Science.gov

Sample records for fascicularis dra polymorphism

  1. Major histocompatibility complex locus DRA polymorphism in the endangered Sorraia horse and related breeds.

    PubMed

    Luís, C; Cothran, E G; Oom, M M; Bailey, E

    2005-02-01

    The major histocompatibility complex (MHC) genes play well-defined roles in eliciting immune responses and combating infectious diseases. This genetic system is among the most polymorphic. The extent of genetic variation within a population has been directly correlated with fitness for many traits. The MHC class II locus DRA polymorphism was analysed in the endangered Sorraia horse, two other Portuguese and four New World horse breeds considered to be historically close to the Sorraia. Comparison of the Sorraia with other breeds demonstrated less MHC variation among Sorraia horses. If DRA polymorphism provides greater disease resistance, selective breeding to increase MHC polymorphism may increase fitness of this population. PMID:16130491

  2. Trans-species polymorphism and selection in the MHC class II DRA genes of domestic sheep.

    PubMed

    Ballingall, Keith T; Rocchi, Mara S; McKeever, Declan J; Wright, Frank

    2010-01-01

    Highly polymorphic genes with central roles in lymphocyte mediated immune surveillance are grouped together in the major histocompatibility complex (MHC) in higher vertebrates. Generally, across vertebrate species the class II MHC DRA gene is highly conserved with only limited allelic variation. Here however, we provide evidence of trans-species polymorphism at the DRA locus in domestic sheep (Ovis aries). We describe variation at the Ovar-DRA locus that is far in excess of anything described in other vertebrate species. The divergent DRA allele (Ovar-DRA*0201) differs from the sheep reference sequences by 20 nucleotides, 12 of which appear non-synonymous. Furthermore, DRA*0201 is paired with an equally divergent DRB1 allele (Ovar-DRB1*0901), which is consistent with an independent evolutionary history for the DR sub-region within this MHC haplotype. No recombination was observed between the divergent DRA and B genes in a range of breeds and typical levels of MHC class II DR protein expression were detected at the surface of leukocyte populations obtained from animals homozygous for the DRA*0201, DRB1*0901 haplotype. Bayesian phylogenetic analysis groups Ovar-DRA*0201 with DRA sequences derived from species within the Oryx and Alcelaphus genera rather than clustering with other ovine and caprine DRA alleles. Tests for Darwinian selection identified 10 positively selected sites on the branch leading to Ovar-DRA*0201, three of which are predicted to be associated with the binding of peptide antigen. As the Ovis, Oryx and Alcelaphus genera have not shared a common ancestor for over 30 million years, the DRA*0201 and DRB1*0901 allelic pair is likely to be of ancient origin and present in the founding population from which all contemporary domestic sheep breeds are derived. The conservation of the integrity of this unusual DR allelic pair suggests some selective advantage which is likely to be associated with the presentation of pathogen antigen to T-cells and the

  3. Trans-Species Polymorphism and Selection in the MHC Class II DRA Genes of Domestic Sheep

    PubMed Central

    Ballingall, Keith T.; Rocchi, Mara S.; McKeever, Declan J.; Wright, Frank

    2010-01-01

    Highly polymorphic genes with central roles in lymphocyte mediated immune surveillance are grouped together in the major histocompatibility complex (MHC) in higher vertebrates. Generally, across vertebrate species the class II MHC DRA gene is highly conserved with only limited allelic variation. Here however, we provide evidence of trans-species polymorphism at the DRA locus in domestic sheep (Ovis aries). We describe variation at the Ovar-DRA locus that is far in excess of anything described in other vertebrate species. The divergent DRA allele (Ovar-DRA*0201) differs from the sheep reference sequences by 20 nucleotides, 12 of which appear non-synonymous. Furthermore, DRA*0201 is paired with an equally divergent DRB1 allele (Ovar-DRB1*0901), which is consistent with an independent evolutionary history for the DR sub-region within this MHC haplotype. No recombination was observed between the divergent DRA and B genes in a range of breeds and typical levels of MHC class II DR protein expression were detected at the surface of leukocyte populations obtained from animals homozygous for the DRA*0201, DRB1*0901 haplotype. Bayesian phylogenetic analysis groups Ovar-DRA*0201 with DRA sequences derived from species within the Oryx and Alcelaphus genera rather than clustering with other ovine and caprine DRA alleles. Tests for Darwinian selection identified 10 positively selected sites on the branch leading to Ovar-DRA*0201, three of which are predicted to be associated with the binding of peptide antigen. As the Ovis, Oryx and Alcelaphus genera have not shared a common ancestor for over 30 million years, the DRA*0201 and DRB1*0901 allelic pair is likely to be of ancient origin and present in the founding population from which all contemporary domestic sheep breeds are derived. The conservation of the integrity of this unusual DR allelic pair suggests some selective advantage which is likely to be associated with the presentation of pathogen antigen to T-cells and the

  4. Novel Polymorphic Microsatellite Markers Reveal Genetic Differentiation between Two Sympatric Types of Galaxea fascicularis

    PubMed Central

    Nakajima, Yuichi; Shinzato, Chuya; Satoh, Noriyuki; Mitarai, Satoshi

    2015-01-01

    The reef-building, scleractinian coral, Galaxea fascicularis, is classified into soft and hard types, based on nematocyst morphology. This character is correlated with the length of the mitochondrial non-coding region (mt-Long: soft colony type, and nematocysts with wide capsules and long shafts; mt-Short: hard colony type, and nematocysts with thin capsules and short shafts). We isolated and characterized novel polymorphic microsatellite markers for G. fascicularis using next-generation sequencing. Based upon the mitochondrial non-coding region, 53 of the 97 colonies collected were mt-Long (mt-L) and 44 were mt-Short (mt-S). Among the 53 mt-L colonies, 27 loci were identified as amplifiable, polymorphic microsatellite loci, devoid of somatic mutations and free of scoring errors. Eleven of those 27 loci were also amplifiable and polymorphic in the 44 mt-S colonies; these 11 are cross-type microsatellite loci. The other 16 loci were considered useful only for mt-L colonies. These 27 loci identified 10 multilocus lineages (MLLs) among the 53 mt-L colonies (NMLL/N = 0.189), and the 11 cross-type loci identified 7 MLLs in 44 mt-S colonies (NMLL/N = 0.159). Significant genetic differentiation between the two types was detected based on the genetic differentiation index (FST = 0.080, P = 0.001). Bayesian clustering also indicated that these two types are genetically isolated. While nuclear microsatellite genotypes also showed genetic differentiation between mitochondrial types, the mechanism of divergence is not yet clear. These markers will be useful to estimate genetic diversity, differentiation, and connectivity among populations, and to understand evolutionary processes, including divergence of types in G. fascicularis. PMID:26147677

  5. RsaI but not DraI polymorphism in CYP2E1 gene increases the risk of gastrointestinal cancer in Malaysians: a case–control study

    PubMed Central

    Chong, Eric Tzyy Jiann; Lee, Chong Cin; Chua, Kek Heng; Chuah, Jitt Aun; Lee, Ping-Chin

    2014-01-01

    Objectives Our study aimed to investigate the association of CYP2E1 C-1019T RsaI and T7678A DraI polymorphisms and factors such as age, gender and ethnicity to the risk of gastrointestinal cancer (GIC) in Malaysians. Design Case–control study. Setting Malaysia. Participants 520 consented healthy blood donors with no previous GIC record and 175 patients with GIC. Measurements C-1019T RsaI and T7678A DraI genotyping of CYP2E1 gene; direct sequencing. Results This study reveals that the variant c2 allele and carrier with at least one c2 allele of C-1019T single nucleotide polymorphism (SNP) significantly increased the risk of GIC but no significant association was found between T7678A SNP and combined analysis of C-1019T and T7678A SNPs to risk of GIC. The Malaysian Chinese had greater risk of GIC compared with the Malays, Indians and KadazanDusun. An increased risk of GIC was observed in individuals aged >40 years and women had a 2.22-fold and 1.58-fold increased risk of stomach and colorectal cancers, respectively, when compared with men. Limitations The future research should be conducted with a larger sample population and including the gene–gene and gene–environmental interactions. Conclusions Our study suggests that the rare c2 allele and carrier with at least one c2 allele of CYP2E1 RsaI polymorphism significantly elevated the risk of GIC and may be used as a genetic biomarker for early screening of GIC in Malaysians. The risk age-group has been shifted to a younger age at 40s and women showed a significant greater risk of stomach and colorectal cancers than men. PMID:24394801

  6. Cytochrome P450 2E1 RsaI/PstI and DraI Polymorphisms Are Risk Factors for Lung Cancer in Mongolian and Han Population in Inner Mongolia

    PubMed Central

    Su, Xiu-lan; Bin, Ba; Cui, Hong-wei; Ran, Mei-rong

    2011-01-01

    Objective To explore the relationship between cytochrome P450 2E1 (CYP2E1) RsaI/PstI and DraI polymorphism and lung cancer susceptibility in Mongolian and Han population in Inner Mongolia of China. Methods CYP2E1 RsaI/PstI and DraI polymorphisms were detected by polymerase chain reaction-restriction fragment length polymorphism in 64 lung cancer patients, 150 healthy Mongolian and 150 healthy Han individuals. The distribution of genotype and allele frequencies of CYP2E1 RsaI/PstI and DraI polymorphisms were studied. Results The risk of lung cancer was increased in individuals with CYP2E1 (cl/cl) and CYP2E1 (DD) with OR values of 2.431 (95%CI=1.082-5.460) and 2.778 (95%CI=1.358-5.683) respectively (P<0.05). When CYP2E1 RsaI/PstI and DraI polymorphisms were combined, the risk of lung cancer was reduced in individuals with CYP2E1 (cl/c2+c2/c2 and DD+CC) with OR values of 0.233 (95%CI=0.088-0.615, P<0.05). In smokers, the susceptibility to lung cancer was higher in the individuals with CYP2E1 (c1/c1) and CYP2E1 (DD) than in the individuals with c2 and C allele (P<0.05, OR=2.643 and 4.308 respectively). There was no significant difference in distribution of CYP2E1 genotype frequency between healthy Mongolian, Han population and lung cancer patients, healthy controls in Inner Mongolia. Conclusion CYP2E1 (c1/c1) and CYP2E1 (DD) are predisposing factors of lung cancer in population in Inner Mongolia. CYP2E1 (c2﹢C) co-mutation may decrease the risk of lung cancer. Smoking exerts synergetic effect with CYP2E1 (c1/c1) and CYP2E1 (DD) on the occurrence of lung cancer. PMID:23483202

  7. The MedDRA paradox.

    PubMed

    Merrill, Gary H

    2008-01-01

    MedDRA (the Medical Dictionary for Regulatory Activities Terminology) is a controlled vocabulary widely used as a medical coding scheme. However, MedDRA's characterization of its structural hierarchy exhibits some confusing and paradoxical features. The goal of this paper is to examine these features, determine whether there is a coherent view of the MedDRA hierarchy that emerges, and explore what lessons are to be learned from this for using MedDRA and similar terminologies in a broad medical informatics context that includes relations among multiple disparate terminologies, thesauri, and ontologies. PMID:18998828

  8. Effect of Genetic Diversity in Swine Leukocyte Antigen-DRA Gene on Piglet Diarrhea

    PubMed Central

    Huang, Xiaoyu; Yang, Qiaoli; Yuan, Junhu; Liu, Lixia; Sun, Wenyang; Jiang, Yingdi; Zhao, Shengguo; Zhang, Shengwei; Huang, Wangzhou; Gun, Shuangbao

    2016-01-01

    The swine leukocyte antigens (SLAs) are the multigene families related to immune responses. Little is known about the effect of the DRA gene on diarrheal disease. This study reported the genetic diversity of the DRA gene in exons 1, 3 and 4 in 290 Chinese Yantai black pigs. No variation was identified in exon 3. In exon 1, three genotypes and two alleles were identified, generated by two single nucleotide polymorphisms (SNPs). In exon 4, there were eight genotypes and five alleles containing seven SNPs were detected with four SNPs being novel SNPs. The low polymorphism found in swine DRA is consistent with the concept that the DRA gene is highly conserved among all mammalian species. Statistical analyses indicated that the genotypes of exon 1 were not significantly associated with piglet diarrhea (p > 0.05); however, genotypes C4C4 (1.80 ± 0.33) and A4E4 (1.66 ± 0.25) of exon 4 were significantly susceptible to diarrhea (p < 0.01). These indicate that the particular genotypes of the DRA gene are susceptible to diarrheal disease, which provides valuable information for disease-resistance breeding in swine. PMID:27429004

  9. Effect of Genetic Diversity in Swine Leukocyte Antigen-DRA Gene on Piglet Diarrhea.

    PubMed

    Huang, Xiaoyu; Yang, Qiaoli; Yuan, Junhu; Liu, Lixia; Sun, Wenyang; Jiang, Yingdi; Zhao, Shengguo; Zhang, Shengwei; Huang, Wangzhou; Gun, Shuangbao

    2016-01-01

    The swine leukocyte antigens (SLAs) are the multigene families related to immune responses. Little is known about the effect of the DRA gene on diarrheal disease. This study reported the genetic diversity of the DRA gene in exons 1, 3 and 4 in 290 Chinese Yantai black pigs. No variation was identified in exon 3. In exon 1, three genotypes and two alleles were identified, generated by two single nucleotide polymorphisms (SNPs). In exon 4, there were eight genotypes and five alleles containing seven SNPs were detected with four SNPs being novel SNPs. The low polymorphism found in swine DRA is consistent with the concept that the DRA gene is highly conserved among all mammalian species. Statistical analyses indicated that the genotypes of exon 1 were not significantly associated with piglet diarrhea (p > 0.05); however, genotypes C₄C₄ (1.80 ± 0.33) and A₄E₄ (1.66 ± 0.25) of exon 4 were significantly susceptible to diarrhea (p < 0.01). These indicate that the particular genotypes of the DRA gene are susceptible to diarrheal disease, which provides valuable information for disease-resistance breeding in swine. PMID:27429004

  10. Earth observation archive activities at DRA Farnborough

    NASA Technical Reports Server (NTRS)

    Palmer, M. D.; Williams, J. M.

    1993-01-01

    Space Sector, Defence Research Agency (DRA), Farnborough have been actively involved in the acquisition and processing of Earth Observation data for over 15 years. During that time an archive of over 20,000 items has been built up. This paper describes the major archive activities, including: operation and maintenance of the main DRA Archive, the development of a prototype Optical Disc Archive System (ODAS), the catalog systems in use at DRA, the UK Processing and Archive Facility for ERS-1 data, and future plans for archiving activities.

  11. Temporal stability of Symbiodinium phylotype in scleractinian coral Galaxea fascicularis from a tropical fringing reef in the South China Sea

    NASA Astrophysics Data System (ADS)

    Zhou, Guowei; Huang, Hui; Dong, Zhijun; Yu, Ziniu

    2011-11-01

    Symbiodinium sp. occurs in a symbiotic association with various marine invertebrates, including the scleractinian corals. Understanding the flexibility and specificity in coral-algal symbiosis can have important implications for predicting the future of coral reefs in the era of global climate change. In the present study, we conducted Symbiodinium phylotype analysis, based on polymerase chain reaction and restriction fragment length polymorphism (PCR-RFLP), in the scleractinian coral, Galaxea fascicularis, from a tropical fringing reef in Hainan Island, over a 1-yr period. Our results showed that Galaxea fascicularis could associate with Symbiodinium clade C and D either individually or simultaneously. However, during the sampling period, the Symbiodinium phylotype did not change significantly in the scleractinian coral Galaxea fascicularis, although the seawater temperature decreased sharply in the winter season. This study further suggests that the shift in Symbiodinium communities in response to seasonally fluctuating environments might not be a universal feature of coral-algal associations.

  12. DRA 2005: The brave new world.

    PubMed

    Lewis, Richard

    2006-01-01

    The Deficit Reduction Act (DRA) of 2005 was signed into law to achieve 39 billion dollars in reductions from federal spending programs, 11 billion dollars from Medicare and Medicaid alone. Conservative estimates indicate that imaging alone accounts for 2.8 billion dollars of that amount. As of the writing of this article, both houses of Congress were reviewing bills with bipartisan support aimed at defusing, at least temporarily, the negative impact of the DRA; however, these bills do not affect the law in totality. Dealing with the changes that the DRA will force upon outpatient imaging practices will require all parties involved in outpatient imaging--physicians, administrators, and staff alike--to make smart, efficient, but practical changes in operational models to effectively survive in this new legislatively mandated environment. PMID:17172096

  13. Continental Monophyly and Molecular Divergence of Peninsular Malaysia's Macaca fascicularis fascicularis

    PubMed Central

    Abdul-Latiff, Muhammad Abu Bakar; Ruslin, Farhani; Faiq, Hamdan; Hairul, Mohd Salleh; Rovie-Ryan, Jeffrine Japning; Abdul-Patah, Pazil; Md-Zain, Badrul Munir

    2014-01-01

    The phylogenetic relationships of long-tailed macaque (Macaca fascicularis fascicularis) populations distributed in Peninsular Malaysia in relation to other regions remain unknown. The aim of this study was to reveal the phylogeography and population genetics of Peninsular Malaysia's M. f. fascicularis based on the D-loop region of mitochondrial DNA. Sixty-five haplotypes were detected in all populations, with only Vietnam and Cambodia sharing four haplotypes. The minimum-spanning network projected a distant relationship between Peninsular Malaysian and insular populations. Genetic differentiation (FST, Nst) results suggested that the gene flow among Peninsular Malaysian and the other populations is very low. Phylogenetic tree reconstructions indicated a monophyletic clade of Malaysia's population with continental populations (NJ = 97%, MP = 76%, and Bayesian = 1.00 posterior probabilities). The results demonstrate that Peninsular Malaysia's M. f. fascicularis belonged to Indochinese populations as opposed to the previously claimed Sundaic populations. M. f. fascicularis groups are estimated to have colonized Peninsular Malaysia ~0.47 million years ago (MYA) directly from Indochina through seaways, by means of natural sea rafting, or through terrestrial radiation during continental shelf emersion. Here, the Isthmus of Kra played a central part as biogeographical barriers that then separated it from the remaining continental populations. PMID:25143948

  14. HyDRa: polishing with a vortex.

    PubMed

    Sohn, Erika; Ruiz, Elfego; Salas, Luis; Luna, Esteban; Herrera, Joel

    2013-09-01

    We present a hydrodynamic, deterministic polishing tool (HyDRa) based on the fluid-jet polishing (FJP) principle. In contrast to other FJP methods, the polishing flux is accelerated with pressurized air and then expelled at high velocity, forming a radial, grazing abrasive pattern that exerts no net force of the tool on the surface to be polished, since the vacuum and thrust forces that are created at the tool's output balance each other out. The grazing effect minimizes microroughness, making it appropriate for finishing high-quality surfaces. The principle of operation as well as polishing results of a series of small etalon plates are presented. PMID:24085071

  15. Using MedDRA: implications for risk management.

    PubMed

    Brown, Elliot G

    2004-01-01

    The introduction of MedDRA, the Medical Dictionary for Regulatory Activities, as a standardised terminology may have a major impact on the performance of risk management. Thus, MedDRA is likely to have an important effect on the analysis of clinical trial safety data. Review of the most commonly used terms in clinical trial tables from the labelling of ten products indicated that each adverse event could be represented by many MedDRA preferred terms; this might theoretically lead to failure to identify differences in adverse event incidence between treatment arms. Possible solutions are proposed. The use of MedDRA in spontaneous reporting systems is a regulatory requirement in some countries. Variability in modes of implementation and use of the terminology are discussed; these may impose additional limitations on any use of spontaneous data for comparative purposes. There are important differences in the ways that safety databases interface with MedDRA and uncertainty about the most appropriate way to manage version changes. The characteristics of MedDRA must be taken into account when establishing methods for signal detection and its use will affect the retrieval of similar cases as required for signal evaluation. The use of MedDRA in the periodic safety update report is discussed. The possible use of MedDRA in pharmacoepidemiology is highly relevant to risk management, and some issues are briefly outlined. With regard to communication of risk, if MedDRA is introduced into existing product labelling, care must be taken that the change itself does not cause misunderstanding; the most appropriate use of MedDRA in this regard remains to be determined. There is a need for careful evaluation of MedDRA in fulfilling its various functions in pharmacovigilance, followed by definitive regulatory guidance on its use. PMID:15154830

  16. Outburst activity of the symbiiotic binary AG Dra

    NASA Astrophysics Data System (ADS)

    Gális, R.; Hric, L.; Leedjärv, L.; Merc, J.

    2016-03-01

    The outburst activity of the symbiotic system AG Dra has been studied using extensive spectroscopic observational material. High luminosity and temperature of the hot component of AG Dra indicate that quasi-steady thermonuclear shell burning takes place on the surface of the white dwarf. The major (cool) outbursts at the beginning of active phases might occur due to enhanced thermonuclear burning triggered by disk instability. Smaller scale hot outbursts might be explained by the accretion disc instability model like in dwarf novae. We discovered significant similarities in photometric and spectroscopic behaviour of AG Dra and prototypical symbiotic star Z And.

  17. Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment

    PubMed Central

    Ebeling, Martin; Küng, Erich; See, Angela; Broger, Clemens; Steiner, Guido; Berrera, Marco; Heckel, Tobias; Iniguez, Leonardo; Albert, Thomas; Schmucki, Roland; Biller, Hermann; Singer, Thomas; Certa, Ulrich

    2011-01-01

    The long-tailed macaque, also referred to as cynomolgus monkey (Macaca fascicularis), is one of the most important nonhuman primate animal models in basic and applied biomedical research. To improve the predictive power of primate experiments for humans, we determined the genome sequence of a Macaca fascicularis female of Mauritian origin using a whole-genome shotgun sequencing approach. We applied a template switch strategy that uses either the rhesus or the human genome to assemble sequence reads. The sixfold sequence coverage of the draft genome sequence enabled discovery of about 2.1 million potential single-nucleotide polymorphisms based on occurrence of a dimorphic nucleotide at a given position in the genome sequence. Homology-based annotation allowed us to identify 17,387 orthologs of human protein-coding genes in the M. fascicularis draft genome, and the predicted transcripts enabled the design of a M. fascicularis–specific gene expression microarray. Using liver samples from 36 individuals of different geographic origin we identified 718 genes with highly variable expression in liver, whereas the majority of the transcriptome shows relatively stable and comparable expression. Knowledge of the M. fascicularis draft genome is an important contribution to both the use of this animal in disease models and the safety assessment of drugs and their metabolites. In particular, this information allows high-resolution genotyping and microarray-based gene-expression profiling for animal stratification, thereby allowing the use of well-characterized animals for safety testing. Finally, the genome sequence presented here is a significant contribution to the global “3R” animal welfare initiative, which has the goal to reduce, refine, and replace animal experiments. PMID:21862625

  18. HyDRa: control of parameters for deterministic polishing.

    PubMed

    Ruiz, E; Salas, L; Sohn, E; Luna, E; Herrera, J; Quiros, F

    2013-08-26

    Deterministic hydrodynamic polishing with HyDRa requires a precise control of polishing parameters, such as propelling air pressure, slurry density, slurry flux and tool height. We describe the HyDRa polishing system and prove how precise, deterministic polishing can be achieved in terms of the control of these parameters. The polishing results of an 84 cm hyperbolic mirror are presented to illustrate how the stability of these parameters is important to obtain high-quality surfaces. PMID:24105579

  19. Evaluating Gaia performances on eclipsing binaries. IV. Orbits and stellar parameters for SV Cam, BS Dra and HP Dra

    NASA Astrophysics Data System (ADS)

    Milone, E. F.; Munari, U.; Marrese, P. M.; Williams, M. D.; Zwitter, T.; Kallrath, J.; Tomov, T.

    2005-10-01

    This is the fourth in a series of papers that aim both to provide reasonable orbits for a number of eclipsing binaries and to evaluate the expected performance of Gaia of these objects and the accuracy that is achievable in the determination of such fundamental stellar parameters as mass and radius. In this paper, we attempt to derive the orbits and physical parameters for three eclipsing binaries in the mid-F to mid-G spectral range. As for previous papers, only the H_P, V_T, BT photometry from the Hipparcos/Tycho mission and ground-based radial velocities from spectroscopy in the region 8480-8740 Å are used in the analyses. These data sets simulate the photometric and spectroscopic data that are expected to be obtained by Gaia, the approved ESA Cornerstone mission to be launched in 2011. The systems targeted in this paper are SV Cam, BS Dra and HP Dra. SV Cam and BS Dra have been studied previously, allowing comparisons of the derived parameters with those from full scale and devoted ground-based investigations. HP Dra has no published orbital solution. SV Cam has a β Lyrae type light curve and the others have Algol-like light curves. SV Cam has the complication of light curve anomalies, usually attributed to spots; BS Dra has non-solar metallicity, and HP Dra appears to have a small eccentricity and a sizeable time derivative in the argument of the periastron. Thus all three provide interesting and different test cases.

  20. Vaginal Stone in a Cynomolgus Macaque (Macaca fascicularis)

    PubMed Central

    Colagross-Schouten, Angela M; Canfield, Don R

    2015-01-01

    A 20-y-old female cynomolgus macaque (Macaca fascicularis) housed in an indoor primate facility presented for poor appetite and acute weakness after several years of no adverse health events. Physical examination revealed a firm, ovoid mass in the caudal abdomen. Further evaluation revealed the mass to be a vaginal calculus composed of calcium carbonate, apatite, and struvite. To our knowledge, this case is the first reported description of a vaginal stone in an NHP. PMID:26678372

  1. Photometric study of the pulsating, eclipsing binary OO DRA

    SciTech Connect

    Zhang, X. B.; Deng, L. C.; Tian, J. F.; Wang, K.; Yan, Z. Z.; Luo, C. Q.; Sun, J. J.; Liu, Q. L.; Xin, H. Q.; Zhou, Q.; Luo, Z. Q.

    2014-12-01

    We present a comprehensive photometric study of the pulsating, eclipsing binary OO Dra. Simultaneous B- and V-band photometry of the star was carried out on 14 nights. A revised orbital period and a new ephemeris were derived from the data. The first photometric solution of the binary system and the physical parameters of the component stars are determined. They reveal that OO Dra could be a detached system with a less-massive secondary component nearly filling its Roche lobe. By subtracting the eclipsing light changes from the data, we obtained the intrinsic pulsating light curves of the hotter, massive primary component. A frequency analysis of the residual light yields two confident pulsation modes in both B- and V-band data with the dominant frequency detected at 41.865 c/d. A brief discussion concerning the evolutionary status and the pulsation nature of the binary system is finally given.

  2. Variations of IR Spectra in carbon Mira, T Dra

    NASA Astrophysics Data System (ADS)

    Sung, H.-I.; Lee, S.-G.

    We have studied variations of physical parameters in the circumstellar envelope of carbon-rich Mira variable, T Dra, at different pulsation phases. After comparing the ISO/SWS spectra of T Dra with spectral energy distributions (SEDs) calculated in models, we could find the best fitted parameters for the physical state of the dust envelope at each phase. The variations of parameters, effective temperature, fraction of SiC grains, mass loss rates and inner radius of shell are found to have nearly the same trend as that of light curve. The other parameters, grain size, optical depth, radius of central star and dust temperature at the inner boundary of envelope, are inversely varing to the light curve. We have found that most physical parameters vary within factor 2, while mass loss rate varies more than factor 3 during pulsation period.

  3. HyDRa: polishing process convergence rate optimization.

    PubMed

    Salas, Luis; Luna, Esteban; Sohn, Erika; Ruiz, Elfego; Herrera, Joel

    2013-10-01

    In an effort to optimize the hydrodynamic radial (HyDRa) polishing process for applications where the amount of material that has to be removed implies long polishing times, we have developed a method to determine the optimum correction fraction that has to be made for a given error map, in terms of the level of determinism of the process, the number of iterations, and their associated polishing runs as well as run times. PMID:24085216

  4. The medical dictionary for regulatory activities (MedDRA).

    PubMed

    Brown, E G; Wood, L; Wood, S

    1999-02-01

    The International Conference on Harmonisation has agreed upon the structure and content of the Medical Dictionary for Regulatory Activities (MedDRA) version 2.0 which should become available in the early part of 1999. This medical terminology is intended for use in the pre- and postmarketing phases of the medicines regulatory process, covering diagnoses, symptoms and signs, adverse drug reactions and therapeutic indications, the names and qualitative results of investigations, surgical and medical procedures, and medical/social history. It can be used for recording adverse events and medical history in clinical trials, in the analysis and tabulations of data from these trials and in the expedited submission of safety data to government regulatory authorities, as well as in constructing standard product information and documentation for applications for marketing authorisation. After licensing of a medicine, it may be used in pharmacovigilance and is expected to be the preferred terminology for international electronic regulatory communication. MedDRA is a hierarchical terminology with 5 levels and is multiaxial: terms may exist in more than 1 vertical axis, providing specificity of terms for data entry and flexibility in data retrieval. Terms in MedDRA were derived from several sources including the WHO's adverse reaction terminology (WHO-ART), Coding Symbols for a Thesaurus of Adverse Reaction Terms (COSTART), International Classification of Diseases (ICD) 9 and ICD9-CM. It will be maintained, further developed and distributed by a Maintenance Support Services Organisation (MSSO). It is anticipated that using MedDRA will improve the quality of data captured on databases, support effective analysis by providing clinically relevant groupings of terms and facilitate electronic communication of data, although as a new tool, users will need to invest time in gaining expertise in its use. PMID:10082069

  5. LUT observations of the mass-transferring binary AI Dra

    NASA Astrophysics Data System (ADS)

    Liao, Wenping; Qian, Shengbang; Li, Linjia; Zhou, Xiao; Zhao, Ergang; Liu, Nianping

    2016-06-01

    Complete UV band light curve of the eclipsing binary AI Dra was observed with the Lunar-based Ultraviolet Telescope (LUT) in October 2014. It is very useful to adopt this continuous and uninterrupted light curve to determine physical and orbital parameters of the binary system. Photometric solutions of the spot model are obtained by using the W-D (Wilson and Devinney) method. It is confirmed that AI Dra is a semi-detached binary with secondary component filling its critical Roche lobe, which indicates that a mass transfer from the secondary component to the primary one should happen. Orbital period analysis based on all available eclipse times suggests a secular period increase and two cyclic variations. The secular period increase was interpreted by mass transfer from the secondary component to the primary one at a rate of 4.12 ×10^{-8}M_{⊙}/yr, which is in agreement with the photometric solutions. Two cyclic oscillations were due to light travel-time effect (LTTE) via the presence of two cool stellar companions in a near 2:1 mean-motion resonance. Both photometric solutions and orbital period analysis confirm that AI Dra is a mass-transferring binary, the massive primary is filling 69 % of its critical Roche lobe. After the primary evolves to fill the critical Roche lobe, the mass transfer will be reversed and the binary will evolve into a contact configuration.

  6. Mechanisms of DRA recycling in intestinal epithelial cells: effect of enteropathogenic E. coli.

    PubMed

    Gujral, Tarunmeet; Kumar, Anoop; Priyamvada, Shubha; Saksena, Seema; Gill, Ravinder K; Hodges, Kim; Alrefai, Waddah A; Hecht, Gail A; Dudeja, Pradeep K

    2015-12-15

    Enteropathogenic Escherichia coli (EPEC) is a food-borne pathogen that causes infantile diarrhea worldwide. EPEC decreases the activity and surface expression of the key intestinal Cl(-)/HCO3(-) exchanger SLC26A3 [downregulated in adenoma (DRA)], contributing to the pathophysiology of early diarrhea. Little is known about the mechanisms governing membrane recycling of DRA. In the current study, Caco-2 cells were used to investigate DRA trafficking under basal conditions and in response to EPEC. Apical Cl(-)/HCO3(-) exchange activity was measured as DIDS-sensitive (125)I(-) uptake. Cell surface biotinylation was performed to assess DRA endocytosis and exocytosis. Inhibition of clathrin-mediated endocytosis by chlorpromazine (60 μM) increased apical Cl(-)/HCO3(-) exchange activity. Dynasore, a dynamin inhibitor, also increased function and surface levels of DRA via decreased endocytosis. Perturbation of microtubules by nocodazole revealed that intact microtubules are essential for basal exocytic (but not endocytic) DRA recycling. Mice treated with colchicine showed a decrease in DRA surface levels as visualized by confocal microscopy. In response to EPEC infection, DRA surface expression was reduced partly via an increase in DRA endocytosis and a decrease in exocytosis. These effects were dependent on the EPEC virulence genes espG1 and espG2. Intriguingly, the EPEC-induced decrease in DRA function was unaltered in the presence of dynasore, suggesting a clathrin-independent internalization of surface DRA. In conclusion, these studies establish the role of clathrin-mediated endocytosis and microtubules in the basal surface expression of DRA and demonstrate that the EPEC-mediated decrease in DRA function and apical expression in Caco-2 cells involves decreased exocytosis. PMID:26447204

  7. New polymorphic variants of human blood clotting factor IX

    SciTech Connect

    Surin, V.L.; Luk`yanenko, A.V.; Tagiev, A.F.; Smirnova, O.V.; Plutalov, O.V.; Berlin, Yu.A.

    1995-04-01

    The polymorphism of Alu-repeats, which are located in the introns of the human factor IX gene (copies 1-3), was studied. To identify polymorphic variants, direct sequencing of PCR products that contained appropriate repeats was used. In each case, 20 unrelated X chromosomes were studied. A polymorphic Dra I site was found near the 3{prime}-end of Alu copy 3 within the region of the polyA tract. A PCR-based testing system with internal control of restriction hydrolysis was suggested. Testing 81 unrelated X chromosomes revealed that the frequency of the polymorphic Dra I site is 0.23. Taq I polymorphism, which was revealed in Alu copy 4 of factor IX gene in our previous work, was found to be closely linked to Dra I polymorphism. Studies in linkage between different types of polymorphisms of the factor IX gene revealed the presence of a rare polymorphism in intron a that was located within the same minisatellite region as the known polymorphic insertion 50 bp/Dde I. However, the size of the insertion in our case was 26 bp. Only one polymorphic variant was found among over 150 unrelated X chromosomes derived from humans from Moscow and its vicinity. 10 refs., 4 figs., 1 tab.

  8. Construction and Validation of a Systematic Ethogram of Macaca fascicularis in a Free Enclosure

    PubMed Central

    Wang, Tao; Ji, Yongjia; Kong, Fei; Zhan, Qunlin; Cheng, Ke; Fang, Liang; Xie, Peng

    2012-01-01

    Behavioral studies in non-human primates have become ideal models for further investigations into advanced cognitive function in humans. To date, there is no systematic ethogram of the cynomolgus monkey (Macaca fascicularis) in a free enclosure. In a field observation of 6012 subjects, 107 distinct behaviors of M. fascicularis were preliminarily described. 83 of these behaviors were then independently validated through a randomized cohort and classified into 12 behavioral categories. 53 of these behaviors were then selected to accurately reflect the daily mundane activity of the species in a free enclosure. These findings systematically document the behavior of M. fascicularis in a free enclosure for use in further investigations. PMID:22662158

  9. Keratin 8 knockdown leads to loss of the chloride transporter DRA in the colon.

    PubMed

    Asghar, M Nadeem; Priyamvada, Shubha; Nyström, Joel H; Anbazhagan, Arivarasu Natarajan; Dudeja, Pradeep K; Toivola, Diana M

    2016-06-01

    Keratins (K) are intermediate filament proteins important in protection from stress. The roles of keratins in the intestine are not clear, but K8 knockout (K8(-/-)) mice develop a Th2-type colonic inflammation, epithelial hyperproliferation, and mild diarrhea caused by a keratin level-dependent decrease in short-circuit current and net sodium and chloride absorption in the distal colon. The lack of K8 leads to mistargeting or altered levels of membrane proteins in colonocytes; however, the main transporter responsible for the keratin-related ion transport defect is unknown. We here analyzed protein and mRNA levels of candidate ion transporters CFTR, PAT-1, NHE-3, and DRA in ileum, cecum, and proximal and distal colon. Although no differences were observed for CFTR, PAT-1, or NHE-3, DRA mRNA levels were decreased by three- to fourfold and DRA protein was almost entirely lost in K8(-/-) cecum and proximal and distal colon compared with K8(+/+), whereas the levels in ileum were normal. In K8(+/-) mice, DRA mRNA levels were unaltered, while decreased DRA protein levels were detected in the proximal colon. Immunofluorescence staining confirmed the loss of DRA in K8(-/-) distal colon, while K8(+/-) displayed a similar but more patchy apical DRA distribution compared with K8(+/+) DRA was similarly decreased when K8 was knocked down in Caco-2 cells, confirming that K8 levels modulate DRA levels in an inflammation-independent manner. Taken together, the loss of DRA in the K8(-/-) mouse colon and cecum explains the dramatic chloride transport defect and diarrheal phenotype after K8 inactivation and identifies K8 as a novel regulator of DRA. PMID:27125276

  10. First analysis of eight Algol-type binaries: EI Aur, XY Dra, BP Dra, DD Her, VX Lac, WX Lib, RZ Lyn, and TY Tri

    NASA Astrophysics Data System (ADS)

    Zasche, P.

    2016-01-01

    The available photometry from the online databases were used for the first light curve analysis of eight eclipsing binary systems EI Aur, XY Dra, BP Dra, DD Her, VX Lac, WX Lib, RZ Lyn, and TY Tri. All these stars are of Algol-type, having the detached components and the orbital periods from 0.92 to 6.8 days. For the systems EI Aur and BP Dra the large amount of the third light was detected during the light curve solution. Moreover, 468 new times of minima for these binaries were derived, trying to identify the period variations. For the systems XY Dra and VX Lac the third bodies were detected with the periods 17.7, and 49.3 years, respectively.

  11. Formalizing MedDRA to support semantic reasoning on adverse drug reaction terms.

    PubMed

    Bousquet, Cédric; Sadou, Éric; Souvignet, Julien; Jaulent, Marie-Christine; Declerck, Gunnar

    2014-06-01

    Although MedDRA has obvious advantages over previous terminologies for coding adverse drug reactions and discovering potential signals using data mining techniques, its terminological organization constrains users to search terms according to predefined categories. Adding formal definitions to MedDRA would allow retrieval of terms according to a case definition that may correspond to novel categories that are not currently available in the terminology. To achieve semantic reasoning with MedDRA, we have associated formal definitions to MedDRA terms in an OWL file named OntoADR that is the result of our first step for providing an "ontologized" version of MedDRA. MedDRA five-levels original hierarchy was converted into a subsumption tree and formal definitions of MedDRA terms were designed using several methods: mappings to SNOMED-CT, semi-automatic definition algorithms or a fully manual way. This article presents the main steps of OntoADR conception process, its structure and content, and discusses problems and limits raised by this attempt to "ontologize" MedDRA. PMID:24680984

  12. Estimation of glomerular filtration rate in cynomolgus monkeys (Macaca fascicularis).

    PubMed

    Iwama, Ryosuke; Sato, Tsubasa; Sakurai, Ken; Takasuna, Kiyoshi; Ichijo, Toshihiro; Furuhama, Kazuhisa; Satoh, Hiroshi

    2014-10-01

    To estimate the glomerular filtration rate (GFR) in cynomolgus monkeys (Macaca fascicularis), a three-blood-sample method using iodixanol was assessed in comparison with the conventional multisample strategy using inulin. Iodixanol and inulin were coadministered intravenously 40 mg I/kg and 50 mg/kg, respectively, to male monkeys, followed by blood collection 60, 90 and 120 min later. A close correlation (r=0.96) was noted between the GFR values estimated by both methods. In clinically healthy monkeys, the basal values were determined to be 3.06 ± 0.50 ml/min/kg. This is the first report, suggesting that serum clearance of iodixanol is a ready-to-use tool for a screening the GFR in monkeys, although it is necessary to perform a more longitudinal study using animals with reduced renal function. PMID:24998395

  13. The near-contact binary star RZ Dra revisited

    NASA Astrophysics Data System (ADS)

    Erdem, A.; Zola, S.; Winiarski, M.

    2011-01-01

    This paper presents the absolute parameters of RZ Dra. New CCD observations were made at the Mt. Suhora Observatory in 2007. Two photometric data sets (1990 BV and 2007 BVRI) were analysed using modern light-curve synthesis methods. Large asymmetries in the light curves may be explained in terms of a dark starspot on the primary component, an A6 type star. Due to this magnetic activity, the primary component would appear to belong to the class of Ap-stars and would show small amplitude with δ Scuti-type pulsations. With this in mind, a time-series analysis of the residual light curves was made. However, we found no evidence of pulsation behaviour in RZ Dra. Combining the solutions of our light curves and Rucinski et al. (2000)'s radial velocity curves, the following absolute parameters of the components were determined: M1 = 1.63 ± 0.03 M ⊙, M2 = 0.70 ± 0.02 M ⊙, R1 = 1.65 ± 0.02R ⊙, R2 = 1.15 ± 0.02 R ⊙, L1 = 9.72 ± 0.30 L ⊙ and L2 = 0.74 ± 0.10 L ⊙. The distance to RZ Dra was calculated as 400 ± 25 pc, taking into account interstellar extinction. The orbital period of the system was studied using updated O- C information. It was found that the orbital period varied in its long-period sinusoidal form, superimposed on a downward parabola. The parabolic term shows a secular period decrease at a slow rate of 0.06 ± 0.02 s per century and is explained by the mass loss via magnetized wind of the Ap-star primary. The tilted sinusoidal form of the period variation may be considered as an apparent change and may be interpreted in terms of the light-time effect due to the presence of a third body.

  14. Ccd Photometry of Neglected Eclipsing Binaries Kz Dra, Lr Cam and Im Vul

    NASA Astrophysics Data System (ADS)

    Pejcha, Ondřej; Motl, David; Zejda, Miloslav; Koss, Karel; Kudrnáčová, Jitka; Hájek, Petr; Šmelcer, Ladislav; Dubovský, Pavol A.; Šafářová, Eva; Wolf, Marek

    2005-04-01

    We present ephemerides and solutions of one Algol-type (KZ Dra) and two overcontact systems (LR Cam and IM Vul) based on V(RI)C CCD observations obtained in the project Prosper (network of amateur observers).

  15. Automatic annotation of ICD-to-MedDRA mappings with SKOS predicates.

    PubMed

    Declerck, Gunnar; Souvignet, Julien; Rodrigues, Jean-Marie; Jaulent, Marie-Christine

    2014-01-01

    Robust alignments between ICD and MedDRA are essential to enable the secondary use of clinical data for pharmacovigilance research. UMLS makes available ICD-to-MedDRA mappings, but they are only poorly specified, which introduces difficulties when exploited in an automatic way. SKOS vocabulary can help achieve quality and machine-processable mappings. We have developed an algorithm based on several simple rules which annotates automatically ICD-to-MedDRA mappings with SKOS predicates. The method was tested and evaluated on a sample of ICD-10-to MedDRA mappings extracted from UMLS. The algorithm demonstrated satisfying performances, especially for skos:exactMatch properties, which suggests that automatic methods can be used to improve the quality of terminology mappings. PMID:25160341

  16. Postdispersal nepotism in male long-tailed macaques (Macaca fascicularis).

    PubMed

    Gerber, Livia; Krützen, Michael; de Ruiter, Jan R; van Schaik, Carel P; van Noordwijk, Maria A

    2016-01-01

    Cooperative behaviors are promoted by kin selection if the costs to the actor are smaller than the fitness benefits to the recipient, weighted by the coefficient of relatedness. In primates, cooperation occurs primarily among female dyads. Due to male dispersal before sexual maturity in many primate species, however, it is unknown whether there are sufficient opportunities for selective tolerance and occasional coalitionary support for kin selection to favor male nepotistic support. We studied the effect of the presence of male kin on correlates of male reproductive success (residence time, duration of high dominance rank) in non-natal male long-tailed macaques (Macaca fascicularis). We found that "related" (i.e., related at the half-sibling level or higher) males in a group have a significantly higher probability to remain in the non-natal group compared to males without relatives. Moreover, males stayed longer in a group when a relative was present at group entry or joined the same group within 3 months upon arrival. Males with co-residing relatives also maintained a high rank for longer than those without. To our knowledge, this is the first demonstration of a potential nepotistic effect on residence and rank maintenance among non-natal males in a social system without long-term alliances. PMID:26811773

  17. Ultrastructural study of the primary olfactory pathway in Macaca fascicularis.

    PubMed

    Herrera, Loren P; Casas, Carlos E; Bates, Margaret L; Guest, James D

    2005-08-01

    Olfactory ensheathing glial cells (OEGs) interact with a wide repertoire of cell types and support extension of olfactory axons (OAs) within the olfactory pathway. OEGs are thought to exclude OAs from contact with all other cells between the olfactory epithelium and the glomerulus of the olfactory bulb. These properties have lead to testing to determine whether OEGs support axonal growth following transplantation. The cellular interactions of transplanted OEGs will probably resemble those that occur within the normal pathway where interactions between OEGs and fibroblasts are prominent. No previous primate studies have focused on these interactions, knowledge of which is important if clinical application is envisioned. We describe the detailed intercellular interactions of OAs with supporting cells throughout the olfactory epithelium, the lamina propria, the fila olfactoria, and the olfactory nerve layer by using transmission electron microscopy in adult Macaca fascicularis. Patterns of OEG ensheathment and variations of the endo- and perineurium formed by olfactory nerve fibroblasts are described. OAs mainly interacted with horizontal basal cells, OEGs, and astrocytes. At both transitional ends of the pathway seamless intercellular interactions were observed, and fibroblast processes were absent. Perineurial cells produced surface basal lamina; however, endoneurial, epineurial, and meningeal fibroblasts did not. Perineurial cells contained intermediate filaments and were distinct from other fibroblasts and meningeal cells. OAs had direct contacts with astrocytes near the glia limitans. The properties of OEGs differed depending on whether astrocytic or fibroblastic processes were present. This indicates the importance of the cellular milieu in the structure and function of OEGs in primates. PMID:15973683

  18. Effects of synthetic glycosides on steroid balance in Macaca fascicularis

    SciTech Connect

    Malinow, M.R.; Elliott, W.H.; McLaughlin, P.; Upson, B.

    1987-01-01

    The predominantly beta-anomer of diosgenin glucoside (DG) was synthesized and its effects on cholesterol homeostasis were tested in monkeys. Cynomolgus macaques (Macaca fascicularis) were fed, during two 3-week periods, a semipurified diet with 0.1% cholesterol and a similar ration containing 1% DG, respectively. A Chow diet was given for 5 weeks between the experimental periods. Cholesterol and bile acid balance were analyzed during the last week of each semipurified diet. Diosgenin glucoside reduced cholesterolemia from 292 mg/dl to 172 mg/dl, decreased intestinal absorption of exogenous cholesterol from 62.4% to 26.0%, and increased secretion of endogenous cholesterol from -0.8 to 93.5 mg/day. The fecal excretion of neutral steroids rose from 40.7 to 157.3 mg/day; that of bile acids changed, nonsignificantly, from 23.1 to 16.0 mg/day. The cholesterol balance was -44 mg/day in the control period, and 88 mg/day in the DG-fed animals. No toxic signs were observed. Thus, when long-term studies demonstrate that the glucoside is well tolerated, DG and other synthetic glycosides with similar activities may be of use in the management of hypercholesterolemia and atherosclerosis.

  19. Cynomolgus macaque (Macaca fascicularis) immunoglobulin heavy chain locus description.

    PubMed

    Yu, Guo-Yun; Mate, Suzanne; Garcia, Karla; Ward, Michael D; Brueggemann, Ernst; Hall, Matthew; Kenny, Tara; Sanchez-Lockhart, Mariano; Lefranc, Marie-Paule; Palacios, Gustavo

    2016-07-01

    Cynomolgus macaques (Macaca fascicularis) have become an important animal model for biomedical research. In particular, it is the animal model of choice for the development of vaccine candidates associated with emerging dangerous pathogens. Despite their increasing importance as animal models, the cynomolgus macaque genome is not fully characterized, hindering molecular studies for this model. More importantly, the lack of knowledge about the immunoglobulin (IG) locus organization directly impacts the analysis of the humoral response in cynomolgus macaques. Recent advances in next generation sequencing (NGS) technologies to analyze IG repertoires open the opportunity to deeply characterize the humoral immune response. However, the IG locus organization for the animal is required to completely dissect IG repertoires. Here, we describe the localization and organization of the rearranging IG heavy (IGH) genes on chromosome 7 of the cynomolgus macaque draft genome. Our annotation comprises 108 functional genes which include 63 variable (IGHV), 38 diversity (IGHD), and 7 joining (IGHJ) genes. For validation, we provide RNA transcript data for most of the IGHV genes and all of the annotated IGHJ genes, as well as proteomic data to validate IGH constant genes. The description and annotation of the rearranging IGH genes for the cynomolgus macaques will significantly facilitate scientific research. This is particularly relevant to dissect the immune response during vaccination or infection with dangerous pathogens such as Ebola, Marburg and other emerging pathogens where non-human primate models play a significant role for countermeasure development. PMID:27233955

  20. Outburst Activity Driven by Evolved Pulsating Star in the Symbiotic Binary AG Dra

    NASA Astrophysics Data System (ADS)

    Gális, R.; Hric, L.; Leedjärv, L.

    2015-12-01

    The symbiotic system AG Dra regularly undergoes quiescent and active stages which consist of the series of individual outbursts. The period analysis of new and historical photometric data, as well as radial velocities, confirmed the presence of the two periods. The longer one around ≈ 550 d is related to the orbital motion and the shorter one ≈355 d could be due to pulsation of the cool component of AG Dra.

  1. Application of the Baade-Wesselink inversion technique to SW Dra, X Ari and U SGR

    NASA Astrophysics Data System (ADS)

    Simon, Norman R.

    1989-03-01

    The Baade-Wesselink inversion technique was applied to three pulsators: the RR(ab) stars SW Dra and X Ari, and the classical Cepheid, U Sgr. A surface brightness parameterization using the V-K color was found to be superior for RR Lyrae stars, while B-V is superior for classical Cepheids. A consistent radius was obtained for SW Dra but not for X Ari.

  2. Mechanical properties of the cement of the stalked barnacle Dosima fascicularis (Cirripedia, Crustacea)

    PubMed Central

    Zheden, Vanessa; Klepal, Waltraud; Gorb, Stanislav N.; Kovalev, Alexander

    2015-01-01

    The stalked barnacle Dosima fascicularis secretes foam-like cement, the amount of which usually exceeds that produced by other barnacles. When Dosima settles on small objects, this adhesive is additionally used as a float which gives buoyancy to the animal. The dual use of the cement by D. fascicularis requires mechanical properties different from those of other barnacle species. In the float, two regions with different morphological structure and mechanical properties can be distinguished. The outer compact zone with small gas-filled bubbles (cells) is harder than the interior one and forms a protective rind presumably against mechanical damage. The inner region with large, gas-filled cells is soft. This study demonstrates that D. fascicularis cement is soft and visco-elastic. We show that the values of the elastic modulus, hardness and tensile stress are considerably lower than in the rigid cement of other barnacles. PMID:25657833

  3. Turritopsis fascicularis Fraser, 1943 (Cnidaria: Hydrozoa): redescription and discussion of its phylogenetic position within the genus.

    PubMed

    Miglietta, Maria Pia

    2016-01-01

    Turritopsis fascicularis Fraser, 1943 was first described off Alligator Reef, Florida, USA, at a depth of 216 m. Presumably a deep-sea species, its validity has often been questioned due to the scarcity of available records. In this paper, T. fascicularis is re-described from some mature colonies from the upper slope of the Gulf of Mexico. Furthermore, new pictures of the colony, polyps, and medusa buds, are provided. A ~600bp sequence of the large ribosomal subunit of the mitochondrial RNA (lsu-rRNA, 16S), also known as the Hydrozoan barcoding molecule, is used for the first time to confirm the validity of T. fascicularis as a species, and analyze its phylogenetic position within the genus Turritopsis. PMID:27394557

  4. Mechanical properties of the cement of the stalked barnacle Dosima fascicularis (Cirripedia, Crustacea).

    PubMed

    Zheden, Vanessa; Klepal, Waltraud; Gorb, Stanislav N; Kovalev, Alexander

    2015-02-01

    The stalked barnacle Dosima fascicularis secretes foam-like cement, the amount of which usually exceeds that produced by other barnacles. When Dosima settles on small objects, this adhesive is additionally used as a float which gives buoyancy to the animal. The dual use of the cement by D. fascicularis requires mechanical properties different from those of other barnacle species. In the float, two regions with different morphological structure and mechanical properties can be distinguished. The outer compact zone with small gas-filled bubbles (cells) is harder than the interior one and forms a protective rind presumably against mechanical damage. The inner region with large, gas-filled cells is soft. This study demonstrates that D. fascicularis cement is soft and visco-elastic. We show that the values of the elastic modulus, hardness and tensile stress are considerably lower than in the rigid cement of other barnacles. PMID:25657833

  5. Slc26a3/Dra and Slc26a6 in Murine Ameloblasts.

    PubMed

    Jalali, R; Zandieh-Doulabi, B; DenBesten, P K; Seidler, U; Riederer, B; Wedenoja, S; Micha, D; Bronckers, A L J J

    2015-12-01

    Formation of apatite crystals during enamel development generates protons. To sustain mineral accretion, maturation ameloblasts need to buffer these protons. The presence of cytosolic carbonic anhydrases, the basolateral Na(+) bicarbonate cotransporter Nbce1, and the basolateral anion exchanger Ae2a,b in maturation ameloblasts suggests that these cells secrete bicarbonates into the forming enamel, but it is unknown by which mechanism. Solute carrier (Slc) family 26A encodes different anion exchangers that exchange Cl(-)/HCO3 (-), including Slc26a3/Dra, Slc26a6/Pat-1, and Slc26a4/pendrin. Previously, we showed that pendrin is expressed in ameloblasts but is not critical for enamel formation. In this study, we tested the hypothesis that maturation ameloblasts express Dra and Slc26a6 to secrete bicarbonate into the enamel space in exchange for Cl(-). Real-time polymerase chain reaction detected mRNA transcripts for Dra and Slc26a6 in mouse incisor enamel organs, and Western blotting confirmed their translation into protein. Both isoforms were immunolocalized in ameloblasts, principally at maturation stage. Mice with null mutation of either Dra or Slc26a6 had a normal dental or skeletal phenotype without changes in mineral density, as measured by micro-computed tomography. In enamel organs of Slc26a6-null mice, Dra and pendrin protein levels were both elevated by 52% and 55%, respectively. The amount of Slc26a6 protein was unchanged in enamel organs of Ae2a,b- and Cftr-null mice but reduced in Dra-null mice by 36%. Our data show that ameloblasts express Dra, pendrin, or Slc26a6 but each of these separately is not critical for formation of dental enamel. The data suggest that in ameloblasts, Slc26a isoforms can functionally compensate for one another. PMID:26394631

  6. Beneficial Insect Attraction to Milkweeds (Asclepias speciosa, Asclepias fascicularis) in Washington State, USA.

    PubMed

    James, David G; Seymour, Lorraine; Lauby, Gerry; Buckley, Katie

    2016-01-01

    Native plant and beneficial insect associations are relatively unstudied yet are important in native habitat restoration programs for improving and sustaining conservation biological control of arthropod pests in agricultural crops. Milkweeds (Asclepias spp.) are currently the focus of restoration programs in the USA aimed at reversing a decline in populations of the milkweed-dependent monarch butterfly (Danaus plexippus); however, little is known of the benefits of these plants to other beneficial insects. Beneficial insects (predators, parasitoids, pollinators) attracted to two milkweed species (Asclepias speciosa, Asclepias fascicularis) in central Washington State, WA, USA were identified and counted on transparent sticky traps attached to blooms over five seasons. Combining all categories of beneficial insects, means of 128 and 126 insects per trap were recorded for A. speciosa and A. fascicularis, respectively. Predatory and parasitic flies dominated trap catches for A. speciosa while parasitic wasps were the most commonly trapped beneficial insects on A. fascicularis. Bees were trapped commonly on both species, especially A. speciosa with native bees trapped in significantly greater numbers than honey bees. Beneficial insect attraction to A. speciosa and A. fascicularis was substantial. Therefore, these plants are ideal candidates for habitat restoration, intended to enhance conservation biological control, and for pollinator conservation. In central Washington, milkweed restoration programs for enhancement of D. plexippus populations should also provide benefits for pest suppression and pollinator conservation. PMID:27367733

  7. The HLA-DRA*0102 allele: correct nucleotide sequence and associated HLA haplotypes.

    PubMed

    Kralovicova, J; Marsh, S G E; Waller, M J; Hammarstrom, L; Vorechovsky, I

    2002-09-01

    Here we correct the nucleotide sequence of a single known variant of the HLA-DRA gene. We show that the coding regions of the HLA-DRA*0101 and HLA-DRA*0102 alleles do not differ at two codons as reported previously, but only in codon 217. Using nucleotide sequencing and DNA samples from individuals homozygous in the major histocompatibility complex, we found that the variant, leucine 217-encoding HLA-DRA*0102 allele was present on the haplotypes HLA-B*0801, DRB1*03011, DQB1*0201 (ancestral haplotype AH8.1), HLA-B*07021, DRB1*15011, DQB1*0602 (AH7.1), HLA-B*1501, DRB1*15011, DQB1*0602, HLA-B*1501, DRB1*1402, DQB1*03011 and HLA-A3, B*07021, DRB1*1301, DQB1*0603. The HLA-DRA*0101 allele coding for valine 217 was observed on the haplotypes HLA-B*5701, DRB1*0701, DQB1*03032 (AH57.1), HLA-DRB1*04011, DQB1*0302, HLA-DRB1*0701, DQB1*0202, and HLA-DRB1*0101, DQB1*05011. PMID:12445311

  8. The Mutual Influences between Depressed Macaca fascicularis Mothers and Their Infants

    PubMed Central

    Xie, Liang; Wang, Tao; Fang, Liang; Yang, Deyu; Melgiri, Narayan D.; Xie, Peng

    2014-01-01

    Objective To assess the influence of infant rearing on the behavior of depressed adult female Macaca fascicularis and the influence of depressed infant-rearing adult female Macaca fascicularis on their infants in a free enclosure environment. Methods Here, 20 depressed subjects and then 20 healthy subjects were randomly selected from a total population of 1007 adult female Macaca fascicularis subjects. Four depressed subjects and eight healthy subjects were rearing infants. By focal observation, three trained observers video-recorded the selected subjects over a total observational period of 560 hours. The video footage was analyzed by qualified blinded analysts that coded the raw footage into quantitative behavioral data (i.e., durations of 53 pre-defined behavioral items across 12 behavioral categories) for statistical analysis. Results Between infant-rearing and non-rearing healthy subjects, ten differential behaviors distributed across five behavioral categories were identified. Between infant-rearing and non-rearing depressed subjects, nine behaviors distributed across five behavioral categories were identified. Between infant-rearing healthy and infant-rearing depressed subjects, fifteen behaviors distributed across six behavioral categories were identified. Conclusion Infant-rearing depressed adult female Macaca fascicularis subjects may have a worse psychological status as compared to non-rearing depressed counterparts. Infant rearing may negatively influence depressed Macaca fascicularis mothers. Infant-rearing depressed subjects were less adequate at raising infants as compared to infant-rearing healthy subjects. Thus, maternal depression in this macaque species may negatively impact infatile development, which is consistent with previous findings in humans. PMID:24599092

  9. [MedDRA and its applications in statistical analysis of adverse events].

    PubMed

    Lu, Meng-jie; Liu, Yu-xiu

    2015-11-01

    Safety assessment in clinical trials is dependent on an in-depth analysis of the adverse events to a great extent. However, there are difficulties in summary classification, data management and statistical analysis of the adverse events because of the different expressions on the same adverse events caused by regional, linguistic, ethnic, cultural and other differences. In order to ensure the normative expressions, it's necessary to standardize the terms in recording the adverse events. MedDRA (medical dictionary for regulatory activities) has been widely recommended and applied in the world as a powerful support for the adverse events reporting in clinical trials. In this paper, the development history, applicable scope, hierarchy structure, encoding term selection and standardized query strategies of the MedDRA is introduced. Furthermore, the practical process of adverse events encoding with MedDRA is proposed. Finally, the framework of statistical analysis about adverse events is discussed. PMID:26911031

  10. Determining correspondences between high-frequency MedDRA concepts and SNOMED: a case study

    PubMed Central

    2010-01-01

    Background The Systematic Nomenclature of Medicine Clinical Terms (SNOMED CT) is being advocated as the foundation for encoding clinical documentation. While the electronic medical record is likely to play a critical role in pharmacovigilance - the detection of adverse events due to medications - classification and reporting of Adverse Events is currently based on the Medical Dictionary of Regulatory Activities (MedDRA). Complete and high-quality MedDRA-to-SNOMED CT mappings can therefore facilitate pharmacovigilance. The existing mappings, as determined through the Unified Medical Language System (UMLS), are partial, and record only one-to-one correspondences even though SNOMED CT can be used compositionally. Efforts to map previously unmapped MedDRA concepts would be most productive if focused on concepts that occur frequently in actual adverse event data. We aimed to identify aspects of MedDRA that complicate mapping to SNOMED CT, determine pattern in unmapped high-frequency MedDRA concepts, and to identify types of integration errors in the mapping of MedDRA to UMLS. Methods Using one years' data from the US Federal Drug Administrations Adverse Event Reporting System, we identified MedDRA preferred terms that collectively accounted for 95% of both Adverse Events and Therapeutic Indications records. After eliminating those already mapping to SNOMED CT, we attempted to map the remaining 645 Adverse-Event and 141 Therapeutic-Indications preferred terms with software assistance. Results All but 46 Adverse-Event and 7 Therapeutic-Indications preferred terms could be composed using SNOMED CT concepts: none of these required more than 3 SNOMED CT concepts to compose. We describe the common composition patterns in the paper. About 30% of both Adverse-Event and Therapeutic-Indications Preferred Terms corresponded to single SNOMED CT concepts: the correspondence was detectable by human inspection but had been missed during the integration process, which had created

  11. Biosorption and desorption of Cd2+ from wastewater by dehydrated shreds of Cladophora fascicularis

    NASA Astrophysics Data System (ADS)

    Deng, Liping; Zhu, Xiaobin; Su, Yingying; Su, Hua; Wang, Xinting

    2008-02-01

    The adsorption and desorption of algae Cladophora fascicularis and their relation with initial Cd2+ concentration, initial pH, and co-existing ions were studied. Adsorption equilibrium and biosorption kinetics were established from batch experiments. The adsorption equilibrium was adequately described by the Langmuir isotherm, and biosorption kinetics was in pseudo-second order model. The experiment on co-existing ions showed that the biosorption capacity of biomass decreased with an increasing concentration of competing ions. Desorption experiments indicated that EDTA was efficient desorbent for recovery from Cd2+. With high capacities of metal biosorption and desorption, the biomass of Cladophora fascicularis is promising as a cost-effective biosorbent for the removal of Cd2+ from wastewater.

  12. [Application analysis of adverse drug reaction terminology WHOART and MedDRA].

    PubMed

    Liu, Jing; Xie, Yan-ming; Gai, Guo-zhong; Liao, Xing

    2015-12-01

    Drug safety has always been a global focus. Discovery and accurate information acquisition of adverse drug reaction have been the most crucial concern. Terminology of adverse drug reaction makes adverse reaction medical report meaningful, standardized and accurate. This paper discussed the domestic use of the terminology WHOART and MedDRA in terms of content, structure, and application situation. It also analysed the differences between the two terminologies and discusses the future trend of application in our country PMID:27245013

  13. Spectral Line Variations of Symbiotic Stars EG And, AG Dra, and BX Mon and Its Interpretation

    NASA Astrophysics Data System (ADS)

    Yoon, Tae Seog; Kim, Soo Hyun; Moon, Hyeonwoo; Kim, Kyu-Seob; Oh, Hyungil

    2013-02-01

    We present some results obtained by high resolution spectroscopic observations for symbiotic stars EG And, AG Dra, and BX Mon in recent years which were performed with 1.8-m reflector and echelle spectrograph BOES at Bohyunsan Optical Astronomy Observatory, Youngcheon, South Korea. The variations of Hα emission line during a night and the variations of H Balmer lines and He I emission lines among several analyzed lines over months and years are shown and discussed.

  14. Proceedings of the Inaugural Pediatric Dermatology Research Alliance (PeDRA) Conference

    PubMed Central

    Siegel, Dawn H.; Choate, Keith; Drolet, Beth A.; Frieden, Ilona J.; Teng, Joyce M.; Tom, Wynnis; Williams, Mary; Eichenfield, Lawrence F.; Paller, Amy S.

    2014-01-01

    Abstract/Statement of the problem Skin disease research involving children currently faces several major hurdles and as a result, many therapies are only available for off-label use in children and many of the most pressing clinical needs of our pediatric population remain unsolved. A strategic planning committee of the Society for Pediatric Dermatology (SPD) identified the need for an organized, inclusive research alliance to augment the resources of individual practitioners and pre-existing smaller collaborative groups and facilitate robust, multicenter basic, translational, and clinical research and therapeutic trials. A December 2011 National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS) Roundtable on Pediatric Dermatology further detailed the therapeutic gaps and barriers to translation of scientific advances to clinical practice. Building on these forums, in July 2012, a group of interested investigators met in Monterey, CA to develop the infrastructure for collaborative pediatric skin research, now called the Pediatric Dermatology Research Alliance (PeDRA). The vision of PeDRA is to create sustainable collaborative research networks to better understand, prevent, treat and cure dermatologic diseases in children. From that starting point, subcommittees and expert members were added, stakeholders identified, and seed funding garnered, with the first PeDRA stand-alone research meeting* realized in Chicago, IL in October 2013. PMID:25318428

  15. Isolation and cDNA characteristics of MHC-DRA genes from gayal (Bos frontalis) and gaytle (Bos frontalis × Bos taurus)

    PubMed Central

    Sun, Yongke; Zhang, Xiaomin; Xi, Dongmei; Li, Guozhi; Wang, Liping; Zheng, Huanli; Du, Min; Gu, Zhaobing; Yang, Yulin; Yang, Yuai

    2015-01-01

    The mammalian major histocompatibility complex (MHC) plays important roles in pathogen recognition and disease resistance. In the present study, the coding sequence and the 5′- and 3′-untranslated regions of MHC class II DR alpha chain (the DRA gene) from rare gayal and gaytle were cloned and analyzed to dissect structural and functional variations. The nucleotide and amino acid sequences for the DRA genes in gayal (Bofr-DRA) and gaytle (Bofr × BoLA-DRA) were almost identical to those for cattle and yak (99%). Compared to yak, two amino acids substitutions in the signal peptide (SP) domain for gayal were found within all Bos animals. Except for only one replacement in the amino acid within the α2 domain of the DRA protein in gayal, the additional residues were highly conserved across the species investigated. The 20 peptide-binding sites (PBS) of Bofr-DRA and Bofr × BoLA-DRA were essentially reserved in the α1 domain among all species investigated. The lesser degree of substitution in Bofr-DRA is concordant with the concept that the DRA gene is highly conserved among all mammals. The very high degree of conservativity of the DRA gene among ruminants, including gayal, suggests its recent evolutionary separation. PMID:26019649

  16. Identification of a novel yolk protein in the hermatypic coral Galaxea fascicularis.

    PubMed

    Hayakawa, Hideki; Andoh, Tadashi; Watanabe, Toshiki

    2007-03-01

    The reef-building (or hermatypic) coral Galaxea fascicularis (Anthozoa, Hexacorallia, Scleractinia) has an annual reproductive cycle. Females of G. fascicularis release packages (or ;bundles') of eggs for external fertilization, whereas male individuals form bundles consisting of sperm and infertile ;pseudo-eggs' that are thought to confer buoyancy to the male bundle. In the egg of G. fascicularis, four proteins (GfEP-1 to 4) were found to be stored in high abundance, and three of them (GfEP-1, 2 and 3) are generated by processing of a vitellogenin (Vg)-like precursor. In the present study, a cDNA encoding GfEP-4 was cloned and its sequence determined (GenBank/EMBL/DDBJ accession no. AB259859). The amino acid sequence of this protein does not exhibit similarity to known proteins, including Vgs or other yolk proteins found in some invertebrates. The expression of GfEP-4 mRNA was observed in females, and also in the majority of males examined, although expression levels were lower than in females. The GfEP-4 protein was detected in pseudo-eggs, where its concentration was 20-100 times lower than in eggs. In contrast, GfEP-1, 2 and 3 were not detected in pseudo-eggs. A protein (28 kDa) which cross-reacted with anti-GfEP-4 antibodies was detected in eggs of the coral Montipora digitata, suggesting the possibility that homologs of this protein are present in the eggs of other scleractinian corals. PMID:17551245

  17. The rhesus (Macaca mulatta) and crab-eating (Macaca fascicularis) monkeys in cardiovascular and aerospace research

    NASA Technical Reports Server (NTRS)

    Erickson, H. H.; Ritzman, J. R.

    1977-01-01

    Two nonhuman primate species were used to investigate the effects of gravitoinertial forces on pilot incapacitation and performance impairment, to define human physiologic tolerance and safe exposure limits to these environments, and to obtain data which can be used to evolve new methods to improve man's G tolerance to match the structural capability of new generation aircraft. The macaca fascicularis was used to study the effects of environmental stress and atheroscelerosis on cerebral blood flow and function agents on myocardial and cardiovascular function were studied in the macaca mulatta.

  18. Biochemical analyses of the cement float of the goose barnacle Dosima fascicularis--a preliminary study.

    PubMed

    Zheden, Vanessa; Klepal, Waltraud; von Byern, Janek; Bogner, Fabian Robert; Thiel, Karsten; Kowalik, Thomas; Grunwald, Ingo

    2014-09-01

    The goose barnacle Dosima fascicularis produces an excessive amount of adhesive (cement), which has a double function, being used for attachment to various substrata and also as a float (buoy). This paper focuses on the chemical composition of the cement, which has a water content of 92%. Scanning electron microscopy with EDX was used to measure the organic elements C, O and N in the foam-like cement. Vibrational spectroscopy (FTIR, Raman) provided further information about the overall secondary structure, which tended towards a β-sheet. Disulphide bonds could not be detected by Raman spectroscopy. The cystine, methionine, histidine and tryptophan contents were each below 1% in the cement. Analyses of the cement revealed a protein content of 84% and a total carbohydrate content of 1.5% in the dry cement. The amino acid composition, 1D/2D-PAGE and MS/MS sequence analysis revealed a de novo set of peptides/proteins with low homologies with other proteins such as the barnacle cement proteins, largely with an acidic pI between 3.5 and 6.0. The biochemical composition of the cement of D. fascicularis is similar to that of other barnacles, but it shows interesting variations. PMID:25237772

  19. Dark calcification and the daily rhythm of calcification in the scleractinian coral, Galaxea fascicularis

    NASA Astrophysics Data System (ADS)

    Al-Horani, F. A.; Tambutté, É.; Allemand, D.

    2007-09-01

    The rate of calcification in the scleractinian coral Galaxea fascicularis was followed during the daytime using 45Ca tracer. The coral began the day with a low calcification rate, which increased over time to a maximum in the afternoon. Since the experiments were carried out under a fixed light intensity, these results suggest that an intrinsic rhythm exists in the coral such that the calcification rate is regulated during the daytime. When corals were incubated for an extended period in the dark, the calcification rate was constant for the first 4 h of incubation and then declined, until after one day of dark incubation, calcification ceased, possibly as a result of the depletion of coral energy reserves. The addition of glucose and Artemia reduced the dark calcification rate for the short duration of the experiment, indicating an expenditure of oxygen in respiration. Artificial hypoxia reduced the rate of dark calcification to about 25% compared to aerated coral samples. It is suggested that G. fascicularis obtains its oxygen needs from the surrounding seawater during the nighttime, whereas during the day time the coral exports oxygen to the seawater.

  20. Phylogenetic relationships of Malaysia’s long-tailed macaques, Macaca fascicularis, based on cytochrome b sequences

    PubMed Central

    Abdul-Latiff, Muhammad Abu Bakar; Ruslin, Farhani; Fui, Vun Vui; Abu, Mohd-Hashim; Rovie-Ryan, Jeffrine Japning; Abdul-Patah, Pazil; Lakim, Maklarin; Roos, Christian; Yaakop, Salmah; Md-Zain, Badrul Munir

    2014-01-01

    Abstract Phylogenetic relationships among Malaysia’s long-tailed macaques have yet to be established, despite abundant genetic studies of the species worldwide. The aims of this study are to examine the phylogenetic relationships of Macaca fascicularis in Malaysia and to test its classification as a morphological subspecies. A total of 25 genetic samples of M. fascicularis yielding 383 bp of Cytochrome b (Cyt b) sequences were used in phylogenetic analysis along with one sample each of M. nemestrina and M. arctoides used as outgroups. Sequence character analysis reveals that Cyt b locus is a highly conserved region with only 23% parsimony informative character detected among ingroups. Further analysis indicates a clear separation between populations originating from different regions; the Malay Peninsula versus Borneo Insular, the East Coast versus West Coast of the Malay Peninsula, and the island versus mainland Malay Peninsula populations. Phylogenetic trees (NJ, MP and Bayesian) portray a consistent clustering paradigm as Borneo’s population was distinguished from Peninsula’s population (99% and 100% bootstrap value in NJ and MP respectively and 1.00 posterior probability in Bayesian trees). The East coast population was separated from other Peninsula populations (64% in NJ, 66% in MP and 0.53 posterior probability in Bayesian). West coast populations were divided into 2 clades: the North-South (47%/54% in NJ, 26/26% in MP and 1.00/0.80 posterior probability in Bayesian) and Island-Mainland (93% in NJ, 90% in MP and 1.00 posterior probability in Bayesian). The results confirm the previous morphological assignment of 2 subspecies, M. f. fascicularis and M. f. argentimembris, in the Malay Peninsula. These populations should be treated as separate genetic entities in order to conserve the genetic diversity of Malaysia’s M. fascicularis. These findings are crucial in aiding the conservation management and translocation process of M. fascicularis populations

  1. All-trans-retinoic Acid Increases SLC26A3 DRA (Down-regulated in Adenoma) Expression in Intestinal Epithelial Cells via HNF-1β*

    PubMed Central

    Priyamvada, Shubha; Anbazhagan, Arivarasu N.; Gujral, Tarunmeet; Borthakur, Alip; Saksena, Seema; Gill, Ravinder K.; Alrefai, Waddah A.; Dudeja, Pradeep K.

    2015-01-01

    All-trans-retinoic acid (ATRA) is an active vitamin A derivative known to modulate a number of physiological processes, including growth and development, differentiation, and gene transcription. The protective effect of ATRA in gut inflammation and diarrheal diseases has been documented. In this regard, down-regulated in adenoma (DRA, a key luminal membrane Cl− transporter involved in NaCl absorption) has been shown to be suppressed in intestinal inflammation. This suppression of DRA is associated with diarrheal phenotype. Therefore, current studies were undertaken to examine the effects of ATRA on DRA expression. DRA mRNA levels were significantly elevated (∼4-fold) in response to ATRA with induction starting as early as 8 h of incubation. Similarly, ATRA increased DRA protein expression by ∼50%. Furthermore, DRA promoter activity was significantly increased in response to ATRA indicating transcriptional activation. ATRA effects on DRA expression appeared to be mediated via the RAR-β receptor subtype, as ATRA remarkably induced RAR-β mRNA levels, whereas RAR-β knockdown substantially attenuated the ability of ATRA to increase DRA expression. Results obtained from agonist (CH-55) and antagonist (LE-135) studies further confirmed that ATRA exerts its effects through RAR-β. Furthermore, ATRA treatment resulted in a significant increase in HNF-1β mRNA levels. The ability of ATRA to induce DRA expression was inhibited in the presence of HNF-1β siRNA indicative of its involvement in ATRA-induced effects on DRA expression. In conclusion, ATRA may act as an antidiarrheal agent by increasing DRA expression via the RAR-β/HNF-1β-dependent pathway. PMID:25887398

  2. Crystal structure of the GlnZ-DraG complex reveals a different form of PII-target interaction

    PubMed Central

    Rajendran, Chitra; Gerhardt, Edileusa C. M.; Bjelic, Sasa; Gasperina, Antonietta; Scarduelli, Marcelo; Pedrosa, Fábio O.; Chubatsu, Leda S.; Merrick, Mike; Souza, Emanuel M.; Winkler, Fritz K.; Huergo, Luciano F.; Li, Xiao-Dan

    2011-01-01

    Nitrogen metabolism in bacteria and archaea is regulated by a ubiquitous class of proteins belonging to the PIIfamily. PII proteins act as sensors of cellular nitrogen, carbon, and energy levels, and they control the activities of a wide range of target proteins by protein-protein interaction. The sensing mechanism relies on conformational changes induced by the binding of small molecules to PII and also by PII posttranslational modifications. In the diazotrophic bacterium Azospirillum brasilense, high levels of extracellular ammonium inactivate the nitrogenase regulatory enzyme DraG by relocalizing it from the cytoplasm to the cell membrane. Membrane localization of DraG occurs through the formation of a ternary complex in which the PII protein GlnZ interacts simultaneously with DraG and the ammonia channel AmtB. Here we describe the crystal structure of the GlnZ-DraG complex at 2.1 Å resolution, and confirm the physiological relevance of the structural data by site-directed mutagenesis. In contrast to other known PII complexes, the majority of contacts with the target protein do not involve the T-loop region of PII. Hence this structure identifies a different mode of PII interaction with a target protein and demonstrates the potential for PII proteins to interact simultaneously with two different targets. A structural model of the AmtB-GlnZ-DraG ternary complex is presented. The results explain how the intracellular levels of ATP, ADP, and 2-oxoglutarate regulate the interaction between these three proteins and how DraG discriminates GlnZ from its close paralogue GlnB. PMID:22074780

  3. Detection of cerebral aneurysms in MRA, CTA and 3D-RA data sets

    NASA Astrophysics Data System (ADS)

    Hentschke, Clemens M.; Beuing, Oliver; Nickl, Rosa; Tönnies, Klaus D.

    2012-03-01

    We propose a system to automatically detect cerebral aneurysms in 3D X-ray rotational angiography images (3D-RA), magnetic resonance angiography images (MRA) and computed tomography angiography images (CTA). After image normalization, initial candidates are found by applying a blob-enhancing filter on the data sets. Clusters are computed by a modified k-means algorithm. A post-processing step reduces the false positive (FP) rate on the basis of computed features. This is implemented as a rule-based system that is adapted according to the modality. In MRA, clusters are excluded that are not neighbored to a vessel. As a final step, FP are further reduced by applying a threshold classification on a feature. Our method was tested on 93 angiographic data sets containing aneurysm and non-aneurysm cases. We achieved 95 % sensitivity with an average rate of 2.6 FP per data set (FP/DS) in case of 3D-RA, 89 % sensitivity at 6.6 FP/DS for MRA and 95 % sensitivity at 37.6 FP/DS with CTA, respectively. We showed that our post-processing approach eliminates FP in MRA with only a slight decrease of sensitivity. In contrast to other approaches, our algorithm does not require a vessel segmentation and does not require training of distributional properties.

  4. VizieR Online Data Catalog: BVR photometry of IZ Mon and AR Dra (Yang+, 2016)

    NASA Astrophysics Data System (ADS)

    Yang, Y.-G.; Dai, H.-F.; Zhou, Z.; Li, Q.

    2016-07-01

    CCD Photometry for IZ Mon and AR Dra, was acquired using the 60cm telescope and the 85cm telescope at the Xinglong station (XLs) of National Astronomical Observatories of China (NAOC). Two telescopes are equipped with the standard Johnson-Cousins UBVRcIc. filters. We then obtained the individual observations as heliocentric Julian dates and differential magnitude, which are listed in Table1. The complete light curves for IZ Mon were obtained on 2009 January 20, 22, 24, 25, and 26, and March 1, using the 85cm telescope. The exposure times are fixed to be 20, 15, and 15s for BVR bands, respectively. A total of 961, 960, and 959 effective images in BVR bands are obtained. Another primary eclipse for IZ Mon was monitored on 2011 January 17. AR Dra was observed on 2009 February 20, 25, 26, and 27, with the 65cm telescope. The typical exposure times are 50, 40 and 40s for BVR bands, which depend on the condition of weather. In total, we obtained 733, 728 and 356 images in B, V and R bands, respectively. (6 data files).

  5. Power Requirements for The NASA Mars Design Reference Architecture (DRA) 5.0

    NASA Technical Reports Server (NTRS)

    Cataldo, Robert L.

    2009-01-01

    This paper summarizes the power systems analysis results from NASA s recent Mars DRA 5.0 study which examined three architecture options and resulting mission requirements for a human Mars landing mission in the post-2030 timeframe. DRA 5.0 features a long approximately 500 day surface stay split mission using separate cargo and crewed Mars transfer vehicles. Two cargo flights, utilizing minimum energy trajectories, pre-deploy a cargo lander to the surface and a habitat lander into a 24-hour elliptical Mars parking orbit where it remains until the arrival of the crew during the next mission opportunity approximately 26 months later. The pre-deployment of cargo poses unique challenges for set-up and emplacement of surface assets that results in the need for self or robotically deployed designs. Three surface architecture options were evaluated for breadth of science content, extent of exploration range/capability and variations in system concepts and technology. This paper describes the power requirements for the surface operations of the three mission options, power system analyses including discussion of the nuclear fission, solar photovoltaic and radioisotope concepts for main base power and long range mobility.

  6. Characterization of cement float buoyancy in the stalked barnacle Dosima fascicularis (Crustacea, Cirripedia)

    PubMed Central

    Zheden, Vanessa; Kovalev, Alexander; Gorb, Stanislav N.; Klepal, Waltraud

    2015-01-01

    Dosima fascicularis is the only barnacle which can drift autonomously at the water surface with a foam-like cement float. The cement secreted by the animal contains numerous gas-filled cells of different size. When several individuals share one float, their size and not their number is crucial for the production of both volume and mass of the float. The gas content within the cells of the foam gives positive static buoyancy to the whole float. The volume of the float, the gas volume and the positive static buoyancy are positively correlated. The density of the cement float without gas is greater than that of seawater. This study shows that the secreted cement consists of more than 90% water and the gas volume is on average 18.5%. Our experiments demonstrate that the intact foam-like cement float is sealed to the surrounding water. PMID:25657839

  7. Characterization of cement float buoyancy in the stalked barnacle Dosima fascicularis (Crustacea, Cirripedia).

    PubMed

    Zheden, Vanessa; Kovalev, Alexander; Gorb, Stanislav N; Klepal, Waltraud

    2015-02-01

    Dosima fascicularis is the only barnacle which can drift autonomously at the water surface with a foam-like cement float. The cement secreted by the animal contains numerous gas-filled cells of different size. When several individuals share one float, their size and not their number is crucial for the production of both volume and mass of the float. The gas content within the cells of the foam gives positive static buoyancy to the whole float. The volume of the float, the gas volume and the positive static buoyancy are positively correlated. The density of the cement float without gas is greater than that of seawater. This study shows that the secreted cement consists of more than 90% water and the gas volume is on average 18.5%. Our experiments demonstrate that the intact foam-like cement float is sealed to the surrounding water. PMID:25657839

  8. Neuroblastoma at the trigeminal nerve in a cynomolgus monkey (Macaca fascicularis).

    PubMed

    Ide, Tetsuya; Moriyama, Akiko; Uchida, Kazuyuki; Chambers, James K; Okazaki, Takanobu; Kobayashi, Kinji; Nakatsuji, Shunji; Matsumoto, Masahiro

    2016-07-01

    A male cynomolgus monkey (Macaca fascicularis) of 5 years and 11 months of age from the vehicle control group of a 4-week repeated oral dose toxicity study had a spontaneously occurring mass lesion directly attached to the proximal part of the left trigeminal nerve. Histologically, the mass was characterized by a multifocal nodular appearance. Nodular zones showed low to moderate cellularity and were composed of small round cells exhibiting nuclear uniformity. On the other hand, inter-nodular zones were composed of nerve fiber containing septa and closely aggregated highly pleomorphic cells. Immunohistochemically, the small round cells were strongly immunopositive for synaptophysin, neuN, and class III beta-tubulin, while the highly pleomorphic cells were weakly immunopositive for neuN and occasionally immunopositive for class III beta-tubulin and doublecortin, suggesting that the tumor had originated from a neuronal lineage cell. Based on these findings, the mass was diagnosed as a neuroblastoma at the trigeminal nerve. PMID:27559245

  9. Hiding and perspective taking in long-tailed macaques (Macaca fascicularis).

    PubMed

    Kummer, H; Anzenberger, G; Hemelrijk, C K

    1996-03-01

    Seven long-tailed macaques (Macaca fascicularis) were trained by threats not to drink from a juice nipple as long as an experimenter was facing them. However, they were allowed to drink when the experimenter was standing with his or her back turned. During transfer tests, the monkeys had a choice between 2 juice nipples, one uncovered and the other hidden from the experimenter by a wooden screen, while the experimenter was facing them. We tested whether the monkeys would then prefer to drink behind the screen, thus demonstrating that they transferred knowledge acquired during training. Results did not yield a significant outcome, suggesting that the macaques did not transfer the observable "experimenter's visible open eyes" and that they did not take the experimenter's perspective. PMID:8851557

  10. Peripheral Ossifying Fibroma and Juxtacortical Chondrosarcoma in Cynomolgus Monkeys (Macaca fascicularis)

    PubMed Central

    Schmelting, Barthel; Zöller, Martina; Kaspareit, Joachim

    2011-01-01

    Literature on spontaneous primary bone tumors in nonhuman primates is sparse. This case report describes 2 different neoplastic bone lesions in 2 adult cynomolgus monkeys (Macaca fascicularis), including macroscopic, radiographic, histologic, and immunohistochemical findings. In one monkey, a firm mass located at the palatogingival junction of the left rostral maxilla was confirmed to be a peripheral ossifying fibroma in light of its histologic and immunohistochemical characteristics. In another monkey, a lobulated tumor at the right distal femur that radiographically showed moderate radiopacity with splotchy areas of mineralization was confirmed to be a juxtacortical chondrosarcoma on histologic examination. The 2 neoplastic bone lesions revealed rare histologic and immunohistochemical characteristics and contribute to the known tumor spectrum of cynomolgus monkeys. PMID:21333171

  11. Neuroblastoma at the trigeminal nerve in a cynomolgus monkey (Macaca fascicularis)

    PubMed Central

    Ide, Tetsuya; Moriyama, Akiko; Uchida, Kazuyuki; Chambers, James K.; Okazaki, Takanobu; Kobayashi, Kinji; Nakatsuji, Shunji; Matsumoto, Masahiro

    2016-01-01

    A male cynomolgus monkey (Macaca fascicularis) of 5 years and 11 months of age from the vehicle control group of a 4-week repeated oral dose toxicity study had a spontaneously occurring mass lesion directly attached to the proximal part of the left trigeminal nerve. Histologically, the mass was characterized by a multifocal nodular appearance. Nodular zones showed low to moderate cellularity and were composed of small round cells exhibiting nuclear uniformity. On the other hand, inter-nodular zones were composed of nerve fiber containing septa and closely aggregated highly pleomorphic cells. Immunohistochemically, the small round cells were strongly immunopositive for synaptophysin, neuN, and class III beta-tubulin, while the highly pleomorphic cells were weakly immunopositive for neuN and occasionally immunopositive for class III beta-tubulin and doublecortin, suggesting that the tumor had originated from a neuronal lineage cell. Based on these findings, the mass was diagnosed as a neuroblastoma at the trigeminal nerve. PMID:27559245

  12. Infection by Brazilian and Dutch swine hepatitis E virus strains induces haematological changes in Macaca fascicularis

    PubMed Central

    2013-01-01

    Background Hepatitis E virus (HEV) has been described as an emerging pathogen in Brazil and seems to be widely disseminated among swine herds. An autochthonous human case of acute hepatitis E was recently reported. To obtain a better understanding of the phenotypic profiles of both human and swine HEV strains, a experimental study was conducted using the animal model, Macaca fascicularis. Methods Six cynomolgus monkeys (Macaca fascicularis) were inoculated intravenously with swine HEV genotype 3 that was isolated from naturally and experimentally infected pigs in Brazil and the Netherlands. Two other monkeys were inoculated with HEV genotype 3 that was recovered from Brazilian and Argentinean patients with locally acquired acute and fulminant hepatitis E. The haematological, biochemical, and virological parameters of all animals were monitored for 67 days. Results Subclinical hepatitis was observed in all monkeys after inoculation with HEV genotype 3 that was recovered from the infected swine and human patients. HEV RNA was detected in the serum and/or faeces of 6 out of the 8 cynomolgus monkeys between 5 and 53 days after inoculation. The mild inflammation of liver tissues and elevations of discrete liver enzymes were observed. Seroconversions to anti-HEV IgM and/or IgG were detected in 7 animals. Reactivities to anti-HEV IgA were also detected in the salivary samples of 3 animals. Interestingly, all of the infected monkeys showed severe lymphopenia and a trend toward monocytosis, which coincided with elevations in alanine aminotransferase and antibody titres. Conclusions The ability of HEV to cross the species barrier was confirmed for both the swine (Brazilian and Dutch) and human (Argentinean) strains, thus reinforcing the zoonotic risk of hepatitis E in South America. Cynomolgus monkeys that were infected with HEV genotype 3 developed subclinical hepatitis that was associated with haematological changes. Haematological approaches should be considered in

  13. Epizoic acoelomorph flatworms impair zooplankton feeding by the scleractinian coral Galaxea fascicularis.

    PubMed

    Wijgerde, Tim; Schots, Pauke; Van Onselen, Eline; Janse, Max; Karruppannan, Eric; Verreth, Johan A J; Osinga, Ronald

    2013-01-15

    Many scleractinian coral species host epizoic acoelomorph flatworms, both in aquaculture and in situ. These symbiotic flatworms may impair coral growth and health through light-shading, mucus removal and disruption of heterotrophic feeding. To quantify the effect of epizoic flatworms on zooplankton feeding, we conducted video analyses of single polyps of Galaxea fascicularis (Linnaeus 1767) grazing on Artemia nauplii in the presence and absence of symbiotic flatworms. 18S DNA analysis revealed that flatworms inhabiting G. fascicularis belonged to the genus Waminoa (Convolutidae), which were hosted at a density of 3.6±0.4 individuals polyp(-1). Polyps hosting flatworms exhibited prey capture rates of 2.2±2.5, 3.4±4.5 and 2.7±3.4 nauplii polyp(-1) 30 min(-1) at prey concentrations of 250, 500 and 1,000 nauplii L(-1), respectively. Polyps that had their flatworms removed displayed prey capture rates of 2.7±1.6, 4.8±4.1 and 16.9±10.3 nauplii polyp(-1) 30 min(-1). Significant main and interactive effects of flatworm presence and ambient prey concentration were found, reflected by the fact that flatworms significantly impaired host feeding rates at the highest prey density of 1,000 nauplii L(-1). In addition, flatworms displayed kleptoparasitism, removing between 0.1±0.3 and 0.6±1.1 nauplii 30 min(-1) from the oral disc of their host, or 5.3±3.3 to 50.0±2.1% of prey acquired by the coral. We suggest classifying the coral-associated Waminoa sp. as an epizoic parasite, as its presence may negatively affect growth and health of the host. PMID:23336072

  14. Study of the gastrointestinal parasitic fauna of captive non-human primates (Macaca fascicularis).

    PubMed

    Zanzani, Sergio Aurelio; Gazzonis, Alessia Libera; Epis, Sara; Manfredi, Maria Teresa

    2016-01-01

    The aim of this study was to examine helminths and protozoans in cynomolgus macaques (Macaca fascicularis) imported from registered breeding facilities in China and their relation to health risks for non-human primate handlers in biomedical research centers and in breeding facilities. Fresh fecal samples were collected from a total of 443 M. fascicularis and analyzed by copromicroscopical analysis, immunoenzymatic, or molecular assays. As to helminths, whose eggs were shed in 2.03% of the samples, Trichuris and Oesophagostomum were the only two taxa found, with low prevalence and low eggs per gram (EPG) values. Protozoans were more frequently detected (87.40%), with Entamoeba coli (85.19%) and Endolimax nana (79.26%) as the most prevalent species shed. Other parasites found by fecal smear examination were uninucleated-cyst-producing Entamoebas (78.52%), Iodamoeba bütschlii (42.96%), and Chilomastix mesnili (24.44%), while cysts of Balantidium coli (22.2%) were only observed by sedimentation. No coproantigens of Giardia duodenalis, Cryptosporidium spp., and Entamoeba histolytica complex were detected. Blastocystis sp. infection was noticed in 87.63% of macaques by PCR. These cynomolgus monkeys were infected with many subtypes (ST1, ST2, ST3, ST5, and ST7), where the predominant Blastocystis sp. subtypes were ST2 (77.5%), followed by ST1 (63.5%). Data collected confirmed the presence of potentially zoonotic parasites and a high parasite diversity, suggesting the need for appropriate and sensitive techniques to adequately control them and related health risks for handlers of non-human primates in biomedical research centers and in breeding facilities. PMID:26374536

  15. Methods and pitfalls in searching drug safety databases utilising the Medical Dictionary for Regulatory Activities (MedDRA).

    PubMed

    Brown, Elliot G

    2003-01-01

    The Medical Dictionary for Regulatory Activities (MedDRA) is a unified standard terminology for recording and reporting adverse drug event data. Its introduction is widely seen as a significant improvement on the previous situation, where a multitude of terminologies of widely varying scope and quality were in use. However, there are some complexities that may cause difficulties, and these will form the focus for this paper. Two methods of searching MedDRA-coded databases are described: searching based on term selection from all of MedDRA and searching based on terms in the safety database. There are several potential traps for the unwary in safety searches. There may be multiple locations of relevant terms within a system organ class (SOC) and lack of recognition of appropriate group terms; the user may think that group terms are more inclusive than is the case. MedDRA may distribute terms relevant to one medical condition across several primary SOCs. If the database supports the MedDRA model, it is possible to perform multiaxial searching: while this may help find terms that might have been missed, it is still necessary to consider the entire contents of the SOCs to find all relevant terms and there are many instances of incomplete secondary linkages. It is important to adjust for multiaxiality if data are presented using primary and secondary locations. Other sources for errors in searching are non-intuitive placement and the selection of terms as preferred terms (PTs) that may not be widely recognised. Some MedDRA rules could also result in errors in data retrieval if the individual is unaware of these: in particular, the lack of multiaxial linkages for the Investigations SOC, Social circumstances SOC and Surgical and medical procedures SOC and the requirement that a PT may only be present under one High Level Term (HLT) and one High Level Group Term (HLGT) within any single SOC. Special Search Categories (collections of PTs assembled from various SOCs by

  16. pH-dependent structural change of the extracellular sensor domain of the DraK histidine kinase from Streptomyces coelicolor

    SciTech Connect

    Yeo, Kwon Joo; Kim, Eun Hye; Hwang, Eunha; Han, Young-Hyun; Eo, Yumi; Kim, Hyun Jung; Kwon, Ohsuk; Hong, Young-Soo; Cheong, Chaejoon; Cheong, Hae-Kap

    2013-02-15

    Highlights: ► We described the biochemical and biophysical properties of the extracellular sensory domain (ESD) of DraK histidine kinase. ► The ESD of DraK showed a reversible pH-dependent conformational change in a wide pH range. ► The E83 is an important residue for the pH-dependent conformational change. -- Abstract: Recently, the DraR/DraK (Sco3063/Sco3062) two-component system (TCS) of Streptomycescoelicolor has been reported to be involved in the differential regulation of antibiotic biosynthesis. However, it has not been shown that under which conditions and how the DraR/DraK TCS is activated to initiate the signal transduction process. Therefore, to understand the sensing mechanism, structural study of the sensory domain of DraK is highly required. Here, we report the biochemical and biophysical properties of the extracellular sensory domain (ESD) of DraK. We observed a reversible pH-dependent conformational change of the ESD in a pH range of 2.5–10. Size-exclusion chromatography and AUC (analytical ultracentrifugation) data indicated that the ESD is predominantly monomeric in solution and exists in equilibrium between monomer and dimer states in acidic condition. Using NMR (nuclear magnetic resonance) and CD (circular dichroism) spectroscopy, our findings suggest that the structure of the ESD at low pH is more structured than that at high pH. In particular, the glutamate at position 83 is an important residue for the pH-dependent conformational change. These results suggest that this pH-dependent conformational change of ESD may be involved in signal transduction process of DraR/DraK TCS.

  17. DRA/NASA/ONERA Collaboration on Icing Research. Part 2; Prediction of Airfoil Ice Accretion

    NASA Technical Reports Server (NTRS)

    Wright, William B.; Gent, R. W.; Guffond, Didier

    1997-01-01

    This report presents results from a joint study by DRA, NASA, and ONERA for the purpose of comparing, improving, and validating the aircraft icing computer codes developed by each agency. These codes are of three kinds: (1) water droplet trajectory prediction, (2) ice accretion modeling, and (3) transient electrothermal deicer analysis. In this joint study, the agencies compared their code predictions with each other and with experimental results. These comparison exercises were published in three technical reports, each with joint authorship. DRA published and had first authorship of Part 1 - Droplet Trajectory Calculations, NASA of Part 2 - Ice Accretion Prediction, and ONERA of Part 3 - Electrothermal Deicer Analysis. The results cover work done during the period from August 1986 to late 1991. As a result, all of the information in this report is dated. Where necessary, current information is provided to show the direction of current research. In this present report on ice accretion, each agency predicted ice shapes on two dimensional airfoils under icing conditions for which experimental ice shapes were available. In general, all three codes did a reasonable job of predicting the measured ice shapes. For any given experimental condition, one of the three codes predicted the general ice features (i.e., shape, impingement limits, mass of ice) somewhat better than did the other two. However, no single code consistently did better than the other two over the full range of conditions examined, which included rime, mixed, and glaze ice conditions. In several of the cases, DRA showed that the user's knowledge of icing can significantly improve the accuracy of the code prediction. Rime ice predictions were reasonably accurate and consistent among the codes, because droplets freeze on impact and the freezing model is simple. Glaze ice predictions were less accurate and less consistent among the codes, because the freezing model is more complex and is critically

  18. Reduced heterotrophy in the stony coral Galaxea fascicularis after life-long exposure to elevated carbon dioxide

    NASA Astrophysics Data System (ADS)

    Smith, Joy N.; Strahl, Julia; Noonan, Sam H. C.; Schmidt, Gertraud M.; Richter, Claudio; Fabricius, Katharina E.

    2016-06-01

    Ocean acidification imposes many physiological, energetic, structural and ecological challenges to stony corals. While some corals may increase autotrophy under ocean acidification, another potential mechanism to alleviate some of the adverse effects on their physiology is to increase heterotrophy. We compared the feeding rates of Galaxea fascicularis colonies that have lived their entire lives under ocean acidification conditions at natural carbon dioxide (CO2) seeps with colonies living under present-day CO2 conditions. When provided with the same quantity and composition of zooplankton as food, corals acclimatized to high CO2 showed 2.8 to 4.8 times depressed rates of zooplankton feeding. Results were consistent over four experiments, from two expeditions and both in field and chamber measurements. Unless replenished by other sources, reduced zooplankton uptake in G. fascicularis acclimatized to ocean acidification is likely to entail a shortage of vital nutrients, potentially jeopardizing their health and survival in future oceans.

  19. Reduced heterotrophy in the stony coral Galaxea fascicularis after life-long exposure to elevated carbon dioxide.

    PubMed

    Smith, Joy N; Strahl, Julia; Noonan, Sam H C; Schmidt, Gertraud M; Richter, Claudio; Fabricius, Katharina E

    2016-01-01

    Ocean acidification imposes many physiological, energetic, structural and ecological challenges to stony corals. While some corals may increase autotrophy under ocean acidification, another potential mechanism to alleviate some of the adverse effects on their physiology is to increase heterotrophy. We compared the feeding rates of Galaxea fascicularis colonies that have lived their entire lives under ocean acidification conditions at natural carbon dioxide (CO2) seeps with colonies living under present-day CO2 conditions. When provided with the same quantity and composition of zooplankton as food, corals acclimatized to high CO2 showed 2.8 to 4.8 times depressed rates of zooplankton feeding. Results were consistent over four experiments, from two expeditions and both in field and chamber measurements. Unless replenished by other sources, reduced zooplankton uptake in G. fascicularis acclimatized to ocean acidification is likely to entail a shortage of vital nutrients, potentially jeopardizing their health and survival in future oceans. PMID:27255977

  20. Reduced heterotrophy in the stony coral Galaxea fascicularis after life-long exposure to elevated carbon dioxide

    PubMed Central

    Smith, Joy N.; Strahl, Julia; Noonan, Sam H. C.; Schmidt, Gertraud M.; Richter, Claudio; Fabricius, Katharina E.

    2016-01-01

    Ocean acidification imposes many physiological, energetic, structural and ecological challenges to stony corals. While some corals may increase autotrophy under ocean acidification, another potential mechanism to alleviate some of the adverse effects on their physiology is to increase heterotrophy. We compared the feeding rates of Galaxea fascicularis colonies that have lived their entire lives under ocean acidification conditions at natural carbon dioxide (CO2) seeps with colonies living under present-day CO2 conditions. When provided with the same quantity and composition of zooplankton as food, corals acclimatized to high CO2 showed 2.8 to 4.8 times depressed rates of zooplankton feeding. Results were consistent over four experiments, from two expeditions and both in field and chamber measurements. Unless replenished by other sources, reduced zooplankton uptake in G. fascicularis acclimatized to ocean acidification is likely to entail a shortage of vital nutrients, potentially jeopardizing their health and survival in future oceans. PMID:27255977

  1. The Long-Term Spectroscopic Misadventures of AG Dra with a Nod toward V407 Cyg: Degenerates Behaving Badly

    NASA Technical Reports Server (NTRS)

    Shore, S.N.; Genovali, K.; Wahlgren, G. M.

    2013-01-01

    We present some results of an ongoing study of the long-term spectroscopic variations of AG Dra, a prototypical eruptive symbiotic system. We discuss the effects of the environment and orbital modulation in this system and some of the physical processes revealed by a comparison with the nova outburst of the symbiotic-like recurrent nova V407 Cyg 2010.

  2. Variations in the orbital periods of the Algol-type eclipsing binaries RZ Cas and Z Dra

    NASA Astrophysics Data System (ADS)

    Khaliullina, A. I.

    2016-05-01

    A detailed study of variations of the orbital periods of the Algol-type eclipsing binary systems RZ Cas and Z Dra is presented. The fairly complex variations of the periods of both systems can be represented as a superposition of a secular increase of the period, slow periodic fluctuations, and quasiperiodic oscillations with a small amplitude occurring on timescales of decades. The secular increase of the period can be explained by the steady mass transfer from the less massive to the more massive component with conservation of the total angular momentum. The mass-transfer rate is 5.7 × 10-9 M ⊙/yr for RZ Cas and 3.0×10-8 M ⊙/yr for Z Dra. To explain the long-period cyclic variations of the orbital periods of RZCas and Z Dra, it must be assumed that the eclipsing binaries move in long-period orbits. RZ Cas moves with a period of 133 yr around a third body withmass M 3 > 0.55 M ⊙, while Z Dra moves with a period of 60 yr around a third body with mass M 3 > 0.7 M ⊙. The residual fluctuations of the periods may be due to a superposition of variations due to magnetic cycles and non-stationary ejections of matter.

  3. Mitochondrial DNA variation within and among regional populations of longtail macaques (Macaca fascicularis) in relation to other species of the fascicularis group of macaques.

    PubMed

    Smith, David Glenn; McDonough, John W; George, Debra A

    2007-02-01

    An 835 base pair (bp) fragment of mitochondrial DNA (mtDNA) was sequenced to characterize genetic variation within and among 1,053 samples comprising five regional populations each of longtail macaques (Macaca fascicularis) and rhesus macaques (Macaca mulatta), and one sample each of Japanese (M. fuscata) and Taiwanese (M. cyclopis) macaques. The mtDNA haplotypes of longtail macaques clustered in two large highly structured clades (Fas1 and Fas2) of a neighbor-joining tree that were reciprocally monophyletic with respect to those representing rhesus macaques, Japanese macaques, and Taiwanese macaques. Both clades exhibited haplotypes of Indonesian and Malaysian longtail macaques widely dispersed throughout them; however, longtail macaques from Indochina, Philippines, and Mauritius each clustered in a separate well-defined clade together with one or a few Malaysian and/or Indonesian longtail macaques, suggesting origins on the Sunda shelf. Longtail macaques from Malaysia and Indonesia were far more genetically diverse, and those from Mauritius were far less diverse than any other population studied. Nucleotide diversity between mtDNA sequences of longtail macaques from different geographic regions is, in some cases, greater than that between Indian and Chinese rhesus macaques. Approximately equal amounts of genetic diversity are due to differences among animals in the same regional population, different regional populations, and different species. A greater proportion of genetic variance was explained by interspecies differences when Japanese and Taiwanese macaques were regarded as regional populations of rhesus macaques than when they were treated as separate species. Rhesus macaques from China were more closely related to both Taiwanese and Japanese macaques than to their own conspecifics from India. PMID:17177314

  4. Evaluating semantic relatedness and similarity measures with Standardized MedDRA Queries.

    PubMed

    Bill, Robert W; Liu, Ying; McInnes, Bridget T; Melton, Genevieve B; Pedersen, Ted; Pakhomov, Serguei

    2012-01-01

    A potential use of automated concept similarity and relatedness measures is to improve automatic detection of clinical text that relates to a condition indicative of an adverse drug reaction. This is also one of the purposes of the Medical Dictionary for Regulatory Activities (MedDRA) Standardized Queries (SMQ). An expert panel evaluates SMQs for their ability to detect a condition of interest and thus qualifies them as a reference standard for evaluating automated approaches. We compare similarity and relatedness measurement methods on rates of correctly identifying intra-category and inter-category concept pairs from SMQ data to create ROC curves of each method's sensitivity and specificity. Results indicate an information content measure, specifically the Resnik method, achieved the highest results as measured by area under the curve, but using two different measures as predictors, Resnik and Lin, obtained the highest score. Overall, using SMQ data resulted in a productive method of evaluating automated semantic relatedness and similarity scores. PMID:23304271

  5. Lunar-based Ultraviolet Telescope study of the well-known Algol-type binary TW Dra

    NASA Astrophysics Data System (ADS)

    Liao, Wen-Ping; Qian, Sheng-Bang; Zejda, Miloslav; Zhu, Li-Ying; Li, Lin-Jia

    2016-06-01

    By using the Lunar-based Ultraviolet Telescope (LUT) from 2014 December 2 to December 4, the first near-UV light curve of the well-known Algol-type binary TW Dra is reported, which is analyzed with the 2013 version of the W-D code. Our solutions confirmed that TW Dra is a semi-detached binary system where the secondary component fills its Roche lobe. The mass ratio and a high inclination are obtained (q = 0.47, i = 86.68°). Based on 589 available data spanning more than one century, the complex period changes are studied. Secular increase and three cyclical changes are found in the corresponding orbital period analysis. The secular increase changes reveal mass transfer from the secondary component to the primary one at a rate of 6.8 × 10‑7 M ⊙ yr‑1. One large cyclical change of 116.04 yr may be caused by disturbance of visual component ADS 9706B orbiting TW Dra (ADS 9706A), while the other two cyclical changes with shorter periods of 22.47 and 37.27 yr can be explained as the result of two circumbinary companions that are orbiting around TW Dra, where the two companions are in simple 3 : 5 orbit-rotation resonances. TW Dra itself is a basic binary in a possible sextuple system with the configuration (1 + 1) + (1 + 1) + (1 + 1), which further suggests that multiplicity may be a fairly common phenomenon in close binary systems.

  6. Engineering Macaca fascicularis cytochrome P450 2C20 to reduce animal testing for new drugs.

    PubMed

    Rua, Francesco; Sadeghi, Sheila J; Castrignanò, Silvia; Di Nardo, Giovanna; Gilardi, Gianfranco

    2012-12-01

    In order to develop in vitro methods as an alternative to P450 animal testing in the drug discovery process, two main requisites are necessary: 1) gathering of data on animal homologues of the human P450 enzymes, currently very limited, and 2) bypassing the requirement for both the P450 reductase and the expensive cofactor NADPH. In this work, P450 2C20 from Macaca fascicularis, homologue of the human P450 2C8 has been taken as a model system to develop such an alternative in vitro method by two different approaches. In the first approach called "molecular Lego", a soluble self-sufficient chimera was generated by fusing the P450 2C20 domain with the reductase domain of cytochrome P450 BM3 from Bacillus megaterium (P450 2C20/BMR). In the second approach, the need for the redox partner and also NADPH were both obviated by the direct immobilization of the P450 2C20 on glassy carbon and gold electrodes. Both systems were then compared to those obtained from the reconstituted P450 2C20 monooxygenase in presence of the human P450 reductase and NADPH using paclitaxel and amodiaquine, two typical drug substrates of the human P450 2C8. The K(M) values calculated for the 2C20 and 2C20/BMR in solution and for 2C20 immobilized on electrodes modified with gold nanoparticles were 1.9 ± 0.2, 5.9 ± 2.3, 3.0 ± 0.5 μM for paclitaxel and 1.2 ± 0.2, 1.6±0.2 and 1.4 ± 0.2 μM for amodiaquine, respectively. The data obtained not only show that the engineering of M. fascicularis did not affect its catalytic properties but also are consistent with K(M) values measured for the microsomal human P450 2C8 and therefore show the feasibility of developing alternative in vitro animal tests. PMID:22819650

  7. Sulfate secretion and chloride absorption are mediated by the anion exchanger DRA (Slc26a3) in the mouse cecum.

    PubMed

    Whittamore, Jonathan M; Freel, Robert W; Hatch, Marguerite

    2013-07-15

    Inorganic sulfate (SO₄²⁻) is essential for a multitude of physiological processes. The specific molecular pathway has been identified for uptake from the small intestine but is virtually unknown for the large bowel, although there is evidence for absorption involving Na⁺-independent anion exchange. A leading candidate is the apical chloride/bicarbonate (Cl⁻/HCO₃⁻) exchanger DRA (down-regulated in adenoma; Slc26a3), primarily linked to the Cl⁻ transporting defect in congenital chloride diarrhea. The present study set out to characterize transepithelial ³⁵SO₄²⁻ and ³⁶Cl⁻ fluxes across the isolated, short-circuited cecum from wild-type (WT) and knockout (KO) mice and subsequently to define the contribution of DRA. The cecum demonstrated simultaneous net SO₄²⁻ secretion (-8.39 ± 0.88 nmol·cm⁻²·h⁻¹) and Cl⁻ absorption (10.85 ± 1.41 μmol·cm⁻²·h⁻¹). In DRA-KO mice, SO₄²⁻ secretion was reversed to net absorption via a 60% reduction in serosal to mucosal SO₄²⁻ flux. Similarly, net Cl⁻ absorption was abolished and replaced by secretion, indicating that DRA represents a major pathway for transcellular SO₄²⁻ secretion and Cl⁻ absorption. Further experiments including the application of DIDS (500 μM), bumetanide (100 μM), and substitutions of extracellular Cl⁻ or HCO₃⁻/CO₂ helped to identify specific ion dependencies and driving forces and suggested that additional anion exchangers were operating at both apical and basolateral membranes supporting SO₄²⁻ transport. In conclusion, DRA contributes to SO₄²⁻ secretion via DIDS-sensitive HCO₃⁻/SO₄²⁻ exchange, in addition to being the principal DIDS-resistant Cl⁻/HCO₃⁻ exchanger. With DRA linked to the pathogenesis of other gastrointestinal diseases extending its functional characterization offers a more complete picture of its role in the intestine. PMID:23660504

  8. Rotational modulation and flares on RS CVn and BY Dra-type stars. I - Photometry and spot models for BY Dra, AU Mic, AR Lac, II Peg and V 711 Tau (= HR 1099)

    NASA Technical Reports Server (NTRS)

    Rodono, M.; Cutispoto, G.; Pazzani, V.; Catalano, S.; Byrne, P. B.

    1986-01-01

    Multicolor wide-band photometry of five active stars is presented. The observations were carried out at several places before, during and after the period of IUE observations for the purpose of determining the location, sizes, and evolution of photospheric spots at the time when chromospheric, transition region, and coronal activity data were obtained from UV and radio observations. II Peg, BY Dra, and AU Mic show fairly stable quasi-sinusoidal light curves, while AR Lac and V 711 Tau show double-peaked light curves. For V 711 Tau, a remarkable evolution of the spotted area extent and/or longitude distribution is found. Small, but definite color variations that are consistent with the cool spot hypothesis have also been detected for BY Dra, II Peg and V 711 Tau.

  9. Compete to Play: Trade-Off with Social Contact in Long-Tailed Macaques (Macaca fascicularis)

    PubMed Central

    Ballesta, Sébastien; Reymond, Gilles; Pozzobon, Mathieu; Duhamel, Jean-René

    2014-01-01

    Many animal species engage in various forms of solitary object play, but this activity seems to be of particular importance in primates. If playing objects constitute a valuable resource, and access to such objects is limited, a competitive context may arise. We inserted a unique toy within a mini-colony of long-tailed macaque (Macaca fascicularis) and compared their behaviors to sessions without playing object. An automatic color-based 3D video device was used to track the positions of each animal and the toy, and this data was categorized into 5 exclusive behaviors (resting, locomotion, foraging, social contact and object play). As expected, the delay to first access to the object reflected the hierarchy of the colony, indicating that a competition took place to own this unique resource of entertainment. In addition, we found that the amount of object play was not correlated with social or foraging behavior, suggesting independent motivational mechanisms. Conversely, object playing time was negatively correlated with idling time, thus indicating its relation to pastime activities. Interestingly, the amount of social contacts in the group was significantly reduced by the heightened competitive context, suggesting that competitors are more likely to be perceived as potential threat requiring caution, as shown in humans. Experimental manipulation of competitive contexts in primates reveals common mental processes involved in social judgment, and shows that access to valuable resources can be a sufficient cause for variations in group cohesion. PMID:25551755

  10. Telomere length of the colonial coral Galaxea fascicularis at different developmental stages

    NASA Astrophysics Data System (ADS)

    Tsuta, H.; Hidaka, M.

    2013-06-01

    The ability to estimate coral age using soft tissue would be useful for population biology or aging studies on corals. In this study, we investigated whether telomere length can be used to estimate coral age. We applied single telomere length analysis to a colonial coral, Galaxea fascicularis, and estimated telomere lengths of specific coral chromosomes at different developmental stages. If the telomere shortened at each cell division, the telomere length of the coral would be longest in sperm and shortest in adult colonies. However, the mean telomere length of sperm, planula larvae, and polyps was approximately 4 kb, with no significant differences among the developmental stages. The telomerase restriction fragment (TRF) analysis also showed no significant difference in the mean TRF length among the developmental stages. Our results suggested that telomere length is maintained during developmental stages and that estimating the age of colonial coral based on telomere length may not be possible. However, our findings can be used to examine avoidance of aging and rejuvenation during regeneration and asexual reproduction in colonial corals.

  11. Generation of haploid embryonic stem cells from Macaca fascicularis monkey parthenotes

    PubMed Central

    Yang, Hui; Liu, Zhen; Ma, Yu; Zhong, Cuiqing; Yin, Qi; Zhou, Chikai; Shi, Linyu; Cai, Yijun; Zhao, Hanzhi; Wang, Hui; Tang, Fan; Wang, Yan; Zhang, Chenchen; Liu, Xin-yuan; Lai, Dongmei; Jin, Ying; Sun, Qiang; Li, Jinsong

    2013-01-01

    Recent success in the derivation of haploid embryonic stem cells (haESCs) from mouse via parthenogenesis and androgenesis has enabled genetic screening in mammalian cells and generation of gene-modified animals. However, whether haESCs can be derived from primates remains unknown. Here, we report the derivation of haESCs from parthenogenetic blastocysts of Macaca fascicularis monkeys. These cells, termed as PG-haESCs, are pluripotent and can differentiate to cells of three embryonic germ layers in vitro or in vivo. Interestingly, the haploidy of one monkey PG-haESC line (MPH1) is more stable compared with that of the other one (MPH2), as shown by the existence of haploid cells for more than 140 days without fluorescence-activated cell sorting (FACS) enrichment of haploid cells. Importantly, transgenic monkey PG-haESC lines can be generated by lentivirus- and piggyBac transposon-mediated gene transfer. Moreover, genetic screening is feasible in monkey PG-haESCs. Our results demonstrate that PG-haESCs can be generated from monkeys, providing an ideal tool for genetic analyses in primates. PMID:23856644

  12. Infinium Monkeys: Infinium 450K Array for the Cynomolgus macaque (Macaca fascicularis)

    PubMed Central

    Ong, Mei-Lyn; Tan, Peck Yean; MacIsaac, Julia L; Mah, Sarah M; Buschdorf, Jan Paul; Cheong, Clara Y; Stunkel, Walter; Chan, Louiza; Gluckman, Peter D.; Chng, Keefe; Kobor, Michael S.; Meaney, Michael J; Holbrook, Joanna D

    2014-01-01

    The Infinium Human Methylation450 BeadChip Array (Infinium 450K) is a robust and cost-efficient survey of genome-wide DNA methylation patterns. Macaca fascicularis (Cynomolgus macaque) is an important disease model; however, its genome sequence is only recently published, and few tools exist to interrogate the molecular state of Cynomolgus macaque tissues. Although the Infinium 450K is a hybridization array designed to the human genome, the relative conservation between the macaque and human genomes makes its use in macaques feasible. Here, we used the Infinium 450K array to assay DNA methylation in 11 macaque muscle biopsies. We showed that probe hybridization efficiency was related to the degree of sequence identity between the human probes and the macaque genome sequence. Approximately 61% of the Human Infinium 450K probes could be reliably mapped to the Cynomolgus macaque genome and contain a CpG site of interest. We also compared the Infinium 450K data to reduced representation bisulfite sequencing data generated on the same samples and found a high level of concordance between the two independent methodologies, which can be further improved by filtering for probe sequence identity and mismatch location. We conclude that the Infinium 450K array can be used to measure the DNA methylome of Cynomolgus macaque tissues using the provided filters. We also provide a pipeline for validation of the array in other species using a simple BLAST-based sequence identify filter. PMID:24815017

  13. Measuring pad-pad pinch strength in a non-human primate: Macaca fascicularis.

    PubMed

    Banks, Jacob J; Lavender, Steven A; Buford, John A; Sommerich, Carolyn M

    2007-12-01

    The primary purpose of this study was to establish a methodology for determining and perhaps predicting (via regression analysis of anthropometric measures) Macaca fascicularis isometric pinch strength for a specific task. The larger purpose of this work was to properly scale a pinching task for the monkeys in order to study dose-response relationships in a non-human primate model for carpal tunnel syndrome. Three female and one male macaque (n=4) of varying size and age were trained to perform a left-handed pad-pad pinch. The task required 60 degrees of wrist flexion at a static pinching distance of 3 cm between the thumb and fingers. Subjects were trained for a period of 20-weeks. After that time, an analysis of performance gradients found that they had each reached a plateau in their force output. Pinch strength for the four animals ranged from 29.4 to 59.8 N. Regression analysis revealed that body mass (kg) and wrist circumference (cm) were both predictive of pinch strength, exhibiting adjusted R(2) values of 0.93 (p=0.024) and 0.96 (p=0.015), respectively. Thus, the results suggest that maximal pinch strength could be acceptably estimated in future subjects using either the wrist circumference or the body mass measures, as both were strong predictors of pad-pad pinch strength. PMID:17035044

  14. Cryopreservation of epididymal spermatozoa collected by needle biopsy from cynomolgus monkeys (Macaca fascicularis).

    PubMed

    Feradis, A H; Pawitri, D; Suatha, I K; Amin, M R; Yusuf, T L; Sajuthi, D; Budiarsa, I N; Hayes, E S

    2001-04-01

    We have examined the motility, morphology, and cryopreservation of epididymal spermatozoa collected by needle biopsy from cynomolgus monkeys (Macaca fascicularis). At collection, epididymal sperm (23 x 10(6) +/- 4 x 10(6) sperm/sample; 611 x 10(6) +/- 116 x 10(6) sperm/ ml; n = 18) were alive (79 +/- 2%), motile (67 +/- 2%), and exhibited intact membranes (65 +/- 2%). Sperm maintained at room temperature in handling medium exhibited decreased motility over time, but head-to-head agglutination was limited. Tris egg-yolk extender containing 6% glycerol and dimethylsulfoxide (DMSO) did not significantly affect functional morphology, whereas extender containing propanediol significantly reduced motility, survival, and membrane integrity. Cryostorage reduced all measures of functional morphology independent of cryoprotectant. Post-thaw motility was superior for glycerol and DMSO compared to propanediol. Variation in glycerol concentration (4, 6, and 8%) produced equivocal effects on sperm functional morphology post-thaw. Needle biopsy may be a useful technique for laboratory and field-based collection of spermatozoa from nonhuman primates. PMID:11491402

  15. Vasopressin and oxytocin systems in the brain and upper spinal cord of Macaca fascicularis.

    PubMed

    Caffé, A R; Van Ryen, P C; Van der Woude, T P; Van Leeuwen, F W

    1989-09-15

    This paper describes the vasopressin (VP) and oxytocin (OXT) immunoreactive structures in the brain and upper spinal cord of the adult male and female Macaca fascicularis. Immunocytochemistry following intraventricular application of colchicine displayed VP neurons in the diagonal band of Broca (DBB), bed nucleus of the stria terminalis (BST), medial amygdaloid nucleus, dorsomedial hypothalamic nucleus, area of the locus coeruleus (LC), solitary tract nuclei (NTS), and the dorsal horn of the cervical spinal cord in addition to those known to exist in the paraventricular, supraoptic, and suprachiasmatic hypothalamic nuclei. Furthermore, a dense accumulation of VP fibers was observed in areas such as the DBB, medial septum, BST, amygdala, hippocampus, ventral tegmental area, periaquaductal gray, dorsal and ventral raphe, area of Forel, LC region, parabrachial nuclei, and NTS. The lateral septum and lateral habenula displayed no and very few VP fibers, respectively. No extrahypothalamic OXT neurons were found in the brain of this macaque monkey. Dense concentrations of OXT fibers were demonstrated in the amygdala, NTS, and marginal layer of the cervical spinal cord. No sexual dimorphism was found in this primate VP or OXT system. The results show a distribution of the central VP and OXT systems in this primate which is quite different from that in the rat. However, in various aspects it agrees with current data on the VP and OXT systems of the human brain. The present results suggest, therefore, that this monkey might serve as a better model for the human VP system than the rat. PMID:2778107

  16. Compete to play: trade-off with social contact in long-tailed macaques (Macaca fascicularis).

    PubMed

    Ballesta, Sébastien; Reymond, Gilles; Pozzobon, Mathieu; Duhamel, Jean-René

    2014-01-01

    Many animal species engage in various forms of solitary object play, but this activity seems to be of particular importance in primates. If playing objects constitute a valuable resource, and access to such objects is limited, a competitive context may arise. We inserted a unique toy within a mini-colony of long-tailed macaque (Macaca fascicularis) and compared their behaviors to sessions without playing object. An automatic color-based 3D video device was used to track the positions of each animal and the toy, and this data was categorized into 5 exclusive behaviors (resting, locomotion, foraging, social contact and object play). As expected, the delay to first access to the object reflected the hierarchy of the colony, indicating that a competition took place to own this unique resource of entertainment. In addition, we found that the amount of object play was not correlated with social or foraging behavior, suggesting independent motivational mechanisms. Conversely, object playing time was negatively correlated with idling time, thus indicating its relation to pastime activities. Interestingly, the amount of social contacts in the group was significantly reduced by the heightened competitive context, suggesting that competitors are more likely to be perceived as potential threat requiring caution, as shown in humans. Experimental manipulation of competitive contexts in primates reveals common mental processes involved in social judgment, and shows that access to valuable resources can be a sufficient cause for variations in group cohesion. PMID:25551755

  17. Gene expression profiling in the Cynomolgus macaque Macaca fascicularis shows variation within the normal birth range

    PubMed Central

    2011-01-01

    Background Although an adverse early-life environment has been linked to an increased risk of developing the metabolic syndrome, the molecular mechanisms underlying altered disease susceptibility as well as their relevance to humans are largely unknown. Importantly, emerging evidence suggests that these effects operate within the normal range of birth weights and involve mechanisms of developmental palsticity rather than pathology. Method To explore this further, we utilised a non-human primate model Macaca fascicularis (Cynomolgus macaque) which shares with humans the same progressive history of the metabolic syndrome. Using microarray we compared tissues from neonates in the average birth weight (50-75th centile) to those of lower birth weight (5-25th centile) and studied the effect of different growth trajectories within the normal range on gene expression levels in the umbilical cord, neonatal liver and skeletal muscle. Results We identified 1973 genes which were differentially expressed in the three tissue types between average and low birth weight animals (P < 0.05). Gene ontology analysis identified that these genes were involved in metabolic processes including cellular lipid metabolism, cellular biosynthesis, cellular macromolecule synthesis, cellular nitrogen metabolism, cellular carbohydrate metabolism, cellular catabolism, nucleotide and nucleic acid metabolism, regulation of molecular functions, biological adhesion and development. Conclusion These differences in gene expression levels between animals in the upper and lower percentiles of the normal birth weight range may point towards early life metabolic adaptations that in later life result in differences in disease risk. PMID:21999700

  18. Photometric analysis of overcontact binaries AK Her, HI Dra, V1128 Tau, and V2612 Oph

    SciTech Connect

    Çalışkan, Ş.; Özavcı, İ.; Baştürk, Ö.; Şenavcı, H. V.; Kılıçoğlu, T.; Yılmaz, M.; Selam, S. O.; Latković, O.; Djurašević, G.; Cséki, A. E-mail: ozavci@science.ankara.edu.tr E-mail: hvsenavci@ankara.edu.tr E-mail: mesutyilmaz@ankara.edu.tr E-mail: olivia@aob.rs E-mail: attila@aob.rs

    2014-12-01

    We analyze new, high quality multicolor light curves of four overcontact binaries: AK Her, HI Dra, V1128 Tau, and V2612 Oph, and determine their orbital and physical parameters using the modeling program of G. Djurasevic and recently published results of radial velocity studies. The achieved precision in absolute masses is between 10% and 20%, and the precision in absolute radii is between 5% and 10%. All four systems are W UMa-type binaries with bright or dark spots indicative of mass and energy transfer or surface activity. We estimate the distances and the ages of the systems using the luminosities computed through our analysis, and perform an O – C study for V1128 Tau, which reveals a complex period variation that can be interpreted in terms of mass loss/exchange and either the presence of the third body, or the magnetic activity on one of the components. We conclude that further observations of these systems are needed to deepen our understanding of their nature and variability.

  19. Inhibition of progesterone secretion during the luteal phase by two luteinizing hormone-releasing hormone agonists in Macaca fascicularis.

    PubMed

    Raynaud, J P; Mary, I; Moguilewsky, M; Mouren, M; Labrie, F

    1980-12-01

    The administration of 200 microgram of the potent luteinizing hormone-releasing hormone (LHRH) agonist [D-Leu6,des-Gly-NH2(10)]LHRH ethylamide on day 6 following the plasma estradiol peak to 11 female monkeys (Macaca fascicularis) during two consecutive menstrual cycles decreased plasma progesterone levels by 40.0% +/- 3.9% as compared with previous control cycles. The plasma estradiol profile and the cycle length were not affected significantly by the treatment. Similar results were obtained with 25 microgram of [D-Ser(TBU)6,des-Gly-NH2(10)]LHRH ethylamide administered to one monkey at the same period of the cycle, such treatment leading to a 41% inhibition of circulating progesterone levels. Although plasma progesterone levels were still reduced in the two post-treatment cycles in monkeys treated with the high dose (200 microgram) of [D-Leu6,des-Gly-NH2(10)]LHRH ethylamide, the recovery cycle was normal after the administration of a lower dose (25 microgram) of [D-Ser(TBU)6, des-Gly-NH2(10)] LHRH ethylamide. The M. fascicularis monkey thus appears as a valid model with which to study the inhibitory effects of LHRH agonists on luteal function. PMID:6778718

  20. Stimulus-Food Pairings Produce Stimulus-Directed Touch Screen Responding in Cynomolgus Monkeys ("Macaca Fascicularis") with or without a Positive Response Contingency

    ERIC Educational Resources Information Center

    Bullock, Christopher E.; Myers, Todd M.

    2009-01-01

    Acquisition and maintenance of touch-screen responding was examined in naive cynomolgus monkeys ("Macaca fascicularis") under automaintenance and classical conditioning arrangements. In the first condition of Experiment 1, we compared acquisition of screen touching to a randomly positioned stimulus (a gray square) that was either stationary or…

  1. A structural study of the interaction between the Dr haemagglutinin DraE and derivatives of chloramphenicol

    SciTech Connect

    Pettigrew, David M.; Roversi, Pietro; Davies, Stephen G.; Russell, Angela J.; Lea, Susan M.

    2009-06-01

    The structures of two Dr adhesin (DraE) complexes with chloramphenicol derivatives, namely chloramphenicol succinate and bromamphenicol, have been solved. The structures reveal important functional groups for small-molecule binding and imply possible modifications to the molecule that would permit a more wide-ranging interaction without the toxic side effects associated with chloramphenicol. Dr adhesins are expressed on the surface of uropathogenic and diffusely adherent strains of Escherichia coli. The major adhesin subunit (DraE/AfaE) of these organelles mediates attachment of the bacterium to the surface of the host cell and possibly intracellular invasion through its recognition of the complement regulator decay-accelerating factor (DAF) and/or members of the carcinoembryonic antigen (CEA) family. The adhesin subunit of the Dr haemagglutinin, a Dr-family member, additionally binds type IV collagen and is inhibited in all its receptor interactions by the antibiotic chloramphenicol (CLM). In this study, previous structural work is built upon by reporting the X-ray structures of DraE bound to two chloramphenicol derivatives: chloramphenicol succinate (CLS) and bromamphenicol (BRM). The CLS structure demonstrates that acylation of the 3-hydroxyl group of CLM with succinyl does not significantly perturb the mode of binding, while the BRM structure implies that the binding pocket is able to accommodate bulkier substituents on the N-acyl group. It is concluded that modifications of the 3@@hydroxyl group would generate a potent Dr haemagglutinin inhibitor that would not cause the toxic side effects that are associated with the normal bacteriostatic activity of CLM.

  2. Immunization of Macaca fascicularis (Macaca irus) monkeys with Streptococcus mutans: specificity of antibody responses in saliva.

    PubMed

    Emmings, F G; Evans, R T; Genco, R J

    1976-04-01

    M fascicularis monkeys were immunized subcutaneously in the vicinity of the major salivary glands and by retrograde infusion into the parotid duct, with a vaccine containing Formalin-killed S mutans strain 6715 cells and culture-fluid antigens. Indirect immunofluorescent staining was used to titrate and classify antibodies. Subcutaneous immunization induced only a serum response, whereas intraductal infusion stimulated both an IgA antibody response in the parotid fluid and a serum response. Immunized and nonimmunized control groups were orally infected with S mutans strain 6715. The establishment in dental plaque was quantitated by recovery of the infecting organism on selective media and by immunofluorescent staining of plaque smears taken from individual tooth surfaces. The establishment of S mutans strain 6715 was noticeably inhibited in immune monkeys. Immunofluorescent assays for antibody also showed that serum and parotid fluid containing serum IgA antibodies cross reacted with other d serotype and a serotype strains but not representative b and c strains. Immune and control groups were then orally infected with S mutans strain GS-5, a c serotype strain, and no inhibition in establishment was detected of the non-cross-reacting type c organism in the immune group. A latter series of booster immunizations via the intraductal route resulted in a significant decrease in parotid fluid flow. Histological investigations showed inflammatory cell infiltration and replacement of epithelium by connective tissue in the glands from immunized monkeys. A separate group of monkeys, younger than the first, was immunized with the same vaccine via the duct only. In this group, immunizations were given at shorter intervals, but the immunization response was similar to that observed in the first group. The investigations reviewed here and new experiments reported show that immunization of monkeys with S mutan strain 6715 via the parotid duct elicited a reproducible IgA antibody

  3. Toxicological consequences of feeding PCB congeners to infant rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) monkeys.

    PubMed

    Arnold, D L; Bryce, F; Mes, J; Tryphonas, H; Hayward, S; Malcolm, S

    1999-01-01

    In a study designed to minimize interspecies extrapolation of toxicological data, nine rhesus (Macaca mulatta) and 15 cynomolgus (M. fascicularis) day-old infant monkeys were separated from their dams following parturition and hand-reared using a liquid non-human primate formulation. The infants were randomly divided into a control and a treated group which received a mixture of polychlorinated biphenyl (PCB) congeners analogous to those found in breast milk from Canadian women. The concentration of congeners in the dosing media resulted in each infant receiving a total of 7.5 microg PCB congeners/kg body weight/day. The congeners were added either to the liquid formulation or to corn oil and administered to the back of the monkey's mouth for 20 weeks. Monthly blood and adipose specimens were obtained during the dosing period and then periodically until the monkey was necropsied or taken off test (minimum of 66 weeks on test) for congener analysis. Parameters such as body weight, formula consumption, tooth eruption, somatic measurements, haematology and serum biochemistry were monitored throughout the study. In addition, a qualitative evaluation of the absorption and depletion of the various congeners was undertaken as was an immunological evaluation. For the monitored parameters, very few differences were found to be statistically significant. For the immunological parameters, the only statistically differences found were a reduction over time for immunoglobulins M and G antibodies to sheep red blood cells (cyno, P = 0.025; rhesus, P = 0.002) and a treatment-related reduction in the levels of the HLA-DR cell surface marker (mean percent, P = 0.016; absolute levels, P = 0.027). There were some qualitative differences regarding absorption and depletion rates for the various congeners, but it could not be definitely ascertained whether these differences were due to species differences or dosing mode. However, statistically significant differences were found for

  4. Pharmacokinetics of 2 Formulations of Buprenorphine in Macaques (Macaca mulatta and Macaca fascicularis)

    PubMed Central

    Nunamaker, Elizabeth A; Halliday, Lisa C; Moody, David E; Fang, Wenfang B; Lindeblad, Matthew; Fortman, Jeffrey D

    2013-01-01

    Buprenorphine is the cornerstone of pain management in nonhuman primates, but the pharmacokinetics of this widely used drug are unknown. The purpose of this study was to evaluate the pharmacokinetic profiles of buprenorphine (0.01 and 0.03 mg/kg IM) and sustained-release buprenorphine (0.2 mg/kg SC) in 2 macaque species (M. mulatta and M. fascicularis) by using mass spectrometry. The pharmacokinetics did not differ significantly between species, and buprenorphine was dose-proportional at the tested doses. The low and high doses of buprenorphine had elimination half-lives of 2.6 ± 0.7 and 5.3 ± 2.0 h, respectively, but the low-dose data were constrained by the sensitivity of the analytical method. Sustained-release buprenorphine had an elimination half-life of 42.6 ± 26.2 h. The AUC0-Tlast of buprenorphine were 9.1 ± 4.3 and 39.0 ± 25.1 ng×h/mL for the low and high doses, respectively, and sustained-release buprenorphine had an AUC0-Tlast of 177 ± 74 ng×h/mL. Assuming a hypothesized therapeutic buprenorphine plasma concentration threshold of 0.1 ng/mL in macaques, these results suggest that buprenorphine doses of 0.01 mg/kg IM should be administered every 6 to 8 h, whereas doses of 0.03 mg/kg IM can be administered every 12 h. These results further demonstrate that a single 0.2-mg/kg SC injection of sustained-release buprenorphine maintains plasma concentrations above 0.1 ng/mL for 5 d in macaques. These findings support a new dosing strategy using sustained-release buprenorphine to improve pain management, decrease animal stress, improve animal welfare, and simplify the postoperative management of nonhuman primates in laboratory animal and zoological settings. PMID:23562033

  5. The photocurrent, noise and spectral sensitivity of rods of the monkey Macaca fascicularis.

    PubMed Central

    Baylor, D A; Nunn, B J; Schnapf, J L

    1984-01-01

    Visual transduction in rods of the cynomolgus monkey, Macaca fascicularis, was studied by recording membrane current from single outer segments projecting from small pieces of retina. Light flashes evoked transient outward-going photocurrents with saturating amplitudes of up to 34 pA. A flash causing twenty to fifty photoisomerizations gave a response of half the saturating amplitude. The response-stimulus relation was of the form 1-e-x where x is flash strength. The response to a dim flash usually had a time to peak of 150-250 ms and resembled the impulse response of a series of six low-pass filters. From the average spectral sensitivity of ten rods the rhodopsin was estimated to have a peak absorption near 491 nm. The spectral sensitivity of the rods was in good agreement with the average human scotopic visibility curve determined by Crawford (1949), when the human curve was corrected for lens absorption and self-screening of rhodopsin. Fluctuations in the photocurrent evoked by dim lights were consistent with a quantal event about 0.7 pA in peak amplitude. A steady light causing about 100 photoisomerizations s-1 reduced the flash sensitivity to half the dark-adapted value. At higher background levels the rod rapidly saturated. These results support the idea that dim background light desensitizes human scotopic vision by a mechanism central to the rod outer segments while scotopic saturation may occur within the outer segments. Recovery of the photocurrent after bright flashes was marked by quantized step-like events. The events had the properties expected if bleached rhodopsin in the disks occasionally caused an abrupt blockage of the dark current over about one-twentieth of the length of the outer segment. It is suggested that superposition of these events after bleaching may contribute to the threshold elevation measured psychophysically. The current in darkness showed random fluctuations which disappeared in bright light. The continuous component of the noise

  6. Theta(1) and gamma Tauri: Understanding the coronal structure of Hyades giants. EUV spectroscopy of BY Dra systems

    NASA Technical Reports Server (NTRS)

    Stern, Robert A.

    1995-01-01

    These programs involve: (1) analysis and interpretation of EUVE spectrometer observations of the active giant beta Cet in comparison to the Hyades giant theta(1) Tau, and (2) analysis and interpretation of EUVE spectrometer observations of the BY Dra systems FK Aqr, DH Leo, and BH Lyn. EUVE carried out observations of beta Cet, but has yet to perform an observation of theta(1) Tau. In beta Cet, a number of Fe lines from high ionization species were observed, up to Fe XXIV. The spectrum overall resembles that seen in the active binary Capella (alpha Aur). All three BY Dra systems were observed by EUVE, and show evidence of high temperature (approximately 10(exp 7) K) plasma; FK Aqr and DH Leo show significant variability in their Deep Survey lightcurves. In FK Aqr, spectral differences between its 'quiescent' and 'active' states suggest possible differences in the plasma density. In DH Leo, the Deep Survey lightcurve, taken over nearly 8 days, shows a distinct period of approximately 1.05 days, similar to the photometric period. The emission measure distributions of all three systems are rather similar in shape, and can be well-represented by a power law with slope approximately 1.5 from 6.2-7.0 in log T.

  7. Physiological properties of retinal Muller glial cells from the cynomolgus monkey, Macaca fascicularis--a comparison to human Muller cells.

    PubMed

    Pannicke, Thomas; Biedermann, Bernd; Uckermann, Ortrud; Weick, Michael; Bringmann, Andreas; Wolf, Sebastian; Wiedemann, Peter; Habermann, Gunnar; Buse, Eberhard; Reichenbach, Andreas

    2005-06-01

    Retinae from rabbits and laboratory rodents are often used as 'models' of the human retina, although there are anatomical differences. To test whether monkey eyes provide a better model, a physiological study of Muller glial cells was performed comparing isolated cells and retinal wholemounts from the cynomolgus monkey, Macaca fascicularis and from man. The membrane conductance of Muller cells from both species was dominated by inward and outward K(+) currents. Cells displayed glutamate uptake currents and responded to nucleotides by intracellular Ca(2+) increases. However, there were also species differences, such as a lack of GABA(A) receptors and of Ca(2+)-dependent K(+) currents in monkey cells. Thus, the use of Muller cells from cynomolgus monkeys may be advantageous for investigating a few specific properties; in general, monkey cells are no more similar to human cells than those from standard laboratory animals. PMID:15797768

  8. Genetic differentiation and connectivity of morphological types of the broadcast-spawning coral Galaxea fascicularis in the Nansei Islands, Japan.

    PubMed

    Nakajima, Yuichi; Zayasu, Yuna; Shinzato, Chuya; Satoh, Noriyuki; Mitarai, Satoshi

    2016-03-01

    Population connectivity resulting from larval dispersal is essential for the maintenance or recovery of populations in marine ecosystems, including coral reefs. Studies of species diversity and genetic connectivity within species are essential for the conservation of corals and coral reef ecosystems. We analyzed mitochondrial DNA sequence types and microsatellite genotypes of the broadcast-spawning coral, Galaxea fascicularis, from four regions in the subtropical Nansei Islands in the northwestern Pacific Ocean. Two types (soft and hard types) of nematocyst morphology are known in G. fascicularis and are significantly correlated with the length of a mitochondrial DNA noncoding sequence (soft type: mt-L; hard type: mt-S type). Using microsatellites, significant genetic differentiation was detected between the mitochondrial DNA sequence types in all regions. We also found a third genetic cluster (mt-L+), and this unexpected type may be a cryptic species of Galaxea. High clonal diversity was detected in both mt-L and mt-S types. Significant genetic differentiation, which was found among regions within a given type (F ST = 0.009-0.024, all Ps ≤ 0.005 in mt-L; 0.009-0.032, all Ps ≤ 0.01 in mt-S), may result from the shorter larval development than in other broadcast-spawning corals, such as the genus Acropora. Nevertheless, intraspecific genetic diversity and connectivity have been maintained, and with both sexual and asexual reproduction, this species appears to have a potential for the recovery of populations after disturbance. PMID:27087925

  9. Test Review: Beaver, J. M., & Carter, M. A. (2006). "The Developmental Reading Assessment--Second Edition" (DRA2). Upper Saddle River, NJ--Pearson

    ERIC Educational Resources Information Center

    McCarty, Allison M.; Christ, Theodore J.

    2010-01-01

    This article reviews the "Developmental Reading Assessment--Second Edition" (DRA2), a teacher-administered assessment that identifies students' instructional level, along with their strengths and weaknesses in reading. Once teachers calculate and interpret scores, the data can purportedly be used to inform, and possibly individualize, instruction.…

  10. Introducing SummerTime: A package for high-precision computation of sums appearing in DRA1 method

    NASA Astrophysics Data System (ADS)

    Lee, Roman N.; Mingulov, Kirill T.

    2016-06-01

    We present the Mathematica  package SummerTime  for arbitrary-precision computation of sums appearing in the results of DRA method (Lee, 2010). So far these results include the following families of the integrals: 3-loop onshell massless vertices, 3-loop onshell mass operator type integrals, 4-loop QED-type tadpoles, 4-loop massless propagators (Lee et al., 2010; Lee and Smirnov, 2011; Lee et al., 2011, 2012). The package can be used for high-precision numerical computation of the expansion of the integrals from the above families around arbitrary space-time dimension. In addition, this package contains convenient tools for the calculation of multiple zeta values, harmonic polylogarithms and other transcendental numbers expressed in terms of nested sums with factorized summand.

  11. HLA-DRA is associated with Parkinson's disease in Iranian population.

    PubMed

    Jamshidi, J; Movafagh, A; Emamalizadeh, B; Zare Bidoki, A; Manafi, A; Ghasemi Firouzabadi, S; Shahidi, G-A; Kazeminasab, S; Petramfar, P; Fazeli, A; Motallebi, M; Mortazavi-Tabatabaei, S A; Kowsari, A; Jafarian, Z; Darvish, H

    2014-12-01

    The rs3129882, a noncoding variant in HLA-DR, was found to be associated with Parkinson's disease (PD) using several genome-wide association studies. The aim of this replication study was to explore the relationship between this variant and PD in Iranian population. Genomic DNA was extracted from peripheral blood samples, and the rs3129882 SNP was genotyped using a PCR-RFLP method in 520 PD patients and 520 healthy Iranian controls. Significant differences were found in allele frequencies between patients and controls (χ(2) = 4.64, P = 0.031). Under additive and dominant models, the association of the SNP with PD risk is significant, where the A allele was observed to be protective. The results suggest that rs3129882 polymorphism may be a risk factor for PD in Iranian. This is the first study reporting such an association in this population. More replication studies are needed to confirm this data. PMID:25319953

  12. Association between CYP2E1 polymorphisms and risk of gastric cancer: An updated meta-analysis of 32 case-control studies

    PubMed Central

    ZHANG, MING-XING; LIU, KAI; WANG, FU-GANG; WEN, XIAO-WEN; SONG, XI-LIN

    2016-01-01

    Previous studies suggested that RsaI/PstI and DraI polymorphisms on cytochrome P450 2E1 (CYP2E1) may be associated with susceptibility to gastric cancer (GC). However, this association remains ambiguous. A meta-analysis of previously published studies was performed in an attempt to elucidate this association. The odds ratio and 95% confidence interval were used to assess the strength of the association. In the overall analyses of RsaI/PstI and DraI, no association was identified. In the subgroup analyses, RsaI/PstI was identified to increase the risk of GC in the smoking population. In addition, in the previous studies of interactions with other genes, RsaI/PstI was revealed to be associated with increased GC risks when glutathione S-transferase-µ-1 or glutathione S-transferase θ-1 was null or DraI was homozygous wild-type. However, these stratified analyses were lacking credibility due to the limitation of correlational study numbers. In conclusion, CYP2E1 polymorphisms revealed no association with the risk of GC. PMID:27284439

  13. An SNP marker at the STAT6 locus can identify the hybrids between rhesus (Macaca mulatta) and long-tailed macaques (M. fascicularis) in Thailand: a rapid and simple screening method and its application.

    PubMed

    Jadejaroen, Janya; Kawamoto, Yoshi; Hamada, Yuzuru; Malaivijitnond, Suchinda

    2016-01-01

    A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay was developed to genetically discriminate rhesus (Macaca mulatta) macaques from long-tailed (M. fascicularis) macaques. The 745 bp PCR amplicon of the STAT6 locus that spans a potentially species-diagnostic single nucleotide polymorphism (SNP) marker was digested with ApaI and gel electrophoresed to give (1) two (234 and 511 bp), (2) one (745 bp) and (3) three (234, 511 and 745 bp) band patterns that correspond to the genotypes G/G (long-tailed macaque specific homozygote), A/A (rhesus macaque specific homozygote) and A/G (hybrid specific heterozygote), respectively. The diagnostic robustness and efficiency of this PCR-RFLP assay was tested on wild rhesus and long-tailed macaques inhabiting Thailand and a known hybrid population. The Indochinese and Sundaic long-tailed macaque samples (n = 18) all showed a homozygous G/G pattern, while the Indochinese rhesus macaques (n = 10) all showed a homozygous A/A pattern. The rhesus/long-tailed hybrid population at Khao Khieow Open Zoo, which resulted from an introduced group of rhesus macaques that hybridized with the indigenous long-tailed macaques about 20 years ago, revealed 47% (56/118 samples analyzed) with the heterogenous A/G genotype. In addition, the frequency of the rhesus-specific allele A significantly decreased in the hybrid population during 2006-2014, where a strong association between the STAT6 genotype and the morphology of the individuals was detected. In conclusion, a robust PCR-RFLP assay allows a simple, effective and inexpensive approach, in particular for field studies, to assess hybrid individuals between rhesus and long-tailed macaques. Although this assay cannot conclusively identify all the hybrids over two or more generations, it at least can allow the evaluation of the process of hybridization, and so it is applicable to the assessment of the status of natural or anthropogenic hybridization between the two

  14. Polymorphic light eruption

    MedlinePlus

    ... outdoors. Wear a sun hat. Wear sunglasses with UV protection. Use a lip balm with sunscreen. Alternative Names Polymorphic light eruption; Photodermatosis; PMLE Images Polymorphic light eruption on ...

  15. Pharmacokinetics of Cefovecin in Cynomolgus Macaques (Macaca fascicularis), Olive Baboons (Papio anubis), and Rhesus Macaques (Macaca mulatto)

    SciTech Connect

    Raabe, Brigitte M.; Lovaglio, Jamie A.; Grover, GScott; Brown, Scott A.; Boucher, Joseph F.; Yuan, Yang; Civil, Jacqueline R.; Gillhouse, Kimberly A.; Stubbs, Makeida N.; Hoggatt, Amber F.; Halliday, Lisa C.; Fortman, Jeffrey D.

    2011-05-01

    Cefovecin sodium is a long-acting, third-generation, cephalosporin antibiotic approved for the treatment of skin infections in dogs and cats. The pharmacokinetic properties of cefovecin were evaluated in cynomolgus macaques (Macaca fascicularis), olive baboons (Papio anubis), and rhesus macaques (Macaca mulatto) by using a single-dose (8 mg/kg SC) dosing regimen. Plasma cefovecin concentrations were determined by using ultra-performance liquid chromatography with tandem mass spectrometry, and a noncompartmental model was used to determine pharmacokinetic parameters. The half-life of cefovecin was 4.95 {+-} 1.47 h in cynomolgus macaques, 9.17 {+-} 1.84 h in olive baboons, and 8.40 {+-} 2.53 h in rhesus macaques. These values are considerably lower than the half-lives previously published for dogs (133 h) and cats (166 h). The extended half-life of cefovecin in dogs and cats is speculated to be due to active reabsorption of drug in the kidney tubules because plasma clearance is well below the normal glomerular filtration rate. In nonhuman primates, renal clearance rates approximated plasma clearance rates, suggesting that active renal reabsorption of cefovecin does not occur in these species. The pharmacokinetic properties of cefovecin in nonhuman primates are vastly different from the pharmacokinetic properties in dogs and cats, precluding its use as a long-acting antibiotic in nonhuman primates. This study highlights the importance of performing pharmacokinetic studies prior to extralabel drug usage.

  16. Attenuation of Neurovirulence, Biodistribution, and Shedding of a Poliovirus:Rhinovirus Chimera after Intrathalamic Inoculation in Macaca fascicularis

    PubMed Central

    Dobrikova, Elena Y.; Goetz, Christian; Walters, Robert W.; Lawson, Sarah K.; Peggins, James O.; Muszynski, Karen; Ruppel, Sheryl; Poole, Karyol; Giardina, Steven L.; Vela, Eric M.; Estep, James E.

    2012-01-01

    A dependence of poliovirus on an unorthodox translation initiation mode can be targeted selectively to drive viral protein synthesis and cytotoxicity in malignant cells. Transformed cells are naturally susceptible to poliovirus, due to widespread ectopic upregulation of the poliovirus receptor, Necl-5, in ectodermal/neuroectodermal cancers. Viral tumor cell killing and the host immunologic response it engenders produce potent, lasting antineoplastic effects in animal tumor models. Clinical application of this principle depends on unequivocal demonstration of safety in primate models for paralytic poliomyelitis. We conducted extensive dose-range-finding, toxicity, biodistribution, shedding, and neutralizing antibody studies of the prototype oncolytic poliovirus recombinant, PVS-RIPO, after intrathalamic inoculation in Macaca fascicularis. These studies suggest that intracerebral PVS-RIPO inoculation does not lead to viral propagation in the central nervous system (CNS), does not cause histopathological CNS lesions or neurological symptoms that can be attributed to the virus, is not associated with extraneural virus dissemination or replication and does not induce shedding of virus with stool. Intrathalamic PVS-RIPO inoculation induced neutralizing antibody responses against poliovirus serotype 1 in all animals studied. PMID:22171271

  17. Sex-dependent expression of mRNA encoding a major egg protein in the gonochoric coral Galaxea fascicularis

    NASA Astrophysics Data System (ADS)

    Hayakawa, H.; Nakano, Y.; Andoh, T.; Watanabe, T.

    2005-11-01

    A cDNA encoding a major egg protein was cloned in Galaxea fascicularis, a hermatypic coral with a gonochoric breeding system, and gene expression at the transcriptional level was compared between female and functional male colonies. In an electrophoretic analysis, four soluble proteins were present in high abundance in the female egg, but not in the pseudo-eggs of functional males. Partial amino acid sequences of one of the major proteins named GfEP-1 (88 kDa) were determined, and a cDNA fragment of about 2 kb containing a partial GfEP-1 sequence was isolated. The deduced amino acid sequence exhibited sequence similarities to vertebrate and invertebrate vitellogenins. GfEP-1 transcripts were detected in both sexes 0 1 month before spawning. However, the mRNA levels were significantly higher in females than in functional males. The expression of GfEP-1 may be utilized in sexing and also monitoring effects of environmental and anthropogenic factors on vitellogenesis and sex determination.

  18. Visible lesion laser thresholds in Cynomolgus (Macaca fascicularis) retina with a 1064 nm 12-ns pulsed laser

    NASA Astrophysics Data System (ADS)

    Oliver, Jeffrey W.; Stolarski, David J.; Noojin, Gary D.; Hodnett, Harvey M.; Imholte, Michelle L.; Rockwell, Benjamin A.; Kumru, Semih S.

    2007-02-01

    A series of experiments in a new animal model for retinal damage, cynomolgus monkeys (Macaca fascicularis), have been conducted to determine the damage threshold for 12.5-nanosecond laser exposures at 1064 nm. These results provide a direct comparison to threshold values obtained in rhesus monkey (Macaca mulatta), which is the model historically used in establishing retinal maximum permissible exposure (MPE) limits. In this study, the irradiance level of a collimated Gaussian laser beam of 2.5 mm diameter at the cornea was randomly varied to produce a rectangular grid of exposures on the retina. Exposures sites were fundoscopically evaluated at post-irradiance intervals of 1 hour and 24 hours. Probit analysis was performed on dose-response data to obtain probability of response curves. The 50% probability of damage (ED50) values for 1 and 24 hours post-exposure are 28.5(22.7-38.4) μJ and 17.0(12.9-21.8) μJ, respectively. These values compare favorably to data obtained with the rhesus model, 28.7(22.3-39.3) μJ and 19.1(13.6-24.4) μJ, suggesting that the cynomolgus monkey may be a suitable replacement for rhesus monkey in photoacoustic minimum visible lesion threshold studies.

  19. Thoracic Radiography as a Refinement Methodology for the Study of H1N1 Influenza in Cynomologus Macaques (Macaca fascicularis)

    PubMed Central

    Brining, Douglas L; Mattoon, John S; Kercher, Lisa; LaCasse, Rachael A; Safronetz, David; Feldmann, Heinz; Parnell, Michael J

    2010-01-01

    Recent advances in the technology associated with digital radiography have created new opportunities for biomedical research applications. Here we evaluated the use of thoracic radiography as a noninvasive refinement methodology for the cynomologus macaque (Macaca fascicularis) model of H1N1 infection. Thoracic radiographic evaluations of macaques infected with any of 3 strains of emerging H1N1 swine-associated influenza virus isolated during the recent pandemic were compared with those of macaques infected with the currently circulating Kawasaki strain of H1N1 influenza. Ventrodorsal, right, and left lateral thoracic radiographs were obtained at days 0, 1, 6, 8, 11, and 14 after infection. A board-certified veterinary radiologist who was blinded to the study design evaluated the images. Numeric scores of extent and severity of lung involvement assigned to each radiograph were compared and demonstrated a significant and substantial difference among groups. The radiographic evaluation allowed for noninvasive assessment of lung involvement, disease onset, progression, and resolution of radiographic changes associated with H1N1 influenza infection. PMID:21262125

  20. Molecular detection and prevalence of Giardia duodenalis and Cryptosporidium spp. among long-tailed macaques (Macaca fascicularis) in Thailand.

    PubMed

    Sricharern, Wanat; Inpankaew, Tawin; Keawmongkol, Sarawan; Supanam, Juthamas; Stich, Roger W; Jittapalapong, Sathaporn

    2016-06-01

    Giardia duodenalis and Cryptosporidium spp. are divergent protozoal intestinal parasites that infect human beings and other animals, including non-human primates. Although long-tailed macaques (Macaca fascicularis) reside in human communities in Thailand, the prevalence of Giardia spp. and Cryptosporidium spp. in these primates has not been previously investigated. The objective of this study was to evaluate long-tailed macaques living near human communities as possible hosts of these intestinal parasites. In 2014, 200 fecal samples were randomly collected from long-tailed macaques living in different areas of Lopburi province, Thailand, and tested with a panel of PCR assays for Giardia spp. and Cryptosporidium spp. G. duodenalis assemblage B was most frequently detected (6%), while assemblage A and an inconclusive assemblage were detected in single samples, for a total G. duodenalis infection rate of 7%. Two samples (1%) tested positive for Cryptosporidium spp., which were both classified as monkey genotypes. No significant associations were found between G. duodenalis infection and sex or location of macaques. This study indicates that long-tailed macaques can carry G. duodenalis and, to a lesser extent, Cryptosporidium spp. monkey genotype. These results warrant education of residents and tourists to limit contact with long-tailed macaques and to take hygienic precautions to mitigate risk of zoonotic and anthroponotic transmission of these parasites between people and macaques. PMID:26892616

  1. Aureisphaera galaxeae gen. nov., sp. nov., a marine member of the family Flavobacteriaceae isolated from the hard coral Galaxea fascicularis.

    PubMed

    Yoon, Jaewoo; Yasumoto-Hirose, Mina; Kasai, Hiroaki

    2015-06-01

    A novel Gram-stain negative, spherical, non-motile, strictly aerobic, heterotrophic, yellow pigmented bacterium, designated strain 04OKA003-7(T) was isolated from the hard coral Galaxea fascicularis L. collected at Akajima, Okinawa, Japan. Phylogenetic analysis based on the 16S rRNA gene sequence revealed the novel isolate is affiliated with the family Flavobacteriaceae of the phylum Bacteroidetes and that it showed highest sequence similarity (92.9 %) to Vitellibacter aestuarii JC2436(T) and Aureitalea marina S1-66(T). The strain could be differentiated phenotypically from recognized members of the family Flavobacteriaceae. The major fatty acids of strain 04OKA003-7(T) were identified as iso-C15:0 and iso-C17:0 3-OH as defined by the MIDI system. The DNA G+C content was determined to be 41 mol%, the major respiratory quinone was identified as menaquinone 6 (MK-6) and a polar lipid profile was present consisting of phosphatidylethanolamine, two unidentified aminolipids and an unidentified lipid. From the distinct phylogenetic position and combination of genotypic and phenotypic characteristics, the strain is considered to represent a novel genus for which the name Aureisphaera galaxeae gen. nov., sp. nov. is proposed. The type strain of A. galaxeae is 04OKA003-7(T) (=KCTC 32993(T) = NBRC 110018(T)). PMID:25795444

  2. Nuclear Thermal Rocket/Vehicle Characteristics And Sensitivity Trades For NASA's Mars Design Reference Architecture (DRA) 5.0 Study

    NASA Technical Reports Server (NTRS)

    Borowski, Stanley K.; McCurdy, David R.; Packard, Thomas W.

    2009-01-01

    This paper summarizes Phase I and II analysis results from NASA's recent Mars DRA 5.0 study which re-examined mission, payload and transportation system requirements for a human Mars landing mission in the post-2030 timeframe. Nuclear thermal rocket (NTR) propulsion was again identified as the preferred in-space transportation system over chemical/aerobrake because of its higher specific impulse (I(sub sp)) capability, increased tolerance to payload mass growth and architecture changes, and lower total initial mass in low Earth orbit (IMLEO) which is important for reducing the number of Ares-V heavy lift launches and overall mission cost. DRA 5.0 features a long surface stay (approximately 500 days) split mission using separate cargo and crewed Mars transfer vehicles (MTVs). All vehicles utilize a common core propulsion stage with three 25 klbf composite fuel NERVA-derived NTR engines (T(sub ex) approximately 2650 - 2700 K, p(sub ch) approximately 1000 psia, epsilon approximately 300:1, I(sub sp) approximately 900 - 910 s, engine thrust-toweight ratio approximately 3.43) to perform all primary mission maneuvers. Two cargo flights, utilizing 1-way minimum energy trajectories, pre-deploy a cargo lander to the surface and a habitat lander into a 24-hour elliptical Mars parking orbit where it remains until the arrival of the crewed MTV during the next mission opportunity (approximately 26 months later). The cargo payload elements aerocapture (AC) into Mars orbit and are enclosed within a large triconicshaped aeroshell which functions as payload shroud during launch, then as an aerobrake and thermal protection system during Mars orbit capture and subsequent entry, descent and landing (EDL) on Mars. The all propulsive crewed MTV is a 0-gE vehicle design that utilizes a fast conjunction trajectory that allows approximately 6-7 month 1-way transit times to and from Mars. Four 12.5 kW(sub e) per 125 square meter rectangular photovoltaic arrays provide the crewed MTV with

  3. Localization of a candidate colon tumor-suppressor gene (DRA) to 7q22-q31. 1 by fluorescence in situ hybridization

    SciTech Connect

    Taguchi, T.; Testa, J.R. ); Papas, T.S.; Schweinfest, C. )

    1994-03-01

    The authors have previously reported that the DRA gene is located on chromosome 7. This assignment was based on Southern blot hybridization of a DRA cDNA to genomic DNA from rodent-human somatic cell hybrids. In this report, they localize the DRA gene to chromosome band 7q22-q31.1 by fluorescence in situ hybridization (FISH) with a full-length (2.9 kb) cDNA as probe. Metaphase spreads from normal human lymphocytes were prepared according to the method of Fan et al. The cDNA clone 611C was labeled with biotin-11-dUTP using a nick-translation kit (Oncor) followed by purification on a Sephadex G50-fine column. FISH and detection of immunofluorescence were performed according to the technique of Pinkel et al. with minor modifications. The chromosome preparations were stained with both diamidino-2-phenylindole and propidium iodide (Oncor) and observed with a Zeiss Axiophot fluorescence microscope. Hybridization was detected on chromosome 7 in 22 of 47 spreads examined. Of 89 fluorescent signals on all chromosomes, 44 (49%) were located on 7q. All signals on chromosome 7 appeared to be located at 7q22-q31.1. Hybridization is in the vicinity of the met protooncogene locus at 7q31.

  4. Large-scale polymorphism discovery in macaque G-protein coupled receptors

    PubMed Central

    2013-01-01

    Background G-protein coupled receptors (GPCRs) play an inordinately large role in human health. Variation in the genes that encode these receptors is associated with numerous disorders across the entire spectrum of disease. GPCRs also represent the single largest class of drug targets and associated pharmacogenetic effects are modulated, in part, by polymorphisms. Recently, non-human primate models have been developed focusing on naturally-occurring, functionally-parallel polymorphisms in candidate genes. This work aims to extend those studies broadly across the roughly 377 non-olfactory GPCRs. Initial efforts include resequencing 44 Indian-origin rhesus macaques (Macaca mulatta), 20 Chinese-origin rhesus macaques, and 32 cynomolgus macaques (M. fascicularis). Results Using the Agilent target enrichment system, capture baits were designed for GPCRs off the human and rhesus exonic sequence. Using next generation sequencing technologies, nearly 25,000 SNPs were identified in coding sequences including over 14,000 non-synonymous and more than 9,500 synonymous protein-coding SNPs. As expected, regions showing the least evolutionary constraint show greater rates of polymorphism and greater numbers of higher frequency polymorphisms. While the vast majority of these SNPs are singletons, roughly 1,750 non-synonymous and 2,900 synonymous SNPs were found in multiple individuals. Conclusions In all three populations, polymorphism and divergence is highly concentrated in N-terminal and C-terminal domains and the third intracellular loop region of GPCRs, regions critical to ligand-binding and signaling. SNP frequencies in macaques follow a similar pattern of divergence from humans and new polymorphisms in primates have been identified that may parallel those seen in humans, helping to establish better non-human primate models of disease. PMID:24119066

  5. Detection and quantification of male-specific fetal DNA in the serum of pregnant cynomolgus monkeys (Macaca fascicularis).

    PubMed

    Yasmin, Lubna; Takano, Jun-Ichiro; Nagai, Yasushi; Otsuki, Junko; Sankai, Tadashi

    2015-02-01

    Because of their developmental similarities to humans, nonhuman primates are often used as a model to study fetal development for potential clinical applications in humans. The detection of fetal DNA in maternal plasma or serum offers a source of fetal genetic material for prenatal diagnosis. However, no such data have been reported for cynomolgus monkeys (Macaca fascicularis), an important model in biomedical research. We have developed a specific, highly sensitive PCR system for detecting and quantifying male-specific fetal DNA in pregnant cynomolgus monkeys. We used multiplex quantitative real-time PCR to analyze cell-free DNA in maternal blood serum obtained from 46 pregnant monkeys at gestational weeks 5, 12, and 22. The presence of SRY gene and DYS14 Y chromosomal sequences was determined in 28 monkeys with male-bearing pregnancies. According to confirmation of fetal sex at birth, the probe and primers for detecting the Y chromosomal regions at each time point revealed 100% specificity of the PCR test and no false-positive or false-negative results. Increased levels of the SRY-specific sequences (mean, 4706 copies/mL serum DNA; range, 1731 to 12,625) and DYS14-specific sequences (mean, 54,814 copies/mL serum DNA; range, 4175-131,250 copies) were detected at week 22. The SRY- and DYS14-specific probes appear to be an effective combination of markers in a multiplex PCR system. To our knowledge, this report is the first to describe the detection of cell-free DNA in cynomolgus monkeys. PMID:25730760

  6. The effect of different flow regimes on the growth and metabolic rates of the scleractinian coral Galaxea fascicularis

    NASA Astrophysics Data System (ADS)

    Schutter, M.; Crocker, J.; Paijmans, A.; Janse, M.; Osinga, R.; Verreth, A. J.; Wijffels, R. H.

    2010-09-01

    To study the effect of water flow on coral growth, four series of ten coral nubbins of Galaxea fascicularis were exposed to four different flow regimes (0, 10, 20, and 25 cm s-1, bidirectional flow) for 42 weeks. Buoyant weight, surface area, and polyp number were measured at regular intervals. Net photosynthesis and dark respiration were measured at the corresponding flow speeds, and daily amount of photosynthetic carbon left for coral growth was calculated. Finally, skeletal density and CN content, chlorophyll concentration and dry weight of coral tissue were determined for each coral. Specific growth rate (in day-1) decreased with time in each flow treatment. Absence of flow resulted in significantly lower growth rates. Average specific growth rate calculated over the entire experiment was not significantly different between 10 and 20 cm s-1, while it was significantly higher at 25 cm s-1. From 10 to 25 cm s-1, average net photosynthetic rate decreased and average dark respiration rate did not change significantly. Scope for growth based on phototrophic carbon decreased with increasing flow. Growth was not positively correlated with either photosynthesis or respiration, or scope for growth. It is suggested that higher flow rates reduce the chance of disturbance of coral growth by competing algae or cyanobacteria, allowing corals to grow more readily with the maximum specific growth rate possible under the given environmental conditions. Notably, other effects of increased flow, such as increased respiratory rates and increased (in)organic nutrient uptake, might have been equally responsible for the increased growth of the corals in 25 cm s-1.

  7. Diurnal pituitary-adrenal activity during schedule-induced polydipsia of water and ethanol in cynomolgus monkeys (Macaca fascicularis)

    PubMed Central

    Helms, Christa M.; Gonzales, Steven W.; Green, Heather L.; Szeliga, Kendall T.; Rogers, Laura S.M.; Grant, Kathleen A.

    2013-01-01

    Rationale Intermittent delivery of an important commodity (e.g., food pellets) generates excessive behaviors as an adjunct to the schedule of reinforcement (adjunctive behaviors) that are hypothesized to be due to conflict between engaging and escaping a situation where reinforcement is delivered, but at sub-optimal rates. Objectives This study characterized the endocrine correlates during schedule-induced polydipsia (SIP) of water and ethanol using a longitudinal approach in non-human primates. Methods Plasma adrenocorticotropic hormone (ACTH) and cortisol were measured in samples from awake cynomolgus monkeys (Macaca fascicularis, 11 adult males) obtained at the onset, midday and offset of their 12-h light cycle. The monkeys were induced to drink water and ethanol (4% w/v, in water) using a fixed time (FT) 300-s interval schedule of pellet delivery. The induction fluid changed every 30 sessions in the following order: water, 0.5 g/kg ethanol, 1.0 g/kg ethanol, and 1.5 g/kg ethanol. Following induction, ethanol and water were concurrently available for 22 h/d. Results The FT300-s schedule gradually increased ACTH, but not cortisol, during water induction to a plateau sustained throughout ethanol induction in every monkey. Upon termination of the schedule, ACTH decreased to baseline and cortisol below baseline. Diurnal ACTH and cortisol were unrelated to the dose of ethanol, but ACTH rhythm flattened at 0.5 g/kg/d and remained flattened. Conclusions The coincidence of elevated ACTH with the initial experience of drinking to intoxication may have altered the mechanisms involved in the transition to heavy drinking. PMID:23508555

  8. Population Recovery of Nicobar Long-Tailed Macaque Macaca fascicularis umbrosus following a Tsunami in the Nicobar Islands, India.

    PubMed

    Velankar, Avadhoot D; Kumara, Honnavalli N; Pal, Arijit; Mishra, Partha Sarathi; Singh, Mewa

    2016-01-01

    Natural disasters pose a threat to isolated populations of species with restricted distributions, especially those inhabiting islands. The Nicobar long tailed macaque.Macaca fascicularis umbrosus, is one such species found in the three southernmost islands (viz. Great Nicobar, Little Nicobar and Katchal) of the Andaman and Nicobar archipelago, India. These islands were hit by a massive tsunami (Indian Ocean tsunami, 26 December 2004) after a 9.2 magnitude earthquake. Earlier studies [Umapathy et al. 2003; Sivakumar, 2004] reported a sharp decline in the population of M. f. umbrosus after thetsunami. We studied the distribution and population status of M. f. umbrosus on thethree Nicobar Islands and compared our results with those of the previous studies. We carried out trail surveys on existing paths and trails on three islands to get encounter rate as measure of abundance. We also checked the degree of inundation due to tsunami by using Normalized Difference Water Index (NDWI) on landsat imageries of the study area before and after tsunami. Theencounter rate of groups per kilometre of M. f. umbrosus in Great Nicobar, Little Nicobar and Katchal was 0.30, 0.35 and 0.48 respectively with the mean group size of 39 in Great Nicobar and 43 in Katchal following the tsunami. This was higher than that reported in the two earlier studies conducted before and after the tsunami. Post tsunami, there was a significant change in the proportion of adult males, adult females and immatures, but mean group size did not differ as compared to pre tsunami. The results show that population has recovered from a drastic decline caused by tsunami, but it cannot be ascertained whether it has reached stability because of the altered group structure. This study demonstrates the effect of natural disasters on island occurring species. PMID:26886197

  9. Population Recovery of Nicobar Long-Tailed Macaque Macaca fascicularis umbrosus following a Tsunami in the Nicobar Islands, India

    PubMed Central

    Velankar, Avadhoot D.; Kumara, Honnavalli N.

    2016-01-01

    Natural disasters pose a threat to isolated populations of species with restricted distributions, especially those inhabiting islands. The Nicobar long tailed macaque.Macaca fascicularis umbrosus, is one such species found in the three southernmost islands (viz. Great Nicobar, Little Nicobar and Katchal) of the Andaman and Nicobar archipelago, India. These islands were hit by a massive tsunami (Indian Ocean tsunami, 26 December 2004) after a 9.2 magnitude earthquake. Earlier studies [Umapathy et al. 2003; Sivakumar, 2004] reported a sharp decline in the population of M. f. umbrosus after thetsunami. We studied the distribution and population status of M. f. umbrosus on thethree Nicobar Islands and compared our results with those of the previous studies. We carried out trail surveys on existing paths and trails on three islands to get encounter rate as measure of abundance. We also checked the degree of inundation due to tsunami by using Normalized Difference Water Index (NDWI) on landsat imageries of the study area before and after tsunami. Theencounter rate of groups per kilometre of M. f. umbrosus in Great Nicobar, Little Nicobar and Katchal was 0.30, 0.35 and 0.48 respectively with the mean group size of 39 in Great Nicobar and 43 in Katchal following the tsunami. This was higher than that reported in the two earlier studies conducted before and after the tsunami. Post tsunami, there was a significant change in the proportion of adult males, adult females and immatures, but mean group size did not differ as compared to pre tsunami. The results show that population has recovered from a drastic decline caused by tsunami, but it cannot be ascertained whether it has reached stability because of the altered group structure. This study demonstrates the effect of natural disasters on island occurring species. PMID:26886197

  10. Hydrostratigraphic Drilling Record Assessment (HyDRA): Assessing the Consistency and Quantitative Utility of Water Well Drillers' Logs

    NASA Astrophysics Data System (ADS)

    Bohling, G.; Helm, C. F.; Butler, J. J., Jr.

    2014-12-01

    The Hydrostratigraphic Drilling Record Assessment (HyDRA) project is a three-year study to develop improved methods for building groundwater flow models from drillers' logs. Lithologic logs recorded by water well drillers represent a voluminous source of information regarding hydrostratigraphy. However, developing quantitative models from drillers' logs is challenging due to the idiosyncratic nature of each driller's approach to describing sediments and lithologies as well as variability in the amount of care invested in the description process. This presentation uses three approaches to assess the consistency and utility of drillers' logs from 250 wells in the vicinity of a continuously monitored "index" well in the High Plains Aquifer in Thomas County, Kansas. The first assessment procedure will examine logs from wells in the vicinity of the index well to determine whether they show evidence of lateral confinement of a region immediately surrounding the index well, as seems to be indicated by the index well hydrograph. The second will apply a cross-validation procedure to determine the degree of consistency among logs at different wells and identify logs that are most out of keeping with logs at nearby wells. The logs are cast in quantitative terms by first representing the sediment descriptions using 72 standardized lithology terms, further categorizing the standardized lithologies into five hydraulic property categories, and then computing the proportions of the hydraulic property categories over regular ten-foot-intervals in each well. The cross-validation procedure involves using a cross-entropy measure to compare the actual category proportions in each well to those interpolated from neighboring wells. Finally, results of a groundwater flow model using property fields developed from the drillers' logs will be briefly discussed. Comparisons between observed and simulated water levels at the index well and other continuously and annually monitored wells in the

  11. Crystallographic Structure of the Human Leukocyte Antigen DRA, DRB3*0101: Models of a Directional Alloimmune Respone and Autoimmunity

    SciTech Connect

    Parry,C.; Gorski, J.; Stern, L.

    2007-01-01

    We describe structural studies of the human leukocyte antigen DR52a, HLA-DRA/DRB3*0101, in complex with an N-terminal human platelet integrin {alpha}II{sub B}{beta}III glycoprotein peptide which contains a Leu/Pro dimorphism. The 33:Leu dimorphism is the epitope for the T cell directed response in neonatal alloimmune thrombocytopenia and post-transfusion purpura in individuals with the {alpha}II{sub B}{beta}III 33:Pro allele, and defines the unidirectional alloimmune response. This condition is always associated with DR52a. The crystallographic structure has been refined to 2.25 {angstrom}. There are two {alpha}{beta} heterodimers to the asymmetric unit in space group P4{sub 1}2{sub 1}2. The molecule is characterized by two prominent hydrophobic pockets at either end of the peptide binding cleft and a deep, narrower and highly charged P4 opening underneath the beta 1 chain. Further, the peptide in the second molecule displays a sharp upward turn after pocket P9. The structure reveals the role of pockets and the distinctive basic P4 pocket, shared by DR52a and DR3, in selecting their respective binding peptide repertoire. We observe an interesting switch in a residue from the canonically assigned pocket 6 seen in prior class II structures to pocket 4. This occludes the P6 pocket helping to explain the distinctive '1-4-9' peptide binding motif. A {beta}57 Asp {yields} Val substitution abrogates the salt-bridge to {alpha}76 Arg and along with a hydrophobic {beta}37 is important in shaping the P9 pocket. DRB3*0101 and DRB1*0301 belong to an ancestral haplotype and are associated with many autoimmune diseases linked to antigen presentation, but whereas DR3 is susceptible to type 1 diabetes DR52a is not. This dichotomy is explored for clues to the disease.

  12. Drug-Induced Liver Injury Associated With Antidepressive Psychopharmacotherapy: An Explorative Assessment Based on Quantitative Signal Detection Using Different MedDRA Terms.

    PubMed

    Gahr, Maximilian; Zeiss, René; Lang, Dirk; Connemann, Bernhard J; Hiemke, Christoph; Schönfeldt-Lecuona, Carlos

    2016-06-01

    Drug-induced liver injury is a major problem of pharmacotherapy and is also frequent with antidepressive psychopharmacotherapy. However, there are only few studies using a consistent methodologic approach to study hepatotoxicity of a larger group of antidepress ants. We performed a quantitative signal detection analysis using data from the Uppsala Monitoring Centre from the WHO that records adverse drug reaction (ADR) data from worldwide sources; we retrieved substance- and country-specific (Australia, France, Germany, Italy, Spain, the United Kingdom, and the United States) ADR data and calculated reporting odds ratios as measures for disproportionality within a case/noncase approach. To allow for identification of agents that cause severe forms of hepatotoxic ADRs, we used 2 terms of the MedDRA ("drug-related hepatic disorders-comprehensive search" [DRHD-CS] and "… -severe events only" [DRHD-SEO]). Distribution of signals was heterogeneous throughout the different data sets, and consistent findings were present for only a few substances: agomelatine (AGM) and tianeptine as well as both positive control agents (amineptine, nefazodone) generated signals related to DRHD-CS and DRHD-SEO in all analyzed data sets. Tri- and tetracyclic antidepressants (here amitriptyline, clomipramine, mianserin, mirtazapine, trimipramine) were associated with hepatotoxicity in several data sets. Using 2 MedDRA terms did not allow for detection of agents that cause severe hepatotoxic ADR. Our results support the findings of previous, primarily literature-based, systematic analyses of hepatotoxicity related to antidepressive psychopharmacotherapy. No new safety information could be generated. Application of 2 MedDRA terms did not increase the substance-specific safety information. PMID:26470856

  13. Affinity enrichment and functional characterization of TRAX1, a novel transcription activator and X1-sequence-binding protein of HLA-DRA.

    PubMed Central

    Itoh-Lindstrom, Y; Peterlin, B M; Ting, J P

    1995-01-01

    The promoters of all class II major histocompatibility (MHC) genes contain a positive regulatory motif, the X element. The DNA-binding proteins specific for this element are presumed to play a critical role in gene expression, although there is a paucity of functional studies supporting this role. In this study, the X-box-binding proteins of HLA-DRA were affinity purified from HeLa nuclear extracts. Fractions 46 to 48 contained an X-box-binding activity and were determined by electrophoretic mobility shift assays to be specific for the X1 element. This X1 sequence-binding-protein, transcriptional activator X1 (TRAX1), was shown to be a specific transcriptional activator of the HLA-DRA promoter in an in vitro transcription assay. By UV cross-linking analysis, the approximate molecular mass of TRAX1 including the bound DNA was determined to be 40 kDa. When the TRAX1 complex was incubated with antibodies against a known recombinant X-box-binding protein, RFX1, and tested in electrophoretic mobility shift assays, TRAX1 was neither shifted nor blocked by the antibody. Further analysis with methylation interference showed that TRAX1 bound to the 5' end of the X1 sequence at -109 and -108 and created hypersensitive sites at -114, -113, and -97. This methylation interference pattern is distinct from those of the known X1-binding proteins RFX1, RFX, NF-Xc, and NF-X. Taken together, our results indicate that TRAX1 is a novel X1-sequence-binding protein and transcription activator of HLA-DRA. PMID:7799935

  14. Stress in cynomolgus monkeys (Macaca fascicularis) subjected to long-distance transport and simulated transport housing conditions.

    PubMed

    Fernström, A L; Sutian, W; Royo, F; Westlund, K; Nilsson, T; Carlsson, H-E; Paramastri, Y; Pamungkas, J; Sajuthi, D; Schapiro, S J; Hau, J

    2008-11-01

    The stress associated with transportation of non-human primates used in scientific research is an important but almost unexplored part of laboratory animal husbandry. The procedures and routines concerning transport are not only important for the animals' physical health but also for their mental health as well. The transport stress in cynomolgus monkeys (Macaca fascicularis) was studied in two experiments. In Experiment 1, 25 adult female cynomolgus monkeys were divided into five groups of five animals each that received different diets during the transport phase of the experiment. All animals were transported in conventional single animal transport cages with no visual or tactile contact with conspecifics. The animals were transported by lorry for 24 h at ambient temperatures ranging between 20 degrees C and 35 degrees C. Urine produced before, during and after transport was collected and analysed for cortisol by enzyme-linked immunosorbent assay (ELISA). All monkeys exhibited a significant increase in cortisol excretion per time unit during the transport and on the first day following transport.Although anecdotal reports concerning diet during transport, including the provision of fruits and/or a tranquiliser, was thought likely to influence stress responses, these were not corrobated by the present study. In Experiment 2, behavioural data were collected from 18 cynomolgus macaques before and after transfer from group cages to either single or pair housing, and also before and after a simulated transport, in which the animals were housed in transport cages. The single housed monkeys were confined to single transport cages and the pair housed monkeys were kept in their pairs in double size cages. Both pair housed and singly housed monkeys showed clear behavioural signs of stress soon after their transfer out of their group cages.However, stress-associated behaviours were more prevalent in singly housed animals than in pair housed animals, and these behaviours

  15. Automated segmentation of cerebral vasculature with aneurysms in 3DRA and TOF-MRA using geodesic active regions: An evaluation study

    SciTech Connect

    Bogunovic, Hrvoje; Pozo, Jose Maria; Villa-Uriol, Maria Cruz; and others

    2011-01-15

    Purpose: To evaluate the suitability of an improved version of an automatic segmentation method based on geodesic active regions (GAR) for segmenting cerebral vasculature with aneurysms from 3D x-ray reconstruction angiography (3DRA) and time of flight magnetic resonance angiography (TOF-MRA) images available in the clinical routine. Methods: Three aspects of the GAR method have been improved: execution time, robustness to variability in imaging protocols, and robustness to variability in image spatial resolutions. The improved GAR was retrospectively evaluated on images from patients containing intracranial aneurysms in the area of the Circle of Willis and imaged with two modalities: 3DRA and TOF-MRA. Images were obtained from two clinical centers, each using different imaging equipment. Evaluation included qualitative and quantitative analyses of the segmentation results on 20 images from 10 patients. The gold standard was built from 660 cross-sections (33 per image) of vessels and aneurysms, manually measured by interventional neuroradiologists. GAR has also been compared to an interactive segmentation method: isointensity surface extraction (ISE). In addition, since patients had been imaged with the two modalities, we performed an intermodality agreement analysis with respect to both the manual measurements and each of the two segmentation methods. Results: Both GAR and ISE differed from the gold standard within acceptable limits compared to the imaging resolution. GAR (ISE) had an average accuracy of 0.20 (0.24) mm for 3DRA and 0.27 (0.30) mm for TOF-MRA, and had a repeatability of 0.05 (0.20) mm. Compared to ISE, GAR had a lower qualitative error in the vessel region and a lower quantitative error in the aneurysm region. The repeatability of GAR was superior to manual measurements and ISE. The intermodality agreement was similar between GAR and the manual measurements. Conclusions: The improved GAR method outperformed ISE qualitatively as well as

  16. Polymorphous computing fabric

    DOEpatents

    Wolinski, Christophe Czeslaw; Gokhale, Maya B.; McCabe, Kevin Peter

    2011-01-18

    Fabric-based computing systems and methods are disclosed. A fabric-based computing system can include a polymorphous computing fabric that can be customized on a per application basis and a host processor in communication with said polymorphous computing fabric. The polymorphous computing fabric includes a cellular architecture that can be highly parameterized to enable a customized synthesis of fabric instances for a variety of enhanced application performances thereof. A global memory concept can also be included that provides the host processor random access to all variables and instructions associated with the polymorphous computing fabric.

  17. A population-genetic study of crab-eating macaques (Macaca fascicularis) on the island of Angaur, Palau, Micronesia.

    PubMed

    Kawamoto, Y; Nozawa, K; Matsubayashi, K; Gotoh, S

    1988-01-01

    Blood protein polymorphisms of an introduced population of the crab-eating macaques on Angaur Island, Palau, Micronesia, were examined electrophoretically to assess genetic variability. Results showed a high degree of genetic heterozygosity and some distinctive features in the genetic constitution of this island population. Negative evidence is presented regarding ancestry from a single pair of macaques. Their origin is discussed in relation to the genetic structure of the present population. PMID:3256533

  18. Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta)

    PubMed Central

    Zhang, Xu; Zhang, Qu; Su, Bing

    2016-01-01

    Retroposition is an RNA-mediated mechanism to generate gene duplication, and is believed to play an important role in genome evolution and phenotypic adaptation in various species including primates. Previous studies suggested an elevated rate of recent retroposition in the rhesus macaque genome. To better understand the impact of retroposition on macaque species which have undergone an adaptive radiation approximately 3–6 million years ago, we developed a bioinformatics pipeline to identify recently derived retrocopies in cynomolgus monkeys. As a result, we identified seven experimentally validated young retrocopies, all of which are polymorphic in cynomolgus monkeys. Unexpectedly, five of them are also present in rhesus monkeys and are still segregating. Molecular evolutionary analysis indicates that the observed inter-specific polymorphism is attribute to ancestral polymorphism. Further population genetics analysis provided strong evidence of balancing selection on at least one case (Crab-eating monkey retrocopy 6, or CER6) in both species. CER6 is in adjacent with an immunoglobulin related gene and may be involved in host-pathogen interaction, a well-known target of balancing selection. Altogether, our data support that retroposition is an important force to shape genome evolution and species adaptation. PMID:27600022

  19. Emergence and evolution of inter-specific segregating retrocopies in cynomolgus monkey (Macaca fascicularis) and rhesus macaque (Macaca mulatta).

    PubMed

    Zhang, Xu; Zhang, Qu; Su, Bing

    2016-01-01

    Retroposition is an RNA-mediated mechanism to generate gene duplication, and is believed to play an important role in genome evolution and phenotypic adaptation in various species including primates. Previous studies suggested an elevated rate of recent retroposition in the rhesus macaque genome. To better understand the impact of retroposition on macaque species which have undergone an adaptive radiation approximately 3-6 million years ago, we developed a bioinformatics pipeline to identify recently derived retrocopies in cynomolgus monkeys. As a result, we identified seven experimentally validated young retrocopies, all of which are polymorphic in cynomolgus monkeys. Unexpectedly, five of them are also present in rhesus monkeys and are still segregating. Molecular evolutionary analysis indicates that the observed inter-specific polymorphism is attribute to ancestral polymorphism. Further population genetics analysis provided strong evidence of balancing selection on at least one case (Crab-eating monkey retrocopy 6, or CER6) in both species. CER6 is in adjacent with an immunoglobulin related gene and may be involved in host-pathogen interaction, a well-known target of balancing selection. Altogether, our data support that retroposition is an important force to shape genome evolution and species adaptation. PMID:27600022

  20. Schistosoma haematobium detection in snails by DraI PCR and Sh110/Sm-Sl PCR: further evidence of the interruption of schistosomiasis transmission in Morocco

    PubMed Central

    2014-01-01

    Background This is the first study in Morocco to estimate snail infection rates at the last historic transmission sites of schistosomiasis, known to be free from new infection among humans since 2004. Screening of large numbers of snails for infection is one way to confirm that Schistosoma haematobium transmission has stopped and does not resurge. Methods A total of 2703 Bulinus truncatus snails were collected from 24 snail habitats in five provinces of Morocco: Errachidia, El Kelaa des Sraghna, Tata, Beni Mellal, and Chtouka Ait Baha. All visible snails were collected with a scoop net or by hand. We used waders and gloves as simple precautions. Snails were morphologically identified according to Moroccan Health Ministry guide of schistosomiasis (1982). All snails were analyzed in pools by molecular tool, using primers from the newly identified repeated DNA sequence, termed DraI, in the S. haematobium group. To distinguish S. bovis and S. haematobium, the snails were analyzed by Sh110/Sm-Sl PCR that was specific of S. haematobium. Results The results showed that snails from Errachidia, Chtouka Ait Baha, sector of Agoujgal in Tata and sector of Mbarkiya in El kelaa des Sraghna were negative for DraI PCR; but, snails from remaining snail habitats of El Kelaa des Sraghna, Tata and Beni Mellal were positive. This led to suggest the presence of circulating schistosome species (S. haematobium, S. bovis or others) within these positive snail habitats. Subsequently, confirmation with S. haematobium species specific molecular assay, Sh110/Sm-Sl PCR, showed that none of the collected snails were infected by S. haematobium in all historic endemic areas. Conclusion The absence of S. haematobium infection in snails supports the argument of S. haematobium transmission interruption in Morocco. PMID:24962624

  1. Polymorphism of triphenyl phosphite

    NASA Astrophysics Data System (ADS)

    Baran, J.; Davydova, N. A.; Drozd, M.

    2014-03-01

    The glass-forming liquid triphenyl phosphite (TPP) has recently attracted much attention due to the possible existence of a polyamorphism, i.e., the existence of two or more amorphous phases. In the present work we provide experimental evidence of the existence of a polymorphism in TPP. In addition to the already known conventional crystalline phase, which melts at 299.1 K, it has been found that TPP can crystallize in another polymorphic phase. The new polymorph can be obtained from the liquid phase due to direct cooling from the room temperature up to 245 K where it is held for 15 min and then heated up to 270 K. At 270 K crystallization of the new polymorph occurs, which melts at 291.6 K.

  2. Proteomic identification of differentially expressed genes in neural stem cells and neurons differentiated from embryonic stem cells of cynomolgus monkey (Macaca fascicularis) in vitro.

    PubMed

    Akama, Kuniko; Horikoshi, Tomoe; Nakayama, Takashi; Otsu, Masahiro; Imaizumi, Noriaki; Nakamura, Megumi; Toda, Tosifusa; Inuma, Michiko; Hirano, Hisashi; Kondo, Yasushi; Suzuki, Yutaka; Inoue, Nobuo

    2011-02-01

    Understanding neurogenesis is valuable for the treatment of nervous system disorders. However, there is currently limited information about the molecular events associated with the transition from primate ES cells to neural cells. We therefore sought to identify the proteins involved in neurogenesis, from Macaca fascicularis ES cells (CMK6 cell line) to neural stem (NS) cells to neurons using two-dimensional gel electrophoresis (2-DE), peptide mass fingerprinting (PMF), and liquid chromatography-tandem mass spectrometry (LC-MS-MS). During the differentiation of highly homogeneous ES cells to NS cells, we identified 17 proteins with increased expression, including fatty acid binding protein 7 (FABP7), collapsin response mediator protein 2 (CRMP2), and cellular retinoic acid binding protein 1 (CRABP1), and seven proteins with decreased expression. In the differentiation of NS cells to neurons, we identified three proteins with increased expression, including CRMP2, and 10 proteins with decreased expression. Of these proteins, FABP7 is a marker of NS cells, CRMP2 is involved in axon guidance, and CRABP1 is thought to regulate retinoic acid access to its nuclear receptors. Western blot analysis confirmed the upregulation of FABP7 and CRABP1 in NS cells, and the upregulation of CRMP2 in NS cells and neurons. RT-PCR results showed that CRMP2 and FABP7 mRNAs were also upregulated in NS cells, while CRABP1 mRNA was unchanged. These results provide insight into the molecular basis of monkey neural differentiation. PMID:21047566

  3. Sequence divergence, polymorphism and evolution of the middle-wave and long-wave visual pigment genes of great apes and Old World monkeys.

    PubMed

    Dulai, K S; Bowmaker, J K; Mollon, J D; Hunt, D M

    1994-10-01

    In man, the spectral shift between the middle-wave (MW) and long-wave (LW) visual pigments is largely achieved by amino acid substitution at two codons, both located in exon 5. A third amino acid site coded by exon 3 is polymorphic between pigments. We have studied the equivalent regions of the cone opsin genes in two members of the Hominidea (the gorilla, Gorilla gorilla and the chimpanzee, Pan troglodytes) and in three members of the Cercopithecoidea family of Old World primates (the diana monkey, Cercopithecus diana, the talapoin monkey, Miopithecus talapoin, and the crab-eating macaque, Macaca fascicularis). No variation in the codons that specify the amino acids involved in spectral tuning were found. We predict therefore that the MW and LW pigments of gorilla and chimpanzee have similar spectral characteristics to those of man. Multiple copies of the same opsin gene sequence were identified in the chimpanzee, talapoin and macaque and we also show that non-human Old World primates are similar to man in showing a bunching of polymorphic sites in exon 3. We discuss the ancestry of the separate MW and LW genes of Old World primates and the equivalent polymorphic gene of the marmoset, a New World primate. PMID:7975287

  4. Species identification of oral viridans streptococci by restriction fragment polymorphism analysis of rRNA genes.

    PubMed Central

    Rudney, J D; Larson, C J

    1993-01-01

    Oral streptococci formerly classified as Streptococcus sanguis have been divided into six genetic groups. Methods to identify those species by genotype are needed. This study compared restriction fragment polymorphisms of rRNA genes (ribotypes) for seven S. gordonii, three S. sanguis, four S. oralis, three S. mitis, one S. crista, and seven S. parasanguis strains classified in previous DNA hybridization studies, as well as one clinical isolate. DNA was digested with HindIII, PvuII, HindIII and PvuII combined, EcoRI, BamHI, AatII, AlwNI, and DraII. DNA fragments were hybridized with a digoxigenin-labeled cDNA probe obtained by reverse transcription of Escherichia coli 16S and 23S rRNA. S. oralis, S. mitis, and S. parasanguis all showed an isolated 2,290-bp band in AatII ribotypes that was absent from S. gordonii, S. sanguis, and S. crista. The last three groups showed species-specific bands with AatII and also with PvuII. S. oralis could be distinguished from S. mitis and S. parasanguis in AlwNI and DraII ribotypes. S. mitis and S. parasanguis could not be distinguished, since they shared multiple bands in PvuII, AlwNI, and EcoRI patterns. The clinical isolate in the panel was very similar to S. sanguis by all enzymes used. Our findings suggest that ribotyping may be useful for genotypic identification of oral viridans streptococci. Initial digests of clinical isolates might be made with AatII, followed by PvuII or AlwNI. Isolates then could be identified by comparing ribotype patterns with those of reference strains. This approach could facilitate clinical studies of these newly defined species. Images PMID:7691875

  5. Absent in Melanoma 2 (AIM2) is an important mediator of interferon-dependent and -independent HLA-DRA and HLA-DRB gene expression in colorectal cancers.

    PubMed

    Lee, J; Li, L; Gretz, N; Gebert, J; Dihlmann, S

    2012-03-01

    Absent in Melanoma 2 (AIM2) is a member of the HIN-200 family of hematopoietic, IFN-inducible, nuclear proteins, associated with both, infection defense and tumor pathology. Recently, AIM2 was found to act as a DNA sensor in innate immunity. In addition, we and others have previously demonstrated a high frequency of AIM2-alterations in microsatellite unstable (MSI-H) tumors. To further elucidate AIM2 function in colorectal tumors, we here addressed AIM2-responsive target genes by microarray based gene expression profiling of 22 244 human genes. A total of 111 transcripts were significantly upregulated, whereas 80 transcripts turned out to be significantly downregulated in HCT116 cells, constitutively expressing AIM2, compared with AIM2-negative cells. Among the upregulated genes that were validated by quantitative PCR and western blotting we recognized several interferon-stimulated genes (ISGs: IFIT1, IFIT2, IFIT3, IFI6, IRF7, ISG15, HLA-DRA, HLA-DRB, TLR3 and CIITA), as well as genes involved in intercellular adhesion and matrix remodeling. Expression of ISGs correlated with expression of AIM2 in 10 different IFN-γ treated colorectal cancer cell lines. Moreover, small interfering RNA-mediated knock-down of AIM2 resulted in reduced expression of HLA-DRA, HLA-DRB and CIITA in IFN-γ-treated cells. IFN-γ independent induction of HLA-DR genes and their encoded proteins was also demonstrated upon doxycyclin-regulated transient induction of AIM2. Luciferase reporter assays revealed induction of the HLA-DR promoter upon AIM2 transfection in different cell lines. STAT-signaling was not involved in IFN-γ independent induction of ISGs, arguing against participation of cytokines released in an autostimulating manner. Our data indicate that AIM2 mediates both IFN-γ dependent and independent induction of several ISGs, including genes encoding the major histocompatibility complex (MHC) class II antigens HLA-DR-α and -β. This suggests a novel role of the IFN/AIM2/ISG

  6. Physical volcanology, geochemistry and basin evolution of the Ediacaran volcano-sedimentary succession in the Bas Draâ inlier (Ouarzazate Supergroup, Western Anti-Atlas, Morocco)

    NASA Astrophysics Data System (ADS)

    Karaoui, Brahim; Breitkreuz, Christoph; Mahmoudi, Abdelkader; Youbi, Nasrrddine

    2014-11-01

    New geologic mapping, lithofacies and granulometric analysis, and geochemistry from the volcano-sedimentary successions of the central part of the Bas Draâ inlier, Western Anti-Atlas, constrain the Ediacaran Ouarzazate Supergroup evolution during the post-collisional stage of the Pan-African orogeny. Volcanosedimentary facies analysis is the key aspect of the present contribution. We distinguished sixteen terrestrial volcanosedimentary lithofacies in the Bas Draâ succession (BDS), which reaches a total thickness of 2000 m. BDS evolution can be grouped into four units (Aouinet Aït Oussa I to IV, AO I-AO IV). The earliest volcanic activity produced rhyolitic ignimbrite sheets (AO I), which had been considered as lava flows by previous workers, and which were presumably related to caldera system(s). During AO II, a complex of high-silica andesitic and rhyolitic lavas formed, punctuated by the explosive eruption of a high-temperature silica-rich magma leading to the formation of parataxitic ignimbrite. AO III consists of basalt and andesite lava fields and small explosive, in parts phreatomagmatic volcanic vents. It is dissected by fluvial systems depositing external non-volcanic and local volcanic debris. BDS evolution terminated with the formation of a large SiO2-rich lava dome complex (AO IV), accompanied by small basalt effusive event. Volcanosedimentary facies analysis infers that the BDS evolved in a continental extensional setting developing in a low topography under humid paleoclimatic conditions. Alteration textures are dominated by a piemontite-calcite-albite-quartz (+ iron oxides) assemblage. Chemical analysis of BDS volcanic and subvolcanic rocks belongs to high-k calc-alkaline and alkali-calcic to alkaline magmatic trend typical for a post-collision setting. Trace elements spidergrams show a pattern typical for subduction-related suites of orogenic belts. REE patterns show moderate enrichment in LREE relative to flat HREE, with strong negative Eu

  7. Données nouvelles sur le contenu organique des dépôts phosphatés du gisement de Ras-Draâ (Tunisie)

    NASA Astrophysics Data System (ADS)

    Ben Hassen, Aida; Trichet, Jean; Disnar, Jean-Robert; Belayouni, Habib

    2009-04-01

    The study of the organic matter (OM) content of phosphatic sediments from the Ras-Draâ deposit, Tunisia, was carried on the two separated lithological fractions constituting the bulk sediments, namely phosphatic grains (pellets) and their associated matrices. The geochemical characterization of the OM present in pellets and in their matrices by CNS elemental analysis and RE pyrolysis indicates that: (i) the TOC content is higher in matrices (where it reaches 4.00%), than in pellets in the same strata where it does not exceed 1.62%; (ii) the presence of more or less oxidized marine planktonic OM in both fractions; (iii) a low degree of diagenetic evolution of the OM in both fractions (RE Tmax globally < than 430 °C). The chemical extraction of the humic substances (HS) from both fractions followed by the separation of fractions according to the IHSS procedure, systematically indicates a higher abundance of extractable humic compounds (HC) in the pellets (C HC ˜ 70% of the sum of TOC in the separated fractions, TOCfr) and a variable but lower extraction yield in matrices (C HC ˜ 18% TOCfr). This significant difference between both fractions excludes the possibility that pellets formed authigenically from, and within, their matrix. This is consistent with recent findings suggesting that these pellets could be fish feces.

  8. Thrombophilic polymorphisms in Israel.

    PubMed

    Zoossmann-Diskin, Avshalom; Gazit, Ephraim; Peleg, Leah; Shohat, Mordechai; Turner, David

    2008-01-01

    Three thrombophilic polymorphisms, FV G1691A, FII G20210A and MTHFR C677T were investigated in Israeli populations by FRET, (fluorescence resonance energy transfer) real-time PCR. We observe extensive variability in the frequencies of each of the polymorphisms, as has been observed in the study of other polymorphisms in these populations. Very high allele frequencies for FV G1691A (the highest 0.087 in Turkish and Greek Jews) and FII G20210A (the highest 0.061 in Georgian Jews) in some of the Israeli populations justify a clinical investigation to assess their risk for venous thrombosis. Principal Coordinates Analysis demonstrates that the Jewish populations are interspersed among the non-Jewish populations. The resemblance of some Jewish populations to certain non-Jewish populations coincides with findings based on classical markers. PMID:18583164

  9. Disappearing Polymorphs Revisited

    PubMed Central

    Bučar, Dejan-Krešimir; Lancaster, Robert W; Bernstein, Joel

    2015-01-01

    Nearly twenty years ago, Dunitz and Bernstein described a selection of intriguing cases of polymorphs that disappear. The inability to obtain a crystal form that has previously been prepared is indeed a frustrating and potentially serious problem for solid-state scientists. This Review discusses recent occurrences and examples of disappearing polymorphs (as well as the emergence of elusive crystal forms) to demonstrate the enduring relevance of this troublesome, but always captivating, phenomenon in solid-state research. A number of these instances have been central issues in patent litigations. This Review, therefore, also highlights the complex relationship between crystal chemistry and the law. PMID:26031248

  10. A novel wireless recording and stimulating multichannel epicortical grid for supplementing or enhancing the sensory-motor functions in monkey (Macaca fascicularis).

    PubMed

    Zippo, Antonio G; Romanelli, Pantaleo; Torres Martinez, Napoleon R; Caramenti, Gian C; Benabid, Alim L; Biella, Gabriele E M

    2015-01-01

    Artificial brain-machine interfaces (BMIs) represent a prospective step forward supporting or replacing faulty brain functions. So far, several obstacles, such as the energy supply, the portability and the biocompatibility, have been limiting their effective translation in advanced experimental or clinical applications. In this work, a novel 16 channel chronically implantable epicortical grid has been proposed. It provides wireless transmission of cortical recordings and stimulations, with induction current recharge. The grid has been chronically implanted in a non-human primate (Macaca fascicularis) and placed over the somato-motor cortex such that 13 electrodes recorded or stimulated the primary motor cortex and three the primary somatosensory cortex, in the deeply anaesthetized animal. Cortical sensory and motor recordings and stimulations have been performed within 3 months from the implant. In detail, by delivering motor cortex epicortical single spot stimulations (1-8 V, 1-10 Hz, 500 ms, biphasic waves), we analyzed the motor topographic precision, evidenced by tunable finger or arm movements of the anesthetized animal. The responses to light mechanical peripheral sensory stimuli (blocks of 100 stimuli, each single stimulus being <1 ms and interblock intervals of 1.5-4 s) have been analyzed. We found 150-250 ms delayed cortical responses from fast finger touches, often spread to nearby motor stations. We also evaluated the grid electrical stimulus interference with somatotopic natural tactile sensory processing showing no suppressing interference with sensory stimulus detection. In conclusion, we propose a chronically implantable epicortical grid which can accommodate most of current technological restrictions, representing an acceptable candidate for BMI experimental and clinical uses. PMID:26029061

  11. A novel wireless recording and stimulating multichannel epicortical grid for supplementing or enhancing the sensory-motor functions in monkey (Macaca fascicularis)

    PubMed Central

    Zippo, Antonio G.; Romanelli, Pantaleo; Torres Martinez, Napoleon R.; Caramenti, Gian C.; Benabid, Alim L.; Biella, Gabriele E. M.

    2015-01-01

    Artificial brain-machine interfaces (BMIs) represent a prospective step forward supporting or replacing faulty brain functions. So far, several obstacles, such as the energy supply, the portability and the biocompatibility, have been limiting their effective translation in advanced experimental or clinical applications. In this work, a novel 16 channel chronically implantable epicortical grid has been proposed. It provides wireless transmission of cortical recordings and stimulations, with induction current recharge. The grid has been chronically implanted in a non-human primate (Macaca fascicularis) and placed over the somato-motor cortex such that 13 electrodes recorded or stimulated the primary motor cortex and three the primary somatosensory cortex, in the deeply anaesthetized animal. Cortical sensory and motor recordings and stimulations have been performed within 3 months from the implant. In detail, by delivering motor cortex epicortical single spot stimulations (1–8 V, 1–10 Hz, 500 ms, biphasic waves), we analyzed the motor topographic precision, evidenced by tunable finger or arm movements of the anesthetized animal. The responses to light mechanical peripheral sensory stimuli (blocks of 100 stimuli, each single stimulus being <1 ms and interblock intervals of 1.5–4 s) have been analyzed. We found 150–250 ms delayed cortical responses from fast finger touches, often spread to nearby motor stations. We also evaluated the grid electrical stimulus interference with somatotopic natural tactile sensory processing showing no suppressing interference with sensory stimulus detection. In conclusion, we propose a chronically implantable epicortical grid which can accommodate most of current technological restrictions, representing an acceptable candidate for BMI experimental and clinical uses. PMID:26029061

  12. Immunoreactivity for Choline Acetyltransferase of Peripheral-Type (pChAT) in the Trigeminal Ganglion Neurons of the Non-Human Primate Macaca fascicularis

    PubMed Central

    Koga, Tsuneyuki; Bellier, Jean-Pierre; Kimura, Hiroshi; Tooyama, Ikuo

    2013-01-01

    Transcripts of the choline acetyltransferase (ChAT) gene reveal a number of different splice variants including ChAT of a peripheral type (pChAT). Immunohistochemical staining of the brain using an antibody against pChAT clearly revealed peripheral cholinergic neurons, but failed to detect cholinergic neurons in the central nervous system. In rodents, pChAT-immunoreactivity has been detected in cholinergic parasympathetic postganglionic and enteric ganglion neurons. In addition, pChAT has been observed in non-cholinergic neurons such as peripheral sensory neurons in the trigeminal and dorsal root ganglia. The common type of ChAT (cChAT) has been investigated in many parts of the brain and the spinal cord of non-human primates, but little information is available about the localization of pChAT in primate species. Here, we report the detection of pChAT immunoreactivity in trigeminal ganglion (TG) neurons and its co-localization with Substance P (SP) and/or calcitonin gene-related peptide (CGRP) in the cynomolgus monkey, Macaca fascicularis. Neurons positive for pChAT were observed in a rather uniform pattern in approximately half of the trigeminal neurons throughout the TG. Most pChAT-positive neurons had small or medium-sized cell bodies. Double-immunofluorescence staining showed that 85.1% of SP-positive cells and 74.0% of CGRP-positive cells exhibited pChAT immunoreactivity. Most pChAT-positive cells were part of a larger population of neurons that co-expressed SP and/or CGRP. PMID:23720604

  13. There Is More than One Way to Crack an Oyster: Identifying Variation in Burmese Long-Tailed Macaque (Macaca fascicularis aurea) Stone-Tool Use

    PubMed Central

    Tan, Amanda; Tan, Say Hoon; Vyas, Dhaval; Malaivijitnond, Suchinda; Gumert, Michael D.

    2015-01-01

    We explored variation in patterns of percussive stone-tool use on coastal foods by Burmese long-tailed macaques (Macaca fascicularis aurea) from two islands in Laem Son National Park, Ranong, Thailand. We catalogued variation into three hammering classes and 17 action patterns, after examining 638 tool-use bouts across 90 individuals. Hammering class was based on the stone surface used for striking food, being face, point, and edge hammering. Action patterns were discriminated by tool material, hand use, posture, and striking motion. Hammering class was analyzed for associations with material and behavioural elements of tool use. Action patterns were not, owing to insufficient instances of most patterns. We collected 3077 scan samples from 109 macaques on Piak Nam Yai Island’s coasts, to determine the proportion of individuals using each hammering class and action pattern. Point hammering was significantly more associated with sessile foods, smaller tools, faster striking rates, smoother recoil, unimanual use, and more varied striking direction, than were face and edge hammering, while both point and edge hammering were significantly more associated with precision gripping than face hammering. Edge hammering also showed distinct differences depending on whether such hammering was applied to sessile or unattached foods, resembling point hammering for sessile foods and face hammering for unattached foods. Point hammering and sessile edge hammering compared to prior descriptions of axe hammering, while face and unattached edge hammering compared to pound hammering. Analysis of scans showed that 80% of individuals used tools, each employing one to four different action patterns. The most common patterns were unimanual point hammering (58%), symmetrical-bimanual face hammering (47%) and unimanual face hammering (37%). Unimanual edge hammering was relatively frequent (13%), compared to the other thirteen rare action patterns (<5%). We compare our study to other stone

  14. Quantitative Real-Time Polymerase Chain Reaction Measurement of HLA-DRA Gene Expression in Whole Blood Is Highly Reproducible and Shows Changes That Reflect Dynamic Shifts in Monocyte Surface HLA-DR Expression during the Course of Sepsis

    PubMed Central

    Tina, Elisabet; Bäckman, Anders; Magnuson, Anders; Strålin, Kristoffer; Söderquist, Bo; Källman, Jan

    2016-01-01

    Introduction A decrease in the expression of monocyte surface protein HLA-DR (mHLA-DR), measured by flow cytometry (FCM), has been suggested as a marker of immunosuppression and negative outcome in severe sepsis. However, FCM is not always available due to sample preparation that limits its use to laboratory operational hours. In this prospective study we evaluated dynamic changes in mHLA-DR expression during sepsis in relation to changes in HLA-DRA gene expression and Class II transactivator (CIITA), measured by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR). Aims The aims of this study were: 1. to validate the robustness of qRT-PCR measurement of HLA-DRA- and CIITA–mRNA expression, in terms of reproducibility; and 2. to see if changes in expression of these genes reflect changes in mHLA-DR expression during the course of severe and non-severe bacteraemic sepsis. Methods and Findings Blood samples were collected from 60 patients with bacteraemic sepsis on up to five occasions during Days 1–28 after hospital admission. We found the reproducibility of the qRT-PCR method to be high by demonstrating low threshold variations (<0.11 standard deviation (SD)) of the qRT-PCR system, low intra-assay variation of Ct-values within triplicates (≤0.15 SD) and low inter-assay variations (12%) of the calculated target gene ratios. Our results also revealed dynamic HLA-DRA expression patterns during the course of sepsis that reflected those of mHLA-DR measured by FCM. Furthermore, HLA-DRA and mHLA-DR recovery slopes in patients with non-severe sepsis differed from those in patients with severe sepsis, shown by mixed model for repeated measurements (p<0.05). However, during the first seven days of sepsis, PCR-measurements showed a higher magnitude of difference between the two sepsis groups. Mean differences (95% CI) between severe sepsis (n = 20) and non-severe sepsis (n = 40) were; on day 1–2, HLA-DRA 0.40 (0.28–0.59) p<0.001, CIITA 0.48 (0.32–0.72) p = 0

  15. Enzyme polymorphisms in Canarium

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fifty-two accessions of Canarium involving seven species, C. ovatum, C. album, C. megalanthum, C. harveyi, C. indicum, C. mehenbethene, and C. odontophyllum were studied for isozyme polymorphisms. Starch gel electrophoresis with a histidine-citrate buffer system (pH 6.5) was employed to assay six en...

  16. Polymorphous Perversity in Texts

    ERIC Educational Resources Information Center

    Johnson-Eilola, Johndan

    2012-01-01

    Here's the tricky part: If we teach ourselves and our students that texts are made to be broken apart, remixed, remade, do we lose the polymorphous perversity that brought us pleasure in the first place? Does the pleasure of transgression evaporate when the borders are opened?

  17. Investigation of Uranium Polymorphs

    SciTech Connect

    Sweet, Lucas E.; Henager, Charles H.; Hu, Shenyang Y.; Johnson, Timothy J.; Meier, David E.; Peper, Shane M.; Schwantes, Jon M.

    2011-08-01

    The UO3-water system is complex and has not been fully characterized, even though these species are common throughout the nuclear fuel cycle. As an example, most production schemes for UO3 result in a mixture of up to six or more different polymorphic phases, and small differences in these conditions will affect phase genesis that ultimately result in measureable changes to the end product. As a result, this feature of the UO3-water system may be useful as a means for determining process history. This research effort attempts to better characterize the UO3-water system with a variety of optical techniques for the purpose of developing some predictive capability for estimating process history in polymorphic phases of unknown origin. Three commercially relevant preparation methods for the production of UO3 were explored. Previously unreported low temperature routes to β- and γ-UO3 were discovered. Raman and fluorescence spectroscopic libraries were established for pure and mixed polymorphic forms of UO3 in addition to the common hydrolysis products of UO3. An advantage of the sensitivity of optical fluorescence microscopy over XRD has been demonstrated. Preliminary aging studies of the α and γ forms of UO3 have been conducted. In addition, development of a 3-D phase field model used to predict phase genesis of the system was initiated. Thermodynamic and structural constants that will feed the model have been gathered from the literature for most of the UO3 polymorphic phases.

  18. Novel experimental methods for investigating high speed friction of titanium-aluminum-vanadium/tool steel interface and dynamic failure of extrinsically toughened DRA composites

    NASA Astrophysics Data System (ADS)

    Irfan, Mohammad Abdulaziz

    effects the sliding resistance of the interface. The experimental results deduced from the response of the sliding interface to step changes in normal pressure and the applied shear stress reinforce the importance of including frictional memory in the development of rate dependent state variable friction models. The second part of the thesis presents an investigation into the dynamic deformation and failure of extrinsically toughened DRA composites. Experiments were conducted using the split Hopkinson pressure bar to investigate the deformation and flow behavior under dynamic compression loading. A modified Hopkinson bar apparatus was used to explore the dynamic fracture behavior of three different extrinsically toughened DRA composites. The study was paralleled by systematic exploration of the failure modes in each composite. For all the composites evaluated the dynamic crack propagation characteristics of the composites are observed to be strongly dependent on the volume fraction of the ductile phase reinforcement in the composite, the yield stress of the ductile phase reinforcement, the micro-structural arrangement of the ductile phase reinforcements with respect to the notch, and the impact velocity employed in the particular experiment.

  19. The most plausible explanation of the cyclic period changes in close binaries: the case of the RS CVn-type binary WW Dra

    NASA Astrophysics Data System (ADS)

    Liao, W.-P.; Qian, S.-B.

    2010-07-01

    Cyclic period changes are a fairly common phenomenon in close binary systems and are usually explained as being caused either by the magnetic activity of one or both components or by the light travel time effect (LTTE) of a third body. We searched the orbital period changes in 182 EA-type (including the 101 Algol systems used by Hall), 43 EB-type and 53 EW-type binaries with known mass ratio and spectral type of the secondary component. We reproduced and improved the diagram in Hall according to the new collected data. Our plots do not support the conclusion derived by Hall that cyclic period changes are restricted to binaries having a secondary component with spectral type later than F5. The presence of period changes among systems with a secondary component of early type indicates that magnetic activity is one, but not the only, cause of the period variation. It is discovered that cyclic period changes, probably resulting from the presence of a third body, are more frequent in EW-type binaries among close systems. Therefore, the most plausible explanation of the cyclic period changes is the LTTE through the presence of a third body. Using the century-long historical record of the times of light minimum, we analysed the cyclic period change in the Algol binary WW Dra. It is found that the orbital period of the binary shows a ~112.2-yr cyclic variation with an amplitude of ~0.1977d. The cyclic oscillation can be attributed to the LTTE by means of a third body with a mass no less than 6.43Msolar. However, no spectral lines of the third body were discovered, indicating that it may be a candidate black hole. The third body is orbiting the binary at a distance closer than 14.4 au and may play an important role in the evolution of this system.

  20. Genetic Heterogeneity of Borrelia burgdorferi Sensu Lato in the Southern United States Based on Restriction Fragment Length Polymorphism and Sequence Analysis

    PubMed Central

    Lin, T.; Oliver, J. H.; Gao, L.; Kollars, T. M.; Clark, K. L.

    2001-01-01

    Fifty-six strains of Borrelia burgdorferi sensu lato, isolated from ticks and vertebrate animals in Missouri, South Carolina, Georgia, Florida, and Texas, were identified and characterized by PCR-restriction fragment length polymorphism (RFLP) analysis of rrf (5S)-rrl (23S) intergenic spacer amplicons. A total of 241 to 258 bp of intergenic spacers between tandemly duplicated rrf (5S) and rrl (23S) was amplified by PCR. MseI and DraI restriction fragment polymorphisms were used to analyze these strains. PCR-RFLP analysis results indicated that the strains represented at least three genospecies and 10 different restriction patterns. Most of the strains isolated from the tick Ixodes dentatus in Missouri and Georgia belonged to the genospecies Borrelia andersonii. Excluding the I. dentatus strains, most southern strains, isolated from the ticks Ixodes scapularis and Ixodes affinis, the cotton rat (Sigmodon hispidus), and cotton mouse (Peromyscus gossypinus) in Georgia and Florida, belonged to Borrelia burgdorferi sensu stricto. Seven strains, isolated from Ixodes minor, the wood rat (Neotoma floridana), the cotton rat, and the cotton mouse in South Carolina and Florida, belonged to Borrelia bissettii. Two strains, MI-8 from Florida and TXW-1 from Texas, exhibited MseI and DraI restriction patterns different from those of previously reported genospecies. Eight Missouri tick strains (MOK-3a group) had MseI patterns similar to that of B. andersonii reference strain 21038 but had a DraI restriction site in the spacer. Strain SCGT-8a had DraI restriction patterns identical to that of strain 25015 (B. bissettii) but differed from strain 25015 in its MseI restriction pattern. Strain AI-1 had the same DraI pattern as other southern strains in the B. bissettii genospecies but had a distinct MseI profile. The taxonomic status of these atypical strains needs to be further evaluated. To clarify the taxonomic positions of these atypical Borrelia strains, the complete sequences of

  1. Polymorphism of phosphoric oxide

    USGS Publications Warehouse

    Hill, W.L.; Faust, G.T.; Hendricks, S.B.

    1943-01-01

    The melting points and monotropic relationship of three crystalline forms of phosphoric oxide were determined by the method of quenching. Previous vapor pressure data are discussed and interpreted to establish a pressure-temperature diagram (70 to 600??) for the one-component system. The system involves three triple points, at which solid, liquid and vapor (P4O10) coexist in equilibrium, namely: 420?? and 360 cm., 562?? and 43.7 cm. and 580?? and 55.5 cm., corresponding to the hexagonal, orthorhombic and stable polymorphs, respectively, and at least two distinct liquids, one a stable polymer of the other, which are identified with the melting of the stable form and the hexagonal modification, respectively. Indices of refraction of the polymorphs and glasses were determined. The density and the thermal, hygroscopic and structural properties of the several phases are discussed.

  2. Facts and fictions about polymorphism.

    PubMed

    Cruz-Cabeza, Aurora J; Reutzel-Edens, Susan M; Bernstein, Joel

    2015-12-01

    We present new facts about polymorphism based on (i) crystallographic data from the Cambridge Structural Database (CSD, a database built over 50 years of community effort), (ii) 229 solid form screens conducted at Hoffmann-La Roche and Eli Lilly and Company over the course of 8+ and 15+ years respectively and (iii) a dataset of 446 polymorphic crystals with energies and properties computed with modern DFT-d methods. We found that molecular flexibility or size has no correlation with the ability of a compound to be polymorphic. Chiral molecules, however, were found to be less prone to polymorphism than their achiral counterparts and compounds able to hydrogen bond exhibit only a slightly higher propensity to polymorphism than those which do not. Whilst the energy difference between polymorphs is usually less than 1 kcal mol(-1), conformational polymorphs are capable of differing by larger values (up to 2.5 kcal mol(-1) in our dataset). As overall statistics, we found that one in three compounds in the CSD are polymorphic whilst at least one in two compounds from the Roche and Lilly set display polymorphism with a higher estimate of up to three in four when compounds are screened intensively. Whilst the statistics provide some guidance of expectations, each compound constitutes a new challenge and prediction and realization of targeted polymorphism still remains a holy grail of materials sciences. PMID:26400501

  3. [Polymorphs of clopidogrel bisulfate].

    PubMed

    Liu, Yi; Huang, Hai-Wei; Wu, Jian-Min; Shi, Ya-Qin; Yang, La-Hu

    2013-08-01

    This paper is to report the polymorphism of raw materials of clopidogrel bisulfate at home and abroad. By the analysis of Fourier transform infrared spectroscopy (FTIR) and powder X-ray diffraction (p-XRD), samples are roughly classified into two groups, except one patent material. And the differential scanning calorimeter (DSC) examination showed more detailed information for these materials. The results of the study could provide comprehensive basis for the quality evaluation of clopidogrel bisulfate. PMID:24187849

  4. Abnormal glucose tolerance and insulin resistance in polycystic ovary syndrome amongst the Taiwanese population- not correlated with insulin receptor substrate-1 Gly972Arg/Ala513Pro polymorphism

    PubMed Central

    Lin, Ta-Chin; Yen, Jui-Mei; Gong, Kum-Bing; Kuo, Tsung-Cheng; Ku, Dong-Chi; Liang, Shu-Fen; Wu, Ming-Jiuan

    2006-01-01

    Background Insulin resistance and glucose dysmetabolism in polycystic ovary syndrome (PCOS) are related with the polymorphisms in the genes encoding the insulin receptor substrate (IRS) proteins, especially Gly972Arg/Ala513Pro polymorphism being reported to be associated with type-2 diabetes and PCOS. We intended to assess the prevalence of abnormal glucose tolerance (AGT) and insulin resistance in Taiwanese PCOS women. We also tried to assess whether the particular identity of Gly972Arg/Ala513Pro polymorphic alleles of the IRS-1 gene mutation can be used as an appropriate diagnostic indicator for PCOS. Methods We designed a prospective clinical study. Forty-seven Taiwanese Hoklo and Hakka women, diagnosed with PCOS were enrolled in this study as were forty-five healthy Hoklo and Hakka women as the control group. Insulin resistance was evaluated with fasting insulin, fasting glucose/insulin ratio, and homeostasis model assessment index for insulin resistance (HOMAIR). The genomic DNA of the subjects was amplified by PCR and digested by restriction fragmented length polymorphism (RFLP) with Bst N1 used for codon 972 and Dra III for codon 513. Results AGT was found in 46.8% of these PCOS patients and was significantly related to high insulin resistance rather than the low insulin resistance. Those patients with either insulin resistance or AGT comprised the majority of PCOS affected patients (AGT + fasting insulin ≥17: 83%, AGT + glucose/insulin ratio ≥6.5: 85.1%, AGT + HOMAIR ≥ 2: 87.2%, and AGT + HOMAIR ≥ 3.8: 72.3%). None of the tested samples revealed any polymorphism due to the absence of any Dra III recognition site or any Bst N1 recognition site in the amplified PCR fragment digested by restriction fragmented length polymorphism. Conclusion There is significantly high prevalence of AGT and insulin resistance in PCOS women, but Gly972Arg and Ala513Pro polymorphic alleles of IRS-1 are rare and are not associated with the elevated risk of PCOS amongst

  5. The sweet taste quality is linked to a cluster of taste fibers in primates: lactisole diminishes preference and responses to sweet in S fibers (sweet best) chorda tympani fibers of M. fascicularis monkey

    PubMed Central

    Wang, Yiwen; Danilova, Vicktoria; Cragin, Tiffany; Roberts, Thomas W; Koposov, Alexey; Hellekant, Göran

    2009-01-01

    Background Psychophysically, sweet and bitter have long been considered separate taste qualities, evident already to the newborn human. The identification of different receptors for sweet and bitter located on separate cells of the taste buds substantiated this separation. However, this finding leads to the next question: is bitter and sweet also kept separated in the next link from the taste buds, the fibers of the taste nerves? Previous studies in non-human primates, P. troglodytes, C. aethiops, M. mulatta, M. fascicularis and C. jacchus, suggest that the sweet and bitter taste qualities are linked to specific groups of fibers called S and Q fibers. In this study we apply a new sweet taste modifier, lactisole, commercially available as a suppressor of the sweetness of sugars on the human tongue, to test our hypothesis that sweet taste is conveyed in S fibers. Results We first ascertained that lactisole exerted similar suppression of sweetness in M. fascicularis, as reported in humans, by recording their preference of sweeteners and non- sweeteners with and without lactisole in two-bottle tests. The addition of lactisole significantly diminished the preference for all sweeteners but had no effect on the intake of non-sweet compounds or the intake of water. We then recorded the response to the same taste stimuli in 40 single chorda tympani nerve fibers. Comparison between single fiber nerve responses to stimuli with and without lactisole showed that lactisole only suppressed the responses to sweeteners in S fibers. It had no effect on the responses to any other stimuli in all other taste fibers. Conclusion In M. fascicularis, lactisole diminishes the attractiveness of compounds, which taste sweet to humans. This behavior is linked to activity of fibers in the S-cluster. Assuming that lactisole blocks the T1R3 monomer of the sweet taste receptor T1R2/R3, these results present further support for the hypothesis that S fibers convey taste from T1R2/R3 receptors, while

  6. Polymorphic Electronic Circuits

    NASA Technical Reports Server (NTRS)

    Stoica, Adrian

    2004-01-01

    Polymorphic electronics is a nascent technological discipline that involves, among other things, designing the same circuit to perform different analog and/or digital functions under different conditions. For example, a circuit can be designed to function as an OR gate or an AND gate, depending on the temperature (see figure). Polymorphic electronics can also be considered a subset of polytronics, which is a broader technological discipline in which optical and possibly other information- processing systems could also be designed to perform multiple functions. Polytronics is an outgrowth of evolvable hardware (EHW). The basic concepts and some specific implementations of EHW were described in a number of previous NASA Tech Briefs articles. To recapitulate: The essence of EHW is to design, construct, and test a sequence of populations of circuits that function as incrementally better solutions of a given design problem through the selective, repetitive connection and/or disconnection of capacitors, transistors, amplifiers, inverters, and/or other circuit building blocks. The evolution is guided by a search-and-optimization algorithm (in particular, a genetic algorithm) that operates in the space of possible circuits to find a circuit that exhibits an acceptably close approximation of the desired functionality. The evolved circuits can be tested by computational simulation (in which case the evolution is said to be extrinsic), tested in real hardware (in which case the evolution is said to be intrinsic), or tested in random sequences of computational simulation and real hardware (in which case the evolution is said to be mixtrinsic).

  7. Polymorphic Evolutionary Games.

    PubMed

    Fishman, Michael A

    2016-06-01

    In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. PMID:27016340

  8. Polymorphism of Alcohol Metabolizing Gene ADH3 Predisposes to Development of Alcoholic Pancreatitis in North Indian Population

    PubMed Central

    Singh, Divya; Negi, Tajwar S.; Upadhyay, Ghanshyam; Choudhuri, Gourdas

    2015-01-01

    Background and aim: Genetic factors regulating alcohol metabolism could predispose in developing alcoholic pancreatitis (ACP). Studies revealed that alcohol could be metabolized by both ways, oxidative and non-oxidative. The main oxidative pathway includes alcohol dehydrogenase (ADH), aldehyde dehydrogenase (ALDH), and cytochrome P450 enzyme. We investigated the association of polymorphisms in these enzymes with the alcoholic pancreatitis in the north Indian population. Method: Patients with alcoholic pancreatitis (ACP; n = 72), tropical calcific pancreatitis (TCP; n = 75), alcoholic controls (AC; n = 40), and healthy controls (HC; n = 100) were included in the study. Blood samples were collected from the subjects in EDTA coated vials. DNA was extracted and genotyping for ADH3, ALDH2, and CYP2E1 was done by PCR-RFLP (polymerase chain reaction—restriction fragment length polymorphism). The products were analyzed by gel electrophoresis. Result: The frequency distribution of ADH3*1/*1 genotype was significantly higher in ACP group (59.7%) compared with TCP (38.7%), HC (42%), and AC (37.5%) and was found to be associated with increased risk of alcoholic pancreatitis. There was no statistically significant difference between the frequency distribution of ADH3*1/*1, ADH3*1/*2, and ADH3*2/*2 genotypes between TCP and HC or healthy alcoholics. ALDH2 gene was monomorphic in our population, and the frequencies for CYP2E1 intron 6 Dra I polymorphism were comparable in all the four groups. Conclusion: This study shows that carriers of ADH3*1/*1 individuals consuming alcohol are at higher risk for alcoholic pancreatitis than those with other genotypes such as ADH3*1/*2 and ADH3*2/*2. PMID:26734614

  9. Preferential Nucleation during Polymorphic Transformations

    PubMed Central

    Sharma, H.; Sietsma, J.; Offerman, S. E.

    2016-01-01

    Polymorphism is the ability of a solid material to exist in more than one phase or crystal structure. Polymorphism may occur in metals, alloys, ceramics, minerals, polymers, and pharmaceutical substances. Unresolved are the conditions for preferential nucleation during polymorphic transformations in which structural relationships or special crystallographic orientation relationships (OR’s) form between the nucleus and surrounding matrix grains. We measured in-situ and simultaneously the nucleation rates of grains that have zero, one, two, three and four special OR’s with the surrounding parent grains. These experiments show a trend in which the activation energy for nucleation becomes smaller – and therefore nucleation more probable - with increasing number of special OR’s. These insights contribute to steering the processing of polymorphic materials with tailored properties, since preferential nucleation affects which crystal structure forms, the average grain size and texture of the material, and thereby - to a large extent - the final properties of the material. PMID:27484579

  10. Preferential Nucleation during Polymorphic Transformations

    NASA Astrophysics Data System (ADS)

    Sharma, H.; Sietsma, J.; Offerman, S. E.

    2016-08-01

    Polymorphism is the ability of a solid material to exist in more than one phase or crystal structure. Polymorphism may occur in metals, alloys, ceramics, minerals, polymers, and pharmaceutical substances. Unresolved are the conditions for preferential nucleation during polymorphic transformations in which structural relationships or special crystallographic orientation relationships (OR’s) form between the nucleus and surrounding matrix grains. We measured in-situ and simultaneously the nucleation rates of grains that have zero, one, two, three and four special OR’s with the surrounding parent grains. These experiments show a trend in which the activation energy for nucleation becomes smaller – and therefore nucleation more probable - with increasing number of special OR’s. These insights contribute to steering the processing of polymorphic materials with tailored properties, since preferential nucleation affects which crystal structure forms, the average grain size and texture of the material, and thereby - to a large extent - the final properties of the material.

  11. Preferential Nucleation during Polymorphic Transformations.

    PubMed

    Sharma, H; Sietsma, J; Offerman, S E

    2016-01-01

    Polymorphism is the ability of a solid material to exist in more than one phase or crystal structure. Polymorphism may occur in metals, alloys, ceramics, minerals, polymers, and pharmaceutical substances. Unresolved are the conditions for preferential nucleation during polymorphic transformations in which structural relationships or special crystallographic orientation relationships (OR's) form between the nucleus and surrounding matrix grains. We measured in-situ and simultaneously the nucleation rates of grains that have zero, one, two, three and four special OR's with the surrounding parent grains. These experiments show a trend in which the activation energy for nucleation becomes smaller - and therefore nucleation more probable - with increasing number of special OR's. These insights contribute to steering the processing of polymorphic materials with tailored properties, since preferential nucleation affects which crystal structure forms, the average grain size and texture of the material, and thereby - to a large extent - the final properties of the material. PMID:27484579

  12. Nucleation of polymorphic amyloid fibrils.

    PubMed

    Auer, Stefan

    2015-03-10

    One and the same protein can self-assemble into amyloid fibrils with different morphologies. The phenomenon of fibril polymorphism is relevant biologically because different fibril polymorphs can have different toxicity, but there is no tool for predicting which polymorph forms and under what conditions. Here, we consider the nucleation of polymorphic amyloid fibrils occurring by direct polymerization of monomeric proteins into fibrils. We treat this process within the framework of our newly developed nonstandard nucleation theory, which allows prediction of the concentration dependence of the nucleation rate for different fibril polymorphs. The results highlight that the concentration dependence of the nucleation rate is closely linked with the protein solubility and a threshold monomer concentration below which fibril formation becomes biologically irrelevant. The relation between the nucleation rate, the fibril solubility, the threshold concentration, and the binding energies of the fibril building blocks within fibrils might prove a valuable tool for designing new experiments to control the formation of particular fibril polymorphs. PMID:25762329

  13. New polymorphous computing fabric.

    SciTech Connect

    Wolinski, C.; Gokhale, M.; McCabe, K. P.

    2002-01-01

    This paper introduces a new polymorphous computing Fabric well suited to DSP and Image Processing and describes its implementation on a Configurable System on a Chip (CSOC). The architecture is highly parameterized and enables customization of the synthesized Fabric to achieve high performance for a specific class of application. For this reason it can be considered to be a generic model for hardware accelerator synthesis from a high level specification. Another important innovation is the Fabric uses a global memory concept, which gives the host processor random access to all the variables and instructions on the Fabric. The Fabric supports different computing models including MIMD, SPMD and systolic flow and permits dynamic reconfiguration. We present a specific implementation of a bank of FIR filters on a Fabric composed of 52 cells on the Altera Excalibur ARM running at 33 MHz. The theoretical performance of this Fabric is 1.8 GMACh. For the FIR application we obtain 1.6 GMAC/s real performance. Some automatic tools have been developed like the tool to provide a host access utility and assembler.

  14. Coding polymorphism for phylogeny reconstruction.

    PubMed

    Kornet, D J; Turner, H

    1999-06-01

    The methodology of coding polymorphic taxa has received limited attention to date. A search of the taxonomic literature revealed seven types of coding methods. Apart from ignoring polymorphic characters (sometimes called the fixed-only method), two main categories can be distinguished: methods that identify the start of a new character state with the origin of an evolutionary novelty, and methods that identify the new state with the fixation of a novelty. The methods of the first category introduce soft reversals, yielding signals that support cladograms incompatible with true phylogenies. We conclude that coding the plesiomorphy is the method to be preferred, unless the ancestral state is unknown, in which case coding as ambiguous is recommended. This holds for coding polymorphism in species as well as in supraspecific taxa. In this light we remark on methods proposed by previous authors. PMID:12066713

  15. Adaptive dynamics of saturated polymorphisms.

    PubMed

    Kisdi, Éva; Geritz, Stefan A H

    2016-03-01

    We study the joint adaptive dynamics of n scalar-valued strategies in ecosystems where n is the maximum number of coexisting strategies permitted by the (generalized) competitive exclusion principle. The adaptive dynamics of such saturated systems exhibits special characteristics, which we first demonstrate in a simple example of a host-pathogen-predator model. The main part of the paper characterizes the adaptive dynamics of saturated polymorphisms in general. In order to investigate convergence stability, we give a new sufficient condition for absolute stability of an arbitrary (not necessarily saturated) polymorphic singularity and show that saturated evolutionarily stable polymorphisms satisfy it. For the case [Formula: see text], we also introduce a method to construct different pairwise invasibility plots of the monomorphic population without changing the selection gradients of the saturated dimorphism. PMID:26676357

  16. Genetics Home Reference: catecholaminergic polymorphic ventricular tachycardia

    MedlinePlus

    ... for This Page Cerrone M, Napolitano C, Priori SG. Catecholaminergic polymorphic ventricular tachycardia: A paradigm to understand ... on PubMed Central Liu N, Ruan Y, Priori SG. Catecholaminergic polymorphic ventricular tachycardia. Prog Cardiovasc Dis. 2008 ...

  17. Crystal Polymorphs of Barbital: News about a Classic Polymorphic System

    PubMed Central

    2013-01-01

    Barbital is a hypnotic agent that has been intensely studied for many decades. The aim of this work was to establish a clear and comprehensible picture of its polymorphic system. Four of the six known solid forms of barbital (denoted I0, III, IV, and V) were characterized by various analytical techniques, and the thermodynamic relationships between the polymorph phases were established. The obtained data permitted the construction of the first semischematic energy/temperature diagram for the barbital system. The modifications I0, III, and V are enantiotropically related to one another. Polymorph IV is enantiotropically related to V and monotropically related to the other two forms. The transition points for the pairs I0/III, I0/V, and III/IV lie below 20 °C, and the transition point for IV/V is above 20 °C. At room temperature, the order of thermodynamic stability is I0 > III > V > IV. The metastable modification III is present in commercial samples and has a high kinetic stability. The solid-state NMR spectra provide information on aspects of crystallography (viz., the asymmetric units and the nature of hydrogen bonding). The known correlation between specific N–H···O=C hydrogen bonding motifs of barbiturates and certain IR characteristics was used to predict the H-bonded pattern of polymorph IV. PMID:24283960

  18. Amplified fragment length polymorphism and virulence polymorphism in Puccinia hordei

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Puccinia hordei is the causal agent of barley leaf rust. To study the genetic diversity in P. hordei, 45 isolates with diverse virulence patterns and geographical origins were analyzed using amplified fragment length polymorphism markers. Two pathotypes of Puccinia graminis f. sp. tritici and one is...

  19. Polymorphism in pleistocene land snails.

    PubMed

    Owen, D F

    1966-04-01

    Under suitable conditions the colors and patterns of the shells of land snails may be preserved for thousands of years. In a late Pleistocene population of Limicolaria martensiana all the major color forms that occur in modern living snails may be distinguished, and the basic polymorphism is at least 8,000 to 10,000 year old. PMID:17830234

  20. Effect of EGF, AREG and LIF genes polymorphisms on reproductive traits in pigs.

    PubMed

    Mucha, Aurelia; Ropka-Molik, Katarzyna; Piórkowska, Katarzyna; Tyra, Mirosław; Oczkowicz, Maria

    2013-02-01

    The aim of our study was to determine the associations between mutations in the EGF, AREG, LIF genes and the reproductive traits in pigs. We examined sows of two Polish breeds, which are used as a dam line in Polish breeding: Large White and Landrace. The reproductive traits investigated were: number of piglets born alive (NBA), number of alive piglets on 21st day (N21), age of sows at first farrowing (AFF) and interval between two successive litters (IBTSL). Polymorphisms in AREG and LIF (C4950G) genes were detected by using PCR-RFLP methods, with restriction enzymes StyI and DraIII, respectively, in EGF gene by using PCR method, while C6988T in LIF gene by PCR-SSCP methods. The statistically significant differences were found at the locus EGF: sows with BB genotype showed higher number of piglets born alive (NBA) and higher number of alive piglets on 21st day (N21) (P<0.01 and P<0.05) when compared to the other genotypes. At the LIF1 locus sows of AA genotype had higher number of NBA (P<0.01) when compared to BB genotype, and at the LIF3 sows of BB had better results for this trait when compared to AA and AB genotype (P<0.01 and P<0.05). In our study, we obtained also statistically significant results for association between AREG gene and reproductive traits. In parities 2 to 4, statistically significant differences were observed between sows of A1A1 and A1A2 genotype of the AREG gene for NBA (P<0.05) and between AA and BB genotypes of the LIF1 gene for NBA and N21 (P<0.01 and P<0.05). PMID:23313365

  1. Neutral behavior of shared polymorphism

    PubMed Central

    Clark, Andrew G.

    1997-01-01

    Several cases have been described in the literature where genetic polymorphism appears to be shared between a pair of species. Here we examine the distribution of times to random loss of shared polymorphism in the context of the neutral Wright–Fisher model. Order statistics are used to obtain the distribution of times to loss of a shared polymorphism based on Kimura’s solution to the diffusion approximation of the Wright–Fisher model. In a single species, the expected absorption time for a neutral allele having an initial allele frequency of ½ is 2.77 N generations. If two species initially share a polymorphism, that shared polymorphism is lost as soon as either of two species undergoes fixation. The loss of a shared polymorphism thus occurs sooner than loss of polymorphism in a single species and has an expected time of 1.7 N generations. Molecular sequences of genes with shared polymorphism may be characterized by the count of the number of sites that segregate in both species for the same nucleotides (or amino acids). The distribution of the expected numbers of these shared polymorphic sites also is obtained. Shared polymorphism appears to be more likely at genetic loci that have an unusually large number of segregating alleles, and the neutral coalescent proves to be very useful in determining the probability of shared allelic lineages expected by chance. These results are related to examples of shared polymorphism in the literature. PMID:9223256

  2. IPD: the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Marsh, Steven G E

    2007-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer cell immunoglobulin-like receptors (KIRs); IPD-MHC, a database of sequences of the major histocompatibility complex (MHC) of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC, share the same database structure. PMID:18449992

  3. The Single Nucleotide Polymorphism Consortium

    NASA Technical Reports Server (NTRS)

    Morgan, Michael

    2003-01-01

    I want to discuss both the Single Nucleotide Polymorphism (SNP) Consortium and the Human Genome Project. I am afraid most of my presentation will be thin on law and possibly too high on rhetoric. Having been engaged in a personal and direct way with these issues as a trained scientist, I find it quite difficult to be always as objective as I ought to be.

  4. Parasitic polymorphism of Coccidioides spp

    PubMed Central

    2014-01-01

    Background Coccidioides spp. is the ethiological agent of coccidioidomycosis, an infection that can be fatal. Its diagnosis is complicated, due to that it shares clinical and histopathological characteristics with other pulmonary mycoses. Coccidioides spp. is a dimorphic fungus and, in its saprobic phase, grows as a mycelium, forming a large amount of arthroconidia. In susceptible persons, arthroconidia induce dimorphic changes into spherules/endospores, a typical parasitic form of Coccidioides spp. In addition, the diversity of mycelial parasitic forms has been observed in clinical specimens; they are scarcely known and produce errors in diagnosis. Methods We presented a retrospective study of images from specimens of smears with 15% potassium hydroxide, cytology, and tissue biopsies of a histopathologic collection from patients with coccidioidomycosis seen at a tertiary-care hospital in Mexico City. Results The parasitic polymorphism of Coccidioides spp. observed in the clinical specimens was as follows: i) spherules/endospores in different maturation stages; ii) pleomorphic cells (septate hyphae, hyphae composed of ovoid and spherical cells, and arthroconidia), and iii) fungal ball formation (mycelia with septate hyphae and arthroconidia). Conclusions The parasitic polymorphism of Coccidioides spp. includes the following: spherules/endospores, arthroconidia, and different forms of mycelia. This knowledge is important for the accurate diagnosis of coccidioidomycosis. In earlier studies, we proposed the integration of this diversity of forms in the Coccidioides spp. parasitic cycle. The microhabitat surrounding the fungus into the host would favor the parasitic polymorphism of this fungus, and this environment may assist in the evolution toward parasitism of Coccidioides spp. PMID:24750998

  5. Polymorphic transporters and platinum pharmacodynamics

    PubMed Central

    Sprowl, Jason A.; Ness, Rachel A.; Sparreboom, Alex

    2013-01-01

    Summary Several solute carriers and ATP-binding cassette transporters have been implicated in the influx or efflux of platinum-based chemotherapeutic agents such as cisplatin, carboplatin, and oxaliplatin. Given that many of these proteins are highly polymorphic, the genetic status of these proteins could be an important contributor to the extensive interindividual pharmacokinetic variability associated with the clinical use of these agents. In this review article, we provide an updated overview of the various transporters that have shown promise in animal models or patient populations in facilitating the movement of platinum-based agents across cell membranes, and how their function is associated with drug disposition or pharmacodynamic effects. PMID:22986709

  6. Analysis of the bacterial diversity existing on animal hide and wool: development of a preliminary PCR-restriction fragment length polymorphism fingerprint database for identifying isolates.

    PubMed

    Chen, Yu; Gao, Hongwei; Zhang, Yanming; Deng, Mingjun; Wu, Zhenxing; Zhu, Laihua; Duan, Qing; Xu, Biao; Liang, Chengzhu; Yue, Zhiqin; Xiao, Xizhi

    2012-01-01

    Twenty-one bacterial strains were isolated from imported cattle hide and rabbit wool using two types of media, nutrient broth, and nutrient broth with serum. The bacteria identified were Brevibacillus laterosporus, Leclercia adecarboxylata, Peptococcus niger, Bacillus circulans, Raoultella ornithinolytica, Bacillus subtilis, Bacillus cereus, Bacillus thermobacillus, Bacillus choshinensis, Bacillus sphaericus, Acinetobacter haemolyticus, Sphingomonas paucimobilis, Bacillus thuringiensis, Staphylococcus intermedius, Mycobacteria, Moraxella, Klebsiella pneumoniae, Ralstonia pickettii, Staphylococcus chromogenes, Comamonas testosteroni, and Cupriavidus pauculus. The 16s rDNA gene of each bacterium was amplified using the universal primers 27f and 1492r. The amplicons were digested with AvaI, BamHI, BgII, DraI, EcoRI, EcoRV, HindIII, HinfI, HpaI, PstI, SmaI, TaqII, XbaI, XmaI, AluI, XhoI, and PvuI individually. A specific fingerprint from the PCR-restriction fragment length polymorphism method based on 16s rDNA was obtained for each bacterium. The results showed that the method developed was useful not only for bacterial identification but also for the etiological investigation of pathogens in imported animal hair and wool. PMID:23451394

  7. Pharmacogenetics and human genetic polymorphisms.

    PubMed

    Daly, Ann K

    2010-08-01

    The term pharmacogenetics was first used in the late 1950s and can be defined as the study of genetic factors affecting drug response. Prior to formal use of this term, there was already clinical data available in relation to variable patient responses to the drugs isoniazid, primaquine and succinylcholine. The subject area developed rapidly, particularly with regard to genetic factors affecting drug disposition. There is now comprehensive understanding of the molecular basis for variable drug metabolism by the cytochromes P450 and also for variable glucuronidation, acetylation and methylation of certain drugs. Some of this knowledge has already been translated to the clinic. The molecular basis of variation in drug targets, such as receptors and enzymes, is generally less well understood, although there is consistent evidence that polymorphisms in the genes encoding the beta-adrenergic receptors and the enzyme vitamin K epoxide reductase is of clinical importance. The genetic basis of rare idiosyncratic adverse drug reactions had also been examined. Susceptibility to reactions affecting skin and liver appears to be determined in part by the HLA (human leucocyte antigen) genotype, whereas reactions affecting the heart and muscle may be determined by polymorphisms in genes encoding ion channels and transporters respectively. Genome-wide association studies are increasingly being used to study drug response and susceptibility to adverse drug reactions, resulting in identification of some novel pharmacogenetic associations. PMID:20626352

  8. Polymorphism and Structure of Carbons

    NASA Astrophysics Data System (ADS)

    Delhaès, P.; Issi, J. P.; Bonnamy, S.; Launois, P.

    In this chapter, our purpose is to introduce carbon materials, situating the nanotubes inside this polymorphic zoo. We aim at giving the reader the basic notions on carbon materials structural and physical properties, necessary for the understanding of the following chapters. The introductory section gives a historical background about the peculiar carbon element and the numerous carbon materials which have been identified up to now. Then in a second part a classical thermodynamic approach is presented to describe the crystalline and non-crystalline forms of carbon, up to fullerenes and nanotubes. It is shown that the choice of the processing ways, including the crucial role played by the temperature, is fundamental to control the final type of material. In particular the different processes to prepare non-crystalline graphitic carbons are described in Sect. 1.3. Based on the texture symmetries different types of classical carbon materials are presented in relation with their numerous industrial applications. Then a general introduction is given concerning mainly the transport properties of the crystalline forms, including the intercalation compounds, but also their `avatars' as pregraphitic carbons. In a final part, this panorama, which is going from the classical forms to the more molecular ones including nanotubes, is completed by the presentation of similar compounds. Starting from neighboring elements in the periodic classification we show that doped carbons and parent compounds present a similar polymorphism which enlarges this general introduction.

  9. Spinning up the polymorphs of calcium carbonate

    PubMed Central

    Boulos, Ramiz A.; Zhang, Fei; Tjandra, Edwin S.; Martin, Adam D.; Spagnoli, Dino; Raston, Colin L.

    2014-01-01

    Controlling the growth of the polymorphs of calcium carbonate is important in understanding the changing environmental conditions in the oceans. Aragonite is the main polymorph in the inner shells of marine organisms, and can be readily converted to calcite, which is the most stable polymorph of calcium carbonate. Both of these polymorphs are significantly more stable than vaterite, which is the other naturally occurring polymorph of calcium carbonate, and this is reflected in its limited distribution in nature. We have investigated the effect of high shear forces on the phase behaviour of calcium carbonate using a vortex fluidic device (VFD), with experimental parameters varied to explore calcium carbonate mineralisation. Variation of tilt angle, rotation speed and temperature allow for control over the size, shape and phase of the resulting calcium carbonate. PMID:24448077

  10. Temporal Expression of Peripheral Blood Leukocyte Biomarkers in a Macaca fascicularis Infection Model of Tuberculosis; Comparison with Human Datasets and Analysis with Parametric/Non-parametric Tools for Improved Diagnostic Biomarker Identification

    PubMed Central

    Wareham, Alice; Lewandowski, Kuiama S.; Williams, Ann; Dennis, Michael J.; Sharpe, Sally; Vipond, Richard; Silman, Nigel; Ball, Graham

    2016-01-01

    A temporal study of gene expression in peripheral blood leukocytes (PBLs) from a Mycobacterium tuberculosis primary, pulmonary challenge model Macaca fascicularis has been conducted. PBL samples were taken prior to challenge and at one, two, four and six weeks post-challenge and labelled, purified RNAs hybridised to Operon Human Genome AROS V4.0 slides. Data analyses revealed a large number of differentially regulated gene entities, which exhibited temporal profiles of expression across the time course study. Further data refinements identified groups of key markers showing group-specific expression patterns, with a substantial reprogramming event evident at the four to six week interval. Selected statistically-significant gene entities from this study and other immune and apoptotic markers were validated using qPCR, which confirmed many of the results obtained using microarray hybridisation. These showed evidence of a step-change in gene expression from an ‘early’ FOS-associated response, to a ‘late’ predominantly type I interferon-driven response, with coincident reduction of expression of other markers. Loss of T-cell-associate marker expression was observed in responsive animals, with concordant elevation of markers which may be associated with a myeloid suppressor cell phenotype e.g. CD163. The animals in the study were of different lineages and these Chinese and Mauritian cynomolgous macaque lines showed clear evidence of differing susceptibilities to Tuberculosis challenge. We determined a number of key differences in response profiles between the groups, particularly in expression of T-cell and apoptotic makers, amongst others. These have provided interesting insights into innate susceptibility related to different host `phenotypes. Using a combination of parametric and non-parametric artificial neural network analyses we have identified key genes and regulatory pathways which may be important in early and adaptive responses to TB. Using comparisons

  11. Temporal Expression of Peripheral Blood Leukocyte Biomarkers in a Macaca fascicularis Infection Model of Tuberculosis; Comparison with Human Datasets and Analysis with Parametric/Non-parametric Tools for Improved Diagnostic Biomarker Identification.

    PubMed

    Javed, Sajid; Marsay, Leanne; Wareham, Alice; Lewandowski, Kuiama S; Williams, Ann; Dennis, Michael J; Sharpe, Sally; Vipond, Richard; Silman, Nigel; Ball, Graham; Kempsell, Karen E

    2016-01-01

    A temporal study of gene expression in peripheral blood leukocytes (PBLs) from a Mycobacterium tuberculosis primary, pulmonary challenge model Macaca fascicularis has been conducted. PBL samples were taken prior to challenge and at one, two, four and six weeks post-challenge and labelled, purified RNAs hybridised to Operon Human Genome AROS V4.0 slides. Data analyses revealed a large number of differentially regulated gene entities, which exhibited temporal profiles of expression across the time course study. Further data refinements identified groups of key markers showing group-specific expression patterns, with a substantial reprogramming event evident at the four to six week interval. Selected statistically-significant gene entities from this study and other immune and apoptotic markers were validated using qPCR, which confirmed many of the results obtained using microarray hybridisation. These showed evidence of a step-change in gene expression from an 'early' FOS-associated response, to a 'late' predominantly type I interferon-driven response, with coincident reduction of expression of other markers. Loss of T-cell-associate marker expression was observed in responsive animals, with concordant elevation of markers which may be associated with a myeloid suppressor cell phenotype e.g. CD163. The animals in the study were of different lineages and these Chinese and Mauritian cynomolgous macaque lines showed clear evidence of differing susceptibilities to Tuberculosis challenge. We determined a number of key differences in response profiles between the groups, particularly in expression of T-cell and apoptotic makers, amongst others. These have provided interesting insights into innate susceptibility related to different host `phenotypes. Using a combination of parametric and non-parametric artificial neural network analyses we have identified key genes and regulatory pathways which may be important in early and adaptive responses to TB. Using comparisons between

  12. Polymorphs and Versatile Solvates of 7-Hydroxyisoflavone.

    PubMed

    Gong, Ningbo; Zhang, Guoshun; Jin, Guimin; Du, Guanhua; Lu, Yang

    2016-04-01

    7-hydroxyisoflavone has been crystallized, identified, and characterized as 2 solvent-free conformational polymorphs and 5 solvates, which differ from each other in the mode of packing and in molecular conformation. All the 7 crystal structures were previously unreported. The conformational polymorphs and solvates were compared by Hirshfeld surface and fingerprint plot analysis and were spectroscopically characterized by powder X-ray diffraction, differential scanning calorimetry, and thermal gravimetric analysis. Hydrogen bond played an important role in the formation of polymorphs. From this study, we can predict that more solvates could be cultivated in other polarity solvents such as isopropanol or 2-butanol at appropriate conditions. PMID:26935882

  13. [Relationship of MTHFR gene polymorphisms with infertility].

    PubMed

    Guo, Kai-min; Tian, Run-hui; Wang, Hong-liang

    2016-02-01

    The folate metabolic pathway plays important roles in cellular physiology by participating in nucleotide synthesis, DNA repair and methylation, and maintenance and stability of the genome. Methylenetetrahydrofolate reductase (MTHFR) is a key regulatory enzyme involved in folate metabolism. Polymorphisms of MTHFR may change the level of homocysteine and affect DNA synthesis and methylation, leading to an increased oxidative stress and disturbed methylation reactions and consequently affecting reproductive function. This article presents an overview on MTHFR gene polymorphisms, proposing that multicentered, large-sample and long-term prospective studies are needed to reveal the relationship between MTHFR gene polymorphisms and infertility. PMID:26939404

  14. Vibrational study of tamoxifen citrate polymorphism

    NASA Astrophysics Data System (ADS)

    Gamberini, M. C.; Baraldi, C.; Tinti, A.; Palazzoli, F.; Ferioli, V.

    2007-09-01

    The trans isomer of ( Z)-2-[ p-(1,2-diphenyl-butenyl)phenoxy]- N, N-dimethyletylamine (tamoxifen) is well known for its endocrine activity as an antiestrogenic agent. Its citrate salt, a widely used pharmaceutical agent, appears in three main polymorphic forms, two of which are well known (I and II) and another form not yet well evidenced. A vibrational study has been conducted for identifying the two known polymorphic forms of tamoxifen citrate (I and II) and for characterising the other form (form III) examined in this study. Other techniques for the characterization of the different polymorphs, such as XRDP, have been used.

  15. Rivastigmine hydrogen tartrate polymorphs: Solid-state characterisation of transition and polymorphic conversion via milling

    NASA Astrophysics Data System (ADS)

    Amaro, Maria Inês; Simon, Alice; Cabral, Lúcio Mendes; de Sousa, Valéria Pereira; Healy, Anne Marie

    2015-11-01

    Rivastigmine (RHT) is an active pharmaceutical ingredient that is used for the treatment of mild to moderately severe dementia in Alzheimer's disease, and is known to present two polymorphic forms and to amorphise upon granulation. To date there is no information in the scientific or patent literature on polymorphic transition and stability. Hence, the aim of the current study was to gain a fundamental understanding of the polymorphic forms by (1) evaluating RHT thermodynamic stability (monotropy or enantiotropy) and (2) investigating the potential for polymorphic transformation upon milling. The two polymorphic and amorphous forms were characterised using X-ray powder diffractometry, thermal analyses, infra-red spectroscopy and water sorption analysis. The polymorphic transition was found to be spontaneous (ΔG0 < 0) and exothermic (ΔH0 < 0), indicative of a monotropic polymorph pair. The kinetic studies showed a fast initial polymorphic transition characterised by a heterogeneous nucleation, followed by a slow crystal growth. Ball milling can be used to promote the polymorphic transition and for the production of RHT amorphous form.

  16. Kinetic Trapping of Metastable Amino Acid Polymorphs

    PubMed Central

    2015-01-01

    Second harmonic generation (SHG) microscopy measurements indicate that inkjet-printed racemic solutions of amino acids can produce nanocrystals trapped in metastable polymorph forms upon rapid solvent evaporation. Polymorphism impacts the composition, distribution, and physico-kinetic properties of organic solids, with energetic arguments favoring the most stable polymorph. In this study, unfavored noncentrosymmetric crystal forms were observed by SHG microscopy. Polarization-dependent SHG measurement and synchrotron X-ray microdiffraction analysis of individual printed drops are consistent with formation of homochiral crystal production. Fundamentally, these results provide evidence supporting the ubiquity of Ostwald’s Rule of Stages, describing the hypothesized transitioning of crystals between metastable polymorphic forms in the early stages of crystal formation. Practically, the presence of homochiral metastable forms has implications on chiral resolution and on solid form preparations relying on rapid solvent evaporation. PMID:24451055

  17. Simple sequence repeat polymorphisms in peanut

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Genetic mapping, forward genetic analyses, and marker-assisted selection (MAS) have been intractable in intraspecific populations of cultivated peanut (Arachis hypogaea), primarily because domestication and breeding bottlenecks have narrowed genetic diversity and depleted DNA polymorphisms. The DNA...

  18. Kinetic trapping of metastable amino acid polymorphs.

    PubMed

    Chowdhury, Azhad U; Dettmar, Christopher M; Sullivan, Shane Z; Zhang, Shijie; Jacobs, Kevin T; Kissick, David J; Maltais, Thora; Hedderich, Hartmut G; Bishop, Patricia A; Simpson, Garth J

    2014-02-12

    Second harmonic generation (SHG) microscopy measurements indicate that inkjet-printed racemic solutions of amino acids can produce nanocrystals trapped in metastable polymorph forms upon rapid solvent evaporation. Polymorphism impacts the composition, distribution, and physico-kinetic properties of organic solids, with energetic arguments favoring the most stable polymorph. In this study, unfavored noncentrosymmetric crystal forms were observed by SHG microscopy. Polarization-dependent SHG measurement and synchrotron X-ray microdiffraction analysis of individual printed drops are consistent with formation of homochiral crystal production. Fundamentally, these results provide evidence supporting the ubiquity of Ostwald's Rule of Stages, describing the hypothesized transitioning of crystals between metastable polymorphic forms in the early stages of crystal formation. Practically, the presence of homochiral metastable forms has implications on chiral resolution and on solid form preparations relying on rapid solvent evaporation. PMID:24451055

  19. Persistent hydrogen bonding in polymorphic crystal structures.

    PubMed

    Galek, Peter T A; Fábián, László; Allen, Frank H

    2009-02-01

    The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability. PMID:19155561

  20. Purification of polymorphic components of complex genomes

    DOEpatents

    Stodolsky, Marvin

    1991-01-01

    A method is disclosed for processing related subject and reference macromolecule populations composed of complementary strands into their respective subject and reference populations of representative fragments and effectuating purification of unique polymorphic subject fragments.

  1. Purification of polymorphic components of complex genomes

    DOEpatents

    Stodolsky, M.

    1988-01-21

    A method for processing related subject and reference macromolecule composed of complementary strand into their respective subject and reference populations of representative fragments and effectuating purification of unique polymorphic subject fragments. 1 fig.

  2. Purification of polymorphic components of complex genomes

    DOEpatents

    Stodolsky, M.

    1991-07-16

    A method is disclosed for processing related subject and reference macromolecule populations composed of complementary strands into their respective subject and reference populations of representative fragments and effectuating purification of unique polymorphic subject fragments. 1 figure.

  3. Gene polymorphisms and chronic obstructive pulmonary disease

    PubMed Central

    Wu, Xiaodan; Yuan, Bowei; López, Elena; Bai, Chunxue; Wang, Xiangdong

    2014-01-01

    The genetic component was suggested to contribute to the development of chronic obstructive pulmonary disease (COPD), a major and growing public health burden. The present review aims to characterize the evidence that gene polymorphisms contribute to the aetiology of COPD and related traits, and explore the potential relationship between certain gene polymorphisms and COPD susceptibility, severity, lung function, phenotypes, or drug effects, even though limited results from related studies lacked consistency. Most of these studies were association studies, rather than confirmatory studies. More large-sized and strictly controlled studies are needed to prove the relationship between gene polymorphisms and the reviewed traits. More importantly, prospective confirmatory studies beyond initial association studies will be necessary to evaluate true relationships between gene polymorphisms and COPD and help individualized treatment for patients with COPD. PMID:24256364

  4. Impact polymorphs of quartz: experiments and modelling

    NASA Astrophysics Data System (ADS)

    Price, M. C.; Dutta, R.; Burchell, M. J.; Cole, M. J.

    2013-09-01

    We have used the light gas gun at the University of Kent to perform a series of impact experiments firing quartz projectiles onto metal, quartz and sapphire targets. The aim is to quantify the amount of any high pressure quartz polymorphs produced, and use these data to develop our hydrocode modelling to enable the predict ion of the quantity of polymorphs produced during a planetary scale impact.

  5. DNA polymorphism identity determination using flow cytometry

    DOEpatents

    Nolan, John P.; White, P. Scott; Cai, Hong

    2001-01-01

    DNA polymorphism identity determination using flow cytometry. Primers designed to be immobilized on microspheres are allowed to anneal to the DNA strand under investigation, and are extended by either DNA polymerase using fluorescent dideoxynucleotides or ligated by DNA ligase to fluorescent reporter oligonucleotides. The fluorescence of either the dideoxynucleotide or the reporter oligonucleotide attached to the immobilized primer is measured by flow cytometry, thereby identifying the nucleotide polymorphism on the DNA strand.

  6. Glycidamide genotoxicity modulated by Caspases genes polymorphisms.

    PubMed

    de Lima, João Pereira; Silva, Susana N; Rueff, José; Pingarilho, Marta

    2016-08-01

    Acrylamide (AA) is amongst acknowledged carcinogenic dietary factors. Its DNA-reactive metabolite is glycidamide (GA). The present study intended to correlate the role of key polymorphic genes of apoptosis (CASP7, CASP8, CASP9, CASP10, LTA and TNFRSF1B) with biomarkers of effect of DNA damage, namely the sister chromatid exchange assay (SCE) and the comet assay in whole blood cells exposed to GA. The aim was to assess as a proof of concept the role that pro-apoptotic effector proteins might have in the yields of genotoxic effects when those effector proteins are coded by polymorphic genes. Whole blood from a small group of volunteers was exposed to GA to assess DNA damage and the volunteers were genotyped for polymorphic genes related to apoptosis pathways. A relation between the induction of SCE and several variants of the polymorphism CASP8 rs1035142 G>T was observed. Also, a relation between the % tail DNA and the CASP10 I522L polymorphism was found. Furthermore, associations between % tail DNA and several SNP-SNP interactions of CASP8 and CASP10 were found. A possible correlation between DNA damage and the genetic susceptibility, bestowed by polymorphic genes in the apoptosis inducing pathways was verified. PMID:27062911

  7. New polymorphs of an old drug: conformational and synthon polymorphism of 5-nitrofurazone.

    PubMed

    Pogoda, Dorota; Janczak, Jan; Videnova-Adrabinska, Veneta

    2016-04-01

    Two new polymorphic forms of 5-nitrofurazone (5-nitro-2-furaldehyde semicarbazone) have been synthesized and structurally characterized by single-crystal and powder X-ray diffraction methods, vibrational spectroscopy (FT-IR and temperature Raman), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA) and Hirshfeld surface analysis. The compound crystallizes in three different polymorphic forms P21/a (polymorph α), P21 (polymorph β) and P21/c (polymorph γ), the crystal structures of two of which (polymorphs β and γ) represent new structure determinations. The solid-state molecular organization in the three crystal forms is analyzed and discussed in terms of molecular conformation, crystal packing and hydrogen-bonded networks. All three crystals are formed from trans geometrical isomers, but the molecular conformation of the α-polymorph is syn-anti-anti-anti, while that of β- and γ-polymorphs is syn-anti-syn-syn. As a consequence of this the hydrogen-bond donor and acceptor sites of the molecules are oriented differently, which in turn results in different hydrogen-bond connectivity and packing patterns. PMID:27048728

  8. An overview of famotidine polymorphs: solid-state characteristics, thermodynamics, polymorphic transformation and quality control.

    PubMed

    Lin, Shan-Yang

    2014-07-01

    Crystal polymorphism of pharmaceuticals has well-known profound effects on the physical, chemical, and pharmaceutical properties of drugs, which can result in changes in the solubility, stability, dissolution, bioavailability, and efficacy of drugs. In this review article, famotidine (FAM), which has a well-known trade name of Pepcid®, was selected as a model drug. Although FAM has three polymorphs (forms A, B and C), forms A and B have been commonly discussed. The active pharmaceutical ingredient (API) in the commercial version of FAM is the metastable form B. FAM has been a concern of FDA because of the physical properties, solubilities, bioavailabilities, or bioequivalencies of the different polymorphic forms. In addition, a patent infringement suit of FAM polymorph had been made sound legal arguments in the pharmaceutical market. We review the solid-state characteristics, thermodynamics, polymorphic transformation, and quality control of FAM in drug products. In particular, pharmaceutical processes, such as grinding, compression, and heating temperature have a significant effect on the polymorphic transformation of FAM. Moreover, environmental humidity and residual water content should be well controlled to prevent polymorphic transformation of FAM during pharmaceutical processing. Several thermal and spectroscopic analytical techniques used for qualitative and quantitative determinations of polymorphic transformation of FAM after different treatments or quality control of FAM in the commercial tablets before and after the expiration dates have been discussed. PMID:24577998

  9. Polymorphism of SARS-CoV genomes.

    PubMed

    Shang, Lei; Qi, Yan; Bao, Qi-Yu; Tian, Wei; Xu, Jian-Cheng; Feng, Ming-Guang; Yang, Huan-Ming

    2006-04-01

    In this work, severe acute respiratory syndrome associated coronavirus (SARS-CoV) genome BJ202 (AY864806) was completely sequenced. The genome was directly accessed from the stool sample of a patient in Beijing. Comparative genomics methods were used to analyze the sequence variations of 116 SARS-CoV genomes (including BJ202) available in the NCBI GenBank. With the genome sequence of GZ02 as the reference, there were 41 polymorphic sites identified in BJ202 and a total of 278 polymorphic sites present in at least two of the 116 genomes. The distribution of the polymorphic sites was biased over the whole genome. Nearly half of the variations (50.4%, 140/278) clustered in the one third of the whole genome at the 3' end (19.0 kb-29.7 kb). Regions encoding Orf10-11, Orf3/4, E, M and S protein had the highest mutation rates. A total of 15 PCR products (about 6.0 kb of the genome) including 11 fragments containing 12 known polymorphic sites and 4 fragments without identified polymorphic sites were cloned and sequenced. Results showed that 3 unique polymorphic sites of BJ202 (positions 13 804, 15 031 and 20 792) along with 3 other polymorphic sites (26 428, 26 477 and 27 243) all contained 2 kinds of nucleotides. It is interesting to find that position 18379 which has not been identified to be polymorphic in any of the other 115 published SARS-CoV genomes is actually a polymorphic site. The nucleotide composition of this site is A (8) to G (6). Among 116 SARS-CoV genomes, 18 types of deletions and 2 insertions were identified. Most of them were related to a 300 bp region (27,700-28,000) which encodes parts of the putative ORF9 and ORF10-11. A phylogenetic tree illustrating the divergence of whole BJ202 genome from 115 other completely sequenced SARS-CoVs was also constructed. BJ202 was phylogeneticly closer to BJ01 and LLJ-2004. PMID:16625834

  10. Angiotensinogen polymorphism and ischemic stroke risk

    PubMed Central

    Bao, Huan; Hao, Jun-Jie; Yang, Yu-Mei; Xu, Xia-Hong; Wang, Yue; Zuo, Lian; Lu, Jing; Zhang, Jing; Zhang, Yue; Xu, Si-Yi; Wang, Xuan; Li, Ying; Li, Gang

    2015-01-01

    The angiotensinogen M235T polymorphism was associated with ischemic stroke risk. However, the results were controversial. Thus, a meta-analysis was conducted. NCBI, Medline, Web of Science and Embase databases were systematically searched. Summary odds ratios (ORs) and corresponding 95% confidence intervals (CIs) were estimated using random-effects models. There was a significant association between angiotensinogen M235T polymorphism and ischemic stroke risk (OR = 1.69; 95% CI, 1.35-2.11; P < 0.001). In the stratified analysis by ethnicity, we found that this polymorphism was significantly associated with ischemic stroke in Asian (OR = 1.85; 95% CI, 1.45-2.35; P < 0.001). In the age subgroup, we found that angiotensinogen M235T polymorphism could increase both early-onset ischemic stroke risk (OR = 1.88; 95% CI, 1.33-2.43; P < 0.001) and late-onset ischemic stroke risk (OR = 1.20; 95% CI, 1.01-1.39; P = 0.04). This meta-analysis suggested that angiotensinogen M235T polymorphism was associated with ischemic stroke. PMID:26550208

  11. The Basques according to polymorphic Alu insertions.

    PubMed

    de Pancorbo, M M; López-Martínez, M; Martínez-Bouzas, C; Castro, A; Fernández-Fernández, I; de Mayolo, G A; de Mayolo, A A; de Mayolo, P A; Rowold, D J; Herrera, R J

    2001-08-01

    Polymorphic Alu insertions provide a set of DNA markers of interest in human population genetics. Approximately 1000-2000 of these insertions have not reached fixation within the human genome. Each one of these polymorphic loci most probably resulted from a unique insertional event, and therefore all individuals possessing the insertion are related by descent not just state. In addition, the direction of mutational change is toward the gain of the Alu element at a particular locus. Therefore, the improved knowledge of both the ancestral state and the direction of mutational change greatly facilitates the analysis of population relationships. As a result, Alu insertion polymorphisms represent a significant tool for population genetic studies. In this study, polymorphic Alu insertions have been employed to ascertain phylogenetic relationships among Basque groups and worldwide populations. The Basques are considered to be a geographic isolate with a unique language and customs. They may be direct descendants of Cro-Magnon enclaves from the upper Paleolithic (38,000 to 10,000 years). The Basques are distributed among narrow valleys in northeastern Spain with little migration between them until recently. This characteristic may have had an effect on allelic frequency distributions. With the aim of studying this possible effect, we have analyzed six autosomal polymorphic Alu loci from four different sites within the Spanish Basque region in order to ascertain any genetic heterogeneity among the Basques. The results are consistent with a lack of homogeneity among these four autochthonous Basque groups. PMID:11511929

  12. Hapsembler: An Assembler for Highly Polymorphic Genomes

    NASA Astrophysics Data System (ADS)

    Donmez, Nilgun; Brudno, Michael

    As whole genome sequencing has become a routine biological experiment, algorithms for assembly of whole genome shotgun data has become a topic of extensive research, with a plethora of off-the-shelf methods that can reconstruct the genomes of many organisms. Simultaneously, several recently sequenced genomes exhibit very high polymorphism rates. For these organisms genome assembly remains a challenge as most assemblers are unable to handle highly divergent haplotypes in a single individual. In this paper we describe Hapsembler, an assembler for highly polymorphic genomes, which makes use of paired reads. Our experiments show that Hapsembler produces accurate and contiguous assemblies of highly polymorphic genomes, while performing on par with the leading tools on haploid genomes. Hapsembler is available for download at http://compbio.cs.toronto.edu/hapsembler.

  13. Polymorphism of Amyloid Fibrils In Vivo.

    PubMed

    Annamalai, Karthikeyan; Gührs, Karl-Heinz; Koehler, Rolf; Schmidt, Matthias; Michel, Henri; Loos, Cornelia; Gaffney, Patricia M; Sigurdson, Christina J; Hegenbart, Ute; Schönland, Stefan; Fändrich, Marcus

    2016-04-01

    Polymorphism is a wide-spread feature of amyloid-like fibrils formed in vitro, but it has so far remained unclear whether the fibrils formed within a patient are also affected by this phenomenon. In this study we show that the amyloid fibrils within a diseased individual can vary considerably in their three-dimensional architecture. We demonstrate this heterogeneity with amyloid fibrils deposited within different organs, formed from sequentially non-homologous polypeptide chains and affecting human or animals. Irrespective of amyloid type or source, we found in vivo fibrils to be polymorphic. These data imply that the chemical principles of fibril assembly that lead to such polymorphism are fundamentally conserved in vivo and in vitro. PMID:26954430

  14. Crystal Polymorphism in a Carbamazepine Derivative: Oxcarbazepine

    PubMed Central

    LUTKER, KATIE M.; MATZGER, ADAM J.

    2011-01-01

    Although crystal polymorphism of carbamazepine (CBZ), an anticonvulsant used to treat epilepsy, has been known for decades, the phenomenon has only recently been noted for its keto-derivative oxcarbazepine (OCB). Here it is demonstrated that OCB possesses at least three anhydrous polymorphs. Although all forms are morphologically similar, making differentiation between crystal modifications by optical microscopy difficult, powder X-ray diffraction, Raman spectroscopy, and thermomicroscopy show distinctive differences. These techniques provide an efficient method of distinguishing between the three polymorphs. The crystal structure of form II of OCB is reported for the first time and the structure of form I has been redetermined at low temperature. Remarkably, both the molecular conformation and crystal packing of form II are in excellent agreement with the blind prediction made in 2007. PMID:19603503

  15. Single Nucleotide Polymorphisms and Osteoarthritis

    PubMed Central

    Wang, Ting; Liang, Yuting; Li, Hong; Li, Haibo; He, Quanze; Xue, Ying; Shen, Cong; Zhang, Chunhua; Xiang, Jingjing; Ding, Jie; Qiao, Longwei; Zheng, Qiping

    2016-01-01

    Abstract Osteoarthritis (OA) is a complex disorder characterized by degenerative articular cartilage and is largely attributed to genetic risk factors. Single nucleotide polymorphisms (SNPs) are common DNA variants that have shown promising and efficiency, compared with positional cloning, to map candidate genes of complex diseases, including OA. In this study, we aim to provide an overview of multiple SNPs from a number of genes that have recently been linked to OA susceptibility. We also performed a comprehensive meta-analysis to evaluate the association of SNP rs7639618 of double von Willebrand factor A domains (DVWA) gene with OA susceptibility. A systematic search of studies on the association of SNPs with susceptibility to OA was conducted in PubMed and Google scholar. Studies subjected to meta-analysis include human and case-control studies that met the Hardy–Weinberg equilibrium model and provide sufficient data to calculate an odds ratio (OR). A total of 9500 OA cases and 9365 controls in 7 case-control studies relating to SNP rs7639618 were included in this study and the ORs with 95% confidence intervals (CIs) were calculated. Over 50 SNPs from different genes have been shown to be associated with either hip (23), or knee (20), or both (13) OA. The ORs of these SNPs for OA and the subtypes are not consistent. As to SNP rs7639618 of DVWA, increased knee OA risk was observed in all genetic models analyzed. Specifically, people from Asian with G-allele showed significantly increased risk of knee OA (A versus G: OR = 1.28, 95% CI 1.13–1.46; AA versus GG: OR = 1.60, 95% CI 1.25–2.05; GA versus GG: OR = 1.31, 95% CI 1.18–1.44; AA versus GA+GG: OR = 1.34, 95% CI 1.12–1.61; AA+GA versus GG: OR = 1.40, 95% CI 1.19–1.64), but not in Caucasians or with hip OA. Our results suggest that multiple SNPs play different roles in the pathogenesis of OA and its subtypes; SNP rs7639618 of DVWA gene is associated with a significantly increased

  16. Vitamin D receptor polymorphisms and cancer.

    PubMed

    Gandini, Sara; Gnagnarella, Patrizia; Serrano, Davide; Pasquali, Elena; Raimondi, Sara

    2014-01-01

    It was suggested that vitamin D levels influence cancer development. The vitamin D receptor (VDR) is a crucial mediator for the cellular effects of vitamin D. In fact It has been hypothesized that polymorphisms in the VDR gene affect cancer risk and the relevance of VDR gene restriction fragment length polymorphisms for various types of cancer has been investigated by a great number of studies. However, results from previous studies on the association of VDR polymorphisms with different cancer types are somewhat contradictory, and the role of VDR in the etiology of cancer is still equivocal. We have performed a systematic review of the literature to analyze the relevance of more VDR polymorphisms (Fok1, Bsm1, Taq1, Apa1, and Cdx2) for individual malignancies, including cancer of the skin (melanoma and nonmelanoma skin cancer), ovarian cancer, renal cell carcinoma, bladder cancer, non-Hodgkin lymphoma, leukemia, thyroid carcinoma, esophageal adenocarcinoma, hepatocellular carcinoma, sarcoma, head and neck and oral squamous cell carcinoma. Up to June 2012, we identified 79 independent studies for a total of 52427 cases and 62225 controls. Significant associations with VDR polymorphisms have been reported for prostate (Fok1, Bsm1, Taq1), breast (Fok1, Bsm1, Apa1), colon-rectum (Fok1, Bsm1, Taq1) and skin cancer (Fok1, Bsm1, Taq1). Very few studies reported risk estimates for the other cancer sites. Conflicting data have been reported for most malignancies and at present it is still not possible to make any definitive statements about the importance of the VDR genotype for cancer risk. It seems probable that interactions with other factors such as calcium and vitamin D intake, 25(OH)D plasma levels and UV radiation exposure play a decisive role in cancer risk. To conclude, there is some indication that VDR polymorphisms may modulate the risk of some cancer sites and in future studies VDR genetic variation should be integrated also with prediagnostic indicator of

  17. Regulatory polymorphisms underlying complex disease traits.

    PubMed

    Knight, Julian C

    2005-02-01

    There is growing evidence that genetic variation plays an important role in the determination of individual susceptibility to complex disease traits. In contrast to coding sequence polymorphisms, where the consequences of non-synonymous variation may be resolved at the level of the protein phenotype, defining specific functional regulatory polymorphisms has proved problematic. This has arisen for a number of reasons, including difficulties with fine mapping due to linkage disequilibrium, together with a paucity of experimental tools to resolve the effects of non-coding sequence variation on gene expression. Recent studies have shown that variation in gene expression is heritable and can be mapped as a quantitative trait. Allele-specific effects on gene expression appear relatively common, typically of modest magnitude and context specific. The role of regulatory polymorphisms in determining susceptibility to a number of complex disease traits is discussed, including variation at the VNTR of INS, encoding insulin, in type 1 diabetes and polymorphism of CTLA4, encoding cytotoxic T lymphocyte antigen, in autoimmune disease. Examples where regulatory polymorphisms have been found to play a role in mongenic traits such as factor VII deficiency are discussed, and contrasted with those polymorphisms associated with ischaemic heart disease at the same gene locus. Molecular mechanisms operating in an allele-specific manner at the level of transcription are illustrated, with examples including the role of Duffy binding protein in malaria. The difficulty of resolving specific functional regulatory variants arising from linkage disequilibrium is demonstrated using a number of examples including polymorphism of CCR5, encoding CC chemokine receptor 5, and HIV-1 infection. The importance of understanding haplotypic structure to the design and interpretation of functional assays of putative regulatory variation is highlighted, together with discussion of the strategic use of

  18. Polymorphs calcium carbonate on temperature reaction

    SciTech Connect

    Chong, Kai-Yin; Chia, Chin-Hua; Zakaria, Sarani

    2014-09-03

    Calcium carbonate (CaCO{sub 3}) has three different crystal polymorphs, which are calcite, aragonite and vaterite. In this study, effect of reaction temperature on polymorphs and crystallite structure of CaCO{sub 3} was investigated. X-ray powder diffraction (XRD), fourier transform infrared (FTIR), and variable pressure scanning electron microscope (VPSEM) were used to characterize the obtained CaCO{sub 3} particles. The obtained results showed that CaCO{sub 3} with different crystal and particle structures can be formed by controlling the temperature during the synthesis process.

  19. [Polymorphic loci and polymorphism analysis of short tandem repeats within XNP gene].

    PubMed

    Liu, Qi-Ji; Gong, Yao-Qin; Guo, Chen-Hong; Chen, Bing-Xi; Li, Jiang-Xia; Guo, Yi-Shou

    2002-01-01

    To select polymorphic short tandem repeat markers within X-linked nuclear protein (XNP) gene, genomic clones which contain XNP gene were recognized by homologous analysis with XNP cDNA. By comparing the cDNA with genomic DNA, non-exonic sequences were identified, and short tandem repeats were selected from non-exonic sequences by using BCM search Launcher. Polymorphisms of the short tandem repeats in Chinese population were evaluated by PCR amplification and PAGE. Five short tandem repeats were identified from XNP gene, two of which were polymorphic. Four and 11 alleles were observed in Chinese population for XNPSTR1 and XNPSTR4, respectively. Heterozygosities were 47% for XNPSTR1 and 70% for XNPSTR4. XNPSTR1 and XNPSTR4 localized within 3' end and intron 10, respectively. Two polymorphic short tandem repeats have been identified within XNP gene and will be useful for linkage analysis and gene diagnosis of XNP gene. PMID:12182071

  20. Single nucleotide polymorphism discovery in rainbow trout

    Technology Transfer Automated Retrieval System (TEKTRAN)

    To enhance capabilities for genetic analyses in rainbow trout, a large suite of polymorphic markers that are amenable to high-throughput genotyping protocols must be developed. However, the evolutionarily recent whole genome duplication event complicates the use of standard approaches in the discove...

  1. Idealized powder diffraction patterns for cellulose polymorphs

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cellulose samples are routinely analyzed by X-ray diffraction to determine their crystal type (polymorph) and crystallinity. However, the connection is seldom made between those efforts and the crystal structures of cellulose that have been determined with synchrotron X-radiation and neutron diffrac...

  2. Difficulties in Learning Inheritance and Polymorphism

    ERIC Educational Resources Information Center

    Liberman, Neomi; Beeri, Catriel; Kolikant, Yifat Ben-David

    2011-01-01

    This article reports on difficulties related to the concepts of inheritance and polymorphism, expressed by a group of 22 in-service CS teachers with an experience with the procedural paradigm, as they coped with a course on OOP. Our findings are based on the analysis of tests, questionnaires that the teachers completed in the course, as well as on…

  3. Single nucleotide polymorphisms in caprine calpastatin gene.

    PubMed

    Sharma, R; Maitra, A; Pandey, A K; Singh, L V; Mishra, B P

    2013-04-01

    The calpains and calpastatin (CAST) make up a major cytosolic proteolytic system, the calpain-calpastatin system, found in mammalian tissues. The relative levels of the components of the calpain-calpastatin system determine the extent of meat tenderization during postmortem storage. Calpastatin (CAST) is a protein inhibitor of the ubiquitous calcium-dependent proteases-micro-calpain and m-calpain. Polymorphisms in the bovine, ovine and pig CAST gene have been associated with meat tenderness but little is known about how caprine CAST gene may affect goat meat quality traits. In this study we selected different parts of the CAST gene: 1) that have been previously reported to be polymorphic, intron 5 and 12 and 3'UTR; 2) first time explored (exon 3, 7 and 8 and part of intron 7 and 8) to investigate polymorphic status of caprine CAST gene. Using comparative sequencing ten novel SN Ps located in exon 3 and intron 5, 7 and 8 were identified. Previously reported SNPs in intron 5, 3'UTR and intron 12 were absent. Sequence analysis revealed a non synonymous amino acid variation in exon 3, which would result in Lys/Arg substitution in the corresponding protein sequence. Considerable variation was detected in intronic regions. Twenty-four InDel were also recognized in intronic regions (15) and 3'UTR (9). All the sequences shared high homology with published bovine and ovine sequences. Three PCR-RFLP loci have been established for further analyzing genetic polymorphism in indigenous goats. PMID:23866627

  4. Raman phonon spectra of pentacene polymorphs

    NASA Astrophysics Data System (ADS)

    Brillante, A.; Della Valle, R. G.; Farina, L.; Girlando, A.; Masino, M.; Venuti, E.

    2002-05-01

    We report for the first time lattice phonon Raman spectra of pentacene measured by means of a Raman microprobe technique. We experimentally prove the existence of two polymorphs, as expected from recent structural studies. A comparison with Quasi Harmonic Lattice Dynamics calculations, previously performed starting from the available X-ray data, help us in identifying the phase to which each crystal belongs.

  5. Characterization of Polymorphic Forms of Rifaximin.

    PubMed

    Kogawa, Ana Carolina; Antonio, Selma Gutierrez; Salgado, Hérida Regina Nunes

    2016-07-01

    Rifaximin is a gut-selective oral antimicrobial that has no systemic adverse effects compared with placebo. It is used for the treatment of hepatic encephalopathy, traveler's diarrhea, irritable bowel syndrome, Clostridium difficile infection, ulcerative colitis, and acute diarrhea. The crystalline form present in rifaximin, α, has minimal systemic absorption compared to the amorphous form. The objective of this study was to obtain polymorphic forms of rifaximin using recrystallization processes. The forms were characterized and studied by thermal analysis, X-ray powder diffraction, scanning electron microscopy, and solubility testing. Six polymorphic forms of rifaximin, designated I-VI, were obtained by the crystallization process by evaporation of the solvent. Some polymorphic forms obtained in this work may not have the same excellent tolerability as the reference medicine; therefore, studies such as these are extremely important and point to the need for greater requirements by the regulatory agencies overseeing polymorph analysis of the raw materials used in the manufacture of medicines marketed globally. These analyses are not required in the majority of official compendia. Partnerships among industries, research centers, and universities would be a viable way to consolidate research in this area and contribute to improving the quality of solid drugs. PMID:27455934

  6. Saitohin polymorphism and executive dysfunction in schizophrenia.

    PubMed

    Bosia, Marta; Buonocore, Mariachiara; Guglielmino, Carmelo; Pirovano, Adele; Lorenzi, Cristina; Marcone, Alessandra; Bramanti, Placido; Cappa, Stefano F; Aguglia, Eugenio; Smeraldi, Enrico; Cavallaro, Roberto

    2012-10-01

    Saitohin (STH) is an intronless gene nested within the human tau gene, which contains a single nucleotide polymorphism (A/G), suggested to be involved in the physiopathology and clinical course of several neurodegenerative and neuropsychiatric diseases. Recently, an association between this polymorphism and frontal hypoperfusion and clinical prognosis in frontotemporal dementia was reported. The present study sought to evaluate the possible role of the STH polymorphism as a concurring factor of cognitive decline in schizophrenia, a disease sharing both early psychotic manifestations, a core deficit of executive functions and hypofrontality with frontotemporal lobe dementia. 220 clinically stabilized patients with schizophrenia were assessed with the Wisconsin Card Sorting Test (WCST) for evaluation of executive functions and compared for STH allele frequency with 48 patients affected by frontotemporal dementia and 47 healthy subjects. There was no significant difference in allelic distribution between the healthy controls and all other groups, while we observed a significantly greater frequency of G allele among both patients with frontotemporal dementia (p = 0.037) and schizophrenia patients with poor performances of WCST (p = 0.044), compared to schizophrenia patients with best WCST performances. Among the patients with schizophrenia, stratified for age and gender, the STH polymorphism resulted in a significant predictor of WCST performance (p = 0.007). These results suggest a possible contribution of STH gene products on the heterogeneity of core frontal executive functions deterioration, probably through complex interactions with mechanism involved in neurodevelopment and neurodegeneration. PMID:22187337

  7. Four new polymorphic forms of suplatast tosilate.

    PubMed

    Nagai, Keiko; Ushio, Takanori; Miura, Hidenori; Nakamura, Takashi; Moribe, Kunikazu; Yamamoto, Keiji

    2014-01-01

    We found four new polymorphic forms (γ-, ε-, ζ-, and η-forms) of suplatast tosilate (ST) by recrystallization and seeding with ST-analogous compounds; three polymorphic forms (α-, β-, and δ-forms) of ST have been previously reported. The physicochemical properties of these new forms were investigated using infrared (IR) spectroscopy, solid-state nuclear magnetic resonance (NMR) spectroscopy, differential scanning calorimetry, and powder X-ray diffractometry. The presence of hydrogen bonds in the new forms was assessed from the IR and solid-state NMR spectra. The crystal structures of the ε- and η-forms were determined from their powder X-ray diffraction data using the direct space approach and the Monte Carlo method, followed by Rietveld refinement. The structures determined for the ε- and η-forms supported the presence of hydrogen bonds between the ST molecules, as the IR and solid-state NMR spectra indicated. The thermodynamic characteristics of the seven polymorphic forms were evaluated by determining the solubility of each form. The α-form was the most insoluble in 2-propanol at 35°C, and was thus concluded to be the most stable form. The ε-form was the most soluble, and a polymorphic transition from the ε- to the α-form was observed during solubility testing. PMID:24211359

  8. Molecular basis for amyloid-[beta] polymorphism

    SciTech Connect

    Colletier, Jacques-Philippe; Laganowsky, Arthur; Landau, Meytal; Zhao, Minglei; Soriaga, Angela B.; Goldschmidt, Lukasz; Flot, David; Cascio, Duilio; Sawaya, Michael R.; Eisenberga, David

    2011-10-19

    Amyloid-beta (A{beta}) aggregates are the main constituent of senile plaques, the histological hallmark of Alzheimer's disease. A{beta} molecules form {beta}-sheet containing structures that assemble into a variety of polymorphic oligomers, protofibers, and fibers that exhibit a range of lifetimes and cellular toxicities. This polymorphic nature of A{beta} has frustrated its biophysical characterization, its structural determination, and our understanding of its pathological mechanism. To elucidate A{beta} polymorphism in atomic detail, we determined eight new microcrystal structures of fiber-forming segments of A{beta}. These structures, all of short, self-complementing pairs of {beta}-sheets termed steric zippers, reveal a variety of modes of self-association of A{beta}. Combining these atomic structures with previous NMR studies allows us to propose several fiber models, offering molecular models for some of the repertoire of polydisperse structures accessible to A{beta}. These structures and molecular models contribute fundamental information for understanding A{beta} polymorphic nature and pathogenesis.

  9. Polymorphism Control in Nanostructured Metal Oxides

    NASA Astrophysics Data System (ADS)

    Sood, Shantanu

    Polymorphic phase transformations are common to all nanocrystalline binary metal oxides. The polymorphic nature of such metal oxides makes available a large number of phases with differing crystal structures, each stable under certain conditions of temperature, pressure, and/or particle size. These different crystal structures translate to unique physical and chemical properties for each structural class of polymorphs. Thus predicting when polymorphic phase transitions are likely to occur becomes important to the synthesis of stable functional materials with desired properties. Theoretical calculations using a heuristic approach have resulted in an accurate estimation of the critical particle size predicting metastable to stable phase transitions. This formula is applied to different case studies: for anatase to rutile titania; gamma-Alumina to alpha-Alumina; and tetragonal to monoclinic zirconia. The theoretical values calculated have been seen to be very close to the experimental results from the literature. Manifestation of the effect of phase transitions in nanostructured metal oxides was provided in the study of metastable to stable phase transitions in WO3. Nanowires of tungsten trioxide have been synthesized in-situ inside an electron microscope. Such structure of tungsten trioxide result due to a metastable to stable phase transformation, from the cubic to the monoclinic phase. The transformation is massive and complete. The structures formed are unique one-dimensional nanowires. Such a method can be scaled inside any equipment equipped with an electron gun, for example lithography systems either using STEM or E-beam lithography. Another study on nanowire formation in binary metal oxides involved the synthesis of stable orthorhombic MoO3 by means of blend electrospinning. Both a traditional single jet electrospinning set up and a novel high-throughput process to get high aspect ratio nanowires. The latter is a jet-controlled and flow controlled

  10. Human Diallelic Insertion/Deletion Polymorphisms

    PubMed Central

    Weber, James L.; David, Donna; Heil, Jeremy; Fan, Ying; Zhao, Chengfeng; Marth, Gabor

    2002-01-01

    We report the identification and characterization of 2,000 human diallelic insertion/deletion polymorphisms (indels) distributed throughout the human genome. Candidate indels were identified by comparison of overlapping genomic or cDNA sequences. Average confirmation rate for indels with a ⩾2-nt allele-length difference was 58%, but the confirmation rate for indels with a 1-nt length difference was only 14%. The vast majority of the human diallelic indels were monomorphic in chimpanzees and gorillas. The ratio of deletion:insertion mutations was 4.1. Allele frequencies for the indels were measured in Europeans, Africans, Japanese, and Native Americans. New alleles were generally lower in frequency than old alleles. This tendency was most pronounced for the Africans, who are likely to be closest among the four groups to the original modern human population. Diallelic indels comprise ∼8% of all human polymorphisms. Their abundance and ease of analysis make them useful for many applications. PMID:12205564

  11. Hyphenated spectroscopy as a polymorph screening tool.

    PubMed

    Aaltonen, Jaakko; Strachan, Clare J; Pöllänen, Kati; Yliruusi, Jouko; Rantanen, Jukka

    2007-06-28

    Polymorph screening of a model compound (nitrofurantoin) was performed. Nitrofurantoin was crystallized from acetone-water mixtures with varying process parameters. Two anhydrate forms (alpha and beta) and one monohydrate form (II) were crystallized in the polymorph screen. The solid forms were analyzed with three complementary spectroscopic techniques: near-infrared (NIR) spectroscopy, Raman spectroscopy and terahertz pulsed spectroscopy (TPS), and the results of the solid phase analysis were verified with X-ray powder diffraction (XRPD). NIR and Raman spectroscopy were coupled to achieve a rapid and comprehensive method of solid phase analysis. The hyphenated NIR/Raman spectroscopic data were analyzed with a multivariate method, principal component analysis (PCA). The combination was found effective in screening solid forms due to the complementary characteristics of the methods. NIR spectroscopy is powerful in differentiating between anhydrate and hydrate forms and intermolecular features, whereas Raman spectroscopy is sensitive to intramolecular alterations in the molecular backbone. PMID:17367979

  12. Adiponectin gene polymorphisms: Association with childhood obesity

    PubMed Central

    Fraga, Vanêssa Gomes; Gomes, Karina Braga

    2014-01-01

    The current childhood obesity epidemic represents a particular challenge for public health. Understanding of the etiological mechanisms of obesity remains integral in treating this complex disorder. In recent years, studies have elucidated the influence of hormones secreted by adipose tissue named adipokines. Adiponectin is a adipokine that exhibits important anti-inflammatory, insulin-sensitizing and anti-atherogenic properties and it is strongly associated to obesity development. It is well known that adiponectin levels decrease with obesity. Furthermore, studies show that some single nucleotide polymorphisms in the gene encoding adiponectin, ADIPOQ, may influence the expression of this protein. The objective of this paper is to provide an up-to-date review of ADIPOQ polymorphisms in the context of childhood obesity.

  13. Kinetics versus Thermodynamics in Virus Capsid Polymorphism.

    PubMed

    Moerman, Pepijn; van der Schoot, Paul; Kegel, Willem

    2016-07-01

    Virus coat proteins spontaneously self-assemble into empty shells in aqueous solution under the appropriate physicochemical conditions, driven by an interaction free energy per bond on the order of 2-5 times the thermal energy kBT. For this seemingly modest interaction strength, each protein building block nonetheless gains a very large binding free energy, between 10 and 20 kBT. Because of this, there is debate about whether the assembly process is reversible or irreversible. Here we discuss capsid polymorphism observed in in vitro experiments from the perspective of nucleation theory and of the thermodynamics of mass action. We specifically consider the potential contribution of a curvature free energy term to the effective interaction potential between the proteins. From these models, we propose experiments that may conclusively reveal whether virus capsid assembly into a mixture of polymorphs is a reversible or an irreversible process. PMID:27027925

  14. Androgen receptor gene polymorphism in zebra species

    PubMed Central

    Ito, Hideyuki; Langenhorst, Tanya; Ogden, Rob; Inoue-Murayama, Miho

    2015-01-01

    Androgen receptor genes (AR) have been found to have associations with reproductive development, behavioral traits, and disorders in humans. However, the influence of similar genetic effects on the behavior of other animals is scarce. We examined the loci AR glutamine repeat (ARQ) in 44 Grevy's zebras, 23 plains zebras, and three mountain zebras, and compared them with those of domesticated horses. We observed polymorphism among zebra species and between zebra and horse. As androgens such as testosterone influence aggressiveness, AR polymorphism among equid species may be associated with differences in levels of aggression and tameness. Our findings indicate that it would be useful to conduct further studies focusing on the potential association between AR and personality traits, and to understand domestication of equid species. PMID:26236645

  15. IPD—the Immuno Polymorphism Database

    PubMed Central

    Robinson, James; Mistry, Kavita; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G. E.

    2010-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; IPD-human platelet antigens, alloantigens expressed only on platelets and IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines. The data is currently available online from the website and ftp directory. PMID:19875415

  16. IPD--the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Mistry, Kavita; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G E

    2010-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors, IPD-MHC, is a database of sequences of the Major Histocompatibility Complex of different species; IPD-human platelet antigens, alloantigens expressed only on platelets and IPD-ESTDAB, which provides access to the European Searchable Tumour cell-line database, a cell bank of immunologically characterised melanoma cell lines. The data is currently available online from the website and ftp directory. PMID:19875415

  17. Genetic polymorphisms and idiopathic generalized epilepsies.

    PubMed

    Lucarini, Nazzareno; Verrotti, Alberto; Napolioni, Valerio; Bosco, Guido; Curatolo, Paolo

    2007-09-01

    In recent years, progress in understanding the genetic basis of idiopathic generalized epilepsies has proven challenging because of their complex inheritance patterns and genetic heterogeneity. Genetic polymorphisms offer a convenient avenue for a better understanding of the genetic basis of idiopathic generalized epilepsy by providing evidence for the involvement of a given gene in these disorders, and by clarifying its pathogenetic mechanisms. Many of these genes encode for some important central nervous system ion channels (KCNJ10, KCNJ3, KCNQ2/KCNQ3, CLCN2, GABRG2, GABRA1, SCN1B, and SCN1A), while many others encode for ubiquitary enzymes that play crucial roles in various metabolic pathways (HP, ACP1, ME2, LGI4, OPRM1, GRIK1, BRD2, EFHC1, and EFHC2). We review the main genetic polymorphisms reported in idiopathic generalized epilepsy, and discusses their possible functional significance in the pathogenesis of seizures. PMID:17765802

  18. Calorimetric determinations and theoretical calculations of polymorphs of thalidomide

    NASA Astrophysics Data System (ADS)

    Lara-Ochoa, F.; Pérez, G. Espinosa; Mijangos-Santiago, F.

    2007-09-01

    The analysis of the thermograms of thalidomide obtained for the two reported polymorphs α and β by differential scanning calorimetry (DSC) shows some inconsistencies that are discussed in the present work. The conception of a new polymorph form, named β ∗, allowed us to explain the observed thermal behavior more satisfactorily. This new polymorph shows enantiotropy with both α and β polymorphs, reflected in the unique endotherm obtained in the DSC-thermograms, when a heating rate of 10 °C/min is applied. Several additional experiments, such as re-melting of both polymorph forms, showed that there is indeed a new polymorph with an endotherm located between the endotherms of α and β. IR, Raman, and powder X-ray permit us to characterize the isolated compound, resulting from the re-melting of both polymorph forms. Mechanical calculations were performed to elucidate the conformations of each polymorph, and ab initio quantum chemical calculations were performed to determine the energy of the more stable conformers and the spatial cell energy for both polymorphs α and β. These results suggested a possible conformation for the newly discovered polymorph β ∗.

  19. Preparation and Crystallographic Analysis of Gliclazide Polymorphs

    PubMed Central

    Rajamma, A. J.; Sateesha, S. B.; Narode, M. K.; Prashanth, V. R. S. S.; Karthik, A. M.

    2015-01-01

    Since the introduction of gliclazide in the pharmaceutical industry, a large number of research groups have been engaged in various investigations aiming to enhance its biomedical application. But, very limited efforts have been made to study polymorphism of gliclazide. Therefore, this study focuses on solvent-induced polymorphism of gliclazide and its characterization by thermal methods. Three polymorphs namely, Form-I, II and III and an amorphous powder were produced from different solvents and solvent mixtures. Crystals were analyzed using infrared spectroscopy, differential scanning calorimetry, X-ray powder diffraction and single crystal x-ray diffraction. Polymorph Form-I is found to exist in centro-symmetric triclinic P-1 space group and has endothermic peak at 162.93°. Form-II has endothermic peak from 171.2° to 172.35° and exists in centro-symmetric monoclinic P21/a space group while Form-III has endothermic peak from 168.93° to 169.86° and exists in centro-symmetric monoclinic P21/n space group. The equilibrium solubility values of Form-I, II, III and the amorphous form were 0.4825±0.025, 0.2341±0.042, 0.2581±0.038 and 0.5213±0.072 mg/ml, respectively. The Form-I has relatively higher solubility and similar to that of amorphous gliclazide. Form-II and Form-III are relatively most stable and least soluble. However, there was no remarkable difference in their aqueous solubility under the conditions in which study was conducted. PMID:25767316

  20. Preparation and crystallographic analysis of gliclazide polymorphs.

    PubMed

    Rajamma, A J; Sateesha, S B; Narode, M K; Prashanth, V R S S; Karthik, A M

    2015-01-01

    Since the introduction of gliclazide in the pharmaceutical industry, a large number of research groups have been engaged in various investigations aiming to enhance its biomedical application. But, very limited efforts have been made to study polymorphism of gliclazide. Therefore, this study focuses on solvent-induced polymorphism of gliclazide and its characterization by thermal methods. Three polymorphs namely, Form-I, II and III and an amorphous powder were produced from different solvents and solvent mixtures. Crystals were analyzed using infrared spectroscopy, differential scanning calorimetry, X-ray powder diffraction and single crystal x-ray diffraction. Polymorph Form-I is found to exist in centro-symmetric triclinic P-1 space group and has endothermic peak at 162.93°. Form-II has endothermic peak from 171.2° to 172.35° and exists in centro-symmetric monoclinic P21/a space group while Form-III has endothermic peak from 168.93° to 169.86° and exists in centro-symmetric monoclinic P21/n space group. The equilibrium solubility values of Form-I, II, III and the amorphous form were 0.4825±0.025, 0.2341±0.042, 0.2581±0.038 and 0.5213±0.072 mg/ml, respectively. The Form-I has relatively higher solubility and similar to that of amorphous gliclazide. Form-II and Form-III are relatively most stable and least soluble. However, there was no remarkable difference in their aqueous solubility under the conditions in which study was conducted. PMID:25767316

  1. Distinct germline polymorphisms underlie glioma morphologic heterogeneity

    PubMed Central

    Jenkins, Robert B.; Wrensch, Margaret R.; Johnson, Derek; Fridley, Brooke L.; Decker, Paul A.; Xiao, Yuanyuan; Kollmeyer, Thomas M.; Rynearson, Amanda L.; Fink, Stephanie; Rice, Terri; McCoy, Lucie S.; Halder, Chandralekha; Kosel, Matthew L.; Giannini, Caterina; Tihan, Tarik; O’Neill, Brian P.; Lachance, Daniel H.; Yang, Ping; Wiemels, Joseph; Wiencke, John K.

    2010-01-01

    Two recent genome-wide association studies reported that single nucleotide polymorphisms (SNPs) in (or near) TERT (5p15), CCDC26 (8q24), CDKN2A/B (9p21), PHLDB1 (11q23), and RTEL1 (20q13) are associated with infiltrating glioma. From these reports it was not clear if the SNP associations predispose to glioma in general or whether they are specific to certain glioma grades or morphologic subtypes. To identify hypothesized associations between susceptibility loci and tumor subtype, we genotyped two case/control groups composed of the spectrum of infiltrating glioma subtypes, and stratified the analyses by type. We report that specific germline polymorphisms are associated with different glioma subtypes. CCDC26 (8q24) region polymorphisms are strongly associated with oligodendroglial tumor risk (rs4295627, OR=2.05, p=8.3*10−11), but not glioblastoma risk. The opposite is true of RTEL (20q13) region polymorphisms which are significantly associated with glioblastoma (rs2297440, OR = 0.56, p= 4.6*10−10) but not oligodendroglial tumor. The SNPs in or near CCDC26 (8q24) are associated with oligodendroglial tumors regardless of combined 1p and 19q deletion status; however, the association is greatest for those with combined deletion (rs4295627, OR=2.77, p=2.6*10-9). These observations generate hypotheses concerning the possible mechanisms by which specific SNPs (or alterations in linkage disequilibrium with such SNPs) are associated with glioma development. PMID:21356187

  2. IL-10 gene polymorphism and herpesvirus infections.

    PubMed

    Hurme, M; Haanpää, M; Nurmikko, T; Wang, X-Y; Virta, M; Pessi, T; Kilpinen, S; Hulkkonen, J; Helminen, M

    2003-01-01

    Genetics has an important role in resistance to various infections and it also may modify the clinical picture of an infectious disease. Here, we briefly review our recent data demonstrating that the polymorphism of the IL-10 gene is associated with resistance to some common herpesviruses and, additionally, that this same gene is involved in the regulation of the severity of the infection and in the reactivation process. PMID:12627487

  3. Androgen receptor polymorphism (CAG repeats) and androgenicity.

    PubMed

    Canale, D; Caglieresi, C; Moschini, C; Liberati, C D; Macchia, E; Pinchera, A; Martino, E

    2005-09-01

    Objective Polymorphism of the androgen receptor (AR) has been related to various pathophysiological conditions, such as osteoporosis and infertility. The objectives of this study were to evaluate the frequency of distribution in a normal Italian population and to assess CAG repeats (CAGr) in other conditions, such as hypoandrogenism, potentially influenced by AR polymorphism. Patients and measurements CAGr polymorphism was determined in a group of 91 healthy normoandrogenized subjects, 29 hypoandrogenized patients (hypoplasia of prostate and seminal vesicles, reduced beard or body hair, etc.) and 29 infertile patients by direct sequencing. Results The mean (+/- SD) number of CAG repeats [(CAGr)n] was 21.5 (+/- 1.7) in the control group, 21.4 (+/- 2.0) in the infertile patients and 24.0 (+/- 2.9) in the hypoandrogenic males. The difference was statistically significant between this last group and the other two (P < 0.0001), while there was no difference between normal controls and infertile patients. The frequency distribution showed a shift towards higher CAG length in hypoandrogenized patients compared to controls and infertile patients. If we used a cut-off point of 24.9 (2 SD above the mean), the percentage of patients with 25 or more CAGr repeats was 38% among hypoandrogenized patients, 7% among infertile patients and 5% among the control group. In hypoandrogenized subjects (CAGr)n correlated slightly with testis and prostate volume. The number of CAG repeats was not associated with any of the hormonal parameters, including testosterone, evaluated in the three groups. Conclusions Our normal population, representing subjects from Central Italy, is superimposable on other European populations with regard to (CAGr)n distribution. Hypoandrogenic males have a shift in the frequency distribution towards longer (CAGr)n. Infertile patients are not statistically different from the control group. These findings suggest that, given the same amount of circulating

  4. Innate Immune Gene Polymorphisms in Tuberculosis

    PubMed Central

    Sadee, Wolfgang

    2012-01-01

    Tuberculosis (TB) is a leading cause worldwide of human mortality attributable to a single infectious agent. Recent studies targeting candidate genes and “case-control” association have revealed numerous polymorphisms implicated in host susceptibility to TB. Here, we review current progress in the understanding of causative polymorphisms in host innate immune genes associated with TB pathogenesis. We discuss genes encoding several types of proteins: macrophage receptors, such as the mannose receptor (MR, CD206), dendritic cell-specific ICAM-3-grabbing nonintegrin (DC-SIGN, CD209), Dectin-1, Toll-like receptors (TLRs), complement receptor 3 (CR3, CD11b/CD18), nucleotide oligomerization domain 1 (NOD1) and NOD2, CD14, P2X7, and the vitamin D nuclear receptor (VDR); soluble C-type lectins, such as surfactant protein-A (SP-A), SP-D, and mannose-binding lectin (MBL); phagocyte cytokines, such as tumor necrosis factor (TNF), interleukin-1β (IL-1β), IL-6, IL-10, IL-12, and IL-18; chemokines, such as IL-8, monocyte chemoattractant protein 1 (MCP-1), RANTES, and CXCL10; and other important innate immune molecules, such as inducible nitric oxide synthase (iNOS) and solute carrier protein 11A1 (SLC11A1). Polymorphisms in these genes have been variably associated with susceptibility to TB among different populations. This apparent variability is probably accounted for by evolutionary selection pressure as a result of long-term host-pathogen interactions in certain regions or populations and, in part, by lack of proper study design and limited knowledge of molecular and functional effects of the implicated genetic variants. Finally, we discuss genomic technologies that hold promise for resolving questions regarding the evolutionary paths of the human genome, functional effects of polymorphisms, and corollary impacts of adaptation on human health, ultimately leading to novel approaches to controlling TB. PMID:22825450

  5. Polymorphic microsatellites and Wilson disease (WD)

    PubMed Central

    Stewart, E. A.; White, A.; Tomfohrde, J.; Osborne-Lawrence, S.; Prestridge, L.; Bonne-Tamir, B.; Scheinberg, I. H.; George-Hyslop, P. St; Giagheddu, M.; Kim, J.-W.; Seo, J. K.; Lo, W. H.-y.; Ivanova-Smolenskaya, I. A.; Limborska, S. A.; Cavalli-Sforza, L. L.; Farrer, L. A.; Bowcock, A. M.

    1993-01-01

    Wilson disease (WD), an autosomal recessive disorder of copper metabolism, has been previously mapped to chromosome 13q. Highly informative PCR-based polymorphic microsatellites closely linked to the WD locus (WND) at 13q14.3, as well as sequence-tagged sites for closely linked loci, are described. Two polymorphic microsatellite markers at D13S118 and D13S119 lie within 3 cM of WND. Two others (D13S227 and D13S228) were derived from a yeast artificial chromosome containing D13S31. These were placed on a genetic linkage map of chromosome 13 and were typed in 74 multiplex WD families from a variety of geographic origins (166 affected members). Multipoint analysis provides very high odds that the location of WND is between D13S31/D13S227/D13S228 and D13S59. Previous odds with RFLP-based markers were only 7:1 more likely than any other location. Current odds are 5,000:1. Preclinical testing of three cases of WD by using the highly informative polymorphic microsatellite markers is described. The markers described here ensure that 95% of predictive tests using DNA from both parents and from at least one affected sib will have an accuracy >99%. PMID:8213814

  6. Introgressive hybridization in a trophically polymorphic cichlid

    PubMed Central

    Hulsey, C Darrin; García-de-León, Francisco J

    2013-01-01

    Trophically polymorphic species could represent lineages that are rapidly diverging along an ecological axis or could phenotypically mark the collapse of species through introgressive hybridization. We investigated patterns of introgression between the trophically polymorphic cichlid fish Herichthys minckleyi and its relative H. cyanoguttatus using a combination of population genetics and species tree analyses. We first examined the distribution of mitochondrial haplotypes within the alternative H. minckleyi pharyngeal jaw morphotypes that are endemic to the small desert valley of Cuatro Ciénegas. We recovered two clusters of mitochondrial haplotypes. The first contained a number of slightly differentiated cytochrome b (cytb) haplotypes that showed some phylogeographic signal and were present in both jaw morphotypes. The other haplotype was monomorphic, highly differentiated from the other cluster, present in equal frequencies in the morphotypes, and identical to H. cyanoguttatus haplotypes found outside Cuatro Ciénegas. Then, we investigated whether H. minckleyi individuals with the H. cyanoguttatus cytb were more evolutionarily similar to H. cyanoguttatus or other H. minckleyi using a species tree analysis of 84 nuclear loci. Both H. minckleyi pharyngeal morphotypes, regardless of their cytb haplotype, were quite distinct from H. cyanoguttatus. However, hybridization could be blurring subdivision within H. minckleyi as the alternative jaw morphotypes were not genetically distinct from one another. Accounting for introgression from H. cyanoguttatus will be essential to understand the evolution of the trophically polymorphic cichlid H. minckleyi. PMID:24340193

  7. Introgressive hybridization in a trophically polymorphic cichlid.

    PubMed

    Hulsey, C Darrin; García-de-León, Francisco J

    2013-11-01

    Trophically polymorphic species could represent lineages that are rapidly diverging along an ecological axis or could phenotypically mark the collapse of species through introgressive hybridization. We investigated patterns of introgression between the trophically polymorphic cichlid fish Herichthys minckleyi and its relative H. cyanoguttatus using a combination of population genetics and species tree analyses. We first examined the distribution of mitochondrial haplotypes within the alternative H. minckleyi pharyngeal jaw morphotypes that are endemic to the small desert valley of Cuatro Ciénegas. We recovered two clusters of mitochondrial haplotypes. The first contained a number of slightly differentiated cytochrome b (cytb) haplotypes that showed some phylogeographic signal and were present in both jaw morphotypes. The other haplotype was monomorphic, highly differentiated from the other cluster, present in equal frequencies in the morphotypes, and identical to H. cyanoguttatus haplotypes found outside Cuatro Ciénegas. Then, we investigated whether H. minckleyi individuals with the H. cyanoguttatus cytb were more evolutionarily similar to H. cyanoguttatus or other H. minckleyi using a species tree analysis of 84 nuclear loci. Both H. minckleyi pharyngeal morphotypes, regardless of their cytb haplotype, were quite distinct from H. cyanoguttatus. However, hybridization could be blurring subdivision within H. minckleyi as the alternative jaw morphotypes were not genetically distinct from one another. Accounting for introgression from H. cyanoguttatus will be essential to understand the evolution of the trophically polymorphic cichlid H. minckleyi. PMID:24340193

  8. Genotyping for cytochrome P450 polymorphisms.

    PubMed

    Daly, Ann K; King, Barry P; Leathart, Julian B S

    2006-01-01

    Protocols for the extraction of DNA from human blood and for genotyping for a number of common cytochrome P450 polymorphisms using either polymerase chain reaction (PCR)-restriction fragment length polymorphism or PCR-single-strand conformational polymorphism (SSCP) analysis are described. Rapid high-throughput techniques are also available for analyses of this type, but they require access to specialized equipment and are not considered here. General guidelines for performing amplification using PCR are described together with electrophoresis protocols for analysis of restriction digests of PCR products with agarose and polyacrylamide gels including the use of polyacrylamide-based gels for SSCP analysis. Protocols for the following specific isoforms and alleles are also provided: CYP1A1 (*2B and *4 alleles), CYP2C8 (*3 and *4 alleles), CYP2C9 (*2, *3, and *11 alleles), CYP2C19 (*2 and *3 alleles), CYP2D6 (*3, *4, *5, and *6 alleles), CYP2E1 (*5A, *5B, and *6 alleles), and CYP3A5 (*3 allele). PMID:16719392

  9. Chromosome-length polymorphism in fungi.

    PubMed Central

    Zolan, M E

    1995-01-01

    The examination of fungal chromosomes by pulsed-field gel electrophoresis has revealed that length polymorphism is widespread in both sexual and asexual species. This review summarizes characteristics of fungal chromosome-length polymorphism and possible mitotic and meiotic mechanisms of chromosome length change. Most fungal chromosome-length polymorphisms are currently uncharacterized with respect to content and origin. However, it is clear that long tandem repeats, such as tracts of rRNA genes, are frequently variable in length and that other chromosomal rearrangements are suppressed during normal mitotic growth. Dispensable chromosomes and dispensable chromosome regions, which have been well documented for some fungi, also contribute to the variability of the fungal karyotype. For sexual species, meiotic recombination increases the overall karyotypic variability in a population while suppressing genetic translocations. The range of karyotypes observed in fungi indicates that many karyotypic changes may be genetically neutral, at least under some conditions. In addition, new linkage combinations of genes may also be advantageous in allowing adaptation of fungi to new environments. PMID:8531892

  10. Glucosyltransferase gene polymorphism among Streptococcus mutans strains.

    PubMed Central

    Chia, J S; Hsu, T Y; Teng, L J; Chen, J Y; Hahn, L J; Yang, C S

    1991-01-01

    Genetic polymorphisms in genes coding for the glucosyltransferases were detected among Streptococcus mutans serotype c strains by Southern blot analysis with DNA probes located within the gtfB gene (H. Aoki, T. Shiroza, M. Hayakawa, S. Sato, and H. K. Kuramitsu, Infect. Immun. 53:587-594, 1986). Restriction endonucleases were used to examine genomic DNAs isolated from serotype a to h strains. The variations were readily detected among 33 strains of serotype c by EcoRI and PstI restriction enzyme digestions. Serotypes e and f, which are genetically similar to serotype c, also had comparable polymorphism; however, serotypes a, b, d, g, and h did not hybridize to the same DNA probes in parallel experiments. Further analysis of enzymatic activities for glucan synthesis and sucrose-dependent adherence revealed no significant differences among the serotype c strains. Our results suggested that genetic polymorphisms existing in S. mutans serotype c strains may reflect a complexity in genes coding for the glucosyltransferases, which are produced ubiquitously in members of the S. mutans group. Images PMID:1826894

  11. Inflammasome polymorphisms in juvenile systemic lupus erythematosus.

    PubMed

    Pontillo, Alessandra; Reis, Edione C; Liphaus, Bernadete L; Silva, Clovis A; Carneiro-Sampaio, Magda

    2015-01-01

    Inflammasome is the cytoplasmic complex responsible for pro-IL1 β cleavage and secretion of IL-1β. Recently our group reported the first association between polymorphisms in the inflammasome receptor NLRP1 and adult-onset systemic lupus erythematosus (SLE) "di per se" and especially in SLE-associated renal disease, suggesting the involvement of NLRP1-inflammasome in the immune dysregulation characteristic of SLE patients. Considering that juvenile-onset SLE (JSLE) is more severe than adult SLE, and that the genetic background plays a major role in the early development of autoimmune diseases, we analysed selected polymorphisms in inflammasome genes (NLRP1, NLRP3, CARD8, IL1B, TNFAIP3) of children and adolescents with JSLE (n = 90) and in healthy controls (n = 144). A single polymorphism in IL1B, and not NLRP1, gene resulted in association with JSLE, suggesting that IL-1 β is involved in the pathogenesis of SLE, but different genes could play specific role in adult- or early-onset disease. PMID:26182076

  12. Interleukin-1 gene polymorphisms and toxoplasmic retinochoroiditis

    PubMed Central

    Moreira, Paula R.; Costa, Germano C.; Dutra, Walderez O.; Oréfice, Fernando; Teixeira, Antônio L.

    2008-01-01

    Purpose It has been proposed that cytokine gene polymorphisms can predispose individuals to disease by enhancing inflammatory processes. Considering the relevance of interleukin-1 (IL-1) in the pathogenesis of toxoplasmic retinochoroiditis (TR), we investigated whether IL1A −889 C/T and IL1B +3954C/T promoter polymorphisms are associated with TR in humans. Methods We performed a cross-sectional study that involved 100 Brazilian TR patients and 100 age- and gender-matched control subjects. Genomic DNA was obtained from oral swabs of all participants and amplified using polymerase chain reaction (PCR) with specific primers flanking the locus −889 of IL1A and +3954 of IL1B. PCR products were submitted to digestion and analyzed by PAGE to distinguish C and T alleles. Results There was no significant difference in the genotype or allele distributions of the IL1A −889 C/T and IL1B +3954C/T polymorphisms in patients with TR when compared with controls. However, in a subgroup analysis, the frequency of genotype and allele distributions of IL1A −889 C/T differed significantly between TR patients with and without recurrent episodes. Conclusion This study suggests that the genotypes related with a high production of IL-1a may be associated with the recurrence of TR. PMID:18941541

  13. Genetic polymorphisms linked to susceptibility to malaria

    PubMed Central

    2011-01-01

    The influence of host genetics on susceptibility to Plasmodium falciparum malaria has been extensively studied over the past twenty years. It is now clear that malaria parasites have imposed strong selective forces on the human genome in endemic regions. Different genes have been identified that are associated with different malaria related phenotypes. Factors that promote severity of malaria include parasitaemia, parasite induced inflammation, anaemia and sequestration of parasitized erythrocytes in brain microvasculature. Recent advances in human genome research technologies such as genome-wide association studies (GWAS) and fine genotyping tools have enabled the discovery of several genetic polymorphisms and biomarkers that warrant further study in host-parasite interactions. This review describes and discusses human gene polymorphisms identified thus far that have been shown to be associated with susceptibility or resistance to P. falciparum malaria. Although some polymorphisms play significant roles in susceptibility to malaria, several findings are inconclusive and contradictory and must be considered with caution. The discovery of genetic markers associated with different malaria phenotypes will help elucidate the pathophysiology of malaria and enable development of interventions or cures. Diversity in human populations as well as environmental effects can influence the clinical heterogeneity of malaria, thus warranting further investigations with a goal of developing new interventions, therapies and better management against malaria. PMID:21929748

  14. Colour Polymorphism Protects Prey Individuals and Populations Against Predation

    PubMed Central

    Karpestam, Einat; Merilaita, Sami; Forsman, Anders

    2016-01-01

    Colour pattern polymorphism in animals can influence and be influenced by interactions between predators and prey. However, few studies have examined whether polymorphism is adaptive, and there is no evidence that the co-occurrence of two or more natural prey colour variants can increase survival of populations. Here we show that visual predators that exploit polymorphic prey suffer from reduced performance, and further provide rare evidence in support of the hypothesis that prey colour polymorphism may afford protection against predators for both individuals and populations. This protective effect provides a probable explanation for the longstanding, evolutionary puzzle of the existence of colour polymorphisms. We also propose that this protective effect can provide an adaptive explanation for search image formation in predators rather than search image formation explaining polymorphism. PMID:26902799

  15. A quantitative study of eosinophil polymorphs in Hodgkin's disease.

    PubMed

    Fuggle, W J; Crocker, J; Smith, P J

    1984-03-01

    Eosinophil polymorphonuclear leucocytes (polymorphs) were counted in 45 specimens from patients with Hodgkin's disease and five specimens from patients with reactive follicular hyperplasia. The use of chlorazol fast pink BK, a little known stain for eosinophil polymorphs, combined with image analysis facilitated rapid and reliable counting. Significant differences were found between the mean percentages of eosinophil polymorphs in the Rye subtypes of Hodgkin's disease. The numbers of eosinophil polymorphs in specimens from patients with reactive follicular hyperplasia were very low and could not be counted. PMID:6699190

  16. Impact of Candidate Genetic Polymorphisms in Prostate Cancer: An Overview.

    PubMed

    Salvi, S; Conteduca, V; Gurioli, G; Calistri, D; Casadio, V; De Giorgi, U

    2016-02-01

    In the last few years, the presence of single nucleotide polymorphisms (SNPs) has been investigated in many tumors as predictor of disease aggressiveness and clinical outcome. We searched for relevant articles from 1998 to 2015 about the impact of SNPs in prostate cancer. Particularly, in this article, we review the pathogenetic, prognostic and predictive significance of gene polymorphisms in prostate tumor, providing a brief overview of studies in which the possible role of genetic variants was investigated in clinical settings. Because conflicting results often emerge about the impact of gene polymorphisms in prostate cancer, further larger studies are warranted in order to introduce gene polymorphism into clinical practice as biomarkers. PMID:26518421

  17. Detecting high-resolution polymorphisms in human coding loci by combining PCR and single-strand conformation polymorphism (SSCP) analysis.

    PubMed

    Poduslo, S E; Dean, M; Kolch, U; O'Brien, S J

    1991-07-01

    A strategy is described that allows the development of polymorphic genetic markers to be characterized in individual genes. Segments of the 3' untranslated regions are amplified, and polymorphisms are detected by digestion with frequently cutting enzymes and with the detection of single-stranded conformation polymorphisms. This allows these genes, or DNA segments, to be placed on the linkage maps of human chromosomes. Polymorphisms in two genes have been identified using this approach. A HaeIII polymorphism was detected in the KIT proto-oncogene, physically assigned to chromosome 4q11-12. This polymorphism is linked to other chromosome 4p markers and is in linkage disequilibrium with a HindIII polymorphism previously described at this locus. We have also identified in the insulin-like growth factor1 receptor gene (IGF1R) a 2-bp deletion that is present at a frequency of .25 in the Caucasian population. Pedigree analysis with this insertion/deletion polymorphism placed the IGF1R gene at the end of the current linkage map of chromosome 15q, consistent with the physical assignment of 15q2526. Thus, polymorphisms in specific genes can be used to related the physical, genetic, and comparative maps of mammalian genomes and to simplify the testing of candidate genes for human diseases. PMID:1676559

  18. Polymorphism in phenobarbital: discovery of a new polymorph and crystal structure of elusive form V.

    PubMed

    Roy, Saikat; Goud, N Rajesh; Matzger, Adam J

    2016-03-10

    This report highlights the discovery of a new polymorph of the anticonvulsant drug phenobarbital (PB) using polymer-induced heteronucleation (PIHn) and unravelling the crystal structure of the elusive form V. Both forms are characterized by structural, thermal and VT-Raman spectroscopy methods to elucidate phase transformation behavior and shed light on stability relationships. PMID:26926048

  19. Genetic polymorphisms associated with exertional rhabdomyolysis.

    PubMed

    Deuster, Patricia A; Contreras-Sesvold, Carmen L; O'Connor, Francis G; Campbell, William W; Kenney, Kimbra; Capacchione, John F; Landau, Mark E; Muldoon, Sheila M; Rushing, Elisabeth J; Heled, Yuval

    2013-08-01

    Exertional rhabdomyolysis (ER) occurs in young, otherwise healthy, individuals principally during strenuous exercise, athletic, and military training. Although many risk factors have been offered, it is unclear why some individuals develop ER when participating in comparable levels of physical exertion under identical environmental conditions and others do not. This study investigated possible genetic polymorphisms that might help explain ER. DNA samples derived from a laboratory-based study of persons who had never experienced an episode of ER (controls) and clinical ER cases referred for testing over the past several years were analyzed for single nucleotide polymorphisms (SNPs) in candidate genes. These included angiotensin I converting enzyme (ACE), α-actinin-3 (ACTN3), creatine kinase muscle isoform (CKMM), heat shock protein A1B (HSPA1B), interleukin 6 (IL6), myosin light chain kinase (MYLK), adenosine monophosphate deaminase 1 (AMPD1), and sickle cell trait (HbS). Population included 134 controls and 47 ER cases. The majority of ER cases were men (n = 42/47, 89.4 %); the five women with ER were Caucasian. Eighteen African Americans (56.3 %) were ER cases. Three SNPs were associated with ER: CKMM Ncol, ACTN3 R577X, and MYLK C37885A. ER cases were 3.1 times more likely to have the GG genotype of CKMM (odds ratio/OR = 3.1, confidence interval/CI 1.33-7.10), 3.0 times for the XX genotype of ACTN3 SNP (OR = 2.97, CI 1.30-3.37), and 5.7 times for an A allele of MYLK (OR = 21.35, CI 2.60-12.30). All persons with HbS were also ER cases. Three distinct polymorphisms were associated with ER. Further work will be required to replicate these findings and determine the mechanism(s) whereby these variants might confer susceptibility. PMID:23543093

  20. The extensive polymorphism of KIR genes

    PubMed Central

    Middleton, Derek; Gonzelez, Faviel

    2010-01-01

    The functions of human natural killer (NK) cells are controlled by diverse families of antigen receptors. Prominent among these are the killer cell immunoglobulin-like receptors (KIR), a family of genes clustered in one of the most variable regions of the human genome. Within this review we discuss the vast polymorphism of the KIR gene complex which rivals that of the human leucocyte antigen (HLA) complex. There are several aspects to this polymorphism. Initially there is presence/absence of individual KIR genes, with four of these genes, termed framework genes, being present in all individuals tested to date, except on those very occasional instances when the gene has been deleted. Within each gene, alleles are present at different frequencies. We provide details of a new website that enables convenient searching for data on KIR gene, allele and genotype frequencies in different populations and show how these frequencies vary in different worldwide populations and the high probability of individuals differing in their KIR repertoire when both gene and allele polymorphism is considered. The KIR genes present in an individual may be classified into A and/or B haplotypes, which respectively have a more inhibitory role or a more activating role on the function of the NK cell. Family studies have been used to ascertain the make-up of these haplotypes, inclusion of allele typing enabling determination of whether one or two copies of a particular gene is present. In addition to genetic diversification the KIR gene complex shows differences at the functional level with different alleles having different protein expression levels and different avidity with their HLA ligand. PMID:20028428

  1. MMP-3 gene polymorphisms and Osteosarcoma.

    PubMed

    Adiguzel, Mustafa; Horozoglu, Cem; Kilicoglu, Onder; Ozger, Harzem; Acar, Leyla; Ergen, Arzu

    2016-03-01

    Osteosarcoma (OSA) is the most common adolescence cancer among all primary bone tumors next only to multiplemyeloma. It has a substantially worse prognosis and ability to metastasize to lung. MMPs (matrix metalloproteinases) are among the major proteases that take part in regulation of ECM (extracellular matrix). MMPs play an active role in the formation of the osteoid tissue, rich in collagens and other ECM proteoglycans. They also take part in pro-osteoclast, osteoclast, osteoblast, and osteoid formation. Many members of the MMP gene family have been linked to human cancers. It has been shown that MMPs particularly play a role in the tumor's acquisition of an invasive and metastatic character. In our study, the E45K and T102T polymorphisms of MMP-3 were studied using the PCR-RFLP method in 135 Turkish subjects (54 subjects with osteosarcoma and 81 healthy controls). We found that frequencies of E45K G allele (p:0,010, χ²:6,710, OR:1,429, 95% Cl: 1,019-1,858) and AG genotype (p:0,001, χ²:14,753, OR:2,32, 95% Cl: 1,491-3,626) were elevated in patients compared to controls. Besides, there was a significant difference in.E45K AA genotype between study groups (p:0,004, χ²:8,182, OR: 2,929, 95% Cl: 1,38-6,19). There were no significant differences between any genotypes or allele in the control and patient groups for MMP-3 T102T polymorphism. Our findings indicate that the G allele and AG genotype of MMP-3 E45K polymorphism is associated with increased risk of osteosarcoma in adolescent population of Turkey. PMID:27145630

  2. Nucleosomes Shape DNA Polymorphism and Divergence

    PubMed Central

    Langley, Sasha A.; Karpen, Gary H.; Langley, Charles H.

    2014-01-01

    An estimated 80% of genomic DNA in eukaryotes is packaged as nucleosomes, which, together with the remaining interstitial linker regions, generate higher order chromatin structures [1]. Nucleosome sequences isolated from diverse organisms exhibit ∼10 bp periodic variations in AA, TT and GC dinucleotide frequencies. These sequence elements generate intrinsically curved DNA and help establish the histone-DNA interface. We investigated an important unanswered question concerning the interplay between chromatin organization and genome evolution: do the DNA sequence preferences inherent to the highly conserved histone core exert detectable natural selection on genomic divergence and polymorphism? To address this hypothesis, we isolated nucleosomal DNA sequences from Drosophila melanogaster embryos and examined the underlying genomic variation within and between species. We found that divergence along the D. melanogaster lineage is periodic across nucleosome regions with base changes following preferred nucleotides, providing new evidence for systematic evolutionary forces in the generation and maintenance of nucleosome-associated dinucleotide periodicities. Further, Single Nucleotide Polymorphism (SNP) frequency spectra show striking periodicities across nucleosomal regions, paralleling divergence patterns. Preferred alleles occur at higher frequencies in natural populations, consistent with a central role for natural selection. These patterns are stronger for nucleosomes in introns than in intergenic regions, suggesting selection is stronger in transcribed regions where nucleosomes undergo more displacement, remodeling and functional modification. In addition, we observe a large-scale (∼180 bp) periodic enrichment of AA/TT dinucleotides associated with nucleosome occupancy, while GC dinucleotide frequency peaks in linker regions. Divergence and polymorphism data also support a role for natural selection in the generation and maintenance of these super

  3. Trophic radiation through polymorphism in cichlid fishes.

    PubMed

    Sage, R D; Selander, R K

    1975-11-01

    Several morphologically defined species of cichlid fishes (Cichlasoma) endemic to the Cuatro Cienegas basin of Mexico and differing in tooth structure, body shape, and diet are allelically identical at 27 gene loci. The presence of only one Mendelian population in each of three drainage systems studied and the occurrence of two of the morphotypes in the same broods indicate that the supposed species are morphs. That trophic radiation in the Cuatro Cienegas cichlids has been achieved through ecological polymorphism rather than speciation raises questions regarding the genetic basis for the extensive intralacustrine radiation of cichlids in Africa and elsewhere. PMID:16592286

  4. Trophic radiation through polymorphism in cichlid fishes

    PubMed Central

    Sage, Richard D.; Selander, Robert K.

    1975-01-01

    Several morphologically defined species of cichlid fishes (Cichlasoma) endemic to the Cuatro Cienegas basin of Mexico and differing in tooth structure, body shape, and diet are allelically identical at 27 gene loci. The presence of only one Mendelian population in each of three drainage systems studied and the occurrence of two of the morphotypes in the same broods indicate that the supposed species are morphs. That trophic radiation in the Cuatro Cienegas cichlids has been achieved through ecological polymorphism rather than speciation raises questions regarding the genetic basis for the extensive intralacustrine radiation of cichlids in Africa and elsewhere. Images PMID:16592286

  5. What Determines the Ice Polymorph in Clouds?

    PubMed

    Hudait, Arpa; Molinero, Valeria

    2016-07-20

    Ice crystals in the atmosphere nucleate from supercooled liquid water and grow by vapor uptake. The structure of the ice polymorph grown has strong impact on the morphology and light scattering of the ice crystals, modulates the amount of water vapor in ice clouds, and can impact the molecular uptake and reactivity of atmospheric aerosols. Experiments and molecular simulations indicate that ice nucleated and grown from deeply supercooled liquid water is metastable stacking disordered ice. The ice polymorph grown from vapor has not yet been determined. Here we use large-scale molecular simulations to determine the structure of ice that grows as a result of uptake of water vapor in the temperature range relevant to cirrus and mixed-phase clouds, elucidate the molecular mechanism of the formation of ice at the vapor interface, and compute the free energy difference between cubic and hexagonal ice interfaces with vapor. We find that vapor deposition results in growth of stacking disordered ice only under conditions of extreme supersaturation, for which a nonequilibrium liquid layer completely wets the surface of ice. Such extreme conditions have been used to produce stacking disordered frost ice in experiments and may be plausible in the summer polar mesosphere. Growth of ice from vapor at moderate supersaturations in the temperature range relevant to cirrus and mixed-phase clouds, from 200 to 260 K, produces exclusively the stable hexagonal ice polymorph. Cubic ice is disfavored with respect to hexagonal ice not only by a small penalty in the bulk free energy (3.6 ± 1.5 J mol(-1) at 260 K) but also by a large free energy penalty at the ice-vapor interface (89.7 ± 12.8 J mol(-1) at 260 K). The latter originates in higher vibrational entropy of the hexagonal-terminated ice-vapor interface. We predict that the free energy penalty against the cubic ice interface should decrease strongly with temperature, resulting in some degree of stacking disorder in ice grown from

  6. Human lymphocyte polymorphisms detected by quantitative two-dimensional electrophoresis

    SciTech Connect

    Goldman, D.; Merril, C.R.

    1983-09-01

    A survey of 186 soluble lymphocyte proteins for genetic polymorphism was carried out utilizing two-dimensional electrophoresis of /sup 14/C-labeled phytohemagglutinin (PHA)-stimulated human lymphocyte proteins. Nineteen of these proteins exhibited positional variation consistent with independent genetic polymorphism in a primary sample of 28 individuals. Each of these polymorphisms was characterized by quantitative gene-dosage dependence insofar as the heterozygous phenotype expressed approximately 50% of each allelic gene product as was seen in homozygotes. Patterns observed were also identical in monozygotic twins, replicate samples, and replicate gels. The three expected phenotypes (two homozygotes and a heterozygote) were observed in each of 10 of these polymorphisms while the remaining nine had one of the homozygous classes absent. The presence of the three phenotypes, the demonstration of gene-dosage dependence, and our own and previous pedigree analysis of certain of these polymorphisms supports the genetic basis of these variants. Based on this data, the frequency of polymorphic loci for man is: P . 19/186 . .102, and the average heterozygosity is .024. This estimate is approximately 1/3 to 1/2 the rate of polymorphism previously estimated for man in other studies using one-dimensional electrophoresis of isozyme loci. The newly described polymorphisms and others which should be detectable in larger protein surveys with two-dimensional electrophoresis hold promise as genetic markers of the human genome for use in gene mapping and pedigree analyses.

  7. Association between Tryptophan Hydroxylase 2 Gene Polymorphism and Completed Suicide

    ERIC Educational Resources Information Center

    Fudalej, Sylwia; Ilgen, Mark; Fudalej, Marcin; Kostrzewa, Grazyna; Barry, Kristen; Wojnar, Marcin; Krajewski, Pawel; Blow, Frederic; Ploski, Rafal

    2010-01-01

    The association between suicide and a single nucleotide polymorphism (rs1386483) was examined in the recently identified tryptophan hydroxylase 2 (TPH2) gene. Blood samples of 143 suicide victims and 162 age- and sex-matched controls were examined. The frequency of the TT genotype in the TPH2 polymorphism was higher in suicide victims than in…

  8. Association Between NAT2 Polymorphisms and Lung Cancer Susceptibility.

    PubMed

    Liu, Chang; Cui, Wei; Cong, Lin; Wang, Li; Ruan, Xinjian; Jia, Jia; Liu, Yanfang; Jia, Xiaoyan; Zhang, Xia

    2015-12-01

    To further investigate the association between NAT2 polymorphisms and lung cancer susceptibility.In terms of phenotypes, we investigated the acetylator status of NAT2 polymorphisms associated with lung cancer risk. Additionally, in view of genotypes, we mainly analyzed 5 single nucleotide polymorphisms (SNPs) in NAT2 gene, namely C282T, A803G, C481T, G590A, and G857A. Twenty-six eligible studies were included in our meta-analysis by searching PubMed, Embase, and CNKI databases. We used odds ratios (ORs) with corresponding 95% confidence intervals (CIs) to evaluate the susceptibility to lung cancer associated with NAT2 polymorphisms.Overall, based on phenotypes, the pooled ORs showed no significant association between NAT2 polymorphisms and lung cancer susceptibility. In the subgroup analyses by ethnicity and source of control, there was still no significant association. In terms of genotypes, overall, no obvious relationship was observed between NAT2 polymorphisms and lung cancer risk. But increased risk of lung cancer was found in association with NAT2 C282T polymorphism (TT vs. CC + TC: OR = 1.58, 95% CI = 1.11-2.25).Our meta-analysis demonstrates that TT genotype in NAT2 C282T polymorphism may be a risk factor for lung cancer susceptibility. Additionally, the acetylator status of 5 SNPs in NAT2 gene may not be associated with lung cancer risk. PMID:26656326

  9. Polymorphisms in Autophagy Genes and Susceptibility to Tuberculosis

    PubMed Central

    Alisjahbana, Bachti; Sahiratmadja, Edhyana; Parwati, Ida; Oosting, Marije; Plantinga, Theo S.; Joosten, Leo A. B.; Netea, Mihai G.; Ottenhoff, Tom H. M.; van de Vosse, Esther; van Crevel, Reinout

    2012-01-01

    Recent data suggest that autophagy is important for intracellular killing of Mycobacterium tuberculosis, and polymorphisms in the autophagy gene IRGM have been linked with susceptibility to tuberculosis (TB) among African-Americans, and with TB caused by particular M. tuberculosis genotypes in Ghana. We compared 22 polymorphisms of 14 autophagy genes between 1022 Indonesian TB patients and 952 matched controls, and between patients infected with different M. tuberculosis genotypes, as determined by spoligotyping. The same autophagy polymorphisms were studied in correlation with ex-vivo production of TNF, IL-1β, IL-6, IL-8, IFN-γ and IL-17 in healthy volunteers. No association was found between TB and polymorphisms in the genes ATG10, ATG16L2, ATG2B, ATG5, ATG9B, IRGM, LAMP1, LAMP3, P2RX7, WIPI1, MTOR and ATG4C. Associations were found between polymorphisms in LAMP1 (p = 0.02) and MTOR (p = 0.02) and infection with the successful M. tuberculosis Beijing genotype. The polymorphisms examined were not associated with M. tuberculosis induced cytokines, except for a polymorphism in ATG10, which was linked with IL-8 production (p = 0.04). All associations found lost statistical significance after correction for multiple testing. This first examination of a broad set of polymorphisms in autophagy genes fails to show a clear association with TB, with M. tuberculosis Beijing genotype infection or with ex-vivo pro-inflammatory cytokine production. PMID:22879892

  10. Effects of human SAMHD1 polymorphisms on HIV-1 susceptibility

    SciTech Connect

    White, Tommy E.; Brandariz-Nuñez, Alberto; Valle-Casuso, Jose Carlos; Knowlton, Caitlin; Kim, Baek; Sawyer, Sara L.; Diaz-Griffero, Felipe

    2014-07-15

    SAMHD1 is a human restriction factor that prevents efficient infection of macrophages, dendritic cells and resting CD4+ T cells by HIV-1. Here we explored the antiviral activity and biochemical properties of human SAMHD1 polymorphisms. Our studies focused on human SAMHD1 polymorphisms that were previously identified as evolving under positive selection for rapid amino acid replacement during primate speciation. The different human SAMHD1 polymorphisms were tested for their ability to block HIV-1, HIV-2 and equine infectious anemia virus (EIAV). All studied SAMHD1 variants block HIV-1, HIV-2 and EIAV infection when compared to wild type. We found that these variants did not lose their ability to oligomerize or to bind RNA. Furthermore, all tested variants were susceptible to degradation by Vpx, and localized to the nuclear compartment. We tested the ability of human SAMHD1 polymorphisms to decrease the dNTP cellular levels. In agreement, none of the different SAMHD1 variants lost their ability to reduce cellular levels of dNTPs. Finally, we found that none of the tested human SAMHD1 polymorphisms affected the ability of the protein to block LINE-1 retrotransposition. - Highlights: • Human SAMHD1 single-nucleotide polymorphisms block HIV-1 and HIV-2 infection. • SAMHD1 polymorphisms do not affect its ability to block LINE-1 retrotransposition. • SAMHD1 polymorphisms decrease the cellular levels of dNTPs.

  11. TPMT Polymorphism: When Shield Becomes Weakness.

    PubMed

    Katara, Pramod; Kuntal, Himani

    2016-06-01

    Thiopurine methyltransferase (TPMT) is a cytoplasmic transmethylase present in both prokaryotes and eukaryotes. In humans, it shows its presence in almost all of the tissues, predominantly in liver and kidney. TPMT is one of the important metabolic enzymes of phase II metabolic pathway and catalyzes methylation of thiopurine drugs such as azathioprine, 6-thioguanine and 6-mercaptopurine, which are used to treat patients with neoplasia and autoimmune disease as well as transplant recipients. In this sense, TPMT acts as shield against toxic effect of these drugs. Pharmacogenomic studies revealed that genetic polymorphism in TPMT is responsible for variable and, in some cases, adverse drug reaction. Those human groups who carry variants of TPMT (i.e., [Formula: see text], [Formula: see text], [Formula: see text]) are at high risk, because they are unable to metabolize thiopurine drugs thus becoming a weakness of patients against these drugs. Keeping in the mind the importance of TPMT, this review discusses the existence and distribution of various TPMT variants throughout different ethnic groups and risk of adverse drug reactions to them, and how they can avoid this risk of side effects. The review also highlighted factors responsible for variable reactions of TPMT, how this TPMT polymorphism can be considered in drug designing process to avoid toxic effects, designing precautions against them and more importantly designing personalized medicine. PMID:26297310

  12. From Single Nucleotide Polymorphism to Transcriptional Mechanism

    PubMed Central

    Martini, Sebastian; Nair, Viji; Patel, Sanjeevkumar R.; Eichinger, Felix; Nelson, Robert G.; Weil, E. Jennifer; Pezzolesi, Marcus G.; Krolewski, Andrzej S.; Randolph, Ann; Keller, Benjamin J.; Werner, Thomas; Kretzler, Matthias

    2013-01-01

    Genome-wide association studies have proven to be highly effective at defining relationships between single nucleotide polymorphisms (SNPs) and clinical phenotypes in complex diseases. Establishing a mechanistic link between a noncoding SNP and the clinical outcome is a significant hurdle in translating associations into biological insight. We demonstrate an approach to assess the functional context of a diabetic nephropathy (DN)-associated SNP located in the promoter region of the gene FRMD3. The approach integrates pathway analyses with transcriptional regulatory pattern-based promoter modeling and allows the identification of a transcriptional framework affected by the DN-associated SNP in the FRMD3 promoter. This framework provides a testable hypothesis for mechanisms of genomic variation and transcriptional regulation in the context of DN. Our model proposes a possible transcriptional link through which the polymorphism in the FRMD3 promoter could influence transcriptional regulation within the bone morphogenetic protein (BMP)-signaling pathway. These findings provide the rationale to interrogate the biological link between FRMD3 and the BMP pathway and serve as an example of functional genomics-based hypothesis generation. PMID:23434934

  13. Intronic polymorphisms of cytochromes P450

    PubMed Central

    2010-01-01

    The cytochrome P450 enzymes active in drug metabolism are highly polymorphic. Most allelic variants have been described for enzymes encoded by the cytochrome P450 family 2 (CYP2) gene family, which has 252 different alleles. The intronic polymorphisms in the cytochrome P450 genes account for only a small number of the important variant alleles; however, the most important ones are CYP2D6*4 and CYP2D6*41, which cause abolished and reduced CYP2D6 activity, respectively, and CYP3A5*3 and CYP3A5*5, common in Caucasian populations, which cause almost null activity. Their discoveries have been based on phenotypic alterations within individuals in a population, and their identification has, in several cases, been difficult and taken a long time. In light of the next-generation sequencing projects, it is anticipated that further alleles with intronic mutations will be identified that can explain the hitherto unidentified genetic basis of inter-individual differences in cytochrome P450-mediated drug and steroid metabolism. PMID:20846929

  14. Polymorphic collaboration in the global grid

    NASA Astrophysics Data System (ADS)

    McQuay, William K.

    2006-05-01

    Next generation collaborative systems must be able to represent the same information in different forms on a broad spectrum of devices and resources from low end personal digital assistants (PDA) to high performance computers (HPC). Users might be on a desktop then switch to a laptop and then to a PDA while accessing the global grid. The user preference profile for a collaboration session should be capable of moving with them as well as be automatically adjusted for the device type. Collaborative systems must be capable of representing the same information in many forms for different domains and on many devices and thus be polymorphic. Polymorphic collaboration will provide an ability for multiple heterogeneous resources (human to human, human to machine and machine to machine) to share information and activities, as well as the ability to regulate collaborative sessions based on client characteristics and needs; reuse user profiles, tool category choices, and settings in future collaboration session by same or different users; use intelligent agents to assist collaborative systems in learning user/resource preferences and behaviors, and autonomously derive optimal information to provide to users and decision makers. This paper discusses ongoing research in next generation collaborative environments with the goal of making electronic collaboration as easy to use as the telephone - collaboration at the touch of the screen.

  15. Counterintuitive compaction behavior of clopidogrel bisulfate polymorphs.

    PubMed

    Khomane, Kailas S; More, Parth K; Bansal, Arvind K

    2012-07-01

    Being a density violator, clopidogrel bisulfate (CLP) polymorphic system (forms I and II) allows us to study individually the impact of molecular packing (true density) and thermodynamic properties such as heat of fusion on the compaction behavior. These two polymorphs of CLP were investigated for in-die and out-of-die compaction behavior using CTC profile, Heckel, and Walker equations. Compaction studies were performed on a fully instrumented rotary tabletting machine. Detailed examinations of the molecular packing of each form revealed that arrangement of the sulfate anion differs significantly in both crystal forms, thus conferring different compaction behavior to two forms. Close cluster packing of molecules in form I offers a rigid structure, which has poor compressibility and hence resists deformation under compaction pressure. This results into lower densification, higher yield strength, and mean yield pressure, as compared with form II at a given pressure. However, by virtue of higher bonding strength, form I showed superior tabletability, despite its poor compressibility and deformation behavior. Form I, having higher true density and lower heat of fusion showed higher bonding strength. Hence, true density and not heat of fusion can be considered predictor of bonding strength of the pharmaceutical powders. PMID:22488254

  16. Dynamically Alterable Arrays of Polymorphic Data Types

    NASA Technical Reports Server (NTRS)

    James, Mark

    2006-01-01

    An application library package was developed that represents data packets for Deep Space Network (DSN) message packets as dynamically alterable arrays composed of arbitrary polymorphic data types. The software was to address a limitation of the present state of the practice for having an array directly composed of a single monomorphic data type. This is a severe limitation when one is dealing with science data in that the types of objects one is dealing with are typically not known in advance and, therefore, are dynamic in nature. The unique feature of this approach is that it enables one to define at run-time the dynamic shape of the matrix with the ability to store polymorphic data types in each of its indices. Existing languages such as C and C++ have the restriction that the shape of the array must be known in advance and each of its elements be a monomorphic data type that is strictly defined at compile-time. This program can be executed on a variety of platforms. It can be distributed in either source code or binary code form. It must be run in conjunction with any one of a number of Lisp compilers that are available commercially or as shareware.

  17. IPD—the Immuno Polymorphism Database

    PubMed Central

    Robinson, James; Waller, Matthew J.; Stoehr, Peter; Marsh, Steven G. E.

    2005-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute. PMID:15608253

  18. IPD--the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Waller, Matthew J; Stoehr, Peter; Marsh, Steven G E

    2005-01-01

    The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-like Receptors; IPD-MHC, a database of sequences of the Major Histocompatibility Complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. Those sections with similar data, such as IPD-KIR and IPD-MHC share the same database structure. The sharing of a common database structure makes it easier to implement common tools for data submission and retrieval. The data are currently available online from the website and ftp directory; files will also be made available in different formats to download from the website and ftp server. The data will also be included in SRS, BLAST and FASTA search engines at the European Bioinformatics Institute. PMID:15608253

  19. IPD—the Immuno Polymorphism Database

    PubMed Central

    Robinson, James; Halliwell, Jason A.; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G. E.

    2013-01-01

    The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project. PMID:23180793

  20. IPD--the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Halliwell, Jason A; McWilliam, Hamish; Lopez, Rodrigo; Marsh, Steven G E

    2013-01-01

    The Immuno Polymorphism Database (IPD), http://www.ebi.ac.uk/ipd/ is a set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. The IPD project stores all the data in a set of related databases. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of killer-cell immunoglobulin-like receptors, IPD-MHC, a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. The data is currently available online from the website and FTP directory. This article describes the latest updates and additional tools added to the IPD project. PMID:23180793

  1. Bitter Taste Receptor Polymorphisms and Human Aging

    PubMed Central

    Carrai, Maura; Crocco, Paolina; Montesanto, Alberto; Canzian, Federico; Rose, Giuseppina; Rizzato, Cosmeri

    2012-01-01

    Several studies have shown that genetic factors account for 25% of the variation in human life span. On the basis of published molecular, genetic and epidemiological data, we hypothesized that genetic polymorphisms of taste receptors, which modulate food preferences but are also expressed in a number of organs and regulate food absorption processing and metabolism, could modulate the aging process. Using a tagging approach, we investigated the possible associations between longevity and the common genetic variation at the three bitter taste receptor gene clusters on chromosomes 5, 7 and 12 in a population of 941 individuals ranging in age from 20 to 106 years from the South of Italy. We found that one polymorphism, rs978739, situated 212 bp upstream of the TAS2R16 gene, shows a statistically significant association (p = 0.001) with longevity. In particular, the frequency of A/A homozygotes increases gradually from 35% in subjects aged 20 to 70 up to 55% in centenarians. These data provide suggestive evidence on the possible correlation between human longevity and taste genetics. PMID:23133589

  2. A gene feature enumeration approach for describing HLA allele polymorphism.

    PubMed

    Mack, Steven J

    2015-12-01

    HLA genotyping via next generation sequencing (NGS) poses challenges for the use of HLA allele names to analyze and discuss sequence polymorphism. NGS will identify many new synonymous and non-coding HLA sequence variants. Allele names identify the types of nucleotide polymorphism that define an allele (non-synonymous, synonymous and non-coding changes), but do not describe how polymorphism is distributed among the individual features (the flanking untranslated regions, exons and introns) of a gene. Further, HLA alleles cannot be named in the absence of antigen-recognition domain (ARD) encoding exons. Here, a system for describing HLA polymorphism in terms of HLA gene features (GFs) is proposed. This system enumerates the unique nucleotide sequences for each GF in an HLA gene, and records these in a GF enumeration notation that allows both more granular dissection of allele-level HLA polymorphism and the discussion and analysis of GFs in the absence of ARD-encoding exon sequences. PMID:26416087

  3. Investigation of transferrin polymorphism in Garole sheep.

    PubMed

    Yadav, Devesh K; Taraphder, Subhash; Sahoo, Ajit K; Dhara, K C

    2010-03-01

    The aim of this study was to determine the genetics of polymorph systems of Transferrin in Garole sheep breed. The present study was conducted on 95 adult Garole sheep comprising 52 ewes and 43 rams, maintained at Sheep and Goat Breeding Farm of West Bengal University of Animal and Fishery Sciences, West Bengal, during the period from April-September, 2009. The polymorphism of transferrin was determined through SDS-Polyacrylamide gel electrophoresis technique. It was found that the transferrin type was controlled by five codominant alleles (TfA, TfB, TfC TfD and TfE) in Garole sheep. These five alleles, because of co-dominant nature of inheritance, determined the occurrence of nine transferrin genotypes in the analyzed flock. Four (TfAA, TfBB, TfCC and TfDD) of these were homozygous and the remaining five (TfAD, TfBC, TfBD, TfCD and TfDE) heterozygous. It was found that the TfDD genotype (0.263) was predominant while TfDE genotype (0.042) was least common in the analyzed flock. Frequencies of other genotypes were as: TfCD(0.242), TfBD(0.126), TfCC(0.084), TfBB(0.074), TfAA(0.063), TfAD and TfBC (0.053 for each genotype ) in whole population. From the result it was found that in whole population combined, the heterozygotic genotypic frequency (0.516) was more than that of homozygotic genotypic frequency (0.484). Considerable variations were recognized in the frequencies of transferrin alleles. In the whole population frequencies of transferrin alleles were found to be TfA = 0.089, TfB = 0.163, TfC = 0.232, TfD = 0.495 and TfE = 0.021. Transferrin system has shown an absence of genetic equilibrium among the analyzed herd (chi2 value = 51.31). In conclusion, there were polymorphism in Transferrin types and the presence of differences among the frequencies of the five alleles by categories could be a source of genetic variation in Garole sheep. PMID:20349135

  4. Gene Polymorphisms and Pharmacogenetics in Rheumatoid Arthritis

    PubMed Central

    Rego-Pérez, Ignacio; Fernández-Moreno, Mercedes; Blanco, Francisco J

    2008-01-01

    Rheumatoid arthritis (RA) is a systemic, chronic and inflammatory disease of unknown etiology with genetic predisposition. The advent of new biological agents, as well as the more traditional disease-modifying antirheumatic drugs, has resulted in highly efficient therapies for reducing the symptoms and signs of RA; however, not all patients show the same level of response in disease progression to these therapies. These variations suggest that RA patients may have different genetic regulatory mechanisms. The extensive polymorphisms revealed in non-coding gene-regulatory regions in the immune system, as well as genetic variations in drug-metabolizing enzymes, suggest that this type of variation is of functional and evolutionary importance and may provide clues for developing new therapeutic strategies. Pharmacogenetics is a rapidly advancing area of research that holds the promise that therapies will soon be tailored to an individual patient’s genetic profile. PMID:19506728

  5. AMPD1 polymorphism and response to regadenoson

    PubMed Central

    Saab, Rayan; Zouk, Aline N; Mastouri, Ronald; Skaar, Todd C; Philips, Santosh; Kreutz, Rolf P

    2016-01-01

    Aims AMPD1 c.34C>T (rs17602729) polymorphism results in AMPD1 deficiency. We examined the association of AMPD1 deficiency and variability of hemodynamic response to regadenoson. Subjects & methods Genotyping for c.34C>T was performed in 267 patients undergoing regadenoson cardiac stress testing. Results Carriers of c.34C >T variant exhibited higher relative changes in systolic blood pressure (SBP) compared with wild-type subjects ([%] SBP change to peak: 12 ± 25 vs 5 ± 13%; p = 0.01) ([%] SBP change to nadir: −3 ± 15 vs −7 ± 11%; p = 0.04). Change in heart rate was similar between groups, but side effects were more common in carriers of the variant (+LR = 4.2; p = 0.04). Conclusion AMPD1 deficiency may be involved in the modulation of regadenoson’s systemic effects. PMID:26554440

  6. Amyloid Fibrils: Formation, Polymorphism, and Inhibition.

    PubMed

    Härd, Torleif

    2014-02-01

    Amyloid fibrils with cross-β spine basic architectures are prevalent and stable forms of peptides and proteins. Recent research has provided significant contributions to our understanding of the mechanisms of fibril formation and to the surprising diversity and persistence of structural polymorphism in amyloid fibrils. There have also been successful demonstrations of how molecules can be engineered to inhibit unwanted amyloid formation by different mechanisms. Future research in these areas will include investigations of mechanisms for primary nucleation and the structure of oligomeric intermediates, the general role of secondary nucleation events (autocatalysis), elucidation of the mechanisms and implications of preservation of structural morphology in amyloid propagation, and research into the largely unexplored phenomenon of cross-seeding, by which amyloid fibrils of one species induce the formation of amyloid by another species. PMID:26276617

  7. Diosgenone: a second P21 polymorph

    PubMed Central

    Hernández Linares, María-Guadalupe; Guerrero-Luna, Gabriel; Bernès, Sylvain; Flores-Alamo, Marcos; Fernández-Herrera, María A.

    2012-01-01

    Diosgenone [(20S,22R,25R)-spirost-4-en-3-one, C27H40O3] has been proposed as a new therapeutic alternative for the treatment of malaria. The first X-ray structure report for diosgenone was by Piro et al. [(2002). Z. Naturforsch. Teil C, 57, 947–950] in the space group P21 (Z′ = 2). We now report a new polymorph in the same space group, with two mol­ecules in the asymmetric unit. Both mol­ecules have similar conformations, characterized by a skewed envelope A ring, which contains the C=C bond conjugated with the ketone functionality at C3. The dimorphism results from a modification of the relative orientation of the mol­ecules in the asymmetric unit: two independent mol­ecules were arranged anti­parallel in the Piro report, while they are parallel in the present determination. PMID:22904824

  8. Clinical Challenges in Catecholaminergic Polymorphic Ventricular Tachycardia.

    PubMed

    Imberti, Jacopo F; Underwood, Katherine; Mazzanti, Andrea; Priori, Silvia G

    2016-08-01

    Catecholaminergic polymorphic ventricular tachycardia (CPVT) is an inheritable cardiac disorder associated with exercise- and stress-induced sudden death in young individuals. Although important steps forward have been made in the comprehension and treatment of this disease, several aspects remain unclear. Firstly, from an epidemiological standpoint the actual prevalence of CPVT is still unknown and possibly underestimated. In addition, the diagnostic process remains very challenging and can be supported by genetic analysis in only about half of the cases. Finally, up to one third of CPVT patients continue to present complex arrhythmias despite beta blocker treatment; the role of newer therapeutic options, such as flecainide and left cardiac sympathetic denervation, needs to be further elucidated. All these points constitute challenges for the cardiologist in the management of CPVT patients and fuel research into new diagnostic, prognostic and therapeutic approaches. PMID:26948768

  9. New source of genetic polymorphisms in Lepidoptera?

    PubMed

    Hundsdoerfer, Anna K; Wink, Michael

    2005-01-01

    The variability level of the ISSR (inter-simple sequences repeat) primer (GACA)4 was examined in the three Lepidoptera families Pyralidae, Sphingidae and Pieridae. Our study shows that the tetra-repeat (GACA)n is evidently present in sufficient numbers in these butterflies to provide informative DNA fingerprints. The variability is mostly rather high, but within a comparable range to other ISSR studies. Although less polymorphisms may be encountered in some butterfly families, this study indicates that high variability of this marker may be a common characteristic of Lepidoptera genomes. An appeal for a minimal level of standardization of ISSR-PCR data analysis is formulated to enable an exact comparison between the groups of organisms studied with this fingerprint technique. PMID:16163839

  10. Amyloid Polymorphism: Structural Basis and Neurobiological Relevance

    PubMed Central

    Tycko, Robert

    2015-01-01

    Summary Our understanding of the molecular structures of amyloid fibrils that are associated with neurodegenerative diseases, of mechanisms by which disease-associated peptides and proteins aggregate into fibrils, and of structural properties of aggregation intermediates has advanced considerably in recent years. Detailed molecular structural models for certain fibrils and aggregation intermediates are now available. It is now well established that amyloid fibrils are generally polymorphic at the molecular level, with a given peptide or protein being capable of forming a variety of distinct, self-propagating fibril structures. Recent results from structural studies and from studies involving cell cultures, transgenic animals, and human tissue provide initial evidence that molecular structural variations in amyloid fibrils and related aggregates may correlate with or even produce variations in disease development. This article reviews our current knowledge of the structural and mechanistic aspects of amyloid formation, as well as current evidence for the biological relevance of structural variations. PMID:25950632

  11. Does colour polymorphism enhance survival of prey populations?

    PubMed

    Wennersten, Lena; Forsman, Anders

    2009-06-22

    That colour polymorphism may protect prey populations from predation is an old but rarely tested hypothesis. We examine whether colour polymorphic populations of prey exposed to avian predators in an ecologically valid visual context were exposed to increased extinction risk compared with monomorphic populations. We made 2976 artificial pastry prey, resembling Lepidoptera larvae, in four different colours and presented them in 124 monomorphic and 124 tetramorphic populations on tree trunks and branches such that they would be exposed to predation by free-living birds, and monitored their 'survival'. Among monomorphic populations, there was a significant effect of prey coloration on survival, confirming that coloration influenced susceptibility to visually oriented predators. Survival of polymorphic populations was inferior to that of monomorphic green populations, but did not differ significantly from monomorphic brown, yellow or red populations. Differences in survival within polymorphic populations paralleled those seen among monomorphic populations; the red morph most frequently went extinct first and the green morph most frequently survived the longest. Our findings do not support the traditional protective polymorphism hypothesis and are in conflict with those of earlier studies. As a possible explanation to our findings, we offer a competing 'giveaway cue' hypothesis: that polymorphic populations may include one morph that attracts the attention of predators and that polymorphic populations therefore may suffer increased predation compared with some monomorphic populations. PMID:19324729

  12. A model of ecological and evolutionary consequences of color polymorphism.

    PubMed

    Forsman, Anders; Ahnesjö, Jonas; Caesar, Sofia; Karlsson, Magnus

    2008-01-01

    We summarize direct and indirect effects on fitness components of animal color pattern and present a synthesis of theories concerning the ecological and evolutionary dynamics of chromatic multiple niche polymorphisms. Previous endeavors have aimed primarily at identifying conditions that promote the evolution and maintenance of polymorphisms. We consider in a conceptual model also the reciprocal influence of color polymorphism on population processes and propose that polymorphism entails selective advantages that may promote the ecological success of polymorphic species. The model begins with an evolutionary branching event from mono- to polymorphic condition that, under the influence of correlational selection, is predicted to promote the evolution of physical integration of coloration and other traits (cf. multi-trait coevolution and complex phenotypes). We propose that the coexistence within a population of alternative ecomorphs with coadapted gene complexes promotes utilization of diverse environmental resources, population stability and persistence, colonization success, and range expansions, and enhances the evolutionary potential and speciation. Conversely, we predict polymorphic populations to be less vulnerable to environmental change and at lower risk of range contractions and extinctions compared with monomorphic populations. We offer brief suggestions as to how these falsifiable predictions may be tested. PMID:18376544

  13. Identification of polymorphism in ethylone hydrochloride: synthesis and characterization.

    PubMed

    Maheux, Chad R; Alarcon, Idralyn Q; Copeland, Catherine R; Cameron, T Stanley; Linden, Anthony; Grossert, J Stuart

    2016-08-01

    Ethylone, a synthetic cathinone with psychoactive properties, is a designer drug which has appeared on the recreational drug market in recent years. Since 2012, illicit shipments of ethylone hydrochloride have been intercepted with increasing frequency at the Canadian border. Analysis has revealed that ethylone hydrochloride exists as two distinct polymorphs. In addition, several minor impurities were detected in some seized exhibits. In this study, the two conformational polymorphs of ethylone hydrochloride have been synthesized and fully characterized by FTIR, FT-Raman, powder XRD, GC-MS, ESI-MS/MS and NMR ((13) C CPMAS, (1) H, (13) C). The two polymorphs can be distinguished by vibrational spectroscopy, solid-state nuclear magnetic resonance spectroscopy and X-ray diffraction. The FTIR data are applied to the identification of both polymorphs of ethylone hydrochloride (mixed with methylone hydrochloride) in a laboratory submission labelled as 'Ocean Snow Ultra'. The data presented in this study will assist forensic scientists in the differentiation of the two ethylone hydrochloride polymorphs. This report, alongside our recent article on the single crystal X-ray structure of a second polymorph of this synthetic cathinone, is the first to confirm polymorphism in ethylone hydrochloride. © 2015 Canada Border Services Agency. Drug Testing and Analysis published by John Wiley & Sons, Ltd. © 2015 Canada Border Services Agency. Drug Testing and Analysis published by John Wiley & Sons, Ltd. PMID:26344849

  14. The human serum paraoxonase/arylesterase polymorphism.

    PubMed Central

    Eckerson, H W; Wyte, C M; La Du, B N

    1983-01-01

    The heterozygous human serum paraoxonase phenotype can be clearly distinguished from both homozygous phenotypes on the basis of its distinctive ratio of paraoxonase to arylesterase activities. A trimodal distribution of the ratio values was found with 348 individual serum samples, measuring the ratio of paraoxonase activity (with 1 M NaCl in the assay) to arylesterase activity, using phenylacetate. The three modes corresponded to the three paraoxonase phenotypes, A, AB, and B (individual genotypes), and the expected Mendelian segregation of the trait was observed within families. The paraoxonase/arylesterase activity ratio showed codominant inheritance. We have defined the genetic locus determining the aromatic esterase (arylesterase) responsible for the polymorphic paraoxonase activity as esterase-A (ESA) and have designated the two common alleles at this locus by the symbols ESA*A and ESA*B. The frequency of the ESA*A allele was estimated to be .685, and that of the ESA*B allele, 0.315, in a sample population of unrelated Caucasians from the United States. We postulate that a single serum enzyme, with both paraoxonase and arylesterase activity, exists in two different isozymic forms with qualitatively different properties, and that paraoxon is a "discriminating" substrate (having a polymorphic distribution of activity) and phenylacetate is a "nondiscriminating" substrate for the two isozymes. Biochemical evidence for this interpretation includes the cosegregation of the degree of stimulation of paraoxonase activity by salt and paraoxonase/arylesterase activity ratio characteristics; the very high correlation between both the basal (non-salt stimulated) and salt-stimulated paraoxonase activities with arylesterase activity; and the finding that phenylacetate is an inhibitor for paraoxonase activities in both A and B types of enzyme. PMID:6316781

  15. Mitochondrial Mutations and Polymorphisms in Psychiatric Disorders

    PubMed Central

    Sequeira, Adolfo; Martin, Maureen V.; Rollins, Brandi; Moon, Emily A.; Bunney, William E.; Macciardi, Fabio; Lupoli, Sara; Smith, Erin N.; Kelsoe, John; Magnan, Christophe N.; van Oven, Mannis; Baldi, Pierre; Wallace, Douglas C.; Vawter, Marquis P.

    2012-01-01

    Mitochondrial deficiencies with unknown causes have been observed in schizophrenia (SZ) and bipolar disorder (BD) in imaging and postmortem studies. Polymorphisms and somatic mutations in mitochondrial DNA (mtDNA) were investigated as potential causes with next generation sequencing of mtDNA (mtDNA-Seq) and genotyping arrays in subjects with SZ, BD, major depressive disorder (MDD), and controls. The common deletion of 4,977 bp in mtDNA was compared between SZ and controls in 11 different vulnerable brain regions and in blood samples, and in dorsolateral prefrontal cortex (DLPFC) of BD, SZ, and controls. In a separate analysis, association of mitochondria SNPs (mtSNPs) with SZ and BD in European ancestry individuals (n = 6,040) was tested using Genetic Association Information Network (GAIN) and Wellcome Trust Case Control Consortium 2 (WTCCC2) datasets. The common deletion levels were highly variable across brain regions, with a 40-fold increase in some regions (nucleus accumbens, caudate nucleus and amygdala), increased with age, and showed little change in blood samples from the same subjects. The common deletion levels were increased in the DLPFC for BD compared to controls, but not in SZ. Full mtDNA genome resequencing of 23 subjects, showed seven novel homoplasmic mutations, five were novel synonymous coding mutations. By logistic regression analysis there were no significant mtSNPs associated with BD or SZ after genome wide correction. However, nominal association of mtSNPs (p < 0.05) to SZ and BD were found in the hypervariable region of mtDNA to T195C and T16519C. The results confirm prior reports that certain brain regions accumulate somatic mutations at higher levels than blood. The study in mtDNA of common polymorphisms, somatic mutations, and rare mutations in larger populations may lead to a better understanding of the pathophysiology of psychiatric disorders. PMID:22723804

  16. Consequences of POR mutations and polymorphisms.

    PubMed

    Miller, Walter L; Agrawal, Vishal; Sandee, Duanpen; Tee, Meng Kian; Huang, Ningwu; Choi, Ji Ha; Morrissey, Kari; Giacomini, Kathleen M

    2011-04-10

    P450 oxidoreductase (POR) transports electrons from NADPH to all microsomal cytochrome P450 enzymes, including steroidogenic P450c17, P450c21 and P450aro. Severe POR mutations A287P (in Europeans) and R457H (in Japanese) cause the Antley-Bixler skeletal malformation syndrome (ABS) plus impaired steroidogenesis (causing genital anomalies), but the basis of ABS is unclear. We have characterized the activities of ∼40 POR variants, showing that assays based on P450c17 activities, but not cytochrome c assays, correlate with the clinical phenotype. The human POR gene is highly polymorphic: the A503V sequence variant, which decreases P450c17 activities to ∼60%, is found on ∼28% of human alleles. A promoter polymorphism (∼8% of Asians and ∼13% of Caucasians) at -152 reduces transcriptional activity by half. Screening of 35 POR variants showed that most mutants lacking activity with P450c17 or cytochrome c also lacked activity to support CYP1A2 and CYP2C19 metabolism of EOMCC (a fluorogenic non-drug substrate), although there were some remarkable differences: Q153R causes ABS and has ∼30% of wild-type activity with P450c17 but had 144% of WT activity with CYP1A2 and 284% with CYP2C19. The effects of POR variants on CYP3A4, which metabolizes nearly 50% of clinically used drugs, was examined with multiple, clinically relevant drug substrates, showing that A287P and R457H dramatically reduce drug metabolism, and that A503V variably impairs drug metabolism. The degree of activity can vary with the drug substrate assayed, as the drugs can influence the conformation of the P450. POR is probably an important contributor to genetic variation in both steroidogenesis and drug metabolism. PMID:21070833

  17. Consequences of POR mutations and polymorphisms

    PubMed Central

    Miller, Walter L.; Agrawal, Vishal; Sandee, Duanpen; Tee, Meng Kian; Huang, Ningwu; Choi, Ji Ha; Morrissey, Kari; Giacomini, Kathleen M.

    2015-01-01

    P450 oxidoreductase (POR) transports electrons from NADPH to all microsomal cytochrome P450 enzymes, including steroidogenic P450c17, P450c21 and P450aro. Severe POR mutations A287P (in Europeans) and R457H (in Japanese) cause the Antley-Bixler skeletal malformation syndrome (ABS) plus impaired steroidogenesis (causing genital anomalies), but the basis of ABS is unclear. We have characterized the activities of ~40 POR variants, showing that assays based on P450c17 activities, but not cytochrome c assays, correlate with the clinical phenotype. The human POR gene is highly polymorphic: the A503V sequence variant, which decreases P450c17 activities to ~60%, is found on ~28% of human alleles. A promoter polymorphism (~8% of Asians and ~13% of Caucasians) at −152 reduces transcriptional activity by half. Screening of 35 POR variants showed that most mutants lacking activity with P450c17 or cytochrome c also lacked activity to support CYP1A2 and CYP2C19 metabolism of EOMCC (a fluorogenic non-drug substrate), although there were some remarkable differences: Q153R causes ABS and has ~30% of wild-type activity with P450c17 but had 144% of WT activity with CYP1A2 and 284% with CYP2C19. The effects of POR variants on CYP3A4, which metabolizes nearly 50% of clinically used drugs, was examined with multiple, clinically-relevant drug substrates, showing that A287P and R457H dramatically reduce drug metabolism, and that A503V variably impairs drug metabolism. The degree of activity can vary with the drug substrate assayed, as the drugs can influence the conformation of the P450. POR is probably an important contributor to genetic variation in both steroidogenesis and drug metabolism. PMID:21070833

  18. Emergence of stable polymorphisms driven by evolutionary games between mutants

    PubMed Central

    Huang, Weini; Haubold, Bernhard; Hauert, Christoph; Traulsen, Arne

    2012-01-01

    Under neutrality, polymorphisms are maintained through the balance between mutation and drift. Under selection, a variety of mechanisms may be involved in the maintenance of polymorphisms, for example, sexual selection or host-parasite coevolution on the population level or heterozygote advantage in diploid individuals. Here we address the emergence of polymorphisms in a population of interacting haploid individuals. In our model, each mutation generates a new evolutionary game characterized by a payoff matrix with an additional row and an additional column. Hence, in general, the fitness of new mutations is frequency-dependent rather than constant. This dynamical process is distinct from the sequential fixation of advantageous traits and naturally leads to the emergence of polymorphisms under selection. It causes substantially higher diversity than observed under the established models of neutral or frequency-independent selection. Our framework allows for the coexistence of an arbitrary number of types, but predicts an intermediate average diversity. PMID:22735447

  19. Prioritizing sequence polymorphisms for potential association with phenotype

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The millions of SNP, insertions and deletions revealed by next generation sequencing (NGS), are certain to include polymorphisms responsible for phenotypic variation. Distinguishing causal from benign variants may allow genomic predictions that are robust across populations. While variants underly...

  20. Chromosome Polymorphism in Microtus (Alexandromys) mujanensis (Arvicolinae, Rodentia).

    PubMed

    Lemskaya, Natalya A; Kartavtseva, Irina V; Rubtsova, Nadezhda V; Golenishchev, Fedor N; Sheremetyeva, Irina N; Graphodatsky, Alexander S

    2015-01-01

    The Muya Valley vole (Microtus mujanensis) has a constant diploid chromosome number of 2n = 38, but an unstable karyotype with polymorphic chromosome pairs. Here, we describe 4 karyotypic variants involving 2 polymorphic chromosome pairs, MMUJ8 and MMUJ14, in 6 animals from Buryatia using a combination of GTG-banding and chromosome painting with M. agrestis probes. We suggest that the polymorphic pairs MMUJ8 and MMUJ14 were formed through pericentric inversions that played a major role during karyotype evolution of the species. We also propose that the stable diploid number with some ongoing polymorphism in the number of chromosome arms indicates that this evolutionarily young endemic species of Russian Far East is on the way to karyotype and likely species stabilization. PMID:26314555

  1. Complement Factor H Polymorphism in Age-Related Macular Degeneration

    PubMed Central

    Klein, Robert J.; Zeiss, Caroline; Chew, Emily Y.; Tsai, Jen-Yue; Sackler, Richard S.; Haynes, Chad; Henning, Alice K.; SanGiovanni, John Paul; Mane, Shrikant M.; Mayne, Susan T.; Bracken, Michael B.; Ferris, Frederick L.; Ott, Jurg; Barnstable, Colin; Hoh., Josephine

    2006-01-01

    Age-related macular degeneration (AMD) is a major cause of blindness in the elderly. We report a genome-wide screen of 96 cases and 50 controls for polymorphisms associated with AMD. Among 116,204 single-nucleotide polymorphisms genotyped, an intronic and common variant in the complement factor H gene (CFH) is strongly associated with AMD (nominal P value <10−7). In individuals homozygous for the risk allele, the likelihood of AMD is increased by a factor of 7.4 (95% confidence interval 2.9 to 19). Resequencing revealed a polymorphism in linkage disequilibrium with the risk allele representing a tyrosine-histidine change at amino acid 402. This polymorphism is in a region of CFH that binds heparin and C-reactive protein. The CFH gene is located on chromosome 1 in a region repeatedly linked to AMD in family-based studies. PMID:15761122

  2. Polymorphisms of Chicken TLR3 and 7 in Different Breeds

    PubMed Central

    Ruan, Wenke; An, Jian; Wu, Yanhua

    2015-01-01

    Toll-like receptors (TLRs) mediate immune responses via the recognition of pathogen-associated molecular patterns (PAMPs), thus playing important roles in host defense. Among the chicken (Ch) TLR family, ChTLR3 and 7 have been shown to recognize viral RNA. In our earlier studies, we have reported polymorphisms of TLR1, 2, 4, 5, 15 and 21. In the present study, we amplified TLR3 and 7 genes from different chicken breeds and analyzed their sequences. We identified 7 amino acid polymorphism sites in ChTLR3 with 6 outer part sites and 1 inner part site, and 4 amino acid polymorphism sites in ChTLR7 with 3 outer part sites and 1 inner part site. These results demonstrate that ChTLR genes are polymorphic among different chicken breeds, suggesting a varied resistance across numerous chicken breeds. This information might help improve chicken health by breeding and vaccination. PMID:25781886

  3. Physical and structural basis for polymorphism in amyloid fibrils

    PubMed Central

    Tycko, Robert

    2014-01-01

    As our understanding of the molecular structures of amyloid fibrils has matured over the past 15 years, it has become clear that, while amyloid fibrils do have well-defined molecular structures, their molecular structures are not uniquely determined by the amino acid sequences of their constituent peptides and proteins. Self-propagating molecular-level polymorphism is a common phenomenon. This article reviews current information about amyloid fibril structures, variations in molecular structures that underlie amyloid polymorphism, and physical considerations that explain the development and persistence of amyloid polymorphism. Much of this information has been obtained through solid state nuclear magnetic resonance measurements. The biological significance of amyloid polymorphism is also discussed briefly. Although this article focuses primarily on studies of fibrils formed by amyloid-β peptides, the same principles apply to many amyloid-forming peptides and proteins. PMID:25179159

  4. [Study of Chloroplast DNA Polymorphism in the Sunflower (Helianthus L.)].

    PubMed

    Markina, N V; Usatov, A V; Logacheva, M D; Azarin, K V; Gorbachenko, C F; Kornienko, I V; Gavrilova, V A; Tihobaeva, V E

    2015-08-01

    The polymorphism of microsatellite loci of chloroplast genome in six Helianthus species and 46 lines of cultivated sunflower H. annuus (17 CMS lines and 29 Rf-lines) were studied. The differences between species are confined to four SSR loci. Within cultivated forms of the sunflower H. annuus, the polymorphism is absent. A comparative analysis was performed on sequences of the cpDNA inbred line 3629, line 398941 of the wild sunflower, and the American line HA383 H. annuus. As a result, 52 polymorphic loci represented by 27 SSR and 25 SNP were found; they can be used for genotyping of H. annuus samples, including cultural varieties: twelve polymorphic positions, of which eight are SSR and four are SNP. PMID:26601486

  5. Single Nucleotide Polymorphisms for Pig Identification and Parentage Exclusion

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Single nucleotide polymorphisms have become an important type of marker for commercial diagnostic and parentage genotyping applications as automated genotyping systems have been developed that yield accurate genotypes. Unfortunately, a large number of highly informative public SNP markers tested in ...

  6. Unsolvated ruthenium(II) benzene dichloride: The beta polymorph

    NASA Astrophysics Data System (ADS)

    Galli, Simona; Giacobbe, Carlotta; Tabacaru, Aurel; Xhaferaj, Nertil; Pettinari, Claudio

    2014-06-01

    A novel polymorph of the unsolvated species [Ru2(benzene)2Cl4] (β form in the following) was serendipitously isolated as a polycrystalline powder. Its molecular and crystal structure was unraveled by means of state-of-the-art X-ray powder diffraction structure determination methods applied to laboratory data, and was compared to those of both the α polymorph and the CHCl3 solvate, throwing light on some discrepant results recently appeared in the literature. The thermal behavior of the α and β polymorphs was investigated by coupling thermogravimetric analyses to variable-temperature X-ray powder diffraction experiments. No temperature-stimulated phase transformation could be detected between the two polymorphs, each preserving its structural features up to decomposition, suggesting that kinetic, more than thermodynamic, factors regulate their isolation.

  7. Structural features of two polymorphs of ammonium uranyl crotonate

    NASA Astrophysics Data System (ADS)

    Savchenkov, A. V.; Peresypkina, E. V.; Pushkin, D. V.; Virovets, A. V.; Serezhkina, L. B.; Serezhkin, V. N.

    2014-09-01

    X-ray crystallography, FTIR spectroscopy and thermal analysis were conducted for crystals of two polymorphs of NH4UO2(C3H5COO)3, which are the first examples of uranyl tricarboxylate complexes with ions of unsaturated aliphatic monocarboxylic acid. The main structural units of both polymorphs are anionic complexes [UO2(C3H5COO)3]-. Uranium atoms adopt hexagonal bipyramidal coordination polyhedron, and crotonate ions realize bidentate cyclic type of coordination. Due to different packing of ammonium ions and [UO2(C3H5COO)3]- complexes triclinic crystals of α-polymorph have layer structure and cubic crystals of β-polymorph have three dimensional structure. Features of three dimensional packing of R+ ions and [UO2L3]- complexes in structures of 25 known R[UO2L3] compounds are discussed.

  8. Discovery of single nucleotide polymorphisms and mutations by pyrosequencing.

    PubMed

    Ronaghi, Mostafa; Elahi, Elahe

    2002-01-01

    Comparative genomics, analyzing variation among individual genomes, is an area of intense investigation. DNA sequencing is usually employed to look for polymorphisms and mutations. Pyrosequencing, a real-time DNA sequencing method, is emerging as a popular platform for comparative genomics. Here we review the use of this technology for mutation scanning, polymorphism discovery and chemical haplotyping. We describe the methodology and accuracy of this technique and discuss how to reduce the cost for large-scale analysis. PMID:18628881

  9. Melanoma risk is associated with vitamin D receptor gene polymorphisms.

    PubMed

    Zeljic, Katarina; Kandolf-Sekulovic, Lidija; Supic, Gordana; Pejovic, Janko; Novakovic, Marijan; Mijuskovic, Zeljko; Magic, Zvonko

    2014-06-01

    Previous studies have reported that vitamin D receptor (VDR) gene polymorphisms are associated with the occurrence of various cancers, including melanoma. The aim of the current study was to investigate the association of VDR gene polymorphisms with melanoma risk, clinicopathological characteristics, and vitamin D levels. The study group included 117 patients (84 patients with superficial spreading melanoma and 33 patients with nodular melanoma). The control group included 122 sex-matched and age-matched healthy-blood donors of the same ethnicity. VDR gene polymorphisms FokI, EcoRV, TaqI, and ApaI were genotyped by real-time PCR. In 60 patients, the total 25-hydroxyvitamin D levels were evaluated in serum samples by direct chemiluminescence. Associations among parameters were considered to be significant if the P value was less than 0.05. Significant differences in the frequencies of VDR genotypes were observed between cases and the control group for FokI and TaqI polymorphisms (P<0.0001; P=0.005, respectively). Heterozygous Ff as well as mutant FF genotypes of the FokI polymorphism were associated with increased melanoma risk compared with the wild-type form [odds ratio (OR)=3.035, P=0.003; OR=9.276, P<0.0001, respectively]. A significantly increased melanoma risk was observed for the heterozygous Tt (OR=2.302, P=0.011) and the mutated variant tt (OR=3.697, P=0.003) of the TaqI polymorphism in comparison with the wild-type genotype. None of the polymorphisms studied was associated with clinicopathological characteristics and vitamin D serum level. Our results suggest that FokI and TaqI polymorphisms in the VDR gene may be considered as potential biomarkers for melanoma susceptibility. Low vitamin D levels in melanoma patients indicate the need for vitamin D supplementation. PMID:24638155

  10. Genetic Polymorphisms Influence Cognition in Patients Undergoing Carotid Interventions.

    PubMed

    Hitchner, Elizabeth; Morrison, Doug; Liao, Phoebe; Rosen, Allyson; Zhou, Wei

    2016-09-01

    While carotid interventions help decrease the risk of stroke, nearly 40% of patients experience cognitive deterioration. Genetic polymorphism in apolipoprotein E (ApoE) and brain-derived neurotrophic factor (BDNF) have been implicated in cognitive impairment; however, it is unclear whether they may influence cognitive changes in patients undergoing carotid intervention. In this study, we seek to assess the role of genetic polymorphisms in carotid intervention-related cognitive change. Polymorphisms related to cognitive function were chosen for this preliminary analysis. Over 2 years, patients undergoing carotid interventions were prospectively recruited. Patients underwent neuropsychological testing 2 weeks prior to and at 1 month following their procedure. Saliva samples were collected for genetic analysis. Logistic regressions were used to identify associations between polymorphisms and cognitive measures. A total of 91 patients were included; all were male with an average age of 70 years. The majority of patients exhibited hypertension (95%) and a history of smoking (81%). Presence of ApoE 4 allele was associated with depression (p= 0.047). After correcting for age and genetic polymorphisms in BDNF and serotonin transporter (5-HTT), ApoE 4 allele was associated with depression (p= 0.044) and showed a trend with baseline cognitive impairment (p= 0.10). Age ≥ 70 years was associated with baseline cognitive impairment after adjusting for the three genetic polymorphisms (p= 0.03). Patients with ApoE 4 and BDNF A polymorphisms performed less well on the visual and verbal memory measures, respectively. Polymorphisms in ApoE and BDNF may provide insight on cognition in patients undergoing carotid interventions; however, the mechanism of this relationship remains unclear. PMID:27574384

  11. [BCL1 POLYMORPHISM OF GLUCOCORTICOID RECEPTOR GENE AND RESPIRATORY DISEASES].

    PubMed

    Prystupa, L N; Garbuzova, V Yu; Kmyta, V V

    2015-01-01

    The article analyses the results of investigating the connection between BCL1-polymorphism of glucocorticoid receptor gene and respiratory diseases. Its role in increasing sensitivity to glucocorticoids is proved here. The authors investigated the association of Bcl1 polymorphism with predisposition to bronchial asthma, chronic obstructive pulmonary disease, with the nicotine addiction degree and with progressing disorders of pulmonary function in cystic fibrosis. PMID:26118026

  12. Relationship of MTHFR gene polymorphisms with renal and cardiac disease

    PubMed Central

    Trovato, Francesca M; Catalano, Daniela; Ragusa, Angela; Martines, G Fabio; Pirri, Clara; Buccheri, Maria Antonietta; Di Nora, Concetta; Trovato, Guglielmo M

    2015-01-01

    AIM: To investigate the effects of different methylenetetrahydrofolate reductase (MTHFR) 677C>T gene polymorphism and hyperhomocysteinemia for the development of renal failure and cardiovascular events, which are controversial. METHODS: We challenged the relationship, if any, of MTHFR 677C>T and MTHFR 1298A>C polymorphisms with renal and heart function. The present article is a reappraisal of these concepts, investigating within a larger population, and including a subgroup of dialysis patients, if the two most common MTHFR polymorphisms, C677T and A1298C, as homozygous, heterozygous or with a compound heterozygous state, show different association with chronic renal failure requiring hemodialysis. MTHFR polymorphism could be a favorable evolutionary factor, i.e., a protective factor for many ominous conditions, like cancer and renal failure. A similar finding was reported in fatty liver disease in which it is suggested that MTHFR polymorphisms could have maintained and maintain their persistence by an heterozygosis advantage mechanism. We studied a total of 630 Italian Caucasian subject aged 54.60 ± 16.35 years, addressing to the increased hazard of hemodialysis, if any, according to the studied MTHFR genetic polymorphisms. RESULTS: A favorable association with normal renal function of MTHFR polymorphisms, and notably of MTHFR C677T is present independently of the negative effects of left ventricular hypertrophy, increased Intra-Renal arterial Resistance and hyperparathyroidism. CONCLUSION: MTHFR gene polymorphisms could have a protective role on renal function as suggested by their lower frequency among our dialysis patients in end-stage renal failure; differently, the association with left ventricular hypertrophy and reduced left ventricular relaxation suggest some type of indirect, or concurrent mechanism. PMID:25664255

  13. Epitaxial stabilization and phase instability of VO2 polymorphs

    DOE PAGESBeta

    Lee, Shinbuhm; Ivanov, Ilia N.; Keum, Jong K.; Lee, Ho Nyung

    2016-01-20

    The VO2 polymorphs, i.e., VO2(A), VO2(B), VO2(M1) and VO2(R), have a wide spectrum of functionalities useful for many potential applications in information and energy technologies. However, synthesis of phase pure materials, especially in thin film forms, has been a challenging task due to the fact that the VO2 polymorphs are closely related to each other in a thermodynamic framework. Here, we report epitaxial stabilization of the VO2 polymorphs to synthesize high quality single crystalline thin films and study the phase stability of these metastable materials. We selectively deposit all the phases on various perovskite substrates with different crystallographic orientations. Bymore » investigating the phase instability, phonon modes and transport behaviours, not only do we find distinctively contrasting physical properties of the VO2 polymorphs, but that the polymorphs can be on the verge of phase transitions when heated as low as ~400 °C. In conclusion, our successful epitaxy of both VO2(A) and VO2(B) phases, which are rarely studied due to the lack of phase pure materials, will open the door to the fundamental studies of VO2 polymorphs for potential applications in advanced electronic and energy devices.« less

  14. Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection.

    PubMed

    Ding, Hong; Dwaraknath, Shyam S; Garten, Lauren; Ndione, Paul; Ginley, David; Persson, Kristin A

    2016-05-25

    With the ultimate goal of finding new polymorphs through targeted synthesis conditions and techniques, we outline a computational framework to select optimal substrates for epitaxial growth using first principle calculations of formation energies, elastic strain energy, and topological information. To demonstrate the approach, we study the stabilization of metastable VO2 compounds which provides a rich chemical and structural polymorph space. We find that common polymorph statistics, lattice matching, and energy above hull considerations recommends homostructural growth on TiO2 substrates, where the VO2 brookite phase would be preferentially grown on the a-c TiO2 brookite plane while the columbite and anatase structures favor the a-b plane on the respective TiO2 phases. Overall, we find that a model which incorporates a geometric unit cell area matching between the substrate and the target film as well as the resulting strain energy density of the film provide qualitative agreement with experimental observations for the heterostructural growth of known VO2 polymorphs: rutile, A and B phases. The minimal interfacial geometry matching and estimated strain energy criteria provide several suggestions for substrates and substrate-film orientations for the heterostructural growth of the hitherto hypothetical anatase, brookite, and columbite polymorphs. These criteria serve as a preliminary guidance for the experimental efforts stabilizing new materials and/or polymorphs through epitaxy. The current screening algorithm is being integrated within the Materials Project online framework and data and hence publicly available. PMID:27145398

  15. Identification of conserved and polymorphic STRs for personal genomes

    PubMed Central

    2014-01-01

    Background Short tandem repeats (STRs) are abundant in human genomes. Numerous STRs have been shown to be associated with genetic diseases and gene regulatory functions, and have been selected as genetic markers for evolutionary and forensic analyses. High-throughput next generation sequencers have fostered new cutting-edge computing techniques for genome-scale analyses, and cross-genome comparisons have facilitated the efficient identification of polymorphic STR markers for various applications. Results An automated and efficient system for detecting human polymorphic STRs at the genome scale is proposed in this study. Assembled contigs from next generation sequencing data were aligned and calibrated according to selected reference sequences. To verify identified polymorphic STRs, human genomes from the 1000 Genomes Project were employed for comprehensive analyses, and STR markers from the Combined DNA Index System (CODIS) and disease-related STR motifs were also applied as cases for evaluation. In addition, we analyzed STR variations for highly conserved homologous genes and human-unique genes. In total 477 polymorphic STRs were identified from 492 human-unique genes, among which 26 STRs were retrieved and clustered into three different groups for efficient comparison. Conclusions We have developed an online system that efficiently identifies polymorphic STRs and provides novel distinguishable STR biomarkers for different levels of specificity. Candidate polymorphic STRs within a personal genome could be easily retrieved and compared to the constructed STR profile through query keywords, gene names, or assembled contigs. PMID:25560225

  16. Color polymorphism in an aphid is maintained by attending ants

    PubMed Central

    Watanabe, Saori; Murakami, Taiga; Yoshimura, Jin; Hasegawa, Eisuke

    2016-01-01

    The study of polymorphisms is particularly informative for enhancing our understanding of phenotypic and genetic diversity. The persistence of polymorphism in a population is generally explained by balancing selection. Color polymorphisms that are often found in many insects and arthropods are prime examples of the maintenance of polymorphisms via balancing selection. In some aphids, color morphs are maintained through frequency-dependent predation by two predatory insects. However, the presence of color polymorphism in ant-attended aphids cannot be explained by traditional balancing selection because these aphids are free from predation. We examined the selective advantages of the existence of two color (red and green) morphs in the ant-attended aphid, Macrosiphoniella yomogicola, in fields. We measured the degree of ant attendance on aphid colonies with different proportions of color morphs. The results show that the ants strongly favor aphid colonies with intermediate proportions of the two color morphs. The relationship between the degree of ant attendance and the proportion of color morphs in the field is convex when aphid colony size and ant colony size are controlled. This function has a peak of approximately 65% of green morphs in a colony. This system represents the first case of a balancing polymorphism that is not maintained by opposing factors but by a symbiotic relationship. PMID:27617289

  17. Epitaxial stabilization and phase instability of VO2 polymorphs

    NASA Astrophysics Data System (ADS)

    Lee, Shinbuhm; Ivanov, Ilia N.; Keum, Jong K.; Lee, Ho Nyung

    2016-01-01

    The VO2 polymorphs, i.e., VO2(A), VO2(B), VO2(M1) and VO2(R), have a wide spectrum of functionalities useful for many potential applications in information and energy technologies. However, synthesis of phase pure materials, especially in thin film forms, has been a challenging task due to the fact that the VO2 polymorphs are closely related to each other in a thermodynamic framework. Here, we report epitaxial stabilization of the VO2 polymorphs to synthesize high quality single crystalline thin films and study the phase stability of these metastable materials. We selectively deposit all the phases on various perovskite substrates with different crystallographic orientations. By investigating the phase instability, phonon modes and transport behaviours, not only do we find distinctively contrasting physical properties of the VO2 polymorphs, but that the polymorphs can be on the verge of phase transitions when heated as low as ~400 °C. Our successful epitaxy of both VO2(A) and VO2(B) phases, which are rarely studied due to the lack of phase pure materials, will open the door to the fundamental studies of VO2 polymorphs for potential applications in advanced electronic and energy devices.

  18. Epitaxial stabilization and phase instability of VO2 polymorphs

    PubMed Central

    Lee, Shinbuhm; Ivanov, Ilia N.; Keum, Jong K.; Lee, Ho Nyung

    2016-01-01

    The VO2 polymorphs, i.e., VO2(A), VO2(B), VO2(M1) and VO2(R), have a wide spectrum of functionalities useful for many potential applications in information and energy technologies. However, synthesis of phase pure materials, especially in thin film forms, has been a challenging task due to the fact that the VO2 polymorphs are closely related to each other in a thermodynamic framework. Here, we report epitaxial stabilization of the VO2 polymorphs to synthesize high quality single crystalline thin films and study the phase stability of these metastable materials. We selectively deposit all the phases on various perovskite substrates with different crystallographic orientations. By investigating the phase instability, phonon modes and transport behaviours, not only do we find distinctively contrasting physical properties of the VO2 polymorphs, but that the polymorphs can be on the verge of phase transitions when heated as low as ~400 °C. Our successful epitaxy of both VO2(A) and VO2(B) phases, which are rarely studied due to the lack of phase pure materials, will open the door to the fundamental studies of VO2 polymorphs for potential applications in advanced electronic and energy devices. PMID:26787259

  19. Epitaxial stabilization and phase instability of VO2 polymorphs.

    PubMed

    Lee, Shinbuhm; Ivanov, Ilia N; Keum, Jong K; Lee, Ho Nyung

    2016-01-01

    The VO2 polymorphs, i.e., VO2(A), VO2(B), VO2(M1) and VO2(R), have a wide spectrum of functionalities useful for many potential applications in information and energy technologies. However, synthesis of phase pure materials, especially in thin film forms, has been a challenging task due to the fact that the VO2 polymorphs are closely related to each other in a thermodynamic framework. Here, we report epitaxial stabilization of the VO2 polymorphs to synthesize high quality single crystalline thin films and study the phase stability of these metastable materials. We selectively deposit all the phases on various perovskite substrates with different crystallographic orientations. By investigating the phase instability, phonon modes and transport behaviours, not only do we find distinctively contrasting physical properties of the VO2 polymorphs, but that the polymorphs can be on the verge of phase transitions when heated as low as ~400 °C. Our successful epitaxy of both VO2(A) and VO2(B) phases, which are rarely studied due to the lack of phase pure materials, will open the door to the fundamental studies of VO2 polymorphs for potential applications in advanced electronic and energy devices. PMID:26787259

  20. Color polymorphism in an aphid is maintained by attending ants.

    PubMed

    Watanabe, Saori; Murakami, Taiga; Yoshimura, Jin; Hasegawa, Eisuke

    2016-09-01

    The study of polymorphisms is particularly informative for enhancing our understanding of phenotypic and genetic diversity. The persistence of polymorphism in a population is generally explained by balancing selection. Color polymorphisms that are often found in many insects and arthropods are prime examples of the maintenance of polymorphisms via balancing selection. In some aphids, color morphs are maintained through frequency-dependent predation by two predatory insects. However, the presence of color polymorphism in ant-attended aphids cannot be explained by traditional balancing selection because these aphids are free from predation. We examined the selective advantages of the existence of two color (red and green) morphs in the ant-attended aphid, Macrosiphoniella yomogicola, in fields. We measured the degree of ant attendance on aphid colonies with different proportions of color morphs. The results show that the ants strongly favor aphid colonies with intermediate proportions of the two color morphs. The relationship between the degree of ant attendance and the proportion of color morphs in the field is convex when aphid colony size and ant colony size are controlled. This function has a peak of approximately 65% of green morphs in a colony. This system represents the first case of a balancing polymorphism that is not maintained by opposing factors but by a symbiotic relationship. PMID:27617289

  1. Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA polymorphisms are valuable for several applications including genotyping, molecular mapping and marker-assisted selection. The Affymetrix Wheat GeneChip was used to survey expression level polymorphisms (ELPs) and single-feature polymorphisms (SFPs) between two near-isogenic wheat genotypes (BC7...

  2. Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    DNA polymorphisms are valuable for several applications including genotyping, molecular mapping and marker-assisted selection. The Affymetrix Wheat GeneChip was used to survey expression level polymorphisms (ELPs) and single-feature polymorphisms (SFPs) between two near-isogenic wheat genotypes (BC...

  3. Gene Polymorphism Studies in a Teaching Laboratory

    NASA Astrophysics Data System (ADS)

    Shultz, Jeffry

    2009-02-01

    I present a laboratory procedure for illustrating transcription, post-transcriptional modification, gene conservation, and comparative genetics for use in undergraduate biology education. Students are individually assigned genes in a targeted biochemical pathway, for which they design and test polymerase chain reaction (PCR) primers. In this example, students used genes annotated for the steroid biosynthesis pathway in soybean. The authoritative Kyoto encyclopedia of genes and genomes (KEGG) interactive database and other online resources were used to design primers based first on soybean expressed sequence tags (ESTs), then on ESTs from an alternate organism if soybean sequence was unavailable. Students designed a total of 50 gene-based primer pairs (37 soybean, 13 alternative) and tested these for polymorphism state and similarity between two soybean and two pea lines. Student assessment was based on acquisition of laboratory skills and successful project completion. This simple procedure illustrates conservation of genes and is not limited to soybean or pea. Cost per student estimates are included, along with a detailed protocol and flow diagram of the procedure.

  4. Insertional Polymorphisms of Endogenous Feline Leukemia Viruses

    PubMed Central

    Roca, Alfred L.; Nash, William G.; Menninger, Joan C.; Murphy, William J.; O'Brien, Stephen J.

    2005-01-01

    The number, chromosomal distribution, and insertional polymorphisms of endogenous feline leukemia viruses (enFeLVs) were determined in four domestic cats (Burmese, Egyptian Mau, Persian, and nonbreed) using fluorescent in situ hybridization and radiation hybrid mapping. Twenty-nine distinct enFeLV loci were detected across 12 of the 18 autosomes. Each cat carried enFeLV at only 9 to 16 of the loci, and many loci were heterozygous for presence of the provirus. Thus, an average of 19 autosomal copies of enFeLV were present per cat diploid genome. Only five of the autosomal enFeLV sites were present in all four cats, and at only one autosomal locus, B4q15, was enFeLV present in both homologues of all four cats. A single enFeLV occurred in the X chromosome of the Burmese cat, while three to five enFeLV proviruses occurred in each Y chromosome. The X chromosome and nine autosomal enFeLV loci were telomeric, suggesting that ectopic recombination between nonhomologous subtelomeres may contribute to enFeLV distribution. Since endogenous FeLVs may affect the infectiousness or pathogenicity of exogenous FeLVs, genomic variation in enFeLVs represents a candidate for genetic influences on FeLV leukemogenesis in cats. PMID:15767400

  5. Apolipoprotein E Polymorphism in Tuberculosis Patients

    NASA Astrophysics Data System (ADS)

    Naserpour Farivar, Taghi; Sharifi Moud, Batool; Sargazi, Mansur; Moeenrezakhanlou, Alireza

    In this study, we aimed to determine the significance of association between Tuberculosis and apolipoprotein E polymorphism. The apolipoprotein E genotypes were assayed in 250 tuberculosis patients by polymerase chain reaction followed by enzymatic digestion with Hha I. The results were compared with the results of the same experiments on 250 sex and age matched control peoples. Present results showed that in studied populations, prevalence of E4 genotype was lower in controls than in patients (8 v. 13.2%; OR = 1.75, p<0.05) and prevalence of E3 genotype was high in controls than in patients (86 v.51%; OR = 0.17, p<0.05). Statistically significant difference was found between patients and controls with respect to ɛ2 allele frequencies, while ɛ2 allele frequency was found to be much less prevalent in controls (6%) than in patients (35.8%; OR = 8.72, p<0.05). Also, our study revealed that there is an association between apolipoprotein E genotypes and amplitude to tuberculosis in studied populations. However, large population-based studies are needed to understand the exact role played by the locus in causing the condition.

  6. Serum protein polymorphism in Bali (Indonesia).

    PubMed

    Constans, J; Gouaillard, C; Breguet, G

    1986-01-01

    Serum samples from Bali, obtained in three different ethnic groups and in one isolated village were tested by isoelectric focusing electrophoresis for Gc, Pi, Tf and Hp subtyping. In addition to the three common alleles Gc1F, Gc1S and Gc2, two variants Gc1A1 and Gc1A8 were observed. In the Pi system, five alleles were present: PiM1, PiM2, PiM3, PiM4 and PiX. The Tf variability was exceptional with the presence of eight alleles: TfB1, TfC1, TfC2, TfC3, TfC4, TfC8, TfD1 and TfDchi. For Hp, there were two common alleles Hp1S and Hp1FS and two rare ones: Hp1F and Hp2SS. As expected, the genetic polymorphism is reduced in the isolated community. The anthropological significance of these genetic data is discussed. PMID:3493727

  7. Polymorphic Admixture Typing in Human Ethnic Populations

    PubMed Central

    Dean, Michael; Stephens, J. Claiborne; Winkler, Cheryl; Lomb, Deborah A.; Ramsburg, Mark; Boaze, Raleigh; Stewart, Claudia; Charbonneau, Lauren; Goldman, David; Albaugh, Bernard J.; Goedert, James J.; Beasley, R. Palmer; Hwang, Lu-Yu; Buchbinder, Susan; Weedon, Michael; Johnson, Patricia A.; Eichelberger, Mary; O'Brien, Stephen J.

    1994-01-01

    A panel of 257 RFLP loci was selected on the basis of high heterozygosity in Caucasian DNA surveys and equivalent spacing throughout the human genome. Probes from each locus were used in a Southern blot survey of allele frequency distribution for four human ethnic groups: Caucasian, African American, Asian (Chinese), and American Indian (Cheyenne). Nearly all RFLP loci were polymorphic in each group, albeit with a broad range of differing allele frequencies (δ). The distribution of frequency differences (δ values) was used for three purposes: (1) to provide estimates for genetic distance (differentiation) among these ethnic groups, (2) to revisit with a large data set the proportion of human genetic variation attributable to differentiation within ethnic groups, and (3) to identify loci with high δ values between recently admixed populations of use in mapping by admixture linkage disequilibrium (MALD). Although most markers display significant allele frequency differences between ethnic groups, the overall genetic distances between ethnic groups were small (.066–.098), and <10% of the measured overall molecular genetic diversity in these human samples can be attributed to “racial” differentiation. The median δ values for pairwise comparisons between groups fell between .15 and .20, permitting identification of highly informative RFLP loci for MALD disease association studies. PMID:7942857

  8. Dispersal Polymorphisms in Invasive Fire Ants.

    PubMed

    Helms, Jackson A; Godfrey, Aaron

    2016-01-01

    In the Found or Fly (FoF) hypothesis ant queens experience reproduction-dispersal tradeoffs such that queens with heavier abdomens are better at founding colonies but are worse flyers. We tested predictions of FoF in two globally invasive fire ants, Solenopsis geminata (Fabricius, 1804) and S. invicta (Buren, 1972). Colonies of these species may produce two different monogyne queen types-claustral queens with heavy abdomens that found colonies independently, and parasitic queens with small abdomens that enter conspecific nests. Claustral and parasitic queens were similarly sized, but the abdomens of claustral queens weighed twice as much as those of their parasitic counterparts. Their heavier abdomens adversely impacted morphological predictors of flight ability, resulting in 32-38% lower flight muscle ratios, 55-63% higher wing loading, and 32-33% higher abdomen drag. In lab experiments maximum flight durations in claustral S. invicta queens decreased by about 18 minutes for every milligram of abdomen mass. Combining our results into a simple fitness tradeoff model, we calculated that an average parasitic S. invicta queen could produce only 1/3 as many worker offspring as a claustral queen, but could fly 4 times as long and have a 17- to 36-fold larger potential colonization area. Investigations of dispersal polymorphisms and their associated tradeoffs promises to shed light on range expansions in invasive species, the evolution of alternative reproductive strategies, and the selective forces driving the recurrent evolution of parasitism in ants. PMID:27082115

  9. Genetic polymorphisms and esophageal cancer risk.

    PubMed

    Hiyama, Toru; Yoshihara, Masaharu; Tanaka, Shinji; Chayama, Kazuaki

    2007-10-15

    The aim of this paper is to review and evaluate, in a comprehensive manner, the published data regarding the contribution of genetic polymorphisms to risk of esophageal cancer, including squamous cell carcinoma (SCC) and adenocarcinoma, in humans. All relevant studies available in MEDLINE and published before February 2007 were identified. Studies carried out in humans and that compared esophageal cancer patients with at least 1 standard control group were considered for analysis. One-hundred studies and 3 meta-analyses were identified. Eighty (80%) studies were conducted in Asian countries, particularly China including Taiwan (60 (60%) studies). The most intensively examined genes were those encoding carcinogen metabolic enzymes. The most widely studied gene was GSTM1 (15 studies), followed by ALDH2 (11 studies). ALDH2, MTHFR C677T, CYP1A1 Ile/Val, CYP1A1MspI, CYP2E1, GSTP1, GSTM1 and GSTT1 were examined by meta-analyses and significant relations were found between ALDH2*1*2 and the CYP1A1 Val allele and increased risk of esophageal cancer. In addition, increased risk of esophageal SCC was consistently associated with the ADH2*1*2 and the p53 codon 72 Pro/Pro genotypes. Cohort studies that simultaneously consider multiple genetic and environmental factors possibly involved in esophageal carcinogenesis are needed to ascertain not only the relative contribution of these factors to tumor development but also the contributions of their putative interactions. PMID:17674367

  10. Epitaxial Retrieval of a Disappearing Polymorph

    PubMed Central

    2014-01-01

    Recrystallization of [PdCl2([9]aneS2O)] ([9]aneS2O = 1-oxa-4,7-dithiacyclononane), 1, and [PtCl2([9]aneS2O)], 2, by diffusion of Et2O vapor into solutions of the complexes in MeNO2 yielded three phases of 1 and two phases of 2. The known phase of 1, herein designated α-1, was obtained under ambient conditions. A second phase, designated β-1, was initially also obtained by this method; however, following the advent of a third phase, γ-1, all subsequent efforts over a period of a year to crystallize β-1 yielded either γ-1, obtained by carrying out the recrystallization at elevated temperature, or α-1, commonly found throughout the study. This persistent absence of a phase which could initially be crystallized with ease led us to the conclusion that β-1 was an example of a “disappearing polymorph”. The first phase obtained of 2, designated α-2, was obtained by recrystallization under ambient conditions and is isomorphous and isostructural with α-1. The second phase β-2 was obtained by slight elevation of the recrystallization temperature and was found to be isomorphous and isostructural with β-1. Subsequently, β-2 was used to seed the growth of the disappearing polymorph β-1. No third phase of 2 (γ-2) has been isolated thus far. PMID:25598741

  11. Evaluation of the compaction of sulfathiazole polymorphs.

    PubMed

    Picker-Freyer, Katharina Maria; Liao, Xiangmin; Zhang, Guifang; Wiedmann, Timothy Scott

    2007-08-01

    The aim of this study was to relate the tableting performance assessed by an instrumented tableting machine to the mechanical properties measured by nanoindentation. Three different polymorphic forms of sulfathiazole were prepared by recrystallization, and the density and X-ray powder diffraction patterns were measured and compared with theoretical density and simulated powder patterns, respectively. Tablets were prepared using a series of applied pressures, and the results were subjected to energy analysis, three dimensional (3D) modeling, and the traditional Heckel analysis. With these approaches, form I was found to be consistently the most brittle material, but the subtle differences between forms II and III were only revealed by 3D modeling. The rank order of the crushing force was found to be I is congruent to II < III. From nanoindentation, form III was found to be much harder than forms I and II, and III also had a much higher Young's modulus. The energy calculations of the nanoindentation curves showed that form III was distinct from forms I and II, which is consistent with the presence of slip planes that are only present in form III. However, in this system, there was little correspondence between the macroscopic and microscopic measurements, and thus particle-particle interactions may to be of paramount importance. PMID:17565752

  12. Long, polymorphic microsatellites in simple organisms.

    PubMed

    Field, D; Wills, C

    1996-02-22

    We have examined the phylogenetic distribution of the longest, perfect microsatellites in GenBank. Despite the large contributions of model higher-eukaryotic organisms to GenBank, the selective cloning of long microsatellites from these organisms as genetic markers, and the relative lack of concentration on the microsatellites in lower eukaryotes and prokaryotes, we found that simple organisms, defined here as slime molds, fungi, protists, prokaryotes, viruses, organelles and plasmids, contributed 78 of the 375 examined sequences. These 78 simple-organism microsatellites are characterized predominantly by trinucleotide repeats, nearly half of which lie in exons, and in general show a bias towards A+T rich motifs. Simple-organism microsatellites represented more than once in GenBank displayed length polymorphisms when independent clones were compared. These facts collectively raise speculation as to the role of these 'junk' sequences in such highly economical genomes, especially when precise changes in long microsatellites are known to regulate critical virulence factors in several prokaryotes. Regardless of their biological significance, simple-organism microsatellites may provide a general source of molecular markers to track disease outbreaks and the evolution of microorganisms in unprecedented detail. PMID:8728984

  13. Lactotransferrin Gene Polymorphism Associated with Caries Experience.

    PubMed

    Doetzer, Andrea D; Brancher, João A; Pecharki, Giovana D; Schlipf, Nina; Werneck, Renata; Mira, Marcelo T; Riess, Olaf; Bauer, Peter; Trevilatto, Paula Cristina

    2015-01-01

    Dental caries is a common multifactorial disease, resulting from the interaction of biofilm, cariogenic diet and host response over time. Lactotransferrin (LTF) is a main salivary glycoprotein, which modulates the host immune-inflammatory and antibacterial response. Although a genetic component for caries outcome has been identified, little is known over the genetic aspects underlying its susceptibility. Thus, the aim of this study was to investigate the association between LTF polymorphisms and caries susceptibility. Six hundred seventy seven 12-year-old students were selected: 346 with (DMFT ≥ 1) and 331 without caries experience (DMFT = 0). Also, individuals concentrating higher levels of disease (polarization group, DMFT ≥ 2, n = 253) were tested against those with DMFT ≤ 1 (n = 424). Along with clinical parameters, three representative LTF tag SNPs (rs6441989, rs2073495, rs11716497) were genotyped and the results were evaluated using univariate and multivariate analyses. Allele A for tag SNP rs6441989 was found to be significantly less frequent in the polarization group, conferring a protective effect against caries experience [AA + AG × GG (OR: 0.710, 95% CI: 0.514-0.980, p = 0.045)], and remained significantly associated with caries protection in the presence of gingivitis (p = 0.020) and plaque (p = 0.035). These results might contribute to the understanding of the genetic control of caries susceptibility in humans. PMID:25998152

  14. [Genomic medicine. Polymorphisms and microarray applications].

    PubMed

    Spalvieri, Mónica P; Rotenberg, Rosa G

    2004-01-01

    This update shows new concepts related to the significance of DNA variations among individuals, as well as to their detection by using a new technology. The sequencing of the human genome is only the beginning of what will enable us to understand genetic diversity. The unit of DNA variability is the polymorphism of a single nucleotide (SNP). At present, studies on SNPs are restricted to basic research but the large number of papers on this subject makes feasible their entrance into clinical practice. We illustrate here the use of SNPs as molecular markers in ethnical genotyping, gene expression in some diseases and as potential targets in pharmacological response, and also introduce the technology of arrays. Microarrays experiments allow the quantification and comparison of gene expression on a large scale, at the same time, by using special chips and array designs. Conventional methods provide data from up to 20 genes, while a single microarray may provide information about thousands of them simultaneously, leading to a more rapid and accurate genotyping. Biotechnology improvements will facilitate our knowledge of each gene sequence, the frequency and exact location of SNPs and their influence on cellular behavior. Although experimental efficiency and validity of results from microarrays are still controversial, the knowledge and characterization of a patient's genetic profile will lead, undoubtedly, to advances in prevention, diagnosis, prognosis and treatment of human diseases. PMID:15637833

  15. Dispersal Polymorphisms in Invasive Fire Ants

    PubMed Central

    Helms, Jackson A.; Godfrey, Aaron

    2016-01-01

    In the Found or Fly (FoF) hypothesis ant queens experience reproduction-dispersal tradeoffs such that queens with heavier abdomens are better at founding colonies but are worse flyers. We tested predictions of FoF in two globally invasive fire ants, Solenopsis geminata (Fabricius, 1804) and S. invicta (Buren, 1972). Colonies of these species may produce two different monogyne queen types—claustral queens with heavy abdomens that found colonies independently, and parasitic queens with small abdomens that enter conspecific nests. Claustral and parasitic queens were similarly sized, but the abdomens of claustral queens weighed twice as much as those of their parasitic counterparts. Their heavier abdomens adversely impacted morphological predictors of flight ability, resulting in 32–38% lower flight muscle ratios, 55–63% higher wing loading, and 32–33% higher abdomen drag. In lab experiments maximum flight durations in claustral S. invicta queens decreased by about 18 minutes for every milligram of abdomen mass. Combining our results into a simple fitness tradeoff model, we calculated that an average parasitic S. invicta queen could produce only 1/3 as many worker offspring as a claustral queen, but could fly 4 times as long and have a 17- to 36-fold larger potential colonization area. Investigations of dispersal polymorphisms and their associated tradeoffs promises to shed light on range expansions in invasive species, the evolution of alternative reproductive strategies, and the selective forces driving the recurrent evolution of parasitism in ants. PMID:27082115

  16. MTHFR genetic polymorphism increases the risk of preterm delivery

    PubMed Central

    Nan, Yanrong; Li, Hongmei

    2015-01-01

    Aims: This study aimed to investigate the association between the methylene tetrahydrofolate reductase (MTHFR) gene C677T and A1298C polymorphisms and premature delivery susceptibility. Methods: With matched age and gender, 108 premature delivery pregnant women as cases and 108 healthy pregnant women as controls were recruited in this case-control study. The cases and controls had same gestational weeks. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was adopted to analyze C677T and A1298C polymorphisms of the participants. Linkage disequilibrium (LD) and haplotype analysis were conducted by Haploview software. The differences for frequencies of gene type, allele and haplotypes in cases and controls were tested by chi-square test. The relevant risk of premature delivery was represented by odds ratios (ORs) with 95% confidence intervals (95% CIs). Results: TT gene type frequency of C677T polymorphsim was higher in cases than the controls (P=0.004, OR=3.077, 95% CI=1.469-6.447), so was allele T (P=0.002, OR=1.853, 95% CI=1.265-2.716). Whereas, CC gene type of A1298C polymorphism had a lower distribution in cases than the controls (P=0.008, OR=0.095, 95% CI=0.012-0.775), so was allele C (P=0.047, OR=0.610, 95% CI=0.384-0.970). Haplotype analysis and linkage disequilibrium test conducted on the alleles of two polymorphisms in MTHFR gene, we discovered that haplotype T-A had a higher distribution in cases, which indicated that susceptible haplotype T-A was the candidate factor for premature delivery. Conclusions: Gene type TT of MTHFR C677T polymorphism might make premature delivery risk rise while gene type CC of A1298C polymorphism might have protective influence on premature delivery. PMID:26261642

  17. Association between HRH4 polymorphisms and ankylosing spondylitis susceptibility

    PubMed Central

    Ran, Bo; Wang, Yongcheng; Zhang, Yonggang; Mao, Keya; Wang, Yan

    2015-01-01

    Target: The purpose of the study was to investigate the association between the histamine H4 receptor (HRH4) polymorphisms and the susceptibility to ankylosing spondylitis (AS). Methods: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method was used to analyze the HRH4 rs8088140 and rs657132 polymorphisms. Linkage disequilibrium and haplotype analyses were conducted with Haploview software. The genotypes distributions of HRH4 polymorphisms in the control group were tested by Hardy-Weinberg equilibrium (HWE), allele, genotype and haplotype frequencies between the cases and control groups were compared by χ2 test. The controls were matched with cases by age and gender. The relative risk of AS with HRH4 polymorphisms was represented by odds ratio (OR) with 95% confidence interval (CI) calculated by χ2 test. Results: The genotypes distributions of HRH4 rs8088140, rs657132 polymorphisms in controls conformed to HWE. The frequency of rs657132 AA genotype in the case group was obviously higher than that in the control group (P=0.040), and so was the A allele (OR=2.572, 95% CI=1.475-4.486, P=0.022). The frequency differences of A-A haplotype between two groups had statistical significance (P=0.011, OR=2.071, 95% CI=1.172-3.660) through haplotype analysis, indicating A-A might be the susceptible haplotype to AS. Conclusion: The AA genotypes of HRH4 rs657132 polymorphism may be the susceptible factors for AS, and rs657132 plays a role in generation of AS. In addition, A-A haplotype in rs8088140-rs657132 is also increased the risk of AS. PMID:26823878

  18. Polymorphism of human cytochrome P-450.

    PubMed

    Guengerich, F P; Umbenhauer, D R; Churchill, P F; Beaune, P H; Böcker, R; Knodell, R G; Martin, M V; Lloyd, R S

    1987-03-01

    The cytochrome P-450 forms involved in debrisoquine 4-hydroxylation (P-450DB), phenacetin O-deethylation (P-450PA), S-mephenytoin 4-hydroxylation (P-450MP), and nifedipine 1,4-oxidation (P-450NF) have been purified to electrophoretic homogeneity from human liver microsomes. All of these reactions show in vivo polymorphism in humans. Evidence for the roles of the purified proteins in these processes comes from in vitro reconstitution and immunoinhibition studies. The rat orthologs of these enzymes are as follows--P-450DB: P-450UT-H; P-450PA: P-450ISF-G; P-450MP: P-450UT-I; P-450NF: P-450PCN-E. Only in the case of P-450UT-H is the primary rat ortholog the same cytochrome P-450 which catalyses the catalytic reaction under consideration. Reconstitution and immunochemical studies establish that the following reactions are catalysed by the individual P-450s--P-450DB: debrisoquine 4-hydroxylation, sparteine delta 5-oxidation, bufuralol 1'-hydroxylation, encainide O-demethylation, and propanolol 4-hydroxylation; P-450PA: phenacetin O-deethylation; P-450MP: S-mephenytoin 4-hydroxylation and tolbutamide methyl hydroxylation; P-450NF: oxidation of nifedipine and 16 other substituted dihydropyridines, estradiol 2- and 4-hydroxylation, aldrin epoxidation, benzphetamine N-demethylation and 6 beta-hydroxylation of testosterone, androstenedione and cortisol. A cDNA clone has been isolated that corresponds to rat P-450UT-H, as shown by a number of criteria. Studies with this probe establish that the sex and strain variation in debrisoquine 4-hydroxylase and related activities is related to differences in the levels of a 2.0 kb length mRNA present.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:3577206

  19. Human enamel thickness and ENAM polymorphism

    PubMed Central

    Daubert, Diane M; Kelley, Joanna L; Udod, Yuriy G; Habor, Carolina; Kleist, Chris G; Furman, Ilona K; Tikonov, Igor N; Swanson, Willie J; Roberts, Frank A

    2016-01-01

    The tooth enamel development gene, enamelin (ENAM), showed evidence of positive selection during a genome-wide scan of human and primate DNA for signs of adaptive evolution. The current study examined the hypothesis that a single-nucleotide polymorphism (SNP) C14625T (rs7671281) in the ENAM gene identified in the genome-wide scan is associated with a change in enamel phenotype. African Americans were selected as the target population, as they have been reported to have a target SNP frequency of approximately 50%, whereas non-Africans are predicted to have a 96% SNP frequency. Digital radiographs and DNA samples from 244 teeth in 133 subjects were analysed, and enamel thickness was assessed in relation to SNP status, controlling for age, sex, tooth number and crown length. Crown length was found to increase with molar number, and females were found to have thicker enamel. Teeth with larger crowns also had thicker enamel, and older subjects had thinner enamel. Linear regression and generalized estimating equations were used to investigate the relationship between enamel thickness of the mandibular molars and ENAM SNP status; enamel in subjects with the derived allele was significantly thinner (P=0.040) when the results were controlled for sex, age, tooth number and crown length. The derived allele demonstrated a recessive effect on the phenotype. The data indicate that thinner dental enamel is associated with the derived ENAM genotype. This is the first direct evidence of a dental gene implicated in human adaptive evolution as having a phenotypic effect on an oral structure. PMID:27357321

  20. Polymorphisms of the chicken antiviral MX gene.

    PubMed

    Watanabe, T

    2007-01-01

    The Mx gene was originally found in laboratory mice in an infection experiment using influenza virus (Lindermann, 1962). Almost all of the mouse strains in that experiment died from the infection, and only the A2G strain had resistance to the virus. This resistant character was shown to be inherited as a single autosomal dominant trait (Lindermann et al., 1963; Lindermann, 1964; Haller et al., 1979). A congenic mouse strain was established by introducing the Mx+ allele of the A2G resistant strain into the Mx- sensitive inbred strain BALB/c (Staeheli et al., 1984). By immunizing parental BALB/c mice with extracts of interferon (IFN)-treated cultured cells from congenic BALB/c-Mx+ mice, a specific antibody against Mx protein was obtained (Horisberger et al., 1983; Staeheli et al., 1985). The Mx protein was detected in the nucleus of IFN-alpha/beta-treated mouse cells by immunofluorescence using the anti-Mx antibody (Dreiding et al., 1985). Thereafter, by using the antibody as an indicator, cDNA encoding the Mx protein was cloned from a cDNA library constructed from IFN-treated cells of congenic BALB/c-Mx+ mice (Staeheli et al., 1986a). IFN-treated Mx+ mouse cells contained a 3.5-kb Mx mRNA in the Northern blot, while Mx- cells failed to express the transcript. The functional Mx+ gene from an A2G mouse was found to contain 14 exons and encode 631 amino acids. The Mx- allelic mouse strains were found to be missing sequence of exons 9 through 11 or to contain a point mutation that converts lysine at position 389 to a stop codon (Staeheli et al., 1988). If these polymorphisms of the Mx gene could be detected in domestic animals, it would be possible to produce breeds that show resistance to infectious diseases. PMID:17675880

  1. The polymorphisms of the chromatin fiber

    NASA Astrophysics Data System (ADS)

    Boulé, Jean-Baptiste; Mozziconacci, Julien; Lavelle, Christophe

    2015-01-01

    In eukaryotes, the genome is packed into chromosomes, each consisting of large polymeric fibers made of DNA bound with proteins (mainly histones) and RNA molecules. The nature and precise 3D organization of this fiber has been a matter of intense speculations and debates. In the emerging picture, the local chromatin state plays a critical role in all fundamental DNA transactions, such as transcriptional control, DNA replication or repair. However, the molecular and structural mechanisms involved remain elusive. The purpose of this review is to give an overview of the tremendous efforts that have been made for almost 40 years to build physiologically relevant models of chromatin structure. The motivation behind building such models was to shift our representation and understanding of DNA transactions from a too simplistic ‘naked DNA’ view to a more realistic ‘coated DNA’ view, as a step towards a better framework in which to interpret mechanistically the control of genetic expression and other DNA metabolic processes. The field has evolved from a speculative point of view towards in vitro biochemistry and in silico modeling, but is still longing for experimental in vivo validations of the proposed structures or even proof of concept experiments demonstrating a clear role of a given structure in a metabolic transaction. The mere existence of a chromatin fiber as a relevant biological entity in vivo has been put into serious questioning. Current research is suggesting a possible reconciliation between theoretical studies and experiments, pointing towards a view where the polymorphic and dynamic nature of the chromatin fiber is essential to support its function in genome metabolism.

  2. Human enamel thickness and ENAM polymorphism.

    PubMed

    Daubert, Diane M; Kelley, Joanna L; Udod, Yuriy G; Habor, Carolina; Kleist, Chris G; Furman, Ilona K; Tikonov, Igor N; Swanson, Willie J; Roberts, Frank A

    2016-01-01

    The tooth enamel development gene, enamelin (ENAM), showed evidence of positive selection during a genome-wide scan of human and primate DNA for signs of adaptive evolution. The current study examined the hypothesis that a single-nucleotide polymorphism (SNP) C14625T (rs7671281) in the ENAM gene identified in the genome-wide scan is associated with a change in enamel phenotype. African Americans were selected as the target population, as they have been reported to have a target SNP frequency of approximately 50%, whereas non-Africans are predicted to have a 96% SNP frequency. Digital radiographs and DNA samples from 244 teeth in 133 subjects were analysed, and enamel thickness was assessed in relation to SNP status, controlling for age, sex, tooth number and crown length. Crown length was found to increase with molar number, and females were found to have thicker enamel. Teeth with larger crowns also had thicker enamel, and older subjects had thinner enamel. Linear regression and generalized estimating equations were used to investigate the relationship between enamel thickness of the mandibular molars and ENAM SNP status; enamel in subjects with the derived allele was significantly thinner (P=0.040) when the results were controlled for sex, age, tooth number and crown length. The derived allele demonstrated a recessive effect on the phenotype. The data indicate that thinner dental enamel is associated with the derived ENAM genotype. This is the first direct evidence of a dental gene implicated in human adaptive evolution as having a phenotypic effect on an oral structure. PMID:27357321

  3. Chromosomal Polymorphisms Involved in Reproductive Failure in the Romanian Population

    PubMed Central

    Mierla, D; Stoian, V

    2012-01-01

    Cytogenetic heteromorphisms are described as variations at specific chromosomal regions with no impact on phenotype. The purpose of this study was to investigate the effects of these chromosomal polymorphisms involved in reproductive failure in the Romanian population. One thousand eight hundred and nine infertile patients, who were referred to Life Memorial Hospital, Bucharest, Romania, between January 2008 and April 2011, were investigated in this retrospective study. The frequency of chromosomal polymorphic variations was calculated for these patients. The control group is represented by 1116 fetuses investigated by amniocentesis between January 2009 and April 2011. In this study 122 (6.74%) infertile patients and 63 fetuses (5.65%) showed chromosomal polymorphic variations. The differences between the two groups was not statistically significant (p <0.242) but there was statistical significance for some specific chromosomal polymorphisms [inv(9),1qh+, 9qh+, fra(17)]. Some chromosomal polymorphic variations appear to be associated with reproductive failure. The statistically significantly higher incidence of heterochromatic variations found in infertile individuals emphasizes the need to assess their role in infertility and subfertility. PMID:24052728

  4. Vitamin D Receptor Polymorphism and Breast Cancer Risk

    PubMed Central

    Lu, Demin; Jing, Lei; Zhang, Suzhan

    2016-01-01

    Abstract The objective was to perform a meta-analysis to summarize the available evidence from prospective nested case-control studies on the association of vitamin D receptor (VDR) polymorphism and the risk of breast cancer. We searched PubMed, ISI web of science, EMBASE, and reference lists for included articles. Study specific odds ratios (ORs) and 95% confidence intervals (CIs) were pooled by using fixed-effect or random-effects models. Eight studies were included in the meta-analysis. There were no association between Fok1 gene allele contrast f versus F (OR: 0.859; 95%CI: 0.685–1.079), ff versus FF (OR: 0.893; 95%CI: 0.763–1.045), recessive models ff versus FF+Ff (OR: 0.932; 95%CI: 0.796–1.092), and dominant models ff+Ff versus FF (OR: 0.899; 95%CI: 0.780–1.037). The estimated VDR polymorphism showed no significant association between Bsm1, Taq1, Apa1 polymorphism, and breast cancer risk. In the Caucasian ethnic subgroup, no association was found between allele contrast, recessive models, and dominant models on Fok1, Bsm1 polymorphism, and breast cancer risk. VDR polymorphism (Fok1, Bsm1, Taq1, and Apa1) were not associated with the risk of breast cancer in the general population as well as Caucasian population. PMID:27149457

  5. Turner syndrome and genetic polymorphism: a systematic review

    PubMed Central

    de Marqui, Alessandra Bernadete Trovó

    2015-01-01

    Objective: To present the main results of the literature on genetic polymorphisms in Turner syndrome and their association with the clinical signs and the etiology of this chromosomal disorder. Data sources: The review was conducted in the PubMed database without any time limit, using the terms Turner syndrome and genetic polymorphism. A total of 116 articles were found, and based on the established inclusion and exclusion criteria 17 were selected for the review. Data synthesis: The polymorphisms investigated in patients with Turner syndrome were associated with growth deficit, causing short stature, low bone mineral density, autoimmunity and cardiac abnormalities, which are frequently found in patients with Turner syndrome. The role of single nucleotide polymorphisms in the etiology of Turner syndrome, i.e., in chromosomal nondisjunction, was also confirmed. Conclusions: Genetic polymorphisms appear to be associated with Turner syndrome. However, in view of the small number of published studies and their contradictory findings, further studies in different populations are needed in order to clarify the role of genetic variants in the clinical signs and etiology of the Turner syndrome. PMID:25765448

  6. Association of TNF, MBL, and VDR Polymorphisms with Leprosy Phenotypes

    PubMed Central

    Sapkota, Bishwa R.; Macdonald, Murdo; Berrington, William R.; Misch, E. Ann; Ranjit, Chaman; Siddiqui, M. Ruby; Kaplan, Gilla; Hawn, Thomas R.

    2010-01-01

    Background Although genetic variants in tumor necrosis factor (TNF), mannose binding lectin (MBL), and the vitamin D receptor (VDR) have been associated with leprosy clinical outcomes these findings have not been extensively validated. Methods We used a case-control study design with 933 patients in Nepal, which included 240 patients with type I reversal reaction (RR), and 124 patients with erythema nodosum leprosum (ENL) reactions. We compared genotype frequencies in 933 cases and 101 controls of 7 polymorphisms, including a promoter region variant in TNF (G−308A), three polymorphisms in MBL (C154T, G161A and G170A), and three variants in VDR (FokI, BsmI, and TaqI). Results We observed an association between TNF −308A and protection from leprosy with an odds ratio (OR) of 0.52 (95% confidence interval (CI) of 0.29 to 0.95, P = 0.016). MBL polymorphism G161A was associated with protection from lepromatous leprosy (OR (95% CI) = 0.33 (0.12–0.85), P = 0.010). VDR polymorphisms were not associated with leprosy phenotypes. Conclusion These results confirm previous findings of an association of TNF −308A with protection from leprosy and MBL polymorphisms with protection from lepromatous leprosy. The statistical significance was modest and will require further study for conclusive validation. PMID:20650301

  7. Excess polymorphism at the Adh locus in Drosophila melanogaster.

    PubMed

    Kreitman, M E; Aguadé, M

    1986-09-01

    The evolutionary history of a region of DNA encompassing the Adh locus is studied by comparing patterns of variation in Drosophila melanogaster and its sibling species, D. simulans. An unexpectedly high level of silent polymorphism in the Adh coding region relative to the 5' and 3' flanking regions in D. melanogaster is revealed by a populational survey of restriction polymorphism using a four-cutter filter hybridization technique as well as by direct sequence comparisons. In both of these studies, a region of the Adh gene encompassing the three coding exons exhibits a frequency of polymorphism equal to that of a 4-kb 5' flanking region. In contrast, an interspecific sequence comparison shows a two-fold higher level of divergence in the 5' flanking sequence compared to the structural locus. Analysis of the patterns of variation suggest an excess of polymorphism within the D. melanogaster Adh locus, rather than lack of polymorphism in the 5' flanking region. An approach is outlined for testing neutral theory predictions about patterns of variation within and between species. This approach indicates that the observed patterns of variation are incompatible with an infinite site neutral model. PMID:3021568

  8. Association of TNF, MBL, and VDR polymorphisms with leprosy phenotypes.

    PubMed

    Sapkota, Bishwa R; Macdonald, Murdo; Berrington, William R; Misch, E Ann; Ranjit, Chaman; Siddiqui, M Ruby; Kaplan, Gilla; Hawn, Thomas R

    2010-10-01

    Although genetic variants in tumor necrosis factor (TNF), mannose binding lectin (MBL), and the vitamin D receptor (VDR) have been associated with leprosy clinical outcomes, these findings have not been extensively validated. We used a case-control study design with 933 patients in Nepal, which included 240 patients with type I reversal reaction (RR), and 124 patients with erythema nodosum leprosum (ENL) reactions. We compared genotype frequencies in 933 cases and 101 controls of seven polymorphisms, including a promoter region variant in TNF (G -308A), three polymorphisms in MBL (C154T, G161A and G170A), and three variants in VDR (FokI, BsmI, and TaqI). We observed an association between TNF -308A and protection from leprosy with an odds ratio of 0.52 (95% confidence interval = 0.29-0.95, p = 0.016). MBL polymorphism G161A was associated with protection from lepromatous leprosy (odds ratio = 0.33, 95% confidence interval = 0.12-0.85, p = 0.010). VDR polymorphisms were not associated with leprosy phenotypes. These results confirm previous findings of an association of TNF -308A with protection from leprosy and MBL polymorphisms with protection from lepromatous leprosy. The statistical significance was modest and will require further study for conclusive validation. PMID:20650301

  9. Development of novel polymorphic microsatellite markers in Siganus fuscescens.

    PubMed

    Mao, X Q; Li, Z B; Ning, Y F; Shangguan, J B; Yuan, Y; Huang, Y S; Li, B B

    2016-01-01

    Rabbitfish, Siganus fuscescens, is widely distributed in the Indo-Pacific regions and eastern Mediterranean. Its dwelling place includes reef flats, coral reef regions, and seagrass meadows in tropical area and reef areas or shallow waters in locations at high latitudes. In the present study, 10 new polymorphic microsatellite markers were screened from 30 wild S. fuscescens individuals, using a method of fast isolation protocol and amplified fragment length polymorphism of sequences containing repeats. The number of polymorphic alleles per locus was 3 to 5 with a mean of 4.3, while the value of polymorphic information content ranged from 0.283 to 0.680. The values of the observed and expected heterozygosities were in the range 0.3333-0.8462 and 0.3011-0.7424, respectively. Deviation from Hardy-Weinberg equilibrium was not observed in this study. These polymorphic loci are expected to be effective in evaluating the genetic diversity, population structure, and gene flow and in determining the paternity in S. fuscescens, as well as for conservation management. PMID:27525874

  10. Quasiparticle bands and spectra of Ga2O3 polymorphs

    NASA Astrophysics Data System (ADS)

    Furthmüller, J.; Bechstedt, F.

    2016-03-01

    Within the framework of density functional theory and Hedin's G W approximation for single-particle excitations, we present quasiparticle band structures and densities of states for two gallium oxide polymorphs: rhombohedral α -Ga2O3 and monoclinic β -Ga2O3 . The gap problem is attacked. In addition, their electron effective mass tensors are given. Solving the Bethe-Salpeter equation we also calculate excitonic optical spectra of the two polymorphs. The treatment of excitonic effects allows for a trustable prediction of optical properties from the band gap to the ultraviolet region. In addition, for few other polymorphs we also discuss the frequency-dependent dielectric tensor within the independent-particle approximation (random phase approximation) and densities of states on density functional level. We demonstrate that apart from subtle details, the overall densities of states and optical spectra, in particular the isotropically averaged spectra, are rather similar for all polymorphs, while the electronic dielectric constants vary with the structure. For all polymorphs, complete sets of elastic constants are given.

  11. Polymorphic behavior of isonicotinamide in cooling crystallization from various solvents

    NASA Astrophysics Data System (ADS)

    Hansen, Thomas B.; Taris, Alessandra; Rong, Ben-Guang; Grosso, Massimiliano; Qu, Haiyan

    2016-09-01

    In this work the nucleation of different polymorphs of isonicotinamide (INA) from different solvents has been studied. The metastable zone width of INA in cooling crystallization from five different solvents has been investigated and attempts have been made to reveal the link between the INA molecular self-association to the polymorphism of the nucleated crystals using ATR FT-IR (Attenuated Total Reflectance Fourier Transform Infrared) and Raman spectroscopy. Raman and IR spectra of INA dissolved in different solvents have demonstrated that the INA molecules might associate in different configurations, whereas, the link between the structure of the molecular self-association and the structure of the nucleated polymorph is complicated by the influence of INA concentration. This is consistent with our previous study with piroxicam. The cooling crystallization of INA from five different solvents resulted in two different polymorphs depending on the initial concentration of the solution. The results obtained in the present work showed that information about self-association of an API (Active Pharmaceutical Ingredient) in a given solvent is not sufficient to predict the polymorphic behavior in all scenarios.

  12. Relationship between TBX20 gene polymorphism and congenital heart disease.

    PubMed

    Yang, X F; Zhang, Y F; Zhao, C F; Liu, M M; Si, J P; Fang, Y F; Xing, W W; Wang, F L

    2016-01-01

    Congenital heart disease in children is a type of birth defect. Previous studies have suggested that the transcription factor, TBX20, is involved in the occurrence and development of congenital heart disease in children; however, the specific regulatory mechanisms are yet to be evaluated. Hence, this study aimed to evaluate the relationship between the TBX20 polymorphism and the occurrence and development of congenital heart disease. The TBX20 gene sequence was obtained from the NCBI database and the polymorphic locus candidate was predicted. Thereafter, the specific gene primers were designed for the restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR) of DNA extracted from the blood of 80 patients with congenital heart disease and 80 controls. The results of the PCR were subjected to correlation analysis to identify the differences between the amplicons and to determine the relationship between the TBX20 gene polymorphism and congenital heart disease. One of the single nucleotide polymorphic locus was found to be rs3999950: c.774T>C (Ala265Ala). The TC genotype frequency in the patients was higher than that in the controls, similar to that for the C locus. The odds ratio of the TC genotypes was above 1, indicating that the presence of the TC genotype increases the incidence of congenital heart diseases. Thus, rs3999950 may be associated with congenital heart disease, and TBX20 may predispose children to the defect. PMID:27323105

  13. Genetic polymorphisms in Pakistani women with polycystic ovary syndrome.

    PubMed

    Liaqat, Irfana; Jahan, Nusrat; Krikun, Graciela; Taylor, Hugh S

    2015-03-01

    Polycystic ovary syndrome (PCOS) is the major cause of anovulatory infertility. Although the genetic basis of PCOS is not well understood, it is a common metabolic and endocrine disorder. This study investigates the possible genomic variants associated with PCOS in Pakistani women from the Punjab region. DNA samples from 96 patients with genetically unrelated PCOS and 96 controls were analyzed by direct sequencing to determine the polymorphisms of different loci on follicle-stimulating hormone receptor (fshr), follicle-stimulating hormone β (fshrβ), luteinizing hormone chorionic gonadotropin (lhcgr), luteinizing hormone β (lhβ), estrogen receptor α (esr1), and estrogen receptor β (esr2) genes. Significant associations were observed within the genotype frequencies, allele frequencies, and multi-single-nucleotide polymorphism (SNP) haplotype analysis of most polymorphisms studied. This study identified new SNPs at positions 605+52 Del/T in lhcgr genes occurring in this particular subpopulation. The strong r (2) value suggests that polymorphisms in the fshr and esr1 genes were in linkage disequilibrium. Our study provides evidence of statistically significant associations between susceptibility to PCOS in Pakistani women and the gene polymorphisms mentioned earlier. This suggests that the susceptible loci for PCOS lie within or very close to the chromosomal regions spanning these genes. PMID:25100445

  14. Geographic variation in animal colour polymorphisms and its role in speciation.

    PubMed

    McLean, Claire A; Stuart-Fox, Devi

    2014-11-01

    Polymorphic species, in which multiple variants coexist within a population, are often used as model systems in evolutionary biology. Recent research has been dominated by the hypothesis that polymorphism can be a precursor to speciation. To date, the majority of research regarding polymorphism and speciation has focused on whether polymorphism is maintained within a population or whether morphs within populations may diverge to form separate species (sympatric speciation); however, the geographical context of speciation in polymorphic systems is likely to be both diverse and complex. In this review, we draw attention to the geographic variation in morph composition and frequencies that characterises many, if not most polymorphic species. Recent theoretical and empirical developments suggest that such variation in the number, type and frequency of morphs present among populations can increase the probability of speciation. Thus, the geographical context of a polymorphism requires a greater research focus. Here, we review the prevalence, causes and evolutionary consequences of geographic variation in polymorphism in colour-polymorphic animal species. The prevalence and nature of geographic variation in polymorphism suggests that polymorphism may be a precursor to and facilitate speciation more commonly than appreciated previously. We argue that a better understanding of the processes generating geographic variation in polymorphism is vital to understanding how polymorphism can promote speciation. PMID:24528520

  15. Typing classical polymorphisms by real-time PCR: analysis of the GPT and ALAD protein polymorphisms in the Jewish populations.

    PubMed

    Zoossmann-Diskin, Avshalom; Swinburne, Sarah; Shohat, Mordechai; Peleg, Leah; Gazit, Ephraim; Turner, David

    2008-01-01

    Expanding the already extensive data array on classical polymorphisms in new populations is beneficial to full characterization of the intricate relationships between human populations. This can be done in a short time on a large-scale by using real-time PCR. The red-cell enzymes Delta-aminolevulinate dehydratase (ALAD) and glutamate pyruvate transaminase (GPT) have each two alleles that can be separated by protein electrophoresis. They were previously characterized by protein electrophoresis in some of the Jewish populations. We designed primers and probes for fluorescence resonance energy transfer detection of the ALAD and GPT alleles to type Jewish populations including some in which these polymorphisms have not been studied in the past. The methods described here allow fast and efficient determination of these common classical polymorphisms. When used in large-scale population studies, these methods are not only faster, but also cheaper than amplification followed by restriction enzyme digestion and gel electrophoresis. The frequency of ALAD*1 among Jews ranges from 0.781 to 0.960 and that of GPT*1 from 0.412 to 0.773. A maximum likelihood tree based on the ALAD and GPT polymorphisms and five other red-cells enzymes polymorphisms depicts quite accurately the known historic, anthropological, and geographic relations between the Jewish populations. PMID:18432999

  16. The Y Alu polymorphism in southern African populations and its relationship to other Y-specific polymorphisms

    SciTech Connect

    Spurdle, A.B.; Jenkins, T. ); Hammer, M.F. )

    1994-02-01

    Y-linked polymorphisms were studied in a number of African populations. The frequency of the alleles of a Y-specific Alu insertion polymorphism, termed the [open quotes]Y Alu polymorphism,[close quotes] was determined in 889 individuals from 23 different African population groups. A trend in frequency was observed, with the insert largely absent in Caucasoid populations, at intermediate frequency in the Khoisan, and at high frequency in Negroids. The insert predates diversification of Homo sapiens, since it occurs in all groups. The Alu insertion is believed to result from a unique mutation event, and comparisons between this and several other Y-linked polymorphisms were carried out in an attempt to validate their usefulness in population and evolutionary studies. The p21A1/Taql and pDP31/EcoRI polymorphisms and 49a/TaqI alleles were all shown to have arisen on more than one occasion, and evidence exists for a preraciation crossover event between the Y-linked pseudoautosomal XY275 locus and the Y chromosome pseudoautosomal boundary. 33 refs., 4 figs., 5 tabs.

  17. Reverse random amplified microsatellite polymorphism reveals enhanced polymorphisms in the 3' end of simple sequence repeats in the pepper genome.

    PubMed

    Min, Woong-Ki; Han, Jung-Heon; Kang, Won-Hee; Lee, Heung-Ryul; Kim, Byung-Dong

    2008-09-30

    Microsatellites or simple sequence repeats (SSR) are widely distributed in eukaryotic genomes and are informative genetic markers. Despite many advantages of SSR markers such as a high degree of allelic polymorphisms, co-dominant inheritance, multi-allelism, and genome-wide coverage in various plant species, they also have shortcomings such as low polymorphic rates between genetically close lines, especially in Capsicum annuum. We developed an alternative technique to SSR by normalizing and alternating anchored primers in random amplified microsatellite polymorphisms (RAMP). This technique, designated reverse random amplified microsatellite polymorphism (rRAMP), allows the detection of nucleotide variation in the 3' region flanking an SSR using normalized anchored and random primer combinations. The reproducibility and frequency of polymorphic loci in rRAMP was vigorously enhanced by translocation of the 5' anchor of repeat sequences to the 3' end position and selective use of moderate arbitrary primers. In our study, the PCR banding pattern of rRAMP was highly dependent on the frequency of repeat motifs and primer combinations with random primers. Linkage analysis showed that rRAMP markers were well scattered on an intra-specific pepper map. Based on these results, we suggest that this technique is useful for studying genetic diversity, molecular fingerprinting, and rapidly constructing molecular maps for diverse plant species. PMID:18483466

  18. Investigation of the Polymorphs and Hydrolysis of Uranium Trioxide

    SciTech Connect

    Sweet, Lucas E.; Blake, Thomas A.; Henager, Charles H.; Hu, Shenyang Y.; Johnson, Timothy J.; Meier, David E.; Peper, Shane M.; Schwantes, Jon M.

    2013-04-01

    This work focuses on progress in gaining a better understanding of the polymorphic nature of the UO3-water system, one of several important materials associated with the nuclear fuel cycle. The UO3-water system is complex and has not been fully characterized, even though these species are common throughout the fuel cycle. Powder x-ray diffraction, Raman and fluorescence characterization was performed on polymorphic forms of UO3 and UO3 hydrolysis products for the purpose of developing some predictive capability of estimating process history and utility, e.g. for polymorphic phases of unknown origin. Specifically, we have investigated three industrially relevant production pathways of UO3 and discovered a previously unknown low temperature route to β-UO3. Pure phases of UO3, hydrolysis products and starting materials were used to establish optical spectroscopic signatures for these compounds.

  19. Mitochondrial DNA hypervariable region 1 polymorphism in Singapore Chinese population.

    PubMed

    Shee, Cheng-Yap; Chong, Michelle S M; Ng, Irene; Chia, Tet-Fatt

    2005-03-01

    Sequence polymorphisms of hypervariable region 1 were analyzed in 100 unrelated Singaporean Chinese. Ninety-five different haplotypes resulting from 113 variable sites were found between nucleotide positions 16045 and 16364. Single nucleotide polymorphism at nucleotide positions 16223, 16045, 16129, 16362 and 16189 was amongst the five highest frequencies observed in the sequences, whilst the most frequent haplotype was 16045-16223. Based on polymorphic sites observed at HV1, haplogroups A, F1a, M7b1, B5a and D4b were the most commonly observed clusters. The haplotype, nucleotide diversity and the average number of nucleotide differences were found to be 0.999, 0.028 and 9.082, respectively. The cytosine-stretch region located around nucleotide position 16189 was observed in 22% of this population sample. Transitions were found to be more predominant than transversions. PMID:15708338

  20. Mu opioid receptor polymorphism, early social adversity, and social traits.

    PubMed

    Carver, Charles S; Johnson, Sheri L; Kim, Youngmee

    2016-10-01

    A polymorphism in the mu opioid receptor gene OPRM1 (rs1799971) has been investigated for its role in sensitivity to social contexts. Evidence suggests that the G allele of this polymorphism is associated with higher levels of sensitivity. This study tested for main effects of the polymorphism and its interaction with a self-report measure of childhood adversity as an index of negative environment. Outcomes were several personality measures relevant to social connection. Significant interactions were obtained, such that the negative impact of childhood adversity on personality was greater among G carriers than among A homozygotes on measures of agreeableness, interdependence, anger proneness, hostility, authentic pride, life engagement, and an index of (mostly negative) feelings coloring one's world view. Findings support the role of OPRM1 in sensitivity to negative environments. Limitations are noted, including the lack of a measure of advantageous social environment to assess sensitivity to positive social contexts. PMID:26527429

  1. Computation of the Gibbs free energy difference between polymorphs

    NASA Astrophysics Data System (ADS)

    Sinkovits, Daniel W.; Kumar, Sanat K.

    2015-03-01

    Semi-crystalline polymers commonly crystallize into several different polymorphs; for example, the alpha and beta phases of isotactic polypropylene. While it is possible to favor particular polymorphs by kinetic means, such as with varying degrees of supercooling or through the use of different solvents in solution casting, we focus on the question of thermodynamic stability; that is, which polymorph possesses the lowest Gibbs free energy for a given temperature and pressure. We implement a version of the Bennett Acceptance Ratio method and find phase diagrams for several polymers. We also demonstrate agreement with phonon analysis in the quasi-harmonic approximation. The advantages and drawbacks of these methods will be discussed. Multidisciplinary University Research Initiative (MURI).

  2. DNA Polymorphisms in Lentinula edodes, the Shiitake Mushroom

    PubMed Central

    Kulkarni, Rajiv K.

    1991-01-01

    DNA restriction fragment length polymorphisms (RFLPs) were examined in Lentinula edodes strains. Genomic DNA from strain 70 was cloned in plasmid vector pUC19, and 18 random clones containing low-copy DNA sequences were used to probe seven strains in Southern DNA-DNA hybridizations. Each cloned fragment revealed DNA polymorphism. An RFLP genotype was determined for each strain and the genetic relatedness was assessed. The coefficients of genetic similarity among the seven strains ranged from 0.43 to 0.90. The inheritance of RFLP markers was examined in single spore isolates. Homokaryons displayed a loss of polymorphic bands compared with the parent dikaryon. Hybrids constructed by crossing compatible homokaryons displayed the inheritance of RFLP markers from each parent homokaryon. Images PMID:16348509

  3. Hepatitis-related hepatocellular carcinoma: Insights into cytokine gene polymorphisms.

    PubMed

    Dondeti, Mahmoud Fathy; El-Maadawy, Eman Anwar; Talaat, Roba Mohamed

    2016-08-14

    Hepatocellular carcinoma (HCC) is a primary liver cancer, which is one of the most prevalent cancers among humans. Many factors are involved in the liver carcinogenesis as lifestyle and environmental factors. Hepatitis virus infections are now recognized as the chief etiology of HCC; however, the precise mechanism is still enigmatic till now. The inflammation triggered by the cytokine-mediated immune response, was reported to be the closest factor of HCC development. Cytokines are immunoregulatory proteins produced by immune cells, functioning as orchestrators of the immune response. Genes of cytokines and their receptors are known to be polymorphic, which give rise to variations in their genes. These variations have a great impact on the expression levels of the secreted cytokines. Therefore, cytokine gene polymorphisms are involved in the molecular mechanisms of several diseases. This piece of work aims to shed much light on the role of cytokine gene polymorphisms as genetic host factor in hepatitis related HCC. PMID:27570418

  4. Hepatitis-related hepatocellular carcinoma: Insights into cytokine gene polymorphisms

    PubMed Central

    Dondeti, Mahmoud Fathy; El-Maadawy, Eman Anwar; Talaat, Roba Mohamed

    2016-01-01

    Hepatocellular carcinoma (HCC) is a primary liver cancer, which is one of the most prevalent cancers among humans. Many factors are involved in the liver carcinogenesis as lifestyle and environmental factors. Hepatitis virus infections are now recognized as the chief etiology of HCC; however, the precise mechanism is still enigmatic till now. The inflammation triggered by the cytokine-mediated immune response, was reported to be the closest factor of HCC development. Cytokines are immunoregulatory proteins produced by immune cells, functioning as orchestrators of the immune response. Genes of cytokines and their receptors are known to be polymorphic, which give rise to variations in their genes. These variations have a great impact on the expression levels of the secreted cytokines. Therefore, cytokine gene polymorphisms are involved in the molecular mechanisms of several diseases. This piece of work aims to shed much light on the role of cytokine gene polymorphisms as genetic host factor in hepatitis related HCC. PMID:27570418

  5. Modeling Polymorphic Molecular Crystals with Electronic Structure Theory.

    PubMed

    Beran, Gregory J O

    2016-05-11

    Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed. PMID:27008426

  6. High-pressure polymorphism of acetylsalicylic acid (aspirin): Raman spectroscopy

    NASA Astrophysics Data System (ADS)

    Crowell, Ethan L.; Dreger, Zbigniew A.; Gupta, Yogendra M.

    2015-02-01

    Micro-Raman spectroscopy was used to elucidate the high-pressure polymorphic behavior of acetylsalicylic acid (ASA), an important pharmaceutical compound known as aspirin. Using a diamond anvil cell (DAC), single crystals of the two polymorphic phases of aspirin existing at ambient conditions (ASA-I and ASA-II) were compressed to 10 GPa. We found that ASA-I does not transform to ASA-II, but instead transforms to a new phase (ASA-III) above ∼2 GPa. It is demonstrated that this transformation primarily introduces structural changes in the bonding and arrangement of the acetyl groups and is reversible upon the release of pressure. In contrast, a less dense ASA-II shows no transition in the pressure range studied, though it appears to exhibit a disordered structure above 7 GPa. Our results suggest that ASA-III is the most stable polymorph of aspirin at high pressures.

  7. Sampling Polymorphs of Ionic Solids using Random Superlattices

    NASA Astrophysics Data System (ADS)

    Stevanović, Vladan

    2016-02-01

    Polymorphism offers rich and virtually unexplored space for discovering novel functional materials. To harness this potential approaches capable of both exploring the space of polymorphs and assessing their realizability are needed. One such approach devised for partially ionic solids is presented. The structure prediction part is carried out by performing local density functional theory relaxations on a large set of random supperlattices (RSLs) with atoms distributed randomly over different planes in a way that favors cation-anion coordination. Applying the RSL sampling on MgO, ZnO, and SnO2 reveals that the resulting probability of occurrence of a given structure offers a measure of its realizability explaining fully the experimentally observed, metastable polymorphs in these three systems.

  8. Polymorphic phases of sp3-hybridized carbon under cold compression.

    PubMed

    Zhou, Rulong; Zeng, Xiao Cheng

    2012-05-01

    It is well established that graphite can be transformed into superhard carbons under cold compression (Mao et al. Science 2003, 302, 425). However, structure of the superhard carbon is yet to be determined experimentally. We have performed an extensive structural search for the high-pressure crystalline phases of carbon using the evolutionary algorithm. Nine low-energy polymorphic structures of sp(3)-hybridized carbon result from the unbiased search. These new polymorphic carbon structures together with previously reported low-energy sp(3)-hybridized carbon structures (e.g., M-carbon, W-carbon, and Cco-C(8) or Z-carbon) can be classified into three groups on the basis of different ways of stacking two (or more) out of five (A-E) types of buckled graphene layers. Such a classification scheme points out a simple way to construct a variety of sp(3)-hybridized carbon allotropes via stacking buckled graphene layers in different combinations of the A-E types by design. Density-functional theory calculations indicate that, among the nine low-energy crystalline structures, seven are energetically more favorable than the previously reported most stable crystalline structure (i.e., Cco-C(8) or Z-carbon) in the pressure range 0-25 GPa. Moreover, several newly predicted polymorphic sp(3)-hybridized carbon structures possess elastic moduli and hardness close to those of the cubic diamond. In particular, Z-carbon-4 possesses the highest hardness (93.4) among all the low-energy sp(3)-hybridized carbon structures predicted today. The calculated electronic structures suggest that most polymorphic carbon structures are optically transparent. The simulated X-ray diffraction (XRD) spectra of a few polymorphic structures are in good agreement with the experimental spectrum, suggesting that samples from the cold-compressed graphite experiments may consist of multiple polymorphic phases of sp(3)-hybridized carbon. PMID:22490007

  9. African origin of human-specific polymorphic Alu insertions

    SciTech Connect

    Batzer, M.A.; Alegria-Hartman, M. ); Stoneking, M. ); Bazan, H.; Kass, D.H.; Shaikh, T.H.; Scheer, W.D. ); Novick, G.E.; Herrera, R.J. ); Ioannou, P.A. )

    1994-12-06

    Alu elements are a family of interspersed repeats that have mobilized throughout primate genomes by retroposition from a few [open quotes]master[close quotes] genes. Among the 500,000 Alu elements in the human genome are members of the human-specific subfamily that are not fixed in the human species. Four such polymorphic human-specific Alu insertions were analyzed by a rapid, PCR-based assay. These four polymorphic Alu insertions were shown to be absent from the genomes of a number of nonhuman primates, consistent with their arising as human genetic polymorphisms sometime after the human/African ape divergence. Analysis of 664 unrelated individuals from 16 population groups from around the world revealed substantial levels of variation within population groups and significant genetic differentiation among groups. No significant associations were found among the four loci, consistent with their location on different chromosomes. A maximum-likelihood tree of population relationships showed four major groupings consisting of Africa, Europe, Asia/Americas, and Australia/New Guinea, which is concordant with similar trees based on other loci. A particularly useful feature of the polymorphic Alu insertions is that the ancestral state is known to be the absence of the Alu element, and the presence of the Alu element at a particular chromosomal site reflects a single, unique event in human evolution. A hypothetical ancestral group can then be included in the tree analysis, with the frequency of each insertion set to zero. The ancestral group connected to the maximum-likelihood tree within the African branch, which suggests an African origin of these polymorphic Alu insertions. These data are concordant with other diverse data sets, which lends further support to the recent African origin hypothesis for modern humans. Polymorphic Alu insertions represent a source of genetic variation for studying human population structure and evolution. 45 refs., 2 figs., 1 tab.

  10. Associations between vitamin D receptor polymorphisms and breast cancer risk.

    PubMed

    Wang, Jie; He, Qi; Shao, Yu-Guo; Ji, Min; Bao, Wei

    2013-12-01

    Many epidemiologic studies have investigated the association between vitamin D receptor (VDR) gene polymorphisms and breast cancer risk, but the results were inconsistent. We performed a meta-analysis of 31 studies on VDR polymorphisms, including FokI, BsmI, TaqI, and ApaI, and breast cancer risk published before May 2013. For FokI, the allele of f was found to be associated with increased risk of breast cancer compared with F (OR, 1.19; 95% CI, 1.03-1.36). Patients with ff genotype were at significantly higher risk of breast cancer compared with those with FF genotype (OR, 1.95; 95% CI, 1.66-2.29). In subgroup analysis by race, Fok1 polymorphism was significantly associated with breast cancer risk for Caucasian population (f vs. F: OR, 1.35; 95% CI, 1.14-1.59; ff vs. FF: OR, 2.18; 95% CI, 1.86-2.54; ff vs. FF + Ff: OR, 1.16; 95% CI, 1.03-1.30). For ApaI, aa genotype was associated with increased breast cancer risk in Asian population based on four studies (aa vs. Aa + AA, OR, 1.49; 95% CI, 1.12-1.98). No significant association was found between breast cancer risk and ApaI and TaqI polymorphism in different models and populations. Our updated meta-analysis showed that Fok1 polymorphism is associated with breast cancer risk both in general population and in Caucasian population. ApaI polymorphism might be associated with breast cancer risk in Asian population. Large well-designed epidemiological studies are necessary to clarify the risk identified in the current meta-analysis. PMID:23900677

  11. Association Between IL-10 Gene Polymorphism and Diabetic Retinopathy

    PubMed Central

    Dong, Hongtao; Li, Qiuming; Wang, Menghua; Wan, Guangming

    2015-01-01

    Background Genetic and environmental factors both play important roles in the occurrence and progression of diabetic retinopathy (DR). IL-10 592 gene polymorphism is associated with diabetes pathogenesis. This study analyzed the relationship between IL-10 gene promoter-592 loci polymorphism (SNP) in a diabetic model rats with DR. Material/Methods Streptozotocin (STZ) was injected through the tail vein to establish a diabetic rat model. The rats were randomly divided into 2 groups for 3 months’ feeding, including 100 rats in the diabetes-positive control group and 100 rats only injected with citric acid buffer as the blank control group. Fundus fluorescein angiography (FFA) was used to observe retinal vascular changes. Polymerase chain reaction-restriction fragment polymorphisms assay (PCR-RFLP) was used to detect IL-10 gene promoter-592 loci polymorphism in DNA samples. Enzyme-linked immunosorbent assay (ELISA) was performed to test serum IL-10 concentration. Results Serum IL-10 level in DR rats was 33.18±5.0 pg/mL and in the control rats it was 53.33±4.16 pg/mL in (P<0.01). Diabetes susceptibility with IL-10-592 genotype frequency and gene frequency analysis showed that IL-10-592 genotype frequency and allele frequency were significantly different in the DR group compared with the control group (P<0.01). Conclusions IL-10 592 polymorphism was associated with DR susceptibility, suggesting that the gene polymorphism might be a risk factor for DR. PMID:26492380

  12. Polymorphism of the DNA Base Excision Repair Genes in Keratoconus

    PubMed Central

    Wojcik, Katarzyna A.; Synowiec, Ewelina; Sobierajczyk, Katarzyna; Izdebska, Justyna; Blasiak, Janusz; Szaflik, Jerzy; Szaflik, Jacek P.

    2014-01-01

    Keratoconus (KC) is a degenerative corneal disorder for which the exact pathogenesis is not yet known. Oxidative stress is reported to be associated with this disease. The stress may damage corneal biomolecules, including DNA, and such damage is primarily removed by base excision repair (BER). Variation in genes encoding BER components may influence the effectiveness of corneal cells to cope with oxidative stress. In the present work we genotyped 5 polymorphisms of 4 BER genes in 284 patients and 353 controls. The A/A genotype of the c.–1370T>A polymorphism of the DNA polymerase γ (POLG) gene was associated with increased occurrence of KC, while the A/T genotype was associated with decreased occurrence of KC. The A/G genotype and the A allele of the c.1196A>G polymorphism of the X-ray repair cross-complementing group 1 (XRCC1) were associated with increased, and the G/G genotype and the G allele, with decreased KC occurrence. Also, the C/T and T as well as C/C genotypes and alleles of the c.580C>T polymorphism of the same gene displayed relationship with KC occurrence. Neither the g.46438521G>C polymorphism of the Nei endonuclease VIII-like 1 (NEIL1) nor the c.2285T>C polymorphism of the poly(ADP-ribose) polymerase-1 (PARP-1) was associated with KC. In conclusion, the variability of the XRCC1 and POLG genes may play a role in KC pathogenesis and determine the risk of this disease. PMID:25356504

  13. Polymorphisms of human N-acetyltransferases and cancer risk.

    PubMed

    Agúndez, José A G

    2008-07-01

    Human arylamine N-acetyltransferases (CoASAc; NAT, EC 2.3.1.5) NAT1 and NAT2 play a key role in the metabolism of drugs and environmental chemicals and in the metabolic activation and detoxification of procarcinogens. Phenotyping analyses have revealed an association between NAT enzyme activities and the risk of developing several forms of cancer. As genotyping procedures have become available for NAT1 and NAT2 gene variations, hundreds of association studies on NAT polymorphisms and cancer risk have been conducted. Here we review the findings obtained from these studies. Evidence for a putative association of NAT1 polymorphism and myeloma, lung and bladder cancer, as well as association of NAT2 polymorphisms with non-Hodgkin lymphoma, liver, colorectal and bladder cancer have been reported. In contrast, no consistent evidence for a relevant association of NAT polymorphisms with brain, head & neck, breast, gastric, pancreatic or prostate cancer have been described. Although preliminary data are available, further well-powered studies are required to fully elucidate the role of NAT1 in most human cancers, and that of NAT2 in astrocytoma, meningioma, esophageal, renal, cervical and testicular cancers, as well as in leukaemia and myeloma. This review discusses controversial findings on cancer risk and putative causes of heterogeneity in the proposed associations, and it identifies topics that require further investigation, particularly mechanisms underlying association of NAT polymorphisms and risk for subsets of cancer patients with specific exposures, putative epistatic contribution of polymorphism for other xenobiotic-metabolising enzymes such as glutathione S-transferases of Cytochrome P450 enzymes, and genetic plus environmental interaction. PMID:18680472

  14. The association between IGF-1 polymorphisms and high myopia

    PubMed Central

    Zhang, Xiaoyu; Zhou, Xingtao; Qu, Xinhua

    2015-01-01

    Background: The potential association between IGF-1 polymorphisms and high myopia has been investigated in previous studies, but the actual relationship remains controversial. Accordingly, we conducted a meta-analysisincludingcase-control and cohort studies to assess the existing relationship between high myopia and IGF-1 polymorphisms. We searched MEDLINE, EMBASE, and OVID. Odds ratios (OR) with 95% confidence intervals (CI) were derived for single-nucleotide polymorphisms (SNPs) involved in the studies obtained from the retrospective database search. Analyses of heterogeneity, sensitivity, and publication bias were also conducted. The findings from this meta-analysis were based on approximately 2,187 high myopia cases and 1,183 controls, and were used to assess the association between three IGF-1 genetic polymorphisms (rs6214, rs12423791, and rs5742632) and high myopia risks. We investigated the association of the IGF-1 gene SNP rs6214, but no statistical association was observed in the resulting odds ratios (OR) in the allelic (OR = 1.06, 95% CI = 0.89-1.25), dominant (OR = 1.07, 95% CI = 0.90-1.27), or recessive models (OR = 1.06, 95% CI = 0.89-1.26), or in the homozygote (OR = 1.12, 95% CI = 0.91-1.38) and heterozygote comparisons (OR = 1.06, 95% CI = 0.88-1.27). Simultaneously, two other selected SNPs, rs12423791 and rs5742632, were also studied, but similarly, no statistical association existed between these polymorphisms and the risk of high myopia. In conclusions, no statistical association between IGF-1 polymorphisms (rs6214, rs12423791, and rs5742632) and the risk of high myopia was observed following the reported meta-analysis. PMID:26309715

  15. Emergence of Polymorphic Mating Strategies in Robot Colonies

    PubMed Central

    Elfwing, Stefan; Doya, Kenji

    2014-01-01

    Polymorphism has fascinated evolutionary biologists since the time of Darwin. Biologists have observed discrete alternative mating strategies in many different species. In this study, we demonstrate that polymorphic mating strategies can emerge in a colony of hermaphrodite robots. We used a survival and reproduction task where the robots maintained their energy levels by capturing energy sources and physically exchanged genotypes for the reproduction of offspring. The reproductive success was dependent on the individuals' energy levels, which created a natural trade-off between the time invested in maintaining a high energy level and the time invested in attracting mating partners. We performed experiments in environments with different density of energy sources and observed a variety in the mating behavior when a robot could see both an energy source and a potential mating partner. The individuals could be classified into two phenotypes: 1) forager, who always chooses to capture energy sources, and 2) tracker, who keeps track of potential mating partners if its energy level is above a threshold. In four out of the seven highest fitness populations in different environments, we found subpopulations with distinct differences in genotype and in behavioral phenotype. We analyzed the fitnesses of the foragers and the trackers by sampling them from each subpopulation and mixing with different ratios in a population. The fitness curves for the two subpopulations crossed at about 25% of foragers in the population, showing the evolutionary stability of the polymorphism. In one of those polymorphic populations, the trackers were further split into two subpopulations: (strong trackers) and (weak trackers). Our analyses show that the population consisting of three phenotypes also constituted several stable polymorphic evolutionarily stable states. To our knowledge, our study is the first to demonstrate the emergence of polymorphic evolutionarily stable strategies within a

  16. A two-stage model for Cepaea polymorphism

    PubMed Central

    Cook, L. M.

    1998-01-01

    The history of the study of snails in the genus Cepaea is briefly outlined. Cepaea nemoralis and C. hortensis are polymorphic for genetically controlled shell colour and banding, which has been the main interest of the work covered. Random drift, selective predation and climatic selection, both at a macro- and micro-scale, all affect gene frequency. The usual approach to understanding maintenance of the polymorphism, has been to look for centripetal effects on frequency. Possible processes include balance of mutation pressure and drift, heterozygote advantage, relational balance heterosis, frequency-dependent predation, multi-niche selective balance, or some combination of these. Mutational balance is overlaid by more substantial forces. There is some evidence for heterosis. Predation by birds may protect the polymorphism, and act apostatically to favour distinct morphs. Although not substantiated for Cepaea, many studies show that predators behave in the appropriate manner, while shell colour polymorphisms in molluscs occur most commonly in species exposed to visually searching predators. It is not known whether different thermal properties of the shells help to generate equilibria. Migration between colonies is probably greater than originally thought. The present geographical range has been occupied for less than 5000 generations. Climatic and human modification alter snail habitats relatively rapidly, which in turn changes selection pressures. A simple simulation shows that migration coupled with selection which fluctuates but is not centripetal, may retain polymorphism for sufficiently long to account for the patterns we see today. There may therefore be a two-stage basis to the polymorphism, comprising long-term but weak balancing forces coupled with fluctuating selection which does not necessarily balance but results in very slow elimination. Persistence of genetic variants in this way may provide the conditions for evolution of a balanced genome.

  17. Asymmetric Dispersal Can Maintain Larval Polymorphism: A Model Motivated by Streblospio benedicti

    PubMed Central

    Zakas, Christina; Hall, David W.

    2012-01-01

    Polymorphism in traits affecting dispersal occurs in a diverse variety of taxa. Typically, the maintenance of a dispersal polymorphism is attributed to environmental heterogeneity where parental bet-hedging can be favored. There are, however, examples of dispersal polymorphisms that occur across similar environments. For example, the estuarine polychaete Streblospio benedicti has a highly heritable offspring dimorphism that affects larval dispersal potential. We use analytical models of dispersal to determine the conditions necessary for a stable dispersal polymorphism to exist. We show that in asexual haploids, sexual haploids, and in sexual diploids in the absence of overdominance, asymmetric dispersal is required in order to maintain a dispersal polymorphism when patches do not vary in intrinsic quality. Our study adds an additional factor, dispersal asymmetry, to the short list of mechanisms that can maintain polymorphism in nature. The region of the parameter space in which polymorphism is possible is limited, suggesting why dispersal polymorphisms within species are rare. PMID:22576818

  18. Genomic and genotyping characterization of haplotype-based polymorphic microsatellites in Prunus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Efficient utilization of microsatellites in genetic studies remains impeded largely due to the unknown status of their primer reliability, chromosomal location, and allele polymorphism. Discovery and characterization of microsatellite polymorphisms in a taxon will disclose the unknowns and gain new ...

  19. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    NASA Astrophysics Data System (ADS)

    Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

    2015-07-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib.

  20. Investigation of a Privileged Polymorphic Motif: a Dimeric ROY Derivative

    PubMed Central

    Lutker, Katie M.; Tolstyka, Zachary P.; Matzger, Adam J.

    2009-01-01

    Bis(5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrilyl)acetylene, a derivative of the highly polymorphic compound 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile (ROY) that possesses two chromophores electronically coupled through a triple bond, was found to be trimorphic. Structural data for two of these forms indicates that symmetry is maintained in one structure and broken in the other leading to spontaneous differentiation of the methyl-thiophenecarbonitrile units. This study contributes to the mounting evidence that ROY and its derivatives are particularly prone to polymorphism. PMID:19367341

  1. Kappa-casein polymorphisms among cattle breeds and bison herds

    USGS Publications Warehouse

    Cronin, M.A.; Cockett, N.

    1993-01-01

    We identified the HindIII restriction site polymorphism Of kappa-casein in cattle reported by Pinder et al. (Animal Genetics 22, 11, 1991) and found an additonal polymorphism (RsaI) in cattle and bison. The Hin dIII and Rsa I restriction sites were mapped and three haplotypes (alleles) were identified. Preliminary screening of 39 cattle and 71 bison revealed one allele restricted to cattle, one restricted to bison, and one shared by the species. No fixed allelic differences were observed among cattle breeds or among bison herds or subspecies.

  2. Novel polymorphs of the anti-Trypanosoma cruzi drug benznidazole

    NASA Astrophysics Data System (ADS)

    Honorato, Sara Braga; Mendonça, Jorge Souza; Boechat, Nubia; Oliveira, Alcemira Conceição; Mendes Filho, Josué; Ellena, Javier; Ayala, Alejandro Pedro

    2014-01-01

    Benznidazole (N-benzyl-2-(2-nitro-1H-imidazol-1-yl)acetamide), is a nitro-heterocyclic drug used in the treatment of Chagas disease. Despite the fact that this drug was released more than 30 years ago, little information about its solid state properties is available in the literature. In this study, it was verified that this drug exhibits three polymorphs, which were characterized in situ by X-ray powder diffraction, thermal analysis, hot stage microscopy and infrared spectroscopy. The thermodynamic relationships among these polymorphs were also discussed.

  3. An orthorhombic polymorph of 10,11-dihydrocarbamazepine.

    PubMed

    Harrison, William T A; Yathirajan, H S; Anilkumar, H G

    2006-05-01

    The title compound (systematic name: 10,11-dihydro-5H-dibenz[b,f]azepine-5-carboxamide), C15H14N2O, is shown to crystallize as an orthorhombic polymorph to complement the known monoclinic form. The molecular conformations of both forms are very similar, involving a bent conformation for the seven-membered azepine ring and an overall ;butterfly' shape. The molecules assemble into chains by way of N-H...O bonds and N-H...pi interactions in both crystal modifications. The two polymorphs appear to form due to different van der Waals interactions between the layer-like sheets of molecules. PMID:16679591

  4. The Pressure-Induced Polymorphic Transformations in Fluconazole.

    PubMed

    Gorkovenko, Ekaterina A; Kichanov, Sergey E; Kozlenko, Denis P; Belushkin, Alexandr V; Wąsicki, Jan; Nawrocik, Wojciech; Mielcarek, Jadwiga; Dubrovinsky, Leonid S; Lathe, Christian; Savenko, Boris N

    2015-12-01

    The structural properties and Raman spectra of fluconazole have been studied by means of X-ray diffraction and Raman spectroscopy at pressures up to 2.5 and 5.5 GPa, respectively. At a pressure of 0.8 GPa, a polymorphic phase transition from the initial form I to a new triclinic form VIII has been observed. At higher pressure of P = 3.2 GPa, possible transformation into another new polymorphic form IX has been detected. The unit cell parameters and volumes, and vibration modes as functions of pressure have been obtained for the different forms of fluconazole. PMID:26367523

  5. Polymorphisms and genes associated with puberty in heifers.

    PubMed

    Fortes, Marina R S; Nguyen, Loan To; Porto Neto, Laercio R; Reverter, Antonio; Moore, Stephen S; Lehnert, Sigrid A; Thomas, Milton G

    2016-07-01

    Puberty onset is a multifactorial process influenced by genetic determinants and environmental conditions, especially nutritional status. Genes, genetic variations, and regulatory networks compose the molecular basis of achieving puberty. In this article, we reviewed the discovery of multiple polymorphisms and genes associated with heifer puberty phenotypes and discuss the opportunities to use this evolving knowledge of genetic determinants for breeding early pubertal Bos indicus-influenced cattle. The discovery of polymorphisms and genes was mainly achieved through candidate gene studies, quantitative trait loci analyses, genome-wide association studies, and recently, global gene expression studies (transcriptome). These studies are recapitulated and summarized in the current review. PMID:27238439

  6. Applications of random amplified polymorphic DNA (RAPD) in molecular ecology.

    PubMed

    Hadrys, H; Balick, M; Schierwater, B

    1992-05-01

    Molecular genetic markers have been developed into powerful tools to analyse genetic relationships and genetic diversity. As an extension to the variety of existing techniques using polymorphic DNA markers, the Random Amplified Polymorphic DNA (RAPD) technique may be used in molecular ecology to determine taxonomic identity, assess kinship relationships, analyse mixed genome samples, and create specific probes. Main advantages of the RAPD technology include (i) suitability for work on anonymous genomes, (ii) applicability to problems where only limited quantities of DNA are available, (iii) efficiency and low expense. PMID:1344984

  7. Molecular docking study of conformational polymorph: building block of crystal chemistry.

    PubMed

    Dubey, Rashmi; Tewari, Ashish Kumar; Singh, Ved Prakash; Singh, Praveen; Dangi, Jawahar Singh; Puerta, Carmen; Valerga, Pedro; Kant, Rajni

    2013-01-01

    Two conformational polymorphs of novel 2-[2-(3-cyano-4,6-dimethyl-2-oxo-2H-pyridin-1-yl)-ethoxy]-4,6-dimethyl nicotinonitrile have been developed. The crystal structure of both polymorphs (1a and 1b) seems to be stabilized by weak interactions. A difference was observed in the packing of both polymorphs. Polymorph 1b has a better binding affinity with the cyclooxygenase (COX-2) receptor than the standard (Nimesulide). PMID:24250264

  8. Large number of replacement polymorphisms in rapidly evolving genes of Drosophila. Implications for genome-wide surveys of DNA polymorphism.

    PubMed Central

    Schmid, K J; Nigro, L; Aquadro, C F; Tautz, D

    1999-01-01

    We present a survey of nucleotide polymorphism of three novel, rapidly evolving genes in populations of Drosophila melanogaster and D. simulans. Levels of silent polymorphism are comparable to other loci, but the number of replacement polymorphisms is higher than that in most other genes surveyed in D. melanogaster and D. simulans. Tests of neutrality fail to reject neutral evolution with one exception. This concerns a gene located in a region of high recombination rate in D. simulans and in a region of low recombination rate in D. melanogaster, due to an inversion. In the latter case it shows a very low number of polymorphisms, presumably due to selective sweeps in the region. Patterns of nucleotide polymorphism suggest that most substitutions are neutral or nearly neutral and that weak (positive and purifying) selection plays a significant role in the evolution of these genes. At all three loci, purifying selection of slightly deleterious replacement mutations appears to be more efficient in D. simulans than in D. melanogaster, presumably due to different effective population sizes. Our analysis suggests that current knowledge about genome-wide patterns of nucleotide polymorphism is far from complete with respect to the types and range of nucleotide substitutions and that further analysis of differences between local populations will be required to understand the forces more completely. We note that rapidly diverging and nearly neutrally evolving genes cannot be expected only in the genome of Drosophila, but are likely to occur in large numbers also in other organisms and that their function and evolution are little understood so far. PMID:10581279

  9. Polymorphism in 3-acetyl-4-hydroxy-2H-chromen-2-one.

    PubMed

    Ghouili, Afef; Brahmia, Ameni; Ben Hassen, Rached

    2015-10-01

    A new polymorph (denoted polymorph II) of 3-acetyl-4-hydroxy-2H-chromen-2-one, C11H8O4, was obtained unexpectedly during an attempt to recrystallize the compound from salt-melted ice, and the structure is compared with that of the original polymorph (denoted polymorph I) [Lyssenko & Antipin (2001). Russ. Chem. Bull. 50, 418-431]. Strong intramolecular O-H...O hydrogen bonds are observed equally in the two polymorphs [O...O = 2.4263 (13) Å in polymorph II and 2.442 (1) Å in polymorph I], with a slight delocalization of the hydroxy H atom towards the ketonic O atom in polymorph II [H...O = 1.32 (2) Å in polymorph II and 1.45 (3) Å in polymorph I]. In both crystal structures, the packing of the molecules is dominated and stabilized by weak intermolecular C-H...O hydrogen bonds. Additional π-π stacking interactions between the keto-enol hydrogen-bonded rings stabilize polymorph I [the centres are separated by 3.28 (1) Å], while polymorph II is stabilized by interactions between α-pyrone rings, which are parallel to one another and separated by 3.670 (5) Å. PMID:26422214

  10. Searching the Cambridge Structural Database for the 'best' representative of each unique polymorph.

    PubMed

    van de Streek, Jacco

    2006-08-01

    A computer program has been written that removes suspicious crystal structures from the Cambridge Structural Database and clusters the remaining crystal structures as polymorphs or redeterminations. For every set of redeterminations, one crystal structure is selected to be the best representative of that polymorph. The results, 243,355 well determined crystal structures grouped by unique polymorph, are presented and analysed. PMID:16840806

  11. Surface Accuracy Measurement Sensor for Deployable Reflector Antennas (SAMS DRA)

    NASA Technical Reports Server (NTRS)

    Neiswander, R. S.

    1980-01-01

    Specifications, system configurations, and concept tests for surface measurement sensors for deployable reflector antennas are presented. Two approaches toward the optical measurement of remote target displacements are discussed: optical ranging, in which the basic measurement is target-to-sensor range; and in particular, optical angular sensing, in which the principle measurements are of target angular displacements lateral to the line of sight. Four representative space antennas are examined.

  12. Genetic study of eight AKT1 gene polymorphisms and their interaction with DRD2 gene polymorphisms in tardive dyskinesia.

    PubMed

    Zai, Clement C; Romano-Silva, Marco A; Hwang, Rudi; Zai, Gwyneth C; Deluca, Vincenzo; Müller, Daniel J; King, Nicole; Voineskos, Aristotle N; Meltzer, Herbert Y; Lieberman, Jeffrey A; Potkin, Steven G; Remington, Gary; Kennedy, James L

    2008-12-01

    Tardive dyskinesia (TD) is a motor adverse effect of chronic antipsychotic medication. It has been suggested to involve dopamine neurotransmission system changes. AKT1 acts downstream of the D(2) receptor that is blocked by all antipsychotics to some degree. The AKT1 gene has not been investigated in TD. We examined eight polymorphisms spanning the AKT1 gene and their association with TD in our schizophrenia sample of 193 Caucasians, 76 of which with TD. AKT1 polymorphisms and haplotypes were not significantly associated with TD. However, we detected a significant interaction between rs6275 of DRD2 and rs3730358 of AKT1 (p<1 x 10(-5)). PMID:18838251

  13. Nestling polymorphism in a cuckoo-host system.

    PubMed

    Sato, Nozomu J; Tanaka, Keita D; Okahisa, Yuji; Yamamichi, Masato; Kuehn, Ralph; Gula, Roman; Ueda, Keisuke; Theuerkauf, Jörn

    2015-12-21

    Virulence of avian brood parasites can trigger a coevolutionary arms race, which favours rejection of parasitic eggs or chicks by host parents, and in turn leads to mimicry in parasite eggs or chicks [1-7]. The appearance of host offspring is critical to enable host parents to detect parasites. Thus, increasing accuracy of parasites' mimicry can favour a newly emerged host morph to escape parasites' mimicry. If parasites catch up with the hosts with a newly acquired mimetic morph, host polymorphism should be maintained through apostatic (negative frequency-dependent) selection, which favours hosts rarer morphs [1-3,7]. Among population-wide polymorphism, uniformity of respective host morphs in single host nests stochastically prevents parasites from targeting any specific morph of hosts and thus helps parents detect parasitism. Polymorphism in such a state is well-known in egg appearances of hosts of brood parasitic birds [2,3,7], which might also occur in chick appearances when arms races escalate. Here, we present evidence of polymorphism in chick skin coloration in a cuckoo-host system: the fan-tailed gerygone Gerygone flavolateralis and its specialist brood parasite, the shining bronze-cuckoo Chalcites lucidus in New Caledonia (Figure 1A-C). PMID:26702649

  14. PARP1 Val762Ala polymorphism reduces enzymatic activity

    SciTech Connect

    Wang Xiaogan; Wang Zhaoqi; Tong Weimin . E-mail: tong@iarc.fr; Shen Yan

    2007-03-02

    Poly(ADP-ribose) polymerase 1 (PARP1) modifies a variety of nuclear proteins by poly(ADP-ribosyl)ation, and plays diverse roles in molecular and cellular processes. A common PARP1 single nucleotide polymorphism (SNP) at codon 762, resulting in the substitution of alanine (Ala) for valine (Val) in the catalytic domain has been implicated in susceptibility to cancer. To characterize the functional effect of this polymorphism on PARP1, we performed in vitro enzymatic analysis on PARP1-Ala762 and PARP1-Val762. We found that PARP1-Ala762 displayed 57.2% of the activity of PARP1-Val762 for auto-poly(ADP-ribosyl)ation and 61.9% of the activity of PARP1-Val762 for trans-poly(ADP-ribosyl)ation of histone H1. The kinetic characterization revealed that the K {sub m} of PARP1-Ala762 was increased to a 1.2-fold of the K {sub m} of PARP1-Val762 for trans-poly(ADP-ribosyl)ation. Thus, the PARP1 Val762Ala polymorphism reduces the enzymatic activity of PARP1 by increasing K {sub m}. This finding suggests that different levels of poly(ADP-ribosyl)ation by PARP1 might aid in understanding Cancer risk of carriers of the PARP1 Val762Ala polymorphism.

  15. Genome-Wide Patterns of Nucleotide Polymorphism in Domesticated Rice

    PubMed Central

    Hernandez, Ryan D; Boyko, Adam; Fledel-Alon, Adi; York, Thomas L; Polato, Nicholas R; Olsen, Kenneth M; Nielsen, Rasmus; McCouch, Susan R; Bustamante, Carlos D; Purugganan, Michael D

    2007-01-01

    Domesticated Asian rice (Oryza sativa) is one of the oldest domesticated crop species in the world, having fed more people than any other plant in human history. We report the patterns of DNA sequence variation in rice and its wild ancestor, O. rufipogon, across 111 randomly chosen gene fragments, and use these to infer the evolutionary dynamics that led to the origins of rice. There is a genome-wide excess of high-frequency derived single nucleotide polymorphisms (SNPs) in O. sativa varieties, a pattern that has not been reported for other crop species. We developed several alternative models to explain contemporary patterns of polymorphisms in rice, including a (i) selectively neutral population bottleneck model, (ii) bottleneck plus migration model, (iii) multiple selective sweeps model, and (iv) bottleneck plus selective sweeps model. We find that a simple bottleneck model, which has been the dominant demographic model for domesticated species, cannot explain the derived nucleotide polymorphism site frequency spectrum in rice. Instead, a bottleneck model that incorporates selective sweeps, or a more complex demographic model that includes subdivision and gene flow, are more plausible explanations for patterns of variation in domesticated rice varieties. If selective sweeps are indeed the explanation for the observed nucleotide data of domesticated rice, it suggests that strong selection can leave its imprint on genome-wide polymorphism patterns, contrary to expectations that selection results only in a local signature of variation. PMID:17907810

  16. Polymorphic copper iodide clusters: insights into the mechanochromic luminescence properties.

    PubMed

    Benito, Quentin; Le Goff, Xavier F; Maron, Sébastien; Fargues, Alexandre; Garcia, Alain; Martineau, Charlotte; Taulelle, Francis; Kahlal, Samia; Gacoin, Thierry; Boilot, Jean-Pierre; Perruchas, Sandrine

    2014-08-13

    An in-depth study of mechanochromic and thermochromic luminescent copper iodide clusters exhibiting structural polymorphism is reported and gives new insights into the origin of the mechanochromic luminescence properties. The two different crystalline polymorphs exhibit distinct luminescence properties with one being green emissive and the other one being yellow emissive. Upon mechanical grinding, only one of the polymorphs exhibits great modification of its emission from green to yellow. Interestingly, the photophysical properties of the resulting partially amorphous crushed compound are closed to those of the other yellow polymorph. Comparative structural and optical analyses of the different phases including a solution of clusters permit us to establish a correlation between the Cu-Cu bond distances and the luminescence properties. In addition, the local structure of the [Cu4I4P4] cluster cores has been probed by (31)P and (65)Cu solid-state NMR analysis, which readily indicates that the grinding process modifies the phosphorus and copper atoms environments. The mechanochromic phenomenon is thus explained by the disruption of the crystal packing within intermolecular interactions inducing shortening of the Cu-Cu bond distances in the [Cu4I4] cluster core and eventually modification of the emissive state. These results definitely establish the role of cuprophilic interactions in the mechanochromism of copper iodide clusters. More generally, this study constitutes a step further into the understanding of the mechanism involved in the mechanochromic luminescent properties of metal-based compounds. PMID:25076411

  17. Prediction of polymorphic transformations of paracetamol in solid dispersions.

    PubMed

    Maniruzzaman, Mohammed; Islam, Muhammad T; Moradiya, Hiren G; Halsey, Sheelagh A; Slipper, Ian J; Chowdhry, Babur Z; Snowden, Martin J; Douroumis, Dennis

    2014-06-01

    A novel approach employing variable-temperature X-ray powder diffraction (VTXRPD) was used to exploit its suitability as an off-line predictive tool to study the polymorphic transformations of paracetamol (PMOL) in melt-extruded hydrophilic polymer matrices. Physical mixtures (PMs) and extruded formulations of PMOL with either polyvinyl caprolactam graft copolymer (Soluplus®) or vinylpyrrolidone-vinyl acetate copolymer (Kollidon®) in the solid state were characterized by using differential scanning calorimetry, hot-stage microscopy, and scanning electron microscopy. The experimental findings from VTXRPD showed that the stable Form I (monoclinic) of PMOL transformed to the metastable polymorph Form II (orthorhombic) at temperatures varying from 112°C to 120°C, in both the PMs and extrudates suggesting an effect of both temperature and identity of the polymers. The findings obtained from VTXRD analysis for both the PMs and the extruded formulations were confirmed by in-line near-infrared (NIR) monitoring during the extrusion processing. In the NIR study, PMOL underwent the same pattern of polymorphic transformations as those detected using VTXPRD. The results of this study suggest that VTXRPD can be used to predict the polymorphic transformation of drugs in polymer matrices during extrusion processing and provides a better understanding of extrusion processing parameters. PMID:24788533

  18. [Intraspecific genetic polymorphism of Russian sturgeon Acipencer gueldenstaedtii].

    PubMed

    Timoshkina, N N; Barmintseva, A E; Usatov, A V; Miuge, N S

    2009-09-01

    Three populations (Azov, Caspian, and Black Sea) of Russian sturgeon Acipenser queldenstaedtii were tested for polymorphism at nuclear (RAPD and microsatellites) and mitochondrial (PCR identification of two mito-types) markers. In addition, morphometric analysis of he representatives of Azov population was carried out. According to the morphological characters, the Black Sea population occupied an intermediate position between the Caspian and Azov populations, reflecting the phylogeography of this species. In agreement with the morphometric data, genetic distances (the data of STR analysis) also placed the Black Sea population between the Caspian and Azov populations (FST = 0.058 and 0.043). The genetic distance between the Azov and Caspian population was somewhat higher (FST = 0.070). The highest allelic polymorphism at four microsatellite loci was found observed in Caspian population, while the lowest polymorphism was in the Sea of Azov. RAPD analysis distinguished high polymorphism within the populations, although it was not feasible for interpopulation analysis. Using the method differentiating the "baerii-like" and typical "gueldenstaedtii" mitotypes, the absence of the "baerii-like" marker in the Black Sea population was demonstrated. The frequency of this marker in Caspian and Azov populations constituted 31.1 and 1.8%, respectively. Possible evolutionary reasons for the interpopulation differences observed are discussed. PMID:19824546

  19. Isolation and characterization of polymorphic microsatellite markers from Coilia ectenes.

    PubMed

    Rong, X J; Xu, Y J; Wang, Q Y; Liao, M J; Liu, X Z; Pan, C Y; Zhang, Z; Wang, Y G

    2013-01-01

    Coilia ectenes (Jordan and Seale 1905) is an important anadromous species that is an important resource at risk of extinction because of over-fishing, pollution, and coastal construction. To evaluate the genetic diversity of C. ectenes for use in breeding programs, elite microsatellite-enriched libraries were constructed and novel microsatellite markers were developed, and applied to genetically detect wild populations. Out of 92 randomly selected and sequenced clones, 89 contained a CA or GA repeat motif. Twenty-two pairs of primers were designed to investigate the polymorphism and genetic structure of a wild population collected from the Yellow River estuary, China. It was found that 2 loci were monomorphic and 20 loci were polymorphic. The number of alleles per polymorphic loci ranged from 3 to 13, with an average of 7.9. The expected heterozygosity per locus ranged from 0.05 to 0.89, with an average of 0.68. The isolated polymorphic markers are expected to be of use in future genetic breeding programs for C. ectenes, and in the assessment of genetic variation within this species. PMID:24338395

  20. The Role of Matrix Metalloproteinase Polymorphisms in Ischemic Stroke.

    PubMed

    Chang, Jason J; Stanfill, Ansley; Pourmotabbed, Tayebeh

    2016-01-01

    Stroke remains the fifth leading cause of mortality in the United States with an annual rate of over 128,000 deaths per year. Differences in incidence, pathogenesis, and clinical outcome have long been noted when comparing ischemic stroke among different ethnicities. The observation that racial disparities exist in clinical outcomes after stroke has resulted in genetic studies focusing on specific polymorphisms. Some studies have focused on matrix metalloproteinases (MMPs). MMPs are a ubiquitous group of proteins with extensive roles that include extracellular matrix remodeling and blood-brain barrier disruption. MMPs play an important role in ischemic stroke pathophysiology and clinical outcome. This review will evaluate the evidence for associations between polymorphisms in MMP-1, 2, 3, 9, and 12 with ischemic stroke incidence, pathophysiology, and clinical outcome. The role of polymorphisms in MMP genes may influence the presentation of ischemic stroke and be influenced by racial and ethnic background. However, contradictory evidence for the role of MMP polymorphisms does exist in the literature, and further studies will be necessary to consolidate our understanding of these multi-faceted proteins. PMID:27529234

  1. MicroRNA polymorphisms: a giant leap towards personalized medicine

    PubMed Central

    Mishra, Prasun J

    2010-01-01

    “An individual’s genetic inheritance of microRNA polymorphisms associated with disease progression, prognosis and treatment holds the key to create safer and more personalized drugs and can be a giant leap towards personalized medicine.” PMID:20428464

  2. Polymorphism in Core-Chlorinated Naphthalene Tetracarboxylic Diimide Thin Films

    NASA Astrophysics Data System (ADS)

    Purdum, Geoffrey; May, Falk; Yao, Nan; Weitz, Thomas; Loo, Yueh-Lin

    2015-03-01

    Polymorphism within organic semiconductors can play a critical role in device performance, as some packing motifs may be more favorable to charge transport than others. As-evaporated polycrystalline thin-films of core-chlorinated naphthalene tetracarboxylic diimides (NTCDI-1) adopt a triclinic polymorph that is not different from those of single crystals grown via physical-vapor transport. Exposing these thin-films to saturated vapors of select organic solvents, such as those of acetone and chloroform, induces structural transformation; thermally evaporated films convert from the triclinic polymorph to a monoclinic polymorph that was reported for solution-grown single crystals. Isothermal transformations are well described by second-order Avrami kinetics; molecular dynamic simulations give us insight into how solvents induce different kinds of favorable molecule-molecule interactions. Interestingly, the surface energy of the underlying substrate also plays a role in determining the rate of transformation; the rate of transformation is 2x and 4x faster on hexamethyldisilazane modified-Si/SiO2 compared to on Si/SiO2 and octadecyltrichlorosilane modified-Si/SiO2, respectively.

  3. Impact of ESR1 Gene Polymorphisms on Migraine Susceptibility

    PubMed Central

    Li, Li; Liu, Ruozhuo; Dong, Zhao; Wang, Xiaolin; Yu, Shengyuan

    2015-01-01

    Abstract An increasing number of studies have explored genetic associations between the functionally important polymorphisms in estrogen receptor 1 (ESR1) gene and migraine susceptibility. The previously reported associations have nevertheless been inconsistent. The present work incorporating the published data derived from 8 publications was performed to assess the impact of these polymorphisms on incident migraine. Strength of the genetic risk was estimated by means of an odds ratio along with the 95% confidence interval (OR and 95% CI). From the results, we found individuals who harbored the 325-GG genotype, compared with those harboring the CC genotype or CG and CC combined genotypes, had almost 50% greater risk of migraine. The same genetic models showed notable associations in subgroups of Caucasians and migraine with aura (MA). For 594G>A, a moderately increased risk of migraine was seen under AG versus GG. The AA + AG versus GG model, however, showed a borderline association with migraine. Subgroup analyses according to ethnicity and subtype of migraine provided statistical evidence of significantly increased risk of migraine in Caucasians and of a marginal association with MA, respectively. Both 325C>G and 594G>A polymorphisms showed no major effects either in males or in females. Based on the statistical data, we conclude some of the ESR1 gene polymorphisms may have major contributions to the pathogenesis of migraine in Caucasian populations. PMID:26334887

  4. Permanent tooth calcification in chimpanzees (Pan troglodytes): patterns and polymorphisms.

    PubMed

    Kuykendall, K L; Conroy, G C

    1996-01-01

    Tooth calcification is an important developmental marker for use in constructing models for early hominid life history, particularly for its application to the fossil record. As chimpanzees are commonly utilized in interspecific comparisons in such research, this study aims to improve available baseline data for tooth calcification patterns in chimpanzees (Pan troglodytes), and to quantify basic patterns and polymorphisms. We present an analysis of developmental patterns for the left mandibular dentition (I1-M3) based on intraoral radiographs obtained from a cross-sectional sample of chimpanzees (58 males, 60 females) housed at LEMSIP (NYU Medical Center) and Yerkes (Emory University). No significant differences with previous descriptions of the basic sequences of tooth calcification in chimpanzees were found, but variation in such patterns was documented for the first time. In the overall sequence, polymorphisms between the canine and the group (M2 P4 P3) reached significant levels. This is due to the relative delay in canine crown formation compared to other teeth. Differences in the basic sequence between males and females were recorded, but are due to minor shifts in the percentages of occurrence for polymorphic sequences which are common to both genders. Perhaps our most important findings are that a) different polymorphic sequences occur in tooth calcification and tooth emergence in chimpanzees, and b) developmental relationships among teeth fluctuate throughout tooth calcification. Thus, characterizations of dental developmental patterns based on particular stages of development cannot necessarily be extrapolated to other stages without supporting data. PMID:8928717

  5. Interferon-gamma Genetic Polymorphism and Expression in Kawasaki Disease

    PubMed Central

    Huang, Ying-Hsien; Hsu, Yu-Wen; Lu, Hsing-Fang; Wong, Henry Sung-Ching; Yu, Hong-Ren; Kuo, Hsing-Chun; Huang, Fu-Chen; Chang, Wei-Chiao; Kuo, Ho-Chang

    2016-01-01

    Abstract Kawasaki disease (KD) is a systemic vasculitis of unknown etiology. IFNG gene encoding interferon (IFN)-γ, produced by natural killer cells and T cells, has been suggested to play an important role in the immunopathogenesis of Kawasaki disease. The aim of this study was to examin the correlation of gene polymorphisms of the IFNG gene and plasma levels of IFN-γ in KD patients and their outcomes. A total of 950 subjects (381 KD and 569 controls) were recruited. Three tagging single-nucleotide polymorphisms (rs2069718, rs1861493, rs2069705) were selected for TaqMan allelic discrimination assay. Clinical phenotypes, coronary artery lesions (CAL), coronary artery aneurysms (CAA) and intravenous immunoglobulin (IVIG) treatment outcomes were collected for analysis. Plasma IFN-γ levels were also measured with an enzyme-linked immunosorbent assay. Polymorphisms of the IFNG gene were significantly different between the normal controls and KD patients. The G allele of rs1861493 conferred a better response to IVIG treatment in KD patients. AA allele frequencies of rs1861493 were also associated with a significantly higher risk of CAA in KD patients. Furthermore, the plasma IFN-γ level was lower in the AA allele than in the GG allele of rs1861493 both before and after IVIG treatment in KD patients. This study provides the first evidence supporting an association between IFNG gene polymorphisms, susceptibility of KD, IVIG responsiveness, and plasma IFN-γ levels in KD patients. PMID:27124053

  6. Computational Assembly of Polymorphic Amyloid Fibrils Reveals Stable Aggregates

    PubMed Central

    Smaoui, Mohamed Raef; Poitevin, Frédéric; Delarue, Marc; Koehl, Patrice; Orland, Henri; Waldispühl, Jérôme

    2013-01-01

    Amyloid proteins aggregate into polymorphic fibrils that damage tissues of the brain, nerves, and heart. Experimental and computational studies have examined the structural basis and the nucleation of short fibrils, but the ability to predict and precisely quantify the stability of larger aggregates has remained elusive. We established a complete classification of fibril shapes and developed a tool called CreateFibril to build such complex, polymorphic, modular structures automatically. We applied stability landscapes, a technique we developed to reveal reliable fibril structural parameters, to assess fibril stability. CreateFibril constructed HET-s, Aβ, and amylin fibrils up to 17 nm in length, and utilized a novel dipolar solvent model that captured the effect of dipole-dipole interactions between water and very large molecular systems to assess their aqueous stability. Our results validate experimental data for HET-s and Aβ, and suggest novel (to our knowledge) findings for amylin. In particular, we predicted the correct structural parameters (rotation angles, packing distances, hydrogen bond lengths, and helical pitches) for the one and three predominant HET-s protofilaments. We reveal and structurally characterize all known Aβ polymorphic fibrils, including structures recently classified as wrapped fibrils. Finally, we elucidate the predominant amylin fibrils and assert that native amylin is more stable than its amyloid form. CreateFibril and a database of all stable polymorphic fibril models we tested, along with their structural energy landscapes, are available at http://amyloid.cs.mcgill.ca. PMID:23442919

  7. Structural and electrical properties of polymorphic pentacene thin films

    NASA Astrophysics Data System (ADS)

    Stadlober, Barbara; Satzinger, Valentin; Maresch, Hannes; Somitsch, Dieter; Haase, Anja; Pichler, Heinz; Rom, Werner; Jakopic, Georg

    2003-11-01

    Due to its outstanding carrier transport capabilities the aromatic hydrocarbon pentacene is still one of the most promising out of all organic semiconducting materials investigated so far. Pentacene appears in several polymorphic structures that significantly differ with respect to the d(001) spacing. It is shown, that precise control of the epitaxial growth process of thin films enables not only to adjust the formation of the polymorphic phases, but also to influence grain size and shape. The relative volume fraction of the pentacene polymorphs is determined by several parameters which are substrate material, deposition rate, film thickness and substrate temperature. A comparison of X-ray diffraction and Raman measurements reveals that the phase with the smaller layer-by-layer spacing grows on top of the other]. Moreover, there is a strict correlation between evaporation rate and maximum grain size. In addition to structural we also investigated the electrical properties of pentacene thin films focussing on polymorphism and its influence on the transport properties. Apart from the fact that the charge carrier mobility is strongly influenced by the grain size it turned out that the bulk phase is related to a lower intrinisic mobility than the thin film phase.

  8. A Simplified Technique for Evaluating Human "CCR5" Genetic Polymorphism

    ERIC Educational Resources Information Center

    Falteisek, Lukáš; Cerný, Jan; Janštová, Vanda

    2013-01-01

    To involve students in thinking about the problem of AIDS (which is important in the view of nondecreasing infection rates), we established a practical lab using a simplified adaptation of Thomas's (2004) method to determine the polymorphism of HIV co-receptor CCR5 from students' own epithelial cells. CCR5 is a receptor involved in…

  9. Genetic polymorphisms predicting the outcome of bone marrow transplants.

    PubMed

    Dickinson, Anne M; Middleton, Peter G; Rocha, Vanderson; Gluckman, Eliane; Holler, Ernst

    2004-12-01

    Analysis of non-histocompatibility leucocyte antigen (HLA) functional genomics, together with conventional risk factors in haematopoietic stem cell transplantation (HSCT) can lead to predicting outcome in HLA-matched sibling transplant recipients. Polymorphisms of cytokine genes including tumour necrosis factor alpha, interleukin-10, interferon gamma and interleukin (IL)-6, associate with more severe acute graft-versus-host disease (aGvHD). Donor genotype for IL-1 receptor antagonist (IL-1Ra) has been associated with reduced aGvHD severity. Other genotypes (patient IL-1Ra, IL-6 and donor IL-1 alpha) have been associated with chronic GvHD, or overall survival (Vitamin D receptor and oestrogen receptor). Polymorphisms within genes associated with host defence/inflammatory responses (mannose binding lectin genes, myeloperoxidase genes and the FC gamma receptors) have been associated with infections. Polymorphisms of pharmacogenes, such as methylenetetrahydrofolate-reductase, have been associated with aGvHD and other post-transplant complications. The NOD2 gene polymorphism, associated with Crohn's disease, has been shown to be associated with risk of gut GvHD. The majority of the studies have been carried out in single centre HLA-matched sibling cohorts and in relatively few matched unrelated donor transplants. This review gives an overall perspective of the current field of non-HLA genetics with regard to HSCT outcome, clinical relevance and potential application of the results to clinical management of HSCT. PMID:15566351

  10. Association between ERCC5 gene polymorphisms and breast cancer risk.

    PubMed

    Na, Nari; Dun, Eer; Ren, Lidong; Li, Guoxin

    2015-01-01

    We conducted a case-control study to evaluate the association between ERCC5 polymorphism and breast cancer risk. 325 breast cancer patients and 325 controls were recruited in our study between January 2011 and March 2014. ERCC5 rs1047768, rs2094258, rs2296147, rs751402 and rs873601 polymorphisms were genotyped, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) assay. By logistic regression analysis, we found that individuals with AA genotype of rs2094258 was associated with increased risk of breast cancer when compared with wide-type genotype, and the OR (95% CI) was 1.80 (1.12-2.92) for AA genotype. Individuals with GA+GG genotype of rs2094258 were significantly correlated with increased risk of breast cancer in tobacco smokers, and the OR (95% CI) was 7.35 (1.21-47.20). In conclusion, our study indicated that ERCC5 rs2094258 polymorphism may contribute to the risk of breast cancer. PMID:26045839

  11. The Role of Matrix Metalloproteinase Polymorphisms in Ischemic Stroke

    PubMed Central

    Chang, Jason J.; Stanfill, Ansley; Pourmotabbed, Tayebeh

    2016-01-01

    Stroke remains the fifth leading cause of mortality in the United States with an annual rate of over 128,000 deaths per year. Differences in incidence, pathogenesis, and clinical outcome have long been noted when comparing ischemic stroke among different ethnicities. The observation that racial disparities exist in clinical outcomes after stroke has resulted in genetic studies focusing on specific polymorphisms. Some studies have focused on matrix metalloproteinases (MMPs). MMPs are a ubiquitous group of proteins with extensive roles that include extracellular matrix remodeling and blood-brain barrier disruption. MMPs play an important role in ischemic stroke pathophysiology and clinical outcome. This review will evaluate the evidence for associations between polymorphisms in MMP-1, 2, 3, 9, and 12 with ischemic stroke incidence, pathophysiology, and clinical outcome. The role of polymorphisms in MMP genes may influence the presentation of ischemic stroke and be influenced by racial and ethnic background. However, contradictory evidence for the role of MMP polymorphisms does exist in the literature, and further studies will be necessary to consolidate our understanding of these multi-faceted proteins. PMID:27529234

  12. The role of MBL2 gene polymorphism in sepsis incidence

    PubMed Central

    Liu, Lei; Ning, Bo

    2015-01-01

    Aim: This case-control study was aimed to explore the role of mannose-binding lectin 2 (MBL2) gene rs1800450 polymorphism (codon 54 A/B, G230A) in the development of sepsis in Han Chinese. Methods: MBL2 rs1800450 polymorphism was genotyped by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). MBL serum level was detected by enzyme-linked immunosorbent assay (ELISA). Associations between rs1800450 and sepsis susceptibility was detected by Chi-square test and represented by odds ratios (ORs) and 95% confidence intervals (CIs). Correlation of rs1800450 genotypes and MBL serum level was assessed using t test. Result: Variant A allele frequency was significantly observed in cases than that in controls, indicating a significant association with the susceptibility of sepsis (OR = 1.979, 95% CI = 1.200-3.262). GA genotype also relate to the onset of sepsis (OR = 2.090, 95% CI = 1.163-3.753). MBL serum concentrations were significantly different between case and control groups (P<0.001). Meanwhile, variant allele carriers had lower serum level compared with wild homozygous (P<0.001). Conclusion: Variant A allele in MBL2 gene rs1800450 polymorphism might increase the risk of sepsis via decrease the MBL serum level. PMID:26823854

  13. Systematic Identification of Balanced Transposition Polymorphisms in Saccharomyces cerevisiae

    PubMed Central

    Faddah, Dina A.; Ganko, Eric W.; McCoach, Caroline; Pickrell, Joseph K.; Hanlon, Sean E.; Mann, Frederick G.; Mieczkowska, Joanna O.; Jones, Corbin D.; Lieb, Jason D.; Vision, Todd J.

    2009-01-01

    High-throughput techniques for detecting DNA polymorphisms generally do not identify changes in which the genomic position of a sequence, but not its copy number, varies among individuals. To explore such balanced structural polymorphisms, we used array-based Comparative Genomic Hybridization (aCGH) to conduct a genome-wide screen for single-copy genomic segments that occupy different genomic positions in the standard laboratory strain of Saccharomyces cerevisiae (S90) and a polymorphic wild isolate (Y101) through analysis of six tetrads from a cross of these two strains. Paired-end high-throughput sequencing of Y101 validated four of the predicted rearrangements. The transposed segments contained one to four annotated genes each, yet crosses between S90 and Y101 yielded mostly viable tetrads. The longest segment comprised 13.5 kb near the telomere of chromosome XV in the S288C reference strain and Southern blotting confirmed its predicted location on chromosome IX in Y101. Interestingly, inter-locus crossover events between copies of this segment occurred at a detectable rate. The presence of low-copy repetitive sequences at the junctions of this segment suggests that it may have arisen through ectopic recombination. Our methodology and findings provide a starting point for exploring the origins, phenotypic consequences, and evolutionary fate of this largely unexplored form of genomic polymorphism. PMID:19503594

  14. A Polymorphism in Mitochondrial DNA Associated with IQ?

    ERIC Educational Resources Information Center

    Skuder, Patricia; And Others

    1995-01-01

    Of 100 DNA markers examined in an allelic association study, only 1 showed a replicated association with IQ in samples totaling 107 children. How the gene marked by the particular restriction fragment length polymorphism was tracked and its mitochondrial origin identified is described. (SLD)

  15. Association between ERCC5 gene polymorphisms and gastric cancer risk.

    PubMed

    Guo, B W; Yang, L; Zhao, R; Hao, S Z

    2016-01-01

    We investigate the role of ERCC5 gene polymorphisms (rs17655 and rs751402) in the development of gastric cancer in a Chinese population. A total of 142 gastric cancer patients whose diagnoses were confirmed by pathology, and 274 control subjects were recruited from Tangshan Gongren Hospital between March 2013 and March 2015. Genotyping of ERCC5 rs17655 and rs751402 polymorphisms was performed by polymerase chain reaction-restriction fragment length polymorphism. Compared with the control subjects, we found that gastric cancer patients were more likely to be older, smoke tobacco, drink alcohol, and suffer from Helicobacter pylori infection. Using a chi-square test, a significant difference was observed in the distribution ofERCC5 rs751402 genotypes between patient and control groups (chi-square = 7.79, P = 0.02). In addition, unconditional multiple logistic regression analysis revealed that the AA genotype of rs751402 significantly increased gastric cancer risk compared to the GG genotype [odds ratio (OR) = 2.61, 95%CI = 1.23-5.49; P = 0.005]. Moreover, we found that the AA genotype correlated with elevated risk of gastric cancer when compared to the GG+AG genotype under a recessive model (OR = 2.21, 95%CI = 1.11-4.39; P = 0.01). In conclusion, we suggest that the ERCC5 rs751402 polymorphism is associated with development of gastric cancer. PMID:27323183

  16. Molecular understanding of the compaction behavior of indomethacin polymorphs.

    PubMed

    Khomane, Kailas S; More, Parth K; Raghavendra, Guru; Bansal, Arvind K

    2013-02-01

    Polymorphs enable us to gain molecular insights into the compaction behavior of pharmaceutical powders. Two polymorphs (α and γ) of indomethacin (IMC) were investigated for in-die and out-of-die compaction behavior using compressibility, tabletability and compactibility (CTC) profile, stress-strain relationship, and Heckel, Kawakita and Walker equations. Compaction studies were performed on a fully instrumented rotary tabletting machine. CTC analysis revealed that the γ-form has increased compressibility while the α-form showed greater compactibility. The α-form also showed increased tabletability over the γ-form at all the compaction pressures. Lower values of Py (Heckel parameter) and 1/b (Kawakita parameter) indicated increased deformation behavior of γ-form. Stress-strain analysis also supports the increased compressibility of γ-form. In addition, Walker analysis showed higher compressibility coefficient (W) for α-form, consistent with its greater tabletability. Thus, tabletability of IMC polymorphs was governed by the compactibility of the material. Detailed examination of crystallographic data revealed that the presence of a slip plane system in the γ-form offered it increased compressibility and deformation behavior. However, the α-form showed greater compactibility by virtue of closer molecular packing (higher true density). Hence, although direct correlation between tabletability and the presence of slip planes in the crystals has been reported, prediction solely based on this crystallographic feature must be avoided. The present work reiterates the influence of the crystal packing on the tabletability of the pharmaceutical polymorphs. PMID:23301663

  17. Single Nucleotide Polymorphisms Predict Symptom Severity of Autism Spectrum Disorder

    ERIC Educational Resources Information Center

    Jiao, Yun; Chen, Rong; Ke, Xiaoyan; Cheng, Lu; Chu, Kangkang; Lu, Zuhong; Herskovits, Edward H.

    2012-01-01

    Autism is widely believed to be a heterogeneous disorder; diagnosis is currently based solely on clinical criteria, although genetic, as well as environmental, influences are thought to be prominent factors in the etiology of most forms of autism. Our goal is to determine whether a predictive model based on single-nucleotide polymorphisms (SNPs)…

  18. Bulk segregant analysis using single nucleotide polymorphism microarrays

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Bulk segregant analysis using microarrays, and extreme array mapping have recently been used to rapidly identify genomic regions associated with phenotypes in multiple species. These experiments, however require the identification of single feature polymorphisms between the cross parents for each ne...

  19. Sleep and COMT Polymorphism in ADHD Children: Preliminary Actigraphic Data

    ERIC Educational Resources Information Center

    Gruber, Reut; Grizenko, Natalie; Schwartz, George; Amor, Leila Ben; Gauthier, Julie; de Guzman, Rosherrie; Joober, Ridha

    2006-01-01

    Objective: To examine whether COMT (catechol-O-methyltransferase) polymorphism modulates aspects of sleep in children diagnosed with attention-deficit/hyperactivity disorder (ADHD). Method: Nightly sleep actigraphic recordings during a double-blind, placebo-controlled, crossover clinical study (1 week of 0.5 mg/kg MPH; 1 week of placebo) were…

  20. A Laboratory Exercise for Genotyping Two Human Single Nucleotide Polymorphisms

    ERIC Educational Resources Information Center

    Fernando, James; Carlson, Bradley; LeBard, Timothy; McCarthy, Michael; Umali, Finianne; Ashton, Bryce; Rose, Ferrill F., Jr.

    2016-01-01

    The dramatic decrease in the cost of sequencing a human genome is leading to an era in which a wide range of students will benefit from having an understanding of human genetic variation. Since over 90% of sequence variation between humans is in the form of single nucleotide polymorphisms (SNPs), a laboratory exercise has been devised in order to…

  1. Polymorphism among EST-based markers in tomato

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cultivated tomato (Lycopersicon esculentum Mill.) has a narrow genetic base. This is in part due to population genetic processes such as founder events, genetic bottlenecks, and natural and artificial selection during domestication. We characterize the nucleotide polymorphism in 26 EST-based markers...

  2. Discovery, Validation and Characterization of 1039 Cattle Single Nucleotide Polymorphisms

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We identified approximately 13000 putative single nucleotide polymorphisms (SNPs) by comparison of repeat-masked BAC-end sequences from the cattle RPCI-42 BAC library with whole-genome shotgun contigs of cattle genome assembly Btau 1.0. Genotyping of a subset of these SNPs was performed on a panel ...

  3. PEROXIDASE GENE POLYMORPHISM IN BUFFALOGRASS AND OTHER GRASSES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Plant peroxidases are a family of related proteins possessing highly conserved domains. Degenerate oligonucleotide primers based on these conserved domains can be used to amplify DNA sequences coding for peroxidases from plants with unsequenced genomes. Polymorphisms in peroxidase genes among buffa...

  4. High polymorphism at microsatellite loci in the Chinese donkey.

    PubMed

    Zhang, R F; Xie, W M; Zhang, T; Lei, C Z

    2016-01-01

    To reveal the genetic diversity and phylogenetic relationships between Chinese donkey breeds, 415 individuals representing ten breeds were investigated using ten microsatellite markers. The observed number of alleles, mean effective number of alleles (NE), mean expected heterozygosity (HE), and polymorphic information content (PIC) of each breed and polymorphic locus were analyzed. The results showed that seven (HTG7, HTG10, AHT4, HTG6, HMS6, HMS3, and HMS7) of ten microsatellite loci were polymorphic. The mean PIC, HE, and NE of seven polymorphic loci for the ten donkey breeds were 0.7679, 0.8072, and 6.0275, respectively. These results suggest that domestic Chinese donkey breeds possess higher levels of genetic diversity and heterozygosity than foreign donkeys. A neighbor-joining tree based on Nei's standard genetic distance showed that there was close genetic distance among Xinjiang, Qingyang, Xiji, and Guanzhong donkey breeds. In addition, Mongolia and Dezhou donkey breeds were placed in the same category. The phylogenetic tree revealed that the genetic relationships between Chinese donkey breeds are consistent with their geographic distribution and breeding history. PMID:27420967

  5. Development of a fingerprinting panel using medically relevant polymorphisms

    PubMed Central

    Cross, Deanna S; Ivacic, Lynn C; McCarty, Catherine A

    2009-01-01

    Background For population based biorepositories to be of use, rigorous quality control and assurance must be maintained. We have designed and validated a panel of polymorphisms for individual sample identification consisting of 36 common polymorphisms that have been implicated in a wide range of diseases and an additional sex marker. This panel uniquely identifies our biorepository of approximately 20,000 samples and would continue to uniquely identify samples in biorepositories of over 100 million samples. Methods A panel of polymorphisms associated with at least one disease state in multiple populations was constructed using a cut-off of 0.20 or greater confirmed minor allele frequency in a European Caucasian population. The fingerprinting assay was tested using the MALDI-TOF mass spectrometry method of allele determination on a Sequenom platform with a panel of 28 Caucasian HapMap samples; the results were compared with known genotypes to ensure accuracy. The frequencies of the alleles were compared to the expected frequencies from dbSNP and any genotype that did not achieve Hardy Weinberg equilibrium was excluded from the final assay. Results The final assay consisted of the AMG sex marker and 36 medically relevant polymorphisms with representation on each chromosome, encompassing polymorphisms on both the Illumina 550K bead array and the Affymetrix 6.0 chip (with over a million polymorphisms) platform. The validated assay has a P(ID) of 6.132 × 10-15 and a Psib(ID) of 3.077 × 10-8. This assay allows unique identification of our biorepository of 20,000 individuals as well and ensures that as we continue to recruit individuals they can be uniquely fingerprinted. In addition, diseases such as cancer, heart disease diabetes, obesity, and respiratory disease are well represented in the fingerprinting assay. Conclusion The polymorphisms in this panel are currently represented on a number of common genotyping platforms making QA/QC flexible enough to accommodate a

  6. Do polymorphisms in chemosensory genes matter for human ingestive behavior?

    PubMed Central

    Hayes, John E.; Feeney, Emma L.; Allen, Alissa L.

    2013-01-01

    In the last decade, basic research in chemoreceptor genetics and neurobiology have revolutionized our understanding of individual differences in chemosensation. From an evolutionary perspective, chemosensory variations appear to have arisen in response to different living environments, generally in the avoidance of toxins and to better detect vital food sources. Today, it is often assumed that these differences may drive variable food preferences and choices, with downstream effects on health and wellness. A growing body of evidence indicates chemosensory variation is far more complex than previously believed. However, just because a genetic polymorphism results in altered receptor function in cultured cells or even behavioral phenotypes in the laboratory, this variation may not be sufficient to influence food choice in free living humans. Still, there is ample evidence to indicate allelic variation in TAS2R38 predicts variation in bitterness of synthetic pharmaceuticals (e.g., propylthiouracil) and natural plant compounds (e.g., goitrin), and this variation associates with differential intake of alcohol and vegetables. Further, this is only one of 25 unique bitter taste genes (TAS2Rs) in humans, and emerging evidence suggests other TAS2Rs may also contain polymorphisms that a functional with respect to ingestive behavior. For example, TAS2R16 polymorphisms are linked to the bitterness of naturally occurring plant compounds and alcoholic beverage intake, a TAS2R19 polymorphism predicts differences in quinine bitterness and grapefruit bitterness and liking, and TAS2R31 polymorphisms associate with differential bitterness of plant compounds like aristolochic acid and the sulfonyl amide sweeteners saccharin and acesulfame-K. More critically with respect to food choices, these polymorphisms may vary independently from each other within and across individuals, meaning a monolithic one-size-fits-all approach to bitterness needs to be abandoned. Nor are genetic

  7. Do polymorphisms in chemosensory genes matter for human ingestive behavior?

    PubMed

    Hayes, John E; Feeney, Emma L; Allen, Alissa L

    2013-12-01

    In the last decade, basic research in chemoreceptor genetics and neurobiology have revolutionized our understanding of individual differences in chemosensation. From an evolutionary perspective, chemosensory variations appear to have arisen in response to different living environments, generally in the avoidance of toxins and to better detect vital food sources. Today, it is often assumed that these differences may drive variable food preferences and choices, with downstream effects on health and wellness. A growing body of evidence indicates chemosensory variation is far more complex than previously believed. However, just because a genetic polymorphism results in altered receptor function in cultured cells or even behavioral phenotypes in the laboratory, this variation may not be sufficient to influence food choice in free living humans. Still, there is ample evidence to indicate allelic variation in TAS2R38 predicts variation in bitterness of synthetic pharmaceuticals (e.g., propylthiouracil) and natural plant compounds (e.g., goitrin), and this variation associates with differential intake of alcohol and vegetables. Further, this is only one of 25 unique bitter taste genes (TAS2Rs) in humans, and emerging evidence suggests other TAS2Rs may also contain polymorphisms that a functional with respect to ingestive behavior. For example, TAS2R16 polymorphisms are linked to the bitterness of naturally occurring plant compounds and alcoholic beverage intake, a TAS2R19 polymorphism predicts differences in quinine bitterness and grapefruit bitterness and liking, and TAS2R31 polymorphisms associate with differential bitterness of plant compounds like aristolochic acid and the sulfonyl amide sweeteners saccharin and acesulfame-K. More critically with respect to food choices, these polymorphisms may vary independently from each other within and across individuals, meaning a monolithic one-size-fits-all approach to bitterness needs to be abandoned. Nor are genetic

  8. Mutations and a polymorphism in the tuberin gene

    SciTech Connect

    Northup, H.; Rodriguez, J.A.; Au, K.S.; Rodriguez, E.

    1994-09-01

    Two deletions and a polymorphism have been identified in the recently described tuberin gene. The tuberin gene (designated TSC2) when mutated causes tuberous sclerosis complex (TSC). Fifty-three affected individuals (30 from families with multiple affected and 23 isolated cases) were screened with the tuberin cDNA for gross deletions or rearrangements. Both deletions were found in families with multiple affected members (family designations: HOU-5 and HOU-22). The approximate size of the deletion in HOU-5 is ten kilobases and eliminates a BamHI restriction site. The deletion includes a portion of the 5{prime} half of the tuberin cDNA. The deletion in HOU-22 occurs in the 3{prime} half of the gene. The deletions are being further characterized. A HindIII restriction site polymorphism was detected by a 0.5 kilobase probe from the 5{prime} coding region of the tuberin gene in an individual from a family linked to chromosome 9 (posterior probability of linkage 93%). The polymorphism did not segregate with TSC in the family. The family had previously been shown to give negative results with multiple markers on chromosome 16. The polymorphism was also seen in one individual among a panel of 20 randomly selected unaffected individuals. Thirty-five additional affected probands (five from families and 30 isolated cases) are being tested with the tuberin cDNA. Testing for subtle mutations is our panel of 80 affected probands is underway utilizing SSCP. Additional mutations or polymorphisms detected will be reported. The tuberin cDNA was a kind gift of The European Chromosome 16 Tuberous Sclerosis Consortium.

  9. CC chemokine receptor 5 gene polymorphisms in beryllium disease.

    PubMed

    Sato, H; Silveira, L; Spagnolo, P; Gillespie, M; Gottschall, E B; Welsh, K I; du Bois, R M; Newman, L S; Maier, L A

    2010-08-01

    CC chemokine receptor 5 (CCR5) is expressed on type-1 T-helper cells, which are involved in the pathogenesis of the granulomatous lung disease chronic beryllium disease (CBD). CCR5 gene (CCR5) polymorphisms are associated with sarcoidosis severity. The present study explores associations between CCR5 polymorphisms and CBD and its disease progression. Eight CCR5 polymorphisms were genotyped in CBD (n = 88), beryllium sensitisation (BeS; n = 86) and beryllium-exposed nondiseased controls (n = 173) using PCR with sequence-specific primers. Pulmonary function and bronchoalveolar lavage data were examined for associations with genotypes. There were no significant differences in genotype and allele frequency between CBD, BeS individuals and controls. In CBD, associations were found with decline in forced expiratory volume in 1 s and forced vital capacity and the CCR5 -3458 thymidine (T)T genotype (p<0.0001), and an increase in alveolar-arterial oxygen tension difference at rest (p = 0.003) and at maximum exercise (p = 0.01) and the -5663 adenine allele. Increased bronchoalveolar lavage lymphocyte numbers were associated with CCR5 -2459 guanine/-2135T (p = 0.01) only in the combined CBD and BeS group. This is the first study showing that CCR5 polymorphisms are associated with worsening pulmonary function over time in CBD, suggesting that CCR5 is important in the progression of pulmonary function in CBD. Further studies would be useful to clarify the mechanism whereby CCR5 polymorphisms affect progression of CBD. PMID:20075058

  10. The interleukin-1 family gene polymorphisms and Graves' disease.

    PubMed

    Khalilzadeh, O; Anvari, M; Esteghamati, A; Momen-Heravi, F; Mahmoudi, M; Rashidi, A; Amiri, H M; Ranjbar, M; Tabataba-Vakili, S; Amirzargar, A

    2010-09-01

    Genetic factors, including cytokine gene polymorphisms, are potential contributors to the pathogenesis of the Graves' disease (GD). We attempted in this study to determine the association between GD and the following polymorphisms in the interleukin-1 (IL-1) family genes: IL-1alpha (-889C/T), IL-1ss (-511C/T), IL-1ss (+3962C/T), IL-1R (Pst-1 1970C/T) and IL-1RA (Mspa-I 11100C/T). We studied 107 patients with an established diagnosis of GD and 140 healthy controls. Cytokine typing was performed by the polymerase chain reaction with sequence-specific primers assay. Genotype distributions among patients were in Hardy-Weinberg equilibrium for all polymorphisms. The frequency of the IL-1alpha -889T allele was significantly higher in patients than in controls (51.9% vs. 31.6%, OR=2.33, 95% CI=1.61-3.38; p<0.0001). The IL-1RA Msp-I 11100C allele was significantly more frequent in patients than in controls (50.0% vs. 22.9%, OR=3.38, 95% CI=2.29-4.97, p<0.0001). No significant associations were found for other polymorphisms. Although the IL-1 family has well-known roles in GD pathogenesis, the contributions of their genetic variations to the disease are unclear. In this study, we documented a highly significant association between GD and polymorphism in IL-1alpha and IL-1RA genes. Further studies in other populations are necessary to confirm our results. PMID:20400062

  11. Habitat-based polymorphism is common in stream fishes.

    PubMed

    Senay, Caroline; Boisclair, Daniel; Peres-Neto, Pedro R

    2015-01-01

    Morphological differences (size and shape) across habitats are common in lake fish where differences relate to two dominant contrasting habitats: the pelagic and littoral habitat. Repeated occurrence of littoral and pelagic morphs across multiple populations of several lake fish species has been considered as important evidence that polymorphism is adaptive in these systems. It has been suggested that these habitat-based polymorphic differences are due to the temporal stability of the differences between littoral and pelagic habitats. Although streams are spatially heterogeneous, they are also more temporally dynamic than lakes and it is still an open question whether streams provide the environmental conditions that promote habitat-based polymorphism. We tested whether fish from riffle, run and pool habitats, respectively, differed consistently in their morphology. Our test compared patterns of morphological variation (size and shape) in 10 fish species from the three stream habitat types in 36 separate streams distributed across three watersheds. For most species, body size and shape (after controlling for body size) differed across riffle, run and pool habitats. Unlike many lake species, the nature of these differences was not consistent across species, possibly because these species use these habitat types in different ways. Our results suggest that habitat-based polymorphism is an important feature also in stream fishes despite the fact that streams are temporally variable in contrast to lake systems. Future research is required to assess whether the patterns of habitat-based polymorphism encountered in streams have a genetic basis or they are simply the result of within generation phenotypic plasticity. PMID:25041645

  12. Polymorphic minisatellites in the mitochondrial DNAs of Oryza and Brassica.

    PubMed

    Honma, Yujiro; Yoshida, Yu; Terachi, Toru; Toriyama, Kinya; Mikami, Tetsuo; Kubo, Tomohiko

    2011-08-01

    Polymorphic analyses of angiosperm mitochondrial DNA are rare in comparison with chloroplast DNA, because few target sequences in angiosperm mitochondrial DNA are known. Minisatellites, a tandem array of repeated sequences with a repeat unit of 10 to ~100 bp, are popular target sequences of animal mitochondria, but Beta vulgaris is the only known angiosperm species for which such an analysis has been conducted. From this lack of information, it was uncertain as to whether polymorphic minisatellites existed in other angiosperm species. Ten plant mitochondrial DNAs were found to contain minisatellite-like repeated sequences, most of which were located in intergenic regions but a few occurred in gene coding and intronic regions. Oryza and Brassica accessions were selected as models for the investigation of minisatellite polymorphism because substantial systematic information existed. PCR analysis of 42 Oryza accessions revealed length polymorphisms in four of the five minisatellites. The mitochondrial haplotypes of the 16 Oryza accessions with chromosomal complement (genome) types of CC, BBCC and CCDD were identical but were clearly distinguished from BB-genome accessions, a result consistent with the notion that the cytoplasmic donor parent of the amphidiploid species might be the CC-genome species. Twenty-nine accessions of six major cultivated species of Brassica were classified into five mitochondrial haplotypes based on two polymorphic minisatellites out of six loci. The haplotypes of Brassica juncea and Brassica carinata accessions were identical to Brassica rapa and Brassica nigra accessions, respectively. The haplotypes of Brassica napus accessions were heterogeneous and unique, results that were consistent with previous studies. PMID:21562713

  13. BRCA1 polymorphism in breast cancer patients from Argentina

    PubMed Central

    JAURE, OMAR; ALONSO, ELIANA N.; BRAICO, DIEGO AGUILERA; NIETO, ALVARO; OROZCO, MANUELA; MORELLI, CECILIA; FERRO, ALEJANDRO M.; BARUTTA, ELENA; VINCENT, ESTEBAN; MARTÍNEZ, DOMINGO; MARTÍNEZ, IGNACIO; MAEGLI, MARIA INES; FRIZZA, ALEJANDRO; KOWALYZYN, RUBEN; SALVADORI, MARISA; GINESTET, PAUL; GONZALEZ DONNA, MARIA L.; BALOGH, GABRIELA A.

    2015-01-01

    Breast cancer is the most common type of cancer in females in Argentina, with an incidence rate similar to that in the USA. However, the contribution of the BRCA1 or BRCA2 mutation in breast cancer incidence has not yet been investigated in Argentina. In order to evaluate which BRCA1 polymorphisms or mutations characterize female breast cancer in Argentina, the current study enrolled 206 females with breast cancer from several hospitals from the southeast of Argentina. A buccal smear sample was obtained in duplicate from each patient and the DNA samples were processed for polymorphism analysis using the single-strand conformational polymorphism technique. The polymorphisms in BRCA1 were investigated using a combination of 15 primers to analyze exons 2, 3, 5, 20 and 11 (including the 11.1 to 11.12 regions). The BRCA1 mutations were confirmed by direct sequencing. Samples were successfully examined from 154 females and, among these, 16 mutations were identified in the BRCA1 gene representing 13.9% of the samples analyzed. One patient was identified with a polymorphism in exon 2 (0.86%), four in exon 20 (3.48%), four in exon 11.3 (3.48%), one in exon 11.7 (0.86%), two in exon 11.8 (1.74%), one in exon 11.10 (0.86%) and one in exon 11.11 (0.86%). The most prevalent alteration in BRCA1 was located in exon 11 (11 out of 16 patients; 68.75%). The objective of our next study is to evaluate the prevalence of mutations in the BRCA2 gene and analyze the BRCA1 gene in the healthy relatives of BRCA1 mutation carriers. PMID:25624909

  14. A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads.

    PubMed

    Kang, Houxiang; Zhu, Dan; Lin, Runmao; Opiyo, Stephen Obol; Jiang, Ning; Shiu, Shin-Han; Wang, Guo-Liang

    2016-06-01

    Identification of polymorphic transposable elements (TEs) is important because TE polymorphism creates genetic diversity and influences the function of genes in the host genome. However, de novo scanning of polymorphic TEs remains a challenge. Here, we report a novel computational method, called PTEMD (polymorphic TEs and their movement detection), for de novo discovery of genome-wide polymorphic TEs. PTEMD searches highly identical sequences using reads supported breakpoint evidences. Using PTEMD, we identified 14 polymorphic TE families (905 sequences) in rice blast fungus Magnaporthe oryzae, and 68 (10,618 sequences) in maize. We validated one polymorphic TE family experimentally, MoTE-1; all MoTE-1 family members are located in different genomic loci in the three tested isolates. We found that 57.1% (8 of 14) of the PTEMD-detected polymorphic TE families in M. oryzae are active. Furthermore, our data indicate that there are more polymorphic DNA transposons in maize than their counterparts of retrotransposons despite the fact that retrotransposons occupy largest fraction of genomic mass. We demonstrated that PTEMD is an effective tool for identifying polymorphic TEs in M. oryzae and maize genomes. PTEMD and the genome-wide polymorphic TEs in M. oryzae and maize are publically available at http://www.kanglab.cn/blast/PTEMD_V1.02.htm. PMID:27098848

  15. A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads

    PubMed Central

    Kang, Houxiang; Zhu, Dan; Lin, Runmao; Opiyo, Stephen Obol; Jiang, Ning; Shiu, Shin-Han; Wang, Guo-Liang

    2016-01-01

    Identification of polymorphic transposable elements (TEs) is important because TE polymorphism creates genetic diversity and influences the function of genes in the host genome. However, de novo scanning of polymorphic TEs remains a challenge. Here, we report a novel computational method, called PTEMD (polymorphic TEs and their movement detection), for de novo discovery of genome-wide polymorphic TEs. PTEMD searches highly identical sequences using reads supported breakpoint evidences. Using PTEMD, we identified 14 polymorphic TE families (905 sequences) in rice blast fungus Magnaporthe oryzae, and 68 (10,618 sequences) in maize. We validated one polymorphic TE family experimentally, MoTE-1; all MoTE-1 family members are located in different genomic loci in the three tested isolates. We found that 57.1% (8 of 14) of the PTEMD-detected polymorphic TE families in M. oryzae are active. Furthermore, our data indicate that there are more polymorphic DNA transposons in maize than their counterparts of retrotransposons despite the fact that retrotransposons occupy largest fraction of genomic mass. We demonstrated that PTEMD is an effective tool for identifying polymorphic TEs in M. oryzae and maize genomes. PTEMD and the genome-wide polymorphic TEs in M. oryzae and maize are publically available at http://www.kanglab.cn/blast/PTEMD_V1.02.htm. PMID:27098848

  16. Formation of β Polymorphs in Milk Fats with Large Differences in Triacylglycerol Profiles.

    PubMed

    Tzompa-Sosa, Daylan A; Ramel, Pere R; van Valenberg, Hein J F; van Aken, George A

    2016-05-25

    In this study, we characterized the polymorphism of milk fat (MF) with various TAG compositions during isothermal crystallization at 20 °C. TAG composition of MF from seven individual cows was determined using GC-FID and MALDI-TOF MS, and MF polymorphism was studied using X-ray diffraction. Results showed that TAG profile determines the polymorphic behavior of MF. Saturated TAG with carbon numbers 34-38 promoted the formation of α polymorphs, whereas unsaturated TAG with 52-54 promoted the formation of the β polymorphs. Furthermore, MFs with unsaturated fatty acid profiles were increased in unsaturated TAG with 52-54 carbons. The presence of MF crystals in the β polymorph has been controversial over the years as most authors mainly find MF crystals in the α and β' form. In our work, we showed that the β polymorph is formed in MF on the basis of its TAG composition. PMID:27121766

  17. Genetic polymorphism of toll-like receptors 4 gene by polymerase chain reaction-restriction fragment length polymorphisms, polymerase chain reaction-single-strand conformational polymorphism to correlate with mastitic cows

    PubMed Central

    Gupta, Pooja H.; Patel, Nirmal A.; Rank, D. N.; Joshi, C. G.

    2015-01-01

    Aim: An attempt has been made to study the toll-like receptors 4 (TLR4) gene polymorphism from cattle DNA to correlate with mastitis cows. Materials and Methods: In present investigation, two fragments of TLR4 gene named T4CRBR1 and T4CRBR2 of a 316 bp and 382 bp were amplified by polymerase chain reaction (PCR), respectively from Kankrej (22) and Triple cross (24) cattle. The genetic polymorphisms in the two populations were detected by a single-strand conformational polymorphism in the first locus and by digesting the fragments with restriction endonuclease Alu I in the second one. Results: Results showed that both alleles (A and B) of two loci were found in all the two populations and the value of polymorphism information content indicated that these were highly polymorphic. Statistical results of χ2 test indicated that two polymorphism sites in the two populations fit with Hardy–Weinberg equilibrium (p<0.05). Meanwhile, the effect of polymorphism of TLR4 gene on the somatic cell score (SCS) indicated the cattle with allele a in T4CRBR1 showed lower SCS than that of allele B (p<0.05). Thus, the allele A might play an important role in mastitis resistance in cows. Conclusion: The relationship between the bovine mastitis trait and the polymorphism of TLR4 gene indicated that the bovine TLR4 gene may play an important role in mastitis resistance. PMID:27047144

  18. Cerebral Baylisascaris larva migrans in a cynomolgus macaque (Macaca fascicularis).

    PubMed

    Shoieb, Ahmed; Radi, Zaher A

    2014-08-01

    An incidental, asymptomatic, focal inflammatory lesion was detected in brain cerebrum of an approximately 6-year-old, female cynomolgus macaque from a chronic toxicology study. No gross lesions were noted at necropsy. Microscopically, the lesion contained a cross-section of larvae approximately 70-80 μm in diameter, a centrally located intestine flanked on either side by large triangular excretory columns, and prominent single lateral cuticular alae. Mixed inflammatory cells of eosinophils, macrophages, and lymphocytes admixed with abundant connective tissue stroma and necrosis surrounded the larvae. Histochemical stains for trichrome revealed significant amount of fibrous connective tissue. The morphology of the larvae was compatible with Baylisascaris spp. Based on the microscopic and histochemical examination, a diagnosis of neural Baylisascaris spp. larva migrans was made. PMID:24795276

  19. Tracking cells implanted into cynomolgus monkeys (Macaca fascicularis) using MRI.

    PubMed

    Ito-Fujishiro, Yasuyo; Koie, Hiroshi; Shibata, Hiroaki; Okabayashi, Sachi; Katakai, Yuko; Ohno, Chieko; Kanayama, Kiichi; Yasutomi, Yasuhiro; Ageyama, Naohide

    2016-07-29

    Regenerative therapy with stem cell transplantation is used to treat various diseases such as coronary syndrome and Buerger's disease. For instance, stem-cell transplantation into the infarcted myocardium is an innovative and promising strategy for treating heart failure due to ischemic heart disease. Basic studies using small animals have shown that transplanted cells improve blood flow in the infarcted region. Magnetic resonance imaging (MRI) can noninvasively identify and track transplanted cells labeled with superparamagnetic iron oxide (SPIO). Although clinical regenerative therapies have been clinically applied to patients, the fate of implanted cells remains unknown. In addition, follow-up studies have shown that some adverse events can occur after recovery. Therefore, the present study evaluated the ability of MRI using a 3T scanner to track implanted peripheral blood mononuclear cells labeled with SPIO on days 0 and 7 after intramuscular (i.m.) and intravenous (i.v.) injection into a cynomolgus monkey. Labeled cells were visualized at the liver and triceps surae muscle on MR images using T1- and T2-weighted sequences and histologically localized by Prussian blue staining. The transplanted cells were tracked without abnormal clinical manifestations throughout this study. Hence, MRI of cynomolgus monkey transplanted SPIO-labeled cells is a safe and efficient method of tracking labeled cells that could help to determine the mechanisms involved in regenerative therapy. PMID:27062993

  20. Tracking cells implanted into cynomolgus monkeys (Macaca fascicularis) using MRI

    PubMed Central

    Ito-Fujishiro, Yasuyo; Koie, Hiroshi; Shibata, Hiroaki; Okabayashi, Sachi; Katakai, Yuko; Ohno, Chieko; Kanayama, Kiichi; Yasutomi, Yasuhiro; Ageyama, Naohide

    2016-01-01

    Regenerative therapy with stem cell transplantation is used to treat various diseases such as coronary syndrome and Buerger’s disease. For instance, stem-cell transplantation into the infarcted myocardium is an innovative and promising strategy for treating heart failure due to ischemic heart disease. Basic studies using small animals have shown that transplanted cells improve blood flow in the infarcted region. Magnetic resonance imaging (MRI) can noninvasively identify and track transplanted cells labeled with superparamagnetic iron oxide (SPIO). Although clinical regenerative therapies have been clinically applied to patients, the fate of implanted cells remains unknown. In addition, follow-up studies have shown that some adverse events can occur after recovery. Therefore, the present study evaluated the ability of MRI using a 3T scanner to track implanted peripheral blood mononuclear cells labeled with SPIO on days 0 and 7 after intramuscular (i.m.) and intravenous (i.v.) injection into a cynomolgus monkey. Labeled cells were visualized at the liver and triceps surae muscle on MR images using T1- and T2-weighted sequences and histologically localized by Prussian blue staining. The transplanted cells were tracked without abnormal clinical manifestations throughout this study. Hence, MRI of cynomolgus monkey transplanted SPIO-labeled cells is a safe and efficient method of tracking labeled cells that could help to determine the mechanisms involved in regenerative therapy. PMID:27062993

  1. Spectral sensitivity of cones of the monkey Macaca fascicularis.

    PubMed Central

    Baylor, D A; Nunn, B J; Schnapf, J L

    1987-01-01

    1. Spectral sensitivities of cones in the retina of cynomolgus monkeys were determined by recording photocurrents from single outer segments with a suction electrode. 2. The amplitude and shape of the response to a flash depended upon the number of photons absorbed but not the wave-length, so that the 'Principle of Univariance' was obeyed. 3. Spectra were obtained from five 'blue', twenty 'green', and sixteen 'red' cones. The wave-lengths of maximum sensitivity were approximately 430, 531 and 561 nm, respectively. 4. The spectra of the three types of cones had similar shapes when plotted on a log wave number scale, and were fitted by an empirical expression. 5. There was no evidence for the existence of subclasses of cones with different spectral sensitivities. Within a class, the positions of the individual spectra on the wave-length axis showed a standard deviation of less than 1.5 nm. 6. Psychophysical results on human colour matching (Stiles & Burch, 1955; Stiles & Burch, 1959) were well predicted from the spectral sensitivities of the monkey cones. After correction for pre-retinal absorption and pigment self-screening, the spectra of the red and green cones matched the respective pi 5 and pi 4 mechanisms of Stiles (1953, 1959). PMID:3443931

  2. Visual transduction in cones of the monkey Macaca fascicularis.

    PubMed Central

    Schnapf, J L; Nunn, B J; Meister, M; Baylor, D A

    1990-01-01

    1. Visual transduction in macaque cones was studied by measuring the membrane current of single outer segments projecting from small pieces of retina. 2. The response to a brief flash of light was diphasic and resembled the output of a bandpass filter with a peak frequency near 5 Hz. After the initial reduction in dark current there was a rebound increase which resulted from an increase in the number of open light-sensitive channels. The response to a step of light consisted of a prominent initial peak followed by a steady phase of smaller amplitude. 3. Responses to dim light were linear and time-invariant, suggesting that responses to single photons were linearly additive. From the flash sensitivity and the effective collecting area the peak amplitude of the single photon response was estimated as about 30 fA. 4. With flashes of increasing strength the photocurrent amplitude usually saturated along a curve that was gentler than an exponential but steeper than a Michaelis relation. The response reached the half-saturating amplitude at roughly 650 photoisomerizations. 5. The response-intensity relation was flatter in the steady state than shortly after a light step was turned on, indicating that bright light desensitized the transduction with a delay. This desensitization was not due to a reduction in pigment content. In the steady state, a background of intensity I lowered the sensitivity to a weak incremental test flash by a factor 1/(1 + I/IO), where IO was about 2.6 x 10(4) photoisomerizations s-1, or about 3.3 log trolands for the red- and green-sensitive cones. 6. Bleaching exposures produced permanent reductions in flash sensitivity but had little effect on the kinetics or saturating amplitude of subsequent flash responses. The sensitivity reductions were consistent with the expected reductions in visual pigment content and gave photosensitivities of about 8 x 10(-9) microns2 (free solution value) for the red- and green-sensitive pigments. During a steady bleaching exposure the final exponential decline of the photocurrent had a rate constant given by the product of the light intensity and the photosensitivity. 7. In some cells it was possible to measure a light-induced increase in current noise. The power spectrum of the noise resembled the spectrum of the dim flash response and the magnitude of the noise was consistent with a single photon response roughly 20 fA in size. 8. The membrane current recorded in darkness was noisy, with a variance near 0.12 pA2 in the band 0-20 Hz.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:2100987

  3. Mapping of mitochondrial ferritin in the brainstem of Macaca fascicularis.

    PubMed

    Yang, Mingchun; Yang, Hongkuan; Guan, Hongpeng; Bellier, Jean-Pierre; Zhao, Shiguang; Tooyama, Ikuo

    2016-07-22

    Mitochondrial ferritin (FtMt), a recently-studied iron storage protein, which we suspect is an important defense against oxidative stress in neurons and elsewhere. The 242-amino acid FtMt precursor protein is cleaved to mature protein (of molecular weight about 22-kDa) in the mitochondrial matrix. Compared with the ubiquitously expressed traditional ferritin (H-ferritin and L-ferritin), FtMt has been found in fewer locations including the testis, heart and brain. Previous studies have reported that the expression of FtMt in mouse and human brain is predominantly localized to neurons and partly to glial cells, and FtMt exerts protective effects on neurons by maintaining normal function and regulates apoptosis in Alzheimer's disease and Parkinson's disease. To find out the function of FtMt in neurodegenerative disease, we had a novel antibody made against human FtMt and characterized it via Western blot analysis, immunoabsorption testing, and double immunofluorescence histochemistry. Then we used this new FtMt antibody to map the distribution of FtMt in the monkey brainstem. We demonstrated widespread distribution of FtMt immunoreactivity throughout the monkey brainstem, with variable staining intensity. FtMt immunoreactivity was observed in the extrapyramidal system, sensory trigeminal nerve nuclei, some motor nuclei including ambiguous nucleus, dorsal motor nucleus of the vagus and hypoglossal nucleus, and some dorsal column nuclei such as the gracile nucleus and cuneate nucleus. In addition, double immunohistochemical stainings confirmed that FtMt immunoreactivity was co-localized with catecholaminergic neurons in the locus coeruleus (63.64%), substantia nigra pars compacta (69.18%), and ventral tegmental area (56.89%). The distribution of FtMt which we found in the brainstem implies possible involvement of FtMt in several physiological mechanisms, especially in the catecholaminergic neurons, and the possibility of significant involvement in neurodegenerative disease. PMID:27133573

  4. Reaching and grasping behavior in Macaca fascicularis: a kinematic study.

    PubMed

    Sartori, Luisa; Camperio Ciani, Andrea; Bulgheroni, Maria; Castiello, Umberto

    2013-01-01

    The prehensile hand is one of the major traits distinguishing primates from other mammal species. All primates, in fact, are able to grasp an object and hold it in part or entirely using a single hand. Although there is a wealth of behavioral data regarding grasping movements in humans and apes, there is relatively little material on macaques, the animal model often used to investigate neuronal mechanisms responsible for grip control in humans. To date, evidence regarding free-ranging macaques is confined to observational data, while quantitative reports describe studies carried out in laboratory settings or in captivity. The purpose of the present study was to provide the first kinematic descriptions of basic grip behavior with regard to precision and power grips in free-ranging macaque monkeys. Video footage of those animals grasping objects was analyzed frame-by-frame using digitalization techniques. The results revealed that the two types of grips considered are each characterized by specific kinematic signatures. It was also found that hand kinematics was scaled depending on the type of grasp needing to be adopted and the intrinsic properties of the object to be grasped. In accordance with data concerning humans, these findings indicate that the intrinsic features of an object affect the planning and control of reach-to-grasp movements even in free-ranging macaques. The data presented here take research in the field of comparative reach-to-grasp kinematics in human and non-human primates another step forward as they are based on precise measurements of spontaneous grasping movements by animals living/acting in their natural environment. PMID:23064847

  5. '1-Antitrypsin polymorphism and systematics of eastern North American wolves

    USGS Publications Warehouse

    Mech, L.D.; Federoff, N.E.

    2002-01-01

    We used data on the polymorphic status of '1-antitrypsin ('1AT) to study the relationship of Minnesota wolves to the gray wolf (Canis lupus), which was thought to have evolved in Eurasia, and to red wolves (Canis rufus) and coyotes (Canis latrans), which putatively evolved in North America. Recent evidence had indicated that Minnesota wolves might be more closely related to red wolves and coyotes. Samples from wild-caught Minnesota wolves and from captive wolves, at least some of which originated in Alaska and western Canada, were similarly polymorphic for '1AT, whereas coyote and red wolf samples were all monomorphic. Our findings, in conjunction with earlier results, are consistent with the Minnesota wolf being a gray wolf of Eurasian origin or possibly a hybrid between the gray wolf of Eurasian origin and the proposed North American wolf.

  6. Latitude-correlated genetic polymorphisms: selection or gene flow?

    PubMed

    Ciminelli, B M; Jodice, C; Scozzari, R; Corbo, R M; Nahum, M; Pompei, F; Santachiara-Benerecetti, S A; Santolamazza, C; Morpurgo, G P; Modiano, G

    2000-08-01

    Latitude-correlated polymorphisms can be due to either selection-driven evolution or gene flow. To discriminate between them, we propose an approach that studies subpopulations springing from a single population that have lived for generations at different latitudes and have had a low genetic admixture. These requirements are fulfilled to a large extent by Ashkenazi and Sephardi Jews. The original population lived at a latitude of 35 degrees N, where the Sephardis still live. The Ashkenazis, however, moved to a latitude of 50 degrees N, starting about 10 centuries ago. The present study examines 3 latitude-correlated polymorphisms: PGP, PGM1, and AHSG. We found that PGP*2 and AHSG*2 alleles most likely underwent selection-driven evolution, but that PGM1*ts allele was not similarly affected. Since temperature might have been considered a reasonable selective factor, we also studied a population living at >800 m above sea level from Aosta Valley (Italy). PMID:11048786

  7. Glutathione S-transferase class {pi} polymorphism in baboons

    SciTech Connect

    Aivaliotis, M.J.; Cantu, T.; Gilligan, R.

    1995-02-01

    Glutathione S-transferase (GST) comprises a family of isozymes with broad substrate specificities. One or more GST isozymes are present in most animal tissues and function in several detoxification pathways through the conjugation of reduced glutathione with various electrophiles, thereby reducing their potential toxicity. Four soluble GST isozymes encoded by genes on different chromosomes have been identified in humans. The acidic class pi GST, GSTP (previously designated GST-3), is widely distributed in adult tissues and appears to be the only GST isozyme present in leukocytes and placenta. Previously reported electrophoretic analyses of erythrocyte and leukocyte extracts revealed single bands of activity, which differed slightly in mobility between the two cell types, or under other conditions, a two-banded pattern. To our knowledge, no genetically determined polymorphisms have previously been reported in GSTP from any species. We now report a polymorphism of GSTP in baboon leukocytes, and present family data that verifies autosomal codominant inheritance. 14 refs., 2 figs., 1 tab.

  8. Flow-cytometry-based DNA hybidization and polymorphism analysis

    NASA Astrophysics Data System (ADS)

    Cai, Hong; Kommander, Kristina; White, P. S.; Nolan, John P.

    1998-05-01

    Functional analysis of the human genome, including the quantification of differential gene expression and the identification of polymorphic sites and disease genes, is an important element of the Human Genome Project. Current methods of analysis are mainly gel-based assays that are not well- suited to rapid genome-scale analyses. To analyze DNA sequence on a large scale, robust and high throughput assays are needed. We are developing a suite of microsphere-based approaches employing fluorescence detection to screen and analyze genomic sequence. Our approaches include competitive DNA hybridization to measure DNA or RNA targets in unknown samples, and oligo ligation or extension assays to analyze single-nucleotide polymorphisms. Apart from the advantages of sensitivity, simplicity, and low sample consumption, these flow cytometric approaches have the potential for high throughput multiplexed analysis using multicolored microspheres and automated sample handling.

  9. Folate: metabolism, genes, polymorphisms and the associated diseases.

    PubMed

    Nazki, Fakhira Hassan; Sameer, Aga Syed; Ganaie, Bashir Ahmad

    2014-01-01

    Folate being an important vitamin of B Complex group in our diet plays an important role not only in the synthesis of DNA but also in the maintenance of methylation reactions in the cells. Folate metabolism is influenced by several processes especially its dietary intake and the polymorphisms of the associated genes involved. Aberrant folate metabolism, therefore, affects both methylation as well as the DNA synthesis processes, both of which have been implicated in the development of various diseases. This paper reviews the current knowledge of the processes involved in folate metabolism and consequences of deviant folate metabolism, particular emphasis is given to the polymorphic genes which have been implicated in the development of various diseases in humans, like vascular diseases, Down's syndrome, neural tube defects, psychiatric disorders and cancers. PMID:24091066

  10. HLA-B polymorphisms and intracellular assembly modes.

    PubMed

    Raghavan, Malini; Geng, Jie

    2015-12-01

    Human leukocyte antigen (HLA) class I molecules are ligands for antigen receptors of cytotoxic T cells (CTL) and inhibitory receptors of natural killer (NK) cells. The high degree of HLA class I polymorphism allows for the selection of distinct and diverse sets of antigenic peptide ligands for presentation to CTL. The extensive polymorphisms of the HLA class I genes also result in large variations in their intracellular folding and assembly characteristics. Recent findings indicate that North American HLA-B variants differ significantly in the stabilities of their peptide-deficient forms and in the requirements for the endoplasmic reticulum (ER)-resident factor tapasin for proper assembly. In HIV-infected individuals, the presence of tapasin-independent HLA-B allotypes links to more rapid progression to death. Further studies are important to better understand how the intrinsic structural characteristics of HLA class I folding intermediates affect immune responses mediated by CTL and NK cells. PMID:26239417

  11. Polymorphism in magic-sized Au144(SR)60 clusters

    NASA Astrophysics Data System (ADS)

    Jensen, Kirsten M. Ø.; Juhas, Pavol; Tofanelli, Marcus A.; Heinecke, Christine L.; Vaughan, Gavin; Ackerson, Christopher J.; Billinge, Simon J. L.

    2016-06-01

    Ultra-small, magic-sized metal nanoclusters represent an important new class of materials with properties between molecules and particles. However, their small size challenges the conventional methods for structure characterization. Here we present the structure of ultra-stable Au144(SR)60 magic-sized nanoclusters obtained from atomic pair distribution function analysis of X-ray powder diffraction data. The study reveals structural polymorphism in these archetypal nanoclusters. In addition to confirming the theoretically predicted icosahedral-cored cluster, we also find samples with a truncated decahedral core structure, with some samples exhibiting a coexistence of both cluster structures. Although the clusters are monodisperse in size, structural diversity is apparent. The discovery of polymorphism may open up a new dimension in nanoscale engineering.

  12. Polymorphism in magic-sized Au144(SR)60 clusters

    PubMed Central

    Jensen, Kirsten M.Ø.; Juhas, Pavol; Tofanelli, Marcus A.; Heinecke, Christine L.; Vaughan, Gavin; Ackerson, Christopher J.; Billinge, Simon J. L.

    2016-01-01

    Ultra-small, magic-sized metal nanoclusters represent an important new class of materials with properties between molecules and particles. However, their small size challenges the conventional methods for structure characterization. Here we present the structure of ultra-stable Au144(SR)60 magic-sized nanoclusters obtained from atomic pair distribution function analysis of X-ray powder diffraction data. The study reveals structural polymorphism in these archetypal nanoclusters. In addition to confirming the theoretically predicted icosahedral-cored cluster, we also find samples with a truncated decahedral core structure, with some samples exhibiting a coexistence of both cluster structures. Although the clusters are monodisperse in size, structural diversity is apparent. The discovery of polymorphism may open up a new dimension in nanoscale engineering. PMID:27297400

  13. A new polymorph of Ln polysulfides (Ln = Pr and Nd)

    SciTech Connect

    Yanagisawa, Y.; Kume, S.

    1986-04-01

    A new polymorph of rare earth polysulfides was synthesized under high temperature-pressure conditions. Its X-ray diffraction patterns were indexed on an orthorhombic unit cell with the lattice constants of a = 0.8025, b = 1.6152 and c = 0.4062 for PrS/sub 2/ and a = 0.7977, b = 1.6012 and c = 0.4027 nm, for NdS/sub 2/. The calculated densities of the orthorhombic polysulfides are nearly the same as those of the allotropic phases with monoclinic symmetry. To compare the stability of the two polymorphs, the Madelung energies of the structures were calculated and that of the monoclinic phase, which is synthesized without applying pressures, was found to be lower than that of the orthorhombic phase.

  14. Influence of amorphous structure on polymorphism in vanadia

    NASA Astrophysics Data System (ADS)

    Stone, Kevin H.; Schelhas, Laura T.; Garten, Lauren M.; Shyam, Badri; Mehta, Apurva; Ndione, Paul F.; Ginley, David S.; Toney, Michael F.

    2016-07-01

    Normally we think of the glassy state as a single phase and therefore crystallization from chemically identical amorphous precursors should be identical. Here we show that the local structure of an amorphous precursor is distinct depending on the initial deposition conditions, resulting in significant differences in the final state material. Using grazing incidence total x-ray scattering, we have determined the local structure in amorphous thin films of vanadium oxide grown under different conditions using pulsed laser deposition (PLD). Here we show that the subsequent crystallization of films deposited using different initial PLD conditions result in the formation of different polymorphs of VO2. This suggests the possibility of controlling the formation of metastable polymorphs by tuning the initial amorphous structure to different formation pathways.

  15. Associations of MICA Polymorphisms with Inflammatory Rheumatic Diseases

    PubMed Central

    Wang, Qingwen; Zhou, Xiaodong

    2015-01-01

    Inflammatory rheumatic diseases are characterized by inflammation resulting from the immune dysregulation that usually attacks joints, skin and internal organs. Many of them are considered as complex disease that may be predisposed by multiple genes and/or genetic loci, and triggered by environmental factors such as microbiome and cellular stress. The major histocompatibility complex class I chain-related gene A (MICA) is a highly polymorphic gene that encodes protein variants expressed under cellular stress conditions, and these MICA variants play important roles in immune activation and surveillance. Recently, accumulating evidences from both genetic and functional studies have suggested that MICA polymorphisms may be associated with various rheumatic diseases, and the expression of MICA variants may attribute to the altered immune responses in the diseases. The objective of this review is to discuss potential genetic associations and pathological relevance of MICA in inflammatory rheumatic diseases that may help us to understand pathogenesis contributing to the development of these diseases. PMID:26862354

  16. Complement factor H polymorphism and age-related macular degeneration.

    PubMed

    Edwards, Albert O; Ritter, Robert; Abel, Kenneth J; Manning, Alisa; Panhuysen, Carolien; Farrer, Lindsay A

    2005-04-15

    Age-related macular degeneration (AMD) is a common, late-onset, and complex trait with multiple risk factors. Concentrating on a region harboring a locus for AMD on 1q25-31, the ARMD1 locus, we tested single-nucleotide polymorphisms for association with AMD in two independent case-control populations. Significant association (P = 4.95 x 10(-10)) was identified within the regulation of complement activation locus and was centered over a tyrosine-402 --> histidine-402 protein polymorphism in the gene encoding complement factor H. Possession of at least one histidine at amino acid position 402 increased the risk of AMD 2.7-fold and may account for 50% of the attributable risk of AMD. PMID:15761121

  17. Interleukin polymorphisms in aggressive periodontitis: A literature review

    PubMed Central

    Maney, Pooja; Owens, Jessica Leigh

    2015-01-01

    Aggressive periodontitis (AgP), occurs in a younger age group (≤35 years) and is associated with the rapid destruction of periodontal attachment and supporting bone. Genetic polymorphisms are allelic variants that occur in at least 1% of the population that could potentially alter the function of the proteins that they encode. Interleukins are a group of cytokines that have complex immunological functions including proliferation, migration, growth and differentiation of cells and play a key role in the immunopathogenesis of periodontal disease. The aim of this review was to summarize the findings of studies that reported associations or potential associations of polymorphisms in the interleukin family of cytokines, specifically with AgP. PMID:26015661

  18. Polymorphism in magic-sized Au144(SR)60 clusters.

    PubMed

    Jensen, Kirsten M Ø; Juhas, Pavol; Tofanelli, Marcus A; Heinecke, Christine L; Vaughan, Gavin; Ackerson, Christopher J; Billinge, Simon J L

    2016-01-01

    Ultra-small, magic-sized metal nanoclusters represent an important new class of materials with properties between molecules and particles. However, their small size challenges the conventional methods for structure characterization. Here we present the structure of ultra-stable Au144(SR)60 magic-sized nanoclusters obtained from atomic pair distribution function analysis of X-ray powder diffraction data. The study reveals structural polymorphism in these archetypal nanoclusters. In addition to confirming the theoretically predicted icosahedral-cored cluster, we also find samples with a truncated decahedral core structure, with some samples exhibiting a coexistence of both cluster structures. Although the clusters are monodisperse in size, structural diversity is apparent. The discovery of polymorphism may open up a new dimension in nanoscale engineering. PMID:27297400

  19. Correlation between nanomechanics and polymorphic conformations in amyloid fibrils.

    PubMed

    Usov, Ivan; Mezzenga, Raffaele

    2014-11-25

    Amyloid fibrils occur in diverse morphologies, but how polymorphism affects the resulting mechanical properties is still not fully appreciated. Using formalisms from the theory of elasticity, we propose an original way of averaging the second area moment of inertia for non-axisymmetric fibrils, which constitutes the great majority of amyloid fibrils. By following this approach, we derive theoretical expressions for the bending properties of the most common polymorphic forms of amyloid fibrils (twisted ribbons, helical ribbons, and nanotubes), and we benchmark the predictions to experimental cases. These results not only allow an accurate estimation of the amyloid fibrils' elastic moduli but also bring insight into the structure-property relationships in the nanomechanics of amyloid systems, such as in the closure of helical ribbons into nanotubes. PMID:25275956

  20. Polymorphism in Bi2(SO4)3

    NASA Astrophysics Data System (ADS)

    Subban, Chinmayee V.; Rousse, Gwenaëlle; Courty, Matthieu; Barboux, Philippe; Tarascon, Jean-Marie

    2014-12-01

    A new polymorph of Bi2(SO4)3 was prepared by reaction of LiBiO2 with H2SO4 and its crystal structure was solved from X-ray powder diffraction. This new polymorph crystallizes in C2/c space group with lattice parameters a = 17.3383(3) Å, b = 6.77803(12) Å, c = 8.30978(13) Å, β = 101.4300(12)°. Bi2(SO4)3 presents a layered structure made of SO4 sulfate groups and signs of stereochemically active Bi3+ lone pairs. The new Bi2(SO4)3 absorbs water to form Bi2(H2O)2(SO4)2(OH)2 through an intermediate Bi2O(OH)2SO4 phase, and the transition is reversible when heated under vacuum.

  1. Methyltetrahydrofolate reductase polymorphism influences onset of Huntington's disease.

    PubMed

    Brune, N; Andrich, J; Gencik, M; Saft, C; Müller, Th; Valentin, S; Przuntek, H; Epplen, J T

    2004-01-01

    Onset of Huntington's disease (HD) negatively correlates with CAG repeat length of the HD gene, which encodes the protein huntingtin. This protein interacts with the homocysteine metabolizing enzyme cystathionine betasynthase (CBS). Objective of this study was to analyze the impact of CAG repeats, polymorphisms of various homocysteine metabolizing enzymes, like CBS, Methyltetrahydrofolate Reductase (MTHTR), Methionine Synthase Reductase (MSR) and methionine synthase (MS) on HD onset in 171 patients. The significant impact of CAG repeats on HD onset (chi2= 25.54, FG = 4, p<0.0001) with a significant correlation between both (R= -0.521, p=0.01) was obvious. HD patients with the homozygous MTHFR-1298-CC significantly (p = 0.024) earlier experienced HD symptoms. There was no influence demonstrable of CBS, MSR and MS. Determination of MTHFR polymorphisms and CAG repeats enables screening for subjects with putative early HD onset in order to study neuroprotective compounds in their efficacy to delay HD symptoms. PMID:15354395

  2. Development and characterization of polymorphic microsatellite markers in Linum usitatissimum.

    PubMed

    Deng, Xin; Long, Songhua; He, Dongfeng; Li, Xiang; Wang, Yufu; Liu, Jia; Chen, Xinbo

    2010-01-01

    Thirty-five microsatellite loci were isolated and characterized in Linum usitatissimum using enriched genomic libraries. These loci were screened in eight cultivars from different countries and regions and were found to be polymorphic, with the number of alleles per locus ranging from two to six, and observed and expected heterozygosities ranging from 0.125 to 0.375 (mean 0.013) and from 0.233 to 0.842 (mean 0.601), respectively. These polymorphic new microsatellite loci will be useful for genetic linkage map construction, germplasm classification and identification, gene identification and quantitative trait loci mapping, and marker-assisted selection in breeding in L. usitatissimum. PMID:19882206

  3. CYP2D6 polymorphism in patients with eating disorders.

    PubMed

    Peñas-Lledó, E M; Dorado, P; Agüera, Z; Gratacós, M; Estivill, X; Fernández-Aranda, F; Llerena, A

    2012-04-01

    CYP2D6 polymorphism is associated with variability in drug response, endogenous metabolism (that is, serotonin), personality, neurocognition and psychopathology. The relationship between CYP2D6 genetic polymorphism and the risk of eating disorders (ED) was analyzed in 267 patients with ED and in 285 controls. A difference in the CYP2D6 active allele distribution was found between these groups. Women carrying more than two active genes (ultrarapid metabolizers) (7.5 vs 4.6%) or two (67 vs 58.9%) active genes were more frequent among patients with ED, whereas those with one (20.6 vs 30.2%) or zero active genes (4.9 vs 6.3%) were more frequent among controls (P<0.05). Although further research is needed, present findings suggest an association between CYP2D6 and ED. CYP2D6 allele distribution in patients with ED seems related to increased enzyme activity. PMID:20877302

  4. Structural characterization of ice polymorphs from self-avoiding walks

    NASA Astrophysics Data System (ADS)

    Herrero, Carlos P.

    2014-08-01

    Topological properties of crystalline ice structures are studied by means of self-avoiding walks on their H-bond networks. The number of self-avoiding walks, Cn, for eight ice polymorphs has been obtained by direct enumeration up to walk length n=27. This has allowed us to determine the ‘connective constant' or effective coordination number μ of these structures as the limit of the ratio Cn/Cn-1 for large n. This structure-dependent parameter μ is related with other topological characteristics of ice polymorphs, such as the mean and minimum ring size, or the topological density of network sites. A correlation between the connective constant and the configurational entropy of hydrogen-disordered ice structures is discussed.

  5. Genetic polymorphisms as a risk factor for dyslipidemia in children

    PubMed Central

    Santos, Izabela R.; Fernandes, Ana Paula; Sousa, Marinez O.; Ferreira, Cláudia N.; Gomes, Karina B.

    2013-01-01

    Dyslipidemia is an important etiological factor for development of cardiovascular disease, which is the leading cause of deaths in adults. Given the growing global epidemic of dyslipidemia, lipoprotein metabolism disorders have become an important health problem not only in adulthood, but have also emerged as an increasingly risk factor in childhood. Although several genome-wide association studies in multiple large population-based cohorts of adults and meta-analyses have identified susceptibility genes or loci, especially in lipid-related traits, it is of great importance to evaluate genetic predisposition at an early age. Recent findings suggest that the identification of polymorphisms in the metabolism of lipids in childhood may help fight subclinical atherosclerosis and its progression to cardiovascular complications in adulthood. Therefore, the aim of this study was to review genetic polymorphisms as risk factors associated with dyslipidemia in children and adolescents.

  6. Association of TLR and TREM-1 gene polymorphisms with atherosclerosis severity in a Russian population

    PubMed Central

    Kutikhin, Anton G.; Ponasenko, Anastasia V.; Khutornaya, Maria V.; Yuzhalin, Arseniy E.; Zhidkova, Irina I.; Salakhov, Ramil R.; Golovkin, Alexey S.; Barbarash, Olga L.; Barbarash, Leonid S.

    2016-01-01

    Local vascular immune response is primarily initiated via Toll-like receptors (TLRs) and triggering receptor expressed on myeloid cells-1 (TREM-1). We previously showed that certain TLR and TREM-1 gene polymorphisms are associated with coronary artery disease (CAD). Therefore, we hypothesized that these gene polymorphisms are associated with atherosclerosis severity. This study included 292 consecutive patients with CAD who were admitted to the Research Institute for Complex Issues of Cardiovascular Diseases (Kemerovo, Russian Federation) during 2011–2012. Sample genotyping was performed in 96-well format using the TaqMan SNP genotyping assay. We found that C/C genotype of the rs3804099 polymorphism within TLR2 gene and T/T genotype of the rs4711668 polymorphism within TREM-1 gene were significantly associated with severe coronary atherosclerosis while C allele of the rs5743551 polymorphism within TLR1 gene, A/G genotype of the rs4986790 polymorphism and C/T genotype of the rs4986791 polymorphism within TLR4 gene, and C allele of the rs3775073 polymorphism within TLR6 gene were significantly associated with severe noncoronary atherosclerosis. However, A/A genotype of the rs5743810 polymorphism within TLR6 gene was significantly associated with mild noncoronary atherosclerosis. We conclude that certain TLR and TREM-1 gene polymorphisms are significantly associated with atherosclerosis severity in a Russian population. PMID:27200266

  7. Association of TLR and TREM-1 gene polymorphisms with atherosclerosis severity in a Russian population.

    PubMed

    Kutikhin, Anton G; Ponasenko, Anastasia V; Khutornaya, Maria V; Yuzhalin, Arseniy E; Zhidkova, Irina I; Salakhov, Ramil R; Golovkin, Alexey S; Barbarash, Olga L; Barbarash, Leonid S

    2016-09-01

    Local vascular immune response is primarily initiated via Toll-like receptors (TLRs) and triggering receptor expressed on myeloid cells-1 (TREM-1). We previously showed that certain TLR and TREM-1 gene polymorphisms are associated with coronary artery disease (CAD). Therefore, we hypothesized that these gene polymorphisms are associated with atherosclerosis severity. This study included 292 consecutive patients with CAD who were admitted to the Research Institute for Complex Issues of Cardiovascular Diseases (Kemerovo, Russian Federation) during 2011-2012. Sample genotyping was performed in 96-well format using the TaqMan SNP genotyping assay. We found that C/C genotype of the rs3804099 polymorphism within TLR2 gene and T/T genotype of the rs4711668 polymorphism within TREM-1 gene were significantly associated with severe coronary atherosclerosis while C allele of the rs5743551 polymorphism within TLR1 gene, A/G genotype of the rs4986790 polymorphism and C/T genotype of the rs4986791 polymorphism within TLR4 gene, and C allele of the rs3775073 polymorphism within TLR6 gene were significantly associated with severe noncoronary atherosclerosis. However, A/A genotype of the rs5743810 polymorphism within TLR6 gene was significantly associated with mild noncoronary atherosclerosis. We conclude that certain TLR and TREM-1 gene polymorphisms are significantly associated with atherosclerosis severity in a Russian population. PMID:27200266

  8. Complex patterns of intragenic polymorphism at the PDGFA locus.

    PubMed

    Bonthron, D T; Smith, S J; Campbell, R

    1999-11-01

    The human platelet-derived growth factor A chain gene (PDGFA) on chromosome 7p22 encodes an important mitogen. Within PDGFA lies a complex minisatellite structure that results in partial duplications of exon 4 and the IVS4 splice donor site. Here, we show that the PDGFA genes of four ape species and an Old-World monkey all have similar complex minisatellites at this position. Comparison of their structures suggests evolutionary constraints resulting from the protein-coding function of the minisatellite. Nonetheless, the IVS4 minisatellite seems to have undergone independent expansion events in different primate lineages. Within the human IVS4 minisatellite, an embedded pentanucleotide repeat, based on the sequence (CCTCC)n, shows frequent subunit sequence variation but only rare length polymorphism. In contrast, within IVS3 of human PDGFA, we have discovered a second minisatellite which, unlike the IVS4 minisatellite, is highly polymorphic. The subunit sequences of these two minisatellites, which lie less than 0.5 kb apart, are non-identical, but share a CnT-rich core. Two new single nucleotide polymorphisms (SNPs), in exon 3 and IVS4, are in linkage disequilibrium, despite flanking the two minisatellite regions. Reverse transcription-polymerase chain reaction analysis of the exon 3 SNP in human foetal tissues demonstrated biallelic expression of PDGFA in all tissues examined. The unusual location of PDGFA exon 4 between two minisatellite sequences, together with its partial duplication, may have functional implications, particularly for the splicing of the gene. The high level of polymorphism demonstrated in this region will also be valuable for disease-association and linkage studies of the PDGFA locus. PMID:10598812

  9. Ten polymorphic microsatellite DNA markers for the platypus, Ornithorhynchus anatinus.

    PubMed

    Kolomyjec, Stephen H; Grant, Tom R; Blair, David

    2008-09-01

    We identified and optimized 10 microsatellite loci for the platypus, Ornithorhynchus anatinus (Monotremata: Ornithorhynchidae), and screened 21 individuals from the southern tablelands area of New South Wales, Australia. Each polymorphic locus possessed between two and 12 alleles with observed heterozygosities between 0.118 and 0.950. The intent of this effort was to provide informative loci for studies on the population genetics of this species. PMID:21585993

  10. [Mitochondrial DNA Polymorphism in Different Populations of Spangled Orloff Chickens].

    PubMed

    Oyuna, N Yu; Moiseyeva, I G; Sevastianova, A A; Vakhrameev, A B; Alexandrov, A V; Kuzevanova, A Yu; Alimov, A A; Sulimova, G E

    2015-09-01

    For the first time, the genetic diversity of the Spangled Orloff chickens was studied by analyzing the polymorphism of the hypervariable region in the D-loop of mitochondrial DNA (mtDNA). Samples for the analysis were collected at the farms ofthe All-Russia Poultry Research and Technological Institute (VNITIP), the All-Russia Institute of Farm Animal Genetics and Breeding (VNIIGRZh), and the Moscow Zoo. The D-loop partial sequences (between nucleotide positions 57 and 523) were determined according to the reference sequence of Gallus gallus spadiceus mtDNA, NC_007235 in 39 individuals obtained from these populations (GenBank Accession Nos. KM391754-KM391792). In the analyzed mtDNA fragment, a total of 20 polymorphic sites localized between positions 167 and 368, as well as at position 446, were described in Spangled Orloff chickens. One polymorphic site at position 221 (haplogroup E, haplotype ORL-2) was unique. All of the identified nucleotide changes were transition-type substitutions. Overall, based on the analysis of poly- morphic sites in the hypervariable fragment of the D-loop of Spangled Orloff chicken mtDNA, we found seven haplotypes belonging to four haplogroups (A, B, C, and E). Haplogroup E (haplotypes ORL-1, ORL-2, and ORL-3) was present in the majority of the studied individual, with the frequencies of 0.77 in the total sample and 0.47 in the VNIIGRZh farm population. Haplogroups A (haplotypes ORL-4 and ORL-7), B (ORL-6), and C (ORL-5) were found only in samples from the VNIIGRZh farm. The studied mtDNA region revealed a lower level of polymorphism in the VNITIP and Moscow Zoo populations, which only had the ORL-1 and ORL-3 haplotypes belonging to Haplogroup E, respectively. Our data suggested that the studied Spangled Orloff chicken populations differed in the composition and frequencies of mtDNA haplogroups and haplotypes. PMID:26606802

  11. Leptin receptor gene polymorphisms in severely pre-eclamptic women.

    PubMed

    Rigó, János; Szendei, György; Rosta, Klára; Fekete, Andrea; Bögi, Krisztina; Molvarec, Attila; Rónai, Zsolt; Vér, Agota

    2006-09-01

    Variants of the leptin receptor gene (LEPR) may modulate the effect of elevated serum leptin levels in pre-eclampsia. The aim of our study was to evaluate the LEPR gene polymorphisms Lys109Arg (A109G) and Gln223Arg (A223G) in severely pre-eclamptic women. In a case-control study, we analyzed blood samples from 124 severely pre-eclamptic patients and 107 healthy control women by the polymerase chain reaction-restriction fragment length polymorphism method. The Pearson chi2 test was used to estimate odds ratios (OR) and 95% confidence intervals (CI). The association was adjusted for maternal age, pre-pregnancy body mass index and primiparity with logistic regression analysis. Pregnant women with the LEPR 223G allele (223A/G or 223G/G genotype) had almost double the risk of developing severe pre-eclampsia compared with patients with the 223A/A genotype (adjusted OR = 1.92, 95% CI: 1.07-3.41). Genotype variants of LEPR A109G alone did not affect the risk of severe pre-eclampsia. Haplotype estimation of A109G and A223G polymorphisms of the LEPR gene revealed that the G-A haplotype versus other pooled haplotypes was significantly less common in the pre-eclamptic group (p < 0.01), while the G-G haplotype versus others was overrepresented among severely pre-eclamptic patients (p < 0.01), compared with controls. In conclusion, our data indicate that LEPR A223G polymorphism may individually modify the risk of severe pre-eclampsia. PMID:17071538

  12. Polymorphism in Cs[AgZn(NCS)4].

    PubMed

    Güneş, Minna; Valkonen, Jussi

    2002-12-01

    The title compound, caesium silver zinc tetrathiocyanate, crystallizes in two polymorphic forms, in space groups P2(1)/n and C2/c. Both structures form a continuous three-dimensional network. The structure in C2/c contains a delocalized Ag atom in a binuclear-like anion, where two [Ag(NCS)(4)] units (delocalized Ag as an average) share two common NCS(-) ligands. PMID:12466595

  13. Association between serotonin transporter gene polymorphism and recurrent aphthous stomatitis

    PubMed Central

    Manchanda, Aastha; Iyengar, Asha R.; Patil, Seema

    2016-01-01

    Background: Anxiety-related traits have been attributed to sequence variability in the genes coding for serotonin transmission in  the brain. Two alleles, termed long (L) and short (S) differing by 44 base pairs, are found in a polymorphism identified in the promoter region of serotonin transporter gene. The presence of the short allele  and SS and LS genotypes is found to be associated with the reduced expression of this gene decreasing the uptake of serotonin in the brain leading to various anxiety-related traits. Recurrent aphthous stomatitis (RAS) is an oral mucosal disease with varied etiology including the presence of stress, anxiety, and genetic influences. The present study aimed to determine this serotonin transporter gene polymorphism in patients with RAS and compare it with normal individuals. Materials and Methods: This study included 20 subjects with various forms of RAS and 20 normal healthy age- and gender-matched individuals. Desquamated oral mucosal cells were collected for DNA extraction and subjected to polymerase chain reaction for studying insertion/deletion in the 5-HTT gene-linked polymorphic region. Cross tabulations followed by Chi-square tests were performed to compare the significance of findings, P < 0.05 was considered statistically significant. Results: The LS genotype was the most common genotype found in the subjects with aphthous stomatitis (60%) and controls (40%). The total percentage of LS and SS genotypes and the frequency of S allele were found to be higher in the subjects with aphthous stomatitis as compared to the control group although a statistically significant correlation could not be established, P = 0.144 and 0.371, respectively. Conclusion: Within the limitations of this study, occurrence of RAS was not found to be associated with polymorphic promoter region in serotonin transporter gene. PMID:27274339

  14. Polymorphic microsatellite loci for primitively eusocial wasp Ropalidia marginata.

    PubMed

    Johny, S; Chakraborty, S; Gadagkar, R; Nagaraju, J

    2009-07-01

    We report here development and characterization of 48 novel microsatellite markers for Ropalidia marginata, a tropical, primitively eusocial polistine wasp from peninsular India. Thirty-two microsatellites showed polymorphism in a wild population of R. marginata (N = 38) collected from Bangalore, India. These markers will facilitate answering some interesting questions in ecology and evolutionary biology of this wasp, such as population structure, serial polygyny, intra-colony genetic relatedness and the pattern of queen succession. PMID:21564866

  15. Uncoupling protein 2 gene polymorphisms are associated with obesity

    PubMed Central

    2012-01-01

    Background Uncoupling protein 2 (UCP2) gene polymorphisms have been reported as genetic risk factors for obesity and type 2 diabetes mellitus (T2DM). We examined the association of commonly observed UCP2 G(−866)A (rs659366) and Ala55Val (C > T) (rs660339) single nucleotide polymorphisms (SNPs) with obesity, high fasting plasma glucose, and serum lipids in a Balinese population. Methods A total of 603 participants (278 urban and 325 rural subjects) were recruited from Bali Island, Indonesia. Fasting plasma glucose (FPG), triglyceride (TG), high density lipoprotein cholesterol (HDL-C), low density lipoprotein cholesterol (LDL-C) and total cholesterol (TC) were measured. Obesity was determined based on WHO classifications for adult Asians. Participants were genotyped for G(−866)A and Ala55Val polymorphisms of the UCP2 gene. Results Obesity prevalence was higher in urban subjects (51%) as compared to rural subjects (23%). The genotype, minor allele (MAF), and heterozygosity frequencies were similar between urban and rural subjects for both SNPs. All genotype frequencies were in Hardy-Weinberg equilibrium. A combined analysis of genotypes and environment revealed that the urban subjects carrying the A/A genotype of the G(−866)A SNP have higher BMI than the rural subjects with the same genotype. Since the two SNPs showed strong linkage disequilibrium (D’ = 0.946, r2 = 0.657), a haplotype analysis was performed. We found that the AT haplotype was associated with high BMI only when the urban environment was taken into account. Conclusions We have demonstrated the importance of environmental settings in studying the influence of the common UCP2 gene polymorphisms in the development of obesity in a Balinese population. PMID:22533685

  16. Genetic polymorphism of the LW blood group system.

    PubMed

    Sistonen, P; Green, C A; Lomas, C G; Tippett, P

    1983-10-01

    Family studies of rare LW(a-b+) propositi confirm the recent finding based on frequency studies that the LW blood groups are polymorphic in Finland (Sistonen & Tippett, 1982); they are controlled by two alleles LWa (0.97) and LWb (0.03) independent from most other common blood group loci. Lod scores for LW and the loci for 27 markers are presented. PMID:6418057

  17. Chromatin fiber polymorphism triggered by variations of DNA linker lengths

    PubMed Central

    Collepardo-Guevara, Rosana; Schlick, Tamar

    2014-01-01

    Deciphering the factors that control chromatin fiber structure is key to understanding fundamental chromosomal processes. Although details remain unknown, it is becoming clear that chromatin is polymorphic depending on internal and external factors. In particular, different lengths of the linker DNAs joining successive nucleosomes (measured in nucleosome-repeat lengths or NRLs) that characterize different cell types and cell cycle stages produce different structures. NRL is also nonuniform within single fibers, but how this diversity affects chromatin fiber structure is not clear. Here we perform Monte Carlo simulations of a coarse-grained oligonucleosome model to help interpret fiber structure subject to intrafiber NRL variations, as relevant to proliferating cells of interphase chromatin, fibers subject to remodeling factors, and regulatory DNA sequences. We find that intrafiber NRL variations have a profound impact on chromatin structure, with a wide range of different architectures emerging (highly bent narrow forms, canonical and irregular zigzag fibers, and polymorphic conformations), depending on the NRLs mixed. This stabilization of a wide range of fiber forms might allow NRL variations to regulate both fiber compaction and selective DNA exposure. The polymorphic forms spanning canonical to sharply bent structures, like hairpins and loops, arise from large NRL variations and are surprisingly more compact than uniform NRL structures. They are distinguished by tail-mediated far-nucleosome interactions, in addition to the near-nucleosome interactions of canonical 30-nm fibers. Polymorphism is consistent with chromatin’s diverse biological functions and heterogeneous constituents. Intrafiber NRL variations, in particular, may contribute to fiber bending and looping and thus to distant communication in associated regulatory processes. PMID:24847063

  18. Y-Single Nucleotide Polymorphisms Diversity in Chinese Indigenous Horse

    PubMed Central

    Han, Haoyuan; Zhang, Qin; Gao, Kexin; Yue, Xiangpeng; Zhang, Tao; Dang, Ruihua; Lan, Xianyong; Chen, Hong; Lei, Chuzhao

    2015-01-01

    In contrast to high genetic diversity of mitochondrial DNA (mtDNA), equine Y chromosome shows extremely low variability, implying limited patrilines in the domesticated horse. In this study, we applied direct sequencing and restriction fragment length polymorphism (RFLP) methods to investigate the polymorphisms of 33 Y chromosome specific loci in 304 Chinese indigenous horses from 13 breeds. Consequently, two Y-single nucleotide polymorphisms (SNPs) (Y-45701/997 and Y-50869) and one Y-indel (Y-45288) were identified. Of those, the Y-50869 (T>A) revealed the highest variation frequency (24.67%), whereas it was only 3.29% and 1.97% in Y-45288 (T/-) and Y-45701/997 (G>T) locus, respectively. These three mutations accounted for 27.96% of the total samples and identified five Y-SNP haplotypes, demonstrating genetic diversity of Y chromosome in Chinese horses. In addition, all the five Y-SNP haplotypes were shared by different breeds. Among 13 horse breeds analyzed, Balikun horse displayed the highest nucleotide diversity (π = 5.6×10−4) and haplotype diversity (h = 0.527), while Ningqiang horse showed the lowest nucleotide diversity (π = 0.00000) and haplotype diversity (h = 0.000). The results also revealed that Chinese horses had a different polymorphic pattern of Y chromosome from European and American horses. In conclusion, Chinese horses revealed genetic diversity of Y chromosome, however more efforts should be made to better understand the domestication and paternal origin of Chinese indigenous horses. PMID:26104513

  19. Salting out the polar polymorph: Analysis by alchemical solvent transformation

    NASA Astrophysics Data System (ADS)

    Duff, Nathan; Dahal, Yuba Raj; Schmit, Jeremy D.; Peters, Baron

    2014-01-01

    We computationally examine how adding NaCl to an aqueous solution with α- and γ-glycine nuclei alters the structure and interfacial energy of the nuclei. The polar γ-glycine nucleus in pure aqueous solution develops a melted layer of amorphous glycine around the nucleus. When NaCl is added, a double layer is formed that stabilizes the polar glycine polymorph and eliminates the surface melted layer. In contrast, the non-polar α-glycine nucleus is largely unaffected by the addition of NaCl. To quantify the stabilizing effect of NaCl on γ-glycine nuclei, we alchemically transform the aqueous glycine solution into a brine solution of glycine. The alchemical transformation is performed both with and without a nucleus in solution and for nuclei of α-glycine and γ-glycine polymorphs. The calculations show that adding 80 mg/ml NaCl reduces the interfacial free energy of a γ-glycine nucleus by 7.7 mJ/m2 and increases the interfacial free energy of an α-glycine nucleus by 3.1 mJ/m2. Both results are consistent with experimental reports on nucleation rates which suggest: J(α, brine) < J(γ, brine) < J(α, water). For γ-glycine nuclei, Debye-Hückel theory qualitatively, but not quantitatively, captures the effect of salt addition. Only the alchemical solvent transformation approach can predict the results for both polar and non-polar polymorphs. The results suggest a general "salting out" strategy for obtaining polar polymorphs and also a general approach to computationally estimate the effects of solvent additives on interfacial free energies for nucleation.

  20. Can paternal leakage maintain sexually antagonistic polymorphism in the cytoplasm?

    PubMed Central

    Kuijper, B; Lane, N; Pomiankowski, A

    2015-01-01

    A growing number of studies in multicellular organisms highlight low or moderate frequencies of paternal transmission of cytoplasmic organelles, including both mitochondria and chloroplasts. It is well established that strict maternal inheritance is selectively blind to cytoplasmic elements that are deleterious to males – ’mother's curse’. But it is not known how sensitive this conclusion is to slight levels of paternal cytoplasmic leakage. We assess the scope for polymorphism when individuals bear multiple cytoplasmic alleles in the presence of paternal leakage, bottlenecks and recurrent mutation. When fitness interactions among cytoplasmic elements within an individual are additive, we find that sexually antagonistic polymorphism is restricted to cases of strong selection on males. However, when fitness interactions among cytoplasmic elements are nonlinear, much more extensive polymorphism can be supported in the cytoplasm. In particular, mitochondrial mutants that have strong beneficial fitness effects in males and weak deleterious fitness effects in females when rare (i.e. ’reverse dominance’) are strongly favoured under paternal leakage. We discuss how such epistasis could arise through preferential segregation of mitochondria in sex-specific somatic tissues. Our analysis shows how paternal leakage can dampen the evolution of deleterious male effects associated with predominant maternal inheritance of cytoplasm, potentially explaining why ’mother's curse’ is less pervasive than predicted by earlier work. PMID:25653025

  1. Assessment of CASP gene polymorphisms in periodontal disease.

    PubMed

    Kang, S W; Kim, S K; Chung, J H; Ban, J Y

    2015-01-01

    Caspases (CASP) are intracellular proteases that play roles as mediators of apoptosis. Activation of caspase 3 is enhanced in chronic periodontitis. Thus, we hypothesized that single nucleotide polymorphisms (SNPs) of CASP genes might be associated with this condition in the Korean population. To investigate whether such polymorphisms might be involved in the development of periodontal disease, 51 patients and 33 control subjects were assessed. A total of 201 CASP gene SNPs were analyzed with genotypes being determined using and Axiom(TM) genome-wide human assay. SNPStats and SPSS 18.0 were used for the analysis of genetic data and logistic regression models were utilized to evaluate odds ratios, 95% confidence intervals, and P values. Of the 201 SNPs, only three (rs12108497, rs4647602, and rs113420705, all in the CASP3 gene) were significantly associated with chronic periodontitis (P < 0.05). The minor allele frequencies of these SNPs were higher in the patient group than in the control group. In addition, the TC and GT haplotypes formed by rs4647602 and rs113420705 were found to be associated with chronic this disease (TC haplotype, P = 0.0039; GT haplotype, P = 0.002). These results suggest that CASP3 gene polymorphisms may be associated with susceptibility to periodontal disease in the Korean population. PMID:26782454

  2. Twinning of cubic diamond explains reported nanodiamond polymorphs

    NASA Astrophysics Data System (ADS)

    Németh, Péter; Garvie, Laurence A. J.; Buseck, Peter R.

    2015-12-01

    The unusual physical properties and formation conditions attributed to h-, i-, m-, and n-nanodiamond polymorphs has resulted in their receiving much attention in the materials and planetary science literature. Their identification is based on diffraction features that are absent in ordinary cubic (c-) diamond (space group: Fd-3m). We show, using ultra-high-resolution transmission electron microscope (HRTEM) images of natural and synthetic nanodiamonds, that the diffraction features attributed to the reported polymorphs are consistent with c-diamond containing abundant defects. Combinations of {113} reflection and <011> rotation twins produce HRTEM images and d-spacings that match those attributed to h-, i-, and m-diamond. The diagnostic features of n-diamond in TEM images can arise from thickness effects of c-diamonds. Our data and interpretations strongly suggest that the reported nanodiamond polymorphs are in fact twinned c-diamond. We also report a new type of twin (<11> rotational), which can give rise to grains with dodecagonal symmetry. Our results show that twins are widespread in diamond nanocrystals. A high density of twins could strongly influence their applications.

  3. Twinning of cubic diamond explains reported nanodiamond polymorphs.

    PubMed

    Németh, Péter; Garvie, Laurence A J; Buseck, Peter R

    2015-01-01

    The unusual physical properties and formation conditions attributed to h-, i-, m-, and n-nanodiamond polymorphs has resulted in their receiving much attention in the materials and planetary science literature. Their identification is based on diffraction features that are absent in ordinary cubic (c-) diamond (space group: Fd-3m). We show, using ultra-high-resolution transmission electron microscope (HRTEM) images of natural and synthetic nanodiamonds, that the diffraction features attributed to the reported polymorphs are consistent with c-diamond containing abundant defects. Combinations of {113} reflection and <011> rotation twins produce HRTEM images and d-spacings that match those attributed to h-, i-, and m-diamond. The diagnostic features of n-diamond in TEM images can arise from thickness effects of c-diamonds. Our data and interpretations strongly suggest that the reported nanodiamond polymorphs are in fact twinned c-diamond. We also report a new type of twin (<121> rotational), which can give rise to grains with dodecagonal symmetry. Our results show that twins are widespread in diamond nanocrystals. A high density of twins could strongly influence their applications. PMID:26671288

  4. Scent of a Dragonfly: Sex Recognition in a Polymorphic Coenagrionid

    PubMed Central

    Conti, Eric; Rebora, Manuela; Salerno, Gianandrea

    2015-01-01

    In polymorphic damselflies discrimination of females from males is complex owing to the presence of androchrome and gynochrome females. To date there is no evidence that damselflies use sensory modalities other than vision (and tactile stimuli) in mate searching and sex recognition. The results of the present behavioural and electrophysiological investigations on Ischnura elegans, a polymorphic damselfly, support our hypothesis that chemical cues could be involved in Odonata sex recognition. The bioassays demonstrate that males in laboratory prefer female to male odour, while no significant difference was present in male behavior between stimuli from males and control. The bioassays suggest also some ability of males to distinguish between the two female morphs using chemical stimuli. The ability of male antennae to perceive odours from females has been confirmed by electrophysiological recordings. These findings are important not only to get insight into the chemical ecology of Odonata, and to shed light into the problem of olfaction in Paleoptera, but could be useful to clarify the controversial aspects of the mating behavior of polymorphic coenagrionids. Behavioural studies in the field are necessary to investigate further these aspects. PMID:26305118

  5. Configurational entropy of hydrogen-disordered ice polymorphs

    SciTech Connect

    Herrero, Carlos P. Ramírez, Rafael

    2014-06-21

    The configurational entropy of several H-disordered ice polymorphs is calculated by means of a thermodynamic integration along a path between a totally H-disordered state and one fulfilling the Bernal-Fowler ice rules. A Monte Carlo procedure based on a simple energy model is used, so that the employed thermodynamic path drives the system from high temperatures to the low-temperature limit. This method turns out to be precise enough to give reliable values for the configurational entropy s{sub th} of different ice phases in the thermodynamic limit (number of molecules N → ∞). The precision of the method is checked for the ice model on a two-dimensional square lattice. Results for the configurational entropy are given for H-disordered arrangements on several polymorphs, including ices Ih, Ic, II, III, IV, V, VI, and XII. The highest and lowest entropy values correspond to ices VI and XII, respectively, with a difference of 3.3% between them. The dependence of the entropy on the ice structures has been rationalized by comparing it with structural parameters of the various polymorphs, such as the mean ring size. A particularly good correlation has been found between the configurational entropy and the connective constant derived from self-avoiding walks on the ice networks.

  6. Vitamin D receptor gene polymorphisms in breast cancer.

    PubMed

    Buyru, Nur; Tezol, Ayda; Yosunkaya-Fenerci, Elif; Dalay, Nejat

    2003-12-31

    Breast cancer is the leading cause of cancer death among women around the world and its incidence is annually increasing. The vitamin D receptor (VDR) gene is a member of the nuclear receptor superfamily, which is expressed in breast tissue and known to modulate the rate of cell proliferation. Association between the VDR gene polymorphisms and cancer development has been suggested by several studies. However, the relationship between VDR polymorphisms and breast cancer is controversial and has not been confirmed by all studies. The purpose of this study was to investigate the genotype frequencies and association of the VDR Bsm I and Taq I polymorphisms with breast cancer in Turkish patients. In this study, 78 patients with breast cancer and 27 healthy individuals were enrolled. The prevalence of the VDR Taq I and Bsm I alleles and the genotype frequencies in patients with breast cancer was similar to that in the normal population. Our data indicate that no significant differences exist between the patients and control subjects. PMID:14749534

  7. High proportions of deleterious polymorphisms in constrained human genes.

    PubMed

    Subramanian, Sankar

    2011-01-01

    Previous studies on human mitochondrial genomes showed that the ratio of intra-specific diversities at nonsynonymous-to-synonymous positions was two to ten times higher than the ratio of interspecific divergences at these positions, suggesting an excess of slightly deleterious nonsynonymous polymorphisms. However, such an overabundance of nonsynonymous single nucleotide polymorphisms (SNPs) was not found in human nuclear genomes. Here, genome-wide estimates using >14,000 human-chimp nuclear genes and 1 million SNPs from four human genomes showed a significant proportion of deleterious nonsynonymous SNPs (∼ 15%). Importantly, this study reveals a negative correlation between the magnitude of selection pressure and the proportion of deleterious SNPs on human genes. The proportion of deleterious amino acid replacement polymorphisms is 3.5 times higher in genes under high purifying selection compared with that in less constrained genes (28% vs. 8%). These results are explained by differences in the extent of contribution of mildly deleterious mutations to diversity and substitution. PMID:20974690

  8. Twinning of cubic diamond explains reported nanodiamond polymorphs

    PubMed Central

    Németh, Péter; Garvie, Laurence A. J.; Buseck, Peter R.

    2015-01-01

    The unusual physical properties and formation conditions attributed to h-, i-, m-, and n-nanodiamond polymorphs has resulted in their receiving much attention in the materials and planetary science literature. Their identification is based on diffraction features that are absent in ordinary cubic (c-) diamond (space group: Fd-3m). We show, using ultra-high-resolution transmission electron microscope (HRTEM) images of natural and synthetic nanodiamonds, that the diffraction features attributed to the reported polymorphs are consistent with c-diamond containing abundant defects. Combinations of {113} reflection and <011> rotation twins produce HRTEM images and d-spacings that match those attributed to h-, i-, and m-diamond. The diagnostic features of n-diamond in TEM images can arise from thickness effects of c-diamonds. Our data and interpretations strongly suggest that the reported nanodiamond polymorphs are in fact twinned c-diamond. We also report a new type of twin (<11> rotational), which can give rise to grains with dodecagonal symmetry. Our results show that twins are widespread in diamond nanocrystals. A high density of twins could strongly influence their applications. PMID:26671288

  9. Gene polymorphisms of fibrinolytic enzymes in coal workers' pneumoconiosis

    SciTech Connect

    Chang, L.C.; Tseng, J.C.; Hua, C.C.; Liu, Y.C.; Shieh, W.B.; Wu, H.P.

    2006-03-15

    The authors assessed the gene polymorphisms of missense C/T polymorphism in exon 6 of the urokinase-plasminogen activator (PLAU) gene (PLAU P141L), A/u-repeat in intron 8 of the tissue-type plasminogen activator (PLAT) gene (PLAT TPA25 Alu insertion), and 4G/5G in the promoter region of the serine proteinase inhibitor, clade E (SERPINE) or plasminogen activator inhibitor type 1 gene (SERPINE1 -675 4G/5G) in 153 healthy volunteers and 154 retired coal miners with coal miners' pneumoconiosis (CWP). The CWP subjects included 94 individuals with simple pneumoconiosis and 60 individuals with progressive massive fibrosis presenting with worse pulmonary function. The distributions of genotypes of these three genes did not differ between the control and CWP subjects or between subjects with simple pneumoconiosis and those with progressive massive fibrosis. However, by assessing duration of work and its interaction with genotypes by means of logistic regression, the authors found the missense C/T polymorphism in exon 6 of the PLAU gene to be an effect modifier of the association between work duration and the development of progressive massive fibrosis.

  10. Myeloperoxidase promoter region polymorphism and lung cancer risk.

    PubMed

    Wu, Xifeng; Schabath, Matthew B; Spitz, Margaret R

    2003-01-01

    Historically, myeloperoxidase activity and subsequent production of hypochlorous acid has been associated with the killing of host-invading microorganisms (bacteria, viruses, and fungi). Currently, there is a wealth of evidence that the MPO polymorphism and enzyme activity is associated with a wide range of pathological and biological processes, including lung cancer carcinogenesis. Although the molecular epidemiology reports reviewed in this chapter are not in complete agreement on all aspects of their findings, it is evident that the MPO polymorphism contributes to the modulation of overall lung cancer risk. Four of the five molecular epidemiologic studies reviewed in this chapter utilized similar case-control study designs with quite different sources of populations. These studies all demonstrate that the MPO variant genotype modulates overall lung cancer risk. However, these studies are not in agreement regarding age and gender effects, and gene-environmental interactions. The nested case control study designed utilized by Misra et al. (35) is a valid and sound approach, but their results found no evidence of an association. Certainly, heterogeneity in study populations can contribute to the variability between these studies. Additionally, epidemiologic issues such as case-control matching and sources of control populations may contribute to the conflicting findings. Thus, the publication of inconsistent or null studies as well as other positive findings is certainly encouraged to elucidate the range of effects associated with the MPO polymorphism and lung cancer risk. PMID:12407737

  11. Polymorphism influences singlet fission rates in tetracene thin films

    DOE PAGESBeta

    Arias, Dylan H.; Ryerson, Joseph L.; Cook, Jasper D.; Damrauer, Niels H.; Johnson, Justin C.

    2015-11-06

    Here, we report the effect of crystal structure and crystallite grain size on singlet fission (SF) in polycrystalline tetracene, one of the most widely studied SF and organic semiconductor materials. SF has been comprehensively studied in one polymoprh (Tc I), but not in the other, less stable polymorph (Tc II). Using carefully controlled thermal evaporation deposition conditions and high sensitivity ultrafast transient absorption spectroscopy, we found that for large crystallite size samples, SF in nearly pure Tc II films is significantly faster than SF in Tc I films. We also discovered that crystallite size has a minimal impact on themore » SF rate in Tc II films, but a significant influence in Tc I films. Large crystallites exhibit SF times of 125 ps and 22 ps in Tc I and Tc II, respectively, whereas small crystallites have SF times of 31 ps and 33 ps. Our results demonstrate first, that attention must be paid to polymorphism in obtaining a self-consistent rate picture for SF in tetracene and second, that control of polymorphism can play a significant role towards achieving a mechanistic understanding of SF in polycrystalline systems. In this latter context we show that conventional theory based on non-covalent tetracene couplings is insufficient, thus highlighting the need for models that capture the delocalized and highly mobile nature of excited states in elucidating the full photophysical picture.« less

  12. Structures and energetics of Ga2O3 polymorphs

    NASA Astrophysics Data System (ADS)

    Yoshioka, S.; Hayashi, H.; Kuwabara, A.; Oba, F.; Matsunaga, K.; Tanaka, I.

    2007-08-01

    First-principles calculations are made for five Ga2O3 polymorphs. The structure of ɛ-Ga2O3 with the space group Pna 21 (No. 33, orthorhombic), which is sometimes called κ-Ga2O3 in the literature, is consistent with experimental reports. The structure of γ-Ga2O3 is optimized within 14 inequivalent configurations of defective spinel structures. Phonon dispersion curves of four polymorphs are obtained. The volume expansivity, bulk modulus, and specific heat at constant volume are computed as a function of temperature within the quasi-harmonic approximation. The Helmholtz free energies of the polymorphs are thus compared. The expansivity shows a relationship of β<ɛ<α<δ, while β<ɛ<δ<α for the bulk modulus. The formation free energies have the tendency β<ɛ<α<δ<γ at low temperatures. With the increase of temperature, the difference in free energy between the β-phase and the ɛ-phase becomes smaller. Eventually the ɛ phase becomes more stable at above 1600 K.

  13. Androgen receptor and monoamine oxidase polymorphism in wild bonobos.

    PubMed

    Garai, Cintia; Furuichi, Takeshi; Kawamoto, Yoshi; Ryu, Heungjin; Inoue-Murayama, Miho

    2014-12-01

    Androgen receptor gene (AR), monoamine oxidase A gene (MAOA) and monoamine oxidase B gene (MAOB) have been found to have associations with behavioral traits, such as aggressiveness, and disorders in humans. However, the extent to which similar genetic effects might influence the behavior of wild apes is unclear. We examined the loci AR glutamine repeat (ARQ), AR glycine repeat (ARG), MAOA intron 2 dinucleotide repeat (MAin2) and MAOB intron 2 dinucleotide repeat (MBin2) in 32 wild bonobos, Pan paniscus, and compared them with those of chimpanzees, Pan troglodytes, and humans. We found that bonobos were polymorphic on the four loci examined. Both loci MAin2 and MBin2 in bonobos showed a higher diversity than in chimpanzees. Because monoamine oxidase influences aggressiveness, the differences between the polymorphisms of MAin2 and MBin2 in bonobos and chimpanzees may be associated with the differences in aggression between the two species. In order to understand the evolution of these loci and AR, MAOA and MAOB in humans and non-human primates, it would be useful to conduct future studies focusing on the potential association between aggressiveness, and other personality traits, and polymorphisms documented in bonobos. PMID:25606465

  14. IMGT/HLA and the Immuno Polymorphism Database.

    PubMed

    Robinson, James; Halliwell, Jason A; Marsh, Steven G E

    2014-01-01

    The IMGT/HLA Database (http://www.ebi.ac.uk/ipd/imgt/hla/) was first released over 15 years ago, providing the HLA community with a searchable repository of highly curated HLA sequences. The HLA complex is located within the 6p21.3 region of human chromosome 6 and contains more than 220 genes of diverse function. Many of the genes encode proteins of the immune system and are highly polymorphic, with some genes currently having over 3,000 known allelic variants. The Immuno Polymorphism Database (IPD) (http://www.ebi.ac.uk/ipd/) expands on this model, with a further set of specialist databases related to the study of polymorphic genes in the immune system. The IPD project works with specialist groups or nomenclature committees who provide and curate individual sections before they are submitted to IPD for online publication. IPD currently consists of four databases: IPD-KIR contains the allelic sequences of killer-cell immunoglobulin-like receptors; IPD-MHC is a database of sequences of the major histocompatibility complex of different species; IPD-HPA, alloantigens expressed only on platelets; and IPD-ESTDAB, which provides access to the European Searchable Tumour Cell-Line Database, a cell bank of immunologically characterized melanoma cell lines. Through the work of the HLA Informatics Group and in collaboration with the European Bioinformatics Institute we are able to provide public access to this data through the website http://www.ebi.ac.uk/ipd/. PMID:25048120

  15. Polymorphism influences singlet fission rates in tetracene thin films

    SciTech Connect

    Arias, Dylan H.; Ryerson, Joseph L.; Cook, Jasper D.; Damrauer, Niels H.; Johnson, Justin C.

    2015-11-06

    Here, we report the effect of crystal structure and crystallite grain size on singlet fission (SF) in polycrystalline tetracene, one of the most widely studied SF and organic semiconductor materials. SF has been comprehensively studied in one polymoprh (Tc I), but not in the other, less stable polymorph (Tc II). Using carefully controlled thermal evaporation deposition conditions and high sensitivity ultrafast transient absorption spectroscopy, we found that for large crystallite size samples, SF in nearly pure Tc II films is significantly faster than SF in Tc I films. We also discovered that crystallite size has a minimal impact on the SF rate in Tc II films, but a significant influence in Tc I films. Large crystallites exhibit SF times of 125 ps and 22 ps in Tc I and Tc II, respectively, whereas small crystallites have SF times of 31 ps and 33 ps. Our results demonstrate first, that attention must be paid to polymorphism in obtaining a self-consistent rate picture for SF in tetracene and second, that control of polymorphism can play a significant role towards achieving a mechanistic understanding of SF in polycrystalline systems. In this latter context we show that conventional theory based on non-covalent tetracene couplings is insufficient, thus highlighting the need for models that capture the delocalized and highly mobile nature of excited states in elucidating the full photophysical picture.

  16. Alcohol and aldehyde dehydrogenase polymorphisms in Chinese and Indian populations.

    PubMed

    Tan, Ene-Choo; Lim, Leslie; Leong, Jern-Yi; Lim, Jing-Yan; Lee, Arthur; Yang, Jun; Tan, Chay-Hoon; Winslow, Munidasa

    2010-01-01

    The association between two functional polymorphisms in alcohol dehydrogenase (ADH2/ADH1B) and aldehyde dehydrogenase (ALDH2) genes and alcohol dependence was examined in 182 Chinese and Indian patients undergoing treatment for alcohol dependence and 184 screened control subjects from Singapore. All subjects were screened by the Alcohol Use Disorders Identification Test (AUDIT). Patients were also administered the Severity of Alcohol Dependence Questionnaire (SADQ). Polymorphisms were genotyped by allele-specific polymerase chain reaction and selected genotypes confirmed by DNA sequencing or restriction fragment length polymorphism. Our results showed that frequencies of ADH1B*2 and ALDH2*2 were higher in controls compared to alcohol-dependent subjects for both Chinese and Indians. Frequencies of these two alleles were also higher in the 104 Chinese controls compared to the 80 Indian controls. None of the eight Chinese who were homozygous for both protective alleles was alcohol dependent. The higher frequencies of the protective alleles could explain the lower rate of alcohol dependence in Chinese. PMID:20025435

  17. Scent of a Dragonfly: Sex Recognition in a Polymorphic Coenagrionid.

    PubMed

    Frati, Francesca; Piersanti, Silvana; Conti, Eric; Rebora, Manuela; Salerno, Gianandrea

    2015-01-01

    In polymorphic damselflies discrimination of females from males is complex owing to the presence of androchrome and gynochrome females. To date there is no evidence that damselflies use sensory modalities other than vision (and tactile stimuli) in mate searching and sex recognition. The results of the present behavioural and electrophysiological investigations on Ischnura elegans, a polymorphic damselfly, support our hypothesis that chemical cues could be involved in Odonata sex recognition. The bioassays demonstrate that males in laboratory prefer female to male odour, while no significant difference was present in male behavior between stimuli from males and control. The bioassays suggest also some ability of males to distinguish between the two female morphs using chemical stimuli. The ability of male antennae to perceive odours from females has been confirmed by electrophysiological recordings. These findings are important not only to get insight into the chemical ecology of Odonata, and to shed light into the problem of olfaction in Paleoptera, but could be useful to clarify the controversial aspects of the mating behavior of polymorphic coenagrionids. Behavioural studies in the field are necessary to investigate further these aspects. PMID:26305118

  18. Association Between COX-2 Polymorphisms and Lung Cancer Risk

    PubMed Central

    Wang, Weiwei; Fan, Xinyun; Zhang, Yong; Yang, Yi; Yang, Siyuan; Li, Gaofeng

    2015-01-01

    Background Multiple relevant risk factors for lung cancer have been reported in different populations, but results of previous studies were not consistent. Therefore, a meta-analysis is necessary to summarize these outcomes and reach a relatively comprehensive conclusion. Material/Methods STATA 12.0 software was used for all statistical of the relationship between COX-2 polymorphisms and lung cancer risk. Inter-study heterogeneity was examined with the Q statistic (significance level at P<0.1). The publication bias among studies in the meta-analysis was analyzed with Begg’s funnel plot and Egger’s test. Hardy-Weinberg equilibrium was tested in all controls of the studies. Results COX-2 rs20417 polymorphism had a significant association with reduced risk of lung cancer under homozygous and recessive models, and similar results were observed in white and population-based subgroups under 2 and 3 contrasts, respectively. Additionally, rs2066826 polymorphism manifested a strong correlation with increased risk of lung cancer under 5 genetic models. Conclusions In COX-2 gene, rs20417 may have a certain relationship with reduced risk of lung cancer, while rs2066826 may increase the risk of lung cancer. PMID:26624903

  19. Role of moisture on the physical stability of polymorphic olanzapine.

    PubMed

    Paisana, Maria C; Wahl, Martin A; Pinto, João F

    2016-07-25

    The focus of this study was the understanding of the hydrate transformations of anhydrous olanzapine Forms I and II (the most common polymorphs) upon exposure to different moisture conditions (11, 53, 75, 93% RH) and direct contact with water (e.g. aqueous slurry) and the impact of hydration on the aqueous dissolution rates of the polymorphs. The kinetics of reversible transformations (anhydrate-hydrate phases) and the identification of polymorphs were evaluated by differential scanning calorimetry, thermogravimetry, infrared (DRIFT) and X-ray powder diffraction. The results showed that anhydrous Forms I and II have undergone water vapor phase induced transformations at 93% and 75% RH, respectively. At 93% RH Forms I and II showed to hydrate into dihydrates D and B, respectively, the latter with a higher hydration rate. The conversion of Form I into the dihydrate D showed to affect the dissolution rate of olanzapine (f2<50). As slurries both forms showed to hydrate into a mixture of two different Forms - dihydrate B and higher hydrate. The study provided an understanding of the conversion pathways of the different forms when they were exposed to humid air or aqueous environments, resembling the transformations that might occur during processing, storage or during the persecution of dissolution tests to assess the quality of dosage forms delivering olanzapine. PMID:27234701

  20. Association between apolipoprotein E gene polymorphism and depression.

    PubMed

    Feng, Fang; Lu, Shan-Shan; Hu, Cai-Yun; Gong, Feng-Feng; Qian, Zhen-Zhong; Yang, Hui-Yun; Wu, Yi-Le; Zhao, Yuan-Yuan; Bi, Peng; Sun, Ye-Huan

    2015-08-01

    We performed an updated meta-analysis to obtain a more precise estimation of the relationship between apolipoprotein E (ApoE) gene polymorphism and susceptibility to depression, as previous reports have been inconsistent. Twenty studies with 2286 depression patients and 3845 controls were included. Odds ratios (OR) with 95% confidence intervals (CI) were calculated to assess the association between ApoE gene polymorphism and depression using a random effects model. Results showed a significant association between ApoE gene polymorphism and susceptibility to depression in the overall population (ε2/ε3 genotype versus ε3/ε3: OR 0.76, 95% CI 0.59-0.99). Subgroup analyses indicated an association in the Caucasian population (ε2 allele versus ε3: OR 0.75, 95% CI 0.58-0.97) as well as in late-life depression (LLD) patients (ε3/ε4 genotype versus ε3/ε3: OR 1.34, 95% CI 1.07-1.68, and ε4 allele versus ε3: OR 1.30, 95% CI 1.06-1.59). We concluded that the ε2/ε3 genotype likely provided a protective effect against depression in the overall population and the ε2 allele acted as a protective factor for depression in the Caucasian population while the ε4 allele and ε3/ε4 genotype were associated with an increased risk of depression in the LLD subjects. PMID:25979253