachapoal River. Other regions of activity are near the San José volcano, the source of the Maipo River, and two previously recognized lineaments that correspond to the southern extension of the Pocuro fault and Olivares River. A temporary array of seismographs, installed in the high Maipo River (1996) and San José volcano (1997) regions, established the hypocentral location of events with errors of less than 1 km. These events are clustered along no particular lineament approximately 25 km away from the San José and Maipo volcanoes. Recurrence intervals, based on a frequency magnitude relationship for lower magnitude events, indicate that earthquakes with magnitudes of 4.7 and 7 have a repeat time of 1 and 1200 years, respectively. Focal mechanisms of the two largest events indicate horizontal maximum and minimum compressive stresses with σ1 varying from a NW-SE orientation in the north to E-W at the southern extreme.

Forest stand conditions after 13 years of gypsy moth infestation

Treesearch

David L. Feicht; Sandra L. C. Fosbroke; Mark J. Twery

1993-01-01

Of 603 central Pennsylvania plots that were established in 1978 to measure the short-term impact of repeated gypsy moth (Lymantria dispar) defoliation, 228 were selected for continued study in 1985. Individual observations of defoliation and tree vigor were continued through 1992. Although two gypsy moth outbreaks occurred across central Pennsylvania...

Questioning the Scholarly Discussion around Decentralization in Turkish Education System

ERIC Educational Resources Information Center

Yildiz, Soner Onder

2016-01-01

From the beginning of Turkish Republic till date, Turkish Education System (TES) has been steered by a handful of politicians and civil servants, who enjoy maximum centralized authority. Over the years, therefore, centralized management has repeatedly been blamed for the deadlocks hampering progress in the TES. Turkish scholars often seem to find…

Mitogen-activated protein kinase is required for the behavioral desensitization that occurs after repeated injections of angiotensin II

PubMed Central

Vento, Peter J.; Daniels, Derek

2013-01-01

Angiotensin II (AngII) acts on central angiotensin type 1 (AT1) receptors to increase water and saline intake. Prolonged exposure to AngII in cell culture models results in a desensitization of the AT1 receptor that is thought to involve receptor internalization, and a behavioral correlate of this desensitization has been shown in rats after repeated central injections of AngII. Specifically, rats given repeated injections of AngII drink less water than controls after a subsequent test injection of AngII. Under the same conditions, however, repeated injections of AngII have no effect on AngII-induced saline intake. Given earlier studies indicating that separate intracellular signaling pathways mediate AngII-induced water and saline intake, we hypothesized that the desensitization observed in rats may be incomplete, leaving the receptor able to activate mitogen-activated protein (MAP) kinases (ERK1/2), which play a role in AngII-induced saline intake without affecting water intake. In support of this hypothesis, we found no difference in MAP kinase phosphorylation after an AngII test injection in rats given prior treatment with repeated injections of vehicle, AngII, or Sar1,Ile4,Ile8-AngII (SII), an AngII analog that activates MAP kinase without G protein coupling. In addition, we found that pretreatment with the MAP kinase inhibitor U0126 completely blocked the desensitizing effect of repeated AngII injections on water intake. Furthermore, AngII-induced water intake was reduced similarly by repeated injections of AngII or SII. The results suggest that G protein-independent signaling is sufficient to produce behavioral desensitization of the angiotensin system and that the desensitization requires MAP kinase activation. PMID:22581747

Mitogen-activated protein kinase is required for the behavioural desensitization that occurs after repeated injections of angiotensin II.

PubMed

Vento, Peter J; Daniels, Derek

2012-12-01

Angiotensin II (Ang II) acts on central angiotensin type 1 (AT(1)) receptors to increase water and saline intake. Prolonged exposure to Ang II in cell culture models results in a desensitization of the AT(1) receptor that is thought to involve receptor internalization, and a behavioural correlate of this desensitization has been shown in rats after repeated central injections of Ang II. Specifically, rats given repeated injections of Ang II drink less water than control animals after a subsequent test injection of Ang II. In the same conditions, however, repeated injections of Ang II have no effect on Ang II-induced saline intake. Given earlier studies indicating that separate intracellular signalling pathways mediate Ang II-induced water and saline intake, we hypothesized that the desensitization observed in rats may be incomplete, leaving the receptor able to activate mitogen-activated protein (MAP) kinases (ERK1/2), which play a role in Ang II-induced saline intake without affecting water intake. In support of this hypothesis, we found no difference in MAP kinase phosphorylation after an Ang II test injection in rats given prior treatment with repeated injections of vehicle, Ang II or Sar(1),Ile(4),Ile(8)-Ang II (SII), an Ang II analogue that activates MAP kinase without G protein coupling. In addition, we found that pretreatment with the MAP kinase inhibitor U0126 completely blocked the desensitizing effect of repeated Ang II injections on water intake. Furthermore, Ang II-induced water intake was reduced to a similar extent by repeated injections of Ang II or SII. The results suggest that G protein-independent signalling is sufficient to produce behavioural desensitization of the angiotensin system and that the desensitization requires MAP kinase activation.

DAT Genotype Modulates Brain and Behavioral Responses Elicited by Cigarette Cues

PubMed Central

Franklin, Teresa R; Lohoff, Falk W; Wang, Ze; Sciortino, Nathan; Harper, Derek; Li, Yin; Jens, Will; Cruz, Jeffrey; Kampman, Kyle; Ehrman, Ron; Berrettini, Wade; Detre, John A; O'Brien, Charles P; Childress, Anna Rose

2011-01-01

We previously demonstrated differential activation of the mesocorticolimbic reward circuitry in response to cigarette cues independent of withdrawal. Despite robust effects, we noted considerable individual variability in brain and subjective responses. As dopamine (DA) is critical for reward and its predictive signals, genetically driven variation in DA transmission may account for the observed differences. Evidence suggests that a variable number of tandem repeats (VNTRs) polymorphism in the DA transporter (DAT) SLC6A3 gene may influence DA transport. Brain and behavioral responses may be enhanced in probands carrying the 9-repeat allele. To test this hypothesis, perfusion fMR images were acquired during cue exposure in 19 smokers genotyped for the 40 bp VNTR polymorphism in the SLC6A3 gene. Contrasts between groups revealed that 9-repeat (9-repeats) had a greater response to smoking (vs nonsmoking) cues than smokers homozygous for the 10-repeat allele (10/10-repeats) bilaterally in the interconnected ventral striatal/pallidal/orbitofrontal cortex regions (VS/VP/OFC). Activity was increased in 9-repeats and decreased in 10/10-repeats in the VS/VP/OFC (p<0.001 for all analyses). Brain activity and craving was strongly correlated in 10/10-repeats in these regions and others (anterior cingulate, parahippocampal gyrus, and insula; r2 = 0.79–0.86, p<0.001 in all regions). Alternatively, there were no significant correlations between brain and behavior in 9-repeats. There were no differences in cigarette dependence, demographics, or resting baseline neural activity between groups. These results provide evidence that genetic variation in the DAT gene contributes to the neural and behavioral responses elicited by smoking cues. PMID:18704100

Hypothermic and antipyretic effects of ACTH (1-24) and alpha-melanotropin in guinea-pigs

NASA Technical Reports Server (NTRS)

Kandasamy, S. B.; Williams, B. A.

1984-01-01

Intracerebroventricular administration of adrenocorticotropin (ACTH 1-24) and alpha-melanotropin (alpha-MSH), peptides which occur naturally in brain induced dose-related hypothermia in guinea-pigs at room temperature (21 C) and also produced greater hypothermia at low (10 C) ambient temperature. However, when the experiments were repeated in a warm (30 C) environment, no effect on body temperature was observed. These results indicate that the peptides did not reduce the central set-point of temperature control. The hypothermia induced by ACTH and alpha-MSH was not mediated via histamine H1- or H2-receptors and serotonin since the H1-receptor antagonist, mepyramine, the H2-receptor antagonist, cimetidine, and the serotonin antagonist, methysergide, had no antagonistic effects. The peptides were antipyretic since they reduced pyrogen-induced-fever and hyperthermia due to prostaglandin E2, norepinephrine and dibutyryl cAMP, at a dose which did not affect normal body temperature. The powerful central effects of these peptides on normal body temperature, fever and hyperthermia, together with their presence of the brain regions important to temperature control, suggest that they participate in thermoregulation.

Somatotopic organization of cortical fields in the lateral sulcus of Homo sapiens: evidence for SII and PV.

PubMed

Disbrow, E; Roberts, T; Krubitzer, L

2000-02-28

The human somatosensory cortex in the Sylvian fissure was examined using functional magnetic resonance imaging to describe the number and internal organization of cortical fields present. Somatic stimuli were applied to the lips, face, hand, trunk, and foot of 18 human subjects. Activity patterns were transposed onto three-dimensional magnetic resonance images of the brain so that the location of activity associated with the different stimuli could be related to specific regions of the cortex. There were several consistent findings. First, there were three regions of activity in the lateral sulcus associated with stimulation of the contralateral body. The most consistent locus of activation was on the upper bank of the lateral sulcus, continuing onto the operculum. The other two areas, one rostral and one caudal to this large central area, were smaller and were activated less consistently. Second, when activity patterns in the large central area resulting from stimulation of all body parts were considered, this region appeared to contain two fields that corresponded in location and somatotopic organization to the second somatosensory area (SII) and the parietal ventral area (PV). Finally, patterns of activation within SII and PV were somewhat variable across subjects. Repeated within-subject stimulus presentation indicated that differences across subjects were not due to inconsistent stimulus presentation. Comparisons with other mammals suggest that some features of organization are found only in primates. It is hypothesized that these features may be associated with manual dexterity and coordination of the hands, a characteristic generally restricted to the primate lineage.

Transmission Reinforcements in the Central American Regional Power System

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

Elizondo, Marcelo A.; Vallem, Mallikarjuna R.; Samaan, Nader A.

The Central American regional interconnected power system (SER) connects the countries members of the Central American regional electricity market (MER): Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica, and Panama. The SER was a result of a long term regional effort, and was initially conceived to transfer 300 MW between countries. However, the current transfer limits between countries range from 70 MW to 300 MW. Regional entities, like CRIE (Regional Commission of Electrical Interconnection), EOR (Central American Regional System Operator), and CDMER (Board of Directors of the Central American Market) are working on coordinating the national transmission expansion plans with regionalmore » transmission planning efforts. This paper presents experience in Central America region to recommend transmission reinforcements to achieve 300 MW transfer capacity between any pair of member countries of the Central American regional electricity market (MER). This paper also provides a methodology for technical analysis and for coordination among the regional and national entities. This methodology is unique for transmission systems of these characteristics.« less

Enhanced central serotonin release from slices of rat hypothalamus following repeated nialamide administration: evidence supporting the overactive serotonin receptor theory of depression

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

Offord, S.J.

1986-01-01

Researchers are suggesting unipolar affective disorders may be related to an abnormality in biogenic amine receptor-sensitivity. This abnormality may be a result of a dysfunction in central serotonin (5-HT) release mechanisms. 5-HT neurotransmission is modulated by presynaptic autoreceptors, which are members of the 5-HT/sub 1/ receptor subtype. The autoreceptor is thought to play an important role in the homeostasis of the central 5-HT synapse and could be a site at which some antidepressants mediate their therapeutic effect. The number of 5-HT/sub 1/ type receptor binding sites are reduced and behavior mediated by this receptor is abolished following repeated injections ofmore » monoamine oxidase inhibitor type antidepressants. These changes did not occur following a single injection. It was hypothesized that repeated treatment with a monoamine oxidase inhibitor would reduce the sensitivity of 5-HT autoreceptors and enhance 5-HT release. Rats were pretreated with single or repeated (twice daily for 7 days) intraperitoneal injections of nialamide (40 mg/kg) or chlorimipramine (10 mg/kg) and the ability of the autoreceptor agonist to inhibit potassium-induced /sup 3/H-5-HT release was evaluated using an in vitro superfusion system. These changes in 5-HT autoreceptor activity are consistent with other reports evaluating monoamine oxidase inhibitors on 5-HT/sub 1/ type receptors. It is hypothesized that the changes in 5-HT neurotransmission are related to the antidepressant mechanism of monoamine oxidase inhibitors.« less

Kaiser Permanente Creatinine Safety Program: A Mechanism to Ensure Widespread Detection and Care for Chronic Kidney Disease.

PubMed

Sim, John J; Rutkowski, Mark P; Selevan, David C; Batech, Michael; Timmins, Royann; Slezak, Jeff M; Jacobsen, Steven J; Kanter, Michael H

2015-11-01

Chronic kidney disease is highly prevalent but is challenging to diagnose because of the need to establish chronicity. Within the current healthcare environment, a single abnormal creatinine measurement often can go without a follow-up, which can lead to missed diagnoses or diagnostic errors. The Kaiser Permanente Southern California creatinine safety program (the Creatinine SureNet) was created to help ensure that all single abnormal creatinine results had a follow-up evaluation. In the period February 1, 2010, to March 1, 2014, the electronic health records were used to capture individuals with single abnormal creatinine results that went >90 days without a repeat measurement. A coordinated effort among a centralized regional nurse and providers was used to communicate with patients and order a repeat creatinine measurement. A total of 12,396 individuals were identified (84% ambulatory care encounters). A total of 6981 individuals (52%) followed up with a repeat measurement. Female patients, non-Hispanic whites, and older individuals were more likely to obtain a repeat measurement. Subsequently, 3668 individuals had chronic kidney disease confirmed. Within 6 months, 1550 patients had chart documentation of their chronic kidney disease and 336 patients had a nephrology consultation. The ambulatory care environment, given its high volume and various prioritizations, is an under-recognized area where diagnostic errors are not uncommon and failure to follow up on abnormal test results can occur routinely. The Kaiser Permanente Southern California Creatinine SureNet program leverages the electronic health records and its multidisciplinary resources in an effort to ensure that patients with potential chronic kidney disease are identified and managed properly. Copyright © 2015 Elsevier Inc. All rights reserved.

Exaggerated phosphorylation of brain tau protein in CRH KO mice exposed to repeated immobilization stress.

PubMed

Kvetnansky, Richard; Novak, Petr; Vargovic, Peter; Lejavova, Katarina; Horvathova, Lubica; Ondicova, Katarina; Manz, George; Filipcik, Peter; Novak, Michal; Mravec, Boris

2016-07-01

Neuroendocrine and behavioral stress responses are orchestrated by corticotropin-releasing hormone (CRH) and norepinephrine (NE) synthesizing neurons. Recent findings indicate that stress may promote development of neurofibrillary pathology in Alzheimer's disease. Therefore, we investigated relationships among stress, tau protein phosphorylation, and brain NE using wild-type (WT) and CRH-knockout (CRH KO) mice. We assessed expression of phosphorylated tau (p-tau) at the PHF-1 epitope and NE concentrations in the locus coeruleus (LC), A1/C1 and A2/C2 catecholaminergic cell groups, hippocampus, amygdala, nucleus basalis magnocellularis, and frontal cortex of unstressed, singly stressed or repeatedly stressed mice. Moreover, gene expression and protein levels of tyrosine hydroxylase (TH) and CRH receptor mRNA were determined in the LC. Plasma corticosterone levels were also measured. Exposure to a single stress increases tau phosphorylation throughout the brain in WT mice when compared to singly stressed CRH KO animals. In contrast, repeatedly stressed CRH KO mice showed exaggerated tau phosphorylation relative to WT controls. We also observed differences in extent of tau phosphorylation between investigated structures, e.g. the LC and hippocampus. Moreover, CRH deficiency leads to different responses to stress in gene expression of TH, NE concentrations, CRH receptor mRNA, and plasma corticosterone levels. Our data indicate that CRH effects on tau phosphorylation are dependent on whether stress is single or repeated, and differs between brain regions. Our findings indicate that CRH attenuates mechanisms responsible for development of stress-induced tau neuropathology, particularly in conditions of chronic stress. However, the involvement of central catecholaminergic neurons in these mechanisms remains unclear and is in need of further investigation.

QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically

PubMed Central

Pérez-Quintero, Alvaro L.; Lamy, Léo; Gordon, Jonathan L.; Escalon, Aline; Cunnac, Sébastien; Szurek, Boris; Gagnevin, Lionel

2015-01-01

Transcription Activator-Like (TAL) effectors from Xanthomonas plant pathogenic bacteria can bind to the promoter region of plant genes and induce their expression. DNA-binding specificity is governed by a central domain made of nearly identical repeats, each determining the recognition of one base pair via two amino acid residues (a.k.a. Repeat Variable Di-residue, or RVD). Knowing how TAL effectors differ from each other within and between strains would be useful to infer functional and evolutionary relationships, but their repetitive nature precludes reliable use of traditional alignment methods. The suite QueTAL was therefore developed to offer tailored tools for comparison of TAL effector genes. The program DisTAL considers each repeat as a unit, transforms a TAL effector sequence into a sequence of coded repeats and makes pair-wise alignments between these coded sequences to construct trees. The program FuncTAL is aimed at finding TAL effectors with similar DNA-binding capabilities. It calculates correlations between position weight matrices of potential target DNA sequence predicted from the RVD sequence, and builds trees based on these correlations. The programs accurately represented phylogenetic and functional relationships between TAL effectors using either simulated or literature-curated data. When using the programs on a large set of TAL effector sequences, the DisTAL tree largely reflected the expected species phylogeny. In contrast, FuncTAL showed that TAL effectors with similar binding capabilities can be found between phylogenetically distant taxa. This suite will help users to rapidly analyse any TAL effector genes of interest and compare them to other available TAL genes and should improve our understanding of TAL effectors evolution. It is available at http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi. PMID:26284082

AlphaII-spectrin interacts with Tes and EVL, two actin-binding proteins located at cell contacts.

PubMed

Rotter, Björn; Bournier, Odile; Nicolas, Gael; Dhermy, Didier; Lecomte, Marie-Christine

2005-06-01

The spectrin-based membrane skeleton, a multi-protein scaffold attached to diverse cellular membranes, is presumed to be involved in the stabilization of membranes, the establishment of membrane domains as well as in vesicle trafficking and nuclear functions. Spectrin tetramers made of alpha- and beta-subunits are linked to actin microfilaments, forming a network that binds a multitude of proteins. The most prevalent alpha-spectrin subunit in non-erythroid cells, alphaII-spectrin, contains two particular spectrin repeats in its central region, alpha9 and alpha10, which host an Src homology 3 domain, a tissue-specific spliced sequence of 20 residues, a calmodulin-binding site and major cleavage sites for caspases and calpains. Using yeast two-hybrid screening of kidney libraries, we identified two partners of the alpha9-alpha10 repeats: the potential tumour suppressor Tes, an actin-binding protein mainly located at focal adhesions; and EVL (Ena/vasodilator-stimulated phosphoprotein-like protein), another actin-binding protein, equally recruited at focal adhesions. Interactions between spectrin and overexpressed Tes and EVL were confirmed by co-immunoprecipitation. In vitro studies showed that the interaction between Tes and spectrin is mediated by a LIM (Lin-11, Isl-1 and Mec3) domain of Tes and by the alpha10 repeat of alphaII-spectrin whereas EVL interacts with the Src homology 3 domain located within the alpha9 repeat. Moreover, we describe an in vitro interaction between Tes and EVL, and a co-localization of these two proteins at focal adhesions. These interactions between alphaII-spectrin, Tes and EVL indicate new functions for spectrin in actin dynamics and focal adhesions.

The population structure and recent colonization history of Oregon threespine stickleback determined using RAD-seq

PubMed Central

Catchen, Julian; Bassham, Susan; Wilson, Taylor; Currey, Mark; O’Brien, Conor; Yeates, Quick; Cresko, William A.

2013-01-01

Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem we are studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been de-glaciated in the last 20,000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed RAD-seq based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin, and central Oregon sites, analyzed their genetic diversity using RAD-seq, performed STRUCTURE analyses, reconstructed their phylogeographic history, and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history. PMID:23718143

Molecular identification and characterization of clustered regularly interspaced short palindromic repeat (CRISPR) gene cluster in Taylorella equigenitalis.

PubMed

Hara, Yasushi; Hayashi, Kyohei; Nakajima, Takuya; Kagawa, Shizuko; Tazumi, Akihiro; Moore, John E; Matsuda, Motoo

2013-09-01

Clustered regularly interspaced short palindromic repeats (CRISPRs), of approximately 10,000 base pairs (bp) in length, were shown to occur in the Japanese Taylorella equigenitalis strain, EQ59. The locus was composed of the putative CRISPRs-associated with 5 (cas5), RAMP csd1, csd2, recB, cas1, a leader region, 13 CRISPR consensus sequence repeats (each 32 bp; 5'-TCAGCCACGTTCGCGTGGCTGTGTGTTTAAAG-3'). These were in turn separated by 12 non repetitive unique spacer regions of similar length. In addition, a leader region, a transposase/IS protein, a leader region, and cas3 were also seen. All seven putative open reading frames carry their ribosome binding sites. Promoter consensus sequences at the -35 and -10 regions and putative intrinsic ρ-independent transcription terminator regions also occurred. A possible long overlap of 170 bp in length occurred between the recB and cas1 loci. Positive reverse transcription PCR signals of cas5, RAMP csd1, csd2-recB/cas1, and cas3 were generated. A putative secondary structure of the CRISPR consensus repeats was constructed. Following this, CRISPR results of the T. equigenitalis EQ59 isolate were subsequently compared with those from the Taylorella asinigenitalis MCE3 isolate.

Corneal topography with an aberrometry-topography system.

PubMed

Mülhaupt, Michael; Dietzko, Sven; Wolffsohn, James; Bandlitz, Stefan

2018-05-07

To investigate the agreement between the central corneal radii and corneal eccentricity measurements generated by the new Wave Analyzer 700 Medica (WAV) compared to the Keratograph 4 (KER) and to test the repeatability of the instruments. 20 subjects (10 male, mean age 29.1 years, range 21-50 years) were recruited from the students and staff of the Cologne School of Optometry. Central corneal radii for the flat (r c/fl ) and steep (r c/st ) meridian as well as corneal eccentricity for the nasal (e nas ), temporal (e temp ), inferior (e inf ) and superior (e sup ) directions were measured using WAV and KER by one examiner in a randomized order. Central radii of the flat (r c/fl ) and steep (r c/st ) meridian measured with both instruments were statically significantly correlated (r = 0.945 and r = 0.951; p < 0.001). Comparison between the WAV and KER showed that r c/fl and r c/st measured with WAV were significantly steeper than those measured with KER (p < 0.001). Corneal eccentricities were statistically significantly correlated in all meridians (p < 0.05). Compared to KER, e temp and e sup measured with WAV were greater (p < 0.05), while there were no statistically significant differences for e nas and e inf (p = 0.350 and p = 0.083). For the central radii, repeated measurements were not significantly different for the KER or WAV (p > 0.05). Limits of agreement (LoA) indicate a better repeatability for the KER compared to WAV. Corneal topography measurements captured with the WAV were strongly correlated with the KER. However, due to the differences in measured corneal radii and eccentricities, the devices cannot be used interchangeably. For corneal topography the KER demonstrated better repeatability. Copyright © 2018 British Contact Lens Association. Published by Elsevier Ltd. All rights reserved.

Is mammalian chromosomal evolution driven by regions of genome fragility?

PubMed Central

Ruiz-Herrera, Aurora; Castresana, Jose; Robinson, Terence J

2006-01-01

Background A fundamental question in comparative genomics concerns the identification of mechanisms that underpin chromosomal change. In an attempt to shed light on the dynamics of mammalian genome evolution, we analyzed the distribution of syntenic blocks, evolutionary breakpoint regions, and evolutionary breakpoints taken from public databases available for seven eutherian species (mouse, rat, cattle, dog, pig, cat, and horse) and the chicken, and examined these for correspondence with human fragile sites and tandem repeats. Results Our results confirm previous investigations that showed the presence of chromosomal regions in the human genome that have been repeatedly used as illustrated by a high breakpoint accumulation in certain chromosomes and chromosomal bands. We show, however, that there is a striking correspondence between fragile site location, the positions of evolutionary breakpoints, and the distribution of tandem repeats throughout the human genome, which similarly reflect a non-uniform pattern of occurrence. Conclusion These observations provide further evidence that certain chromosomal regions in the human genome have been repeatedly used in the evolutionary process. As a consequence, the genome is a composite of fragile regions prone to reorganization that have been conserved in different lineages, and genomic tracts that do not exhibit the same levels of evolutionary plasticity. PMID:17156441

Action of cholinergic poisons on the central nervous system and effectiveness of potential antidotes. Annual report 1 Jul 81-30 Jun 82

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

Samson, F.; Nelson, S.

The research aim was to determine the effects of soman, related organophosphate toxins and potential antidotes on brain regional functions in rats: The (/sup 14/C)-2-deoxyglucose procedure (2-DG) was used for mapping brain regional glucose use. Quantitative autoradiography was used for muscarinic and nicotinic cholinergic receptors. The 2-DG procedure gives a quantitative measure of glucose utilization in brain regions and is in index of the 'functional activity' in brain regions and systems. Values were determined in controls, rats with soman induced seizures, seizures induced by convulsants (DFP, strychnine, picrotoxin, pentylenetetrazol, penicillin) and soman pretreated with TAB. Brain regional cholinergic receptor mapsmore » were prepared and some regional muscarinic and nicotinic receptor densities have been quantified. Soman (112 micrograms/kg i.m.) causes strong, continuous seizures and a dramatic (2-6 fold) increase in the rate of glucose use in 10 major brain regions. Most intense increases were in septum, substants nigra reticularis and outer layer of hippcampal dendata gyrus. The overt seizures of rats induced by convulsants DFP, strychnine, picrotoxin, pentylenetetrazol and penicillin (in hippocampus) were strikingly different from that of rats with soman seizures. High doses (2X LD50) of soman in rats protected with TAB caused a 50% depression of glucose use in most brain regions. The effects of repeated soman exposure on muscarinic and nicotinic receptors are under study.« less

The complete chloroplast genome of Cinnamomum camphora and its comparison with related Lauraceae species.

PubMed

Chen, Caihui; Zheng, Yongjie; Liu, Sian; Zhong, Yongda; Wu, Yanfang; Li, Jiang; Xu, Li-An; Xu, Meng

2017-01-01

Cinnamomum camphora , a member of the Lauraceae family, is a valuable aromatic and timber tree that is indigenous to the south of China and Japan. All parts of Cinnamomum camphora have secretory cells containing different volatile chemical compounds that are utilized as herbal medicines and essential oils. Here, we reported the complete sequencing of the chloroplast genome of Cinnamomum camphora using illumina technology. The chloroplast genome of Cinnamomum camphora is 152,570 bp in length and characterized by a relatively conserved quadripartite structure containing a large single copy region of 93,705 bp, a small single copy region of 19,093 bp and two inverted repeat (IR) regions of 19,886 bp. Overall, the genome contained 123 coding regions, of which 15 were repeated in the IR regions. An analysis of chloroplast sequence divergence revealed that the small single copy region was highly variable among the different genera in the Lauraceae family. A total of 40 repeat structures and 83 simple sequence repeats were detected in both the coding and non-coding regions. A phylogenetic analysis indicated that Calycanthus is most closely related to Lauraceae , both being members of Laurales , which forms a sister group to Magnoliids . The complete sequence of the chloroplast of Cinnamomum camphora will aid in in-depth taxonomical studies of the Lauraceae family in the future. The genetic sequence information will also have valuable applications for chloroplast genetic engineering.

Preliminary toxicity study of dichloromethane extract of Kielmeyera coriacea stems in mice and rats.

PubMed

Obici, Simoni; Otobone, Fernanda Jacques; da Silva Sela, Vânia Ramos; Ishida, Kelly; da Silva, José Carlos; Nakamura, Celso Vataru; Garcia Cortez, Diógenes Aparício; Audi, Elisabeth Aparecida

2008-01-04

Kielmeyera coriacea Mart. (Clusiaceae), known as "Pau Santo" or "Saco de Boi" in the central Brazilian plateau region, is used to treat several tropical diseases. The present study evaluated the toxic effects of dichloromethane (DcM) extract of Kielmeyera coriacea stems, administered to rodents. In the acute toxicity tests, mice receiving doses of this extract by the oral and intraperitoneal routes, showed reversible effects, with LD50 values of 1503.0 and 538.8 mg/kg, respectively. In the repeated-dose oral (90 days) toxicity tests, male and female Wistar rats were treated by gavage with different doses of DcM extract (5, 25 or 125 mg/kg). In biochemical and haematological evaluations, the results varied widely in respect to dose and sex, with no linear profile, and did not show clinical correlations. In the histopathological examinations, the groups exhibited some changes, but there were no significant differences between the groups compared to the controls. In conclusion, these investigations appeared to indicate the safety of acute and repeated oral administration of the DcM extract of Kielmeyera coriacea stems, which can therefore be continuously used with safety.

A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.

PubMed

Beloglazova, Natalia; Brown, Greg; Zimmerman, Matthew D; Proudfoot, Michael; Makarova, Kira S; Kudritska, Marina; Kochinyan, Samvel; Wang, Shuren; Chruszcz, Maksymilian; Minor, Wladek; Koonin, Eugene V; Edwards, Aled M; Savchenko, Alexei; Yakunin, Alexander F

2008-07-18

Clustered regularly interspaced short palindromic repeats (CRISPRs) together with the associated CAS proteins protect microbial cells from invasion by foreign genetic elements using presently unknown molecular mechanisms. All CRISPR systems contain proteins of the CAS2 family, suggesting that these uncharacterized proteins play a central role in this process. Here we show that the CAS2 proteins represent a novel family of endoribonucleases. Six purified CAS2 proteins from diverse organisms cleaved single-stranded RNAs preferentially within U-rich regions. A representative CAS2 enzyme, SSO1404 from Sulfolobus solfataricus, cleaved the phosphodiester linkage on the 3'-side and generated 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides. The crystal structure of SSO1404 was solved at 1.6A resolution revealing the first ribonuclease with a ferredoxin-like fold. Mutagenesis of SSO1404 identified six residues (Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37) that are important for enzymatic activity and suggested that Asp-10 might be the principal catalytic residue. Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs.

Dual Megathrust Slip Behaviors of the 2014 Iquique Earthquake Sequence

NASA Astrophysics Data System (ADS)

Meng, L.; Huang, H.; Burgmann, R.; Ampuero, J. P.; Strader, A. E.

2014-12-01

The transition between seismic rupture and aseismic creep is of central interest to better understand the mechanics of subduction processes. A M 8.2 earthquake occurred on April 1st, 2014 in the Iquique seismic gap of Northern Chile. This event was preceded by a 2-week-long foreshock sequence including a M 6.7 earthquake. Repeating earthquakes are found among the foreshock sequence that migrated towards the mainshock area, suggesting a large scale slow-slip event on the megathrust preceding the mainshock. The variations of the recurrence time of repeating earthquakes highlights the diverse seismic and aseismic slip behaviors on different megathrust segments. The repeaters that were active only before the mainshock recurred more often and were distributed in areas of substantial coseismic slip, while other repeaters occurred both before and after the mainshock in the area complementary to the mainshock rupture. The spatial and temporal distribution of the repeating earthquakes illustrate the essential role of propagating aseismic slip in leading up to the mainshock and aftershock activities. Various finite fault models indicate that the coseismic slip generally occurred down-dip from the foreshock activity and the mainshock hypocenter. Source imaging by teleseismic back-projection indicates an initial down-dip propagation stage followed by a rupture-expansion stage. In the first stage, the finite fault models show slow initiation with low amplitude moment rate at low frequency (< 0.1 Hz), while back-projection shows a steady initiation at high frequency (> 0.5 Hz). This indicates frequency-dependent manifestations of seismic radiation in the low-stress foreshock region. In the second stage, the high-frequency rupture remains within an area of low gravity anomaly, suggesting possible upper-crustal structures that promote high-frequency generation. Back-projection also shows an episode of reverse rupture propagation which suggests a delayed failure of asperities in the foreshock area. Our results highlight the complexity of the interactions between large-scale aseismic slow-slip and dynamic ruptures of megathrust earthquakes.

Association of GPs’ risk attitudes, level of empathy, and burnout status with PSA testing in primary care

PubMed Central

Pedersen, Anette F; Carlsen, Anders H; Vedsted, Peter

2015-01-01

Background Rates of prostate specific antigen (PSA) test ordering vary among GPs. Aim To examine whether GPs’ risk attitude, level of empathy, and burnout status are associated with PSA testing. Design and setting Register and questionnaire study including 129 solo GPs (active in the Central Denmark Region) and 76 672 of their adult male patients with no history of or current prostate cancer diagnosis. Method PSA tests from 2012 were retrieved from a register and classified as incident (that is, the first PSA test within 24 months), repeated normal, or repeated raised tests. This was merged with information on GPs’ risk attitudes, empathy, and burnout status from a 2012 survey. Results Patients registered with a GP with a high score on anxiety caused by uncertainty (odds ratio [OR] 1.03, 95% confidence interval [CI] = 1.00 to 1.06, P = 0.025) or concern about bad outcomes (OR 1.04; 95% CI = 1.00 to 1.08, P = 0.034) were more likely to have an incident PSA test, whereas those registered with a GP with increased tolerance for ambiguity were less likely (OR 0.98, 95% CI = 0.96 to 1.00, P = 0.025). Patients registered with a GP reporting high tolerance for ambiguity (OR 0.96, 95% CI = 0.94 to 0.99, P = 0.009) or high propensity to risk-taking (OR 0.97, 95% CI = 0.93 to 1.00, P = 0.047) were less likely to have a repeated normal PSA test. Conclusion Various aspects of GPs’ risk-taking attitudes were associated with patients’ probability of having an incident and a repeated normal PSA test. The probability of having a repeated raised PSA test was not influenced by any of the psychological factors. Burnout and empathy were not associated with PSA testing. PMID:26541183

Myotonin protein-kinase [AGC]n trinucleotide repeat in seven nonhuman primates

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

Novelli, G.; Sineo, L.; Pontieri, E.

Myotonic dystrophy (DM) is due to a genomic instability of a trinucleotide [AGC]n motif, located at the 3{prime} UTR region of a protein-kinase gene (myotonin protein kinase, MT-PK). The [AGC] repeat is meiotically and mitotically unstable, and it is directly related to the manifestations of the disorder. Although a gene dosage effect of the MT-PK has been demonstrated n DM muscle, the mechanism(s) by which the intragenic repeat expansion leads to disease is largely unknown. This non-standard mutational event could reflect an evolutionary mechanism widespread among animal genomes. We have isolated and sequenced the complete 3{prime}UTR region of the MT-PKmore » gene in seven primates (macaque, orangutan, gorilla, chimpanzee, gibbon, owl monkey, saimiri), and examined by comparative sequence nucleotide analysis the [AGC]n intragenic repeat and the surrounding nucleotides. The genomic organization, including the [AGC]n repeat structure, was conserved in all examined species, excluding the gibbon (Hylobates agilis), in which the [AGC]n upstream sequence (GGAA) is replaced by a GA dinucleotide. The number of [AGC]n in the examined species ranged between 7 (gorilla) and 13 repeats (owl monkeys), with a polymorphism informative content (PIC) similar to that observed in humans. These results indicate that the 3{prime}UTR [AGC] repeat within the MT-PK gene is evolutionarily conserved, supporting that this region has important regulatory functions.« less

40 CFR 81.243 - Central Minnesota Intrastate Air Quality Control Region.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Central Minnesota Intrastate Air... Air Quality Control Regions § 81.243 Central Minnesota Intrastate Air Quality Control Region. The Central Minnesota Intrastate Air Quality Control Region consists of the territorial area encompassed by...

40 CFR 81.243 - Central Minnesota Intrastate Air Quality Control Region.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Central Minnesota Intrastate Air... Air Quality Control Regions § 81.243 Central Minnesota Intrastate Air Quality Control Region. The Central Minnesota Intrastate Air Quality Control Region consists of the territorial area encompassed by...

40 CFR 81.243 - Central Minnesota Intrastate Air Quality Control Region.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Central Minnesota Intrastate Air... Air Quality Control Regions § 81.243 Central Minnesota Intrastate Air Quality Control Region. The Central Minnesota Intrastate Air Quality Control Region consists of the territorial area encompassed by...

40 CFR 81.243 - Central Minnesota Intrastate Air Quality Control Region.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 18 2013-07-01 2013-07-01 false Central Minnesota Intrastate Air... Air Quality Control Regions § 81.243 Central Minnesota Intrastate Air Quality Control Region. The Central Minnesota Intrastate Air Quality Control Region consists of the territorial area encompassed by...

40 CFR 81.243 - Central Minnesota Intrastate Air Quality Control Region.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 18 2014-07-01 2014-07-01 false Central Minnesota Intrastate Air... Air Quality Control Regions § 81.243 Central Minnesota Intrastate Air Quality Control Region. The Central Minnesota Intrastate Air Quality Control Region consists of the territorial area encompassed by...

40 CFR 81.105 - South Central Pennsylvania Intrastate Air Quality Control Region.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 17 2010-07-01 2010-07-01 false South Central Pennsylvania Intrastate... Designation of Air Quality Control Regions § 81.105 South Central Pennsylvania Intrastate Air Quality Control Region. The South Central Pennsylvania Intrastate Air Quality Control Region consists of the territorial...

40 CFR 81.157 - North Central Wisconsin Intrastate Air Quality Control Region.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 18 2012-07-01 2012-07-01 false North Central Wisconsin Intrastate Air... Air Quality Control Regions § 81.157 North Central Wisconsin Intrastate Air Quality Control Region. The North Central Wisconsin Intrastate Air Quality Control Region consists of the territorial area...

40 CFR 81.157 - North Central Wisconsin Intrastate Air Quality Control Region.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 18 2013-07-01 2013-07-01 false North Central Wisconsin Intrastate Air... Air Quality Control Regions § 81.157 North Central Wisconsin Intrastate Air Quality Control Region. The North Central Wisconsin Intrastate Air Quality Control Region consists of the territorial area...

40 CFR 81.157 - North Central Wisconsin Intrastate Air Quality Control Region.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 17 2010-07-01 2010-07-01 false North Central Wisconsin Intrastate Air... Air Quality Control Regions § 81.157 North Central Wisconsin Intrastate Air Quality Control Region. The North Central Wisconsin Intrastate Air Quality Control Region consists of the territorial area...

40 CFR 81.157 - North Central Wisconsin Intrastate Air Quality Control Region.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 18 2014-07-01 2014-07-01 false North Central Wisconsin Intrastate Air... Air Quality Control Regions § 81.157 North Central Wisconsin Intrastate Air Quality Control Region. The North Central Wisconsin Intrastate Air Quality Control Region consists of the territorial area...

40 CFR 81.157 - North Central Wisconsin Intrastate Air Quality Control Region.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 17 2011-07-01 2011-07-01 false North Central Wisconsin Intrastate Air... Air Quality Control Regions § 81.157 North Central Wisconsin Intrastate Air Quality Control Region. The North Central Wisconsin Intrastate Air Quality Control Region consists of the territorial area...

Contrasting Patterns of rDNA Homogenization within the Zygosaccharomyces rouxii Species Complex

PubMed Central

Chand Dakal, Tikam; Giudici, Paolo; Solieri, Lisa

2016-01-01

Arrays of repetitive ribosomal DNA (rDNA) sequences are generally expected to evolve as a coherent family, where repeats within such a family are more similar to each other than to orthologs in related species. The continuous homogenization of repeats within individual genomes is a recombination process termed concerted evolution. Here, we investigated the extent and the direction of concerted evolution in 43 yeast strains of the Zygosaccharomyces rouxii species complex (Z. rouxii, Z. sapae, Z. mellis), by analyzing two portions of the 35S rDNA cistron, namely the D1/D2 domains at the 5’ end of the 26S rRNA gene and the segment including the internal transcribed spacers (ITS) 1 and 2 (ITS regions). We demonstrate that intra-genomic rDNA sequence variation is unusually frequent in this clade and that rDNA arrays in single genomes consist of an intermixing of Z. rouxii, Z. sapae and Z. mellis-like sequences, putatively evolved by reticulate evolutionary events that involved repeated hybridization between lineages. The levels and distribution of sequence polymorphisms vary across rDNA repeats in different individuals, reflecting four patterns of rDNA evolution: I) rDNA repeats that are homogeneous within a genome but are chimeras derived from two parental lineages via recombination: Z. rouxii in the ITS region and Z. sapae in the D1/D2 region; II) intra-genomic rDNA repeats that retain polymorphisms only in ITS regions; III) rDNA repeats that vary only in their D1/D2 domains; IV) heterogeneous rDNA arrays that have both polymorphic ITS and D1/D2 regions. We argue that an ongoing process of homogenization following allodiplodization or incomplete lineage sorting gave rise to divergent evolutionary trajectories in different strains, depending upon temporal, structural and functional constraints. We discuss the consequences of these findings for Zygosaccharomyces species delineation and, more in general, for yeast barcoding. PMID:27501051

Propagation properties of hollow sinh-Gaussian beams in quadratic-index medium

NASA Astrophysics Data System (ADS)

Zou, Defeng; Li, Xiaohui; Pang, Xingxing; Zheng, Hairong; Ge, Yanqi

2017-10-01

Based on the Collins integral formula, the analytical expression for a hollow sinh-Gaussian (HsG) beam propagating through the quadratic-index medium is derived. The propagation properties of a single HsG beam and their interactions have been studied in detail with numerical examples. The results show that inhomogeneity can support self-repeating intensity distributions of HsG beams. With high-ordered beam order n, HsG beams could maintain their initial dark hollow distributions for a longer distance. In addition, interference fringes appear at the interactional region. The central intensity is a prominent peak for two in-phase beams, which is zero for two out-of phase beams. By tuning the initial beam phase shift, the distribution of the fringes can be controlled.

18F-FPEB, a PET radiopharmaceutical for quantifying metabotropic glutamate 5 receptors: a first-in-human study of radiochemical safety, biokinetics, and radiation dosimetry.

PubMed

Wong, Dean F; Waterhouse, Rikki; Kuwabara, Hiroto; Kim, Jongho; Brašić, James R; Chamroonrat, Wichana; Stabins, Michael; Holt, Daniel P; Dannals, Robert F; Hamill, Terence G; Mozley, P David

2013-03-01

Identification of safe and valid PET radioligands for metabotropic glutamate receptor, type 5 (mGluR5), is essential to measure changes in brain mGluR5 in neuropsychiatric disorders, to confirm central mGluR5 occupancy of drug candidates, and to guide dose selection for obtaining an optimum therapeutic window. Here we present the results of a first-in-human study assessing the safety and effectiveness of a novel PET radiopharmaceutical, (18)F-3-fluoro-5-[(pyridin-3-yl)ethynyl]benzonitrile ((18)F-FPEB), for quantifying regional brain concentrations of mGluR5. Quantification of whole-body biokinetics was conducted in 6 healthy adults (3 men and 3 women). The radiation safety profile was estimated with OLINDA/EXM software. Subsequently, pairs of dynamic brain scans were obtained for 11 healthy men to identify optimal methods for derivation of regional distribution volume and binding potential and to determine the repeatability of measurement. The whole-body effective radiation dose was approximately 17 μSv/MBq (62 mrem/mCi), with the gallbladder receiving the highest dose of 190 μSv/MBq. In brain studies, time-activity curves showed high accumulation in the insula/caudate nucleus, moderate uptake in the thalamus, and the lowest concentration in the cerebellum/pons. The plasma reference graphical analysis method appeared optimal for (18)F-FPEB; it showed acceptable test-retest variability of nondisplaceable binding potential (<10%) and identified the highest nondisplaceable binding potential values (from ∼0.5 in the globus pallidus to ∼3.5 in the insula) for target regions. Safety assessments revealed no clinically meaningful changes in vital signs, electrocardiogram, or laboratory values. (18)F-FPEB is safe and well tolerated, and its regional cerebral distribution is consistent with previous reports in the literature for metabotropic glutamate receptors. The repeatability of measurement suggests that (18)F-FPEB is suitable for quantifying mGluR5 in humans.

REPPER—repeats and their periodicities in fibrous proteins

PubMed Central

Gruber, Markus; Söding, Johannes; Lupas, Andrei N.

2005-01-01

REPPER (REPeats and their PERiodicities) is an integrated server that detects and analyzes regions with short gapless repeats in protein sequences or alignments. It finds periodicities by Fourier Transform (FTwin) and internal similarity analysis (REPwin). FTwin assigns numerical values to amino acids that reflect certain properties, for instance hydrophobicity, and gives information on corresponding periodicities. REPwin uses self-alignments and displays repeats that reveal significant internal similarities. Both programs use a sliding window to ensure that different periodic regions within the same protein are detected independently. FTwin and REPwin are complemented by secondary structure prediction (PSIPRED) and coiled coil prediction (COILS), making the server a versatile analysis tool for sequences of fibrous proteins. REPPER is available at . PMID:15980460

Expression levels of DNA replication and repair genes predict regional somatic repeat instability in the brain but are not altered by polyglutamine disease protein expression or age.

PubMed

Mason, Amanda G; Tomé, Stephanie; Simard, Jodie P; Libby, Randell T; Bammler, Theodor K; Beyer, Richard P; Morton, A Jennifer; Pearson, Christopher E; La Spada, Albert R

2014-03-15

Expansion of CAG/CTG trinucleotide repeats causes numerous inherited neurological disorders, including Huntington's disease (HD), several spinocerebellar ataxias and myotonic dystrophy type 1. Expanded repeats are genetically unstable with a propensity to further expand when transmitted from parents to offspring. For many alleles with expanded repeats, extensive somatic mosaicism has been documented. For CAG repeat diseases, dramatic instability has been documented in the striatum, with larger expansions noted with advancing age. In contrast, only modest instability occurs in the cerebellum. Using microarray expression analysis, we sought to identify the genetic basis of these regional instability differences by comparing gene expression in the striatum and cerebellum of aged wild-type C57BL/6J mice. We identified eight candidate genes enriched in cerebellum, and validated four--Pcna, Rpa1, Msh6 and Fen1--along with a highly associated interactor, Lig1. We also explored whether expression levels of mismatch repair (MMR) proteins are altered in a line of HD transgenic mice, R6/2, that is known to show pronounced regional repeat instability. Compared with wild-type littermates, MMR expression levels were not significantly altered in R6/2 mice regardless of age. Interestingly, expression levels of these candidates were significantly increased in the cerebellum of control and HD human samples in comparison to striatum. Together, our data suggest that elevated expression levels of DNA replication and repair proteins in cerebellum may act as a safeguard against repeat instability, and may account for the dramatically reduced somatic instability present in this brain region, compared with the marked instability observed in the striatum.

Validation of an enzyme-linked immunosorbent assay for the quantification of human IgG directed against the repeat region of the circumsporozoite protein of the parasite Plasmodium falciparum

PubMed Central

2012-01-01

Background Several pre-erythrocytic malaria vaccines based on the circumsporozoite protein (CSP) antigen of Plasmodium falciparum are in clinical development. Vaccine immunogenicity is commonly evaluated by the determination of anti-CSP antibody levels using IgG-based assays, but no standard assay is available to allow comparison of the different vaccines. Methods The validation of an anti-CSP repeat region enzyme-linked immunosorbent assay (ELISA) is described. This assay is based on the binding of serum antibodies to R32LR, a recombinant protein composed of the repeat region of P. falciparum CSP. In addition to the original recombinant R32LR, an easy to purify recombinant His-tagged R32LR protein has been constructed to be used as solid phase antigen in the assay. Also, hybridoma cell lines have been generated producing human anti-R32LR monoclonal antibodies to be used as a potential inexhaustible source of anti-CSP repeats standard, instead of a reference serum. Results The anti-CSP repeats ELISA was shown to be robust, specific and linear within the analytical range, and adequately fulfilled all validation criteria as defined in the ICH guidelines. Furthermore, the coefficient of variation for repeatability and intermediate precision did not exceed 23%. Non-interference was demonstrated for R32LR-binding sera, and the assay was shown to be stable over time. Conclusions This ELISA, specific for antibodies directed against the CSP repeat region, can be used as a standard assay for the determination of humoral immunogenicity in the development of any CSP-based P. falciparum malaria vaccine. PMID:23173602

In vitro characterization of the RS motif in N-terminal head domain of goldfish germinal vesicle lamin B3 necessary for phosphorylation of the p34cdc2 target serine by SRPK1☆

PubMed Central

Yamaguchi, Akihiko; Iwatani, Miho; Ogawa, Mariko; Kitano, Hajime; Matsuyama, Michiya

2013-01-01

The nuclear envelopes surrounding the oocyte germinal vesicles of lower vertebrates (fish and frog) are supported by the lamina, which consists of the protein lamin B3 encoded by a gene found also in birds but lost in the lineage leading to mammals. Like other members of the lamin family, goldfish lamin B3 (gfLB3) contains two putative consensus phosphoacceptor p34cdc2 sites (Ser-28 and Ser-398) for the M-phase kinase to regulate lamin polymerization on the N- and C-terminal regions flanking a central rod domain. Partial phosphorylation of gfLB3 occurs on Ser-28 in the N-terminal head domain in immature oocytes prior to germinal vesicle breakdown, which suggests continual rearrangement of lamins by a novel lamin kinase in fish oocytes. We applied the expression-screening method to isolate lamin kinases by using phosphorylation site Ser-28-specific monoclonal antibody and a vector encoding substrate peptides from a goldfish ovarian cDNA library. As a result, SRPK1 was screened as a prominent lamin kinase candidate. The gfLB3 has a short stretch of the RS repeats (9-SRASTVRSSRRS-20) upstream of the Ser-28, within the N-terminal head. This stretch of repeats is conserved among fish lamin B3 but is not found in other lamins. In vitro phosphorylation studies and GST-pull down assay revealed that SRPK1 bound to the region of sequential RS repeats (9–20) with affinity and recruited serine into the active site by a grab-and-pull manner. These results indicate SRPK1 may phosphorylate the p34cdc2 site in the N-terminal head of GV-lamin B3 at the RS motifs, which have the general property of aggregation. PMID:23772390

Effect of central neurotropic substances on the hypophysisadrenal cortex system during immobilization of animals

NASA Technical Reports Server (NTRS)

Ryzhenkov, V. Y.

1980-01-01

The immobilization of guinea pigs for 5, 12, 24 and 48 hours, by securing to a slab, results in a persistent rise of the blood plasma 17-oxycorticosteroid concentration. Repeated administration of phenobarbital (50 mg/kg) and of the sodium salt of gamma-oxybutyric acid (500 mg/kg), as well as the combined administration of central m- and n-cholinolytics with small doses of phenobarbital tends to inhibit activation of the adrenal cortex during 48 hour immobilization of the animals. Repeated administration of aminazine (20 mg/kg) tends to decrease activation of the adrenal cortex. The administration of reserpine (0.1-5 mg/kg) 12-18 hours before immobilization of guinea pigs increases the response of the hypophysis-adrenal cortex system.

40 CFR 81.127 - Central New York Intrastate Air Quality Control Region.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Central New York Intrastate Air... Air Quality Control Regions § 81.127 Central New York Intrastate Air Quality Control Region. The Central New York Intrastate Air Quality Control Region consists of the territorial area encompassed by the...

40 CFR 81.95 - Central Florida Intrastate Air Quality Control Region.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Quality Control Regions § 81.95 Central Florida Intrastate Air Quality Control Region. The Central Florida Intrastate Air Quality Control Region consists of the territorial area encompassed by the boundaries of the... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Central Florida Intrastate Air Quality...

40 CFR 81.95 - Central Florida Intrastate Air Quality Control Region.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Quality Control Regions § 81.95 Central Florida Intrastate Air Quality Control Region. The Central Florida Intrastate Air Quality Control Region consists of the territorial area encompassed by the boundaries of the... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Central Florida Intrastate Air Quality...

A novel tandem repeat sequence located on human chromosome 4p: isolation and characterization.

PubMed

Kogi, M; Fukushige, S; Lefevre, C; Hadano, S; Ikeda, J E

1997-06-01

In an effort to analyze the genomic region of the distal half of human chromosome 4p, to where Huntington disease and other diseases have been mapped, we have isolated the cosmid clone (CRS447) that was likely to contain a region with specific repeat sequences. Clone CRS447 was subjected to detailed analysis, including chromosome mapping, restriction mapping, and DNA sequencing. Chromosome mapping by both a human-CHO hybrid cell panel and FISH revealed that CRS447 was predominantly located in the 4p15.1-15.3 region. CRS447 was shown to consist of tandem repeats of 4.7-kb units present on chromosome 4p. A single EcoRI unit was subcloned (pRS447), and the complete sequence was determined as 4752 nucleotides. When pRS447 was used as a probe, the number of copies of this repeat per haploid genome was estimated to be 50-70. Sequence analysis revealed that it contained two internal CA repeats and one putative ORF. Database search established that this sequence was unreported. However, two homologous STS markers were found in the database. We concluded that CRS447/pRS447 is a novel tandem repeat sequence that is mainly specific to human chromosome 4p.

From NGS assembly challenges to instability of fungal mitochondrial genomes: A case study in genome complexity.

PubMed

Misas, Elizabeth; Muñoz, José Fernando; Gallo, Juan Esteban; McEwen, Juan Guillermo; Clay, Oliver Keatinge

2016-04-01

The presence of repetitive or non-unique DNA persisting over sizable regions of a eukaryotic genome can hinder the genome's successful de novo assembly from short reads: ambiguities in assigning genome locations to the non-unique subsequences can result in premature termination of contigs and thus overfragmented assemblies. Fungal mitochondrial (mtDNA) genomes are compact (typically less than 100 kb), yet often contain short non-unique sequences that can be shown to impede their successful de novo assembly in silico. Such repeats can also confuse processes in the cell in vivo. A well-studied example is ectopic (out-of-register, illegitimate) recombination associated with repeat pairs, which can lead to deletion of functionally important genes that are located between the repeats. Repeats that remain conserved over micro- or macroevolutionary timescales despite such risks may indicate functionally or structurally (e.g., for replication) important regions. This principle could form the basis of a mining strategy for accelerating discovery of function in genome sequences. We present here our screening of a sample of 11 fully sequenced fungal mitochondrial genomes by observing where exact k-mer repeats occurred several times; initial analyses motivated us to focus on 17-mers occurring more than three times. Based on the diverse repeats we observe, we propose that such screening may serve as an efficient expedient for gaining a rapid but representative first insight into the repeat landscapes of sparsely characterized mitochondrial chromosomes. Our matching of the flagged repeats to previously reported regions of interest supports the idea that systems of persisting, non-trivial repeats in genomes can often highlight features meriting further attention. Copyright © 2016 Elsevier Ltd. All rights reserved.

Disruption of Higher Order DNA Structures in Friedreich’s Ataxia (GAA)n Repeats by PNA or LNA Targeting

PubMed Central

Bergquist, Helen; Rocha, Cristina S. J.; Álvarez-Asencio, Rubén; Nguyen, Chi-Hung; Rutland, Mark. W.; Smith, C. I. Edvard; Good, Liam; Nielsen, Peter E.; Zain, Rula

2016-01-01

Expansion of (GAA)n repeats in the first intron of the Frataxin gene is associated with reduced mRNA and protein levels and the development of Friedreich’s ataxia. (GAA)n expansions form non-canonical structures, including intramolecular triplex (H-DNA), and R-loops and are associated with epigenetic modifications. With the aim of interfering with higher order H-DNA (like) DNA structures within pathological (GAA)n expansions, we examined sequence-specific interaction of peptide nucleic acid (PNA) with (GAA)n repeats of different lengths (short: n=9, medium: n=75 or long: n=115) by chemical probing of triple helical and single stranded regions. We found that a triplex structure (H-DNA) forms at GAA repeats of different lengths; however, single stranded regions were not detected within the medium size pathological repeat, suggesting the presence of a more complex structure. Furthermore, (GAA)4-PNA binding of the repeat abolished all detectable triplex DNA structures, whereas (CTT)5-PNA did not. We present evidence that (GAA)4-PNA can invade the DNA at the repeat region by binding the DNA CTT strand, thereby preventing non-canonical-DNA formation, and that triplex invasion complexes by (CTT)5-PNA form at the GAA repeats. Locked nucleic acid (LNA) oligonucleotides also inhibited triplex formation at GAA repeat expansions, and atomic force microscopy analysis showed significant relaxation of plasmid morphology in the presence of GAA-LNA. Thus, by inhibiting disease related higher order DNA structures in the Frataxin gene, such PNA and LNA oligomers may have potential for discovery of drugs aiming at recovering Frataxin expression. PMID:27846236

Heterogeneity of the Epstein-Barr Virus (EBV) Major Internal Repeat Reveals Evolutionary Mechanisms of EBV and a Functional Defect in the Prototype EBV Strain B95-8.

PubMed

Ba Abdullah, Mohammed M; Palermo, Richard D; Palser, Anne L; Grayson, Nicholas E; Kellam, Paul; Correia, Samantha; Szymula, Agnieszka; White, Robert E

2017-12-01

Epstein-Barr virus (EBV) is a ubiquitous pathogen of humans that can cause several types of lymphoma and carcinoma. Like other herpesviruses, EBV has diversified through both coevolution with its host and genetic exchange between virus strains. Sequence analysis of the EBV genome is unusually challenging because of the large number and lengths of repeat regions within the virus. Here we describe the sequence assembly and analysis of the large internal repeat 1 of EBV (IR1; also known as the BamW repeats) for more than 70 strains. The diversity of the latency protein EBV nuclear antigen leader protein (EBNA-LP) resides predominantly within the exons downstream of IR1. The integrity of the putative BWRF1 open reading frame (ORF) is retained in over 80% of strains, and deletions truncating IR1 always spare BWRF1. Conserved regions include the IR1 latency promoter (Wp) and one zone upstream of and two within BWRF1. IR1 is heterogeneous in 70% of strains, and this heterogeneity arises from sequence exchange between strains as well as from spontaneous mutation, with interstrain recombination being more common in tumor-derived viruses. This genetic exchange often incorporates regions of <1 kb, and allelic gene conversion changes the frequency of small regions within the repeat but not close to the flanks. These observations suggest that IR1-and, by extension, EBV-diversifies through both recombination and breakpoint repair, while concerted evolution of IR1 is driven by gene conversion of small regions. Finally, the prototype EBV strain B95-8 contains four nonconsensus variants within a single IR1 repeat unit, including a stop codon in the EBNA-LP gene. Repairing IR1 improves EBNA-LP levels and the quality of transformation by the B95-8 bacterial artificial chromosome (BAC). IMPORTANCE Epstein-Barr virus (EBV) infects the majority of the world population but causes illness in only a small minority of people. Nevertheless, over 1% of cancers worldwide are attributable to EBV. Recent sequencing projects investigating virus diversity to see if different strains have different disease impacts have excluded regions of repeating sequence, as they are more technically challenging. Here we analyze the sequence of the largest repeat in EBV (IR1). We first characterized the variations in protein sequences encoded across IR1. In studying variations within the repeat of each strain, we identified a mutation in the main laboratory strain of EBV that impairs virus function, and we suggest that tumor-associated viruses may be more likely to contain DNA mixed from two strains. The patterns of this mixing suggest that sequences can spread between strains (and also within the repeat) by copying sequence from another strain (or repeat unit) to repair DNA damage. Copyright © 2017 Ba abdullah et al.

Advancing The Cancer Genome Atlas glioma MRI collections with expert segmentation labels and radiomic features

PubMed Central

Bakas, Spyridon; Akbari, Hamed; Sotiras, Aristeidis; Bilello, Michel; Rozycki, Martin; Kirby, Justin S.; Freymann, John B.; Farahani, Keyvan; Davatzikos, Christos

2017-01-01

Gliomas belong to a group of central nervous system tumors, and consist of various sub-regions. Gold standard labeling of these sub-regions in radiographic imaging is essential for both clinical and computational studies, including radiomic and radiogenomic analyses. Towards this end, we release segmentation labels and radiomic features for all pre-operative multimodal magnetic resonance imaging (MRI) (n=243) of the multi-institutional glioma collections of The Cancer Genome Atlas (TCGA), publicly available in The Cancer Imaging Archive (TCIA). Pre-operative scans were identified in both glioblastoma (TCGA-GBM, n=135) and low-grade-glioma (TCGA-LGG, n=108) collections via radiological assessment. The glioma sub-region labels were produced by an automated state-of-the-art method and manually revised by an expert board-certified neuroradiologist. An extensive panel of radiomic features was extracted based on the manually-revised labels. This set of labels and features should enable i) direct utilization of the TCGA/TCIA glioma collections towards repeatable, reproducible and comparative quantitative studies leading to new predictive, prognostic, and diagnostic assessments, as well as ii) performance evaluation of computer-aided segmentation methods, and comparison to our state-of-the-art method. PMID:28872634

Mechanical Properties of β-Catenin Revealed by Single-Molecule Experiments

PubMed Central

Valbuena, Alejandro; Vera, Andrés Manuel; Oroz, Javier; Menéndez, Margarita; Carrión-Vázquez, Mariano

2012-01-01

β-catenin is a central component of the adaptor complex that links cadherins to the actin cytoskeleton in adherens junctions and thus, it is a good candidate to sense and transmit mechanical forces to trigger specific changes inside the cell. To fully understand its molecular physiology, we must first investigate its mechanical role in mechanotransduction within the cadherin system. We have studied the mechanical response of β-catenin to stretching using single-molecule force spectroscopy and molecular dynamics. Unlike most proteins analyzed to date, which have a fixed mechanical unfolding pathway, the β-catenin armadillo repeat region (ARM) displays low mechanostability and multiple alternative unfolding pathways that seem to be modulated by its unstructured termini. These results are supported by steered molecular dynamics simulations, which also predict its mechanical stabilization and unfolding pathway restrictions when the contiguous α-helix of the C-terminal unstructured region is included. Furthermore, simulations of the ARM/E-cadherin cytosolic tail complex emulating the most probable stress geometry occurring in vivo show a mechanical stabilization of the interaction whose magnitude correlates with the length of the stretch of the cadherin cytosolic tail that is in contact with the ARM region. PMID:23083718

Association between arginine vasopressin 1a receptor (AVPR1a) promoter region polymorphisms and prepulse inhibition.

PubMed

Levin, Raz; Heresco-Levy, Uriel; Bachner-Melman, Rachel; Israel, Salomon; Shalev, Idan; Ebstein, Richard P

2009-07-01

Arginine vasopressin and the arginine vasopressin 1a (AVPR1a) gene contribute to a range of social behaviors both in lower vertebrates and in humans. Human promoter-region microsatellite repeat regions (RS1 and RS3) in the AVPR1a gene region have been associated with autism spectrum disorders, prosocial behavior and social cognition. Prepulse inhibition (PPI) of the startle response to auditory stimuli is a largely autonomic response that resonates with social cognition in both animal models and humans. Reduced PPI has been observed in disorders including schizophrenia that are distinguished by deficits in social skills. In the current investigation association was examined between PPI and the AVPR1a RS1 and RS repeat regions and PPI in a group of 113 nonclinical subjects. Using a robust family-based strategy, association was observed between AVPR1a promoter-region repeat length, especially RS3) and PPI (30 ms: global p=0.04; 60 ms p=0.006; 120 ms p=0.008). Notably, longer RS3 alleles were associated with greater levels of prepulse inhibition. Using a short/long classification scheme for the repeat regions, significant association was also observed between all three PPI intervals (30, 60 and 120 ms) and both RS1 and RS3 polymorphisms (PBAT: FBAT-PC(2) statistic p=0.047). Tests of within-subject effects (SPSS GLM) showed significant sexxRS3 interactions at 30 ms (p=0.045) and 60 ms (p=0.01). Longer alleles, especially in male subjects, are associated with significantly higher PPI response, consistent with a role for the promoter repeat region in partially molding social behavior in both animals and humans. This is the first report in humans demonstrating a role of the AVPR1a gene in contributing to the PPI response to auditory stimuli.

Structures of ω repressors bound to direct and inverted DNA repeats explain modulation of transcription

PubMed Central

Weihofen, Wilhelm Andreas; Cicek, Aslan; Pratto, Florencia; Alonso, Juan Carlos; Saenger, Wolfram

2006-01-01

Repressor ω regulates transcription of genes required for copy number control, accurate segregation and stable maintenance of inc18 plasmids hosted by Gram-positive bacteria. ω belongs to homodimeric ribbon-helix-helix (RHH2) repressors typified by a central, antiparallel β-sheet for DNA major groove binding. Homodimeric ω2 binds cooperatively to promotors with 7 to 10 consecutive non-palindromic DNA heptad repeats (5′-A/TATCACA/T-3′, symbolized by →) in palindromic inverted, converging (→←) or diverging (←→) orientation and also, unique to ω2 and contrasting other RHH2 repressors, to non-palindromic direct (→→) repeats. Here we investigate with crystal structures how ω2 binds specifically to heptads in minimal operators with (→→) and (→←) repeats. Since the pseudo-2-fold axis relating the monomers in ω2 passes the central C–G base pair of each heptad with ∼0.3 Å downstream offset, the separation between the pseudo-2-fold axes is exactly 7 bp in (→→), ∼0.6 Å shorter in (→←) but would be ∼0.6 Å longer in (←→). These variations grade interactions between adjacent ω2 and explain modulations in cooperative binding affinity of ω2 to operators with different heptad orientations. PMID:16528102

40 CFR 81.104 - Central Pennsylvania Intrastate Air Quality Control Region.

Code of Federal Regulations, 2011 CFR

2011-07-01

... Quality Control Region. 81.104 Section 81.104 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.104 Central Pennsylvania Intrastate Air Quality Control Region. The Central Pennsylvania Intrastate Air Quality Control Region consists of the territorial area encompassed by...

40 CFR 81.104 - Central Pennsylvania Intrastate Air Quality Control Region.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Quality Control Region. 81.104 Section 81.104 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY... Air Quality Control Regions § 81.104 Central Pennsylvania Intrastate Air Quality Control Region. The Central Pennsylvania Intrastate Air Quality Control Region consists of the territorial area encompassed by...

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

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

Bond, C.E.; Hodes, M.E.

1994-09-01

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 designingmore » 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.« less

The repeat organizer, a specialized insulator element within the intergenic spacer of the Xenopus rRNA genes.

PubMed Central

Robinett, C C; O'Connor, A; Dunaway, M

1997-01-01

We have identified a novel activity for the region of the intergenic spacer of the Xenopus laevis rRNA genes that contains the 35- and 100-bp repeats. We devised a new assay for this region by constructing DNA plasmids containing a tandem repeat of rRNA reporter genes that were separated by the 35- and 100-bp repeat region and a rRNA gene enhancer. When the 35- and 100-bp repeat region is present in its normal position and orientation at the 3' end of the rRNA reporter genes, the enhancer activates the adjacent downstream promoter but not the upstream rRNA promoter on the same plasmid. Because this element can restrict the range of an enhancer's activity in the context of tandem genes, we have named it the repeat organizer (RO). The ability to restrict enhancer action is a feature of insulator elements, but unlike previously described insulator elements the RO does not block enhancer action in a simple enhancer-blocking assay. Instead, the activity of the RO requires that it be in its normal position and orientation with respect to the other sequence elements of the rRNA genes. The enhancer-binding transcription factor xUBF also binds to the repetitive sequences of the RO in vitro, but these sequences do not activate transcription in vivo. We propose that the RO is a specialized insulator element that organizes the tandem array of rRNA genes into single-gene expression units by promoting activation of a promoter by its proximal enhancers. PMID:9111359

Genetic Studies of the Prp17 Gene of Saccharomyces Cerevisiae: A Domain Essential for Function Maps to a Nonconserved Region of the Protein

PubMed Central

Seshadri, V.; Vaidya, V. C.; Vijayraghavan, U.

1996-01-01

The PRP17 gene product is required for the second step of pre-mRNA splicing reactions. The C-terminal half of this protein bears four repeat units with homology to the β transducin repeat. Missense mutations in three temperature-sensitive prp17 mutants map to a region in the N-terminal half of the protein. We have generated, in vitro, 11 missense alleles at the β transducin repeat units and find that only one affects function in vivo. A phenotypically silent missense allele at the fourth repeat unit enhances the slow-growing phenotype conferred by an allele at the third repeat, suggesting an interaction between these domains. Although many missense mutations in highly conserved amino acids lack phenotypic effects, deletion analysis suggests an essential role for these units. Only mutations in the N-terminal nonconserved domain of PRP17 are synthetically lethal in combination with mutations in PRP16 and PRP18, two other gene products required for the second splicing reaction. A mutually allele-specific interaction between prp17 and snr7, with mutations in U5 snRNA, was observed. We therefore suggest that the functional region of Prp17p that interacts with Prp18p, Prp16p, and U5 snRNA is in the N terminal region of the protein. PMID:8722761

Molecular identification and characterization of clustered regularly interspaced short palindromic repeats (CRISPRs) in a urease-positive thermophilic Campylobacter sp. (UPTC).

PubMed

Tasaki, E; Hirayama, J; Tazumi, A; Hayashi, K; Hara, Y; Ueno, H; Moore, J E; Millar, B C; Matsuda, M

2012-02-01

Novel clustered regularly-interspaced short palindromic repeats (CRISPRs) locus [7,500 base pairs (bp) in length] occurred in the urease-positive thermophilic Campylobacter (UPTC) Japanese isolate, CF89-12. The 7,500 bp gene loci consisted of the 5'-methylaminomethyl-2-thiouridylate methyltransferase gene, putative (P) CRISPR associated (p-Cas), putative open reading frames, Cas1 and Cas2, leader sequence region (146 bp), 12 CRISPRs consensus sequence repeats (each 36 bp) separated by a non-repetitive unique spacer region of similar length (26-31 bp) and the phosphatidyl glycerophosphatase A gene. When the CRISPRs loci in the UPTC CF89-12 and five C. jejuni isolates were compared with one another, these six isolates contained p-Cas, Cas1 and Cas2 within the loci. Four to 12 CRISPRs consensus sequence repeats separated by a non-repetitive unique spacer region occurred in six isolates and the nucleotide sequences of those repeats gave approximately 92-100% similarity with each other. However, no sequence similarity occurred in the unique spacer regions among these isolates. The putative σ(70) transcriptional promoter and the hypothetical ρ-independent terminator structures for the CRISPRs and Cas were detected. No in vivo transcription of p-Cas, Cas1 and Cas2 was confirmed in the UPTC cells.

Entry into the nuclear pore complex is controlled by a cytoplasmic exclusion zone containing dynamic GLFG-repeat nucleoporin domains.

PubMed

Fiserova, Jindriska; Spink, Matthew; Richards, Shane A; Saunter, Christopher; Goldberg, Martin W

2014-01-01

Nuclear pore complexes (NPCs) mediate nucleocytoplasmic movement. The central channel contains proteins with phenylalanine-glycine (FG) repeats, or variations (GLFG, glycine-leucine-phenylalanine-glycine). These are 'intrinsically disordered' and often represent weak interaction sites that become ordered upon interaction. We investigated this possibility during nuclear transport. Using electron microscopy of S. cerevisiae, we show that NPC cytoplasmic filaments form a dome-shaped structure enclosing GLFG domains. GLFG domains extend out of this structure and are part of an 'exclusion zone' that might act as a partial barrier to entry of transport-inert proteins. The anchor domain of a GLFG nucleoporin locates exclusively to the central channel. By contrast, the localisation of the GLFG domains varied between NPCs and could be cytoplasmic, central or nucleoplasmic and could stretch up to 80 nm. These results suggest a dynamic exchange between ordered and disordered states. In contrast to diffusion through the NPC, transport cargoes passed through the exclusion zone and accumulated near the central plane. We also show that movement of cargo through the NPC is accompanied by relocation of GLFG domains, suggesting that binding, restructuring and movement of these domains could be part of the translocation mechanism.

A Comparative Proteomic Analysis of the Simple Amino Acid Repeat Distributions in Plasmodia Reveals Lineage Specific Amino Acid Selection

PubMed Central

Dalby, Andrew R.

2009-01-01

Background Microsatellites have been used extensively in the field of comparative genomics. By studying microsatellites in coding regions we have a simple model of how genotypic changes undergo selection as they are directly expressed in the phenotype as altered proteins. The simplest of these tandem repeats in coding regions are the tri-nucleotide repeats which produce a repeat of a single amino acid when translated into proteins. Tri-nucleotide repeats are often disease associated, and are also known to be unstable to both expansion and contraction. This makes them sensitive markers for studying proteome evolution, in closely related species. Results The evolutionary history of the family of malarial causing parasites Plasmodia is complex because of the life-cycle of the organism, where it interacts with a number of different hosts and goes through a series of tissue specific stages. This study shows that the divergence between the primate and rodent malarial parasites has resulted in a lineage specific change in the simple amino acid repeat distribution that is correlated to A–T content. The paper also shows that this altered use of amino acids in SAARs is consistent with the repeat distributions being under selective pressure. Conclusions The study shows that simple amino acid repeat distributions can be used to group related species and to examine their phylogenetic relationships. This study also shows that an outgroup species with a similar A–T content can be distinguished based only on the amino acid usage in repeats, and suggest that this might be a useful feature for proteome clustering. The lineage specific use of amino acids in repeat regions suggests that comparative studies of SAAR distributions between proteomes gives an insight into the mechanisms of expansion and the selective pressures acting on the organism. PMID:19597555

Insights into intragenic and extragenic effectors of prion propagation using chimeric prion proteins

PubMed Central

Kalastavadi, Tejas; Tank, Elizabeth MH

2008-01-01

The study of fungal prion proteins affords remarkable opportunities to elucidate both intragenic and extragenic effectors of prion propagation. The yeast prion protein Sup35 and the self-perpetuating [PSI+] prion state is one of the best characterized fungal prions. While there is little sequence homology among known prion proteins, one region of striking similarity exists between Sup35p and the mammalian prion protein PrP. This region is comprised of roughly five octapeptide repeats of similar composition. The expansion of the repeat region in PrP is associated with inherited prion diseases. In order to learn more about the effects of PrP repeat expansions on the structural properties of a protein that undergoes a similar transition to a self-perpetuating aggregate, we generated chimeric Sup35-PrP proteins. Using both in vivo and in vitro systems we described the effect of repeat length on protein misfolding, aggregation, amyloid formation and amyloid stability. We found that repeat expansions in the chimeric prion proteins increase the propensity to initiate prion propagation and enhance the formation of amyloid fibers without significantly altering fiber stability. PMID:19098443

Combined deficiency of MSH2 and Sμ region abolishes class switch recombination.

PubMed

Leduc, Claire; Haddad, Dania; Laviolette-Malirat, Nathalie; Nguyen Huu, Ngoc-Sa; Khamlichi, Ahmed Amine

2010-10-01

Class switch recombination (CSR) is mediated by G-rich tandem repeated sequences termed switch regions. Transcription of switch regions generates single-stranded R loops that provide substrates for activation-induced cytidine deaminase. Mice deficient in MSH2 have a mild defect in CSR and analysis of their switch junctions has led to a model in which MSH2 is more critical for switch recombination events outside than within the tandem repeats. It is also known that deletion of the whole Sμ region severely impairs but does not abrogate CSR despite the lack of detectable R loops. Here, we demonstrate that deficiency of both MSH2 and the Sμ region completely abolishes CSR and that the abrogation occurs at the genomic level. This finding further supports the crucial role of MSH2 outside the tandem repeats. It also indicates that during CSR, MSH2 has access to activation-induced cytidine deaminase targets in R-loop-deficient Iμ-Cμ sequences rarely used in CSR, suggesting an MSH2-dependent DNA processing activity at the Iμ exon that may decrease with transcription elongation across the Sμ region.

Methods for sequencing GC-rich and CCT repeat DNA templates

DOEpatents

Robinson, Donna L.

2007-02-20

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.

Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens.

PubMed

Maze, Ian; Feng, Jian; Wilkinson, Matthew B; Sun, HaoSheng; Shen, Li; Nestler, Eric J

2011-02-15

Repeated cocaine exposure induces persistent alterations in genome-wide transcriptional regulatory networks, chromatin remodeling activity and, ultimately, gene expression profiles in the brain's reward circuitry. Virtually all previous investigations have centered on drug-mediated effects occurring throughout active euchromatic regions of the genome, with very little known concerning the impact of cocaine exposure on the regulation and maintenance of heterochromatin in adult brain. Here, we report that cocaine dramatically and dynamically alters heterochromatic histone H3 lysine 9 trimethylation (H3K9me3) in the nucleus accumbens (NAc), a key brain reward region. Furthermore, we demonstrate that repeated cocaine exposure causes persistent decreases in heterochromatization in this brain region, suggesting a potential role for heterochromatic regulation in the long-term actions of cocaine. To identify precise genomic loci affected by these alterations, chromatin immunoprecipitation followed by massively parallel DNA sequencing (ChIP-Seq) was performed on NAc. ChIP-Seq analyses confirmed the existence of the H3K9me3 mark mainly within intergenic regions of the genome and identified specific patterns of cocaine-induced H3K9me3 regulation at repetitive genomic sequences. Cocaine-mediated decreases in H3K9me3 enrichment at specific genomic repeats [e.g., long interspersed nuclear element (LINE)-1 repeats] were further confirmed by the increased expression of LINE-1 retrotransposon-associated repetitive elements in NAc. Such increases likely reflect global patterns of genomic destabilization in this brain region after repeated cocaine administration and open the door for future investigations into the epigenetic and genetic basis of drug addiction.

Repeatability and reproducibility of corneal thickness using SOCT Copernicus HR.

PubMed

Vidal, Silvia; Viqueira, Valentín; Mas, David; Domenech, Begoña

2013-05-01

The aim of this study is to determine the reliability of corneal thickness measurements derived from SOCT Copernicus HR (Fourier domain OCT). Thirty healthy eyes of 30 subjects were evaluated. One eye of each patient was chosen randomly. Images were obtained of the central (up to 2.0 mm from the corneal apex) and paracentral (2.0 to 4.0 mm) cornea. We assessed corneal thickness (central and paracentral) and epithelium thickness. The intra-observer repeatability data were analysed using the intra-class correlation coefficient (ICC) for a range of 95 per cent within-subject standard deviation (S(W)) and the within-subject coefficient of variation (C(W)). The level of agreement by Bland-Altman analysis was also represented for the study of the reproducibility between observers and agreement between methods of measurement (automatic versus manual). The mean value of the central corneal thickness (CCT) was 542.4 ± 30.1 μm (SD). There was a high intra-observer agreement, finding the best result in the central sector with an intra-class correlation coefficient of 0.99, 95 per cent CI (0.989 to 0.997) and the worst, in the minimum corneal thickness, with an intra-class correlation coefficient of 0.672, 95 per cent CI (0.417 to 0.829). Reproducibility between observers was very high. The best result was found in the central sector thickness obtained both manually and automatically with an intra-class correlation coefficient of 0.990 in both cases and the worst result in the maximum corneal thickness with an intra-class correlation coefficient of 0.827. The agreement between measurement methods was also very high with intra-class correlation coefficient greater than 0.91. On the other hand the repeatability and reproducibility for epithelial measurements was poor. Pachymetric mapping with SOCT Copernicus HR was found to be highly repeatable and reproducible. We found that the device lacks an appropriate ergonomic design as proper focusing of the laser beam onto the cornea for anterior segment scanning required that patients were positioned slightly farther away from the machine head-rest than in the setup for retinal imaging. © 2013 The Authors. Clinical and Experimental Optometry © 2013 Optometrists Association Australia.

Reducing unplanned pregnancy and abortion in Zimbabwe through postabortion contraception.

PubMed

Johnson, Brooke R; Ndhlovu, Singatsho; Farr, Sherry L; Chipato, Tsungai

2002-06-01

In many countries, women treated for complications from spontaneous or unsafely induced abortion lack access to contraceptive services. As a result, many of them soon have a subsequent unplanned pregnancy or a repeat abortion, placing their health at increased risk. This report presents the results of a prospective intervention study on postabortion family planning conducted in the two largest public hospitals in Zimbabwe. Women at Harare Central Hospital, in the capital, received a postabortion family planning intervention, and Mpilo Central Hospital, in Bulawayo, served as the control site. The study cohort was 982 women, 527 of whom were followed for a 12-month period. During the follow-up period, significantly more women used highly effective methods of contraception, significantly fewer unplanned pregnancies occurred, and fewer repeat abortions were performed at the intervention site than at the control site. These results offer compelling evidence that ward-based contraceptive services provided to women treated for incomplete abortion can significantly reduce subsequent unplanned pregnancies. The results also suggest that postabortion family planning services can reduce the incidence of repeat abortion.

Meiotic synapsis of homogeneously staining regions (HSRs) in chromosome 1 of Mus musculus.

PubMed

Winking, H; Reuter, C; Traut, W

1993-05-01

About 50 copies of a long-range repeat DNA family with a repeat size of roughly 100 kb and with sequence homology to mRNAs are clustered in the G-light band D of chromosome 1 of the house mouse, Mus musculus. We studied amplified versions of the cluster which are found in many wild populations of M. musculus. They are cytogenetically conspicuous as one or two C-band positive homogeneously staining regions (single- and double band HSRs) which increase the mitotic length of chromosome 1. The double band HSR was phylogenetically derived from a single band HSR by a paracentric inversion. In homozygous condition, such HSRs contribute, albeit not as much as expected from their mitotic length, to the synaptonemal complex (SC) length of chromosome 1. In HSR heterozygous animals an elongation of the SCs was not noticeable. In single band HSR heterozygous males, synapsis proceeds regularly and continuously from the distal telomere towards the centromeric end without forming buckles. Thus, the single band HSR has no adverse effect on pairing. The same straight pairing behaviour was found in the majority of double band HSR heterozygous spermatocytes. This shows that extensive nonhomologous pairing can take place in the earliest phase of synapsis. Synapsis was discontinuous, leaving the central part of the bivalent 1 asynapsed, in only 14.3% of double band HSR heterozygous cells. In such cells the chromosome 1 SC is completed at a later stage of meiosis. The delay is presumably an effect of the inversion that includes one HSR band and the segment between the two HSR bands.

Isolation and molecular analysis of inv dup(15) and construction of a physical map of a common breakpoint in order to elucidate their mechanism of formation.

PubMed

Wandstrat, A E; Schwartz, S

2000-11-01

An inverted duplication of chromosome 15 [inv dup(15)] is the most common supernumerary marker chromosome, comprising approximately 50% of all chromosomes in this class. Structurally, the inv dup(15) is a mirror image with the central axis defining a distal break within either the heterochromatic alpha-satellite array or along the euchromatin in the long (q) arm of the chromosome. There are several types of inv dup(15), classified by the amount of euchromatic material present. Generally, they are bisatellited, pseudodicentric and have a breakpoint in 15q11-q14. A suggested mechanism of formation of inv dup(15) involves illegitimate recombination between homologous chromosomes followed by nondisjunction and centromere inactivation. The proximal portion of chromosome 15 contains several low-copy repeat sequence families and it has been hypothesized that errors in pairing among these repeats may result in structural rearrangements of this chromosome including the inv dup(15). To test this hypothesis and to determine the mechanism of formation, the inv dup(15) from four cases was isolated in somatic cell hybrids and polymerase chain reaction microsatellite markers were used to determine the origin of exchange. Two appeared to result from interchromosomal and two from intrachromosomal exchange, one of which occurred post-recombination. In addition, a detailed physical map of the breakpoint region in the largest inv dup(15) was constructed placing eight new sequence-tagged sites and ten new bacterial artificial chromosome markers in the region.

Adolescent social defeat alters N-methyl-D-aspartic acid receptor expression and impairs fear learning in adulthood.

PubMed

Novick, Andrew M; Mears, Mackenzie; Forster, Gina L; Lei, Yanlin; Tejani-Butt, Shanaz M; Watt, Michael J

2016-05-01

Repeated social defeat of adolescent male rats results in adult mesocortical dopamine hypofunction, impaired working memory, and increased contextual anxiety-like behavior. Given the role of glutamate in dopamine regulation, cognition, and fear and anxiety, we investigated potential changes to N-methyl-D-aspartic acid (NMDA) receptors following adolescent social defeat. As both NMDA receptors and mesocortical dopamine are implicated in the expression and extinction of conditioned fear, a separate cohort of rats was challenged with a classical fear conditioning paradigm to investigate whether fear learning is altered by adolescent defeat. Quantitative autoradiography was used to measure 3H-MK-801 binding to NMDA receptors in regions of the medial prefrontal cortex, caudate putamen, nucleus accumbens, amygdala and hippocampus. Assessment of fear learning was achieved using an auditory fear conditioning paradigm, with freezing toward the auditory tone used as a measure of conditioned fear. Compared to controls, adolescent social defeat decreased adult NMDA receptor expression in the infralimbic region of the prefrontal cortex and central amygdala, while increasing expression in the CA3 region of the hippocampus. Previously defeated rats also displayed decreased conditioned freezing during the recall and first extinction periods, which may be related to the observed decreases and increases in NMDA receptors within the central amygdala and CA3, respectively. The alteration in NMDA receptors seen following adolescent social defeat suggests that dysfunction of glutamatergic systems, combined with mesocortical dopamine deficits, likely plays a role in the some of the long-term behavioral consequences of social stressors in adolescence seen in both preclinical and clinical studies. Copyright © 2016 Elsevier B.V. All rights reserved.

The population structure and recent colonization history of Oregon threespine stickleback determined using restriction-site associated DNA-sequencing.

PubMed

Catchen, Julian; Bassham, Susan; Wilson, Taylor; Currey, Mark; O'Brien, Conor; Yeates, Quick; Cresko, William A

2013-06-01

Understanding how genetic variation is partitioned across genomes within and among populations is a fundamental problem in ecological and evolutionary genetics. To address this problem, we studied the threespine stickleback fish, which has repeatedly undergone parallel phenotypic and genetic differentiation when oceanic fish have invaded freshwater habitats. While significant evolutionary genetic research has been performed using stickleback from geographic regions that have been deglaciated in the last 20 000 years, less research has focused on freshwater populations that predate the last glacial maximum. We performed restriction-site associated DNA-sequencing (RAD-seq) based population genomic analyses on stickleback from across Oregon, which was not glaciated during the last maximum. We sampled stickleback from coastal, Willamette Basin and central Oregon sites, analysed their genetic diversity using RAD-seq, performed structure analyses, reconstructed their phylogeographic history and tested the hypothesis of recent stickleback introduction into central Oregon, where incidence of this species was only recently documented. Our results showed a clear phylogeographic break between coastal and inland populations, with oceanic populations exhibiting the lowest levels of divergence from one another. Willamette Basin and central Oregon populations formed a clade of closely related populations, a finding consistent with a recent introduction of stickleback into central Oregon. Finally, genome-wide analysis of genetic diversity (π) and correlations of alleles within individuals in subpopulations (FIS) supported a role for introgressive hybridization in coastal populations and a recent expansion in central Oregon. Our results exhibit the power of next-generation sequencing genomic approaches such as RAD-seq to identify both historical population structure and recent colonization history. © 2013 John Wiley & Sons Ltd.

Somatic instability of the expanded allele of IT-15 from patients with Huntington disease

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

Stine, O.C.; Pleasant, N.; Ross, C.A.

1994-09-01

Huntington`s disease (HD) is an inherited neurodegenerative disorder caused by an expanded trinucleotide repeat in the gene IT-15. Although the expanded allele of IT-15 is unstable during gametogenesis, particularly, spermatogenesis, it is not clear if there is somatic stability. There are two reports of stability and one of instability. In order to test whether somatic instability occurs in the expansions found in HD, we have compared amplified genomic DNA isolated from either blood or distinct regions of autopsied brains of persons with Huntington disease. We find that somatic variation occurs in at least two ways. First, in cases with longermore » repeats (n > 47), the cerebellum often (8 of 9 cases) has a smaller number of repeats (2 to 10 less) than other tested regions of the brain. The larger the expanded allele, the larger the reduction in size of the repeat in the cerebellum (r=0.94, p<0.0001, df=12). Second, regardless of the repeat size, the number of amplification products from genomic DNA isolated from the cerebellum is smaller than that from genomic DNA from other forebrain regions such as the dorsal parietal cortex. As the length of the expanded allele increases, the number of amplification products increase in either tissue (r=0.86, p<0.001, df=12). Therefore our data demonstrates somatic instability especially for longer repeats.« less

High Regional Variation in Urethroplasty in the United States

PubMed Central

Figler, Bradley D.; Gore, John L.; Holt, Sarah K.; Voelzke, Bryan B.; Wessells, Hunter

2015-01-01

Purpose We identified clinical and regional factors associated with the use of urethroplasty vs repeat endoscopic management for urethral stricture disease. Materials and Methods We analyzed claims for patients 18 to 65 years old in the 2007 to 2011 MarketScan ® Commercial Claims and Encounters Database with a diagnosis of urethral stricture. The primary outcome was treatment with urethroplasty vs repeat endoscopic management, defined as more than 2 dilations or direct vision internal urethrotomies. The likelihood of urethroplasty vs repeat endoscopic management was determined for each major metropolitan area in the United States. Multivariate logistic regression was done to identify factors associated with urethroplasty. Results We identified 41,056 patients with urethral stricture, yielding a diagnosis rate of 296/100,000 men in MarketScan. Repeat endoscopic management and urethroplasty were performed in 2,700 and 1,444 patients, respectively. Compared to patients treated with repeat endoscopic management those with urethroplasty were younger (median age 44 vs 54 years) and more likely to have a Charlson comorbidity score of 0 (84% vs 77%), have traveled out of a metropolitan area for care (34% vs 17%) and have a reconstructive urologist in the treatment metropolitan area (76% and 62%, each p < 0.001). When controlling for age and Charlson comorbidity score, travel out of a metropolitan area (OR 2.7, 95% CI 2.2–3.3) and a reconstructive urologist in the treatment metropolitan area (OR 2.0, 95% CI 1.7–2.5) were associated with a greater likelihood of urethroplasty vs repeat endoscopic management. Conclusions Despite the well established benefits of urethroplasty compared to repeat endoscopic management a strong bias for repeat endoscopic management exists in many regions in the United States. PMID:25072180

Length and sequence variability in mitochondrial control region of the milkfish, Chanos chanos.

PubMed

Ravago, Rachel G; Monje, Virginia D; Juinio-Meñez, Marie Antonette

2002-01-01

Extensive length variability was observed in the mitochondrial control region of the milkfish, Chanos chanos. The nucleotide sequence of the control region and flanking regions was determined. Length variability and heteroplasmy was due to the presence of varying numbers of a 41-bp tandemly repeated sequence and a 48-bp insertion/deletion (indel). The structure and organization of the milkfish control region is similar to that of other teleost fish and vertebrates. However, extensive variation in the copy number of tandem repeats (4-20 copies) and the presence of a relatively large (48-bp) indel, are apparently uncommon in teleost fish control region sequences reported to date. High sequence variability of control region peripheral domains indicates the potential utility of selected regions as markers for population-level studies.

The post-LGM deglaciation in Central and Southeast Switzerland: New insights from surface exposure dating

NASA Astrophysics Data System (ADS)

Boxleitner, Max; Maisch, Max; Brandova, Dagmar; Egli, Markus; Ochs, Susan Ivy; Christl, Marcus

2017-04-01

The deglaciation of the Alps after the Last Glacial Maximum was not a linear process. Moraines as traces of glacier re-advances show that the climate within the general Late-Pleistocene-warming is characterized by repeated cold intervals. While moraine series resulting from these cold spells have been already described for many Alpine valleys at the beginning of the 20th century, absolute chronologies of the Lateglacial climate and glacier development are still fragmentary. The advent of surface exposure dating as a new absolute dating method some 30 years ago made it possible to directly target the deposition-age of moraines. But still many questions regarding the local-to-regional glacier development and its coupling to the overall climate change remain open. In the framework of my PhD-project we study key sites in Central (Uri) and Southeast (Engadine) Switzerland with the aim to develop an absolute post-LGM chronology. More than 50 rock-samples from boulders of different moraine complexes from both regions have been analyzed using 10Be-surface-expsure-dating. Our results show that especially the Younger Dryas plays not unexpected an important role as a very pronounced cold interval. With our results we will refine the understanding of the glacier development in the Swiss Alps during the Lateglacial and the Holocene and improve estimates of equilibrium lines of altitude (ELA) of glaciers from the LGM to the beginning of the Holocene.

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved

PubMed Central

Long, Hannah K.; King, Hamish W.; Patient, Roger K.; Odom, Duncan T.; Klose, Robert J.

2016-01-01

DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species. PMID:27084945

Investigating the stratigraphy and palaeoenvironments for a suite of newly discovered mid-Cretaceous vertebrate fossil-localities in the Winton Formation, Queensland, Australia

NASA Astrophysics Data System (ADS)

Tucker, Ryan T.; Roberts, Eric M.; Darlington, Vikie; Salisbury, Steven W.

2017-08-01

The Winton Formation of central Queensland is recognized as a quintessential source of mid-Cretaceous terrestrial faunas and floras in Australia. However, sedimentological investigations linking fossil assemblages and palaeoenvironments across this unit remain limited. The intent of this study was to interpret depositional environments and improve stratigraphic correlations between multiple fossil localities within the preserved Winton Formation in the Eromanga Basin, including Isisford, Lark Quarry, and Bladensburg National Park. Twenty-three facies and six repeated facies associations were documented, indicating a mosaic of marginal marine to inland alluvial depositional environments. These developed synchronously with the final regression of the Eromanga Seaway from central Australia during the late Albian-early Turonian. Investigations of regional- and local-scale structural features and outcrop, core and well analysis were combined with detrital zircon provenance signatures to help correlate stratigraphy and vertebrate faunas across the basin. Significant palaeoenvironmental differences exist between the lower and upper portions of the preserved Winton Formation, warranting informal subdivisions; a lower tidally influenced fluvial-deltaic member and an upper inland alluvial member. This work further demonstrates that the Isisford fauna is part of the lower member of the preserved Winton Formation; whereas, fossil localities around Winton, including Lark Quarry and Bladensburg National Park, are part of the upper member of the Winton Formation. These results permit a more meaningful framework for both regional and global comparisons of the Winton flora and fauna.

Woodland-to-forest transition during prolonged drought in Minnesota after ca. AD 1300.

PubMed

Shuman, Bryan; Henderson, Anna K; Plank, Colin; Stefanova, Ivanka; Ziegler, Susy S

2009-10-01

Interactions among multiple causes of ecological perturbation, such as climate change and disturbance, can produce "ecological surprises." Here, we examine whether climate-fire-vegetation interactions can produce ecological changes that differ in direction from those expected from the effects of climate change alone. To do so, we focus on the "Big Woods" of central Minnesota, USA, which was shaped both by climate and fire. The deciduous Big Woods forest replaced regional woodlands and savannas after the severity of regional fire regimes declined at ca. AD 1300. A trend toward wet conditions has long been assumed to explain the forest expansion, but we show that water levels at two lakes within the region (Wolsfeld Lake and Bufflehead Pond) were low when open woodlands were transformed into the Big Woods. Water levels were high instead at ca. 2240-795 BC when regional fire regimes were most severe. Based on the correlation between water levels and fire-regime severity, we infer that prolonged or repeated droughts after ca. AD 1265 reduced the biomass and connectivity of fine fuels (grasses) within the woodlands. As a result, regional fire severity declined and allowed tree populations to expand. Tree-ring data from the region show a peak in the recruitment of key Big Woods tree species during the AD 1930s drought and suggest that low regional moisture balance need not have been a limiting factor for forest expansion. The regional history, thus, demonstrates the types of counterintuitive ecosystem changes that may arise as climate changes in the future.

Faunistic Composition, Ecological Properties and Zoogeographical Composition of the Family Elateridae (Coleoptera) of the Central Anatolian Region of Turkey

PubMed Central

Kabalak, Mahmut; Sert, Osman

2011-01-01

The focus of this study was to understand the faunistic composition, ecological properties and zoogeographical composition of Elateridae (Coleoptera) of the Central Anatolian region. 72 species belonging to seven subfamilies and 25 genera were identified. The major part of the Elateridae fauna of the Central Anatolian region is formed by the subfamilies Elaterinae and Cardiophorinae. The genus Cardiophorus was the most species-rich genus. The species composition of the Elateridae fauna of the Central Anatolian region is partially consistent with known Elateridae fauna of Turkey. The Central Anatolian region shares most species with the European part of the Western Palaearctic as does the Elateridae fauna of Turkey. Detailed localities of nine species are given for the first time for Turkey, with emphasis on the Central Anatolian region. PMID:21864150

Central neuropeptide Y plays an important role in mediating the adaptation mechanism against chronic stress in male rats.

PubMed

Yang, Yu; Babygirija, Reji; Zheng, Jun; Shi, Bei; Sun, Weinan; Zheng, Xiaojiao; Zhang, Fan; Cao, Yu

2018-02-07

Exposure to continuous life stress often causes gastrointestinal (GI) symptoms. Studies have shown that neuropeptide Y (NPY) counteracts the biological actions of corticotrophin-releasing factor (CRF), and is involved in the termination of the stress response. However, in chronic repeated restraint stress (CRS) conditions, the actions of NPY on GI motility remain controversial. To evaluate the role of NPY in mediation of the adaptation mechanism and GI motility in CRS conditions, a CRS rat model was set up. Central CRF and NPY expression levels were analyzed, serum corticosterone and NPY concentrations were measured, and GI motor function was evaluated. The NPY Y1 receptor antagonist BIBP-3226 was centrally administered before stress loading, and on days, 1-5, of repeated stress, the central CRF and the serum corticosterone concentrations were measured. In addition, gastric and colonic motor functions were evaluated. The elevated central CRF expression and corticosterone concentration caused by acute stress began to fall after 3 days of stress loading, while central NPY expression and serum NPY began to increase. GI dysmotility also returned to a normal level. Pretreatment with BIBP-3226 abolished the adaptation mechanism, and significantly increased CRF expression and the corticosterone concentration, which resulted in delayed gastric emptying and accelerated fecal pellet output. Inhibited gastric motility and enhanced distal colonic motility were also recorded. CRS-produced adaptation, over-expressed central CRF, and GI dysmotility observed in acute restraint stress were restored to normal levels. Central NPY via the Y1 receptor plays an important role in mediating the adaptation mechanism against chronic stress. Copyright © 2018 Endocrine Society.

Are There Multiple Populations of Fast Radio Bursts?

NASA Astrophysics Data System (ADS)

Palaniswamy, Divya; Li, Ye; Zhang, Bing

2018-02-01

The repeating FRB 121102 (the “repeater”) shows repetitive bursting activities and was localized in a host galaxy at z = 0.193. On the other hand, despite dozens of hours of telescope time spent on follow-up observations, no other fast radio bursts (FRBs) have been observed to repeat. Yet, it has been speculated that the repeater is the prototype of FRBs, and that other FRBs should show similar repeating patterns. Using the published data, we compare the repeater with other FRBs in the observed time interval (Δt)–flux ratio (S i /S i+1) plane. We find that whereas other FRBs occupy the upper (large S i /S i+1) and right (large Δt) regions of the plane due to the non-detections of other bursts, some of the repeater bursts fall into the lower left region of the plot (short interval and small flux ratio) excluded by the non-detection data of other FRBs. The trend also exists even if one only selects those bursts detectable by the Parkes radio telescope. If other FRBs were similar to the repeater, our simulations suggest that the probability that none of them have been detected to repeat with the current searches would be ∼(10‑4–10‑3). We suggest that the repeater is not representative of the entire FRB population, and that there is strong evidence of more than one population of FRBs.

Development of the nowcasting system for the XVII Asiad at Korea Meteorological Administration

NASA Astrophysics Data System (ADS)

Park, Kyungjeen; Kim, Juwon; Jang, Taekyu; Hwang, Seung On; Park, Yunho; Kim, Yoonjae; Park, Seonjoo; Joo, Sangwon; Noh, Hae Mi

2014-05-01

The XVII Asiad, known as the 2014 Asian game, is the largest sporting event in Asia. It will be held in Incheon, South Korea from September 19 to October 4, with 437 events in 36 sports. To support this game, Korea Meteorological Administration developed Incheon Data Assimilation and Prediction System (IDAPS) for nowcasting and very short range forecasts. The domain is centered at Incheon city and covers the central region of the Korean peninsula and adjacent seas. It repeats analysis and forecast processes with 1 hour cycling interval. IDAPS has approximately 1 km horizontal resolution with 324 x 360 grids and 70 vertical layers. Three dimensional variational data assimilation is applied to assimilate AWS, windprofiler, buoy, sonde, aircraft, scatwinds, rain rate, and radar products. The details of IDAPS and the experiment results will be given during the conference.

40 CFR 81.47 - Central Oklahoma Intrastate Air Quality Control Region.

Code of Federal Regulations, 2012 CFR

2012-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air Quality Control Regions § 81.47 Central Oklahoma Intrastate Air Quality Control Region. The Metropolitan Oklahoma Intrastate Air Quality Control Region has been renamed the Central Oklahoma Intrastate...

40 CFR 81.47 - Central Oklahoma Intrastate Air Quality Control Region.

Code of Federal Regulations, 2011 CFR

2011-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air Quality Control Regions § 81.47 Central Oklahoma Intrastate Air Quality Control Region. The Metropolitan Oklahoma Intrastate Air Quality Control Region has been renamed the Central Oklahoma Intrastate...

40 CFR 81.47 - Central Oklahoma Intrastate Air Quality Control Region.

Code of Federal Regulations, 2014 CFR

2014-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air Quality Control Regions § 81.47 Central Oklahoma Intrastate Air Quality Control Region. The Metropolitan Oklahoma Intrastate Air Quality Control Region has been renamed the Central Oklahoma Intrastate...

40 CFR 81.47 - Central Oklahoma Intrastate Air Quality Control Region.

Code of Federal Regulations, 2013 CFR

2013-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air Quality Control Regions § 81.47 Central Oklahoma Intrastate Air Quality Control Region. The Metropolitan Oklahoma Intrastate Air Quality Control Region has been renamed the Central Oklahoma Intrastate...

40 CFR 81.47 - Central Oklahoma Intrastate Air Quality Control Region.

Code of Federal Regulations, 2010 CFR

2010-07-01

... (CONTINUED) AIR PROGRAMS (CONTINUED) DESIGNATION OF AREAS FOR AIR QUALITY PLANNING PURPOSES Designation of Air Quality Control Regions § 81.47 Central Oklahoma Intrastate Air Quality Control Region. The Metropolitan Oklahoma Intrastate Air Quality Control Region has been renamed the Central Oklahoma Intrastate...

Correlation of FCGRT genomic structure with serum immunoglobulin, albumin and farletuzumab pharmacokinetics in patients with first relapsed ovarian cancer.

PubMed

O'Shannessy, Daniel J; Bendas, Katie; Schweizer, Charles; Wang, Wenquan; Albone, Earl; Somers, Elizabeth B; Weil, Susan; Meredith, Rhonda K; Wustner, Jason; Grasso, Luigi; Landers, Mark; Nicolaides, Nicholas C

2017-07-01

Farletuzumab (FAR) is a humanized monoclonal antibody (mAb) that binds to folate receptor alpha. A Ph3 trial in ovarian cancer patients treated with carboplatin/taxane plus FAR or placebo did not meet the primary statistical endpoint. Subgroup analysis demonstrated that subjects with high FAR exposure levels (Cmin>57.6μg/mL) showed statistically significant improvements in PFS and OS. The neonatal Fc receptor (fcgrt) plays a central role in albumin/IgG stasis and mAb pharmacokinetics (PK). Here we evaluated fcgrt sequence and association of its promoter variable number tandem repeats (VNTR) and coding single nucleotide variants (SNV) with albumin/IgG levels and FAR PK in the Ph3 patients. A statistical correlation existed between high FAR Cmin and AUC in patients with the highest quartile of albumin and lowest quartile of IgG1. Analysis of fcgrt identified 5 different VNTRs in the promoter region and 9 SNVs within the coding region, 4 which are novel. Copyright © 2017. Published by Elsevier Inc.

The ancient Yakuts: a population genetic enigma

PubMed Central

Keyser, Christine; Hollard, Clémence; Gonzalez, Angela; Fausser, Jean-Luc; Rivals, Eric; Alexeev, Anatoly Nikolayevich; Riberon, Alexandre; Crubézy, Eric; Ludes, Bertrand

2015-01-01

This study is part of an ongoing project aiming at determining the ethnogenesis of an eastern Siberian ethnic group, the Yakuts, on the basis of archaeological excavations carried out over a period of 10 years in three regions of Yakutia: Central Yakutia, the Vilyuy River basin and the Verkhoyansk area. In this study, genetic analyses were carried out on skeletal remains from 130 individuals of unknown ancestry dated mainly from the fifteenth to the nineteenth century AD. Kinship studies were conducted using sets of commercially available autosomal and Y-chromosomal short tandem repeats (STRs) along with hypervariable region I sequences of the mitochondrial DNA. An unexpected and intriguing finding of this work was that the uniparental marker systems did not always corroborate results from autosomal DNA analyses; in some cases, false-positive relationships were observed. These discrepancies revealed that 15 autosomal STR loci are not sufficient to discriminate between first degree relatives and more distantly related individuals in our ancient Yakut sample. The Y-STR analyses led to similar conclusions, because the current Y-STR panels provided the limited resolution of the paternal lineages. PMID:25487336

Resilience landscapes for Congo basin rainforests vs. climate and management impacts

NASA Astrophysics Data System (ADS)

Pietsch, Stephan Alexander; Gautam, Sishir; Elias Bednar, Johannes; Stanzl, Patrick; Mosnier, Aline; Obersteiner, Michael

2015-04-01

Past climate change caused severe disturbances of the Central African rainforest belt, with forest fragmentation and re-expansion due to drier and wetter climate conditions. Besides climate, human induced forest degradation affected biodiversity, structure and carbon storage of Congo basin rainforests. Information on climatically stable, mature rainforest, unaffected by human induced disturbances, provides means of assessing the impact of forest degradation and may serve as benchmarks of carbon carrying capacity over regions with similar site and climate conditions. BioGeoChemical (BGC) ecosystem models explicitly consider the impacts of site and climate conditions and may assess benchmark levels over regions devoid of undisturbed conditions. We will present a BGC-model validation for the Western Congolian Lowland Rainforest (WCLRF) using field data from a recently confirmed forest refuge, show model - data comparisons for disturbed und undisturbed forests under different site and climate conditions as well as for sites with repeated assessment of biodiversity and standing biomass during recovery from intensive exploitation. We will present climatic thresholds for WCLRF stability, and construct resilience landscapes for current day conditions vs. climate and management impacts.

HIV, international travel and tourism: global issues and Pacific perspectives.

PubMed

Lewis, N D; Bailey, J

AIDS, like plagues throughout human history, has been blamed repeatedly on foreigners. This has heightened ramifications, from the personal to the geopolitical, in an era of escalating population movement and rapid international travel. By the end of 1990, the World Health Organization had estimated that the total number of AIDS cases worldwide was close to 1.3 million. Recent estimates suggest that by the year 2000, 38-100 million adults and over 10 million children will have been infected with HIV. Seventy-five to eighty-five percent of that number will be from the developing world. AIDS has rapidly become pandemic, with wide-ranging consequences for humankind. Human population movement is an important component in the natural history of AIDS. With respect to this, a central consideration is the relationship between AIDS and international travel, especially tourism. In this paper, after reviewing HIV in the Asia-Pacific region, we present the epidemiology of HIV in the Pacific Islands, discuss its impact with particular reference to population movement, and explore some of the specific challenges that the Pacific Island region faces.

40 CFR 81.219 - Central Oregon Intrastate Air Quality Control Region.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 17 2010-07-01 2010-07-01 false Central Oregon Intrastate Air Quality... Quality Control Regions § 81.219 Central Oregon Intrastate Air Quality Control Region. The Central Oregon... outermost boundaries of the area so delimited): In the State of Oregon: Crook County, Deschutes County, Hood...

40 CFR 81.219 - Central Oregon Intrastate Air Quality Control Region.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 18 2013-07-01 2013-07-01 false Central Oregon Intrastate Air Quality... Quality Control Regions § 81.219 Central Oregon Intrastate Air Quality Control Region. The Central Oregon... outermost boundaries of the area so delimited): In the State of Oregon: Crook County, Deschutes County, Hood...

40 CFR 81.219 - Central Oregon Intrastate Air Quality Control Region.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 18 2012-07-01 2012-07-01 false Central Oregon Intrastate Air Quality... Quality Control Regions § 81.219 Central Oregon Intrastate Air Quality Control Region. The Central Oregon... outermost boundaries of the area so delimited): In the State of Oregon: Crook County, Deschutes County, Hood...

40 CFR 81.219 - Central Oregon Intrastate Air Quality Control Region.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 18 2014-07-01 2014-07-01 false Central Oregon Intrastate Air Quality... Quality Control Regions § 81.219 Central Oregon Intrastate Air Quality Control Region. The Central Oregon... outermost boundaries of the area so delimited): In the State of Oregon: Crook County, Deschutes County, Hood...

40 CFR 81.219 - Central Oregon Intrastate Air Quality Control Region.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 17 2011-07-01 2011-07-01 false Central Oregon Intrastate Air Quality... Quality Control Regions § 81.219 Central Oregon Intrastate Air Quality Control Region. The Central Oregon... outermost boundaries of the area so delimited): In the State of Oregon: Crook County, Deschutes County, Hood...

Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates

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

Jackson, P.J.; Walthers, E.A.; Richmond, K.L.

1997-04-01

PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five Polymorphisms differed by the presence Of two to six copies of the 12-bp tandem repeat 5{prime}-CAATATCAACAA-3{prime}. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats aremore » generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations. 22 refs., 4 figs., 3 tabs.« less

Characterization of carotenoid hydroxylase gene promoter in Haematococcus pluvialis.

PubMed

Meng, C X; Wei, W; Su, Z- L; Qin, S

2006-10-01

Astaxanthin, a high-value ketocarotenoid is mainly used in fish aquaculture. It also has potential in human health due to its higher antioxidant capacity than beta-carotene and vitamin E. The unicellular green alga Haematococcus pluvialis is known to accumulate astaxanthin in response to environmental stresses, such as high light intensity and salt stress. Carotenoid hydroxylase plays a key role in astaxanthin biosynthesis in H. pluvialis. In this paper, we report the characterization of a promoter-like region (-378 to -22 bp) of carotenoid hydroxylase gene by cloning, sequence analysis and functional verification of its 919 bp 5'-flanking region in H. pluvialis. The 5'-flanking region was characterized using micro-particle bombardment method and transient expression of LacZ reporter gene. Results of sequence analysis showed that the 5'-flanking region might have putative cis-acting elements, such as ABA (abscisic acid)-responsive element (ABRE), C-repeat/dehydration responsive element (C-repeat/DRE), ethylene-responsive element (ERE), heat-shock element (HSE), wound-responsive element (WUN-motif), gibberellin-responsive element (P-box), MYB-binding site (MBS) etc., except for typical TATA and CCAAT boxes. Results of 5' deletions construct and beta-galactosidase assays revealed that a highest promoter-like region might exist from -378 to -22 bp and some negative regulatory elements might lie in the region from -919 to -378 bp. Results of site-directed mutagenesis of a putative C-repeat/DRE and an ABRE-like motif in the promoter-like region (-378 to -22 bp) indicated that the putative C-repeat/DRE and ABRE-like motif might be important for expression of carotenoid hydroxylase gene.

[Comparative analysis of clustered regularly interspaced short palindromic repeats (CRISPRs) loci in the genomes of halophilic archaea].

PubMed

Zhang, Fan; Zhang, Bing; Xiang, Hua; Hu, Songnian

2009-11-01

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic archaea, of which the whole genome sequences are available at present time. We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarchaeal genomes. We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilic archaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.

Acute and repeated ECS treatment increases CRF, POMC and PENK gene expression in selected regions of the rat hypothalamus.

PubMed

Garcia-Garcia, L; Llewellyn-Jones, V; Fernandez Fernandez, I; Fuentes, J A; Manzanares, J

1998-01-05

The purpose of this study was to investigate the effects of acute and repeated electroconvulsive shock (ECS) on corticotropin releasing factor (CRF), proopiomelanocortin (POMC) and proenkephalin (PENK) gene expression in selected regions of the brain and pituitary of the rat. Acute ECS increased CRF gene expression in the paraventricular nucleus (PVN) by 20%, an effect that was further enhanced to 38% when rats received repeated ECS treatment. Acute and repeated ECS increased POMC gene expression in the arcuate nucleus (ARC) by 49-59% but failed to alter these mRNA levels in the anterior lobe (AL) of the pituitary gland. PENK gene expression was increased by 35% in the nucleus accumbens (NA) and by 180% the ventromedial nucleus (VMN) after acute or repeated ECS treatment but no significant changes were found in the PVN or striatum (ST). Taken together, these results indicate a differential CRF and opioid gene expression regulation after acute or repeated ECS treatment that may be relevant to their therapeutic or side effects in depression.

ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants

PubMed Central

Kapil, Aditi; Rai, Piyush Kant; Shanker, Asheesh

2014-01-01

Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1–6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants. Database URL: www.compubio.in/chlorossrdb/ PMID:25380781

ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants.

PubMed

Kapil, Aditi; Rai, Piyush Kant; Shanker, Asheesh

2014-01-01

Simple sequence repeats (SSRs) are regions in DNA sequence that contain repeating motifs of length 1-6 nucleotides. These repeats are ubiquitously present and are found in both coding and non-coding regions of genome. A total of 534 complete chloroplast genome sequences (as on 18 September 2014) of Viridiplantae are available at NCBI organelle genome resource. It provides opportunity to mine these genomes for the detection of SSRs and store them in the form of a database. In an attempt to properly manage and retrieve chloroplastic SSRs, we designed ChloroSSRdb which is a relational database developed using SQL server 2008 and accessed through ASP.NET. It provides information of all the three types (perfect, imperfect and compound) of SSRs. At present, ChloroSSRdb contains 124 430 mined SSRs, with majority lying in non-coding region. Out of these, PCR primers were designed for 118 249 SSRs. Tetranucleotide repeats (47 079) were found to be the most frequent repeat type, whereas hexanucleotide repeats (6414) being the least abundant. Additionally, in each species statistical analyses were performed to calculate relative frequency, correlation coefficient and chi-square statistics of perfect and imperfect SSRs. In accordance with the growing interest in SSR studies, ChloroSSRdb will prove to be a useful resource in developing genetic markers, phylogenetic analysis, genetic mapping, etc. Moreover, it will serve as a ready reference for mined SSRs in available chloroplast genomes of green plants. Database URL: www.compubio.in/chlorossrdb/ © The Author(s) 2014. Published by Oxford University Press.

ROHHAD Syndrome: The Girl who Forgets to Breathe.

PubMed

Sanklecha, Mukesh; Sundaresan, Suba; Udani, Vrajesh

2016-04-01

ROHHAD syndrome is an exceedingly rare cause of central hypoventilation. A 7-year-old girl with ROHHAD syndrome who had central hypoventilation, rapid weight gain, multiple cardiac arrests and hyperprolactinemia. She required prolonged and repeated ventilation, and finally died due to complications of ventilation. ROHHAD Syndrome should be suspected in any child who presents with obesity, behavioral changes or autonomic instability following a neural crest tumor.

Central noradrenergic mechanisms and the acute stress response during painful stimulation.

PubMed

Chapman, C Richard; Bradshaw, David H; Donaldson, Gary W; Jacobson, Robert C; Nakamura, Yoshio

2014-12-01

Events that threaten tissue integrity including noxious stimulation activate central noradrenergic circuits, particularly locus coeruleus and its projections. Recent advances in theory hold that an adaptive, defensive shift in brain activity takes place in response to threat. In principle, this shift may accentuate the autonomic and central biomarkers of the perception of painful events and the experience of pain itself. We have examined the effects of an alpha-2 agonist on pupil dilation responses, skin conductance responses, near field somatosensory evoked potentials and pain reports in normal volunteers undergoing repeated trials of painful fingertip stimulation delivered at low, medium and high intensities. In a double-blinded study, 114 healthy male and female volunteers underwent repeated noxious stimulation under baseline, placebo and active drug conditions where the active drug was the alpha-2 agonist tizanidine 4 mg. In contrast to baseline and placebo conditions, tizanidine 4 mg significantly reduced the magnitudes of the mean pupil dilation response, the mean skin conductance response, the mean near field somatosensory evoked potential peak-to-peak amplitude and the mean pain intensity rating. Stimulus intensity significantly altered all three biomarkers and the pain report in a graded fashion. There were no sex differences. These findings support the hypotheses that painful events activate central noradrenergic circuits, and that these circuits play a role in the autonomic and central arousal associated with pain. © The Author(s) 2014.

Volcano hazards in the Three Sisters region, Oregon

USGS Publications Warehouse

Scott, William E.; Iverson, R.M.; Schilling, S.P.; Fisher, B.J.

2001-01-01

Three Sisters is one of three potentially active volcanic centers that lie close to rapidly growing communities and resort areas in Central Oregon. Two types of volcanoes exist in the Three Sisters region and each poses distinct hazards to people and property. South Sister, Middle Sister, and Broken Top, major composite volcanoes clustered near the center of the region, have erupted repeatedly over tens of thousands of years and may erupt explosively in the future. In contrast, mafic volcanoes, which range from small cinder cones to large shield volcanoes like North Sister and Belknap Crater, are typically short-lived (weeks to centuries) and erupt less explosively than do composite volcanoes. Hundreds of mafic volcanoes scattered through the Three Sisters region are part of a much longer zone along the High Cascades of Oregon in which birth of new mafic volcanoes is possible. This report describes the types of hazardous events that can occur in the Three Sisters region and the accompanying volcano-hazard-zonation map outlines areas that could be at risk from such events. Hazardous events include landslides from the steep flanks of large volcanoes and floods, which need not be triggered by eruptions, as well as eruption-triggered events such as fallout of tephra (volcanic ash) and lava flows. A proximal hazard zone roughly 20 kilometers (12 miles) in diameter surrounding the Three Sisters and Broken Top could be affected within minutes of the onset of an eruption or large landslide. Distal hazard zones that follow river valleys downstream from the Three Sisters and Broken Top could be inundated by lahars (rapid flows of water-laden rock and mud) generated either by melting of snow and ice during eruptions or by large landslides. Slow-moving lava flows could issue from new mafic volcanoes almost anywhere within the region. Fallout of tephra from eruption clouds can affect areas hundreds of kilometers (miles) downwind, so eruptions at volcanoes elsewhere in the Cascade Range also contribute to volcano hazards in Central Oregon. This report is intended to aid scientists, government officials, and citizens as they work together to reduce the risk from volcano hazards through public education and emergency-response planning.

Comparison of central corneal thickness measurements by rotating Scheimpflug camera, ultrasonic pachymetry, and scanning-slit corneal topography.

PubMed

Amano, Shiro; Honda, Norihiko; Amano, Yuki; Yamagami, Satoru; Miyai, Takashi; Samejima, Tomokazu; Ogata, Miyuki; Miyata, Kazunori

2006-06-01

To compare central corneal thickness measurements and their reproducibility when taken by a rotating Scheimpflug camera, ultrasonic pachymetry, and scanning-slit corneal topography/pachymetry. Experimental study. Seventy-four eyes of 64 subjects without ocular abnormalities other than cataract. Corneal thickness measurements were compared among the 3 methods in 54 eyes of 54 subjects. Two sets of measurements were repeated by a single examiner for each pachymetry in another 10 eyes of 5 subjects, and the intraexaminer repeatability was assessed as the absolute difference of the first and second measurements. Two experienced examiners took one measurement for each pachymetry in another 10 eyes of 5 subjects, and the interexaminer reproducibility was assessed as the absolute difference of the 2 measurements of the first and second examiners. Central corneal thickness measurements by the 3 methods, absolute difference of the first and second measurements by a single examiner, absolute difference of the 2 measurements by 2 examiners, and relative amount of variation. The average measurements of central corneal thickness by a rotating Scheimpflug camera, scanning-slit topography, and ultrasonic pachymetry were 538+/-31.3 microm, 541+/-40.7 microm, and 545+/-31.3 microm, respectively. There were no statistically significant differences in the measurement results among the 3 methods (P = 0.569, repeated-measures analysis of variance). There was a significant linear correlation between the rotating Scheimpflug camera and ultrasonic pachymetry (r = 0.908, P<0.0001), rotating Scheimpflug camera and scanning-slit topography (r = 0.930, P<0.0001), and ultrasonic pachymetry and scanning-slit topography (r = 0.887, P<0.0001). Ultrasonic pachymetry had the smallest intraexaminer variability, and scanning-slit topography had the largest intraexaminer variability among the 3 methods. There were similar variations in interexaminer reproducibility among the 3 methods. Mean corneal thicknesses were comparable among rotating Scheimpflug camera, ultrasonic pachymetry, and scanning-slit topography with the acoustic equivalent correction factor. The measurements of the 3 instruments had significant linear correlations with one another, and all methods had highly satisfactory measurement repeatability.

Novel variants of the 5S rRNA genes in Eruca sativa.

PubMed

Singh, K; Bhatia, S; Lakshmikumaran, M

1994-02-01

The 5S ribosomal RNA (rRNA) genes of Eruca sativa were cloned and characterized. They are organized into clusters of tandemly repeated units. Each repeat unit consists of a 119-bp coding region followed by a noncoding spacer region that separates it from the coding region of the next repeat unit. Our study reports novel gene variants of the 5S rRNA genes in plants. Two families of the 5S rDNA, the 0.5-kb size family and the 1-kb size family, coexist in the E. sativa genome. The 0.5-kb size family consists of the 5S rRNA genes (S4) that have coding regions similar to those of other reported plant 5S rDNA sequences, whereas the 1-kb size family consists of the 5S rRNA gene variants (S1) that exist as 1-kb BamHI tandem repeats. S1 is made up of two variant units (V1 and V2) of 5S rDNA where the BamHI site between the two units is mutated. Sequence heterogeneity among S4, V1, and V2 units exists throughout the sequence and is not limited to the noncoding spacer region only. The coding regions of V1 and V2 show approximately 20% dissimilarity to the coding regions of S4 and other reported plant 5S rDNA sequences. Such a large variation in the coding regions of the 5S rDNA units within the same plant species has been observed for the first time. Restriction site variation is observed between the two size classes of 5S rDNA in E. sativa.(ABSTRACT TRUNCATED AT 250 WORDS)

Stability of Tandem Repeats in the Drosophila Melanogaster HSR-Omega Nuclear RNA

PubMed Central

Hogan, N. C.; Slot, F.; Traverse, K. L.; Garbe, J. C.; Bendena, W. G.; Pardue, M. L.

1995-01-01

The Drosophila melanogaster Hsr-omega locus produces a nuclear RNA containing >5 kb of tandem repeat sequences. These repeats are unique to Hsr-omega and show concerted evolution similar to that seen with classical satellite DNAs. In D. melanogaster the monomer is ~280 bp. Sequences of 191/2 monomers differ by 8 +/- 5% (mean +/- SD), when all pairwise comparisons are considered. Differences are single nucleotide substitutions and 1-3 nucleotide deletions/insertions. Changes appear to be randomly distributed over the repeat unit. Outer repeats do not show the decrease in monomer homogeneity that might be expected if homogeneity is maintained by recombination. However, just outside the last complete repeat at each end, there are a few fragments of sequence similar to the monomer. The sequences in these flanking regions are not those predicted for sequences decaying in the absence of recombination. Instead, the fragmentation of the sequence homology suggests that flanking regions have undergone more severe disruptions, possibly during an insertion or amplification event. Hsr-omega alleles differing in the number of repeats are detected and appear to be stable over a few thousand generations; however, both increases and decreases in repeat numbers have been observed. The new alleles appear to be as stable as their predecessors. No alleles of less than ~5 kb nor more than ~16 kb of repeats were seen in any stocks examined. The evidence that there is a limit on the minimum number of repeats is consistent with the suggestion that these repeats are important in the function of the unusual Hsr-omega nuclear RNA. PMID:7540581

Bioclimatic conditions of the winter months in Western Kazakhstan and their dynamics in relation to climate change

NASA Astrophysics Data System (ADS)

Nyssanbayeva, Aiman S.; Cherednichenko, Alexandr V.; Cherednichenko, Vladimir S.; Abayev, Nurlan N.; Madibekov, Azamat S.

2018-03-01

The territory of West Kazakhstan is an intensively developing region. The main oil and gas fields are concentrated there. In addition, this region is well-known as a region of nomad cattle breeding. Both of industry and agriculture demand a lot of employees, working in the open air in wintertime. Severe winter conditions, primary very low temperatures, and strong winds characterize the region. In this work, we calculated and analyzed the spatial and temporal distributions of effective temperatures in the region and their dynamics due to the global warming in the last decades. To calculate the equivalent temperature (WCET) was used the method of OFCM 2003. Nowadays, it is known as a common method for similar studies. It was shown that in the observed region, WCET is significantly lower than the ambient temperature. Repeatability of WCET, corresponding to «increasing risk», «high risk» is high in the main part of the region. Global warming in the region results in returning extremely high temperatures of the air, decreasing repeatability of the average gradation of WCET approximately on 4%, but there is no any visible changing repeatability of extreme WCET. Obtained results can be used for planning any construction work in the open air and agriculture branches.

Bioclimatic conditions of the winter months in Western Kazakhstan and their dynamics in relation to climate change.

PubMed

Nyssanbayeva, Aiman S; Cherednichenko, Alexandr V; Cherednichenko, Vladimir S; Abayev, Nurlan N; Madibekov, Azamat S

2018-03-05

The territory of West Kazakhstan is an intensively developing region. The main oil and gas fields are concentrated there. In addition, this region is well-known as a region of nomad cattle breeding. Both of industry and agriculture demand a lot of employees, working in the open air in wintertime. Severe winter conditions, primary very low temperatures, and strong winds characterize the region. In this work, we calculated and analyzed the spatial and temporal distributions of effective temperatures in the region and their dynamics due to the global warming in the last decades. To calculate the equivalent temperature (WCET) was used the method of OFCM 2003. Nowadays, it is known as a common method for similar studies. It was shown that in the observed region, WCET is significantly lower than the ambient temperature. Repeatability of WCET, corresponding to «increasing risk», «high risk» is high in the main part of the region. Global warming in the region results in returning extremely high temperatures of the air, decreasing repeatability of the average gradation of WCET approximately on 4%, but there is no any visible changing repeatability of extreme WCET. Obtained results can be used for planning any construction work in the open air and agriculture branches.

Inverted repeats in the promoter as an autoregulatory sequence for TcrX in Mycobacterium tuberculosis

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

Bhattacharya, Monolekha; Das, Amit Kumar, E-mail: amitk@hijli.iitkgp.ernet.in

Highlights: Black-Right-Pointing-Pointer The regulatory sequences recognized by TcrX have been identified. Black-Right-Pointing-Pointer The regulatory region comprises of inverted repeats segregated by 30 bp region. Black-Right-Pointing-Pointer The mode of binding of TcrX with regulatory sequence is unique. Black-Right-Pointing-Pointer In silico TcrX-DNA docked model binds one of the inverted repeats. Black-Right-Pointing-Pointer Both phosphorylated and unphosphorylated TcrX binds regulatory sequence in vitro. -- Abstract: TcrY, a histidine kinase, and TcrX, a response regulator, constitute a two-component system in Mycobacterium tuberculosis. tcrX, which is expressed during iron scarcity, is instrumental in the survival of iron-dependent M. tuberculosis. However, the regulator of tcrX/Y has notmore » been fully characterized. Crosslinking studies of TcrX reveal that it can form oligomers in vitro. Electrophoretic mobility shift assays (EMSAs) show that TcrX recognizes two regions in the promoter that are comprised of inverted repeats separated by {approx}30 bp. The dimeric in silico model of TcrX predicts binding to one of these inverted repeat regions. Site-directed mutagenesis and radioactive phosphorylation indicate that D54 of TcrX is phosphorylated by H256 of TcrY. However, phosphorylated and unphosphorylated TcrX bind the regulatory sequence with equal efficiency, which was shown with an EMSA using the D54A TcrX mutant.« less

Cis-acting regulatory sequences promote high-frequency gene conversion between repeated sequences in mammalian cells.

PubMed

Raynard, Steven J; Baker, Mark D

2004-01-01

In mammalian cells, little is known about the nature of recombination-prone regions of the genome. Previously, we reported that the immunoglobulin heavy chain (IgH) mu locus behaved as a hotspot for mitotic, intrachromosomal gene conversion (GC) between repeated mu constant (Cmu) regions in mouse hybridoma cells. To investigate whether elements within the mu gene regulatory region were required for hotspot activity, gene targeting was used to delete a 9.1 kb segment encompassing the mu gene promoter (Pmu), enhancer (Emu) and switch region (Smu) from the locus. In these cell lines, GC between the Cmu repeats was significantly reduced, indicating that this 'recombination-enhancing sequence' (RES) is necessary for GC hotspot activity at the IgH locus. Importantly, the RES fragment stimulated GC when appended to the same Cmu repeats integrated at ectopic genomic sites. We also show that deletion of Emu and flanking matrix attachment regions (MARs) from the RES abolishes GC hotspot activity at the IgH locus. However, no stimulation of ectopic GC was observed with the Emu/MARs fragment alone. Finally, we provide evidence that no correlation exists between the level of transcription and GC promoted by the RES. We suggest a model whereby Emu/MARS enhances mitotic GC at the endogenous IgH mu locus by effecting chromatin modifications in adjacent DNA.

Centromere Pairing in Early Meiotic Prophase Requires Active Centromeres and Precedes Installation of the Synaptonemal Complex in Maize[W

PubMed Central

Zhang, Jing; Pawlowski, Wojciech P.; Han, Fangpu

2013-01-01

Pairing of homologous chromosomes in meiosis is critical for their segregation to daughter cells. In most eukaryotes, clustering of telomeres precedes and facilitates chromosome pairing. In several species, centromeres also form pairwise associations, known as coupling, before the onset of pairing. We found that, in maize (Zea mays), centromere association begins at the leptotene stage and occurs earlier than the formation of the telomere bouquet. We established that centromere pairing requires centromere activity and the sole presence of centromeric repeats is not sufficient for pairing. In several species, homologs of the ZIP1 protein, which forms the central element of the synaptonemal complex in budding yeast (Saccharomyces cerevisiae), play essential roles in centromere coupling. However, we found that the maize ZIP1 homolog ZYP1 installs in the centromeric regions of chromosomes after centromeres form associations. Instead, we found that maize STRUCTURAL MAINTENANCE OF CHROMOSOMES6 homolog forms a central element of the synaptonemal complex, which is required for centromere associations. These data shed light on the poorly understood mechanism of centromere interactions and suggest that this mechanism may vary somewhat in different species. PMID:24143803

Centromere pairing in early meiotic prophase requires active centromeres and precedes installation of the synaptonemal complex in maize.

PubMed

Zhang, Jing; Pawlowski, Wojciech P; Han, Fangpu

2013-10-01

Pairing of homologous chromosomes in meiosis is critical for their segregation to daughter cells. In most eukaryotes, clustering of telomeres precedes and facilitates chromosome pairing. In several species, centromeres also form pairwise associations, known as coupling, before the onset of pairing. We found that, in maize (Zea mays), centromere association begins at the leptotene stage and occurs earlier than the formation of the telomere bouquet. We established that centromere pairing requires centromere activity and the sole presence of centromeric repeats is not sufficient for pairing. In several species, homologs of the ZIP1 protein, which forms the central element of the synaptonemal complex in budding yeast (Saccharomyces cerevisiae), play essential roles in centromere coupling. However, we found that the maize ZIP1 homolog ZYP1 installs in the centromeric regions of chromosomes after centromeres form associations. Instead, we found that maize structural maintenance of chromosomes6 homolog forms a central element of the synaptonemal complex, which is required for centromere associations. These data shed light on the poorly understood mechanism of centromere interactions and suggest that this mechanism may vary somewhat in different species.

Beam orbit simulation in the central region of the RIKEN AVF cyclotron

NASA Astrophysics Data System (ADS)

Toprek, Dragan; Goto, Akira; Yano, Yasushige

1999-04-01

This paper describes the modification design of the central region for h=2 mode of acceleration in the RIKEN AVF cyclotron. we made a small modification to the electrode shape in the central region for optimization of the beam transmission. The central region is equipped with an axial injection system. The spiral type inflector is used for axial injection. The electric field distribution in the inflector and in four acceleration gaps has been numerically calculated from an electric potential map produced by the program RELAX3D. The magnetic field is measured. The geometry of the central region has been tested with the computations of orbits carried out by means of the computer code CYCLONE. The optical properties of the spiral inflector and the central region are studied by using the program CASINO and CYCLONE, respectively. We have also made an effort to minimize the inflector fringe field effects using the RELAX3D program.

Pleistocene refugia and polytopic replacement of diploids by tetraploids in the Patagonian and Subantarctic plant Hypochaeris incana (Asteraceae, Cichorieae).

PubMed

Tremetsberger, Karin; Urtubey, Estrella; Terrab, Anass; Baeza, Carlos M; Ortiz, María Angeles; Talavera, María; König, Christiane; Temsch, Eva M; Kohl, Gudrun; Talavera, Salvador; Stuessy, Tod F

2009-09-01

We report the phylogeographic pattern of the Patagonian and Subantarctic plant Hypochaeris incana endemic to southeastern South America. We applied amplified fragment length polymorphism (AFLP) and chloroplast DNA (cpDNA) analysis to 28 and 32 populations, respectively, throughout its distributional range and assessed ploidy levels using flow cytometry. While cpDNA data suggest repeated or simultaneous parallel colonization of Patagonia and Tierra del Fuego by several haplotypes and/or hybridization, AFLPs reveal three clusters corresponding to geographic regions. The central and northern Patagonian clusters (approximately 38-51 degrees S), which are closer to the outgroup, contain mainly tetraploid, isolated and highly differentiated populations with low genetic diversity. To the contrary, the southern Patagonian and Fuegian cluster (approximately 51-55 degrees S) contains mainly diploid populations with high genetic diversity and connected by high levels of gene flow. The data suggest that H. incana originated at the diploid level in central or northern Patagonia, from where it migrated south. All three areas, northern, central and southern, have similar levels of rare and private AFLP bands, suggesting that all three served as refugia for H. incana during glacial times. In southern Patagonia and Tierra del Fuego, the species seems to have expanded its populational system in postglacial times, when the climate became warmer and more humid. In central and northern Patagonia, the populations seem to have become restricted to favourable sites with increasing temperature and decreasing moisture and there was a parallel replacement of diploids by tetraploids in local populations.

Does Money Matter: Earnings Patterns Among a National Sample of the US State Governmental Public Health Agency Workforce

PubMed Central

Castrucci, Brian C.; Leider, Jonathon P.; Liss-Levinson, Rivka; Sellers, Katie

2015-01-01

Context: Earnings have been shown to be a critical point in workforce recruitment and retention. However, little is known about how much governmental public health staff are paid across the United States. Objective: To characterize earnings among state health agency central office employees. Design: A cross-sectional survey was conducted of state health agency central office employees in late 2014. The sampling approach was stratified by 5 (paired HHS) regions. Balanced repeated replication weights were used to correctly calculate variance estimates, given the complex sampling design. Descriptive and bivariate statistical comparisons were conducted. A linear regression model was used to examine correlates of earnings among full-time employees. Setting and Participants: A total of 9300 permanently employed, full-time state health agency central office staff who reported earnings information. Main Outcome Measure: Earnings are the main outcomes examined in this article. Results: Central office staff earn between $55 000 and $65 000 on average annually. Ascending supervisory status, educational attainment, and tenure are all associated with greater earnings. Those employed in clinical and laboratory positions and public health science positions earn more than their colleagues in administrative positions. Disparities exist between men and women, with men earning more, all else being equal (P < .001). Racial/ethnic disparities also exist, after accounting for other factors. Conclusions: This study provides baseline information to characterize the workforce and key challenges that result from earnings levels, including disparities in earnings that persist after accounting for education and experience. Data from the survey can inform strategies to address earnings issues and help reduce disparities. PMID:26422496

Does Money Matter: Earnings Patterns Among a National Sample of the US State Governmental Public Health Agency Workforce.

PubMed

Castrucci, Brian C; Leider, Jonathon P; Liss-Levinson, Rivka; Sellers, Katie

2015-01-01

Earnings have been shown to be a critical point in workforce recruitment and retention. However, little is known about how much governmental public health staff are paid across the United States. To characterize earnings among state health agency central office employees. A cross-sectional survey was conducted of state health agency central office employees in late 2014. The sampling approach was stratified by 5 (paired HHS) regions. Balanced repeated replication weights were used to correctly calculate variance estimates, given the complex sampling design. Descriptive and bivariate statistical comparisons were conducted. A linear regression model was used to examine correlates of earnings among full-time employees. A total of 9300 permanently employed, full-time state health agency central office staff who reported earnings information. Earnings are the main outcomes examined in this article. Central office staff earn between $55,000 and $65,000 on average annually. Ascending supervisory status, educational attainment, and tenure are all associated with greater earnings. Those employed in clinical and laboratory positions and public health science positions earn more than their colleagues in administrative positions. Disparities exist between men and women, with men earning more, all else being equal (P < .001). Racial/ethnic disparities also exist, after accounting for other factors. This study provides baseline information to characterize the workforce and key challenges that result from earnings levels, including disparities in earnings that persist after accounting for education and experience. Data from the survey can inform strategies to address earnings issues and help reduce disparities.

A study of reconstruction accuracy for a cardiac SPECT system with multi-segmental collimation

NASA Astrophysics Data System (ADS)

Yu, D.-C.; Chang, W.; Pan, T.-S.

1997-06-01

To improve the geometric efficiency of cardiac SPECT imaging, the authors previously proposed to use a multi-segmental collimation with a cylindrical geometry. The proposed collimator consists of multiple parallel-hole collimators with most of the segments directed toward a small central region, where the patient's heart should be positioned. This technique provides a significantly increased detection efficiency for the central region, but at the expense of reduced efficiency for the surrounding region. The authors have used computer simulations to evaluate the implication of this technique on the accuracy of the reconstructed cardiac images. Two imaging situations were simulated: 1) the heart well placed inside the central region, and 2) the heart shifted and partially outside the central region. A neighboring high-uptake liver was simulated for both imaging situations. The images were reconstructed and corrected for attenuation with ML-EM and OS-FM methods using a complete attenuation map. The results indicate that errors caused by projection truncation are not significant and are not strongly dependent on the activity of the liver when the heart is well positioned within the central region. When the heart is partially outside the central region, hybrid emission data (a combination of high-count projections from the central region and low-count projections from the background region) can be used to restore the activity of the truncated section of the myocardium. However, the variance of the image in the section of the myocardium outside the central region is increased by 2-3 times when 10% of the collimator segments are used to image the background region.

East and central farming and forest region and Atlantic basin diversified farming region: LRRs N and S

Treesearch

Brad D. Lee; John M. Kabrick

2017-01-01

The central, unglaciated US east of the Great Plains to the Atlantic coast corresponds to the area covered by LRR N (East and Central Farming and Forest Region) and S (Atlantic Basin Diversified Farming Region). These regions roughly correspond to the Interior Highlands, Interior Plains, Appalachian Highlands, and the Northern Coastal Plains.

Molecular characterization and in situ mRNA localization of the neural recognition molecule J1-160/180: a modular structure similar to tenascin

PubMed Central

1993-01-01

The oligodendrocyte-derived extracellular matrix glycoprotein J1- 160/180 is a recognition molecule expressed exclusively in the central nervous system. J1-160/180 has been shown to be adhesive for astrocytes and repellent towards neurons and growth cones. We report here the complete nucleotide sequence of J1-160/180 in the rat. The predicted amino acid sequence showed a structural architecture very similar to tenascin: a cysteine-rich amino terminal region is followed by 4.5 epidermal growth factor-like repeats, 9 fibronectin type III homologous repeats and a domain homologous to fibrinogen. Sequence comparison analysis revealed highest homology of rat J1-160/180 to mouse tenascin and chicken restrictin with a similarity of 66% and 85%, respectively. The J1-160/180-coding mRNA is derived from a single copy gene. Using the polymerase chain reaction we could show that two J1-160/180 isoforms are generated by alternative splicing of the sixth fibronectin type III homologous repeat. Localization of J1-160/180 mRNA by in situ hybridization in the cerebellum, hippocampus and olfactory bulb confirmed the expression of J1-160/180 by oligodendrocytes with a peak of transcription at 7-14 d after birth, indicating a functional role during myelination. In addition, J1-160/180-specific RNA was found in a small subset of neurons in all three structures of the CNS analyzed. These neurons continue to express J1-160/180 in the adult. PMID:7679676

Measurement of central corneal thickness with optical low-coherence reflectometry and ultrasound pachymetry in normal and post-femtosecond laser in situ keratomileusis eyes.

PubMed

Huang, Jinhai; Liao, Na; Savini, Giacomo; Li, Yuanguang; Bao, Fangjun; Yu, Ye; Yu, Ayong; Wang, Qinmei

2015-02-01

To determine the repeatability and reproducibility of measurements of central corneal thickness (CCT) using optical low-coherence reflectometry (Lenstar LS900; Haag Streit) in normal eyes and post-femtosecond laser in situ keratomileusis (post-FS-LASIK) eyes and evaluate their agreement with ultrasound (US) pachymetry. CCT was measured using Lenstar and US pachymetry sequentially in normal and post-FS-LASIK eyes by 2 experienced observers. Intraoperator repeatability and interoperator reproducibility were assessed by within-subject standard deviation, test-retest repeatability, coefficient of variation (CoV), and intraclass correlation coefficient. Paired t-tests and Bland-Altman plots were used for analyzing agreement between the 2 devices. In this study, 55 healthy subjects and 50 post-FS-LASIK patients were recruited. Test-retest repeatability of Lenstar was within 10 μm, CoV was less than 1.0%, and intraclass correlation coefficient was more than 0.9 in both normal and post-FS-LASIK groups. Mean difference between these methods was 1.4 ± 4.2 μm and -1.7 ± 5.4 μm, respectively. Moreover, measurements of CCT showed narrow 95% limits of agreement (range, normal group: -6.8 and 9.6 μm; post-FS-LASIK group: -12.4 and 8.9 μm), which implied good agreement. Measurements of CCT using Lenstar showed excellent intraoperator repeatability and interoperator reproducibility both in normal eyes and post-FS-LASIK eyes. Measurements of CCT using Lenstar and US pachymetry showed good agreement and both can be used interchangeably.

Characterization of the fusion core in zebrafish endogenous retroviral envelope protein

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

Shi, Jian; State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071; Zhang, Huaidong

2015-05-08

Zebrafish endogenous retrovirus (ZFERV) is the unique endogenous retrovirus in zebrafish, as yet, containing intact open reading frames of its envelope protein gene in zebrafish genome. Similarly, several envelope proteins of endogenous retroviruses in human and other mammalian animal genomes (such as syncytin-1 and 2 in human, syncytin-A and B in mouse) were identified and shown to be functional in induction of cell–cell fusion involved in placental development. ZFERV envelope protein (Env) gene appears to be also functional in vivo because it is expressible. After sequence alignment, we found ZFERV Env shares similar structural profiles with syncytin and other type Imore » viral envelopes, especially in the regions of N- and C-terminal heptad repeats (NHR and CHR) which were crucial for membrane fusion. We expressed the regions of N + C protein in the ZFERV Env (residues 459–567, including predicted NHR and CHR) to characterize the fusion core structure. We found N + C protein could form a stable coiled-coil trimer that consists of three helical NHR regions forming a central trimeric core, and three helical CHR regions packing into the grooves on the surface of the central core. The structural characterization of the fusion core revealed the possible mechanism of fusion mediated by ZFERV Env. These results gave comprehensive explanation of how the ancient virus infects the zebrafish and integrates into the genome million years ago, and showed a rational clue for discovery of physiological significance (e.g., medicate cell–cell fusion). - Highlights: • ZFERV Env shares similar structural profiles with syncytin and other type I viral envelopes. • The fusion core of ZFERV Env forms stable coiled-coil trimer including three NHRs and three CHRs. • The structural mechanism of viral entry mediated by ZFERV Env is disclosed. • The results are helpful for further discovery of physiological function of ZFERV Env in zebrafish.« less

Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition.

PubMed

Voogdt, Carlos G P; Bouwman, Lieneke I; Kik, Marja J L; Wagenaar, Jaap A; van Putten, Jos P M

2016-01-07

Toll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization, and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein architecture with 22 extracellular leucine rich repeats flanked by a N- and C-terminal leucine rich repeat domain, a membrane-spanning region, and an intracellular TIR domain. The receptor is phylogenetically most similar to TLR5 of birds and most distant to fish TLR5. Transcript analysis revealed acTLR5 expression in multiple lizard tissues. Stimulation of acTLR5 with TLR ligands demonstrated unique responsiveness towards bacterial flagellin in both reptile and human cells. Comparison of acTLR5 and human TLR5 using purified flagellins revealed differential sensitivity to Pseudomonas but not Salmonella flagellin, indicating development of species-specific flagellin recognition during the divergent evolution of mammals and reptiles. Our discovery of reptile TLR5 fills the evolutionary gap regarding TLR conservation across vertebrates and provides novel insights in functional evolution of host-microbe interactions.

Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition

PubMed Central

Voogdt, Carlos G. P.; Bouwman, Lieneke I.; Kik, Marja J. L.; Wagenaar, Jaap A.; van Putten, Jos P. M.

2016-01-01

Toll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization, and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein architecture with 22 extracellular leucine rich repeats flanked by a N- and C-terminal leucine rich repeat domain, a membrane-spanning region, and an intracellular TIR domain. The receptor is phylogenetically most similar to TLR5 of birds and most distant to fish TLR5. Transcript analysis revealed acTLR5 expression in multiple lizard tissues. Stimulation of acTLR5 with TLR ligands demonstrated unique responsiveness towards bacterial flagellin in both reptile and human cells. Comparison of acTLR5 and human TLR5 using purified flagellins revealed differential sensitivity to Pseudomonas but not Salmonella flagellin, indicating development of species-specific flagellin recognition during the divergent evolution of mammals and reptiles. Our discovery of reptile TLR5 fills the evolutionary gap regarding TLR conservation across vertebrates and provides novel insights in functional evolution of host-microbe interactions. PMID:26738735

Genetic Diversity of Blumeria graminis f. sp. hordei in Central Europe and Its Comparison with Australian Population

PubMed Central

Komínková, Eva; Dreiseitl, Antonín; Malečková, Eva; Doležel, Jaroslav

2016-01-01

Population surveys of Blumeria graminis f. sp. hordei (Bgh), a causal agent of more than 50% of barley fungal infections in the Czech Republic, have been traditionally based on virulence tests, at times supplemented with non-specific Restriction fragment length polymorphism or Random amplified polymorphic DNA markers. A genomic sequence of Bgh, which has become available recently, enables identification of potential markers suitable for population genetics studies. Two major strategies relying on transposable elements and microsatellites were employed in this work to develop a set of Repeat junction markers, Single sequence repeat and Single nucleotide polymorphism markers. A resolution power of the new panel of markers comprising 33 polymorphisms was demonstrated by a phylogenetic analysis of 158 Bgh isolates. A core set of 97 Czech isolates was compared to a set 50 Australian isolates on the background of 11 diverse isolates collected throughout the world. 73.2% of Czech isolates were found to be genetically unique. An extreme diversity of this collection was in strong contrast with the uniformity of the Australian one. This work paves the way for studies of population structure and dynamics based on genetic variability among different Bgh isolates originating from geographically limited regions. PMID:27875588

A Novel Family of Sequence-specific Endoribonucleases Associated with the Clustered Regularly Interspaced Short Palindromic Repeats

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

Beloglazova, Natalia; Brown, Greg; Zimmerman, Matthew D.

Clustered regularly interspaced short palindromic repeats (CRISPRs) together with the associated CAS proteins protect microbial cells from invasion by foreign genetic elements using presently unknown molecular mechanisms. All CRISPR systems contain proteins of the CAS2 family, suggesting that these uncharacterized proteins play a central role in this process. Here we show that the CAS2 proteins represent a novel family of endoribonucleases. Six purified CAS2 proteins from diverse organisms cleaved single-stranded RNAs preferentially within U-rich regions. A representative CAS2 enzyme, SSO1404 from Sulfolobus solfataricus, cleaved the phosphodiester linkage on the 3'-side and generated 5'-phosphate- and 3'-hydroxyl-terminated oligonucleotides. The crystal structure ofmore » SSO1404 was solved at 1.6{angstrom} resolution revealing the first ribonuclease with a ferredoxin-like fold. Mutagenesis of SSO1404 identified six residues (Tyr-9, Asp-10, Arg-17, Arg-19, Arg-31, and Phe-37) that are important for enzymatic activity and suggested that Asp-10 might be the principal catalytic residue. Thus, CAS2 proteins are sequence-specific endoribonucleases, and we propose that their role in the CRISPR-mediated anti-phage defense might involve degradation of phage or cellular mRNAs.« less

Glider and Vision: two new families of miniature inverted-repeat transposable elements in Xenopus laevis genome.

PubMed

Lepetit, D; Pasquet, S; Olive, M; Thézé, N; Thiébaud, P

2000-01-01

We have characterised from Xenopus laevis two new short interspersed repetitive elements, we have named Glider and Vision, that belong to the family of miniature inverted-repeat transposable elements (MITEs). Glider was first characterised in an intronic region of the alpha-tropomyosin (alpha-TM) gene and database search has revealed the presence of this element in 10 other Xenopus laevis genes. Glider elements are about 150 bp long and for some of them, their terminal inverted repeats are flanked by potential target-site duplications. Evidence for the mobility of Glider element has been provided by the presence/absence of one element at corresponding location in duplicated alpha-TM genes. Vision element has been identified in the promoter region of the cyclin dependant kinase 2 gene (cdk2) where it is boxed in a Glider element. Vision is 284bp long and is framed by 14-bp terminal inverted repeats that are flanked by 7-bp direct repeats. We have estimated that there are about 20,000 and 300 copies of Glider and Vision respectively scattered throughout the Xenopus laevis genome. Every MITEs elements but two described in our study are found either in 5' or in 3' regulatory regions of genes suggesting a potential role in gene regulation.

Reconstructing Fire Disturbances in Coastal Temperate Rainforests on the Central Coast of British Columbia, Canada

NASA Astrophysics Data System (ADS)

Hoffman, Kira; Smith, Dan; Lertzman, Ken; Starzomski, Brian

2015-04-01

The coastal temperate rainforests of British Columbia's Central Coast are comprised of old growth, mixed-age stands and a mosaic of non-forested bogs. This region receives approximately 4000 mm of annual rainfall, and fire disturbances caused by lightning are thought to be very rare. Because of the late successional characteristics of these forests and the presumed lack of visible fire evidence, fires have been estimated to occur at up to 6000-year return intervals. We attempt to distinguish the roles of natural and cultural (First Nations) fires using multiple lines of evidence from tree ring records, fire-scarred trees, soil charcoal and archaeological evidence from First Nations settlement areas. To reconstruct the Holocene fire history of the study area located on Hecate Island (N 51 38 W -128 05), thirty 400m2 forest mensuration plots were systematically established in a 287-hectare area burned in 1893. Analyses focused on the relationship between fire events and climate recorded in tree rings and instrumental records, as well as nutrient concentrations and pH of soils and plant community characteristics. Four fire events (1893, 1776, 1525, 1372) were recorded in forty-five living, fire-scarred western redcedar (Thuja plicata), yellow cedar (Xanthocyparis nootkatensis) and shore pine (Pinus contorta var. contorta) trees. Five additional fire events (1785 Cal BP, 2760 Cal BP, 3355 Cal BP, 4735 Cal BP, 7740 Cal BP) were dated with accelerated mass spectrometry radiocarbon dating of in situ macro charcoal (> 5mm) buried in stratigraphy in both organic and mineral soils. The short intervals between fire events, coupled with the long history of First Nations settlement and land use in the study area, suggest purposeful and repeated low-intensity ground fires. Our research demonstrates that fires are more widespread and common than previously recorded on the very wet Central Coast of British Columbia. It is important to incorporate cultural fires into fire history research to better understand the ecological legacies associated with repeat fire disturbances in coastal temperate rainforests.

The complete chloroplast DNA sequence of Eleutherococcus senticosus (Araliaceae); comparative evolutionary analyses with other three asterids.

PubMed

Yi, Dong-Keun; Lee, Hae-Lim; Sun, Byung-Yun; Chung, Mi Yoon; Kim, Ki-Joong

2012-05-01

This study reports the complete chloroplast (cp) DNA sequence of Eleutherococcus senticosus (GenBank: JN 637765), an endangered endemic species. The genome is 156,768 bp in length, and contains a pair of inverted repeat (IR) regions of 25,930 bp each, a large single copy (LSC) region of 86,755 bp and a small single copy (SSC) region of 18,153 bp. The structural organization, gene and intron contents, gene order, AT content, codon usage, and transcription units of the E. senticosus chloroplast genome are similar to that of typical land plant cp DNA. We aligned and analyzed the sequences of 86 coding genes, 19 introns and 113 intergenic spacers (IGS) in three different taxonomic hierarchies; Eleutherococcus vs. Panax, Eleutherococcus vs. Daucus, and Eleutherococcus vs. Nicotiana. The distribution of indels, the number of polymorphic sites and nucleotide diversity indicate that positional constraint is more important than functional constraint for the evolution of cp genome sequences in Asterids. For example, the intron sequences in the LSC region exhibited base substitution rates 5-11-times higher than that of the IR regions, while the intron sequences in the SSC region evolved 7-14-times faster than those in the IR region. Furthermore, the Ka/Ks ratio of the gene coding sequences supports a stronger evolutionary constraint in the IR region than in the LSC or SSC regions. Therefore, our data suggest that selective sweeps by base collection mechanisms more frequently eliminate polymorphisms in the IR region than in other regions. Chloroplast genome regions that have high levels of base substitutions also show higher incidences of indels. Thirty-five simple sequence repeat (SSR) loci were identified in the Eleutherococcus chloroplast genome. Of these, 27 are homopolymers, while six are di-polymers and two are tri-polymers. In addition to the SSR loci, we also identified 18 medium size repeat units ranging from 22 to 79 bp, 11 of which are distributed in the IGS or intron regions. These medium size repeats may contribute to developing a cp genome-specific gene introduction vector because the region may use for specific recombination sites.

Thermal denaturation of the BRCT tandem repeat region of human tumour suppressor gene product BRCA1.

PubMed

Pyrpassopoulos, Serapion; Ladopoulou, Angela; Vlassi, Metaxia; Papanikolau, Yannis; Vorgias, Constantinos E; Yannoukakos, Drakoulis; Nounesis, George

2005-04-01

Reduced stability of the tandem BRCT domains of human BReast CAncer 1 (BRCA1) due to missense mutations may be critical for loss of function in DNA repair and damage-induced checkpoint control. In the present thermal denaturation study of the BRCA1 BRCT region, high-precision differential scanning calorimetry (DSC) and circular dichroism (CD) spectroscopy provide evidence for the existence of a denatured state that is structurally very similar to the native. Consistency between theoretical structure-based estimates of the enthalpy (DeltaH) and heat capacity change (DeltaCp) and the calorimetric results is obtained when considering partial thermal unfolding contained in the region of the conserved hydrophobic pocket formed at the interface of the two BRCT repeats. The structural integrity of this region has been shown to be crucial for the interaction of BRCA1 with phosphorylated peptides. In addition, cancer-causing missense mutations located at the inter-BRCT-repeat interface have been linked to the destabilization of the tandem BRCT structure.

[A young woman with central facial nerve palsy].

PubMed

Broere, Christiaan M; de Witte, B R René; Claes, J F H M Franka

2014-01-01

The distinction between central and peripheral facial nerve palsy can be difficult but is very important for the workup and treatment. A tumefactive demyelinating lesion (TDL) is a rare condition that can sometimes cause diagnostic difficulties due to its similarity to a brain tumour. We present a 20-year-old female patient who visited her GP with a discrete right-sided drooping corner of her mouth. The GP started treatment with oral glucorticoids because of presumed Bell's palsy and referred her to the neurology outpatient clinic. Repeated neurological examination showed central facial palsy on the right side of the face. An MRI study of the brain revealed a single large contrast-enhanced abnormality in the left hemisphere that was diagnosed as TDL after exclusion of other causes. In view of the limited number of clinical symptoms, an expectative policy was conducted. The patient recovered spontaneously and repeated MRI studies showed partial regression of TDL. TDL is often considered to be a first presentation of multiple sclerosis. Accurate analysis with MRI can help in making a diagnosis without the need for a biopsy.

Reproducibility of regional DEXA examinations of abdominal fat and lean tissue.

PubMed

Tallroth, Kaj; Kettunen, Jyrki A; Kujala, Urho M

2013-01-01

The aim of this study was to develop and test the validity of a new repeatable method to delimit abdominal areas for follow-up of fat mass (FM) and lean tissue mass (LM) in DEXA examinations. 37 male volunteers underwent two DEXA examinations. Total body FM and LM measurements and corresponding abdominal measurements in a carefully defined region were calculated from the first scan. After repositioning of the subjects and a second scan, the delimited region was copied and the abdominal tissues re-calculated. The mean LM of the abdominal area was 2.804 kg (SD 0.556), and the mean FM was 1.026 kg (SD 0.537). The intra-class correlation coefficient for the repeated abdominal LM, FM, and LM/FM ratio measurements was 0.99. The mean difference (bias) for the repeated abdominal LM measurements was -13 g (95% confidence interval (CI) -193.0 to 166.8), and for the repeated abdominal FM measurements it was -35 g (95% CI -178.9 to 108.5). The results indicate that regional DEXA is a sensitive method with excellent reproducibility in the measurements of the abdominal fat and lean tissues. The method may serve as a useful tool for evaluation and follow-up of various dietary and training programmes.

Reproducibility of Regional DEXA Examinations of Abdominal Fat and Lean Tissue

PubMed Central

Tallroth, Kaj; Kettunen, Jyrki A.; Kujala, Urho M.

2013-01-01

Objective The aim of this study was to develop and test the validity of a new repeatable method to delimit abdominal areas for follow-up of fat mass (FM) and lean tissue mass (LM) in DEXA examinations. Methods 37 male volunteers underwent two DEXA examinations. Total body FM and LM measurements and corresponding abdominal measurements in a carefully defined region were calculated from the first scan. After repositioning of the subjects and a second scan, the delimited region was copied and the abdominal tissues re-calculated. Results The mean LM of the abdominal area was 2.804 kg (SD 0.556), and the mean FM was 1.026 kg (SD 0.537). The intra-class correlation coefficient for the repeated abdominal LM, FM, and LM/FM ratio measurements was 0.99. The mean difference (bias) for the repeated abdominal LM measurements was −13 g (95% confidence interval (CI) −193.0 to 166.8), and for the repeated abdominal FM measurements it was −35 g (95% CI −178.9 to 108.5). Conclusions The results indicate that regional DEXA is a sensitive method with excellent reproducibility in the measurements of the abdominal fat and lean tissues. The method may serve as a useful tool for evaluation and follow-up of various dietary and training programmes. PMID:23615566

A survey of FRAXE allele sizes in three populations

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

Zhong, N.; Ju, W.; Curley, D.

1996-08-09

FRAXE is a fragile site located at Xq27-8, which contains polymorphic triplet GCC repeats associated with a CpG island. Similar to FRAXA, expansion of the GCC repeats results in an abnormal methylation of the CpG island and is associated with a mild mental retardation syndrome (FRAXE-MR). We surveyed the GCC repeat alleles of FRAXE from 3 populations. A total of 665 X chromosomes including 416 from a New York Euro-American sample (259 normal and 157 with FRAXA mutations), 157 from a Chinese sample (144 normal and 13 FRAXA), and 92 from a Finnish sample (56 normal and 36 FRAXA) weremore » analyzed by polymerase chain reaction. Twenty-seven alleles, ranging from 4 to 39 GCC repeats, were observed. The modal repeat number was 16 in the New York and Finnish samples and accounted for 24% of all the chromosomes tested (162/665). The modal repeat number in the Chinese sample was 18. A founder effect for FRAXA was suggested among the Finnish FRAXA samples in that 75% had the FRAXE 16 repeat allele versus only 30% of controls. Sequencing of the FRAXE region showed no imperfections within the GCC repeat region, such as those commonly seen in FRAXA. The smaller size and limited range of repeats and the lack of imperfections suggests the molecular mechanisms underlying FRAXE triplet mutations may be different from those underlying FRAXA. 27 refs., 4 figs., 1 tab.« less

Thermodynamics in landscape ecology: The importance of integrating measurement and modeling of landscape entropy

Treesearch

Samuel A. Cushman

2015-01-01

Entropy and the second law of thermodynamics are the central organizing principles of nature. Or perhaps more accurately, the second law is the central disorganizing principle. Hot things cool down. Cold things warm up. You cannot get something for nothing. You always pay more than you get. Things fall apart. You cannot repeat the past. We grow old and die. It is all...

Identification and Analysis of Novel Amino-Acid Sequence Repeats in Bacillus anthracis str. Ames Proteome Using Computational Tools

PubMed Central

Hemalatha, G. R.; Rao, D. Satyanarayana; Guruprasad, L.

2007-01-01

We have identified four repeats and ten domains that are novel in proteins encoded by the Bacillus anthracis str. Ames proteome using automated in silico methods. A “repeat” corresponds to a region comprising less than 55-amino-acid residues that occur more than once in the protein sequence and sometimes present in tandem. A “domain” corresponds to a conserved region with greater than 55-amino-acid residues and may be present as single or multiple copies in the protein sequence. These correspond to (1) 57-amino-acid-residue PxV domain, (2) 122-amino-acid-residue FxF domain, (3) 111-amino-acid-residue YEFF domain, (4) 109-amino-acid-residue IMxxH domain, (5) 103-amino-acid-residue VxxT domain, (6) 84-amino-acid-residue ExW domain, (7) 104-amino-acid-residue NTGFIG domain, (8) 36-amino-acid-residue NxGK repeat, (9) 95-amino-acid-residue VYV domain, (10) 75-amino-acid-residue KEWE domain, (11) 59-amino-acid-residue AFL domain, (12) 53-amino-acid-residue RIDVK repeat, (13) (a) 41-amino-acid-residue AGQF repeat and (b) 42-amino-acid-residue GSAL repeat. A repeat or domain type is characterized by specific conserved sequence motifs. We discuss the presence of these repeats and domains in proteins from other genomes and their probable secondary structure. PMID:17538688

A Novel MAPT Mutation, G55R, in a Frontotemporal Dementia Patient Leads to Altered Tau Function

PubMed Central

Guzman, Elmer; Barczak, Anna; Chodakowska-Żebrowska, Małgorzata; Barcikowska, Maria; Feinstein, Stuart

2013-01-01

Over two dozen mutations in the gene encoding the microtubule associated protein tau cause a variety of neurodegenerative dementias known as tauopathies, including frontotemporal dementia (FTD), PSP, CBD and Pick's disease. The vast majority of these mutations map to the C-terminal region of tau possessing microtubule assembly and microtubule dynamics regulatory activities as well as the ability to promote pathological tau aggregation. Here, we describe a novel and non-conservative tau mutation (G55R) mapping to an alternatively spliced exon encoding part of the N-terminal region of the protein in a patient with the behavioral variant of FTD. Although less well understood than the C-terminal region of tau, the N-terminal region can influence both MT mediated effects as well as tau aggregation. The mutation changes an uncharged glycine to a basic arginine in the midst of a highly conserved and very acidic region. In vitro, 4-repeat G55R tau nucleates microtubule assembly more effectively than wild-type 4-repeat tau; surprisingly, this effect is tau isoform specific and is not observed in a 3-repeat G55R tau versus 3-repeat wild-type tau comparison. In contrast, the G55R mutation has no effect upon the abilities of tau to regulate MT growing and shortening dynamics or to aggregate. Additionally, the mutation has no effect upon kinesin translocation in a microtubule gliding assay. Together, (i) we have identified a novel tau mutation mapping to a mutation deficient region of the protein in a bvFTD patient, and (ii) the G55R mutation affects the ability of tau to nucleate microtubule assembly in vitro in a 4-repeat tau isoform specific manner. This altered capability could markedly affect in vivo microtubule function and neuronal cell biology. We consider G55R to be a candidate mutation for bvFTD since additional criteria required to establish causality are not yet available for assessment. PMID:24086739

Prevalence of human immunodeficiency virus RNA and antibody in first-time, lapsed, and repeat blood donations across five international regions and relative efficacy of alternative screening scenarios.

PubMed

Bruhn, Roberta; Lelie, Nico; Custer, Brian; Busch, Michael; Kleinman, Steven

2013-10-01

Twenty-one blood organizations from five geographical regions provided HIV individual donation (ID)-NAT and serology data on 11,787,610 donations. Infections were classified as anti-HIV-/RNA+ window period (WP), anti-HIV+/RNA+ concordant positive (CP) or anti-HIV+/RNA- elite controller (EC). Residual risk and efficacy of several screening scenarios were estimated for first time, lapsed and repeat donations. WP residual risk estimates assumed a 50% infectious dose of 3.16 virions and a 50% detection limit of 2.7 HIV RNA copies/mL for ID-NAT and 10,000 copies/mL for p24Ag. Infectivity for CP (100%) and EC (2.2%) donations was estimated based on viral load distributions and 100-fold reduced infectivity by antibody neutralization as reported elsewhere. Efficacy was calculated as proportion of transmission risk removed from baseline (i.e. in absence of any screening). There was no significant difference in transmission risk between lapsed and repeat donations in any region. Risk was 3.8-fold higher in first time than combined lapsed/repeat donations in South Africa but not in other regions. Screening strategies were most efficacious at interdicting infectious transfusions in first time (98.7-99.8%) followed by lapsed (97.6-99.7%) and repeat (86.8-97.7%) donations in all regions combined. In each donor category the efficacy of ID-NAT alone (97.7-99.8%) was superior to that of minipool (MP)-NAT/anti-HIV (95.0-99.6%) and p24 Ag/anti-HIV (89.8-99.1%). Efficacy patterns were similar by donor/donation status in each region despite large differences in HIV prevalence and transmission risk. As similar data become available for HBV and HCV, this modeling may be useful in cost effectiveness analyses of alternative testing scenarios. © 2013 American Association of Blood Banks.

Top surface blade residues and the central channel water molecules are conserved in every repeat of the integrin-like β-propeller structures.

PubMed

Denesyuk, Alexander; Denessiouk, Konstantin; Johnson, Mark S

2018-02-01

An integrin-like β-propeller domain contains seven repeats of a four-stranded antiparallel β-sheet motif (blades). Previously we described a 3D structural motif within each blade of the integrin-type β-propeller. Here, we show unique structural links that join different blades of the β-propeller structure, which together with the structural motif for a single blade are repeated in a β-propeller to provide the functional top face of the barrel, found to be involved in protein-protein interactions and substrate recognition. We compare functional top face diagrams of the integrin-type β-propeller domain and two non-integrin type β-propeller domains of virginiamycin B lyase and WD Repeat-Containing Protein 5. Copyright © 2017 Elsevier Inc. All rights reserved.

Role of Hsp-70 responses in cold acclimation of HUVEC-12 cells.

PubMed

Guan, Hao; Hu, Dahai; Zhao, Zhijing; Cai, Weixia; Zhou, Qin; Yang, Ximing; Yan, Ying; Zhu, Xiongxiang

2015-01-01

Endothelial recovery is a central feature of tissues after frostbite injuries. Thermo tolerance plays an important role in protecting cells against injury after frozen and thawing. The present study aimed to quantitatively assess the injury of human umbilical vein endothelial cells HUVEC-12 after repeated low temperature. Pretreatments (HUVEC-12) cells were repeatedly exposed to cold (1°C/min decrement to -20°C). Their proliferation, death, apoptosis, and protein and mRNA expressions of HSP70 were determined. Endothelial cells after repeated cold exposures were more resistant to apoptosis and necrosis than normal cells. The expressions of HSP70 in cells after repeated cold exposures were significantly higher than in normal HUVEC-12 cells (P < 0.05). Cold acclimation may induce the expression of HSP-70 which plays a protective role in the temperature tolerance.

Recombination-dependent replication and gene conversion homogenize repeat sequences and diversify plastid genome structure.

PubMed

Ruhlman, Tracey A; Zhang, Jin; Blazier, John C; Sabir, Jamal S M; Jansen, Robert K

2017-04-01

There is a misinterpretation in the literature regarding the variable orientation of the small single copy region of plastid genomes (plastomes). The common phenomenon of small and large single copy inversion, hypothesized to occur through intramolecular recombination between inverted repeats (IR) in a circular, single unit-genome, in fact, more likely occurs through recombination-dependent replication (RDR) of linear plastome templates. If RDR can be primed through both intra- and intermolecular recombination, then this mechanism could not only create inversion isomers of so-called single copy regions, but also an array of alternative sequence arrangements. We used Illumina paired-end and PacBio single-molecule real-time (SMRT) sequences to characterize repeat structure in the plastome of Monsonia emarginata (Geraniaceae). We used OrgConv and inspected nucleotide alignments to infer ancestral nucleotides and identify gene conversion among repeats and mapped long (>1 kb) SMRT reads against the unit-genome assembly to identify alternative sequence arrangements. Although M. emarginata lacks the canonical IR, we found that large repeats (>1 kilobase; kb) represent ∼22% of the plastome nucleotide content. Among the largest repeats (>2 kb), we identified GC-biased gene conversion and mapping filtered, long SMRT reads to the M. emarginata unit-genome assembly revealed alternative, substoichiometric sequence arrangements. We offer a model based on RDR and gene conversion between long repeated sequences in the M. emarginata plastome and provide support that both intra-and intermolecular recombination between large repeats, particularly in repeat-rich plastomes, varies unit-genome structure while homogenizing the nucleotide sequence of repeats. © 2017 Botanical Society of America.

The myotonic dystrophy kinase 3{prime}-untranslated region and its effect on gene expression

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

Ang, C.W.Y.; Sabourin, L.A.; Narang, M.A.

1994-09-01

Myotonic dystrophy (DM) is an autosomal dominant neuromuscular disease involving the expansion of an unstable CTG repeat in the 3{prime}-untranslated (3{prime}-UTR) region of the DM kinase (DMK) gene. Increased levels of mRNA in congenital compared to normal tissue have been shown, suggesting elevated DMK levels may be responsible for the disease phenotype. To study the effect of the DMK 3{prime}UTR on gene expression, a reporter gene system was constructed using the constitutive CMV promoter with the chloramphenicol acetyl transferase (CAT) open reading frame and the DMK 3{prime}UTR containing from 5 repeats up to 90 repeats. Transient transfection into a rhabdomyosarcomamore » cell line shows a three-fold increase in CAT activity from constructs containing a wildtype 3{prime}UTR (5 and 20 repeats) compared to a control construct containing only a poly(A) signal. Reporter constructs with repeats in the protomutation (50 repeats) and mutation (90 repeats) range show a greater than 10-fold increase over control CAT activity. These results suggest the presence of elements in the DMK 3{prime}UTR capable of conferring increased gene expression. We are currently investigating cell-specific activity of the constructs and conducting deletion mapping to identify regulatory elements in the 3{prime}-UTR.« less

Divergence in centromere structure distinguishes related genomes in Coix lacryma-jobi and its wild relative.

PubMed

Han, Yonghua; Wang, Guixiang; Liu, Zhao; Liu, Jinhua; Yue, Wei; Song, Rentao; Zhang, Xueyong; Jin, Weiwei

2010-02-01

Knowledge about the composition and structure of centromeres is critical for understanding how centromeres perform their functional roles. Here, we report the sequences of one centromere-associated bacterial artificial chromosome clone from a Coix lacryma-jobi library. Two Ty3/gypsy-class retrotransposons, centromeric retrotransposon of C. lacryma-jobi (CRC) and peri-centromeric retrotransposon of C. lacryma-jobi, and a (peri)centromere-specific tandem repeat with a unit length of 153 bp were identified. The CRC is highly homologous to centromere-specific retrotransposons reported in grass species. An 80-bp DNA region in the 153-bp satellite repeat was found to be conserved to centromeric satellite repeats from maize, rice, and pearl millet. Fluorescence in situ hybridization showed that the three repetitive sequences were located in (peri-)centromeric regions of both C. lacryma-jobi and Coix aquatica. However, the 153-bp satellite repeat was only detected on 20 out of the 30 chromosomes in C. aquatica. Immunostaining with an antibody against rice CENH3 indicates that the 153-bp satellite repeat and CRC might be both the major components for functional centromeres, but not all the 153-bp satellite repeats or CRC sequences are associated with CENH3. The evolution of centromeric repeats of C. lacryma-jobi during the polyploidization was discussed.

CRISPR Detection From Short Reads Using Partial Overlap Graphs.

PubMed

Ben-Bassat, Ilan; Chor, Benny

2016-06-01

Clustered regularly interspaced short palindromic repeats (CRISPR) are structured regions in bacterial and archaeal genomes, which are part of an adaptive immune system against phages. CRISPRs are important for many microbial studies and are playing an essential role in current gene editing techniques. As such, they attract substantial research interest. The exponential growth in the amount of bacterial sequence data in recent years enables the exploration of CRISPR loci in more and more species. Most of the automated tools that detect CRISPR loci rely on fully assembled genomes. However, many assemblers do not handle repetitive regions successfully. The first tool to work directly on raw sequence data is Crass, which requires reads that are long enough to contain two copies of the same repeat. We present a method to identify CRISPR repeats from raw sequence data of short reads. The algorithm is based on an observation differentiating CRISPR repeats from other types of repeats, and it involves a series of partial constructions of the overlap graph. This enables us to avoid many of the difficulties that assemblers face, as we merely aim to identify the repeats that belong to CRISPR loci. A preliminary implementation of the algorithm shows good results and detects CRISPR repeats in cases where other existing tools fail to do so.

Two tandemly repeated telomere-associated sequences in Nicotiana plumbaginifolia.

PubMed

Chen, C M; Wang, C T; Wang, C J; Ho, C H; Kao, Y Y; Chen, C C

1997-12-01

Two tandemly repeated telomere-associated sequences, NP3R and NP4R, have been isolated from Nicotiana plumbaginifolia. The length of a repeating unit for NP3R and NP4R is 165 and 180 nucleotides respectively. The abundance of NP3R, NP4R and telomeric repeats is, respectively, 8.4 x 10(4), 6 x 10(3) and 1.5 x 10(6) copies per haploid genome of N. plumbaginifolia. Fluorescence in situ hybridization revealed that NP3R is located at the ends and/or in interstitial regions of all 10 chromosomes and NP4R on the terminal regions of three chromosomes in the haploid genome of N. plumbaginifolia. Sequence homology search revealed that not only are NP3R and NP4R homologous to HRS60 and GRS, respectively, two tandem repeats isolated from N. tabacum, but that NP3R and NP4R are also related to each other, suggesting that they originated from a common ancestral sequence. The role of these repeated sequences in chromosome healing is discussed based on the observation that two to three copies of a telomere-similar sequence were present in each repeating unit of NP3R and NP4R.

Fraud in a population-based study of headache: prevention, detection and correction

PubMed Central

2014-01-01

Background In medicine, research misconduct is historically associated with laboratory or pharmaceutical research, but the vulnerability of epidemiological surveys should be recognized. As these surveys underpin health policy and allocation of limited resources, misreporting can have far-reaching implications. We report how fraud in a nationwide headache survey occurred and how it was discovered and rectified before it could cause harm. Methods The context was a door-to-door survey to estimate the prevalence and burden of headache disorders in Pakistan. Data were collected from all four provinces of Pakistan by non-medical interviewers and collated centrally. Measures to ensure data integrity were preventative, detective and corrective. We carefully selected and trained the interviewers, set rules of conduct and gave specific warnings regarding the consequences of falsification. We employed two-fold fraud detection methods: comparative data analysis, and face-to-face re-contact with randomly selected participants. When fabrication was detected, data shown to be unreliable were replaced by repeating the survey in new samples according to the original protocol. Results Comparative analysis of datasets from the regions revealed unfeasible prevalences and gender ratios in one (Multan). Data fabrication was suspected. During a surprise-visit to Multan, of a random sample of addresses selected for verification, all but one had been falsely reported. The data (from 840 cases) were discarded, and the survey repeated with new interviewers. The new sample of 800 cases was demographically and diagnostically consistent with other regions. Conclusion Fraud in community-based surveys is seldom reported, but no less likely to occur than in other fields of medical research. Measures should be put in place to prevent, detect and, where necessary, correct it. In this instance, had the data from Multan been pooled with those from other regions before analysis, a damaging fraud might have escaped notice. PMID:24916996

Structural insight into the role of Streptococcus parasanguinis Fap1 within oral biofilm formation

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

Garnett, James A.; Simpson, Peter J.; Taylor, Jonathan

2012-01-06

Highlights: Black-Right-Pointing-Pointer Crystal structure of Streptococcus parasanguinis Fap1-NR{sub {alpha}} at pH 5.0. Black-Right-Pointing-Pointer pH-dependent conformational changes mediated through electrostatic potential of Fap1-NR{sub {alpha}}. Black-Right-Pointing-Pointer Fap1 facilitates pH-dependent biofilms. Black-Right-Pointing-Pointer We model inter-Fap1 biofilm interactions. -- Abstract: The fimbriae-associated protein 1 (Fap1) is a major adhesin of Streptococcus parasanguinis, a primary colonizer of the oral cavity that plays an important role in the formation of dental plaque. Fap1 is an extracellular adhesive surface fibre belonging to the serine-rich repeat protein (SRRP) family, which plays a central role in the pathogenesis of streptococci and staphylococci. The N-terminal adhesive region of Fap1 (Fap1-NR)more » is composed of two domains (Fap1-NR{sub {alpha}} and Fap1-NR{sub {beta}}) and is projected away from the bacterial surface via the extensive serine-rich repeat region, for adhesion to the salivary pellicle. The adhesive properties of Fap1 are modulated through a pH switch in which a reduction in pH results in a rearrangement between the Fap1-NR{sub {alpha}} and Fap1-NR{sub {beta}} domains, which assists in the survival of S. parasanguinis in acidic environments. We have solved the structure of Fap1-NR{sub {alpha}} at pH 5.0 at 3.0 A resolution and reveal how subtle rearrangements of the 3-helix bundle combined with a change in electrostatic potential mediates 'opening' and activation of the adhesive region. Further, we show that pH-dependent changes are critical for biofilm formation and present an atomic model for the inter-Fap1-NR interactions which have been assigned an important role in the biofilm formation.« less

Effect of CpG dinucleotides within IgH switch region repeats on immunoglobulin class switch recombination.

PubMed

Zhang, Zheng Z; Hsieh, Chih-Lin; Okitsu, Cindy Yen; Han, Li; Yu, Kefei; Lieber, Michael R

2015-08-01

Immunoglobulin (Ig) heavy chains undergo class switch recombination (CSR) to change the heavy chain isotype from IgM to IgG, A or E. The switch regions are several kilobases long, repetitive, and G-rich on the nontemplate strand. They are also relatively depleted of CpG (also called CG) sites for unknown reasons. Here we use synthetic switch regions at the IgH switch alpha (Sα) locus to test the effect of CpG sites and to try to understand why the IgH switch sequences evolved to be relatively depleted of CpG. We find that even just two CpG sites within an 80 bp synthetic switch repeat iterated 15 times (total switch region length of 1200 bp containing 30 CpG sites) are sufficient to dramatically reduce both Ig CSR and transcription through the switch region from the upstream Iα sterile transcript promoter, which is the promoter that directs transcripts through the Sα region. De novo DNA methylation occurs at the four CpG sites in and around the Iα promoter when each 80 bp Iα switch repeat contains the two CpG sites. Thus, a relatively low density of CpG sites within the switch repeats can induce upstream CpG methylation at the IgH alpha locus, and cause a substantial decrease in transcription from the sterile transcript promoter. This effect is likely the reason that switch regions evolved to contain very few CpG sites. We discuss these findings as they relate to DNA methylation and to Ig CSR. Copyright © 2015 Elsevier Ltd. All rights reserved.

Associations between mutations and a VNTR in the human phenylalanine hydroxylase gene

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

Goltsov, A.A.; Eisensmith, R.C.; Woo, S.L.C.

1992-09-01

The HindIII RFLP in the human phenylalanine hydroxylase (PAH) gene is caused by the presence of an AT-rich (70%) minisatellite region. This region contains various multiples of 30-bp tandem repeats and is located 3 kb downstream of the final exon of the gene. PCR-mediated amplification of this region from haplotyped PAH chromosomes indicates that the previously reported 4.0-kb HindIII allele contains three of these repeats, while the 4.4-kb HindIII allele contains 12 of these repeats. The 4.2-kb HindIII fragment can contain six, seven, eight, or nine copies of this repeat. These variations permit more detailed analysis of mutant haplotypes 1,more » 5, 6, and, possibly, others. Kindred analysis in phenylketonuria families demonstrates Mendelian segregation of these VNTR alleles, as well as associations between theses alleles and certain PAH mutations. The R261Q mutation, associated with haplotype 1, is associated almost exclusively with an allele containing eight repeats; the R408W mutation, when occurring on a haplotype 1 background, may also be associated with the eight-repeat VNTR allele. Other PAH mutations associated with haplotype 1, R252W and P281L, do not appear to segregate with specific VNTR alleles. The IVS-10 mutation, when associated with haplotype 6, is associated exclusively with an allele containing seven repeats. The combined use of this VNTR system and the existing RFLP haplotype system will increase the performance of prenatal diagnostic tests based on haplotype analysis. In addition, this VNTR may prove useful in studies concerning the origins and distributions of PAH mutations in different human populations. 32 refs., 3 figs., 3 tabs.« less

Poor methodological detail precludes experimental repeatability and hampers synthesis in ecology.

PubMed

Haddaway, Neal R; Verhoeven, Jos T A

2015-10-01

Despite the scientific method's central tenets of reproducibility (the ability to obtain similar results when repeated) and repeatability (the ability to replicate an experiment based on methods described), published ecological research continues to fail to provide sufficient methodological detail to allow either repeatability of verification. Recent systematic reviews highlight the problem, with one example demonstrating that an average of 13% of studies per year (±8.0 [SD]) failed to report sample sizes. The problem affects the ability to verify the accuracy of any analysis, to repeat methods used, and to assimilate the study findings into powerful and useful meta-analyses. The problem is common in a variety of ecological topics examined to date, and despite previous calls for improved reporting and metadata archiving, which could indirectly alleviate the problem, there is no indication of an improvement in reporting standards over time. Here, we call on authors, editors, and peer reviewers to consider repeatability as a top priority when evaluating research manuscripts, bearing in mind that legacy and integration into the evidence base can drastically improve the impact of individual research reports.

Design of the central region in the Warsaw K-160 cyclotron

NASA Astrophysics Data System (ADS)

Toprek, Dragan; Sura, Josef; Choinski, Jaroslav; Czosnyka, Tomas

2001-08-01

This paper describes the design of the central region for h=2 and 3 modes of acceleration in the Warsaw K-160 cyclotron. The central region is unique and compatible with the two above-mentioned harmonic modes of operation. Only one spiral type inflector will be used. The electric field distribution in the inflector and in the four acceleration gaps has been numerically calculated from an electric potential map produced by the program RELAX3D. The geometry of the central region has been tested with the computations of orbits carried out by means of the computer code CYCLONE. The optical properties of the spiral inflector and the central region were studied by using the programs CASINO and CYCLONE, respectively.

Generation of Aptamers from A Primer-Free Randomized ssDNA Library Using Magnetic-Assisted Rapid Aptamer Selection

NASA Astrophysics Data System (ADS)

Tsao, Shih-Ming; Lai, Ji-Ching; Horng, Horng-Er; Liu, Tu-Chen; Hong, Chin-Yih

2017-04-01

Aptamers are oligonucleotides that can bind to specific target molecules. Most aptamers are generated using random libraries in the standard systematic evolution of ligands by exponential enrichment (SELEX). Each random library contains oligonucleotides with a randomized central region and two fixed primer regions at both ends. The fixed primer regions are necessary for amplifying target-bound sequences by PCR. However, these extra-sequences may cause non-specific bindings, which potentially interfere with good binding for random sequences. The Magnetic-Assisted Rapid Aptamer Selection (MARAS) is a newly developed protocol for generating single-strand DNA aptamers. No repeat selection cycle is required in the protocol. This study proposes and demonstrates a method to isolate aptamers for C-reactive proteins (CRP) from a randomized ssDNA library containing no fixed sequences at 5‧ and 3‧ termini using the MARAS platform. Furthermore, the isolated primer-free aptamer was sequenced and binding affinity for CRP was analyzed. The specificity of the obtained aptamer was validated using blind serum samples. The result was consistent with monoclonal antibody-based nephelometry analysis, which indicated that a primer-free aptamer has high specificity toward targets. MARAS is a feasible platform for efficiently generating primer-free aptamers for clinical diagnoses.

Extraction of edge-based and region-based features for object recognition

NASA Astrophysics Data System (ADS)

Coutts, Benjamin; Ravi, Srinivas; Hu, Gongzhu; Shrikhande, Neelima

1993-08-01

One of the central problems of computer vision is object recognition. A catalogue of model objects is described as a set of features such as edges and surfaces. The same features are extracted from the scene and matched against the models for object recognition. Edges and surfaces extracted from the scenes are often noisy and imperfect. In this paper algorithms are described for improving low level edge and surface features. Existing edge extraction algorithms are applied to the intensity image to obtain edge features. Initial edges are traced by following directions of the current contour. These are improved by using corresponding depth and intensity information for decision making at branch points. Surface fitting routines are applied to the range image to obtain planar surface patches. An algorithm of region growing is developed that starts with a coarse segmentation and uses quadric surface fitting to iteratively merge adjacent regions into quadric surfaces based on approximate orthogonal distance regression. Surface information obtained is returned to the edge extraction routine to detect and remove fake edges. This process repeats until no more merging or edge improvement can take place. Both synthetic (with Gaussian noise) and real images containing multiple object scenes have been tested using the merging criteria. Results appeared quite encouraging.

EXCESS CANCER MORTALITY IN AGRICULTURAL REGIONS OF MINNESOTA

EPA Science Inventory

Because of its unique geology, Minnesota can be divided into four agricultural regions: south-central region one (corn, soybeans); west-central region two (wheat, corn, soybeans); northwest region three (wheat, sugar beets, potatoes); and northeast region four (forested and urban...

The Hayward Fault - Is It Due for a Repeat of the Powerful 1868 Earthquake?

USGS Publications Warehouse

Brocher, Thomas M.; Boatwright, Jack; Lienkaemper, James J.; Prentice, Carol S.; Schwartz, David P.; Bundock, Howard

2008-01-01

On October 21, 1868, a magnitude 6.8 earthquake struck the San Francisco Bay region. Although the region was then sparsely populated, this quake on the Hayward Fault was one of the most destructive in California?s history. Recent studies show that such powerful Hayward Fault quakes have repeatedly jolted the region in the past. U.S. Geological Survey (USGS) scientists describe this fault as a tectonic time bomb, due anytime for another magnitude 6.8 to 7.0 earthquake. Because such a quake could cause hundreds of deaths, leave thousands homeless, and devastate the region?s economy, the USGS and other organizations are working together with new urgency to help prepare Bay Area communities for this certain future quake.

Endogenous opioid systems: physiological role in the self-limitation of seizures.

PubMed

Tortella, F C; Long, J B; Holaday, J W

1985-04-15

Immediately following a seizure, the severity of subsequent seizures is significantly reduced. The involvement of endogenous opioid systems as a physiological regulator of this postseizure inhibition was studied in rats using repeated maximal electroshock (MES) seizures. Both the opiate antagonist (-)-naloxone and morphine tolerance abolished the progressive seizure protection associated with repeated MES. We propose that endogenous opioids, activated by a prior seizure, provide a central homeostatic inhibitory mechanism which may be responsible for the initiation of a postictal refractory state in the epileptic.

Comparison of laboratory and ambulatory measures of central blood pressure and pulse wave reflection: hitting the target or missing the mark?

PubMed

Burns, Matthew J; Seed, Jeremy D; Incognito, Anthony V; Doherty, Connor J; Notay, Karambir; Millar, Philip J

2018-04-01

Prior studies demonstrating clinical significance of noninvasive estimates of central blood pressure (BP) and pulse wave reflection have relied primarily on discrete resting measures. The aim of this study was to compare central BP and pulse wave reflection measures sampled during a single resting laboratory visit against those obtained under ambulatory conditions. The secondary aim was to investigate the reproducibility of ambulatory central BP and pulse wave reflection measurements. Forty healthy participants (21 males; 24 ± 3 years) completed three measurements of brachial artery pulse wave analysis (Oscar 2 with SphygmoCor Inside) in the laboratory followed by 24 hours of ambulatory monitoring. Seventeen participants repeated the 24-hour ambulatory monitoring visit after at least 1 week. Ambulatory measures were divided into daytime (9 AM-9 PM), nighttime (1 AM-6 AM), and 24-hour periods. Compared with laboratory measurements, central systolic BP, augmentation pressure, and augmentation index (with and without heart rate normalization) were higher (all P < .01) during daytime and 24-hour periods but lower during the nighttime period (all P < .001). The drop in nighttime brachial systolic BP was larger than central systolic pressure (Δ -20 ± 6 vs. -15 ± 6 mm Hg; P < .0001). Repeat ambulatory measurements of central BP and pulse wave reflection displayed good-to-excellent intraclass correlation coefficients (r = 0.58-0.86; all P < .01), although measures of pulse wave reflection had higher coefficients of variation (14%-41%). The results highlight absolute differences in central BP and pulse wave reflection between discrete laboratory and ambulatory conditions. The use of ambulatory measures of central BP and pulse wave reflection warrant further investigation for clinical prognostic value. Copyright © 2018 American Heart Association. Published by Elsevier Inc. All rights reserved.

Specific Armadillo Repeat Sequences Facilitate β-Catenin Nuclear Transport in Live Cells via Direct Binding to Nucleoporins Nup62, Nup153, and RanBP2/Nup358*

PubMed Central

Sharma, Manisha; Jamieson, Cara; Johnson, Michael; Molloy, Mark P.; Henderson, Beric R.

2012-01-01

β-Catenin transduces the Wnt signal from the membrane to nucleus, and certain gene mutations trigger its nuclear accumulation leading to cell transformation and cancer. β-Catenin shuttles between the nucleus and cytoplasm independent of classical Ran/transport receptor pathways, and this movement was previously hypothesized to involve the central Armadillo (Arm) domain. Fluorescence recovery after photobleaching (FRAP) assays were used to delineate functional transport regions of the Arm domain in living cells. The strongest nuclear import/export activity was mapped to Arm repeats R10–12 using both in vivo FRAP and in vitro export assays. By comparison, Arm repeats R3–8 of β-catenin were highly active for nuclear import but displayed a comparatively weak export activity. We show for the first time using purified components that specific Arm sequences of β-catenin interact directly in vitro with the FG repeats of the nuclear pore complex (NPC) components Nup62, Nup98, and Nup153, indicating an independent ability of β-catenin to traverse the NPC. Moreover, a proteomics screen identified RanBP2/Nup358 as a binding partner of Arm R10–12, and β-catenin was confirmed to interact with endogenous and ectopic forms of Nup358. We further demonstrate that knock-down of endogenous Nup358 and Nup62 impeded the rate of nuclear import/export of β-catenin to a greater extent than that of importin-β. The Arm R10–12 sequence facilitated transport even when β-catenin was bound to the Arm-binding partner LEF-1, and its activity was stimulated by phosphorylation at Tyr-654. These findings provide functional evidence that the Arm domain contributes to regulated β-catenin transport through direct interaction with the NPC. PMID:22110128

Does Dry Eye Affect Repeatability of Corneal Topography Measurements?

PubMed

Doğan, Aysun Şanal; Gürdal, Canan; Köylü, Mehmet Talay

2018-04-01

The purpose of this study was to assess the repeatability of corneal topography measurements in dry eye patients and healthy controls. Participants underwent consecutive corneal topography measurements (Sirius; Costruzione Strumenti Oftalmici, Florence, Italy). Two images with acquisition quality higher than 90% were accepted. The following parameters were evaluated: minimum and central corneal thickness, aqueous depth, apex curvature, anterior chamber volume, horizontal anterior chamber diameter, iridocorneal angle, cornea volume, and average simulated keratometry. Repeatability was assessed by calculating intra-class correlation coefficient. Thirty-three patients with dry eye syndrome and 40 healthy controls were enrolled to the study. The groups were similar in terms of age (39 [18-65] vs. 30.5 [18-65] years, p=0.198) and gender (M/F: 4/29 vs. 8/32, p=0.366). Intra-class correlation coefficients among all topography parameters within both groups showed excellent repeatability (>0.90). The anterior segment measurements provided by the Sirius corneal topography system were highly repeatable for dry eye patients and are sufficiently reliable for clinical practice and research.

Exploring the repeat protein universe through computational protein design

DOE PAGES

Brunette, TJ; Parmeggiani, Fabio; Huang, Po-Ssu; ...

2015-12-16

A central question in protein evolution is the extent to which naturally occurring proteins sample the space of folded structures accessible to the polypeptide chain. Repeat proteins composed of multiple tandem copies of a modular structure unit are widespread in nature and have critical roles in molecular recognition, signalling, and other essential biological processes. Naturally occurring repeat proteins have been re-engineered for molecular recognition and modular scaffolding applications. In this paper, we use computational protein design to investigate the space of folded structures that can be generated by tandem repeating a simple helix–loop–helix–loop structural motif. Eighty-three designs with sequences unrelatedmore » to known repeat proteins were experimentally characterized. Of these, 53 are monomeric and stable at 95 °C, and 43 have solution X-ray scattering spectra consistent with the design models. Crystal structures of 15 designs spanning a broad range of curvatures are in close agreement with the design models with root mean square deviations ranging from 0.7 to 2.5 Å. Finally, our results show that existing repeat proteins occupy only a small fraction of the possible repeat protein sequence and structure space and that it is possible to design novel repeat proteins with precisely specified geometries, opening up a wide array of new possibilities for biomolecular engineering.« less

Vibroseis Monitoring of San Andreas Fault in California

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

Korneev, Valeri; Nadeau, Robert

2004-06-11

A unique data set of seismograms for 720 source-receiver paths has been collected as part of a controlled source Vibroseis experiment San Andreas Fault (SAF) at Parkfield. In the experiment, seismic waves repeatedly illuminated the epicentral region of the expected M6 event at Parkfield from June 1987 until November 1996. For this effort, a large shear-wave vibrator was interfaced with the 3-component (3-C) borehole High-Resolution Seismic Network (HRSN), providing precisely timed collection of data for detailed studies of changes in wave propagation associated with stress and strain accumulation in the fault zone (FZ). Data collected by the borehole network weremore » examined for evidence of changes associated with the nucleation process of the anticipated M6 earthquake at Parkfield. These investigations reported significant traveltime changes in the S coda for paths crossing the fault zone southeast of the epicenter and above the rupture zone of the 1966 M6 earthquake. Analysis and modeling of these data and comparison with observed changes in creep, water level, microseismicity, slip-at-depth and propagation from characteristic repeating microearthquakes showed temporal variations in a variety of wave propagation attributes that were synchronous with changes in deformation and local seismicity patterns. Numerical modeling suggests 200 meters as an effective thickness of SAF. The observed variations can be explained by velocity 6 percent velocity variation within SAF core. Numerical modeling studies and a growing number of observations have argued for the propagation of fault-zone guided waves (FZGW) within a SAF zone that is 100 to 200 m wide at seismogenic depths and with 20 to 40 percent lower shear-wave velocity than the adjacent unfaulted rock. Guided wave amplitude tomographic inversion for SAF using microearthquakes, shows clearly that FZGW are significantly less attenuated in a well-defined region of the FZ. This region plunges to the northwest along the northwest boundary of the region of highest moment release and separates locked and slipping sections of the SAF at depth, as determined independently from geodesy, seismicity and the recurrence rates of characteristically repeating microearthquakes. The mechanism for low FZGW attenuation in the zone is possibly due to dewatering by fracture closure and/or fault-normal compression, or changes in fracture orientation due to a complex stress or strain field at the boundary between creeping and locked zones of the San Andreas Fault. Temporal changes of FZGW correlates with changes in overall seismicity. Active monitoring of changes in FZGW has a potential for imaging and detecting of changes in stress within FZ cores. Since FZGW primarily propagate in the low-velocity core region of fault zones, they sample the most active zone of fault deformation and provide greater structural detail of the inner fault core than body waves which propagate primarily outside of the central core region. FZGW also can be used for FZ continuity studies.« less

Canadian forest products shipped into the north-central region.

Treesearch

Eugene M. Carpenter

1972-01-01

Documents the imports of Canadian forest products into the north central region and relates import trends to the potential for expanding markets for the region's surplus volume of hardwood growing stock. More than 42% of the $2.1 billion of forest products imported from Canada in 1969 came into the north central region. The value of forest imports has increased...

A Feature-adaptive Subdivision Method for Real-time 3D Reconstruction of Repeated Topology Surfaces

NASA Astrophysics Data System (ADS)

Lin, Jinhua; Wang, Yanjie; Sun, Honghai

2017-03-01

It's well known that rendering for a large number of triangles with GPU hardware tessellation has made great progress. However, due to the fixed nature of GPU pipeline, many off-line methods that perform well can not meet the on-line requirements. In this paper, an optimized Feature-adaptive subdivision method is proposed, which is more suitable for reconstructing surfaces with repeated cusps or creases. An Octree primitive is established in irregular regions where there are the same sharp vertices or creases, this method can find the neighbor geometry information quickly. Because of having the same topology structure between Octree primitive and feature region, the Octree feature points can match the arbitrary vertices in feature region more precisely. In the meanwhile, the patches is re-encoded in the Octree primitive by using the breadth-first strategy, resulting in a meta-table which allows for real-time reconstruction by GPU hardware tessellation unit. There is only one feature region needed to be calculated under Octree primitive, other regions with the same repeated feature generate their own meta-table directly, the reconstruction time is saved greatly for this step. With regard to the meshes having a large number of repeated topology feature, our algorithm improves the subdivision time by 17.575% and increases the average frame drawing time by 0.2373 ms compared to the traditional FAS (Feature-adaptive Subdivision), at the same time the model can be reconstructed in a watertight manner.

Comparative analysis of the 5{prime} genomic and promoter regions between the mouse (Hdh) and human Huntington disease (HD) gene

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

Kalchman, M.; Lin, B.; Nasir, J.

1994-09-01

The mouse homologue of the Huntington disease gene (Hdh) has recently been cloned and mapped to a region of synteny with the human, on mouse chromosome 5. The two genes share a high degree of both coding (90% amino acid) and nucleotide (86.2%) identity. We have subsequently performed a detailed comparison of the genomic organization of the 5{prime} region of the two genes encompassing the promoter region and first five exons of both the human and mouse genes. The comparative sequence analysis of the promoter region between HD and Hdh reveals two highly conserved regions. One region (-56 to -118)more » (+1 is the ATG start codon), shared 84% nucleotide identity and another region (-130 to -206) had 81% nucleotide identity. Nine putative Sp1 sites appear in the human promoter region contrasted with only 3 in a similar region in the mouse. Furthermore, 17 and 20 base pair direct repeats present in the HD 5{prime} region are absent in the similar Hdh region. Although both the mouse and human intron/exon boundaries conform to the GT/AG rule, the intron sizes between HD and Hdh are markedly different. The first four introns in Hdh are 15, 7, 5 and 0.5 kb compared to sizes of 10, 15, 7 and 0.5 kb, respectively. Comparison between the mouse and human intronic sequences immediately adjacent to the first five exons (excluding exon 1) reveals only about 46 to 50% identity within the first 60 bp of intronic sequence. Furthermore, we have identified novel polymorphic di-, tri- and tetra-nucleotide repeats in Hdh introns of various mouse strains that are not present in the human. For example, polymorphic CT repeats are present in introns 2 and 4 of Hdh and a novel mouse 56 AAG trinucleotide repeat (interrupted by an AAGG) is also located within intron 2. This information concerning the promoter and genomic organization of both HD and Hdh is critical for designing appropriate gene targetting vectors for studying the normal function of the HD and Hdh genes in model systems.« less

Imaging a Time-variant Earthquake Focal Region along an Interplate Boundary

NASA Astrophysics Data System (ADS)

Tsuruga, K.; Kasahara, J.; Hasada, Y.; Fujii, N.

2010-12-01

We show a preliminary result of a trial for detecting a time-variant earthquake focal region along an interplate boundary by means of a new imaging method through a numerical simulation. Remarkable seismic reflections from the interplate boundaries of a subducting oceanic plate have been observed in Japan Trench (Mochizuki et al, 2005) and in Nankai Trough (Iidaka et al., 2003). Those strong seismic reflection existing in the current aseismic zones suggest the existence of fluid along the subduction boundary, and it is considered that they closely relate to a future huge earthquake. Seismic ACROSS has a potential to monitor some changes of transfer function along the propagating ray paths, by using an accurately-controlled transmission and receiving of the steady continuous signals repeatedly (Kumazawa et al., 2000). If the physical state in a focal region along the interplate would be changed enough in the time and space, for instance, by increasing or decreasing of fluid flow, we could detect some differences of the amplitude and/or travel-time of the particular reflection phases from the time-variant target region. In this study, we first investigated the seismic characteristics of seismograms and their differences before and after the change of a target region through a numerical simulation. Then, as one of the trials, we attempted to make an image of such time-variant target region by applying a finite-difference back-propagation technique in the time and space to the differences of waveforms (after Kasahara et al., 2010). We here used a 2-D seismic velocity model in the central Japan (Tsuruga et al., 2005), assuming a time-variant target region with a 200-m thickness along a subducting Philippine Sea plate at 30 km in depth. Seismograms were calculated at a 500-m interval for 260 km long by using FDM software (Larsen, 2000), in the case that P- and S-wave velocities (Vp amd Vs) in the target region decreased about 30 % before to after the change (e.g., Vp=3.5 km/s to 2.5 km/s). After applying the new imaging method to the differences between both seismograms at each receiver, it is clear that the remarkable signals related with the target change were focused around the target region during a particular back-propagation time. As a preliminary result, it is not still easy to exactly identify the geometry and shape of the target region. However, we can conclude that it is almost possible to decide the location of the target region by means of an optimized receiver array together with the seismic source which can transmit the accurate and steady signals repeatedly as like as ACROSS even if a single source.

Long-term response of surface water acid neutralizing capacity in a central Appalachian (USA) river basin to declining acid deposition

NASA Astrophysics Data System (ADS)

Kline, Kathleen M.; Eshleman, Keith N.; Garlitz, James E.; U'Ren, Sarah H.

2016-12-01

Long-term changes in acid-base chemistry resulting from declining regional acid deposition were examined using data from repeating synoptic surveys conducted within the 275 km2 Upper Savage River Watershed (USRW) in western Maryland (USA); a randomly-selected set of 40 stream reaches was sampled 36 times between 1999 and 2014 to: (1) repeatedly characterize the acid-base status of the entire river basin; (2) determine whether an extensive network of streams of varying order has shown signs of recovery in acid neutralizing capacity (ANC); and (3) understand the key factors controlling the rate of ANC recovery across the river network. Several non-parametric analyses of trends (i.e., Mann Kendall Trend: MKT tests; and Regional Kendall Trend: RKT) in streamwater acid-base chemistry suggest that USRW has significantly responded to declining acid deposition during the study period; the two most robust, statistically significant trends were decreasing surface water SO42- (∼1.5 μeq L-1 yr-1) and NO3- (∼1 μeq L-1 yr-1) concentrations-consistent with observed downward trends in regional wet S and N deposition. Basin-wide decreasing trends in K+, Mg2+, and Ca2+ were also observed, while Na+ concentrations increased. Significant ANC recovery was observed in 10-20% of USRW stream reaches (depending on the p level used), but the magnitude of the trend relative to natural variability was apparently insufficient to allow detection of a basin-wide ANC trend using the RKT test. Watershed factors, such as forest disturbances and increased application of road deicing salts, appeared to contribute to substantial variability in concentrations of NO3- and Na+ in streams across the basin, but these factors did not affect our overall interpretation of the results as a systematic recovery of USRW from regional acidification. Methodologically, RKT appears to be a robust method for identifying basin-wide trends using synoptic data, but MKT results for individual systems should be examined closely (e.g., to identify trends for specific subpopulations).

Global and regional dissemination and evolution of Burkholderia pseudomallei

PubMed Central

Chewapreecha, Claire; Holden, Matthew T. G.; Vehkala, Minna; Välimäki, Niko; Yang, Zhirong; Harris, Simon R; Mather, Alison E.; Tuanyok, Apichai; De Smet, Birgit; Le Hello, Simon; Bizet, Chantal; Mayo, Mark; Wuthiekanun, Vanaporn; Limmathurotsakul, Direk; Phetsouvanh, Rattanaphone; Spratt, Brian G; Corander, Jukka; Keim, Paul; Dougan, Gordon; Dance, David A. B.; Currie, Bart J; Parkhill, Julian; Peacock, Sharon J.

2017-01-01

The environmental bacterium Burkholderia pseudomallei causes an estimated 165,000 cases of human melioidosis per year worldwide, and is also classified as a biothreat agent. We used whole genome sequences of 469 B. pseudomallei isolates from 30 countries collected over 79 years to explore its geographic transmission. Our data point to Australia as an early reservoir, with transmission to Southeast Asia followed by onward transmission to South Asia, and East Asia. Repeated reintroduction was observed within the Malay Peninsula, and between countries bordered by the Mekong river. Our data support an African origin of the Central and South American isolates with introduction of B. pseudomallei into the Americas between 1650 and 1850, providing a temporal link with the slave trade. We also identified geographically distinct genes/variants in Australasian or Southeast Asian isolates alone, with virulence-associated genes being among those overrepresented. This provides a potential explanation for clinical manifestations of melioidosis that are geographically restricted. PMID:28112723

Role of Chromatin assembly factor 1 in DNA replication of Plasmodium falciparum.

PubMed

Gupta, Mohit Kumar; Agarawal, Meetu; Banu, Khadija; Reddy, K Sony; Gaur, Deepak; Dhar, Suman Kumar

2018-01-01

Nucleosome assembly in P. falciparum could be the key process in maintaining its genomic integrity as DNA replicates more than once per cell cycle during several stages of its life cycle. Here, we report the functional characterization of P. falciparum chromatin assembly factor 1 (CAF1), which interacts with several proteins namely PfCAF2, Histones, PfHP1 and others. Consistent with the above findings, we demonstrate the presence of PfCAF1 at the telomeric repeat regions, central and subtelomeric var genes of multiple var gene family along with PfHP1. Further, we report the upregulation of PfCAF1 after treatment with genotoxic agents like MMS and HU. Together, these findings establish role of PfCAF1 in heterochromatin maintenance and as histone chaperone in nucleosome assembly and DNA damage repair. Copyright © 2017 Elsevier Inc. All rights reserved.

Pneumonic Plague Outbreak, Northern Madagascar, 2011

PubMed Central

Richard, Vincent; Herindrainy, Perlinot; Soanandrasana, Rahelinirina; Ratsitoharina, Maherisoa; Rakotomanana, Fanjasoa; Andrianalimanana, Samuel; Scholz, Holger C.; Rajerison, Minoarisoa

2015-01-01

Yersinia pestis, the causative agent of plague, is endemic to Madagascar, particularly to the central highlands. Although plague has not been previously reported in northern Madagascar, an outbreak of pneumonic plague occurred in this remote area in 2011. Over a 27-day period, 17 suspected, 2 presumptive, and 3 confirmed human cases were identified, and all 15 untreated 20 patients died. Molecular typing of Y. pestis isolated from 2 survivors and 5 Rattus rattus rat samples identified the Madagascar-specific 1.ORI3-k single-nucleotide polymorphism genotype and 4 clustered regularly interspaced short palindromic repeat patterns. This outbreak had a case-fatality rate of 100% for nontreated patients. The Y. pestis 1.ORI3-k single-nucleotide polymorphism genotype might cause larger epidemics. Multidrug-resistant strains and persistence of the pathogen in natural foci near human settlements pose severe risks to populations in plague-endemic regions and require outbreak response strategies. PMID:25530466

Direct observation of TALE protein dynamics reveals a two-state search mechanism

PubMed Central

Cuculis, Luke; Abil, Zhanar; Zhao, Huimin; Schroeder, Charles M.

2015-01-01

Transcription activator-like effector (TALE) proteins are a class of programmable DNA-binding proteins for which the fundamental mechanisms governing the search process are not fully understood. Here we use single-molecule techniques to directly observe TALE search dynamics along DNA templates. We find that TALE proteins are capable of rapid diffusion along DNA using a combination of sliding and hopping behaviour, which suggests that the TALE search process is governed in part by facilitated diffusion. We also observe that TALE proteins exhibit two distinct modes of action during the search process—a search state and a recognition state—facilitated by different subdomains in monomeric TALE proteins. Using TALE truncation mutants, we further demonstrate that the N-terminal region of TALEs is required for the initial non-specific binding and subsequent rapid search along DNA, whereas the central repeat domain is required for transitioning into the site-specific recognition state. PMID:26027871

Direct observation of TALE protein dynamics reveals a two-state search mechanism.

PubMed

Cuculis, Luke; Abil, Zhanar; Zhao, Huimin; Schroeder, Charles M

2015-06-01

Transcription activator-like effector (TALE) proteins are a class of programmable DNA-binding proteins for which the fundamental mechanisms governing the search process are not fully understood. Here we use single-molecule techniques to directly observe TALE search dynamics along DNA templates. We find that TALE proteins are capable of rapid diffusion along DNA using a combination of sliding and hopping behaviour, which suggests that the TALE search process is governed in part by facilitated diffusion. We also observe that TALE proteins exhibit two distinct modes of action during the search process-a search state and a recognition state-facilitated by different subdomains in monomeric TALE proteins. Using TALE truncation mutants, we further demonstrate that the N-terminal region of TALEs is required for the initial non-specific binding and subsequent rapid search along DNA, whereas the central repeat domain is required for transitioning into the site-specific recognition state.

Floating plastic debris in the Central and Western Mediterranean Sea.

PubMed

Ruiz-Orejón, Luis F; Sardá, Rafael; Ramis-Pujol, Juan

2016-09-01

In two sea voyages throughout the Mediterranean (2011 and 2013) that repeated the historical travels of Archduke Ludwig Salvator of Austria (1847-1915), 71 samples of floating plastic debris were obtained with a Manta trawl. Floating plastic was observed in all the sampled sites, with an average weight concentration of 579.3 g dw km(-2) (maximum value of 9298.2 g dw km(-2)) and an average particle concentration of 147,500 items km(-2) (the maximum concentration was 1,164,403 items km(-2)). The plastic size distribution showed microplastics (<5 mm) in all the samples. The most abundant particles had a surface area of approximately 1 mm(2) (the mesh size was 333 μm). The general estimate obtained was a total value of 1455 tons dw of floating plastic in the entire Mediterranean region, with various potential spatial accumulation areas. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Congenital toxoplasmosis with ocular involvment--case report].

PubMed

Constantin, Farah; Denislam, Dogan

2014-01-01

Two thirds of the congenital toxoplasmosis cases describe minimal or inapparent symptoms present at birth, being diagnosed from a psychomotor retard. The forms of chorioretinitis may be described by repeated outbursts in the first years of life. Chorioretinitis or focal necrotizing retinitis usually develops in a bilateral way, being progressive and leading to blindness. Usually there is only one focal inflammatory beginning at the edge of a pigmented scar and the local inflammatory process may extend through successive spikes in other regions of the retina. Active chorioretinitis is expressed clinically by a blurred misty eyesight, with the advent of scotomas, photophobia, and if the macula is involved, the loss of the central eyesight may occur. In this paper I present the patient R.A., 6 years old from Constanta who is hospitalized in the Clinic of Infectious Diseases for investigations and treatment continuity because positive IgG Toxoplasma was previously found. The child has spastic quadriplegia and profound mental retardation.

Investigating the impact of land-use land-cover change on Indian summer monsoon daily rainfall and temperature during 1951–2005 using a regional climate model

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

Halder, Subhadeep; Saha, Subodh K.; Dirmeyer, Paul A.

Daily moderate rainfall events, which constitute a major portion of seasonal summer monsoon rainfall over central India, have decreased significantly during the period 1951 through 2005. On the other hand, mean and extreme near-surface daily temperature during the monsoon season have increased by a maximum of 1–1.5 °C. Using simulations made with a high-resolution regional climate model (RegCM4) and prescribed land cover of years 1950 and 2005, it is demonstrated that part of the changes in moderate rainfall events and temperature have been caused by land-use/land-cover change (LULCC), which is mostly anthropogenic. Model simulations show that the increase in seasonal mean and extreme temperature over centralmore » India coincides with the region of decrease in forest and increase in crop cover. Our results also show that LULCC alone causes warming in the extremes of daily mean and maximum temperatures by a maximum of 1–1.2 °C, which is comparable with the observed increasing trend in the extremes. Decrease in forest cover and simultaneous increase in crops not only reduces the evapotranspiration over land and large-scale convective instability, but also contributes toward decrease in moisture convergence through reduced surface roughness. These factors act together in reducing significantly the moderate rainfall events and the amount of rainfall in that category over central India. Additionally, the model simulations are repeated by removing the warming trend in sea surface temperatures over the Indian Ocean. As a result, enhanced warming at the surface and greater decrease in moderate rainfall events over central India compared to the earlier set of simulations are noticed. Results from these additional experiments corroborate our initial findings and confirm the contribution of LULCC in the decrease in moderate rainfall events and increase in daily mean and extreme temperature over India. Therefore, this study demonstrates the important implications of LULCC over India during the monsoon season. Although, the regional climate model helps in better resolving land–atmosphere feedbacks over the Indian region, the inferences do depend on the fidelity of the model in capturing the features of Indian monsoon realistically. Lastly, it is proposed that similar studies using a suite of climate models will further enrich our understanding about the role of LULCC in the Indian monsoon climate.« less

Investigating the impact of land-use land-cover change on Indian summer monsoon daily rainfall and temperature during 1951–2005 using a regional climate model

DOE PAGES

Halder, Subhadeep; Saha, Subodh K.; Dirmeyer, Paul A.; ...

2016-05-10

Daily moderate rainfall events, which constitute a major portion of seasonal summer monsoon rainfall over central India, have decreased significantly during the period 1951 through 2005. On the other hand, mean and extreme near-surface daily temperature during the monsoon season have increased by a maximum of 1–1.5 °C. Using simulations made with a high-resolution regional climate model (RegCM4) and prescribed land cover of years 1950 and 2005, it is demonstrated that part of the changes in moderate rainfall events and temperature have been caused by land-use/land-cover change (LULCC), which is mostly anthropogenic. Model simulations show that the increase in seasonal mean and extreme temperature over centralmore » India coincides with the region of decrease in forest and increase in crop cover. Our results also show that LULCC alone causes warming in the extremes of daily mean and maximum temperatures by a maximum of 1–1.2 °C, which is comparable with the observed increasing trend in the extremes. Decrease in forest cover and simultaneous increase in crops not only reduces the evapotranspiration over land and large-scale convective instability, but also contributes toward decrease in moisture convergence through reduced surface roughness. These factors act together in reducing significantly the moderate rainfall events and the amount of rainfall in that category over central India. Additionally, the model simulations are repeated by removing the warming trend in sea surface temperatures over the Indian Ocean. As a result, enhanced warming at the surface and greater decrease in moderate rainfall events over central India compared to the earlier set of simulations are noticed. Results from these additional experiments corroborate our initial findings and confirm the contribution of LULCC in the decrease in moderate rainfall events and increase in daily mean and extreme temperature over India. Therefore, this study demonstrates the important implications of LULCC over India during the monsoon season. Although, the regional climate model helps in better resolving land–atmosphere feedbacks over the Indian region, the inferences do depend on the fidelity of the model in capturing the features of Indian monsoon realistically. Lastly, it is proposed that similar studies using a suite of climate models will further enrich our understanding about the role of LULCC in the Indian monsoon climate.« less

Changes of Glaciation and Their Probable Impact on Water Resources in Central Asia

NASA Astrophysics Data System (ADS)

Severskiy, I.

2009-04-01

In the Central Asia the main limiting factor of sustainable development is increasing water shortage. Even now the overwhelming part of territory of Kazakhstan and the adjacent countries of Central Asia are characterized by a condition of the strongest water stress. Fresh water deficiency is, to this or that extent, observed practically on all the territory of Central Asia and transboundary character of the main rivers is one of the main risk factors for sustainable development of national economy of the countries in this region. For the last 20 years a great number of scientific publications appeared in which their authors express an increasingly serious fears about significant reduction of water resources in the arid regions of the world as a reaction to global warming. One of the arguments substantiating such forecasts is the indisputable fact of a continuous intensive degradation of glaciers. Predominating opinion about the inevitability of glaciers disappearance in Central Asia Mountains cannot be accepted as an axiom. Taking into account stability in the sum of precipitation and especially in the snow resources, one can suppose that glaciers in this region will not disappear during this century. Despite the reduction of glaciers, annual runoff volumes and runoff distribution within a year remained unchanged during the last decades. During the same period, norms of atmospheric precipitation and maximum snow-water storage in the zone of runoff formation remained stable. All these suggest the existence of a certain compensation mechanism. Research, based on data analysis of repeated photogrammetric surveys of a group of glaciers and temperature regime of permafrost in Zailiyskiy Alatau range (Northern Tien Shan), suggests that such mechanism can be more and more significant (with climate warming) participation of melting waters of underground ice (buried glaciers, rock glaciers, permafrost) in runoff formation. During last decade the Global Climate system developed in direction of cooling, not warming. It's very clear reflects in change in state of the mountain's glaciation. This rate calculated on the basis of comparative analyses of the data of unified glaciers inventories composed for years 1955, 1979, 1990, 2000, and 2008. The maximum rate of glaciers area reduction in Northern Tien Shan is observed during 1970s and after that during period from middle 1980s to 2008 it significant decreased. In our days this rate is lesser than in middle 1950s. Changes in state of climate was clear reflects in state of perennial permafrost. The ground temperature in perennial permafrost layer in Northern Tien Shan (on the depth of 15m on elevation 3400 a.s.l.) during period from 1974 to 1995 was increased by 0.5-0.6. But after that this process of ground warming was stopped and temperature of above perennial permafrost layer during last 12 years was remain stable about minus 0.2°C. According to the results of research, dispute on continue reduction of glaciation is no reasons to expect significant shortage of regional water resources in Central Asia at least up to coming decades.

Expanded CAG/CTG Repeat DNA Induces a Checkpoint Response That Impacts Cell Proliferation in Saccharomyces cerevisiae

PubMed Central

Sundararajan, Rangapriya; Freudenreich, Catherine H.

2011-01-01

Repetitive DNA elements are mutational hotspots in the genome, and their instability is linked to various neurological disorders and cancers. Although it is known that expanded trinucleotide repeats can interfere with DNA replication and repair, the cellular response to these events has not been characterized. Here, we demonstrate that an expanded CAG/CTG repeat elicits a DNA damage checkpoint response in budding yeast. Using microcolony and single cell pedigree analysis, we found that cells carrying an expanded CAG repeat frequently experience protracted cell division cycles, persistent arrests, and morphological abnormalities. These phenotypes were further exacerbated by mutations in DSB repair pathways, including homologous recombination and end joining, implicating a DNA damage response. Cell cycle analysis confirmed repeat-dependent S phase delays and G2/M arrests. Furthermore, we demonstrate that the above phenotypes are due to the activation of the DNA damage checkpoint, since expanded CAG repeats induced the phosphorylation of the Rad53 checkpoint kinase in a rad52Δ recombination deficient mutant. Interestingly, cells mutated for the MRX complex (Mre11-Rad50-Xrs2), a central component of DSB repair which is required to repair breaks at CAG repeats, failed to elicit repeat-specific arrests, morphological defects, or Rad53 phosphorylation. We therefore conclude that damage at expanded CAG/CTG repeats is likely sensed by the MRX complex, leading to a checkpoint response. Finally, we show that repeat expansions preferentially occur in cells experiencing growth delays. Activation of DNA damage checkpoints in repeat-containing cells could contribute to the tissue degeneration observed in trinucleotide repeat expansion diseases. PMID:21437275

A History of Repeated Failures: Stratigraphy of the Currituck and Cape Fear Slide Complexes on the Central U.S. Atlantic Margin

NASA Astrophysics Data System (ADS)

Hill, J. C.; Brothers, D. S.; Ten Brink, U. S.

2016-12-01

The Currituck and Cape Fear Slide complexes, offshore of North Carolina, are two of the largest (>150 km3) submarine slope failure provinces on the U.S. Atlantic margin. Detailed stratigraphy of these slides and the surrounding regions is derived from a combination of high-resolution sparker multichannel seismic (MCS) data collected by the USGS in 2012, airgun MCS collected as part of the NSF GeoPRISMs Community Seismic Experiment in 2014 & legacy industry airgun MCS data collected in 1970s and 80s. Both the Currituck and Cape Fear Slide complexes are located in regions with high sediment input that resulted in the development of a broad, low gradient (<6°) margin with thick slope sediment accumulation since at least the Miocene. Bedding parallel failure planes highlight the influence of subsurface stratigraphy here. Differential compaction across buried scarps and other erosional surfaces found in proximity to many of the headwalls may have contributed to excess pore pressure in these zones, setting the stage for repeated failures. Within the Currituck Slide complex, there appear to be several buried mass transport deposits (MTDs) within both the Quaternary and Pliocene sections that may be related to buried scarps found beneath both the upper and lower headwalls. At the Cape Fear Slide, the Quaternary section upslope of a large salt diapir displays evidence of possible downslope creep folding within strata that downlap onto a possible buried failure plane. While submarine slope failure along this portion of the margin has long been linked with hydrate dissociation and/or salt tectonics, features that are pervasive along the margin, our new stratigraphic analyses suggest that antecedent margin physiography and sediment loading may be critical factors in determining the locations of large-scale slope failures.

Asymmetric Assembly of Merkel Cell Polyomavirus Large T-Antigen Origin Binding Domains at the Viral Origin

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

C Harrison; G Meinke; H Kwun

2011-12-31

The double-stranded DNA polyomavirus Merkel cell polyomavirus (MCV) causes Merkel cell carcinoma, an aggressive but rare human skin cancer that most often affects immunosuppressed and elderly persons. As in other polyomaviruses, the large T-antigen of MCV recognizes the viral origin of replication by binding repeating G(A/G)GGC pentamers. The spacing, number, orientation, and necessity of repeats for viral replication differ, however, from other family members such as SV40 and murine polyomavirus. We report here the 2.9 {angstrom} crystal structure of the MCV large T-antigen origin binding domain (OBD) in complex with a DNA fragment from the MCV origin of replication. Consistentmore » with replication data showing that three of the G(A/G)GGC-like binding sites near the center of the origin are required for replication, the crystal structure contains three copies of the OBD. This stoichiometry was verified using isothermal titration calorimetry. The affinity for G(A/G)GGC-containing double-stranded DNA was found to be {approx} 740 nM, approximately 8-fold weaker than the equivalent domain in SV40 for the analogous region of the SV40 origin. The difference in affinity is partially attributable to DNA-binding residue Lys331 (Arg154 in SV40). In contrast to SV40, a small protein-protein interface is observed between MCV OBDs when bound to the central region of the origin. This protein-protein interface is reminiscent of that seen in bovine papilloma virus E1 protein. Mutational analysis indicates, however, that this interface contributes little to DNA binding energy.« less

Systematic detection and classification of earthquake clusters in Italy

NASA Astrophysics Data System (ADS)

Poli, P.; Ben-Zion, Y.; Zaliapin, I. V.

2017-12-01

We perform a systematic analysis of spatio-temporal clustering of 2007-2017 earthquakes in Italy with magnitudes m>3. The study employs the nearest-neighbor approach of Zaliapin and Ben-Zion [2013a, 2013b] with basic data-driven parameters. The results indicate that seismicity in Italy (an extensional tectonic regime) is dominated by clustered events, with smaller proportion of background events than in California. Evaluation of internal cluster properties allows separation of swarm-like from burst-like seismicity. This classification highlights a strong geographical coherence of cluster properties. Swarm-like seismicity are dominant in regions characterized by relatively slow deformation with possible elevated temperature and/or fluids (e.g. Alto Tiberina, Pollino), while burst-like seismicity are observed in crystalline tectonic regions (Alps and Calabrian Arc) and in Central Italy where moderate to large earthquakes are frequent (e.g. L'Aquila, Amatrice). To better assess the variation of seismicity style across Italy, we also perform a clustering analysis with region-specific parameters. This analysis highlights clear spatial changes of the threshold separating background and clustered seismicity, and permits better resolution of different clusters in specific geological regions. For example, a large proportion of repeaters is found in the Etna region as expected for volcanic-induced seismicity. A similar behavior is observed in the northern Apennines with high pore pressure associated with mantle degassing. The observed variations of earthquakes properties highlight shortcomings of practices using large-scale average seismic properties, and points to connections between seismicity and local properties of the lithosphere. The observations help to improve the understanding of the physics governing the occurrence of earthquakes in different regions.

Analysis of simian immunodeficiency virus sequence variation in tissues of rhesus macaques with simian AIDS.

PubMed Central

Kodama, T; Mori, K; Kawahara, T; Ringler, D J; Desrosiers, R C

1993-01-01

One rhesus macaque displayed severe encephalomyelitis and another displayed severe enterocolitis following infection with molecularly cloned simian immunodeficiency virus (SIV) strain SIVmac239. Little or no free anti-SIV antibody developed in these two macaques, and they died relatively quickly (4 to 6 months) after infection. Manifestation of the tissue-specific disease in these macaques was associated with the emergence of variants with high replicative capacity for macrophages and primary infection of tissue macrophages. The nature of sequence variation in the central region (vif, vpr, and vpx), the env gene, and the nef long terminal repeat (LTR) region in brain, colon, and other tissues was examined to see whether specific genetic changes were associated with SIV replication in brain or gut. Sequence analysis revealed strong conservation of the intergenic central region, nef, and the LTR. However, analysis of env sequences in these two macaques and one other revealed significant, interesting patterns of sequence variation. (i) Changes in env that were found previously to contribute to the replicative ability of SIVmac for macrophages in culture were present in the tissues of these animals. (ii) The greatest variability was located in the regions between V1 and V2 and from "V3" through C3 in gp120, which are different in location from the variable regions observed previously in animals with strong antibody responses and long-term persistent infection. (iii) The predominant sequence change of D-->N at position 385 in C3 is most surprising, since this change in both SIV and human immunodeficiency virus type 1 has been associated with dramatically diminished affinity for CD4 and replication in vitro. (iv) The nature of sequence changes at some positions (146, 178, 345, 385, and "V3") suggests that viral replication in brain and gut may be facilitated by specific sequence changes in env in addition to those that impart a general ability to replicate well in macrophages. These results demonstrate that complex selective pressures, including immune responses and varying cell and tissue specificity, can influence the nature of sequence changes in env. Images PMID:8411355

Tularaemia in Berlin - two independent cases in travellers returning from central Anatolia, Turkey, February 2011.

PubMed

Schubert, A; Splettstoesser, W; Bätzing-Feigenbaum, J

2011-05-05

Tularaemia, though rare, has recently been increasingly reported in Germany. Most cases are indigenous infections. This report describes two epidemiologically independent infections with Francisella tularensis subspecies holarctica detected in Berlin in February 2011 that were acquired in central Anatolia, Turkey. In Turkey, there have been repeated tularaemia outbreaks since 2000 and the disease should therefore be considered as a differential diagnosis in travellers returning from that country.

Interactions between mafic eruptions and glacial ice or snow: implications of the 2010 Eyjafjallajökull, Iceland, eruption for hazard assessments in the central Oregon Cascades

NASA Astrophysics Data System (ADS)

McKay, D.; Cashman, K. V.

2010-12-01

The 2010 eruption of Eyjafjallajökull, Iceland, demonstrated the importance of addressing hazards specific to mafic eruptions in regions where interactions with glacial ice or snow are likely. One such region is the central Oregon Cascades, where there are hundreds of mafic vents, many of which are Holocene in age. Here we present field observations and quantitative analyses of tephra deposits from recent eruptions at Sand Mountain, Yapoah Cone, and Collier Cone (all <4 ka). These deposits differ from typical Cascade cinder cone deposits in several ways. Most significantly, the Sand Mountain eruption produced a relatively large tephra blanket (~1 km3) that is unusually fine-grained: average clast size is 0.063 - 0.5 mm, in contrast to tephra from typical Cascade cinder cones, which are dominated by small lapilli-sized clasts rather than ash. The eruption of Eyjafjallajökull earlier this year prompted us to investigate the role that ice or snow may have played in the production of unusually fine-grained tephra during the Sand Mountain eruption. The eruption date of Sand Mountain is not well constrained, but it likely occurred during the Neoglacial phase of ice advance, which lasted from ~2 to 8 ka in the central Oregon Cascades (Marcott et al., 2009). During the Neoglacial, winter snowfall was likely ~23% greater and summer temperatures ~1.4°C cooler than present (Marcott, 2009). Although ice did not advance to the elevation of the Sand Mountain vents during this time, the eruption could have occurred through several meters of snow. We have also seen very fine-grained tephra at Yapoah Cone, which is located at a higher elevation and may have interacted with glacial ice. In addition to being characterized by unusually fine grainsize, the Yapoah tephra blanket is deposited directly on top of hyaloclastite in several locations. Tephra from Collier Cone is not characterized by unusually fine grainsize, but several sections of the deposit exhibit features that suggest deposition on top of, or interbedding with, snow that later melted away. Identification of features in mafic tephra that suggest interactions with glacial ice or snow has significant implications for regional volcanic hazard assessments. Specifically, the unique hazards posed by Eyjafjallajökull, especially hazards to air travel caused by unusually fine-grained tephra, could be repeated in the Cascades. Although glacial ice is presently limited to elevations above ~2300 m in the central Oregon Cascades, winter snowpack can exceed 5 m at elevations of ~1800 m and above. If a cinder cone eruption were to occur during winter months, interaction with snow could generate phreatomagmatic activity and outburst flooding similar to the 2010 eruption of Eyjafjallajökull, along with similar hazards to regional air travel and nearby infrastructure. For this reason, we suggest that seasonality should be an important consideration in volcanic hazard assessments for the central Oregon Cascades.

Monitoring post-fire vegetation rehabilitation projects: A common approach for non-forested ecosystems

USGS Publications Warehouse

Wirth, Troy A.; Pyke, David A.

2007-01-01

Emergency Stabilization and Rehabilitation (ES&R) and Burned Area Emergency Response (BAER) treatments are short-term, high-intensity treatments designed to mitigate the adverse effects of wildfire on public lands. The federal government expends significant resources implementing ES&R and BAER treatments after wildfires; however, recent reviews have found that existing data from monitoring and research are insufficient to evaluate the effects of these activities. The purpose of this report is to: (1) document what monitoring methods are generally used by personnel in the field; (2) describe approaches and methods for post-fire vegetation and soil monitoring documented in agency manuals; (3) determine the common elements of monitoring programs recommended in these manuals; and (4) describe a common monitoring approach to determine the effectiveness of future ES&R and BAER treatments in non-forested regions. Both qualitative and quantitative methods to measure effectiveness of ES&R treatments are used by federal land management agencies. Quantitative methods are used in the field depending on factors such as funding, personnel, and time constraints. There are seven vegetation monitoring manuals produced by the federal government that address monitoring methods for (primarily) vegetation and soil attributes. These methods vary in their objectivity and repeatability. The most repeatable methods are point-intercept, quadrat-based density measurements, gap intercepts, and direct measurement of soil erosion. Additionally, these manuals recommend approaches for designing monitoring programs for the state of ecosystems or the effect of management actions. The elements of a defensible monitoring program applicable to ES&R and BAER projects that most of these manuals have in common are objectives, stratification, control areas, random sampling, data quality, and statistical analysis. The effectiveness of treatments can be determined more accurately if data are gathered using an approach that incorporates these six monitoring program design elements and objectives, as well as repeatable procedures to measure cover, density, gap intercept, and soil erosion within each ecoregion and plant community. Additionally, using a common monitoring program design with comparable methods, consistently documenting results, and creating and maintaining a central database for query and reporting, will ultimately allow a determination of the effectiveness of post-fire rehabilitation activities region-wide.

Biological, immunological and functional properties of two novel multi-variant chimeric recombinant proteins of CSP antigens for vaccine development against Plasmodium vivax infection.

PubMed

Shabani, Samaneh H; Zakeri, Sedigheh; Salmanian, Ali H; Amani, Jafar; Mehrizi, Akram A; Snounou, Georges; Nosten, François; Andolina, Chiara; Mourtazavi, Yousef; Djadid, Navid D

2017-10-01

The circumsporozoite protein (CSP) of the malaria parasite Plasmodium vivax is a major pre-erythrocyte vaccine candidate. The protein has a central repeat region that belongs to one of repeat families (VK210, VK247, and the P. vivax-like). In the present study, computer modelling was employed to select chimeric proteins, comprising the conserved regions and different arrangements of the repeat elements (VK210 and VK247), whose structure is similar to that of the native counterparts. DNA encoding the selected chimeras (named CS127 and CS712) were synthetically constructed based on E. coli codons, then cloned and expressed. Mouse monoclonal antibodies (mAbs; anti-Pv-210-CDC and -Pv-247-CDC), recognized the chimeric antigens in ELISA, indicating correct conformation and accessibility of the B-cell epitopes. ELISA using IgG from plasma samples collected from 221 Iranian patients with acute P. vivax showed that only 49.32% of the samples reacted to both CS127 and CS712 proteins. The dominant subclass for the two chimeras was IgG1 (48% of the positive responders, OD 492 =0.777±0.420 for CS127; 48.41% of the positive responders, OD 492 =0.862±0.423 for CS712, with no statistically significant difference P>0.05; Wilcoxon signed ranks test). Binding assays showed that both chimeric proteins bound to immobilized heparan sulphate and HepG2 hepatocyte cells in a concentration-dependent manner, saturable at 80μg/mL. Additionally, anti-CS127 and -CS712 antibodies raised in mice recognized the native protein on the surface of P. vivax sporozoite with high intensity, confirming the presence of common epitopes between the recombinant forms and the native proteins. In summary, despite structural differences at the molecular level, the expression levels of both chimeras were satisfactory, and their conformational structure retained biological function, thus supporting their potential for use in the development of vivax-based vaccine. Copyright © 2017 Elsevier Ltd. All rights reserved.

Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice.

PubMed

Ma, Jianxin; Jackson, Scott A

2006-02-01

The abundance of repetitive DNA varies greatly across centromeres within an individual or between different organisms. To shed light on the molecular mechanisms of centromere repeat proliferation, we performed structural analysis of LTR-retrotransposons, mostly centromere retrotransposons of rice (CRRs), and phylogenetic analysis of CentO satellite repeats harbored in the core region of the rice chromosome 4 centromere (CEN4). The data obtained demonstrate that the CRRs in the centromeric region we investigated have been enriched more significantly by recent rounds of segmental duplication than by original integration of active elements, suggesting that segmental duplication is an important process for CRR accumulation in the centromeric region. Our results also indicate that segmental duplication of large arrays of satellite repeats is primarily responsible for the amplification of satellite repeats, contributing to rapid reshuffling of CentO satellites. Intercentromere satellite homogenization was revealed by genome-wide comparison of CentO satellite monomers. However, a 10-bp duplication present in nearly half of the CEN4 monomers was found to be completely absent in rice centromere 8 (CEN8), suggesting that CEN4 and CEN8 may represent two different stages in the evolution of rice centromeres. These observations, obtained from the only complex eukaryotic centromeres to have been completely sequenced thus far, depict the evolutionary dynamics of rice centromeres with respect to the nature, timing, and process of centromeric repeat amplification.

A 200kW central receiver CPV system

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

Lasich, John, E-mail: jbl@raygen.com; Thomas, Ian, E-mail: ithomas@raygen.com; Hertaeg, Wolfgang

2015-09-28

Raygen Resources has recently completed a Central Receiver CPV (CSPV) pilot plant in Central Victoria, Australia. The system is under final commissioning and initial operation is expected in late April 2015. The pilot demonstrates a full scale CSPV repeatable unit in a form that is representative of a commercial product and provides a test bed to prove out performance and reliability of the CSPV technology. Extensive testing of the system key components: dense array module, wireless solar powered heliostat and control system has been performed in the laboratory and on sun. Results from this key component testing are presented herein.

Analysis of sequence repeats of proteins in the PDB.

PubMed

Mary Rajathei, David; Selvaraj, Samuel

2013-12-01

Internal repeats in protein sequences play a significant role in the evolution of protein structure and function. Applications of different bioinformatics tools help in the identification and characterization of these repeats. In the present study, we analyzed sequence repeats in a non-redundant set of proteins available in the Protein Data Bank (PDB). We used RADAR for detecting internal repeats in a protein, PDBeFOLD for assessing structural similarity, PDBsum for finding functional involvement and Pfam for domain assignment of the repeats in a protein. Through the analysis of sequence repeats, we found that identity of the sequence repeats falls in the range of 20-40% and, the superimposed structures of the most of the sequence repeats maintain similar overall folding. Analysis sequence repeats at the functional level reveals that most of the sequence repeats are involved in the function of the protein through functionally involved residues in the repeat regions. We also found that sequence repeats in single and two domain proteins often contained conserved sequence motifs for the function of the domain. Copyright © 2013 Elsevier Ltd. All rights reserved.

The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa.

PubMed

Budde, K B; González-Martínez, S C; Hardy, O J; Heuertz, M

2013-07-01

Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation-coastal or swamp vs terra firme-in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees.

The ancient tropical rainforest tree Symphonia globulifera L. f. (Clusiaceae) was not restricted to postulated Pleistocene refugia in Atlantic Equatorial Africa

PubMed Central

Budde, K B; González-Martínez, S C; Hardy, O J; Heuertz, M

2013-01-01

Understanding the history of forests and their species' demographic responses to past disturbances is important for predicting impacts of future environmental changes. Tropical rainforests of the Guineo-Congolian region in Central Africa are believed to have survived the Pleistocene glacial periods in a few major refugia, essentially centred on mountainous regions close to the Atlantic Ocean. We tested this hypothesis by investigating the phylogeographic structure of a widespread, ancient rainforest tree species, Symphonia globulifera L. f. (Clusiaceae), using plastid DNA sequences (chloroplast DNA [cpDNA], psbA-trnH intergenic spacer) and nuclear microsatellites (simple sequence repeats, SSRs). SSRs identified four gene pools located in Benin, West Cameroon, South Cameroon and Gabon, and São Tomé. This structure was also apparent at cpDNA. Approximate Bayesian Computation detected recent bottlenecks approximately dated to the last glacial maximum in Benin, West Cameroon and São Tomé, and an older bottleneck in South Cameroon and Gabon, suggesting a genetic effect of Pleistocene cycles of forest contraction. CpDNA haplotype distribution indicated wide-ranging long-term persistence of S. globulifera both inside and outside of postulated forest refugia. Pollen flow was four times greater than that of seed in South Cameroon and Gabon, which probably enabled rapid population recovery after bottlenecks. Furthermore, our study suggested ecotypic differentiation—coastal or swamp vs terra firme—in S. globulifera. Comparison with other tree phylogeographic studies in Central Africa highlighted the relevance of species-specific responses to environmental change in forest trees. PMID:23572126

Resection of Grade III cranial horn tears of the equine medial meniscus alter the contact forces on medial tibial condyle at full extension: an in-vitro cadaveric study.

PubMed

Fowlie, Jennifer; Arnoczky, Steven; Lavagnino, Michael; Maerz, Tristan; Stick, John

2011-12-01

To evaluate the magnitude and distribution of joint contact pressure on the medial tibial condyle after grade III cranial horn tears of the medial meniscus. Experimental study. Cadaveric equine stifles (n = 6). Cadaveric stifles were mounted in a materials testing system and electronic pressure sensors were placed between the medial tibial condyle and medial meniscus. Specimens were loaded parallel to the longitudinal axis of the tibia to 1800 N at 130°, 140°, 150°, and 160° stifle angle. Peak pressure and contact area were recorded from the contact maps. Testing was repeated after surgical creation of a grade III cranial horn tear of the medial meniscus, and after resection of the simulated tear. In the intact specimens, a significantly smaller contact area was observed at 160° compared with the other angles (P < .05). Creation of a grade III cranial horn tear in the medial meniscus did not significantly alter the pressure or contact area measurements at any stifle angle compared with intact specimens (P > .05). Resection of the tear resulted in significantly higher peak pressures in the central region of the medial tibial condyle at a stifle angle of 160° relative to the intact (P = .026) and torn (P = .012) specimens. Resection of grade III cranial horn tears in the medial meniscus resulted in a central focal region of increased pressure on the medial tibial condyle at 160° stifle angle. © Copyright 2011 by The American College of Veterinary Surgeons.

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved.

PubMed

Long, Hannah K; King, Hamish W; Patient, Roger K; Odom, Duncan T; Klose, Robert J

2016-08-19

DNA methylation is a repressive epigenetic modification that covers vertebrate genomes. Regions known as CpG islands (CGIs), which are refractory to DNA methylation, are often associated with gene promoters and play central roles in gene regulation. Yet how CGIs in their normal genomic context evade the DNA methylation machinery and whether these mechanisms are evolutionarily conserved remains enigmatic. To address these fundamental questions we exploited a transchromosomic animal model and genomic approaches to understand how the hypomethylated state is formed in vivo and to discover whether mechanisms governing CGI formation are evolutionarily conserved. Strikingly, insertion of a human chromosome into mouse revealed that promoter-associated CGIs are refractory to DNA methylation regardless of host species, demonstrating that DNA sequence plays a central role in specifying the hypomethylated state through evolutionarily conserved mechanisms. In contrast, elements distal to gene promoters exhibited more variable methylation between host species, uncovering a widespread dependence on nucleotide frequency and occupancy of DNA-binding transcription factors in shaping the DNA methylation landscape away from gene promoters. This was exemplified by young CpG rich lineage-restricted repeat sequences that evaded DNA methylation in the absence of co-evolved mechanisms targeting methylation to these sequences, and species specific DNA binding events that protected against DNA methylation in CpG poor regions. Finally, transplantation of mouse chromosomal fragments into the evolutionarily distant zebrafish uncovered the existence of a mechanistically conserved and DNA-encoded logic which shapes CGI formation across vertebrate species. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Synthetic Fab Fragments that Bind the HIV-1 gp41 Heptad Repeat Regions

PubMed Central

Liu, Yanyun; Regula, Lauren K.; Stewart, Alex; Lai, Jonathan R.

2011-01-01

Recent work has demonstrated that antibody phage display libraries containing restricted diversity in the complementarity determining regions (CDRs) can be used to target a wide variety of antigens with high affinity and specificity. In the most extreme case, antibodies whose combining sites are comprised of only two residues – tyrosine and serine – have been identified against several protein antigens. [F. A. Fellouse, B. Li, D. M. Compaan, A. A. Peden, S. G. Hymowitz, and S. S. Sidhu, J. Mol. Biol., 348 (2005) 1153–1162.] Here, we report the isolation and characterization of antigen-binding fragments (Fabs) from such “minimalist” diversity synthetic antibody libraries that bind the heptad repeat regions of human immunodeficiency virus type 1 (HIV-1) gp41. We show that these Fabs are highly specific for the HIV-1 epitope and comparable in affinity to a single chain variable fragment (scFv) derived from a natural antibody repertoire that targets the same region. Since the heptad repeat regions of HIV-1 gp41 are required for viral entry, these Fabs have potential for use in therapeutic, research, or diagnostic applications. PMID:21925149

Tandem-repeat protein domains across the tree of life.

PubMed

Jernigan, Kristin K; Bordenstein, Seth R

2015-01-01

Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20-40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species.

Is HL Tauri and FU Orionis system in quiescence?

NASA Technical Reports Server (NTRS)

Lin, D. N. C.; Hayashi, M.; Bell, K. R.; Ohashi, N.

1994-01-01

A recent Nobeyama map of HL Tau reveals that gas is infalling in a flattened region approximately 1400 AU around the central star. The apparent motion of the gas provides the necessary condition for the formation of a Keplerian disk with a radius comparable to the size of the primordial solar nebula. The inferred mass infall rate onto the disk is approximately equal to 5 x 10(exp -6) solar mass/yr, which greatly exceeds the maximum estimate of the accretion rate onto the central star (approximately 7 x 10(exp -7) solar mass/yr). Consequently, mass must currently be accumulating in the disk. The estimated age and disk mass of HL Tau suggest that the accumulated matter has been flushed repeatedly on a timescale less than 10(exp 4) yr. Based on the similarites between their evolution patterns, we propose that HL Tau is an FU Orionis system in quiescence. In addition to HL Tau, 14 out of 86 pre-main-sequence stars in the Taurus-Auriga dark clouds have infrared luminosities much greater than their otherwise normal extinction-corrected stellar luminosities. These sources also tend to have flat spectra which may be due to the reprocessing of radiation by dusty, flattened, collapsing envelopes with infall rates a few 10(exp -6) solar mass/yr. Such rates are much larger than estimated central accretion rates for these systems, which suggests that mass must also be accumulating in these disks. If these sources are FU Orionis stars in quiescence, similar to HL Tau, their age and relative abundance imply that the FU Orionis phase occurs over a timescale of approixmately 10(exp 5) yr, and the quiescent phase between each outburst lasts approximately 10(exp 3) =10(exp 4) yr. These inferred properties are compatible with the scenario that FU Orionis outbursts are regulated by a thermal instability in the inner region of the disk.

Educational Attainment of the Public Health Workforce and Its Implications for Workforce Development.

PubMed

Leider, Jonathon P; Harper, Elizabeth; Bharthapudi, Kiran; Castrucci, Brian C

2015-01-01

Educational attainment is a critical issue in public health workforce development. However, relatively little is known about the actual attainment of staff in state health agencies (SHAs). Ascertain the levels of educational attainment among SHA employees, as well as the correlates of attainment. Using a stratified sampling approaching, staff from SHAs were surveyed using the Public Health Workforce Interests and Needs Survey (PH WINS) instrument in late 2014. A nationally representative sample was drawn across 5 geographic (paired adjacent HHS) regions. Descriptive and inferential statistics were analyzed using balanced repeated replication weights to account for complex sampling. A logistic regression was conducted with attainment of a bachelor's degree as the dependent variable and age, region, supervisory status, race/ethnicity, gender, and staff type as independent variables. Web-based survey of SHA central office employees. Educational attainment overall, as well as receipt of a degree with a major in public health. A total of 10,246 permanently-employed SHA central office staff participated in the survey (response rate 46%). Seventy-five percent (95% confidence interval [CI], 74-77) had a bachelor's degree, 38% (95% CI, 37-40) had a master's degree, and 9% (95% CI, 8%-10%) had a doctoral degree. A logistic regression showed Asian staff had the highest odds of having a bachelor's degree (odds ratio [OR] = 2.8; 95% CI, 2.2-3.7) compared with non-Hispanic whites, and Hispanic/Latino staff had lower odds (OR = 0.6; 95% CI, 0.4-0.8). Women had lower odds of having a bachelor's degree than men (OR = 0.5; 95% CI, 0.4-0.6). About 17% of the workforce (95% CI, 16-18) had a degree in public health at any level. Educational attainment among SHA central office staff is high, but relatively few have formal training of any sort in public health. This makes efforts to increase availability of on-the-job training and distance learning all the more critical.

Effects of location and timing of co-activated neurons in the auditory midbrain on cortical activity: implications for a new central auditory prosthesis

NASA Astrophysics Data System (ADS)

Straka, Małgorzata M.; McMahon, Melissa; Markovitz, Craig D.; Lim, Hubert H.

2014-08-01

Objective. An increasing number of deaf individuals are being implanted with central auditory prostheses, but their performance has generally been poorer than for cochlear implant users. The goal of this study is to investigate stimulation strategies for improving hearing performance with a new auditory midbrain implant (AMI). Previous studies have shown that repeated electrical stimulation of a single site in each isofrequency lamina of the central nucleus of the inferior colliculus (ICC) causes strong suppressive effects in elicited responses within the primary auditory cortex (A1). Here we investigate if improved cortical activity can be achieved by co-activating neurons with different timing and locations across an ICC lamina and if this cortical activity varies across A1. Approach. We electrically stimulated two sites at different locations across an isofrequency ICC lamina using varying delays in ketamine-anesthetized guinea pigs. We recorded and analyzed spike activity and local field potentials across different layers and locations of A1. Results. Co-activating two sites within an isofrequency lamina with short inter-pulse intervals (<5 ms) could elicit cortical activity that is enhanced beyond a linear summation of activity elicited by the individual sites. A significantly greater extent of normalized cortical activity was observed for stimulation of the rostral-lateral region of an ICC lamina compared to the caudal-medial region. We did not identify any location trends across A1, but the most cortical enhancement was observed in supragranular layers, suggesting further integration of the stimuli through the cortical layers. Significance. The topographic organization identified by this study provides further evidence for the presence of functional zones across an ICC lamina with locations consistent with those identified by previous studies. Clinically, these results suggest that co-activating different neural populations in the rostral-lateral ICC rather than the caudal-medial ICC using the AMI may improve or elicit different types of hearing capabilities.

Insertion of reticuloendotheliosis virus long terminal repeat into CVI988 strain of Marek’s disease virus results in enhanced growth and protection

USDA-ARS?s Scientific Manuscript database

It has been reported that co-cultivation of a JM/102W strain, a virulent strain of Marek’s disease virus (MDV), with reticuloendotheliosis virus (REV) resulted in the integration of REV long terminal repeat (LTR) into the MDV repeat region. The resulting virus, RM1, was unable to transform T-cells ...

Long interspersed repeated DNA (LINE) causes polymorphism at the rat insulin 1 locus.

PubMed

Lakshmikumaran, M S; D'Ambrosio, E; Laimins, L A; Lin, D T; Furano, A V

1985-09-01

The insulin 1, but not the insulin 2, locus is polymorphic (i.e., exhibits allelic variation) in rats. Restriction enzyme analysis and hybridization studies showed that the polymorphic region is 2.2 kilobases upstream of the insulin 1 coding region and is due to the presence or absence of an approximately 2.7-kilobase repeated DNA element. DNA sequence determination showed that this DNA element is a member of a long interspersed repeated DNA family (LINE) that is highly repeated (greater than 50,000 copies) and highly transcribed in the rat. Although the presence or absence of LINE sequences at the insulin 1 locus occurs in both the homozygous and heterozygous states, LINE-containing insulin 1 alleles are more prevalent in the rat population than are alleles without LINEs. Restriction enzyme analysis of the LINE-containing alleles indicated that at least two versions of the LINE sequence may be present at the insulin 1 locus in different rats. Either repeated transposition of LINE sequences or gene conversion between the resident insulin 1 LINE and other sequences in the genome are possible explanations for this.

Interstitial telomeric sequences in vertebrate chromosomes: Origin, function, instability and evolution.

PubMed

Bolzán, Alejandro D

2017-07-01

By definition, telomeric sequences are located at the very ends or terminal regions of chromosomes. However, several vertebrate species show blocks of (TTAGGG)n repeats present in non-terminal regions of chromosomes, the so-called interstitial telomeric sequences (ITSs), interstitial telomeric repeats or interstitial telomeric bands, which include those intrachromosomal telomeric-like repeats located near (pericentromeric ITSs) or within the centromere (centromeric ITSs) and those telomeric repeats located between the centromere and the telomere (i.e., truly interstitial telomeric sequences) of eukaryotic chromosomes. According with their sequence organization, localization and flanking sequences, ITSs can be classified into four types: 1) short ITSs, 2) subtelomeric ITSs, 3) fusion ITSs, and 4) heterochromatic ITSs. The first three types have been described mainly in the human genome, whereas heterochromatic ITSs have been found in several vertebrate species but not in humans. Several lines of evidence suggest that ITSs play a significant role in genome instability and evolution. This review aims to summarize our current knowledge about the origin, function, instability and evolution of these telomeric-like repeats in vertebrate chromosomes. Copyright © 2017 Elsevier B.V. All rights reserved.

A Legionella pneumophila collagen-like protein encoded by a gene with a variable number of tandem repeats is involved in the adherence and invasion of host cells.

PubMed

Vandersmissen, Liesbeth; De Buck, Emmy; Saels, Veerle; Coil, David A; Anné, Jozef

2010-05-01

Legionella pneumophila is a Gram-negative, facultative intracellular pathogen and the causative agent of Legionnaires' disease, a severe pneumonia in humans. Analysis of the Legionella sequenced genomes revealed a gene with a variable number of tandem repeats (VNTRs), whose number varies between strains. We examined the strain distribution of this gene among a collection of 108 clinical, environmental and hot spring serotype I strains. Twelve variants were identified, but no correlation was observed between the number of repeat units and clinical and environmental strains. The encoded protein contains the C-terminal consensus motif of outer membrane proteins and has a large region of collagen-like repeats that is encoded by the VNTR region. We have therefore annotated this protein Lcl for Legionella collagen-like protein. Lcl was shown to contribute to the adherence and invasion of host cells and it was demonstrated that the number of repeat units present in lcl had an influence on these adhesion characteristics.

SM50 Repeat-Polypeptides Self-Assemble into Discrete Matrix Subunits and Promote Appositional Calcium Carbonate Crystal Growth during Sea Urchin Tooth Biomineralization

PubMed Central

Mao, Yelin; Satchell, Paul G.; Luan, Xianghong; Diekwisch, Thomas G.H.

2015-01-01

The two major proteins involved in vertebrate enamel formation and echinoderm sea urchin tooth biomineralization, amelogenin and SM50, are both characterized by elongated polyproline repeat domains in the center of the macromolecule. To determine the role of polyproline repeat polypeptides in basal deuterostome biomineralization, we have mapped the localization of SM50 as it relates to crystal growth, conducted self-assembly studies of SM50 repeat polypeptides, and examined their effect on calcium carbonate and apatite crystal growth. Electron micrographs of the growth zone of Strongylocentrotus purpuratus sea urchin teeth documented a series of successive events from intravesicular mineral nucleation to mineral deposition at the interface between tooth surface and odontoblast syncytium. Using immunohistochemistry, SM50 was detected within the cytoplasm of cells associated with the developing tooth mineral, at the mineral secreting front, and adjacent to initial mineral deposits, but not in muscles and ligaments. Polypeptides derived from the SM50 polyproline alternating hexa- and hepta-peptide repeat region (SM50P6P7) formed highly discrete, donut-shaped self-assembly patterns. In calcium carbonate crystal growth studies, SM50P6P7 repeat peptides triggered the growth of expansive networks of fused calcium carbonate crystals while in apatite growth studies, SM50P6P7 peptides facilitated the growth of needle-shaped and parallel arranged crystals resembling those found in developing vertebrate enamel. In comparison, SM50P6P7 surpassed the PXX24 polypeptide repeat region derived from the vertebrate enamel protein amelogenin in its ability to promote crystal nucleation and appositional crystal growth. Together, these studies establish the SM50P6P7 polyproline repeat region as a potent regulator in the protein-guided appositional crystal growth that occurs during continuous tooth mineralization and eruption. In addition, our studies highlight the role of species-specific polyproline repeat motifs in the formation of discrete self-assembled matrices and the resulting control of mineral growth. PMID:26194158

SM50 repeat-polypeptides self-assemble into discrete matrix subunits and promote appositional calcium carbonate crystal growth during sea urchin tooth biomineralization.

PubMed

Mao, Yelin; Satchell, Paul G; Luan, Xianghong; Diekwisch, Thomas G H

2016-01-01

The two major proteins involved in vertebrate enamel formation and echinoderm sea urchin tooth biomineralization, amelogenin and SM50, are both characterized by elongated polyproline repeat domains in the center of the macromolecule. To determine the role of polyproline repeat polypeptides in basal deuterostome biomineralization, we have mapped the localization of SM50 as it relates to crystal growth, conducted self-assembly studies of SM50 repeat polypeptides, and examined their effect on calcium carbonate and apatite crystal growth. Electron micrographs of the growth zone of Strongylocentrotus purpuratus sea urchin teeth documented a series of successive events from intravesicular mineral nucleation to mineral deposition at the interface between tooth surface and odontoblast syncytium. Using immunohistochemistry, SM50 was detected within the cytoplasm of cells associated with the developing tooth mineral, at the mineral secreting front, and adjacent to initial mineral deposits, but not in muscles and ligaments. Polypeptides derived from the SM50 polyproline alternating hexa- and hepta-peptide repeat region (SM50P6P7) formed highly discrete, donut-shaped self-assembly patterns. In calcium carbonate crystal growth studies, SM50P6P7 repeat peptides triggered the growth of expansive networks of fused calcium carbonate crystals while in apatite growth studies, SM50P6P7 peptides facilitated the growth of needle-shaped and parallel arranged crystals resembling those found in developing vertebrate enamel. In comparison, SM50P6P7 surpassed the PXX24 polypeptide repeat region derived from the vertebrate enamel protein amelogenin in its ability to promote crystal nucleation and appositional crystal growth. Together, these studies establish the SM50P6P7 polyproline repeat region as a potent regulator in the protein-guided appositional crystal growth that occurs during continuous tooth mineralization and eruption. In addition, our studies highlight the role of species-specific polyproline repeat motifs in the formation of discrete self-assembled matrices and the resulting control of mineral growth. Copyright © 2015 Elsevier GmbH. All rights reserved.

The minisatellite of the GPI/AMF/NLK/MF gene: interspecies conservation and transcriptional activity.

PubMed

Williams, R R; Hassan-Walker, A F; Lavender, F L; Morgan, M; Faik, P; Ragoussis, J

2001-05-16

Minisatellites are tandemly repeated DNA sequences found throughout the genomes of all eukaryotes. They are regions often prone to instability and hence hypervariability; thus repeat unit sequence is generally not conserved beyond closely related species. We have studied the minisatellite located in intron 9 of the human glucose phosphate isomerase (GPI) gene (also known as neuroleukin, autocrine motility factor, maturation and differentiation factor) and have found, by Zoo blotting coupled with PCR amplification and DNA sequencing, that similar repeat units are present in seven other species of mammal. There is also evidence for the presence of the minisatellite in chicken. The repeat unit does not appear to be present at any other locus in these genomes. Minisatellite DNA has been reported to be involved in recombination activity, control of gene expression of nearby gene(s) (both transcriptional and translational), whilst others form protein coding regions. The high level of conservation exhibited by the GPI minisatellite, coupled with the unique location, strongly suggests a functional role. Our results from transient and stable transfections using luciferase reporter constructs have shown that the GPI minisatellite region can act to increase transcription from the SV40 promoter, CMV promoter and the human GPI promoter.

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

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

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

1994-09-01

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

Forest soils bibliography for the North-Central Region (including subject matter index through 1972).

Treesearch

Willard H. Carmean

1973-01-01

Includes 793 publications dealing with forest soils in the North-Central States (Minnesota, Wisconsin, Michigan, Iowa, Missouri, Illinois, and Indiana); Ohio; and the Northern Plains States (Kansas, Nebraska, and the Dakotas). Includes some publications from other regions considered applicable to conditions in the North-Central Region.

Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8)

PubMed Central

Russo, James J.; Bohenzky, Roy A.; Chien, Ming-Cheng; Chen, Jing; Yan, Ming; Maddalena, Dawn; Parry, J. Preston; Peruzzi, Daniela; Edelman, Isidore S.; Chang, Yuan; Moore, Patrick S.

1996-01-01

The genome of the Kaposi sarcoma-associated herpesvirus (KSHV or HHV8) was mapped with cosmid and phage genomic libraries from the BC-1 cell line. Its nucleotide sequence was determined except for a 3-kb region at the right end of the genome that was refractory to cloning. The BC-1 KSHV genome consists of a 140.5-kb-long unique coding region flanked by multiple G+C-rich 801-bp terminal repeat sequences. A genomic duplication that apparently arose in the parental tumor is present in this cell culture-derived strain. At least 81 ORFs, including 66 with homology to herpesvirus saimiri ORFs, and 5 internal repeat regions are present in the long unique region. The virus encodes homologs to complement-binding proteins, three cytokines (two macrophage inflammatory proteins and interleukin 6), dihydrofolate reductase, bcl-2, interferon regulatory factors, interleukin 8 receptor, neural cell adhesion molecule-like adhesin, and a D-type cyclin, as well as viral structural and metabolic proteins. Terminal repeat analysis of virus DNA from a KS lesion suggests a monoclonal expansion of KSHV in the KS tumor. PMID:8962146

Gross rearrangements within the 5'-untranslated region of the picornaviral genomes.

PubMed

Pilipenko, E V; Blinov, V M; Agol, V I

1990-06-11

An analysis of reported nucleotide sequences revealed several cases of gross rearrangements in the 5'-untranslated region (5-UTR) of picornaviral genomes. A large (greater than 100 nt) duplication was discovered in a downstream region of poliovirus 5-UTR involved in the translational control. Properties of the poliovirus mutants with large deletions [Kuge and Nomoto (1987) J. Virol. 61, 1478-1487] show that a single copy of the appropriate repeating unit is compatible with a wild type phenotype of the virus. In contrast to poliovirus and another enterovirus genomes, human rhinovirus RNAs contain only a single copy of this repeating unit. Another similarly large repeat was found in an upstream segment of the bovine enterovirus 5-UTR. A comparison of the primary and secondary structures of cardio- and aphthovirus 5-UTRs demonstrated the existence of a large (ca. 250 nucleotides) insertion/deletion in a region preceding the poly(C) tract. The two latter rearrangements appear to involve elements of the viral genome replication machinery. Possible origin as well as evolutionary and functional implications of these structural peculiarities are discussed.

Wildlife-associated recreation in the North Central Region: participation patterns and management implications

Treesearch

Allan Marsinko; John Dwyer

2002-01-01

The North Central Region (IA, IL, IN, MI, MN, MO, WI) is a diverse area of the United States. Compared to the remainder of the country, the region as a whole is demographically similar in terms of mean age, education, household income, and gender. However, the North Central region has a higher proportion of Whites and a slightly lower proportion of people residing in...

Y-chromosomal diversity of the Valachs from the Czech Republic: model for isolated population in Central Europe

PubMed Central

Ehler, Edvard; Vaněk, Daniel; Stenzl, Vlastimil; Vančata, Václav

2011-01-01

Aim To evaluate Y-chromosomal diversity of the Moravian Valachs of the Czech Republic and compare them with a Czech population sample and other samples from Central and South-Eastern Europe, and to evaluate the effects of genetic isolation and sampling. Methods The first sample set of the Valachs consisted of 94 unrelated male donors from the Valach region in northeastern Czech Republic border-area. The second sample set of the Valachs consisted of 79 men who originated from 7 paternal lineages defined by surname. No close relatives were sampled. The third sample set consisted of 273 unrelated men from the whole of the Czech Republic and was used for comparison, as well as published data for other 27 populations. The total number of samples was 3244. Y-short tandem repeat (STR) markers were typed by standard methods using PowerPlex® Y System (Promega) and Yfiler® Amplification Kit (Applied Biosystems) kits. Y-chromosomal haplogroups were estimated from the haplotype information. Haplotype diversity and other intra- and inter-population statistics were computed. Results The Moravian Valachs showed a lower genetic variability of Y-STR markers than other Central European populations, resembling more to the isolated Balkan populations (Aromuns, Csango, Bulgarian, and Macedonian Roma) than the surrounding populations (Czechs, Slovaks, Poles, Saxons). We illustrated the effect of sampling on Valach paternal lineages, which includes reduction of discrimination capacity and variability inside Y-chromosomal haplogroups. Valach modal haplotype belongs to R1a haplogroup and it was not detected in the Czech population. Conclusion The Moravian Valachs display strong substructure and isolation in their Y chromosomal markers. They represent a unique Central European population model for population genetics. PMID:21674832

Repeat migration and disappointment.

PubMed

Grant, E K; Vanderkamp, J

1986-01-01

This article investigates the determinants of repeat migration among the 44 regions of Canada, using information from a large micro-database which spans the period 1968 to 1971. The explanation of repeat migration probabilities is a difficult task, and this attempt is only partly successful. May of the explanatory variables are not significant, and the overall explanatory power of the equations is not high. In the area of personal characteristics, the variables related to age, sex, and marital status are generally significant and with expected signs. The distance variable has a strongly positive effect on onward move probabilities. Variables related to prior migration experience have an important impact that differs between return and onward probabilities. In particular, the occurrence of prior moves has a striking effect on the probability of onward migration. The variable representing disappointment, or relative success of the initial move, plays a significant role in explaining repeat migration probabilities. The disappointment variable represents the ratio of actural versus expected wage income in the year after the initial move, and its effect on both repeat migration probabilities is always negative and almost always highly significant. The repeat probabilities diminish after a year's stay in the destination region, but disappointment in the most recent year still has a bearing on the delayed repeat probabilities. While the quantitative impact of the disappointment variable is not large, it is difficult to draw comparisons since similar estimates are not available elsewhere.

The complete chloroplast genome sequence of Cephalotaxus oliveri (Cephalotaxaceae): evolutionary comparison of cephalotaxus chloroplast DNAs and insights into the loss of inverted repeat copies in gymnosperms.

PubMed

Yi, Xuan; Gao, Lei; Wang, Bo; Su, Ying-Juan; Wang, Ting

2013-01-01

We have determined the complete chloroplast (cp) genome sequence of Cephalotaxus oliveri. The genome is 134,337 bp in length, encodes 113 genes, and lacks inverted repeat (IR) regions. Genome-wide mutational dynamics have been investigated through comparative analysis of the cp genomes of C. oliveri and C. wilsoniana. Gene order transformation analyses indicate that when distinct isomers are considered as alternative structures for the ancestral cp genome of cupressophyte and Pinaceae lineages, it is not possible to distinguish between hypotheses favoring retention of the same IR region in cupressophyte and Pinaceae cp genomes from a hypothesis proposing independent loss of IRA and IRB. Furthermore, in cupressophyte cp genomes, the highly reduced IRs are replaced by short repeats that have the potential to mediate homologous recombination, analogous to the situation in Pinaceae. The importance of repeats in the mutational dynamics of cupressophyte cp genomes is also illustrated by the accD reading frame, which has undergone extreme length expansion in cupressophytes. This has been caused by a large insertion comprising multiple repeat sequences. Overall, we find that the distribution of repeats, indels, and substitutions is significantly correlated in Cephalotaxus cp genomes, consistent with a hypothesis that repeats play a role in inducing substitutions and indels in conifer cp genomes.

Nucleosome exclusion from the interspecies-conserved central AT-rich region of the Ars insulator.

PubMed

Takagi, Haruna; Inai, Yuta; Watanabe, Shun-ichiro; Tatemoto, Sayuri; Yajima, Mamiko; Akasaka, Koji; Yamamoto, Takashi; Sakamoto, Naoaki

2012-01-01

The Ars insulator is a boundary element identified in the upstream region of the arylsulfatase (HpArs) gene in the sea urchin, Hemicentrotus pulcherrimus, and possesses the ability to both block enhancer-promoter communications and protect transgenes from silent chromatin. To understand the molecular mechanism of the Ars insulator, we investigated the correlation between chromatin structure, DNA structure and insulator activity. Nuclease digestion of nuclei isolated from sea urchin embryos revealed the presence of a nuclease-hypersensitive site within the Ars insulator. Analysis of micrococcal nuclease-sensitive sites in the Ars insulator, reconstituted with nucleosomes, showed the exclusion of nucleosomes from the central AT-rich region. Furthermore, the central AT-rich region in naked DNA was sensitive to nucleotide base modification by diethylpyrocarbonate (DEPC). These observations suggest that non-B-DNA structures in the central AT-rich region may inhibit nucleosomal formation, which leads to nuclease hypersensitivity. Furthermore, comparison of nucleotide sequences between the HpArs gene and its ortholog in Strongylocentrotus purpuratus revealed that the central AT-rich region of the Ars insulator is conserved, and this conserved region showed significant enhancer blocking activity. These results suggest that the central AT-rich nucleosome-free region plays an important role in the function of the Ars insulator.

Short- and long-term variability of radon progeny concentration in dwellings in the Czech Republic.

PubMed

Slezáková, M; Navrátilová Rovenská, K; Tomásek, L; Holecek, J

2013-03-01

In this paper, repeated measurements of radon progeny concentration in dwellings in the Czech Republic are described. Two distinct data sets are available: one based on present measurements in 170 selected dwellings in the Central Bohemian Pluton with a primary measurement carried out in the 1990s and the other based on 1920 annual measurements in 960 single-family houses in the Czech Republic in 1992 and repeatedly in 1993. The analysis of variance model with random effects is applied to data to evaluate the variability of measurements. The calculated variability attributable to repeated measurements is compared with results from other countries. In epidemiological studies, ignoring the variability of measurements may lead to biased estimates of risk of lung cancer.

Genetic determinants of mate recognition in Brachionus manjavacas (Rotifera)

PubMed Central

Snell, Terry W; Shearer, Tonya L; Smith, Hilary A; Kubanek, Julia; Gribble, Kristin E; Welch, David B Mark

2009-01-01

Background Mate choice is of central importance to most animals, influencing population structure, speciation, and ultimately the survival of a species. Mating behavior of male brachionid rotifers is triggered by the product of a chemosensory gene, a glycoprotein on the body surface of females called the mate recognition pheromone. The mate recognition pheromone has been biochemically characterized, but little was known about the gene(s). We describe the isolation and characterization of the mate recognition pheromone gene through protein purification, N-terminal amino acid sequence determination, identification of the mate recognition pheromone gene from a cDNA library, sequencing, and RNAi knockdown to confirm the functional role of the mate recognition pheromone gene in rotifer mating. Results A 29 kD protein capable of eliciting rotifer male circling was isolated by high-performance liquid chromatography. Two transcript types containing the N-terminal sequence were identified in a cDNA library; further characterization by screening a genomic library and by polymerase chain reaction revealed two genes belonging to each type. Each gene begins with a signal peptide region followed by nearly perfect repeats of an 87 to 92 codon motif with no codons between repeats and the final motif prematurely terminated by the stop codon. The two Type A genes contain four and seven repeats and the two Type B genes contain three and five repeats, respectively. Only the Type B gene with three repeats encodes a peptide with a molecular weight of 29 kD. Each repeat of the Type B gene products contains three asparagines as potential sites for N-glycosylation; there are no asparagines in the Type A genes. RNAi with Type A double-stranded RNA did not result in less circling than in the phosphate-buffered saline control, but transfection with Type B double-stranded RNA significantly reduced male circling by 17%. The very low divergence between repeat units, even at synonymous positions, suggests that the repeats are kept nearly identical through a process of concerted evolution. Information-rich molecules like surface glycoproteins are well adapted for chemical communication and aquatic animals may have evolved signaling systems based on these compounds, whereas insects use cuticular hydrocarbons. Conclusion Owing to its critical role in mating, the mate recognition pheromone gene will be a useful molecular marker for exploring the mechanisms and rates of selection and the evolution of reproductive isolation and speciation using rotifers as a model system. The phylogenetic variation in the mate recognition pheromone gene can now be studied in conjunction with the large amount of ecological and population genetic data being gathered for the Brachionus plicatilis species complex to understand better the evolutionary drivers of cryptic speciation. PMID:19740420

Genetic determinants of mate recognition in Brachionus manjavacas (Rotifera).

PubMed

Snell, Terry W; Shearer, Tonya L; Smith, Hilary A; Kubanek, Julia; Gribble, Kristin E; Welch, David B Mark

2009-09-09

Mate choice is of central importance to most animals, influencing population structure, speciation, and ultimately the survival of a species. Mating behavior of male brachionid rotifers is triggered by the product of a chemosensory gene, a glycoprotein on the body surface of females called the mate recognition pheromone. The mate recognition pheromone has been biochemically characterized, but little was known about the gene(s). We describe the isolation and characterization of the mate recognition pheromone gene through protein purification, N-terminal amino acid sequence determination, identification of the mate recognition pheromone gene from a cDNA library, sequencing, and RNAi knockdown to confirm the functional role of the mate recognition pheromone gene in rotifer mating. A 29 kD protein capable of eliciting rotifer male circling was isolated by high-performance liquid chromatography. Two transcript types containing the N-terminal sequence were identified in a cDNA library; further characterization by screening a genomic library and by polymerase chain reaction revealed two genes belonging to each type. Each gene begins with a signal peptide region followed by nearly perfect repeats of an 87 to 92 codon motif with no codons between repeats and the final motif prematurely terminated by the stop codon. The two Type A genes contain four and seven repeats and the two Type B genes contain three and five repeats, respectively. Only the Type B gene with three repeats encodes a peptide with a molecular weight of 29 kD. Each repeat of the Type B gene products contains three asparagines as potential sites for N-glycosylation; there are no asparagines in the Type A genes. RNAi with Type A double-stranded RNA did not result in less circling than in the phosphate-buffered saline control, but transfection with Type B double-stranded RNA significantly reduced male circling by 17%. The very low divergence between repeat units, even at synonymous positions, suggests that the repeats are kept nearly identical through a process of concerted evolution. Information-rich molecules like surface glycoproteins are well adapted for chemical communication and aquatic animals may have evolved signaling systems based on these compounds, whereas insects use cuticular hydrocarbons. Owing to its critical role in mating, the mate recognition pheromone gene will be a useful molecular marker for exploring the mechanisms and rates of selection and the evolution of reproductive isolation and speciation using rotifers as a model system. The phylogenetic variation in the mate recognition pheromone gene can now be studied in conjunction with the large amount of ecological and population genetic data being gathered for the Brachionus plicatilis species complex to understand better the evolutionary drivers of cryptic speciation.

Intraoperative mapping during repeat awake craniotomy reveals the functional plasticity of adult cortex.

PubMed

Southwell, Derek G; Hervey-Jumper, Shawn L; Perry, David W; Berger, Mitchel S

2016-05-01

OBJECT To avoid iatrogenic injury during the removal of intrinsic cerebral neoplasms such as gliomas, direct electrical stimulation (DES) is used to identify cortical and subcortical white matter pathways critical for language, motor, and sensory function. When a patient undergoes more than 1 brain tumor resection as in the case of tumor recurrence, the use of DES provides an unusual opportunity to examine brain plasticity in the setting of neurological disease. METHODS The authors examined 561 consecutive cases in which patients underwent DES mapping during surgery forglioma resection. "Positive" and "negative" sites-discrete cortical regions where electrical stimulation did (positive) or did not (negative) produce transient sensory, motor, or language disturbance-were identified prior to tumor resection and documented by intraoperative photography for categorization into functional maps. In this group of 561 patients, 18 were identified who underwent repeat surgery in which 1 or more stimulation sites overlapped with those tested during the initial surgery. The authors compared intraoperative sensory, motor, or language mapping results between initial and repeat surgeries, and evaluated the clinical outcomes for these patients. RESULTS A total of 117 sites were tested for sensory (7 sites, 6.0%), motor (9 sites, 7.7%), or language (101 sites, 86.3%) function during both initial and repeat surgeries. The mean interval between surgical procedures was 4.1 years. During initial surgeries, 95 (81.2%) of 117 sites were found to be negative and 22 (18.8%) of 117 sites were found to be positive. During repeat surgeries, 103 (88.0%) of 117 sites were negative and 14 (12.0%) of 117 were positive. Of the 95 sites that were negative at the initial surgery, 94 (98.9%) were also negative at the repeat surgery, while 1 (1.1%) site was found to be positive. Of the 22 sites that were initially positive, 13 (59.1%) remained positive at repeat surgery, while 9 (40.9%) had become negative for function. Overall, 6 (33.3%) of 18 patients exhibited loss of function at 1 or more motor or language sites between surgeries. Loss of function at these sites was not associated with neurological impairment at the time of repeat surgery, suggesting that neurological function was preserved through neural circuit reorganization or activation of latent functional pathways. CONCLUSIONS The adult central nervous system reorganizes motor and language areas in patients with glioma. Ultimately, adult neural plasticity may help to preserve motor and language function in the presence of evolving structural lesions. The insight gained from this subset of patients has implications for our understanding of brain plasticity in clinical settings.

A 150-ka-long record for the volcano-tectonic deformation of Central Anatolian Volcanic Province

NASA Astrophysics Data System (ADS)

Karabacak, Volkan; Tonguç Uysal, I.; Ünal-İmer, Ezgi; Mutlu, Halim; Zhao, Jian-xin

2017-04-01

The Anatolian Block represents one of the most outstanding examples of intra-plate deformation related to continental collision. Deformation related to the convergence of the Afro-Arabian continent toward north gives rise to widespread and intense arc volcanism in the Central Anatolia. All the usual studies on dating the volcano-tectonic deformation of the region are performed entirely on volcanic events of the geological record resulted in eruptions. However, without volcanic eruption, magma migration and related fluid pressurization also generate crustal deformation. In the current study has been funded by the Scientific and Technological Research Council of Turkey with the project no. 115Y497, we focused on fracture systems and their carbonate veins around the Ihlara Valley (Cappadocia) surrounded by well-known volcanic centers with latest activities of the southern Central Anatolian Volcanic Province. We dated 37 samples using the Uranium-series technique and analyzed their isotope systematics from fissure veins, which are thought to be controlled by the young volcanism in the region. Our detailed fracture analyses in the field show that there is a regional dilatation as a result of a NW-SE striking extension which is consistent with the results of recent GPS studies. The Uranium-series results indicate that fracture development and associated carbonate vein deposition occurred in the last 150 ka. Carbon and oxygen isotope systematics have almost remained unchanged in the studied time interval. Although veins in the region were precipitated from fluids primarily of meteoric origin, fluids originating from water-rock interaction also contribute for the deposition of carbonate veins. The age distribution indicates that the crustal deformation intensified during 7 different period at about 4.7, 34, 44, 52, 83, 91, 149 ka BP. Four of these periods (4.7, 34, 91, 149 ka BP) correspond to the volcanic activities suggested in the previous studies. The three crustal deformation periods occurred at 44, 52, and 83 ka BP were dated in addition to the known. They are interpreted to have possibly occurred without any eruption in the late Pleistocene and were controlled by magma movements and/or associated fluid pressure. Such crustal deformation controlled by volcanism is dated for the first time in the literature with a sampling other than extrusive material. The obtained age data revealed that crustal deformation linked to the young volcanism in the Central Anatolian Volcanic Province was repeated in short-term strain cycles of 8-10 ka and that the duration of activity lasted approximately 1100 ± 1000 years in each period, possibly triggered fracture development without any eruption in some periods.

Design of the central region in the Gustaf Werner cyclotron at the Uppsala university

NASA Astrophysics Data System (ADS)

Toprek, Dragan; Reistad, Dag; Lundstrom, Bengt; Wessman, Dan

2002-07-01

This paper describes the design of the central region in the Gustaf Werner cyclotron for h=1, 2 and 3 modes of acceleration. The electric field distribution in the inflector and in the four acceleration gaps has been numerically calculated from an electric potential map produced by the program RELAX3D. The geometry of the central region has been tested with the computations of orbits carried out by means of the computer code CYCLONE. The optical properties of the spiral inflector and the central region were studied by using the programs CASINO and CYCLONE, respectively.

Impacts of the 2016 outburst flood on the Bhote Koshi River valley, central Nepal

NASA Astrophysics Data System (ADS)

Cook, Kristen; Andermann, Christoff; Gimbert, Florent; Hovius, Niels; Adhikari, Basanta

2017-04-01

The central Nepal Himalaya is a region of rapid erosion where fluvial processes are largely driven by the annual Indian Summer Monsoon, which delivers up to several meters of precipitation each year. However, the rivers in this region are also subject to rare catastrophic floods caused by the sudden failure of landslide or moraine dams. Because these floods happen rarely, it has been difficult to isolate their impact on the rivers and adjacent hillslopes, and their importance for the long-term evolution of Himalayan rivers is poorly constrained. On the 5th of July, 2016, the Bhote Koshi River in central Nepal was hit by a glacial lake outburst flood (GLOF). The flood passed through a seismic and hydrological observatory installed along the river in June 2015, and we have used the resulting data to constrain the timing, duration, and bedload transport properties of the outburst flood. The impact of the flood on the river can be further observed with hourly time-lapse photographs, daily measurements of suspended sediment load, repeat lidar surveys, and satellite imagery. Overall, our observatory data span two monsoon seasons, allowing us to evaluate the impacts of the outburst flood relative to the annual monsoon flood. The outburst flood affected the river on several timescales. In the short term, it transported large amounts of coarse sediment and restructured the river bed during the hours of the flood pulse itself. Over intermediate timescales it resulted in elevated bedload and suspended load transport for several weeks following the flood. Over longer timescales the flood undercut and destabilized the river banks and hillslopes in a number of locations, leading to bank collapses, slumps, and landslides. We map changes in the channel and associated mass wasting using rapidEye imagery from Oct. 2015 and Oct. 2016. We also use repeat terrestrial lidar scans to quantify the magnitude of change in multiple locations along the river channel and to measure bank erosion and ongoing failures and slumps. The changes to the river bed vary along stream, ranging from up to 10 meters of channel lowering to several meters of deposition. Bank erosion ranges from simple collapses of vertical banks to large scale slumps that extend >200 m up the hillslope. Following the flood, bank and hillslope erosion continued through the monsoon season. These post-flood collapses have caused considerable damage to infrastructure, destroying houses and roads, and are likely to remain active and continue affecting the system for the next years. Our data all indicate that, despite the very short duration of the flood itself, its impact on the river outstripped the monsoon floods of 2015 and 2016.

MEG adaptation reveals action representations in posterior occipitotemporal regions.

PubMed

Hauswald, Anne; Tucciarelli, Raffaele; Lingnau, Angelika

2018-06-01

When we observe other people's actions, a number of parietal and precentral regions known to be involved in the planning and execution of actions are recruited for example seen as power decreases in alpha and beta frequencies indicative of increased activation. It has been argued that this recruitment reflects the process of simulating the observed action, thereby providing access to the meaning of the action. Alternatively, it has been suggested that rather than providing access to the meaning of an action, parietal and precentral regions might be recruited as a consequence of action understanding. A way to distinguish between these alternatives is to examine where in the brain and at which time point it is possible to discriminate between different types of actions (e.g., pointing or grasping) irrespective of the way these are performed. To this aim, we presented participants with videos of simple hand actions performed with the left or right hand towards a target on the left or the right side while recording magnetoencephalography (MEG) data. In each trial, participants were presented with two subsequent videos (S1, S2) depicting either the same (repeat trials) or different (non-repeat trials) actions. We predicted that areas that are sensitive to the type of action should show stronger adaptation (i.e., a smaller decrease in alpha and beta power) in repeat in comparison to non-repeat trials. Indeed, we observed less alpha and beta power decreases during the presentation of S2 when the action was repeated compared to when two different actions were presented indicating adaptation of neuronal populations that are selective for the type of action. Sources were obtained exclusively in posterior occipitotemporal regions, supporting the notion that an early differentiation of actions occurs outside the motor system. Copyright © 2018 Elsevier Ltd. All rights reserved.

The Nitrogen-Fixation Island Insertion Site Is Conserved in Diazotrophic Pseudomonas stutzeri and Pseudomonas sp. Isolated from Distal and Close Geographical Regions

PubMed Central

Venieraki, Anastasia; Dimou, Maria; Vezyri, Eleni; Vamvakas, Alexandros; Katinaki, Pagona-Artemis; Chatzipavlidis, Iordanis; Tampakaki, Anastasia; Katinakis, Panagiotis

2014-01-01

The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution. PMID:25251496

The nitrogen-fixation island insertion site is conserved in diazotrophic Pseudomonas stutzeri and Pseudomonas sp. isolated from distal and close geographical regions.

PubMed

Venieraki, Anastasia; Dimou, Maria; Vezyri, Eleni; Vamvakas, Alexandros; Katinaki, Pagona-Artemis; Chatzipavlidis, Iordanis; Tampakaki, Anastasia; Katinakis, Panagiotis

2014-01-01

The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution.

Design of the central region for axial injection in the VINCY cyclotron

NASA Astrophysics Data System (ADS)

Milinković, Ljiljana; Toprek, Dragan

1996-02-01

This paper describes the design of the central region for h = 1, h = 2 and h = 4 modes of acceleration in the VINCY cyclotron. The result which is worth reported in that the central region is unique and compatible with the three above mentioned harmonic modes of operation. Only one spiral type inflector will be used. The central region is designed to operate with two external ion sources: (a) an ECR ion source with the maximum extraction voltage of 25 kV for heavy ions, and (b) a multicusp ion source with the maximum extraction voltage of 30 kV for H - and D - ions. Heavy ions will be accelerated by the second and fourth harmonics, D - ions by the second harmonic and H - ions by the first harmonic of the RF field. The central region is equipped with an axial injection system. The electric field distribution in the inflector and in the four acceleration gaps has been numerically calculated from an electric potential map produced by the program RELAX3D. The geometry of the central region has been tested with the computations of orbits carried out by means of the computer code CYCLONE. The optical properties of the spiral inflector and the central region were studied by using the programs CASINO and CYCLONE respectively. We have also made an effort to minimize the inflector fringe field using the RELAX3D program.

Molecular epidemiology of Plasmodium vivax in Latin America: polymorphism and evolutionary relationships of the circumsporozoite gene

PubMed Central

2013-01-01

Background The origins and dispersal of Plasmodium vivax to its current worldwide distribution remains controversial. Although progress on P. vivax genetics and genomics has been achieved worldwide, information concerning New World parasites remains fragmented and largely incomplete. More information on the genetic diversity in Latin America (LA) is needed to better explain current patterns of parasite dispersion and evolution. Methods Plasmodium vivax circumsporozoite protein gene polymorphism was investigated using polymerase chain reaction amplification and restriction fragment length polymorphism (PCR-RFLP), and Sanger sequencing in isolates from the Pacific Ocean coast of Mexico, Nicaragua, and Peru. In conjunction with worldwide sequences retrieved from the Genbank, mismatch distribution analysis of central repeat region (CRR), frequency estimation of unique repeat types and phylogenetic analysis of the 3′ terminal region, were performed to obtain an integrative view of the genetic relationships between regional and worldwide isolates. Results Four RFLP subtypes, vk210a, b, c and d were identified in Southern Mexico and three subtypes vk210a, e and f in Nicaragua. The nucleotide sequences showed that Mexican vk210a and all Nicaraguan isolates were similar to other American parasites. In contrast, vk210b, c and d were less frequent, had a domain ANKKAEDA in their carboxyl end and clustered with Asian isolates. All vk247 isolates from Mexico and Peru had identical RFLP pattern. Their nucleotide sequences showed two copies of GGQAAGGNAANKKAGDAGA at the carboxyl end. Differences in mismatch distribution parameters of the CRR separate vk247 from most vk210 isolates. While vk247 isolates display a homogeneous pattern with no geographical clustering, vk210 isolates display a heterogeneous geographically clustered pattern which clearly separates LA from non-American isolates, except vk210b, c and d from Southern Mexico. Conclusions The presence of vk210a in Mexico and vk210e, f and g in Nicaragua are consistent with other previously reported LA isolates and reflect their circulation throughout the continent. The vk210b, c and d are novel genotypes in LA. Their genetic relationships and low variability within these vk210 and/or within the vk247 parasites in Southern Mexico suggest its recent introduction and/or recent expansion to this region. The global analysis of P. vivax csp suggests this parasite introduction to the region and likely LA by different independent events. PMID:23855807

Persistent Bloodstream Infection with Kocuria rhizophila Related to a Damaged Central Catheter

PubMed Central

Becker, Karsten; Mérens, Audrey; Ferroni, Agnès; Dubern, Béatrice; Vu-Thien, Hoang

2012-01-01

A case of persistent bloodstream infection with Kocuria rhizophila related to a damaged central venous catheter in a 3-year-old girl with Hirschsprung's disease is reported. The strain was identified as K. rhizophila by 16S rRNA gene sequencing and matrix-assisted laser desorption ionization–time of flight mass spectrometry. Arbitrarily primed PCR analysis showed a clonal strain. The repeated septic episodes were resolved with the catheter repair. PMID:22259211

Comparison of Repeatability and Agreement between Swept-Source Optical Biometry and Dual-Scheimpflug Topography.

PubMed

Jung, Soyeon; Chin, Hee Seung; Kim, Na Rae; Lee, Kang Won; Jung, Ji Won

2017-01-01

To assess the repeatability and agreement of parameters obtained with two biometers and to compare the predictability. Biometry was performed on 101 eyes with cataract using the IOLMaster 700 and the Galilei G6. Three measurements were obtained per eye with each device, and repeatability was evaluated. The axial length (AL), anterior chamber depth (ACD), keratometry (K), white-to-white (WTW) corneal diameter, central corneal thickness (CCT), and lens thickness (LT) were measured and postoperative predictability was compared. Measurements could not be obtained with the IOLMaster 700 in one eye and in seven eyes with the Galilei G6 due to dense cataract. Both the IOLMaster 700 and Galilei G6 showed good repeatability, although the IOLMaster 700 showed better repeatability than the Galilei G6. There were no statistically significant differences in AL, ACD, steepest K, WTW, and LT ( P > 0.050), although flattest K, mean K, and CCT differed ( P < 0.050). The proportion of eyes with an absolute prediction error within 0.5 D was 85.0% for the IOLMaster 700 and was 80.0% for the Galilei G6 based on the SRK/T formula. Two biometers showed high repeatability and relatively good agreements. The swept-source optical biometer demonstrated better repeatability, penetration, and an overall lower prediction error.

Muscle deoxygenation and neural drive to the muscle during repeated sprint cycling.

PubMed

Racinais, Sébastien; Bishop, David; Denis, Romain; Lattier, Grégory; Mendez-Villaneuva, Alberto; Perrey, Stéphane

2007-02-01

To investigate muscle deoxygenation and neural drive-related changes during repeated cycling sprints in a fatiguing context. Nine healthy male subjects performed a repeated-sprint test (consisting of 10 x 6-s maximal sprints interspaced by 30 s of recovery). Oxygen uptake was measured breath-by-breath; muscle deoxygenation of the vastus lateralis was assessed continuously using the near-infrared spectroscopy technique. Surface electromyograms (RMS) of both vastus lateralis and biceps femoris were also recorded. Furthermore, before and after the repeated-sprint test, the percentage of muscle activation by voluntary drive (twitch-interpolated method) was measured during a maximal voluntary contraction. Consistent with previous research, our data showed a significant power decrement during repeated-sprint exercise. There was also a progressive muscle deoxygenation, but our data showed that the ability of the subjects to use available O2 throughout the entire repeated-sprint test was well preserved. Our data displayed a significant decrement in the RMS activity during the acceleration phase of each sprint across the repeated-sprint exercise. Moreover, decrement in motor drive was confirmed after exercise by a significant decrease in both percentage of voluntary activation and RMS/M-wave ratio during a maximal voluntary contraction. In this experimental design, our findings suggest that the ability to repeat short-duration (6 s) sprints was associated with the occurrence of both peripheral and central fatigue.

Revisiting the TALE repeat.

PubMed

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

2014-04-01

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

Occult lymph node metastasis and risk of regional recurrence in papillary thyroid cancer after bilateral prophylactic central neck dissection: A multi-institutional study.

PubMed

Lee, Young Chan; Na, Se Young; Park, Gi Cheol; Han, Ju Hyun; Kim, Seung Woo; Eun, Young Gyu

2017-02-01

The impact of occult lymph node metastasis on regional recurrence after prophylactic central neck dissection for preoperative, nodal-negative papillary thyroid cancer is controversial. We investigated risk factors for regional lymph node recurrence in papillary thyroid cancer patients who underwent total thyroidectomy and bilateral prophylactic central neck dissection. Analysis was according to clinicopathologic characteristics and occult lymph node metastasis patterns. This multicenter study enrolled 211 consecutive patients who underwent total thyroidectomy with bilateral prophylactic central neck dissection for papillary thyroid cancer without evidence of central lymph node metastasis on preoperative imaging. Clinicopathologic features and central lymph node metastasis patterns were analyzed for predicting regional recurrence. Multivariate Cox regression analysis was used to identify independent factors for recurrence. Median follow-up time was 43 months (24-95 months). Ten patients (4.7%) showed regional lymph node recurrence. The estimated 5-year, regional recurrence-free survival was 95.2%. Tumor size ≥1 cm, central lymph node metastasis, lymph node ratio, and prelaryngeal lymph node metastasis were associated with regional recurrence in univariate analysis (P < .05). In multivariate analysis, a lymph node ratio ≥ 0.26 was a significant risk factor for regional lymph node recurrence (odds ratio = 11.63, P = .003). Lymph node ratio ≥ 0.26 was an independent predictor of worse recurrence-free survival on Cox regression analysis (hazard ratio = 11.49, P = .002). Although no significant association was observed between the presence of occult lymph node metastasis and regional recurrence, lymph node ratio ≥ 0.26 was an independent predictor of regional lymph node recurrence in papillary thyroid cancer patients who underwent total thyroidectomy and bilateral prophylactic central neck dissection. Copyright © 2016 Elsevier Inc. All rights reserved.

Scaling and self-organized criticality in proteins I

PubMed Central

Phillips, J. C.

2009-01-01

The complexity of proteins is substantially simplified by regarding them as archetypical examples of self-organized criticality (SOC). To test this idea and elaborate on it, this article applies the Moret–Zebende SOC hydrophobicity scale to the large-scale scaffold repeat protein of the HEAT superfamily, PR65/A. Hydrophobic plasticity is defined and used to identify docking platforms and hinges from repeat sequences alone. The difference between the MZ scale and conventional hydrophobicity scales reflects long-range conformational forces that are central to protein functionality. PMID:19218446

spa typing for epidemiological surveillance of Staphylococcus aureus.

PubMed

Hallin, Marie; Friedrich, Alexander W; Struelens, Marc J

2009-01-01

The spa typing method is based on sequencing of the polymorphic X region of the protein A gene (spa), present in all strains of Staphylococcus aureus. The X region is constituted of a variable number of 24-bp repeats flanked by well-conserved regions. This single-locus sequence-based typing method combines a number of technical advantages, such as rapidity, reproducibility, and portability. Moreover, due to its repeat structure, the spa locus simultaneously indexes micro- and macrovariations, enabling the use of spa typing in both local and global epidemiological studies. These studies are facilitated by the establishment of standardized spa type nomenclature and Internet shared databases.

The role of the 2008 Mw 7.9 Wenchuan earthquake in topographic evolution: seismically induced landslides and the associated isostatic response

NASA Astrophysics Data System (ADS)

Ren, Z.; Zhang, Z.; Zhang, H.; Zheng, W.; Zhang, P. Z.

2017-12-01

The widely held understanding that reverse-faulting earthquakes play an important role in building mountains has been challenged by recent studies suggesting that co-seismic landslides of the 2008 Mw 7.9 Wenchuan earthquake led to a net co-seismic lowering of surface height. We use precise estimates of co-seismic landslide volumes to calculate the long-term isostatic response to landsliding during the 2008 Wenchuan earthquake. The total isostatic respond volume is 2.0 km3 which did not change much associated with thickness of Te, however, the distribution of the rebound changes associated with thickness of Te. The total co-seismic mass change could be 1.8 km3. The maximum isostatic response due to Wenchuan earthquake may have been as high as 0.9 meters in the highest Pengguan massif of the central Longmen Shan. We also find that the average net uplift is 0.16 meters within the total landslide region due to the Wenchuan earthquake. Our findings suggest that the local topographic evolution of the middle Longmen Shan region is closely related to repeated tectonic events such as the 2008 Wenchuan Earthquake.

Coseismic seafloor deformation in the trench region during the Mw8.8 Maule megathrust earthquake.

PubMed

Maksymowicz, A; Chadwell, C D; Ruiz, J; Tréhu, A M; Contreras-Reyes, E; Weinrebe, W; Díaz-Naveas, J; Gibson, J C; Lonsdale, P; Tryon, M D

2017-04-05

The M w 8.8 megathrust earthquake that occurred on 27 February 2010 offshore the Maule region of central Chile triggered a destructive tsunami. Whether the earthquake rupture extended to the shallow part of the plate boundary near the trench remains controversial. The up-dip limit of rupture during large subduction zone earthquakes has important implications for tsunami generation and for the rheological behavior of the sedimentary prism in accretionary margins. However, in general, the slip models derived from tsunami wave modeling and seismological data are poorly constrained by direct seafloor geodetic observations. We difference swath bathymetric data acquired across the trench in 2008, 2011 and 2012 and find ~3-5 m of uplift of the seafloor landward of the deformation front, at the eastern edge of the trench. Modeling suggests this is compatible with slip extending seaward, at least, to within ~6 km of the deformation front. After the M w 9.0 Tohoku-oki earthquake, this result for the Maule earthquake represents only the second time that repeated bathymetric data has been used to detect the deformation following megathrust earthquakes, providing methodological guidelines for this relatively inexpensive way of obtaining seafloor geodetic data across subduction zone.

Exploratory studies on a passively triggered vacuum spark

NASA Astrophysics Data System (ADS)

Rout, R. K.; Auluck, S. K. H.; Nagpal, J. S.; Kulkarni, L. V.

1999-12-01

The results of an experimental investigation on a passively triggered vacuum spark device are presented. The diagnostics include the current, x-ray and optical emission measurements. The sharp dips in the current derivative signal indicate the occurrence of pinching at an early stage of the discharge (at current icons/Journals/Common/approx" ALT="approx" ALIGN="TOP"/>5 kA). A well-confined plasma with a central hot region was recorded using a streak camera. The pinched plasma was observed to undergo kink-type oscillations with a time period of 10-15 ns. Repeated plasma fronts were seen to move from the anode to the cathode with an average velocity of icons/Journals/Common/approx" ALT="approx" ALIGN="TOP"/>5 × 106 cm s-1. Soft x-ray emission having a radiation intensity of a few hundred mR per discharge was observed. The x-ray signals obtained using photodiodes showed multiple bursts. A soft x-ray pinhole camera recorded micro-pinches of icons/Journals/Common/approx" ALT="approx" ALIGN="TOP"/>100 µm. The x-ray emitting regions were confined to the inter-electrode gap. The x-ray emission characteristics were influenced by the electrolytic resistance, which was connected across the spark gap to initiate discharge.

Probing the Active Galactic Nuclei using optical spectroscopy

NASA Astrophysics Data System (ADS)

Vivek, M.

Variability studies offer one of the best tools for understanding the physical conditions present in regions close to the central engine in an AGN. We probed the various properties of AGN through time variability studies of spectral lines in the optical wavelengths using the 2m telescope in IUCAA Girawali observatory. The absorption line variability studies are mainly concentrated in understanding the nature of outflows in quasars. Quasar outflows have a huge impact on the evolution of central supermassive blackholes, their host galaxies and the surrounding intergalactic medium. Studying the variability in these Broad Absorption Lines (BALs) can help us understand the structure, evolution, and basic physical properties of these outflows. We conducted a repeated Low ionization BAL monitoring program with 27 LoBALs (Low Ionization BALs) at z 0.3-2.1 covering timescales from 3.22 to 7.69 years in the quasar rest frame. We see a variety of phenomena, including some BALs that either appeared or disappeared completely and some BALs which do not vary over the observation period. In one case, the excited fine structure lines have changed dramatically. One source shows signatures of radiative acceleration. Here, we present the results from this program. Emission line studies are concentrated in understanding the peculiar characteristics of a dual-AGN source SDSS J092712.64+294344.0.

Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge.

PubMed

Cao, Huiluo; Dong, Chunming; Bougouffa, Salim; Li, Jiangtao; Zhang, Weipeng; Shao, Zongze; Bajic, Vladimir B; Qian, Pei-Yuan

2016-03-08

In the dark ocean, the SAR324 group of Delta-proteobacteria has been associated with a chemolithotrophic lifestyle. However, their electron transport chain for energy generation and information system has not yet been well characterized. In the present study, four SAR324 draft genomes were extracted from metagenomes sampled from hydrothermal plumes in the South Mid-Atlantic Ridge. We describe novel electron transport chain components in the SAR324 group, particularly the alternative complex III, which is involved in energy generation. Moreover, we propose that the C-type cytochrome, for example the C553, may play a novel role in electron transfer, adding to our knowledge regarding the energy generation process in the SAR324 cluster. The central carbon metabolism in the described SAR324 genomes exhibits several new features other than methanotrophy e.g. aromatic compound degradation. This suggests that methane oxidation may not be the main central carbon metabolism component in SAR324 cluster bacteria. The reductive acetyl-CoA pathway may potentially be essential in carbon fixation due to the absence of components from the Calvin-Benson cycle. Our study provides insight into the role of recombination events in shaping the genome of the SAR324 group based on a larger number of repeat regions observed, which has been overlooked thus far.

Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge

PubMed Central

Cao, Huiluo; Dong, Chunming; Bougouffa, Salim; Li, Jiangtao; Zhang, Weipeng; Shao, Zongze; Bajic, Vladimir B.; Qian, Pei-Yuan

2016-01-01

In the dark ocean, the SAR324 group of Delta-proteobacteria has been associated with a chemolithotrophic lifestyle. However, their electron transport chain for energy generation and information system has not yet been well characterized. In the present study, four SAR324 draft genomes were extracted from metagenomes sampled from hydrothermal plumes in the South Mid-Atlantic Ridge. We describe novel electron transport chain components in the SAR324 group, particularly the alternative complex III, which is involved in energy generation. Moreover, we propose that the C-type cytochrome, for example the C553, may play a novel role in electron transfer, adding to our knowledge regarding the energy generation process in the SAR324 cluster. The central carbon metabolism in the described SAR324 genomes exhibits several new features other than methanotrophy e.g. aromatic compound degradation. This suggests that methane oxidation may not be the main central carbon metabolism component in SAR324 cluster bacteria. The reductive acetyl-CoA pathway may potentially be essential in carbon fixation due to the absence of components from the Calvin-Benson cycle. Our study provides insight into the role of recombination events in shaping the genome of the SAR324 group based on a larger number of repeat regions observed, which has been overlooked thus far. PMID:26953077

Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages

PubMed Central

Santos, Juan C; Coloma, Luis A; Summers, Kyle; Caldwell, Janalee P; Ree, Richard; Cannatella, David C

2009-01-01

The Neotropics contains half of remaining rainforests and Earth's largest reservoir of amphibian biodiversity. However, determinants of Neotropical biodiversity (i.e., vicariance, dispersals, extinctions, and radiations) earlier than the Quaternary are largely unstudied. Using a novel method of ancestral area reconstruction and relaxed Bayesian clock analyses, we reconstructed the biogeography of the poison frog clade (Dendrobatidae). We rejected an Amazonian center-of-origin in favor of a complex connectivity model expanding over the Neotropics. We inferred 14 dispersals into and 18 out of Amazonia to adjacent regions; the Andes were the major source of dispersals into Amazonia. We found three episodes of lineage dispersal with two interleaved periods of vicariant events between South and Central America. During the late Miocene, Amazonian, and Central American-Chocoan lineages significantly increased their diversity compared to the Andean and Guianan-Venezuelan-Brazilian Shield counterparts. Significant percentage of dendrobatid diversity in Amazonia and Chocó resulted from repeated immigrations, with radiations at <10.0 million years ago (MYA), rather than in situ diversification. In contrast, the Andes, Venezuelan Highlands, and Guiana Shield have undergone extended in situ diversification at near constant rate since the Oligocene. The effects of Miocene paleogeographic events on Neotropical diversification dynamics provided the framework under which Quaternary patterns of endemism evolved. PMID:19278298

Polymorphic CA repeats in the IGF-I gene and breast cancer.

PubMed

Yu, H; Li, B D; Smith, M; Shi, R; Berkel, H J; Kato, I

2001-11-01

Insulin-like growth factor (IGF)-I is a potent mitogen for breast cancer cells and may play a role in the disease. Although the involvement of IGF-I phenotype in breast cancer has been studied extensively, little is known about IGF-I genotype in relation to the disease. The IGF-I gene contains a polymorphic region composed of multiple cytosine-adenine dinucleotides (CA repeats). Studies of other genes indicate that the CA-repeat region in the promoter of a gene may affect transcription activity and that the length of the repeat is inversely correlated with transactivation. To examine if the IGF-I polymorphism is associated with breast cancer, we compared the length of CA repeats in the IGF-I gene between 53 breast cancer patients and 53 controls. Genomic DNA extracted from peripheral blood was used to determine the number of CA repeats through PCR amplification and DNA sequencing. Associations between CA repeats and breast cancer were assessed using unconditional logistic regression analysis. The results showed that the median number of CA repeats was 19, ranging from 15 to 23, and that compared to women without 19 CA repeats, women with 19 CA repeats were more likely to be breast cancer patients (OR = 2.87, 95%CI: 1.16-7.06) after adjusting for age, race, menopausal status, age at menopause, and alcohol use. The study also suggested possible synergistic interplay between IGF-I genotype and phenotype as women with 19 CA repeats and high plasma IGF-I had a much higher odds ratio for breast cancer (OR = 5.12, 95%CI: 1.42-18.5) than those with only one of the conditions. If our observations can be confirmed in larger studies, the findings will provide further evidence to support the role of IGF-I in breast cancer and the link between genetic polymorphism and cancer susceptibility.

EPA's Role with the Regional Environmental Center (REC) for Central and Eastern Europe

EPA Pesticide Factsheets

The Regional Environmental Center (REC) for Central and Eastern Europe provides assistance in solving environmental problems in Central and Eastern Europe by promoting cooperation among governments, non-governmental organizations, businesses and others.

Comparison of simple sequence repeats in 19 Archaea.

PubMed

Trivedi, S

2006-12-05

All organisms that have been studied until now have been found to have differential distribution of simple sequence repeats (SSRs), with more SSRs in intergenic than in coding sequences. SSR distribution was investigated in Archaea genomes where complete chromosome sequences of 19 Archaea were analyzed with the program SPUTNIK to find di- to penta-nucleotide repeats. The number of repeats was determined for the complete chromosome sequences and for the coding and non-coding sequences. Different from what has been found for other groups of organisms, there is an abundance of SSRs in coding regions of the genome of some Archaea. Dinucleotide repeats were rare and CG repeats were found in only two Archaea. In general, trinucleotide repeats are the most abundant SSR motifs; however, pentanucleotide repeats are abundant in some Archaea. Some of the tetranucleotide and pentanucleotide repeat motifs are organism specific. In general, repeats are short and CG-rich repeats are present in Archaea having a CG-rich genome. Among the 19 Archaea, SSR density was not correlated with genome size or with optimum growth temperature. Pentanucleotide density had an inverse correlation with the CG content of the genome.

Correlation between fibroin amino acid sequence and physical silk properties.

PubMed

Fedic, Robert; Zurovec, Michal; Sehnal, Frantisek

2003-09-12

The fiber properties of lepidopteran silk depend on the amino acid repeats that interact during H-fibroin polymerization. The aim of our research was to relate repeat composition to insect biology and fiber strength. Representative regions of the H-fibroin genes were sequenced and analyzed in three pyralid species: wax moth (Galleria mellonella), European flour moth (Ephestia kuehniella), and Indian meal moth (Plodia interpunctella). The amino acid repeats are species-specific, evidently a diversification of an ancestral region of 43 residues, and include three types of regularly dispersed motifs: modifications of GSSAASAA sequence, stretches of tripeptides GXZ where X and Z represent bulky residues, and sequences similar to PVIVIEE. No concatenations of GX dipeptide or alanine, which are typical for Bombyx silkworms and Antheraea silk moths, respectively, were found. Despite different repeat structure, the silks of G. mellonella and E. kuehniella exhibit similar tensile strength as the Bombyx and Antheraea silks. We suggest that in these latter two species, variations in the repeat length obstruct repeat alignment, but sufficiently long stretches of iterated residues get superposed to interact. In the pyralid H-fibroins, interactions of the widely separated and diverse motifs depend on the precision of repeat matching; silk is strong in G. mellonella and E. kuehniella, with 2-3 types of long homogeneous repeats, and nearly 10 times weaker in P. interpunctella, with seven types of shorter erratic repeats. The high proportion of large amino acids in the H-fibroin of pyralids has probably evolved in connection with the spinning habit of caterpillars that live in protective silk tubes and spin continuously, enlarging the tubes on one end and partly devouring the other one. The silk serves as a depot of energetically rich and essential amino acids that may be scarce in the diet.

Obstetric and psychological characteristics of women seeking multiple abortions in the region of Monastir (Tunisia): results of a cross-sectional design.

PubMed

El Mhamdi, Sana; Ben Salah, Arwa; Bouanene, Ines; Hlaiem, Imen; Hadhri, Saloua; Maatouk, Wahiba; Soltani, Mohamed

2015-05-10

Repeat abortion is a public health concern favored by many obstetric and social factors. The purpose of our study was to identify associated factors to repeated abortion in the region of Monastir (Tunisia). Common mental disorders (CMD) such as anxiety and depression were also evaluated in women seeking voluntary repeated abortion. We carried out a cross sectional study between January and April 2013 in the Reproductive Health Center (RHC) of the region of Monastir in Tunisia (This study is part of a prospective design on mental disorders and intimate partner violence among women seeking abortions in the RHC). Among women referred to the RHC we selected those seeking voluntary abortion (medical or surgical method). Data on women's demographic characters, knowledge and practices about contraceptive methods and abortion were collected the abortion day via a structured questionnaire. Data about anxiety and depression status were evaluated during the post-abortal control visit at 3-4 weeks following pregnancy termination. Of the 500 interviewed women, 211 (42.2 %; CI95% [37.88 - 46.52]) were seeking repeated abortions. Multivariate analysis showed that increased age, lower level of women school education, single status, poor knowledge about birth control methods and history of conflict/abuse by a male partner, were uniquely associated with undergoing repeat compared with initial abortion. CMD were significantly higher in women undergoing second or subsequent abortion (51.1 %) single and lower educated women. Women relating a history of conflicts/abuse report more CMD than others (30.6 % vs 20.8 %). Health facilities providing abortion services need to pay more attention to women seeking repeat abortion. Further studies are needed to well establish the relation between the number of abortion and the occurrence and the severity of CMD.

Recurrent postoperative CRPS I in patients with abnormal preoperative sympathetic function.

PubMed

Ackerman, William E; Ahmad, Mahmood

2008-02-01

A complex regional pain syndrome of an extremity that has previously resolved can recur after repeat surgery at the same anatomic site. Complex regional pain syndrome is described as a disease of the autonomic nervous system. The purpose of this study was to evaluate preoperative and postoperative sympathetic function and the recurrence of complex regional pain syndrome type I (CRPS I) in patients after repeat carpal tunnel surgery. Thirty-four patients who developed CRPS I after initial carpal tunnel releases and required repeat open carpal tunnel surgeries were studied. Laser Doppler imaging (LDI) was used to assess preoperative sympathetic function 5-7 days prior to surgery and to assess postoperative sympathetic function 19-22 days after surgery or 20-22 days after resolution of the CRPS I. Sympathetic nervous system function was prospectively examined by testing reflex-evoked vasoconstrictor responses to sympathetic stimuli recorded with LDI of both hands. Patients were assigned to 1 of 2 groups based on LDI responses to sympathetic provocation. Group I (11 of 34) patients had abnormal preoperative LDI studies in the hands that had prior surgeries, whereas group II (23 of 34) patients had normal LDI studies. Each patient in this study had open repeat carpal tunnel surgery. In group I, 8 of 11 patients had recurrent CRPS I, whereas in group II, 3 of 23 patients had recurrent CRPS I. All of the recurrent CRPS I patients were successfully treated with sympathetic blockade, occupational therapy, and pharmacologic modalities. Repeat LDI after recurrent CRPS I resolution was abnormal in 8 of 8 group I patients and in 1 of 3 group II patients. CRPS I can recur after repeat hand surgery. Our study results may, however, identify those individuals who may readily benefit from perioperative therapies. Prognostic I.

Topographical distribution of decrements and recovery in muscarinic receptors from rat brains repeatedly exposed to sublethal doses of soman

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

Churchill, L.; Pazdernik, T.L.; Jackson, J.L.

1984-08-01

(3H)Quinuclidinyl benzilate binding to rat brain muscarinic receptors decreased after repeated exposure to soman, a potent organophosphorus cholinesterase inhibitor. The topographical distribution of this decrement was analyzed by quantitative receptor autoradiography. After 4 weeks of soman, three times a week, quinuclidinyl benzilate binding decreased to 67 to 80% of control in frontal and parietal cortex, caudate-putamen, lateral septum, hippocampal body, dentate gyrus, superior colliculus, nucleus of the fifth nerve, and central grey. Minor or no decreases were observed in thalamic or hypothalamic nuclei, reticular formation, pontine nuclei, inferior colliculus, nucleus of the seventh nerve, and cerebellum. Scatchard analyses of saturationmore » curves using frontal cortex sections from soman-treated rats revealed a decrease in maximal quinuclidinyl benzilate binding from that in control rats and a return toward control levels by 24 days without any significant change in affinity. These brain areas showing significant decrements in muscarinic receptors recovered with a similar time course. An estimate of the time for 50% recovery for some of the brain areas was 14 days for superior colliculus, 16 days for cortex, and 19 days for hippocampal body. The application of quantitative receptor autoradiography to analyze receptor alterations has been valuable in localizing the telencephalon as a region more susceptible to change in receptor concentration.« less

Research on fatigue cracking growth parameters in asphaltic mixtures using computed tomography

NASA Astrophysics Data System (ADS)

Braz, D.; Lopes, R. T.; Motta, L. M. G.

2004-01-01

Distress of asphalt concrete pavement due to repeated bending from traffic loads has been a well-recognized problem in Brazil. If it is assumed that fatigue cracking growth is governed by the conditions at the crack tip, and that the crack tip conditions can be characterized by the stress intensity factor, then fatigue cracking growth as a function of stress intensity range Δ K can be determined. Computed tomography technique is used to detect crack evolution in asphaltic mixtures which were submitted to fatigue tests. Fatigue tests under conditions of controlled stress were carried out using diametral compression equipment and repeat loading. The aim of this work is imaging several specimens at different stages of the fatigue tests. In preliminary studies it was noted that the trajectory of a crack was influenced by the existence of voids in the originally unloaded specimens. Cracks would first be observed in the central region of a specimen, propagating in the direction of the extremities. Analyzing the graphics, that represent the fatigue cracking growth (d c/d N) as a function of stress intensity factor (Δ K), it is noticed that the curve has practically shown the same behavior for all specimens at the same level of the static tension rupture stress. The experimental values obtained for the constants A and n (of the Paris-Erdogan Law) present good agreement with the results obtained by Liang and Zhou.

Recombination, rearrangement, reshuffling, and divergence in a centromeric region of rice.

PubMed

Ma, Jianxin; Bennetzen, Jeffrey L

2006-01-10

Centromeres have many unusual biological properties, including kinetochore attachment and severe repression of local meiotic recombination. These properties are partly an outcome, partly a cause, of unusual DNA structure in the centromeric region. Although several plant and animal genomes have been sequenced, most centromere sequences have not been completed or analyzed in depth. To shed light on the unique organization, variability, and evolution of centromeric DNA, detailed analysis of a 1.97-Mb sequence that includes centromere 8 (CEN8) of japonica rice was undertaken. Thirty-three long-terminal repeat (LTR)-retrotransposon families (including 11 previously unknown) were identified in the CEN8 region, totaling 245 elements and fragments that account for 67% of the region. The ratio of solo LTRs to intact elements in the CEN8 region is approximately 0.9:1, compared with approximately 2.2:1 in noncentromeric regions of rice. However, the ratio of solo LTRs to intact elements in the core of the CEN8 region ( approximately 2.5:1) is higher than in any other region investigated in rice, suggesting a hotspot for unequal recombination. Comparison of the CEN8 region of japonica and its orthologous segments from indica rice indicated that approximately 15% of the intact retrotransposons and solo LTRs were inserted into CEN8 after the divergence of japonica and indica from a common ancestor, compared with approximately 50% for previously studied euchromatic regions. Frequent DNA rearrangements were observed in the CEN8 region, including a 212-kb subregion that was found to be composed of three rearranged tandem repeats. Phylogenetic analysis also revealed recent segmental duplication and extensive rearrangement and reshuffling of the CentO satellite repeats.

Neural activity associated with repetitive simulation of episodic counterfactual thoughts.

PubMed

De Brigard, Felipe; Parikh, Natasha; Stewart, Gregory W; Szpunar, Karl K; Schacter, Daniel L

2017-11-01

When people revisit past autobiographical events they often imagine alternative ways in which such events could have occurred. Often these episodic counterfactual thoughts (eCFT) are momentary and fleeting, but sometimes they are simulated frequently and repeatedly. However, little is known about the neural differences between frequently versus infrequently repeated eCFT. The current study explores this issue. In a three-session study, participants were asked to simulate alternative ways positive, negative, and neutral autobiographical memories could have occurred. Half of these eCFT were repeatedly re-simulated while the other half were not. Immediately after, participants were asked to simulate all these eCFT again while undergoing fMRI. A partial least squares analysis on the resultant fMRI data revealed that eCFT that were not frequently repeated preferentially engaged brain regions including middle (BA 21) and superior temporal gyri (BA 38/39), middle (BA 11) and superior frontal gyri (BA 9), and hippocampus. By contrast, frequently repeated eCFT preferentially engaged regions including medial frontal gyri (BA 10), anterior cingulate cortex, insula, and inferior parietal lobule (BA 40). Direct contrasts for each type of eCFT were also conducted. The results of these analyses suggest differential contributions of regions traditionally associated with eCFT, such as BA 10, anterior cingulate cortex, and hippocampus, as a function of kind of eCFT and frequency of repetition. Consequences for future research on eCFT and rumination are considered. Copyright © 2017 Elsevier Ltd. All rights reserved.

Repeat-Associated Plasticity in the Helicobacter pylori RD Gene Family▿ †

PubMed Central

Shak, Joshua R.; Dick, Jonathan J.; Meinersmann, Richard J.; Perez-Perez, Guillermo I.; Blaser, Martin J.

2009-01-01

The bacterium Helicobacter pylori is remarkable for its ability to persist in the human stomach for decades without provoking sterilizing immunity. Since repetitive DNA can facilitate adaptive genomic flexibility via increased recombination, insertion, and deletion, we searched the genomes of two H. pylori strains for nucleotide repeats. We discovered a family of genes with extensive repetitive DNA that we have termed the H. pylori RD gene family. Each gene of this family is composed of a conserved 3′ region, a variable mid-region encoding 7 and 11 amino acid repeats, and a 5′ region containing one of two possible alleles. Analysis of five complete genome sequences and PCR genotyping of 42 H. pylori strains revealed extensive variation between strains in the number, location, and arrangement of RD genes. Furthermore, examination of multiple strains isolated from a single subject's stomach revealed intrahost variation in repeat number and composition. Despite prior evidence that the protein products of this gene family are expressed at the bacterial cell surface, enzyme-linked immunosorbent assay and immunoblot studies revealed no consistent seroreactivity to a recombinant RD protein by H. pylori-positive hosts. The pattern of repeats uncovered in the RD gene family appears to reflect slipped-strand mispairing or domain duplication, allowing for redundancy and subsequent diversity in genotype and phenotype. This novel family of hypervariable genes with conserved, repetitive, and allelic domains may represent an important locus for understanding H. pylori persistence in its natural host. PMID:19749042

Repeat-associated plasticity in the Helicobacter pylori RD gene family.

PubMed

Shak, Joshua R; Dick, Jonathan J; Meinersmann, Richard J; Perez-Perez, Guillermo I; Blaser, Martin J

2009-11-01

The bacterium Helicobacter pylori is remarkable for its ability to persist in the human stomach for decades without provoking sterilizing immunity. Since repetitive DNA can facilitate adaptive genomic flexibility via increased recombination, insertion, and deletion, we searched the genomes of two H. pylori strains for nucleotide repeats. We discovered a family of genes with extensive repetitive DNA that we have termed the H. pylori RD gene family. Each gene of this family is composed of a conserved 3' region, a variable mid-region encoding 7 and 11 amino acid repeats, and a 5' region containing one of two possible alleles. Analysis of five complete genome sequences and PCR genotyping of 42 H. pylori strains revealed extensive variation between strains in the number, location, and arrangement of RD genes. Furthermore, examination of multiple strains isolated from a single subject's stomach revealed intrahost variation in repeat number and composition. Despite prior evidence that the protein products of this gene family are expressed at the bacterial cell surface, enzyme-linked immunosorbent assay and immunoblot studies revealed no consistent seroreactivity to a recombinant RD protein by H. pylori-positive hosts. The pattern of repeats uncovered in the RD gene family appears to reflect slipped-strand mispairing or domain duplication, allowing for redundancy and subsequent diversity in genotype and phenotype. This novel family of hypervariable genes with conserved, repetitive, and allelic domains may represent an important locus for understanding H. pylori persistence in its natural host.

Analysis of the platypus genome suggests a transposon origin for mammalian imprinting.

PubMed

Pask, Andrew J; Papenfuss, Anthony T; Ager, Eleanor I; McColl, Kaighin A; Speed, Terence P; Renfree, Marilyn B

2009-01-01

Genomic imprinting is an epigenetic phenomenon that results in monoallelic gene expression. Many hypotheses have been advanced to explain why genomic imprinting evolved in mammals, but few have examined how it arose. The host defence hypothesis suggests that imprinting evolved from existing mechanisms within the cell that act to silence foreign DNA elements that insert into the genome. However, the changes to the mammalian genome that accompanied the evolution of imprinting have been hard to define due to the absence of large scale genomic resources between all extant classes. The recent release of the platypus genome has provided the first opportunity to perform comparisons between prototherian (monotreme; which appear to lack imprinting) and therian (marsupial and eutherian; which have imprinting) mammals. We compared the distribution of repeat elements known to attract epigenetic silencing across the entire genome from monotremes and therian mammals, particularly focusing on the orthologous imprinted regions. There is a significant accumulation of certain repeat elements within imprinted regions of therian mammals compared to the platypus. Our analyses show that the platypus has significantly fewer repeats of certain classes in the regions of the genome that have become imprinted in therian mammals. The accumulation of repeats, especially long terminal repeats and DNA elements, in therian imprinted genes and gene clusters is coincident with, and may have been a potential driving force in, the development of mammalian genomic imprinting. These data provide strong support for the host defence hypothesis.

Analysis of the platypus genome suggests a transposon origin for mammalian imprinting

PubMed Central

Pask, Andrew J; Papenfuss, Anthony T; Ager, Eleanor I; McColl, Kaighin A; Speed, Terence P; Renfree, Marilyn B

2009-01-01

Background Genomic imprinting is an epigenetic phenomenon that results in monoallelic gene expression. Many hypotheses have been advanced to explain why genomic imprinting evolved in mammals, but few have examined how it arose. The host defence hypothesis suggests that imprinting evolved from existing mechanisms within the cell that act to silence foreign DNA elements that insert into the genome. However, the changes to the mammalian genome that accompanied the evolution of imprinting have been hard to define due to the absence of large scale genomic resources between all extant classes. The recent release of the platypus genome has provided the first opportunity to perform comparisons between prototherian (monotreme; which appear to lack imprinting) and therian (marsupial and eutherian; which have imprinting) mammals. Results We compared the distribution of repeat elements known to attract epigenetic silencing across the entire genome from monotremes and therian mammals, particularly focusing on the orthologous imprinted regions. There is a significant accumulation of certain repeat elements within imprinted regions of therian mammals compared to the platypus. Conclusions Our analyses show that the platypus has significantly fewer repeats of certain classes in the regions of the genome that have become imprinted in therian mammals. The accumulation of repeats, especially long terminal repeats and DNA elements, in therian imprinted genes and gene clusters is coincident with, and may have been a potential driving force in, the development of mammalian genomic imprinting. These data provide strong support for the host defence hypothesis. PMID:19121219

Localization of deformations within the amygdala in individuals with psychopathy.

PubMed

Yang, Yaling; Raine, Adrian; Narr, Katherine L; Colletti, Patrick; Toga, Arthur W

2009-09-01

Despite the repeated findings of impaired fear conditioning and affective recognition in psychopathic individuals, there has been a paucity of brain imaging research on the amygdala and no evidence suggesting which regions within the amygdala may be structurally compromised in individuals with psychopathy. To detect global and regional anatomical abnormalities in the amygdala in individuals with psychopathy. Cross-sectional design using structural magnetic resonance imaging. Participants were recruited from high-risk communities (temporary employment agencies) in the Los Angeles, California, area and underwent imaging at a hospital research facility at the University of Southern California. Twenty-seven psychopathic individuals as defined by the Hare Psychopathy Checklist-Revised and 32 normal controls matched on age, sex, and ethnicity. Amygdala volumes were examined using traditional volumetric analyses and surface-based mesh modeling methods were used to localize regional surface deformations. Individuals with psychopathy showed significant bilateral volume reductions in the amygdala compared with controls (left, 17.1%; right, 18.9%). Surface deformations were localized in regions in the approximate vicinity of the basolateral, lateral, cortical, and central nuclei of the amygdala. Significant correlations were found between reduced amygdala volumes and increased total and facet psychopathy scores, with correlations strongest for the affective and interpersonal facets of psychopathy. Results provide the first evidence, to our knowledge, of focal amygdala abnormalities in psychopathic individuals and corroborate findings from previous lesion studies. Findings support prior hypotheses of amygdala deficits in individuals with psychopathy and indicate that amygdala abnormalities contribute to emotional and behavioral symptoms of psychopathy.

Structure of thrombospondin type 3 repeats in bacterial outer membrane protein A reveals its intra-repeat disulfide bond-dependent calcium-binding capability

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

Dai, Shuyan; Sun, Cancan; Tan, Kemin

Eukaryotic thrombospondin type 3 repeat (TT3R) is an efficient calcium ion (Ca2+) binding motif only found in mammalian thrombospondin family. TT3R has also been found in prokaryotic cellulase Cel5G, which was thought to forfeit the Ca2+-binding capability due to the formation of intra-repeat disulfide bonds, instead of the inter-repeat ones possessed by eukaryotic TT3Rs. In this study, we have identified an enormous number of prokaryotic TT3R-containing proteins belonging to several different protein families, including outer membrane protein A (OmpA), an important structural protein connecting the outer membrane and the periplasmic peptidoglycan layer in gram-negative bacteria. Here, we report the crystalmore » structure of the periplasmic region of OmpA from Capnocytophaga gingivalis, which contains a linker region comprising five consecutive TT3Rs. The structure of OmpA-TT3R exhibits a well-ordered architecture organized around two tightly-coordinated Ca2+ and confirms the presence of abnormal intra-repeat disulfide bonds. Further mutagenesis studies showed that the Ca2+-binding capability of OmpA-TT3R is indeed dependent on the proper formation of intra-repeat disulfide bonds, which help to fix a conserved glycine residue at its proper position for Ca2+ coordination. Additionally, despite lacking inter repeat disulfide bonds, the interfaces between adjacent OmpA-TT3Rs are enhanced by both hydrophobic and conserved aromatic-proline interactions.« less

Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility in Japanese Black cattle.

PubMed

Arishima, Taichi; Sasaki, Shinji; Isobe, Tomohiro; Ikebata, Yoshihisa; Shimbara, Shinichi; Ikeda, Shogo; Kawashima, Keisuke; Suzuki, Yutaka; Watanabe, Manabu; Sugano, Sumio; Mizoshita, Kazunori; Sugimoto, Yoshikazu

2017-12-06

Repeat breeding, which is defined as cattle failure to conceive after three or more inseminations in the absence of clinical abnormalities, is a substantial problem in cattle breeding. To identify maternal genetic variants of repeat breeding in Japanese Black cattle, we selected 29 repeat-breeding heifers that failed to conceive following embryo transfer (ET) and conducted a genome-wide association study (GWAS) using the traits. We found that a single-nucleotide polymorphism (SNP; g.92,377,635A > G) in the upstream region of the FOXP3 gene on the X chromosome was highly associated with repeat breeding and failure to conceive following ET (P = 1.51 × 10 -14 ). FOXP3 is a master gene for differentiation of regulatory T (T reg ) cells that function in pregnancy maintenance. Reporter assay results revealed that the activity of the FOXP3 promoter was lower in reporter constructs with the risk-allele than in those with the non-risk-allele by approximately 0.68 fold. These findings suggest that the variant in the upstream region of FOXP3 with the risk-allele decreased FOXP3 transcription, which in turn, could reduce the number of maternal T reg cells and lead to infertility. The frequency of the risk-allele in repeat-breeding heifers is more than that in cows, suggesting that the risk-allele could be associated with infertility in repeat-breeding heifers. This GWAS identified a maternal variant in the upstream region of FOXP3 that was associated with infertility in repeat-breeding Japanese Black cattle that failed to conceive using ET. The variant affected the level of FOXP3 mRNA expression. Thus, the results suggest that the risk-allele could serve as a useful marker to reduce and eliminate animals with inferior fertility in Japanese Black cattle.

The Neuropsychology of Starvation: Set-Shifting and Central Coherence in a Fasted Nonclinical Sample

PubMed Central

Pender, Sarah; Gilbert, Sam J.; Serpell, Lucy

2014-01-01

Objectives Recent research suggests certain neuropsychological deficits occur in anorexia nervosa (AN). The role of starvation in these deficits remains unclear. Studies of individuals without AN can elucidate our understanding of the effect of short-term starvation on neuropsychological performance. Methods Using a within-subjects repeated measures design, 60 healthy female participants were tested once after fasting for 18 hours, and once when satiated. Measures included two tasks to measure central coherence and a set-shifting task. Results Fasting exacerbated set-shifting difficulties on a rule-change task. Fasting was associated with stronger local and impaired global processing, indicating weaker central coherence. Conclusions Models of AN that propose a central role for set-shifting difficulties or weak central coherence should also consider the impact of short-term fasting on these processes. PMID:25338075

Regional Strategic Appraisal of Central America

DTIC Science & Technology

2003-04-07

effective region, to increase its competitiveness in the face of the challenges from globalization . Therefore, I recommend a deepening of the regional...centroamericanos, 1970 a 1999, Mexico City, Mach 2000. 7 Agosin, Bloom and Gitli, Globalization , Liberalization, and Sustainable Human Development in Central...Bloom, and Eduardo Gitli, “ Globalization , Liberalization, and Sustainable Human Development in Central America,” February, 2000; available from <http

Health disparities among the western, central and eastern rural regions of China after a decade of health promotion and disease prevention programming.

PubMed

Zhang, Xi-Fan; Tian, Xiang-Yang; Cheng, Yu-Lan; Feng, Zhan-Chun; Wang, Liang; Southerland, Jodi

2015-08-01

Health disparities between the western, central and eastern regions of rural China, and the impact of national health improvement policies and programming were assessed. A total of 400 counties were randomly sampled. ANOVA and Logistic regression modeling were employed to estimate differences in health outcomes and determinants. Significant differences were found between the western, central and eastern rural regions in community infrastructure and health outcomes. From 2000 to 2010, health indicators in rural China were improved significantly, and the infant mortality rate (IMR), maternal mortality rate (MMR) and under 5 mortality rate (U5MR) had fallen by 62.79%, 71.74% and 61.92%, respectively. Central rural China had the greatest decrease in IMR (65.05%); whereas, western rural China had the greatest reduction in MMR (72.99%) but smallest reduction in U5MR (57.36%). Despite these improvements, Logistic regression analysis showed regional differences in key health outcome indicators (odds ratios): IMR (central: 2.13; western: 5.31), U5MR (central: 2.25; western: 5.69), MMR (central: 1.94; western: 3.31), and prevalence of infectious diseases (central: 1.62; western: 3.58). The community infrastructure and health outcomes of the western and central rural regions of China have been improved markedly during the first decade of the 21st century. However, health disparities still exist across the three regions. National efforts to increase per capita income, community empowerment and mobilization, community infrastructure, capacity of rural health facilities, and health literacy would be effective policy options to attain health equity.