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Sample records for acid repeat region

  1. Understanding and identifying amino acid repeats.

    PubMed

    Luo, Hong; Nijveen, Harm

    2014-07-01

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

  2. Nucleic acid recognition by tandem helical repeats.

    PubMed

    Rubinson, Emily H; Eichman, Brandt F

    2012-02-01

    Protein domains constructed from tandem α-helical repeats have until recently been primarily associated with protein scaffolds or RNA recognition. Recent crystal structures of human mitochondrial termination factor MTERF1 and Bacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA revealed two new superhelical tandem repeat architectures capable of wrapping around the double helix in unique ways. Unlike DNA sequence recognition motifs that rely mainly on major groove read-out, MTERF and ALK motifs locate target sequences and aberrant nucleotides within DNA by resculpting the double-helix through extensive backbone contacts. Comparisons between MTERF and ALK repeats, together with recent advances in ssRNA recognition by Pumilio/FBF (PUF) domains, provide new insights into the fundamental principles of protein-nucleic acid recognition. PMID:22154606

  3. Amino acid repeats and the structure and evolution of proteins.

    PubMed

    Albà, M M; Tompa, P; Veitia, R A

    2007-01-01

    Many proteins have repeats or runs of single amino acids. The pathogenicity of some repeat expansions has fueled proteomic, genomic and structural explorations of homopolymeric runs not only in human but in a wide variety of other organisms. Other types of amino acid repetitive structures exhibit more complex patterns than homopeptides. Irrespective of their precise organization, repetitive sequences are defined as low complexity or simple sequences, as one or a few residues are particularly abundant. Prokaryotes show a relatively low frequency of simple sequences compared to eukaryotes. In the latter the percentage of proteins containing homopolymeric runs varies greatly from one group to another. For instance, within vertebrates, amino acid repeat frequency is much higher in mammals than in amphibians, birds or fishes. For some repeats, this is correlated with the GC-richness of the regions containing the corresponding genes. Homopeptides tend to occur in disordered regions of transcription factors or developmental proteins. They can trigger the formation of protein aggregates, particularly in 'disease' proteins. Simple sequences seem to evolve more rapidly than the rest of the protein/gene and may have a functional impact. Therefore, they are good candidates to promote rapid evolutionary changes. All these diverse facets of homopolymeric runs are explored in this review. PMID:18753788

  4. The 213-amino-acid leucine-rich repeat region of the listeria monocytogenes InlB protein is sufficient for entry into mammalian cells, stimulation of PI 3-kinase and membrane ruffling.

    PubMed

    Braun, L; Nato, F; Payrastre, B; Mazié, J C; Cossart, P

    1999-10-01

    The Listeria monocytogenes InlB protein is a 630-amino-acid surface protein that mediates entry of the bacterium into a wide variety of cell types, including hepatocytes, fibroblasts and epithelial cells such as Vero, HEp-2 and HeLa cells. Invasion stimulates host proteins tyrosine phosphorylation, PI 3-kinase activity and rearrangements in the actin cytoskeleton. We previously showed that InlB is sufficient for entry of InlB-coated latex beads into cells and recent results indicate that purified InlB can stimulate PI 3-kinase activity and is thus the first bacterial agonist of this lipid kinase. In this study, we identified the region of InlB responsible for entry and stimulation of signal transduction events. Eight monoclonal antibodies directed against InlB were raised and, of those, five inhibited bacterial entry. These five antibodies recognized epitopes within the leucine-rich repeat (LRR) region and/or the inter-repeat (IR) region. InlB-staphylococcal protein A (SPA) fusion proteins and recombinant InlB derivatives were generated and tested for their capacity to mediate entry into cultured mammalian cells. All the InlB derivatives that carried the amino-terminal 213-amino-acid LRR region conferred invasiveness to the normally non-invasive bacterium L. innocua or to inert latex beads and the corresponding purified polypeptides inhibited bacterial entry. In addition, the 213-amino-acid LRR region was able to stimulate PI 3-kinase activity and changes in the actin cytoskeleton (membrane ruffling). These properties were not detected with purified internalin, another invasion protein of L. monocytogenes that displays LRRs similar to those of InlB. Taken together, these results show that the first 213 amino acids of InlB are critical for its specific properties. PMID:10540282

  5. Inhibition of breast cancer cell proliferation in repeated and non-repeated treatment with zoledronic acid

    PubMed Central

    2012-01-01

    Background Zoledronic acid is used to treat bone metastases and has been shown to reduce skeletal-related events and exert antitumor activity. The present in vitro study investigates the mechanism of action of Zoledronic Acid on breast cancer cell lines with different hormonal and HER2 patterns. Furthermore, we investigated the efficacy of repeated versus non-repeated treatments. Methods The study was performed on 4 breast cancer cell lines (BRC-230, SkBr3, MCF-7 and MDA-MB-231). Non-repeated treatment (single exposure of 168 hrs’ duration) with zoledronic acid was compared with repeated treatment (separate exposures, each of 48 hrs’ duration, for a total of 168 hrs) at different dosages. A dose–response profile was generated using sulforhodamine B assay. Apoptosis was evaluated by TUNEL assay and biomolecular characteristics were analyzed by western blot. Results Zoledronic acid produced a dose-dependent inhibition of proliferation in all cell lines. Anti-proliferative activity was enhanced with the repeated treatment, proving to be statistically significant in the triple-negative lines. In these lines repeated treatment showed a cytocidal effect, with apoptotic cell death caused by caspase 3, 8 and 9 activation and decreased RAS and pMAPK expression. Apoptosis was not observed in estrogen receptor-positive line: p21 overexpression suggested a slowing down of cell cycle. A decrease in RAS and pMAPK expression was seen in HER2-overexpressing line after treatment. Conclusions The study suggests that zoledronic acid has an antitumor activity in breast cancer cell lines. Its mechanism of action involves the decrease of RAS and RHO, as in osteoclasts. Repeated treatment enhances antitumor activity compared to non-repeated treatment. Repeated treatment has a killing effect on triple-negative lines due to apoptosis activation. Further research is warranted especially in the treatment of triple-negative breast cancer. PMID:23173568

  6. Activating frataxin expression by repeat-targeted nucleic acids

    PubMed Central

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

    2016-01-01

    Friedreich's ataxia is an incurable genetic disorder caused by a mutant expansion of the trinucleotide GAA within an intronic FXN RNA. This expansion leads to reduced expression of frataxin (FXN) protein and evidence suggests that transcriptional repression is caused by an R-loop that forms between the expanded repeat RNA and complementary genomic DNA. Synthetic agents that increase levels of FXN protein might alleviate the disease. We demonstrate that introducing anti-GAA duplex RNAs or single-stranded locked nucleic acids into patient-derived cells increases FXN protein expression to levels similar to analogous wild-type cells. Our data are significant because synthetic nucleic acids that target GAA repeats can be lead compounds for restoring curative FXN levels. More broadly, our results demonstrate that interfering with R-loop formation can trigger gene activation and reveal a new strategy for upregulating gene expression. PMID:26842135

  7. Repeat polymorphisms in the low-complexity regions of Plasmodium falciparum ABC transporters and associations with in vitro antimalarial responses.

    PubMed

    Okombo, John; Abdi, Abdirahman I; Kiara, Steven M; Mwai, Leah; Pole, Lewa; Sutherland, Colin J; Nzila, Alexis; Ochola-Oyier, Lynette Isabella

    2013-12-01

    The Plasmodium falciparum genome is rich in regions of low amino acid complexity which evolve with few constraints on size. To explore the extent of diversity in these loci, we sequenced repeat regions in pfmdr1, pfmdr5, pfmdr6, pfmrp2, and the antigenic locus pfmsp8 in laboratory and cultured-adapted clinical isolates. We further assessed associations between the repeats and parasite in vitro responses to 7 antimalarials to determine possible adaptive roles of these repeats in drug tolerance. Our results show extensive repeat variations in the reference and clinical isolates in all loci. We also observed a modest increase in dihydroartemisinin activity in parasites harboring the pfmdr1 sequence profile 7-2-10 (reflecting the number of asparagine repeats, number of aspartate repeats, and number of asparagine repeats in the final series of the gene product) (P = 0.0321) and reduced sensitivity to chloroquine, mefloquine, quinine, and dihydroartemisinin in those with the 7-2-11 profile (P = 0.0051, 0.0068, 0.0011, and 0.0052, respectively). Interestingly, we noted an inverse association between two drugs whereby isolates with 6 asparagine repeats encoded by pfmdr6 were significantly more susceptible to piperaquine than those with 8 (P = 0.0057). Against lumefantrine, those with 8 repeats were, however, more sensitive (P = 0.0144). In pfmrp2, the 7-DNNNTS/NNNNTS (number of DNNNTS or NNNNTS motifs; underlining indicates dimorphism) repeat group was significantly associated with a higher lumefantrine 50% inhibitory concentration (IC50) (P = 0.008) than in those without. No associations were observed with pfmsp8. These results hint at the probable utility of some repeat conformations as markers of in vitro antimalarial response; hence, biochemical functional studies to ascertain their role in P. falciparum are required. PMID:24080667

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

    ERIC Educational Resources Information Center

    Nicholson, John W.; Wilson, Alan D.

    2004-01-01

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

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

    PubMed Central

    Boursaux-Eude, Caroline; Guiso, Nicole

    2000-01-01

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

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

    SciTech Connect

    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.

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

    PubMed

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

    2014-05-01

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

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

    PubMed Central

    2009-01-01

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

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

    PubMed

    Palmer, William H; Obbard, Darren J

    2016-01-01

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

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

    PubMed Central

    Palmer, William H.; Obbard, Darren J.

    2016-01-01

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

  15. Improvement of myocardial ischemic dysfunction with dichloroacetic acid: experimental study by repeated ischemia in dogs.

    PubMed

    Okuda, K; Nohara, R; Fujita, M; Tamaki, N; Konishi, J; Sasayama, S

    1995-12-01

    We investigated metabolic factors related to the recovery of myocardial function during ischemia and after reperfusion using dichloroacetic acid (DCA) in canine models with repeated 10-min regional ischemia and reperfusion. Administration of 100 mg/kg DCA, which activates pyruvate dehydrogenase, improved regional wall motion significantly as compared with the nontreated controls (p < 0.05). The mechanism was studied by determining changes in myocardial levels of pH, glucose, lactate, and nonesterified fatty acids (NEFA). Glucose extraction was increased significantly during ischemia and reperfusion by the pretreatment of DCA (p < 0.01). the calculated contribution of glucose to myocardial oxidative metabolism during ischemia and reperfusion was greater than that of NEFA and lactate in case of DCA treatment. The uptake of [99mTc]pyrophosphate (PYP), which reflects myocardial injury, was also significantly suppressed by DCA (p < 0.01). pH was not affected by an infusion of DCA. These findings suggest that the activation of glucose metabolism by DCA, which is impaired and reduced during ischemia and reperfusion, may be responsible for the improved myocardial function after reperfusion. PMID:8606539

  16. ASICs Do Not Play a Role in Maintaining Hyperalgesia Induced by Repeated Intramuscular Acid Injections

    PubMed Central

    Gautam, Mamta; Benson, Christopher J.; Ranier, Jon D.; Light, Alan R.; Sluka, Kathleen A.

    2012-01-01

    Repeated intramuscular acid injections produce long-lasting mechanical hyperalgesia that depends on activation of ASICs. The present study investigated if pH-activated currents in sensory neurons innervating muscle were altered in response to repeated acid injections, and if blockade of ASICs reverses existing hyperalgesia. In muscle sensory neurons, the mean acid-evoked current amplitudes and the biophysical properties of the ASIC-like currents were unchanged following acidic saline injections when compared to neutral pH saline injections or uninjected controls. Moreover, increased mechanical sensitivity of the muscle and paw after the second acid injection was unaffected by local blockade of ASICs (A-317567) in the muscle. As a control, electron microscopic analysis showed that the tibial nerve was undamaged after acid injections. Our previous studies demonstrated that ASICs are important in the development of hyperalgesia to repeated acid injections. However, the current data suggest that ASICs are not involved in maintaining hyperalgesia to repeated intramuscular acid injections. PMID:22191025

  17. The Repeat Region of the Circumsporozoite Protein is Critical for Sporozoite Formation and Maturation in Plasmodium

    PubMed Central

    Patzewitz, Eva-Maria; Wall, Richard J.; Hopp, Christine S.; Poulin, Benoit; Mohmmed, Asif; Malhotra, Pawan; Coppi, Alida; Sinnis, Photini; Tewari, Rita

    2014-01-01

    The circumsporozoite protein (CSP) is the major surface protein of the sporozoite stage of malaria parasites and has multiple functions as the parasite develops and then migrates from the mosquito midgut to the mammalian liver. The overall structure of CSP is conserved among Plasmodium species, consisting of a species-specific central tandem repeat region flanked by two conserved domains: the NH2-terminus and the thrombospondin repeat (TSR) at the COOH-terminus. Although the central repeat region is an immunodominant B-cell epitope and the basis of the only candidate malaria vaccine in Phase III clinical trials, little is known about its functional role(s). We used the rodent malaria model Plasmodium berghei to investigate the role of the CSP tandem repeat region during sporozoite development. Here we describe two mutant parasite lines, one lacking the tandem repeat region (ΔRep) and the other lacking the NH2-terminus as well as the repeat region (ΔNΔRep). We show that in both mutant lines oocyst formation is unaffected but sporozoite development is defective. PMID:25438048

  18. Kinetics of D-lactic acid production by Sporolactobacillus sp. strain CASD using repeated batch fermentation.

    PubMed

    Zhao, Bo; Wang, Limin; Li, Fengsong; Hua, Dongliang; Ma, Cuiqing; Ma, Yanhe; Xu, Ping

    2010-08-01

    D-lactic acid was produced by Sporolactobacillus sp. strain CASD in repeated batch fermentation with one- and two-reactor systems. The strain showed relatively high energy consumption in its growth-related metabolism in comparison with other lactic acid producers. When the fermentation was repeated with 10% (v/v) of previous culture to start a new batch, D-lactic acid production shifted from being cell-maintenance-dependent to cell-growth-dependent. In comparison with the one-reactor system, D-lactic acid production increased approximately 9% in the fourth batch of the two-reactor system. Strain CASD is an efficient D-lactic acid producer with increased growth rate at the early stage of repeated cycles, which explains the strain's physiological adaptation to repeated batch culture and improved performance in the two-reactor fermentation system. From a kinetic point of view, two-reactor fermentation system was shown to be an alternative for conventional one-reactor repeated batch operation. PMID:20374976

  19. Ab initio detection of fuzzy amino acid tandem repeats in protein sequences

    PubMed Central

    2012-01-01

    Background Tandem repetitions within protein amino acid sequences often correspond to regular secondary structures and form multi-repeat 3D assemblies of varied size and function. Developing internal repetitions is one of the evolutionary mechanisms that proteins employ to adapt their structure and function under evolutionary pressure. While there is keen interest in understanding such phenomena, detection of repeating structures based only on sequence analysis is considered an arduous task, since structure and function is often preserved even under considerable sequence divergence (fuzzy tandem repeats). Results In this paper we present PTRStalker, a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences. In the reported results we show that by feeding PTRStalker with amino acid sequences from the UniProtKB/Swiss-Prot database we detect novel tandemly repeated structures not captured by other state-of-the-art tools. Experiments with membrane proteins indicate that PTRStalker can detect global symmetries in the primary structure which are then reflected in the tertiary structure. Conclusions PTRStalker is able to detect fuzzy tandem repeating structures in protein sequences, with performance beyond the current state-of-the art. Such a tool may be a valuable support to investigating protein structural properties when tertiary X-ray data is not available. PMID:22536906

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

    SciTech Connect

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

    1994-09-01

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

  1. Identification of antigenic epitopes in an alanine-rich repeating region of a surface protein antigen of Streptococcus mutants.

    PubMed Central

    Okahashi, N; Takahashi, I; Nakai, M; Senpuku, H; Nisizawa, T; Koga, T

    1993-01-01

    A surface protein antigen (PAc) of Streptococcus mutans with a molecular mass of 190 kDa is considered to play an important role in the initial attachment of this streptococcus to the tooth surface. Two internal repeating amino acid sequences are present in the PAc molecule. One repeating region located in the N-terminal region is rich in alanine (A-region), and the other, located in the central region, is rich in proline (P-region). To identify antigenic epitopes on the A-region of the PAc protein, 82 sequential overlapping synthetic decapeptides covering one of the repetitive units of the A-region were synthesized. In the epitope scanning analyses using murine antisera raised against recombinant PAc (rPAc), multiple antigenic epitopes were found in the repetitive unit of the A-region, and some of them reacted with antisera to rPAc from BALB/c, B10, B10.D2, and B10.BR mice. In particular, a peptide YEAALKQY (residues 366 to 373) was recognized by anti-rPAc sera from all four strains of mice. The reactivities of anti-rPAc sera in the epitope scanning were confirmed by using a purified synthetic peptide, NAKATYEAALKQYEADLAA (corresponding to residues 361 to 379). Furthermore, antisera against a surface protein antigen PAg (SpaA) of Streptococcus sobrinus from BALB/c mice reacted strongly to residues 330 to 337, 362 to 369, and 366 to 373 of the PAc protein by the epitope scanning analysis. An AKATYEAALKQY (residues 362 to 373 of the PAc protein)-like sequence, AKANYEAKLAQY, was found within the A-region of S. sobrinus PAg, suggesting that the amino acid sequences AKA-YEA and YEA-L-QY may be major cross-reactive epitopes of the S. mutans PAc protein and the S. sobrinus PAg protein. PMID:7681043

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

    PubMed Central

    Kim, Byoung Sik; Gavin, Hannah E.

    2015-01-01

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

  3. Low Density Lipoprotein Receptor Class A Repeats Are O-Glycosylated in Linker Regions*

    PubMed Central

    Pedersen, Nis Borbye; Wang, Shengjun; Narimatsu, Yoshiki; Yang, Zhang; Halim, Adnan; Schjoldager, Katrine Ter-Borch Gram; Madsen, Thomas Daugbjerg; Seidah, Nabil G.; Bennett, Eric Paul; Levery, Steven B.; Clausen, Henrik

    2014-01-01

    The low density lipoprotein receptor (LDLR) is crucial for cholesterol homeostasis and deficiency in LDLR functions cause hypercholesterolemia. LDLR is a type I transmembrane protein that requires O-glycosylation for stable expression at the cell surface. It has previously been suggested that LDLR O-glycosylation is found N-terminal to the juxtamembrane region. Recently we identified O-glycosylation sites in the linker regions between the characteristic LDLR class A repeats in several LDLR-related receptors using the “SimpleCell” O-glycoproteome shotgun strategy. Herein, we have systematically characterized O-glycosylation sites on recombinant LDLR shed from HEK293 SimpleCells and CHO wild-type cells. We find that the short linker regions between LDLR class A repeats contain an evolutionarily conserved O-glycosylation site at position −1 of the first cysteine residue of most repeats, which in wild-type CHO cells is glycosylated with the typical sialylated core 1 structure. The glycosites in linker regions of LDLR class A repeats are conserved in LDLR from man to Xenopus and found in other homologous receptors. O-Glycosylation is controlled by a large family of polypeptide GalNAc transferases. Probing into which isoform(s) contributed to glycosylation of the linker regions of the LDLR class A repeats by in vitro enzyme assays suggested a major role of GalNAc-T11. This was supported by expression of LDLR in HEK293 cells, where knock-out of the GalNAc-T11 isoform resulted in the loss of glycosylation of three of four linker regions. PMID:24798328

  4. Repetitive sequences in the crocodilian mitochondrial control region: poly-A sequences and heteroplasmic tandem repeats.

    PubMed

    Ray, David A; Densmore, Llewellyn D

    2003-06-01

    Heteroplasmic tandem repeats in the mitochondrial control region have been documented in a wide variety of vertebrate species. We have examined the control region from 11 species in the family Crocodylidae and identified two different types of heteroplasmic repetitive sequences in the conserved sequence block (CSB) domain-an extensive poly-A tract that appears to be involved in the formation of secondary structure and a series of tandem repeats located downstream ranging from approximately 50 to approximately 80 bp in length. We describe this portion of the crocodylian control region in detail and focus on members of the family Crocodylidae. We then address the origins of the tandemly repeated sequences in this family and suggest hypotheses to explain possible mechanisms of expansion/contraction of the sequences. We have also examined control region sequences from Alligator and Caiman and offer hypotheses for the origin of tandem repeats found in those taxa. Finally, we present a brief analysis of intraindividual and interindividual haplotype variation by examining representatives of Morelet's crocodile (Crocodylus moreletii). PMID:12716979

  5. Correlation between zoledronic acid infusion and repeat vertebroplasty surgery in osteoporotic patients.

    PubMed

    Lin, Tung-Yi; Yang, Shih-Chieh; Tsai, Tsung-Ting; Lai, Po-Liang; Fu, Tsai-Sheng; Niu, Chi-Chien; Chen, Lih-Huei; Chen, Wen-Jer

    2016-05-01

    Objective The incidence of bone fractures rapidly increases as people age, mostly due to bone loss resulting from osteoporosis. The purpose of this study is to compare the rates of repeat vertebroplasty in osteoporotic patients treated with or without zoledronic acid (ZOL) infusion following initial vertebroplasty. Research design and methods We conducted a retrospective chart review of osteoporotic patients who underwent vertebroplasty from June 2009 to June 2012. Patients with existing vertebral fracture(s) were retrospectively divided into two groups according to whether or not they received zoledronic acid infusion after initial vertebroplasty. Zoledronic acid infusion was intravenously administered once a year for three consecutive years, as a single 5 mg dose in 100 mL solution infused over at least 15 minutes. The primary efficacy variable was the number of patients requiring repeat vertebroplasty procedures after the initial surgery due to subsequent vertebral fractures. The Cox proportional hazards model was used to compare the risk ratios of repeat vertebroplasty between these two groups. Results A total of 1646 patients, including 456 males and 1190 females (age range: 65-89 years), were enrolled. Compared to the 1595 patients who did not receive osteoporosis medication, the 51 patients treated with zoledronic acid infusion demonstrated a significantly lower rate of repeat vertebroplasty. In the ZOL-treated group, only 4% of the patients (2/51) required a second vertebroplasty, compared to 13% (206/1595) in the non-ZOL-treated group (p = 0.032). Conclusions The results indicate that osteoporotic patients who undergo vertebroplasty are significantly less likely to require reoperation if treated with zoledronic acid infusion. However, since the number of male patients in the ZOL-treated group was limited, and since Taiwan's National Health System program does not cover the cost of receiving zoledronic acid infusions for male patients, the

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

    PubMed Central

    2013-01-01

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

  7. Broader pattern of tandem repeats in the mitochondrial control region of Perciformes

    NASA Astrophysics Data System (ADS)

    Cui, Zhaoxia; Liu, Yuan; Chu, Ka Hou

    2010-07-01

    Perciformes, the largest order of vertebrates with 20 suborders, is the most diverse fish order that dominates vertebrate ocean life. The complete mitochondrial control region (CR) of Trichiurus japonicus (Trichiuridae, Scombroidei) and Pampus sp. (Stromateidae, Stromateoidei) were amplified and sequenced. Together with data from GenBank, the tandem repeats in the mitochondrial CR from 48 species, which covered nine suborders of Perciformes, are reported in this study. The tandem repeats tend to be long in the suborder Percoidei and Stromateoidei. The identical repeats in 21 species of Cichlidae suggest a common origin and have existed before species divergence. Larimichthys crocea shows tandem repeats instead of the typical structure of the central conserved sequence blocks, which was first reported in Perciformes and vertebrates. This might have resulted from interruption of the polymerase activity during the H-strand synthesis. The four broader patterns presented here for the tandem repeats, including those in both the 5' and 3' ends, only in the either 5' or 3' end, and in the central conserved domain of the control region, will be useful for understanding the evolution of species.

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

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

  9. Transcription-Associated R-Loop Formation across the Human FMR1 CGG-Repeat Region

    PubMed Central

    Loomis, Erick W.; Sanz, Lionel A.; Chédin, Frédéric; Hagerman, Paul J.

    2014-01-01

    Expansion of a trinucleotide (CGG) repeat element within the 5′ untranslated region (5′UTR) of the human FMR1 gene is responsible for a number of heritable disorders operating through distinct pathogenic mechanisms: gene silencing for fragile X syndrome (>200 CGG) and RNA toxic gain-of-function for FXTAS (∼55–200 CGG). Existing models have focused almost exclusively on post-transcriptional mechanisms, but co-transcriptional processes could also contribute to the molecular dysfunction of FMR1. We have observed that transcription through the GC-rich FMR1 5′UTR region favors R-loop formation, with the nascent (G-rich) RNA forming a stable RNA:DNA hybrid with the template DNA strand, thereby displacing the non-template DNA strand. Using DNA:RNA (hybrid) immunoprecipitation (DRIP) of genomic DNA from cultured human dermal fibroblasts with both normal (∼30 CGG repeats) and premutation (55repeats) alleles, we provide evidence for FMR1 R-loop formation in human genomic DNA. Using a doxycycline (DOX)-inducible episomal system in which both the CGG-repeat and transcription frequency can be varied, we further show that R-loop formation increases with higher expression levels. Finally, non-denaturing bisulfite mapping of the displaced single-stranded DNA confirmed R-loop formation at the endogenous FMR1 locus and further indicated that R-loops formed over CGG repeats may be prone to structural complexities, including hairpin formation, not commonly associated with other R-loops. These observations introduce a new molecular feature of the FMR1 gene that is directly affected by CGG-repeat expansion and is likely to be involved in the associated cellular dysfunction. PMID:24743386

  10. Nonneutral evolution of tandem repeats in the mitochondrial DNA control region of lagomorphs.

    PubMed

    Casane, D; Dennebouy, N; de Rochambeau, H; Mounolou, J C; Monnerot, M

    1997-08-01

    The mitochondrial DNA of the European rabbit (Oryctolagus cuniculus) contains a tandem array of 153-bp repeats in the vicinity of the replication origin of the H-stand. Variation among molecules in the number of these repeats results in inter- and intraindividual length polymorphism (heteroplasmy). Generally, in an individual, one predominant molecular type is observed, the others representing a low percentage of the mtDNA content. At the tissue level, we observe a particular distribution of this polymorphism in the gonads compared with liver, kidneys, or brain, implying a relationship between the differentiation status of the cells and the types of new mtDNA molecules which appear and accumulate during lifetime. Similar tandem repeats were also found in the mtDNA noncoding region of European hares (Lepus europaeus), a cottontail (Sylvilagus floridanus), and a pika (Ochotona rufescens). The lengths and the sequences of these units evolve rapidly and in a concerted way, but the number of repeats is maintained in a narrow range, and an internal 20-bp segment is highly conserved. Constraints restrict the evolution of the primary sequence of these repeated units, the number of which is probably controlled by a stabilizing selection. PMID:9254915

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

    PubMed

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

    2015-01-01

    The purpose of this study was to investigate the effect of repeated harvesting on the content of caffeic acid (CA) and seven species of caffeoylquinic acids (CQAs) in sweet potato leaves using a newly developed high-performance liquid chromatography method. Six cultivars and two breeding lines were used in this study. Leaves were collected at monthly intervals from 1st harvest (May) to 4th harvest (August) in 2011 and 2012. ANOVA analysis revealed that the contents of CQAs were significantly different among all cultivars and breeding lines, but no significant differences were found for CA. No annual variation was confirmed in CA and CQAs. Repeated harvest of sweet potato leaves affected the content of only 4-CQA and 5-CQA. Post-hoc comparisons using Tukey's method indicated that the contents of 4-CQA and 5-CQA in sweet potato leaves harvested at first time were significantly higher compared to those at the other harvest times. PMID:25971339

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    DOEpatents

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

    1995-06-27

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

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

    DOEpatents

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

    1995-01-01

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

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

    PubMed

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

    2012-06-01

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

  17. Regional adaptation of collagen in skeletal muscle to repeated bouts of strenuous eccentric exercise.

    PubMed

    Takagi, Ryo; Ogasawara, Riki; Tsutaki, Arata; Nakazato, Koichi; Ishii, Naokata

    2016-09-01

    This study investigated the injured region-specific alterations of factors related to the "repeated bout effect" (RBE), i.e., when the first bout of eccentric exercise generates resistance to injuries from the second bout of the same exercise. Wistar rats were divided into single injury (SI) and repeated injury (RI) groups. The right gastrocnemius muscle was subjected to a bout of eccentric contractions (ECs) at the age of 14 weeks in the SI group and 10 and 14 weeks in the RI group. The number of injured fibers after the last bout of ECs was lower in RI than in SI. In the SI group, injured fibers after ECs were mainly located in the superficial region of muscle and expressed myosin heavy chain (MHC) IIx and IIb. Prior to the second bout of ECs, the fiber-type composition in the RI group showed decreased MHC IIx and IIb fibers and increased MHC IIa fibers compared with those in the SI group. However, most regenerating fibers showed either MHC IIx or IIb expression. Heat shock protein 72 and total collagen contents in whole muscle were higher in the RI group than in the SI group; however, only the collagen expression in the RI group was more intense than that in the SI group in the superficial region of muscle. These findings suggest that increased collagen may play a more important role in the injured region of muscle than the other factors in RBE. PMID:27469054

  18. Tetra-amino-acid tandem repeats are involved in HsdS complementation in type IC restriction-modification systems.

    PubMed

    Adamczyk-Popławska, Monika; Kondrzycka, Aneta; Urbanek, Katarzyna; Piekarowicz, Andrzej

    2003-11-01

    All known type I restriction and modification (R-M) systems of Escherichia coli and Salmonella enterica belong to one of four discrete families: type IA, IB, IC or ID. The classification of type I systems from a wide range of other genera is mainly based on complementation and molecular evidence derived from the comparison of the amino acid similarity of the corresponding subunits. This affiliation was seldom based on the strictest requirement for membership of a family, which depends on relatedness as demonstrated by complementation tests. This paper presents data indicating that the type I NgoAV R-M system from Neisseria gonorrhoeae, despite the very high identity of HsdM and HsdR subunits with members of the type IC family, does not show complementation with E. coli type IC R-M systems. Sequence analysis of the HsdS subunit of several different potential type IC R-M systems shows that the presence of different tetra-amino-acid sequence repeats, e.g. TAEL, LEAT, SEAL, TSEL, is characteristic for type IC R-M systems encoded by distantly related bacteria. The other regions of the HsdS subunits potentially responsible for subunit interaction are also different between a group of distantly related bacteria, but show high similarity within these bacteria. Complementation between the NgoAV R-M system and members of the EcoR124 R-M family can be restored by changing the tetra-amino-acid repeat within the HsdS subunit. The authors propose that the type IC family of R-M systems could consist of several complementation subgroups whose specificity would depend on differences in the conserved regions of the HsdS polypeptide. PMID:14600243

  19. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines.

    PubMed Central

    Powell, W; Morgante, M; McDevitt, R; Vendramin, G G; Rafalski, J A

    1995-01-01

    Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of several (dA)n.(dT)n mononucleotide stretches in chloroplast genomes. A chloroplast (cp) SSR was identified in three pine species (Pinus contorta, Pinus sylvestris, and Pinus thunbergii) 312 bp upstream of the psbA gene. DNA amplification of this repeated region from 11 pine species identified nine length variants. The polymorphic amplified fragments were isolated and the DNA sequence was determined, confirming that the length polymorphism was caused by variation in the length of the repeated region. In the pines, the chloroplast genome is transmitted through pollen and this PCR assay may be used to monitor gene flow in this genus. Analysis of 305 individuals from seven populations of Pinus leucodermis Ant. revealed the presence of four variants with intrapopulational diversities ranging from 0.000 to 0.629 and an average of 0.320. Restriction fragment length polymorphism analysis of cpDNA on the same populations previously failed to detect any variation. Population subdivision based on cpSSR was higher (Gst = 0.22, where Gst is coefficient of gene differentiation) than that revealed in a previous isozyme study (Gst = 0.05). We anticipate that SSR loci within the chloroplast genome should provide a highly informative assay for the analysis of the genetic structure of plant populations. Images Fig. 2 PMID:7644491

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

    PubMed

    Pelassa, Ilaria; Fiumara, Ferdinando

    2015-01-01

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

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

    NASA Technical Reports Server (NTRS)

    Nelson, Kevin E.; Miller, Stanley L.

    1992-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  4. Structure and organization of Marchantia polymorpha chloroplast genome. IV. Inverted repeat and small single copy regions.

    PubMed

    Kohchi, T; Shirai, H; Fukuzawa, H; Sano, T; Komano, T; Umesono, K; Inokuchi, H; Ozeki, H; Ohyama, K

    1988-09-20

    We characterized the genes in the regions of large inverted repeats (IRA and IRB, 10,058 base-pairs each) and a small single copy (SSC 19,813 bp) of chloroplast DNA from Marchantia polymorpha. The inverted repeat (IR) regions contain genes for four ribosomal RNAs (16 S, 23 S, 4.5 S and 5 S rRNAs) and five transfer RNAs (valine tRNA(GAC), isoleucine tRNA(GAU), alanine tRNA(UGC), arginine tRNA(ACG) and asparagine tRNA(GUU)). The gene organization of the IR regions in the liverwort chloroplast genome is conserved, although the IR regions are smaller (10,058 base-pairs) than any reported in higher plant chloroplasts. The small single-copy region (19,813 base-pairs) encoded genes for 17 open reading frames, a leucine tRNA(UAG) and a proline tRNA(GGG)-like sequence. We identified 12 open reading frames by homology of their coding sequences to a 4Fe-4S-type ferredoxin protein, a bacterial nitrogenase reductase component (Fe-protein), five human mitochondrial components of NADH dehydrogenase (ND1, ND4, ND4L, ND5 and ND6), two Escherichia coli ribosomal proteins (S15 and L21), two putative proteins encoded in the kinetoplast maxicircle DNA of Leishmania tarentolae (LtORF 3 and LtORF 4), and a bacterial permease inner membrane component (encoded by malF in E. coli or hisQ in Salmonella typhimurium). PMID:3199437

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

    PubMed Central

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

    2016-01-01

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

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

    SciTech Connect

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

    2005-10-10

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

  7. Repeated dose and reproductive/developmental toxicity of perfluorododecanoic acid in rats.

    PubMed

    Kato, Hina; Fujii, Sakiko; Takahashi, Mika; Matsumoto, Mariko; Hirata-Koizumi, Mutsuko; Ono, Atsushi; Hirose, Akihiko

    2015-11-01

    Perfluoroalkyl carboxylic acids (PFCAs) are a series of environmental contaminants that have received attention because of their possible adverse effects on wildlife and human health. Although many toxicological studies have been performed on perfluorooctanoic acid with carbon chain length C8, available toxicity data on PFCAs with longer chains are still insufficient to evaluate their hazard. A combined repeated dose and reproductive/developmental toxicity screening study for perfluorododecanoic acid (PFDoA; C12) was conducted in accordance with OECD guideline 422 to fill these toxicity data gaps. PFDoA was administered by gavage to male and female rats at 0.1, 0.5, or 2.5 mg/kg/day. The administration of PFDoA at 0.5 and 2.5 mg/kg/day for 42-47 days mainly affected the liver, in which hypertrophy, necrosis, and inflammatory cholestasis were noted. Body weight gain was markedly inhibited in the 2.5 mg/kg/day group, and a decrease in hematopoiesis in the bone marrow and atrophic changes in the spleen, thymus, and adrenal gland were also observed. Regarding reproductive/developmental toxicity, various histopathological changes, including decreased spermatid and spermatozoa counts, were observed in the male reproductive organs, while continuous diestrous was observed in the females of the 2.5 mg/kg/day group. Seven of twelve females receiving 2.5 mg/kg/day died during late pregnancy while four other females in this group did not deliver live pups. No reproductive or developmental parameters changed at 0.1 or 0.5 mg/kg/day. Based on these results, the NOAELs of PFDoA were concluded to be 0.1 mg/kg/day for repeated dose toxicity and 0.5 mg/kg/day for reproductive/developmental toxicity. PMID:24753098

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

    PubMed

    Chen, Pengcheng; Tao, Shengtao; Zheng, Pu

    2016-07-01

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

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

    PubMed Central

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

    1990-01-01

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

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2016-01-01

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

  12. A region of euchromatin coincides with an extensive tandem repeat on the mouse (Mus musculus) inactive X chromosome.

    PubMed

    Darrow, Emily M; Seberg, Andrew P; Das, Sunny; Figueroa, Debbie M; Sun, Zhuo; Moseley, Shawn C; Chadwick, Brian P

    2014-09-01

    Euchromatic features are largely absent from the human inactive X chromosome (Xi), with the exception of several large tandem repeats that can be detected as euchromatin bands at metaphase. Despite residing megabases apart, these tandem repeats make frequent inactive X-specific interactions. The mouse homologue has been reported for at least one of the tandem repeats, but whether the mouse Xi is also characterized by distinct bands of euchromatin remains unknown. We examined the mouse Xi for the presence of euchromatin bands by examining the pattern of histone H3 dimethylated at lysine 4 and detected two major signals. The first band resides in the subtelomeric region of band XF5 and may correspond to the pseudoautosomal region. The second band localizes to XE3 and coincides with an extensive complex repeat composed of a large tandem and inverted repeat segment as well as several large short interspersed nuclear element (SINE)-rich tandem repeats. Fluorescence in situ hybridization reveals that sequences with homology to the repeat region are scattered along the length of the Y chromosome. Immunofluorescence analysis of histone H3 trimethylated at lysine 9 on metaphase chromosomes indicates that the repeat region corresponds to a band of constitutive heterochromatin on the male X and female active X chromosomes, whereas the euchromatin signal appears to be female specific. These data suggest that the band of euchromatin observed at XE3 is unique to the mouse Xi, comparable to the chromatin arrangement of several large tandem repeats located on the human X chromosome. PMID:24821208

  13. Repeated-batch production of kojic acid in a cell-retention fermenter using Aspergillus oryzae M3B9.

    PubMed

    Wan, H M; Chen, C C; Giridhar, R; Chang, T S; Wu, W T

    2005-06-01

    A cell-retention fermenter was used for the pilot-scale production of kojic acid using an improved strain of Aspergillus oryzae in repeated-batch fermentations. Among the various carbon and nitrogen sources used, sucrose and yeast extract promoted pellet morphology of fungi and higher kojic acid production. Repeated-batch culture using a medium replacement ratio of 75% gave a productivity of 5.3 gL(-1)day(-1) after 11.5 days of cultivation. While batch culture in shake-flasks resulted in a productivity of 5.1 gL(-1)day(-1), a productivity of 5 gL(-1)day(-1) was obtained in a pilot-scale fermenter. By converting the batch culture into repeated batches, the non-productive downtime of cleaning, filling and sterilizing the fermenter between each batch were eliminated, thereby increasing the kojic acid productivity. PMID:15895266

  14. Branched-chain amino acid supplementation during repeated prolonged skiing exercises at altitude.

    PubMed

    Bigard, A X; Lavier, P; Ullmann, L; Legrand, H; Douce, P; Guezennec, C Y

    1996-09-01

    This study was conducted to test the hypothesis that a branched-chain amino acid (BCAA) supplementation would minimize changes in body composition and alterations in plasma amino acid profile induced by prolonged exercises at altitude. Twenty-four highly trained subjects participated in six successive sessions of ski mountaineering (6-8 hr duration, altitude 2,500-4,100 m). Twelve subjects took a dietary supplement of BCAA (BCAA group) and 12 took a dietary supplement that was 98% carbohydrate (C group). Body weight decreased in C subjects (-2.1%, p < .01), while the body weight loss recorded in the BCAA group was not statistically significant (-1.2%, NS). Changes in body composition that resulted from repeated skiing exercise at altitude were not significantly minimized by BCAA administration. Peak power output recorded during an incremental bicycle exercise decreased in C subjects but did not change significantly in BCAA subjects. Results of this study demonstrate that neither changes in body composition related to the ski mountaineering program nor muscular performance during isometric contraction was significantly affected by BCAA administration. PMID:8876349

  15. Evaluation of kojic acid production in a repeated-batch PCS biofilm reactor.

    PubMed

    Liu, Jui-Ming; Yu, Ting-Chu; Lin, Shin-Ping; Hsu, Ren-Jun; Hsu, Kai-Di; Cheng, Kuan-Chen

    2016-01-20

    In this study, kojic acid, a secondary metabolite as an industrially important compound, was produced by Aspergillus oryzae (A. oryzae), which was immobilized in plastic composite support (PCS) bioreactor. Nitrogen deficient medium was applied to increase the production of KA in PCS-immobilized bioreactor. The efficiency of immobilized culture for kojic acid (KA) production and the effect of morphology of A. oryzae on KA production were evaluated. After three cycles of cultivation, 83.47 g/L of KA was produced in PCS bioreactor in nitrogen deficient medium with productivity of 3.09 g/L/d, which is higher than free suspension culture in batch fermentation. The morphology of A. oryzae mycelium changed under nitrogen starvation. Feather-like mycelium was observed with increasing KA production. RNA expression (kojA and kojT) results indicated that the nitrogen deficient environment had strong influence on KA production on the transcriptional level. PCS immobilized fermentation system, which allowed a repeated-batch fermentation with higher production and productivity, is a potential tool in industrial production of KA. PMID:26657710

  16. The major clotting protein from guinea pig seminal vesicle contains eight repeats of a 24-amino acid domain.

    PubMed Central

    Moore, J T; Hagstrom, J; McCormick, D J; Harvey, S; Madden, B; Holicky, E; Stanford, D R; Wieben, E D

    1987-01-01

    The complete amino acid sequence of the major clotting protein from the guinea pig seminal vesicle (SVP-1) has been determined by nucleotide sequencing of cDNA clones corresponding to the 3' terminus of an mRNA that codes for a protein precursor to SVP-1. The first 40 amino acids of the derived protein sequence are identical to those determined by N-terminal sequencing of SVP-1 isolated from the lumen of the seminal vesicle. This finding confirms that SVP-1 is cleaved from the C terminus of a larger precursor protein. The portion of the nucleotide sequence that codes for SVP-1 contains eight highly homologous but imperfect repeats of a 72-nucleotide domain. This repeated structure is also evident at the amino acid level. The consensus 24-amino acid repeat unit contains two lysine and three glutamine residues. Since the clotting of SVP-1 is known to involve the formation of gamma-glutamyl-epsilon-lysine crosslinks, it is likely that the 24-amino acid repeating unit is the unit of function of SVP-1. PMID:3477802

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

    PubMed Central

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

    1998-01-01

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

  18. Telomerase Activity in the Various Regions of Mouse Brain: Non-Radioactive Telomerase Repeat Amplification Protocol (TRAP) Assay

    PubMed Central

    Grin, Yossi; Admoni, Tamar; Priel, Esther

    2014-01-01

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

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

    PubMed

    Grin, Yossi; Admoni, Tamar; Priel, Esther

    2014-01-01

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

  20. Alteration of brain levels of neurotransmitters and amino acids in male F344 rats induced by three-week repeated inhalation exposure to 1-bromopropane.

    PubMed

    Suda, Megumi; Honma, Takeshi; Miyagawa, Muneyuki; Wang, Rui-Sheng

    2008-08-01

    The present study investigated the effects of 1-bromopropane (1BP) on brain neuroactive substances of rats to determine the extent of its toxicity to the central nervous system (CNS). We measured the changes in neurotransmitters (acetylcholine, catecholamine, serotonin and amino acids) and their metabolites or precursors in eight brain regions after inhalation exposure to 1BP at 50 to 1,000 ppm for 8 h per day for 7 d per week for 3 wk. Rats were sacrificed at 2 h (Case 1), or at 19 h (Case 2) after the end of exposure. In Case 1, the level of 5-hydroxyindoleacetic acid (5HIAA) was lowered in some brain regions by 1BP exposure. The decrease of 5HIAA in the frontal cortex was statistically significant at 50 ppm 1BP exposure. In Case 2, gamma-amino butyric acid (GABA) and taurine were decreased in many brain regions of exposed rats, and a significant decrease of taurine in the midbrain occurred at 50 ppm 1BP exposure. In both cases of 2-h and 19-h intervals from the end of exposure to sacrifice, aspartate and glutamine levels were elevated in many brain regions, but the acetylcholine level did not change in any brain region. Three-week repeated exposure to 1BP produced significantly changes in amino acid contents of rat brains, particularly at 1,000 ppm. PMID:18716383

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

    PubMed

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

    2015-04-01

    Deep-sea tubeworms in the annelid family Siboglinidae have drawn considerable interest regarding their ecology and evolutionary biology. As adults, they lack a digestive tract and rely on endosymbionts for nutrition. Moreover, they are important members of chemosynthetic environments including hydrothermal vents, cold seeps, muddy sediments, and whale bones. Evolution and diversification of siboglinids has been associated with host-symbiont relationships and reducing habitats. Despite their importance, the taxonomy and phylogenetics of this clade are debated due to conflicting results. In this study, 10 complete and 2 partial mitochondrial genomes and one transcriptome were sequenced and analyzed to address siboglinid evolution. Notably, repeated nucleotide motifs were found in control regions of these mt genomes, which may explain previous challenges of sequencing siboglinid mt genomes. Phylogenetic analyses of amino acid and nucleotide datasets were conducted in order to infer evolutionary history. Both analyses generally had strong nodal support and suggest Osedax is most closely related to the Vestimentifera+Sclerolinum clade, rather than Frenulata, as recently reported. These results imply Osedax, the only siboglinid lineage with heterotrophic endosymbionts, evolved from a lineage utilizing chemoautotrophic symbionts. PMID:25721539

  2. Improvement of short tandem repeat analysis of samples highly contaminated by humic acid.

    PubMed

    Seo, Seung Bum; Jin, Hong Xuan; Lee, Hye Young; Ge, Jianye; King, Jonathan L; Lyoo, Sung Hee; Shin, Dong Hoon; Lee, Soong Deok

    2013-10-01

    We investigated several methods for obtaining successful short tandem repeat (STR) results from high-humic acid (HA)-content samples. DNA purification efficiency was tested for QIAquick(®) PCR Purification, QIAamp(®) DNA Investigator and Prepfiler™ Forensic DNA Extraction kits. HA-removal capacity of Inhibitor Remover and InhibitEX(®) Tablet was tested. Experiments on overcoming HA effects on STR amplification were conducted using an AmpliTaq Gold(®) DNA Polymerase and a TaKaRa Ex Taq™ Hot Start Version (Ex Taq HS) with BSA addition. QIAquick kit was most efficient in HA removal and Ex Taq HS showed high resistance to HA. Increasing the amounts of Taq polymerases and BSA addition were shown to be efficient in overcoming PCR inhibition, but BSA addition was superior to the former method. Inhibitor Remover and InhibitEX(®) Tablet did not positively affect the STR results. This study will help achieve better STR results with high-HA-content samples. PMID:24112347

  3. A dynamic G-quadruplex region regulates the HIV-1 long terminal repeat promoter.

    PubMed

    Perrone, Rosalba; Nadai, Matteo; Frasson, Ilaria; Poe, Jerrod A; Butovskaya, Elena; Smithgall, Thomas E; Palumbo, Manlio; Palù, Giorgio; Richter, Sara N

    2013-08-22

    G-Quadruplexes, noncanonical nucleic acid structures, act as silencers in the promoter regions of human genes; putative G-quadruplex forming sequences are also present in promoters of other mammals, yeasts, and prokaryotes. Here we show that also the HIV-1 LTR promoter exploits G-quadruplex-mediated transcriptional regulation with striking similarities to eukaryotic promoters and that treatment with a G-quadruplex ligand inhibits HIV-1 infectivity. Computational analysis on 953 HIV-1 strains substantiated a highly conserved G-rich sequence corresponding to Sp1 and NF-κB binding sites. Biophysical/biochemical analysis proved that two mutually exclusive parallel-like intramolecular G-quadruplexes, stabilized by small molecule ligands, primarily fold in this region. Mutations disrupting G-quadruplex formation enhanced HIV promoter activity in cells, whereas treatment with a G-quadruplex ligand impaired promoter activity and displayed antiviral effects. These findings disclose the possibility of inhibiting the HIV-1 LTR promoter by G-quadruplex-interacting small molecules, providing a new pathway to development of anti-HIV-1 drugs with unprecedented mechanism of action. PMID:23865750

  4. Loss of parvalbumin-immunoreactivity in mouse brain regions after repeated intermittent administration of esketamine, but not R-ketamine.

    PubMed

    Yang, Chun; Han, Mei; Zhang, Ji-Chun; Ren, Qian; Hashimoto, Kenji

    2016-05-30

    Clinical use of the rapid antidepressant drug ketamine is limited, due to psychotomimetic side effects. R-ketamine appears to be a potent, long-lasting and safer antidepressant, relative to S-ketamine (esketamine), since it is free of psychotomimetic side effects. Repeated, intermittent administration of esketamine (10mg/kg, once per week for 8-weeks), but not R-ketamine, caused loss of parvalbumin (PV)-immunoreactivity in the medial prefrontal cortex and hippocampus of mouse brains, regions associated with psychosis. This study suggests that repeated intermittent use of R-ketamine is safer than esketamine in the treatment of depression. PMID:27043274

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

    PubMed

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

    2015-01-01

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

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

    PubMed

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

    2007-12-19

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

  7. Optimization of L-(+)-lactic acid production by ring and disc plastic composite supports through repeated-batch biofilm fermentation.

    PubMed Central

    Ho, K L; Pometto, A L; Hinz, P N

    1997-01-01

    Four customized bioreactors, three with plastic composite supports (PCS) and one with suspended cells (control), were operated as repeated-batch fermentors for 66 days at pH 5 and 37 degrees C. The working volume of each customized reactor was 600 ml, and each reactor's medium was changed every 2 to 5 days for 17 batches. The performance of PCS bioreactors in long-term biofilm repeated-batch fermentation was compared with that of suspended-cell bioreactors in this research. PCS could stimulate biofilm formation, supply nutrients to attached and free suspended cells, and reduce medium channelling for lactic acid production. Compared with conventional repeated-batch fermentation, PCS bioreactors shortened the lag time by threefold (control, 11 h; PCS, 3.5 h) and sixfold (control, 9 h; PCS, 1.5 h) at yeast extract concentrations of 0.4 and 0.8% (wt/vol), respectively. They also increased the lactic acid productivity of Lactobacillus casei subsp. rhamnosus (ATCC 11443) by 40 to 70% and shortened the total fermentation time by 28 to 61% at all yeast extract concentrations. The fastest productivity of the PCS bioreactors (4.26 g/liter/h) was at a starting glucose concentration of 10% (wt/vol), whereas that of the control (2.78 g/liter/h) was at 8% (wt/vol). PCS biofilm lactic acid fermentation can drastically improve the fermentation rate with reduced complex-nutrient addition. PMID:9212403

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

    PubMed

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

    2016-07-01

    In order to efficiently produce l-lactic acid from non-food feedstocks, sweet sorghum juice (SSJ), which is rich of fermentable sugars, was directly used for l-lactic acid fermentation by Lactobacillus rhamnosus LA-04-1. A membrane integrated repeated batch fermentation (MIRB) was developed for productivity improvement. High-cell-density fermentation was achieved with a final cell density (OD620) of 42.3, and the CCR effect was overcomed. When SSJ (6.77gL(-1) glucose, 4.51gL(-1) fructose and 50.46gL(-1) sucrose) was used as carbon source in MIRB process, l-lactic acid productivity was increased significantly from 1.45gL(-1)h(-1) (batch 1) to 17.55gL(-1)h(-1) (batch 6). This process introduces an effective way to produce l-lactic acid from SSJ. PMID:27023384

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

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

    PubMed

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

    2016-02-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  13. DRY DEPOSITION MODULE FOR REGIONAL ACID DEPOSITION

    EPA Science Inventory

    Methods to compute surface dry deposition velocities for sulfur dioxide, sulfate, ozone, NO plus NO2, and nitric acid vapor over much of the North American continent have been developed for use with atmospheric numerical models of long-range transport and deposition. The resultin...

  14. 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. PMID:25899867

  15. 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. PMID:24621225

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

    PubMed

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

    2016-04-01

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

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

    PubMed Central

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

    2013-01-01

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

  18. The transcription factor-like nuclear regulator (TFNR) contains a novel 55-amino-acid motif repeated nine times and maps closely to SMN1.

    PubMed

    Kelter, A R; Herchenbach, J; Wirth, B

    2000-12-15

    The transcription factor-like nuclear regulator (TFNR) is a novel human gene that maps on 5q13, distal to the duplicated region that includes SMN1, the spinal muscular atrophy (SMA) determining gene. The location of TFNR allowed us to design an evolutionary model of the SMA region. The 9.5-kb TFNR transcript is highly expressed in cerebellum and weakly in all other tissues tested. TFNR encodes a protein of 2254 amino acids (aa) and contains nine repeats of a novel 55-aa motif, of yet unknown function. The coding region is organized in 32 exons. Alternative splicing of exon 15 results in a truncated protein of 796 aa. TFNR comprises a series of polypeptides that range from 55 to 250 kDa. Immunocytological studies showed that the TFNR protein is present exclusively in the nucleus, where it is concentrated in several nuclear structures. Amino acids 155-474 show significant homology to TFC5, a subunit of the yeast transcription factor TFIIIB, suggesting that TFNR is a putative transcription factor. Based on its proximity to SMN1 and its expression pattern, TFNR may be a candidate gene for atypical forms of SMA with cerebral atrophy and axonal neuropathy that have been shown to carry large deletions in the SMA region. PMID:11161782

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

    PubMed

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

    2012-05-01

    Well defined estimates of mutation rates are a prerequisite for the use of short tandem repeat (STR-) loci in relationship testing. We investigated 65 isolated genetic inconsistencies, which were observed within 50,796 allelic transfers at 23 STR-loci (ACTBP2 (SE33), CD4, CSF1PO, F13A1, F13B, FES, FGA, vWA, TH01, TPOX, D2S1338, D3S1358, D5S818, D7S820, D8S1132, D8S1179, D12S391, D13S317, D16S539, D17S976, D18S51, D19S433, D21S11) in Caucasoid families residing in Austria and Switzerland. Sequencing data of repeat and flanking regions and the median of all theoretically possible mutational steps showed valuable information to characterise the mutational events with regard to parental origin, change of repeat number (mutational step size) and direction of mutation (losses and gains of repeats). Apart from predominant single-step mutations including one case with a double genetic inconsistency, two double-step and two apparent four-step mutations could be identified. More losses than gains of repeats and more mutations originating from the paternal than the maternal lineage were observed (31 losses, 22 gains, 12 losses or gains and 47 paternal, 11 maternal mutations and 7 unclear of parental origin). The mutation in the paternal germline was 3.3 times higher than in the maternal germline. The results of our study show, that apart from the vast majority of single-step mutations rare multi-step mutations can be observed. Therefore, the interpretation of mutational events should not rigidly be restricted to the shortest possible mutational step, because rare but true multi-step mutations can easily be overlooked, if haplotype analysis is not possible. PMID:21873136

  20. Fatty acid profile and Unigene-derived simple sequence repeat markers in tung tree (Vernicia fordii)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Tung tree (Vernicia fordii) provides the sole source of tung oil widely used in industry. Lack of fatty acid composition and molecular markers hinders biochemical, genetic and breeding research. The objectives of this study were to determine fatty acid profiles and develop unigene-derived simple se...

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

    SciTech Connect

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

    2005-12-20

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

  2. Analysis of complex repeat sequences within the spinal muscular atrophy (SMA) candidate region in 5q13

    SciTech Connect

    Davies, K.E.; Morrison, K.E.; Daniels, R.I.

    1994-09-01

    We previously reported that the 400 kb interval flanked the polymorphic loci D5S435 and D5S557 contains blocks of a chromosome 5 specific repeat. This interval also defines the SMA candidate region by genetic analysis of recombinant families. A YAC contig of 2-3 Mb encompassing this area has been constructed and a 5.5 kb conserved fragment, isolated from a YAC end clone within the above interval, was used to obtain cDNAs from both fetal and adult brain libraries. We describe the identification of cDNAs with stretches of high DNA sequence homology to exons of {beta} glucuronidase on human chromosome 7. The cDNAs map both to the candidate region and to an area of 5p using FISH and deletion hybrid analysis. Hybridization to bacteriophage and cosmid clones from the YACs localizes the {beta} glucuronidase related sequences within the 400 kb region of the YAC contig. The cDNAs show a polymorphic pattern on hybridization to genomic BamH1 fragments in the size range of 10-250 kb. Further analysis using YAC fragmentation vectors is being used to determine how these {beta} glucuronidase related cDNAs are distributed within 5q13. Dinucleotide repeats within the region are being investigated to determine linkage disequilibrium with the disease locus.

  3. EMISSION INVENTORY APPLICATIONS TO REGIONAL ACID DEPOSITION MODELING

    EPA Science Inventory

    A comprehensive Regional Acid Deposition Model (RADM) is being developed and a simpler fast-turn-around 'engineering' model(s) (EM) is being designed by the National Center for Atmospheric Research as part of the National Acid Precipitation Assessment Program (NAPAP). This paper ...

  4. Internalin of Listeria monocytogenes with an intact leucine-rich repeat region is sufficient to promote internalization.

    PubMed Central

    Lecuit, M; Ohayon, H; Braun, L; Mengaud, J; Cossart, P

    1997-01-01

    Listeria monocytogenes can use two different surface proteins, internalin (InlA) and InlB, to invade mammalian cells. The exact role of these invasiveness factors in vivo remains to be determined. In cultured cells, InlA is necessary to promote Listeria entry into human epithelial cells, such as Caco-2 cells, whereas InlB is necessary to promote Listeria internalization in several other cell types, including hepatocytes, fibroblasts, and epithelioid cells, such as Vero, HeLa, CHO, or Hep-2 cells. We have recently reported that the InlA receptor on Caco-2 cells is the cell adhesion molecule E-cadherin and demonstrated that nonpermissive fibroblasts become permissive for internalin-mediated entry when transfected with the gene coding for LCAM, the chicken homolog of the human E-cadherin gene. In this study, we demonstrate for the first time that the internalin protein alone is sufficient to promote internalization into cells expressing its receptor. Indeed, internalin confers invasiveness to both Enterococcus faecalis and internalin-coated latex beads. As shown by transmission electron microscopy, these beads were phagocytosed via a "zipper" mechanism similar to that observed during the internalin-E-cadherin-mediated entry of Listeria. Moreover, a functional analysis of internalin demonstrates that its amino-terminal region, encompassing the leucine-rich repeat (LRR) region and the inter-repeat (IR) region, is necessary and sufficient to promote bacterial entry into cells expressing its receptor. Several lines of evidence suggest that the LRR region would interact directly with E-cadherin, whereas the IR region would be required for a proper folding of the LRR region. PMID:9393831

  5. Geographic variation within a tandemly repeated mitochondrial DNA D-loop region of a North American freshwater fish, Pylodictis olivaris.

    PubMed

    Padhi, Abinash

    2014-03-15

    The present study reports the distribution of a 35-bp mitochondrial DNA (mtDNA) D-loop tandemly repeated sequence in the populations of a North American freshwater catfish, Pylodictis olivaris, and the important role of a past geological event in the phylogeographic pattern of this species. A total of 330 individuals of flathead catfish, representing 34 drainages throughout the species' native range in the United States, were collected. While more than 70% of individuals sampled from the Southeastern Gulf Coast drainages were characterized by the presence of a 35-bp mtDNA D-loop tandem repeat proximal to the 5' end, more than 95% of samples from the Mississippi River and its tributaries, as well as from the drainages of the Southwest Gulf Coast region, lack this tandem repeat. Concomitantly, phylogenetic analyses revealed the existence of two distinct matrilineal lineages (lineage I and II) of P. olivaris, which were estimated to have diverged from a common ancestor sometime between 0.70 and 2.05myr ago. While one lineage is comprised of samples from the Mississippi River and its tributaries and rivers draining to the Southwest Gulf Coast, the other lineage is comprised of samples from the Southeastern Gulf Coast drainages. Each lineage also has two sub-lineages, which also showed geographic specificity. PMID:24440244

  6. different Roles for the axin interactions with the SAMP versus the second twenty amino acid repeat of adenomatous polyposis coli.

    PubMed

    Schneikert, Jean; Ruppert, Jan Gustav; Behrens, Jürgen; Wenzel, Eva Maria

    2014-01-01

    Wnt signalling is prevented by the proteosomal degradation of β-catenin, which occurs in a destruction complex containing adenomatous polyposis coli (APC), APC-like (APCL), Axin and Axin2. Truncating mutations of the APC gene result in the constitutive stabilisation of β-catenin and the initiation of colon cancer, although tumour cells tolerate the expression of wild-type APCL. Using the colocalisation of overexpressed Axin, APC and APCL constructs as a readout of interaction, we found that Axin interacted with the second twenty amino acid repeat (20R2) of APC and APCL. This interaction involved a domain adjacent to the C-terminal DIX domain of Axin. We identified serine residues within the 20R2 of APCL that were involved in Axin colocalisation, the phosphorylation of truncated APCL and the down-regulation of β-catenin. Our results indicated that Axin, but not Axin2, displaced APC, but not APCL, from the cytoskeleton and stimulated its incorporation into bright cytoplasmic dots that others have recognised as β-catenin destruction complexes. The SAMP repeats in APC interact with the N-terminal RGS domain of Axin. Our data showed that a short domain containing the first SAMP repeat in truncated APC was required to stimulate Axin oligomerisation. This was independent of Axin colocalisation with 20R2. Our data also suggested that the RGS domain exerted an internal inhibitory constraint on Axin oligomerisation. Considering our data and those from others, we discuss a working model whereby β-catenin phosphorylation involves Axin and the 20R2 of APC or APCL and further processing of phospho-β-catenin occurs upon the oligomerisation of Axin that is induced by binding the SAMP repeats in APC. PMID:24722208

  7. The regional costs and benefits of acid rain control

    SciTech Connect

    Berkman, M.P.

    1991-01-01

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

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

    PubMed Central

    Bolton, Amanda Nicholle; Saatman, Kathryn Eileen

    2014-01-01

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

  9. Short tandem repeats haplotyping of the HLA region in preimplantation HLA matching.

    PubMed

    Fiorentino, Francesco; Kahraman, Semra; Karadayi, Hüseyin; Biricik, Anil; Sertyel, Semra; Karlikaya, Güvenc; Saglam, Yaman; Podini, Daniele; Nuccitelli, Andrea; Baldi, Marina

    2005-08-01

    Recently, preimplantation genetic diagnosis (PGD) has been considered for several indications beyond its original purpose, not only to test embryos for genetic disease but also to select embryos for a nondisease trait, such as specific human leukocyte antigen (HLA) genotypes, related to immune compatibility with an existing affected child in need of a haematopoetic stem cell (HSC) transplant. We have optimized an indirect single-cell HLA typing protocol based on a multiplex fluorescent polymerase chain reaction (PCR) of short tandem repeat (STR) markers scattered throughout the HLA complex. The assay was clinically applied in 60 cycles from 45 couples. A conclusive HLA-matching diagnosis was achieved in 483/530 (91.1%) of the embryos tested. In total, 74 (15.3%) embryos revealed an HLA match with the affected siblings, 55 (11.4%) of which resulted unaffected and 46 (9.5%) have been transferred to the patients. Nine pregnancies were achieved, five healthy HLA-matched children have already been delivered and cord blood HSCs, were transplanted to three affected siblings, resulting in a successful haematopoietic reconstruction. PMID:15886713

  10. Computational Finishing of Large Sequence Contigs Reveals Interspersed Nested Repeats and Gene Islands in the rf1-associated Region of Maize

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The architecture of grass genomes varies on multiple levels. Large long terminal repeat (LTR) retrotransposon clusters occupy significant portions of the intergenic regions, and islands of protein-encoding genes are interspersed among the repeat clusters. Hence, advanced assembly techniques are requ...

  11. Repeatability and variation of region-of-interest methods using quantitative diffusion tensor MR imaging of the brain

    PubMed Central

    2012-01-01

    Background Diffusion tensor imaging (DTI) is increasingly used in various diseases as a clinical tool for assessing the integrity of the brain’s white matter. Reduced fractional anisotropy (FA) and an increased apparent diffusion coefficient (ADC) are nonspecific findings in most pathological processes affecting the brain’s parenchyma. At present, there is no gold standard for validating diffusion measures, which are dependent on the scanning protocols, methods of the softwares and observers. Therefore, the normal variation and repeatability effects on commonly-derived measures should be carefully examined. Methods Thirty healthy volunteers (mean age 37.8 years, SD 11.4) underwent DTI of the brain with 3T MRI. Region-of-interest (ROI) -based measurements were calculated at eleven anatomical locations in the pyramidal tracts, corpus callosum and frontobasal area. Two ROI-based methods, the circular method (CM) and the freehand method (FM), were compared. Both methods were also compared by performing measurements on a DTI phantom. The intra- and inter-observer variability (coefficient of variation, or CV%) and repeatability (intra-class correlation coefficient, or ICC) were assessed for FA and ADC values obtained using both ROI methods. Results The mean FA values for all of the regions were 0.663 with the CM and 0.621 with the FM. For both methods, the FA was highest in the splenium of the corpus callosum. The mean ADC value was 0.727 ×10-3 mm2/s with the CM and 0.747 ×10-3 mm2/s with the FM, and both methods found the ADC to be lowest in the corona radiata. The CV percentages of the derived measures were < 13% with the CM and < 10% with the FM. In most of the regions, the ICCs were excellent or moderate for both methods. With the CM, the highest ICC for FA was in the posterior limb of the internal capsule (0.90), and with the FM, it was in the corona radiata (0.86). For ADC, the highest ICC was found in the genu of the corpus callosum (0.93) with the CM and in

  12. MapRepeat: an approach for effective assembly of repetitive regions in prokaryotic genomes

    PubMed Central

    Mariano, Diego CB; Pereira, Felipe L; Ghosh, Preetam; Barh, Debmalya; Figueiredo, Henrique CP; Silva, Artur; Ramos, Rommel TJ; Azevedo, Vasco AC

    2015-01-01

    The newest technologies for DNA sequencing have led to the determination of the primary structure of the genomes of organisms, mainly prokaryotes, with high efficiency and at lower costs. However, the presence of regions with repetitive sequences, in addition to the short reads produced by the Next-Generation Sequencing (NGS) platforms, created a lot of difficulty in reconstructing the original genome in silico. Thus, even today, genome assembly continues to be one of the major challenges in bioinformatics specifically when repetitive sequences are considered. In this paper, we present an approach to assemble repetitive regions in prokaryotic genomes. Our methodology enables (i) the identification of these regions through visual tools, (ii) the characterization of sequences on the extremities of gaps and (iii) the extraction of consensus sequences based on mapping of raw data to a reference genome. We also present a case study on the assembly of regions that encode ribosomal RNAs (rRNA) in the genome of Corynebacterium ulcerans FRC11, in order to show the efficiency of the strategies presented here. The proposed methods and tools will help in finishing genome assemblies, besides reducing the running time and associated costs. Availability All scripts are available at http://github.com/dcbmariano/maprepeat PMID:26229287

  13. Enhancing gamma-aminobutyric acid content in germinated brown rice by repeated treatment of soaking and incubation.

    PubMed

    Thitinunsomboon, Somboon; Keeratipibul, Suwimon; Boonsiriwit, Athip

    2013-02-01

    Gamma-aminobutyric acid (GABA), commonly produced by germination of brown rice grain, is a free amino acid which could help relieving or preventing non-communicable diseases in human. Several research works have been conducted on GABA production from germinated brown rice. However, the yielded GABA (10.1-69.2 mg/100 g germinated brown rice) was comparatively low; thus the amount was insufficient to be used as active ingredients in functional foods. The objective of this study was to explore alternative methods in order to gain higher yield of GABA. A new process of repeated soaking (in tap water at 35 °C, 3 h) and incubation (at 37 °C, 21 h) during germination was developed. The amount of GABA produced was highest at 116.88 ± 9.24 mg/100 g germinated brown rice (dry basis). However, an unpleasant odour was generated by some microorganisms during long germination. Lactic acid was applied at soaking step to overcome this problem; whereby 0.5% lactic acid solution (vol./vol.) could effectively control the microorganisms without impairing GABA producing ability and sensory qualities. PMID:23345323

  14. The heptad repeat region is a major selection target in MERS-CoV and related coronaviruses

    PubMed Central

    Forni, Diego; Filippi, Giulia; Cagliani, Rachele; De Gioia, Luca; Pozzoli, Uberto; Al-Daghri, Nasser; Clerici, Mario; Sironi, Manuela

    2015-01-01

    Middle East respiratory syndrome coronavirus (MERS-CoV) originated in bats and spread to humans via zoonotic transmission from camels. We analyzed the evolution of the spike (S) gene in betacoronaviruses (betaCoVs) isolated from different mammals, in bat coronavirus populations, as well as in MERS-CoV strains from the current outbreak. Results indicated several positively selected sites located in the region comprising the two heptad repeats (HR1 and HR2) and their linker. Two sites (R652 and V1060) were positively selected in the betaCoVs phylogeny and correspond to mutations associated with expanded host range in other coronaviruses. During the most recent evolution of MERS-CoV, adaptive mutations in the HR1 (Q/R/H1020) arose in camels or in a previous host and spread to humans. We determined that different residues at position 1020 establish distinct inter- and intra-helical interactions and affect the stability of the six-helix bundle formed by the HRs. A similar effect on stability was observed for a nearby mutation (T1015N) that increases MERS-CoV infection efficiency in vitro. Data herein indicate that the heptad repeat region was a major target of adaptive evolution in MERS-CoV-related viruses; these results are relevant for the design of fusion inhibitor peptides with antiviral function. PMID:26404138

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

    SciTech Connect

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

    2006-01-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  19. Repeated Administration of Hyaluronic Acid Coated Liposomes with Improved Pharmacokinetics and Reduced Immune Response.

    PubMed

    Zhang, Quan; Deng, Caifeng; Fu, Yao; Sun, Xun; Gong, Tao; Zhang, Zhirong

    2016-06-01

    PEGylated liposomes (PEG-Lip) have been widely used as a drug carrier for their good stealth property in blood circulation. However, the second injection of PEG-Lip was reported to result in the accelerated blood clearance (ABC) phenomenon and trigger hypersensitivity reactions in sensitive individuals for its complement activation effect. To avoid adverse immune responses, HA was selected to modify liposomes to afford HA modified liposomes (HA-Lip). Repeated administrations of PEG-Lip and HA-Lip were performed in rats. Our results showed that PEG-Lip induced the ABC phenomenon accompanied by a greatly increased accumulation of PEG-Lip in the liver. In contrast, HA-Lip showed good stealth property without inducing either the ABC phenomenon or an increase in liver uptake. Moreover, HA-Lip did not trigger complement activation in human serum in vitro and in rat blood in vivo. Consequently, HA modification represents a viable strategy to prolong the blood circulation time of liposomes without inducing the ABC phenomenon and adverse immune responses. PMID:27112287

  20. Poly(2-thiophen-3-yl-malonic acid), a polythiophene with two carboxylic acids per repeating unit.

    PubMed

    Bertran, Oscar; Armelin, Elaine; Estrany, Francesc; Gomes, Alex; Torras, Juan; Alemán, Carlos

    2010-05-20

    A new substituted polythiophene derivative bearing malonic acid, poly(2-thiophen-3-yl-malonic acid), has been prepared and characterized using a strategy that combines both experimental and theoretical methodologies. The chemical structure of this material has been investigated using FTIR and (1)H NMR, and its molecular conformation has been determined using quantum mechanical calculations. Interestingly, the arrangement of the inter-ring dihedral angles was found to depend on the ionization degree of the material, that is, on the pH, which has been found completely soluble in aqueous base solution. Thus, the preferred anti-gauche conformation changes to syn-gauche when the negatively charged carboxylate groups transforms into neutral carboxylic acid. UV-vis experiments and quantum mechanical calculations on model systems with a head-to-tail regiochemistry showed that the lowest pi-pi* transition energy is 2.25 and 2.39 eV for the negatively charged and the neutral polymer, respectively. These values are slightly larger than those previously reported for other polythiophenes with bulky polar side groups. The polymer presents a good thermal stability with a decomposition temperature above 215 degrees C and an electrical conductivity of 10(-5) S/cm, which is characteristic of semiconductor materials. Scanning electron microscopy micrographs showed that, after doping, the surface of this material displays regular distribution pores with irregular sizes. This surface suggests that poly(2-thiophen-3-yl-malonic acid) is a candidate for potential applications such as selective membranes for electrodialysis, wastewater treatment, or ion-selective membranes for biomedical uses. PMID:20411968

  1. Regional Changes in Cerebral Oxygenation During Repeated Passive Movement Measured by Functional Near-infrared Spectroscopy

    PubMed Central

    Sugawara, Kazuhiro; Onishi, Hideaki; Tsubaki, Atsuhiro; Takai, Haruna; Tokunaga, Yuta; Tamaki, Hiroyuki

    2015-01-01

    The aim of this study is to investigate the influence of passive movement repetition frequency at 1.5-Hz and 1-Hz on changes in cerebral oxygenation and assess the temporal properties of these changes using functional near-infrared spectroscopy (fNIRS). No significant differences in systemic hemodynamics were observed between resting and passive movement phases for either 1.5-Hz or 1-Hz trial. Changes in cortical oxygenation as measured by fNIRS in bilateral supplementary motor cortex (SMC), left primary motor cortex (M1), left primary somatosensory cortex (S1), and left posterior association area (PAA) during passive movement of the right index finger revealed greater cortical activity at only 1.5-Hz movement frequency. However, there were no significant differences in the time for peak oxyhemoglobin (oxyHb) among regions (bilateral SMC, 206.4 ± 14.4 s; left M1, 199.1 ± 14.8 s; left S1, 207.3 ± 9.4 s; left PAA, 219.1 ± 10.2 s). Therefore, our results that passive movement above a specific frequency may be required to elicit a changed in cerebral oxygenation, and the times of peak ΔoxyHb did not differ significantly among measured regions. PMID:26635590

  2. TMAO promotes fibrillization and microtubule assembly activity in the C-terminal repeat region of tau.

    PubMed

    Scaramozzino, Francesca; Peterson, Dylan W; Farmer, Patrick; Gerig, J T; Graves, Donald J; Lew, John

    2006-03-21

    Alzheimer's disease most closely correlates with the appearance of the neurofibrillary tangles (NFTs), intracellular fibrous aggregates of the microtubule-associated protein, tau. Under native conditions, tau is an unstructured protein, and its physical characterization has revealed no clues about the three-dimensional structural determinants essential for aggregation or microtubule binding. We have found that the natural osmolyte trimethylamine N-oxide (TMAO) induces secondary structure in a C-terminal fragment of tau (tau(187)) and greatly promotes both self-aggregation and microtubule (MT) assembly activity. These processes could be distinguished, however, by a single-amino acid substitution (Tyr(310) --> Ala), which severely inhibited aggregation but had no effect on MT assembly activity. The inability of this mutant to aggregate could be completely reversed by TMAO. We propose a model in which TMAO induces partial order in tau(187), resulting in conformers that may correspond to on-pathway intermediates of either aggregation or tau-dependent MT assembly or both. These studies set the stage for future high-resolution structural characterization of these intermediates and the basis by which Tyr(310) may direct pathologic versus normal tau function. PMID:16533051

  3. Amino acid sequence of the serine-repeat antigen (SERA) of Plasmodium falciparum determined from cloned cDNA.

    PubMed

    Bzik, D J; Li, W B; Horii, T; Inselburg, J

    1988-09-01

    We report the isolation of cDNA clones for a Plasmodium falciparum gene that encodes the complete amino acid sequence of a previously identified exported blood stage antigen. The Mr of this antigen protein had been determined by sodium dodecylsulphate-polyacrylamide gel electrophoresis analysis, by different workers, to be 113,000, 126,000, and 140,000. We show, by cDNA nucleotide sequence analysis, that this antigen gene encodes a 989 amino acid protein (111 kDa) that contains a potential signal peptide, but not a membrane anchor domain. In the FCR3 strain the serine content of the protein was 11%, of which 57% of the serine residues were localized within a 201 amino acid sequence that included 35 consecutive serine residues. The protein also contained three possible N-linked glycosylation sites and numerous possible O-linked glycosylation sites. The mRNA was abundant during late trophozoite-schizont parasite stages. We propose to identity this antigen, which had been called p126, by the acronym SERA, serine-repeat antigen, based on its complete structure. The usefulness of the cloned cDNA as a source of a possible malaria vaccine is considered in view of the previously demonstrated ability of the antigen to induce parasite-inhibitory antibodies and a protective immune response in Saimiri monkeys. PMID:2847041

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

    PubMed Central

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

    2011-01-01

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

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

    SciTech Connect

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

    1994-09-01

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

  6. Protection against syphilis correlates with specificity of antibodies to the variable regions of Treponema pallidum repeat protein K.

    PubMed

    Morgan, Cecilia A; Lukehart, Sheila A; Van Voorhis, Wesley C

    2003-10-01

    Syphilis has been recognized as a disease since the late 1400s, yet there is no practical vaccine available. One impediment to the development of a vaccine is the lack of understanding of multiple reinfections in humans despite the development of robust immune responses during the first episode. It has been shown that the Treponema pallidum repeat protein K (TprK) differs in seven discrete variable (V) regions in isolates and that the antibody response during infection is directed to these V regions. Immunization with TprK confers significant protection against infection with the homologous strain. We hypothesize that the antigenic diversity of TprK is involved in immune evasion, which contributes to the lack of heterologous protection. Here, using the rabbit model, we show a correlation between limited heterologous protection and tprK diversity in the challenge inoculum. We demonstrate that antibody responses to the V regions of one TprK molecule show limited cross-reactivity with heterologous TprK V regions. PMID:14500480

  7. Repeated Batch Fermentation Biotechnology for the Biosynthesis of Lipid and Gamma-Linolenic Acid by Cunninghamella bainieri 2A1

    PubMed Central

    Ganjali Dashti, Marjan; Abdeshahian, Peyman; Wan Yusoff, Wan Mohtar; Kalil, Mohd Sahaid; Abdul Hamid, Aidil

    2014-01-01

    The biosynthesis of biomedical products including lipid and gamma-linolenic acid (GLA) by Cunninghamella bainieri 2A1 was studied in repeated batch fermentation. Three key process variables, namely, glucose concentration, ammonium tartrate concentration, and harvesting time, were optimized using response surface methodology. Repeated batch fermentation was carried out by the cultivation of Cunninghamella bainieri 2A1 in nitrogen-limited medium with various nitrogen concentration (1–4 g/L) and glucose concentration (20–40 g/L) at three time intervals (12 h, 24 h, and 48 h). Experimental results showed that the highest lipid concentration of 6.2 g/L and the highest GLA concentration of 0.4 g/L were obtained in optimum conditions, where 20.2 g/L glucose, 2.12 g/L ammonium tartrate, and 48 h harvesting time were utilized. Statistical results showed that the interaction between glucose and ammonium tartrate concentration had highly significant effects on lipid and GLA biosynthesis (P < 0.01). Moreover, harvesting time had a significant interaction effect with glucose and ammonium tartrate concentration on lipid production (P < 0.05). PMID:25147817

  8. Effect of intraperitoneal administered ginseng total saponins on hyperalgesia induced by repeated intramuscular injection of acidic saline in rats.

    PubMed

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

    2014-06-01

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

  9. Identification of an Alu-repeat-mediated deletion of OPTN upstream region in a patient with a complex ocular phenotype.

    PubMed

    Schilter, Kala F; Reis, Linda M; Sorokina, Elena A; Semina, Elena V

    2015-11-01

    Genetic causes of ocular conditions remain largely unknown. To reveal the molecular basis for a congenital ocular phenotype associated with glaucoma we performed whole-exome sequencing (WES) and whole-genome copy number analyses of patient DNA. WES did not identify a causative variant. Copy number variation analysis identified a deletion of 10p13 in the patient and his unaffected father; the deletion breakpoint contained a single 37-bp sequence that is normally present in two distinct Alu repeats separated by ~181 kb. The deletion removed part of the upstream region of optineurin (OPTN) as well as the upstream sequence and two coding exons of coiled-coil domain containing 3 (CCDC3); analysis of the patient's second allele showed normal OPTN and CCDC3 sequences. Studies of zebrafish orthologs identified expression in the developing eye for both genes. OPTN is a known factor in dominant adult-onset glaucoma and Amyotrophic Lateral Sclerosis (ALS). The deletion eliminates 98 kb of the OPTN upstream sequence leaving only ~1 kb of the proximal promoter region. Comparison of transcriptional activation capability of the 3 kb normal and the rearranged del(10)(p13) OPTN promoter sequences demonstrated a statistically significant decrease for the deleted allele; sequence analysis of the entire deleted region identified multiple conserved elements with possible cis-regulatory activity. Additional screening of CCDC3 indicated that heterozygous loss-of-function alleles are unlikely to cause congenital ocular disease. In summary, we report the first regulatory region deletion involving OPTN, caused by Alu-mediated nonallelic homologous recombination and possibly contributing to the patient's ocular phenotype. In addition, our data indicate that Alu-mediated rearrangements of the OPTN upstream region may represent a new source of affected alleles in human conditions. Evaluation of the upstream OPTN sequences in additional ocular and ALS patients may help to determine the role

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

    SciTech Connect

    Wang Xiaojia Li Chuangen; Chi Xiaojing; Wang Ming

    2011-06-20

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

  11. Functional analysis of a highly conserved abundant larval transcript-2 (alt-2) intron 2 repeat region of lymphatic filarial parasites.

    PubMed

    Sakthidevi, Moorthy; Hoti, Sugeerappa Laxmanappa; Kaliraj, Perumal

    2014-06-01

    The filarial-specific protein abundant larval transcript-2 (ALT-2) is expressed exclusively in the infective larval stage (L3) and is a crucial protein for establishing immunopathogenesis in human hosts. The alt-2 gene has a conserved minisatellite repeat (29 or 27bp) in intron 2 (IR2) whose significance within lymphatic filarial species is unknown. Here, we report the role of IR2 in the regulation of alt-2 gene expression using an in vitro model. Using electrophoretic mobility shift assays, we identified the presence of a putative nuclear protein binding region within IR2. Subsequent transient expression experiments in eukaryotic cell lines demonstrated that the IR2 downregulated the expression of a downstream luciferase reporter gene, which was further validated with RT-PCR. We therefore identify IR2 as a suppressor element that regulates L3 stage-specific expression of alt-2. PMID:24681262

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

    SciTech Connect

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

    2007-03-15

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

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

    PubMed

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

    1992-06-01

    DNA sequence analyses of several human immunodeficiency virus (HIV) isolates revealed extensive genetic diversity in the env gene and, to a lesser extent, in other regions of the viral genome, including the long terminal repeat (LTR) sequences. Since the LTRs contain elements responsible for the control of transcription, the difference in the LTR region may play a crucial role in the overall replication rate of HIV. To evaluate the role of the LTR, we have constructed a number of infectious hybrid HIV molecular clones containing LTRs from different proviral DNAs linked to the body of the viral genome, and analyzed them in a transient expression system. Both parental and hybrid proviral DNAs were transfected into human rhabdomyosarcoma cells for monitoring virus production. Proviral DNA designate pZ6 (HIVZr6) showed a high level of virus in the medium of the transfected culture in comparison to the pHXB2 (HIVHTLV-III) and pARV (HIVSF-2) DNAs. Hybrid proviral DNAs containing viral genes from pZ6, linked to LTR U3 sequences of pHXB2 and pARV at the 5' end, showed virus production similar to the levels observed with pZ6. These results indicate that the extent of virus production does not correlate with the LTR U3 sequences, and may involve other regions of the viral genome. PMID:1351391

  14. Comprehensive Treatment of Periorbital Region with Hyaluronic Acid

    PubMed Central

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

    2015-01-01

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

  15. Comprehensive Treatment of Periorbital Region with Hyaluronic Acid.

    PubMed

    Bravo, Bruna Souza Felix; Rocha, Camila Roos Mariano Da; Bastos, Julien Toni De; Silva, Priscila Mara Chaves E

    2015-06-01

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

  16. Antibodies to the leucine-rich repeat region of internalin block entry of Listeria monocytogenes into cells expressing E-cadherin.

    PubMed

    Mengaud, J; Lecuit, M; Lebrun, M; Nato, F; Mazie, J C; Cossart, P

    1996-12-01

    Internalin, a surface protein essential for entry of Listeria monocytogenes EGD into epithelial cells, was used as an antigen to raise nine monoclonal antibodies. These monoclonal antibodies recognized seven distinct epitopes which were located in three different regions of the protein. Three of them inhibited internalin-mediated entry and recognized the amino-terminal leucine-rich repeat region of the protein, suggesting that this region is essential for entry. PMID:8945603

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2014-04-22

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2016-01-01

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

  2. Merozoite Surface Antigen 2 Proteins of Babesia bovis Vaccine Breakthrough Isolates Contain a Unique Hypervariable Region Composed of Degenerate Repeats

    PubMed Central

    Berens, Shawn J.; Brayton, Kelly A.; Molloy, John B.; Bock, Russell E.; Lew, Ala E.; McElwain, Terry F.

    2005-01-01

    The merozoite surface antigen 2 (MSA-2) proteins of Babesia bovis are members of the variable merozoite surface antigen (VMSA) family that have been implicated in erythrocyte invasion and are important targets for antibody-mediated blocking of invasion. Extensive sequence variation in another VMSA member, MSA-1, has been shown in all vaccine breakthrough isolates. To test the hypothesis that the msa-2 genes of vaccine breakthrough isolates would also encode a diverse set of proteins, the complete msa-2 locus was characterized from 12 Australian B. bovis strains and isolates, including two vaccine strains and eight vaccine breakthrough isolates, and compared to the loci in previously and newly characterized American strains. In contrast to American strains, the msa-2 loci of all Australian strains and isolates examined contain, in addition to msa-2c, only a solitary gene (designated msa-2a/b) closely related to American strain msa-2a and msa-2b. Nevertheless, the proteins encoded by these genes are quite diverse both between and within geographic regions and harbor evidence of genetic exchange among other VMSA family members, including msa-1. Moreover, all but one of the Australian breakthrough isolate MSA-2a/b proteins is markedly different from the vaccine strain from which immune escape occurred, consistent with their role in strain-specific protective immunity. The densest distribution of polymorphisms occurs in a hypervariable region (HVR) within the carboxy third of the molecule that is highly proline rich. Variation in length and content of the HVR is primarily attributable to differences in the order and number of degenerate nucleotide repeats encoding three motifs of unknown function. PMID:16239512

  3. Immune Responses Induced by Gene Gun or Intramuscular Injection of DNA Vaccines That Express Immunogenic Regions of the Serine Repeat Antigen from Plasmodium falciparum

    PubMed Central

    Belperron, Alexia A.; Feltquate, David; Fox, Barbara A.; Horii, Toshihiro; Bzik, David J.

    1999-01-01

    The liver- and blood-stage-expressed serine repeat antigen (SERA) of Plasmodium falciparum is a candidate protein for a human malaria vaccine. We compared the immune responses induced in mice immunized with SERA-expressing plasmid DNA vaccines delivered by intramuscular (i.m.) injection or delivered intradermally by Gene Gun immunization. Mice were immunized with a pcdna3 plasmid encoding the entire 47-kDa domain of SERA (amino acids 17 to 382) or the N-terminal domain (amino acids 17 to 110) of SERA. Minimal antibody responses were detected following DNA vaccination with the N-terminal domain of SERA, suggesting that the N-terminal domain alone is not highly immunogenic by this route of vaccine delivery. Immunization of mice by Gene Gun delivery of the 47-kDa domain of SERA elicited a significantly higher serum antibody titer to the antigen than immunization of mice by i.m. injection with the same plasmid did. The predominant isotype subclass of the antibodies elicited to the SERA protein following i.m. and Gene Gun immunizations with SERA plasmid DNA was immunoglobulin G1. Coimmunization of mice with SERA plasmid DNA and a plasmid expressing the hepatitis B surface antigen (pCMV-s) by the i.m. route resulted in higher anti-SERA titers than those generated in mice immunized with the SERA DNA plasmid alone. Vaccination with DNA may provide a viable alternative or may be used in conjunction with protein-based subunit vaccines to maximize the efficacy of a human malaria vaccine that includes immunogenic regions of the SERA protein. PMID:10496891

  4. Immune responses induced by gene gun or intramuscular injection of DNA vaccines that express immunogenic regions of the serine repeat antigen from Plasmodium falciparum.

    PubMed

    Belperron, A A; Feltquate, D; Fox, B A; Horii, T; Bzik, D J

    1999-10-01

    The liver- and blood-stage-expressed serine repeat antigen (SERA) of Plasmodium falciparum is a candidate protein for a human malaria vaccine. We compared the immune responses induced in mice immunized with SERA-expressing plasmid DNA vaccines delivered by intramuscular (i.m.) injection or delivered intradermally by Gene Gun immunization. Mice were immunized with a pcdna3 plasmid encoding the entire 47-kDa domain of SERA (amino acids 17 to 382) or the N-terminal domain (amino acids 17 to 110) of SERA. Minimal antibody responses were detected following DNA vaccination with the N-terminal domain of SERA, suggesting that the N-terminal domain alone is not highly immunogenic by this route of vaccine delivery. Immunization of mice by Gene Gun delivery of the 47-kDa domain of SERA elicited a significantly higher serum antibody titer to the antigen than immunization of mice by i.m. injection with the same plasmid did. The predominant isotype subclass of the antibodies elicited to the SERA protein following i.m. and Gene Gun immunizations with SERA plasmid DNA was immunoglobulin G1. Coimmunization of mice with SERA plasmid DNA and a plasmid expressing the hepatitis B surface antigen (pCMV-s) by the i.m. route resulted in higher anti-SERA titers than those generated in mice immunized with the SERA DNA plasmid alone. Vaccination with DNA may provide a viable alternative or may be used in conjunction with protein-based subunit vaccines to maximize the efficacy of a human malaria vaccine that includes immunogenic regions of the SERA protein. PMID:10496891

  5. Amino Acids in Nine Ligand-Prefer Ramachandran Regions

    PubMed Central

    Cao, Chen; Wang, Lincong; Chen, Xiaoyang; Zou, Shuxue; Wang, Guishen; Xu, Shutan

    2015-01-01

    Several secondary structures, such as π-helix and left-handed helix, have been frequently identified at protein ligand-binding sites. A secondary structure is considered to be constrained to a specific region of dihedral angles. However, a comprehensive analysis of the correlation between main chain dihedral angles and ligand-binding sites has not been performed. We undertook an extensive analysis of the relationship between dihedral angles in proteins and their distance to ligand-binding sites, frequency of occurrence, molecular potential energy, amino acid composition, van der Waals contacts, and hydrogen bonds with ligands. The results showed that the values of dihedral angles have a strong preference for ligand-binding sites at certain regions in the Ramachandran plot. We discovered that amino acids preceding the ligand-prefer ϕ/ψ box residues are exposed more to solvents, whereas amino acids following ligand-prefer ϕ/ψ box residues form more hydrogen bonds and van der Waals contacts with ligands. Our method exhibited a similar performance compared with the program Ligsite-csc for both ligand-bound structures and ligand-free structures when just one ligand-binding site was predicted. These results should be useful for the prediction of protein ligand-binding sites and for analysing the relationship between structure and function. PMID:26491686

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

    PubMed Central

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

    2011-01-01

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

  7. Triplet repeat polymorphism in the transmembrane region of the MICA gene: A strong association of six GCT repetitions with Behçet disease

    PubMed Central

    Mizuki, Nobuhisa; Ota, Masao; Kimura, Minoru; Ohno, Shigeaki; Ando, Hitoshi; Katsuyama, Yoshihiko; Yamazaki, Masaaki; Watanabe, Koji; Goto, Kaori; Nakamura, Satoshi; Bahram, Seiamak; Inoko, Hidetoshi

    1997-01-01

    A member of a novel family of the human major histocompatibility complex (MHC) class I genes termed MIC (MHC class I chain-related genes), MICA, has been recently identified near the HLA-B gene on the short arm of human chromosome 6. The predicted amino acid sequence of the MICA chain suggests that it folds similarly to typical class I chains and may have the capacity to bind peptides or other short ligands. Therefore, MICA is predicted to have a specialized function in antigen presentation or T cell recognition. During nucleotide sequence analyses of the MICA genomic clone, we found a triplet repeat microsatellite polymorphism of (GCT/AGC)n in the transmembrane (TM) region of the MICA gene. In 68 HLA homozygous B cell lines, 5 distinct alleles of this microsatellite sequence were detected. One of them contained an additional one base insertion that created a frameshift mutation resulting in a premature termination codon in the TM region. This particular allele may encode a soluble, secreted form of the MICA molecule. In addition, we have investigated this microsatellite polymorphism in 77 Japanese patients with Behçet disease, which is known to be associated with HLA-B51. The microsatellite allele consisting of 6 repetitions of GCT/AGC was present at significantly higher frequency in the patient group (Pc = 0.00055) than in a control population. Furthermore, the (GCT/AGC)6 allele was present in all B51 positive patients and in an additional 13 B51 negative patients. These results suggest the possibility of a primary association of Behçet disease with MICA rather than HLA-B. PMID:9037047

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

    PubMed Central

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

    2014-01-01

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

  9. 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.

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

    PubMed

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

    2016-06-01

    Enterococcus faecalis RKY1 was used to produce l-lactic acid from hydrol, soybean curd residues (SCR), and malt. Hydrol was efficiently metabolized to l-lactic acid with optical purity of >97.5%, though hydrol contained mixed sugars such as glucose, maltose, maltotriose, and maltodextrin. Combined utilization of hydrol, SCR, and malt was enough to sustain lactic acid fermentation by E. faecalis RKY1. In order to reduce the amount of nitrogen sources and product inhibition, cell-recycle repeated-batch fermentation was employed, where a high cell mass (26.3g/L) was obtained. Lactic acid productivity was improved by removal of lactic acid from fermentation broth by membrane filtration and by linearly increased cell density. When the total of 10 repeated-batch fermentations were carried out using 100g/L hydrol, 150g/L SCR hydrolyzate, and 20g/L malt hydrolyzate as the main nutrients, lactic acid productivity was increased significantly from 3.20g/L/h to 6.37g/L/h. PMID:26970921

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

    PubMed

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

    2015-08-01

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

  12. Mutations in Conserved Regions of the Predicted RAG2 Kelch Repeats Block Initiation of V(D)J Recombination and Result in Primary Immunodeficiencies†

    PubMed Central

    Gomez, Carlos A.; Ptaszek, Leon M.; Villa, Anna; Bozzi, Fabio; Sobacchi, Cristina; Brooks, Edward G.; Notarangelo, Luigi D.; Spanopoulou, Eugenia; Pan, Z. Q.; Vezzoni, Paolo; Cortes, Patricia; Santagata, Sandro

    2000-01-01

    The V(D)J recombination reaction is composed of multiple nucleolytic processing steps mediated by the recombination-activating proteins RAG1 and RAG2. Sequence analysis has suggested that RAG2 contains six kelch repeat motifs that are predicted to form a six-bladed β-propeller structure, with the second β-strand of each repeat demonstrating marked conservation both within and between kelch repeat-containing proteins. Here we demonstrate that mutations G95R and ΔI273 within the predicted second β-strand of repeats 2 and 5 of RAG2 lead to immunodeficiency in patients P1 and P2. Green fluorescent protein fusions with the mutant proteins reveal appropriate localization to the nucleus. However, both mutations reduce the capacity of RAG2 to interact with RAG1 and block recombination signal cleavage, therefore implicating a defect in the early steps of the recombination reaction as the basis of the clinical phenotype. The present experiments, performed with an extensive panel of site-directed mutations within each of the six kelch motifs, further support the critical role of both hydrophobic and glycine-rich regions within the second β-strand for RAG1-RAG2 interaction and recombination signal recognition and cleavage. In contrast, multiple mutations within the variable-loop regions of the kelch repeats had either mild or no effects on RAG1-RAG2 interaction and hence on the ability to mediate recombination. In all, the data demonstrate a critical role of the RAG2 kelch repeats for V(D)J recombination and highlight the importance of the conserved elements of the kelch motif. PMID:10891502

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

    SciTech Connect

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

    1994-01-01

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

  14. Activation of NMDA receptors in the brainstem, RVM and NGC, mediates mechanical hyperalgesia produced by repeated intramuscular injections of acidic saline in rats

    PubMed Central

    Da Silva, LFS; DeSantana, JM; Sluka, KA

    2010-01-01

    Repeated injections of acidic saline into the gastrocnemius muscle induced both muscle and cutaneous hypersensitivity. We have previously shown that microinjection of local anesthetic into either the rostral ventromedial medulla (RVM) or the nucleus reticularis gigantocellularis (NGC) reverses this muscle and cutaneous hypersensitivity. Although prior studies show that NMDA receptors in the RVM play a clear role in mediating visceral and inflammatory hypersensitivity, the role of NMDA receptors in the NGC, or in non-inflammatory muscle pain is unclear. Therefore, the present study evaluated involvement of the NMDA receptors in the RVM and NGC in muscle and cutaneous hypersensitivity induced by repeated intramuscular injections of acidic saline. Repeated intramuscular injections of acidic saline, 5 days apart, resulted in a bilateral decrease in the withdrawal thresholds of the paw and muscle in all groups 24 h after the second injection. Microinjection of NMDA receptor antagonists into the RVM reversed both the muscle and cutaneous hypersensitivity. However, microinjection of NMDA receptor antagonists into the NGC only reversed cutaneous, but not muscle hypersensitivity. These results suggest that NMDA receptors in the RVM mediate both muscle and cutaneous hypersensitivity, but those in the NGC mediated only cutaneous hypersensitivity after muscle insult. PMID:19853525

  15. The cpc-2 gene of Neurospora crassa encodes a protein entirely composed of WD-repeat segments that is involved in general amino acid control and female fertility.

    PubMed

    Müller, F; Krüger, D; Sattlegger, E; Hoffmann, B; Ballario, P; Kanaan, M; Barthelmess, I B

    1995-07-28

    Phenotypic and molecular studies of the mutation U142 indicate that the cpc-2+ gene is required to activate general amino acid control under conditions of amino acid limitation in the vegetative growth phase, and for formation of protoperithecia in preparation for the sexual phase of the life cycle of Neurospora crassa. The cpc-2 gene was cloned by complementation of the cpc-2 mutation in a his-2ts bradytrophic background. Genomic and cDNA sequence analysis indicated a 1636 bp long open reading frame interrupted by four introns. The deduced 316 amino acid polypeptide reveals 70% positional identity over its full length with G-protein beta-subunit-related polypeptides found in humans, rat (RACK1), chicken, tobacco and Chlamydomonas. With the exception of RACK1 the function of these proteins is obscure. All are entirely made up of seven WD-repeats. Expression studies of cpc-2 revealed one abundant transcript in the wild type; in the mutant its level is drastically reduced. In mutant cells transformed with the complementing sequence, the transcript level, enzyme regulation and female fertility are restored. In the wild type the cpc-2 transcript is down-regulated under conditions of amino acid limitation. With cpc-2 a new element involved in general amino acid control has been identified, indicating a function for a WD-repeat protein that belongs to a class that is conserved throughout the evolution of eukaryotes. PMID:7651339

  16. Allelic ladder characterization of the short tandem repeat polymorphism located in the 5{prime} flanking region to the human coagulation factor XIII A subunit gene

    SciTech Connect

    Puers, C.; Lins, A.M.; Sprecher, C.J.

    1994-09-01

    The short tandem repeat (STR) polymorphism present within the 5{prime} untranslated region of the human coagulation factor XIII A subunit gene, HUM-F13A01 [AAAG]{sub n}, was evaluated using an allelic ladder, i.e., a standard size marker consisting of amplified alleles from the locus. The allelic ladder was constructed by pooling 12 polymerase chain reaction (PCR)-amplified alleles identified by their differential migration in denaturing polyacrylamide gel electrophoresis. This standard marker was used to distinguish 14 different alleles observed at this locus. Sequence analyses indicate that 13 of the alleles contain 4 through 16 iterations of the tandemly repeated AAAG sequence, respectively. The remaining allele carries four repeats and displays a deletion of two consecutive nucleotides (GT), one base distal to the repeat region. The allelic ladder was employed to type 326 F13A01 chromosomes rapidly and reliably in representatives of a German Caucasian population. Population data were analyzed with respect to Hardy-Weinberg Equilibrium (HWE) and compared with those of a previously studied Houston, Texas, Caucasian population. 27 refs., 2 figs., 1 tab.

  17. Bidirectional cell-surface anchoring function of C-terminal repeat region of peptidoglycan hydrolase of Lactococcus lactis IL1403.

    PubMed

    Tarahomjoo, Shirin; Katakura, Yoshio; Satoh, Eiichi; Shioya, Suteaki

    2008-02-01

    With the aim of constructing an efficient protein display system for lactic acid bacteria (LABs), the effect of fusion direction on the cell-surface binding activity of the C-terminal region of the peptidoglycan hydrolase (CPH) of Lactococcus lactis IL1403 was studied. CPH fused to the alpha-amylase (AMY) of Streptococcus bovis 148 either at its C-terminus (CPH-AMY) or at its N-terminus (AMY-CPH) was expressed intracellularly in Escherichia coli. This domain was able to direct binding of AMY to the surface of L. lactis ATCC 19435 in both constructs. However, the number of bound molecules per cell and the specific activity for starch digestion in the case of CPH-AMY were 3 and 14 times greater than those in the case of AMY-CPH, respectively. Of the LABs tested, L. lactis ATCC 19435 showed the highest binding capability for CPH-AMY, up to 6 x 10(4) molecules per cell, with a dissociation rate constant of 5.00 x 10(-5) s(-1). The binding of CPH-AMY to the surface of Lactobacillus delbrueckii ATCC 9649 cells was very stable with a dissociation rate constant of 6.96 x 10(-6) s(-1). The production of CPH-AMY in the soluble form increased 3-fold as a result of coexpression with a molecular chaperone, trigger factor. The results of this study suggest the usefulness of CPH as a bidirectional anchor protein for the production of cell-surface adhesive enzymes in E. coli. Furthermore, the importance of the fusion direction of CPH in determining cell-surface binding and enzymatic activities was shown. PMID:18343337

  18. Plasmodium falciparum: an epitope within a highly conserved region of the 47-kDa amino-terminal domain of the serine repeat antigen is a target of parasite-inhibitory antibodies.

    PubMed

    Fox, B A; Xing-Li, P; Suzue, K; Horii, T; Bzik, D J

    1997-02-01

    Previously, the Plasmodium falciparum serine repeat antigen has been shown to be protective in primate models of malaria immunity and also to be a target of in vitro parasite-inhibitory antibodies. To further define parasite-inhibitory epitopes a series of deletions from the amino-terminal 47-kDa domain of the serine repeat antigen (SERA) were constructed as glutathione-S-transferase fusion proteins. Several GST-SERA fusion proteins were used to vaccinate mice with Freund's adjuvant and the resulting immune sera were used to assay for the inhibition of P. falciparum invasion of erythrocytes in vitro. The minimal epitope shown to be the target of invasion-blocking antibodies was SERA amino acids 17-165. Additional GST-SERA deletion constructs of the 47-kDa domain were developed and evaluated for reactivity, by Western immunoblot analysis, with a parasite-inhibitory murine monoclonal antibody (mAb 43E5), a parasite-inhibitory pooled goat polyclonal sera, and a pooled human Nigerian immune serum. The parasite-inhibitory epitope defined by mAb 43E5 was mapped to SERA amino acids 17-110 and, at least, part of the epitope was defined to include amino acids in the region of amino acids 59-72. The parasite-inhibitory epitope recognized by mAb 43E5 appears to be well conserved between diverse geographical isolates of P. falciparum. The results have relevance for malaria vaccine development and suggest that an appropriately designed recombinant SERA antigen produced from a synthetic gene in Escherichia coli may be an effective component of a candidate malaria vaccine. PMID:9030663

  19. A 1. 8-Mb YAC contig in Xp11. 23: Identification of Cpg islands and physical mapping of CA repeats in a region of high gene density

    SciTech Connect

    Coleman, M.P.; Nemeth, A.H.; Campbell, L.; Raut, C.P.; Davies, K.E. ); Weissenbach, J. )

    1994-05-15

    The genes ARAF1, SYN1, TIMP, and PFC are clustered within 70 kb of one another, and, as reported in the accompanying paper, at least four more genes map within 400 kb: a cluster of Krueppel-type zinc finger genes (including ZNF21, ZNF41, and ZNF81) and ELK-1, a member of the ets oncogene superfamily. This gene-rich region is of particular interest because of the large number of disease genes mapping to Xp11.23: At least three eye diseases (retinitis pigmentosa type 2, congenital stationary night blindness CSNB1, and Aland Island eye disease), Wiskott-Aldrich syndrome, X-linked nephrolithiasis, and a translocation breakpoint associated with synovial sarcoma. The authors have constructed a 1.8-Mb YAC contig in this region, confirming the link between TIMP and OATL1 reported by Knight et al. (1994) and extending the map in the distal direction. To investigate the likelihood that more genes are located within this region, they have carried out detailed mapping of rare-cutter restriction sites in these YACs and identified seven CpG islands. At least six of these islands are located over 50 kb from any known gene locations, suggesting that the region contains at least this many as yet unidentified genes. They have also mapped the physical locations of six highly polymorphic CA repeats within the contig, thus integrating the physical, genetic, and transcriptional maps of the region and facilitating the mapping and identification of disease genes. Together with the report by Knight et al., these data indicate the following order of loci: Xpter-DXS1264-DXS1055-DXS1003-DXS1146-DXS1266-(ZNF41, ARAF1)-SYN1 CA repeat-SYN1 (3[prime] end)-TIMP-SYN1 (5[prime] end)-PFC CA repeat-PFC-(DXS426, ELK1)-(DXS1265, ZNF81)-ZNF21-DXS1267-OATL1-Xcen. 40 refs., 4 figs., 3 tabs.

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

    SciTech Connect

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

    2005-05-27

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

  1. Pericentromeric Regions of Soybean (Glycine max L. Merr.) Chromosomes Consist of Retroelements and Tandemly Repeated DNA and Are Structurally and Evolutionarily Labile

    PubMed Central

    Lin, Jer-Young; Jacobus, Barbara Hass; SanMiguel, Phillip; Walling, Jason G.; Yuan, Yinan; Shoemaker, Randy C.; Young, Nevin D.; Jackson, Scott A.

    2005-01-01

    Little is known about the physical makeup of heterochromatin in the soybean (Glycine max L. Merr.) genome. Using DNA sequencing and molecular cytogenetics, an initial analysis of the repetitive fraction of the soybean genome is presented. BAC 076J21, derived from linkage group L, has sequences conserved in the pericentromeric heterochromatin of all 20 chromosomes. FISH analysis of this BAC and three subclones on pachytene chromosomes revealed relatively strict partitioning of the heterochromatic and euchromatic regions. Sequence analysis showed that this BAC consists primarily of repetitive sequences such as a 102-bp tandem repeat with sequence identity to a previously characterized ∼120-bp repeat (STR120). Fragments of Calypso-like retroelements, a recently inserted SIRE1 element, and a SIRE1 solo LTR were present within this BAC. Some of these sequences are methylated and are not conserved outside of G. max and G. soja, a close relative of soybean, except for STR102, which hybridized to a restriction fragment from G. latifolia. These data present a picture of the repetitive fraction of the soybean genome that is highly concentrated in the pericentromeric regions, consisting of rapidly evolving tandem repeats with interspersed retroelements.

  2. Protective Efficacy of a Plasmodium vivax Circumsporozoite Protein-Based Vaccine in Aotus nancymaae Is Associated with Antibodies to the Repeat Region

    PubMed Central

    Yadava, Anjali; Hall, Cysha E.; Sullivan, JoAnn S.; Nace, Douglas; Williams, Tyrone; Collins, William E.; Ockenhouse, Christian F.; Barnwell, John W.

    2014-01-01

    We have previously reported that Vivax Malaria Protein 001 (VMP001), a vaccine candidate based on the circumsporozoite protein of Plasmodium vivax, is immunogenic in mice and rhesus monkeys in the presence of various adjuvants. In the present study, we evaluated the immunogenicity and efficacy of VMP001 formulated with a TLR9 agonist in a water-in-oil emulsion. Following immunization, the vaccine efficacy was assessed by challenging Aotus nancymaae monkeys with P. vivax sporozoites. Monkeys from both the low- and high-dose vaccine groups generated strong humoral immune responses to the vaccine (peak median titers of 291,622), and its subunits (peak median titers to the N-term, central repeat and C-term regions of 22,188; 66,120 and 179,947, respectively). 66.7% of vaccinated monkeys demonstrated sterile protection following challenge. Protection was associated with antibodies directed against the central repeat region. The protected monkeys had a median anti-repeat titer of 97,841 compared to 14,822 in the non-protected monkeys. This is the first report demonstrating P. vivax CSP vaccine-induced protection of Aotus monkeys challenged with P. vivax sporozoites. PMID:25329054

  3. 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. PMID:24622844

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

    SciTech Connect

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

    2005-07-20

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

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

    PubMed

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

    2014-06-01

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

  6. Immunogenicity of IMS 1113 plus soluble subunit and chimeric proteins containing Mycoplasma hyopneumoniae P97 C-terminal repeat regions.

    PubMed

    Barate, Abhijit K; Cho, Youngjae; Truong, Quang Lam; Hahn, Tae-Wook

    2014-03-01

    The surface adhesin P97 mediates the adherence of Mycoplasma hyopneumoniae to swine cilia. Two reiterated repeats R1 and R2 are located at the C-terminus of P97. The purpose of this study was to evaluate the immunogenicity of Montanide adjuvant IMS 1113 plus soluble subunit proteins rR1, rR1R2 and their chimeric forms coupled with B subunit of the heat-labile enterotoxin of Escherichia coli (LTB). Each recombinant protein in this study was capable of eliciting anti-R1 specific humoral antibodies (IgG), mucosal antibodies (IgG and IgA) and IFN-γ production. The chimeric protein rLTBR1R2 elicited the quickest humoral antibody response among the recombinant proteins. Serum and bronchoalveolar lavage analysis revealed that each recombinant protein was capable of inducing both Th1 and Th2 responses. Importantly, all of the proteins induced an anti-R1-specific Th2-biased response in both humoral and mucosal compartments, similar to the response observed in a natural infection or vaccination process. These observations indicate that rR1, rR1R2, rLTBR1 and rLTBR1R2 with IMS 1113 might represent a promising subunit vaccine strategy against porcine enzootic pneumonia in pigs. PMID:24461070

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

    SciTech Connect

    Ji, Y.

    1999-01-01

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

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

    PubMed

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

    2016-09-01

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

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

    PubMed Central

    Grewal, SIS.; Klar, AJS.

    1997-01-01

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

  10. Functional analysis of the long terminal repeats of intracisternal A-particle genes: Sequences within the U3 region determine both the efficiency and direction of promoter activity

    SciTech Connect

    Christy, R.J.; Huang, R.C.C.

    1988-03-01

    The transcriptional activity of five intracisternal A-particle (IAP) long terminal repeats (LTRs) in mouse embryonal carcinoma PCC3-A/1 cells and in Ltk/sup -/ cells was determined. The authors tested the promoter activity of the LTRs by coupling them to the reporter gene chloramphenicol acetyltransferase (CAT) or guanosine-xanthine phosphoribosyltransferase (gpt). Each LTR was tested for promoter function in both the sense (5' to 3') and antisense (3' to 5') orientation preceding the reporter gene. The transcriptional activity of individual IAP gene LTRs varied considerably, and the LTR from IAP81 possessed promoter activity in both directions. The bidirectional activity of the IAP81 LTR was confirmed by monitoring Ecogpt expression in stably transfected Ltk/sup -/ cells, with the initiation sites for sense and antisense transcription being localized to within the IAP81 LTR by S1 nuclease mapping. Deletions of LTR81 show that for normal 5'-to-3' gene transcription (sense direction), the /sup 3'/U3/R region determines the basal level of transcription, whereas sequences within the /sup 5'/U3 region enhance transcription four- to fivefold. Deletion mapping for antisense transcription indicates that a 64-base-pair region (nucleotides 47 to 110) within the U3 region is essential for activity. These data indicate that the U3 region contains all the regulatory elements for bidirectional transcription in IAP LTRs.

  11. Phylogenetic analysis of encapsulated and non-encapsulated Trichinella species by studying the 5S rDNA tandemly repeated intergenic region.

    PubMed

    van der Giessen, J W B; Fonville, M; Briels, I; Pozio, E

    2005-09-01

    The identification of sequence regions in the genomes of pathogens which can be useful to distinguish among species and genotypes, is of great importance for epidemiological, molecular, and phylogenetic studies. The 5S ribosomal DNA intergenic spacer region has been identified as a good target to distinguish among eight Trichinella species and genotypes. The recent discovery of two non-encapsulated species in this genus, Trichinella papuae and Trichinella zimbabwensis, which can infect both mammals and reptiles, has suggested analyzing their 5S rDNA. Amplification of the tandem repeats of the 5S rDNA intergenic region of encapsulated species of Trichinella shows a 751bp fragment, whereas the three non-encapsulated species show a fragment of 800bp with T. pseudospiralis showing an additional fragment of 522bp. Although the size of the 800bp PCR fragments of T. papuae and T. zimbabwensis are similar to that of T. pseudospiralis, there are differences in the 5S rDNA intergenic regions among the three non-encapsulated species. Phylogenetic analysis of the 5S rDNA intergenic regions shows a clustering together of the three non-encapsulated Trichinella species that is well separated from the encapsulated ones. In addition, a single PCR-based method allows distinguishing non-encapsulated and encapsulated species. PMID:16076532

  12. Repeating thermocouple

    SciTech Connect

    Falk, R. A.

    1985-06-04

    Disclosed herein is a repeating use thermocouple assembly and method of making the same in which a cavity adjacent the tip of the thermocouple is filled with a thermosetting foundry sand and baked in place to provide support for the thermocouple tube without causing stresses during use which could cause breakage of the thermocouple tube.

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

    PubMed

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

    2014-12-23

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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2012-03-01

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

  16. Repeated vapor ethanol exposure induces transient histone modifications in the brain that are modified by genotype and brain region

    PubMed Central

    Finegersh, Andrey; Ferguson, Carolyn; Maxwell, Seth; Mazariegos, David; Farrell, Daniel; Homanics, Gregg E.

    2015-01-01

    Background: Emerging research implicates ethanol (EtOH)-induced epigenetic modifications in regulating gene expression and EtOH consumption. However, consensus on specific epigenetic modifications induced by EtOH has not yet emerged, making it challenging to identify mechanisms and develop targeted treatments. We hypothesized that chronic intermittent EtOH (CIE) induces persistent changes in histone modifications across the cerebral cortex (CCx), nucleus accumbens (NAc), and prefrontal cortex (PFC), and that these histone modifications are altered in a knock-in mouse strain with altered sensitivity to EtOH. Methods: C57BL/6J (B6) mice and α1SHLA knockin mice on a B6 background were exposed to 16 h of vapor EtOH or room air followed by 8 h of room air for 4 consecutive days and sacrificed at multiple time points up to 72 h following exposure. Histone modifications were assessed using Western blot and dot blot. RT-qPCR was used to study expression of chromatin modifying enzymes in NAc and PFC. Results: In NAc, CIE significantly increased acetylation of histone subunit H3 at lysine 9 (H3K9ac) but not lysine 14 (H3K14ac) or lysine 27 (H3K27ac). In PFC, CIE significantly increased H3K9ac but not H3K14 or H3K27ac. There were no significant changes at 8 or 72 h after EtOH exposure in either NAc or PFC. CIE was also associated with increased expression of Kat2b, Kat5, and Tet1 in NAc but not PFC. In CCx, CIE had a significant effect on levels of H3K18ac; there was also a significant effect of the α1SHLA mutation on levels of H3K27me3, H3K14ac, and H3K18ac as well as a trend for H3S10pK14ac. Conclusions: The EtOH-induced histone modifications observed were transient and varied significantly between brain regions. A genetic mutation that altered sensitivity to EtOH was associated with altered induction of histone modifications during CIE. These results have implications for studying EtOH-induced histone modifications and EtOH sensitivity. PMID:26300722

  17. Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize

    PubMed Central

    Zhang, Qiang; Arbuckle, John; Wessler, Susan R.

    2000-01-01

    A 314-bp DNA element called Heartbreaker-hm1 (Hbr-hm1) was previously identified in the 3′ untranslated region of a mutant allele of the maize disease resistance gene HM1. This element has structural features of miniature inverted-repeat transposable elements (MITEs) and is a member of a large family of approximately 4,000 copies in the maize genome. Unlike previously described MITEs, most members of the Hbr family display over 90% sequence identity. This, coupled with the insertion of an Hbr element into an allele of the HM1 gene, suggested that this family might have spread recently throughout the genome. Consistent with this view is the finding that Hbr insertion sites are remarkably polymorphic. Ten of ten loci containing Hbr elements were found to be polymorphic for the presence or absence of Hbr among a collection of maize inbred lines and teosinte strains. Despite the fact that over 80% of the maize genome contain moderate to highly repetitive DNA, we find that randomly chosen Hbr elements are predominantly in single or low copy regions. Furthermore, when used to query both the public and private databases of plant genes, over 50% of the sequences flanking these Hbr elements resulted in significant “hits.” Taken together, these data indicate that the presence or absence of Hbr elements is a significant contributory factor to the high level of polymorphism associated with maize genic regions. PMID:10655501

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    PubMed

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

    2015-12-01

    Exposure to nerve agents results in severe seizures or status epilepticus caused by the inhibition of acetylcholinesterase, a critical enzyme that breaks down acetylcholine to terminate neurotransmission. Prolonged seizures cause brain damage and can lead to long-term consequences. Current countermeasures are only modestly effective against the brain damage supporting interest in the evaluation of new and efficacious therapies. The nutraceutical alpha-linolenic acid (LIN) is an essential omega-3 polyunsaturated fatty acid that has a wide safety margin. Previous work showed that a single intravenous injection of alpha-linolenic acid (500 nmol/kg) administered before or after soman significantly protected against soman-induced brain damage when analyzed 24h after exposure. Here, we show that administration of three intravenous injections of alpha-linolenic acid over a 7 day period after soman significantly improved motor performance on the rotarod, enhanced memory retention, exerted an anti-depressant-like activity and increased animal survival. This dosing schedule significantly reduced soman-induced neuronal degeneration in four major vulnerable brain regions up to 21 days. Taken together, alpha-linolenic acid reduces the profound behavioral deficits induced by soman possibly by decreasing neuronal cell death, and increases animal survival. PMID:26386148

  20. The Pentapeptide Repeat Proteins

    SciTech Connect

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

    2006-01-01

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

  1. A novel repetitive sequence, termed the JNK repeat family, located on an extra heterochromatic region of chromosome 2R of Japanese rye.

    PubMed

    Nagaki, K; Tsujimoto, H; Sasakuma, T

    1999-01-01

    Among cultivated rye, Seccale cereale L., collected in Japan, we found an extra heterochromatin on the long-arm interstitial region of chromosome 2R. This extra heterochromatin was polymorphic in the population. The plants with the extra heterochromatin showed a specific DNA fragment of 1.2 kb in digests prepared with the restriction enzyme Dral. The fragment was cloned and used as a probe for fluorescent in-situ hybridization (FISH). The clone, pScJNK1, showed a hybridization signal at the extra heterochromatic region. The segregation of the number of signals corresponded to the number of the extra heterochromatin of the 2R chromosome, indicating that the sequence might construct the heterochromatin. Southern hybridization using the clone as a probe showed a ladder pattern, suggesting that the sequence was a tandem repeat. Three sequences homologous to pScJNK1 were isolated; these were 1192 1232 bp, 44.7-45.9% in GC content, highly homologous (> 93%) with each other, and did not show any significant homology to other sequences in a DNA database. Slot blot hybridization using pScJNK1 as a probe indicated that there were about 4000 copies of the sequence in the haploid genome carrying the extra heterochromatin, whereas less than 20 copies existed in the genome without the heterochromatin. Southern hybridization using MspI and HapII indicated that all of the second cytosine nucleotides in CCGG sites in the sequence were methylated in the extra heterochromatin. PMID:10328621

  2. An interferon regulatory factor binding site in the U5 region of the bovine leukemia virus long terminal repeat stimulates Tax-independent gene expression.

    PubMed

    Kiermer, V; Van Lint, C; Briclet, D; Vanhulle, C; Kettmann, R; Verdin, E; Burny, A; Droogmans, L

    1998-07-01

    Bovine leukemia virus (BLV) replication is controlled by both cis- and trans-acting elements. The virus-encoded transactivator, Tax, is necessary for efficient transcription from the BLV promoter, although it is not present during the early stages of infection. Therefore, sequences that control Tax-independent transcription must play an important role in the initiation of viral gene expression. This study demonstrates that the R-U5 sequence of BLV stimulates Tax-independent reporter gene expression directed by the BLV promoter. R-U5 was also stimulatory when inserted immediately downstream from the transcription initiation site of a heterologous promoter. Progressive deletion analysis of this region revealed that a 46-bp element corresponding to the 5' half of U5 is principally responsible for the stimulation. This element exhibited enhancer activity when inserted upstream or downstream from the herpes simplex virus thymidine kinase promoter. This enhancer contains a binding site for the interferon regulatory factors IRF-1 and IRF-2. A 3-bp mutation that destroys the IRF recognition site caused a twofold decrease in Tax-independent BLV long terminal repeat-driven gene expression. These observations suggest that the IRF binding site in the U5 region of BLV plays a role in the initiation of virus replication. PMID:9621009

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

    SciTech Connect

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

    1994-11-15

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

  4. Involvement of long terminal repeat U3 sequences overlapping the transcription control region in human immunodeficiency virus type 1 mRNA 3' end formation.

    PubMed Central

    DeZazzo, J D; Kilpatrick, J E; Imperiale, M J

    1991-01-01

    In retroviral proviruses, the poly(A) site is present in both long terminal repeats (LTRs) but used only in the 3' position. One mechanism to account for this selective poly(A) site usage is that LTR U3 sequences, transcribed only from the 3' poly(A) site, are required in the RNA for efficient processing. To test this possibility, mutations were made in the human immunodeficiency virus type 1 (HIV-1) U3 region and the mutated LTRs were inserted into simple and complex transcription units. HIV-1 poly(A) site usage was then quantitated by S1 nuclease analysis following transfection of each construct into human 293 cells. The results showed that U3 sequences confined to the transcription control region were required for efficient usage of the HIV-1 poly(A) site, even when it was placed 1.5 kb from the promoter. Although the roles of U3 in processing and transcription activation were separable, optimal 3' end formation was partly dependent on HIV-1 enhancer and SP1 binding site sequences. Images PMID:1996111

  5. Motifs within the CA-repeat-rich region of Surfactant Protein B (SFTPB) intron 4 differentially affect mRNA splicing

    PubMed Central

    Yang, Wenjun; Ni, Lan; Silveyra, Patricia; Wang, Guirong; Noutsios, Georgios T; Singh, Anamika; DiAngelo, Susan L; Sanusi, Olabisi; Raval, Manmeet; Floros, Joanna

    2013-01-01

    The first half of the surfactant protein B (SP-B) gene intron 4 is a CA-repeat-rich region that contains 11 motifs. To study the role of this region on SP-B mRNA splicing, minigenes were generated by systematic removal of motifs from either the 5′ or 3′ end. These were transfected in CHO cells to study their splicing efficiency. The latter was determined as the ratio of completely to incompletely spliced SP-B RNA. Our results indicate that SP-B intron 4 motifs differentially affect splicing. Motifs 8 and 9 significantly enhanced and reduced splicing of intron 4, respectively. RNA mobility shift assays performed with a Motif 8 sequence that contains a CAUC cis-element and cell extracts resulted in a RNA:protein shift that was lost upon mutation of the element. Furthermore, in silico analysis of mRNA secondary structure stability for minigenes with and without motif 8 indicated a correlation between mRNA stability and splicing ratio. We conclude that differential loss of specific intron 4 motifs results in one or more of the following: a) altered splicing, b) differences in RNA stability and c) changes in secondary structure. These, in turn, may affect SP-B content in lung health or disease. PMID:23687636

  6. Expression of fluorescent proteins within the repeat long region of the Marek's disease virus genome allows direct identification of infected cells while retaining full pathogenicity.

    PubMed

    Jarosinski, Keith W; Donovan, Kathleen M; Du, Guixin

    2015-04-01

    Marek's disease virus (MDV) is a lymphotropic alphaherpesvirus and causes Marek's disease (MD) in chickens. RLORF4 is an MDV-specific gene located in the repeat long (RL) regions of the genome and is directly involved in attenuation. In this report, we generated recombinant (r)MDVs in which eGFP or mRFP was inserted in-frame of the 3' end of the RLORF4 gene. In vitro growth was unaffected and infected cells could be identified by using fluorescent microscopy. Interestingly, though inserted in-frame with RLORF4, eGFP and mRFP were expressed alone, confirming mRNA expression and splicing within the RL of MDV is complex. In vivo, rMDVs expressing mRFP or eGFP caused tumors similar to wild-type MDV. Fluorescent protein expression could be seen in spleen, tumor, and feather follicle epithelial cells. These results show that expression of fluorescent proteins within the RL region results in fluorescent rMDVs that still maintains full pathogenicity in the chicken. PMID:25725150

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  9. DNA sequence analysis of a 5.27-kb direct repeat occurring adjacent to the regions of S-episome homology in maize mitochondria.

    PubMed Central

    Houchins, J P; Ginsburg, H; Rohrbaugh, M; Dale, R M; Schardl, C L; Hodge, T P; Lonsdale, D M

    1986-01-01

    The DNA sequence of the 5270-bp repeated DNA element from the mitochondrial genome of the fertile cytoplasm of maize has been determined. The repeat is a major site of recombination within the mitochondrial genome and sequences related to the R1(S1) and R2(S2) linear episomes reside immediately adjacent to the repeat. The terminal inverted repeats of the R1 and R2 homologous sequences form one of the two boundaries of the repeat. Frame-shift mutations have introduced 11 translation termination codons into the transcribed S2/R2 URFI gene. The repeated sequence, though recombinantly active, appears to serve no biological function. Images Fig. 7. PMID:3792299

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

    PubMed Central

    Xu, Ke; Lipsky, Robert H

    2015-01-01

    For more than 40 years following its approval by the Food and Drug Administration (FDA) as an anesthetic, ketamine, a non-competitive N-methyl-D-aspartic acid (NMDA) receptor antagonist, has been used as a tool of psychiatric research. As a psychedelic drug, ketamine induces psychotic symptoms, cognitive impairment, and mood elevation, which resemble some symptoms of schizophrenia. Recreational use of ketamine has been increasing in recent years. However, little is known of the underlying molecular mechanisms responsible for ketamine-associated psychosis. Recent animal studies have shown that repeated ketamine administration significantly increases NMDA receptor subunit gene expression, in particular subunit 1 (NR1 or GluN1) levels. This results in neurodegeneration, supporting a potential mechanism where up-regulation of NMDA receptors could produce cognitive deficits in chronic ketamine abuse patients. In other studies, NMDA receptor gene variants are associated with addictive behavior. Here, we focus on the roles of NMDA receptor gene subunits in ketamine abuse and ketamine psychosis and propose that full sequencing of NMDA receptor genes may help explain individual vulnerability to ketamine abuse and ketamine-associated psychosis. PMID:25245072

  11. Identification of amino acid residues of a designed ankyrin repeat protein potentially involved in intermolecular interactions with CD4: analysis by molecular dynamics simulations.

    PubMed

    Nimmanpipug, Piyarat; Khampa, Chalermpon; Lee, Vannajan Sanghiran; Nangola, Sawitree; Tayapiwatana, Chatchai

    2011-11-01

    We applied molecular dynamics simulations to investigate the binding properties of a designed ankyrin repeat protein, the DARPin-CD4 complex. DARPin 23.2 has been reported to disturb the human immunodeficiency virus (HIV) viral entry process by Schweizer et al. The protein docking simulation was analysed by comparing the specific ankyrin binder (DARPin 23.2) to an irrelevant control (2JAB) in forming a composite with CD4. To determine the binding free energy of both ankyrins, the MM/PBSA and MM/GBSA protocols were used. The free energy decomposition of both complexes were analysed to explore the role of certain amino acid residues in complex configuration. Interestingly, the molecular docking analysis of DARPin 23.2 revealed a similar CD4 interaction regarding the gp120 theoretical anchoring motif. In contrast, the binding of control ankyrin to CD4 occurred at a different location. This observation suggests that there is an advantage to the molecular modification of DARPin 23.2, an enhanced affinity for CD4. PMID:21962990

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

    SciTech Connect

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

    2008-07-11

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

  13. Development of a chimeric Plasmodium berghei strain expressing the repeat region of the P. vivax circumsporozoite protein for in vivo evaluation of vaccine efficacy.

    PubMed

    Espinosa, Diego A; Yadava, Anjali; Angov, Evelina; Maurizio, Paul L; Ockenhouse, Christian F; Zavala, Fidel

    2013-08-01

    The development of vaccine candidates against Plasmodium vivax-the most geographically widespread human malaria species-is challenged by technical difficulties, such as the lack of in vitro culture systems and availability of animal models. Chimeric rodent Plasmodium parasites are safe and useful tools for the preclinical evaluation of new vaccine formulations. We report the successful development and characterization of chimeric Plasmodium berghei parasites bearing the type I repeat region of P. vivax circumsporozoite protein (CSP). The P. berghei-P. vivax chimeric strain develops normally in mosquitoes and produces highly infectious sporozoites that produce patent infection in mice that are exposed to the bites of as few as 3 P. berghei-P. vivax-infected mosquitoes. Using this transgenic parasite, we demonstrate that monoclonal and polyclonal antibodies against P. vivax CSP strongly inhibit parasite infection and thus support the notion that these antibodies play an important role in protective immunity. The chimeric parasites we developed represent a robust model for evaluating protective immune responses against P. vivax vaccines based on CSP. PMID:23716612

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

    SciTech Connect

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

    1994-09-01

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

  15. Evaluation of a Multilocus Variable-Number Tandem-Repeat Analysis Scheme for Typing Human Brucella Isolates in a Region of Brucellosis Endemicity▿ †

    PubMed Central

    Kattar, Mireille M.; Jaafar, Rola F.; Araj, George F.; Le Flèche, Philippe; Matar, Ghassan M.; Abi Rached, Roland; Khalife, Simon; Vergnaud, Gilles

    2008-01-01

    Brucellosis remains an important anthropozoonosis worldwide. Brucella species are genetically homogeneous, and thus, the typing of Brucella species for epidemiological purposes by conventional molecular typing methods has remained elusive. Although many methods could segregate isolates into the phylogenetically recognized taxa, limited within-species genetic diversity has been identified. Recently, multilocus variable-number tandem-repeat analysis (MLVA) was found to have a high degree of resolution when it was applied to collections of Brucella isolates from geographically widespread locations, and an assay comprising 16 such loci (MLVA-16) was proposed. This scheme includes eight minisatellite loci (panel 1) and eight microsatellites (panel 2, which is subdivided into panels 2A and 2B). The utility of MLVA-16 for the subtyping of human Brucella isolates from geographically restricted regions needs to be further evaluated, and genotyping databases with worldwide coverage must be progressively established. In the present study, MLVA-16 was applied to the typing of 42 human Brucella isolates obtained from 41 patients recovered from 2002 to 2006 at a tertiary-care center in Lebanon. All isolates were identified as Brucella melitensis by MLVA-16 and were found to be closely related to B. melitensis isolates from neighboring countries in the Middle East when their genotypes were queried against those in the web-based Brucella2007 MLVA database (http://mlva.u-psud.fr/). Panel 2B, which comprised the most variable loci, displayed a very high discriminatory power, while panels 1 and 2A showed limited diversity. The most frequent genotype comprised seven isolates obtained over 7 weeks in 2002, demonstrating an outbreak from a common source. Two isolates obtained from one patient 5 months apart comprised another genotype, indicating relapsing disease. These findings confirm that MLVA-16 has a good discriminatory power for species determination, typing of B. melitensis

  16. Triggering of repeated earthquakes

    NASA Astrophysics Data System (ADS)

    Sobolev, G. A.; Zakrzhevskaya, N. A.; Sobolev, D. G.

    2016-03-01

    Based on the analysis of the world's earthquakes with magnitudes M ≥ 6.5 for 1960-2013, it is shown that they cause global-scale coherent seismic oscillations which most distinctly manifest themselves in the period interval of 4-6 min during 1-3 days after the event. After these earthquakes, a repeated shock has an increased probability to occur in different seismically active regions located as far away as a few thousand km from the previous event, i.e., a remote interaction of seismic events takes place. The number of the repeated shocks N( t) decreases with time, which characterizes the memory of the lithosphere about the impact that has occurred. The time decay N( t) can be approximated by the linear, exponential, and powerlaw dependences. No distinct correlation between the spatial locations of the initial and repeated earthquakes is revealed. The probable triggering mechanisms of the remote interaction between the earthquakes are discussed. Surface seismic waves traveling several times around the Earth's, coherent oscillations, and global source are the most preferable candidates. This may lead to the accumulation and coalescence of ruptures in the highly stressed or weakened domains of a seismically active region, which increases the probability of a repeated earthquake.

  17. RepeatsDB: a database of tandem repeat protein structures

    PubMed Central

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

    2014-01-01

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

  18. Regional distribution and postnatal changes of D-amino acids in rat brain.

    PubMed

    Hamase, K; Homma, H; Takigawa, Y; Fukushima, T; Santa, T; Imai, K

    1997-03-15

    Regional distribution of D-amino acids in rat brain was studied by the modified highly sensitive analytical method which was previously developed. The method includes fluorogenic derivatization of each amino acid, isolation of each amino acid by reverse-phase HPLC, followed by enantiomeric separation with Pirkle-type chiral stationary phases. D-Amino acid contents were determined in the cerebrum, cerebellum, hippocampus, medulla oblongata, pituitary gland and pineal gland. D-Aspartic acid was observed in the pineal gland (3524 +/- 263 nmol/g, data are for male rats of 6 weeks of age) and the pituitary gland (80.5 +/- 9.0 nmol/g). D-Serine was found in various regions of the brain except for the cerebellum and medulla oblongata. D-Alanine was observed exclusively in the pituitary gland (25.9 +/- 4.4 nmol/g), whereas D-leucine was found in the pineal gland (3.4 +/- 0.4 nmol/g) and the hippocampus (1.6 +/- 0.07 nmol/g). No other D-amino acids were detected in the brain. The contents of D-aspartic acid in the pituitary gland and D-serine in the pineal gland were higher in female rats. In contrast the contents of D-alanine in the pituitary gland and D-leucine in the pineal gland and the hippocampus were higher in males. Postnatal changes of D-aspartic acid and D-leucine in the pineal gland and D-alanine in the pituitary gland were also investigated. The results described in this paper suggested that distinct regulatory mechanisms exist for individual D-amino acids in the corresponding region of rat brain. PMID:9101716

  19. Chiroptical study of α-aliphatic amino acid films in the vacuum ultraviolet region.

    PubMed

    Tanaka, Masahito; Yagi-Watanabe, Kazutoshi; Kaneko, Fusae; Nakagawa, Kazumichi

    2010-11-11

    A series of natural circular dichroism (CD) and absorption spectra for films of α-aliphatic amino acids--such as alanine, aminobutyric acid, norvaline, norleucine, valine, leucine, and isoleucine--in the vacuum ultraviolet (VUV) region were observed with the absolute values of optical constants at the undulator-based CD beamline TERAS BL5. Preliminary predictions of some CD spectra were also performed, based on quantum-chemical calculations using the crystal structure. Although the absorption spectra show similar features to each other, significant differences between the CD spectra were found, especially in the 7-8 eV region. The CD spectra of aliphatic amino acids with branched alkyl groups in the side-chain--such as valine, leucine, and isoleucine--exhibit strong negative CD peaks in this energy region. In contrast, the corresponding CD peaks were weak or absent in the spectra of amino acids with straight alkyl groups. Our simple calculation, and the absorption spectra of alkanes, suggest that this difference partly originates from the contribution of the alkyl group. Clear discrepancies between the CD spectra of these amino acids in solutions and those in the solid state were also observed; this is probably caused by the different molecular structures in each state. Our results clearly indicated that CD spectra in the VUV region were very sensitive to the conformations of chiral molecules. PMID:20958008

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

    NASA Astrophysics Data System (ADS)

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

    2013-04-01

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

  1. Vibrational analysis of amino acids and short peptides in hydrated media. II. Role of KLLL repeats to induce helical conformations in minimalist LK-peptides.

    PubMed

    Guiffo-Soh, Guy; Hernandez, Belén; Coïc, Yves-Marie; Boukhalfa-Heniche, Fatima-Zohra; Ghomi, Mahmoud

    2007-11-01

    Aqueous solution secondary structures of minimalist LK-peptides, with the generic sequence defined as KLL(KLLL)nKLLK, have been analyzed by means of circular dichroism (CD) and Raman scattering techniques. Our discussion in the present paper is mainly focused on four synthetic peptides (from 5 to 19 amino acids), KLLLK, KLLKLLLKLLK, KLLKLLLKLLLKLLK, and KLLKLLLKLLLKLLLKLLK, corresponding to the repeat unit, and to the peptide chains with the values of n = 1-3, respectively. CD and Raman spectra were analyzed in order to study both structural features of the peptide chains and their capability to form aggregates. On the basis of the obtained results it was concluded that the conformational flexibility of the shortest peptides (5-mer and 11-mer) is high enough to adopt random, beta-type, and helical chains in aqueous solution. However, the 11-mer shows a clear tendency to form beta-strands in phosphate buffer. The conformational equilibrium can be completely shifted to beta-type structures upon increasing ionic strength, i.e., in PBS and tris buffers. This equilibrium can also be shifted toward helical chains in the presence of methanol. Finally, the longest peptides (15-mer and 19-mer) are shown to form alpha-helical chains with an amphipathic character in aqueous solution. The possibility of bundle formation between helical chains is discussed over the temperature-dependent H-D exchange on labile hydrogens and particularly by considering the particular behavior of an intense Raman mode at 1127 cm-1 originating from the leucine residue side chain. The conformational dependence of this mode observed upon selective deuteration has never been documented up to now. PMID:17918991

  2. Codon repeats in genes associated with human diseases: fewer repeats in the genes of nonhuman primates and nucleotide substitutions concentrated at the sites of reiteration.

    PubMed Central

    Djian, P; Hancock, J M; Chana, H S

    1996-01-01

    Five human diseases are due to an excessive number of CAG repeats in the coding regions of five different genes. We have analyzed the repeat regions in four of these genes from nonhuman primates, which are not known to suffer from the diseases. These primates have CAG repeats at the same sites as in human alleles, and there is similar polymorphism of repeat number, but this number is smaller than in the human genes. In some of the genes, the segment of poly(CAG) has expanded in nonhuman primates, but the process has advanced further in the human lineage than in other primate lineages, thereby predisposing to diseases of CAG reiteration. Adjacent to stretches of homogeneous present-day codon repeats, previously existing codons of the same kind have undergone nucleotide substitutions with high frequency. Where these lead to amino acid substitutions, the effect will be to reduce the length of the original homopolymeric stretch in the protein. PMID:8552651

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

    PubMed Central

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

    2015-01-01

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

  4. [Principal component analysis of mineral elements and fatty acids composition in flaxseed from ten different regions].

    PubMed

    Xing, Li; Zhao, Feng-Min; Cao, You-Fu; Wang, Mei; Mei, Shuai; Li, Shao-Ping; Cai, Zhi-Yong

    2014-09-01

    Flaxseed is a kind of biomass with high edible and medical value. It is rich in many kinds of nutrients and mineral elements. China is one of the important producing places of flaxseed. In order to explore the main characteristic constituents of mineral elements and fatty acids in flaxseed, the study of analyzing the mineral elements and fatty acid composition from 10 different regions was carried out. The contents of seventeen kinds of mineral elements in flaxseed were determined by inductively coupled plasma mass spectrometry (ICP-MS). The contents of fatty acids of the flaxseed oil obtained under the same conditions were determined by gas chromatography-mass spectrometer (GC-MS). The principal component analysis (PCA) method was applied to the study of analyzing the mineral elements and fatty acid compositions in flaxseeds. The difference in mineral elements and fatty acids of flaxseed from different regions were discussed. The main characteristic constituents of mineral elements and fatty acids were analyzed. The results showed that K, Sr, Mg, Ni, Co, Cr, Cd, Se, Zn and Cu were the main characteristic constituents of the mineral elements. At the same time, C16:0, C18:0, C18: 2, C18:3, C20:0 and C20:1 were the main characteristic constituents of the fatty acids. The combination of ICP-MS, GS-MS and PCA can reveal the characteristics and difference of mineral elements and fatty acids from different regions. The results would provide important theoretical basis for the reasonable and effective utilization of flaxseed. PMID:25532360

  5. Sequence repeats and protein structure

    NASA Astrophysics Data System (ADS)

    Hoang, Trinh X.; Trovato, Antonio; Seno, Flavio; Banavar, Jayanth R.; Maritan, Amos

    2012-11-01

    Repeats are frequently found in known protein sequences. The level of sequence conservation in tandem repeats correlates with their propensities to be intrinsically disordered. We employ a coarse-grained model of a protein with a two-letter amino acid alphabet, hydrophobic (H) and polar (P), to examine the sequence-structure relationship in the realm of repeated sequences. A fraction of repeated sequences comprises a distinct class of bad folders, whose folding temperatures are much lower than those of random sequences. Imperfection in sequence repetition improves the folding properties of the bad folders while deteriorating those of the good folders. Our results may explain why nature has utilized repeated sequences for their versatility and especially to design functional proteins that are intrinsically unstructured at physiological temperatures.

  6. 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

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

    NASA Astrophysics Data System (ADS)

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

    2015-02-01

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

  8. Machine learning and hurdle models for improving regional predictions of stream water acid neutralizing capacity

    NASA Astrophysics Data System (ADS)

    Povak, Nicholas A.; Hessburg, Paul F.; Reynolds, Keith M.; Sullivan, Timothy J.; McDonnell, Todd C.; Salter, R. Brion

    2013-06-01

    In many industrialized regions of the world, atmospherically deposited sulfur derived from industrial, nonpoint air pollution sources reduces stream water quality and results in acidic conditions that threaten aquatic resources. Accurate maps of predicted stream water acidity are an essential aid to managers who must identify acid-sensitive streams, potentially affected biota, and create resource protection strategies. In this study, we developed correlative models to predict the acid neutralizing capacity (ANC) of streams across the southern Appalachian Mountain region, USA. Models were developed using stream water chemistry data from 933 sampled locations and continuous maps of pertinent environmental and climatic predictors. Environmental predictors were averaged across the upslope contributing area for each sampled stream location and submitted to both statistical and machine-learning regression models. Predictor variables represented key aspects of the contributing geology, soils, climate, topography, and acidic deposition. To reduce model error rates, we employed hurdle modeling to screen out well-buffered sites and predict continuous ANC for the remainder of the stream network. Models predicted acid-sensitive streams in forested watersheds with small contributing areas, siliceous lithologies, cool and moist environments, low clay content soils, and moderate or higher dry sulfur deposition. Our results confirmed findings from other studies and further identified several influential climatic variables and variable interactions. Model predictions indicated that one quarter of the total stream network was sensitive to additional sulfur inputs (i.e., ANC < 100 µeq L-1), while <10% displayed much lower ANC (<50 µeq L-1). These methods may be readily adapted in other regions to assess stream water quality and potential biotic sensitivity to acidic inputs.

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

    PubMed

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

    2008-01-01

    Rain samples were collected from Warri and Port Harcourt, two major oil-producing cities of Nigeria in April-June, July-August, and September-October 2005 and 2006. Awka, a "non-oil" city was used as control. Samples were collected from three points, using clean plastic basins fastened to a table, 2 m above ground level and 115 m away from tall buildings and trees. Water samples were filtered and acidity determined using digital pH meter. The results show that the rain samples were acidic. The pH values for the 2 years under study show that the rainfall in Warri was more acidic than that of Port Harcourt. Oil exploration and other anthropogenic sources may be responsible for the acid rain in the Niger Delta region of Nigeria. PMID:18758657

  10. Does the autoantibody immunodominant region on thyroid peroxidase include amino acid residues 742-771?

    PubMed

    Xiong, Z; Farilla, L; Guo, J; McLachlan, S; Rapoport, B

    2001-03-01

    Identification of the thyroid peroxidase (TPO) amino acid residues that comprise the autoantibody immunodominant region is an important goal that has proven difficult because of the conformational nature of the epitopes involved. Recent data suggest that the immunodominant region has been located. Thus, by autoantibody recognition of tryptic fragments of native TPO, as well as of conformational portions of TPO expressed as cell-free translates, the autoantibody immunodominant region appears to include amino acid residues 742-771, near the C terminus of the ectodomain. To evaluate this deduction, we expressed as cell-free translates the full TPO ectodomain, as well as TPO truncated after residues 741 and 771. The epitopic integrity of these molecules was first confirmed by immunoprecipitation by patient sera containing TPO autoantibodies. However, autoantibody recognition could involve a minority of TPO autoantibodies with the individual sera, not fulfilling the strict criteria for immunodominance. In order to obtain definitive data, we performed immunoprecipitations on these TPO variants with four recombinant human monoclonal autoantibodies that define the immunodominant region. All four monoclonal autoantibodies immunoprecipitated TPO 1-741 to the same extent as they did TPO 1-771 and the full TPO ectodomain, indicating that the immunodominant region comprises (at least in large part) amino acid residues upstream of residue 741. PMID:11327613

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    PubMed

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

    2007-06-01

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

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

    EPA Science Inventory

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

  14. Protein Repeats from First Principles.

    PubMed

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

    2016-01-01

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

  15. Protein Repeats from First Principles

    PubMed Central

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

    2016-01-01

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

  16. Protein Repeats from First Principles

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

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

    PubMed

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

    1992-05-01

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

  18. The C-Terminal Acidic Region of Calreticulin Mediates Phosphatidylserine Binding and Apoptotic Cell Phagocytosis.

    PubMed

    Wijeyesakere, Sanjeeva Joseph; Bedi, Sukhmani Kaur; Huynh, David; Raghavan, Malini

    2016-05-01

    Calreticulin is a calcium-binding chaperone that is normally localized in the endoplasmic reticulum. Calreticulin is detectable on the surface of apoptotic cells under some apoptosis-inducing conditions, where it promotes the phagocytosis and immunogenicity of dying cells. However, the precise mechanism by which calreticulin, a soluble protein, localizes to the outer surface of the plasma membrane of dying cells is unknown, as are the molecular mechanisms that are relevant to calreticulin-induced cellular phagocytosis. Calreticulin comprises three distinct structural domains: a globular domain, an extended arm-like P-domain, and a C-terminal acidic region containing multiple low-affinity calcium binding sites. We show that calreticulin, via its C-terminal acidic region, preferentially interacts with phosphatidylserine (PS) compared with other phospholipids and that this interaction is calcium dependent. Additionally, exogenous calreticulin binds apoptotic cells via a higher-affinity calcium-dependent mode that is acidic region dependent. Exogenous calreticulin also binds live cells, including macrophages, via a second, lower-affinity P-domain and globular domain-dependent, but calcium-independent binding mode that likely involves its generic polypeptide binding site. Truncation constructs lacking the acidic region or arm-like P-domain of calreticulin are impaired in their abilities to induce apoptotic cell phagocytosis by murine peritoneal macrophages. Taken together, the results of this investigation provide the first molecular insights into the phospholipid binding site of calreticulin as a key anchor point for the cell surface expression of calreticulin on apoptotic cells. These findings also support a role for calreticulin as a PS-bridging molecule that cooperates with other PS-binding factors to promote the phagocytosis of apoptotic cells. PMID:27036911

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

    USGS Publications Warehouse

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

    2004-01-01

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

  20. Formic and acetic acid over the central Amazon region, Brazil 1. Dry season

    SciTech Connect

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

    1988-02-20

    We have determined the atmospheric concentrations of formic and acetic acid in the gas phase, in aerosols, and in rain during the dry season (July--August 1985) in the Amazonia region of Brazil. At ground level the average concentrations of gas phase formic and acetic acid were 1.6 +- 0.6 and 2.2 +- 1.0 ppb, respectively. The diurnal behavior of both acids at ground level and their vertical distribution in the forest canopy point to the existence of vegetative sources as well as to production by chemical reactions in the atmosphere. Dry deposition of the gaseous acids appears to be a major sink. The concentrations of formic and acetic acid in the gas phase were about 2 orders of magnitude higher than concentrations of the corresponding species in the atmospheric aerosol. About 50--60%/sub 0/ of the aerosol (total) formate and acetate were in the size fraction below 1.0 ..mu..m diameter.

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

    PubMed

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

    2000-09-01

    The alpha-amylase from Bacillus sp. no. 195 (BAA) consists of two domains: one is the catalytic domain similar to alpha-amylases from animals and Streptomyces in the N-terminal region; the other is the functionally unknown domain composed of an approx. 90-residue direct repeat in the C-terminal region. The gene coding for BAA was expressed in Streptomyces lividans TK24. Three active forms of the gene products were found. The pH and thermal profiles of BAAs, and their catalytic activities for p-nitrophenyl maltopentaoside and soluble starch, showed almost the same behaviours. The largest, 69 kDa, form (BAA-alpha) was of the same molecular mass as that of the mature protein estimated from the nucleotide sequence, and had raw-starch-binding and -degrading abilities. The second largest, 60 kDa, form (BAA-beta), whose molecular mass was the same as that of the natural enzyme from Bacillus sp. no. 195, was generated by proteolytic processing between the two repeat sequences in the C-terminal region, and had lower activities for raw starch binding and degrading than those of BAA-alpha. The smallest, 50 kDa, form (BAA-gamma) contained only the N-terminal catalytic domain as a result of removal of the C-terminal repeat sequence, which led to loss of binding and degradation of insoluble starches. Thus the starch adsorption capacity and raw-starch-degrading activity of BAAs depends on the existence of the repeat sequence in the C-terminal region. BAA-alpha was specifically adsorbed on starch or dextran (alpha-1,4 or alpha-1,6 glucan), and specifically desorbed with maltose or beta-cyclodextrin. These observations indicated that the repeat sequence of the enzyme was functional in the starch-binding domain (SBD). We propose the designation of the homologues to the SBD of glucoamylase from Aspergillus niger as family I SBDs, the homologues to that of glucoamylase from Rhizopus oryzae as family II, and the homologues of this repeat sequence of BAA as family III. PMID:10947962

  2. DNA Instability Maintains the Repeat Length of the Yeast RNA Polymerase II C-terminal Domain.

    PubMed

    Morrill, Summer A; Exner, Alexandra E; Babokhov, Michael; Reinfeld, Bradley I; Fuchs, Stephen M

    2016-05-27

    The C-terminal domain (CTD) of RNA polymerase II in eukaryotes is comprised of tandemly repeating units of a conserved seven-amino acid sequence. The number of repeats is, however, quite variable across different organisms. Furthermore, previous studies have identified evidence of rearrangements within the CTD coding region, suggesting that DNA instability may play a role in regulating or maintaining CTD repeat number. The work described here establishes a clear connection between DNA instability and CTD repeat number in Saccharomyces cerevisiae First, analysis of 36 diverse S. cerevisiae isolates revealed evidence of numerous past rearrangements within the DNA sequence that encodes the CTD. Interestingly, the total number of CTD repeats was relatively static (24-26 repeats in all strains), suggesting a balancing act between repeat expansion and contraction. In an effort to explore the genetic plasticity within this region, we measured the rates of repeat expansion and contraction using novel reporters and a doxycycline-regulated expression system for RPB1 In efforts to determine the mechanisms leading to CTD repeat variability, we identified the presence of DNA secondary structures, specifically G-quadruplex-like DNA, within the CTD coding region. Furthermore, we demonstrated that mutating PIF1, a G-quadruplex-specific helicase, results in increased CTD repeat length polymorphisms. We also determined that RAD52 is necessary for CTD repeat expansion but not contraction, identifying a role for recombination in repeat expansion. Results from these DNA rearrangements may help explain the CTD copy number variation seen across eukaryotes, as well as support a model of CTD expansion and contraction to maintain CTD integrity and overall length. PMID:27026700

  3. DNA Instability Maintains the Repeat Length of the Yeast RNA Polymerase II C-terminal Domain*

    PubMed Central

    Morrill, Summer A.; Exner, Alexandra E.; Babokhov, Michael; Reinfeld, Bradley I.

    2016-01-01

    The C-terminal domain (CTD) of RNA polymerase II in eukaryotes is comprised of tandemly repeating units of a conserved seven-amino acid sequence. The number of repeats is, however, quite variable across different organisms. Furthermore, previous studies have identified evidence of rearrangements within the CTD coding region, suggesting that DNA instability may play a role in regulating or maintaining CTD repeat number. The work described here establishes a clear connection between DNA instability and CTD repeat number in Saccharomyces cerevisiae. First, analysis of 36 diverse S. cerevisiae isolates revealed evidence of numerous past rearrangements within the DNA sequence that encodes the CTD. Interestingly, the total number of CTD repeats was relatively static (24–26 repeats in all strains), suggesting a balancing act between repeat expansion and contraction. In an effort to explore the genetic plasticity within this region, we measured the rates of repeat expansion and contraction using novel reporters and a doxycycline-regulated expression system for RPB1. In efforts to determine the mechanisms leading to CTD repeat variability, we identified the presence of DNA secondary structures, specifically G-quadruplex-like DNA, within the CTD coding region. Furthermore, we demonstrated that mutating PIF1, a G-quadruplex-specific helicase, results in increased CTD repeat length polymorphisms. We also determined that RAD52 is necessary for CTD repeat expansion but not contraction, identifying a role for recombination in repeat expansion. Results from these DNA rearrangements may help explain the CTD copy number variation seen across eukaryotes, as well as support a model of CTD expansion and contraction to maintain CTD integrity and overall length. PMID:27026700

  4. Detection of copiapite in the northern Mawrth Vallis region of Mars: Evidence of acid sulfate alteration

    NASA Astrophysics Data System (ADS)

    Farrand, William H.; Glotch, Timothy D.; Horgan, Briony

    2014-10-01

    The Mawrth Vallis region on Mars is associated with extensive layered deposits containing a stratigraphic sequence of Fe/Mg smectites overlain by Al phyllosilicates. Earlier studies have reported restricted exposures of the ferric sulfate mineral jarosite on top of the sequence. In this paper we have used CRISM data covering the northern portion of the Mawrth Vallis region to find a new jarosite exposure and multiple occurrences of the mixed valence Fe-sulfate mineral copiapite (Fe2+Fe3+4(SO4)6(OH)2·20(H2O)). HiRISE imagery indicate that the copiapite exposures lie on top of the Al phyllosilicates and thus post-date that unit either as a coating or as extensive veins. The presumed copiapite exposures are associated with high values of a “SINDX” parameter derived from CRISM data. Application of several spectral matching metrics over a spectral subsection indicated several candidates for the high SINDX phase including copiapite, ferricopiapite and metavoltine (another mixed valence Fe-sulfate mineral). Visible and near infrared CRISM spectra of the high SINDX areas are most consistent with the phase being copiapite. On Earth copiapite generally occurs as efflorescent coatings in acid mine drainage environments or in association with acid sulfate soils. The presence of jarosite and copiapite indicates the presence of acidic waters. Such acid waters could have contributed to the formation of the underlying Al phyllosilicate minerals. A possible mode of origin for these minerals in this region would involve a fluctuating ground water table and the weathering of Fe sulfide minerals.

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

    PubMed Central

    2009-01-01

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

  6. A validation of two-dimensional in vivo regional strain computed from displacement encoding with stimulated echoes (DENSE), in reference to tagged magnetic resonance imaging and studies in repeatability.

    PubMed

    Kar, Julia; Knutsen, Andrew K; Cupps, Brian P; Pasque, Michael K

    2014-03-01

    Fast cine displacement encoding with stimulated echoes (DENSE) has comparative advantages over tagged MRI (TMRI) including higher spatial resolution and faster post-processing. This study computed regional radial and circumferential myocardial strains with DENSE displacements and validated it in reference to TMRI, according to American Heart Association (AHA) guidelines for standardized segmentation of regions in the left ventricle (LV). This study was therefore novel in examining agreement between the modalities in 16 AHA recommended LV segments. DENSE displacements were obtained with spatiotemporal phase unwrapping and TMRI displacements obtained with a conventional tag-finding algorithm. A validation study with a rotating phantom established similar shear strain between modalities prior to in vivo studies. A novel meshfree nearest node finite element method (NNFEM) was used for rapid computation of Lagrange strain in both phantom and in vivo studies in both modalities. Also novel was conducting in vivo repeatability studies for observing recurring strain patterns in DENSE and increase confidence in it. Comprehensive regional strain agreements via Bland-Altman analysis between the modalities were obtained. Results from the phantom study showed similar radial-circumferential shear strains from the two modalities. Mean differences in regional in vivo circumferential strains were -0.01 ± 0.09 (95% limits of agreement) from comparing the modalities and -0.01 ± 0.07 from repeatability studies. Differences and means from comparison and repeatability studies were uncorrelated (p > 0.05) indicating no increases in differences with increased strain magnitudes. Bland-Altman analysis and similarities in regional strain distribution within the myocardium showed good agreements between DENSE and TMRI and show their interchangeability. NNFEM was also established as a common framework for computing strain in both modalities. PMID:24150239

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

    PubMed Central

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

    2004-01-01

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

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

    PubMed

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

    2004-08-01

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

  9. Proximate and fatty acid composition of some commercially important fish species from the Sinop region of the Black Sea.

    PubMed

    Kocatepe, Demet; Turan, Hülya

    2012-06-01

    The proximate and fatty acid compositions of the commercially important fish species (Engraulis encrasicolus, Alosa alosa, Belone belone, Scorpaena porcus, Pomatomus saltatrix, Mullus barbatus) from the Sinop region of the Black Sea were examined. The fat contents ranged from 1.26% (for scorpion fish) to 18.12% (for shad). The protein contents were min 14.54% (for red mullet) and maximum 20.26% (for belone). The fatty acid compositions of the fish ranged from 27.83 to 35.91% for saturated fatty acids, 19.50-33.80% for monounsaturated fatty acids and 15.25-40.02% for polyunsaturated fatty acids. Among the saturated fatty acids, palmitic acid (16:0) (17.75-22.20%) was the dominant fatty acid for all the fish species. As a second saturated fatty acid, myristic acid (14:0) was observed in four of the fish species and its content ranged from 4.72 to 7.31%. Whereas, for the other two fish species, the second saturated fatty acid was stearic acid (18:0) ranging between 4.54 and 10.64%. Among the monounsaturated fatty acids, those occurring in the highest proportions were oleic acid (18:1n-9c) (11.67-22.45%) and palmitoleic acid (16:1) (4.50-9.40%). Docosahexaenoic acid (22:6n-3) (5.41-28.52%), eicosapentaenoic acid (20:5n-3) (4.68-11.06) and linoleic acid (18:2n-6) (1.38-3.49%) were dominant polyunsaturated fatty acids, respectively. All the species, in particular the belone, the anchovy and the shad had high levels of the n-3 series. PMID:22322400

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

    PubMed

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

    2014-02-01

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

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

    SciTech Connect

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

    1986-02-01

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

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

    PubMed Central

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

    2015-01-01

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

  13. Formation of the Arabidopsis Pentatricopeptide Repeat Family1[W

    PubMed Central

    Rivals, Eric; Bruyère, Clémence; Toffano-Nioche, Claire; Lecharny, Alain

    2006-01-01

    In Arabidopsis (Arabidopsis thaliana) the 466 pentatricopeptide repeat (PPR) proteins are putative RNA-binding proteins with essential roles in organelles. Roughly half of the PPR proteins form the plant combinatorial and modular protein (PCMP) subfamily, which is land-plant specific. PCMPs exhibit a large and variable tandem repeat of a standard pattern of three PPR variant motifs. The association or not of this repeat with three non-PPR motifs at their C terminus defines four distinct classes of PCMPs. The highly structured arrangement of these motifs and the similar repartition of these arrangements in the four classes suggest precise relationships between motif organization and substrate specificity. This study is an attempt to reconstruct an evolutionary scenario of the PCMP family. We developed an innovative approach based on comparisons of the proteins at two levels: namely the succession of motifs along the protein and the amino acid sequence of the motifs. It enabled us to infer evolutionary relationships between proteins as well as between the inter- and intraprotein repeats. First, we observed a polarized elongation of the repeat from the C terminus toward the N-terminal region, suggesting local recombinations of motifs. Second, the most N-terminal PPR triple motif proved to evolve under different constraints than the remaining repeat. Altogether, the evidence indicates different evolution for the PPR region and the C-terminal one in PCMPs, which points to distinct functions for these regions. Moreover, local sequence homogeneity observed across PCMP classes may be due to interclass shuffling of motifs, or to deletions/insertions of non-PPR motifs at the C terminus. PMID:16825340

  14. STREAM CHEMISTRY IN THE EASTERN UNITED STATES: I. SYNOPTIC SURVEY DESIGN, ACID-BASE STATUS, AND REGIONAL PATTERNS

    EPA Science Inventory

    To assess the regional acid-base status of streams in the Mid-Atlantic and Southeastern United States, spring baseflow chemistry was surveyed in a probability sample of 500 stream reaches representing a population of 64,300 reaches. Approximately half of the streams had acid neut...

  15. EFFECTS OF ACIDIC DEPOSITION ON STREAMS IN THE APPALACHIAN MOUNTAINS AND PIEDMONT REGION OF THE MID-ATLANTIC UNITED STATES

    EPA Science Inventory

    Streams in the Appalachian Mountain area of the Mid-Atlantic receive some of the largest acidic deposition loadings of any region of the United States. ompilation of survey data from the Mid-Appalachians yields a consistent picture of the acid-base status of streams. cidic stream...

  16. Modeling analysis of the benefits of Crassulacean acid metabolism (CAM) for sustainable agriculture in arid regions

    NASA Astrophysics Data System (ADS)

    Bartlett, M. S.; Vico, G.; Porporato, A. M.

    2012-12-01

    In view of the pressing needs to sustainably manage water and soil resources, especially in arid and semi-arid regions, here we propose a new carbon assimilation model that couples a simple yet mechanistic description of Crassulacean acid metabolism (CAM) photosynthesis to the soil-plant-atmosphere continuum. The model captures the full coupling of the CAM photosynthetic pathway with fluctuations in environmental conditions (cycles of light availability and air humidity, changes in soil moisture as driven by plant transpiration and rainfall occurrence). As such, the model is capable of reproducing the different phases of CAM, including daytime stomatal closure and photosynthesis from malic acid, afternoon stomatal opening for direct carbon assimilation, and nighttime stomatal opening for CO2 uptake and malic acid synthesis. Thanks to its versatility, our model allows us to relate CAM productivity, for both obligate and facultative CAM plants, to various soil moisture conditions including hydroclimatic scenarios of rainfall frequency and intensity as well as different night-time conditions of temperature, wind speed, and humidity. Our analyses show the potential productive benefits of CAM cultivation in dryland environments as feedstock and possible biofuel source, in terms of sustainable water use and economic benefits. In particular, the model is used to explore conditions where CAM plant resiliency to water stress makes these plants a more sustainable alternative to C3 and C4 species for potential deficit irrigation.

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

    PubMed

    Whitfield, Colin J; Watmough, Shaun A

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2003-04-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2008-12-01

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

  20. Regional characters of cloud water chemistry over severe acid rain areas of China

    SciTech Connect

    Zhilai Shen; Hui Xiao; Hengchi Lei; Meiyuan Huang

    1996-12-31

    The results and discussion are presented of measurements of cloud water chemistry made over severe add rain areas, such as Chongqing, Chengdu, Guiyang, Guangzhou, Nanchang, and Changsha in China from 1985 to 1993. Analyses indicate that acid cloud water is widespread in these areas, the range of cloud water pH is large within an area, the highest acidity is not over big city, and the difference of average values of pH is not obvious in different areas. In some areas, for example Chongqing, the annual variation of average pH is large. The range of average of total ion concentrations of cloud water is also large and the maximum is six more than minimum. The relationship between the acidity and ion concentration of cloud water is unlinear. The chemistry parameters of cloud water exhibit an obvious region character in Southwest China (Chongqing, Chengdu and Guiyang) SO4= is a dominant anion and SO4=/NO3- is more than 8, Ca++ and NH4+ are the main cation, Ca++/NH4+>1 (in the remaining areas, Ca++/NH4+<1), the cloud water acidity is higher than that of ground rain, indicating that there is an acidification process below cloud. In South China (Guangzhou and Guiyang) NO3 is same important as SO4= and SO4=/NO3- is about 1. In Central China (Nanchang and Changsha) the total ion concentration is highest on comparison with other areas and the value is more than that of ground rainwater, meaning probably that there is an influence of cloud microphysical process on cloud water and rainwater chemistry.

  1. A Further Analysis of the Relationship between Yellow Ripe-Fruit Color and the Capsanthin-Capsorubin Synthase Gene in Pepper (Capsicum sp.) Indicated a New Mutant Variant in C. annuum and a Tandem Repeat Structure in Promoter Region

    PubMed Central

    Gui, Xiao-Ling; Chang, Xiao-Bei; Gong, Zhen-Hui

    2013-01-01

    Mature pepper (Capsicum sp.) fruits come in a variety of colors, including red, orange, yellow, brown, and white. To better understand the genetic and regulatory relationships between the yellow fruit phenotype and the capsanthin-capsorubin synthase gene (Ccs), we examined 156 Capsicum varieties, most of which were collected from Northwest Chinese landraces. A new ccs variant was identified in the yellow fruit cultivar CK7. Cluster analysis revealed that CK7, which belongs to the C. annuum species, has low genetic similarity to other yellow C. annuum varieties. In the coding sequence of this ccs allele, we detected a premature stop codon derived from a C to G change, as well as a downstream frame-shift caused by a 1-bp nucleotide deletion. In addition, the expression of the gene was detected in mature CK7 fruit. Furthermore, the promoter sequences of Ccs from some pepper varieties were examined, and we detected a 176-bp tandem repeat sequence in the promoter region. In all C. annuum varieties examined in this study, the repeat number was three, compared with four in two C. chinense accessions. The sequence similarity ranged from 84.8% to 97.7% among the four types of repeats, and some putative cis-elements were also found in every repeat. This suggests that the transcriptional regulation of Ccs expression is complex. Based on the analysis of the novel C. annuum mutation reported here, along with the studies of three mutation types in yellow C. annuum and C. chinense accessions, we suggest that the mechanism leading to the production of yellow color fruit may be not as complex as that leading to orange fruit production. PMID:23637942

  2. Functional characterization of a complex protein-DNA-binding domain located within the human immunodeficiency virus type 1 long terminal repeat leader region.

    PubMed Central

    Malim, M H; Fenrick, R; Ballard, D W; Hauber, J; Böhnlein, E; Cullen, B R

    1989-01-01

    Transcriptional trans activation of the human immunodeficiency virus type 1 (HIV-1) long terminal repeat (LTR) by the viral tat trans activator is mediated by an LTR-specific sequence located immediately 3' to the start of transcription initiation. We have used a range of molecular techniques to examine DNA-protein interactions that occur in the vicinity of this cis-acting sequence. Our results demonstrate the existence of a sequence-specific DNA-protein interaction involving the HIV-1 leader DNA and map this binding event to between -2 and +21 base pairs relative to the HIV-1 LTR transcription start site. Evidence suggesting that this interaction involves three distinct protein-DNA contact sites extending along one side of the DNA helix is presented. Mutation of these sites was found to ablate protein-DNA binding yet was observed to have no effect on either the basal or tat trans-activated level of HIV-1 LTR-specific gene expression. We therefore conclude that this DNA-protein interaction has a function distinct from the regulation of HIV-1 LTR-specific gene expression. Images PMID:2545899

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

    SciTech Connect

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

    2010-09-15

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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  5. Repeated Course Enrollments.

    ERIC Educational Resources Information Center

    Windham, Patricia

    This report resents tables of repeated course enrollment data in Florida community colleges for the fall 1993 cohort. Overall, the percent of repeats in college preparatory courses was greater than that of college credit courses. Within ICS codes, the highest percentage of credit repeat enrollments was in mathematics; the second highest was in…

  6. Analysis of acid rain effects on vegetation in eco-regions in China based on AVHRR/NDVI

    NASA Astrophysics Data System (ADS)

    Jin, Jiaxin; Jiang, Hong; Zhang, Xiuying; Xu, Xiaobin

    2010-09-01

    The vegetation, as the main component of the ecosystems, is the main receptor of acid rain pollution. Because of the discrepancy of the vegetation characteristics and environment, the responses of the different types of vegetation to acid rain in different regions are different. In this paper, we chose 9 eco-regions in southern China as study area, based on the acid rain and NOAA/NDVI data from 1992 to 2006, and revealed the impact of acid rain on the vegetation by using spatial interpolation, cluster analysis and curve fitting. The result shows that the most tropical and subtropical moist broadleaf forests were positively correlated with the acidity of precipitation and the growth was inhibited obviously. On the contrary, the growth of temperate coniferous forests was promoted by acid rain to some extent. In generally, the vegetation in the condition of the weak acid rain grew better, especially the Qin Ling Mountains deciduous forests and the Changjiang Plain evergreen forests. For South China-Vietnam subtropical evergreen forest, Yunnan Plateau subtropical evergreen forests and Qionglai-Minshan conifer forests, the significant difference of NDVI between the different gradients of acid rain lasted almost the whole year, while that of the other eco-regions only appeared most obviously in Winter.

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

    PubMed Central

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

    1993-01-01

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

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

    EPA Science Inventory

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

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

    PubMed

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

    2015-12-01

    These studies probed the relationship between intrinsic efficacy and tolerance/cross-tolerance between ∆(9)-THC and synthetic cannabinoid drugs of abuse (SCBs) by examining in vivo effects and cellular changes concomitant with their repeated administration in mice. Dose-effect relationships for hypothermic effects were determined in order to confirm that SCBs JWH-018 and JWH-073 are higher efficacy agonists than ∆(9)-THC in mice. Separate groups of mice were treated with saline, sub-maximal hypothermic doses of JWH-018 or JWH-073 (3.0mg/kg or 10.0mg/kg, respectively) or a maximally hypothermic dose of 30.0mg/kg ∆(9)-THC once per day for 5 consecutive days while core temperature and locomotor activity were monitored via biotelemetry. Repeated administration of all drugs resulted in tolerance to hypothermic effects, but not locomotor effects, and this tolerance was still evident 14 days after the last drug administration. Further studies treated mice with 30.0mg/kg ∆(9)-THC once per day for 4 days, then tested with SCBs on day 5. Mice with a ∆(9)-THC history were cross-tolerant to both SCBs, and this cross-tolerance also persisted 14 days after testing. Select brain regions from chronically treated mice were examined for changes in CB1 receptor expression and function. Expression and function of hypothalamic CB1Rs were reduced in mice receiving chronic drugs, but cortical CB1R expression and function were not altered. Collectively, these data demonstrate that repeated ∆(9)-THC, JWH-018 and JWH-073 can induce long-lasting tolerance to some in vivo effects, which is likely mediated by region-specific downregulation and desensitization of CB1Rs. PMID:26361728

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

    SciTech Connect

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

    1994-01-01

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

  11. Regional relationships between geomorphic/hydrologic parameters and surface water chemistry relative to acidic deposition

    SciTech Connect

    Rochelle, B.P.; Liff, C.I.; Campbell, W.G.; Cassell, D.L.; Church, M.R.

    1989-01-01

    The authors determined geomorphic and hydrologic parameters for 144 forested, lake watersheds in the Northeast (NE) of the United States based primarily on measurements from topographic maps. These parameters were used to test for relationships with selected surface water chemistry relevant to acidic deposition. Analyses were conducted on regional and subregional scales delineated based on soils, land use, physiography, total sulfur deposition and statistical clustering of selected geomorphic/hydrologic parameters. Significant relationships were found among the geomorphic/hydrologic parameters and the surface water chemistry for the NE. Elevation had the most significant relationship with surface water chemistry, particularly in the mountainous areas of the NE. Other factors occurring consistently as significant predictors of surface water chemistry were maximum relief, relief ratio, runoff, and estimates of basin elongation. Results suggest that elevational parameters might be surrogates for other watershed characteristics, such as soils or spatial deposition patterns.

  12. Production of bacteriocin-like substances by lactic acid bacteria isolated from regional ovine cheese

    PubMed Central

    Nespolo, Cássia Regina; Brandelli, Adriano

    2010-01-01

    Lactic acid bacteria (LAB) were isolated from ovine milk and cheeses manufactured in the South Region of Brazil. Among 112 bacterial isolates investigated, 59 were chosen through a screening for LAB. Among these 59 strains of LAB, 21% showed antimicrobial, proteolytic and lipolytic activities. Based on this screening, Lactobacillus plantarum LCN 17 and Lactobacillus rhamnosus LCN 43 were selected and tested for the production of bacteriocin-like substances (BLS). The BLS produced by both isolates showed antimicrobial activity against Listeria monocytogenes, whereas that produced by L. plantarum LCN 17 presented higher stability to different temperature, pH and enzyme treatments. These strains present potential for production of BLS, and for use as starter cultures. PMID:24031581

  13. Genome-wide in Silico Identification of New Conserved and Functional Retinoic Acid Receptor Response Elements (Direct Repeats Separated by 5 bp)*

    PubMed Central

    Lalevée, Sébastien; Anno, Yannick N.; Chatagnon, Amandine; Samarut, Eric; Poch, Olivier; Laudet, Vincent; Benoit, Gerard; Lecompte, Odile; Rochette-Egly, Cécile

    2011-01-01

    The nuclear retinoic acid receptors interact with specific retinoic acid (RA) response elements (RAREs) located in the promoters of target genes to orchestrate transcriptional networks involved in cell growth and differentiation. Here we describe a genome-wide in silico analysis of consensus DR5 RAREs based on the recurrent RGKTSA motifs. More than 15,000 DR5 RAREs were identified and analyzed for their localization and conservation in vertebrates. We selected 138 elements located ±10 kb from transcription start sites and gene ends and conserved across more than 6 species. We also validated the functionality of these RAREs by analyzing their ability to bind retinoic acid receptors (ChIP sequencing experiments) as well as the RA regulation of the corresponding genes (RNA sequencing and quantitative real time PCR experiments). Such a strategy provided a global set of high confidence RAREs expanding the known experimentally validated RAREs repertoire associated to a series of new genes involved in cell signaling, development, and tumor suppression. Finally, the present work provides a valuable knowledge base for the analysis of a wider range of RA-target genes in different species. PMID:21803772

  14. Genome-wide in silico identification of new conserved and functional retinoic acid receptor response elements (direct repeats separated by 5 bp).

    PubMed

    Lalevée, Sébastien; Anno, Yannick N; Chatagnon, Amandine; Samarut, Eric; Poch, Olivier; Laudet, Vincent; Benoit, Gerard; Lecompte, Odile; Rochette-Egly, Cécile

    2011-09-23

    The nuclear retinoic acid receptors interact with specific retinoic acid (RA) response elements (RAREs) located in the promoters of target genes to orchestrate transcriptional networks involved in cell growth and differentiation. Here we describe a genome-wide in silico analysis of consensus DR5 RAREs based on the recurrent RGKTSA motifs. More than 15,000 DR5 RAREs were identified and analyzed for their localization and conservation in vertebrates. We selected 138 elements located ±10 kb from transcription start sites and gene ends and conserved across more than 6 species. We also validated the functionality of these RAREs by analyzing their ability to bind retinoic acid receptors (ChIP sequencing experiments) as well as the RA regulation of the corresponding genes (RNA sequencing and quantitative real time PCR experiments). Such a strategy provided a global set of high confidence RAREs expanding the known experimentally validated RAREs repertoire associated to a series of new genes involved in cell signaling, development, and tumor suppression. Finally, the present work provides a valuable knowledge base for the analysis of a wider range of RA-target genes in different species. PMID:21803772

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Aktuğ, Bahadır; Kılıçoğlu, Ali

    2006-07-01

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

  17. Repeating covalent structure of streptococcal M protein.

    PubMed Central

    Beachey, E H; Seyer, J M; Kang, A H

    1978-01-01

    We have attempted to identify the covalent structure of the M protein molecule of group A streptococci that is responsible for inducing type-specific, protective immunity. M protein was extracted from type 24 streptococci, purified, and cleaved with cyanogen bromide. Seven cyanogen bromide peptides were purified and further characterized. Together, the peptides account for the entire amino acid content of the M protein molecule. Each of the purified peptides possessed the type-specific determinant that inhibits opsonic antibodies for group A streptococci. The primary structures of the amino-terminal regions of each of the purified peptides was studied by automated Edman degradation. The partial sequences of two of the peptides were found to be identical to each other and to that of the uncleaved M protein molecule through at least the first 27 residues. The amino-terminal sequences of the remaining five peptides were identical to each other through the twentieth residue but completely different from the amino-terminal region of the other two peptides. However, the type-specific immunoreactivity and the incomplete analysis of the primary structure of the seven peptides suggest that the antiphagocytic determinant resides in a repeating amino acid sequence in the M protein molecule. PMID:80011

  18. Immune factors and fatty acid composition in human milk from river/lake, coastal and inland regions of China.

    PubMed

    Urwin, Heidi J; Zhang, Jian; Gao, Yixiong; Wang, Chunrong; Li, Lixiang; Song, Pengkun; Man, Qingqing; Meng, Liping; Frøyland, Livar; Miles, Elizabeth A; Calder, Philip C; Yaqoob, Parveen

    2013-06-01

    Breast milk fatty acid composition may be affected by the maternal diet during gestation and lactation. The influence of dietary and breastmilk fatty acids on breast milk immune factors is poorly defined. We determined the fatty acid composition and immune factor concentrations of breast milk from women residing in river/lake, coastal and inland regions of China, which differ in their consumption of lean fish and oily fish. Breast milk samples were collected on days 3–5 (colostrum), 14 and 28 post-partum (PP) and analysed for soluble CD14 (sCD14), transforming growth factor (TGF)-b1, TGF-b2, secretory IgA (sIgA) and fatty acids. The fatty acid composition of breast milk differed between the regions and with time PP. The concentrations of all four immune factors in breast milk decreased over time, with sCD14, sIgA and TGF-b1 being highest in the colostrum in the river and lake region. Breast milk DHA and arachidonic acid (AA) were positively associated, and g-linolenic acid and EPA negatively associated, with the concentrations of each of the four immune factors. In conclusion, breast milk fatty acids and immune factors differ between the regions in China characterised by different patterns of fish consumption and change during the course of lactation. A higher breast milk DHA and AA concentration is associated with higher concentrations of immune factors in breast milk, suggesting a role for these fatty acids in promoting gastrointestinal and immune maturation of the infant. PMID:23148871

  19. Effect of total hepatectomy and administration of branched-chain amino acids on regional norepinephrine, dopamine, and amino acids in rat brain.

    PubMed Central

    Herlin, P M; James, J H; Nachbauer, C A; Fischer, J E

    1983-01-01

    In rats after total hepatectomy, the effect of infusing glucose alone or combined with branched-chain amino acids on amino acid concentrations in plasma and cerebral cortex and on catecholamine levels in eight different regions of the brain was studied. Infusion of branched-chain amino acids reduced the accumulation of tryptophan, phenylalanine, and tyrosine in plasma, while in cerebral cortex, the concentrations of phenylalanine and tyrosine were normalized and that of tryptophan was reduced greatly. In rats with hepatectomy and glucose infusion alone, norepinephrine levels were decreased in seven of eight brain regions with the exception of striatum, while dopamine was reduced significantly in striatum only. Infusion of branched-chain amino acids resulted in higher norepinephrine in cortex, mesencephalon, and hypothalamus and higher striatal dopamine 18 hours after hepatectomy. Thus, infusing branched-chain amino acids and reducing the accumulation of various neutral amino acids in brain may partially prevent the loss of norepinephrine from brain after total hepatectomy. PMID:6870374

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

    Zhu, Bingqi; Ryan, David K

    2016-03-01

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

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

    SciTech Connect

    Yubao Wang; Miaoqin Lu

    1996-12-31

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

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

    PubMed

    Lin, Tiao-Yin

    2016-07-01

    Phages are the most abundant biological entities and influence prokaryotic communities on Earth. Comparing closely related genomes sheds light on molecular events shaping phage evolution. Simple sequence repeat (SSR) variations impart over half of the genomic changes between T7M and T3, indicating an important role of SSRs in accelerating phage genetic divergence. Differences in coding and noncoding regions of phages infecting different hosts, coliphages T7M and T3, Yersinia phage ϕYeO3-12, and Salmonella phage ϕSG-JL2, frequently arise from SSR variations. Such variations modify noncoding and coding regions; the latter efficiently changes multiple amino acids, thereby hastening protein evolution. Four classes of events are found to drive SSR variations: insertion/deletion of SSR units, expansion/contraction of SSRs without alteration of genome length, changes of repeat motifs, and generation/loss of repeats. The categorization demonstrates the ways SSRs mutate in genomes during phage evolution. Indels are common constituents of genome variations and human diseases, yet, how they occur without preexisting repeat sequence is less understood. Non-repeat-unit-based misalignment-elongation (NRUBME) is proposed to be one mechanism for indels without adjacent repeats. NRUBME or consecutive NRUBME may also change repeat motifs or generate new repeats. NRUBME invoking a non-Watson-Crick base pair explains insertions that initiate mononucleotide repeats. Furthermore, NRUBME successfully interprets many inexplicable human di- to tetranucleotide repeat generations. This study provides the first evidence of SSR variations expediting phage divergence, and enables insights into the events and mechanisms of genome evolution. NRUBME allows us to emulate natural evolution to design indels for various applications. PMID:27133219

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

    PubMed Central

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

    2012-01-01

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

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

    SciTech Connect

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

    1995-11-20

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

  6. D5S818 Typing Discrepancy Between PowerPlex(®) Fusion and Other STR Kits Including GlobalFiler(®) Caused by a One-base Deletion in 31 Nucleotides Upstream of the Repeat Region.

    PubMed

    Fujii, Koji; Iwashima, Yasuki; Watahiki, Haruhiko; Mita, Yusuke; Kitayama, Tetsushi; Nakahara, Hiroaki; Mizuno, Natsuko; Sekiguchi, Kazumasa

    2016-05-01

    Short tandem repeat (STR) typing is widely used in forensic investigation. When the same DNA sample is analyzed with different STR typing kits, a typing discrepancy is occasionally observed. In this study, we examined the cause of a typing discrepancy in a sample at D5S818 locus. This sample was designated as 10, 12 using Identifiler(®) , Identifiler(®) Plus, GlobalFiler(®) , PowerPlex(®) 16HS, and PowerPlex(®) 18D, but as 9.3, 12 using PowerPlex(®) Fusion. Sequencing results indicated that the shorter allele in the sample had a deletion (U31Tdel) at 31 nucleotides upstream of the repeat region (AGAT)10 . This deletion was located in the binding site of the published D5S818 forward primer in PowerPlex(®) 16 and was only 9 and 11 nucleotides downstream of our estimated 5' end position of D5S818 forward primer in GlobalFiler(®) and PowerPlex(®) 18D, respectively. We also examined the effect of primer length on the heterozygous peak balance in this sample. PMID:27122415

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

    USGS Publications Warehouse

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

    2013-01-01

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

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

    PubMed

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

    2013-09-01

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

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

    NASA Astrophysics Data System (ADS)

    Mountjoy, Joshu J.; Barnes, Philip M.

    2011-01-01

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

  10. Identification of a large bent DNA domain and binding sites for serum response factor adjacent to the NFI repeat cluster and enhancer region in the major IE94 promoter from simian cytomegalovirus.

    PubMed Central

    Chang, Y N; Jeang, K T; Chiou, C J; Chan, Y J; Pizzorno, M; Hayward, G S

    1993-01-01

    The major immediate-early (MIE) transactivator proteins of cytomegaloviruses (CMV) play a pivotal role in the initiation of virus-host cell interactions. Therefore, cis- and trans-acting factors influencing the expression of these proteins through their upstream promoter-enhancer regions are important determinants of the outcome of virus infection. S1 nuclease analysis and in vitro transcription assays with the MIE (or IE94) transcription unit of simian CMV (SCMV) (Colburn) revealed a single prominent mRNA start site associated with a canonical TATATAA motif. This initiator region lies adjacent to a 2,400-bp 5'-upstream noncoding sequence that encompasses a newly identified 1,000-bp (A+T)-rich segment containing intrinsically bent DNA (domain C), together with the previously described proximal cyclic AMP response element locus (domain A) and a tandemly repeated nuclear factor I binding site cluster (domain B). Deleted MIE reporter gene constructions containing domain A sequences only yield up to 4-fold stronger basal expression in Vero cells than the intact simian virus 40 promoter-enhancer region, and sequences from position -405 to -69 (ENH-A1) added to a minimal heterologous promoter produced a 50-fold increase of basal expression in an enhancer assay. In contrast, neither the nuclear factor I cluster nor the bent DNA region possessed basal enhancer properties and neither significantly modulated the basal activity of the ENH-A1 segment. A second segment of domain A from position -580 to -450 was also found to possess basal enhancer activity in various cell types. This ENH-A2 region contains three copies of a repeated element that includes the 10-bp palindromic sequence CCATATATGG, which resembles the core motif of serum response elements and proved to bind specifically to the cellular nuclear protein serum response transcription factor. Reporter gene constructions containing four tandem copies of these elements displayed up to 13-fold increased basal enhancer

  11. Serum Uric Acid Level and Diverse Impacts on Regional Arterial Stiffness and Wave Reflection

    PubMed Central

    Bian, Suyan; Guo, Hongyang; Ye, Ping; Luo, Leiming; Wu, Hongmei; Xiao, Wenkai

    2012-01-01

    Background: Both increased arterial stiffness and hyperuricaemia are associated with elevated cardiovascular risks. Little is known about the relations of serum uric acid (UA) level to regional arterial stiffness and wave reflection. The aim of the study was to investigate the gender-specific association of serum UA and indices of arterial function in a community-based investigation in China. Methods: Cross-sectional data from 2374 adults (mean age 58.24 years) who underwent routine laboratory tests, regional pulse wave velocity (PWV) and pulse wave analysis measurements were analyzed in a gender-specific manner. None of the participants had atherosclerotic cardiovascular disease, chronic renal failure, systemic inflammatory disease, gout, or were under treatment which would affect serum UA level. Results: Men had higher serum UA level than women. Subjects with hyperuricaemia had significantly higher carotid-ankle PWV in both genders (P< 0.05), and the carotid-femoral PWV (PWVc-f) was higher in women (P< 0.001) while the augmentation index was marginally lower in men (P = 0.049). Multiple regression analysis showed that serum UA was an independent determinant only for PWVc-f in women (β = 0.104, P = 0.027) when adjusted for atherogenic confounders. No other independent relationship was found between UA level and other surrogates of arterial stiffness. Conclusions: Serum UA levels are associated with alterations in systemic arterial stiffness that differ in men and women. Women might be more susceptible to large vascular damage associated with hyperuricaemia. PMID:23113222

  12. Cooperative Regulation of the Activity of Factor Xa within Prothrombinase by Discrete Amino Acid Regions from Factor Va Heavy Chain†

    PubMed Central

    2008-01-01

    The prothrombinase complex catalyzes the activation of prothrombin to α-thrombin. We have repetitively shown that amino acid region 695DYDY698 from the COOH terminus of the heavy chain of factor Va regulates the rate of cleavage of prothrombin at Arg271 by prothrombinase. We have also recently demonstrated that amino acid region 334DY335 is required for the optimal activity of prothrombinase. To assess the effect of these six amino acid residues on cofactor activity, we created recombinant factor Va molecules combining mutations at amino acid regions 334–335 and 695−698 as follows: factor V3K (334DY335 → KF and 695DYDY698 → KFKF), factor VKF/4A (334DY335 → KF and 695DYDY698 → AAAA), and factor V6A (334DY335 → AA and 695DYDY698 → AAAA). The recombinant factor V molecules were expressed and purified to homogeneity. Factor Va3K, factor VaK4/4A, and factor Va6A had reduced affinity for factor Xa, when compared to the affinity of the wild-type molecule (factor VaWt) for the enzyme. Prothrombinase assembled with saturating concentrations of factor Va3K had a 6-fold reduced second-order rate constant for prothrombin activation compared to the value obtained with prothrombinase assembled with factor VaWt, while prothrombinase assembled with saturating concentrations of factor VaKF/4A and factor Va6A had approximately 1.5-fold reduced second-order rate constants. Overall, the data demonstrate that amino acid region 334–335 together with amino acid region 695−698 from factor Va heavy chain are part of a cooperative mechanism within prothrombinase regulating cleavage and activation of prothrombin by factor Xa. PMID:18991406

  13. Distribution and Evolution of Yersinia Leucine-Rich Repeat Proteins.

    PubMed

    Hu, Yueming; Huang, He; Hui, Xinjie; Cheng, Xi; White, Aaron P; Zhao, Zhendong; Wang, Yejun

    2016-08-01

    Leucine-rich repeat (LRR) proteins are widely distributed in bacteria, playing important roles in various protein-protein interaction processes. In Yersinia, the well-characterized type III secreted effector YopM also belongs to the LRR protein family and is encoded by virulence plasmids. However, little has been known about other LRR members encoded by Yersinia genomes or their evolution. In this study, the Yersinia LRR proteins were comprehensively screened, categorized, and compared. The LRR proteins encoded by chromosomes (LRR1 proteins) appeared to be more similar to each other and different from those encoded by plasmids (LRR2 proteins) with regard to repeat-unit length, amino acid composition profile, and gene expression regulation circuits. LRR1 proteins were also different from LRR2 proteins in that the LRR1 proteins contained an E3 ligase domain (NEL domain) in the C-terminal region or an NEL domain-encoding nucleotide relic in flanking genomic sequences. The LRR1 protein-encoding genes (LRR1 genes) varied dramatically and were categorized into 4 subgroups (a to d), with the LRR1a to -c genes evolving from the same ancestor and LRR1d genes evolving from another ancestor. The consensus and ancestor repeat-unit sequences were inferred for different LRR1 protein subgroups by use of a maximum parsimony modeling strategy. Structural modeling disclosed very similar repeat-unit structures between LRR1 and LRR2 proteins despite the different unit lengths and amino acid compositions. Structural constraints may serve as the driving force to explain the observed mutations in the LRR regions. This study suggests that there may be functional variation and lays the foundation for future experiments investigating the functions of the chromosomally encoded LRR proteins of Yersinia. PMID:27217422

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

    PubMed Central

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

    2012-01-01

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

  15. A 1.8-Mb YAC contig in Xp11.23: identification of CpG islands and physical mapping of CA repeats in a region of high gene density.

    PubMed

    Coleman, M P; Németh, A H; Campbell, L; Raut, C P; Weissenbach, J; Davies, K E

    1994-05-15

    The genes ARAF1, SYN1, TIMP, and PFC are clustered within 70 kb of one another, and, as reported in the accompanying paper (J. Knight et al., 1994, Genomics 21: 180-187), at least four more genes map within 400 kb: a cluster of Krüppel-type zinc finger genes (including ZNF21, ZNF41, and ZNF81) and ELK-1, a member of the ets oncogene superfamily. This gene-rich region is of particular interest because of the large number of disease genes mapping to Xp11.23: at least three eye diseases (retinitis pigmentosa type 2, congenital stationary night blindness CSNB1, and Aland Island eye disease), Wiskott-Aldrich syndrome, X-linked nephrolithiasis, and a translocation breakpoint associated with synovial sarcoma. We have constructed a 1.8-Mb YAC contig in this region, confirming the link between TIMP and OATL1 reported by Knight et al. (1994) and extending the map in the distal direction. To investigate the likelihood that more genes are located within this region, we have carried out detailed mapping of rare-cutter restriction sites in these YACs and identified seven CpG islands. At least six of these islands are located over 50 kb from any known gene locations, suggesting that the region contains at least this many as yet unidentified genes. We have also mapped the physical locations of six highly polymorphic CA repeats within the contig, thus integrating the physical, genetic, and transcriptional maps of the region and facilitating the mapping and identification of disease genes.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:8088827

  16. USING THE REGIONAL ACID DEPOSITION MODEL TO DETERMINE THE NITROGEN DEPOSITION AIRSHED OF THE CHESAPEAKE BAY WATERSHED

    EPA Science Inventory

    The Regional Acid Deposition Model, RADM, an advanced Eulerian model, is used to develop an estimate of the primary airshed of nitrogen oxide (NOx) emissions that is contributing nitrogen deposition to the Chesapeake Bay watershed. rief description of RADM together with a summary...

  17. A domain of human immunodeficiency virus type 1 Vpr containing repeated H(S/F)RIG amino acid motifs causes cell growth arrest and structural defects.

    PubMed Central

    Macreadie, I G; Castelli, L A; Hewish, D R; Kirkpatrick, A; Ward, A C; Azad, A A

    1995-01-01

    Vpr is a virion-associated protein of human immunodeficiency type 1 (HIV-1) whose function in acquired immunodeficiency syndrome (AIDS) has been uncertain. Employing the yeast Saccharomyces cerevisiae as a model to examine the effects of HIV-1 auxiliary proteins on basic cellular functions, we found that the vpr gene caused cell growth arrest and structural defects indicated by osmotic sensitivity and gross cell enlargement. Production of various domains by gene expression showed that this effect arose from within the carboxyl-terminal third of the Vpr protein and implicated the sequence HFRIGCRHSRIG, containing two H(S/F)RIG motifs. Electroporation with a series of peptides containing these motifs caused structural defects in yeast that resulted in osmotic sensitivity. A protein with functions relating to the yeast cytoskeleton, Sac1p [Cleves, A. E., Novick, P.J. & Bankaitis, V.A. (1989) J. Cell Biol. 109, 2939-2950], shows sequence similarity to Vpr, and Vpr's effect in yeast may be to disrupt normal Sac1p functions. The Sac1p equivalent has not yet been described in mammalian cells, but in rhabdomyosarcoma and osteosarcoma cell lines Vpr also caused gross cell enlargement and replication arrest [Levy, D.N., Fernandes, L.S., Williams, W.V. & Weiner, D.B. (1993) Cell 72, 541-550]. We note that there is a correlation between the region containing the H(S/F)RIG motifs and the pathogenicity of primate lentiviruses and we suggest that the function of Vpr may be to bring about cell growth arrest and/or cytoskeletal changes as an early step in HIV-1 infection. Images Fig. 2 Fig. 3 Fig. 4 Fig. 6 Fig. 7 PMID:7708721

  18. Reconfigurable multiport EPON repeater

    NASA Astrophysics Data System (ADS)

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

    2009-11-01

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

  19. Expression of sialic acid and polysialic acid in serogroup B Neisseria meningitidis: divergent transcription of biosynthesis and transport operons through a common promoter region.

    PubMed Central

    Swartley, J S; Ahn, J H; Liu, L J; Kahler, C M; Stephens, D S

    1996-01-01

    We studied capsule-defective (Cap-) serogroup B meningococcal mutants created through Tn916 or omega-fragment mutagenesis. The Cap- phenotypes were the results of insertions in three of four linked genes (synX, synC, and synD) involved in CMP-N-acetylneuraminic acid and polysialic acid capsule biosynthesis, and in ctrA the first of four linked genes involved in capsule membrane transport. Mutations in the CMP-N-acetylneuraminic acid biosynthesis genes synX and synC caused defects in lipooligosaccharide sialylation but not mutations in the putative (alpha2 -> 8)-linked polysialyltransferase (synD) or in ctrA. Reverse transcriptase PCR studies indicated that the four biosynthesis genes (synX to -D) and the capsule transport genes (ctr to -D) were separately transcribed as operons. The operons were separated by a 134-bp intergenic region. Primer extension of synX and ctrA demonstrated that transcription of the operons was divergently initiated from adjacent start sites present in the intergenic region. Both transcriptional start sites were preceded by a perfect -10 Pribnow promoter binding region. The synX to -D, but not the ctrA to -D, transcriptional start site was preceded by a sequence bearing strong homology to the consensus sigma 70 -35 promoter binding sequence. Both promoters showed transcriptional activity when cloned behind a lacZ reporter gene in Escherichia coli. Our results confirm the intrinsic relationship between polysialic acid capsule biosynthesis and lipooligosaccharide sialylation pathways in group B Neisseria meningitidis. Our study also suggests that the intergenic region separating the synX to -D and ctrA to -D operons is an important control point for the regulation of group B capsule expression through coordinated transcriptional regulation of the synX to -D and drA to -D promoters. PMID:8763931

  20. Quantum repeated games revisited

    NASA Astrophysics Data System (ADS)

    Frąckiewicz, Piotr

    2012-03-01

    We present a scheme for playing quantum repeated 2 × 2 games based on Marinatto and Weber’s approach to quantum games. As a potential application, we study the twice repeated Prisoner’s Dilemma game. We show that results not available in the classical game can be obtained when the game is played in the quantum way. Before we present our idea, we comment on the previous scheme of playing quantum repeated games proposed by Iqbal and Toor. We point out the drawbacks that make their results unacceptable.

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

    PubMed Central

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

    2011-01-01

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

  2. Oligomerization of the hydrophobic heptad repeat of gp41.

    PubMed Central

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

    1995-01-01

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

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

    PubMed

    Chen, Yushun; Lin, Lian-Shin

    2009-03-15

    Data from 5 wet deposition stations and 21 streams during 1980-2006 were analyzed to investigate chemical responses of streams to reduced acidic deposition in the central Appalachian Mountain region of West Virginia, USA. Wet deposition of acidic anions (i.e., sulfate, nitrate, and chloride) and hydrogen ions decreased significantly during the studied time period. Stream sulfate showed a delayed response to the reduced acidic deposition, and showed a decrease in the 2000s (-5.54 microeq L(-1) yr(-1)) and the whole period (-0.49 microeq L(-1) yr(-1)). No significant trend of stream nitrate+nitrite and chloride was observed. Stream alkalinity increased in the 1990s (+23.33 microeq L(-1) yr(-1)) and the whole period (+7.26 microeq L(-1) yr(-1)). Stream hydrogen ions decreased in the 1990s (-0.002 microeq L(-1) yr(-1)), 2000s (-0.001 microeq L(-1) yr(-1)), and the whole period (-0.001 microeq L(-1) yr(-1)). Compared with most acidic streams and lakes in the United States and Europe, a lower decreasing rate of hydrogen ions and higher increasing rate of alkalinity were observed in the alkaline West Virginian streams in the 1990s. However, due to their initial negative or zero alkalinity values, those acidic streams showed a higher percent increase in alkalinity than that in the alkaline West Virginian streams (from 800 microeq L(-1) yr(-1) to 1200 microeq L(-1) yr(-1)). Total aluminum in the West Virginian streams decreased in the 1990s (-0.67 micromol L(-1) yr(-1)) and the whole period (-0.22 micromol L(-1) yr(-1)). The current study advanced our understanding of streams' responses to the reduced acidic deposition in the Mid-Appalachians since the passage of the 1970 and 1990 Amendments to the United States Clean Air Act (US CAAA). PMID:19073337

  4. Contribution of Amino Acid Region 334−335 from Factor Va Heavy Chain to the Catalytic Efficiency of Prothrombinase†

    PubMed Central

    2008-01-01

    We have demonstrated that amino acids E323, Y324, E330, and V331 from the factor Va heavy chain are required for the interaction of the cofactor with factor Xa and optimum rates of prothrombin cleavage. We have also shown that amino acid region 332−336 contains residues that are important for cofactor function. Using overlapping peptides, we identified amino acids D334 and Y335 as contributors to cofactor activity. We constructed recombinant factor V molecules with the mutations D334 → K and Y335 → F (factor VKF) and D334 → A and Y335 → A (factor VAA). Kinetic studies showed that while factor VaKF and factor VaAA had a KD for factor Xa similar to the KD observed for wild-type factor Va (factor VaWT), the clotting activities of the mutant molecules were impaired and the kcat of prothrombinase assembled with factor VaKF and factor VaAA was reduced. The second-order rate constant of prothrombinase assembled with factor VaKF or factor VaAA for prothrombin activation was ∼10-fold lower than the second-order rate constant for the same reaction catalyzed by prothrombinase assembled with factor VaWT. We also created quadruple mutants combining mutations in the amino acid region 334–335 with mutations at the previously identified amino acids that are important for factor Xa binding (i.e., E323Y324 and E330V331). Prothrombinase assembled with the quadruple mutant molecules displayed a second-order rate constant up to 400-fold lower than the values obtained with prothrombinase assembled with factor VaWT. The data demonstrate that amino acid region 334–335 is required for the rearrangement of enzyme and substrate necessary for efficient catalysis of prothrombin by prothrombinase. PMID:18537263

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

    PubMed

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

    2016-07-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-09-01

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-03-01

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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

    Roy, Susmita; Dhar, Pubali; Ghosh, Santinath

    2012-12-01

    This study investigated the fatty acid composition of lipid present in breast milk of mothers residing in urban and suburban regions of West Bengal with special emphasis on n-6 and n-3 polyunsaturated fatty acids, which played a crucial role in the growth and development of neonates. Milk samples collected from 135 mothers of middle income group (average monthly income around 'Rs 10,000/-') were analysed by gas liquid chromatography after extraction and transmethylation to determine fatty acid composition. Information about the dietary intake of individual mothers was obtained through food frequency questionnaire. The fractions of n-6 and n-3 polyunsaturated fatty acids available in milk of urban mothers were 13.59 ± 0.94 and 3.65 ± 0.49, respectively, and in suburban mothers 12.74 ± 0.89 and 4.36 ± 0.39, respectively. The green leafy vegetables, fishes and vegetable oils were the major sources of essential fatty acids in the diet of the experimental groups of Bengali mothers. This study revealed a relationship between the alimentary habits of mothers and the concentration of essential fatty acids in breast milk of Bengali mothers. PMID:22575018

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

    SciTech Connect

    Chakravarty, R.; Rice, R.H.

    1989-01-05

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

  13. Grouping of amino acids and recognition of protein structurally conserved regions by reduced alphabets of amino acids.

    PubMed

    Li, Jing; Wang, Wei

    2007-06-01

    Sequence alignment is a common method for finding protein structurally conserved/similar regions. However, sequence alignment is often not accurate if sequence identities between to-be-aligned sequences are less than 30%. This is because that for these sequences, different residues may play similar structural roles and they are incorrectly aligned during the sequence alignment using substitution matrix consisting of 20 types of residues. Based on the similarity of physicochemical features, residues can be clustered into a few groups. Using such simplified alphabets, the complexity of protein sequences is reduced and at the same time the key information encoded in the sequences remains. As a result, the accuracy of sequence alignment might be improved if the residues are properly clustered. Here, by using a database of aligned protein structures (DAPS), a new clustering method based on the substitution scores is proposed for the grouping of residues, and substitution matrices of residues at different levels of simplification are constructed. The validity of the reduced alphabets is confirmed by relative entropy analysis. The reduced alphabets are applied to recognition of protein structurally conserved/similar regions by sequence alignment. The results indicate that the accuracy or efficiency of sequence alignment can be improved with the optimal reduced alphabet with N around 9. PMID:17609897

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

    PubMed

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

    1974-07-01

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

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

    PubMed

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

    2005-06-01

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

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

    PubMed

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

    2015-01-01

    Acidification of blood entering a membrane lung (ML) with lactic acid enhances CO2 removal (VCO2ML). We compared the effects of infusion of acetic, citric, and lactic acids on VCO2ML. Three sheep were connected to a custom-made circuit, consisting of a Hemolung device (Alung Technologies, Pittsburgh, PA), a hemofilter (NxStage, NxStage Medical, Lawrence, MA), and a peristaltic pump recirculating ultrafiltrate before the ML. Blood flow was set at 250 ml/min, gas flow (GF) at 10 L/min, and recirculating ultrafiltrate flow at 100 ml/min. Acetic (4.4 M), citric (0.4 M), or lactic (4.4 M) acids were infused in the ultrafiltrate at 1.5 mEq/min, for 2 hours each, in randomized fashion. VCO2ML was measured by the Hemolung built-in capnometer. Circuit and arterial blood gas samples were collected at baseline and during acid infusion. Hemodynamics and ventilation were monitored. Acetic, citric, or lactic acids similarly enhanced VCO2ML (+35%), from 37.4 ± 3.6 to 50.6 ± 7.4, 49.8 ± 5.6, and 52.0 ± 8.2 ml/min, respectively. Acids similarly decreased pH, increased pCO2, and reduced HCO3 of the post-acid extracorporeal blood sample. No significant effects on arterial gas values, ventilation, or hemodynamics were observed. In conclusion, it is possible to increase VCO2ML by more than one-third using any one of the three metabolizable acids. PMID:26273934

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

    SciTech Connect

    Shiheido, Hirokazu Shimizu, Jun

    2015-02-20

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

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

    PubMed Central

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

    2015-01-01

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

  19. Honesty through repeated interactions.

    PubMed

    Rich, Patricia; Zollman, Kevin J S

    2016-04-21

    In the study of signaling, it is well known that the cost of deception is an essential element for stable honest signaling in nature. In this paper, we show how costs for deception can arise endogenously from repeated interactions between individuals. Utilizing the Sir Philip Sidney game as an illustrative case, we show that repeated interactions can sustain honesty with no observable signal costs, even when deception cannot be directly observed. We provide a number of potential experimental tests for this theory which distinguish it from the available alternatives. PMID:26869213

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

    USGS Publications Warehouse

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

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  2. Acid particles and the tracheobronchial region of the respiratory system. An irritation-signaling model for possible health effects

    SciTech Connect

    Hattis, D.; Wasson, J.M.; Page, G.S.; Stern, B.; Franklin, C.A.

    1987-09-01

    This paper explores some detailed mechanistic hypotheses for the possible action of acid particles on the tracheobronchial region of the human respiratory system. Because of the buffering capacity and volume of mucus produced per day it appears doubtful that ordinary ambient exposures to acid particles could markedly change the overall pH of tracheobronchial mucus considered as a whole. However, it is possible that individual acidic particles could contain enough acid to deliver localized irritant signals that could be the triggers for enhanced mucus secretion and cell division in sensitive portions of the bronchial tree, and thereby contribute to the processes involved in chronic bronchitis. Depending on the exact pH depression required for a signal to be perceived by the tracheobronchial epithelium, the acid content of the incoming particles per unit weight, and the effect of neutralization by ammonia in the upper respiratory tract, the minimum size of an acidic particle required to deliver a perceptible signal might range from about 0.4 to 0.7 microns for portions of the epithelium that are frequently swept by 4-micron mucus droplets. Since particle number per unit weight declines dramatically with increasing particle size, the most potent fraction of particles in terms of signals delivered per /sup +/g/m/sup 3/ is likely to be just above the minimum size that is needed to produce an effective signal. The model developed here makes predictions of the relative potency of particles of different size and acid delivery capacity that could be tested in both experimental animal systems and human epidemiological studies.

  3. Genetic analysis of the cell binding domain region of the chicken fibronectin gene.

    PubMed

    Kubomura, S; Obara, M; Karasaki, Y; Taniguchi, H; Gotoh, S; Tsuda, T; Higashi, K; Ohsato, K; Hirano, H

    1987-11-20

    We have determined the nucleotide sequence of the cell binding domain region of the chicken fibronectin gene and analyzed it evolutionaly. We present here the complete nucleotide sequence of 4.3 kb HindIII/EcoRI segment from the clone lambda FC23 of the chicken fibronectin gene. There were five exons in this segment. When we lined up the amino acid of exons 28, 29 and 31, three alignments, known as the Type III repeat, appeared. Tetrapeptide, -RGDS-, called the cell binding domain, existed in the second repeat, coding exon 30. It was presumed that the Type III repeats were composed of two exons in the chicken gene, the same as in the rat and humans. We found repeatedly appearing amino-acid sequences such as -TIT- (three arrays in these Type III repeats) but also found one of the amino acids substituted in the tripeptide in these Type III repeats (seven arrays). We analyzed these repeats from the point of view of evolution. We used three of the nucleotide sequences (12-18 bp) coding such -TIT- repeats as a unit length for comparing the various homologies after dividing the coding region into 56 segments. The mutual homology of the divided segments to each one of three showed 53% on average. On the other hand, the mutual nucleotide homology of the Type III repeat was 44%. This suggested that the Type III repeat may have been developed by frequent duplication of small gene units. PMID:2823899

  4. Role of the Acidic Hirudin-like COOH-Terminal Amino Acid Region of Factor Va Heavy Chain in the Enhanced Function of Prothrombinase†‡

    PubMed Central

    2008-01-01

    Prothrombinase activates prothrombin through initial cleavage at Arg320 followed by cleavage at Arg271. This pathway is characterized by the generation of an enzymatically active, transient intermediate, meizothrombin, that has increased chromogenic substrate activity but poor clotting activity. The heavy chain of factor Va contains an acidic region at the COOH terminus (residues 680−709). We have shown that a pentapeptide from this region (DYDYQ) inhibits prothrombin activation by prothrombinase by inhibiting meizothrombin generation. To ascertain the function of these regions, we have created a mutant recombinant factor V molecule that is missing the last 30 amino acids from the heavy chain (factor VΔ680−709) and a mutant molecule with the 695DYDY698 → AAAA substitutions (factor V4A). The clotting activities of both recombinant mutant factor Va molecules were impaired compared to the clotting activity of wild-type factor Va (factor VaWt). Using an assay employing purified reagents, we found that prothrombinase assembled with factor VaΔ680−709 displayed an ∼39% increase in kcat, while prothrombinase assembled with factor Va4A exhibited an ∼20% increase in kcat for the activation of prothrombin as compared to prothrombinase assembled with factor VaWt. Gel electrophoresis analyzing prothrombin activation by prothrombinase assembled with the mutant molecules revealed a delay in prothrombin activation with persistence of meizothrombin. Our data demonstrate that the COOH-terminal region of factor Va heavy chain is indeed crucial for coordinated prothrombin activation by prothrombinase because it regulates meizothrombin cleavage at Arg271 and suggest that this portion of factor Va is partially responsible for the enhanced procoagulant function of prothrombinase. PMID:18590276

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

    NASA Technical Reports Server (NTRS)

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

    1988-01-01

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

  6. Repeated Causal Decision Making

    ERIC Educational Resources Information Center

    Hagmayer, York; Meder, Bjorn

    2013-01-01

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

  7. Bidirectional Manchester repeater

    NASA Technical Reports Server (NTRS)

    Ferguson, J.

    1980-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2012-01-01

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

  10. Regional scale patterns in seagrass defences: Phenolic acid content in Zostera noltii

    NASA Astrophysics Data System (ADS)

    Grignon-Dubois, Micheline; Rezzonico, Bernadette; Alcoverro, Teresa

    2012-12-01

    Secondary metabolites play an important role in protecting plants from herbivores or pathogens. Despite this, few studies have investigated the presence and the concentration of those compounds over broad spatial scales in seagrasses. Here we analysed the presence and abundance of specific phenolic compounds of Zostera noltii from four different meadows located across the Atlantic and the Mediterranean coast. Three phenolic acids have been found in the samples of Z. noltii: rosmarinic, caffeic and zosteric acids. The proportion of the three compounds varied substantially with the major proportion comprising rosmarinic acid (RA, mean value 94%) followed by zosteric acid (ZA, mean value 4%) and caffeic acid (CAF, mean value 2%). Z. noltii metabolic compounds varied notably between sites. The highest concentrations in RA were found in the Cadiz Bay with values of 11,254 (55 SD) μg g-1 dry wt, while the lowest were observed in the Alfacs Bay (Ebro) with values of 823 (7 SD) μg g-1 dry wt. The highest concentrations in ZA were also observed in the Cadiz Bay with values of 727 (6 SD) μg g-1 dry wt, while the lowest were observed in the Sa Nitja Bay (Menorca Island) with values of 20 (4 SD) μg g-1 dry wt. Finally, the concentrations in CAF remain very low at each site (17-69 μg g-1 dry wt), with the lowest observed in Arcachon. Their proportions remained relatively constant, indicating that most phenolic acids responded together. Documenting the presence of those compounds in living tissues of Z. noltii and how they vary in abundance between seagrass meadows across large geographical scales is a crucial first step to understand the large-scale level response of the plant to potential pathogens, herbivore outbreaks or other ecological processes.

  11. EFFECTS OF ACID RAIN AND GASEOUS POLLUTANTS ON FOREST PRODUCTIVITY: A REGIONAL SCALE APPROACH

    EPA Science Inventory

    Increased industrialization of the eastern U.S. over the past several decades has led to regional scale buildup of atmospheric pollutants and concern over possible losses in forest productivity within this region. This paper describes the rationale, methodology, and some prelimin...

  12. Assembly of Repeat Content Using Next Generation Sequencing Data

    SciTech Connect

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

    2014-03-17

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

  13. COMPARISON OF SULFUR MEASUREMENTS FROM A REGIONAL FINE PARTICLE NETWORK WITH CONCURRENT ACID MODES NETWORK RESULTS

    EPA Science Inventory

    The Fine Particle Network (FPN), a system of fine particle (less than 2.5 um) samplers, was operated at 41 sites selected from the Environmental Protection Agency Acid MODES program during a two year period in 1988-90. he 24-hour sample results included fine particle mass and the...

  14. [Relationships between soil moisture and needle-fall in Masson pine forests in acid rain region of Chongqing, Southwest China].

    PubMed

    Wang, Yi-Hao; Wang, Yan-Hui; Li, Zhen-Hua; Yu, Peng-Tao; Xiong, Wei; Hao, Jia; Duan, Jian

    2012-10-01

    From March 2009 to November 2011, an investigation was conducted on the spatiotemporal variation of soil moisture and its effects on the needle-fall in Masson pine (Pinus massoniana) forests in acid rain region of Chongqing, Southeast China, with the corresponding soil moisture thresholds determined. No matter the annual precipitation was abundant, normal or less than average, the seasonal variation of soil moisture in the forests could be obviously divided into four periods, i.e., sufficient (before May), descending (from June to July), drought (from August to September), and recovering (from October to November). With increasing soil depth, the soil moisture content increased after an initial decrease, but the difference of the soil moisture content among different soil layers decreased with decreasing annual precipitation. The amount of monthly needle-fall in the forests in growth season was significantly correlated with the water storage in root zone (0-60 cm soil layer), especially in the main root zone (20-50 cm soil layer). Soil field capacity (or capillary porosity) and 82% of field capacity (or 80% of capillary porosity) were the main soil moisture thresholds affecting the litter-fall. It was suggested that in acid rain region, Masson pine forest was easily to suffer from water deficit stress, especially in dry-summer period. The water deficit stress, together with already existed acid rain stress, would further threaten the health of the Masson forest. PMID:23359920

  15. A recombinant chimera composed of repeat region RR1 of Mycoplasma hyopneumoniae adhesin with Pseudomonas exotoxin: in vivo evaluation of specific IgG response in mice and pigs.

    PubMed

    Chen, J R; Liao, C W; Mao, S J; Weng, C N

    2001-06-22

    Using the binding and translocation domain of Pseudomonas exotoxin A [domain III deleted PE termed PE(DeltaIII)] as a vehicle, this study characterized and evaluated a novel application of PE toxin in Mycoplasma hyopneumoniae adhesin used as an immunogen. PCR and sequence analysis revealed that 16 copies of AAKPV(E) in tandem repeat region 1 (RR1) of M. hyopneumoniae 97kDa adhesion were successfully fused to the downstream of PE(DeltaIII) to create a subunit vaccine, i.e. PE(DeltaIII)-RR1. This chimeric protein, over-expressed in inclusion bodies of E. coli BL21(DE3)pLysS, was characterized by a monoclonal antibody (MAb) F2G5 prepared against RR1 of the 97kDa adhesin and was readily purified. The data indicated that the epitope recognized by MAb F2G5 was located in the structure of PE(DeltaIII)-RR1. Using ELISA and Western blot analyses, the specific IgG immune response against RR1 and whole adhesin in mice immunized with PE(DeltaIII)-RR1 was found more marked than that in mice immunized with the M. hyopneumoniae whole cells. Similarly, PE(DeltaIII)-RR1 also stimulated a remarkable IgG response against RR1 in pigs compared to that in pigs immunized with the conventional M. hyopneumoniae vaccine. The PE(DeltaIII)-RR1 would be potentially useful for the future development of a M. hyopneumoniae adhesin vaccine. PMID:11348771

  16. Two-step identification of taro (Colocasia esculenta cv. Xinmaoyu) using specific psbE-petL and simple sequence repeat-sequence characterized amplified regions (SSR-SCAR) markers.

    PubMed

    Dai, H J; Zhang, Y M; Sun, X Q; Xue, J Y; Li, M M; Cao, M X; Shen, X L; Hang, Y Y

    2016-01-01

    Colocasia esculenta cv. Xinmaoyu is an eddoe-type taro cultivar local to Taicang, Jiangsu Province, China; it is characterized by its pure flavor, glutinous texture, and high nutritional value. Due to its excellent qualities, the Trademark Office of the State Administration for Industry and Commerce of the People's Republic of China awarded Xinmaoyu, a geographical indication certification in 2014. Therefore, there is an urgent need to develop an efficient molecular marker for the specific identification of this cultivar, which would greatly facilitate the conservation and utilization of this unique germplasm resource. In the present study, amplifying the psbE-petL fragment from two dasheen-type and seven eddoe-type taro cultivars revealed three conserved insertions/deletions among sequences from the two taro types. Based on these sequence differences, a pair of site-specific primers was designed targeting the psbE-petL sequence from the dasheen-type taro, which specifically amplified a DNA band in all individuals from cultivars of this type, but not in those from the seven eddoe-type cultivars. To discriminate Xinmaoyu from the other eddoe-type taro cultivars, a pair of simple sequence repeat-sequence characterized amplified region (SSR-SCAR) primers was further developed to specifically amplify a DNA band from all Xinmaoyu individuals, but not from individuals of other eddoe-type taro cultivars. In conclusion, through a two-step-screening procedure using psbE-petL and SSR-SCAR markers, we developed a pair of primers that could specifically discriminate Xinmaoyu from nine taro cultivars commonly cultivated in Jiangsu Province and Fujian Province. PMID:27525909

  17. Responses of 20 lake-watersheds in the Adirondack region of New York to historical and potential future acidic deposition.

    PubMed

    Zhou, Qingtao; Driscoll, Charles T; Sullivan, Timothy J

    2015-04-01

    Critical loads (CLs) and dynamic critical loads (DCLs) are important tools to guide the protection of ecosystems from air pollution. In order to quantify decreases in acidic deposition necessary to protect sensitive aquatic species, we calculated CLs and DCLs of sulfate (SO4(2-))+nitrate (NO3-) for 20 lake-watersheds from the Adirondack region of New York using the dynamic model, PnET-BGC. We evaluated lake water chemistry and fish and total zooplankton species richness in response to historical acidic deposition and under future deposition scenarios. The model performed well in simulating measured chemistry of Adirondack lakes. Current deposition of SO4(2-)+NO3-, calcium (Ca2+) weathering rate and lake acid neutralizing capacity (ANC) in 1850 were related to the extent of historical acidification (1850-2008). Changes in lake Al3+ concentrations since the onset of acidic deposition were also related to Ca2+ weathering rate and ANC in 1850. Lake ANC and fish and total zooplankton species richness were projected to increase under hypothetical decreases in future deposition. However, model projections suggest that lake ecosystems will not achieve complete chemical and biological recovery in the future. PMID:25544337

  18. Accumulate repeat accumulate codes

    NASA Technical Reports Server (NTRS)

    Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

    2004-01-01

    In this paper we propose an innovative channel coding scheme called 'Accumulate Repeat Accumulate codes' (ARA). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes, thus belief propagation can be used for iterative decoding of ARA codes on a graph. The structure of encoder for this class can be viewed as precoded Repeat Accumulate (RA) code or as precoded Irregular Repeat Accumulate (IRA) code, where simply an accumulator is chosen as a precoder. Thus ARA codes have simple, and very fast encoder structure when they representing LDPC codes. Based on density evolution for LDPC codes through some examples for ARA codes, we show that for maximum variable node degree 5 a minimum bit SNR as low as 0.08 dB from channel capacity for rate 1/2 can be achieved as the block size goes to infinity. Thus based on fixed low maximum variable node degree, its threshold outperforms not only the RA and IRA codes but also the best known LDPC codes with the dame maximum node degree. Furthermore by puncturing the accumulators any desired high rate codes close to code rate 1 can be obtained with thresholds that stay close to the channel capacity thresholds uniformly. Iterative decoding simulation results are provided. The ARA codes also have projected graph or protograph representation that allows for high speed decoder implementation.

  19. Duct Leakage Repeatability Testing

    SciTech Connect

    Walker, Iain; Sherman, Max

    2014-01-01

    Duct leakage often needs to be measured to demonstrate compliance with requirements or to determine energy or Indoor Air Quality (IAQ) impacts. Testing is often done using standards such as ASTM E1554 (ASTM 2013) or California Title 24 (California Energy Commission 2013 & 2013b), but there are several choices of methods available within the accepted standards. Determining which method to use or not use requires an evaluation of those methods in the context of the particular needs. Three factors that are important considerations are the cost of the measurement, the accuracy of the measurement and the repeatability of the measurement. The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards.

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

    PubMed

    Shiheido, Hirokazu; Shimizu, Jun

    2015-02-20

    BEN domain-containing protein 3 (BEND3) has recently been reported to function as a heterochromatin-associated protein in transcriptional repression in the nucleus. BEND3 should have nuclear localization signals (NLSs) to localize to the nucleus in light of its molecular weight, which is higher than that allowed to pass through nuclear pore complexes. We here analyzed the subcellular localization of deletion/site-directed mutants of human BEND3 by an immunofluorescence assay in an attempt to identify the amino acids essential for its nuclear localization. We found that three basic amino acid residues located in the N-terminal region of BEND3 (BEND356-58, KRK) are essential, suggesting that these residues play a role as a functional NLS. These results provide valuable information for progressing research on BEND3. PMID:25600804

  1. Spectroscopic and Computational Study of Acetic Acid and Its Cyclic Dimer in the Near-Infrared Region.

    PubMed

    Beć, Krzysztof B; Futami, Yoshisuke; Wójcik, Marek J; Nakajima, Takahito; Ozaki, Yukihiro

    2016-08-11

    Anharmonic vibrational analysis of near-infrared (NIR) spectra of acetic acid was carried out by anharmonic quantum chemical calculation in a wide concentration range of its CCl4 solution. By predicting vibrational spectra of acetic acid for the first time over a wide NIR region, it was possible to elucidate the influence of the formation of acetic acid cyclic dimer on its NIR spectrum. Quantum chemical simulations were based on coupled cluster and density functional theory quantum methods. Additionally, Møller-Plesset perturbation theory was employed for the additional calculation of hydrogen bonding stabilization energies. An anharmonic vibrational analysis was performed with the use of generalized second-order vibrational perturbation theory (GVPT2). A hybrid approach was assumed, in which monomeric species was treated by CCSD(T)/aug-cc-pVDZ (harmonic approximation) and B3LYP/SNSD (anharmonic approximation) methods. For the cyclic dimer, B3LYP and B2PLYP single and double hybrid functionals, paired with an SNSD basis set, were employed. DFT calculations were augmented with additional empirical dispersion correction. It was found that quantum chemically calculated vibrational modes in the NIR region are in a good agreement with experimental data. The results of anharmonic vibrational analysis were supported by a harmonic shift analysis, for elucidating the very strong anharmonic coupling observed between stretching modes of hydrogen bonded bridge in the cyclic dimer. However, the calculated wavenumbers for combination modes of double hydrogen bonded bridge in the cyclic dimer, which are very sensitive to the formation of hydrogen bonding, were found to be underestimated by quantum chemical methods. Therefore, by band fitting, the wavenumbers and shape parameters for these bands were found, and the modeled spectra were adjusted accordingly. A high accuracy of simulated spectra was achieved, and a detailed analysis of the experimental NIR spectra of acetic acid

  2. Responses of grape berry anthocyanin and titratable acidity to the projected climate change across the Western Australian wine regions.

    PubMed

    Barnuud, Nyamdorj N; Zerihun, Ayalsew; Mpelasoka, Freddie; Gibberd, Mark; Bates, Bryson

    2014-08-01

    More than a century of observations has established that climate influences grape berry composition. Accordingly, the projected global climate change is expected to impact on grape berry composition although the magnitude and direction of impact at regional and subregional scales are not fully known. The aim of this study was to assess potential impacts of climate change on levels of berry anthocyanin and titratable acidity (TA) of the major grapevine varieties grown across all of the Western Australian (WA) wine regions. Grape berry anthocyanin and TA responses across all WA wine regions were projected for 2030, 2050 and 2070 by utilising empirical models that link these berry attributes and climate data downscaled (to ∼5 km resolution) from the csiro_mk3_5 and miroc3_2_medres global climate model outputs under IPCC SRES A2 emissions scenario. Due to the dependence of berry composition on maturity, climate impacts on anthocyanin and TA levels were assessed at a common maturity of 22 °Brix total soluble solids (TSS), which necessitated the determination of when this maturity will be reached for each variety, region and warming scenario, and future period. The results indicate that both anthocyanin and TA levels will be affected negatively by a warming climate, but the magnitude of the impacts will differ between varieties and wine regions. Compared to 1990 levels, median anthocyanins concentrations are projected to decrease, depending on global climate model, by up to 3-12 % and 9-33 % for the northern wine regions by 2030 and 2070, respectively while 2-18 % reductions are projected in the southern wine regions for the same time periods. Patterns of reductions in the median Shiraz berry anthocyanin concentrations are similar to that of Cabernet Sauvignon; however, the magnitude is lower (up to 9-18 % in southern and northern wine regions respectively by 2070). Similarly, uneven declines in TA levels are projected across the study regions. The largest reductions

  3. Responses of grape berry anthocyanin and titratable acidity to the projected climate change across the Western Australian wine regions

    NASA Astrophysics Data System (ADS)

    Barnuud, Nyamdorj N.; Zerihun, Ayalsew; Mpelasoka, Freddie; Gibberd, Mark; Bates, Bryson

    2014-08-01

    More than a century of observations has established that climate influences grape berry composition. Accordingly, the projected global climate change is expected to impact on grape berry composition although the magnitude and direction of impact at regional and subregional scales are not fully known. The aim of this study was to assess potential impacts of climate change on levels of berry anthocyanin and titratable acidity (TA) of the major grapevine varieties grown across all of the Western Australian (WA) wine regions. Grape berry anthocyanin and TA responses across all WA wine regions were projected for 2030, 2050 and 2070 by utilising empirical models that link these berry attributes and climate data downscaled (to ˜5 km resolution) from the csiro_mk3_5 and miroc3_2_medres global climate model outputs under IPCC SRES A2 emissions scenario. Due to the dependence of berry composition on maturity, climate impacts on anthocyanin and TA levels were assessed at a common maturity of 22 °Brix total soluble solids (TSS), which necessitated the determination of when this maturity will be reached for each variety, region and warming scenario, and future period. The results indicate that both anthocyanin and TA levels will be affected negatively by a warming climate, but the magnitude of the impacts will differ between varieties and wine regions. Compared to 1990 levels, median anthocyanins concentrations are projected to decrease, depending on global climate model, by up to 3-12 % and 9-33 % for the northern wine regions by 2030 and 2070, respectively while 2-18 % reductions are projected in the southern wine regions for the same time periods. Patterns of reductions in the median Shiraz berry anthocyanin concentrations are similar to that of Cabernet Sauvignon; however, the magnitude is lower (up to 9-18 % in southern and northern wine regions respectively by 2070). Similarly, uneven declines in TA levels are projected across the study regions. The largest reductions

  4. Sources of atmospheric acidity in an agricultural-industrial region of São Paulo State, Brazil

    NASA Astrophysics Data System (ADS)

    Da Rocha, G. O.; Franco, A.; Allen, A. G.; Cardoso, A. A.

    2003-04-01

    Surface-based measurements of atmospheric formic acid (HCOOH), acetic acid (CH3COOH), sulfur dioxide (SO2), hydrogen chloride (HCl), and nitric acid (HNO3) were made in central São Paulo State, Brazil, between April 1999 and March 2000. Mean concentrations were 9.0 ppb (HCOOH), 1.3 ppb (CH3COOH), 4.9 ppb (SO2), 0.3 ppb (HCl), and 0.5 ppb (HNO3). Concentrations in sugar cane burning plumes were 1160-4230 ppb (HCOOH), 360-1750 ppb (CH3COOH), 10-630 ppb (SO2), 4-210 ppb (HCl), and 14-90 ppb (HNO3). Higher ambient concentrations of SO2, HCl and HNO3 were measured during the burning season (May-November). Concentrations of SO2 and HCl increased during the evening, and of HCOOH and CH3COOH were lowest in the morning, with peak levels in the afternoon. Ratios obtained between different species showed either nighttime maxima (SO2/HCOOH, SO2/CH3COOH, SO2/HNO3, CH3COOH/HNO3, SO2/HCl and HCOOH/HNO3), daytime maxima (HCOOH/HCl, CH3COOH/HCl and HNO3/HCl), or no clear trends (HCOOH/CH3COOH). Correlation analysis showed that SO2 and HCl were primary emissions from biomass burning and road transport; HCOOH, HNO3 and CH3COOH were products of photochemistry; HCOOH and CH3COOH were emitted directly during combustion as well as from biogenic sources. Biomass burning affected atmospheric acidity on a regional scale, while vehicular emissions had greater impact in urban and adjacent areas. Atmospheric ammonia levels were insufficient to neutralize atmospheric acidity, which was mainly removed by deposition to the surface.

  5. Epigenetics and Triplet-Repeat Neurological Diseases

    PubMed Central

    Nageshwaran, Sathiji; Festenstein, Richard

    2015-01-01

    The term “junk DNA” has been reconsidered following the delineation of the functional significance of repetitive DNA regions. Typically associated with centromeres and telomeres, DNA repeats are found in nearly all organisms throughout their genomes. Repetitive regions are frequently heterochromatinized resulting in silencing of intrinsic and nearby genes. However, this is not a uniform rule, with several genes known to require such an environment to permit transcription. Repetitive regions frequently exist as dinucleotide, trinucleotide, and tetranucleotide repeats. The association between repetitive regions and disease was emphasized following the discovery of abnormal trinucleotide repeats underlying spinal and bulbar muscular atrophy (Kennedy’s disease) and fragile X syndrome of mental retardation (FRAXA) in 1991. In this review, we provide a brief overview of epigenetic mechanisms and then focus on several diseases caused by DNA triplet-repeat expansions, which exhibit diverse epigenetic effects. It is clear that the emerging field of epigenetics is already generating novel potential therapeutic avenues for this group of largely incurable diseases. PMID:26733936

  6. Epigenetics and Triplet-Repeat Neurological Diseases.

    PubMed

    Nageshwaran, Sathiji; Festenstein, Richard

    2015-01-01

    The term "junk DNA" has been reconsidered following the delineation of the functional significance of repetitive DNA regions. Typically associated with centromeres and telomeres, DNA repeats are found in nearly all organisms throughout their genomes. Repetitive regions are frequently heterochromatinized resulting in silencing of intrinsic and nearby genes. However, this is not a uniform rule, with several genes known to require such an environment to permit transcription. Repetitive regions frequently exist as dinucleotide, trinucleotide, and tetranucleotide repeats. The association between repetitive regions and disease was emphasized following the discovery of abnormal trinucleotide repeats underlying spinal and bulbar muscular atrophy (Kennedy's disease) and fragile X syndrome of mental retardation (FRAXA) in 1991. In this review, we provide a brief overview of epigenetic mechanisms and then focus on several diseases caused by DNA triplet-repeat expansions, which exhibit diverse epigenetic effects. It is clear that the emerging field of epigenetics is already generating novel potential therapeutic avenues for this group of largely incurable diseases. PMID:26733936

  7. The C34 Peptide Fusion Inhibitor Binds to the Six-Helix Bundle Core Domain of HIV-1 gp41 by Displacement of the C-Terminal Helical Repeat Region.

    PubMed

    Louis, John M; Baber, James L; Clore, G Marius

    2015-11-17

    The conformational transition of the core domain of HIV-1 gp41 from a prehairpin intermediate to a six-helix bundle is responsible for virus-cell fusion. Several inhibitors which target the N-heptad repeat helical coiled-coil trimer that is fully accessible in the prehairpin intermediate have been designed. One such inhibitor is the peptide C34 derived from the C-heptad repeat of gp41 that forms the exterior of the six-helix bundle. Here, using a variety of biophysical techniques, including dye tagging, size-exclusion chromatography combined with multiangle light scattering, double electron-electron resonance EPR spectroscopy, and circular dichroism, we investigate the binding of C34 to two six-helix bundle mimetics comprising N- and C-heptad repeats either without (core(SP)) or with (core(S)) a short spacer connecting the two. In the case of core(SP), C34 directly exchanges with the C-heptad repeat. For core(S), up to two molecules of C34 bind the six-helix bundle via displacement of the C-heptad repeat. These results suggest that fusion inhibitors such as C34 can target a continuum of transitioning conformational states from the prehairpin intermediate to the six-helix bundle prior to the occurrence of irreversible fusion of viral and target cell membranes. PMID:26506247

  8. Insertions of up to 17 amino acids into a region of alpha-tubulin do not disrupt function in vivo.

    PubMed

    Schatz, P J; Georges, G E; Solomon, F; Botstein, D

    1987-10-01

    Microtubules in yeasts are essential components of the mitotic and meiotic spindle and are necessary for nuclear movement during cell division and mating. The yeast Saccharomyces cerevisiae has two alpha-tubulin genes, TUB1 and TUB3, either of which alone is sufficient for these processes when present in a high enough copy number. Comparisons of sequences from several species reveals the presence of a variable region near the amino terminus of alpha-tubulin proteins. We perturbed the structure of this region in TUB3 by inserting into it 3, 9, or 17 amino acids and tested the ability of these altered proteins to function as the only alpha-tubulin protein in yeast cells. We found that each of these altered proteins was sufficient on its own for mitotic growth, mating, and methods of yeast. We conclude that this region can tolerate considerable variation without losing any of the highly conserved functions of alpha-tubulin. Our results suggest that variability in this region occurs because it can be tolerated, not because it specifies an important function for the protein. PMID:3316988

  9. Efficacy and Safety of Arachidonic Acid for Treatment of School-Age Children in Schistosoma mansoni High-Endemicity Regions

    PubMed Central

    Barakat, Rashida; Abou El-Ela, Nadia E.; Sharaf, Soraya; El Sagheer, Ola; Selim, Sahar; Tallima, Hatem; Bruins, Maaike J.; Hadley, Kevin B.; El Ridi, Rashika

    2015-01-01

    Arachidonic acid (ARA), an omega-6 fatty acid, is a potent schistosomicide that displayed significant and safe therapeutic effects in Schistosoma mansoni-infected schoolchildren in S. mansoni low-prevalence regions. We here report on ARA efficacy and safety in treatment of schoolchildren in S. mansoni high-endemicity areas of Kafr El Sheikh, Egypt. The study was registered with ClinicalTrials.gov (NCT02144389). In total, 268 schoolchildren with light, moderate, or heavy S. mansoni infection were assigned to three study arms of 87, 91, and 90 children and received a single dose of 40 mg/kg praziquantel (PZQ), ARA (10 mg/kg per day for 15 days), or PZQ combined with ARA, respectively. The children were examined before and after treatment for stool parasite egg counts and blood biochemical, hematological, and immunological parameters. ARA, like PZQ, induced moderate cure rates (50% and 60%, respectively) in schoolchildren with light infection and modest cure rates (21% and 20%, respectively) in schoolchildren with high infection. PZQ and ARA combined elicited 83% and 78% cure rates in children with light and heavy infection, respectively. Biochemical and immunological profiles were either unchanged or ameliorated after ARA therapy. Combination of PZQ and ARA might be useful for treatment of children with schistosomiasis in high-endemicity regions. PMID:25624403

  10. Duct Leakage Repeatability Testing

    SciTech Connect

    Walker, Iain; Sherman, Max

    2014-08-01

    The purpose of this report is to evaluate the repeatability of the three most significant measurement techniques for duct leakage using data from the literature and recently obtained field data. We will also briefly discuss the first two factors. The main question to be answered by this study is to determine if differences in the repeatability of these tests methods is sufficient to indicate that any of these methods is so poor that it should be excluded from consideration as an allowed procedure in codes and standards. The three duct leak measurement methods assessed in this report are the two duct pressurization methods that are commonly used by many practitioners and the DeltaQ technique. These are methods B, C and A, respectively of the ASTM E1554 standard. Although it would be useful to evaluate other duct leak test methods, this study focused on those test methods that are commonly used and are required in various test standards, such as BPI (2010), RESNET (2014), ASHRAE 62.2 (2013), California Title 24 (CEC 2012), DOE Weatherization and many other energy efficiency programs.

  11. Repeated measures with zeros.

    PubMed

    Berk, K N; Lachenbruch, P A

    2002-08-01

    Consider repeated measures data with many zeros. For the case with one grouping factor and one repeated measure, we examine several models, assuming that the nonzero data are roughly lognormal. One of the simplest approaches is to model the zeros as left-censored observations from the lognormal distribution. A random effect is assumed for subjects. The censored model makes a strong assumption about the relationship between the zeros and the nonzero values. To check on this, you can instead assume that some of the zeros are 'true' zeros and model them as Bernoulli. Then the other values are modeled with a censored lognormal. A logistic model is used for the Bernoulli p, the probability of a true nonzero. The fit of the pure left-censored lognormal can be assessed by testing the hypothesis that p is 1, as described by Moulton and Halsey. The model can also be simplified by omitting the censoring, leaving a logistic model for the zeros and a lognormal model for the nonzero values. This is approximately equivalent to modeling the zero and nonzero values separately, a two-part model. In contrast to the censored model, this model assumes only a slight relationship (a covariance component) between the occurrence of zeros and the size of the nonzero values. The models are compared in terms of an example with data from children's private speech. PMID:12197298

  12. Analysis of separate isolates of Bordetella pertussis repeated DNA sequences.

    PubMed

    McPheat, W L; Hanson, J H; Livey, I; Robertson, J S

    1989-06-01

    Two independent isolates of a Bordetella pertussis repeated DNA unit were sequenced and shown to be an insertion sequence element with five nucleotide differences between the two copies. The sequences were 1053 bp in length with near-perfect terminal inverted repeats of 28 bp, had three open reading frames, and were each flanked by short direct repeats. The two insertion sequences showed considerable homology to two other B. pertussis repeated DNA sequences reported recently: IS481 and a 530 bp repeated DNA unit. The B. pertussis insertion sequence would appear to comprise a group of closely related sequences differing mainly in flanking direct repeats and the terminal inverted repeats. The two isolates reported here, which were from the adenylate cyclase and agglutinogen 2 regions of the genome, were numbered IS48lvl and IS48lv2 respectively. PMID:2559151

  13. Structural and Energetic Characterization of the Ankyrin Repeat Protein Family

    PubMed Central

    Parra, R. Gonzalo; Espada, Rocío; Verstraete, Nina; Ferreiro, Diego U.

    2015-01-01

    Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins. PMID:26691182

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

    NASA Technical Reports Server (NTRS)

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

    2015-01-01

    The Pahrump Hills region of Gale crater is a approximately 12 millimeter thick section of sedimentary rock in the Murray formation, interpreted as the basal geological unit of Mount Sharp. The Mars Science Laboratory, Curiosity, arrived at the Pahrump Hills in September 2014 and performed a detailed six-month investigation of the sedimentary structures, geochemistry, and mineralogy of the area. During the campaign, Curiosity drilled and delivered three mudstone samples (targets Confidence Hills, Mojave 2, and Telegraph Peak) to its internal instruments, including the CheMin XRD/XRF.

  15. Repeat Customer Success in Extension

    ERIC Educational Resources Information Center

    Bess, Melissa M.; Traub, Sarah M.

    2013-01-01

    Four multi-session research-based programs were offered by two Extension specialist in one rural Missouri county. Eleven participants who came to multiple Extension programs could be called "repeat customers." Based on the total number of participants for all four programs, 25% could be deemed as repeat customers. Repeat customers had…

  16. Characterization of transcriptional regulatory domains of ankyrin repeat cofactor-1

    SciTech Connect

    Zhang, Aihua; Li, Chia-Wei; Chen, J. Don . E-mail: chenjd@umdnj.edu

    2007-07-13

    The ankyrin repeats cofactor-1 (ANCO-1) was recently identified as a p160 coactivator-interacting protein that may inhibit transcriptional activity of nuclear receptors. Here, we have characterized the transcriptional regulatory domains of ANCO-1. Two intrinsic repression domains (RD) were identified: an N-terminal RD1 at residues 318-611 and a C-terminal RD2 at 2369-2663. ANCO-1 also contains an activation domain (AD) capable of stimulating transcription in both mammalian and yeast cells. The minimal AD was delimited to a 70-amino acid region at residues 2076-2145. Overall, full-length ANCO-1 exhibited transcriptional repressor activity, suggesting that RD domains may suppress the AD activity. We further demonstrated that ANCO-1 silencing by siRNA enhanced progesterone receptor-mediated transcription. Together, these results indicate that the transcriptional potential of ANCO-1 may be modulated by a combination of repression and activation signals.

  17. Body regional distribution and stratification of fatty acids in the blubber of New Zealand sea lions: implications for diet predictions.

    PubMed

    Lambert, Antoine; Meynier, Laureline; Donaldson, Laura C; Roe, Wendi D; Morel, Patrick C H

    2013-01-01

    Fatty acids (FAs) from blubber are often analysed to assess the diet of marine mammals. However, distribution of blubber FAs is not necessarily uniform along the body. It is therefore important to understand the deposition of dietary fat to be able to estimate the diet. We analysed the FA compositions of the thoracic ventral (T region) blubber of 28 New Zealand (NZ) sea lions Phocarctos hookeri by-caught by the southern arrow squid Nototodarus sloani fishery. Each blubber sample was divided into an inner and an outer layer. For 16 of these 28 animals, the pelvic dorsal (P) region was also sampled. The influence of body region and layer was statistically tested on the distribution of blubber FAs. We found minimal differences between the P and T regions (3 out of 29 FAs). The outer blubber layer was more concentrated in short-chain monounsaturated FAs, and less concentrated in saturated FAs, but the degree of stratification was small. Diet predictions from quantitative FA signature analysis (QFASA) applied on different body regions were similar. When applied to different blubber layers, QFASA gave some variation in the contribution of rattails (~25 % in outer blubber vs. ~12 % in inner blubber). Nonetheless, diet predicted from both layers was dominated by similar prey species: octopus, hoki and rattails. Hoki and rattails shared a similar ecological niche. Therefore, feeding ecology of NZ sea lions inferred from the inner or the outer blubber would lead to the same conclusions. In the case of NZ sea lions, the outer layer of blubber, if the only sample accessible, could be a useful tissue for diet inference from FAs. PMID:22847500

  18. The influence of temperature and aerosol acidity on biogenic secondary organic aerosol tracers: Observations at a rural site in the central Pearl River Delta region, South China

    NASA Astrophysics Data System (ADS)

    Ding, Xiang; Wang, Xin-Ming; Zheng, Mei

    2011-02-01

    At a rural site in the central Pearl River Delta (PRD) region in south China, fine particle (PM 2.5) samples were collected during fall-winter 2007 to measure biogenic secondary organic aerosol (SOA) tracers, including isoprene SOA tracers (3-methyl-2,3,4-trihydroxy-1-butene, 2-methylglyceric acid, 2-methylthreitol and 2-methylerythritol), α-pinene SOA tracers ( cis-pinonic acid, pinic acid, 3-methyl-1,2,3-butanetricarboxylic acid, 3-hydroxyglutaric acid and 3-hydroxy-4,4-dimethylglutaric acid) and a sesquiterpene SOA tracer (β-caryophyllinic acid). The isoprene-, α-pinene- and sesquiterpene-SOA tracers averaged 30.8 ± 15.9, 6.61 ± 4.39, and 0.54 ± 0.56 ng m -3, respectively; and 2-methyltetrols (sum of 2-methylthreitol and 2-methylerythritol, 27.6 ± 15.1 ng m -3) and cis-pinonic acid (3.60 ± 3.76 ng m -3) were the dominant isoprene- and α-pinene-SOA tracers, respectively. 2-Methyltetrols exhibited significantly positive correlations ( p < 0.05) with ambient temperature, probably resulting from the enhanced isoprene emission strength and tracer formation rate under higher temperature. The significantly positive correlation ( p < 0.05) between 2-methyltetrols and the estimated aerosol acidity with a slope of 59.4 ± 13.4 ng m -3 per μmol [H +] m -3 reflected the enhancement of isoprene SOA formation by aerosol acidity, and acid-catalyzed heterogeneous reaction was probably the major formation pathway for 2-methyltetrols in the PRD region. 2-Methylglyceric acid showed poor correlations with both temperature and aerosol acidity. The α-pinene SOA tracers showed poor correlations with temperature, probably due to the counteraction between temperature effects on the precursor emission/tracer formation and gas/particle partitioning. Among the α-pinene SOA tracers, only cis-pinonic acid and pinic acid exhibited significant correlations with aerosol acidity with slopes of -11.7 ± 3.7 and -2.2 ± 0.8 ng m -3 per μmol [H +] m -3, respectively. The negative

  19. Glutaryl-CoA dehydrogenase deficiency: region-specific analysis of organic acids and acylcarnitines in post mortem brain predicts vulnerability of the putamen.

    PubMed

    Kölker, S; Hoffmann, G F; Schor, D S M; Feyh, P; Wagner, L; Jeffrey, I; Pourfarzam, M; Okun, J G; Zschocke, J; Baric, I; Bain, M D; Jakobs, C; Chalmers, R A

    2003-06-01

    The neurometabolic disorder glutaryl-CoA dehydrogenase (GCDH) deficiency is biochemically characterised by an accumulation of the marker metabolites 3-hydroxyglutaric acid, glutaric acid, and glutarylcarnitine. If untreated, the disease is complicated by acute encephalopathic crises, resulting in neurodegeneration of vulnerable brain regions, in particular the putamen. 3-hydroxyglutaric acid is considered the major neurotoxin in this disease. There are only preliminary data concerning glutaric acid concentrations in the brains of affected children and the distribution of 3-hydroxyglutaric acid and glutarylcarnitine has not been described. In the present study, we investigated post mortem the distribution of 3-hydroxyglutaric and glutaric acids as well as glutarylcarnitine in 14 different brain regions, internal organs, and body fluids (urine, plasma, cerebrospinal fluid) in a 14-year-old boy. 3-Hydroxyglutaric acid showed the highest concentration (62 nmol/g protein) in the putamen among all brain areas investigated. The glutarylcarnitine concentration was also highest in the putamen (7.1 nmol/g protein). We suggest that the regional-specific differences in the relative concentrations of 3-hydroxyglutaric acid contribute to the pattern of neuronal damage in this disease. These results provide an explanatory basis for the high vulnerability of the putamen in this disease, adding to the strong corticostriatal glutamatergic input into the putamen and the high excitotoxic susceptibility of neostriatal medium spiny neurons. PMID:14598231

  20. The influence of different land management practices on the transformation of humic acids in heavy loamy soddy-podzolic soils of the Cis-Urals region

    NASA Astrophysics Data System (ADS)

    Zavyalova, N. E.; Konchits, V. A.

    2011-01-01

    The elemental composition and structure of humic acids were studied in heavy loamy soddy-podzolic soils of the Cis-Urals region under different land management practices. The humic acids in the soil of the long-term clean fallow, overgrown fallow (abandoned plot), and crop rotation plots differed in their composition and properties. The humic acids in the soils of the crop rotation with the regular application of manure and of the overgrown fallow were enriched in the components of both their central (nuclear) and peripheral parts. Such a structure ensured the active participation of humic acids in the carbon cycle with the simultaneous preservation of the soil's fertility.

  1. ST proteins, a new family of plant tandem repeat proteins with a DUF2775 domain mainly found in Fabaceae and Asteraceae

    PubMed Central

    2012-01-01

    Background Many proteins with tandem repeats in their sequence have been described and classified according to the length of the repeats: I) Repeats of short oligopeptides (from 2 to 20 amino acids), including structural cell wall proteins and arabinogalactan proteins. II) Repeats that range in length from 20 to 40 residues, including proteins with a well-established three-dimensional structure often involved in mediating protein-protein interactions. (III) Longer repeats in the order of 100 amino acids that constitute structurally and functionally independent units. Here we analyse ShooT specific (ST) proteins, a family of proteins with tandem repeats of unknown function that were first found in Leguminosae, and their possible similarities to other proteins with tandem repeats. Results ST protein sequences were only found in dicotyledonous plants, limited to several plant families, mainly the Fabaceae and the Asteraceae. ST mRNAs accumulate mainly in the roots and under biotic interactions. Most ST proteins have one or several Domain(s) of Unknown Function 2775 (DUF2775). All deduced ST proteins have a signal peptide, indicating that these proteins enter the secretory pathway, and the mature proteins have tandem repeat oligopeptides that share a hexapeptide (E/D)FEPRP followed by 4 partially conserved amino acids, which could determine a putative N-glycosylation signal, and a fully conserved tyrosine. In a phylogenetic tree, the sequences clade according to taxonomic group. A possible involvement in symbiosis and abiotic stress as well as in plant cell elongation is suggested, although different STs could play different roles in plant development. Conclusions We describe a new family of proteins called ST whose presence is limited to the plant kingdom, specifically to a few families of dicotyledonous plants. They present 20 to 40 amino acid tandem repeat sequences with different characteristics (signal peptide, DUF2775 domain, conservative repeat regions) from the

  2. 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. PMID:12816957

  3. An Adirondack Watershed Data Base: Attribute and mapping information for regional acidic deposition studies

    SciTech Connect

    Rosen, A.E.; Olson, R.J.; Gruendling, G.K.; Bogucki, D.J.; Malanchuk, J.L.; Durfee, R.C.; Turner, R.S.; Adams, K.B.; Wilson, D.L.; Coleman, P.R.

    1988-12-01

    The Adirondack Watershed Data Base (AWDB) provides a means to test hypotheses concerning the relative importance of various watershed attributes that may contribute to increased acidification of Adirondack surface waters. The AWDB is a valuable resource for the study of other ecological phenomena. The AWDB consists of digital watershed boundaries and digital geographic data, stored within a geographic information system, and watershed/lake attribute data stored in a data management system (SAS) for 463 Adirondack headwater lakes. Attributes include watershed morphology, physiography, bedrock, soils, land cover, wetlands, disturbances (e.g., cabins, fire, and logging), beaver activity, precipitation, and atmospheric deposition. Over 600 variables are available for each watershed. These data can be combined with water chemistry data and fish community status for regional-scale examinations of watershed attributes that may account for variability and change in water chemistry and fish populations in the Adirondacks. This report describes the design of the AWDB, documents sources and history of the data; defines the format of the AWDB contents; and characterizes the data using summary statistics, frequency bar charts, and other graphics. In addition, it provides information necessary for researchers using the data base on their own computer systems. 37 refs., 42 figs., 4 tabs.

  4. The Cipher Code of Simple Sequence Repeats in "Vampire Pathogens".

    PubMed

    Zou, Geng; Bello-Orti, Bernardo; Aragon, Virginia; Tucker, Alexander W; Luo, Rui; Ren, Pinxing; Bi, Dingren; Zhou, Rui; Jin, Hui

    2015-01-01

    Blood inside mammals is a forbidden area for the majority of prokaryotic microbes; however, red blood cells tropism microbes, like "vampire pathogens" (VP), succeed in matching scarce nutrients and surviving strong immunity reactions. Here, we found VP of Mycoplasma, Rhizobiales, and Rickettsiales showed significantly higher counts of (AG)n dimeric simple sequence repeats (Di-SSRs) in the genomes, coding and non-coding regions than non Vampire Pathogens (N_VP). Regression analysis indicated a significant correlation between GC content and the span of (AG)n-Di-SSR variation. Gene Ontology (GO) terms with abundance of (AG)3-Di-SSRs shared by the VP strains were associated with purine nucleotide metabolism (FDR < 0.01), indicating an adaptation to the limited availability of purine and nucleotide precursors in blood. Di-amino acids coded by (AG)n-Di-SSRs included all three six-fold code amino acids (Arg, Leu and Ser) and significantly higher counts of Di-amino acids coded by (AG)3, (GA)3, and (TC)3 in VP than N_VP. Furthermore, significant differences (P < 0.001) on the numbers of triplexes formed from (AG)n-Di-SSRs between VP and N_VP in Mycoplasma suggested the potential role of (AG)n-Di-SSRs in gene regulation. PMID:26215592

  5. Conserved Repeat Motifs and Glucan Binding by Glucansucrases of Oral Streptococci and Leuconostoc mesenteroides

    PubMed Central

    Shah, Deepan S. H.; Joucla, Gilles; Remaud-Simeon, Magali; Russell, Roy R. B.

    2004-01-01

    Glucansucrases of oral streptococci and Leuconostoc mesenteroides have a common pattern of structural organization and characteristically contain a domain with a series of tandem amino acid repeats in which certain residues are highly conserved, particularly aromatic amino acids and glycine. In some glucosyltransferases (GTFs) the repeat region has been identified as a glucan binding domain (GBD). Such GBDs are also found in several glucan binding proteins (GBP) of oral streptococci that do not have glucansucrase activity. Alignment of the amino acid sequences of 20 glucansucrases and GBP showed the widespread conservation of the 33-residue A repeat first identified in GtfI of Streptococcus downei. Site-directed mutagenesis of individual highly conserved residues in recombinant GBD of GtfI demonstrated the importance of the first tryptophan and the tyrosine-phenylalanine pair in the binding of dextran, as well as the essential contribution of a basic residue (arginine or lysine). A microplate binding assay was developed to measure the binding affinity of recombinant GBDs. GBD of GtfI was shown to be capable of binding glucans with predominantly α-1,3 or α-1,6 links, as well as alternating α-1,3 and α-1,6 links (alternan). Western blot experiments using biotinylated dextran or alternan as probes demonstrated a difference between the binding of streptococcal GTF and GBP and that of Leuconostoc glucansucrases. Experimental data and bioinformatics analysis showed that the A repeat motif is distinct from the 20-residue CW motif, which also has conserved aromatic amino acids and glycine and which occurs in the choline-binding proteins of Streptococcus pneumoniae and other organisms. PMID:15576779

  6. First Analysis of the ν_5 Band of DNO_3 (deuterated Nitric Acid) in the 11 μm Region

    NASA Astrophysics Data System (ADS)

    Koubek, J.; Perrin, A.; Beckers, H.; Willner, H.

    2009-06-01

    The infrared spectrum of DNO_3 (deuterated nitric acid) was recorded at high resolution (0.0018 cm ^{-1}) in the 800 -1400 cm ^{-1} region on the Bruker IFR 120 HR Fourier transform spectrometer of Wuppertal. The analysis of the ν_5 A-type band of DNO_3 centered at 887.656 cm ^{-1} was performed taking use of the ground state parameters achieved by Drouin et al. This band is perturbed by several resonances. [1] Drouin, Miller, Fry, Petkie, Helminger, Medvedev, J. Mol. Spectrosc. 236 (2006) 29-34 [2] Acknowledgment: The work was supported through the Ministry of Education, Youth and Sports of the Czech Republic (research program LC06071) and scholarship of the French government (Bourse du Gouvernement Francais - Bourse de Doctorat en co-tutelle).

  7. A 750 bp sensory integration region directs global control of the Escherichia coli GadE acid resistance regulator.

    PubMed

    Sayed, Atef K; Foster, John W

    2009-03-01

    Escherichia coli survives pH 2 environments through an acid resistance (AR) system regulated by the transcriptional activator GadE. Numerous proteins control gadE at an upstream, conserved, 798 bp intergenic region. We show this region produces three transcripts starting at -124 (T1), -324/-317 (T2) and -566 (T3) bp from the gadE start codon. Transcriptional lacZ fusions to gadE promoter regions revealed P1 and P3 were active while P2 alone was not. However, pairing P3 with P2 activated P2 and increased expression 20-fold above P3 alone. The fusions were transferred to Salmonella, which lacks this AR system, and plasmid-borne E. coli-specific regulators EvgA, YdeO, GadE and GadX were introduced. Data revealed that YdeO and GadX activate P3, P2 and P3P2, while GadE autoactivates P1 and represses P3 and P3P2. The developing model indicates that different signals activate YdeO, GadX, or an MnmE-dependent regulator, which stimulate gadE transcription from the P3 and P2 promoters. Once made, GadE activates P1 and represses P3 and P2. The P1 region also enables efficient downstream transcription and translation of the P3 or P2 transcripts. Evidence indicates the entire 750 bp sensory integration locus is necessary for a versatile response. PMID:19220752

  8. Early region 1B of adenovirus 2 encodes two coterminal proteins of 495 and 155 amino acid residues.

    PubMed Central

    Anderson, C W; Schmitt, R C; Smart, J E; Lewis, J B

    1984-01-01

    Partial sequence analysis of tryptic peptides has identified the E1B-495R (E1b-57K) (early transcription region 1B of 495 amino acid residues, with an approximate molecular weight of 57,000) protein of adenovirus 2 as encoded by the 495 amino acid open reading frame located in the adenovirus 2 DNA sequence between nucleotides 2016 and 3500. Additional proteins of 16,000 Mr and 18,000 Mr that are related to the E1B-495R protein were identified by cell-free translation of hybridization-selected mRNA. Analysis of [35S]methionine-containing amino terminal tryptic peptides by thin-layer chromatography showed that the E1B-495R, E1B-18K, and E1B-16K proteins all begin at the same initiation codon. The E1B-495R protein from 293 cells also has the same initial tryptic peptide, acetyl-methionyl-glutamyl-arginine. Sequence analysis of E1B-18K tryptic peptides indicated that this protein also has the same carboxy terminus as the E1B-495R protein and that it is derived from an mRNA that is spliced to remove sequences between nucleotides 2250 and 3269, resulting in a protein product of 155 amino acid residues. Analysis of E1B-16K tryptic peptides has not yet revealed the carboxy terminal structure of this protein. Both the E1B-495R and the E1B-155R (E1B-18K) proteins, as well as the E1B-16K protein, were precipitated from cell-free translations and from extracts of infected cells by antiserum against an amino terminal nonapeptide common to these proteins. Images PMID:6323739

  9. A time-series analysis of acidic particulate matter and daily mortality and morbidity in the Buffalo, New York, region.

    PubMed

    Gwynn, R C; Burnett, R T; Thurston, G D

    2000-02-01

    A component of particulate matter (PM) air pollution that may provide one biologically plausible pathway for the observed PM air pollution-health effect associations is aerosol acidity (H(+)). An increasing number of observational studies have demonstrated associations between H(+) and increased adverse health effects in the United States and abroad. Although studies have shown significant H(+) associations with increased morbidity in the United States, similar associations have yet to be shown with daily mortality. We considered a 2.5-year record of daily H(+) and sulfate measurements (May 1988-October 1990) collected in the Buffalo, New York, region in a time-series analysis of respiratory, circulatory, and total daily mortality and hospital admissions. Other copollutants considered included particulate matter [less than/equal to] 10 microm in aerodynamic diameter, coefficient of haze, ozone, carbon monoxide, sulfur dioxide, and nitrogen dioxide. Various modeling techniques were applied to control for confounding of effect estimates due to seasonality, weather, and day-of-week effects. We found multiple significant pollutant-health effect associations--most strongly between SO(4)(2-) and respiratory hospital admissions (as indicated by its t-statistic). Additionally, H(+) and SO(4)(2-) demonstrated the most coherent associations with both respiratory hospital admissions [H(+): relative risk (RR) = 1. 31; 95% confidence interval (CI), 1.14-1.51; and SO(4)(2-): RR = 1. 18, CI, 1.09-1.28] and respiratory mortality (H(+): RR = 1.55, CI, 1. 09-2.20; and SO(4)(2-): RR = 1.24, CI, 1.01-1.52). Thus, acidic sulfate aerosols represent a component of PM air pollution that may contribute to the previously noted adverse effects of PM mass on human health, and the associations demonstrated in this study support the need for further investigations into the potential health effects of acidic aerosols. PMID:10656852

  10. Isocyanic acid in a global chemistry transport model: Tropospheric distribution, budget, and identification of regions with potential health impacts

    NASA Astrophysics Data System (ADS)

    Young, Paul. J.; Emmons, Louisa K.; Roberts, James M.; Lamarque, Jean-FrançOis; Wiedinmyer, Christine; Veres, Patrick; Vandenboer, Trevor C.

    2012-05-01

    This study uses a global chemical transport model to estimate the distribution of isocyanic acid (HNCO). HNCO is toxic, and concentrations exceeding 1 ppbv have been suggested to have negative health effects. Based on fire studies, HNCO emissions were scaled to those of hydrogen cyanide (30%), resulting in yearly total emissions of 1.5 Tg for 2008, from both anthropogenic and biomass burning sources. Loss processes included heterogeneous uptake (pH dependent), dry deposition (like formic acid), and reaction with the OH radical (k = 1 × 10-15 molecule-1 cm3 s-1). Annual mean surface HNCO concentrations were highest over parts of China (maximum of 470 pptv), but episodic fire emissions gave much higher levels, exceeding 4 ppbv in tropical Africa and the Amazon, and exceeding 10 ppbv in Southeast Asia and Siberia. This suggests that large biomass burning events could result in deleterious health effects for populations in these regions. For the tropospheric budget, using the model-calculated pH the HNCO lifetime was 37 days, with the split between dry deposition and heterogeneous loss being 95%:5%. Fixing the heterogeneous loss rate at pH = 7 meant that this process dominated, accounting for ˜70% of the total loss, giving a lifetime of 6 days, and resulting in upper tropospheric concentrations that were essentially zero. However, changing the pH does not notably impact the high concentrations found in biomass burning regions. More observational data is needed to evaluate the model, as well as a better representation of the likely underestimated biofuel emissions, which could mean more populations exposed to elevated HNCO concentrations.

  11. A Neutralizing Monoclonal Antibody Targeting the Acid-Sensitive Region in Chikungunya Virus E2 Protects from Disease

    PubMed Central

    Selvarajah, Suganya; Sexton, Nicole R.; Kahle, Kristen M.; Fong, Rachel H.; Mattia, Kimberly-Anne; Gardner, Joy; Lu, Kai; Liss, Nathan M.; Salvador, Beatriz; Tucker, David F.; Barnes, Trevor; Mabila, Manu; Zhou, Xiangdong; Rossini, Giada; Rucker, Joseph B.; Sanders, David Avram; Suhrbier, Andreas; Sambri, Vittorio; Michault, Alain; Muench, Marcus O.; Doranz, Benjamin J.; Simmons, Graham

    2013-01-01

    The mosquito-borne alphavirus, chikungunya virus (CHIKV), has recently reemerged, producing the largest epidemic ever recorded for this virus, with up to 6.5 million cases of acute and chronic rheumatic disease. There are currently no licensed vaccines for CHIKV and current anti-inflammatory drug treatment is often inadequate. Here we describe the isolation and characterization of two human monoclonal antibodies, C9 and E8, from CHIKV infected and recovered individuals. C9 was determined to be a potent virus neutralizing antibody and a biosensor antibody binding study demonstrated it recognized residues on intact CHIKV VLPs. Shotgun mutagenesis alanine scanning of 98 percent of the residues in the E1 and E2 glycoproteins of CHIKV envelope showed that the epitope bound by C9 included amino-acid 162 in the acid-sensitive region (ASR) of the CHIKV E2 glycoprotein. The ASR is critical for the rearrangement of CHIKV E2 during fusion and viral entry into host cells, and we predict that C9 prevents these events from occurring. When used prophylactically in a CHIKV mouse model, C9 completely protected against CHIKV viremia and arthritis. We also observed that when administered therapeutically at 8 or 18 hours post-CHIKV challenge, C9 gave 100% protection in a pathogenic mouse model. Given that targeting this novel neutralizing epitope in E2 can potently protect both in vitro and in vivo, it is likely to be an important region both for future antibody and vaccine-based interventions against CHIKV. PMID:24069479

  12. Molecular and technological characterization of lactic acid bacteria from traditional fermented sausages of Basilicata region (Southern Italy).

    PubMed

    Bonomo, M G; Ricciardi, A; Zotta, T; Parente, E; Salzano, G

    2008-12-01

    Lactic acid bacteria (LAB) from traditional fermented sausages of the Basilicata region were investigated by ARDRA-PCR and RAPD-PCR for taxonomic identification at species and strain level and characterized on the basis of the growth and acidification at different temperatures, incubation times, levels of NaCl and KNO(2), hydrolysis of sarcoplasmatic and myofibrillar proteins and antimicrobial, peptide/amino acid release and nitrate reductase activities. Lactobacillus sakei was the predominant species (67%) followed by Pediococcus pentosaceus (16%), Leuconostoc carnosum (8%), Lactobacillus plantarum (4%), Lactobacillus brevis (2%) and Leuconostoc pseudomesenteroides (2%). The technological characterization revealed that most of the isolates had good acidifying and proteolytic properties. Moreover, Lb. sakei strains showed antimicrobial ability, while Leuconostoc strains the highest reduction of nitrates. This work was a preliminary study in the formulation of autochthonous starter cultures in order to standardize the production process of sausages, to preserve their typical organoleptic and sensory characteristics and to improve the quality of final product. PMID:22063864

  13. Reversing and nonreversing heat capacity of poly(lactic acid) in the glass transition region by TMDSC

    SciTech Connect

    Pyda, Marek {nmn}; Wunderlich, Bernhard {nmn}

    2005-11-01

    A study of the glass transition of an amorphous and a semicrystalline poly(lactic acid) (PLA) is performed with adiabatic calorimetry, differential scanning calorimetry (DSC), and temperature-modulated DSC (TMDSC). The reversing, total, and nonreversing apparent heat capacities of samples with different contents of L- and D-lactic acid and with various thermal histories were evaluated. Different modes of TMDSC analyses of amorphous and semicrystalline PLA were compared to the total heat capacity from standard DSC. The enthalpy relaxation and the cold crystallization in the glass transition region are largely irreversible. The melting is largely irreversible, but a 100% reversing fraction is observed at low temperatures from 375 to 420 K, which becomes small inside the major melting peak at about 440 K. From the TMDSC of amorphous PLA, the combined information on endothermic and exothermic enthalpy relaxation and glass transition were deconvoluted into the reversing and nonreversing components. The glass transition temperature from the reversing heat capacity and the enthalpy relaxation peaks from the nonreversing component shift to higher temperature for increasingly annealed PLA. The relaxation times for aging decrease on cooling until the glass transition is reached and then increase. This behavior is linked to cooperativity. All quantitative thermal analyses are based on the heat capacity of the solid and liquid, evaluated earlier with the advanced thermal analysis system (ATHAS).

  14. Factors contributing to decreased protein stability when aspartic acid residues are in {beta}-sheet regions.

    SciTech Connect

    Pokkuluri, P. R.; Cai, X.; Raffen, R.; Gu, M.; Stevens, F. J.; Schiffer, M.

    2002-07-01

    Asp residues are significantly under represented in {beta}-sheet regions of proteins, especially in the middle of {beta}-strands, as found by a number of studies using statistical, modeling, or experimental methods. To further understand the reasons for this under representation of Asp, we prepared and analyzed mutants of a {beta}-domain. Two Gln residues of the immunoglobulin light-chain variable domain (V{sub L}) of protein Len were replaced with Asp, and then the effects of these changes on protein stability and protein structure were studied. The replacement of Q38D, located at the end of a {beta}-strand, and that of Q89D, located in the middle of a {beta}-strand, reduced the stability of the parent immunoglobulin VL domain by 2.0 kcal/mol and 5.3 kcal/mol, respectively. Because the Q89D mutant of the wild-type V{sub L}-Len domain was too unstable to be expressed as a soluble protein, we prepared the Q89D mutant in a triple mutant background, V{sub L}-Len M4L/Y27dD/T94H, which was 4.2 kcal/mol more stable than the wild-type V{sub L}-Len domain. The structures of mutants V{sub L}-Len Q38D and V{sub L}-Len Q89D/M4L/Y27dD/T94H were determined by X-ray diffraction at 1.6 A resolution. We found no major perturbances in the structures of these QD mutant proteins relative to structures of the parent proteins. The observed stability changes have to be accounted for by cumulative effects of the following several factors: (1) by changes in main-chain dihedral angles and in side-chain rotomers, (2) by close contacts between some atoms, and, most significantly, (3) by the unfavorable electrostatic interactions between the Asp side chain and the carbonyls of the main chain. We show that the Asn side chain, which is of similar size but neutral, is less destabilizing. The detrimental effect of Asp within a {beta}-sheet of an immunoglobulin-type domain can have very serious consequences. A somatic mutation of a {beta}-strand residue to Asp could prevent the expression of the

  15. The effect of charge reversal mutations in the alpha-helical region of liver fatty acid binding protein on the binding of fatty-acyl CoAs, lysophospholipids and bile acids.

    PubMed

    Hagan, Robert M; Davies, Joanna K; Wilton, David C

    2002-10-01

    Liver fatty acid binding protein (LFABP) is unique among the various types of FABPs in that it can bind a variety of ligands in addition to fatty acids. LFABP is able to bind long chain fatty acids with a 2:1 stoichiometry and the crystal structure has identified two fatty acid binding sites in the binding cavity. The presumed primary site (site 1) involves the fatty acid binding with the carboxylate group buried in the cavity whereas the fatty acid at site 2 has the carboxylate group solvent-exposed within the ligand portal region and in the vicinity of alpha-helix II. The alpha-helical region contains three cationic residues, K20, K31, K33 and modelling studies suggest that K31 on alpha-helix II could make an electrostatic contribution to anionic ligands binding to site 2. The preparation of three charge reversal mutants of LFABP, K20E, K31E and K33E has allowed an investigation of the role of site 2 in ligand binding, particularly those ligands with a bulky anionic head group. The binding of oleoyl CoA, lysophosphatidic acid, lysophosphatidylcholine, lithocholic acid and taurolithocholate 3-sulphate to LFABP has been studied using the alpha-helical mutants. The results support the concept that such ligands bind at site 2 of LFABP where solvent exposure allows the accommodation of their bulky anionic group. PMID:12479568

  16. Amino Acid Region 1000–1008 of Factor V Is a Dynamic Regulator for the Emergence of Procoagulant Activity*

    PubMed Central

    Wiencek, Joesph R.; Na, Mahesheema; Hirbawi, Jamila; Kalafatis, Michael

    2013-01-01

    Single chain factor V (fV) circulates as an Mr 330,000 quiescent pro-cofactor. Removal of the B domain and generation of factor Va (fVa) are vital for procoagulant activity. We investigated the role of the basic amino acid region 1000–1008 within the B domain of fV by constructing a recombinant mutant fV molecule with all activation cleavage sites (Arg709/Arg1018/Arg1545) mutated to glutamine (fVQ3), a mutant fV molecule with region 1000–1008 deleted (fVΔB9), and a mutant fV molecule containing the same deletion with activation cleavage sites changed to glutamine (fVΔB9/Q3). The recombinant molecules along with wild type fV (fVWT) were transiently expressed in COS-7L cells, purified, and assessed for their ability to bind factor Xa (fXa) prior to and following incubation with thrombin. The data showed that fVQ3 was severely impaired in its interaction with fXa before and after incubation with thrombin. In contrast, KD(app) values for fVΔB9 (0.9 nm), fVaΔB9 (0.4 nm), and fVΔB9/Q3 (0.7 nm) were similar to the affinity of fVaWT for fXa (0.3 nm). Two-stage clotting assays revealed that although fVQ3 was deficient in its clotting activity, fVΔB9/Q3 had clotting activity comparable with fVaWT. The kcat value of prothrombinase assembled with fVΔB9/Q3 was minimally affected, whereas the Km value of the reaction was increased 57-fold compared with the Km value obtained with prothrombinase assembled with fVaWT. These findings strongly suggest that amino acid region 1000–1008 of fV is a regulatory sequence protecting the organisms from spontaneous binding to fXa and unnecessary prothrombinase complex formation, which in turn results in catastrophic physiological consequences. PMID:24178294

  17. Intragenic tandem repeat variation between Legionella pneumophila strains

    PubMed Central

    Coil, David A; Vandersmissen, Liesbeth; Ginevra, Christophe; Jarraud, Sophie; Lammertyn, Elke; Anné, Jozef

    2008-01-01

    Background Bacterial genomes harbour a large number of tandem repeats, yet the possible phenotypic effects of those found within the coding region of genes are only beginning to be examined. Evidence exists from other organisms that these repeats can be involved in the evolution of new genes, gene regulation, adaptation, resistance to environmental stresses, and avoidance of the immune system. Results In this study, we have investigated the presence and variability in copy number of intragenic tandemly repeated sequences in the genome of Legionella pneumophila, the etiological agent of a severe pneumonia known as Legionnaires' disease. Within the genome of the Philadelphia strain, we have identified 26 intragenic tandem repeat sequences using conservative selection criteria. Of these, seven were "polymorphic" in terms of repeat copy number between a large number of L. pneumophila serogroup 1 strains. These strains were collected from a wide variety of environments and patients in several geographical regions. Within this panel of strains, all but one of these seven genes exhibited statistically different patterns in repeat copy number between samples from different origins (environmental, clinical, and hot springs). Conclusion These results support the hypothesis that intragenic tandem repeats could play a role in virulence and adaptation to different environments. While tandem repeats are an increasingly popular focus of molecular typing studies in prokaryotes, including in L. pneumophila, this study is the first examining the difference in tandem repeat distribution as a function of clinical or environmental origin. PMID:19077205

  18. [Studies on changes in nucleolar organizer region of human promyelocytic leukemia cells (HL-60) treated with retinoic acid].

    PubMed

    Xie, R L; Wang, Y Q

    1989-12-01

    Changes of nucleolar organizer region in HL-60 cells after treated with retinoic acid (RA) were studied with techniques of silver-staining nucleolar organizer region (Ag-NOR) in metaphase karyotypes, Brachet's reaction and with our improved TEM techniques for studying silver-stained active nucleolar organizer region (Ag-aNOR) in interphase nucleoli. Number of Ag-NOR in HL-60 cells is 4.5/cell on average. The Ag-NOR number of cells treated with RA showed no remarkable difference from that of control group. Ag-aNOR number treated with RA was reduced obviously as compared with that of control group. Meanwhile, the changes of nucleolus number showed by Brachet's reaction were in accordance with those of Ag-aNOR. Therefore, it may be concluded: (1). Though the number of active rRNA genes did not changed after the differentiation of HL-60 cells induced by RA, their expression was clearly inhibited: (2). The relationship between the changes of Brachet-No and Ag-aNOR is in positive correlation (r = 0.98, p less than 0.01). EM examination of Ag-aNOR of HL-60 cells reveals that Ag-protein (RNA polymerase I) only presented in fibrillar centers (FC) and the dense fibrillar components (DFC) of nucleolus. In addition, in control group, large amount of Ag-protein, FC, DFC and granular components (GC) were observed, and there were many large nucleoli in a nucleus, meanwhile, the cells of the treated group tended to be mature, with a decrease in the amount of Ag-protein, FC, DFC and GC accordingly, and the nucleoli reduced both in size and number significantly.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:2626898

  19. Saturation of repeated quantum measurements

    NASA Astrophysics Data System (ADS)

    Haapasalo, Erkka; Heinosaari, Teiko; Kuramochi, Yui

    2016-08-01

    We study sequential measurement scenarios where the system is repeatedly subjected to the same measurement process. We first provide examples of such repeated measurements where further repetitions of the measurement do not increase our knowledge on the system after some finite number of measurement steps. We also prove, however, that repeating the Lüders measurement of an unsharp two-outcome observable never saturates in this sense, and we characterize the observable measured in the limit of infinitely many repetitions. Our result implies that a repeated measurement can be used to correct the inherent noise of an unsharp observable.

  20. Characterization of Arbequina virgin olive oils produced in different regions of Brazil and Spain: Physicochemical properties, oxidative stability and fatty acid profile.

    PubMed

    Borges, Thays H; Pereira, José Alberto; Cabrera-Vique, Carmen; Lara, Luis; Oliveira, Adelson F; Seiquer, Isabel

    2017-01-15

    Production of virgin olive oil is beginning in Brazil. This paper analyzes the characteristics of the EVOO Arbequina from Brazil in comparison with Spanish Arbequina from different regions. Quality parameters, oxidative stability, pigments, colour and fatty acid profile were assessed, and relationships with geographic and climatic conditions were studied. All the samples presented good quality and met EU standards for extra-virgin olive oil, but there were significant differences between regions and countries for many of the parameters evaluated. Major differences between Brazilian and Spanish samples were observed for free acidity and colour of the oils, as well as minor variations in the fatty acid profile. The colour differences were related to rainfall, whereas the fatty acid content was strongly influenced by altitude and temperature. These results highlight the fact that geographic area and environmental factors influence the characteristics of Arbequina oil and play an important role in newly introduced cultivars. PMID:27542498

  1. Comparison of simple sequence repeats in 19 Archaea.

    PubMed

    Trivedi, S

    2006-01-01

    All organisms that have been studied until now have been found to have differential distribution of simple sequence repeats (SSRs), with more SSRs in intergenic than in coding sequences. SSR distribution was investigated in Archaea genomes where complete chromosome sequences of 19 Archaea were analyzed with the program SPUTNIK to find di- to penta-nucleotide repeats. The number of repeats was determined for the complete chromosome sequences and for the coding and non-coding sequences. Different from what has been found for other groups of organisms, there is an abundance of SSRs in coding regions of the genome of some Archaea. Dinucleotide repeats were rare and CG repeats were found in only two Archaea. In general, trinucleotide repeats are the most abundant SSR motifs; however, pentanucleotide repeats are abundant in some Archaea. Some of the tetranucleotide and pentanucleotide repeat motifs are organism specific. In general, repeats are short and CG-rich repeats are present in Archaea having a CG-rich genome. Among the 19 Archaea, SSR density was not correlated with genome size or with optimum growth temperature. Pentanucleotide density had an inverse correlation with the CG content of the genome. PMID:17183484

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

    PubMed Central

    Chu, Chong; Nielsen, Rasmus; Wu, Yufeng

    2016-01-01

    Repeat elements are important components of eukaryotic genomes. One limitation in our understanding of repeat elements is that most analyses rely on reference genomes that are incomplete and often contain missing data in highly repetitive regions that are difficult to assemble. To overcome this problem we develop a new method, REPdenovo, which assembles repeat sequences directly from raw shotgun sequencing data. REPdenovo can construct various types of repeats that are highly repetitive and have low sequence divergence within copies. We show that REPdenovo is substantially better than existing methods both in terms of the number and the completeness of the repeat sequences that it recovers. The key advantage of REPdenovo is that it can reconstruct long repeats from sequence reads. We apply the method to human data and discover a number of potentially new repeats sequences that have been missed by previous repeat annotations. Many of these sequences are incorporated into various parasite genomes, possibly because the filtering process for host DNA involved in the sequencing of the parasite genomes failed to exclude the host derived repeat sequences. REPdenovo is a new powerful computational tool for annotating genomes and for addressing questions regarding the evolution of repeat families. The software tool, REPdenovo, is available for download at https://github.com/Reedwarbler/REPdenovo. PMID:26977803

  3. Occurrence and transport of 17 perfluoroalkyl acids in 12 coastal rivers in south Bohai coastal region of China with concentrated fluoropolymer facilities.

    PubMed

    Wang, Pei; Lu, Yonglong; Wang, Tieyu; Fu, Yaning; Zhu, Zhaoyun; Liu, Shijie; Xie, Shuangwei; Xiao, Yang; Giesy, John P

    2014-07-01

    Perfluoroalkyl acids (PFAAs) are emerging contaminants that have raised great concern in recent years. While PFAAs manufacturing becomes regulated in developed countries, production has been partly shifted to China. Eight fluoropolymer manufacturing facilities located in the South Bohai coastal region, one of the most populated areas of China, have been used to manufacture PFAA-related substances since 2001. The environmental consequence of the intensive production of PFAAs in this region remains largely unknown. We analyzed 17 PFAAs in twelve coastal rivers of this region, and found staggeringly high concentrations of perfluorooctanoic acid (PFOA) ranging from 0.96 to 4534.41 ng/L. The highest concentration was observed in the Xiaoqing River which received effluents from certain fluoropolymer facilities. Principal component analysis indicated similar sources of several perfluoroalkyl carboxylic acids (PFCAs) in all rivers, which indicated that atmospheric transport, wastewater treatment and surface runoff also acted as important supplements to direct discharge to surface water. PMID:24747105

  4. Contribution of Amino Acid Region 659−663 of Factor Va Heavy Chain to the Activity of Factor Xa within Prothrombinase†,‡

    PubMed Central

    2010-01-01

    Factor Va, the cofactor of prothrombinase, is composed of heavy and light chains associated noncovalently in the presence of divalent metal ions. The COOH-terminal region of the heavy chain contains acidic amino acid clusters that are important for cofactor activity. In this work, we have investigated the role of amino acid region 659−663, which contains five consecutive acidic amino acid residues, by site-directed mutagenesis. We have generated factor V molecules in which all residues were mutated to either lysine (factor V5K) or alanine (factor V5A). We have also constructed a mutant molecule with this region deleted (factor VΔ659−663). The recombinant molecules along with wild-type factor V (factor VWT) were transiently expressed in mammalian cells, purified, and assessed for cofactor activity. Two-stage clotting assays revealed that the mutant molecules had reduced clotting activities compared to that of factor VaWT. Kinetic analyses of prothrombinase assembled with the mutant molecules demonstrated diminished kcat values, while the affinity of all mutant molecules for factor Xa was similar to that for factor VaWT. Gel electrophoresis analyses of plasma-derived and recombinant mutant prothrombin activation demonstrated delayed cleavage of prothrombin at both Arg320 and Arg271 by prothrombinase assembled with the mutant molecules, resulting in meizothrombin lingering throughout the activation process. These results were confirmed after analysis of the cleavage of FPR-meizothrombin. Our findings provide new insights into the structural contribution of the acidic COOH-terminal region of factor Va heavy chain to factor Xa activity within prothrombinase and demonstrate that amino acid region 659−663 from the heavy chain of the cofactor contributes to the regulation of the rate of cleavage of prothrombin by prothrombinase. PMID:20722419

  5. Identification of amino acids in the V3 region of gp120 critical for virus neutralization by human HIV-1-specific antibodies.

    PubMed Central

    Broliden, P A; Mäkitalo, B; Akerblom, L; Rosen, J; Broliden, K; Utter, G; Jondal, M; Norrby, E; Wahren, B

    1991-01-01

    The importance of the dependence on single amino acids in the V3 region of HIV-1 gp120 was evaluated for virus neutralization and antibody-dependent cellular cytotoxicity (ADCC). Synthetic overlapping 15-mer peptides and a set of omission peptides covering amino acids 301-317 were used. Sera from 29 HIV-1-infected individuals at different stages of disease were tested for neutralization, ADCC and specific IgG reactivity. Six HIV-1 neutralizing monoclonal antibodies (mAb) acted as controls. All mAb reacted with a region (amino acids 304-318) of gp120, previously shown to induce neutralizing antibodies. The amino acids essential for reactivity were identified to be within the sequence GPGR (amino acids 312-315). The importance of this region for occurrence of neutralizing antibodies in infected humans was investigated using the same set of peptides. Out of 29 individuals, 21 were found to have neutralizing antibodies in titres between 100 and 1000. Among the neutralization-positive sera, 17/21 (81%) reacted with amino acids 304-318, compared with only one of eight sera (13%) negative in neutralization. When any of the four amino acids G, P, G or R were deleted, the seroreactivity decreased considerably. The conserved sequence GPGR was therefore considered to be the most important for neutralization in this region in human sera as well. Thus, the conserved sequence GPGR in the V3 region of gp120 is critical for virus neutralization by human HIV-1-specific antibodies. PMID:1916888

  6. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, Joe N.; Straume, Tore; Bogen, Kenneth T.

    1998-01-01

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

  7. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1998-03-24

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. 14 figs.

  8. Trinucleotide repeat expansion and DRPLA (Smith`s disease): Molecular characterization of atrophin-1

    SciTech Connect

    Margolis, R.L.; Li, S.H.; Li, X.J.; Ross, C.A.

    1994-09-01

    Smith`s disease (also known as dentatorubral pallidoluysian atrophy or DRPLA) is a rare, progressive, fatal neuropsychiatric disorder similar to Huntington`s disease (HD). Smith`s disease is characterized by ataxia, choreoathetosis, myoclonic epilepsy, dementia, and genetic anticipation. Neuropathological findings include prominent cell loss in the dentate nucleus of the cerebellum, the globus pallidus, the red nucleus, and the subthalamic nucleus. An expansion of a CAG trinucleotide repeat encoding polyglutamine in a gene originally identified in our laboratory as part of a program to clone candidate genes for disorders with anticipation has recently been found to cause this disorder. We have identified two families that demonstrate the pathological and genetic features (expanded CAG repeat and anticipation) of this disease. Northern analysis indicates that the gene, which we have termed atrophin-1, is widely expressed as a 5 kb mRNA in normal human brain and peripheral tissues. Brain expression is highest in the cerebellum. The developmental expression of the rat homologues of IT-15 (the gene in which a CAG expansion causes HD) and atrophin-1 were compared. Atrophin-1 was most highly expressed in early rat embryo brain (E16), whereas the greatest expression of IT-15 was in the adult rat brain. Cloning and sequencing of the open reading frame from inserts contained in brain cDNA libraries is in progress. In addition to the CAG repeat, the ORF contains an unusual region of alternating acidic and basic amino acids. Further characterization of atrophin-1, and comparison of it to other genes in which trinucleotide repeat expansion leads to neuropsychiatric disorders, should lead to a better understanding of the pathophysiology by which CAG repeat expansion causes human disease.

  9. Trinucleotide Repeats: A Structural Perspective

    PubMed Central

    Almeida, Bruno; Fernandes, Sara; Abreu, Isabel A.; Macedo-Ribeiro, Sandra

    2013-01-01

    Trinucleotide repeat (TNR) expansions are present in a wide range of genes involved in several neurological disorders, being directly involved in the molecular mechanisms underlying pathogenesis through modulation of gene expression and/or the function of the RNA or protein it encodes. Structural and functional information on the role of TNR sequences in RNA and protein is crucial to understand the effect of TNR expansions in neurodegeneration. Therefore, this review intends to provide to the reader a structural and functional view of TNR and encoded homopeptide expansions, with a particular emphasis on polyQ expansions and its role at inducing the self-assembly, aggregation and functional alterations of the carrier protein, which culminates in neuronal toxicity and cell death. Detail will be given to the Machado-Joseph Disease-causative and polyQ-containing protein, ataxin-3, providing clues for the impact of polyQ expansion and its flanking regions in the modulation of ataxin-3 molecular interactions, function, and aggregation. PMID:23801983

  10. Modeling Repeatedly Flaring δ Sunspots.

    PubMed

    Chatterjee, Piyali; Hansteen, Viggo; Carlsson, Mats

    2016-03-11

    Active regions (ARs) appearing on the surface of the Sun are classified into α, β, γ, and δ by the rules of the Mount Wilson Observatory, California on the basis of their topological complexity. Amongst these, the δ sunspots are known to be superactive and produce the most x-ray flares. Here, we present results from a simulation of the Sun by mimicking the upper layers and the corona, but starting at a more primitive stage than any earlier treatment. We find that this initial state consisting of only a thin subphotospheric magnetic sheet breaks into multiple flux tubes which evolve into a colliding-merging system of spots of opposite polarity upon surface emergence, similar to those often seen on the Sun. The simulation goes on to produce many exotic δ sunspot associated phenomena: repeated flaring in the range of typical solar flare energy release and ejective helical flux ropes with embedded cool-dense plasma filaments resembling solar coronal mass ejections. PMID:27015469

  11. Characterization of the promoter region of the gene for the rat neutral and basic amino acid transporter and chromosomal localization of the human gene.

    PubMed Central

    Yan, N; Mosckovitz, R; Gerber, L D; Mathew, S; Murty, V V; Tate, S S; Udenfriend, S

    1994-01-01

    The promoter region of the rat kidney neutral and basic amino acid transporter (NBAT) gene has been isolated and sequenced. The major transcription initiation site was mapped by primer extension. The entire promoter region and a set of 5' deletions within it were expressed at a high level in LLC-PK1 cells using the luciferase indicator gene. Positive and negative regulatory elements in the promoter region were observed. A human genomic clone of the transporter was also obtained and was used to localize the NBAT gene at the p21 region of chromosome 2. Images PMID:8052618

  12. Characterization of the variable-number tandem repeats in vrrA from different Bacillus anthracis isolates

    SciTech Connect

    Jackson, P.J.; Walthers, E.A.; Richmond, K.L.

    1997-04-01

    PCR analysis of 198 Bacillus anthracis isolates revealed a variable region of DNA sequence differing in length among the isolates. Five Polymorphisms differed by the presence Of two to six copies of the 12-bp tandem repeat 5{prime}-CAATATCAACAA-3{prime}. This variable-number tandem repeat (VNTR) region is located within a larger sequence containing one complete open reading frame that encodes a putative 30-kDa protein. Length variation did not change the reading frame of the encoded protein and only changed the copy number of a 4-amino-acid sequence (QYQQ) from 2 to 6. The structure of the VNTR region suggests that these multiple repeats are generated by recombination or polymerase slippage. Protein structures predicted from the reverse-translated DNA sequence suggest that any structural changes in the encoded protein are confined to the region encoded by the VNTR sequence. Copy number differences in the VNTR region were used to define five different B. anthracis alleles. Characterization of 198 isolates revealed allele frequencies of 6.1, 17.7, 59.6, 5.6, and 11.1% sequentially from shorter to longer alleles. The high degree of polymorphism in the VNTR region provides a criterion for assigning isolates to five allelic categories. There is a correlation between categories and geographic distribution. Such molecular markers can be used to monitor the epidemiology of anthrax outbreaks in domestic and native herbivore populations. 22 refs., 4 figs., 3 tabs.

  13. Upper limits for stereoselective photodissociation of free amino acids in the vacuum ultraviolet region and at the C 1s edge

    SciTech Connect

    Pruemper, Georg; Viefhaus, Jens; Cvejanovic, Slobodan; Rolles, Daniel; Gessner, Oliver; Lischke, Toralf; Hentges, Rainer; Wienberg, Christian; Mahler, Willy; Becker, Uwe; Langer, Burkhard; Prosperi, Tommaso; Zema, Nicola; Turchini, Stefano; Zada, Birgitt; Senf, Fred

    2004-06-01

    We measured the total and partial ion yields of the two chiral amino acids alanine and serine in the gas phase both in the vacuum ultraviolet region and at the C(1s) edge using circularly polarized light. We did not detect any circular dichroism asymmetry larger than 1x10{sup -3}. A similar measurement of fixed-in-space amino acids yielded an upper limit of 1x10{sup -2} for the stereoselective effect of circularly polarized light. The results obtained are relevant for quantitative models of stereoselective photodecomposition of amino acids that try to explain the homochirality of life.

  14. Amino acid substitutions in hepatitis C virus core region predict hepatocarcinogenesis following eradication of HCV RNA by antiviral therapy.

    PubMed

    Akuta, Norio; Suzuki, Fumitaka; Hirakawa, Miharu; Kawamura, Yusuke; Sezaki, Hitomi; Suzuki, Yoshiyuki; Hosaka, Tetsuya; Kobayashi, Masahiro; Kobayashi, Mariko; Saitoh, Satoshi; Arase, Yasuji; Ikeda, Kenji; Kumada, Hiromitsu

    2011-06-01

    Substitution of amino acid (aa) 70 and/or 91 in the core region of HCV genotype 1b (HCV-1b) is an important predictor of hepatocarcinogenesis, but its impact on the development of hepatocellular carcinoma (HCC) following eradication of HCV RNA by antiviral therapy is not clear. 1,273 patients with HCV-related chronic liver disease, with sustained virological response, defined as negative HCV RNA at 24 weeks after cessation of interferon monotherapy or interferon plus ribavirin combination therapy, were included in a follow-up study to evaluate the impact of aa substitution in the core region on hepatocarcinogenesis. Twenty six patients developed HCC during the follow-up. The cumulative rates of new HCC were 3.2%, 4.8%, and 8.6% at the end of 5, 10, and 15 years, respectively. The rates in patients infected with HCV-1b/Gln70(His70) [glutamine (histidine) at aa 70] were significantly higher than in patients infected with HCV-1b/Arg70 (arginine at aa 70) (P = 0.007; log-rank test) and HCV-2a/2b (P < 0.001; log-rank test). The rates in patients infected with HCV-1b/Arg70 were not significantly higher than in those infected with HCV-2a/2b (P = 0.617; log-rank test). Multivariate analysis identified HCV-1b/Gln70(His70) (HR 10.5, P < 0.001), advanced fibrosis (HR 9.03, P = 0.002), and old age (HR 3.09, P = 0.066) as determinants of hepatocarcinogenesis. In conclusion, aa substitution in the core region of HCV-1b at the start of antiviral therapy is an important predictor of HCC following eradication of HCV RNA. This study emphasizes the importance of detection of aa substitutions in the core region before antiviral therapy. PMID:21503914

  15. All-photonic quantum repeaters

    PubMed Central

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

    2015-01-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories. PMID:25873153

  16. All-photonic quantum repeaters

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories.

  17. All-photonic quantum repeaters.

    PubMed

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

    2015-01-01

    Quantum communication holds promise for unconditionally secure transmission of secret messages and faithful transfer of unknown quantum states. Photons appear to be the medium of choice for quantum communication. Owing to photon losses, robust quantum communication over long lossy channels requires quantum repeaters. It is widely believed that a necessary and highly demanding requirement for quantum repeaters is the existence of matter quantum memories. Here we show that such a requirement is, in fact, unnecessary by introducing the concept of all-photonic quantum repeaters based on flying qubits. In particular, we present a protocol based on photonic cluster-state machine guns and a loss-tolerant measurement equipped with local high-speed active feedforwards. We show that, with such all-photonic quantum repeaters, the communication efficiency scales polynomially with the channel distance. Our result paves a new route towards quantum repeaters with efficient single-photon sources rather than matter quantum memories. PMID:25873153

  18. Estimating repeatability of egg size

    USGS Publications Warehouse

    Flint, P.L.; Rockwell, R.F.; Sedinger, J.S.

    2001-01-01

    Measures of repeatability have long been used to assess patterns of variation in egg size within and among females. We compared different analytical approaches for estimating repeatability of egg size of Black Brant. Separate estimates of repeatability for eggs of each clutch size and laying sequence number varied from 0.49 to 0.64. We suggest that using the averaging egg size within clutches results in underestimation of variation within females and thereby overestimates repeatability. We recommend a nested design that partitions egg-size variation within clutches, among clutches within females, and among females. We demonstrate little variation in estimates of repeatability resulting from a nested model controlling for egg laying sequence and a nested model in which we assumed laying sequence was unknown.

  19. Role of portal region lysine residues in electrostatic interactions between heart fatty acid binding protein and phospholipid membranes.

    PubMed

    Herr, F M; Aronson, J; Storch, J

    1996-01-30

    The structure of heart fatty acid binding protein (HFABP) is a flattened beta-barrel comprising 10 antiparallel beta-sheets capped by two alpha-helical segments. The helical cap region is hypothesized to behave as a portal "lid" for the entry and release of ligand from the binding pocket. The transfer of fatty acid from HFABP is thought to occur via effective collisional interactions with membranes, and these interactions are enhanced when transfer is to membranes of net negative charge, thus implying that specific basic residues on the surface of HFABP may govern the transfer process [Wootan, M. G., & Storch, J. (1994) J. Biol. Chem. 269, 10517-10523]. To directly examine the role of charged lysine residues on the HFABP surface in specific interactions with membranes, chemical modification and selective mutagenesis of HFABP were used. All surface lysine residues were neutralized by acetylation of recombinant HFABP with acetic anhydride. In addition, seven mutant HFABPs were generated that resulted in charge alterations in five distinct sites of HFABP. Modification of the protein did not significantly alter the structural or ligand binding properties of HFABP, as assessed by circular dichroism, fluorescence quantum yield, and ligand binding analyses. By using a resonance energy transfer assay, transfer of 2-(9-anthroyloxy)palmitate (2AP) from acetylated HFABP to membranes was significantly slower than transfer from native HFABP. In addition, in distinct contrast to transfer from native protein, the 2AP transfer rate from acetylated HFABP was not increased to acceptor membranes of increased negative charge. Transfer of 2AP from HFABP mutants involving K22, located on alpha-helix I (alpha-I) of the helical cap region, was 3-fold slower than transfer from wild-type protein, whereas rates from a mutant involving the K59 residue, located on the beta 2-turn of the barrel near the helical cap, were 2-fold faster than those of wild type. A double mutant involving K22 and K

  20. The effects of acidic deposition on streams in the Appalachian Mountain and Piedmont region of the mid-Atlantic United States

    SciTech Connect

    Herlihy, A.T.; Kaufman, P.R. ); Church, M.R.; Wigington, P.J. Jr. ); Webb, J.R. ); Sale, M.J. )

    1993-08-01

    Streams in the Appalachian Mountain area of the mid-Atlantic receive some of the largest acidic deposition loadings of any region of the US. A synthesis of the survey data from the mid-Appalachians yields a consistent picture of the acid base status of streams. Acidic streams, and streams with very low acid neutralizing capacity (ANC), are almost all located in small (<20 km[sup 2]), upland, forested catchments in areas of base-poor bedrock. In the subpopulation in the mid-Appalachian area, data from various local surveys show that 6-27% of the streams are acidic, and about 25-50% have ANC less than 50 [mu]eq L[sup [minus]1]. After excluding streams with acid mine drainage, National Stream Survey estimates for the whole region show that there are 2330 km of acidic streams and 7500 km of streams with ANC less than 50 [mu]eq L[sup [minus]1]. Many of the streams with base flow ANC less than 50 [mu]eq L[sup [minus]1] become acidic during storm or snowmelt episodes. Sulfate from atmospheric deposition is the dominant source of strong acid anions in acid mid-Appalachian streams. Their low pH (median, 4.9) and high levels of inorganic monomeric aluminum (median, 129 [mu]g L[sup [minus]1]) leached through soils by acidic deposition are causing damage to aquatic biota. Quantification of the extent of biological effects, however, is not possible with available data. Localized studies have shown that stream water ANC is closely related to bedrock mineralogy. Attempts to quantify this relationship across the mid-Appalachians, however, were frustrated by the lack of adequate scale geologic mapping throughout the region. Sulfate mass balance analyses indicate that soils and surface waters of the region have not yet realized the full effects of elevated sulfur deposition due to watershed sulfate retention. Sulfur retention is likely to decrease in the future, resulting in further losses of stream ANC. 70 refs., 5 figs., 4 tabs.

  1. Two single amino acid substitutions in the intervening region of Newcastle disease virus HN protein attenuate viral replication and pathogenicity

    PubMed Central

    Liu, Bin; Ji, Yanhong; Lin, Zhongqing; Fu, Yuguang; Muhammad Dafallah, Rihab; Zhu, Qiyun

    2015-01-01

    Among the proteins encoded by Newcastle disease virus (NDV), the attachment protein (HN) is an important determinant of virulence and pathogenicity. HN has been molecularly characterized at the protein level; however, the relationship between the molecular character of HN and the animal pathotype it causes has not been well explored. Here, we revisited the intervening region (IR) of the HN stalk and extended the known biological functions of HN. Three distinct substitutions (A89Q, P93A, and L94A) in the IR of genotype VII NDV (G7 strain) HN protein were analyzed. The A89Q and L94A mutations weakened the fusion promotion activity of HN to 44% and 41% of that of wild type, respectively, whereas P93A decreased the neuraminidase activity to 21% of the parental level. At the virus level, P93A and L94A-bearing viruses displayed impaired receptor recognition ability, neuraminidase activity, and fusion-promoting activity, all of which led to virus attenuation. In addition, the L94A-mutated virus showed a dramatic decline in replication and was attenuated in cells and in chickens. Our data demonstrate that the HN biological activities and functions modulated by these specific amino acids in the IR are associated with NDV replication and pathogenicity. PMID:26267791

  2. The impact of mineral fertilizers and lime on the transformation of humic acids in a soddy-podzolic heavy loamy soil of the Cis-Ural region

    NASA Astrophysics Data System (ADS)

    Zav'yalova, N. E.

    2015-06-01

    The composition and structure of humic acids in a soddy-podzolic heavy loamy soil (Retisol) of the Cis-Ural region after the long-term application of mineral fertilizers and lime was studied by the methods of elemental analysis, infrared spectroscopy, and thermogravimetry. It was found that mineral fertilizers and lime did not change the ranges of C, H, O, and N contents and general structure typical of humic acids in soddy-podzolic soils. The long-term anthropogenic impact on the soil resulted in some transformation of the composition and properties of humic acids. Clear absorption bands in the area of 1700 cm-1 (C=O of carbonyl group) and 1620 cm-1 (C=C of aromatic rings), which characterize the benzenoid structures of molecules, were found in the infrared spectra of humic acids from the soil treated with lime at the rate to compensate for the total acidity. Soil liming favored the accumulation of thermodynamically stable fragments of the central part of humic acid molecules and the destruction of peripheral radicals. The application of mineral fertilizers resulted in the enrichment of humic acids with aliphatic fragments. The combined application of mineral fertilizers and lime increased the portion of aromatic structures and, at the same time, enriched humic acids in aliphatic fragments less resistant to pyrolysis. These fragments are biologically and chemically active and can be readily involved in the element turnover processes, thus protecting the stable part of humus from the biological destruction.

  3. Bovine gall-bladder mucin contains two distinct tandem repeating sequences: evidence for scavenger receptor cysteine-rich repeats.

    PubMed Central

    Nunes, D P; Keates, A C; Afdhal, N H; Offner, G D

    1995-01-01

    Gall-bladder mucin is a densely glycosylated macromolecule which is the primary secretory product of the gall-bladder epithelium. It has been shown to bind cholesterol and other biliary lipids and to promote cholesterol crystal nucleation in vitro. In order to understand the molecular basis for mucin-lipid interactions, bovine gall-bladder mucin cDNAs were identified by expression cloning and were isolated and sequenced. The nucleotide sequences of these cDNAs revealed two distinct tandem repeating domains. One of these domains contained a 20-amino acid tandem repeating sequence enriched in threonine, serine and proline. This sequence was similar to, but not identical with, the short tandem repeating sequences identified previously in other mammalian mucins. The other domain contained a 127-amino acid tandem repeating sequence enriched in cysteine and glycine. This repeat displayed considerable sequence similarity to a family of receptor- and ligand-binding proteins containing scavenger receptor cysteine-rich repeats. By analogy with other proteins containing these cysteine-rich repeats, it is possible that, in gall-bladder mucin, this domain serves as a binding site for hydrophobic ligands such as bilirubin, cholesterol and other biliary lipids. Images Figure 4 Figure 5 Figure 6 PMID:7646470

  4. Development of simple sequence repeat markers in cymbopogon species.

    PubMed

    Kumar, Jitendra; Verma, Vijeshwar; Shahi, Ashok Kumar; Qazi, Gulam Nab; Balyan, Harindra Singh

    2007-03-01

    The genus Cymbopogon comprises about 140 species, which produce characteristic aromatic essential oils. However, the phenotypic identification of species of Cymbopogon has been difficult as a result of widespread occurrence of natural variants, which differ in ploidy levels and chemotaxonomic complexities. Therefore, we have developed a set of simple sequence repeat markers from a genomic library of Cymbopogon jwarancusa to help in the precise identification of the species (including accessions) of Cymbopogon. For this purpose, we isolated 16 simple sequence repeat containing genomic deoxyribonucleic acid clones of C. jwarancusa, which contained a total of 32 simple sequence repeats with a range of 1 to 3 simple sequence repeats per clone. The majority (68.8%) of the 32 simple sequence repeats comprised dinucleotide repeat motifs followed by simple sequence repeats with trinucleotide (21.8%) and other higher order repeat motifs. Eighteen (81.8%) of the 22 designed primers for the above simple sequence repeats amplified products of expected sizes, when tried with genomic DNA of C. jwarancusa, the source species. Thirteen (72.2%) of the 18 functional primers detected polymorphism among the three species of Cymbopogon (C. flexuosus, C. pendulus and C. jwarancusa) and amplified a total of 95 alleles (range 1-18 alleles) with a PIC value of 0.44 to 0.96 per simple sequence repeat. Thus, the higher allelic range and high level of polymorphism demonstrated by the newly developed simple sequence repeat markers are likely to have many applications such as in improvement of essential oil quality by authentication of Cymbopogon species and varieties and mapping or tagging the genes controlling agronomically important traits of essential oils, which can further be utilized in marker assisted breeding. PMID:17318781

  5. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants.

    PubMed

    Sharma, Manisha; Pandey, Girdhar K

    2015-01-01

    The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein-protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants. PMID:26793205

  6. Expansion and Function of Repeat Domain Proteins During Stress and Development in Plants

    PubMed Central

    Sharma, Manisha; Pandey, Girdhar K.

    2016-01-01

    The recurrent repeats having conserved stretches of amino acids exists across all domains of life. Subsequent repetition of single sequence motif and the number and length of the minimal repeating motifs are essential characteristics innate to these proteins. The proteins with tandem peptide repeats are essential for providing surface to mediate protein–protein interactions for fundamental biological functions. Plants are enriched in tandem repeat containing proteins typically distributed into various families. This has been assumed that the occurrence of multigene repeats families in plants enable them to cope up with adverse environmental conditions and allow them to rapidly acclimatize to these conditions. The evolution, structure, and function of repeat proteins have been studied in all kingdoms of life. The presence of repeat proteins is particularly profuse in multicellular organisms in comparison to prokaryotes. The precipitous expansion of repeat proteins in plants is presumed to be through internal tandem duplications. Several repeat protein gene families have been identified in plants. Such as Armadillo (ARM), Ankyrin (ANK), HEAT, Kelch-like repeats, Tetratricopeptide (TPR), Leucine rich repeats (LRR), WD40, and Pentatricopeptide repeats (PPR). The structure and functions of these repeat proteins have been extensively studied in plants suggesting a critical role of these repeating peptides in plant cell physiology, stress and development. In this review, we illustrate the structural, functional, and evolutionary prospects of prolific repeat proteins in plants. PMID:26793205

  7. Intramolecular Folding in Human ILPR Fragment with Three C-Rich Repeats

    PubMed Central

    Dhakal, Soma; Lafontaine, Javonne L.; Yu, Zhongbo; Koirala, Deepak; Mao, Hanbin

    2012-01-01

    Enrichment of four tandem repeats of guanine (G) rich and cytosine (C) rich sequences in functionally important regions of human genome forebodes the biological implications of four-stranded DNA structures, such as G-quadruplex and i-motif, that can form in these sequences. However, there have been few reports on the intramolecular formation of non-B DNA structures in less than four tandem repeats of G or C rich sequences. Here, using mechanical unfolding at the single-molecule level, electrophoretic mobility shift assay (EMSA), circular dichroism (CD), and ultraviolet (UV) spectroscopy, we report an intramolecularly folded non-B DNA structure in three tandem cytosine rich repeats, 5'-TGTC4ACAC4TGTC4ACA (ILPR-I3), in the human insulin linked polymorphic region (ILPR). The thermal denaturation analyses of the sequences with systematic C to T mutations have suggested that the structure is linchpinned by a stack of hemiprotonated cytosine pairs between two terminal C4 tracts. Mechanical unfolding and Br2 footprinting experiments on a mixture of the ILPR-I3 and a 5′-C4TGT fragment have further indicated that the structure serves as a building block for intermolecular i-motif formation. The existence of such a conformation under acidic or neutral pH complies with the strand-by-strand folding pathway of ILPR i-motif structures. PMID:22761750

  8. Long terminal repeat of murine retroviral DNAs: sequence analysis, host-proviral junctions, and preintegration site.

    PubMed Central

    Van Beveren, C; Rands, E; Chattopadhyay, S K; Lowy, D R; Verma, I M

    1982-01-01

    The nucleotide sequence of the long terminal repeat (LTR) of three murine retroviral DNAs has been determined. The data indicate that the U5 region (sequences originating from the 5' end of the genome) of various LTRs is more conserved than the U3 region (sequences from the 3' end of the genome). The location and sequence of the control elements such as the 5' cap, "TATA-like" sequences, "CCAAT-box," and presumptive polyadenylic acid addition signal AATAAA in the various LTRs are nearly identical. Some murine retroviral DNAs contain a duplication of sequences within the LTR ranging in size from 58 to 100 base pairs. A variant of molecularly cloned Moloney murine sarcoma virus DNA in which one of the two LTRs integrated into the viral DNA was also analyzed. A 4-base-pair duplication was generated at the site of integration of LTR in the viral DNA. The host-viral junction of two molecularly cloned AKR-murine leukemia virus DNAs (clones 623 and 614) was determined. In the case of AKR-623 DNA, a 3- or 4-base-pair direct repeat of cellular sequences flanking the viral DNA was observed. However, AKR-614 DNA contained a 5-base-pair repeat of cellular sequences. The nucleotide sequence of the preintegration site of AKR-623 DNA revealed that the cellular sequences duplicated during integration are present only once. Finally, a striking homology between the sequences flanking the preintegration site and viral LTRs was observed. Images PMID:6281466

  9. Trends in summer chemistry linked to productivity in lakes recovering from acid deposition in the Adirondack region of New York

    USGS Publications Warehouse

    Momen, B.; Lawrence, G.B.; Nierzwicki-Bauer, S. A.; Sutherland, J.W.; Eichler, L.W.; Harrison, J.P.; Boylen, C.W.

    2006-01-01

    The US Environmental Protection Agency established the Adirondack Effects Assessment Program (AEAP) to evaluate and monitor the status of biological communities in lakes in the Adirondack region of New York that have been adversely affected by acid deposition. This program includes chemical analysis of 30 lakes, sampled two to three times each summer. Results of trends analysis for lake chemistry and chlorophyll a (chlor a) are presented for 1994 to 2003, and a general comparison is made with recent results of the Adirondack Long-Term Monitoring (ALTM) Program, which included chemical analysis of all but two of these lakes (plus an additional 24 lakes) monthly, year-round for 1992-2004. Increases in pH were found in 25 of the 30 AEAP lakes (P < 0.05) and increases in acid-neutralizing capacity (ANC) were found in 12 of the 30 lakes (P < 0.05). Concentrations of both SO 42- and Mg 2+ decreased in 11 lakes (P < 0.05), whereas concentrations of NO 3- decreased in 20 lakes (P < 0.05). Concentrations of NH 4+ decreased in 10 lakes at a significance level of P < 0.05 and in three other lakes based on P < 0.1. Concentrations of inorganic and organic monomeric aluminum generally were below the reporting limit of 1.5 ??mol L-1, but decreases were detected in four and five lakes, respectively (P < 0.1). Concentrations of chlor a increased in seven lakes at a significance level of P < 0.05 and two lakes at a significance level of P < 0.1. A significant inverse correlation was also found between chlor a and NO 3- concentrations in nine lakes at a significance level of P < 0.05 and two lakes at a significance level of P < 0.1. Results of AEAP analysis of lake chemistry were similar to those of the ALTM Program, although decreases in SO 42- concentrations were more evident in the year-round ALTM record. Overall, the results suggest (a) a degree of chemical recovery from acidification during the summer, (b) an increase in phytoplankton productivity, and (c) a decreasing trend in

  10. Regional and global impacts of Criegee intermediates on atmospheric sulphuric acid concentrations and first steps of aerosol formation.

    PubMed

    Percival, Carl J; Welz, Oliver; Eskola, Arkke J; Savee, John D; Osborn, David L; Topping, David O; Lowe, Douglas; Utembe, Steven R; Bacak, Asan; McFiggans, Gordon; Cooke, Michael C; Xiao, Ping; Archibald, Alexander T; Jenkin, Michael E; Derwent, Richard G; Riipinen, Ilona; Mok, Daniel W K; Lee, Edmond P F; Dyke, John M; Taatjes, Craig A; Shallcross, Dudley E

    2013-01-01

    Carbonyl oxides ("Criegee intermediates"), formed in the ozonolysis of alkenes, are key species in tropospheric oxidation of organic molecules and their decomposition provides a non-photolytic source of OH in the atmosphere (Johnson and Marston, Chem. Soc. Rev., 2008, 37, 699, Harrison et al, Sci, Total Environ., 2006, 360, 5, Gäb et al., Nature, 1985, 316, 535, ref. 1-3). Recently it was shown that small Criegee intermediates, C.I.'s, react far more rapidly with SO2 than typically represented in tropospheric models, (Welz, Science, 2012, 335, 204, ref. 4) which suggested that carbonyl oxides could have a substantial influence on the atmospheric oxidation of SO2. Oxidation of 502 is the main atmospheric source of sulphuric acid (H2SO4), which is a critical contributor to aerosol formation, although questions remain about the fundamental nucleation mechanism (Sipilä et al., Science, 2010, 327, 1243, Metzger et al., Proc. Natl. Acad. Sci. U. S. A., 2010 107, 6646, Kirkby et al., Nature, 2011, 476, 429, ref. 5-7). Non-absorbing atmospheric aerosols, by scattering incoming solar radiation and acting as cloud condensation nuclei, have a cooling effect on climate (Intergovernmental Panel on Climate Change (IPCC), Climate Change 2007: The Physical Science Basis, Cambridge University Press, 2007, ref. 8). Here we explore the effect of the Criegees on atmospheric chemistry, and demonstrate that ozonolysis of alkenes via the reaction of Criegee intermediates potentially has a large impact on atmospheric sulphuric acid concentrations and consequently the first steps in aerosol production. Reactions of Criegee intermediates with SO2 will compete with and in places dominate over the reaction of OH with SO2 (the only other known gas-phase source of H2SO4) in many areas of the Earth's surface. In the case that the products of Criegee intermediate reactions predominantly result in H2SO4 formation, modelled particle nucleation rates can be substantially increased by the improved

  11. Approaching improved adhesive bonding repeatability

    NASA Astrophysics Data System (ADS)

    Schlette, Christian; Müller, Tobias; Roβmann, Jürgen; Brecher, Christian

    2016-03-01

    Today, the precision of micro-optics assembly is mostly limited by the accuracy of the bonding process ― and in the case of adhesive bonding by the prediction and compensation of adhesive shrinkage during curing. In this contribution, we present a novel approach to address adhesive bonding based on hybrid control system theory. In hybrid control, dynamic systems are described as "plants" which produce discrete and/or continuous outputs from given discrete and/or continuous inputs, thus yielding a hybrid state space description of the system. The task of hybrid controllers is to observe the plant and to generate a discrete and/or continuous input sequence that guides or holds the plant in a desired target state region while avoiding invalid or unwanted intermediate states. Our approach is based on a series of experiments carried out in order to analyze, define and decouple the dependencies of adhesive shrinkage on multiple parameters, such as application geometries, fixture forces and UV intensities. As some of the dependencies describe continuous effects (e.g. shrinkage from UV intensity) and other dependencies describe discrete state transitions (e.g. fixture removal during curing), the resulting model of the overall bonding process is a hybrid dynamic system in the general case. For this plant model, we then propose a concept of sampling-based parameter search as a basis to design suitable hybrid controllers, which have the potential to optimize process control for a selection of assembly steps, thus improving the repeatability of related production steps like beam-shaping optics or mounting of turning mirrors for fiber coupling.

  12. Mechanisms of RNA-induced toxicity in CAG repeat disorders.

    PubMed

    Nalavade, R; Griesche, N; Ryan, D P; Hildebrand, S; Krauss, S

    2013-01-01

    Several inherited neurodegenerative disorders are caused by CAG trinucleotide repeat expansions, which can be located either in the coding region or in the untranslated region (UTR) of the respective genes. Polyglutamine diseases (polyQ diseases) are caused by an expansion of a stretch of CAG repeats within the coding region, translating into a polyQ tract. The polyQ tract expansions result in conformational changes, eventually leading to aggregate formation. It is widely believed that the aggregation of polyQ proteins is linked with disease development. In addition, in the last couple of years, it has been shown that RNA-mediated mechanisms also have a profound role in neurotoxicity in both polyQ diseases and diseases caused by elongated CAG repeat motifs in their UTRs. Here, we review the different molecular mechanisms assigned to mRNAs with expanded CAG repeats. One aspect is the mRNA folding of CAG repeats. Furthermore, pathogenic mechanisms assigned to CAG repeat mRNAs are discussed. First, we discuss mechanisms that involve the sequestration of the diverse proteins to the expanded CAG repeat mRNA molecules. As a result of this, several cellular mechanisms are aberrantly regulated. These include the sequestration of MBNL1, leading to misregulated splicing; sequestration of nucleolin, leading to reduced cellular rRNA; and sequestration of proteins of the siRNA machinery, resulting in the production of short silencing RNAs that affect gene expression. Second, we discuss the effect of expanded CAG repeats on the subcellular localization, transcription and translation of the CAG repeat mRNA itself. Here we focus on the MID1 protein complex that triggers an increased translation of expanded CAG repeat mRNAs and a mechanism called repeat-associated non-ATG translation, which leads to proteins aberrantly translated from CAG repeat mRNAs. In addition, therapeutic approaches for CAG repeat disorders are discussed. Together, all the findings summarized here show that

  13. Mechanisms of RNA-induced toxicity in CAG repeat disorders

    PubMed Central

    Nalavade, R; Griesche, N; Ryan, D P; Hildebrand, S; Krauß, S

    2013-01-01

    Several inherited neurodegenerative disorders are caused by CAG trinucleotide repeat expansions, which can be located either in the coding region or in the untranslated region (UTR) of the respective genes. Polyglutamine diseases (polyQ diseases) are caused by an expansion of a stretch of CAG repeats within the coding region, translating into a polyQ tract. The polyQ tract expansions result in conformational changes, eventually leading to aggregate formation. It is widely believed that the aggregation of polyQ proteins is linked with disease development. In addition, in the last couple of years, it has been shown that RNA-mediated mechanisms also have a profound role in neurotoxicity in both polyQ diseases and diseases caused by elongated CAG repeat motifs in their UTRs. Here, we review the different molecular mechanisms assigned to mRNAs with expanded CAG repeats. One aspect is the mRNA folding of CAG repeats. Furthermore, pathogenic mechanisms assigned to CAG repeat mRNAs are discussed. First, we discuss mechanisms that involve the sequestration of the diverse proteins to the expanded CAG repeat mRNA molecules. As a result of this, several cellular mechanisms are aberrantly regulated. These include the sequestration of MBNL1, leading to misregulated splicing; sequestration of nucleolin, leading to reduced cellular rRNA; and sequestration of proteins of the siRNA machinery, resulting in the production of short silencing RNAs that affect gene expression. Second, we discuss the effect of expanded CAG repeats on the subcellular localization, transcription and translation of the CAG repeat mRNA itself. Here we focus on the MID1 protein complex that triggers an increased translation of expanded CAG repeat mRNAs and a mechanism called repeat-associated non-ATG translation, which leads to proteins aberrantly translated from CAG repeat mRNAs. In addition, therapeutic approaches for CAG repeat disorders are discussed. Together, all the findings summarized here show that

  14. Trace element uptake by Eleocharis equisetina (spike rush) in an abandoned acid mine tailings pond, northeastern Australia: implications for land and water reclamation in tropical regions.

    PubMed

    Lottermoser, Bernd G; Ashley, Paul M

    2011-10-01

    This study was conducted to determine the uptake of trace elements by the emergent wetland plant species Eleocharis equisetina at the historic Jumna tin processing plant, tropical Australia. The perennial emergent sedge was found growing in acid waters (pH 2.45) and metal-rich tailings (SnAsCuPbZn). E. equisetina displayed a pronounced acid tolerance and tendency to exclude environmentally significant elements (Al, As, Cd, Ce, Co, Cu, Fe, La, Ni, Pb, Se, Th, U, Y, Zn) from its above-substrate biomass. This study demonstrates that geobotanical and biogeochemical examinations of wetland plants at abandoned mined lands of tropical areas can reveal pioneering, metal-excluding macrophytes. Such aquatic macrophytes are of potential use in the remediation of acid mine waters and sulfidic tailings and the reclamation of disturbed acid sulfate soils in subtropical and tropical regions. PMID:21550704

  15. Structural Basis of Neuronal Nitric-oxide Synthase Interaction with Dystrophin Repeats 16 and 17.

    PubMed

    Molza, Anne-Elisabeth; Mangat, Khushdeep; Le Rumeur, Elisabeth; Hubert, Jean-François; Menhart, Nick; Delalande, Olivier

    2015-12-01

    Duchenne muscular dystrophy is a lethal genetic defect that is associated with the absence of dystrophin protein. Lack of dystrophin protein completely abolishes muscular nitric-oxide synthase (NOS) function as a regulator of blood flow during muscle contraction. In normal muscles, nNOS function is ensured by its localization at the sarcolemma through an interaction of its PDZ domain with dystrophin spectrin-like repeats R16 and R17. Early studies suggested that repeat R17 is the primary site of interaction but ignored the involved nNOS residues, and the R17 binding site has not been described at an atomic level. In this study, we characterized the specific amino acids involved in the binding site of nNOS-PDZ with dystrophin R16-17 using combined experimental biochemical and structural in silico approaches. First, 32 alanine-scanning mutagenesis variants of dystrophin R16-17 indicated the regions where mutagenesis modified the affinity of the dystrophin interaction with the nNOS-PDZ. Second, using small angle x-ray scattering-based models of dystrophin R16-17 and molecular docking methods, we generated atomic models of the dystrophin R16-17·nNOS-PDZ complex that correlated well with the alanine scanning identified regions of dystrophin. The structural regions constituting the dystrophin interaction surface involve the A/B loop and the N-terminal end of helix B of repeat R16 and the N-terminal end of helix A' and a small fraction of helix B' and a large part of the helix C' of repeat R17. The interaction surface of nNOS-PDZ involves its main β-sheet and its specific C-terminal β-finger. PMID:26378238

  16. The DNA binding specificity of the basic region of the yeast transcriptional activator GCN4 can be changed by substitution of a single amino acid.

    PubMed Central

    Suckow, M; von Wilcken-Bergmann, B; Müller-Hill, B

    1993-01-01

    The X-ray structure of a GCN4 DNA complex (1) shows, that specific DNA binding of the GCN4 basic region is mediated by a complicated network of base pair and DNA backbone contacts. According to the X-ray structure, alanine -14 of the basic region of GCN4 (we define the first leucine of the leucine zipper as +1) makes a hydrophobic contact to the methyl group of the thymine next to the center of the GCN4 binding site 5' ATGACTCAT 3'. We tested the DNA binding properties of the nineteen derivatives of GCN4, which carry all possible amino acids in position -14 of the basic region. Substitution of alanine -14 of GCN4 by either asparagine or cysteine changes the DNA binding specificity. Serine in this position broadens the specificity for position 1 of the target, whereas other amino acids either retain or decrease GCN4 specificity. Images PMID:8502548

  17. Acid-sensing ion channels in trigeminal ganglion neurons innervating the orofacial region contribute to orofacial inflammatory pain.

    PubMed

    Fu, Hui; Fang, Peng; Zhou, Hai-Yun; Zhou, Jun; Yu, Xiao-Wei; Ni, Ming; Zheng, Jie-Yan; Jin, You; Chen, Jian-Guo; Wang, Fang; Hu, Zhuang-Li

    2016-02-01

    Orofacial pain is a common clinical symptom that is accompanied by tooth pain, migraine and gingivitis. Accumulating evidence suggests that acid-sensing ion channels (ASICs), especially ASIC3, can profoundly affect the physiological properties of nociception in peripheral sensory neurons. The aim of this study is to examine the contribution of ASICs in trigeminal ganglion (TG) neurons to orofacial inflammatory pain. A Western blot (WB), immunofluorescence assay of labelled trigeminal ganglion neurons, orofacial formalin test, cell preparation and electrophysiological experiments are performed. This study demonstrated that ASIC1, ASIC2a and ASIC3 are highly expressed in TG neurons innervating the orofacial region of rats. The amplitude of ASIC currents in these neurons increased 119.72% (for ASIC1-like current) and 230.59% (for ASIC3-like current) in the formalin-induced orofacial inflammatory pain model. In addition, WB and immunofluorescence assay demonstrated a significantly augmented expression of ASICs in orofacial TG neurons during orofacial inflammation compared with the control group. The relative protein density of ASIC1, ASIC2a and ASIC3 also increased 58.82 ± 8.92%, 45.30 ± 11.42% and 55.32 ± 14.71%, respectively, compared with the control group. Furthermore, pharmacological blockade of ASICs and genetic deletion of ASIC1 attenuated the inflammation response. These findings indicate that peripheral inflammation can induce the upregulation of ASICs in TG neurons, causing orofacial inflammatory pain. Additionally, the specific inhibitor of ASICs may have a significant analgesic effect on orofacial inflammatory pain. PMID:26510178

  18. Role of the C-terminal YG repeats of the primer-dependent streptococcal glucosyltransferase, GtfJ, in binding to dextran and mutan.

    PubMed

    Kingston, Kim B; Allen, Donna M; Jacques, Nicholas A

    2002-02-01

    The recombinant primer-dependent glucosyltransferase GtfJ of Streptococcus salivarius possesses a C-terminal glucan-binding domain composed of eighteen 21 aa YG repeats. By engineering a series of C-terminal truncated proteins, the position at which truncation prevented further mutan synthesis was defined to a region of 43 aa, confirming that not all of the YG motifs were required for the formation of mutan by GtfJ. The role of the YG repeats in glucan binding was investigated in detail. Three proteins consisting of 3.8, 7.2 or 11.0 C-terminal YG repeats were expressed in Escherichia coli. Each of the three purified proteins bound to both the 1,6-alpha-linked glucose residues of dextran and the 1,3-alpha-linked glucose residues of mutan, indicating that a protein consisting of nothing but 3.8 YG repeats could attach to either substrate. Secondary structure predictions of the primary amino acid sequence suggested that 37% of the amino acids were capable of forming a structure such that five regions of beta-sheet were separated by regions capable of forming beta-turns and random coils. CD spectral analysis showed that the purified 3.8 YG protein possessed an unordered secondary structure with some evidence of possible beta-sheet formation and that the protein maintained this relatively unordered structure on binding to dextran. PMID:11832518

  19. High-resolution opal records from the eastern tropical Pacific provide evidence for silicic acid leakage from HNLC regions during glacial periods

    NASA Astrophysics Data System (ADS)

    Arellano-Torres, Elsa; Pichevin, Laetitia E.; Ganeshram, Raja S.

    2011-05-01

    A shift from carbonate- to silica-dominated primary production could significantly affect the oceanic carbon cycle via changes in the particulate carbon rain-rate ratio ( C organic:C inorganic fluxes). An increase in C rain rate ratio has been invoked to explain lower glacial pCO 2; however, firm evidence of an ecological shift towards silica-dominated productivity during the last glacial period is lacking. Here, we present new high-resolution reconstructions of biogenic silica and total production over the past 40,000 yr BP in 3 cores from the eastern tropical North Pacific (ETNP) off Mexico and Nicaragua. These records reveal a clear regional pattern of higher siliceous productivity with higher opal accumulation during the last glacial period compared to interglacial times. Higher Si:C and Si:N ratios of glacial sediments in these records suggest a net increase in siliceous production over total production. We attribute this to the additional supply of silicic acid to the ETNP margins favouring diatoms over other non-siliceous algae. This suggestion for increased supply of Si during glacial periods is consistent with the proposed large-scale redistribution of excess silicic acid from High Nitrate Low Chlorophyll (HNLC) regions like the eastern equatorial Pacific (EEP) and the Southern Ocean by the Silicic Acid Leakage Hypothesis (SALH). In these HNLC regions, the Si-isotope composition of diatom frustules (δ 30Si) has provided evidence for the generation of surplus of silicic acid during diatom growth under conditions of higher Fe availability during glacial periods. We suggest that silicic acid leakage from the HNLC regions to the adjoining oceans may have increased the carbon rain rate ratio and ultimately, contributed to the decrease in glacial atmospheric pCO 2.

  20. Genomic repeats, genome plasticity and the dynamics of Mycoplasma evolution

    PubMed Central

    Rocha, Eduardo P. C.; Blanchard, Alain

    2002-01-01

    Mycoplasmas evolved by a drastic reduction in genome size, but their genomes contain numerous repeated sequences with important roles in their evolution. We have established a bioinformatic strategy to detect the major recombination hot-spots in the genomes of Mycoplasma pneumoniae, Mycoplasma genitalium, Ureaplasma urealyticum and Mycoplasma pulmonis. This allowed the identification of large numbers of potentially variable regions, as well as a comparison of the relative recombination potentials of different genomic regions. Different trends are perceptible among mycoplasmas, probably due to different functional and structural constraints. The largest potential for illegitimate recombination in M.pulmonis is found at the vsa locus and its comparison in two different strains reveals numerous changes since divergence. On the other hand, the main M.pneumoniae and M.genitalium adhesins rely on large distant repeats and, hence, homologous recombination for variation. However, the relation between the existence of repeats and antigenic variation is not necessarily straightforward, since repeats of P1 adhesin were found to be anti-correlated with epitopes recognized by patient antibodies. These different strategies have important consequences for the structures of genomes, since large distant repeats correlate well with the major chromosomal rearrangements. Probably to avoid such events, mycoplasmas strongly avoid inverse repeats, in comparison to co-oriented repeats. PMID:11972343

  1. Bovine submaxillary mucin contains multiple domains and tandemly repeated non-identical sequences.

    PubMed Central

    Jiang, W; Woitach, J T; Keil, R L; Bhavanandan, V P

    1998-01-01

    A number of cDNA fragments coding for bovine submaxillary mucin (BSM) were cloned, and the nucleotide sequence of the largest clone, BSM421, was determined. Two peptide sequences determined from the purified apoBSM were found near the N-terminus of the mucin-coding region of BSM421. This clone does not contain a start or stop codon, but its 3' end overlaps with the 5' end of a previously isolated clone, lambdaBSM10. The composite sequence of 1589 amino acid residues consists of five distinct protein domains, which are numbered from the C-terminus. The cysteine-rich domain I can be further divided into a von Willebrand factor type C repeat and a cystine knot. Domains III and V consist of similar repeated peptide sequences with an average of 47 residues. Domains II and IV do not contain such sequences but are similar to domains III and V in being rich in serine and threonine, many of which are predicted to be potential O-glycosylation sites. Domain III also contains two sequences that match the ATP/GTP-binding site motif A (P-loop). Only beta-strands and no alpha-helices are predicted for the partial deduced amino acid sequence. Northern analysis of submaxillary gland RNA with the BSM421 probe detected multiple messages of BSM with sizes from 1.1 to over 10 kb. The tandemly repeated, non-identical peptide sequences of approx. 47 residues in domains III and V of BSM differ from the tandemly repeated, identical 81-residue sequences of pig submaxillary mucin (PSM), although both BSM and PSM contain similar C-terminal domains. In contrast, two peptide sequences of ovine submaxillary mucin are highly similar (86% and 65% identical respectively) to the corresponding sequences in domain V of BSM. PMID:9512479

  2. Reprint of The improvement of the energy resolution in epi-thermal neutron region of Bonner sphere using boric acid water solution moderator.

    PubMed

    Ueda, H; Tanaka, H; Sakurai, Y

    2015-12-01

    Bonner sphere is useful to evaluate the neutron spectrum in detail. We are improving the energy resolution in epi-thermal neutron region of Bonner sphere, using boric acid water solution as a moderator. Its response function peak is narrower than that for polyethylene moderator and the improvement of the resolution is expected. The resolutions between polyethylene moderator and boric acid water solution moderator were compared by simulation calculation. Also the influence in the uncertainty of Bonner sphere configuration to spectrum estimation was simulated. PMID:26508275

  3. The improvement of the energy resolution in epi-thermal neutron region of Bonner sphere using boric acid water solution moderator.

    PubMed

    Ueda, H; Tanaka, H; Sakurai, Y

    2015-10-01

    Bonner sphere is useful to evaluate the neutron spectrum in detail. We are improving the energy resolution in epi-thermal neutron region of Bonner sphere, using boric acid water solution as a moderator. Its response function peak is narrower than that for polyethylene moderator and the improvement of the resolution is expected. The resolutions between polyethylene moderator and boric acid water solution moderator were compared by simulation calculation. Also the influence in the uncertainty of Bonner sphere configuration to spectrum estimation was simulated. PMID:26133664

  4. ¹H NMR-based metabonomics in brain nucleus accumbens and striatum following repeated cocaine treatment in rats.

    PubMed

    Li, Y; Yan, G-Y; Zhou, J-Q; Bu, Q; Deng, P-C; Yang, Y-Z; Lv, L; Deng, Y; Zhao, J-X; Shao, X; Zhu, R-M; Huang, Y-N; Zhao, Y-L; Cen, X-B

    2012-08-30

    Studies have shown a few cerebral metabolites modified by cocaine in brain regions; however, endogenous metabolic profiling has been lacking. Ex vivo (1)H NMR (hydrogen-1 nuclear magnetic resonance) spectroscopy-based metabonomic approach coupled with partial least squares was applied to investigate the changes of cerebral metabolites in nucleus accumbens (NAc) and striatum of rats subjected to cocaine treatment. Our results showed that both single and repeated cocaine treatment can induce significant changes in a couple of cerebral metabolites. The increase of neurotransmitters glutamate and gamma-amino butyric acid (GABA) were observed in NAc and striatum from the rats repeatedly treated with cocaine. Creatine and taurine increased in NAc whereas taurine increased and creatine decreased in striatum after repeated cocaine treatment. Elevation of N-acetylaspartate in NAc and striatum and decrease of lactate in striatum were observed, which may reflect the mitochondria dysregulation caused by cocaine; moreover, alterations of choline, phosphocholine and glycerol in NAc and striatum could be related to membrane disruption. Moreover, groups of rats with and without conditioned place preference (CPP) apparatus are presenting difference in metabolites. Collectively, our results provide the first evidence of metabonomic profiling of NAc and striatum in response to cocaine, exhibiting a regionally-specific alteration patterns. We find that repeated cocaine administration leads to significant metabolite alterations, which are involved in neurotransmitter disturbance, oxidative stress, mitochondria dysregulation and membrane disruption in brain. PMID:22609933

  5. CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

    PubMed Central

    Alkhnbashi, Omer S.; Costa, Fabrizio; Shah, Shiraz A.; Garrett, Roger A.; Saunders, Sita J.; Backofen, Rolf

    2014-01-01

    Motivation: The discovery of CRISPR-Cas systems almost 20 years ago rapidly changed our perception of the bacterial and archaeal immune systems. CRISPR loci consist of several repetitive DNA sequences called repeats, inter-spaced by stretches of variable length sequences called spacers. This CRISPR array is transcribed and processed into multiple mature RNA species (crRNAs). A single crRNA is integrated into an interference complex, together with CRISPR-associated (Cas) proteins, to bind and degrade invading nucleic acids. Although existing bioinformatics tools can recognize CRISPR loci by their characteristic repeat-spacer architecture, they generally output CRISPR arrays of ambiguous orientation and thus do not determine the strand from which crRNAs are processed. Knowledge of the correct orientation is crucial for many tasks, including the classification of CRISPR conservation, the detection of leader regions, the identification of target sites (protospacers) on invading genetic elements and the characterization of protospacer-adjacent motifs. Results: We present a fast and accurate tool to determine the crRNA-encoding strand at CRISPR loci by predicting the correct orientation of repeats based on an advanced machine learning approach. Both the repeat sequence and mutation information were encoded and processed by an efficient graph kernel to learn higher-order correlations. The model was trained and tested on curated data comprising >4500 CRISPRs and yielded a remarkable performance of 0.95 AUC ROC (area under the curve of the receiver operator characteristic). In addition, we show that accurate orientation information greatly improved detection of conserved repeat sequence families and structure motifs. We integrated CRISPRstrand predictions into our CRISPRmap web server of CRISPR conservation and updated the latter to version 2.0. Availability: CRISPRmap and CRISPRstrand are available at http://rna.informatik.uni-freiburg.de/CRISPRmap. Contact: backofen

  6. Entanglement replication via quantum repeated interactions

    NASA Astrophysics Data System (ADS)

    Wendenbaum, Pierre; Platini, Thierry; Karevski, Dragi

    2015-04-01

    We study entanglement creation between two independent XX chains, which are repeatedly coupled locally to spin-1/2 Bell pairs. We show analytically that in the steady state the entanglement of the Bell pairs is perfectly transferred to the chains, generating large-scale interchain pair correlations. However, before the steady state is reached, within a growing causal region around the interacting locus the chains are found in a current driven nonequilibrium steady state (NESS). In the NESS, the chains cross entanglement decays exponentially with respect to the distance to the boundary sites with a typical length scale which is inversely proportional to the driving current.

  7. Effects of different cooking methods on fatty acid profiles in four freshwater fishes from the Laurentian Great Lakes region.

    PubMed

    Neff, Margaret R; Bhavsar, Satyendra P; Braekevelt, Eric; Arts, Michael T

    2014-12-01

    Fish is often promoted as a healthy part of the human diet due its high content of long chain n-3 polyunsaturated fatty acids (LC-PUFA). Previous studies have shown that cooked fish can have different fatty acid profiles than raw fillets, depending on the cooking method and fish species. In this study, the fatty acid content of broiled, baked or fried skinless, boneless fillets of four fish species from the tributaries of the Great Lakes, or connecting rivers, was compared to fatty acid profiles in raw sections from the same fillet. Cooking treatments had little effect on n-3 fatty acid content; however, fried treatments generally had higher n-6 and MUFA content, which is likely a result of the cooking oil used (canola). Broiling or baking is generally the most healthy option presented in this study, as these methods result in lower levels of less-favourable fatty acids; however, the choice of cooking oil may also influence the overall fatty acid content in cooked fish. PMID:24996368

  8. 5'TRU: identification and analysis of translationally regulative 5'untranslated regions in amino acid starved yeast cells.

    PubMed

    Rachfall, Nicole; Heinemeyer, Isabelle; Morgenstern, Burkhard; Valerius, Oliver; Braus, Gerhard H

    2011-06-01

    We describe a method to identify and analyze translationally regulative 5'UTRs (5'TRU) in Saccharomyces cerevisiae. Two-dimensional analyses of (35)S-methionine metabolically labeled cells revealed 13 genes and proteins, whose protein biosynthesis is post-transcriptionally up-regulated on amino acid starvation. The 5'UTRs of the respective mRNAs were further investigated. A plasmid-based reporter-testing system was developed to analyze their capability to influence translation dependent on amino acid availability. Most of the 13 candidate 5'UTRs are able to enhance translation independently of amino acids. Two 5'UTRs generally repressed translation, and the 5'UTRs of ENO1, FBA1, and TPI1 specifically up-regulated translation when cells were starved for amino acids. The TPI1-5'UTR exhibited the strongest effect in the testing system, which is consistent with elevated Tpi1p-levels in amino acid starved cells. Bioinformatical analyses support that an unstructured A-rich 5' leader is beneficial for efficient translation when amino acids are scarce. Accordingly, the TPI1-5'UTR was shown to contain an A-rich tract in proximity to the mRNA-initiation codon, required for its amino acid dependent regulatory function. PMID:21444828

  9. System Using Tandem Repeats of the cA Peptidoglycan-Binding Domain from Lactococcus lactis for Display of both N- and C-Terminal Fusions on Cell Surfaces of Lactic Acid Bacteria▿

    PubMed Central

    Okano, Kenji; Zhang, Qiao; Kimura, Sakurako; Narita, Junya; Tanaka, Tsutomu; Fukuda, Hideki; Kondo, Akihiko

    2008-01-01

    Here, we established a system for displaying heterologous protein to the C terminus of the peptidoglycan-binding domain (cA domain) of AcmA (a major autolysin from Lactococcus lactis). Western blot and flow cytometric analyses revealed that the fusion proteins (cA-AmyA) of the cA domain and α-amylase from Streptococcus bovis 148 (AmyA) are efficiently expressed and successfully displayed on the surfaces of L. lactis cells. AmyA was also displayed on the cell surface while retaining its activity. Moreover, with an increase in the number of cA domains, the quantity of cA-AmyA fusion proteins displayed on the cell surface increased. When three repeats of the cA domain were used as an anchor protein, 82% of α-amylase activity was detected on the cells. The raw starch-degrading activity of AmyA was significantly higher when AmyA was fused to the C terminus of the cA domain than when it was fused to the N terminus. In addition, cA-AmyA fusion proteins were successfully displayed on the cell surfaces of Lactobacillus plantarum and Lactobacillus casei. PMID:18156338

  10. System using tandem repeats of the cA peptidoglycan-binding domain from Lactococcus lactis for display of both N- and C-terminal fusions on cell surfaces of lactic acid bacteria.

    PubMed

    Okano, Kenji; Zhang, Qiao; Kimura, Sakurako; Narita, Junya; Tanaka, Tsutomu; Fukuda, Hideki; Kondo, Akihiko

    2008-02-01

    Here, we established a system for displaying heterologous protein to the C terminus of the peptidoglycan-binding domain (cA domain) of AcmA (a major autolysin from Lactococcus lactis). Western blot and flow cytometric analyses revealed that the fusion proteins (cA-AmyA) of the cA domain and alpha-amylase from Streptococcus bovis 148 (AmyA) are efficiently expressed and successfully displayed on the surfaces of L. lactis cells. AmyA was also displayed on the cell surface while retaining its activity. Moreover, with an increase in the number of cA domains, the quantity of cA-AmyA fusion proteins displayed on the cell surface increased. When three repeats of the cA domain were used as an anchor protein, 82% of alpha-amylase activity was detected on the cells. The raw starch-degrading activity of AmyA was significantly higher when AmyA was fused to the C terminus of the cA domain than when it was fused to the N terminus. In addition, cA-AmyA fusion proteins were successfully displayed on the cell surfaces of Lactobacillus plantarum and Lactobacillus casei. PMID:18156338

  11. Phenotypic and genotypic identification of lactic acid bacteria isolated from traditional pickles of the Çubuk region in Turkey.

    PubMed

    Bağder Elmacı, Simel; Tokatlı, Mehmet; Dursun, Derya; Özçelik, Filiz; Şanlıbaba, Pınar

    2015-05-01

    A total of 152 lactic acid bacteria (LAB) were isolated from pickles produced in the Ankara-Çubuk region. These isolates were clustered into eight groups on the basis of their phenotypic characteristics including cell morphology, CO2 production from glucose, growth at 10 and 45 °C, growth in 6.5 % NaCl, and growth at pH 9.6. API 50 CH carbohydrate fermentation test, 16S ribosomal RNA (rRNA) sequence analysis, and sodium dodecyl sulfate-acrylamide gel electrophoresis (SDS-PAGE) whole-cell protein profile analysis were also performed for precise identification of the isolates at the species level. Molecular identification revealed that the most prevalent LAB species involved in pickle fermentation were Pediococcus ethanolidurans (46 isolates, 30.3 %), Lactobacillus brevis (37 isolates, 24.3 %), Lactobacillus plantarum (37 isolates, 24.3 %), and Lactobacillus buchneri (15 isolates, 9.9 %). Other LAB were found in minor frequencies such as Pediococcus parvulus (8 isolates, 5.3 %), Lactobacillus namurensis (6 isolates, 3.9 %), Lactobacillus diolivorans (1 isolate, 0.7 %), Lactobacillus parabrevis (1 isolate, 0.7 %), and Enterococcus casseliflavus (1 isolate, 0.7 %). When results of phenotypic and genotypic identification methods were compared, differences in the species distribution of LAB associated with pickles were defined between the API and the 16S rRNA sequencing. The API 50 CHL test coincided with the 16S rRNA results in 71 out of the 152 tested isolates, indicating that API gave unreliable identification results. A clear correlation could not be found between the results of whole-cell SDS profiles and 16S rRNA sequencing. Therefore, molecular characterization by 16S rRNA sequencing was considered to be the most reliable method for identifying isolates. The results presented in this work provide insight in to the LAB population associated with traditional Çubuk pickles and constitute a LAB strain resource for further studies involving the development of

  12. Limitations on quantum key repeaters.

    PubMed

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

    2015-01-01

    A major application of quantum communication is the distribution of entangled particles for use in quantum key distribution. Owing to noise in the communication line, quantum key distribution is, in practice, limited to a distance of a few hundred kilometres, and can only be extended to longer distances by use of a quantum repeater, a device that performs entanglement distillation and quantum teleportation. The existence of noisy entangled states that are undistillable but nevertheless useful for quantum key distribution raises the question of the feasibility of a quantum key repeater, which would work beyond the limits of entanglement distillation, hence possibly tolerating higher noise levels than existing protocols. Here we exhibit fundamental limits on such a device in the form of bounds on the rate at which it may extract secure key. As a consequence, we give examples of states suitable for quantum key distribution but unsuitable for the most general quantum key repeater protocol. PMID:25903096

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

    NASA Astrophysics Data System (ADS)

    Provenzano, Virgil; Della Torre, Edward; Bennett, Lawrence H.; ElBidweihy, Hatem

    2014-02-01

    The Gd5Ge2Si2 alloy and the off-stoichiometric Ni50Mn35In15 Heusler alloy belong to a special class of metallic materials that exhibit first-order magnetostructural transitions near room temperature. The magnetic properties of this class of materials have been extensively studied due to their interesting magnetic behavior and their potential for a number of technological applications such as refrigerants for near-room-temperature magnetic refrigeration. The thermally driven first-order transitions in these materials can be field-induced in the reverse order by applying a strong enough field. The field-induced transitions are typically accompanied by the presence of large magnetic hysteresis, the characteristics of which are a complicated function of temperature, field, and magneto-thermal history. In this study we show that the virgin curve, the major loop, and sequentially measured MH loops are the results of both repeatable and non-repeatable processes, in which the starting magnetostructural state, prior to the cycling of field, plays a major role. Using the Gd5Ge2Si2 and Ni50Mn35In15 alloys, as model materials, we show that a starting single phase state results in fully repeatable processes and large magnetic hysteresis, whereas a mixed phase starting state results in non-repeatable processes and smaller hysteresis.

  14. Repeating seismic events in China.

    PubMed

    Schaff, David P; Richards, Paul G

    2004-02-20

    About 10% of seismic events in and near China from 1985 to 2000 were repeating events not more than about 1 kilometer from each other. We cross-correlated seismograms from approximately 14,000 earthquakes and explosions and measured relative arrival times to approximately 0.01 second, enabling lateral location precision of about 100 to 300 meters. Such precision is important for seismic hazard studies, earthquake physics, and nuclear test ban verification. Recognition and measurement of repeating signals in archived data and the resulting improvement in location specificity quantifies the inaccuracy of current procedures for picking onset times and locating events. PMID:14976310

  15. Pure laparoscopic hepatectomy as repeat surgery and repeat hepatectomy

    PubMed Central

    Isetani, Masashi; Morise, Zenichi; Kawabe, Norihiko; Tomishige, Hirokazu; Nagata, Hidetoshi; Kawase, Jin; Arakawa, Satoshi

    2015-01-01

    AIM: To assess clinical outcomes of laparoscopic hepatectomy (LH) in patients with a history of upper abdominal surgery and repeat hepatectomy. METHODS: This study compared the perioperative courses of patients receiving LH at our institution that had or had not previously undergone upper abdominal surgery. Of the 80 patients who underwent LH, 22 had prior abdominal surgeries, including hepatectomy (n = 12), pancreatectomy (n = 3), cholecystectomy and common bile duct excision (n = 1), splenectomy (n = 1), total gastrectomy (n = 1), colectomy with the involvement of transverse colon (n = 3), and extended hysterectomy with extensive lymph-node dissection up to the upper abdomen (n = 1). Clinical indicators including operating time, blood loss, hospital stay, and morbidity were compared among the groups. RESULTS: Eighteen of the 22 patients who had undergone previous surgery had severe adhesions in the area around the liver. However, there were no conversions to laparotomy in this group. In the 58 patients without a history of upper abdominal surgery, the median operative time was 301 min and blood loss was 150 mL. In patients with upper abdominal surgical history or repeat hepatectomy, the operative times were 351 and 301 min, and blood loss was 100 and 50 mL, respectively. The median postoperative stay was 17, 13 and 12 d for patients with no history of upper abdominal surgery, patients with a history, and patients with repeat hepatectomy, respectively. There were five cases with complications in the group with no surgical history, compared to only one case in the group with a prior history. There were no statistically significant differences in the perioperative results between the groups with and without upper abdominal surgical history, or with repeat hepatectomy. CONCLUSION: LH is feasible and safe in patients with a history of upper abdominal surgery or repeat hepatectomy. PMID:25624731

  16. Inhibition of the mutagenicity of bay-region diol epoxides of polycyclic aromatic hydrocarbons by naturally occurring plant phenols: Exceptional activity of ellagic acid

    PubMed Central

    Wood, Alexander W.; Huang, Mou-Tuan; Chang, Richard L.; Newmark, Harold L.; Lehr, Roland E.; Yagi, Haruhiko; Sayer, Jane M.; Jerina, Donald M.; Conney, Allan H.

    1982-01-01

    Ferulic, caffeic, chlorogenic, and ellagic acids, four naturally occurring plant phenols, inhibit the mutagenicity and cytotoxicity of (±)-7β,8α-dihydroxy-9α, 10α-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene (B[a]P 7,8-diol-9,10-epoxide-2), the only known ultimate carcinogenic metabolite of benzo[a]pyrene. The mutagenicity of 0.05 nmol of B[a]P 7,8-diol-9,10-epoxide-2 in strain TA100 of Salmonella typhimurium is inhibited 50% by incubation of the bacteria and the diol epoxide with 150 nmol of ferulic acid, 75 nmol of caffeic acid, 50 nmol of chlorogenic acid or, most strikingly, 1 nmol of ellagic acid in the 0.5-ml incubation mixture. A 3-nmol dose of ellagic acid inhibits mutation induction by 90%. Ellagic acid is also a potent antagonist of B[a]P 7,8-diol-9,10-epoxide-2 in Chinese hamster V79 cells. Mutations to 8-azaguanine resistance induced by 0.2 μM diol epoxide are reduced by 50% when tissue culture media also contains 2 μM ellagic acid. Similar to results obtained with the bacteria, ferulic, caffeic, and chlorogenic acids are approximately two orders of magnitude less active than ellagic acid in the mammalian cell assay. The antimutagenic effects of the plant phenols result from their direct interaction with B[a]P 7,8-diol-9,10-epoxide-2, because a concentration-dependent increase in the rate of diol epoxide disappearance in cell-free solutions of 1:9 dioxane/water, pH 7.0, is observed with all four phenols. In parallel with the mutagenicity studies, ellagic acid is 80-300 times more effective than the other phenols in accelerating the disappearance of B[a]P 7,8-diol-9,10-epoxide-2. Ellagic acid at 10 μM increases the disappearance of B[a]P 7,8-diol-9,10-epoxide-2 by approximately 20-fold relative to the spontaneous and hydronium ion-catalyzed hydrolysis of the diol epoxide at pH 7.0. Ellagic acid is a highly potent inhibitor of the mutagenic activity of bay-region diol epoxides of benzo[a]pyrene, dibenzo[a,h]pyrene, and dibenzo[a,i]pyrene, but higher

  17. Sequence of human tryptophan 2,3-dioxygenase (TDO2): Presence of a glucocorticoid response-like element composed of a GTT repeat and an intronic CCCCT repeat

    SciTech Connect

    Comings, D.E.; Muhleman, D.; Dietz, G.

    1995-09-20

    Abnormalities in serotonin levels have been implicated in a wide range of psychiatric disorders. Tryptophan 2,3-dioxygenase is the rate-limiting enzyme in the catabolism of tryptophan, the precursor of serotonin. As such it is a potential major candidate gene in psychiatric genetics. The regulatory, intron, and exon regions of the human TDO2 gene have been sequenced. Twelve exons were identified. The amino acid sequence of the enzyme was 88% homologous to that of the rat. Compared to the rat, the regulatory region of the human TDO2 gene had an insertion of approximately 1064 bp of random DNA beginning at -293 bp and extending to -1357 bp. This displaced the glucocorticoid response element (GRE) occurring at -1174 bp in the rat to -1500 in the human. The proximal GRE at -419 in the rat was missing in the human. However, within the DNA insert there was a GRE-like microsatellite region containing multiple GTT repeats plus additional GT(n) sequences. This could produce several staggered regions of the sequence TGTTGTnnnTGTTGT similiar to a GRE consensus sequence of TGTTCAnnnTGTTCT. The intron regions 5` and 3` to each exon were sequenced. This allowed each exon to be screened for mutations. This showed a His{r_arrow}Val mutation polymorphism in exon 7. Three introns, 1, 5, and 6, were completely sequenced and examined for polymorphisms. This identified two polymorphisms consisting of G{r_arrow}T and G{r_arrow}A mutations 2 bp apart in intron 6. The 3` end of intron 5` showed an extensive CCCCT pentanucleotide repeat that was markedly polymorphic. These polymorphisms allow the TDO2 gene to be examined for a possible role in psychiatric disorders. 35 refs., 4 figs., 1 tab.

  18. Polymorphic CUG repeats in human mRNAs and their effects on gene expression.

    PubMed

    Tian, Bin; Mukhopadhyay, Rupa; Mathews, Michael B

    2005-01-01

    Expanded CUG repeats in the 3'-untranslated region (UTR) of the gene encoding myotonic dystrophy protein kinase (DMPK) cause myotonic dystrophy type 1 disease (DM1). The presence of such repeats has been found to impede gene expression at several levels in model systems. We took a bioinformatic approach to survey all human mRNA sequences for polymorphic CUG repeats. Our survey revealed that CUG repeats occur widely in various regions of mRNAs, with higher frequency in protein coding regions than 5'-UTRs or 3'-UTRs. About 30 genes were found to contain CUG repeats that are polymorphic in the number of repeats, suggesting the potential to expand or shrink. However, long polymorphic repeats were restricted to the 3'-UTR of the DMPK gene and the coding region of the ribosomal protein L14 gene. Using cell-free translation systems, we showed that extended CUG repeats can inhibit protein synthesis in vitro in the rabbit reticulocyte lysate, but not in wheat germ extracts, consistent with our previous finding of an interaction of CUG repeats with the protein kinase PKR. In transfected cells, CUG repeats can inhibit gene expression both in cis and in trans. However, observations with PKR-minus cells indicate that these effects are not primarily attributable to the interaction of extended CUG repeats with PKR. Northwestern blotting detected the presence in human cells of more CUG-binding proteins than are currently known. PMID:17114933

  19. Characterization and amino acid sequence of a fatty acid-binding protein from human heart.

    PubMed

    Offner, G D; Brecher, P; Sawlivich, W B; Costello, C E; Troxler, R F

    1988-05-15

    The complete amino acid sequence of a fatty acid-binding protein from human heart was determined by automated Edman degradation of CNBr, BNPS-skatole [3'-bromo-3-methyl-2-(2-nitrobenzenesulphenyl)indolenine], hydroxylamine, Staphylococcus aureus V8 proteinase, tryptic and chymotryptic peptides, and by digestion of the protein with carboxypeptidase A. The sequence of the blocked N-terminal tryptic peptide from citraconylated protein was determined by collisionally induced decomposition mass spectrometry. The protein contains 132 amino acid residues, is enriched with respect to threonine and lysine, lacks cysteine, has an acetylated valine residue at the N-terminus, and has an Mr of 14768 and an isoelectric point of 5.25. This protein contains two short internal repeated sequences from residues 48-54 and from residues 114-119 located within regions of predicted beta-structure and decreasing hydrophobicity. These short repeats are contained within two longer repeated regions from residues 48-60 and residues 114-125, which display 62% sequence similarity. These regions could accommodate the charged and uncharged moieties of long-chain fatty acids and may represent fatty acid-binding domains consistent with the finding that human heart fatty acid-binding protein binds 2 mol of oleate or palmitate/mol of protein. Detailed evidence for the amino acid sequences of the peptides has been deposited as Supplementary Publication SUP 50143 (23 pages) at the British Library Lending Division, Boston Spa, Yorkshire LS23 7BQ, U.K., from whom copies may be obtained as indicated in Biochem. J. (1988) 249, 5. PMID:3421901

  20. Tandem-repeat protein domains across the tree of life

    PubMed Central

    Jernigan, Kristin K.

    2015-01-01

    Tandem-repeat protein domains, composed of repeated units of conserved stretches of 20–40 amino acids, are required for a wide array of biological functions. Despite their diverse and fundamental functions, there has been no comprehensive assessment of their taxonomic distribution, incidence, and associations with organismal lifestyle and phylogeny. In this study, we assess for the first time the abundance of armadillo (ARM) and tetratricopeptide (TPR) repeat domains across all three domains in the tree of life and compare the results to our previous analysis on ankyrin (ANK) repeat domains in this journal. All eukaryotes and a majority of the bacterial and archaeal genomes analyzed have a minimum of one TPR and ARM repeat. In eukaryotes, the fraction of ARM-containing proteins is approximately double that of TPR and ANK-containing proteins, whereas bacteria and archaea are enriched in TPR-containing proteins relative to ARM- and ANK-containing proteins. We show in bacteria that phylogenetic history, rather than lifestyle or pathogenicity, is a predictor of TPR repeat domain abundance, while neither phylogenetic history nor lifestyle predicts ARM repeat domain abundance. Surprisingly, pathogenic bacteria were not enriched in TPR-containing proteins, which have been associated within virulence factors in certain species. Taken together, this comparative analysis provides a newly appreciated view of the prevalence and diversity of multiple types of tandem-repeat protein domains across the tree of life. A central finding of this analysis is that tandem repeat domain-containing proteins are prevalent not just in eukaryotes, but also in bacterial and archaeal species. PMID:25653910

  1. Vibrational analysis of amino acids and short peptides in hydrated media. 3. Successive KL repeats induce highly stable beta-strands capable of forming non-H-bonded aggregates.

    PubMed

    Guiffo-Soh, Guy; Hernandez, Belén; Coïc, Yves-Marie; Boukhalfa-Heniche, Fatima-Zohra; Fadda, Giulia; Ghomi, Mahmoud

    2008-01-31

    Circular dichroism (CD) and Raman scattering were applied to the aqueous solution of minimalist LK peptides constructed with successive KL repeats leading to the following generic primary sequence: (KL)nK. Three peptides of this family, a 3-mer (n=1), a 9-mer (n=4), and a 15-mer (n=7), are analyzed in this report. Raman spectra of the 3-mer (KLK, a random chain) and its labile-hydrogen deuterated species yield a set of interesting information for analyzing longer peptides of this series. Although the CD spectrum of the 9-mer (KLKLKLKLK) reveals a signal traditionally assigned to a random structure, the corresponding Raman spectrum allows finding a mixture of conformations in solution, adopting predominantly beta-type structures. This fact proves the utility of Raman spectroscopy to eliminate eventual ambiguity concerning conformational assignments in peptides based only on the use of CD technique. Finally, the 15-mer (KLKLKLKLKLKLKLK) gives rise to CD and Raman spectra clearly assignable to a beta-type structure. On the basis of all the observed results on the 15-mer, we can confirm that this peptide may exist as isolated beta-strands at low concentration (sub-micromolar), flat-oriented at the air/water interface, whereas at high concentrations (millimolar), non-H-bonded immersible aggregates might be formed. A hypothetical model for these beta-strand aggregates could be proposed as stabilized by an interior hydrophobic core and a hydrophilic external face, formed by leucine and lysine side chains, respectively. PMID:18177032

  2. Modeling the Seasonal Ice Zone from the Air: use of repeat aerial hydrographic surveys to constrain a regional ice-ocean model in an area of rapidly evolving ice cover

    NASA Astrophysics Data System (ADS)

    Dewey, S.; Morison, J.; Zhang, J.

    2015-12-01

    The Seasonal Ice Zone of the Beaufort Sea is the area of ocean north of Alaska over which sea ice melts and reforms annually. It contains the more narrow, near-edge marginal ice zone (MIZ). Seasonal Ice Zone Reconnaissance Surveys (SIZRS) measure hydrography along two meridional sections using Air eXpendable CTDs (AXCTDs) and Air eXpendable Current Profilers (AXCPs). These surveys take place aboard U.S. Coast Guard Arctic Domain Awareness flights of opportunity during each melt season (June-October) starting in 2012. The Marginal Ice Zone Modeling and Assimilation System (MIZMAS) is a high-resolution regional ice-ocean model with daily, three-dimensional output encompassing the SIZRS survey area. Direct comparison of the SIZRS data with MIZMAS output as well as with several regional climatologies can constrain the ice-ocean model and help to explain recent changes in subsurface heat content and salinity. For example, observed freshening relative to climatology has been used as a reference to which MIZMAS surface salinity values can be relaxed. MIZMAS may in turn shed light on the physical mechanisms driving the observed freshening. In addition, use of MIZMAS surface fluxes to drive a one-dimensional mixed layer model gives results close to observations when the model is initialized with SIZRS profiles. Because SIZRS observations range in time from the onset of melt to the onset of Fall freeze-up, the comparison of the one-dimensional model with MIZMAS illustrates the relative roles of local and regional processes in forming near-surface temperature maxima and salinity minima. The SIZRS observations and one-dimensional model are used to constrain MIZMAS estimations of stored subsurface heat while establishing the physical drivers of these temperature and salinity changes.

  3. Temperature modulation of thermal tolerance of a CAM-tank bromeliad and the relationship with acid accumulation in different leaf regions.

    PubMed

    Chaves, Cleber Juliano Neves; Leal, Bárbara Simões Santos; Lemos-Filho, José Pires de

    2015-08-01

    Physiological changes that increase plant performance during exposure to high temperatures may play an inverse role during exposure to low temperatures. The objective of this study was to test variations in photosystem II response to heat and cold stress in the leaves of a bromeliad with crassulacean acid metabolism submitted to high or low temperatures. Leaves were maintained under constant temperatures of 10 and 35°C and used to examine possible relationships among physiological responses to high and low temperatures and organic acid accumulation. We also tested if distinct parts of bromeliad leaves show differences in photosynthetic thermotolerance. The samples from leaves maintained at 35°C showed greater heat tolerance values, while those from leaves maintained at 10°C showed lower cold tolerance values. Our results identified a strong negative relationship between the organic acid accumulation and thermal tolerance of bromeliad leaves that largely explained the differences in thermal tolerance among groups. One of these differences occurred among regions of a single leaf, with the base showing critical heat values of up to 8°C higher than the top region, suggesting a possible partitioning of leaf response among its regions. Differences in thermal tolerance were also observed between sampling times, with higher values observed in the morning. PMID:25271368

  4. Bidirectional transcripts of the expanded C9orf72 hexanucleotide repeat are translated into aggregating dipeptide repeat proteins.

    PubMed

    Mori, Kohji; Arzberger, Thomas; Grässer, Friedrich A; Gijselinck, Ilse; May, Stephanie; Rentzsch, Kristin; Weng, Shih-Ming; Schludi, Martin H; van der Zee, Julie; Cruts, Marc; Van Broeckhoven, Christine; Kremmer, Elisabeth; Kretzschmar, Hans A; Haass, Christian; Edbauer, Dieter

    2013-12-01

    Massive GGGGCC repeat expansion in the first intron of the gene C9orf72 is the most common known cause of familial frontotemporal lobar degeneration (FTLD) and amyotrophic lateral sclerosis (ALS). Despite its intronic localization and lack of an ATG start codon, the repeat region is translated in all three reading frames into aggregating dipeptide-repeat (DPR) proteins, poly-(Gly-Ala), poly-(Gly-Pro) and poly-(Gly-Arg). We took an antibody-based approach to further validate the translation of DPR proteins. To test whether the antisense repeat RNA transcript is also translated, we raised antibodies against the predicted products, poly-(Ala-Pro) and poly-(Pro-Arg). Both antibodies stained p62-positive neuronal cytoplasmic inclusions throughout the cerebellum and hippocampus indicating that not only sense but also antisense strand repeats are translated into DPR proteins in the absence of ATG start codons. Protein products of both strands co-aggregate suggesting concurrent translation of both strands. Moreover, an antibody targeting the putative carboxyl terminus of DPR proteins can detect inclusion pathology in C9orf72 repeat expansion carriers suggesting that the non-ATG translation continues through the entire repeat and beyond. A highly sensitive monoclonal antibody against poly-(Gly-Arg), visualized abundant inclusion pathology in all cortical regions and some inclusions also in motoneurons. Together, our data show that the GGGGCC repeat is bidirectionally translated into five distinct DPR proteins that co-aggregate in the characteristic p62-positive TDP-43 negative inclusions found in FTLD/ALS cases with C9orf72 repeat expansion. Novel monoclonal antibodies against poly-(Gly-Arg) will facilitate pathological diagnosis of C9orf72 FTLD/ALS. PMID:24132570

  5. Do Twelfths Terminate or Repeat?

    ERIC Educational Resources Information Center

    Ambrose, Rebecca; Burnison, Erica

    2015-01-01

    When finding the decimal equivalent of a fraction with 12 in the denominator, will it terminate or repeat? This question came from a seventh grader in author Erica Burnison's class as the student was pondering a poster generated by one of her classmates. Not only was the question intriguing, but it also affirmed the belief in the power of…

  6. Variation of intragenic tandem repeat tract of tolA modulates Escherichia coli stress tolerance.

    PubMed

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

    2012-01-01

    In recent work we discovered that the intragenic tandem repeat (TR) region of the tolA gene is highly variable among different Escherichia coli strains. The aim of this study was therefore to investigate the biological function and dynamics of TR variation in E. coli tolA. The biological impact of TR variation was examined by comparing the ability of a set of synthetic tolA variants with in frame repeat copies varying from 2 to 39 to rescue the altered susceptibility of an E. coli ΔtolA mutant to deoxycholic acid, sodium dodecyl sulfate, hyperosmolarity, and infection with filamentous bacteriophage. Interestingly, although each of the TolA variants was able to at least partly rescue the ΔtolA mutant, the extent was clearly dependent on both the repeat number and the type of stress imposed, indicating the existence of opposing selective forces with regard to the optimal TR copy number. Subsequently, TR dynamics in a clonal population were assayed, and we could demonstrate that TR contractions are RecA dependent and enhanced in a DNA repair deficient uvrD background, and can occur at a frequency of 6.9×10(-5). PMID:23094082

  7. Minifish mtDNA has abundance of repeat sequences and inefficient replication in vitro.

    PubMed

    Wang, J; Peng, L-Y; You, C-P; Li, Q-L; Wen, M; Liu, S-J; Hong, Y-H

    2014-01-01

    Paedocypris is a newly described minifish genus endemic to Southeast Asia. Besides a tiny adult size of ~8 mm in length, minifish feature fragmentary habitats of acidic peat blackwater swamps, an unusual reproduction mode, truncated development and one of the smallest known genomes. A complete sequence is absent for the minifish mitochondrial DNA (mtDNA). Here we report the complete mtDNA sequence and its unusual feature in the minifish P. progenetica (Pp). We show that the Pp mtDNA is a circular molecule of 17,382 bp in length and has the same number of similarly oriented genes as in other vertebrates. Specifically, it comprises 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and 1 D-loop. Surprisingly, the D-loop is elusive for amplification by standard PCR conditions. The D-loop possesses a 28-bp dinucleotide TA repeat and more intriguingly, up to 25 copies of a 34-bp tandem repeat sequence. These tandem repeats predict the formation of paired regions. Hence, besides a generally conserved mtDNA with other vertebrates, the Pp mtDNA features an unusual D-loop and compromised DNA replication in vitro. PMID:25470288

  8. Statistical approaches to detecting and analyzing tandem repeats in genomic sequences.

    PubMed

    Anisimova, Maria; Pečerska, Julija; Schaper, Elke

    2015-01-01

    Tandem repeats (TRs) are frequently observed in genomes across all domains of life. Evidence suggests that some TRs are crucial for proteins with fundamental biological functions and can be associated with virulence, resistance, and infectious/neurodegenerative diseases. Genome-scale systematic studies of TRs have the potential to unveil core mechanisms governing TR evolution and TR roles in shaping genomes. However, TR-related studies are often non-trivial due to heterogeneous and sometimes fast evolving TR regions. In this review, we discuss these intricacies and their consequences. We present our recent contributions to computational and statistical approaches for TR significance testing, sequence profile-based TR annotation, TR-aware sequence alignment, phylogenetic analyses of TR unit number and order, and TR benchmarks. Importantly, all these methods explicitly rely on the evolutionary definition of a tandem repeat as a sequence of adjacent repeat units stemming from a common ancestor. The discussed work has a focus on protein TRs, yet is generally applicable to nucleic acid TRs, sharing similar features. PMID:25853125

  9. Pentapeptide Repeat Proteins and Cyanobacteria

    SciTech Connect

    Buchko, Garry W.

    2009-10-16

    Cyanobacteria are unique in many ways and one unusual feature is the presence of a suite of proteins that contain at least one domain with a minimum of eight tandem repeated five-residues (Rfr) of the general consensus sequence A[N/D]LXX. The function of such pentapeptide repeat proteins (PRPs) are still unknown, however, their prevalence in cyanobacteria suggests that they may play some role in the unique biological activities of cyanobacteria. As part of an inter-disciplinary Membrane Biology Grand Challenge at the Environmental Molecular Sciences Laboratory (Pacific Northwest National Laboratory) and Washington University in St. Louis, the genome of Cyanothece 51142 was sequenced and its molecular biology studied with relation to circadian rhythms. The genome of Cyanothece encodes for 35 proteins that contain at least one PRP domain. These proteins range in size from 105 (Cce_3102) to 930 (Cce_2929) kDa with the PRP domains ranging in predicted size from 12 (Cce_1545) to 62 (cce_3979) tandem pentapeptide repeats. Transcriptomic studies with 29 out of the 35 genes showed that at least three of the PRPs in Cyanothece 51142 (cce_0029, cce_3083, and cce_3272) oscillated with repeated periods of light and dark, further supporting a biological function for PRPs. Using X-ray diffraction crystallography, the structure for two pentapeptide repeat proteins from Cyanothece 51142 were determined, cce_1272 (aka Rfr32) and cce_4529 (aka Rfr23). Analysis of their molecular structures suggests that all PRP may share the same structural motif, a novel type of right-handed quadrilateral β-helix, or Rfr-fold, reminiscent of a square tower with four distinct faces. Each pentapeptide repeat occupies one face of the Rfr-fold with four consecutive pentapeptide repeats completing a coil that, in turn, stack upon each other to form “protein skyscrapers”. Details of the structural features of the Rfr-fold are reviewed here together with a discussion for the possible role of end

  10. 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. PMID:9451957

  11. Chromosome-specific DNA Repeat Probes

    SciTech Connect

    Baumgartner, Adolf; Weier, Jingly Fung; Weier, Heinz-Ulrich G.

    2006-03-16

    In research as well as in clinical applications, fluorescence in situ hybridization (FISH) has gained increasing popularity as a highly sensitive technique to study cytogenetic changes. Today, hundreds of commercially available DNA probes serve the basic needs of the biomedical research community. Widespread applications, however, are often limited by the lack of appropriately labeled, specific nucleic acid probes. We describe two approaches for an expeditious preparation of chromosome-specific DNAs and the subsequent probe labeling with reporter molecules of choice. The described techniques allow the preparation of highly specific DNA repeat probes suitable for enumeration of chromosomes in interphase cell nuclei or tissue sections. In addition, there is no need for chromosome enrichment by flow cytometry and sorting or molecular cloning. Our PCR-based method uses either bacterial artificial chromosomes or human genomic DNA as templates with {alpha}-satellite-specific primers. Here we demonstrate the production of fluorochrome-labeled DNA repeat probes specific for human chromosomes 17 and 18 in just a few days without the need for highly specialized equipment and without the limitation to only a few fluorochrome labels.

  12. Specific recognition of guanines in non-duplex regions of nucleic acids with potassium tungstate and hydrogen peroxide

    PubMed Central

    Mao, Wuxiang; Xu, Xiaowei; He, Huan; Huang, Rong; Chen, Xi; Xiao, Heng; Yu, Zhenduo; Liu, Yi; Zhou, Xiang

    2015-01-01

    Structural features of nucleic acids have become an integral part of current biomedical research. Highly selective and readily performed methods with little toxicity that target guanosines in non-duplex nucleic acids are needed, which led us to search for an effective agent for guanosine sequencing. Treatment of DNA or RNA with potassium tungstate and hydrogen peroxide produced damaged guanosines in DNA or RNA sequences. The damaged guanosines in non-duplex DNA could be cleaved by hot piperidine. Similarly, damaged guanosines in non-duplex RNA could be cleaved by aniline acetate. We could identify structural features of nucleic acid using this strategy instead of dimethyl sulphate and Ribonuclease T1. PMID:25355517

  13. The mouse and human excitatory amino acid transporter gene (EAAT1) maps to mouse chromosome 15 and a region of syntenic homology on human chromosome 5

    SciTech Connect

    Kirschner, M.A.; Arriza, J.L.; Amara, S.G.

    1994-08-01

    The gene for human excitatory amino acid transporter (EAAT1) was localized to the distal region of human chromosome 5p13 by in situ hybridization of metaphase chromosome spreads. Interspecific backcross analysis identified the mouse Eaat1 locus in a region of 5p13 homology on mouse chromosome 15. Markers that are linked with EAAT1 on both human and mouse chromosomes include the receptors for leukemia inhibitory factor, interleukin-7, and prolactin. The Eaat1 locus appears not be linked to the epilepsy mutant stg locus, which is also on chromosome 15. The EAAT1 locus is located in a region of 5p deletions that have been associated with mental retardation and microcephaly. 22 refs., 2 figs.

  14. Gadolinium ethoxybenzyl diethylenetriamine pentaacetic acid-enhanced magnetic resonance imaging: A potential utility for the evaluation of regional liver function impairment following transcatheter arterial chemoembolization

    PubMed Central

    XIAO, YU-DONG; PAUDEL, RAMCHANDRA; LIU, HUAN; ZHANG, BIN; MA, CONG; ZHOU, SHUN-KE

    2015-01-01

    The present study aimed to evaluate regional liver function impairment following transcatheter arterial chemoembolization (TACE), assessed by magnetic resonance imaging (MRI) enhanced by gadolinium ethoxybenzyl diethylenetriamine pentaacetic acid (Gd-EOB-DTPA). Additionally, this study evaluated the associations between signal intensity and various clinical factors. A prospective study was conducted between March 2012 and May 2013 with a total of 35 patients. Gd-EOB-DTPA-enhanced MRI was performed 3–5 days after TACE therapy. The signal to noise ratio (SNR) was subsequently calculated for healthy liver tissue regions and peritumoral regions, prior to and 20 min after Gd-EOB-DTPA administration. The correlation between clinical factors and relative SNR was assessed using Pearson’s correlation coefficient or Spearman’s rank correlation coefficient. Prior to Gd-EOB-DTPA administration, the SNR values showed no significant difference (t=1.341, P=0.191) in healthy liver tissue regions (50.53±15.99; range, 11.25–83.46) compared with peritumoral regions (49.81±15.85; range, 12.34–81.53). On measuring at 20 min following Gd-EOB-DTPA administration, the SNR in healthy liver tissue regions (82.55±33.33; range, 31.45–153.02) was significantly higher (t=3.732, P<0.001) compared with that in peritumoral regions (75.77±27.41; range, 31.42–144.49). The relative SNR in peritumoral regions correlated only with the quantity of iodized oil used during TACE therapy (r=0.528, P=0.003); the age, gender, diameter and blood supply of the tumor, or Child-Pugh class of the patient did not correlate with relative SNR. Gd-EOB-DTPA-enhanced MRI may be an effective way to evaluate regional liver function impairment following TACE therapy. PMID:25663880

  15. Response of surface water chemistry to reduced levels of acid precipitation: comparison of trends in two regions of New York, USA

    NASA Astrophysics Data System (ADS)

    Burns, Douglas A.; McHale, Michael R.; Driscoll, Charles T.; Roy, Karen M.

    2006-04-01

    In light of recent reductions in sulphur (S) and nitrogen (N) emissions mandated by Title IV of the Clean Air Act Amendments of 1990, temporal trends and trend coherence in precipitation (1984-2001 and 1992-2001) and surface water chemistry (1992-2001) were determined in two of the most acid-sensitive regions of North America, i.e. the Catskill and Adirondack Mountains of New York. Precipitation chemistry data from six sites located near these regions showed decreasing sulphate (SO42-), nitrate (NO3-), and base cation (CB) concentrations and increasing pH during 1984-2001, but few significant trends during 1992-2001. Data from five Catskill streams and 12 Adirondack lakes showed decreasing trends in SO42- concentrations at all sites, and decreasing trends in NO3-, CB, and H+ concentrations and increasing trends in dissolved organic carbon at most sites. In contrast, acid-neutralizing capacity (ANC) increased significantly at only about half the Adirondack lakes and in one of the Catskill streams. Flow correction prior to trend analysis did not change any trend directions and had little effect on SO42- trends, but it caused several significant non-flow-corrected trends in NO3- and ANC to become non-significant, suggesting that trend results for flow-sensitive constituents are affected by flow-related climate variation. SO42- concentrations showed high temporal coherence in precipitation, surface waters, and in precipitation-surface water comparisons, reflecting a strong link between S emissions, precipitation SO42- concentrations, and the processes that affect S cycling within these regions. NO3- and H+ concentrations and ANC generally showed weak coherence, especially in surface waters and in precipitation-surface water comparisons, indicating that variation in local-scale processes driven by factors such as climate are affecting trends in acid-base chemistry in these two regions.

  16. Response of surface water chemistry to reduced levels of acid precipitation: Comparison of trends in two regions of New York, USA

    USGS Publications Warehouse

    Burns, Douglas A.; McHale, M.R.; Driscoll, C.T.; Roy, K.M.

    2006-01-01

    In light of recent reductions in sulphur (S) and nitrogen (N) emissions mandated by Title IV of the Clean Air Act Amendments of 1990, temporal trends and trend coherence in precipitation (1984-2001 and 1992-2001) and surface water chemistry (1992-2001) were determined in two of the most acid-sensitive regions of North America, i.e. the Catskill and Adirondack Mountains of New York. Precipitation chemistry data from six sites located near these regions showed decreasing sulphate (SO42-), nitrate (NO3-), and base cation (CB) concentrations and increasing pH during 1984-2001, but few significant trends during 1992-2001. Data from five Catskill streams and 12 Adirondack lakes showed decreasing trends in SO42- concentrations at all sites, and decreasing trends in NO3-, CB, and H+ concentrations and increasing trends in dissolved organic carbon at most sites. In contrast, acid-neutralizing capacity (ANC increased significantly at only about half the Adirondack lakes and in one of the Catskill streams. Flow correction prior to trend analysis did not change any trend directions and had little effect on SO42- trends, but it caused several significant non-flow-corrected trends in NO3- and ANC to become non-significant, suggesting that trend results for flow-sensitive constituents are affected by flow-related climate variation. SO42- concentrations showed high temporal coherence in precipitation, surface waters, and in precipitation-surface water comparisons, reflecting a strong link between S emissions, precipitation SO42- concentrations, and the processes that affect S cycling within these regions. NO3- and H+ concentrations and ANC generally showed weak coherence, especially in surface waters and in precipitation-surface water comparisons, indicating that variation in local-scale processes driven by factors such as climate are affecting trends in acid-base chemistry in these two regions. Copyright ?? 2005 John Wiley & Sons, Ltd.

  17. Observations of Soft Gamma Repeaters

    NASA Technical Reports Server (NTRS)

    Kouveliotou, Chryssa

    2004-01-01

    Magnetars (Soft Gamma Repeaters and Anomalous X-ray Pulsars) are a subclass of neutron stars characterized by their recurrent X-ray bursts. While in an active (bursting) state (lasting anywhere between days and years), they are emit&ng hundreds of predominantly soft (kT=30 kev), short (0.1-100 ms long) events. Their quiescent source x-ray light ewes exhibit puhlions rotational period rate changes (spin-down) indicate that their magnetic fields are extremely high, of the order of 10^14- 10^l5 G. Such high B-field objects, dubbed "magnetars", had been predicted to exist in 1992, but the first concrete observational evidence were obtained in 1998 for two of these sources. I will discuss here the history of Soft Gamma Repeaters, and their spectral, timing and flux characteristics both in the persistent and their burst emission.

  18. Utilization of folic acid and iron supplementation services by pregnant women attending an antenatal clinic at a regional referral hospital in Kenya.

    PubMed

    Maina-Gathigi, L; Omolo, J; Wanzala, P; Lindan, C; Makokha, A

    2013-09-01

    To determine utilization of iron and folic acid supplementation services among pregnant women in Kenya. A cross sectional study was conducted at Nyeri Hospital, a regional referral hospital in central Kenya. Women attending the antenatal clinic were selected through systematic sampling. A semi-structured questionnaire was administered to collect information on utilization of folic acid and iron supplementation services. Women who ingested folic acid or iron supplements for >4 days in a week were considered "highly compliant". The health worker in-charge of the antenatal clinic was interviewed about the frequency of supplement stock-outs during the past year. Haemoglobin concentration was measured directly from one drop of capillary blood and measured using portable HEMOCUE B-Hb photometer. Of the 381 women interviewed, only 23.6 % obtained antenatal care in the first trimester; 69.3 and 51.2 % received folic acid and iron supplements, respectively. However, only half (45-58 %) received any information about supplementation. Most women were initiated on folic acid (80.7 %) or iron (67.7 %) after 12 and 16 weeks of gestation, respectively, well after the recommended time period. However, more than 80 % of those who received folic acid and iron were highly compliant. Stock-outs were common at the facility. Of 361 women tested for Hb level, the prevalence of anaemia (Hb levels < 11 g/dl) was 7.8 %. Health workers need to better explain the importance of supplements to pregnant women. Women who come late to antenatal clinic miss opportunities to start supplementation early in pregnancy. Problems with supply chain management exacerbate the problem. PMID:22907273

  19. Repeat Size Determination by Two Molecular Rulers in the Type I-E CRISPR Array.

    PubMed

    Goren, Moran G; Doron, Shany; Globus, Rea; Amitai, Gil; Sorek, Rotem; Qimron, Udi

    2016-09-13

    Prokaryotic adaptive immune systems are composed of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) proteins. These systems adapt to new threats by integrating short nucleic acids, termed spacers, into the CRISPR array. The functional motifs in the repeat and the mechanism by which a constant repeat size is maintained are still elusive. Here, through a series of mutations within the repeat of the CRISPR-Cas type I-E, we identify motifs that are crucial for adaptation and show that they serve as anchor sites for two molecular rulers determining the size of the new repeat. Adaptation products from various repeat mutants support a model in which two motifs in the repeat bind to two different sites in the adaptation complex that are 8 and 16 bp away from the active site. This model significantly extends our understanding of the adaptation process and broadens the scope of its applications. PMID:27626652

  20. A repeating fast radio burst

    NASA Astrophysics Data System (ADS)

    Spitler, L. G.; Scholz, P.; Hessels, J. W. T.; Bogdanov, S.; Brazier, A.; Camilo, F.; Chatterjee, S.; Cordes, J. M.; Crawford, F.; Deneva, J.; Ferdman, R. D.; Freire, P. C. C.; Kaspi, V. M.; Lazarus, P.; Lynch, R.; Madsen, E. C.; McLaughlin, M. A.; Patel, C.; Ransom, S. M.; Seymour, A.; Stairs, I. H.; Stappers, B. W.; van Leeuwen, J.; Zhu, W. W.

    2016-03-01

    Fast radio bursts are millisecond-duration astronomical radio pulses of unknown physical origin that appear to come from extragalactic distances. Previous follow-up observations have failed to find additional bursts at the same dispersion measure (that is, the integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of these bursts has led to the suggestion that they originate in cataclysmic events. Here we report observations of ten additional bursts from the direction of the fast radio burst FRB 121102. These bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB 121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB 121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and which vary on timescales of minutes or less. Although there may be multiple physical origins for the population of fast radio bursts, these repeat bursts with high dispersion measure and variable spectra specifically seen from the direction of FRB 121102 support an origin in a young, highly magnetized, extragalactic neutron star.

  1. A repeating fast radio burst.

    PubMed

    Spitler, L G; Scholz, P; Hessels, J W T; Bogdanov, S; Brazier, A; Camilo, F; Chatterjee, S; Cordes, J M; Crawford, F; Deneva, J; Ferdman, R D; Freire, P C C; Kaspi, V M; Lazarus, P; Lynch, R; Madsen, E C; McLaughlin, M A; Patel, C; Ransom, S M; Seymour, A; Stairs, I H; Stappers, B W; van Leeuwen, J; Zhu, W W

    2016-03-10

    Fast radio bursts are millisecond-duration astronomical radio pulses of unknown physical origin that appear to come from extragalactic distances. Previous follow-up observations have failed to find additional bursts at the same dispersion measure (that is, the integrated column density of free electrons between source and telescope) and sky position as the original detections. The apparent non-repeating nature of these bursts has led to the suggestion that they originate in cataclysmic events. Here we report observations of ten additional bursts from the direction of the fast radio burst FRB 121102. These bursts have dispersion measures and sky positions consistent with the original burst. This unambiguously identifies FRB 121102 as repeating and demonstrates that its source survives the energetic events that cause the bursts. Additionally, the bursts from FRB 121102 show a wide range of spectral shapes that appear to be predominantly intrinsic to the source and which vary on timescales of minutes or less. Although there may be multiple physical origins for the population of fast radio bursts, these repeat bursts with high dispersion measure and variable spectra specifically seen from the direction of FRB 121102 support an origin in a young, highly magnetized, extragalactic neutron star. PMID:26934226

  2. Effect of time period after boric acid injection on 10B absorption in different regions of adult male rat's brain.

    PubMed

    Khojasteh, Nasrin Baghban; Pazirandeh, Ali; Jameie, Behnam; Goodarzi, Samereh

    2012-06-01

    Distribution of (10)B in different regions of rat normal brain was studied. Two groups were chosen as control and trial. Trial group received 2 ml of neutral boron compound. 2, 4 and 6 h after the injection brain removed, coronal sections of forebrain, midbrain and hindbrain were sandwiched between two pieces of polycarbonate. Autoradiography plots of (10)B distribution showed significant differences in three regions with the highest (10)B concentration in the forebrain during 4 h after injection. PMID:22476013

  3. Simple sequence repeats in Haemophilus influenzae.

    PubMed

    Power, Peter M; Sweetman, W A; Gallacher, N J; Woodhall, M R; Kumar, G A; Moxon, E R; Hood, D W

    2009-03-01

    Simple sequence repeat (SSRs) of DNA are subject to high rates of mutation and are important mediators of adaptation in Haemophilus influenzae. Previous studies of the Rd KW20 genome identified the primacy of tetranucleotide SSRs in mediating phase variation (the rapid reversible switching of gene expression) of surface exposed structures such as lipopolysaccharide. The recent sequencing of the genomes of multiple strains of H. influenzae allowed the comparison of the SSRs (repeat units of one to nine nucleotides in length) in detail across four complete H. influenzae genomes and then comparison with a further 12 genomes when they became available. The SSR loci were broadly classified into three groups: (1) those that did not vary; (2) those for which some variation between strains was observed but this could not be linked to variation of gene expression; and (3) those that both varied and were located in regions consistent with mediating phase variable gene expression. Comparative analysis of 988 SSR associated loci confirmed that tetranucleotide repeats were the major mediators of phase variation and extended the repertoire of known tetranucleotide SSR loci by identifying ten previously uncharacterised tetranucleotide SSR loci with the potential to mediate phase variation which were unequally distributed across the H. influenzae pan-genome. Further, analysis of non-tetranucleotide SSR in the 16 strains revealed a number of mononucleotide, dinucleotide, pentanucleotide, heptanucleotide, and octanucleotide SSRs which were consistent with these tracts mediating phase variation. This study substantiates previous findings as to the important role that tetranucleotide SSRs play in H. influenzae biology. Two Brazilian isolates showed the most variation in their complement of SSRs suggesting the possibility of geographic and phenotypic influences on SSR distribution. PMID:19095084

  4. Effects of Non-Natural Amino Acid Incorporation into the Enzyme Core Region on Enzyme Structure and Function

    PubMed Central

    Wong, H. Edward; Kwon, Inchan

    2015-01-01

    Techniques to incorporate non-natural amino acids (NNAAs) have enabled biosynthesis of proteins containing new building blocks with unique structures, chemistry, and reactivity that are not found in natural amino acids. It is crucial to understand how incorporation of NNAAs affects protein function because NNAA incorporation may perturb critical function of a target protein. This study investigates how the site-specific incorporation of NNAAs affects catalytic properties of an enzyme. A NNAA with a hydrophobic and bulky sidechain, 3-(2-naphthyl)-alanine (2Nal), was site-specifically incorporated at six different positions in the hydrophobic core of a model enzyme, murine dihydrofolate reductase (mDHFR). The mDHFR variants with a greater change in van der Waals volume upon 2Nal incorporation exhibited a greater reduction in the catalytic efficiency. Similarly, the steric incompatibility calculated using RosettaDesign, a protein stability calculation program, correlated with the changes in the catalytic efficiency. PMID:26402667

  5. The propeptide region of clotting factor IX is a signal for a vitamin K dependent carboxylase: evidence from protein engineering of amino acid -4.

    PubMed Central

    Galeffi, P; Brownlee, G G

    1987-01-01

    Homologous "propeptide" regions are present in a family of vitamin K-dependent mammalian proteins, including clotting factors II, VII, IX, X, protein C, protein S and bone "gla" proteins. To test the hypothesis that the propeptide is a signal for the correct gamma-carboxylation of the adjacent gamma-carboxy region, we have mutated amino acid -4 of human factor IX from an arginine to a glutamine residue, by M13-directed site-specific mutagenesis of a cDNA clone. After expression of mutant factor IX in dog kidney cells, we find that it is secreted into the medium in a precursor form containing the propeptide, and is inefficiently gamma-carboxylated compared to the control, wild-type, recombinant factor IX. This result supports the hypothesis that the propeptide region is required for efficient gamma-carboxylation of factor IX in dog kidney cells. Furthermore, it confirms previous results that arginine at amino acid -4 is required for correct propeptide processing. Images PMID:3684602

  6. Communication: Protonation process of formic acid from the ionization and fragmentation of dimers induced by synchrotron radiation in the valence region

    NASA Astrophysics Data System (ADS)

    Arruda, Manuela S.; Medina, Aline; Sousa, Josenilton N.; Mendes, Luiz A. V.; Marinho, Ricardo R. T.; Prudente, Frederico V.

    2016-04-01

    The ionization and fragmentation of monomers of organic molecules have been extensively studied in the gas phase using mass spectroscopy. In the spectra of these molecules it is possible to identify the presence of protonated cations, which have a mass-to-charge ratio one unit larger than the parent ion. In this work, we investigate this protonation process as a result of dimers photofragmentation. Experimental photoionization and photofragmentation results of doubly deuterated formic acid (DCOOD) in the gas phase by photons in the vacuum ultraviolet region are presented. The experiment was performed by using a time-of-flight mass spectrometer installed at the Brazilian Synchrotron Light Laboratory and spectra for different pressure values in the experimental chamber were obtained. The coupled cluster approach with single and double substitutions was employed to assist the experimental analysis. Results indicate that protonated formic acid ions are originated from dimer dissociation, and the threshold photoionization of (DCOOD)ṡD+ is also determined.

  7. [Identification of new conserved and variable regions in the 16S rRNA gene of acetic acid bacteria and acetobacteraceae family].

    PubMed

    Chakravorty, S; Sarkar, S; Gachhui, R

    2015-01-01

    The Acetobacteraceae family of the class Alpha Proteobacteria is comprised of high sugar and acid tolerant bacteria. The Acetic Acid Bacteria are the economically most significant group of this family because of its association with food products like vinegar, wine etc. Acetobacteraceae are often hard to culture in laboratory conditions and they also maintain very low abundances in their natural habitats. Thus identification of the organisms in such environments is greatly dependent on modern tools of molecular biology which require a thorough knowledge of specific conserved gene sequences that may act as primers and or probes. Moreover unconserved domains in genes also become markers for differentiating closely related genera. In bacteria, the 16S rRNA gene is an ideal candidate for such conserved and variable domains. In order to study the conserved and variable domains of the 16S rRNA gene of Acetic Acid Bacteria and the Acetobacteraceae family, sequences from publicly available databases were aligned and compared. Near complete sequences of the gene were also obtained from Kombucha tea biofilm, a known Acetobacteraceae family habitat, in order to corroborate the domains obtained from the alignment studies. The study indicated that the degree of conservation in the gene is significantly higher among the Acetic Acid Bacteria than the whole Acetobacteraceae family. Moreover it was also observed that the previously described hypervariable regions V1, V3, V5, V6 and V7 were more or less conserved in the family and the spans of the variable regions are quite distinct as well. PMID:26510592

  8. Evolution of vertebrate IgM: complete amino acid sequence of the constant region of Ambystoma mexicanum mu chain deduced from cDNA sequence.

    PubMed

    Fellah, J S; Wiles, M V; Charlemagne, J; Schwager, J

    1992-10-01

    cDNA clones coding for the constant region of the Mexican axolotl (Ambystoma mexicanum) mu heavy immunoglobulin chain were selected from total spleen RNA, using a cDNA polymerase chain reaction technique. The specific 5'-end primer was an oligonucleotide homologous to the JH segment of Xenopus laevis mu chain. One of the clones, JHA/3, corresponded to the complete constant region of the axolotl mu chain, consisting of a 1362-nucleotide sequence coding for a polypeptide of 454 amino acids followed in 3' direction by a 179-nucleotide untranslated region and a polyA+ tail. The axolotl C mu is divided into four typical domains (C mu 1-C mu 4) and can be aligned with the Xenopus C mu with an overall identity of 56% at the nucleotide level. Percent identities were particularly high between C mu 1 (59%) and C mu 4 (71%). The C-terminal 20-amino acid segment which constitutes the secretory part of the mu chain is strongly homologous to the equivalent sequences of chondrichthyans and of other tetrapods, including a conserved N-linked oligosaccharide, the penultimate cysteine and the C-terminal lysine. The four C mu domains of 13 vertebrate species ranging from chondrichthyans to mammals were aligned and compared at the amino acid level. The significant number of mu-specific residues which are conserved into each of the four C mu domains argues for a continuous line of evolution of the vertebrate mu chain. This notion was confirmed by the ability to reconstitute a consistent vertebrate evolution tree based on the phylogenic parsimony analysis of the C mu 4 sequences. PMID:1382992

  9. Long Tract of Untranslated CAG Repeats Is Deleterious in Transgenic Mice

    PubMed Central

    Lin, Min-Jon; Li, Chui-Yen; Wang, Li-Chun; Chen, Luen-Kui; Pan, Huichin

    2011-01-01

    The most frequent trinucleotide repeat found in human disorders is the CAG sequence. Expansion of CAG repeats is mostly found in coding regions and is thought to cause diseases through a protein mechanism. Recently, expanded CAG repeats were shown to induce toxicity at the RNA level in Drosophila and C. elegans. These findings raise the possibility that CAG repeats may trigger RNA-mediated pathogenesis in mammals. Here, we demonstrate that transgenic mice expressing EGFP transcripts with long CAG repeats in the 3′ untranslated region develop pathogenic features. Expression of the transgene was directed to the muscle in order to compare the resulting phenotype to that caused by the CUG expansion, as occurs in myotonic dystrophy. Transgenic mice expressing 200, but not those expressing 0 or 23 CAG repeats, showed alterations in muscle morphology, histochemistry and electrophysiology, as well as abnormal behavioral phenotypes. Expression of the expanded CAG repeats in testes resulted in reduced fertility due to defective sperm motility. The production of EGFP protein was significantly reduced by the 200 CAG repeats, and no polyglutamine-containing product was detected, which argues against a protein mechanism. Moreover, nuclear RNA foci were detected for the long CAG repeats. These data support the notion that expanded CAG repeat RNA can cause deleterious effects in mammals. They also suggest the possible involvement of an RNA mechanism in human diseases with long CAG repeats. PMID:21283659

  10. Lipid and fatty acid/alcohol compositions of the subarctic copepods Neocalanus cristatus and Eucalanus bungii from various depths in the Oyashio region, western North Pacific.

    PubMed

    Yamada, Yuichiro; Nishida, Shuhei; Graeve, Martin; Kattner, Gerhard

    2016-08-01

    Lipids of Neocalanus cristatus and Eucalanus bungii (C3 to adults), collected in March, May, and December from various depths (0-2000m) were studied in the Oyashio region, western North Pacific. Total lipid and wax ester contents of younger N. cristatus stages increased during the development, being higher in May than in March and December. Major fatty acids of younger N. cristatus were 16:0, 20:5(n-3), and 22:6(n-3) and the dominant alcohols were 16:0, 16:1(n-7), 20:1(n-9)/(n-11) and 22:1(n-11). The energy-rich 20:1 and 22:1 moieties increased from the younger to the adult stages showing the importance of lipid biosynthesis which may be advantageous for successful overwintering and reproduction at depth. The 16:4(n-1) fatty acid, characteristic of a diatom diet increased in May, particularly in the younger stages. Our results suggest that the diatom-dominated feeding mode of younger N. cristatus during the spring bloom is important for an effective accumulation of wax esters. In contrast to N. cristatus, E. bungii accumulated substantial amounts of triacylglycerols. The total lipid and triacylglycerol content increased slightly toward the older developmental stages. The major fatty acids were 16:0, 16:1(n-7), 18:1(n-9) and (n-7), and 20:5(n-3). There was no evidence of developmental or seasonal changes in the fatty acid composition. The differences in the lipid storage modes of both copepods via wax esters or triacylglycerols are species-specific but their fatty acid compositions varied according to diet and developmental stage, especially in N. cristatus. These lipid characteristics are discussed in relation to reproduction, feeding modes, diapause and overwintering strategies. PMID:27087549

  11. Telomerase Repeated Amplification Protocol (TRAP)

    PubMed Central

    Mender, Ilgen; Shay, Jerry W.

    2016-01-01

    Telomeres are found at the end of eukaryotic linear chromosomes, and proteins that bind to telomeres protect DNA from being recognized as double-strand breaks thus preventing end-to-end fusions (Griffith et al., 1999). However, due to the end replication problem and other factors such as oxidative damage, the limited life span of cultured cells (Hayflick limit) results in progressive shortening of these protective structures (Hayflick and Moorhead, 1961; Olovnikov, 1973). The ribonucleoprotein enzyme complex telomerase-consisting of a protein catalytic component hTERT and a functional RNA component hTR or hTERC- counteracts telomere shortening by adding telomeric repeats to the end of chromosomes in ~90% of primary human tumors and in some transiently proliferating stem-like cells (Shay and Wright, 1996; Shay and Wright, 2001). This results in continuous proliferation of cells which is a hallmark of cancer. Therefore, telomere biology has a central role in aging, cancer progression/metastasis as well as targeted cancer therapies. There are commonly used methods in telomere biology such as Telomere Restriction Fragment (TRF) (Mender and Shay, 2015b), Telomere Repeat Amplification Protocol (TRAP) and Telomere dysfunction Induced Foci (TIF) analysis (Mender and Shay, 2015a). In this detailed protocol we describe Telomere Repeat Amplification Protocol (TRAP). The TRAP assay is a popular method to determine telomerase activity in mammalian cells and tissue samples (Kim et al., 1994). The TRAP assay includes three steps: extension, amplification, and detection of telomerase products. In the extension step, telomeric repeats are added to the telomerase substrate (which is actually a non telomeric oligonucleotide, TS) by telomerase. In the amplification step, the extension products are amplified by the polymerase chain reaction (PCR) using specific primers (TS upstream primer and ACX downstream primer) and in the detection step, the presence or absence of telomerase is

  12. Accumulate Repeat Accumulate Coded Modulation

    NASA Technical Reports Server (NTRS)

    Abbasfar, Aliazam; Divsalar, Dariush; Yao, Kung

    2004-01-01

    In this paper we propose an innovative coded modulation scheme called 'Accumulate Repeat Accumulate Coded Modulation' (ARA coded modulation). This class of codes can be viewed as serial turbo-like codes, or as a subclass of Low Density Parity Check (LDPC) codes that are combined with high level modulation. Thus at the decoder belief propagation can be used for iterative decoding of ARA coded modulation on a graph, provided a demapper transforms the received in-phase and quadrature samples to reliability of the bits.

  13. Excision of plastid marker genes using directly repeated DNA sequences.

    PubMed

    Mudd, Elisabeth A; Madesis, Panagiotis; Avila, Elena Martin; Day, Anil

    2014-01-01

    Excision of marker genes using DNA direct repeats makes use of the predominant homologous recombination pathways present in the plastids of algae and plants. The method is simple, efficient, and widely applicable to plants and microalgae. Marker excision frequency is dependent on the length and number of directly repeated sequences. When two repeats are used a repeat size of greater than 600 bp promotes efficient excision of the marker gene. A wide variety of sequences can be used to make the direct repeats. Only a single round of transformation is required, and there is no requirement to introduce site-specific recombinases by retransformation or sexual crosses. Selection is used to maintain the marker and ensure homoplasmy of transgenic plastid genomes. Release of selection allows the accumulation of marker-free plastid genomes generated by marker excision, which is spontaneous, random, and a unidirectional process. Positive selection is provided by linking marker excision to restoration of the coding region of an herbicide resistance gene from two overlapping but incomplete coding regions. Cytoplasmic sorting allows the segregation of cells with marker-free transgenic plastids. The marker-free shoots resulting from direct repeat-mediated excision of marker genes have been isolated by vegetative propagation of shoots in the T0 generation. Alternatively, accumulation of marker-free plastid genomes during growth, development and flowering of T0 plants allows the collection of seeds that give rise to a high proportion of marker-free T1 seedlings. The simplicity and convenience of direct repeat excision facilitates its widespread use to isolate marker-free crops. PMID:24599849

  14. EFFECTS OF NEONATAL METHYLMERCURY EXPOSURE ON DEVELOPMENT OF NUCLEIC ACIDS AND PROTEINS IN RAT BRAIN: REGIONAL SPECIFICITY

    EPA Science Inventory

    Exposure of neonatal rats to methylmercury (1 or 2.5 mg/kg SC daily) during the preweaning period caused regionally-specific alterations in DNA, RNA and protein content in brain. In midbrain + brainstem, where neuronal replication and differentiation conclude early, reduced DNA c...

  15. The Bel1 protein of human foamy virus contains one positive and two negative control regions which regulate a distinct activation domain of 30 amino acids.

    PubMed Central

    Lee, C W; Chang, J; Lee, K J; Sung, Y C

    1994-01-01

    The Bel1 transactivator is essential for the replication of human foamy virus (HFV). To define the functional domains of HFV Bel1, we generated random missense mutations throughout the entire coding sequence of Bel1. Functional analyses of 24 missense mutations have revealed the presence of at least two functional domains in Bel1. One domain corresponds to a basic amino acid-rich motif which acts as a bipartite nuclear targeting sequence. A second, central domain corresponds to a presumed effector region which, when mutated, leads to dominant-negative mutants and/or lacks transactivating ability. In addition, deletion analyses and domain-swapping experiments further showed that Bel1 protein contains a strong carboxy-terminal activation domain. The activating region is also capable of functioning as a transcription-activating domain in yeast cells, although it does not bear any significant sequence homology to the well-characterized acidic activation domain which is known to function only in yeast and mammalian cells. We also demonstrated that the regions of Bel1 from residues 1 to 76 and from residues 153 to 225 repressed transcriptional activation exerted by the Bel1 activation domain. In contrast, the region from residues 82 to 150 appears to overcome an inhibitory effect. These results indicate that Bel1 contains one positive and two negative regulatory domains that modulate a distinct activation domain of Bel1. These regulatory domains of Bel1 cannot affect the function of the VP16 activation domain, suggesting that these domains specifically regulate the activation domain of Bel1. Furthermore, in vivo competition experiments showed that the positive regulatory domain acts in trans. Thus, our results demonstrate that Bel1-mediated transactivation appears to undergo a complex regulatory pathway which provides a novel mode of regulation for a transcriptional activation domain. Images PMID:8139046

  16. Synthesis and biological evaluation of (E)-19-iodo-3,3-dimethyl-18-nonadecenoic acid, a new dimethyl-branched long-chain fatty acid to evaluate regional myocardial fatty acid uptake

    SciTech Connect

    Goodman, M.M.; Ambrose, K.R.; Neff, K.H.; Knapp, F.F. Jr.

    1986-01-01

    The synthetic method for the preparation of (E)-19-iodo-3,3-dimethyl-18-nonadecenoic acid (DMIVN) involved introduction of substituents into the 2- and 5-positions of a thiophene ring followed by sulfur extrusion of a 2,5-dialkyl thiophene derivative to provide a key 3,3-dimethyl-branched fatty acid intermediate, 17-iodo-3,3-dimethylheptadecanoic acid. Myocardial subcellular distribution studies of the /sup 125/I-labeled DMIVN in fasted rats showed a higher association of radioactivity with the microsomes when compared to the results obtained with the 19-carbon straight chain analogue. With the nonfasted rats the distribution profiles of the two analogues showed differences that seemed to correlate with the differences in myocardial retention that fasting and feeding can induce. 5 refs., 3 figs., 2 tabs.

  17. Aminolevulinic acid (ALA)-assisted photodynamic diagnosis of subclinical and latent HPV infection of external genital region.

    PubMed

    Wang, Hong-Wei; Wang, Xiu-Li; Zhang, Ling-Lin; Guo, Ming-Xia; Huang, Zheng

    2008-12-01

    The relatively high recurrence rate of genital warts can be attributed to the unsuccessful elimination of viruses in areas of subclinical and latent infection. Therefore, the identification and treatment of the subclinical and latent infection is a key to reduce the recurrence. The goal of this study is to investigate the usefulness of 5-aminolevulinic acid (ALA)-assisted in situ fluorescence diagnosis of subclinical lesion and latent HPV infection. A total of 30 patients with histologically confirmed genital warts (condylomata acuminata) were subjected to topical application of ALA, acetic acid test, histopathologic examination and HPV DNA subtyping. Topical application of ALA was performed by applying 20% ALA cream to the lesion plus 2-cm margin for 2h followed by fluorescence examination. Correlations between histopathologic examination, aceto-whitening test, HPV DNA subtyping and fluorescence were examined. All warty lesions and subclinical lesions (n=25) showed red fluorescence and harbored HPV DNA (HPV6 or 11). Latent HPV infections at 0.5-2 cm away from the warty lesion also showed red fluorescence. Nonspecific fluorescence was associated with mucosa, inflammatory infiltration and erosive lesion. ALA-assisted photodynamic diagnosis could be employed for the detection of the lesion and subclinical lesion of genital warts. It is also useful in detecting latent HPV infection. PMID:19356665

  18. New insights into atmospheric sources and sinks of isocyanic acid, HNCO, from recent urban and regional observations

    NASA Astrophysics Data System (ADS)

    Roberts, James M.; Veres, Patrick R.; VandenBoer, Trevor C.; Warneke, Carsten; Graus, Martin; Williams, Eric J.; Lefer, Barry; Brock, Charles A.; Bahreini, Roya; Öztürk, Fatma; Middlebrook, Ann M.; Wagner, Nicholas L.; Dubé, William P.; Gouw, Joost A.

    2014-01-01

    Isocyanic acid (HNCO) has only recently been measured in the ambient atmosphere, and many aspects of its atmospheric chemistry are still uncertain. HNCO was measured during three diverse field campaigns: California Nexus—Research at the Nexus of Air Quality and Climate Change (CalNex 2010) at the Pasadena ground site, Nitrogen, Aerosol Composition, and Halogens on a Tall Tower (NACHTT 2011) at the Boulder Atmospheric Observatory (BAO) in Weld County, CO, and Biofuel Crops emission of Ozone precursors intensive (BioCORN 2011), in a cornfield NW of Fort Collins, CO. Mixing ratios varied from below detection limit (~0.003 ppbv) to over 1.2 ppbv during a period when agricultural burning impacted the BAO Tower site. Urban areas, such as the CalNex 2010 Pasadena site, appear to have both primary (combustion) and secondary (photochemical) sources of HNCO, 50 ± 9%, and 33 ± 12%, respectively, while primary sources were responsible for the large mixing ratios of HNCO observed during the wintertime NACHTT study in suburban Colorado. Isocyanic acid during the BioCORN study in rural NE Colorado was closely correlated to ozone and therefore likely photochemically produced as a secondary product from amines or formamide. The removal of HNCO from the lower atmosphere is thought to be due to deposition, as common gas phase loss processes of photolysis and reactions with hydroxyl radicals, are slow. These ambient measurements are consistent with some HNCO deposition, which was evident at night at these surface sites.

  19. Crowding by a repeating pattern

    PubMed Central

    Rosen, Sarah; Pelli, Denis G.

    2015-01-01

    Theinability to recognize a peripheral target among flankers is called crowding. For a foveal target, crowding can be distinguished from overlap masking by its sparing of detection, linear scaling with eccentricity, and invariance with target size.Crowding depends on the proximity and similarity of the flankers to the target. Flankers that are far from or dissimilar to the target do not crowd it. On a gray page, text whose neighboring letters have different colors, alternately black and white, has enough dissimilarity that it might escape crowding. Since reading speed is normally limited by crowding, escape from crowding should allow faster reading. Yet reading speed is unchanged (Chung & Mansfield, 2009). Why? A recent vernier study found that using alternating-color flankers produces strong crowding (Manassi, Sayim, & Herzog, 2012). Might that effect occur with letters and reading? Critical spacing is the minimum center-to-center target–flanker spacing needed to correctly identify the target. We measure it for a target letter surrounded by several equidistant flanker letters of the same polarity, opposite polarity, or mixed polarity: alternately white and black. We find strong crowding in the alternating condition, even though each flanker letter is beyond its own critical spacing (as measured in a separate condition). Thus a periodic repeating pattern can produce crowding even when the individual elements do not. Further, in all conditions we find that, once a periodic pattern repeats (two cycles), further repetition does not affect critical spacing of the innermost flanker. PMID:26024457

  20. Evidence of Recombinant Citrus tristeza virus Isolate Occurring in Acid Lime cv. Pant Lemon Orchard in Uttarakhand Terai Region of Northern Himalaya in India.

    PubMed

    Singh, Jaywant Kumar; Tarafdar, Avijit; Sharma, Susheel Kumar; Biswas, Kajal Kumar

    2013-06-01

    The present study for the first time describes biological and molecular characterization of Citrus tristeza virus (CTV) occurring in the Terai area of Uttarakhand State in Northern Himalaya region of India. Direct antigen coated-ELISA and reverse transcriptase-polymerase chain reaction (RT-PCR) detected the CTV infection in Acid lime cv. Pant lemon (Citrus aurantifolia) orchards of Pantnagar with an estimated disease incidence of 16.6-20.5 %. To know the biological and genetic properties, an isolate, CTV Pant 4 was characterized. Isolate Pant 4 could be graft transmitted to Kinnow, Nagpur and Darjeeling mandarins, Mosambi sweet orange, Kagzi lime, Sweet lime, Sour orange but not to Rough lemon. The sequence analyses of the 5'ORF1a (3038 nucleotides) of LPro domain and 3'end (2058 nt) covering ORF7-ORF10 regions of the CTV genome revealed that Pant 4 was closely related to the previously reported Indian CTV isolate, Kpg3 from Northeastern Himalaya region with 97 and 98 % sequence identity, respectively. Whereas, it differed from the previously reported CTV isolate B165 from Southern India with 79 and 92 % identity, respectively for 5'ORF1a and 3' end regions. Recombination and SplitsTree decomposition analyses indicated that CTV isolate Pant 4 was a recombinant isolate originating from Kpg3 as a major and B165 as a minor donor. PMID:24426255

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

    PubMed

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

    2014-02-28

    Epigenetic gene silencing is seen in several repeat-expansion diseases. In fragile X syndrome, the most common genetic form of mental retardation, a CGG trinucleotide-repeat expansion adjacent to the fragile X mental retardation 1 (FMR1) gene promoter results in its epigenetic silencing. Here, we show that FMR1 silencing is mediated by the FMR1 mRNA. The FMR1 mRNA contains the transcribed CGG-repeat tract as part of the 5' untranslated region, which hybridizes to the complementary CGG-repeat portion of the FMR1 gene to form an RNA·DNA duplex. Disrupting the interaction of the mRNA with the CGG-repeat portion of the FMR1 gene prevents promoter silencing. Thus, our data link trinucleotide-repeat expansion to a form of RNA-directed gene silencing mediated by direct interactions of the trinucleotide-repeat RNA and DNA. PMID:24578575

  2. Promoter-Bound Trinucleotide Repeat mRNA Drives Epigenetic Silencing in Fragile X Syndrome

    PubMed Central

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

    2015-01-01

    Epigenetic gene silencing is seen in several repeat-expansion diseases. In fragile X syndrome, the most common genetic form of mental retardation, a CGG trinucleotide–repeat expansion adjacent to the fragile X mental retardation 1 (FMR1) gene promoter results in its epigenetic silencing. Here, we show that FMR1 silencing is mediated by the FMR1 mRNA. The FMR1 mRNA contains the transcribed CGG-repeat tract as part of the 5′ untranslated region, which hybridizes to the complementary CGG-repeat portion of the FMR1 gene to form an RNA·DNA duplex. Disrupting the interaction of the mRNA with the CGG-repeat portion of the FMR1 gene prevents promoter silencing. Thus, our data link trinucleotide-repeat expansion to a form of RNA-directed gene silencing mediated by direct interactions of the trinucleotide-repeat RNA and DNA. PMID:24578575

  3. Regional vulnerability of the hippocampus to repeated motor activity deprivation.

    PubMed

    Faraji, Jamshid; Soltanpour, Nabiollah; Moeeini, Reza; Hosseini, Seyed Abedin; Pakdel, Shiva; Moharrerie, Alireza; Arjang, Kaveh; Soltanpour, Nasrin; Metz, Gerlinde A S

    2016-03-15

    Spontaneous vertical and horizontal exploratory movements are integral components of rodent behavior. Little is known, however, about the structural and functional consequences of restricted spontaneous exploration. Here, we report two experiments to probe whether restriction in vertical activity (rearing) in rats could induce neuro-hormonal and behavioral disturbances. Rearing movements in rats were deprived for 3h/day for 30 consecutive days by placing the animal into a circular tunnel task. Rats temporarily deprived of rearing behavior showed elevated plasma corticosterone levels but no detectable psychological distress and/or anxiety-related behavior within an elevated plus maze. However, rats emitted a greater number of 22-kHz ultrasonic vocalizations and spent significantly more time vocalizing than controls when deprived of their rearing behavior. Despite intact spatial performance within wet- and dry-land spatial tasks, rearing-deprived rats also exhibited a significant alteration in search strategies within both spatial tasks along with reduced volume and neuron number in the hippocampal subregion CA2. These data suggest a new approach to test the importance of free exploratory behavior in endocrine and structural manifestations. The results support a central role of the CA2 in spontaneous exploratory behavior and vulnerability to psychological stress. PMID:26723539

  4. Isolation of key amino acid residues at the N-terminal end of the core region Streptococcus downei glucansucrase, GTF-I.

    PubMed

    Monchois, V; Vignon, M; Russell, R R

    1999-11-01

    Related streptococcal and Leuconostoc mesenteroides glucansucrases are enzymes of medical and biotechnological interest. Molecular modelling has suggested that the catalytic domain contains a circularly permuted version of the (beta/alpha)8 barrel structure found in the amylase superfamily, and site-directed mutagenesis has identified critical amino acids in this region. In this study, sequential N-terminal truncations of Streptococcus downei GTF-I showed that key amino acids are also present in the first one-third of the core domain. Mutations were introduced at Trp-344, Glu-349 and His-355, residues that are conserved in all glucansucrases and lie within a region which is a target for inhibitory antibodies. W344L, E349L and H355V substitutions were assayed for their effect on mutan synthesis and also on oligosaccharide synthesis with various acceptors. It appeared that Trp-344 and His-355 are involved in the action mechanism of GTF-I; His-355 may also play a role in a binding subsite necessary for oligosaccharide and glucan elongation. PMID:10570812

  5. Regional assessment of the response of the acid-base status of lake watersheds in the Adirondack region of New York to changes in atmospheric deposition using PnET-BGC.

    PubMed

    Chen, Limin; Driscoll, Charles T

    2005-02-01

    Understanding the response of soil and surface waters to changes in atmospheric deposition is critical for guiding future legislation on air pollution. The Adirondack region of New York experiences among the most severe ecological impacts from acidic deposition. The region is characterized by considerable variability in atmospheric deposition, surficial and bedrock geology, hydrologic flow paths, and vegetation resulting in variability in effects of acidic deposition. In this study, an integrated biogeochemical model (PnET-BGC) was applied to 37 forest lake watersheds to assess the response of soil and surface waters of the Adirondacks to changes in atmospheric deposition at a regional scale. Model-simulated surface water chemistry was validated against data from two synoptic surveys conducted in 1984 and 2001. Results indicate that the model is able to capture the observed changes in surface water chemistry during this period. The model was further used to forecast the response of soil and surface waters to three future emission control scenarios. Results indicate that under the Clean Air Act, surface water SO4(2-) concentrations will continue to decrease at a median rate of -0.38 microeq/L-yr, and surface water ANC is predicted to increase at a median rate of 0.11 microeq/L-yr. More aggressive emission reductions will accelerate the rate of recovery. Under an aggressive control scenario, which represents an additional 75% reduction in SO2 emissions beyond the implementation of the Clean Air Act, surface water SO4(2-) concentrations are predicted to decrease at a median rate of -0.88 microeq/L-yr, and surface water ANC is predicted to increase at a median rate of 0.43 microeq/L-yr. Model predictions of several biologically relevant chemical indicators are also reported. PMID:15757340

  6. Amino acid epimerization dating of Quaternary coastal deformation in SE Iberian Peninsula: The region between Aguas and Antas Rivers' mouths

    NASA Astrophysics Data System (ADS)

    Torres, Trinidad; Ortiz, José E.; Sánchez-Palencia, Yolanda

    2016-05-01

    The coastal area between the mouths of the Aguas and Antas Rivers presents a deformed system of raised marine deposits, some of which have been strongly affected by active tectonics. The use of amino acid epimerization dating of Glycymeris shells from raised coastal deposits allowed determining the age of these marine deposits, all of them linked to highstand sea levels in the Mediterranean realm, with ages between MIS 11 and MIS 1. These results allowed corroborating the age of some previously studied sites, and using new sampling sites, the general aminostratigraphy for the Quaternary raised marine deposits on the Mediterranean coast was confirmed. The main deformation event took place after MIS 11 and continued until MIS 5, and was linked to the activity of the Palomares Fault.

  7. 47 CFR 22.1015 - Repeater operation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 2 2010-10-01 2010-10-01 false Repeater operation. 22.1015 Section 22.1015 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) COMMON CARRIER SERVICES PUBLIC MOBILE SERVICES Offshore Radiotelephone Service § 22.1015 Repeater operation. Offshore central stations may be used as repeater stations provided that...

  8. Repeated Reading. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2014

    2014-01-01

    "Repeated reading" is an academic practice that aims to increase oral reading fluency. "Repeated reading" can be used with students who have developed initial word reading skills but demonstrate inadequate reading fluency for their grade level. During "repeated reading," a student sits in a quiet location with a…

  9. Sex- and region-specific alterations of basal amino acid and monoamine metabolism in the brain of aquaporin-4 knockout mice.

    PubMed

    Fan, Yi; Zhang, Jing; Sun, Xiu-Lan; Gao, Lin; Zeng, Xiao-Ning; Ding, Jian-Hua; Cao, Cong; Niu, Ling; Hu, Gang

    2005-11-15

    Aquaporin-4 (AQP4), a predominant water channel of the brain, mediates transmembrane water movement at the blood-brain barrier and brain-cerebrospinal fluid interface. A broad pattern of evidence indicates that AQP4 and regulators of its expression are potential targets for treatment of brain swelling, but whether it participates in the regulation of neurotransmission has not been reported. We examined neurochemical differences between AQP4-knockout and wild-type mice with particular focus on neurotransmission. Basal tissue neurotransmitter and metabolite levels were measured by high-performance liquid chromatography. Significant sex- and region-specific differences of amino acids and monoamines were found in the brain of wild-type and AQP4-knockout mice. In cortex, striatum, and hippocampus of male AQP4-knockout mice, an increase of glutamine and decrease of aspartate were observed. Glutamate was increased only in female AQP4-knockout mice. The lack of AQP4 failed to affect the levels of gamma-aminobutyric acid and taurine. In the medial prefrontal cortex of AQP4-knockout mice, the levels of serotonin and norepinephrine were increased, but no significant change in dopamine level was found. In the striatum of male AQP4-knockout mice, the levels of dopamine and serotonin were remarkably increased, which was not found in female mice. In the hypothalamus of AQP4-knockout mice, only the serotonin level was altered. These results provide the first evidence that the lack of AQP4 expression is accompanied by sex- and region-specific alterations in brain amino acid and monoamine metabolism. PMID:16237719

  10. Identification of the amino acid region involved in the intercellular interaction between the β1 subunits of Na+/K+-ATPase

    PubMed Central

    Tokhtaeva, Elmira; Sachs, George; Sun, Haiying; Dada, Laura A.; Sznajder, Jacob I.; Vagin, Olga

    2012-01-01

    Epithelial junctions depend on intercellular interactions between β1 subunits of the Na+/K+-ATPase molecules of neighboring cells. The interaction between dog and rat subunits is less effective than the interaction between two dog β1 subunits, indicating the importance of species-specific regions for β1–β1 binding. To identify these regions, the species-specific amino acid residues were mapped on a high-resolution structure of the Na+/K+-ATPase β1 subunit to select those exposed towards the β1 subunit of the neighboring cell. These exposed residues were mutated in both dog and rat YFP-linked β1 subunits (YFP–β1) and also in the secreted extracellular domain of the dog β1 subunit. Five rat-like mutations in the amino acid region spanning residues 198–207 of the dog YFP–β1 expressed in Madin–Darby canine kidney (MDCK) cells decreased co-precipitation of the endogenous dog β1 subunit with YFP–β1 to the level observed between dog β1 and rat YFP–β1. In parallel, these mutations impaired the recognition of YFP–β1 by the dog-specific antibody that inhibits cell adhesion between MDCK cells. Accordingly, dog-like mutations in rat YFP–β1 increased both the (YFP–β1)–β1 interaction in MDCK cells and recognition by the antibody. Conversely, rat-like mutations in the secreted extracellular domain of the dog β1 subunit increased its interaction with rat YFP–β1 in vitro. In addition, these mutations resulted in a reduction of intercellular adhesion between rat lung epithelial cells following addition of the secreted extracellular domain of the dog β1 subunit to a cell suspension. Therefore, the amino acid region 198–207 is crucial for both trans-dimerization of the Na+/K+-ATPase β1 subunits and cell–cell adhesion. PMID:22328500

  11. The complete mitochondrial genome sequence of Euphausia pacifica (Malacostraca: Euphausiacea) reveals a novel gene order and unusual tandem repeats.

    PubMed

    Shen, Xin; Wang, Haiqing; Wang, Minxiao; Liu, Bin

    2011-11-01

    Euphausiid krill are dominant organisms in the zooplankton population and play a central role in marine ecosystems. Euphausia pacifica (Malacostraca: Euphausiacea) is one of the most important and dominant crustaceans in the North Pacific Ocean. In this paper, we described the gene content, organization, and codon usage of the E. pacifica mitochondrial genome. The mitochondrial genome of E. pacifica is 16 898 bp in length and contains a standard set of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Translocation of three transfer RNAs (trnL(1), trnL(2), and trnW) was found in the E. pacifica mitochondrial genome when comparing with the pancrustacean ground pattern. The rate of K(a)/K(s) in 13 protein-coding genes among three krill is much less than 1, which indicates a strong purifying selection within this group. The largest noncoding region in the E. pacifica mitochondrial genome contains one section with tandem repeats (4.7 x 154 bp), which are the largest tandem repeats found in malacostracan mitochondrial genomes so far. All analyses based on nucleotide and amino acid data strongly support the monophyly of Stomatopoda, Penaeidae, Caridea, Brachyura, and Euphausiacea. The Bayesian analysis of nucleotide and amino acid datasets strongly supports the close relationship between Euphausiacea and Decapoda, which confirms traditional findings. The maximum likelihood analysis based on amino acid data strongly supports the close relationship between Euphausiacea and Penaeidae, which destroys the monophyly of Decapoda. PMID:22017501

  12. Genomic distribution of simple sequence repeats in Brassica rapa.

    PubMed

    Hong, Chang Pyo; Piao, Zhong Yun; Kang, Tae Wook; Batley, Jacqueline; Yang, Tae-Jin; Hur, Yoon-Kang; Bhak, Jong; Park, Beom-Seok; Edwards, David; Lim, Yong Pyo

    2007-06-30

    Simple Sequence Repeats (SSRs) represent short tandem duplications found within all eukaryotic organisms. To examine the distribution of SSRs in the genome of Brassica rapa ssp. pekinensis, SSRs from different genomic regions representing 17.7 Mb of genomic sequence were surveyed. SSRs appear more abundant in non-coding regions (86.6%) than in coding regions (13.4%). Comparison of SSR densities in different genomic regions demonstrated that SSR density was greatest within the 5'-flanking regions of the predicted genes. The proportion of different repeat motifs varied between genomic regions, with trinucleotide SSRs more prevalent in predicted coding regions, reflecting the codon structure in these regions. SSRs were also preferentially associated with gene-rich regions, with peri-centromeric heterochromatin SSRs mostly associated with retrotransposons. These results indicate that the distribution of SSRs in the genome is non-random. Comparison of SSR abundance between B. rapa and the closely related species Arabidopsis thaliana suggests a greater abundance of SSRs in B. rapa, which may be due to the proposed genome triplication. Our results provide a comprehensive view of SSR genomic distribution and evolution in Brassica for comparison with the sequenced genomes of A. thaliana and Oryza sativa. PMID:17646709

  13. Linear Synchronous Motor Repeatability Tests

    SciTech Connect

    Ward, C.R.

    2002-10-18

    A cart system using linear synchronous motors was being considered for the Plutonium Immobilization Plant (PIP). One of the applications in the PIP was the movement of a stack of furnace trays, filled with the waste form (pucks) from a stacking/unstacking station to several bottom loaded furnaces. A system was ordered to perform this function in the PIP Ceramic Prototype Test Facility (CPTF). This system was installed and started up in SRTC prior to being installed in the CPTF. The PIP was suspended and then canceled after the linear synchronous motor system was started up. This system was used to determine repeatability of a linear synchronous motor cart system for the Modern Pit Facility.

  14. The acidic amino-terminal region of herpes simplex virus type 1 alpha protein ICP27 is required for an essential lytic function.

    PubMed Central

    Rice, S A; Lam, V; Knipe, D M

    1993-01-01

    The herpes simplex virus type 1 (HSV-1) alpha protein ICP27 regulates the transition between the delayed-early and late phases of the viral infection. Previous genetic analyses have suggested that the important functional domains of ICP27 map to its carboxyl-terminal half. One striking feature of the primary sequence of ICP27, however, is an extremely acidic region near its amino terminus. To determine whether this region is required for ICP27 function, we deleted the sequences in the ICP27 gene which encode it (codons 12 through 63). In transient expression assays, the deletion mutant was unable to efficiently repress the expression of a cotransfected reporter gene or to efficiently complement the growth of d27-1, an HSV-1 ICP27 null mutant. These results suggested that the acidic region of ICP27 is involved in a regulatory function required for lytic growth. To test this possibility further, we introduced the mutant allele into the HSV-1 genome by marker transfer. Two independently derived isolates of the mutant virus, designated d1-2a and d1-2b, were recovered and analyzed. Both isolates were defective for growth in Vero cells, exhibiting a 100-fold reduction in virus yield compared with the wild-type infection. Vero cells infected with the d1-2 isolates showed a three- to eightfold reduction in viral DNA replication, a moderate reduction in the expression of viral gamma genes, and a delay in the repression of beta genes. The phenotype of the d1-2 isolates differs substantially from the phenotypes of previously isolated ICP27 mutants, which show much more severe defects in viral gene expression. Our results demonstrate that the amino-terminal half of ICP27 participates in its regulatory activities in both infected and transfected cells. Images PMID:8383210

  15. Regional characteristics of land use in Northeast and Southern Blue Ridge Province: Associations with acid rain effects on surface-water chemistry

    NASA Astrophysics Data System (ADS)

    Liegel, Leon; Cassell, David; Stevens, Donald; Shaffer, Paul; Church, Robbins

    1991-03-01

    The Direct/Delayed Response Project (DDRP) is one of several studies being conducted by the United States Environmental Protection Agency to assess risk to surface waters from acidic deposition in the eastern United States. In one phase of DDRP, land use, wetland, and forest cover data were collected for statistical samples of 145 Northeast lake and 35 Southern Blue Ridge Province stream watersheds in the United States. Land-use and other data then were extrapolated from individual to target watershed populations. Project statistical design allows summarization of results for various subsets of the target population. This article discusses results and implications of the land-use and land-cover characterization for both regions. Forest cover was the primary land use in both regions. In the Northeast, developed (agriculture and urban) land was positively associated with surface-water chemistry values for acid neutralizing capacity, Ca plus Mg, pH, and sulfate in the Pocono/Catskill subregion. Extensive wetlands and beaver activity occur in parts of the Northeast region, whereas topography limits wetland and riparian development in the Southern Blue Ridge Province. Northeast soils have low sulfate adsorption capacity, most watersheds are near sulfur steady state, and lake sulfate concentrations are controlled principally by levels of sulfur deposition. Net annual sulfur retention in Northeast watersheds is positively correlated with occurrence of wetlands and beaver impoundments. In contrast, most Southern Blue Ridge Province soils have high sulfate adsorption capacities, resulting in high net watershed sulfur retention. At the present time, stream sulfate concentrations and percent sulfur retention are controlled principally by soil chemical properties related to adsorption rather than atmospheric deposition and land use.

  16. Recombination hot spot in 3.2-kb region of the Charcot-Marie Tooth type 1A repeat sequences: New tools for molecular diagnosis of hereditary neuropathy with liability to pressure palsies and of Charcot-Marie-Tooth type 1A

    SciTech Connect

    Lopes, J.; LeGuern, E.; Gouider, R.; Tardieu, S.; Abbas, N.

    1996-06-01

    Charcot-Marie-Tooth type 1A (CMT1A) disease and hereditary neuropathy with liability to pressure palsies (HNPP) are autosomal dominant neuropathies, associated, respectively, with duplications and deletions of the same 1.5-Mb region on 17p11.2-p12. These two rearrangements are the reciprocal products of an unequal meiotic crossover between the two chromosome 17 homologues, caused by the misalignment of the CMT1A repeat sequences (CMT1A-REPs), the homologous sequences flanking the 1.5-Mb CMT1A/HNPP monomer unit. In order to map recombination breakpoints within the CMT1A-REPs, a 12.9-kb restriction map was constructed from cloned EcoRI fragments of the proximal and distal CMT1A-REPs. Only 3 of the 17 tested restriction sites were present in the proximal CMT1A-REP but absent in the distal CMT1A-REP, indicating a high degree of homology between these sequences. The rearrangements were mapped in four regions of the CMT1A-REPs by analysis of 76 CMT1A index cases and 38 HNPP patients, who were unrelated. A hot spot of crossover breakpoints located in a 3.2-kb region accounted for three-quarters of the rearrangements, detected after EcoRI/SacI digestion, by the presence of 3.2-kb and 7.8-kb junction fragments in CMT1A and HNPP patients, respectively. These junction fragments, which can be detected on classical Southern blots, permit molecular diagnosis. Other rearrangements can also be detected by gene dosage on the same Southern blots. 25 refs., 4 figs., 2 tabs.

  17. The chromosome localization and the HCF repeats of the human host cell factor gene (HCFC1) are conserved in the mouse homologue

    SciTech Connect

    Frattini, A.; Faranda, S.; Sacco, M.G.; Villa, A.; Vezzoni, P.

    1996-03-01

    The gene encoding the human host cell factor (HCFC1) has recently been cloned and mapped to Xq28. HCFC1 codes for a family of related polypeptides that apparently arise from posttranslational processing. Six extremely conserved 19-amino-acid (aa)-long motifs, unique to HCFC1 and located in the middle of the protein, could play a role in this processing or could be instrumental to the physiological role of the protein. Alternatively, these repeats could have arisen from recent duplications and may not have any specific function. To resolve this issue, we cloned the homologous region from the mouse Hcfc1 gene and demonstrated that the 19-aa motifs are extremely conserved in sequence, number, and genomic organization, while the {open_quotes}linker{close_