Sample records for xi gene frequencies

  1. Group 16SrXI phytoplasma strains, including subgroup 16SrXI-B and a new subgroup, 16SrXI-D, are associated with sugar cane white leaf.

    PubMed

    Zhang, Rong-Yue; Li, Wen-Feng; Huang, Ying-Kun; Wang, Xiao-Yan; Shan, Hong-Li; Luo, Zhi-Ming; Yin, Jiong

    2016-01-01

    Sugar cane white leaf (SCWL) is a serious disease caused by phytoplasmas. In this study, we performed nested PCR with phytoplasma universal primer pairs (P1/P7 and R16F2n/R16R2) for the 16S rRNA gene to detect SCWL phytoplasmas in 31 SCWL samples collected from Baoshan and Lincang, Yunnan, China. We cloned and sequenced the nested PCR products, revealing that the 16S rRNA gene sequences from 31 SCWL samples were all 1247 bp in length and shared more than 99 % nucleotide sequence similarity with the 16S rRNA gene sequences of SCWL phytoplasmas from various countries. Based on the reported 16S rRNA gene sequence data from SCWL isolates of various countries, we conducted phylogenetic and virtual RFLP analysis. In the resulting phylogenetic tree, all SCWL isolates clustered into two branches, with the Lincang and Baoshan SCWL phytoplasma isolates belonging to different branches. The virtual RFLP patterns show that phytoplasmas of the Lincang branch belong to subgroup 16SrXI-B. However, the virtual RFLP patterns revealed by HaeIII digestion of phytoplasmas of the Baoshan branch differed from those of subgroup 16SrXI-B. According to the results of phylogenetic and virtual RFLP analysis, we propose that the phytoplasmas of the Baoshan branch represent a new subgroup, 16SrXI-D. These findings suggest that SCWL is caused by phytoplasmas from group 16SrXI, including subgroup 16SrXI-B and a new subgroup, 16SrXI-D.

  2. Mixing {Xi}--{Xi}' Effects and Static Properties of Heavy {Xi}'s

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

    Aliev, T. M.; Ozpineci, A.; Zamiralov, V. S.

    It is shown the importance of mixing of heavy baryons {Xi}--{Xi}' with the new quantum numbers for analysis of its characteristics. The quark model of Ono is used as an example. Masses of new baryons as well as mixing angles of the states {Xi}--{Xi}' are obtained. The same reasoning is shown to be valid for the interpolating currents of these baryons in the framework of the QCD sum rules.

  3. Myosins XI-K, XI-1, and XI-2 are required for development of pavement cells, trichomes, and stigmatic papillae in Arabidopsis

    PubMed Central

    2012-01-01

    Background The positioning and dynamics of vesicles and organelles, and thus the growth of plant cells, is mediated by the acto-myosin system. In Arabidopsis there are 13 class XI myosins which mediate vesicle and organelle transport in different cell types. So far the involvement of five class XI myosins in cell expansion during the shoot and root development has been shown, three of which, XI-1, XI-2, and XI-K, are essential for organelle transport. Results Simultaneous depletion of Arabidopsis class XI myosins XI-K, XI-1, and XI-2 in double and triple mutant plants affected the growth of several types of epidermal cells. The size and shape of trichomes, leaf pavement cells and the elongation of the stigmatic papillae of double and triple mutant plants were affected to different extent. Reduced cell size led to significant size reduction of shoot organs in the case of triple mutant, affecting bolt formation, flowering time and fertility. Phenotype analysis revealed that the reduced fertility of triple mutant plants was caused by delayed or insufficient development of pistils. Conclusions We conclude that the class XI myosins XI-K, XI-1 and XI-2 have partially redundant roles in the growth of shoot epidermis. Myosin XI-K plays more important role whereas myosins XI-1 and XI-2 have minor roles in the determination of size and shape of epidermal cells, because the absence of these two myosins is compensated by XI-K. Co-operation between myosins XI-K and XI-2 appears to play an important role in these processes. PMID:22672737

  4. Mass formulas for {Xi}{sub c} and {Xi}{sub b} baryons

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

    Aliev, T. M.; Zamiralov, V. S.; Ozpineci, A.

    The importance of taking into account the mixing of the heavy cascade baryons {Xi} and {Xi}' that have new quantum numbers in analyzing their properties is shown. The Ono quark model is considered by way of example. The masses of the new baryons and the {Xi}-{Xi}' mixing angles are obtained. The same approach is applied to the interpolating currents of these baryons within QCD sum rules.

  5. MuPeXI: prediction of neo-epitopes from tumor sequencing data.

    PubMed

    Bjerregaard, Anne-Mette; Nielsen, Morten; Hadrup, Sine Reker; Szallasi, Zoltan; Eklund, Aron Charles

    2017-09-01

    Personalization of immunotherapies such as cancer vaccines and adoptive T cell therapy depends on identification of patient-specific neo-epitopes that can be specifically targeted. MuPeXI, the mutant peptide extractor and informer, is a program to identify tumor-specific peptides and assess their potential to be neo-epitopes. The program input is a file with somatic mutation calls, a list of HLA types, and optionally a gene expression profile. The output is a table with all tumor-specific peptides derived from nucleotide substitutions, insertions, and deletions, along with comprehensive annotation, including HLA binding and similarity to normal peptides. The peptides are sorted according to a priority score which is intended to roughly predict immunogenicity. We applied MuPeXI to three tumors for which predicted MHC-binding peptides had been screened for T cell reactivity, and found that MuPeXI was able to prioritize immunogenic peptides with an area under the curve of 0.63. Compared to other available tools, MuPeXI provides more information and is easier to use. MuPeXI is available as stand-alone software and as a web server at http://www.cbs.dtu.dk/services/MuPeXI .

  6. Ultrabass Sounds of the Giant Star xi Hya

    NASA Astrophysics Data System (ADS)

    2002-05-01

    First Observations of Solar-type Oscillations in a Star Very Different from the Sun Summary About 30 years ago, astronomers realised that the Sun resonates like a giant musical instrument with well-defined periods (frequencies). It forms a sort of large, spherical organ pipe. The energy that excites these sound waves comes from the turbulent region just below the Sun's visible surface. Observations of the solar sound waves (known as " helioseismology ") have resulted in enormous progress in the exploration of the interior of the Sun, otherwise hidden from view. As is the case on Earth, seismic techniques can be applied and the detailed interpretation of the observed oscillation periods has provided quite accurate information about the structure and motions inside the Sun, our central star. It has now also become possible to apply this technique to some solar-type stars. The first observations concerned the northern star eta Bootis (cf. ESO PR 16/94 ). Last year, extensive and much more accurate observations with the 1.2-m Swiss telescope at the ESO La Silla Observatory proved that Alpha Centauri , a solar "twin", behaves very much like the Sun (cf. ESO PR 15/01 ), and that some of the periods are quite similar to those in the Sun. These new observational data were of a superb quality, and that study marked a true break-through in the new research field of " asteroseismology " (seismology of the stars) for solar-type stars. But what about other types of stars, for instance those that are much larger than the Sun? Based on an extremely intensive observing project with the same telescope, an international group of astronomers [1] has found that the giant star xi Hya ("xi" is the small greek letter [2]; "Hya" is an abbreviation of "Hydrae") behaves like a giant sub-ultra-bass instrument . This star is located in the constellation Hydra (the Water-Monster) at a distance of 130 light-years, it has a radius about 10 times that of the Sun and its luminosity is about 60

  7. Cloning and characterization of XiR1, a locus responsible for dagger nematode resistance in grape.

    PubMed

    Hwang, Chin-Feng; Xu, Kenong; Hu, Rong; Zhou, Rita; Riaz, Summaira; Walker, M Andrew

    2010-08-01

    The dagger nematode, Xiphinema index, feeds aggressively on grape roots and in the process, vectors grapevine fanleaf virus (GFLV) leading to the severe viral disease known as fanleaf degeneration. Resistance to X. index and GFLV has been the key objective of grape rootstock breeding programs. A previous study found that resistance to X. index derived from Vitis arizonica was largely controlled by a major quantitative trait locus, XiR1 (X. index Resistance 1), located on chromosome 19. The study presented here develops high-resolution genetic and physical maps in an effort to identify the XiR1 gene(s). The mapping was carried out with 1,375 genotypes in three populations derived from D8909-15, a resistant selection from a cross of V. rupestris A. de Serres (susceptible) x V. arizonica b42-26 (resistant). Resistance to X. index was evaluated on 99 informative recombinants that were identified by screening the three populations with two markers flanking the XiR1 locus. The high-resolution genetic map of XiR1 was primarily constructed with seven DNA markers developed in this study. Physical mapping of XiR1 was accomplished by screening three bacterial artificial chromosome (BAC) libraries constructed from D8909-15, V. vinifera Cabernet Sauvignon and V. arizonica b42-26. A total of 32 BAC clones were identified and the XiR1 locus was delineated within a 115 kb region. Sequence analysis of three BAC clones identified putative nucleotide binding/leucine-rich repeat (NB-LRR) genes. This is the first report of a closely linked major gene locus responsible for ectoparasitic nematode resistance. The markers developed from this study are being used to expedite the breeding of resistant grape rootstocks.

  8. Cloning and characterization of XiR1, a locus responsible for dagger nematode resistance in grape

    PubMed Central

    Hwang, Chin-Feng; Xu, Kenong; Hu, Rong; Zhou, Rita; Riaz, Summaira

    2010-01-01

    The dagger nematode, Xiphinemaindex, feeds aggressively on grape roots and in the process, vectors grapevine fanleaf virus (GFLV) leading to the severe viral disease known as fanleaf degeneration. Resistance to X. index and GFLV has been the key objective of grape rootstock breeding programs. A previous study found that resistance to X. index derived from Vitis arizonica was largely controlled by a major quantitative trait locus, XiR1 (X. index Resistance 1), located on chromosome 19. The study presented here develops high-resolution genetic and physical maps in an effort to identify the XiR1 gene(s). The mapping was carried out with 1,375 genotypes in three populations derived from D8909-15, a resistant selection from a cross of V. rupestris A. de Serres (susceptible) × V. arizonica b42-26 (resistant). Resistance to X. index was evaluated on 99 informative recombinants that were identified by screening the three populations with two markers flanking the XiR1 locus. The high-resolution genetic map of XiR1 was primarily constructed with seven DNA markers developed in this study. Physical mapping of XiR1 was accomplished by screening three bacterial artificial chromosome (BAC) libraries constructed from D8909-15, V. vinifera Cabernet Sauvignon and V. arizonica b42-26. A total of 32 BAC clones were identified and the XiR1 locus was delineated within a 115 kb region. Sequence analysis of three BAC clones identified putative nucleotide binding/leucine-rich repeat (NB-LRR) genes. This is the first report of a closely linked major gene locus responsible for ectoparasitic nematode resistance. The markers developed from this study are being used to expedite the breeding of resistant grape rootstocks. PMID:20490447

  9. Observation of the $$\\Xi_b^0$$ Baryon

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

    Aaltonen, T.; /Helsinki Inst. of Phys.; Alvarez Gonzalez, B.

    The observation of the bottom, strange baryon {Xi}{sup 0}{sub b} through the decay chain {Xi}{sup 0}{sub b} {yields} {Xi}{sup +}{sub c} {pi}{sup -}, where {Xi}{sup +}{sub c} {yields} {Xi}{sup -} {pi}{sup +} {pi}{sup +}, {Xi}{sup -} {yields} {Lambda} {yields} p {pi}{sup -}, is reported using data corresponding to an integrated luminosity of 4.2 ft{sup -1} from p{anti p} collisions at {radical}{ovr s} = 1.96 TeV recorded with the Collider Detector at Fermilab. A signal of 25.3{sup +5.6}{sub -5.4} candidates is observed whose probability of arising from a background fluctuation is 3.6 x 10{sup -12}, corresponding to 6.8 Gaussian standard deviations.more » The {Xi}{sup 0}{sub b} mass is measured to be 5787.8 {+-} 5.0(stat) {+-} 1.3(syst) MeV/c{sup 2}. In addition, the {Xi}{sup -}{sub b} is observed through the process {Xi}{sup -}{sub b} {yields} {Xi}{sup 0}{sub c} {pi}{sup -}, where {Xi}{sup 0}{sub c} {yields} {Xi}{sup -} {pi}{sup +}, {Xi}{sup -} {yields} {Lambda} {pi}{sup -}, and {Lambda} {yields} p {pi}{sup -}.« less

  10. Xi0 and anti-Xi0 Polarization Measurements at 800-GeV/c

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

    Abouzaid, E.; Alavi-Harati, A.; Alexopoulos, T.

    The polarization of {Xi}{sup 0} and {bar {Xi}}{sup 0} hyperons produced by 800 GeV/c protons on a BeO target at a fixed targeting angle of 4.8 mrad is measured by the KTeV experiment at Fermilab. The result of 9.7% for {Xi}{sup 0} polarization shows no significant energy dependence when compared to a result obtained at 400 GeV/c production energy and at twice the targeting angle. The polarization of the {Xi}{sup 0} is measured for the first time and found to be consistent with zero. They also examine the dependence of polarization on production p{sub t}.

  11. Detection of mecC-Positive Staphylococcus aureus (CC130-MRSA-XI) in Diseased European Hedgehogs (Erinaceus europaeus) in Sweden

    PubMed Central

    Monecke, Stefan; Gavier-Widen, Dolores; Mattsson, Roland; Rangstrup-Christensen, Lena; Lazaris, Alexandros; Coleman, David C.; Shore, Anna C.; Ehricht, Ralf

    2013-01-01

    Recently, a novel mec gene conferring beta-lactam resistance in Staphylococcus aureus has been discovered. This gene, mecC, is situated on a SCCmec XI element that has to date been identified in clonal complexes 49, 130, 425, 599 and 1943. Some of the currently known isolates have been identified from animals. This, and observations of mecA alleles that do not confer beta-lactam resistance, indicate that mec genes might have a reservoir in Staphylococcus species from animals. Thus it is important also to screen wildlife isolates for mec genes. Here, we describe mecC-positive Staphylococcus aureus (ST130-MRSA-XI) and the lesions related to the infection in two diseased free-ranging European hedgehogs (Erinaceus europaeus). One was found dead in 2003 in central Sweden, and suffered from S. aureus septicaemia. The other one, found on the island of Gotland in the Baltic Sea in 2011, showed a severe dermatitis and was euthanised. ST130-MRSA-XI isolates were isolated from lesions from both hedgehogs and were essentially identical to previously described isolates from humans. Both isolates carried the complete SCCmec XI element. They lacked the lukF-PV/lukS-PV and lukM/lukF-P83 genes, but harboured a gene for an exfoliative toxin homologue previously described from Staphylococcus hyicus, Staphylococcus pseudintermedius and other S. aureus of the CC130 lineage. To the best of our knowledge, these are the first reported cases of CC130-MRSA-XI in hedgehogs. Given that one of the samples was taken as early as 2003, this was the earliest detection of this strain and of mecC in Sweden. This and several other recent observations suggest that CC130 might be a zoonotic lineage of S. aureus and that SCCmec XI/mecC may have originated from animal pathogens. PMID:23776626

  12. Detection of mecC-positive Staphylococcus aureus (CC130-MRSA-XI) in diseased European hedgehogs (Erinaceus europaeus) in Sweden.

    PubMed

    Monecke, Stefan; Gavier-Widen, Dolores; Mattsson, Roland; Rangstrup-Christensen, Lena; Lazaris, Alexandros; Coleman, David C; Shore, Anna C; Ehricht, Ralf

    2013-01-01

    Recently, a novel mec gene conferring beta-lactam resistance in Staphylococcus aureus has been discovered. This gene, mecC, is situated on a SCCmec XI element that has to date been identified in clonal complexes 49, 130, 425, 599 and 1943. Some of the currently known isolates have been identified from animals. This, and observations of mecA alleles that do not confer beta-lactam resistance, indicate that mec genes might have a reservoir in Staphylococcus species from animals. Thus it is important also to screen wildlife isolates for mec genes. Here, we describe mecC-positive Staphylococcus aureus (ST130-MRSA-XI) and the lesions related to the infection in two diseased free-ranging European hedgehogs (Erinaceus europaeus). One was found dead in 2003 in central Sweden, and suffered from S. aureus septicaemia. The other one, found on the island of Gotland in the Baltic Sea in 2011, showed a severe dermatitis and was euthanised. ST130-MRSA-XI isolates were isolated from lesions from both hedgehogs and were essentially identical to previously described isolates from humans. Both isolates carried the complete SCCmec XI element. They lacked the lukF-PV/lukS-PV and lukM/lukF-P83 genes, but harboured a gene for an exfoliative toxin homologue previously described from Staphylococcus hyicus, Staphylococcus pseudintermedius and other S. aureus of the CC130 lineage. To the best of our knowledge, these are the first reported cases of CC130-MRSA-XI in hedgehogs. Given that one of the samples was taken as early as 2003, this was the earliest detection of this strain and of mecC in Sweden. This and several other recent observations suggest that CC130 might be a zoonotic lineage of S. aureus and that SCCmec XI/mecC may have originated from animal pathogens.

  13. [Correlativity study of the distribution of soil magnetic susceptibility and the heavy metal contents in Xi'an City].

    PubMed

    Chen, Xiu-Duan; Lu, Xin-Wei; Yang, Guang

    2013-03-01

    The magnetic susceptibility and the concentrations of Co, Cr, Cu, Pb, Sn, Sr and Ba in topsoil samples from Xi'an City were measured to study their spatial distribution and their correlation in this study. The results show that the concentrations of all measured heavy metals are higher than their background values in Cinnamon topsoil, which is the main soil type of Xi'an City. The heavy metals concentrations and the magnetic susceptibility of the studied samples display moderate variance. Co, Cr, Cu, Pb, Sn, Sr and Ba are significantly positively correlated with low-frequency magnetic susceptibility, while are significantly negatively correlated with frequency susceptibility. The spatial distribution of low-frequency magnetic susceptibility is identical with the concentrations of Pb and Cu. However, the spatial variation of frequency magnetic susceptibility is different from the concentrations of Co, Cr and Ba. The pollution assessment results show that the heavy metal pollution in topsoil of Xi'an City is moderate. The spatial contribution of the pollution load index was significantly correlated with the magnetic susceptibility of topsoil in Xi'an City. Therefore, soil magnetic susceptibility can be used as an effective monitoring means for heavy metal pollution in urban soil.

  14. Arabidopsis Myosins XI1, XI2, and XIK Are Crucial for Gravity-Induced Bending of Inflorescence Stems

    PubMed Central

    Talts, Kristiina; Ilau, Birger; Ojangu, Eve-Ly; Tanner, Krista; Peremyslov, Valera V.; Dolja, Valerian V.; Truve, Erkki; Paves, Heiti

    2016-01-01

    Myosins and actin filaments in the actomyosin system act in concert in regulating cell structure and dynamics and are also assumed to contribute to plant gravitropic response. To investigate the role of the actomyosin system in the inflorescence stem gravitropism, we used single and multiple mutants affecting each of the 17 Arabidopsis myosins of class VIII and XI. We show that class XI but not class VIII myosins are required for stem gravitropism. Simultaneous loss of function of myosins XI1, XI2, and XIK leads to impaired gravitropic bending that is correlated with altered growth, stiffness, and insufficient sedimentation of gravity sensing amyloplasts in stem endodermal cells. The gravitropic defect of the corresponding triple mutant xi1 xi2 xik could be rescued by stable expression of the functional XIK:YFP in the mutant background, indicating a role of class XI myosins in this process. Altogether, our results emphasize the critical contributions of myosins XI in stem gravitropism of Arabidopsis. PMID:28066484

  15. Donor motivation in Xi'an, China: comparison with Canadian donors.

    PubMed

    O'Brien, S F; Shao, Z-J; Osmond, L; Yi, Q-L; Li, C-Y; An, Q-X

    2013-04-01

    In China, paid donation is prohibited by law. There is little literature assessing donor motivation in China, and comparison with western countries such as Canada is important in understanding the application of Western literature. We compared motivational factors in donors from the city of Xi'an, China, with Canadian donors matched for age, sex and donation status. A total of 218 donors in Xi'an completed an interview about motivation as did 218 Canadian donors matched for age, sex and donation status. Frequencies and percentages of responses to questions were tabulated and compared using the Chi-squared test. Donors in Xi'an and Canada felt a personal responsibility to donate blood (81·2% vs. 78·0%, P = 0·2057), but Xi'an donors were more likely to consider blood donation a social responsibility (81·7% vs. 45·2%, P < 0·0001). Xi'an donors more often believed that society views donation as a normal activity (98·6% vs. 48·4%, P < 0·0001) and that the social atmosphere promotes donation (90·3% vs. 53·5%, P < 0·0001) and saw greater health benefit (52·3% vs. 12·5%, P < 0·0001). Most Xi'an donors believed in balance between their life force (Qi) and blood (86·7% vs. 49·8%, P < 0·0001) but did not believe blood lost from donating would affect this (0·5% vs. 3·8%, P = 0·01). While traditional Chinese beliefs may not be seen as a barrier among people in Xi'an who donate blood, blood donation is seen differently than by Canadian donors. There is a need for more research specific to China to tailor recruitment strategies. © 2012 The Author(s). Vox Sanguinis © 2012 International Society of Blood Transfusion.

  16. Sp1 upregulates the proximal promoter activity of the mouse collagen α1(XI) gene (Col11a1) in chondrocytes.

    PubMed

    Watanabe, Keijirou; Hida, Mariko; Sasaki, Takako; Yano, Hiroyuki; Kawano, Kenji; Yoshioka, Hidekatsu; Matsuo, Noritaka

    2016-02-01

    Type XI collagen is a cartilage-specific extracellular matrix, and is important for collagen fibril formation and skeletal morphogenesis. We have previously reported that NF-Y regulated the proximal promoter activity of the mouse collagen α1(XI) gene (Col11a1) in chondrocytes (Hida et. al. In Vitro Cell. Dev. Biol. Anim. 2014). However, the mechanism of the Col11a1 gene regulation in chondrocytes has not been fully elucidated. In this study, we further characterized the proximal promoter activity of the mouse Col11a1 gene in chondrocytes. Cell transfection experiments with deletion and mutation constructs indicated that the downstream region of the NF-Y binding site (-116 to +1) is also necessary to regulate the proximal promoter activity of the mouse Col11a1 gene. This minimal promoter region has no TATA box and GC-rich sequence; we therefore examined whether the GC-rich sequence (-96 to -67) is necessary for the transcription regulation of the Col11a1 gene. Luciferase assays using a series of mutation constructs exhibited that the GC-rich sequence is a critical element of Col11a1 promoter activity in chondrocytes. Moreover, in silico analysis of this region suggested that one of the most effective candidates was transcription factor Sp1. Consistent with the prediction, overexpression of Sp1 significantly increased the promoter activity. Furthermore, knockdown of Sp1 expression by siRNA transfection suppressed the proximal promoter activity and the expression of endogenous transcript of the mouse Col11a1 gene. Taken together, these results indicate that the transcription factor Sp1 upregulates the proximal promoter activity of the mouse Col11a1 gene in chondrocytes.

  17. Exclusive photoproduction of the cascade (Xi) hyperon

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

    John Price; Bernard Nefkens; Justin Ducote

    2004-09-01

    We report on the first measurement of exclusive {Xi}{sup -}(1321) hyperon photoproduction in {gamma}p {yields} K{sup +}K{sup +}{Xi}{sup -} for 3.2 < E{sub {gamma}} < 3.9 GeV. The final state is identified by the missing mass in p({gamma}, K{sup +}K{sup +})X measured with the CLAS detector at Jefferson Laboratory. We have detected a significant number of the ground-state {Xi}{sup -}(132)1/2{sup +}, and have estimated the total cross section for its production. We have also observed the first excited state {Xi}{sup -}(1530)3/2{sup +}. Photoproduction provides a copious source of {Xi}'s. We discuss the possibilities of a search for the recently proposedmore » {Xi}{sub 5}{sup --} and {Xi}{sub 5}{sup +} pentaquarks.« less

  18. Light {xi} hypernuclei in four-body cluster models

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

    Hiyama, E.; Yamamoto, Y.; Motoba, T.

    Detailed structure calculations in {sub {xi}{sup -}}{sup 12}Be, {sub {xi}{sup -}}{sup 5}H, {sub {xi}{sup -}}{sup 9}Li, {sub {xi}{sup -}}{sup 7}H, and {sub {xi}{sup -}}{sup 10}Li are performed within the framework of the microscopic two-, three-, and four-body cluster models using the Gaussian expansion method. We adopted effective {xi}N interactions derived from the Nijmegen interaction models, which give rise to substantially attractive {xi}-nucleus potentials in accordance with the experimental indications. {sub {xi}{sup -}}{sup 7}H and {sub {xi}{sup -}}{sup 10}Li are predicted to have bound states. we propose to observe the bound states in future (K{sup -},K{sup +}) experiments using {sup 7}Limore » and {sup 10}B targets in addition to the standard {sup 12}C target. The experimental confirmation of these states will provide information on the spin- and isospin-averaged {xi}N interaction.« less

  19. Searches for the pentaquark states {xi}(1860){sup 0} and {xi}(1860){sup --} in neutron-carbon interactions via the EXCHARM experiment

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

    Aleev, A. N.; Amaglobeli, N. S.; Balandin, V. P.

    Results of searches for the pentaquark states {xi}(1860){sup 0} and {xi}(1860){sup --} in neutron-carbon interactions at an average neutron energy of about 51 GeV via the EXCHARM experiment are presented. No such states are found in the {xi}{sup -}{pi}{sup +} and {xi}{sup -}{pi}{sup -} effective-mass spectra examined in this study. Upper limits on the cross sections for {xi}(1860){sup 0} and {xi}(1860){sup --} production are estimated.

  20. Observation of the {Xi}{sub b}{sup 0} Baryon

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

    Aaltonen, T.; Brucken, E.; Devoto, F.

    The observation of the bottom, strange baryon {Xi}{sub b}{sup 0} through the decay chain {Xi}{sub b}{sup 0}{yields}{Xi}{sub c}{sup +}{pi}{sup -}, where {Xi}{sub c}{sup +}{yields}{Xi}{sup -}{pi}{sup +}{pi}{sup +}, {Xi}{sup -}{yields}{Lambda}{pi}{sup -}, and {Lambda}{yields}p{pi}{sup -}, is reported by using data corresponding to an integrated luminosity of 4.2 fb{sup -1} from pp collisions at {radical}(s)=1.96 TeV recorded with the Collider Detector at Fermilab. A signal of 25.3{sub -5.4}{sup +5.6} candidates is observed whose probability of arising from a background fluctuation is 3.6x10{sup -12}, corresponding to 6.8 Gaussian standard deviations. The {Xi}{sub b}{sup 0} mass is measured to be 5787.8{+-}5.0(stat){+-}1.3(syst) MeV/c{sup 2}. In addition,more » the {Xi}{sub b}{sup -} baryon is observed through the process {Xi}{sub b}{sup -}{yields}{Xi}{sub c}{sup 0}{pi}{sup -}, where {Xi}{sub c}{sup 0}{yields}{Xi}{sup -}{pi}{sup +}, {Xi}{sup -}{yields}{Lambda}{pi}{sup -}, and {Lambda}{yields}p{pi}{sup -}.« less

  1. Molecular cloning and biochemical characterization of rabbit factor XI.

    PubMed Central

    Sinha, Dipali; Marcinkiewicz, Mariola; Gailani, David; Walsh, Peter N

    2002-01-01

    Human factor XI, a plasma glycoprotein required for normal haemostasis, is a homodimer (160 kDa) formed by a single interchain disulphide bond linking the Cys-321 of each Apple 4 domain. Bovine, porcine and murine factor XI are also disulphide-linked homodimers. Rabbit factor XI, however, is an 80 kDa polypeptide on non-reducing SDS/PAGE, suggesting that rabbit factor XI exists and functions physiologically either as a monomer, as does prekallikrein, a structural homologue to factor XI, or as a non-covalent homodimer. We have investigated the structure and function of rabbit factor XI to gain insight into the relation between homodimeric structure and factor XI function. Characterization of the cDNA sequence of rabbit factor XI and its amino acid translation revealed that in the rabbit protein a His residue replaces the Cys-321 that forms the interchain disulphide linkage in human factor XI, explaining why rabbit factor XI is a monomer in non-reducing SDS/PAGE. On size-exclusion chromatography, however, purified plasma rabbit factor XI, like the human protein and unlike prekallikrein, eluted as a dimer, demonstrating that rabbit factor XI circulates as a non-covalent dimer. In functional assays rabbit factor XI and human factor XI behaved similarly. Both monomeric and dimeric factor XI were detected in extracts of cells expressing rabbit factor XI. We conclude that the failure of rabbit factor XI to form a covalent homodimer due to the replacement of Cys-321 with His does not impair its functional activity because it exists in plasma as a non-covalent homodimer and homodimerization is an intracellular process. PMID:12084014

  2. Measurement of the Spin of the $$\\Xi(1530)$$ Resonance

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

    Aubert, B.; Bona, M.; Karyotakis, Y.

    The properties of the {Xi}(1530) resonance are investigated in the {Lambda}{sub c}{sup +} {yields} {Xi}{sup -}{pi}{sup +}K{sup +} decay process. The data sample was collected with the BABAR detector at the SLAC PEP-II asymmetric-energy e{sup +}e{sup -} collider operating at center of mass energies 10.58 and 10.54 GeV. The corresponding integrated luminosity is approximately 230 fb{sup -1}. The spin of the {Xi}(1530) is established to be 3/2. The existence of an S-wave amplitude in the {Xi}{sup -}{pi}{sup +} system is inferred, and its interference with the {Xi}(1530)0 amplitude provides the first clear demonstration of the Breit-Wigner phase motion expected formore » the {Xi}(1530). The P{sub 1}(cos {theta}{sub {Xi}{sup -}}) Legendre polynomial moment indicates the presence of a significant S-wave amplitude for {Xi}{sup -}{pi}{sup +} mass values above 1.6 GeV/c{sup 2}, and a dip in the mass distribution at approximately 1.7 GeV/c{sup 2} is interpreted as due to coherent addition of a {Xi}(1690){sup 0} contribution to this amplitude. This would imply J{sup P} = 1/2{sup -} for the {Xi}(1690). Attempts at fitting the {Xi}(1530){sup 0} lineshape yield unsatisfactory results, and this failure is attributed to interference effects associated with the amplitudes describing the K{sup +}{pi}{sup +} and/or {Xi}{sup -}K{sup +} systems.« less

  3. First measurements of J/{psi} decays into {sigma}{sup +}{sigma}{sup -} and {xi}{sup 0}{xi}{sup 0}

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

    Ablikim, M.; Bai, J. Z.; Bai, Y.

    Based on 58x10{sup 6} J/{psi} events collected with the BESII detector at the Beijing Electron-Positron Collider, the baryon pair processes J/{psi}{yields}{sigma}{sup +}{sigma}{sup -} and J/{psi}{yields}{xi}{sup 0}{xi}{sup 0} are observed for the first time. The branching fractions are measured to be B(J/{psi}{yields}{sigma}{sup +}{sigma}{sup -})=(1.50{+-}0.10{+-}0.22)x10{sup -3} and B(J/{psi}{yields}{xi}{sup 0}{xi}{sup 0})=(1.20{+-}0.12{+-}0.21)x10{sup -3}, where the first errors are statistical and the second ones are systematic.

  4. Measurement of the spin of the {xi}(1530) resonance

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

    Aubert, B.; Bona, M.; Karyotakis, Y.

    The properties of the {xi}(1530) resonance are investigated in the {lambda}{sub c}{sup +}{yields}{xi}{sup -}{pi}{sup +}K{sup +} decay process. The data sample was collected with the BABAR detector at the SLAC PEP-II asymmetric-energy e{sup +}e{sup -} collider operating at center-of-mass energies 10.58 and 10.54 GeV. The corresponding integrated luminosity is approximately 230 fb{sup -1}. The spin of the {xi}(1530) is established to be 3/2. The existence of an S-wave amplitude in the {xi}{sup -}{pi}{sup +} system is inferred, and its interference with the {xi}(1530){sup 0} amplitude provides the first clear demonstration of the Breit-Wigner phase motion expected for the {xi}(1530). Themore » P{sub 1}(cos{theta}{sub {xi}}{sub {sup -}}) Legendre polynomial moment indicates the presence of a significant S-wave amplitude for {xi}{sup -}{pi}{sup +} mass values above 1.6 GeV/c{sup 2}, and a dip in the mass distribution at approximately 1.7 GeV/c{sup 2} is interpreted as due to the coherent addition of a {xi}(1690){sup 0} contribution to this amplitude. This would imply J{sup P}=1/2{sup -} for the {xi}(1690). Attempts at fitting the {xi}(1530){sup 0} line shape yield unsatisfactory results, and this failure is attributed to interference effects associated with the amplitudes describing the K{sup +}{pi}{sup +} and/or {xi}{sup -}K{sup +} systems.« less

  5. Search for CP Violation in Hyperon Decay: $$\\Xi^- / \\bar{\\Xi}^+$$ and $$\\Lambda / \\bar{\\Lambda}$$ (in French)

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

    Leros, Nicolas

    2001-06-01

    The HyperCP(EB71) experiment, performed at the Fermi National Accelerator Laboratory in the United States, provides a primary search for direct OP violation in the decays ofmore » $$\\Xi^-/\\bar{\\Xi}^+$$ and $$\\Lambda/ \\bar{\\Lambda}$$ hyperons....« less

  6. First Observation of the Cabibbo-suppressed Decays Xi+(c) ---> Sigma+ pi- pi+ and Xi+(c) ---> Sigma- pi+ pi+ and Measurement of their Branching Ratios

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

    Vazquez-Jauregui, E.; /San Luis Potosi U.; Engelfried, J.

    The authors report the first observation of two Cabibbo-suppressed decay modes, {Xi}{sub c}{sup +} {yields} {Sigma}{sup +}{pi}{sup -}{pi}{sup +} and {Xi}{sub c}{sup +} {yields} {Sigma}{sup -} {pi}{sup +}{pi}{sup +}. They observe 56 {+-} 13 over a background of 21, and 23 {+-} 7 over a background of 12 events, respectively, for the signals. The data were accumulated using the SELEX spectrometer during the 1996-1997 fixed target run at Fermilab, chiefly from a 600 GeV/c {Sigma}{sup -} beam. The branching ratios of the decays relative to the Cabibbo-favored {Xi}{sub c}{sup +} {yields} {Xi}{sup -}{pi}{sup +}{pi}{sup +} are measured to be B({Xi}{submore » c}{sup +} {yields} {Sigma}{sup +}{pi}{sup -}{pi}{sup +})/B({xi}{sub c}{sup +} {yields} {Xi}{sup -} {pi}{sup +}{pi}{sup +}) = 0.50 {+-} 0.20, and B({Xi}{sub c}{sup +} {yields} {Sigma}{sup -}{pi}{sup +}{pi}{sup +})/B({Xi}{sub c}{sup +} {yields} {Xi}{sup -}{pi}{sup +}{pi}{sup +}) = 0.23 {+-} 0.11, respectively. They also report branching ratios for the same decay modes of the {Lambda}{sub c}{sup +} relative to {Lambda}{sub c}{sup +} {yields} pK{sup -}{pi}{sup +}.« less

  7. Light-cone distribution amplitudes of {xi} and their applications

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

    Liu Yonglu; Huang Mingqiu

    We present the light-cone distribution amplitudes of the {xi} baryons up to twist six on the basis of QCD conformal partial wave expansion to the leading order conformal spin accuracy. The nonperturbative parameters relevant to the DAs are determined in the framework of the QCD sum rule. The light-cone QCD sum rule approach is used to investigate both the electromagnetic form factors of {xi} and the exclusive semileptonic decay of {xi}{sub c} as applications. Our estimations on the magnetic moments are {mu}{sub {xi}{sup 0}}=-(1.92{+-}0.34){mu}{sub N} and {mu}{sub {xi}{sup -}}=-(1.19{+-}0.03){mu}{sub N}. The decay width of the process {xi}{sub c}{yields}{xi}e{sup +}{nu}{sub e}more » is evaluated to be {gamma}=8.73x10{sup -14} GeV, which is in accordance with the experimental measurements and other theoretical approaches.« less

  8. Production and Decay of {xi}{sub c}{sup 0} at BABAR

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

    Aubert, B.; Barate, R.; Boutigny, D.

    Using 116.1 fb{sup -1} of data collected by the BABAR detector, we present an analysis of {xi}{sub c}{sup 0} production in B decays and from the cc continuum, with the {xi}{sub c}{sup 0} decaying into {omega}{sup -}K{sup +} and {xi}{sup -}{pi}{sup +} final states. We measure the ratio of branching fractions B({xi}{sub c}{sup 0}{yields}{omega}{sup -}K{sup +})/B({xi}{sub c}{sup 0}{yields}{xi}{sup -}{pi}{sup +}) to be 0.294{+-}0.018{+-}0.016, where the first uncertainty is statistical and the second is systematic. The {xi}{sub c}{sup 0} momentum spectrum is measured on and 40 MeV below the {upsilon}(4S) resonance. From these spectra the branching fraction product B(B{yields}{xi}{sub c}{sup 0}X)xB({xi}{submore » c}{sup 0}{yields}{xi}{sup -}{pi}{sup +}) is measured to be (2.11{+-}0.19{+-}0.25)x10{sup -4}, and the cross-section product {sigma}(e{sup +}e{sup -}{yields}{xi}{sub c}{sup 0}X)xB({xi}{sub c}{sup 0}{yields}{xi}{sup -}{pi}{sup +}) from the continuum is measured to be (388{+-}39{+-}41) fb at a center-of-mass energy of 10.58 GeV.« less

  9. Xi-cam: Flexible High Throughput Data Processing for GISAXS

    NASA Astrophysics Data System (ADS)

    Pandolfi, Ronald; Kumar, Dinesh; Venkatakrishnan, Singanallur; Sarje, Abinav; Krishnan, Hari; Pellouchoud, Lenson; Ren, Fang; Fournier, Amanda; Jiang, Zhang; Tassone, Christopher; Mehta, Apurva; Sethian, James; Hexemer, Alexander

    With increasing capabilities and data demand for GISAXS beamlines, supporting software is under development to handle larger data rates, volumes, and processing needs. We aim to provide a flexible and extensible approach to GISAXS data treatment as a solution to these rising needs. Xi-cam is the CAMERA platform for data management, analysis, and visualization. The core of Xi-cam is an extensible plugin-based GUI platform which provides users an interactive interface to processing algorithms. Plugins are available for SAXS/GISAXS data and data series visualization, as well as forward modeling and simulation through HipGISAXS. With Xi-cam's advanced mode, data processing steps are designed as a graph-based workflow, which can be executed locally or remotely. Remote execution utilizes HPC or de-localized resources, allowing for effective reduction of high-throughput data. Xi-cam is open-source and cross-platform. The processing algorithms in Xi-cam include parallel cpu and gpu processing optimizations, also taking advantage of external processing packages such as pyFAI. Xi-cam is available for download online.

  10. Xi-CAM v1.2.3

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

    PANDOLFI, RONALD; KUMAR, DINESH; VENKATAKRISHNAN, SINGANALLUR

    Xi-CAM aims to provide a community driven platform for multimodal analysis in synchrotron science. The platform core provides a robust plugin infrastructure for extensibility, allowing continuing development to simply add further functionality. Current modules include tools for characterization with (GI)SAXS, Tomography, and XAS. This will continue to serve as a development base as algorithms for multimodal analysis develop. Seamless remote data access, visualization and analysis are key elements of Xi-CAM, and will become critical to synchrotron data infrastructure as expectations for future data volume and acquisition rates rise with continuously increasing throughputs. The highly interactive design elements of Xi-cam willmore » similarly support a generation of users which depend on immediate data quality feedback during high-throughput or burst acquisition modes.« less

  11. Direct Observation of the Strange b Baryon {xi}{sub b}{sup -}

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

    Abazov, V. M.; Alexeev, G. D.; Kalinin, A. M.

    We report the first direct observation of the strange b baryon {xi}{sub b}{sup -}({xi}{sub b}{sup +}). We reconstruct the decay {xi}{sub b}{sup -}{yields}J/{psi}{xi}{sup -}, with J/{psi}{yields}{mu}{sup +}{mu}{sup -}, and {xi}{sup -}{yields}{lambda}{pi}{sup -}{yields}p{pi}{sup -}{pi}{sup -} in pp collisions at {radical}(s)=1.96 TeV. Using 1.3 fb{sup -1} of data collected by the D0 detector, we observe 15.2{+-}4.4(stat){sub -0.4}{sup +1.9}(syst) {xi}{sub b}{sup -} candidates at a mass of 5.774{+-}0.011(stat){+-}0.015(syst) GeV. The significance of the observed signal is 5.5{sigma}, equivalent to a probability of 3.3x10{sup -8} of it arising from a background fluctuation. Normalizing to the decay {lambda}{sub b}{yields}J/{psi}{lambda}, we measure the relative rate ({sigma}({xi}{submore » b}{sup -})xB({xi}{sub b}{sup -}{yields}J/{psi}{xi}{sup -})/{sigma}({lambda}{sub b})xB({lambda}{sub b}{yields}J/{psi}{lambda}))=0.28{+-}0.09(stat){sub -0.08}{sup +0.09}(syst)« less

  12. Molecular and genetic characterization of the Ry adg locus on chromosome XI from Andigena potatoes conferring extreme resistance to potato virus Y.

    PubMed

    Herrera, María Del Rosario; Vidalon, Laura Jara; Montenegro, Juan D; Riccio, Cinzia; Guzman, Frank; Bartolini, Ida; Ghislain, Marc

    2018-05-31

    We have elucidated the Andigena origin of the potato Ry adg gene on chromosome XI of CIP breeding lines and developed two marker assays to facilitate its introgression in potato by marker-assisted selection. Potato virus Y (PVY) is causing yield and quality losses forcing farmers to renew periodically their seeds from clean stocks. Two loci for extreme resistance to PVY, one on chromosome XI and the other on XII, have been identified and used in breeding. The latter corresponds to a well-known source of resistance (Solanum stoloniferum), whereas the one on chromosome XI was reported from S. stoloniferum and S. tuberosum group Andigena as well. To elucidate its taxonomic origin in our breeding lines, we analyzed the nucleotide sequences of tightly linked markers (M45, M6) and screened 251 landraces of S. tuberosum group Andigena for the presence of this gene. Our results indicate that the PVY resistance allele on chromosome XI in our breeding lines originated from S. tuberosum group Andigena. We have developed two marker assays to accelerate the introgression of Ry adg gene into breeding lines by marker-assisted selection (MAS). First, we have multiplexed RYSC3, M6 and M45 DNA markers flanking the Ry adg gene and validated it on potato varieties with known presence/absence of the Ry adg gene and a progeny of 6,521 individuals. Secondly, we developed an allele-dosage assay particularly useful to identify multiplex Ry adg progenitors. The assay based on high-resolution melting analysis at the M6 marker confirmed Ry adg plex level as nulliplex, simplex and duplex progenitors and few triplex progenies. These marker assays have been validated and can be used to facilitate MAS in potato breeding.

  13. Xi-cam: a versatile interface for data visualization and analysis

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

    Pandolfi, Ronald J.; Allan, Daniel B.; Arenholz, Elke

    Xi-cam is an extensible platform for data management, analysis and visualization.Xi-camaims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core ofXi-camis an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. WithXi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data.Xi-cam's plugin-based architecture targetsmore » cross-facility and cross-technique collaborative development, in support of multi-modal analysis.Xi-camis open-source and cross-platform, and available for download on GitHub.« less

  14. Xi-cam: a versatile interface for data visualization and analysis

    DOE PAGES

    Pandolfi, Ronald J.; Allan, Daniel B.; Arenholz, Elke; ...

    2018-05-31

    Xi-cam is an extensible platform for data management, analysis and visualization.Xi-camaims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core ofXi-camis an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. WithXi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data.Xi-cam's plugin-based architecture targetsmore » cross-facility and cross-technique collaborative development, in support of multi-modal analysis.Xi-camis open-source and cross-platform, and available for download on GitHub.« less

  15. Search for the lepton-number-violating decay Xi(-)-->pmu(-)mu(-).

    PubMed

    Rajaram, D; Burnstein, R A; Chakravorty, A; Chan, A; Chen, Y C; Choong, W S; Clark, K; Dukes, E C; Durandet, C; Felix, J; Gidal, G; Gu, P; Gustafson, H R; Ho, C; Holmstrom, T; Huang, M; James, C; Jenkins, C M; Kaplan, D M; Lederman, L M; Leros, N; Longo, M J; Lopez, F; Lu, L C; Luebke, W; Luk, K B; Nelson, K S; Park, H K; Perroud, J-P; Rubin, H A; Teng, P K; Volk, J; White, C G; White, S L; Zyla, P

    2005-05-13

    A sensitive search for the lepton-number-violating decay Xi(-)-->pmu(-)mu(-) has been performed using a sample of approximately 10(9) Xi(-) hyperons produced in 800 GeV/c p-Cu collisions. We obtain B(Xi(-)-->pmu(-)mu(-))<4.0x10(-8) at 90% confidence, improving on the best previous limit by 4 orders of magnitude.

  16. Effect of misspecification of gene frequency on the two-point LOD score.

    PubMed

    Pal, D K; Durner, M; Greenberg, D A

    2001-11-01

    In this study, we used computer simulation of simple and complex models to ask: (1) What is the penalty in evidence for linkage when the assumed gene frequency is far from the true gene frequency? (2) If the assumed model for gene frequency and inheritance are misspecified in the analysis, can this lead to a higher maximum LOD score than that obtained under the true parameters? Linkage data simulated under simple dominant, recessive, dominant and recessive with reduced penetrance, and additive models, were analysed assuming a single locus with both the correct and incorrect dominance model and assuming a range of different gene frequencies. We found that misspecifying the analysis gene frequency led to little penalty in maximum LOD score in all models examined, especially if the assumed gene frequency was lower than the generating one. Analysing linkage data assuming a gene frequency of the order of 0.01 for a dominant gene, and 0.1 for a recessive gene, appears to be a reasonable tactic in the majority of realistic situations because underestimating the gene frequency, even when the true gene frequency is high, leads to little penalty in the LOD score.

  17. Study of excited charm-strange baryons with evidence for new baryons {xi}{sub c}(3055){sup +} and {xi}{sub c}(3123){sup +}

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

    Aubert, B.; Bona, M.; Boutigny, D.

    We present a study of excited charm-strange baryon states produced in e{sup +}e{sup -} annihilations at or near a center-of-mass energy of 10.58 GeV, in a data sample with an integrated luminosity of 384 fb{sup -1} recorded with the BABAR detector at the PEP-II e{sup +}e{sup -} storage rings at the Stanford Linear Accelerator Center. We study strong decays of charm-strange baryons to {lambda}{sub c}{sup +}K{sub S}{sup 0}, {lambda}{sub c}{sup +}K{sup -}, {lambda}{sub c}{sup +}K{sup -}{pi}{sup +}, {lambda}{sub c}{sup +}K{sub S}{sup 0}{pi}{sup -}, {lambda}{sub c}{sup +}K{sub S}{sup 0}{pi}{sup -}{pi}{sup +}, and {lambda}{sub c}{sup +}K{sup -}{pi}{sup +}{pi}{sup -}. This study confirmsmore » the existence of the states {xi}{sub c}(2980){sup +}, {xi}{sub c}(3077){sup +}, and {xi}{sub c}(3077){sup 0}, with a more accurate determination of the {xi}{sub c}(2980){sup +} mass and width. We also present evidence for two new states, {xi}{sub c}(3055){sup +} and {xi}{sub c}(3123){sup +}, decaying through the intermediate-resonant modes {sigma}{sub c}(2455){sup ++}K{sup -} and {sigma}{sub c}(2520){sup ++}K{sup -}, respectively. For each of these baryons, we measure the yield in each final state, determine the statistical significance, and calculate the product of the production cross section and branching fractions. We also measure the masses and widths of these excited charm-strange baryons.« less

  18. Gaucher disease: Gene frequencies in the Ashkenazi Jewish population

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

    Beutler, E.; West, C.; Gelbart, T.

    1993-01-01

    DNA from over 2,000 Ashkenazi Jewish subjects has been examined for the four most common Jewish Gaucher disease mutations, which collectively account for about 96% of the disease-producing alleles in Jewish patients. This population survey has made possible the estimation of gene frequencies for these alleles. Eighty-seven of 1,528 individuals were heterozygous for the 1226G (N370S) mutation, and four presumably well persons were homozygous for this mutation. The gene frequency for the 1226G allele was calculated to be .0311, and when these data were pooled with those obtained previously from another 593 Jewish subjects, a gene frequency of .032 withmore » a standard error of .004 was found. Among 2,305 normal subjects, 10 were found to be heterozygous for the 84GG allele, giving a gene frequency of .00217 with a standard error of .00096. No examples of the IVS2(+1) mutation were found among 1,256 samples screened, and no 1448C (L444P) mutations were found among 1,528 samples examined. Examination of the distribution of Gaucher disease gene frequencies in the general population shows that the ratio of 1226G mutations to 84GG mutations is higher than that in the patient population. This is presumed to be due to the fact that homozygotes for the 1226G mutation often have late-onset disease or no significant clinical manifestations at all. To bring the gene frequency in the patient population into conformity with the gene frequency in the general population, nearly two-thirds of persons with a Gaucher disease genotype would be missing from the patient population, presumably because their clinical manifestations were very mild. 10 refs., 3 tabs.« less

  19. Observation of B{sup +}{yields}{xi}{sub c}{sup 0}{lambda}{sub c}{sup +} and evidence for B{sup 0}{yields}{xi}{sub c}{sup -}{lambda}{sub c}{sup +}

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

    Chistov, R.; Aushev, T.; Balagura, V.

    We report the first observation of the decay B{sup +}{yields}{xi}{sub c}{sup 0}{lambda}{sub c}{sup +} with a significance of 8.7{sigma} and evidence for the decay B{sup 0}{yields}{xi}{sub c}{sup -}{lambda}{sub c}{sup +} with a significance of 3.8{sigma}. The product B(B{sup +}{yields}{xi}{sub c}{sup 0}{lambda}{sub c}{sup +})xB({xi}{sub c}{sup 0}{yields}{xi}{sup +}{pi}{sup -}) is measured to be (4.8{sub -0.9}{sup +1.0}{+-}1.1{+-}1.2)x10{sup -5}, and B(B{sup 0}{yields}{xi}{sub c}{sup -}{lambda}{sub c}{sup +})xB({xi}{sub c}{sup -}{yields}{xi}{sup +}{pi}{sup -}{pi}{sup -}) is measured to be (9.3{sub -2.8}{sup +3.7}{+-}1.9{+-}2.4)x10{sup -5}. The errors are statistical, systematic and the error of the {lambda}{sub c}{sup +}{yields}pK{sup -}{pi}{sup +} branching fraction, respectively. The decay B{sup +}{yields}{xi}{sub c}{sup 0}{lambda}{sub c}{supmore » +} is the first example of a two-body exclusive B{sup +} decay into two charmed baryons. The data used for this analysis was accumulated at the {upsilon}(4S) resonance, using the Belle detector at the e{sup +}e{sup -} asymmetric-energy collider KEKB. The integrated luminosity of the data sample is equal to 357 fb{sup -1}, corresponding to 386x10{sup 6} BB pairs.« less

  20. BRCA1 does not paint the inactive X to localize XIST RNA but may contribute to broad changes in cancer that impact XIST and Xi heterochromatin.

    PubMed

    Pageau, Gayle J; Hall, Lisa L; Lawrence, Jeanne B

    2007-03-01

    The BRCA1 tumor suppressor involved in breast and ovarian cancer is linked to several fundamental cell regulatory processes. Recently, it was reported that BRCA1 supports localization of XIST RNA to the inactive X chromosome (Xi) in women. The apparent cytological overlap between BRCA1 and XIST RNA across the Xi raised the possibility a direct role of BRCA1 in localizing XIST. We report here that BRCA1 does not paint the Xi or XIST territory, as do markers of Xi facultative heterochromatin. A smaller BRCA1 accumulation abuts Xi, although this is not exclusive to Xi. In BRCA1 depleted normal and tumor cells, or BRCA1 reconstituted cells, BRCA1 status does not closely correlate with XIST localization, however in a BRCA1 inducible system over-expression correlated strongly with enhanced XIST expression. We confirm frequent loss of an Xi in tumor cells. In addition to mitotic loss of Xi, we find XIST RNA expression or localization frequently become compromised in cultured breast cancer cells, suggesting Xi heterochromatin may not be fully maintained. We demonstrate that complex epigenetic differences between tumor cell subpopulations can have striking effects on XIST transcription, accumulation, and localization, but this does not strictly correlate with BRCA1. Although BRCA1 can have indirect effects that impact XIST, our results do not indicate a direct and specific role in XIST RNA regulation. Rather, regulatory factors such as BRCA1 that have broad effects on chromatin or gene regulation can impact XIST RNA and the Xi. We provide preliminary evidence that this may occur as part of a wider failure of heterochromatin maintenance in some cancers.

  1. Adjusting for background mutation frequency biases improves the identification of cancer driver genes.

    PubMed

    Evans, Perry; Avey, Stefan; Kong, Yong; Krauthammer, Michael

    2013-09-01

    A common goal of tumor sequencing projects is finding genes whose mutations are selected for during tumor development. This is accomplished by choosing genes that have more non-synonymous mutations than expected from an estimated background mutation frequency. While this background frequency is unknown, it can be estimated using both the observed synonymous mutation frequency and the non-synonymous to synonymous mutation ratio. The synonymous mutation frequency can be determined across all genes or in a gene-specific manner. This choice introduces an interesting trade-off. A gene-specific frequency adjusts for an underlying mutation bias, but is difficult to estimate given missing synonymous mutation counts. Using a genome-wide synonymous frequency is more robust, but is less suited for adjusting biases. Studying four evaluation criteria for identifying genes with high non-synonymous mutation burden (reflecting preferential selection of expressed genes, genes with mutations in conserved bases, genes with many protein interactions, and genes that show loss of heterozygosity), we find that the gene-specific synonymous frequency is superior in the gene expression and protein interaction tests. In conclusion, the use of the gene-specific synonymous mutation frequency is well suited for assessing a gene's non-synonymous mutation burden.

  2. Frequency domain analysis of noise in simple gene circuits

    NASA Astrophysics Data System (ADS)

    Cox, Chris D.; McCollum, James M.; Austin, Derek W.; Allen, Michael S.; Dar, Roy D.; Simpson, Michael L.

    2006-06-01

    Recent advances in single cell methods have spurred progress in quantifying and analyzing stochastic fluctuations, or noise, in genetic networks. Many of these studies have focused on identifying the sources of noise and quantifying its magnitude, and at the same time, paying less attention to the frequency content of the noise. We have developed a frequency domain approach to extract the information contained in the frequency content of the noise. In this article we review our work in this area and extend it to explicitly consider sources of extrinsic and intrinsic noise. First we review applications of the frequency domain approach to several simple circuits, including a constitutively expressed gene, a gene regulated by transitions in its operator state, and a negatively autoregulated gene. We then review our recent experimental study, in which time-lapse microscopy was used to measure noise in the expression of green fluorescent protein in individual cells. The results demonstrate how changes in rate constants within the gene circuit are reflected in the spectral content of the noise in a manner consistent with the predictions derived through frequency domain analysis. The experimental results confirm our earlier theoretical prediction that negative autoregulation not only reduces the magnitude of the noise but shifts its content out to higher frequency. Finally, we develop a frequency domain model of gene expression that explicitly accounts for extrinsic noise at the transcriptional and translational levels. We apply the model to interpret a shift in the autocorrelation function of green fluorescent protein induced by perturbations of the translational process as a shift in the frequency spectrum of extrinsic noise and a decrease in its weighting relative to intrinsic noise.

  3. Aristolochic acid-related nephropathy associated with the popular Chinese herb Xi Xin.

    PubMed

    Yang, Huang-Yu; Lin, J-L; Chen, Kuan-Hsing; Yu, Chun-Chen; Hsu, Po-Yaur; Lin, Chun-Liang

    2006-01-01

    Chinese herbs nephropathy is known as a subacute interstitial nephritis attributed to aristolochic acid. This work describes the case of a 49-year-old male who displayed subacute renal failure induced by ingestion of herbal powder containing Xi Xin, which includes aristolochic acid. Since Xi Xin is a common ingredient in traditional formulae, care needs to be taken in the future to identify the aristolochic acid concentration of different components of Xi Xin. Xi Xin containing aristolochic acid should be forbidden for use in remedies in order to prevent the harmful effects of aristolochic acid.

  4. xiSPEC: web-based visualization, analysis and sharing of proteomics data.

    PubMed

    Kolbowski, Lars; Combe, Colin; Rappsilber, Juri

    2018-05-08

    We present xiSPEC, a standard compliant, next-generation web-based spectrum viewer for visualizing, analyzing and sharing mass spectrometry data. Peptide-spectrum matches from standard proteomics and cross-linking experiments are supported. xiSPEC is to date the only browser-based tool supporting the standardized file formats mzML and mzIdentML defined by the proteomics standards initiative. Users can either upload data directly or select files from the PRIDE data repository as input. xiSPEC allows users to save and share their datasets publicly or password protected for providing access to collaborators or readers and reviewers of manuscripts. The identification table features advanced interaction controls and spectra are presented in three interconnected views: (i) annotated mass spectrum, (ii) peptide sequence fragmentation key and (iii) quality control error plots of matched fragments. Highlighting or selecting data points in any view is represented in all other views. Views are interactive scalable vector graphic elements, which can be exported, e.g. for use in publication. xiSPEC allows for re-annotation of spectra for easy hypothesis testing by modifying input data. xiSPEC is freely accessible at http://spectrumviewer.org and the source code is openly available on https://github.com/Rappsilber-Laboratory/xiSPEC.

  5. Search for Exotic Baryons in 800 GeV pp{yields}p{xi}{sup {+-}}{pi}{sup {+-}}X Reactions

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

    Christian, D.C.; Gottschalk, E.E.; Gutierrez, G.

    We report the results of a high-statistics, sensitive search for narrow baryon resonances decaying to {xi}{sup -}{pi}{sup -}, {xi}{sup -}{pi}{sup +}, {xi}{sup +}{pi}{sup -}, and {xi}{sup +}{pi}{sup +}. The only resonances observed are the well known {xi}{sup 0}(1530) and {xi}{sup 0}(1530). No evidence is found for the states near 1862 MeV, previously reported by NA49 [Phys. Rev. Lett. 92, 042003 (2003)]. At the 95% confidence level, we find the upper limit for the production of a Gaussian enhancement with {sigma}=7.6 MeV in the {xi}{sup -}{pi}{sup -} effective mass spectrum to be 0.3% of the number of observed {xi}{sup 0}(1530){yields}{xi}{sup -}{pi}{supmore » +}. We find similarly restrictive upper limits for an enhancement at 1862 MeV in the {xi}{sup -}{pi}{sup +}, {xi}{sup +}{pi}{sup -}, and {xi}{sup +}{pi}{sup +} mass spectra.« less

  6. The Da Vinci Xi and robotic radical prostatectomy-an evolution in learning and technique.

    PubMed

    Goonewardene, S S; Cahill, D

    2017-06-01

    The da Vinci Xi robot has been introduced as the successor to the Si platform. The promise of the Xi is to open the door to new surgical procedures. For robotic-assisted radical prostatectomy (RARP)/pelvic surgery, the potential is better vision and longer instruments. How has the Xi impacted on operative and pathological parameters as indicators of surgical performance? This is a comparison of an initial series of 42 RARPs with the Xi system in 2015 with a series using the Si system immediately before Xi uptake in the same calendar year, and an Si series by the same surgeon synchronously as the Xi series using operative time, blood loss, and positive margins as surrogates of surgical performance. Subjectively and objectively, there is a learning curve to Xi uptake in longer operative times but no impact on T2 positive margins which are the most reflective single measure of RARP outcomes. Subjectively, the vision of the Xi is inferior to the Si system, and the integrated diathermy system and automated setup are quirky. All require experience to overcome. There is a learning curve to progress from the Si to Xi da Vinci surgical platforms, but this does not negatively impact the outcome.

  7. Da Vinci Xi Robot–Assisted Penetrating Keratoplasty

    PubMed Central

    Chammas, Jimmy; Sauer, Arnaud; Pizzuto, Joëlle; Pouthier, Fabienne; Gaucher, David; Marescaux, Jacques; Mutter, Didier; Bourcier, Tristan

    2017-01-01

    Purpose This study aims (1) to investigate the feasibility of robot-assisted penetrating keratoplasty (PK) using the new Da Vinci Xi Surgical System and (2) to report what we believe to be the first use of this system in experimental eye surgery. Methods Robot-assisted PK procedures were performed on human corneal transplants using the Da Vinci Xi Surgical System. After an 8-mm corneal trephination, four interrupted sutures and one 10.0 monofilament running suture were made. For each procedure, duration and successful completion of the surgery as well as any unexpected events were assessed. The depth of the corneal sutures was checked postoperatively using spectral-domain optical coherence tomography (SD-OCT). Results Robot-assisted PK was successfully performed on 12 corneas. The Da Vinci Xi Surgical System provided the necessary dexterity to perform the different steps of surgery. The mean duration of the procedures was 43.4 ± 8.9 minutes (range: 28.5–61.1 minutes). There were no unexpected intraoperative events. SD-OCT confirmed that the sutures were placed at the appropriate depth. Conclusions We confirm the feasibility of robot-assisted PK with the new Da Vinci Surgical System and report the first use of the Xi model in experimental eye surgery. Operative time of robot-assisted PK surgery is now close to that of conventional manual surgery due to both improvement of the optical system and the presence of microsurgical instruments. Translational Relevance Experimentations will allow the advantages of robot-assisted microsurgery to be identified while underlining the improvements and innovations necessary for clinical use. PMID:28660096

  8. Da Vinci Xi Robot-Assisted Penetrating Keratoplasty.

    PubMed

    Chammas, Jimmy; Sauer, Arnaud; Pizzuto, Joëlle; Pouthier, Fabienne; Gaucher, David; Marescaux, Jacques; Mutter, Didier; Bourcier, Tristan

    2017-06-01

    This study aims (1) to investigate the feasibility of robot-assisted penetrating keratoplasty (PK) using the new Da Vinci Xi Surgical System and (2) to report what we believe to be the first use of this system in experimental eye surgery. Robot-assisted PK procedures were performed on human corneal transplants using the Da Vinci Xi Surgical System. After an 8-mm corneal trephination, four interrupted sutures and one 10.0 monofilament running suture were made. For each procedure, duration and successful completion of the surgery as well as any unexpected events were assessed. The depth of the corneal sutures was checked postoperatively using spectral-domain optical coherence tomography (SD-OCT). Robot-assisted PK was successfully performed on 12 corneas. The Da Vinci Xi Surgical System provided the necessary dexterity to perform the different steps of surgery. The mean duration of the procedures was 43.4 ± 8.9 minutes (range: 28.5-61.1 minutes). There were no unexpected intraoperative events. SD-OCT confirmed that the sutures were placed at the appropriate depth. We confirm the feasibility of robot-assisted PK with the new Da Vinci Surgical System and report the first use of the Xi model in experimental eye surgery. Operative time of robot-assisted PK surgery is now close to that of conventional manual surgery due to both improvement of the optical system and the presence of microsurgical instruments. Experimentations will allow the advantages of robot-assisted microsurgery to be identified while underlining the improvements and innovations necessary for clinical use.

  9. Study of the Rare Hyperon Decay $${\\boldmath \\Omega^\\mp \\to \\Xi^\\mp \\: \\pi^+\\pi^-}$$

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

    Kamaev, O.; Solomey, N.; Burnstein, R.A.

    The authors report a new measurement of the decay {Omega}{sup -} {yields} {Xi}{sup -} {pi}{sup +}{pi}{sup -} with 76 events and a first observation of the decay {bar {Omega}}{sup +} {yields} {bar {Xi}}{sup +} {pi}{sup +}{pi}{sup -} with 24 events, yielding a combined branching ratio (3.74{sub -0.56}{sup +0.67}) x 10{sup -4}. This represents a factor 25 increase in statistics over the best previous measurement. No evidence is seen for CP violation, with {Beta}({Omega}{sup -} {yields} {Xi}{sup -} {pi}{sup +}{pi}{sup -}) = 4.04{sub -0.71}{sup +0.83} x 10{sup -4} and {Beta}({bar {Omega}}{sup +} {yields} {bar {Xi}}{sup +} {pi}{sup +}{pi}{sup -}) = 3.15{submore » -0.89}{sup +1.12} x 10{sup -4}. Contrary to theoretical expectation, they see little evidence for the decays {Omega}{sup -} {yields} {Xi}*{sub 1530}{sup 0} {pi}{sup -} and {bar {Omega}}{sup +} {yields} {bar {Xi}}*{sub 1530}{sup 0} {pi}{sup +} and place a 90% C.L. upper limit on the combined branching ratio {Beta}({Omega}{sup -}({bar {Omega}}{sup +}) {yields} {Xi}*{sub 1530}{sup 0} ({bar {Xi}}*{sub 1530}{sup 0}){pi}{sup {-+}}) < 7.0 x 10{sup -5}.« less

  10. Rapid increase of ozone concentrations in Xi'an, China: Anthropogenically or naturally?

    NASA Astrophysics Data System (ADS)

    Wu, J.; Li, G.; Junji, C.

    2017-12-01

    The air quality in the Guanzhong basin, China has deteriorated recently caused by growing industries, city expansions, and increasing transportation activity. We report here a substantial increasing trend of ozone (O3) concentrations in Xi'an, the largest city of the basin, and the average observed O3 concentration in the afternoon during summertime has increased by 39% from 2013 to 2016. There are two main possible reasons for the rapid O3 increase. Motor vehicle has been reported to increase by 35% in Xi'an, which enhances the O3 precursors emissions to facilitate the O3 formation. In addition, the surface solar radiation at the meteorological site in Xi'an has been observed to intensify by 30%, which increases the photolysis rates to expedite the O3 production. A persistent high O3 episode from 16 to 22 June 2016 in Xi'an has been simulated using the WRF-CHEM model to evaluate the contribution of the transportation emission and solar radiation enhancement on the O3 trend. The model generally performs reasonably well in simulating the temporal variation and spatial distribution of near-surface O3 and NO2 concentrations against measurements in Xi'an. Sensitivity studies have revealed that the enhancement of transportation emissions and the solar radiation explains about 70% of the O3 trend from 2013 to 2016. Considering that large amounts of biogenic emissions are released over the Qinling Mountains on the south of Xi'an, which can be delivered to Xi'an under favorable meteorological conditions, enhancing O3 formation. Therefore, future studies need to be performed to evaluate impacts of the solar radiation enhancement on the biogenic emissions and further the O3 formation in Xi'an.

  11. Factor XI Antisense Oligonucleotide for Prevention of Venous Thrombosis

    PubMed Central

    Büller, Harry R.; Bethune, Claudette; Bhanot, Sanjay; Gailani, David; Monia, Brett P.; Raskob, Gary E.; Segers, Annelise; Verhamme, Peter; Weitz, Jeffrey I.

    2015-01-01

    BACKGROUND Experimental data indicate that reducing factor XI levels attenuates thrombosis without causing bleeding, but the role of factor XI in the prevention of postoperative venous thrombosis in humans is unknown. FXI-ASO (ISIS 416858) is a second-generation antisense oligonucleotide that specifically reduces factor XI levels. We compared the efficacy and safety of FXI-ASO with those of enoxaparin in patients undergoing total knee arthroplasty. METHODS In this open-label, parallel-group study, we randomly assigned 300 patients who were undergoing elective primary unilateral total knee arthroplasty to receive one of two doses of FXI-ASO (200 mg or 300 mg) or 40 mg of enoxaparin once daily. The primary efficacy outcome was the incidence of venous thromboembolism (assessed by mandatory bilateral venography or report of symptomatic events). The principal safety outcome was major or clinically relevant nonmajor bleeding. RESULTS Around the time of surgery, the mean (±SE) factor XI levels were 0.38±0.01 units per milliliter in the 200-mg FXI-ASO group, 0.20±0.01 units per milliliter in the 300-mg FXI-ASO group, and 0.93±0.02 units per milliliter in the enoxaparin group. The primary efficacy outcome occurred in 36 of 134 patients (27%) who received the 200-mg dose of FXI-ASO and in 3 of 71 patients (4%) who received the 300-mg dose of FXI-ASO, as compared with 21 of 69 patients (30%) who received enoxaparin. The 200-mg regimen was noninferior, and the 300-mg regimen was superior, to enoxaparin (P<0.001). Bleeding occurred in 3%, 3%, and 8% of the patients in the three study groups, respectively. CONCLUSIONS This study showed that factor XI contributes to postoperative venous thromboembolism; reducing factor XI levels in patients undergoing elective primary unilateral total knee arthroplasty was an effective method for its prevention and appeared to be safe with respect to the risk of bleeding. (Funded by Isis Pharmaceuticals; FXI-ASO TKA ClinicalTrials.gov number

  12. Decay widths of ground-state and excited {Xi}{sub b} baryons in a nonrelativistic quark model

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

    Limphirat, Ayut; Thailand Center of Excellence in Physics; Department of Applied Physics, Faculty of Sciences and Liberal Arts, Rajamangala University of Technology Isan, Nakhon Ratchasima 30000

    Decay processes of ground and excited bottom baryons are studied in the {sup 3}P{sub 0} nonrelativistic quark model with all model parameters fixed in the sector of light quarks. Using as an input the recent mass of {Xi}{sub b} and the theoretical masses of {Xi}{sub b}{sup *} and {Xi}{sub b}{sup '}, narrow decay widths are predicted for the ground-state bottom baryons {Xi}{sub b}{sup *} and {Xi}{sub b}{sup '}. The work predicts large decay widths, about 100 MeV for the {rho}-type orbital excitation states of {Xi}{sub b}.

  13. Monte Carlo simulation on the effect of different approaches to thalassaemia on gene frequency.

    PubMed

    Habibzadeh, F; Yadollahie, M

    2006-01-01

    We used computer simulation to determine variation in gene, heterozygous and homozygous frequencies induced by 4 different approaches to thalassaemia. These were: supportive therapy only; treat homozygous patients with a hypothetical modality phenotypically only; abort all homozygous fetuses; and prevent marriage between gene carriers. Gene frequency becomes constant with the second or the fourth strategy, and falls over time with the first or the third strategy. Heterozygous frequency varies in parallel with gene frequency. Using the first strategy, homozygous frequency falls over time; with the second strategy it becomes constant; and with the third and fourth strategies it falls to zero after the first generation. No matter which strategy is used, the population gene frequency, in the worst case, will remain constant over time.

  14. Hadronic production of the doubly heavy baryon {Xi}{sub bc} at the LHC

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

    Zhang Jiawei; Wu Xinggang; Zhong Tao

    We investigate the hadronic production of the doubly heavy baryon {Xi}{sub bc} at the Large Hadron Collider (LHC), where contributions from the four (bc)-diquark states (bc){sub 3,6}[{sup 1}S{sub 0}] and (bc){sub 3,6}[{sup 3}S{sub 1}] have been taken into consideration. Numerical results show that under the condition of p{sub T}>4 GeV and |y|<1.5, sizable {Xi}{sub bc} events about 1.7x10{sup 7} and 3.5x10{sup 9} per year can be produced for the center-of-mass energy {radical}(S)=7 TeV and {radical}(S)=14 TeV, respectively. For experimental usage, the total and the interested differential cross sections are estimated under some typical p{sub T} and y cuts for themore » LHC detectors CMS, ATLAS, and LHCb. The main uncertainties are discussed and a comparative study on the hadronic production of {Xi}{sub cc}, {Xi}{sub bc}, and {Xi}{sub bb} at the LHC are also presented.« less

  15. Low frequency of endospore-specific genes in subseafloor sedimentary metagenomes.

    PubMed

    Kawai, Mikihiko; Uchiyama, Ikuo; Takami, Hideto; Inagaki, Fumio

    2015-04-01

    Spore formation is considered to be one of the microbial strategies for long-term survival in subseafloor sedimentary habitats. However, our knowledge of the genetic and physiological characteristics of subseafloor microbes is limited. Here, we studied the distribution and frequency of genes that are related to endospore formation in 10 subseafloor sedimentary metagenomes from Site C9001 off Japan and Site 1229 off Peru. None or very low frequencies of endospore-specific genes (e.g. dpaA, dpaB, sspA, spo0A, spoIIGA, spoIIM, spoIIIAB, spoIVA, spoIVB, yabP, yunB, spoVM) were observed in the subseafloor metagenomes. Based on the number of universally conserved single copy genes, the frequency ratio of putative endospore-formers was estimated to be < 10%, which is consistent with the frequency of Clostridia-derived genomes (2-4%) but is lower than previous estimates based on the concentration of dipicolinic acid. Conceivable explanations for this discrepancy are as follows: the efficiency of lysis and DNA extraction of subseafloor endospore cells may have been lower than those of vegetative cells, conversion factor of dipicolinic acid content per cell may differ, and/or sporulation-related genes and other functional strategies for long-term survival in the deep subseafloor biosphere are evolutionarily distinct from known spore-forming gene repertoires. © 2014 Society for Applied Microbiology and John Wiley & Sons Ltd.

  16. High-Throughput Screening of a Luciferase Reporter of Gene Silencing on the Inactive X Chromosome.

    PubMed

    Keegan, Alissa; Plath, Kathrin; Damoiseaux, Robert

    2018-01-01

    Assays of luciferase gene activity are a sensitive and quantitative reporter system suited to high-throughput screening. We adapted a luciferase assay to a screening strategy for identifying factors that reactivate epigenetically silenced genes. This epigenetic luciferase reporter is subject to endogenous gene silencing mechanisms on the inactive X chromosome (Xi) in primary mouse cells and thus captures the multilayered nature of chromatin silencing in development. Here, we describe the optimization of an Xi-linked luciferase reactivation assay in 384-well format and adaptation of the assay for high-throughput siRNA and chemical screening. Xi-luciferase reactivation screening has applications in stem cell biology and cancer therapy. We have used the approach described here to identify chromatin-modifying proteins and to identify drug combinations that enhance the gene reactivation activity of the DNA demethylating drug 5-aza-2'-deoxycytidine.

  17. A Dependence Study of $$\\Xi^{*0}$$ and $$\\bar{\\Xi}^{*0}$$ in 250 GeV/c $$\\pi^-$$. $K^-$ -nucleon Interactions (in Portuguese)

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

    Seixas de Rezende, Fabio Antonio; /Rio de Janeiro, CBPF

    A direct measurement of the mass number (A) dependence of the production of the hyperon {Xi}*{sup 0} and its opposite {bar {Xi}}*{sup 0} in {pi}{sup -}, K{sup -} beam-nucleon interactions at 250 GeV/c is reported. The data derive from the experiment E769 at Fermilab. The results were obtained for different targets: Be, Al, Cu and W. It was observed the data are found to be well described by the parametrization {sigma}{sub A} = {sigma}{sub 0}A{sup {alpha}}, {alpha} being calculated for different beams. The results obtained are compared with those results of E769 experiment. The results shown here are preliminary.

  18. Multiquadrant robotic colorectal surgery: the da Vinci Xi vs Si comparison.

    PubMed

    Protyniak, Bogdan; Jorden, Jeffrey; Farmer, Russell

    2018-03-01

    The newly introduced da Vinci Xi Surgical System hopes to address the shortcomings of its predecessor, specifically robotic arm restrictions and difficulty working in multiple quadrants. We compare the two robot platforms in multiquadrant surgery at a major colorectal referral center. Forty-four patients in the da Vinci Si group and 26 patients in the Xi group underwent sigmoidectomy or low anterior resection between 2014 and 2016. Patient demographics, operative variables, and postoperative outcomes were compared using descriptive statistics. Both groups were similar in age, sex, BMI, pelvic surgeries, and ASA class. Splenic flexure was mobilized in more (p = 0.045) da Vinci Xi cases compared to da Vinci Si both for sigmoidectomy (50 vs 15.4%) and low anterior resection (60 vs 29%). There was no significant difference in operative time (219.9 vs 224.7 min; p = 0.640), blood loss (170.0 vs 188.1 mL; p = 0.289), length of stay (5.7 vs 6 days; p = 0.851), or overall complications (26.9 vs 22.7%; p = 0.692) between the da Vinci Xi and Si groups, respectively. Single-dock multiquadrant robotic surgery, measured by splenic flexure mobilization with concomitant pelvic dissection, was more frequently performed using the da Vinci Xi platform with no increase in operative time, bleeding, or postoperative complications. The new platform provides surgeons an easier alternative to the da Vinci Si dual docking or combined robotic/laparoscopic multiquadrant surgery.

  19. Study of the strong {sigma}{sub c}{yields}{lambda}{sub c}{pi},{sigma}{sub c}*{yields}{lambda}{sub c}{pi} and {xi}{sub c}*{yields}{xi}{sub c}{pi} decays in a nonrelativistic quark model

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

    Albertus, C.; Nieves, J.; Hernandez, E.

    We present results for the strong widths corresponding to the {sigma}{sub c}{yields}{lambda}{sub c}{pi}, {sigma}{sub c}*{yields}{lambda}{sub c}{pi} and {xi}{sub c}*{yields}{xi}{sub c}{pi} decays. The calculations have been done in a nonrelativistic constituent quark model with wave functions that take advantage of the constraints imposed by heavy quark symmetry. Partial conservation of axial current hypothesis allows us to determine the strong vertices from an analysis of the axial current matrix elements. Our results {gamma}({sigma}{sub c}{sup ++}{yields}{lambda}{sub c}{sup +}{pi}{sup +})=2.41{+-}0.07{+-}0.02 MeV, {gamma}({sigma}{sub c}{sup +}{yields}{lambda}{sub c}{sup +}{pi}{sup 0})=2.79{+-}0.08{+-}0.02 MeV, {gamma}({sigma}{sub c}{sup 0}{yields}{lambda}{sub c}{sup +}{pi}{sup -})=2.37{+-}0.07{+-}0.02 MeV, {gamma}({sigma}{sub c}*{sup ++}{yields}{lambda}{sub c}{sup +}{pi}{sup +})=17.52{+-}0.74{+-}0.12 MeV, {gamma}({sigma}{sub c}*{supmore » +}{yields}{lambda}{sub c}{sup +}{pi}{sup 0})=17.31{+-}0.73{+-}0.12 MeV, {gamma}({sigma}{sub c}*{sup 0}{yields}{lambda}{sub c}{sup +}{pi}{sup -})=16.90{+-}0.71{+-}0.12 MeV, {gamma}({xi}{sub c}*{sup +}{yields}{xi}{sub c}{sup 0}{pi}{sup +}+{xi}{sub c}{sup +}{pi}{sup 0})=3.18{+-}0.10{+-}0.01 MeV, and {gamma}({xi}{sub c}*{sup 0}{yields}{xi}{sub c}{sup +}{pi}{sup -}+{xi}{sub c}{sup 0}{pi}{sup 0})=3.03{+-}0.10{+-}0.01 MeV are in good agreement with experimental determinations.« less

  20. Factor XI and XII as antithrombotic targets.

    PubMed

    Müller, Felicitas; Gailani, David; Renné, Thomas

    2011-09-01

    Arterial and venous thrombosis are major causes of morbidity and mortality, and the incidence of thromboembolic diseases increases as a population ages. Thrombi are formed by activated platelets and fibrin. The latter is a product of the plasma coagulation system. Currently available anticoagulants such as heparins, vitamin K antagonists and inhibitors of thrombin or factor Xa target enzymes of the coagulation cascade that are critical for fibrin formation. However, fibrin is also necessary for terminating blood loss at sites of vascular injury. As a result, anticoagulants currently in clinical use increase the risk of bleeding, partially offsetting the benefits of reduced thrombosis. This review focuses on new targets for anticoagulation that are associated with minimal or no therapy-associated increased bleeding. Data from experimental models using mice and clinical studies of patients with hereditary deficiencies of coagulation factors XI or XII have shown that both of these clotting factors are important for thrombosis, while having minor or no apparent roles in processes that terminate blood loss (hemostasis). Hereditary deficiency of factor XII (Hageman factor) or factor XI, plasma proteases that initiate the intrinsic pathway of coagulation, impairs thrombus formation and provides protection from vascular occlusive events, while having a minimal impact on hemostasis. As the factor XII-factor XI pathway contributes to thrombus formation to a greater extent than to normal hemostasis, pharmacological inhibition of these coagulation factors may offer the exciting possibility of anticoagulation therapies with minimal or no bleeding risk.

  1. Nursing frequency alters circadian patterns of mammary gene expression in lactating mice

    USDA-ARS?s Scientific Manuscript database

    Milking frequency impacts lactation in dairy cattle and in rodent models of lactation. The role of circadian gene expression in this process is unknown. The hypothesis tested was that changing nursing frequency alters the circadian patterns of mammary gene expression. Mid-lactation CD1 mice were stu...

  2. Detection of a compact companion of the mild barium star Xi-1 Ceti

    NASA Technical Reports Server (NTRS)

    Bohm-Vitense, E.; Johnson, H. R.

    1985-01-01

    In the present paper, the observation of a white dwarf companion of the mild Ba star Xi-1 Ceti (= 65 Ceti = HR 649 = HD 13611) is reported, taking into account also the properties of the mild Ba star and of its companion. The UV spectrum of Xi-1 Ceti is discussed along with an interpretation of this spectrum. Attention is given to the effective temperature of the companion, the absorption bands in the spectrum, the radius and mass of the Xi-1 Ceti companion, and questions regarding the obscuration of the companion by the atmosphere of the Ba star. It is found that the overall energy distribution of the Xi-1 Ceti companion can best be matched with a 14,000 K DA white dwarf of log g = 8 or less. However, the absolute intensity is too small and would require a radius too small and a mass too large for such a gravity.

  3. The Obama - Xi Accord: A Need for Further Action

    NASA Astrophysics Data System (ADS)

    Tribett, W. R.; Hope, A. P.; Canty, T. P.; Salawitch, R. J.

    2015-12-01

    Presidents Barrack Obama of the United States and Jinping Xi of China recently announced a bilateral framework to reduce the total carbon emissions of their respective countries. The U.S. agreed to reduce annual carbon emissions such that by 2025, emissions would be 27% below 2005 levels. China agreed to achieve peak carbon emissions around 2030 coupled with a best effort to peak early. Here we analyze the implications of the Obama-Xi accord for total global carbon emissions (GCE) out to year 2060, using projections of population, economic growth, and carbon intensity for the rest of the world as well as various assumptions regarding how emissions from the U.S. and China will evolve after the timeframe of the Obama-Xi accord. Our GCE projections will be compared to those of the four Representative Concentration Pathway (RCP) emission scenarios used in the IPCC Fifth Assessment Report (AR5). The Obama-Xi accord is shown to be a meaningful first step: if followed, the actual GCE will likely fall below RCP 8.5 between now and 2060. The U.S., China, and rest of the world presently emit 4.5, 2.0, and 1.1 tonne of carbon per person per year (tpy), respectively. We show that if the world's nations adopt a strategy of "Contraction and Convergence", such that per capita emission for each country reaches 1.0 tpy by 2060, actual GCE will approach that of RCP 4.5 by year 2060. Such action may be needed to reduce the risk of the most dire global warming forecasts within IPCC AR5.

  4. 2017 Scientific Sessions Sol Sherry Distinguished Lecture in Thrombosis: Factor XI as a Target for New Anticoagulants.

    PubMed

    Weitz, Jeffrey I; Fredenburgh, James C

    2018-02-01

    The goal of anticoagulant therapy is to attenuate thrombosis without compromising hemostasis. Although the direct oral anticoagulants are associated with less intracranial hemorrhage than vitamin K antagonists, bleeding remains their major side effect. Factor XI has emerged as a promising target for anticoagulants that may be safer than those currently available. The focus on factor XI stems from epidemiological evidence of its role in thrombosis, the observation of attenuated thrombosis in factor XI-deficient mice, identification of novel activators, and the fact that factor XI deficiency is associated with only a mild bleeding diathesis. Proof-of-concept comes from the demonstration that compared with enoxaparin, factor XI knockdown reduces venous thromboembolism without increasing bleeding after elective knee arthroplasty. This article rationalizes the selection of factor XI as a target for new anticoagulants, reviews the agents under development, and outlines a potential path forward for their development. © 2017 American Heart Association, Inc.

  5. Level structure and production cross section of {sub {Xi}}{sup 12} Be studied with coupled-channels antisymmetrized molecular dynamics

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

    Matsumiya, H.; Tsubakihara, K.; Kimura, M.

    A theoretical framework of coupled-channels antisymmetrized molecular dynamics that describes the multistrangeness system with mixing between different baryon species is developed and applied to {sub {Lambda}}{sup 12}C and {sub {Xi}}{sup 12}Be. By introducing a minor modification to the YN G-matrix interaction derived from the Nijmegen model-D, the low-lying level structure and production cross section of {sub {Lambda}}{sup 12}C are reasonably described. It is found that the low-lying states of {sub {Xi}}{sup 12}Be are dominated by the {sup 11}B {circle_times} {Xi}{sup -} channel and their order strongly depends on {Xi}N effective interactions used in the calculation. The calculated peak position ofmore » the production cross section depends on the {Xi}N effective interaction and the magnitude of spin-flip and non-spin-flip cross sections of K{sup -}p{yields}K{sup +}{Xi}{sup -} elemental processes. We suggest that the {sup 12}C(K{sup -},K{sup +}){sub {Xi}}{sup 12}Be reaction possibly provides us information about the {Xi}N interaction.« less

  6. 42 CFR 476.86 - Correlation of Title XI functions with Title XVIII functions.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 4 2011-10-01 2011-10-01 false Correlation of Title XI functions with Title XVIII functions. 476.86 Section 476.86 Public Health CENTERS FOR MEDICARE & MEDICAID SERVICES, DEPARTMENT OF...) Qio Review Functions § 476.86 Correlation of Title XI functions with Title XVIII functions. (a...

  7. Da Vinci Xi and Si platforms have equivalent perioperative outcomes during robot-assisted partial nephrectomy: preliminary experience.

    PubMed

    Abdel Raheem, Ali; Sheikh, Abulhasan; Kim, Dae Keun; Alatawi, Atalla; Alabdulaali, Ibrahim; Han, Woong Kyu; Choi, Young Deuk; Rha, Koon Ho

    2017-03-01

    The aims of this study were to compare the perioperative outcomes of da Vinci Xi to Si during robotic-assisted partial nephrectomy (RAPN) and to discuss the feasibility of our novel port placement scheme for the da Vinci Xi platform, to overcome the existing kinetic and technical difficulties we faced with the linear port placement in patients with a small body habitus. A retrospective data analysis of patients who underwent RPN using da Vinci Xi (n = 18) was carried out. The outcomes of the Xi group were compared with the Si group (n = 18) selected using a case-matched methodology. For da Vinci Xi, we applied the universal linear port placement in 12 patients and our modified port placement in the remaining 6 patients. The Xi group had a shorter mean docking time of 17.8 ± 2.6 min compared to the Si group of 20.5 ± 2.1 min (p = 0.002); otherwise, no significant difference was present with regard to the remaining perioperative variables (p > 0.05). The modified Xi port placement had a shorter mean console time of 70.8 ± 9.7 min compared to the universal linear port placement of 89.3 ± 17.2 min (p = 0.03). Moreover, it provided a broader field of vision with excellent robotic arms movement, minimizing collisions and allowing an easier and comfortable surgical assist. Da Vinci Xi appears to be feasible and safe during RPN with similar outcomes to Si. The novel Xi port placement makes surgery easier in patients with low BMI.

  8. Factor XI and Contact Activation as Targets for Antithrombotic Therapy

    PubMed Central

    Gailani, David; Bane, Charles E.; Gruber, Andras

    2015-01-01

    Summary The most commonly used anticoagulants produce therapeutic antithrombotic effects either by inhibiting thrombin or factor Xa, or by lowering the plasma levels of the precursors of these key enzymes, prothrombin and factor X. These drugs do not distinguish between thrombin generation contributing to thrombosis from thrombin generation required for hemostasis. Thus, anticoagulants increase bleeding risk, and many patients who would benefit from therapy go untreated because of comorbidities that place them at unacceptable risk for hemorrhage. Studies in animals demonstrate that components of the plasma contact activation system contribute to experimentally-induced thrombosis, despite playing little or no role in hemostasis. Attention has focused on factor XII, the zymogen of a protease (factor XIIa) that initiates contact activation when blood is exposed to foreign surfaces; and factor XI, the zymogen of the protease factor XIa, which links contact activation to the thrombin generation mechanism. In the case of factor XI, epidemiologic data indicate this protein contributes to stroke and venous thromboembolism, and perhaps myocardial infarction, in humans. A phase 2 trial showing that reduction of factor XI may be more effective than low-molecular-weight heparin at preventing venous thrombosis during knee replacement surgery provides proof of concept for the premise that an antithrombotic effect can be uncoupled from an anticoagulant effect in humans by targeting components of contact activation. Here we review data on the role of factor XI and factor XII in thrombosis, and results of pre-clinical and human trials for therapies targeting these proteins. PMID:25976012

  9. OMEGA{sup -}, XI*{sup -}, SIGMA*{sup -}, and DELTA{sup -} decuplet baryon magnetic moments

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

    Slaughter, Milton Dean

    The properties of the ground-state U spin =(3/2) baryon decuplet magnetic moments DELTA{sup -}, XI*{sup -}, SIGMA*{sup -}, and OMEGA{sup -} and their ground-state spin-(1/2) cousins p, n, LAMBDA, SIGMA{sup +}, SIGMA{sup 0}, SIGMA{sup -}, XI{sup +}, and XI{sup -} have been studied for many years with a modicum of success. The magnetic moments of many are yet to be determined. Of the decuplet baryons, only the magnetic moment of the OMEGA{sup -} has been accurately determined. We calculate the magnetic moments of the physical decuplet U spin =(3/2) quartet members without ascribing any specific form to their quark structuremore » or intraquark interactions.« less

  10. Collagen type XI alpha1 may be involved in the structural plasticity of the vertebral column in Atlantic salmon (Salmo salar L.).

    PubMed

    Wargelius, A; Fjelldal, P G; Nordgarden, U; Grini, A; Krossøy, C; Grotmol, S; Totland, G K; Hansen, T

    2010-04-01

    Atlantic salmon (Salmo salar L.) vertebral bone displays plasticity in structure, osteoid secretion and mineralization in response to photoperiod. Other properties of the vertebral bone, such as mineral content and mechanical strength, are also associated with common malformations in farmed Atlantic salmon. The biological mechanisms that underlie these changes in bone physiology are unknown, and in order to elucidate which factors might be involved in this process, microarray assays were performed on vertebral bone of Atlantic salmon reared under natural or continuous light. Eight genes were upregulated in response to continuous light treatment, whereas only one of them was upregulated in a duplicate experiment. The transcriptionally regulated gene was predicted to code for collagen type XI alpha1, a protein known to be involved in controlling the diameter of fibrillar collagens in mammals. Furthermore, the gene was highly expressed in the vertebrae, where spatial expression was found in trabecular and compact bone osteoblasts and in the chordoblasts of the notochordal sheath. When we measured the expression level of the gene in the tissue compartments of the vertebrae, the collagen turned out to be 150 and 25 times more highly expressed in the notochord and compact bone respectively, relative to the expression in the trabecular bone. Gene expression was induced in response to continuous light, and reduced in compressed vertebrae. The downregulation in compressed vertebrae was due to reduced expression in the compact bone, while expression in the trabecular bone and the notochord was unaffected. These data support the hypothesis that this gene codes for a presumptive collagen type XI alpha1, which may be involved in the regulatory pathway leading to structural adaptation of the vertebral architecture.

  11. Study on collaborative operation in Xi'an international inland port and airport

    NASA Astrophysics Data System (ADS)

    Jia, Guoling

    2017-10-01

    Xi 'an international inland port and airport are the important fulcrums for Shaanxi province to implement the strategy of "One Belt One Road" and to develop its export-oriented economy. Based on the general development situation of Xi 'an international inland port and airport and analyzing their similarities and differences, the external cause and internal cause of synergy are discussed. The contents of synergy from the strategy level, tactics level and business level are explained respectively.

  12. Educational Pico-Satellite Project CUBESAT - University of Tokyo's CUBESAT XI and its Operation Plan

    NASA Astrophysics Data System (ADS)

    Tsuda, Y.; Sako, N.; Eishima, T.; Ito, T.; Arikawa, Y.; Miyamura, N.

    2002-01-01

    University of Tokyo ISSL (Intelligent Space Systems Laboratory) has been developing a pico-satellite called "CubeSat" as an international joint program. In CubeSat project, 10cm cubic satellites have been developed by several universities and launched to the low-earth orbit altogether by Russian rocket "Dnepr". ISSL has developed "XI" series ([sai]: X-factor Investigator) satellites, and the flight model is already fabricated and ready for delivery. The mission of XI satellite is the on-orbit technology demonstration of the ultra-small satellite bus system with an extensive use of commercial-off-the-shelf components. XI transmits the Morse beacon and FM packet telemetry which provides the health data of the satellite. Additionally, XI has a CMOS camera which provides 15,000 pixels panchromatic images as an advanced mission. Ground operation is one of the key issues for CubeSats. Now we are promoting international ground station network in which several universities' ground stations connected by internet collaboratively operate university-built small satellites, which enlarges the link opportunity. Collaboration with amateur HAM engineers is also indispensable for search for the satellite or get beacon signal to estimate the satellite orbit. We are now developing operation concept based on these ideas. As the launch is scheduled in this fall, the operation plan will be fixed at the time of this conference. In this presentation the final design of ISSL's CubeSat XI and operation plan will be presented.

  13. Early clinical experience with the da Vinci Xi Surgical System in general surgery.

    PubMed

    Hagen, Monika E; Jung, Minoa K; Ris, Frederic; Fakhro, Jassim; Buchs, Nicolas C; Buehler, Leo; Morel, Philippe

    2017-09-01

    The da Vinci Xi Surgical System (Intuitive Surgical Inc., Sunnyvale, CA, USA) has been released in 2014 to facilitate minimally invasive surgery. Novel features are targeted towards facilitating complex multi-quadrant procedures, but data is scarce so far. Perioperative data of patients who underwent robotic general surgery with the da Vinci Xi system within the first 6 month after installation were collected and analyzed. The gastric bypass procedures performed with the da Vinci Xi Surgical System were compared to an equal amount of the last procedures with the da Vinci Si Surgical System. Thirty-one foregut (28 Roux-en-Y gastric bypasses), 6 colorectal procedures and 1 revisional biliary procedure were performed. The mean operating room (OR) time was 221.8 (±69.0) minutes for gastric bypasses and 306.5 (±48.8) for colorectal procedures with mean docking time of 9.4 (±3.8) minutes. The gastric bypass procedure was transitioned from a hybrid to a fully robotic approach. In comparison to the last 28 gastric bypass procedures performed with the da Vinci Si Surgical System, the OR time was comparable (226.9 versus 230.6 min, p = 0.8094), but the docking time significantly longer with the da Vinci Xi Surgical System (8.5 versus 6.1 min, p = 0.0415). All colorectal procedures were performed with a single robotic docking. No intraoperative and two postoperative complications occurred. The da Vinci Xi might facilitate single-setups of totally robotic gastric bypass and colorectal surgeries. However, further comparable research is needed to clearly determine the significance of this latest version of the da Vinci Surgical System.

  14. Genome-wide identification, splicing, and expression analysis of the myosin gene family in maize (Zea mays)

    PubMed Central

    Wang, Guifeng; Zhong, Mingyu; Wang, Gang; Song, Rentao

    2014-01-01

    The actin-based myosin system is essential for the organization and dynamics of the endomembrane system and transport network in plant cells. Plants harbour two unique myosin groups, class VIII and class XI, and the latter is structurally and functionally analogous to the animal and fungal class V myosin. Little is known about myosins in grass, even though grass includes several agronomically important cereal crops. Here, we identified 14 myosin genes from the genome of maize (Zea mays). The relatively larger sizes of maize myosin genes are due to their much longer introns, which are abundant in transposable elements. Phylogenetic analysis indicated that maize myosin genes could be classified into class VIII and class XI, with three and 11 members, respectively. Apart from subgroup XI-F, the remaining subgroups were duplicated at least in one analysed lineage, and the duplication events occurred more extensively in Arabidopsis than in maize. Only two pairs of maize myosins were generated from segmental duplication. Expression analysis revealed that most maize myosin genes were expressed universally, whereas a few members (XI-1, -6, and -11) showed an anther-specific pattern, and many underwent extensive alternative splicing. We also found a short transcript at the O1 locus, which conceptually encoded a headless myosin that most likely functions at the transcriptional level rather than via a dominant-negative mechanism at the translational level. Together, these data provide significant insights into the evolutionary and functional characterization of maize myosin genes that could transfer to the identification and application of homologous myosins of other grasses. PMID:24363426

  15. Use of a mobile tower-based robot--The initial Xi robot experience in surgical oncology.

    PubMed

    Yuh, Bertram; Yu, Xian; Raytis, John; Lew, Michael; Fong, Yuman; Lau, Clayton

    2016-01-01

    The da Vinci Xi platform provides expanded movement of the arms relative to the base, theoretically allowing increased versatility in complex multi-field or multi-quadrant surgery. We describe the initial Xi experience in oncologic surgery at a tertiary cancer center. One hundred thirty unique robot-assisted procedures were performed using the Xi between 2014 and 2015, 112 of which were oncology surgeries. For procedures involving multiple quadrants, the robot was re-targeted. Complications were assessed according to Martin criteria and the Clavien-Dindo classification up to 90 days after operation. Thirteen different operations were performed in five oncology subspecialties (urology, gynecology, thoracic, hepatobiliary, and gastrointestinal surgery). Median operative times ranged from 183 min for nephroureterectomy to 543 min for esophagogastrectomy. Median estimated blood loss did not exceed 200 ml for any of the categorized procedures . No patients were transfused intraoperatively and no positioning injuries occurred. Conversions to open operation occurred in three cases (2.7%), though not related to complications or technical considerations. Overall complication rate was 26% with major complication rate of 4%. Readmissions were necessary in 11 (10%) patients. The da Vinci Xi can be safely assimilated into a surgical oncology program. The Xi offers versatility to various oncologic procedures with satisfactory complication and readmission rates. © 2015 Wiley Periodicals, Inc.

  16. [High gene conversion frequency between genes encoding 2-deoxyglucose-6-phosphate phosphatase in 3 Saccharomyces species].

    PubMed

    Piscopo, Sara-Pier; Drouin, Guy

    2014-05-01

    Gene conversions are nonreciprocal sequence exchanges between genes. They are relatively common in Saccharomyces cerevisiae, but few studies have investigated the evolutionary fate of gene conversions or their functional impacts. Here, we analyze the evolution and impact of gene conversions between the two genes encoding 2-deoxyglucose-6-phosphate phosphatase in S. cerevisiae, Saccharomyces paradoxus and Saccharomyces mikatae. Our results demonstrate that the last half of these genes are subject to gene conversions among these three species. The greater similarity and the greater percentage of GC nucleotides in the converted regions, as well as the absence of long regions of adjacent common converted sites, suggest that these gene conversions are frequent and occur independently in all three species. The high frequency of these conversions probably result from the fact that they have little impact on the protein sequences encoded by these genes.

  17. Deteriorating haze situation and the severe haze episode during December 18-25 of 2013 in Xi'an, China, the worst event on record

    NASA Astrophysics Data System (ADS)

    Liu, Xiaodong; Hui, Ying; Yin, Zhi-Yong; Wang, Zhaosheng; Xie, Xiaoning; Fang, Jiangang

    2016-07-01

    Frequent occurrence of haze weather has been considered an urgent environmental problem in China and has attracted much attention worldwide in recent years. In this study, we examined the trend in the occurrence of haze days based on horizontal visibility in Xi'an, a major city in central China, since 2000. There were 49 haze days per year on average in Xi'an during 2000-2013, and the number of haze days has increased significantly since 2008, reaching 102 days in 2013. December is the month of the highest frequency of occurrence. During December 18-25 of 2013, the longest-lasting and most severe haze event in the recent decades occurred. The 8-day mean visibility in Xi'an was only 2.5 km with 5 days below 2 km. The mean air quality index in Xi'an during this period was 486.5, and in four of those days, it reached or exceeded the index's upper limit of 500. The exceptionally high level of PM2.5 concentration was inferred as the main reason of this severe haze episode. The local weather conditions were characterized by weak winds, enhanced atmospheric stability, and high relative humidity. Strong mid-tropospheric zonal flows in combination with weakened East Asian winter monsoon limited the cold air invasion from the higher latitudes, creating a condition of low pressure gradients in the lower troposphere and near the surface for a large region in central and eastern China. With high background emission levels, the suppressed dispersion of air pollutants eventually caused this severe haze episode affecting a large region in China.

  18. Cristobalite X-I: A bridge between low and high density silica polymorphs

    NASA Astrophysics Data System (ADS)

    Shelton, H.; Tiange, B.; Zurek, E.; Smith, J.; Dera, P.

    2017-12-01

    SiO2 is one of the most common compounds found on Earth. Despite its chemical simplicity, and because of its crystal chemical characteristics, SiO2 exhibits a complex phase diagram. SiO2 has a wide variety of thermodynamically stable crystalline phases, as well as numerous metastable crystalline and amorphous polymorphs. Many of the phase transition sequences that produce metastable phases of SiO2 are strongly path-dependent, where the rate of change controls the transition just as much as the final conditions. The elusive metastable polymorphs of SiO2 may provide a better understanding of the factors controlling its densification. On compression of α-cristobalite (the high temperature tetrahedral phase of SiO2) to pressures above 12 GPa, a new polymorph known as cristobalite X-I forms. Existence of cristobalite X-I has been known for several decades, however, consensus regarding the exact atomic arrangement has not yet been reached. The X-I phase constitutes an important step in the silica densification process, separating low-density tetrahedral framework structures from high-density octahedral polymorphs. It is unique in being the only non-quenchable high-density SiO2 phase, which reverts back to the tetrahedral low-density form on decompression at ambient temperature. Our new single crystal synchrotron X-ray diffraction experiments, with quasihydrostatic neon as the pressure medium, revealed the structure of this enigmatic phase to consist of octahedral silicate chains with 4-60°-2 zigzag chain geometry. This geometry has not been considered before, but is closely related to post-quartz, stishovite and seifertite. Density functional theory calculations support this observation, confirming the dynamic stability of the X-I arrangement and reasonably reproducing the pressure at which the transformation takes place. The enthalpy of cristobalite X-I is higher than stishovite and seifertite, but it is favored as a high-pressure successor of cristobalite due to a

  19. Robotic da Vinci Xi-assisted nipple-sparing mastectomy: First clinical report.

    PubMed

    Sarfati, Benjamin; Honart, Jean-Francois; Leymarie, Nicolas; Rimareix, Francoise; Al Khashnam, Heba; Kolb, Frederic

    2018-05-01

    Nipple-sparing mastectomy (NSM) is increasingly popular for the treatment of selected breast cancers and prophylactic mastectomy. Surgical scarring and esthetic outcomes are important patient-related cosmetic considerations. Today, the concept of minimally invasive surgery has become popular, especially using robotic surgery. The authors report the first case of NSM using the latest version of the da Vinci Xi surgical system (Xi). The final incision used to remove the entire mammary gland was located behind the axillary line. In this position, hidden by the arm of the patient, the incision was not visible and was compatible with immediate breast reconstruction. © 2017 Wiley Periodicals, Inc.

  20. Low-frequency ultrasound increases non-viral gene transfer to the mouse lung.

    PubMed

    Xenariou, Stefania; Liang, Hai-Dong; Griesenbach, Uta; Zhu, Jie; Farley, Raymond; Somerton, Lucinda; Singh, Charanjit; Jeffery, Peter K; Scheule, Ronald K; Cheng, Seng H; Geddes, Duncan M; Blomley, Martin; Alton, Eric W F W

    2010-01-01

    The aim of the study was to assess if low-frequency ultrasound (US), in the range of 30-35 kHz, increases non-viral gene transfer to the mouse lung. US is greatly attenuated in the lung due to large energy losses at the air/tissue interfaces. The advantages of low-frequency US, compared with high-frequency US are: (i) increased cavitation (responsible for the formation of transient pores in the cell membrane) and (ii) reduced energy losses during lung penetration. Cationic lipid GL67/plasmid DNA (pDNA), polyethylenimine (PEI)/pDNA and naked pDNA were delivered via intranasal instillation and the animals were then exposed to US (sonoporation) at 0.07 or 0.1 MPa for 10 min. Under these conditions, US did not enhance GL67 or PEI-mediated transfection. It did, however, increase naked pDNA gene transfer by approximately 4 folds. Importantly, this was achieved in the absence of microbubbles, which are crucial for the commonly used high-frequency (1 MHz) sonoporation but may not be able to withstand nebulization in a clinically relevant setup. Lung hemorrhage was also assessed and shown to increase with US pressure in a dose-dependent manner. We have thus, established that low-frequency US can enhance lung gene transfer with naked pDNA and this enhancement is more effective than the previously reported 1 MHz US.

  1. Distribution and source analysis of aluminum in rivers near Xi'an City, China.

    PubMed

    Wang, Dongqi; He, Yanling; Liang, Jidong; Liu, Pei; Zhuang, Pengyu

    2013-02-01

    To study the status and source of aluminum (Al) contamination, a total of 21 sampling sites along six rivers near Xi'an City (Shaanxi province, China) were investigated during 2008-2010. The results indicated that the average concentration of total Al (Al(t)) in the six rivers increased by 1.6 times from 2008 to 2010. The spatial distribution of Al(t) concentrations in the rivers near Xi'an City was significantly different, ranged from 367 μg/L (Bahe River) to 1,978 μg/L (Taiping River). The Al(t) concentration was highest near an industrial area for pulp and paper-making (2,773 μg/L), where the Al level greatly exceeded the water quality criteria of both the USA (Criterion Continuous Concentration, 87 μg/L) and Canada (100 μg/L). The average concentration of inorganic monometric aluminum (Al(im)) was 72 μg/L which would pose threats to fishes and other aquatic lives in the rivers. The concentrations of exchangeable Al (Al(ex)) in the sediment of the Taiping River sampled were relatively high, making it to be an alternative explanation of increasing Al concentrations in the rivers near Xi'an City. Furthermore, an increasing Al level has been detected in the upstream watershed near Xi'an City in recent years, which might indicate another notable pollution source of Al.

  2. Monitoring on Xi'an ground fissures deformation with TerraSAR-X data

    USGS Publications Warehouse

    Zhao, C.; Zhang, Q.; Zhu, W.; Lu, Z.

    2012-01-01

    Owing to the fine resolution of TerraSAR-X data provided since 2007, this paper applied 6 TerraSAR data (strip mode) during 3rd Dec. 2009 to 23rd Mar. 2010 to detect and monitor the active fissures over Xi'an region. Three themes have been designed for high precision detection and monitoring of Xi'an-Chang'an fissures, as small baseline subsets (SBAS) to test the atmospheric effects of differential interferograms pair stepwise, 2-pass differential interferogram with very short baseline perpendicular to generate the whole deformation map with 44 days interval, and finally, corner reflector (CR) technique was used to closely monitor the relative deformation time series between two CRs settled crossing two ground fissures. Results showed that TerraSAR data are a good choice for small-scale ground fissures detection and monitoring, while special considerations should be taken for their great temporal and baseline decorrelation. Secondly, ground fissures in Xi'an were mostly detected at the joint section of stable and deformable regions. Lastly, CR-InSAR had potential ability to monitor relative deformation crossing fissures with millimeter precision.

  3. Tumor necrosis factor-alpha and interleukin-4 gene polymorphisms in Chinese patients with gout.

    PubMed

    Chen, M-L; Tsai, F-J; Tsai, C-H; Huang, C-M

    2007-01-01

    The purpose of this study was to examine whether polymorphisms of interleukin-4 (IL-4) (promoter-590 and intron 3) and tumor necrosis factor-alpha (TNF-alpha) promoter-308 genes are markers of susceptibility to or clinical manifestations of gout in Taiwanese patients. The study included 196 Taiwanese patients with gout and 103 unrelated healthy control subjects living in central Taiwan. Polymorphisms of the IL-4 (promoter-590 and intron 3) and TNF-alpha (promoter-308) genes were typed from genomic DNA. Allelic frequencies and carriage rates were then compared between gout patients and control subjects. The correlation between allelic frequencies, carriage rates and clinical manifestations of gout were evaluated. No significant differences were observed in the allelic frequencies and carriage rates of the IL-4 (promoter-590 and intron 3) and TNF-alpha gene polymorphisms between patients with gout and healthy control subjects. Furthermore, the IL-4 (promoter-590 and intron 3) and TNF-alpha genotypes were not found to be associated with the clinical and laboratory profiles in gout patients. However, there was a significant difference in the TNF-alphapolymorphism genotype between patients with and without hypertriglyceridemia (P=0.001, xi2=11.47, OR=10.3, 95%CI=3.57-29.7). The results of our study suggest that polymorphisms of the IL-4 (promoter-590 and intron 3) and TNF-alpha promoter-308 genes are not related to gout in Chinese patients in Taiwan.

  4. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes

    PubMed Central

    Kawai, Mikihiko; Futagami, Taiki; Toyoda, Atsushi; Takaki, Yoshihiro; Nishi, Shinro; Hori, Sayaka; Arai, Wataru; Tsubouchi, Taishi; Morono, Yuki; Uchiyama, Ikuo; Ito, Takehiko; Fujiyama, Asao; Inagaki, Fumio; Takami, Hideto

    2014-01-01

    Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere. PMID:24624126

  5. High frequency of phylogenetically diverse reductive dehalogenase-homologous genes in deep subseafloor sedimentary metagenomes.

    PubMed

    Kawai, Mikihiko; Futagami, Taiki; Toyoda, Atsushi; Takaki, Yoshihiro; Nishi, Shinro; Hori, Sayaka; Arai, Wataru; Tsubouchi, Taishi; Morono, Yuki; Uchiyama, Ikuo; Ito, Takehiko; Fujiyama, Asao; Inagaki, Fumio; Takami, Hideto

    2014-01-01

    Marine subsurface sediments on the Pacific margin harbor diverse microbial communities even at depths of several hundreds meters below the seafloor (mbsf) or more. Previous PCR-based molecular analysis showed the presence of diverse reductive dehalogenase gene (rdhA) homologs in marine subsurface sediment, suggesting that anaerobic respiration of organohalides is one of the possible energy-yielding pathways in the organic-rich sedimentary habitat. However, primer-independent molecular characterization of rdhA has remained to be demonstrated. Here, we studied the diversity and frequency of rdhA homologs by metagenomic analysis of five different depth horizons (0.8, 5.1, 18.6, 48.5, and 107.0 mbsf) at Site C9001 off the Shimokita Peninsula of Japan. From all metagenomic pools, remarkably diverse rdhA-homologous sequences, some of which are affiliated with novel clusters, were observed with high frequency. As a comparison, we also examined frequency of dissimilatory sulfite reductase genes (dsrAB), key functional genes for microbial sulfate reduction. The dsrAB were also widely observed in the metagenomic pools whereas the frequency of dsrAB genes was generally smaller than that of rdhA-homologous genes. The phylogenetic composition of rdhA-homologous genes was similar among the five depth horizons. Our metagenomic data revealed that subseafloor rdhA homologs are more diverse than previously identified from PCR-based molecular studies. Spatial distribution of similar rdhA homologs across wide depositional ages indicates that the heterotrophic metabolic processes mediated by the genes can be ecologically important, functioning in the organic-rich subseafloor sedimentary biosphere.

  6. [HIV/STD prevalence and related behaviors among male STD clinic attendees in Xi'an and Xianyang cities, Shaanxi province].

    PubMed

    Hu, T; Dong, L F; Ding, Z W; Jia, H; Li, X; Zhang, J S; Song, Y L; Chang, W H

    2017-12-10

    Objective: To compare the prevalence of HIV/STD and related health care seeking behaviors among male STD clinic attendees between Xi'an and Xianyang cities. Methods: During June and July 2016, 206 male STD clinic attendees were studied in Xi'an city, with another 221 male STD clinic attendees in Xianyang city. Cross-sectional questionnaire survey was used to collect attendees'behavioral information. Blood samples were collected via HIV/HCV/Syphilis testing. Results: The prevalence rate of HIV infection was 2.4% (5/206) in Xi'an and 0.9% (2/221) in Xianyang, with no statistical significant difference between the two cities. The prevalence rate of syphilis was 4.9% (10/206) in Xi'an, which was significantly lower than 13.6% (30/221) in Xianyang. The proportion of respondents, diagnosed with other sexually transmitted diseases, in Xi'an was higher than that of Xianyang. The proportions of commercial heterosexual sex and sex with temporary sexual partners in the past 3 months were 18.0% (37/206) and 15.5% (32/206) in Xi'an, lower than 46.6% (103/221) and 15.8% (35/221) in Xianyang ( χ (2)=39.70, Р <0.01; χ (2)=0.01, P =0.93) . The proportions of condom use with commercial sex workers or temporary sexual partners in the past 3 months among Xi'an were 37.8% (14/37) and 6.3% (2/32) , lower than 93.1% (95/102) and 57.1% (20/35) in Xianyang ( χ (2)=49.06, Р <0.01; χ (2)=19.63, Р <0.01) . Conclusion: Differences were noticed between Xi'an and Xianyang city in terms of STD and HIV prevalences, behaviors related to commercial sex and use of condoms among the male STD clinic attendees that calling for targeted actions in control of high risk behavlors in both HIV/AIDS and STDs transmission.

  7. Operative technique and early experience for robotic-assisted laparoscopic nephroureterectomy (RALNU) using da Vinci Xi.

    PubMed

    Darwiche, Fadi; Swain, Sanjaya; Kallingal, George; Punnen, Sanoj; Manoharan, Murugesan; Parekh, Dipen J; Gonzalgo, Mark L

    2015-01-01

    Robotic-assisted laparoscopic nephroureterectomy (RALNU) has been previously utilized for management of upper tract urothelial carcinoma. The da Vinci Xi surgical system was released in April of 2014. We describe our operative technique and early experience for RALNU using the da Vinci Xi system highlighting unique features of this surgical platform. A total of 10 patients with a diagnosis of upper tract urothelial carcinoma underwent RALNU using the da Vinci Xi system between April and November of 2014. A novel, oblique "in line" robotic trocar configuration was utilized to access the upper abdomen (nephrectomy portion) and pelvis (bladder cuff excision) without undocking. The port hopping feature of da Vinci Xi was utilized to facilitate optimal, multi-quadrant visualization during RALNU. Robotic-assisted laparoscopic nephroureterectomy was successfully completed without open conversion in all 10 patients. Mean operative time was 184 min (range 140-300 min), mean estimated blood loss was 121 cc (range 60-300 cc), and mean hospital stay was 2.4 days. Final pathology demonstrated high grade urothelial carcinoma in all patients. Surgical margins were negative in all patients. No intra-operative complications were encountered. One patient developed a pulmonary embolus after being discharged. No patients required a blood transfusion. Mean patient follow-up was 130 days (range 15-210 days). The use of da Vinci Xi with a novel, oblique "in line" port configuration and camera port hopping technique allows for an efficient and reproducible method for RALNU without the need for repositioning the patient or the robot during surgery.

  8. 25 CFR 36.31 - Standard XI-Student promotion requirements.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 1 2012-04-01 2011-04-01 true Standard XI-Student promotion requirements. 36.31 Section 36.31 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR EDUCATION MINIMUM ACADEMIC STANDARDS FOR THE BASIC EDUCATION OF INDIAN CHILDREN AND NATIONAL CRITERIA FOR DORMITORY SITUATIONS Student...

  9. 25 CFR 36.31 - Standard XI-Student promotion requirements.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 1 2011-04-01 2011-04-01 false Standard XI-Student promotion requirements. 36.31 Section 36.31 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR EDUCATION MINIMUM ACADEMIC STANDARDS FOR THE BASIC EDUCATION OF INDIAN CHILDREN AND NATIONAL CRITERIA FOR DORMITORY SITUATIONS Student...

  10. Ground Subsidence Monitoring with MT-InSAR and Mechanism Inversion Over Xi'an, China

    NASA Astrophysics Data System (ADS)

    Peng, M. M.; Zhao, C. Y.; Zhang, Q.; Zhang, J.; Liu, Y. Y.

    2018-04-01

    The ancient Xi'an, China, has been suffering severe land subsidence and ground fissure hazards since the 1960s, which has affected the safety of Subways. Multi-sensor SAR data are conducted to monitor the latest complex ground deformation and its influence on subway line No.3 over Xi'an. Annual deformation rates have been retrieved to reveal the spatiotemporal evolution of ground subsidence in Xi'an city from 2013 to 2017. Meanwhile, the correlation between land subsidence and ground fissures are analyzed by retrieving the deformation differences in both sides of the fissures. Besides, the deformation along subway line No. 3 is analyzed, and the fast deformation section is quantitatively studied. Finally, a flat lying sill model with distributed contractions is implemented to model the InSAR deformation over YHZ subsidence center, which manifests that the ground deformation is mainly caused by groundwater withdrawal.

  11. Decreased mutation frequencies among immunoglobulin G variable region genes during viremic HIV-1 infection.

    PubMed

    Bowers, Elisabeth; Scamurra, Ronald W; Asrani, Anil; Beniguel, Lydie; MaWhinney, Samantha; Keays, Kathryne M; Thurn, Joseph R; Janoff, Edward N

    2014-01-01

    HIV-1 infection is complicated by high rates of opportunistic infections against which specific antibodies contribute to immune defense. Antibody function depends on somatic hypermutation (SHM) of variable regions of immunoglobulin heavy chain genes (VH-D-J). We characterized the frequency of SHM in expressed IgG mRNA immunoglobulin transcripts from control and HIV-1-infected patients. We compared utilization of genes in the most prominent VH family (VH3) and mutation frequencies and patterns of cDNA from VH3-IgG genes from 10 seronegative control subjects and 21 patients with HIV-1 infection (6 without and 15 patients with detectable plasma viremia). Unique IgG VH3 family cDNA sequences (n = 1,565) were PCR amplified, cloned, and sequenced from blood. Sequences were analyzed using online (Vbase) and in-house immunoglobulin alignment resources. Mutation frequencies in the antigen-binding hypervariable complementarity determining regions (CDR1/2) of IgG class-switched B cells were lower among viremic HIV-1-infected patients vs. controls for nucleotides (CDR1/2: 10±5% vs. 13.5±6%, p = 0.03) and amino acids (CDR: 20%±10 vs. 25%±12, p = 0.02) and in structural framework regions. Mutation patterns were similar among groups. The most common VH3 gene, VH3-23, was utilized less frequently among viremic HIV-1-infected patients (p = 0.03), and overall, mutation frequencies were decreased in nearly all VH3 genes compared with controls. B cells from HIV-1-infected patients show decreased mutation frequencies, especially in antigen-binding VH3 CDR genes, and selective defects in gene utilization. Similar mutation patterns suggest defects in the quantity, but not quality, of mutator activity. Lower levels of SHM in IgG class-switched B cells from HIV-1-infected patients may contribute to the increased risk of opportunistic infections and impaired humoral responses to preventative vaccines.

  12. [Heavy metals pollution and analysis of seasonal variation runoff in Xi'an].

    PubMed

    Yuan, Hong-Lin; Li, Xing-Yu; Wang, Xiao-Chang

    2014-11-01

    In order to explore heavy metals pollution situation,changes in characteristics, the correlation between each heavy mental and pollution source analysis of Xi'an various regions in different season in one year. This study collected several samples of Xi'an rainfall typical urban trunk roads throughout the year in 2013 and used inductively coupled plasma mass spectrometry (ICP-MS) to determine the level of Fe, Mn, Pb, Zn, Al, Cd of the samples, then, analyzed the seasonal change of heavy mental. Studies have shown that: the heavy metal of Xi'an road runoff pollutes seriously, the concentration of Fe over three times of the national standard and maintain the higher levels throughout the year, meanwhile the concentration with the intensity of human activities increases. The concentration of Mn and Zn in one year show a trends: winter > autumn > summer> spring. Pb concentration increases with the increase in traffic volume, while showing: winter > spring > summer > autumn. Factor analysis shows: Fe and Al was affected by the same sources-natural sources; Zn, Cd affected by anthropogenic sources of large; Mn, Pb affected by the larger traffic sources.

  13. 25 CFR 36.31 - Standard XI-Student promotion requirements.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 1 2014-04-01 2014-04-01 false Standard XI-Student promotion requirements. 36.31 Section 36.31 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR EDUCATION MINIMUM ACADEMIC... programs, in a minimum of 160 instructional days per academic term or 80 instructional days per semester...

  14. 25 CFR 36.31 - Standard XI-Student promotion requirements.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 1 2013-04-01 2013-04-01 false Standard XI-Student promotion requirements. 36.31 Section 36.31 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR EDUCATION MINIMUM ACADEMIC... programs, in a minimum of 160 instructional days per academic term or 80 instructional days per semester...

  15. Research on Xi Jinping's Thought of Ecological Civilization and Environment Sustainable Development

    NASA Astrophysics Data System (ADS)

    Xiang-chao, Pan

    2018-05-01

    Since the reform and opening up, China’s sustained and rapid economic development, but the environment problem increasingly is prominent in our country. It has seriously affected the sustainability of economic development in China. Environment overall situation is not optimistic, and environmental management is imperative. Since the 18th national congress of the Communist Party of China (CPC), Xi Jin-ping has put forward the thought of building a beautiful China with ecological civilization and realizing the sustainable development of economic construction and environmental protection. Sticking to Xi's Thought of Ecological Civilization is a fundamental guarantee for the sustainable development of environment and building a new era of ecological civilization.

  16. Synthetic gene frequency maps of man and selective effects of climate

    PubMed Central

    Piazza, A.; Menozzi, P.; Cavalli-Sforza, L. L.

    1981-01-01

    The world distribution of 39 independent gene frequencies in human populations is analyzed by multivariate techniques and synthetic geographic maps. Most genetic variation is associated with longitude, with South Asia showing a tendency to be central. Also latitude and, more particularly, distance from the equator play a significant role in a way that suggests that climatic factors exercise selective pressures, especially for certain genes. Images PMID:6941316

  17. Transoral robotic surgery for the base of tongue squamous cell carcinoma: a preliminary comparison between da Vinci Xi and Si.

    PubMed

    Alessandrini, Marco; Pavone, Isabella; Micarelli, Alessandro; Caporale, Claudio

    2017-09-13

    Considering the emerging advantages related to da Vinci Xi robotic platform, the aim of this study is to compare for the first time the operative outcomes of this tool to the previous da Vinci Si during transoral robotic surgery (TORS), both performed for squamous cell carcinomas (SCC) of the base of tongue (BOT). Intra- and peri-operative outcomes of eight patients with early stage (T1-T2) of the BOT carcinoma and undergoing TORS by means of the da Vinci Xi robotic platform (Xi-TORS) are compared with the da Vinci Si group ones (Si-TORS). With respect to Si-TORS group, Xi-TORS group demonstrated a significantly shorter overall operative time, console time, and intraoperative blood loss, as well as peri-operative pain intensity and length of mean hospital stays and nasogastric tube positioning. Considering recent advantages offered by surgical robotic techniques, the da Vinci Xi Surgical System preliminary outcomes could suggest its possible future routine implementation in BOT squamous cell carcinoma procedures.

  18. Conversion of partially reprogrammed cells to fully pluripotent stem cells is associated with further activation of stem cell maintenance- and gamete generation-related genes.

    PubMed

    Kim, Jong Soo; Choi, Hyun Woo; Choi, Sol; Seo, Han Geuk; Moon, Sung-Hwan; Chung, Hyung-Min; Do, Jeong Tae

    2014-11-01

    Somatic cells are reprogrammed to induced pluripotent stem cells (iPSCs) by overexpression of a combination of defined transcription factors. We generated iPSCs from mouse embryonic fibroblasts (with Oct4-GFP reporter) by transfection of pCX-OSK-2A (Oct4, Sox2, and Klf4) and pCX-cMyc vectors. We could generate partially reprogrammed cells (XiPS-7), which maintained more than 20 passages in a partially reprogrammed state; the cells expressed Nanog but were Oct4-GFP negative. When the cells were transferred to serum-free medium (with serum replacement and basic fibroblast growth factor), the XiPS-7 cells converted to Oct4-GFP-positive iPSCs (XiPS-7c, fully reprogrammed cells) with ESC-like properties. During the conversion of XiPS-7 to XiPS-7c, we found several clusters of slowly reprogrammed genes, which were activated at later stages of reprogramming. Our results suggest that partial reprogrammed cells can be induced to full reprogramming status by serum-free medium, in which stem cell maintenance- and gamete generation-related genes were upregulated. These long-term expandable partially reprogrammed cells can be used to verify the mechanism of reprogramming.

  19. Molecular genetic analysis of the F11 gene in 14 Turkish patients with factor XI deficiency: identification of novel and recurrent mutations and their inheritance within families.

    PubMed

    Colakoglu, Seyma; Bayhan, Turan; Tavil, Betül; Keskin, Ebru Yılmaz; Cakir, Volkan; Gümrük, Fatma; Çetin, Mualla; Aytaç, Selin; Berber, Ergul

    2018-01-01

    Factor XI (FXI) deficiency is an autosomal bleeding disease associated with genetic defects in the F11 gene which cause decreased FXI levels or impaired FXI function. An increasing number of mutations has been reported in the FXI mutation database, most of which affect the serine protease domain of the protein. FXI is a heterogeneous disorder associated with a variable bleeding tendency and a variety of causative F11 gene mutations. The molecular basis of FXI deficiency in 14 patients from ten unrelated families in Turkey was analysed to establish genotype-phenotype correlations and inheritance of the mutations in the patients' families. Fourteen index cases with a diagnosis of FXI deficiency and family members of these patients were enrolled into the study. The patients' F11 genes were amplified by polymerase chain reaction and subjected to direct DNA sequencing analysis. The findings were analysed statistically using bivariate correlations, Pearson's correlation coefficient and the nonparametric Mann-Whitney test. Direct DNA sequencing analysis of the F11 genes revealed that all of the 14 patients had a F11 gene mutation. Eight different mutations were identified in the apple 1, apple 2 or serine protease domains, except one which was a splice site mutation. Six of the mutations were recurrent. Two of the mutations were novel missense mutations, p.Val522Gly and p.Cys581Arg, within the catalytic domain. The p.Trp519Stop mutation was observed in two families whereas all the other mutations were specific to a single family. Identification of mutations confirmed the genetic heterogeneity of FXI deficiency. Most of the patients with mutations did not have any bleeding complications, whereas some had severe bleeding symptoms. Genetic screening for F11 gene mutations is important to decrease the mortality and morbidity rate associated with FXI deficiency, which can be life-threatening if bleeding occurs in tissues with high fibrinolytic activity.

  20. Molecular genetic analysis of the F11 gene in 14 Turkish patients with factor XI deficiency: identification of novel and recurrent mutations and their inheritance within families

    PubMed Central

    Colakoglu, Seyma; Bayhan, Turan; Tavil, Betül; Keskin, Ebru Yılmaz; Cakir, Volkan; Gümrük, Fatma; Çetin, Mualla; Aytaç, Selin; Berber, Ergul

    2018-01-01

    Background Factor XI (FXI) deficiency is an autosomal bleeding disease associated with genetic defects in the F11 gene which cause decreased FXI levels or impaired FXI function. An increasing number of mutations has been reported in the FXI mutation database, most of which affect the serine protease domain of the protein. FXI is a heterogeneous disorder associated with a variable bleeding tendency and a variety of causative F11 gene mutations. The molecular basis of FXI deficiency in 14 patients from ten unrelated families in Turkey was analysed to establish genotype-phenotype correlations and inheritance of the mutations in the patients’ families. Material and methods Fourteen index cases with a diagnosis of FXI deficiency and family members of these patients were enrolled into the study. The patients’ F11 genes were amplified by polymerase chain reaction and subjected to direct DNA sequencing analysis. The findings were analysed statistically using bivariate correlations, Pearson’s correlation coefficient and the nonparametric Mann-Whitney test. Results Direct DNA sequencing analysis of the F11 genes revealed that all of the 14 patients had a F11 gene mutation. Eight different mutations were identified in the apple 1, apple 2 or serine protease domains, except one which was a splice site mutation. Six of the mutations were recurrent. Two of the mutations were novel missense mutations, p.Val522Gly and p.Cys581Arg, within the catalytic domain. The p.Trp519Stop mutation was observed in two families whereas all the other mutations were specific to a single family. Discussion Identification of mutations confirmed the genetic heterogeneity of FXI deficiency. Most of the patients with mutations did not have any bleeding complications, whereas some had severe bleeding symptoms. Genetic screening for F11 gene mutations is important to decrease the mortality and morbidity rate associated with FXI deficiency, which can be life-threatening if bleeding occurs in tissues

  1. 40 CFR Appendix Xi to Part 86 - Sampling Plans for Selective Enforcement Auditing of Light-Duty Vehicles

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 19 2010-07-01 2010-07-01 false Sampling Plans for Selective Enforcement Auditing of Light-Duty Vehicles XI Appendix XI to Part 86 Protection of Environment ENVIRONMENTAL... Enforcement Auditing of Light-Duty Vehicles 40% AQL Table 1—Sampling Plan Code Letter Annual sales of...

  2. 25 CFR 36.31 - Standard XI-Student promotion requirements.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 1 2010-04-01 2010-04-01 false Standard XI-Student promotion requirements. 36.31 Section... Instructional Evaluation § 36.31 Standard XI—Student promotion requirements. Each school shall establish and implement a promotion policy which shall be submitted to and approved by the local school board and Agency...

  3. Does transition from the da Vinci Si to Xi robotic platform impact single-docking technique for robot-assisted laparoscopic nephroureterectomy?

    PubMed

    Patel, Manish N; Aboumohamed, Ahmed; Hemal, Ashok

    2015-12-01

    To describe our robot-assisted nephroureterectomy (RNU) technique for benign indications and RNU with en bloc excision of bladder cuff (BCE) and lymphadenectomy (LND) for malignant indications using the da Vinci Si and da Vinci Xi robotic platform, with its pros and cons. The port placement described for Si can be used for standard and S robotic systems. This is the first report in the literature on the use of the da Vinci Xi robotic platform for RNU. After a substantial experience of RNU using different da Vinci robots from the standard to the Si platform in a single-docking fashion for benign and malignant conditions, we started using the newly released da Vinci Xi robot since 2014. The most important differences are in port placement and effective use of the features of da Vinci Xi robot while performing simultaneous upper and lower tract surgery. Patient positioning, port placement, step-by-step technique of single docking RNU-LND-BCE using the da Vinci Si and da Vinci Xi robot are shown in an accompanying video with the goal that centres using either robotic system benefit from the hints and tips. The first segment of video describes RNU-LND-BCE using the da Vinci Si followed by the da Vinci Xi to highlight differences. There was no need for patient repositioning or robot re-docking with the new da Vinci Xi robotic platform. We have experience of using different robotic systems for single docking RNU in 70 cases for benign (15) and malignant (55) conditions. The da Vinci Xi robotic platform helps operating room personnel in its easy movement, allows easier patient side-docking with the help of its boom feature, in addition to easy and swift movements of the robotic arms. The patient clearance feature can be used to avoid collision with the robotic arms or the patient's body. In patients with challenging body habitus and in situations where bladder cuff management is difficult, modifications can be made through reassigning the camera to a different port with

  4. Robotic resections in hepatobiliary oncology - initial experience with Xi da Vinci system in India.

    PubMed

    Chandarana, M; Patkar, S; Tamhankar, A; Garg, S; Bhandare, M; Goel, M

    2017-01-01

    Minimal invasive surgery has proven its advantages over open surgeries in the perioperative period. Food and Drug Administration approved da Vinci robot in 2000. The latest version, da Vinci Xi system has a mobile tower-based robot with several modifications to improve the functionality, versatility, and operative ease. None of the centers have reported exclusively on hepatobiliary oncology using the da Vinci Xi system. We report our initial experience. To study the feasibility, advantages, and discuss the operative technique of da Vinci Xi system in hepatobiliary oncology. Data were analyzed retrospectively from a prospectively maintained database from June 2015 to October 2016. Twenty-five patients with suspected or proven hepatobiliary malignancies were operated. Total robotic technique using da Vinci Xi system was used. Demographic details and perioperative outcomes were noted. Of the 25 surgeries, 14 patients had a suspected gallbladder malignancy, 11 patients had primary or metastatic liver tumor. Median age was 53 years. The average duration of surgery was 225 min with a median blood loss 150 ml. The median postoperative stay was 4 days. The median nodal yield for radical cholecystectomy was seven. Five patients required conversion. Two of these developed postoperative morbidity. Robotic surgery for hepatobiliary oncology is feasible and can be performed safely in experienced hands. Increasing experience in this field may equal or even prove advantageous over conventional or laparoscopic approach in future. A cautious approach with judicious patient selection is the key to establishing robotic surgery as a standard surgical approach.

  5. Model for End-stage Liver Disease excluding INR (MELD-XI) score in critically ill patients: Easily available and of prognostic relevance.

    PubMed

    Wernly, Bernhard; Lichtenauer, Michael; Franz, Marcus; Kabisch, Bjoern; Muessig, Johanna; Masyuk, Maryna; Hoppe, Uta C; Kelm, Malte; Jung, Christian

    2017-01-01

    MELD-XI, an adapted version of Model for End-stage Liver Disease (MELD) score excluding INR, was reported to predict outcomes e.g. in patients with acute heart failure. We aimed to evaluate MELD-XI in critically ill patients admitted to an intensive care unit (ICU) for prognostic relevance. A total of 4381 medical patients (66±14 years, 2862 male) admitted to a German ICU between 2004 and 2009 were included and retrospectively investigated. Admission diagnoses were e.g. myocardial infarction (n = 2034), sepsis (n = 694) and heart failure (n = 688). We divided our patients in two cohorts basing on their MELD-XI score and evaluated the MELD-XI score for its prognostic relevance regarding short-term and long-term survival. Optimal cut-offs were calculated by means of the Youden-Index. Patients with a MELD-XI score >12 had pronounced laboratory signs of organ failure and more comorbidities. MELD-XI >12 was associated with an increase in short-term (27% vs 6%; HR 4.82, 95%CI 3.93-5.93; p<0.001) and long-term (HR 3.69, 95%CI 3.20-4.25; p<0.001) mortality. In a univariate Cox regression analysis for all patients MELD-XI was associated with increased long-term mortality (changes per score point: HR 1.06, 95%CI 1.05-1.07; p<0.001) and remained to be associated with increased mortality after correction in a multivariate regression analysis for renal failure, liver failure, lactate concentration, blood glucose concentration, oxygenation and white blood count (HR 1.04, 95%CI 1.03-1.06; p<0.001). Optimal cut-off for the overall cohort was 11 and varied remarkably depending on the admission diagnosis: myocardial infarction (9), pulmonary embolism (9), cardiopulmonary resuscitation (17) and pneumonia (17). We performed ROC-analysis and compared the AUC: SAPS2 (0.78, 95%CI 0.76-0.80; p<0.0001) and APACHE (0.76, 95%CI 0.74-0.78; p<0.003) score were superior to MELD-XI (0.71, 95%CI 0.68-0.73) for prediction of mortality. The easily calculable MELD-XI score is a robust and reliable

  6. Regulation of organ straightening and plant posture by an actin-myosin XI cytoskeleton.

    PubMed

    Okamoto, Keishi; Ueda, Haruko; Shimada, Tomoo; Tamura, Kentaro; Kato, Takehide; Tasaka, Masao; Morita, Miyo Terao; Hara-Nishimura, Ikuko

    2015-03-23

    Plants are able to bend nearly every organ in response to environmental stimuli such as gravity and light(1,2). After this first phase, the responses to stimuli are restrained by an independent mechanism, or even reversed, so that the organ will stop bending and attain its desired posture. This phenomenon of organ straightening has been called autotropism(3) and autostraightening(4) and modelled as proprioception(5). However, the machinery that drives organ straightening and where it occurs are mostly unknown. Here, we show that the straightening of inflorescence stems is regulated by an actin-myosin XI cytoskeleton in specialized immature fibre cells that are parallel to the stem and encircle it in a thin band. Arabidopsis mutants defective in myosin XI (specifically XIf and XIk) or ACTIN8 exhibit hyperbending of stems in response to gravity, an effect independent of the physical properties of the shoots. The actin-myosin XI cytoskeleton enables organs to attain their new position more rapidly than would an oscillating series of diminishing overshoots in environmental stimuli. We propose that the long actin filaments in elongating fibre cells act as a bending tensile sensor to perceive the organ's posture and trigger the straightening system.

  7. A T8.5 BROWN DWARF MEMBER OF THE {xi} URSAE MAJORIS SYSTEM

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

    Wright, Edward L.; Mace, Gregory; McLean, Ian S.

    The Wide-field Infrared Survey Explorer has revealed a T8.5 brown dwarf (WISE J111838.70+312537.9) that exhibits common proper motion with a solar-neighborhood (8 pc) quadruple star system-{xi} Ursae Majoris. The angular separation is 8.'5, and the projected physical separation is Almost-Equal-To 4000 AU. The sub-solar metallicity and low chromospheric activity of {xi} UMa A argue that the system has an age of at least 2 Gyr. The infrared luminosity and color of the brown dwarf suggests the mass of this companion ranges between 14 and 38 M{sub J} for system ages of 2 and 8 Gyr, respectively.

  8. Use of the new da Vinci Xi® during robotic rectal resection for cancer: a pilot matched-case comparison with the da Vinci Si®.

    PubMed

    Morelli, Luca; Guadagni, Simone; Di Franco, Gregorio; Palmeri, Matteo; Caprili, Giovanni; D'Isidoro, Cristiano; Cobuccio, Luigi; Marciano, Emanuele; Di Candio, Giulio; Mosca, Franco

    2017-03-01

    The aim of this study was to compare the short-term outcomes of robotic rectal resection with total mesorectal excision (TME) for rectal cancer, with the use of the new da Vinci Xi® (Xi-RobTME group) and the da Vinci Si® (Si-RobTME group). Ten patients with histologically confirmed rectal cancer underwent robot-assisted TME with the use of the new da Vinci Xi. The outcomes of Xi-RobTME group were compared with a Si-RobTME group selected using a case-matched methodology. Overall operative times and mean hospital stays were shorter in the Xi-RobTME group. Surgeries were fully robotic with a complete take-down of the splenic flexure in all Xi-RobTME cases, while only four cases of the Si-RobTME group were fully robotic, with two cases of complete take-down of the splenic flexure. The new da Vinci Xi could offer some advantages with respect to the da Vinci Si in rectal resection for cancer. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  9. The in vivo Therapeutic Effect of Free Wanderer Powder (逍 遙 散 xiāo yáo sǎn, Xiaoyaosan) on Mice with 4T1 Cell Induced Breast Cancer Model

    PubMed Central

    Chen, Wen-Fang; Xu, Li; Yu, Chung-Him; Ho, Chui-Kwan; Wu, Ka; Leung, Gina CW; Wong, Man-Sau

    2012-01-01

    In the present study, we investigated the therapeutic effect of a classical TCM formula, Free Wanderer Powder (逍遙散 xiāo yáo sǎn), in a breast cancer mouse model induced with estrogen-insensitive breast cancer 4T1 cells. Ovariectomized Balb/c mice (6-8 weeks) or sham mice were injected into the fourth mammary fat pad with 4T1 cells in which tumors were palpable 7 days after injection. On the eighth day, the mice were divided into 4 groups and tubefed daily with vehicle, Free Wanderer Powder (逍遙散 xiāo yáo sǎn) formula or tamoxifen for 28 days. Tumor growth inhibition and the decrease of the average tumor mass were most evident in mice treated with Free Wanderer Powder (逍遙散 xiāo yáo sǎn). Free Wanderer Powder (逍遙散 xiāo yáo sǎn) treatment significantly reduced Bcl-2 and elevated Bax and p53 protein expressions in breast cancer tumor. These results were further confirmed by immunohistochemisty. Tamoxifen could decrease spleen mass and Bcl-2 protein expression, increase the Bax protein expression as well as exert uterotrophic effects by increasing uterus index and inducing the gene expressions in the uterus. Taken together, these results show that Free Wanderer Powder (逍遙散 xiāo yáo sǎn) treatment induced apoptosis at protein level and inhibited the tumor growth in 4T1-induced ovariectomized Balb/c female mice, indicating the possibility of its future use for treatment of estrogen-insensitive breast caner. PMID:24716117

  10. Frequency of genetic polymorphisms of PXR gene in the Brazilian population.

    PubMed

    Moreira, Ricardo P P; Jorge, Alexander A L; Mendonca, Berenice B; Bachega, Tânia A S S

    2011-01-01

    PXR polymorphisms have been implicated in modulating CYP3A4 and PXR expression, potentially accounting for interindividual differences in drug metabolism. The prevalence of PXR polymorphisms varies among ethnic groups and data on the allelic distribution in the highly mixed Brazilian population is lacking. The aim of this study was to analyze genetic variations in the PXR gene in Brazilians and to compare the results to other ethnic groups. DNA samples from 117 healthy Brazilians underwent PCR amplification and sequencing. Eleven polymorphisms were identified, 3 of which are highly associated with differences in CYP3A4 expression. We also identified 1 new synonymous variant in 1.3% of the alleles. Among the functional polymorphisms, -25913 C>T and -6994T>C occurred at a higher frequency comparedtothe Africanalleles (p < 0.05) but at a lower frequency compared to Caucasian alleles. The 8055 C>T allele was found at a similar frequency to those described in Caucasians and Africans (p > 0.05). We observed that functional variants of the PXR were frequent in our sample of the Brazilian population. Our results suggest that PXR gene variants may be of interest in pharmacogenetic studies involving Brazilians.

  11. Frequency and expression of mutacin biosynthesis genes in isolates of Streptococcus mutans with different mutacin-producing phenotypes.

    PubMed

    Kamiya, Regianne Umeko; Höfling, José Francisco; Gonçalves, Reginaldo Bruno

    2008-05-01

    The aim of this study was to analyse the frequency and expression of biosynthesis genes in 47 Streptococcus mutans isolates with different mutacin-producing phenotypes. Detection of the frequency and expression of genes encoding mutacin types I, II, III and IV were carried out by PCR and semi-quantitative RT-PCR, respectively, using primers specific for each type of biosynthesis gene. In addition, a further eight genes encoding putative bacteriocins, designated bsm 283, bsm 299, bsm 423, bsm 1889c, bsm 1892c, bsm 1896, bsm 1906c and bsm 1914, were also screened. There was a high phenotypic diversity; some Streptococcus mutans isolates presented broad antimicrobial spectra against other Streptococcus mutans clinical isolates, including bacteria resistant to common antibiotics, as well as Staphylococcus aureus, Staphylococcus epidermidis, Enterococcus faecalis and Streptococcus pyogenes. The expression frequency of the bsm gene was higher than that of the previously characterized mutacins (I-IV). There was no positive correlation between the number of indicator strains inhibited (antimicrobial spectra) and the number of biosynthesis genes expressed (Spearman correlation test, r=-0.03, P>0.05). In conclusion, the high diversity of mutacin-producing phenotypes, associated with high frequency of expression of the biosynthesis genes screened, reveals a broad repertoire of genetic determinants encoding antimicrobial peptides that can act in different combinations.

  12. Model for End-stage Liver Disease excluding INR (MELD-XI) score in critically ill patients: Easily available and of prognostic relevance

    PubMed Central

    Wernly, Bernhard; Lichtenauer, Michael; Franz, Marcus; Kabisch, Bjoern; Muessig, Johanna; Masyuk, Maryna; Hoppe, Uta C.; Kelm, Malte; Jung, Christian

    2017-01-01

    Purpose MELD-XI, an adapted version of Model for End-stage Liver Disease (MELD) score excluding INR, was reported to predict outcomes e.g. in patients with acute heart failure. We aimed to evaluate MELD-XI in critically ill patients admitted to an intensive care unit (ICU) for prognostic relevance. Methods A total of 4381 medical patients (66±14 years, 2862 male) admitted to a German ICU between 2004 and 2009 were included and retrospectively investigated. Admission diagnoses were e.g. myocardial infarction (n = 2034), sepsis (n = 694) and heart failure (n = 688). We divided our patients in two cohorts basing on their MELD-XI score and evaluated the MELD-XI score for its prognostic relevance regarding short-term and long-term survival. Optimal cut-offs were calculated by means of the Youden-Index. Results Patients with a MELD-XI score >12 had pronounced laboratory signs of organ failure and more comorbidities. MELD-XI >12 was associated with an increase in short-term (27% vs 6%; HR 4.82, 95%CI 3.93–5.93; p<0.001) and long-term (HR 3.69, 95%CI 3.20–4.25; p<0.001) mortality. In a univariate Cox regression analysis for all patients MELD-XI was associated with increased long-term mortality (changes per score point: HR 1.06, 95%CI 1.05–1.07; p<0.001) and remained to be associated with increased mortality after correction in a multivariate regression analysis for renal failure, liver failure, lactate concentration, blood glucose concentration, oxygenation and white blood count (HR 1.04, 95%CI 1.03–1.06; p<0.001). Optimal cut-off for the overall cohort was 11 and varied remarkably depending on the admission diagnosis: myocardial infarction (9), pulmonary embolism (9), cardiopulmonary resuscitation (17) and pneumonia (17). We performed ROC-analysis and compared the AUC: SAPS2 (0.78, 95%CI 0.76–0.80; p<0.0001) and APACHE (0.76, 95%CI 0.74–0.78; p<0.003) score were superior to MELD-XI (0.71, 95%CI 0.68–0.73) for prediction of mortality. Conclusions The easily

  13. Chondrogenic properties of collagen type XI, a component of cartilage extracellular matrix.

    PubMed

    Li, Ang; Wei, Yiyong; Hung, Clark; Vunjak-Novakovic, Gordana

    2018-08-01

    Cartilage extracellular matrix (ECM) has been used for promoting tissue engineering. However, the exact effects of ECM on chondrogenesis and the acting mechanisms are not well understood. In this study, we investigated the chondrogenic effects of cartilage ECM on human mesenchymal stem cells (MSCs) and identified the contributing molecular components. To this end, a preparation of articular cartilage ECM was supplemented to pellets of chondrogenically differentiating MSCs, pellets of human chondrocytes, and bovine articular cartilage explants to evaluate the effects on cell proliferation and the production of cartilaginous matrix. Selective enzymatic digestion and screening of ECM components were conducted to identify matrix molecules with chondrogenic properties. Cartilage ECM promoted MSC proliferation, production of cartilaginous matrix, and maturity of chondrogenic differentiation, and inhibited the hypertrophic differentiation of MSC-derived chondrocytes. Selective digestion of ECM components revealed a contributory role of collagens in promoting chondrogenesis. The screening of various collagen subtypes revealed strong chondrogenic effect of collagen type XI. Finally, collagen XI was found to promote production and inhibit degradation of cartilage matrix in human articular chondrocyte pellets and bovine articular cartilage explants. Our results indicate that cartilage ECM promotes chondrogenesis and inhibits hypertrophic differentiation in MSCs. Collagen type XI is the ECM component that has the strongest effects on enhancing the production and inhibiting the degradation of cartilage matrix. Copyright © 2018 Elsevier Ltd. All rights reserved.

  14. Coronal Diagnostics of Intermediate Activity Star XI Boo A

    NASA Technical Reports Server (NTRS)

    Drake, Jeremy

    2005-01-01

    The analysis of Xi Boo A proved difficult to adapt to our line-by-line approach because of the strong wings of the RGS instrumental profile, as has been detailed in earlier reports. While progress was also delayed because of problems in using SAS v4, we succeeded in the past year or so to bring the analysis to conclusion. Abundances have been derived using both EPIC and RGS data, confirming earlier EUVE findings of a mild solar-like FIP effect, though with some evidence of a turn-up in abundances of elements with higher FIP. Plasma densities appear normal for a moderately active stellar corona. Xi Boo A nicely bridges the gap between the very active stars and stars like the Sun, and it indeed does appear that these are the stars in which the solar-like FIP effects begins to change to the "inverse FIP" type of effect seen in the very active stars. Probing this divide was the main goal of the proposal. These results are in the process of being prepared for publication, though we have not decided the target journal as yet.

  15. Source contributions of fine particulate matter during one winter haze episodes in Xi'an, China

    NASA Astrophysics Data System (ADS)

    Yang, X.; Wu, Q.

    2017-12-01

    Long-term exposure to high levels of fine particulate matter (PM2.5) is found to be associated with adverse effects on human health, ecological environment and climate change. Identification the major source regions of fine particulate matter are essential to proposing proper joint prevention and control strategies for heavy haze mitigation. In this work, the Comprehensive Air Quality Model with extensions (CAMx) together with the Particulate Source Apportionment Technology (PSAT) and the Weather Research and Forecast Model (WRF), have been applied to analyze the major source regions of PM2.5 in Xi'an during the heavy haze episodes in winter (29, December, 2016 - 5 January 2017), and the framework of the model system is shown in Fig. 1. Firstly, according to the model evaluation of the daily PM2.5 concentrations for the two months, the model has well performance, and the fraction of predictions within a factor of 2 of the observations (FAC2) is 84%, while the correlation coefficient (R) is 0.80 in Xi'an. By using the PSAT in CAMx model, a detailed source region contribution matrix is derived for all points within the Xi'an region and its six surrounding areas, and long-range regional transport. The results show that the local emission in Xi'an is the mainly sources at downtown area, which contributing 72.9% as shown in Fig.2, and the contribution rate of transportations between adjacent areas depends on wind direction. Meanwhile, three different suburban areas selected for detailed analysis in fine particles sources. Comparing to downtown area, the sources of suburban areas are more multiply, and the transportations make the contribution 40%-82%. In the suburban areas, regional inflows play an important role in the fine particles concentrations, indicating a strong need for regional joint emission control efforts. The results enhance the quantitative understanding of the PM2.5 source regions and provide a basis for policymaking to advance the control of pollution

  16. Frequency Modulation of Transcriptional Bursting Enables Sensitive and Rapid Gene Regulation.

    PubMed

    Li, Congxin; Cesbron, François; Oehler, Michael; Brunner, Michael; Höfer, Thomas

    2018-04-25

    Gene regulation is a complex non-equilibrium process. Here, we show that quantitating the temporal regulation of key gene states (transcriptionally inactive, active, and refractory) provides a parsimonious framework for analyzing gene regulation. Our theory makes two non-intuitive predictions. First, for transcription factors (TFs) that regulate transcription burst frequency, as opposed to amplitude or duration, weak TF binding is sufficient to elicit strong transcriptional responses. Second, refractoriness of a gene after a transcription burst enables rapid responses to stimuli. We validate both predictions experimentally by exploiting the natural, optogenetic-like responsiveness of the Neurospora GATA-type TF White Collar Complex (WCC) to blue light. Further, we demonstrate that differential regulation of WCC target genes is caused by different gene activation rates, not different TF occupancy, and that these rates are tuned by both the core promoter and the distance between TF-binding site and core promoter. In total, our work demonstrates the relevance of a kinetic, non-equilibrium framework for understanding transcriptional regulation. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  17. The Aymara of Western Bolivia. IV. Gene frequencies for eight blood groups and 19 protein and erythrocyte enzyme systems.

    PubMed Central

    Ferrell, R E; Bertin, T; Young, R; Barton, S A; Murillo, F; Schull, W J

    1978-01-01

    A total of 315 individuals, mainly of Aymara origin, from western Bolivia were examined for genetic variation at eight red cell antigen and 19 serum protein and red cell enzyme loci. The gene frequencies for polymorphic loci and the discovery of several rare variants are discussed in terms of previous work among the Aymara and the closely related Quechua. The effect of inclusion of related individuals in the sample on gene frequency, variance of gene frequency and genetic distance, is discussed. Images Fig. 1 PMID:736042

  18. Insight into the da Vinci® Xi - technical notes for single-docking left-sided colorectal procedures.

    PubMed

    Ngu, James Chi-Yong; Sim, Sarah; Yusof, Sulaiman; Ng, Chee-Yung; Wong, Andrew Siang-Yih

    2017-12-01

    The adoption of robot-assisted laparoscopic colorectal surgery has been hampered by issues with docking, operative duration, technical difficulties in multi-quadrant access, and cost. The da Vinci® Xi has been designed to overcome some of these limitations. We describe our experience with the system and offer technical insights to its application in left-sided colorectal procedures. Our initial series of left-sided robotic colorectal procedures was evaluated. Patient demographics and operative outcomes were recorded prospectively using a predefined database. Between March 2015 and April 2016, 54 cases of robot-assisted laparoscopic left-sided colorectal procedures were successfully completed with no cases of conversion. The majority were low anterior resections for colorectal malignancies. Using the da Vinci® Xi Surgical System, multi-quadrant surgery involving dissection from the splenic flexure to the pelvis was possible without redocking. The da Vinci® Xi simplifies the docking procedure and makes single-docking feasible for multi-quadrant left-sided colorectal procedures. Copyright © 2016 John Wiley & Sons, Ltd.

  19. Transoral robotic thyroidectomy: a preclinical feasibility study using the da Vinci Xi platform.

    PubMed

    Russell, Jonathon O; Noureldine, Salem I; Al Khadem, Mai G; Chaudhary, Hamad A; Day, Andrew T; Kim, Hoon Yub; Tufano, Ralph P; Richmon, Jeremy D

    2017-09-01

    Transoral thyroid surgery allows the surgeon to conceal incisions within the oral cavity without significantly increasing the amount of required dissection. TORT provides an ideal scarless, midline access to the thyroid gland and bilateral central neck compartments. This approach, however, presents multiple technical challenges. Herein, we present our experience using the latest generation robotic surgical system to accomplish transoral robotic thyroidectomy (TORT). In two human cadavers, the da Vinci Xi surgical system (Intuitive Surgical, Sunnyvale, CA, USA) was used to complete TORT. Total thyroidectomy and bilateral central neck dissection was successfully completed in both cadavers. The da Vinci Xi platform offered several technologic advantages over previous robotic generations including overhead docking, narrower arms, and improved range of motion allowing for improved execution of previously described TORT techniques.

  20. Molecular cloning and characterization of the spaB gene of Streptococcus sobrinus.

    PubMed

    Holt, R G; Perry, S E

    1990-07-01

    A gene of Streptococcus sobrinus 6715 (serotype g) designated spaB and encoding a surface protein antigen was isolated from a cosmid gene bank. A 5.4 kb HindIII/AvaI DNA fragment containing the gene was inserted into plasmid pBR322 to yield plasmid pXI404. Analysis of plasmid-encoded gene products showed that the 5.4 kb fragment of pXI404 encoded a 195 kDa protein. Southern blot experiments revealed that the 5.4 kb chromosomal insert DNA had sequence similarity with genomic DNA of S. sobrinus 6715, S. sobrinus B13 (serotype d) and Streptococcus cricetus HS6 (serotype a). The recombinant SpaB protein (rSpaB) was purified and monospecific antiserum was prepared. With immunological techniques and the anti-rSpaB serum, we have shown: (1) that the rSpaB protein has physico-chemical and antigenic identity with the S. sobrinus SpaB protein, (2) the presence of cross-reactive proteins in the extracellular protein of serotypes a and d of the mutans group of streptococci and (3) that the SpaB protein is expressed on the surface of mutans streptococcal serotypes a, d and g.

  1. Is Xi Jinping a Reformer Similar to Deng Xiaoping

    DTIC Science & Technology

    2017-06-09

    core focus from ideology to economic development by announcing his policy of reform and opening up in 1978. His pragmatic policies resulted in...political stability, ideological openness, and sparked over thirty years of rapid economic growth. After 30 years since reform and opening up, China has...his commitment to rebalancing China’s economy. Despite the lack of significant progress on economic reforms, this paper finds that Xi is a reformer

  2. The extent and nature of television food advertising to children in Xi'an, China.

    PubMed

    Li, Danyang; Wang, Ting; Cheng, Yue; Zhang, Min; Yang, Xue; Zhu, Zhonghai; Liu, Danli; Yang, Wenfang; Zeng, Lingxia

    2016-08-11

    To explore the extent and nature of television food advertising especially unhealthy food advertising to primary school children in Xi'an, China. Television data were recorded for 2 weekdays and 2 weekend days between 6:00 and 22:00 during May and June in 2012 from a total of five television channels most popular with children in Xi'an. Pearson χ (2) tests and logistic regression were applied to determine differences in the proportion of healthy food, unhealthy food and miscellaneous food advertisements for different channels, programs, dates, viewing periods and the use of persuasive marketing tactics. Of the 5527 advertisements transcribed, 25.5 % were for food, among which 48.1 % were considered to be unhealthy. The frequency of food advertisements was 6 per hour per channel, including 3 unhealthy food advertisements. Compared with healthy and miscellaneous food advertisements, more unhealthy food advertisements were shown during afternoon, weekends and children's non-peak viewing times as well as on children's television channels, central television channels and non-children's programmes. Unhealthy foods contributed the highest proportion of all food advertisements containing promotional characters (51.7 %) and premium offers (59.1 %). Both promotional characters and premium offers appeared more on non-children's television channels. The majority of food advertisements were for unhealthy food. More unhealthy food ads were shown in children's non-peak time and afternoon as well as non-children's channels. More children-oriented persuasive marketing tactics were used in unhealthy food ads especially in non-children's channels. Therefore, intervening in the entrance of unhealthy foods into the market and establishing regulations related to food advertising especially unhealthy food advertisements are important strategies to prevent children's exposure to unhealthy food and childhood obesity.

  3. Multiwavelength observations of magnetic fields and related activity on XI Bootis A

    NASA Technical Reports Server (NTRS)

    Saar, Steven H.; Huovelin, J.; Linsky, Jeffrey L.; Giampapa, Mark S.; Jordan, Carole

    1988-01-01

    Preliminary results of coordinated observations of magnetic fields and related activity on the active dwarf, Xi Boo A, are presented. Combining the magnetic fluxes with the linear polarization data, a simple map of the stellar active regions is constructed.

  4. 2 CFR 376.147 - Does an exclusion from participation in Federal health care programs under Title XI of the Social...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Federal health care programs under Title XI of the Social Security Act affect a person's eligibility to..., Medicaid, and other Federal health care programs under Title XI of the Social Security Act, 42 U.S.C. 1320a... Federal Agency Regulations for Grants and Agreements DEPARTMENT OF HEALTH AND HUMAN SERVICES...

  5. The Pioneer XI high field fluxgate magnetometer

    NASA Technical Reports Server (NTRS)

    Acuna, M. A.; Ness, N. F.

    1975-01-01

    The high field fluxgate magnetometer experiment flown aboard the Pioneer XI spacecraft is described. This extremely simple instrument was used to extend the spacecraft's upper-limit measurement capability by approximately an order of magnitude (from 0.14 mT to 1.00 mT) with minimum power and volume requirements. This magnetometer was designed to complement the low-field measurements provided by a helium vector magnetometer and utilizes magnetic ring core sensors with biaxial orthogonal sense coils. The instrument is a single-range, triaxial-fluxgate magnetometer capable of measuring fields of up to 1 mT along each orthogonal axis, with a maximum resolution of 1 microT.

  6. OATYC Journal; Vol. XI, Nos. 1-2, Fall 1985-Spring 1986.

    ERIC Educational Resources Information Center

    Fullen, James, Ed.

    1986-01-01

    "OATYC Journal," which is published by the Ohio Association of Two-Year Colleges, is designed as a forum for the exchange of concepts, methods, and findings relevant to the two-year college classroom. Along with commentaries and letters of reaction from the readership, the two issues of volume XI contain the following: (1) "Focus:…

  7. Validation and Implementation of Marker-Assisted Selection (MAS) for PVY Resistance (Ryadg gene) in a Tetraploid Potato Breeding Program

    USDA-ARS?s Scientific Manuscript database

    The gene Ryadg from S. tuberosum ssp. andigena provides extreme resistance to PVY. This gene has been mapped to chromosome XI and linked PCR-based DNA markers have been identified. Advanced tetraploid russeted potato clones developed by the U.S. Pacific Northwest Potato Breeding Program with Ryadg P...

  8. RESOLVING THE {xi} BOO BINARY WITH CHANDRA, AND REVEALING THE SPECTRAL TYPE DEPENDENCE OF THE CORONAL 'FIP EFFECT'

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

    Wood, Brian E.; Linsky, Jeffrey L., E-mail: brian.wood@nrl.navy.mi, E-mail: jlinsky@jila.colorado.ed

    On 2008 May 2, Chandra observed the X-ray spectrum of {xi} Boo (G8 V+K4 V), resolving the binary for the first time in X-rays and allowing the coronae of the two stars to be studied separately. With the contributions of {xi} Boo A and B to the system's total X-ray emission now observationally established (88.5% and 11.5%, respectively), consideration of mass loss measurements for GK dwarfs of various activity levels (including one for {xi} Boo) leads to the surprising conclusion that {xi} Boo B may dominate the wind from the binary, with {xi} Boo A's wind being very weak despitemore » its active corona. Emission measure (EM) distributions and coronal abundances are computed for both stars and compared with Chandra measurements of other moderately active stars with G8-K5 spectral types, all of which exhibit a narrow peak in EM near log T = 6.6, indicating that the coronal heating process in these stars has a strong preference for this temperature. As is the case for the Sun and many other stars, our sample of stars shows coronal abundance anomalies dependent on the first ionization potential (FIP) of the element. We see no dependence of the degree of 'FIP effect' on activity, but there is a dependence on spectral type, a correlation that becomes more convincing when moderately active main-sequence stars with a broader range of spectral types are considered. This clear dependence of coronal abundances on spectral type weakens if the stellar sample is allowed to be contaminated by evolved stars, interacting binaries, or extremely active stars with log L{sub X} >29, explaining why this correlation has not been recognized in the past.« less

  9. Cloning and sequence analysis of chitin synthase gene fragments of Demodex mites.

    PubMed

    Zhao, Ya-e; Wang, Zheng-hang; Xu, Yang; Xu, Ji-ru; Liu, Wen-yan; Wei, Meng; Wang, Chu-ying

    2012-10-01

    To our knowledge, few reports on Demodex studied at the molecular level are available at present. In this study our group, for the first time, cloned, sequenced and analyzed the chitin synthase (CHS) gene fragments of Demodex folliculorum, Demodex brevis, and Demodex canis (three isolates from each species) from Xi'an China, by designing specific primers based on the only partial sequence of the CHS gene of D. canis from Japan, retrieved from GenBank. Results show that amplification was successful only in three D. canis isolates and one D. brevis isolate out of the nine Demodex isolates. The obtained fragments were sequenced to be 339 bp for D. canis and 338 bp for D. brevis. The CHS gene sequence similarities between the three Xi'an D. canis isolates and one Japanese D. canis isolate ranged from 99.7% to 100.0%, and those between four D. canis isolates and one D. brevis isolate were 99.1%-99.4%. Phylogenetic trees based on maximum parsimony (MP) and maximum likelihood (ML) methods shared the same clusters, according with the traditional classification. Two open reading frames (ORFs) were identified in each CHS gene sequenced, and their corresponding amino acid sequences were located at the catalytic domain. The relatively conserved sequences could be deduced to be a CHS class A gene, which is associated with chitin synthesis in the integument of Demodex mites.

  10. Influence of Problem-Based Learning Model of Learning to the Mathematical Communication Ability of Students of Grade XI IPA SMAN 14 Padang

    NASA Astrophysics Data System (ADS)

    Nisa, I. M.

    2018-04-01

    The ability of mathematical communication is one of the goals of learning mathematics expected to be mastered by students. However, reality in the field found that the ability of mathematical communication the students of grade XI IPA SMA Negeri 14 Padang have not developed optimally. This is evident from the low test results of communication skills mathematically done. One of the factors that causes this happens is learning that has not been fully able to facilitate students to develop mathematical communication skills well. By therefore, to improve students' mathematical communication skills required a model in the learning activities. One of the models learning that can be used is Problem Based learning model Learning (PBL). The purpose of this study is to see whether the ability the students' mathematical communication using the PBL model better than the students' mathematical communication skills of the learning using conventional learning in Class XI IPA SMAN 14 Padang. This research type is quasi experiment with design Randomized Group Only Design. Population in this research that is student of class XI IPA SMAN 14 Padang with sample class XI IPA 3 and class XI IPA 4. Data retrieval is done by using communication skill test mathematically shaped essay. To test the hypothesis used U-Mann test Whitney. Based on the results of data analysis, it can be concluded that the ability mathematical communication of students whose learning apply more PBL model better than the students' mathematical communication skills of their learning apply conventional learning in class XI IPA SMA 14 Padang at α = 0.05. This indicates that the PBL learning model effect on students' mathematical communication ability.

  11. Robot-assisted total mesorectal excision for rectal cancer: case-matched comparison of short-term surgical and functional outcomes between the da Vinci Xi and Si.

    PubMed

    Morelli, Luca; Di Franco, Gregorio; Guadagni, Simone; Rossi, Leonardo; Palmeri, Matteo; Furbetta, Niccolò; Gianardi, Desirée; Bianchini, Matteo; Caprili, Giovanni; D'Isidoro, Cristiano; Mosca, Franco; Moglia, Andrea; Cuschieri, Alfred

    2018-02-01

    Robotic rectal resection with da Vinci Si has some technical limitations, which could be overcome by the new da Vinci Xi. We compare short-term surgical and functional outcomes following robotic rectal resection with total mesorectal excision for cancer, with the da Vinci Xi (Xi-RobTME group) and the da Vinci Si (Si-RobTME group). The first consecutive 30 Xi-RobTME were compared with a Si-RobTME control group of 30 patients, selected using a one-to-one case-matched methodology from our prospectively collected Institutional database, comprising all cases performed between April 2010 and September 2016 by a single surgeon. Perioperative outcomes were compared. The impact of minimally invasive TME on autonomic function and quality of life was analyzed with specific questionnaires. The docking and overall operative time were shorter in the Xi-RobTME group (p < 0.001 and p < 0.05 respectively). The mean differences of overall operative time and docking time were -33.8 min (95% CI -5.1 to -64.5) and -6 min (95% CI -4.1 to -7.9), respectively. A fully-robotic approach with complete splenic flexure mobilization was used in 30/30 (100%) of the Xi-RobTME cases and in 7/30 (23%) of the Si-RobTME group (p < 0.001). The hybrid approach in males and patients with BMI > 25 kg/m 2 was necessary in ten patients (45 vs. 0%, p < 0.001) and in six patients (37 vs. 0%, p < 0.05), in the Si-RobTME and Xi-RobTME groups, respectively. There were no differences in conversion rate, mean hospital stay, pathological data, and in functional outcomes between the two groups before and at 1 year after surgery. The technical advantages offered by the da Vinci Xi seem to be mainly associated with a shorter docking and operative time and with superior ability to perform a fully-robotic approach. Clinical and functional outcomes seem not to be improved, with the introduction of the new Xi platform.

  12. Commercial sex behaviours among involuntary male bachelors: findings from a survey of migrants in Xi'an, China.

    PubMed

    Yang, Xueyan; Li, Shuzhuo; Attané, Isabelle; Feldman, Marcus W

    2015-06-01

    The highly male-biased sex ratio at birth has produced a severe male 'marriage squeeze' in China. However, with an imbalanced sex ratio, the marriage-squeezed or involuntary bachelors can meet their sexual needs only through ways other than marriage. To investigate the commercial sex behaviours of involuntary bachelors, we conducted a survey on reproductive health and family living among male migrant bachelors in Xi'an City, the capital of Shaanxi Province, from December 2009 to January 2010. The prevalence of commercial sex use was 37.2% among unmarried men, 30.1% among married but separated men and 17.2% among married and cohabitating men (χ(2) = 31.33; P = 0.000; df = 2). Marital status, knowledge about acquired immunodeficiency syndrome (AIDS), age and income were associated with the prevalence and frequency of commercial sex behaviours. Condom use was less frequent among involuntary bachelors and was significantly associated with knowledge about AIDS and other sexually transmitted diseases, the frequency of commercial sex behaviours, marital status and age. The higher prevalence of commercial sex behaviours and the lower frequency of condom use indicate a higher risk of disease from commercial sex among involuntary bachelors, implicating both individual and public health. © The Author 2014. Published by Oxford University Press on behalf of Faculty of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  13. Antithrombotic Effect of Antisense Factor XI Oligonucleotide Treatment in Primates

    PubMed Central

    Crosby, Jeffrey R.; Marzec, Ulla; Revenko, Alexey S.; Zhao, Chenguang; Gao, Dacao; Matafonov, Anton; Gailani, David; MacLeod, A. Robert; Tucker, Erik I.; Gruber, Andras; Hanson, Stephen R.; Monia, Brett P.

    2013-01-01

    Objective During coagulation, factor IX (FIX) is activated by two distinct mechanisms mediated by the active proteases of either factors VII (FVIIa) or XI (FXIa). Both coagulation factors may contribute to thrombosis; factor XI, however, plays only a limited role in the arrest of bleeding. Therefore, therapeutic targeting of FXI may produce an antithrombotic effect with relatively low hemostatic risk. Approach and Results We have reported that reducing FXI levels with FXI antisense oligonucleotides (ASOs) produces antithrombotic activity in mice, and that administration of FXI ASOs to primates decreases circulating FXI levels and activity in a dose- and time-dependent manner. Here we evaluated the relationship between FXI plasma levels and thrombogenicity in an established baboon model of thrombosis and hemostasis. In previous studies with this model, antibody-induced inhibition of FXI produced potent antithrombotic effects. In the present report, ASO-mediated reduction of FXI plasma levels by ≥50% resulted in a demonstrable and sustained antithrombotic effect without an increased risk of bleeding. Conclusion These results indicate that reducing FXI levels using ASOs is a promising alternative to direct FXI inhibition, and that targeting FXI may be potentially safer than conventional antithrombotic therapies that can markedly impair primary hemostasis. PMID:23559626

  14. [Gene method for inconsistent hydrological frequency calculation. 2: Diagnosis system of hydrological genes and method of hydrological moment genes with inconsistent characters].

    PubMed

    Xie, Ping; Zhao, Jiang Yan; Wu, Zi Yi; Sang, Yan Fang; Chen, Jie; Li, Bin Bin; Gu, Hai Ting

    2018-04-01

    The analysis of inconsistent hydrological series is one of the major problems that should be solved for engineering hydrological calculation in changing environment. In this study, the diffe-rences of non-consistency and non-stationarity were analyzed from the perspective of composition of hydrological series. The inconsistent hydrological phenomena were generalized into hydrological processes with inheritance, variability and evolution characteristics or regulations. Furthermore, the hydrological genes were identified following the theory of biological genes, while their inheritance bases and variability bases were determined based on composition of hydrological series under diffe-rent time scales. To identify and test the components of hydrological genes, we constructed a diagnosis system of hydrological genes. With the P-3 distribution as an example, we described the process of construction and expression of the moment genes to illustrate the inheritance, variability and evolution principles of hydrological genes. With the annual minimum 1-month runoff series of Yunjinghong station in Lancangjiang River basin as an example, we verified the feasibility and practicability of hydrological gene theory for the calculation of inconsistent hydrological frequency. The results showed that the method could be used to reveal the evolution of inconsistent hydrological series. Therefore, it provided a new research pathway for engineering hydrological calculation in changing environment and an essential reference for the assessment of water security.

  15. Teaching Authorial Style and Literary Technique: "Exemplo XI" of "El Conde Lucanor"

    ERIC Educational Resources Information Center

    Bryant, Stacy

    2016-01-01

    This current study proposes a comparative method of teaching authorial style, using four versions of "Exemplo XI," an often-anthologized tale about the "mago" of Toledo, Don Illán, from the "Conde Lucanor," a series of interlinked tales by the early fourteenth-century author Don Juan Manuel. Teaching a medieval text…

  16. Precision in robotic rectal surgery using the da Vinci Xi system and integrated table motion, a technical note.

    PubMed

    Panteleimonitis, Sofoklis; Harper, Mick; Hall, Stuart; Figueiredo, Nuno; Qureshi, Tahseen; Parvaiz, Amjad

    2017-09-15

    Robotic rectal surgery is becoming increasingly more popular among colorectal surgeons. However, time spent on robotic platform docking, arm clashing and undocking of the platform during the procedure are factors that surgeons often find cumbersome and time consuming. The newest surgical platform, the da Vinci Xi, coupled with integrated table motion can help to overcome these problems. This technical note aims to describe a standardised operative technique of single docking robotic rectal surgery using the da Vinci Xi system and integrated table motion. A stepwise approach of the da Vinci docking process and surgical technique is described accompanied by an intra-operative video that demonstrates this technique. We also present data collected from a prospectively maintained database. 33 consecutive rectal cancer patients (24 male, 9 female) received robotic rectal surgery with the da Vinci Xi during the preparation of this technical note. 29 (88%) patients had anterior resections, and four (12%) had abdominoperineal excisions. There were no conversions, no anastomotic leaks and no mortality. Median operation time was 331 (249-372) min, blood loss 20 (20-45) mls and length of stay 6.5 (4-8) days. 30-day readmission rate and re-operation rates were 3% (n = 1). This standardised technique of single docking robotic rectal surgery with the da Vinci Xi is safe, feasible and reproducible. The technological advances of the new robotic system facilitate the totally robotic single docking approach.

  17. Analysis of bacterial xylose isomerase gene diversity using gene-targeted metagenomics.

    PubMed

    Nurdiani, Dini; Ito, Michihiro; Maruyama, Toru; Terahara, Takeshi; Mori, Tetsushi; Ugawa, Shin; Takeyama, Haruko

    2015-08-01

    Bacterial xylose isomerases (XI) are promising resources for efficient biofuel production from xylose in lignocellulosic biomass. Here, we investigated xylose isomerase gene (xylA) diversity in three soil metagenomes differing in plant vegetation and geographical location, using an amplicon pyrosequencing approach and two newly-designed primer sets. A total of 158,555 reads from three metagenomic DNA replicates for each soil sample were classified into 1127 phylotypes, detected in triplicate and defined by 90% amino acid identity. The phylotype coverage was estimated to be within the range of 84.0-92.7%. The xylA gene phylotypes obtained were phylogenetically distributed across the two known xylA groups. They shared 49-100% identities with their closest-related XI sequences in GenBank. Phylotypes demonstrating <90% identity with known XIs in the database accounted for 89% of the total xylA phylotypes. The differences among xylA members and compositions within each soil sample were significantly smaller than they were between different soils based on a UniFrac distance analysis, suggesting soil-specific xylA genotypes and taxonomic compositions. The differences among xylA members and their compositions in the soil were strongly correlated with 16S rRNA variation between soil samples, also assessed by amplicon pyrosequencing. This is the first report of xylA diversity in environmental samples assessed by amplicon pyrosequencing. Our data provide information regarding xylA diversity in nature, and can be a basis for the screening of novel xylA genotypes for practical applications. Copyright © 2015. Published by Elsevier B.V.

  18. Changing Student Expectations and Graduate Employment: Case Studies from Xi'an, Shaanxi Province

    ERIC Educational Resources Information Center

    Moorman, Adam B. R.

    2011-01-01

    This paper addresses the issue of students' employment expectations, considered a key factor in alleviating graduate unemployment in China. This empirical investigation surveyed students at two higher education institutions in Xi'an, Shaanxi Province, to analyze how expectations were changing. The results contrasted with earlier studies that…

  19. Forward-Backward asymmetry in $$\\Lambda_{b}$$ production and search for the $$\\Xi^{-}_{b}$$ and $$\\Omega^{-}_{b}$$ baryons in $$p\\bar{p}$$ collisions at $$\\sqrt{s} = 1.96$$ TeV

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

    Garcia Gonzalez, Jose Andres

    We present a search for the heavy-flavor baryonsmore » $$\\Xi_{b}$$ (bsd) and $$\\Omega^{-}_{b}$$ in decays $$\\Xi^{-}_{b}$$→ J/ψ$$\\Xi^{-}_{b}$$ → J/ψΛπ-, J/ψ → μ + μ - and $$\\Omega^{-}_{b}$$ → J/ψ$$\\Omega^{-}_{b}$$ J/ψΛ $$K^{-}_{b}$$, J/ψ → μ + μ - respectively.« less

  20. Effects of Dao De Xin Xi Exercise on Balance and Quality of Life in Thai Elderly Women

    PubMed Central

    Intarakamhang, Patrawut; Chintanaprawasee, Pantipa

    2012-01-01

    The objective of this study was to evaluate the effects of a 12-week Dao De Xin Xi exercise, modified short forms of Tai Chi, on balance and quality of life in Thai elderly population. Quasi-Experimental research, pretest-posttest one group design was done at Physical Medicine and Rehabilitation Department, Phramongkutklao Hospital. Thai healthy elderly women over the age of 60, requiring regular Dao De Xin Xi exercise were recruited from either patients or workers in the hospital. A 60-minute Dao De Xin Xi exercise class was set as 3 times per week for 12 weeks. At baseline and 12 weeks, participants were tested in their static balance (Single-Leg Stance Timed Test with eyes open and close), dynamic balance (Expanded Timed Up and Go (ETUG) Test). Quality of life was measured by the abbreviated Thai version of the World Health Organization Quality of Life (WHOQOL-BREF) questionnaire. Fourteen females were studied with mean age of 62.8±4.3 years old. The Single-Leg Stance Timed Test with eyes open and close, Expanded Timed Up and Go (ETUG) Test improved significantly (before versus after exercises p <0.001). Significant improvement in quality of life were also found in each 4 domains, including physical health, psychological, social relationship, and environment (before versus after exercises p =0.001, 0.001, 0.004 and 0.005 respectively). No significant improvement was found only in the right Single-Leg Stance Timed Test with eyes close (p =0.091). A three times per week for 12-week Dao De Xin Xi exercise may help Thai elderly women improve both static, dynamic balance and quality of life. PMID:22980114

  1. Effects of Dao De Xin Xi exercise on balance and quality of life in Thai elderly women.

    PubMed

    Intarakamhang, Patrawut; Chintanaprawasee, Pantipa

    2011-12-29

    The objective of this study was to evaluate the effects of a 12-week Dao De Xin Xi exercise, modified short forms of Tai Chi, on balance and quality of life in Thai elderly population. Quasi-Experimental research, pretest-posttest one group design was done at Physical Medicine and Rehabilitation Department, Phramongkutklao Hospital. Thai healthy elderly women over the age of 60, requiring regular Dao De Xin Xi exercise were recruited from either patients or workers in the hospital. A 60-minute Dao De Xin Xi exercise class was set as 3 times per week for 12 weeks. At baseline and 12 weeks, participants were tested in their static balance (Single-Leg Stance Timed Test with eyes open and close), dynamic balance (Expanded Timed Up and Go (ETUG) Test). Quality of life was measured by the abbreviated Thai version of the World Health Organization Quality of Life (WHOQOL-BREF) questionnaire. Fourteen females were studied with mean age of 62.8±4.3 years old. The Single-Leg Stance Timed Test with eyes open and close, Expanded Timed Up and Go (ETUG) Test improved significantly (before versus after exercises p <0.001). Significant improvement in quality of life were also found in each 4 domains, including physical health, psychological, social relationship, and environment (before versus after exercises p =0.001, 0.001, 0.004 and 0.005 respectively). No significant improvement was found only in the right Single-Leg Stance Timed Test with eyes close (p =0.091). A three times per week for 12-week Dao De Xin Xi exercise may help Thai elderly women improve both static, dynamic balance and quality of life.

  2. 40 CFR Appendix Xi to Part 268 - Metal Bearing Wastes Prohibited From Dilution in a Combustion Unit According to 40 CFR 268.3(c)

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES (CONTINUED) LAND DISPOSAL RESTRICTIONS Pt. 268, App. XI Appendix XI to Part 268—Metal Bearing Wastes Prohibited From Dilution in a Combustion... 40 Protection of Environment 28 2013-07-01 2013-07-01 false Metal Bearing Wastes Prohibited From...

  3. 40 CFR Appendix Xi to Part 268 - Metal Bearing Wastes Prohibited From Dilution in a Combustion Unit According to 40 CFR 268.3(c)

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID WASTES (CONTINUED) LAND DISPOSAL RESTRICTIONS Pt. 268, App. XI Appendix XI to Part 268—Metal Bearing Wastes Prohibited From Dilution in a Combustion... 40 Protection of Environment 27 2014-07-01 2014-07-01 false Metal Bearing Wastes Prohibited From...

  4. Sibling genes as environment: Sibling dopamine genotypes and adolescent health support frequency dependent selection.

    PubMed

    Rauscher, Emily; Conley, Dalton; Siegal, Mark L

    2015-11-01

    While research consistently suggests siblings matter for individual outcomes, it remains unclear why. At the same time, studies of genetic effects on health typically correlate variants of a gene with the average level of behavioral or health measures, ignoring more complicated genetic dynamics. Using National Longitudinal Study of Adolescent Health data, we investigate whether sibling genes moderate individual genetic expression. We compare twin variation in health-related absences and self-rated health by genetic differences at three locations related to dopamine regulation and transport to test sibship-level cross-person gene-gene interactions. Results suggest effects of variation at these genetic locations are moderated by sibling genes. Although the mechanism remains unclear, this evidence is consistent with frequency dependent selection and suggests much genetic research may violate the stable unit treatment value assumption. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. The Distribution of Genotype and Allelic Frequency of IL28B Gene Polymorphism in Andhra Pradesh, India

    PubMed Central

    Sivaprasad, Siddapuram; Rao, Padaki Nagaraja; Gupta, Rajesh; Ashwini, Kaitha; Reddy, Duvvuru Nageshwar

    2012-01-01

    Background The single nucleotide polymorphism (SNP) of IL28B gene on chromosome 19, encoding for the interferon (IFN)-λ-3 is strongly associated with treatment response to pegylated-IFN and ribavirin in patients infected with different genotypes of hepatitis C virus (HCV). Difference between ethnicity and treatment response rates suggesting a key role of host genetics. The IL28B polymorphism (rs12979860C/T) shows a marked differential distribution between racial groups. Aim The present study is aimed to evaluate genotype and allelic frequency of IL28B gene polymorphism (rs12979860C/T) in Andhra Pradesh, India. Methods A total of 220 healthy controls were recruited for the study. The genotyping of SNP rs12979860C/T on IL28B gene was performed by polymerase chain reaction-direct sequencing method. Result The frequency of CC genotype was found to be significantly (59.09%) higher compared to CT (34.09%) and TT (6.81%) genotypes, respectively. The frequency of major allele C is 0.762 whereas minor allele T is 0.238. Conclusion The higher distribution of genotype ‘CC’ of SNP, rs12979860C/T of IL28B gene in study subjects is suggestive of better response of HCV patients to standard anti-HCV therapy. PMID:25755419

  6. The impact on post-operative shoulder function of intraoperative nerve monitoring of cranial nerve XI during modified radical neck dissection.

    PubMed

    Lanišnik, Boštjan; Žitnik, Lidija; Levart, Primož; Žargi, Miha; Rodi, Zoran

    2016-12-01

    Intraoperative monitoring of the cranial nerve XI (CN XI) may decrease shoulder disability following modified radical neck dissection. Prospective study was designed comparing results of Constant Shoulder Score (CSS), Shoulder Pain and Disability Index (SPADI) and EMG score of the trapezius muscle (mT) before and after surgery. One side of the neck was monitored during surgery with intraoperative nerve monitor. EMG scores of the mT 6 months postoperatively were statistically better on monitored as compared to the non-monitored side of the neck (p = 0.041), while the differences of the CSS and SPADI were not statistically significant. Patients with better EMG scores of the mT at 6 weeks recuperated better and with smaller decrease of the CSS. Intraoperative monitoring is beneficial at the beginning of the surgeon's learning curve and in the process of familiarizing with anatomical variation of the CN XI.

  7. High dietary intake of sodium selenite does not affect gene mutation frequency in rat colon and liver.

    PubMed

    Zeng, Huawei; Uthus, Eric O; Ross, Sharon A; Davis, Cindy D

    2009-10-01

    Our previous studies have shown that selenium (Se) is protective against dimethylhydrazine (DMH)-induced preneoplastic colon cancer lesions, and protection against DNA damage has been hypothesized to be one mechanism for the anticancer effect of Se. The present study was designed to determine whether dietary selenite affects somatic mutation frequency in vivo. We used the Big Blue transgenic model to evaluate the in vivo mutation frequency of the cII gene in rats fed either a Se-deficient (0 microg Se/g diet) or Se-supplemented diet (0.2 or 2 microg Se/g diet; n = 3 rats/diet in experiment 1 and n = 5 rats/group in experiment 2) and injected with DMH (25 mg/kg body weight, i.p.). There were no significant differences in body weight between the Se-deficient and Se-supplemented (0.2 or 2 microg Se/g diet) rats, but the activities of liver glutathione peroxidase and thioredoxin reductase and concentration of liver Se were significantly lower (p < 0.0001) in Se-deficient rats compared to rats supplemented with Se. We found no effect of dietary Se on liver 8-hydroxy-2'-deoxyguanosine. Gene mutation frequency was significantly lower in liver (p < 0.001) than that of colon regardless of dietary Se. However, there were no differences in gene mutation frequency in DNA from colon mucosa or liver from rats fed the Se-deficient diet compared to those fed the Se-supplemented (0.2 or 2 microg Se/g diet) diet. Although gene mutations have been implicated in the etiology of cancer, our data suggest that decreasing gene mutation is not likely a key mechanism through which dietary selenite exerts its anticancer action against DMH-induced preneoplastic colon cancer lesions in a Big Blue transgenic rat model.

  8. Dynamic interplay and function of multiple noncoding genes governing X chromosome inactivation

    PubMed Central

    Yue, Minghui; Richard, John Lalith Charles

    2015-01-01

    There is increasing evidence for the emergence of long noncoding RNAs (IncRNAs) as important components, especially in the regulation of gene expression. In the event of X chromosome inactivation, robust epigenetic marks are established in a long noncoding Xist RNA-dependent manner, giving rise to a distinct epigenetic landscape on the inactive X chromosome (Xi). The X inactivation center (Xic is essential for induction of X chromosome inactivation and harbors two topologically associated domains (TADs) to regulate monoallelic Xist expression: one at the noncoding Xist gene and its upstream region, and the other at the antisense Tsix and its upstream region. The monoallelic expression of Xist is tightly regulated by these two functionally distinct TADs as well as their constituting IncRNAs and proteins. In this review, we summarize recent updates in our knowledge of IncRNAs found at the Xic and discuss their overall mechanisms of action. We also discuss our current understanding of the molecular mechanism behind Xist RNA-mediated induction of the repressive epigenetic landscape at the Xi. PMID:26260844

  9. Frequency of familial Mediterranean fever (MEFV) gene mutations in patients with biopsy-proven primary glomerulonephritis.

    PubMed

    Huzmeli, Can; Candan, Ferhan; Bagci, Gokhan; Alaygut, Demet; Yilmaz, Ali; Gedikli, Asim; Bagci, Binnur; Timucin, Meryem; Sezgin, Ilhan; Kayatas, Mansur

    2017-11-01

    Primary glomerulopathies are those disorders that affect glomerular structure, function, or both in the absence of a multisystem disorder. We aimed to evaluate the frequency of MEFV gene mutation to show possible coexistence of FMF in patients diagnosed with biopsy-proven primary glomerulonephritis (GN). A total of 64 patients with biopsy-proven primary GN were included in the study. MEFV gene mutations examined retrospectively. The mean age of patients was 39.6 ± 13.4 (range 18-69), 35 of patients were female and 29 of patients were male. Of the 64 patients, 17 were mesangial proliferative glomerulonephritis (MsPGN), 15 were IgA nephropathy (IgAN), 12 were membranous glomerulonephritis (MGN), 11 were focal segmental glomerulosclerosis (FSGS), three were membranous proliferative glomerulonephritis (MPGN), three were immune complex glomerulonephritis (ICGN), two were minimal change disease (MCD), and one was IgM nephropathy (IgMN). MEFV gene mutation was detected in 35.9% (23) of these patients. The most frequently detected mutations were E148Q and M694V. Twelve cases (18.75% of GN patients) with MEFV gene mutation were diagnosed as FMF phenotype I. The frequency of MEFV gene mutation was detected at a high rate of 35.9%. Further studies with larger populations are needed to clarify the importance of these mutations on clinical progression of glomerulonephritis.

  10. Is da Vinci Xi Better than da Vinci Si in Robotic Rectal Cancer Surgery? Comparison of the 2 Generations of da Vinci Systems.

    PubMed

    Ozben, Volkan; Cengiz, Turgut B; Atasoy, Deniz; Bayraktar, Onur; Aghayeva, Afag; Erguner, Ilknur; Baca, Bilgi; Hamzaoglu, Ismail; Karahasanoglu, Tayfun

    2016-10-01

    We aimed to compare perioperative outcomes for procedures using the latest generation of da Vinci robot versus its previous version in rectal cancer surgery. Fifty-three patients undergoing robotic rectal cancer surgery between January 2010 and March 2015 were included. Patients were classified into 2 groups (Xi, n=28 vs. Si, n=25) and perioperative outcomes were analyzed. The groups had significant differences including operative procedure, hybrid technique and redocking (P>0.05). In univariate analysis, the Xi group had shorter console times (265.7 vs. 317.1 min, P=0.006) and total operative times (321.6 vs. 360.4 min, P=0.04) and higher number of lymph nodes harvested (27.5 vs. 17.0, P=0.008). In multivariate analysis, Xi robot was associated with a shorter console time (odds ratio: 0.09, P=0.004) with no significant differences regarding other outcomes. Both generations of da Vinci robot led to similar short-term outcomes in rectal cancer surgery, but the Xi robot allowed shorter console times.

  11. A Preliminary Investigation into Critical Thinking of Urban Xi'an High School Students

    ERIC Educational Resources Information Center

    Zhou, Qing; Wang, Xiang; Yao, Linna

    2007-01-01

    This paper reports the development of critical thinking of urban high school students in the Chinese city of Xi'an. It presents the assessment of the students' two components of critical thinking: dispositions towards critical thinking and critical thinking skills, using the California Critical Thinking Disposition Inventory and the California…

  12. Synthetic maps of human gene frequencies in Europeans.

    PubMed

    Menozzi, P; Piazza, A; Cavalli-Sforza, L

    1978-09-01

    Multivarate techniques can be used to condense the information for a large number of loci and alleles into one or a few synthetic variables. The geographic distribution of synthetic variables can be plotted by the same technique used in mapping the gene frequency of a single allele. Synthetic maps were constructed for Europe and the Near East, with the use of principal components to condense the information of 38 independent alleles from ten loci. The first principal component summarizes close to 30% of the total information and shows gradients. Maps thus constructed show clines in remarkable agreement with those expected on the basis of the spread of early farming in Europe, thus supporting the hypothesis that this spread was a demic spread rather than a cultural diffusion of farming technology.

  13. Localized N, {lambda}, {sigma}, and {xi} single-particle potentials in finite nuclei calculated with SU{sub 6} quark-model baryon-baryon interactions

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

    Kohno, M.; Fujiwara, Y.

    Localized single-particle potentials for all octet baryons, N, {lambda}, {sigma}, and {xi}, in finite nuclei, {sup 12}C, {sup 16}O, {sup 28}Si, {sup 40}Ca, {sup 56}Fe, and {sup 90}Zr, are calculated using the quark-model baryon-baryon interactions. G matrices evaluated in symmetric nuclear matter in the lowest order Brueckner theory (LOBT) are applied to finite nuclei in local density approximation. Nonlocal potentials are localized by a zero-momentum Wigner transformation. Empirical single-particle properties of the nucleon and the {lambda} hyperon in a nuclear medium have been known to be explained semiquantitatively in the LOBT framework. Attention is focused in the present consideration onmore » predictions for the {sigma} and {xi} hyperons. The unified description for the octet baryon-baryon interactions by the SU{sub 6} quark model enables us to obtain less ambiguous extrapolation to the S=-1 and S=-2 sectors based on the knowledge in the NN sector than other potential models. The {sigma} mean field is shown to be weakly attractive at the surface, but turns out to be repulsive inside, which is consistent with the experimental evidence. The {xi} hyperon s.p. potential is also attractive at the nuclear surface region, and inside it fluctuates around zero. Hence {xi} hypernuclear bound states are unlikely. We also evaluate energy shifts of the {sigma}{sup -} and {xi}{sup -} atomic levels in {sup 28}Si and {sup 56}Fe, using the calculated s.p. potentials.« less

  14. High frequency of DD polymorphism of the angiotensin-converting enzyme gene in Turkish asthmatic patients.

    PubMed

    Urhan, Meral; Degirmenci, Irfan; Harmanci, Emel; Gunes, Hasan V; Metintas, Muzaffer; Basaran, Ayse

    2004-01-01

    The aim of this study is to detect the incidence of the angiotensin-converting enzyme (ACE) gene polymorphism in Turkish asthmatic patients and to examine whether there is an association between the disease and ACE gene polymorphism. In our study, the genomic DNA of 100 asthmatic patients and 88 healthy subjects was analyzed Genomic DNA was isolated from peripheral blood by using standard methods. The intron 16 of the ACE gene was amplified by the polymerase chain reaction (PCR) method using primers ACE and ACEX to examine the presence and absence of a 287-base pair (bp) DNA fragment that showed I/D polymorphism genotypes. PCR products were separated by agarose gel electrophoresis and were visualized by a charge-coupled device camera. Serum ACE activities were measured using an ACE kit. The results were evaluated statistically using the chi-square test and one-way analysis of variance. Although the population of patients with asthma was characterized by a higher frequency (30%) of the DD genotype of ACE, they were characterized by lower frequency (48%) of the ID genotype of ACE (DD, 16%, and ID, 64%, in healthy control subjects). The frequency of the I and D alleles of the ACE gene was not significantly different between asthmatic patients (0.46/0.54) and healthy controls (0.52/ 0.48). In addition, in both asthmatic patients and controls, there was a significant decrease of the levels of ACE activity in individuals that have II genotypes when compared with individuals that have DD genotypes. ACE activities were increased significantly in all asthmatic patients (67.20 +/- 1.95 IU/L) compared with all healthy controls (60.90 +/- 2.12 IU/L).

  15. [Estimation on value of water and soil conservation of agricultural ecosystems in Xi' an metropolitan, Northwest China].

    PubMed

    Yang, Wen-yan; Zhou, Zhong-xue

    2014-12-01

    With the urban eco-environment increasingly deteriorating, the ecosystem services provided by modern urban agriculture are exceedingly significant to maintain and build more suitable environment in a city. Taking Xi' an metropolitan as the study area, based on remote sensing data, DEM data and the economic and social statistics data, the water and soil conservation service of the agricultural ecosystems was valued employing the remote sensing and geographic information system method, covering the reduction values on land waste, soil fertility loss and sediment loss from 2000 to 2011, and analyzed its changes in time and space. The results showed that during the study period, the total value of water and soil conservation service provided by agricultural systems in Xi' an metropolitan was increased by 46,086 and 33.008 billion yuan respectively from period of 2000 to 2005 and from 2005 to 2011. The cultivated land (including grains, vegetables and other farming land), forest (including orchard) and grassland provided higher value on the water and soil conservation service than waters and other land use. Ecosystem service value of water and soil conserva- tion provided by agriculture was gradually decreasing from the southern to the northern in Xi' an metropolitan. There were significantly positive relationship between the ecosystem service value and the vegetation coverage. Forest, orchard and grassland distributed intensively in the southern which had higher vegetation coverage than in northern where covered by more cultivated land, sparse forest and scattered orchard. There were significantly negative correlation between the urbanization level and the value of water and soil conservation. The higher level of urbanization, the lower value there was from built-up area to suburban and to countryside within Xi' an metropolitan.

  16. Genetic variation of the angiotensin-converting enzyme gene: increased frequency of the insertion allele in Koreans.

    PubMed

    Hong, S H; Kang, B Y; Park, W H; Kim, J Q; Lee, C C

    1997-01-01

    In view of the clinical importance of angiotensin-converting enzyme (ACE) as a major marker for cardiovascular diseases, we investigated insertion/deletion (I/D) polymorphism of the ACE gene in Koreans. Genotype frequencies were examined by polymerase chain reaction in 171 patients with coronary artery disease (CAD) and 120 healthy subjects. Allele frequencies of ACE polymorphism in Koreans were not significantly different between patient and control groups. In addition, association between ACE genotypes and the number of stenosed coronary arteries was not detected. ACE genotypes in the CAD group were not associated with body mass index and plasma lipid levels. Thus, our results suggest that, at least in Koreans, I/D polymorphism of the gene is unlikely to be a useful marker for CAD subjects. However, the I allele frequency of Koreans (0.58) was higher than that of Caucasian populations (0.47) but lower than that of Samoan (0.91) and Yanomami (0.85) populations. Here, we discuss the clinical and ethnic importance of ACE polymorphism.

  17. Frequency of the S65C mutation in the hemochromatosis gene in Brazil.

    PubMed

    Oliveira, V C; Caxito, F A; Gomes, K B; Castro, A M; Pardini, V C; Ferreira, A C S

    2009-07-14

    Development of hereditary hemochromatosis is associated with the C282Y, H63D or S65C mutations in the hemochromatosis gene. Though there is extensive knowledge about the former two, there is little information on the mechanism of action and the allelic frequency of the S65C mutation. We examined the prevalence of the S65C mutation of the hemochromatosis gene in Brazilians with clinical suspicion of hereditary hemochromatosis. Genotyping for this mutation was carried out in 633 individuals with clinical suspicion of hereditary hemochromatosis, using the polymerase chain reaction, followed by enzymatic digestion. The sample comprised 77.1% men and 22.9% women, giving a ratio of approximately 3:1; the mean age was 48.8 +/- 13.8 years. More than half (57.3%) of the individuals in the sample were 41 to 60 years old. The frequency of heterozygotes for this mutation was 0.016; no homozygous mutant patients were found. This is the first analysis of the S65C mutation in individuals suspected of having hereditary hemochromatosis in Brazil.

  18. Screening and evolution of a novel protist xylose isomerase from the termite Reticulitermes speratus for efficient xylose fermentation in Saccharomyces cerevisiae.

    PubMed

    Katahira, Satoshi; Muramoto, Nobuhiko; Moriya, Shigeharu; Nagura, Risa; Tada, Nobuki; Yasutani, Noriko; Ohkuma, Moriya; Onishi, Toru; Tokuhiro, Kenro

    2017-01-01

    The yeast Saccharomyces cerevisiae , a promising host for lignocellulosic bioethanol production, is unable to metabolize xylose. In attempts to confer xylose utilization ability in S. cerevisiae , a number of xylose isomerase (XI) genes have been expressed heterologously in this yeast. Although several of these XI encoding genes were functionally expressed in S. cerevisiae , the need still exists for a S. cerevisiae strain with improved xylose utilization ability for use in the commercial production of bioethanol. Although currently much effort has been devoted to achieve the objective, one of the solutions is to search for a new XI gene that would confer superior xylose utilization in S. cerevisiae . Here, we searched for novel XI genes from the protists residing in the hindgut of the termite Reticulitermes speratus . Eight novel XI genes were obtained from a cDNA library, prepared from the protists of the R. speratus hindgut, by PCR amplification using degenerated primers based on highly conserved regions of amino acid sequences of different XIs. Phylogenetic analysis classified these cloned XIs into two groups, one showed relatively high similarities to Bacteroidetes and the other was comparatively similar to Firmicutes . The growth rate and the xylose consumption rate of the S. cerevisiae strain expressing the novel XI, which exhibited highest XI activity among the eight XIs, were superior to those exhibited by the strain expressing the XI gene from Piromyces sp. E2. Substitution of the asparagine residue at position 337 of the novel XI with a cysteine further improved the xylose utilization ability of the yeast strain. Interestingly, introducing point mutations in the corresponding asparagine residues in XIs originated from other organisms, such as Piromyces sp. E2 or Clostridium phytofermentans , similarly improved xylose utilization in S. cerevisiae . A novel XI gene conferring superior xylose utilization in S. cerevisiae was successfully isolated from the

  19. Physical activity level and associated factors among civil servants in Xi'an, China.

    PubMed

    Sun, Lijun; Jiang, Xun; Zhao, Xin; Zhang, Yuhai; Xu, Yongyong; Shang, Lei

    2016-08-01

    This study investigated physical activity levels and associated factors among civil servants in Xi'an, China, to provide reference data for the implementation of health improvement strategies among civil servants. A cross-section study. A random sample of 1000 civil servants aged 18-60 years and employed by the Xi'an civic government was assessed by using the Chinese version of the International Physical Activity Questionnaire. Associations between physical activity and sociodemographic characteristics, family history of chronic disease, and existing disease were evaluated by the Mann-Whitney U-test, Kruskal-Wallis H-test, and binary logistic regression. The response rate was 92.4%. The median physical activity score was 2227 metabolic equivalents of task (MET) minutes per week (interquartile range [IQR]: 1308-3802METmin/week). Among the 924 participants, 7.4% did not meet minimum recommendations for physical activity, 57.3% had moderate activity levels, and 35.4% had high activity levels. Participants spent most of their time on occupational activities (median: 869METmin/week, IQR: 228-1953METmin/week). Female sex (odds ratio [OR]:0.40, 95% confidence interval [CI]:0.29-0.55), age≥51 years (OR: 0.45, 95%CI: 0.27-0.75), and family history of chronic disease (OR: 0.67, 95%CI: 0.48-0.94) were associated with significantly lower odds of a high activity level. Most civil servants in Xi'an, China, have moderate activity levels. Some have high activity levels, but few engage in vigorous-intensity physical activity. Interventions to encourage a high level of physical activity are needed, especially for women, older civil servants, and those with family histories of chronic disease. Copyright © 2015 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

  20. Secondary Ion Mass Spectrometry SIMS XI

    NASA Astrophysics Data System (ADS)

    Gillen, G.; Lareau, R.; Bennett, J.; Stevie, F.

    2003-05-01

    This volume contains 252 contributions presented as plenary, invited and contributed poster and oral presentations at the 11th International Conference on Secondary Ion Mass Spectrometry (SIMS XI) held at the Hilton Hotel, Walt Disney World Village, Orlando, Florida, 7 12 September, 1997. The book covers a diverse range of research, reflecting the rapid growth in advanced semiconductor characterization, ultra shallow depth profiling, TOF-SIMS and the new areas in which SIMS techniques are being used, for example in biological sciences and organic surface characterization. Papers are presented under the following categories: Isotopic SIMS Biological SIMS Semiconductor Characterization Techniques and Applications Ultra Shallow Depth Profiling Depth Profiling Fundamental/Modelling and Diffusion Sputter-Induced Topography Fundamentals of Molecular Desorption Organic Materials Practical TOF-SIMS Polyatomic Primary Ions Materials/Surface Analysis Postionization Instrumentation Geological SIMS Imaging Fundamentals of Sputtering Ion Formation and Cluster Formation Quantitative Analysis Environmental/Particle Characterization Related Techniques These proceedings provide an invaluable source of reference for both newcomers to the field and experienced SIMS users.

  1. Energy levels and radiative rates for transitions in Co XI

    NASA Astrophysics Data System (ADS)

    Aggarwal, K. M.; Keenan, F. P.; Msezane, A. Z.

    2007-10-01

    Aims: In this paper we report calculations for energy levels and radiative rates for transitions in Co xi. Methods: The General purpose Relativistic Atomic Structure Package (grasp) and the Flexible Atomic Code (fac) have been adopted for the calculations of energy levels and radiative rates. Results: Energies for the lowest 287 levels of Co xi, including those among the (1s^22s^22p^6) 3s^23p^5, 3s3p^6, 3s^23p^43d, 3s3p^53d, 3s^23p^33d^2, and 3s^23p^44s configurations, are reported. Additionally, radiative rates and oscillator strengths are reported for all electric dipole (E1) transitions with f ≥ 10-5 among these levels, and similar results for magnetic dipole (M1), electric quadrupole (E2), and magnetic quadrupole (M2) transitions are reported only for those with f≥10-8. Comparisons are made with the available results in the literature, and the accuracy of the present data is assessed. Finally, lifetimes for all excited levels are also listed, although measurements are presently available for only one of these. Tables 1 and 3-6 are only available in electronic form at the CDS via anonymous ftp to cdsarc.u-strasbg.fr (130.79.128.5) or via http://cdsweb.u-strasbg.fr/cgi-bin/qcat?J/A+A/473/995

  2. HLA class II and TNF genes in African Americans from the Southeastern United States: regional differences in allele frequencies.

    PubMed

    Kuffner, Tamara; Whitworth, William; Jairam, Maya; McNicholl, Janet

    2003-06-01

    Knowledge of population major histocompatibility complex gene frequencies is important for construction of organ donor pools and for studies of disease association. Human leukocyte antigen DRB1 (HLA-DRB1), HLA-DQB1, and TNFalpha -308 (G-A) promoter genetic typing was performed in 112 healthy, unrelated African Americans (AAs) from the southeastern United States. Allele frequencies were compared with published frequency data from other AA populations. Our AA population had the highest frequency of HLA- DRB1*09 (6.7%) reported in any AA population. The frequency of the TNF alpha -308A polymorphism was also high (14.4%), when compared with published frequencies in AAs. Significant regional differences in the distribution of most HLA-DRB1 and HLA-DQB1 alleles were observed in all AA populations examined. The AA HLA-DRB1 and -DQB1 frequencies also differed from published Caucasian frequencies. This is the first report describing the distribution of TNF alpha promoter alleles in the Southeastern United States. The high DRB1*09 and TNF alpha -308A allele frequencies of our population most resemble the frequencies of these alleles in certain West African populations. These varying major histocompatibility complex gene frequencies may reflect different regional population structures among AAs in the United States, which may be due to differences in ancestral origins, migration, and racial admixture.

  3. Spatial frequency domain imaging using a snap-shot filter mosaic camera with multi-wavelength sensitive pixels

    NASA Astrophysics Data System (ADS)

    Strömberg, Tomas; Saager, Rolf B.; Kennedy, Gordon T.; Fredriksson, Ingemar; Salerud, Göran; Durkin, Anthony J.; Larsson, Marcus

    2018-02-01

    Spatial frequency domain imaging (SFDI) utilizes a digital light processing (DLP) projector for illuminating turbid media with sinusoidal patterns. The tissue absorption (μa) and reduced scattering coefficient (μ,s) are calculated by analyzing the modulation transfer function for at least two spatial frequencies. We evaluated different illumination strategies with a red, green and blue light emitting diodes (LED) in the DLP, while imaging with a filter mosaic camera, XiSpec, with 16 different multi-wavelength sensitive pixels in the 470-630 nm wavelength range. Data were compared to SFDI by a multispectral camera setup (MSI) consisting of four cameras with bandpass filters centered at 475, 560, 580 and 650 nm. A pointwise system for comprehensive microcirculation analysis was used (EPOS) for comparison. A 5-min arterial occlusion and release protocol on the forearm of a Caucasian male with fair skin was analyzed by fitting the absorption spectra of the chromophores HbO2, Hb and melanin to the estimatedμa. The tissue fractions of red blood cells (fRBC), melanin (/mel) and the Hb oxygenation (S02 ) were calculated at baseline, end of occlusion, early after release and late after release. EPOS results showed a decrease in S02 during the occlusion and hyperemia during release (S02 = 40%, 5%, 80% and 51%). The fRBC showed an increase during occlusion and release phases. The best MSI resemblance to the EPOS was for green LED illumination (S02 = 53%, 9%, 82%, 65%). Several illumination and analysis strategies using the XiSpec gave un-physiological results (e.g. negative S02 ). XiSpec with green LED illumination gave the expected change in /RBC , while the dynamics in S02 were less than those for EPOS. These results may be explained by the calculation of modulation using an illumination and detector setup with a broad spectral transmission bandwidth, with considerable variation in μa of included chromophores. Approaches for either reducing the effective bandwidth of

  4. Ecosystem Services Insights into Water Resources Management in China: A Case of Xi'an City.

    PubMed

    Liu, Jingya; Li, Jing; Gao, Ziyi; Yang, Min; Qin, Keyu; Yang, Xiaonan

    2016-11-24

    Global climate and environmental changes are endangering global water resources; and several approaches have been tested to manage and reduce the pressure on these decreasing resources. This study uses the case study of Xi'an City in China to test reasonable and effective methods to address water resource shortages. The study generated a framework combining ecosystem services and water resource management. Seven ecosystem indicators were classified as supply services, regulating services, or cultural services. Index values for each indicator were calculated, and based on questionnaire results, each index's weight was calculated. Using the Likert method, we calculated ecosystem service supplies in every region of the city. We found that the ecosystem's service capability is closely related to water resources, providing a method for managing water resources. Using Xi'an City as an example, we apply the ecosystem services concept to water resources management, providing a method for decision makers.

  5. [Gene method for inconsistent hydrological frequency calculation. I: Inheritance, variability and evolution principles of hydrological genes].

    PubMed

    Xie, Ping; Wu, Zi Yi; Zhao, Jiang Yan; Sang, Yan Fang; Chen, Jie

    2018-04-01

    A stochastic hydrological process is influenced by both stochastic and deterministic factors. A hydrological time series contains not only pure random components reflecting its inheri-tance characteristics, but also deterministic components reflecting variability characteristics, such as jump, trend, period, and stochastic dependence. As a result, the stochastic hydrological process presents complicated evolution phenomena and rules. To better understand these complicated phenomena and rules, this study described the inheritance and variability characteristics of an inconsistent hydrological series from two aspects: stochastic process simulation and time series analysis. In addition, several frequency analysis approaches for inconsistent time series were compared to reveal the main problems in inconsistency study. Then, we proposed a new concept of hydrological genes origined from biological genes to describe the inconsistent hydrolocal processes. The hydrologi-cal genes were constructed using moments methods, such as general moments, weight function moments, probability weight moments and L-moments. Meanwhile, the five components, including jump, trend, periodic, dependence and pure random components, of a stochastic hydrological process were defined as five hydrological bases. With this method, the inheritance and variability of inconsistent hydrological time series were synthetically considered and the inheritance, variability and evolution principles were fully described. Our study would contribute to reveal the inheritance, variability and evolution principles in probability distribution of hydrological elements.

  6. [Chiparray-based identification of gene expression in HUVECs treated with low frequency electric fields].

    PubMed

    Ulrich, D; Ulrich, F; Silny, J; Unglaub, F; Pallua, N

    2006-06-01

    After high-voltage electric injury, patients often show progressive tissue necrosis and thrombosis of blood vessels even remote from the entry and exit sites of electrical current. Recently, we were able to demonstrate IN VIVO and VITRO the release of several prothrombotic factors. In this study, we report on IN VITRO studies performed to characterize gene expression profiles using a DNA-microarray in HUVECs (human umbilical vein endothelial cells) exposed to low frequency electrical current. HUVECs were plated and grown to confluence in a culture chamber. They were exposed to 25 periods of 50 Hz sinusoidal waves. The periods had field strength of 60 V/cm and duration of 100 ms. Periods were interrupted by 10-second intervals to prevent significant joule heating. Control HUVECs were treated identically except that no electric field was applied. Samples from control and treated cells were taken after six and 24 hours. A PIQOR Immunology Array (Milteny Biotech) containing 1076 cDNAs was used for gene expression analysis. Hybridization of Cy3- and Cy5-labelled samples, image capture, and signal quantification of hybridized arrays were performed. Local background was subtracted from the signal to obtain the net signal intensity and the ratio of Cy5/Cy3. The ratios were normalized to the median of all ratios and the mean of the ratios of four corresponding spots was computed. More than two-fold increases or decreases of the gene expression were regarded as relevant. A total of 413 genes (1s + s) respectively 345 genes (2s + s) could be detected. The results obtained display a distinct expression pattern of up-regulated genes known to be important for hemostasis (e.g. UPA, UPAR, ECE1, PAFAH1B1, PGT, INOS, ENOS, TPA, ICAM1, VCAM1, PAI1, PAI2, VWF, PTGDR, F3, THBD), which was most evident after 24 hours. This expression profile might lead to a hypercoagulated state. Furthermore, the expression of genes involved in angiogenesis was reduced whereas the expression of those

  7. The high frequency of GJB2 gene mutation c.313_326del14 suggests its possible origin in ancestors of Lithuanian population.

    PubMed

    Mikstiene, Violeta; Jakaitiene, Audrone; Byckova, Jekaterina; Gradauskiene, Egle; Preiksaitiene, Egle; Burnyte, Birute; Tumiene, Birute; Matuleviciene, Ausra; Ambrozaityte, Laima; Uktveryte, Ingrida; Domarkiene, Ingrida; Rancelis, Tautvydas; Cimbalistiene, Loreta; Lesinskas, Eugenijus; Kucinskas, Vaidutis; Utkus, Algirdas

    2016-02-19

    Congenital hearing loss (CHL) is diagnosed in 1 - 2 newborns in 1000, genetic factors contribute to two thirds of CHL cases in industrialised countries. Mutations of the GJB2 gene located in the DFNB1 locus (13q11-12) are a major cause of CHL worldwide. The aim of this cross-sectional study was to assess the contribution of the DFNB1 locus containing the GJB2 and GJB6 genes in the development of early onset hearing loss in the affected group of participants, to determine the population-specific mutational profile and DFNB1-related HL burden in Lithuanian population. Clinical data were obtained from a collection of 158 affected participants (146 unrelated probands) with early onset non-syndromic HL. GJB2 and GJB6 gene sequencing and GJB6 gene deletion testing were performed. The data of GJB2 and GJB6 gene sequencing in 98 participants in group of self-reported healthy Lithuanian inhabitants were analysed. Statistic summary, homogeneity tests, and logistic regression analysis were used for the assessment of genotype-phenotype correlation. Our findings show 57.5% of affected participants with two pathogenic GJB2 gene mutations identified. The most prevalent GJB2 mutations were c.35delG, p. (Gly12Valfs*2) (rs80338939) and c.313_326del14, p. (Lys105Glyfs*5) (rs111033253) with allele frequencies 64.7% and 28.3% respectively. GJB6 gene mutations were not identified in the affected group of participants. The statistical analysis revealed significant differences between GJB2(-) and GJB2(+) groups in disease severity (p = 0.001), and family history (p = 0.01). The probability of identification of GJB2 mutations in patients with various HL characteristics was estimated. The carrier rate of GJB2 gene mutations - 7.1% (~1 in 14) was identified in the group of healthy participants and a high frequency of GJB2-related hearing loss was estimated in our population. The results show a very high proportion of GJB2-positive individuals in the research group affected with sensorineural

  8. Study on the adult physique with the Heath-Carter anthropometric somatotype in the Han of Xi'an, China.

    PubMed

    Yang, Li-Tao; Wang, Ning; Li, Zeng-Xian; Liu, Cui; He, Xin; Zhang, Jian-Fei; Han, Hua; Wen, You-Feng; Qian, Yi-Hua; Xi, Huan-Jiu

    2016-03-01

    The study of somatotypes has important significance for medical and physical anthropology as well as sports science. The aim of this study was to understand the somatotype components of the Han population in Xi'an and compare the somatotypes of the Han and five other nationalities in China. The study sample consisted of 429 people of Han nationality (207 males, 222 females) from Xi'an, China, aged ≥20 years old. The Heath-Carter anthropometric method was employed. We evaluated the differences in age and sex by one-way ANOVA and t test. A comparison of somatotypes between the Han and other nationalities was made using the U test. The results showed that the male and female samples all could be classified as having a mesomorphic endomorph profile. The difference in endomorphy was strongest between sexes in all age groups (P < 0.01). There were prominent differences in mesomorphy and ectomorphy between males and females in the 50-59- and ≥60-year-old age groups. In females, the differences in somatotype components appeared to be distinguished between ages (P < 0.01 or P < 0.05). However, in males, there were prominent differences in somatotype components between the 20-29 year olds and all other age groups (P < 0.01 or P < 0.05) except for between those 20-29 and ≥60 years old in endomorphy. Compared with the other five nationalities, there were prominent differences in somatotype components between males and females. These results suggest that the somatotype of the Han population in Xi'an, China, has a predominantly mesomorphic endomorph profile. The endomorphic component shows distinct differences between ages and genders, respectively. Additionally, there are distinct differences in the somatotype components between Xi'an Han and five other nationalities in China in males and females.

  9. Resolving the xi Boo Binary with Chandra, and Revealing the Spectral Type Dependence of the Coronal "Fip Effect"

    NASA Technical Reports Server (NTRS)

    Wood, Brian E.; Linsky, Jeffrey L.

    2010-01-01

    On 2008 May 2, Chandra observed the X-ray spectrum of xi Boo (G8 V+K4 V), resolving the binary for the first time in X-rays and allowing the coronae of the two stars to be studied separately. With the contributions of ξ Boo A and B to the system's total X-ray emission now observationally established (88.5% and 11.5% respectively), consideration of mass loss measurements for GK dwarfs of various activity levels (including one for xi Boo) leads to the surprising conclusion that xi Boo B may dominate the wind from the binary, with xi Boo A's wind being very weak despite its active corona. Emission measure (EM) distributions and coronal abundances are computed for both stars and compared with Chandra measurements of other moderately active stars with G8-K5 spectral types, all of which exhibit a narrow peak in EM near log T = 6.6, indicating that the coronal heating process in these stars has a strong preference for this temperature. As is the case for the Sun and many other stars, our sample of stars shows coronal abundance anomalies dependent on the first ionization potential (FIP) of the element. We see no dependence of the degree of FIP effect on activity, but there is a dependence on spectral type, a correlation that becomes more convincing when moderately active main-sequence stars with a broader range of spectral types are considered. This clear dependence of coronal abundances on spectral type weakens if the stellar sample is allowed to be contaminated by evolved stars, interacting binaries or extremely active stars with logLX 29, explaining why this correlation has not been recognized in the past.

  10. Frequency of mutations in the genes associated with hereditary sensory and autonomic neuropathy in a UK cohort

    PubMed Central

    Davidson, G. L.; Murphy, S. M.; Polke, J. M.; Laura, M.; Salih, M. A. M.; Muntoni, F.; Blake, J.; Brandner, S.; Davies, N.; Horvath, R.; Price, S.; Donaghy, M.; Roberts, M.; Foulds, N.; Ramdharry, G.; Soler, D.; Lunn, M. P.; Manji, H.; Davis, M. B.; Houlden, H.; Reilly, M. M.

    2013-01-01

    The hereditary sensory and autonomic neuropathies (HSAN, also known as the hereditary sensory neuropathies) are a clinically and genetically heterogeneous group of disorders, characterised by a progressive sensory neuropathy often complicated by ulcers and amputations, with variable motor and autonomic involvement. To date, mutations in twelve genes have been identified as causing HSAN. To study the frequency of mutations in these genes and the associated phenotypes, we screened 140 index patients in our inherited neuropathy cohort with a clinical diagnosis of HSAN for mutations in the coding regions of SPTLC1, RAB7, WNK1/HSN2, FAM134B, NTRK1 (TRKA) and NGFB. We identified 25 index patients with mutations in six genes associated with HSAN (SPTLC1, RAB7, WNK1/HSN2, FAM134B, NTRK1 and NGFB); 20 of which appear to be pathogenic giving an overall mutation frequency of 14.3%. Mutations in the known genes for HSAN are rare suggesting that further HSAN genes are yet to be identified. The p.Cys133Trp mutation in SPTLC1 is the most common cause of HSAN in the UK population and should be screened first in all patients with sporadic or autosomal dominant HSAN. PMID:22302274

  11. Frequency of mutations in the genes associated with hereditary sensory and autonomic neuropathy in a UK cohort.

    PubMed

    Davidson, G L; Murphy, S M; Polke, J M; Laura, M; Salih, M A M; Muntoni, F; Blake, J; Brandner, S; Davies, N; Horvath, R; Price, S; Donaghy, M; Roberts, M; Foulds, N; Ramdharry, G; Soler, D; Lunn, M P; Manji, H; Davis, M B; Houlden, H; Reilly, M M

    2012-08-01

    The hereditary sensory and autonomic neuropathies (HSAN, also known as the hereditary sensory neuropathies) are a clinically and genetically heterogeneous group of disorders, characterised by a progressive sensory neuropathy often complicated by ulcers and amputations, with variable motor and autonomic involvement. To date, mutations in twelve genes have been identified as causing HSAN. To study the frequency of mutations in these genes and the associated phenotypes, we screened 140 index patients in our inherited neuropathy cohort with a clinical diagnosis of HSAN for mutations in the coding regions of SPTLC1, RAB7, WNK1/HSN2, FAM134B, NTRK1 (TRKA) and NGFB. We identified 25 index patients with mutations in six genes associated with HSAN (SPTLC1, RAB7, WNK1/HSN2, FAM134B, NTRK1 and NGFB); 20 of which appear to be pathogenic giving an overall mutation frequency of 14.3%. Mutations in the known genes for HSAN are rare suggesting that further HSAN genes are yet to be identified. The p.Cys133Trp mutation in SPTLC1 is the most common cause of HSAN in the UK population and should be screened first in all patients with sporadic or autosomal dominant HSAN.

  12. Allelic frequencies and association with carcass traits of six genes in local subpopulations of Japanese Black cattle.

    PubMed

    Nishimaki, Takahiro; Ibi, Takayuki; Siqintuya; Kobayashi, Naohiko; Matsuhashi, Tamako; Akiyama, Takayuki; Yoshida, Emi; Imai, Kazumi; Matsui, Mayu; Uemura, Keiichi; Eto, Hisayoshi; Watanabe, Naoto; Fujita, Tatsuo; Saito, Yosuke; Komatsu, Tomohiko; Hoshiba, Hiroshi; Mannen, Hideyuki; Sasazaki, Shinji; Kunieda, Tetsuo

    2016-04-01

    Marker-assisted selection (MAS) is expected to accelerate the genetic improvement of Japanese Black cattle. However, verification of the effects of the genes for MAS in different subpopulations is required prior to the application of MAS. In this study, we investigated the allelic frequencies and genotypic effects for carcass traits of six genes, which can be used in MAS, in eight local subpopulations. These genes are SCD, FASN and SREBP1, which are associated with the fatty acid composition of meat, and NCAPG, MC1R and F11, which are associated with carcass weight, coat color and blood coagulation abnormality, respectively. The frequencies of desirable alleles of SCD and FASN were relatively high and that of NCAPG was relatively low, and NCAPG was significantly associated with several carcass traits, including carcass weight. The proportions of genotypic variance explained by NCAPG to phenotypic variance were 4.83 for carcass weight. We thus confirmed that NCAPG is a useful marker for selection of carcass traits in these subpopulations. In addition, we found that the desirable alleles of six genes showed no negative effects on carcass traits. Therefore, selection using these genes to improve target traits should not have negative impacts on carcass traits. © 2015 Japanese Society of Animal Science.

  13. Role of high-spin hyperon resonances in the reaction of $$\\gamma p \\to K^+ K^+ \\Xi^-$$

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

    J. Ka Shing Man, Yongseok Oh, K. Nakayama

    The recent data taken by the CLAS Collaboration at the Thomas Jefferson National Accelerator Facility for the reaction ofmore » $$\\gamma p \\to K^+ K^+ \\Xi^-$$ are reanalyzed within a relativistic meson-exchange model of hadronic interactions. The present model is an extension of the one developed in an earlier work by Nakayama, Oh, and Haberzettl [Phys. Rev. C 74, 035205 (2006)]. In particular, the role of the spin-5/2 and -7/2 hyperon resonances, which were not included in the previous model, is investigated in the present study. It is shown that the contribution of the $$\\Sigma(2030)$$ hyperon having spin-7/2 and positive parity has a key role to bring the model predictions into a fair agreement with the measured data for the $$K^+\\Xi^-$$ invariant mass distribution.« less

  14. Inherited differences in crossing over and gene conversion frequencies between wild strains of Sordaria fimicola from "Evolution Canyon".

    PubMed Central

    Saleem, M; Lamb, B C; Nevo, E

    2001-01-01

    Recombination generates new combinations of existing genetic variation and therefore may be important in adaptation and evolution. We investigated whether there was natural genetic variation for recombination frequencies and whether any such variation was environment related and possibly adaptive. Crossing over and gene conversion frequencies often differed significantly in a consistent direction between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in "Evolution Canyon," Israel. First- and second-generation descendants from selfing the original strains from the harsher, more variable, south-facing slope had higher frequencies of crossing over in locus-centromere intervals and of gene conversion than those from the lusher north-facing slopes. There were some significant differences between strains within slopes, but these were less marked than between slopes. Such inherited variation could provide a basis for natural selection for optimum recombination frequencies in each environment. There were no significant differences in meiotic hybrid DNA correction frequencies between strains from the different slopes. The conversion analysis was made using only conversions to wild type, because estimations of conversion to mutant were affected by a high frequency of spontaneous mutation. There was no polarized segregation of chromosomes at meiosis I or of chromatids at meiosis II. PMID:11779798

  15. Inherited differences in crossing over and gene conversion frequencies between wild strains of Sordaria fimicola from "Evolution Canyon".

    PubMed

    Saleem, M; Lamb, B C; Nevo, E

    2001-12-01

    Recombination generates new combinations of existing genetic variation and therefore may be important in adaptation and evolution. We investigated whether there was natural genetic variation for recombination frequencies and whether any such variation was environment related and possibly adaptive. Crossing over and gene conversion frequencies often differed significantly in a consistent direction between wild strains of the fungus Sordaria fimicola isolated from a harsher or a milder microscale environment in "Evolution Canyon," Israel. First- and second-generation descendants from selfing the original strains from the harsher, more variable, south-facing slope had higher frequencies of crossing over in locus-centromere intervals and of gene conversion than those from the lusher north-facing slopes. There were some significant differences between strains within slopes, but these were less marked than between slopes. Such inherited variation could provide a basis for natural selection for optimum recombination frequencies in each environment. There were no significant differences in meiotic hybrid DNA correction frequencies between strains from the different slopes. The conversion analysis was made using only conversions to wild type, because estimations of conversion to mutant were affected by a high frequency of spontaneous mutation. There was no polarized segregation of chromosomes at meiosis I or of chromatids at meiosis II.

  16. TlBr and TlBr xI 1-x crystals for γ-ray detectors

    NASA Astrophysics Data System (ADS)

    Churilov, Alexei V.; Ciampi, Guido; Kim, Hadong; Higgins, William M.; Cirignano, Leonard J.; Olschner, Fred; Biteman, Viktor; Minchello, Mark; Shah, Kanai S.

    2010-04-01

    TlBr and TlBr xI 1-x are wide bandgap semiconductor materials being investigated for applications in γ-ray spectroscopy. They have a good combination of density and atomic numbers, promising to make them very efficient detectors. Their low melting points and simple cubic and orthorhombic crystal structures are favorable for bulk crystal growth. However, these semiconductors need to be extremely pure to become useful as radiation detectors. Impurities can lead to charge trapping and scattering, reducing the charge transit lengths and limiting the detector thickness to <1 mm. Additional purification steps were implemented to improve the purity and mobility-lifetime product ( μτ) of electrons. Detector-grade TlBr with the electron μτ product of up to 6×10 -3 cm 2/V has been produced, which allowed operation of detectors up to 15 mm thickness. The ternary TlBr xI 1-x was investigated at different compositions to vary the bandgap and explore the effect of added TlI on the long term stability of detectors. The material analysis and detector characterization results are included.

  17. High frequency of coexistent mutations of PIK3CA and PTEN genes in endometrial carcinoma.

    PubMed

    Oda, Katsutoshi; Stokoe, David; Taketani, Yuji; McCormick, Frank

    2005-12-01

    The phosphatidylinositol 3'-kinase (PI3K) pathway is activated in many human cancers. In addition to inactivation of the PTEN tumor suppressor gene, mutations or amplifications of the catalytic subunit alpha of PI3K (PIK3CA) have been reported. However, the coexistence of mutations in these two genes seems exceedingly rare. As PTEN mutations occur at high frequency in endometrial carcinoma, we screened 66 primary endometrial carcinomas for mutations in the helical and catalytic domains of PIK3CA. We identified a total of 24 (36%) mutations in this gene and coexistence of PIK3CA/PTEN mutations at high frequency (26%). PIK3CA mutations were more common in tumors with PTEN mutations (17 of 37, 46%) compared with those without PTEN mutations (7 of 29, 24%). Array comparative genomic hybridization detected 3q24-qter amplification, which covers the PIK3CA gene (3q26.3), in one of nine tumors. Knocking down PTEN expression in the HEC-1B cell line, which possesses both K-Ras and PIK3CA mutations, further enhances phosphorylation of Akt (Ser473), indicating that double mutation of PIK3CA and PTEN has an additive effect on PI3K activation. Our data suggest that the PI3K pathway is extensively activated in endometrial carcinomas, and that combination of PIK3CA/PTEN alterations might play an important role in development of these tumors.

  18. Atomic Data and Spectral Line Intensities for Ni XI

    NASA Technical Reports Server (NTRS)

    Bhatia, A. K.; Landi, E.

    2010-01-01

    Electron impact collision strengths, energy levels, oscillator strengths and spontaneous radiative decay rates are calculated for Ni XI. We include in the calculations the 10 lowest configurations, corresponding to 164 fine structure levels: 3s(sup 2)3p(sup 6), 3s(sup 2)3p(sup 5)3d, 3s(sup 2)3p(sup 4)3d(sup 2), 3s3p(sup 6)3d, 3s(sup 2)3p(sup 5)4l and 3s3p6 4l with l =.s, p, d. Collision strengths are calculated at five incident energies for all transitions: 7.1, 16.8, 30.2, 48.7 and 74.1 Ry above the threshold of each transition. An additional energy, very close to the transition threshold, has been added, whose value is between 0.06 Ry and 0.25 Ry depending on the lower level. Calculations have been carried out using the Flexible Atomic Code and the distorted wave approximation. Excitation rate coefficients are calculated as a function of electron temperature by assuming a Maxwellian electron velocity distribution. Using the excitation rate coefficients and the radiative transition rates of the present work, combined with Close Coupling collision excitation rate coefficient available in the literature for the lowest 17 levels, statistical equilibrium equations for level populations are solved at electron densities covering the 10(exp 8)-10(exp 14) cu cm range and at an electron temperature of logT(sub c)(K)=6.1, corresponding to the maximum abundance of Ni XI. Spectral line intensities are calculated, and their diagnostic relevance is discussed. This dataset will be made available in the next version of the CHIANTI database.

  19. Effect of NET-1 siRNA conjugated sub-micron bubble complex combined with low-frequency ultrasound exposure in gene transfection

    PubMed Central

    Wu, Bolin; Liang, Xitian; Jing, Hui; Han, Xue; Sun, Yixin; Guo, Cunli; Liu, Ying; Cheng, Wen

    2018-01-01

    The present study evaluated the effect of NET-1 siRNA-conjugated sub-micron bubble (SMB) complexes combined with low-frequency ultrasound exposure in gene transfection. The NET-1 gene was highly expressed level in SMMC-7721 human hepatocellular carcinoma cell line. The cells were divided into seven groups and treated with different conditions. The groups with or without low-frequency ultrasound exposure, groups of adherent cells, and suspension cells were separated. The NET-1 siRNA-conjugated SMB complexes were made in the laboratory and tested by Zetasizer Nano ZS90 analyzer. Flow cytometry was used to estimate the transfection efficiency and cellular apoptosis. Western blot and quantitative real-time polymerase chain reaction (qPCR) were used for the estimation of the protein and mRNA expressions, respectively. Transwell analysis determined the migration and invasion capacities of the tumor cells. The results did not show any difference in the transfection efficiency between adherent and suspension cells. However, the NET-1 siRNA-SMB complexes combined with low-frequency ultrasound exposure could enhance the gene transfection effectively. In summary, the NET-1 siRNA-SMB complexes appeared to be promising gene vehicle. PMID:29423111

  20. Total robotic radical rectal resection with da Vinci Xi system: single docking, single phase technique.

    PubMed

    Tamhankar, Anup Sunil; Jatal, Sudhir; Saklani, Avanish

    2016-12-01

    This study aims to assess the advantages of Da Vinci Xi system in rectal cancer surgery. It also assesses the initial oncological outcomes after rectal resection with this system from a tertiary cancer center in India. Robotic rectal surgery has distinct advantages over laparoscopy. Total robotic resection is increasing following the evolution of hybrid technology. The latest Da Vinci Xi system (Intuitive Surgical, Sunnyvale, USA) is enabled with newer features to make total robotic resection possible with single docking and single phase. Thirty-six patients underwent total robotic resection in a single phase and single docking. We used newer port positions in a straight line. Median distance from the anal verge was 4.5 cm. Median robotic docking time and robotic procedure time were 9 and 280 min, respectively. Median blood loss was 100 mL. One patient needed conversion to an open approach due to advanced disease. Circumferential resection margin and longitudinal resection margins were uninvolved in all other patients. Median lymph node yield was 10. Median post-operative stay was 7 days. There were no intra-operative adverse events. The latest Da Vinci Xi system has made total robotic rectal surgery feasible in single docking and single phase. With the new system, four arm total robotic rectal surgery may replace the hybrid technique of laparoscopic and robotic surgery for rectal malignancies. The learning curve for the new system appears to be shorter than anticipated. Early perioperative and oncological outcomes of total robotic rectal surgery with the new system are promising. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  1. Novel DNA variants and mutation frequencies of hMLH1 and hMSH2 genes in colorectal cancer in the Northeast China population.

    PubMed

    Hu, Fulan; Li, Dandan; Wang, Yibaina; Yao, Xiaoping; Zhang, Wencui; Liang, Jing; Lin, Chunqing; Ren, Jiaojiao; Zhu, Lin; Wu, Zhiwei; Li, Shuying; Li, Ye; Zhao, Xiaojuan; Cui, Binbin; Dong, Xinshu; Tian, Suli; Zhao, Yashuang

    2013-01-01

    Research on hMLH1 and hMSH2 mutations tend to focus on Lynch syndrome (LS) and LS-like colorectal cancer (CRC). No studies to date have assessed the role of hMLH1 and hMSH2 genes in mass sporadic CRC (without preselection by MSI or early age of onset). We aimed to identify novel hMLH1 and hMSH2 DNA variants, to determine the mutation frequencies and sites in both sporadic and LS CRC and their relationships with clinicopathological characteristics of CRC in Northeast of China. 452 sporadic and 21 LS CRC patients were screened for germline and somatic mutations in hMLH1 and hMSH2 genes with PCR-SSCP sequencing. We identified 11 hMLH1 and seven hMSH2 DNA variants in our study cohort. Six of them were novel: four in hMLH1 gene (IVS8-16 A>T, c.644 GAT>GTT, c.1529 CAG>CGG and c.1831 ATT>TTT) and two in hMSH2 gene (-39 C>T, insertion AACAACA at c.1127 and deletion AAG at c.1129). In sporadic CRC, germline and somatic mutation frequencies of hMLH1/hMSH2 gene were 15.59% and 17.54%, respectively (p = 0.52). Germline mutations present in hMLH1 and hMSH2 genes were 5.28% and 10.78%, respectively (p<0.01). Somatic mutations in hMLH1 and hMSH2 genes were 6.73% and 11.70%, respectively (p = 0.02). In LS CRC, both germline and somatic mutation frequencies of hMLH1/hMSH2 gene were 28.57%. The most prevalent germline mutation site in hMSH2 gene was c.1168 CTT>TTT (3.90%), a polymorphism. Somatic mutation frequency of hMLH1/hMSH2 gene was significantly different in proximal, distal colon and rectal cancer (p = 0.03). Our findings elucidate the mutation spectrum and frequency of hMLH1 and hMSH2 genes in sporadic and LS CRC, and their relationships with clinicopathological characteristics of CRC.

  2. A high frequency of distinct ATM gene mutations in ataxia-telangiectasia.

    PubMed Central

    Wright, J.; Teraoka, S.; Onengut, S.; Tolun, A.; Gatti, R. A.; Ochs, H. D.; Concannon, P.

    1996-01-01

    The clinical features of the autosomal recessive disorder ataxia-telangiectasia (AT) include a progressive cerebellar ataxia, hypersensitivity to ionizing radiation, and an increased susceptibility to malignancies. Epidemiological studies have suggested that AT heterozygotes may also be at increased risk for malignancy, possibly as a consequence of radiation exposure. A gene mutated in AT patients (ATM) has recently been isolated, making mutation screening in both patients and the general population possible. Because of the relatively large size of the ATM gene, the design of screening programs will depend on the types and distribution of mutations in the general population. In this report, we describe 30 mutations identified in a panel of unrelated AT patients and controls. Twenty-five of the 30 were distinct, and most patients were compound heterozygotes. The most frequently detected mutation was found in three different families and had previously been reported in five others. This corresponds to a frequency of 8% of all reported ATM mutations. Twenty-two of the alterations observed would be predicted to lead to protein truncation at sites scattered throughout the molecule. Two fibroblast cell lines, which displayed normal responses to ionizing radiation, also proved to be heterozygous for truncation mutations of ATM. These observations suggest that the carrier frequency of ATM mutations may be sufficiently high to make population screening practical. However, such screening may need to be done prospectively, that is, by searching for new mutations rather than by screening for just those already identified in AT families. PMID:8808599

  3. Breckinridge Project, initial effort. Report XI, Volume V. Critical review of the design basis. [Critical review

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

    None

    1982-01-01

    Report XI, Technical Audit, is a compendium of research material used during the Initial Effort in making engineering comparisons and decisions. Volumes 4 and 5 of Report XI present those studies which provide a Critical Review of the Design Basis. The Critical Review Report, prepared by Intercontinental Econergy Associates, Inc., summarizes findings from an extensive review of the data base for the H-Coal process design. Volume 4 presents this review and assessment, and includes supporting material; specifically, Design Data Tabulation (Appendix A), Process Flow Sheets (Appendix B), and References (Appendix C). Volume 5 is a continuation of the references ofmore » Appendix C. Studies of a proprietary nature are noted and referenced, but are not included in these volumes. They are included in the Limited Access versions of these reports and may be reviewed by properly cleared personnel in the offices of Ashland Synthetic Fuels, Inc.« less

  4. [Geographical characteristics of single nucleotide polymorphism of candidate genes associated with coronary artery disease in Chinese Han population].

    PubMed

    Wang, Sheng-Huang; Cui, Han-Bin; Wang, Dong-Qi; Chen, Xiao-Min; Zhang, Hong-Kao; Cui, Chang-Cong; Chen, Xin-Yi; Liu, Xin-Hong; Zhang, Zheng; Bai, Feng; Jb, Muhlestein

    2008-01-01

    To investigate the geographical characteristics of single nucleotide polymorphism (SNP) of candidate genes associated with coronary artery disease in Chinese Han population. Study population were Chinese Han nationality recruited from Xi'an, Shiyan and Ningbo districts. Patients with coronary artery disease were defined by coronary angiography with stenosis >or= 50% and control subjects with stenosis < 10%, respectively. The DNA was extracted from peripheral white blood cell by approach comprised proteinase K digestion, phenol and chloroform extraction as well as isopropanol precipitation. The SNP of ATP-binding cassette transporter (ABCA1)-G596A, cholesteryl ester transfer protein (CETP)-Taq1B, Lipoprotein lipase (LPL)-Hind III and LPL-Pvu II were genotyped by PCR-RFLPs, and verified by gene sequencing. A Total of 615 patients undertaken coronary angiography were recruited from cardiac center in Xi'an (220), Ningbo (209) and Shiyan district (186), China (mean age 60 +/- 10 years, 75.9% males). Diabetes mellitus was more prevalent in Xi'an Cohort population than Shiyan and Ningbo cohort (P < 0.01). Plasma total cholesterol, LDL cholesterol and triglyceride levels in Xi'an Cohort population were significantly higher, and HDL-C siginificantly lower than in Shiyan and Ningbo cohort population [HDL-C: (1.17 +/- 0.48) mmol/L vs. (1.25 +/- 0.33) mmol/L and (1.29 +/- 0.44) mmol/L, P < 0.05]. Distribution differences for ABCA1-G596A and CETP-Taq1B genotypes were found in Xi'an Cohort population compared to Ningbo and Shiyan cohorts (for ABCA1, Xi'an: 0.24, 0.53, 0.23 and Shiyan: 0.17, 0.62, 0.21 and Ningbo: 0.34, 0.37, 0.29, for GG, AG, AA, respectively, P < 0.01; and for CETP, Xi'an: 0.29, 0.54, 0.17 and Shiyan: 0.38, 0.40, 0.22 and Ningbo: 0.39, 0.49, 0.12 for B1B1, B1B2, B2B2, respectively, P < 0.01), but not for LPL variants. ABCA1-G596A variant predicted HDL-C [Xi'an: (1.2 +/- 0.3) mmol/L, (1.3 +/- 0.2) mmol/L and (1.4 +/- 0.4) mmol/L, P = 0.01; Shiyan: (1.1 +/- 0

  5. Estimating PM2.5 in Xi'an , China Using Aerosol Optical Depth of Npp Viirs Data and Meteorological Measurements

    NASA Astrophysics Data System (ADS)

    Zhang, K.; Yang, Z.; Zheng, J.; Jiao, J.; Gao, W.

    2018-04-01

    In recent years, the air pollution is becoming more and more serious, which not only causes the decrease of the visibility, but also affects the human health. As the most important pollutant particulate matter, remote sensing satellite measurements have been widely used to estimate PM2.5 concentration on the ground. Visible Infrared Imaging Radiometer Suite (VIIRS) is one of the instruments which is taken in the National Polar-orbiting Partnership (NPP) satellite. In this study, VIIRS was used to retrieve aerosol optical depth (AOD) with the way of dark pixels, and several other major meteorological variables (wind speed, relative humidity, NO2 concentration, ground surface relative humidity and planetary boundary layer height) were combined with AOD to construct a nonlinear multiple regression mode for establishing the relationship between AOD and PM2.5 concentration. The North Basin of Shaanxi province of China, which includes Xi'an, is located in the north of Qinling Mountains, south of the Loess Plateau, and in the central of Weihe basin, with special structure and other adverse weather conditions (static wind, less rain) to cause the frequent haze weather in Xi'an. Xi'an city was selected as the area of the experiment due to its particularity. This research obtained the AOD results from August 1, 2013 to October 30, 2013. The inversion results were compared with ground-based PM2.5 concentration date from air quality monitoring station of Xi'an. The result showed that there is a significant correlation between the two, and the correlation coefficient is 0.783. The inversion result verified that the model of VIIRS data agreed well AOD, which could be used to estimate the surface PM2.5 concentration and monitor the regional air quality.

  6. Screening for bovine leukocyte adhesion deficiency, deficiency of uridine monophosphate synthase, complex vertebral malformation, bovine citrullinaemia, and factor XI deficiency in Holstein cows reared in Turkey.

    PubMed

    Meydan, Hasan; Yildiz, Mehmet A; Agerholm, Jørgen S

    2010-10-07

    Bovine leukocyte adhesion deficiency (BLAD), deficiency of uridine monophosphate synthase (DUMPS), complex vertebral malformation (CVM), bovine citrullinaemia (BC) and factor XI deficiency (FXID) are autosomal recessive hereditary disorders, which have had significant economic impact on dairy cattle breeding worldwide. In this study, 350 Holstein cows reared in Turkey were screened for BLAD, DUMPS, CVM, BC and FXID genotypes to obtain an indication on the importance of these defects in Turkish Holsteins. Genomic DNA was obtained from blood and the amplicons of BLAD, DUMPS, CVM, BC and FXID were obtained by using PCR. PCR products were digested with TaqI, AvaI and AvaII restriction enzymes for BLAD, DUMPS, and BC, respectively. These digested products and PCR product of FXID were analyzed by agarose gel electrophoresis stained with ethidium bromide. CVM genotypes were detected by DNA sequencing. Additionally, all genotypes were confirmed by DNA sequencing to determine whether there was a mutant allele or not. Fourteen BLAD, twelve CVM and four FXID carriers were found among the 350 Holstein cows examined, while carriers of DUMPS and BC were not detected. The mutant allele frequencies were calculated as 0.02, 0.017, and 0.006 for BLAD, CVM and FXID, respectively with corresponding carrier prevalence of 4.0% (BLAD), 3.4% (CVM) and 1.2% (FXID). This study demonstrates that carriers of BLAD, CVM and FXID are present in the Turkish Holstein population, although at a low frequency. The actual number of clinical cases is unknown, but sporadic cases may appear. As artificial insemination is widely used in dairy cattle breeding, carriers of BLAD, CVM and FXID are likely present within the population of breeding sires. It is recommended to screen breeding sires for these defective genes in order to avoid an unwanted spread within the population.

  7. Screening for bovine leukocyte adhesion deficiency, deficiency of uridine monophosphate synthase, complex vertebral malformation, bovine citrullinaemia, and factor XI deficiency in Holstein cows reared in Turkey

    PubMed Central

    2010-01-01

    Background Bovine leukocyte adhesion deficiency (BLAD), deficiency of uridine monophosphate synthase (DUMPS), complex vertebral malformation (CVM), bovine citrullinaemia (BC) and factor XI deficiency (FXID) are autosomal recessive hereditary disorders, which have had significant economic impact on dairy cattle breeding worldwide. In this study, 350 Holstein cows reared in Turkey were screened for BLAD, DUMPS, CVM, BC and FXID genotypes to obtain an indication on the importance of these defects in Turkish Holsteins. Methods Genomic DNA was obtained from blood and the amplicons of BLAD, DUMPS, CVM, BC and FXID were obtained by using PCR. PCR products were digested with TaqI, AvaI and AvaII restriction enzymes for BLAD, DUMPS, and BC, respectively. These digested products and PCR product of FXID were analyzed by agarose gel electrophoresis stained with ethidium bromide. CVM genotypes were detected by DNA sequencing. Additionally, all genotypes were confirmed by DNA sequencing to determine whether there was a mutant allele or not. Results Fourteen BLAD, twelve CVM and four FXID carriers were found among the 350 Holstein cows examined, while carriers of DUMPS and BC were not detected. The mutant allele frequencies were calculated as 0.02, 0.017, and 0.006 for BLAD, CVM and FXID, respectively with corresponding carrier prevalence of 4.0% (BLAD), 3.4% (CVM) and 1.2% (FXID). Conclusion This study demonstrates that carriers of BLAD, CVM and FXID are present in the Turkish Holstein population, although at a low frequency. The actual number of clinical cases is unknown, but sporadic cases may appear. As artificial insemination is widely used in dairy cattle breeding, carriers of BLAD, CVM and FXID are likely present within the population of breeding sires. It is recommended to screen breeding sires for these defective genes in order to avoid an unwanted spread within the population. PMID:20929557

  8. Full Robotic Colorectal Resections for Cancer Combined With Other Major Surgical Procedures: Early Experience With the da Vinci Xi.

    PubMed

    Morelli, Luca; Di Franco, Gregorio; Guadagni, Simone; Palmeri, Matteo; Gianardi, Desirée; Bianchini, Matteo; Moglia, Andrea; Ferrari, Vincenzo; Caprili, Giovanni; D'Isidoro, Cristiano; Melfi, Franca; Di Candio, Giulio; Mosca, Franco

    2017-08-01

    The da Vinci Xi has been developed to overcome some of the limitations of the previous platform, thereby increasing the acceptance of its use in robotic multiorgan surgery. Between January 2015 and October 2015, 10 patients with synchronous tumors of the colorectum and others abdominal organs underwent robotic combined resections with the da Vinci Xi. Trocar positions respected the Universal Port Placement Guidelines provided by Intuitive Surgical for "left lower quadrant," with trocars centered on the umbilical area, or shifted 2 to 3 cm to the right or to the left, depending on the type of combined surgical procedure. All procedures were completed with the full robotic technique. Simultaneous procedures in same quadrant or left quadrant and pelvis, or left/right and upper, were performed with a single docking/single targeting approach; in cases of left/right quadrant or right quadrant/pelvis, we performed a dual-targeting operation. No external collisions or problems related to trocar positions were noted. No patient experienced postoperative surgical complications and the mean hospital stay was 6 days. The high success rate of full robotic colorectal resection combined with other surgical interventions for synchronous tumors, suggest the efficacy of the da Vinci Xi in this setting.

  9. High-frequency transformation of Lobelia erinus L. by Agrobacterium-mediated gene transfer.

    PubMed

    Tsugawa, H; Kagami, T; Suzuki, M

    2004-05-01

    A highly efficient transformation procedure was developed for Lobelia erinus. Leaf or cotyledon discs were inoculated with Agrobacterium tumefaciens strain EHA105 harboring the binary vector plasmid pIG121Hm, which contains a beta-glucuronidase gene with an intron as a reporter gene and both the neomycin phosphotransferase II and hygromycin phosphotransferase genes as selectable markers. The hygromycin-resistant calli produced on the selection medium were transferred to MS medium supplemented with 0.5 mg/l benzyladenine and 0.2 mg/l indole-3-acetic acid for regeneration of adventitious shoots. Transgenic plants were obtained as a result of the high regeneration rate of the transformed calli, which was as high as 83%. In contrast, no transgenic plant was obtained by the procedure of direct shoot formation following inoculation with A. tumefaciens. Transgenic plants flowered 3-4 months after transformation. Integration of the transgenes was detected using PCR and Southern blot analysis, which revealed that one to several copies were integrated into the genomes of the host plants. The transformation frequency at the stage of whole plants was very high--45% per inoculated disc. Copyright 2004 Springer-Verlag

  10. Port positioning and docking for single-stage totally robotic dissection for rectal cancer surgery with the Si and Xi Da Vinci Surgical System.

    PubMed

    Toh, James Wei Tatt; Kim, Seon-Hahn

    2017-11-04

    We have previously reported our technique of single-docking totally robotic dissection for rectal cancer surgery using the Da Vinci ® Si Surgical System in 2009. However, we have since optimised our port placement for the Si system and have developed a novel configuration of port placement and docking for the Da Vinci ® Xi Surgical System. We have performed over 700 cases using this technique with the Si system and have used our Xi technique since 2016 for totally robotic dissection for rectal cancer. We have kept the configuration of port placements for both the Xi and Si system as similar as possible, with the priorities to avoid arm collisions as well as to provide a workable port configuration of two left-handed instruments and one right-handed instrument. To date, there have had no major complications or arm collisions related to this technique of docking, port positioning and instrument placement.

  11. Analysis of magnesium XI line profiles from solar active regions

    NASA Technical Reports Server (NTRS)

    Blake, R. L.; Cowan, R. D.; Felthauser, H.; Fenimore, E. E.; Hockaday, M. P.; Bely-Dubau, F.; Faucher, P.; Steenman-Clark, L.

    1984-01-01

    High-resolution solar spectra of the Mg XI 1s2 1S0-1s2p 1P1 resonance line at 9.169 A and the associated nearby satellite lines obtained from two rocket-borne crystal spectrometer measurements are presented. Comparisons with two independent sets of theoretical calculations for the 1s2nl-1s2pnl dielectronic satellite lines with n = 3-7 indicate electron temperatures of 4-4.5 million K. Measured line widths indicate either that the ion temperature exceeds the electron temperature by about a million K or that about 28 km/s of turbulence is present.

  12. The position of DNA cleavage by TALENs and cell synchronization influences the frequency of gene editing directed by single-stranded oligonucleotides.

    PubMed

    Rivera-Torres, Natalia; Strouse, Bryan; Bialk, Pawel; Niamat, Rohina A; Kmiec, Eric B

    2014-01-01

    With recent technological advances that enable DNA cleavage at specific sites in the human genome, it may now be possible to reverse inborn errors, thereby correcting a mutation, at levels that could have an impact in a clinical setting. We have been developing gene editing, using single-stranded DNA oligonucleotides (ssODNs), as a tool to direct site specific single base changes. Successful application of this technique has been demonstrated in many systems ranging from bacteria to human (ES and somatic) cells. While the frequency of gene editing can vary widely, it is often at a level that does not enable clinical application. As such, a number of stimulatory factors such as double-stranded breaks are known to elevate the frequency significantly. The majority of these results have been discovered using a validated HCT116 mammalian cell model system where credible genetic and biochemical readouts are available. Here, we couple TAL-Effector Nucleases (TALENs) that execute specific ds DNA breaks with ssODNs, designed specifically to repair a missense mutation, in an integrated single copy eGFP gene. We find that proximal cleavage, relative to the mutant base, is key for enabling high frequencies of editing. A directionality of correction is also observed with TALEN activity upstream from the target base being more effective in promoting gene editing than activity downstream. We also find that cells progressing through S phase are more amenable to combinatorial gene editing activity. Thus, we identify novel aspects of gene editing that will help in the design of more effective protocols for genome modification and gene therapy in natural genes.

  13. Class XI Myosins Move Specific Organelles in Pollen Tubes and Are Required for Normal Fertility and Pollen Tube Growth in Arabidopsis1[OPEN

    PubMed Central

    Madison, Stephanie L.; Buchanan, Matthew L.; Glass, Jeremiah D.; McClain, Tarah F.; Park, Eunsook; Nebenführ, Andreas

    2015-01-01

    Pollen tube growth is an essential aspect of plant reproduction because it is the mechanism through which nonmotile sperm cells are delivered to ovules, thus allowing fertilization to occur. A pollen tube is a single cell that only grows at the tip, and this tip growth has been shown to depend on actin filaments. It is generally assumed that myosin-driven movements along these actin filaments are required to sustain the high growth rates of pollen tubes. We tested this conjecture by examining seed set, pollen fitness, and pollen tube growth for knockout mutants of five of the six myosin XI genes expressed in pollen of Arabidopsis (Arabidopsis thaliana). Single mutants had little or no reduction in overall fertility, whereas double mutants of highly similar pollen myosins had greater defects in pollen tube growth. In particular, myo11c1 myo11c2 pollen tubes grew more slowly than wild-type pollen tubes, which resulted in reduced fitness compared with the wild type and a drastic reduction in seed set. Golgi stack and peroxisome movements were also significantly reduced, and actin filaments were less organized in myo11c1 myo11c2 pollen tubes. Interestingly, the movement of yellow fluorescent protein-RabA4d-labeled vesicles and their accumulation at pollen tube tips were not affected in the myo11c1 myo11c2 double mutant, demonstrating functional specialization among myosin isoforms. We conclude that class XI myosins are required for organelle motility, actin organization, and optimal growth of pollen tubes. PMID:26358416

  14. Identification and functional activity of a staphylocoagulase type XI variant originating from staphylococcal food poisoning isolates.

    PubMed

    Suzuki, Y; Matsushita, S; Kubota, H; Kobayashi, M; Murauchi, K; Higuchi, Y; Kato, R; Hirai, A; Sadamasu, K

    2016-09-01

    Staphylocoagulase, an extracellular protein secreted by Staphylococcus aureus, has been used as an epidemiological marker. At least 12 serotypes and 24 genotypes subdivided on the basis of nucleotide sequence have been reported to date. In this study, we identified a novel staphylocoagulase nucleotide sequence, coa310, from staphylococcal food poisoning isolates that had the ability to coagulate plasma, but could not be typed using the conventional method. The protein encoded by coa310 contained the six fundamental conserved domains of staphylocoagulase. The full-length nucleotide sequence of coa310 shared the highest similarity (77·5%) with that of staphylocoagulase-type (SCT) XIa. The sequence of the D1 region, which would be responsible for the determination of SCT, shared the highest similarity (91·8%) with that of SCT XIa. These results suggest that coa310 is a novel variant of SCT XI. Moreover, we demonstrated that coa310 encodes a functioning coagulase, by confirming the coagulating activity of the recombinant protein expressed from coa310. This is the first study to directly demonstrate that Coa310, a putative SCT XI, has coagulating activity. These findings may be useful for the improvement of the staphylocoagulase-typing method, including serotyping and genotyping. This is the first study to identify a novel variant of staphylocoagulase type XI based on its nucleotide sequence and to demonstrate coagulating activity in the variant using a recombinant protein. Elucidation of the variety of staphylocoagulases will provide suggestions for further improvement of the staphylocoagulase-typing method and contribute to our understanding of the epidemiologic characterization of Staphylococcus aureus. © 2016 The Society for Applied Microbiology.

  15. Increased frequency of DNA deletions in pink-eyed unstable mice carrying a mutation in the Werner syndrome gene homologue.

    PubMed

    Lebel, Michel

    2002-01-01

    Werner syndrome (WS) is a rare autosomal recessive disorder characterized by genomic instability and the premature onset of a number of age-related diseases, including cancers. Accumulating evidence indicates that the WS gene product is involved in resolving aberrant DNA structures that may arise during the process of DNA replication and/or transcription. To estimate the frequency of DNA deletions directly in the skin of mouse embryos, mice with a deletion of part of the murine WRN helicase domain were created. These mutant mice were then crossed to the pink-eyed unstable animals, which have a 70 kb internal duplication at the pink-eyed dilution (p) gene. This report indicates that the frequency of deletion of the duplicated sequence at the p locus is elevated in mice with a mutation in the WRN allele when compared with wild-type mice. In addition, the inhibitor of topoisomerase I camptothecin also increases the frequency of deletion at the p locus. This frequency is even more elevated in WRN mutant mice treated with camptothecin. In contrast, while the inhibition of poly(ADP-ribose) polymerase (PARP) activity by 3-aminobenzamide increases the frequency of DNA deletion, mutant WRN mice are not significantly more sensitive to the inhibition of PARP activity than wild-type animals.

  16. Chinese Military Reform in the Age of Xi Jinping: Drivers, Challenges, and Implications

    DTIC Science & Technology

    2017-03-01

    refused to obey commands, Xi has em - phasized it in a way that his immediate predecessors did not. For instance, loyalty to the Party was a major...disposal and appears to be em - ploying them in a reasonably strategic fashion to promote the military reforms. However, some of these tools require his...exercise operational control over units. ■■ Rocket Force C2 and scope of authority. Although authoritative Chinese sources em - phasize consistency in the

  17. [Analysis of the frequencies of genotype combinations of 4 polymorphisms of genes acting on the folate cycle in the Spanish population].

    PubMed

    Martínez-Frías, María Luisa; Bermejo, Eva; Pérez, Belén; Desviat, Lourdes R; Castro, Margarita; Leal, Fátima; Mansilla, Elena; Martínez-Fernández, María Luisa; Rodríguez-Pinilla, Elvira; Rodríguez, Laura; Ugarte, Magdalena

    2008-06-21

    Studies on different populations have shown a great variability of the frequencies of different polymorphisms in genes acting in the folate cycle. The present study was aimed to analyze the frequency in the Spanish population of each genotype combination of four polymorphisms, one of them -1561C-T of the glutamate carboxypeptidase II (GCPII) gene- being the first time that is studied in Spain. The study included a meta-analysis of the published data. Using the Spanish Collaborative Study of Congenital Malformations (ECEMC) Network, blood samples of 190 mother-child couples with newborns without any congenital defect, were obtained from 15 Spanish autonomous regions. The study polymorphisms were the 677C-T and 1298A-C polymorphisms of the methylenetetrahydrofolate reductase (MTHFR), the 66A-G of the methionine synthase reductase (MTRR), and the 1561C-T polymorphism of the GCPII gene. To estimate the range for the population frequencies, 99% confidence intervals were calculated. The frequencies observed in our country were significantly different from others, being similar to those obtained in countries of the Mediterranean European area. The 1561C-T polymorphism of the GCPII gene has a frequency in Spain of 5.11%, which is also similar to the values observed in France (5%) and in Italy (6%). On the other hand, the frequency of the genotypes CTCC, TTAC is quite few, while the genotype TTCC was not observed in any mother or infants. A meta-analysis was performed for a big sample (23,612 individuals) and the results showed that with a 99% of probability the values for the genotype combinations CTCC, TTAC, and TTCC were within 0.10-0.24; 0.20-0.36; and 0.003-0.05, respectively. Our results are important to further analyze the relationship with some health problems and individual susceptibilities. Indeed, considering the published observations of the structure and function of the MTHFR enzyme, it is understandable that those genotype combinations that are quite little

  18. [Frequency of CHEK2 gene mutations in patients with breast cancer from the Republic of Bashkortostan].

    PubMed

    2014-01-01

    Several studies have shown, that mutation in CHEK2 gene can increase the risk of different cancers, including breast cancer (BC). Clearly, that character of mutations distribution in the defined regions is depended on genetic structure of the population. We conducted the screening of mutations c.1100delC, c.444 + 1G>A, de15395, p.I157T andIp.R145Win CHEK2 gene in patients with breast cancer (n = 977) and in control group (n = 1069) originating from the Republic of Bashkortostan. The mutation de15395 in CHEK2 gene was detected with frequency of 1,23% (12/977)in woman with BC and 0.09% (1/1069) in controls (OR:13.28, CI 95%: 1.72-102.33, p = 0.003). Mutations c.1100delC and c.444 + 1G>A were found in BC patients and controls with frequencies of 0.4%, 0.4% (4/977) and 0.09% (1/1069), 0.2% (2/1069), respectively. The missense mutation p.I157T in CHEK2 was found as the most common variant in two studied cohorts (approximately 5%), but differences did not achieved statistical significance. We found the ethnic specificity in distribution of truncating mutations, which occurs mainly among the women of Slavic origin. All three mutations were identified in women of Russian and Ukrainian ethnic origin. Mutations c.1100delC and c.444 + 1G>A in CHEK2 gene were not detected in Bashkirs and Tatars, but CHEK2 de15395 mutation was observed in Tatars.

  19. Gene-Specific Substitution Profiles Describe the Types and Frequencies of Amino Acid Changes during Antibody Somatic Hypermutation.

    PubMed

    Sheng, Zizhang; Schramm, Chaim A; Kong, Rui; Mullikin, James C; Mascola, John R; Kwong, Peter D; Shapiro, Lawrence

    2017-01-01

    Somatic hypermutation (SHM) plays a critical role in the maturation of antibodies, optimizing recognition initiated by recombination of V(D)J genes. Previous studies have shown that the propensity to mutate is modulated by the context of surrounding nucleotides and that SHM machinery generates biased substitutions. To investigate the intrinsic mutation frequency and substitution bias of SHMs at the amino acid level, we analyzed functional human antibody repertoires and developed mGSSP (method for gene-specific substitution profile), a method to construct amino acid substitution profiles from next-generation sequencing-determined B cell transcripts. We demonstrated that these gene-specific substitution profiles (GSSPs) are unique to each V gene and highly consistent between donors. We also showed that the GSSPs constructed from functional antibody repertoires are highly similar to those constructed from antibody sequences amplified from non-productively rearranged passenger alleles, which do not undergo functional selection. This suggests the types and frequencies, or mutational space, of a majority of amino acid changes sampled by the SHM machinery to be well captured by GSSPs. We further observed the rates of mutational exchange between some amino acids to be both asymmetric and context dependent and to correlate weakly with their biochemical properties. GSSPs provide an improved, position-dependent alternative to standard substitution matrices, and can be utilized to developing software for accurately modeling the SHM process. GSSPs can also be used for predicting the amino acid mutational space available for antigen-driven selection and for understanding factors modulating the maturation pathways of antibody lineages in a gene-specific context. The mGSSP method can be used to build, compare, and plot GSSPs; we report the GSSPs constructed for 69 common human V genes (DOI: 10.6084/m9.figshare.3511083) and provide high-resolution logo plots for each (DOI: 10

  20. University of Nottingham Ningbo China and Xi'an Jiaotong-Liverpool University: Globalization of Higher Education in China

    ERIC Educational Resources Information Center

    Feng, Yi

    2013-01-01

    This essay studies the University of Nottingham Ningbo China and Xi'an Jiaotong-Liverpool University--the two Chinese campuses established respectively by the University of Nottingham and the University of Liverpool. They represent successful models of globalization of higher education in China; however their rationale, strategies, curricula,…

  1. Calculation of the {pi}{sup +}{Sigma}{sup +} and {pi}{sup +}{Xi}{sup 0} Scattering Lengths in Lattice QCD

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

    Torok, Aaron

    The {pi}{sup +}{Sigma}{sup +} and {pi}{sup +}{Xi}{sup 0} scattering lengths were calculated in mixed-action Lattice QCD with domain-wall valence quarks on the asqtad-improved coarse MILC configurations at four light-quark masses, and at two light-quark masses on the fine MILC configurations. Heavy Baryon Chiral Perturbation Theory with two and three flavors of light quarks was used to perform the chiral extrapolations. To NNLO in the three-flavor chiral expansion, the kaon-baryon processes that were investigated show no signs of convergence. Using the two-flavor chiral expansion for extrapolation, the pion-hyperon scattering lengths are found to be a{sub {pi}}{sup +}{sub {Sigma}}{sup +} = -0.197{+-}0.017more » fm, and a{sub {pi}}{sup +}{sub {Xi}}{sup 0} = -0.098{+-}0.017 fm, where the comprehensive error includes statistical and systematic uncertainties.« less

  2. Enhanced photovoltaic performance of CH3NH3PbBrXI3-X-based perovskite solar cells via anti-solvent extraction

    NASA Astrophysics Data System (ADS)

    Jiang, Zhaoyi; Zhang, Weijia; Lu, Chaoqun; Ma, Denghao; Liu, Haixu; Yu, Wei; Zhang, Yu; Ma, Qiang; Zhang, Yulong

    2018-06-01

    In this paper, the two-step sequential deposition method was used to prepare the CH3NH3PbBrXI3-X films by introducing CH3NH3Br in the precursors. The surface morphology of the PbI2 films was controlled by anti-solvent extraction (ASE) to improve the microstructure and photo-physical properties of the perovskite films. It was noteworthy that, compared to the compact PbI2 films, the porous PbI2 films facilitated the growth of crystals and bromine incorporation in films, and the prepared perovskite films exhibited enlarged grain size, increased light absorption, enhanced Br incorporation and prolonged carrier lifetime, which resulted in excellent photo-electrical properties of the CH3NH3PbBrXI3-X films. With porous PbI2 templates, the inverted planar perovskite solar cells based on films with appropriate Br incorporation (CH3NH3Br/CH3NH3I mole ratio = 3/7) showed a photovoltaic conversion efficiency (PCE) of 14.9%, and the stability of the devices in air was elevated. Consequently, the high-quality CH3NH3PbBrXI3-X films can be obtained with porous PbI2 templates for improving the performance of the perovskite solar cells.

  3. Genotype distribution and allele frequencies of the genes associated with body composition and locomotion traits in Myanmar native horses.

    PubMed

    Okuda, Yu; Moe, Hla Hla; Moe, Kyaw Kyaw; Shimizu, Yuki; Nishioka, Kenji; Shimogiri, Takeshi; Mannen, Hideyuki; Kanemaki, Misao; Kunieda, Tetsuo

    2017-08-01

    Myanmar native horses are small horses used mainly for drafting carts or carriages in rural areas and packing loads in mountainy areas. In the present study, we investigated genotype distributions and allele frequencies of the LCORL/NCAPG, MSTN and DMRT3 genes, which are associated with body composition and locomotion traits of horses, in seven local populations of Myanmar native horses. The genotyping result of LCORL/NCAPG showed that allele frequencies of C allele associated with higher withers height ranged from 0.08 to 0.27, and 0.13 in average. For MSTN, allele frequencies of C allele associated with higher proportion of Type 2B muscular fiber ranged from 0.05 to 0.23, and 0.09 in average. For DMRT3, allele frequencies of A allele associated with ambling gait ranged from 0 to 0.04, and 0.01 in average. The presences of the minor alleles of these genes at low frequencies suggest a possibility that these horse populations have not been under strong selection pressure for particular locomotion traits and body composition. Our findings of the presence of these minor alleles in Southeast Asian native horses are also informative for considering the origins of these minor alleles associated with body composition and locomotion traits in horse populations. © 2016 Japanese Society of Animal Science.

  4. Modular pathway engineering of Corynebacterium glutamicum to improve xylose utilization and succinate production.

    PubMed

    Jo, Suah; Yoon, Jinkyung; Lee, Sun-Mi; Um, Youngsoon; Han, Sung Ok; Woo, Han Min

    2017-09-20

    Xylose-negative Corynebacterium glutamicum has been engineered to utilize xylose as the sole carbon source via either the xylose isomerase (XI) pathway or the Weimberg pathway. Heterologous expression of xylose isomerase and overexpression of a gene encoding for xylulose kinase enabled efficient xylose utilization. In this study, we show that two functionally-redundant transcriptional regulators (GntR1 and GntR2) present on xylose repress the pentose phosphate pathway genes. For efficient xylose utilization, pentose phosphate pathway genes and a phosphoketolase gene were overexpressed with the XI pathway in C. glutamicum. Overexpression of the genes encoding for transaldolase (Tal), 6-phosphogluconate dehydrogenase (Gnd), or phosphoketolase (XpkA) enhanced the growth and xylose consumption rates compared to the wild-type with the XI pathway alone. However, co-expression of these genes did not have a synergetic effect on xylose utilization. For the succinate production from xylose, overexpression of the tal gene with the XI pathway in a succinate-producing strain improved xylose utilization and increased the specific succinate production rate by 2.5-fold compared to wild-type with the XI pathway alone. Thus, overexpression of the tal, gnd, or xpkA gene could be helpful for engineering C. glutamicum toward production of value-added chemicals with efficient xylose utilization. Copyright © 2017 Elsevier B.V. All rights reserved.

  5. Role of high-spin hyperon resonances in the reaction of {gamma}p{yields}K{sup +}K{sup +}{Xi}{sup -}

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

    Man, J. Ka Shing; Oh, Yongseok; Excited Baryon Analysis Center, Thomas Jefferson National Accelerator Facility, Newport News, Virginia 23606

    The recent data taken by the CLAS Collaboration at the Thomas Jefferson National Accelerator Facility for the reaction of {gamma}p{yields}K{sup +}K{sup +}{Xi}{sup -} are reanalyzed within a relativistic meson-exchange model of hadronic interactions. The present model is an extension of the one developed in an earlier work by Nakayama, Oh, and Haberzettl [Phys. Rev. C 74, 035205 (2006)]. In particular, the role of the spin-5/2 and -7/2 hyperon resonances, which were not included in the previous model, is investigated in the present study. It is shown that the contribution of the {Sigma}(2030) hyperon having spin-7/2 and positive parity has amore » key role to bring the model predictions into a fair agreement with the measured data for the K{sup +}{Xi}{sup -} invariant mass distribution.« less

  6. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes

    PubMed Central

    Hornoy, Benjamin; Pavy, Nathalie; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean

    2015-01-01

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome. Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs. Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. PMID:26560341

  7. Genetic polymorphisms of genes involved in DNA repair and metabolism influence micronucleus frequencies in human peripheral blood lymphocytes.

    PubMed

    Dhillon, Varinderpal S; Thomas, Philip; Iarmarcovai, G; Kirsch-Volders, Micheline; Bonassi, Stefano; Fenech, Michael

    2011-01-01

    The cytokinesis-block micronucleus cytome (CBMNCyt) assay is a widely used technique for measuring DNA damage in human populations. The formation of micronuclei (MN) in dividing cells can result from chromosome breakage due to unrepaired or mis-repaired DNA lesions or chromosome malsegregation due to mitotic malfunction. The sensitivity of the MN assay to polymorphisms in various genes involved in DNA repair, activation/deactivation of carcinogens/chemicals/drugs/alcohol, folate metabolism pathway and micronutrient transport has been extensively reported in the literature. MN frequency is also an important index for determining DNA repair efficiency phenotype (including mis-repair), response to environmental exposure and identifying various dietary factors required for optimal genome stability. The aim of the present study is to review the reported in vivo associations between genotype and MN frequency in humans taking into considerations the presence of interactions with nutrients levels and/or exposure to genotoxins. One hundred and eleven publications linking MN frequency in peripheral blood lymphocytes to gene polymorphism were retrieved from PubMed. After applying exclusion criteria, only 37 studies were evaluated in the present review. Polymorphisms in XRCC1 (Arg280His), ERCC2 (Lys751Gln), CYP2E1 (c1/c2) and MTR (A2756G) were consistently associated with the MN formation. These results contribute substantial evidence to the hypothesis that genotype may influence MN frequency in human cells.

  8. Strange hadron (neutral kaon(short), lambda baryon and Xi baryon) production in deuteron+gold collisions at center of mass energy = 200 GeV at RHIC

    NASA Astrophysics Data System (ADS)

    Jiang, Hai

    The study of identified particles from deuteron(d)+gold(Au) collisions provide a crucial reference to investigate nuclear effects observed in Au+Au collisions where a thermalized partonic state - Quark Gluon Plasma (QGP) - is thought to have been created. The measurements of transverse mass (mT) and momentum (pT) spectra at mid-rapidity (| y| < 1) for the identified strange hadrons: K0S , Λ + Λ and xi- + xi+ from d+Au collisions are presented. The measured pT covers 0.4 < p T < 6.0 GeV/c for K0S and Λ + Λ and 0.6 < pT < 5.0 GeV/c for xi- + xi+. These particles were reconstructed from the topological characteristics of their weak decays in the STAR Time Projection Chamber (TPC). The mT spectra of these particles are well described by a double exponential function which can be understood by two component models: soft (thermal) hadron production at low mT and hard hadron production at high mT. The integrated yields (dN/dy) and mean pT (< pT >) of these particles are calculated from the fit functions for different centralities. The dN/dy normalized to the number of participants (Npart) increase with Npart. The Λ(Λ ) dN/dy values at the mid-rapidity and forward rapidity regions agree with the EPOS model calculations. The measured Λ/ K0S ratios show the greatest baryon enhancement at pT ˜ 2 GeV/c in d+Au collisions. The strangeness enhancement going from d+Au to Au+Au collisions grows with the number of strange quark in a hadron. The magnitude of the enhancement is in the same order as the SPS measurement. The nuclear modification factors RCP normalized to binary collisions indicate that the Cronin effect in d+Au collisions has a distinct particle type dependence. The RCP ratios show a distinct baryon versus meson dependence: the RCP for xi- + xi+ follows that for Λ + Λ while the R CP for the φ is close to that for the K0S . The mechanism based on initial hadron or parton multiple scattering is not sufficient to explain this particle type dependence

  9. Determinants of outcome after intensified therapy of childhood lymphoblastic leukaemia: results from Medical Research Council United Kingdom acute lymphoblastic leukaemia XI protocol.

    PubMed

    Hann, I; Vora, A; Harrison, G; Harrison, C; Eden, O; Hill, F; Gibson, B; Richards, S

    2001-04-01

    The single most important prognostic determinant in childhood acute lymphoblastic leukaemia (ALL) is effective therapy and changes in therapy may influence the significance of other risk factors. The effect of intensified therapy on the importance of currently recognized phenotypic and genotypic determinants of outcome was assessed in 2090 children enrolled on the Medical Research Council United Kingdom acute lymphoblastic leukaemia XI (MRC UKALL XI) protocol. Treatment allocation was not determined by risk factors. Multivariate analysis confirmed the dominant influence on prognosis of age, sex and presenting white cell count (WCC). After allowing for these features, blast karyotype, d 8 marrow blast percentage and remission status at the end of induction therapy were the only remaining significant predictors of outcome. Organomegaly, haemoglobin concentration, French--American--British type, body mass index, presence of central nervous system disease at diagnosis, immunophenotype and presence of TEL/AML1 fusion gene (examined in a subset of 659 patients) either had no significant effect on outcome or were significant only in univariate analysis. Among karyotype abnormalities with an independent influence on prognosis, high hyperdiploidy (> 50 chromosomes) was shown to be favourable, whereas near haploidy (23--29 chromosomes), presence of the Philadelphia chromosome, t(4;11) and abnormalities affecting the short arm of chromosome 9 [abn (9p)] were adverse risk factors. Early responders to therapy, determined by residual marrow infiltration after 8 d of induction therapy, had a good outcome, while the small proportion of patients who did not achieve a complete remission by the end of induction therapy had a poor outcome. A third block of late intensification was shown to improve event-free survival by 8% at 5 years. The effect of these risk factors was not significantly different between those randomized to the third intensification block and those not randomized to

  10. Observation of the {omega}{sub b}{sup -} baryon and measurement of the properties of the {xi}{sub b}{sup -} and {omega}{sub b}{sup -} baryons

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

    Aaltonen, T.; Maki, T.; Mehtala, P.

    We report the observation of the bottom, doubly-strange baryon {omega}{sub b}{sup -} through the decay chain {omega}{sub b}{sup -}{yields}J/{psi}{omega}{sup -}, where J/{psi}{yields}{mu}{sup +}{mu}{sup -}, {omega}{sup -}{yields}{lambda}K{sup -}, and {lambda}{yields}p{pi}{sup -}, using 4.2 fb{sup -1} of data from pp collisions at {radical}(s)=1.96 TeV, and recorded with the Collider Detector at Fermilab. A signal is observed whose probability of arising from a background fluctuation is 4.0x10{sup -8}, or 5.5 Gaussian standard deviations. The {omega}{sub b}{sup -} mass is measured to be 6054.4{+-}6.8(stat){+-}0.9(syst) MeV/c{sup 2}. The lifetime of the {omega}{sub b}{sup -} baryon is measured to be 1.13{sub -0.40}{sup +0.53}(stat){+-}0.02(syst) ps. In addition,more » for the {xi}{sub b}{sup -} baryon we measure a mass of 5790.9{+-}2.6(stat){+-}0.8(syst) MeV/c{sup 2} and a lifetime of 1.56{sub -0.25}{sup +0.27}(stat){+-}0.02(syst) ps. Under the assumption that the {xi}{sub b}{sup -} and {omega}{sub b}{sup -} are produced with similar kinematic distributions to the {lambda}{sub b}{sup 0} baryon, we find ({sigma}({xi}{sub b}{sup -})B({xi}{sub b}{sup -}{yields}J/{psi}{xi}{sup -})/{sigma}({lambda}{sub b}{sup 0})B({lambda}{sub b}{sup 0}{yields}J/{psi}{lambda}))=0.167{sub -0.025}{sup +0.037}(stat){+-}0.012(syst) and ({sigma}({omega}{sub b}{sup -})B({omega}{sub b}{sup -}{yields}J/{psi}{omega}{sup -})/{sigma}({lambda}{sub b}{sup 0})B({lambda}{sub b}{sup 0}{yields}J/{psi}{lambda}))=0.045{sub -0.012}{sup +0.017}(stat){+-} 0.004(syst) for baryons produced with transverse momentum in the range of 6-20 GeV/c.« less

  11. {open_quotes}Horizontal{close_quotes} gene transfer from a transgenic potato line to a bacterial pathogen (Erwinia chrysanthemi) occurs - if at all - at an extremely low frequency

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

    Schlueter, K.; Fuetterer, J.; Potrykus, I.

    1995-10-01

    The frequency of possible {open_quotes}horizontal{close_quotes} gene transfer between a plant and a tightly associated bacterial pathogen was studied in a model system consisting of transgenic Solanum tuberosum, containing a {beta}-lactamase gene linked to a pBR322 origin of replication, and Erwinia chrysanthemi. This experimental system offers optimal conditions for the detection of possible horizontal gene transfer events, even when they occur at very low frequency. Horizontal gene transfer was not detected under conditions mimicking a {open_quotes}natural{close_quotes} infection. The gradual, stepwise alteration of artificial, positive control conditions to idealized natural conditions, however, allowed the characterization of factors that affected gene transfer, andmore » revealed a gradual decrease of the gene transfer frequency from 6.3 x 10{sup -2} under optimal control conditions to a calculated 2.0 x 10{sub -17} under idealized natural conditions. These data, in combination with other published studies, argue that horizontal gene transfer is so rare as to be essentially irrelevant to any realistic assessment of the risk involved in release experiments involving transgenic plants. 22 refs., 3 figs., 2 tabs.« less

  12. The Frequency of c.550delA Mutation of the CANP3 Gene in the Polish LGMD2A Population.

    PubMed

    Dorobek, Małgorzata; Ryniewicz, Barbara; Kabzińska, Dagmara; Fidziańska, Anna; Styczyńska, Maria; Hausmanowa-Petrusewicz, Irena

    2015-11-01

    Limb girdle muscular dystrophy 2A (LGMD2A) is the most frequent LGMD variant in the European population, representing about 40% of LGMD. The c.550delA mutation in the CANP3 (calcium activated neutral protease 3) gene is the most commonly reported mutation in LGMD2A. Prevalence of this mutation in the Polish population has not been previously investigated. The aim of this study was to identify and estimate the frequency of the c.550delA mutation in Polish LGMD2A patients. Polymerase chain reaction-sequencing analysis, restriction fragment length polymorphism polymerase chain reaction method. We analyzed 76 families affected with LGMD and identified 62 probands with mutations in the CANP3 gene. C.550delA was the most common mutation identified, being found in 78% of the LGMD2A families. The remaining mutations observed multiple times were as follows: c.598-612del15ntd; c.2242C>T; c.418dupC; c.1356insT, listed in terms of decreasing frequency. Two novel variants in the CANP3 gene, that is, c.700G>A Gly234Arg and c.661G>A Gly221Ser were also characterized. Overall, mutations in the LGMD2A gene were estimated to be present in 81% of patients with the LGMD phenotype who were without sarcoglycans and dysferlin deficiency on immunocytochemical analysis. The frequency of the heterozygous c.550delA mutation in the healthy Polish population was estimated at 1/124. The c.550delA is the most frequent CANP3 mutation in the Polish population, thus sequencing of exon 4 of this gene could identify the majority of LGMD2A patients in Poland.

  13. LighSail Students Testing - ELaNa XI

    NASA Image and Video Library

    2014-09-23

    Students Alex Diaz and Riki Munakata of California Polytechnic State University testing the LightSail CubeSat. LightSail is a citizen-funded technology demonstration mission sponsored by the Planetary Society using solar propulsion for CubeSats. The spacecraft is designed to “sail” on the energy of solar photons striking the thin, reflective sail material. The first LightSail mission is designed to test the spacecraft’s critical systems, including the sequence to autonomously deploy a Mylar solar sail with an area of 32 square meters (344 square feet). The Planetary Society is planning a second, full solar sailing demonstration flight for 2016. Light is made of packets of energy called photons. While photons have no mass, they have energy and momentum. Solar sails use this momentum as a method of propulsion, creating flight by light. LightSail’s solar sail is packaged into a three-unit CubeSat about the size of a loaf of bread. Launched by NASA’s CubeSat Launch Initiative on the ELaNa XI mission as an auxiliary payload aboard the U.S. Air Force X-37B space plane mission on May 20, 2015.

  14. Asian population frequencies and haplotype distribution of killer cell immunoglobulin-like receptor (KIR) genes among Chinese, Malay, and Indian in Singapore.

    PubMed

    Lee, Yi Chuan; Chan, Soh Ha; Ren, Ee Chee

    2008-11-01

    Killer cell immunoglobulin-like receptors (KIR) gene frequencies have been shown to be distinctly different between populations and contribute to functional variation in the immune response. We have investigated KIR gene frequencies in 370 individuals representing three Asian populations in Singapore and report here the distribution of 14 KIR genes (2DL1, 2DL2, 2DL3, 2DL4, 2DL5, 2DS1, 2DS2, 2DS3, 2DS4, 2DS5, 3DL1, 3DL2, 3DL3, 3DS1) with two pseudogenes (2DP1, 3DP1) among Singapore Chinese (n = 210); Singapore Malay (n = 80), and Singapore Indian (n = 80). Four framework genes (KIR3DL3, 3DP1, 2DL4, 3DL2) and a nonframework pseudogene 2DP1 were detected in all samples while KIR2DS2, 2DL2, 2DL5, and 2DS5 had the greatest significant variation across the three populations. Fifteen significant linkage patterns, consistent with associations between genes of A and B haplotypes, were observed. Eighty-four distinct KIR profiles were determined in our populations, 38 of which had not been described in other populations. KIR haplotype studies were performed using nine Singapore Chinese families comprising 34 individuals. All genotypes could be resolved into corresponding pairs of existing haplotypes with eight distinct KIR genotypes and eight different haplotypes. The haplotype A2 with frequency of 63.9% was dominant in Singapore Chinese, comparable to that reported in Korean and Chinese Han. The A haplotypes predominate in Singapore Chinese, with ratio of A to B haplotypes of approximately 3:1. Comparison with KIR frequencies in other populations showed that Singapore Chinese shared similar distributions with Chinese Han, Japanese, and Korean; Singapore Indian was found to be comparable with North Indian Hindus while Singapore Malay resembled the Thai.

  15. Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes.

    PubMed

    Hornoy, Benjamin; Pavy, Nathalie; Gérardi, Sébastien; Beaulieu, Jean; Bousquet, Jean

    2015-11-11

    Understanding the genetic basis of adaptation to climate is of paramount importance for preserving and managing genetic diversity in plants in a context of climate change. Yet, this objective has been addressed mainly in short-lived model species. Thus, expanding knowledge to nonmodel species with contrasting life histories, such as forest trees, appears necessary. To uncover the genetic basis of adaptation to climate in the widely distributed boreal conifer white spruce (Picea glauca), an environmental association study was conducted using 11,085 single nucleotide polymorphisms representing 7,819 genes, that is, approximately a quarter of the transcriptome.Linear and quadratic regressions controlling for isolation-by-distance, and the Random Forest algorithm, identified several dozen genes putatively under selection, among which 43 showed strongest signals along temperature and precipitation gradients. Most of them were related to temperature. Small to moderate shifts in allele frequencies were observed. Genes involved encompassed a wide variety of functions and processes, some of them being likely important for plant survival under biotic and abiotic environmental stresses according to expression data. Literature mining and sequence comparison also highlighted conserved sequences and functions with angiosperm homologs.Our results are consistent with theoretical predictions that local adaptation involves genes with small frequency shifts when selection is recent and gene flow among populations is high. Accordingly, genetic adaptation to climate in P. glauca appears to be complex, involving many independent and interacting gene functions, biochemical pathways, and processes. From an applied perspective, these results shall lead to specific functional/association studies in conifers and to the development of markers useful for the conservation of genetic resources. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular

  16. An isoform of myosin XI is responsible for the translocation of endoplasmic reticulum in tobacco cultured BY-2 cells.

    PubMed

    Yokota, Etsuo; Ueda, Shunpei; Tamura, Kentaro; Orii, Hidefumi; Uchi, Satoko; Sonobe, Seiji; Hara-Nishimura, Ikuko; Shimmen, Teruo

    2009-01-01

    The involvement of myosin XI in generating the motive force for cytoplasmic streaming in plant cells is becoming evident. For a comprehensive understanding of the physiological roles of myosin XI isoforms, it is necessary to elucidate the properties and functions of each isoform individually. In tobacco cultured BY-2 cells, two types of myosins, one composed of 175 kDa heavy chain (175 kDa myosin) and the other of 170 kDa heavy chain (170 kDa myosin), have been identified biochemically and immunocytochemically. From sequence analyses of cDNA clones encoding heavy chains of 175 kDa and 170 kDa myosin, both myosins have been classified as myosin XI. Immunocytochemical studies using a polyclonal antibody against purified 175 kDa myosin heavy chain showed that the 175 kDa myosin is distributed throughout the cytoplasm as fine dots in interphase BY-2 cells. During mitosis, some parts of 175 kDa myosin were found to accumulate in the pre-prophase band (PPB), spindle, the equatorial plane of a phragmoplast and on the circumference of daughter nuclei. In transgenic BY-2 cells, in which an endoplasmic reticulum (ER)-specific retention signal, HDEL, tagged with green fluorescent protein (GFP) was stably expressed, ER showed a similar behaviour to that of 175 kDa myosin. Furthermore, this myosin was co-fractionated with GFP-ER by sucrose density gradient centrifugation. From these findings, it was suggested that the 175 kDa myosin is a molecular motor responsible for translocating ER in BY-2 cells.

  17. PyCMSXiO: an external interface to script treatment plans for the Elekta® CMS XiO treatment planning system

    NASA Astrophysics Data System (ADS)

    Xing, Aitang; Arumugam, Sankar; Holloway, Lois; Goozee, Gary

    2014-03-01

    Scripting in radiotherapy treatment planning systems not only simplifies routine planning tasks but can also be used for clinical research. Treatment planning scripting can only be utilized in a system that has a built-in scripting interface. Among the commercially available treatment planning systems, Pinnacle (Philips) and Raystation (Raysearch Lab.) have inherent scripting functionality. CMS XiO (Elekta) is a widely used treatment planning system in radiotherapy centres around the world, but it does not have an interface that allows the user to script radiotherapy plans. In this study an external scripting interface, PyCMSXiO, was developed for XiO using the Python programming language. The interface was implemented as a python package/library using a modern object-oriented programming methodology. The package was organized as a hierarchy of different classes (objects). Each class (object) corresponds to a plan object such as the beam of a clinical radiotherapy plan. The interface of classes was implemented as object functions. Scripting in XiO using PyCMSXiO is comparable with Pinnacle scripting. This scripting package has been used in several research projects including commissioning of a beam model, independent three-dimensional dose verification for IMRT plans and a setup-uncertainty study. Ease of use and high-level functions provided in the package achieve a useful research tool. It was released as an open-source tool that may benefit the medical physics community.

  18. Frequency of efflux pump genes mediating ciprofloxacin and antiseptic resistance in methicillin-resistant Staphylococcus aureus isolates.

    PubMed

    Hassanzadeh, Sepideh; Mashhadi, Rahil; Yousefi, Masoud; Askari, Emran; Saniei, Maryam; Pourmand, Mohammad Reza

    2017-10-01

    Efflux pumps are well known as a key role to fluoroquinolone resistance in methicillin-resistant Staphylococcus aureus (MRSA). In this study, among 60 clinical MRSA isolates, 42 isolates (70%) were resistant to ciprofloxacin. MRSA were isolated to detect efflux genes including norA, norB, norC, mepA, sepA, mdeA, qacA/B and smr. Isolates subjected to PCR detection and DNA sequence analysis for these genes. PCR detection showed that 42 isolates (70%) contained at least one efflux pump gene. Among ciprofloxacin-resistant isolates, mdeA and qacA/B genes were found with the highest (61.7%) and lowest (3.3%) frequency, respectively. We also observed that the highest minimum inhibitory concentrations of ciprofloxacin in the presence of mdeA+mepA+norA-C+sepA+smr combination. This type of combination may have the greatest impact on resistance to ciprofloxacin. Finally, compared to previous studies, our study demonstrates that prevalence of ciprofloxacin resistance has been increasing among MRSA clinical isolates. Copyright © 2017 Elsevier Ltd. All rights reserved.

  19. Distribution and genotype frequency of the C1431T and pro12ala polymorphisms of the peroxisome proliferator activator receptor gamma gene in an Iranian population

    PubMed Central

    Rooki, Hassan; Haerian, Monir-Sadat; Azimzadeh, Pedram; Ebrahimi, Mahmoud; Mirhafez, Reza; Ferns, Gordon; Ghayour-Mobarhan, Majid; Zali, Mohammad-Reza

    2013-01-01

    BACKGROUND: Peroxisome proliferator activator receptor gamma (PPARγ) is a nuclear transcription factor regulating multiple genes involved in cell growth, differentiation, carbohydrate and lipid metabolism and energy production. Several genetic variations in the PPARγ gene have been identified to be associated with diabetes, obesity, dyslipidemia, insulin resistance, metabolic syndrome and coronary artery disease. The present study was designed to explore the distribution of two common single nucleotide polymorphisms of the PPARγ gene (C1431T and Pro12Ala) in an Iranian population. MATERIALS AND METHODS: Genotype frequencies for these two polymorphisms were compared for 160 healthy Iranian individuals with reports from other populations. The Genotyping was performed using real-time polymerase chain reaction. RESULTS: The genotype distribution of the C1431T PPARγ polymorphism was 0.869 for the CC genotype, 0.119 for the CT genotype and 0.013 for uncommon TT genotype. Allelic frequencies were 0.93 for C and 0.07 for T allele respectively. For the Pro12Ala polymorphism of PPARγ gene, genotypic distributions and allelic frequencies were, 0.813 for CC, 0.181 for CG and 0.06 for GG and 0.903 for C and 0.097 for G respectively. Allelic and genotypic frequencies for both polymorphisms of PPARγ gene were in Hardy-Weinberg equilibrium. CONCLUSIONS: Iran is a country with an ethnically diverse population and a comparison of allelic and genotypic frequencies of PPARγ C1431T and Pro12Ala polymorphisms between our population and others showed significant differences. PMID:24497707

  20. Frequency of Germline Mutations in 25 Cancer Susceptibility Genes in a Sequential Series of Patients With Breast Cancer

    PubMed Central

    Lin, Nancy U.; Kidd, John; Allen, Brian A.; Singh, Nanda; Wenstrup, Richard J.; Hartman, Anne-Renee; Winer, Eric P.; Garber, Judy E.

    2016-01-01

    Purpose Testing for germline mutations in BRCA1/2 is standard for select patients with breast cancer to guide clinical management. Next-generation sequencing (NGS) allows testing for mutations in additional breast cancer predisposition genes. The frequency of germline mutations detected by using NGS has been reported in patients with breast cancer who were referred for BRCA1/2 testing or with triple-negative breast cancer. We assessed the frequency and predictors of mutations in 25 cancer predisposition genes, including BRCA1/2, in a sequential series of patients with breast cancer at an academic institution to examine the utility of genetic testing in this population. Methods Patients with stages I to III breast cancer who were seen at a single cancer center between 2010 and 2012, and who agreed to participate in research DNA banking, were included (N = 488). Personal and family cancer histories were collected and germline DNA was sequenced with NGS to identify mutations. Results Deleterious mutations were identified in 10.7% of women, including 6.1% in BRCA1/2 (5.1% in non-Ashkenazi Jewish patients) and 4.6% in other breast/ovarian cancer predisposition genes including CHEK2 (n = 10), ATM (n = 4), BRIP1 (n = 4), and one each in PALB2, PTEN, NBN, RAD51C, RAD51D, MSH6, and PMS2. Whereas young age (P < .01), Ashkenazi Jewish ancestry (P < .01), triple-negative breast cancer (P = .01), and family history of breast/ovarian cancer (P = .01) predicted for BRCA1/2 mutations, no factors predicted for mutations in other breast cancer predisposition genes. Conclusion Among sequential patients with breast cancer, 10.7% were found to have a germline mutation in a gene that predisposes women to breast or ovarian cancer, using a panel of 25 predisposition genes. Factors that predict for BRCA1/2 mutations do not predict for mutations in other breast/ovarian cancer susceptibility genes when these genes are analyzed as a single group. Additional cohorts will be helpful to define

  1. HFE gene C282Y, H63D and S65C mutations frequency in the Transylvania region, Romania.

    PubMed

    Trifa, Adrian P; Popp, Radu A; Militaru, Mariela S; Farcaş, Marius F; Crişan, Tania O; Gana, Ionuţ; Cucuianu, Andrei; Pop, Ioan V

    2012-06-01

    HFE-associated haemochromatosis is one of the most frequent autosomal recessive disorders in the Caucasian population. Although most of the cases are homozygous individuals for the C282Y mutation, another two mutations, H63D and S65C, have been reported to be associated with milder forms of the disease. This study was a first attempt to evaluate the distribution of these HFE gene mutations in the Transylvania region. Two-hundred and twenty-five healthy, unrelated volunteers originating from the Transylvania region, Romania, were screened for the HFE gene C282Y, H63D and S65C mutations, using molecular genetics assays (Polymerase Chain Reaction-Restriction Fragments Length Polymorphism). For the C282Y mutation, 7 heterozygotes (3.1%) were found, but no homozygous individual. In the case of the H63D mutation, 40 heterozygotes (17.8%) and 4 homozygotes (1.75%) for the mutant allele were evidenced. We found a compound heterozygous genotype (C282Y/H63D) in one individual (0.45%). Thus, the allele frequencies of the C282Y and H63D were 1.75% and 10.9%, respectively. Three individuals (1.3%) were found to harbour the S65C mutation in a heterozygous state, but none in a homozygous state: the allele frequency of the mutant allele was 0.75%. The distribution of the HFE gene C282Y, H63D and S65C mutations found in our group matches the tendencies observed in other European countries: a decreasing gradient from Northern to Southern Europe for the C282Y mutation; high frequency for the H63D mutation, and low frequency for the S65C mutation in most of the countries.

  2. Breit–Pauli atomic structure calculations for Fe XI

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

    Aggarwal, Sunny, E-mail: sunny.du87@gmail.com; Singh, Jagjit; Mohan, Man

    Energy levels, oscillator strengths, and transition probabilities are calculated for the lowest-lying 165 energy levels of Fe XI using configuration-interaction wavefunctions. The calculations include all the major correlation effects. Relativistic effects are included in the Breit–Pauli approximation by adding mass-correction, Darwin, and spin–orbit interaction terms to the non-relativistic Hamiltonian. For comparison with the calculated ab initio energy levels, we have also calculated the energy levels by using the fully relativistic multiconfiguration Dirac–Fock method. The calculated results are in close agreement with the National Institute of Standards and Technology compilation and other available results. New results are predicted for many ofmore » the levels belonging to the 3s3p{sup 4}3d and 3s3p{sup 3}3d{sup 2} configurations, which are very important in astrophysics, relevant, for example, to the recent observations by the Hinode spacecraft. We expect that our extensive calculations will be useful to experimentalists in identifying the fine structure levels in their future work.« less

  3. Incidence and Carrier Frequency of CFTR Gene Mutations in Pregnancies With Echogenic Bowel in Nova Scotia and Prince Edward Island.

    PubMed

    Miller, Michelle E; Allen, Victoria M; Brock, Jo-Ann K

    2018-03-01

    Fetal echogenic bowel (echogenic bowel) is associated with cystic fibrosis (CF), with a reported incidence ranging from 1% to 13%. Prenatal testing for CF in the setting of echogenic bowel can be done by screening parental or fetal samples for pathogenic CFTR variants. If only one pathogenic variant is identified, sequencing of the CFTR gene can be undertaken, to identify a second pathogenic variant not covered in the standard screening panel. Full gene sequencing, however, also introduces the potential to identify variants of uncertain significance (VUSs) that can create counselling challenges and cause parental anxiety. To provide accurate counselling for families in the study population, the incidence of CF associated with echogenic bowel and the carrier frequency of CFTR variants were investigated. All pregnancies for which CF testing was undertaken for the indication of echogenic bowel (from Nova Scotia and Prince Edward Island) were identified (January 2007-July 2017). The CFTR screening and sequencing results were reviewed, and fetal outcomes related to CF were assessed. A total of 463 pregnancies with echogenic bowel were tested. Four were confirmed to be affected with CF, giving an incidence of 0.9% in this cohort. The carrier frequency of CF among all parents in the cohort was 5.0% (1 in 20); however, when excluding parents of affected fetuses, the carrier frequency for the population was estimated at 4.1% (1 in 25). CFTR gene sequencing identified an additional VUS in two samples. The incidence of CF in pregnancies with echogenic bowel in Nova Scotia and Prince Edward Island is 0.9%, with an estimated population carrier frequency of 4.1%. These results provide the basis for improved counselling to assess the risk of CF in the pregnancy, after parental carrier screening, using Bayesian probability. Counselling regarding VUSs should be undertaken before gene sequencing. Copyright © 2017 Society of Obstetricians and Gynaecologists of Canada. Published by

  4. Gene frequencies and admixture estimates in four Mexican urban centers.

    PubMed

    Lisker, R; Ramirez, E; Briceño, R P; Granados, J; Babinsky, V

    1990-12-01

    We studied 202 individuals from the city of Leon in Guanajuato state, 228 from Merida, Yucatan, 220 from Oaxaca, Oaxaca, and 257 from Saltillo, Coahuila, to learn the distribution of the ABO, MN, Rh, and Duffy blood groups, serum haptoglobin, albumin, and factor Bf types, and red cell hemoglobin and glucose-6-phosphate dehydrogenase types. With the gene frequencies obtained, we performed admixture measurements with a maximum likelihood method, obtaining a trihybrid model for black, Indian, and white ancestry with the following proportions: 0.084, 0.513, and 0.403 in Leon: 0.059, 0.512, and 0.429 in Merida; 0.018, 0.676, and 0.306 in Oaxaca; and 0.073, 0.547, and 0.380 in Saltillo. The general pattern has high Indian ancestry followed by white and black ancestry. This pattern is congruent with most other studies performed in Mexico, including the east coast, where Indian ancestry predominates despite a clear increase in the black contribution.

  5. Coronal Abundances In Xi Boo A, Abundances in the Corona of FK Aqr and the Origin of Cosmic Ray

    NASA Technical Reports Server (NTRS)

    Drake, Jeremy; Oliversen, Ronald J. (Technical Monitor)

    2002-01-01

    Both Xi Boo A and FK Agr observations have been acquired, reduced and analysed. The results of the Xi Boo A study were published in ApJ (Drake, J.J., Kashyap, V., 2001, Up, 547, 428). Work is ongoing to determine the coronet metallicity of FK Aqr based on EUVE spectra and DO photometer data, using the techniques developed in the Drake & Kashyap paper. Preliminary synthetic spectra for FK Aqr have been developed, and further work to heap define the hot plasma emission measure distribution is underway. Progress on spectral analysis has been hampered following the post-doctoral scientist, Vinay Kashyap, taking up new position. A suitable replacement has been difficult to find, but new hire is expected shortly. However, good progress has been made on analysis of DO photometric variations in FK Age, with a publication now ready (Kashyap, V., Drake, J.J., Guedel, M., Audard, M.) for submission to a mainstream astrophysical journal.

  6. Frequency of ace, epa and elrA Genes in Clinical and Environmental Strains of Enterococcus faecalis.

    PubMed

    Lysakowska, Monika Eliza; Denys, Andrzej; Sienkiewicz, Monika

    2012-12-01

    Surface proteins play an important role in the pathogenesis of enterococcal infections. Some of them are candidates for a vaccine, e.g., the frequency of endocarditis in rats vaccinated with Ace protein was 75 % as 12 opposed to 100 % in those who weren't. However, there are other components of enterococcal cells, such as Epa antigens or internalin-like proteins, which may be used in the prophylaxis of infections caused by them. However, also other virulence factors and resistance to antibiotics are important during enterococcal infection. Therefore, the relevance of ace, epa, elrA, other virulence genes, as well as resistance to antibiotics was investigated. 161 Enterococcus faecalis strains isolated from teaching hospitals in Lodz, cultured according to standard microbiological methods, were investigated for the presence of genes encoding surface proteins by PCR. Results were analyzed with χ(2) test. The elrA gene was found in all clinical and environmental strains, the ace gene was also widespread among E. faecalis (96.9 %). Both tested epa genes were found in the majority of isolates (83.25 %). There was correlation between the presence of esp and ace genes (p = 0.046) as well as between epa and agg genes (p = 0.0094; χ(2) test). The presence of the genes encoding surface proteins investigated in our study in the great majority of isolates implies that they would appear to be required during E. faecalis infection. Therefore, they could be excellent targets in therapy of enterococcal infections or, as some studies show, candidates for vaccines.

  7. Frequency of CYP450 enzyme gene polymorphisms in the Greek population: review of the literature, original findings and clinical significance.

    PubMed

    Ragia, Georgia; Giannakopoulou, Efstathia; Karaglani, Makrina; Karantza, Ioanna-Maria; Tavridou, Anna; Manolopoulos, Vangelis G

    2014-01-01

    The cytochrome P450 (CYP450) enzyme family is involved in the oxidative metabolism of many therapeutic drugs and various endogenous substrates. These enzymes are highly polymorphic. Prevalence of CYP450 enzyme gene polymorphisms vary among different populations and substantial inter- and intra-ethnic variability in frequency of CYP450 enzyme gene polymorphisms has been reported. This paper provides an overview and investigation of CYP450 genotypic and phenotypic reports published in the Greek population.

  8. Neutral B-meson mixing from three-flavor lattice QCD: Determination of the SU(3)-breaking ratio \\xi

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

    Bazavov, A.; /Brookhaven; Bernard, C.

    We study SU(3)-breaking effects in the neutral B{sub d}-{bar B}{sub d} and B{sub s}-{bar B}{sub s} systems with unquenched N{sub t}=2+1 lattice quantum chromodynamics (QCD). We calculate the relevant matrix elements on the MILC collaboration's gauge configurations with asqtad-improved staggered sea quarks. For the valence light-quarks (u, d, and s) we use the asqtad action, while for b quarks we use the Fermilab action. We obtain {xi}=f{sub B{sub s}} {radical}{ovr B{sub B{sub s}}}/f{sub B{sub d}}{radical}{ovr B{sub B{sub d}}}=1.268{+-}0.063. We also present results for the ratio of bag parameters B{sub B{sub s}}/B{sub B{sub d}} and the ratio of Cabibbo-Kobayashi-Maskawa matrix elementsmore » |V{sub td}|/|V{sub ts}|. Although we focus on the calculation of {xi}, the strategy and techniques described here will be employed in future extended studies of the B mixing parameters {Delta}M{sub d,s} and {Delta}{Gamma}{sub d,s} in the standard model and beyond.« less

  9. 75 FR 44163 - Implementation of Regulations Required Under Title XI of the Food, Conservation and Energy Act of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-28

    ... Under Title XI of the Food, Conservation and Energy Act of 2008; Conduct in Violation of the Act AGENCY... Act and provide for a fairer market place. DATES: We will consider comments we receive by November 22... clarify conditions for industry compliance with the P&S Act and provide for a fairer market place. We have...

  10. [Mutational frequencies in usherin(USH2A gene) in 26 Colombian individuals with Usher syndrome type II].

    PubMed

    López, Greizy; Gelvez, Nancy Yaneth; Tamayo, Martalucía

    2011-03-01

    Usher syndrome is a disorder characterized by progressive retinitis pigmentosa, prelingual sensory hearing loss and vestibular dysfunction. It is the most frequent cause of deaf-blindness in humans. Three clinical types and twelve genetic subtypes have been characterized. Type II is the most common, and among these cases, nearly 80% have mutations in the USH2A gene. The aim of the study was to establish the mutational frequencies for the short isoform of USH2A gene in Usher syndrome type II. Twenty-six Colombian individuals with Usher syndrome type II were included. SSCP analysis for 20 exons of the short isoform was performed and abnormal patterns were sequenced. Sequencing of exon 13 of the USH2A gene was performed for all the individuals because the most frequent mutation is located in this exon. The most frequent mutation was c.2299delG, identified in the 27% (n=8) of the sample. The second mutation, p.R334W, showed a frequency of 15%. A new variant identified in the 5’UTR region, g.129G>T, was present in 1 individual (4%). Four polymorphisms were identified; one of them is a new deletion in exon 20, first reported in this study. Mutations in the usherin short isoform were identified in 38% of a sample of 26 USH2 cases. Molecular diagnosis was established in 7 of the 26.

  11. Evaluating the Frequency of aac(6')-IIa, ant(2″)-I, intl1, and intl2 Genes in Aminoglycosides Resistant Klebsiella pneumoniae Isolates Obtained from Hospitalized Patients in Yazd, Iran.

    PubMed

    Mokhtari, Hesam; Eslami, Gilda; Zandi, Hengameh; Dehghan-Banadkouki, Amin; Vakili, Mahmood

    2018-01-01

    Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen that could be resistant to many antimicrobial agents. Resistance genes can be carried among gram-negative bacteria by integrons. Enzymatic inactivation is the most important mechanism of resistance to aminoglycosides. In this study, the frequencies of two important resistance gene aac(6')-II a and ant(2″)-I, and genes coding integrase I and II, in K. pneumoniae isolates resistant to aminoglycosides were evaluated. In this cross-sectional study, an attempt was made to assess the antibiotic susceptibility of 130 K. pneumoniae isolates obtained from different samples of patients hospitalized in training hospitals of Yazd evaluated by disk diffusion method. The frequencies of aac(6')-II a, ant(2″)-I, intl1 , and intl2 genes were determined by PCR method. Data were analyzed by chi-square method using SPSS software (Ver. 16). our results showed that resistance to gentamicin, tobramycin, kanamycin, and amikacin were 34.6, 33.8, 43.8, and 14.6%, respectively. The frequencies of aac (6')-II a, ant(2″)-I, intl1 , and intl2 genes were 44.6, 27.7, 90, and 0%, respectively. This study showed there are high frequencies of genes coding aminoglycosides resistance in K. pneumoniae isolates. Hence, it is very important to monitor and inhibit the spread of antibiotic resistance genes.

  12. [Frequency of the most common mutations of the CFTR gene in peruvian patients with cystic fibrosis using the ARMS-PCR technique].

    PubMed

    Aquino, Ruth; Protzel, Ana; Rivera, Juan; Abarca, Hugo; Dueñas, Milagros; Nestarez, Cecilia; Purizaga, Nestor; Diringer, Benoit

    2017-01-01

    To determine the frequency of the ten most common mutations of the CFTR gene reported in Latin Americausing amplification-refractory mutation system-polymerase chain reaction (ARMS-PCR) in patients with cystic fibrosis (CF) in two referral hospitals in Peru during the year 2014. The frequency of the ten most common mutations of the CFTR gene was assessed in patients of the Hospital Nacional Edgardo Rebagliati Martins and the Instituto Nacional de Salud del Niño, both located in Lima, Peru. Blood samples were collected from 36 patients with CF, and the ARMS-PCR technique was used to determine the presence of these mutations. The study group included 73.5% of patients with a known diagnosis of CF in the country when the study was carried out. ARMS-PCR allowed three of the mutations to be identified in a combined 30.6% of the alleles from patients with CF, and 64.9% of the mutated alleles were not identified. The mutations found were p.Phe508del (22,2%), p.Gly542* (6,9%), and p.Arg1162* (1,4%). There is significant variability in both the frequency and type of mutations present in our study population and in what has been reported in other Latin American countries. It is necessary to perform studies that use complete sequencing technology for the CFTR gene to identify other mutations present in our population.

  13. Sources and Dynamics of Inorganic Carbon within the Upper Reaches of the Xi River Basin, Southwest China

    PubMed Central

    Zou, Junyu

    2016-01-01

    The carbon isotopic composition (δ13C) of dissolved and particulate inorganic carbon (DIC; PIC) was used to compare and analyze the origin, dynamics and evolution of inorganic carbon in two headwater tributaries of the Xi River, Southwest China. Carbonate dissolution and soil CO2 were regarded as the primary sources of DIC on the basis of δ13CDIC values which varied along the Nanpan and Beipan Rivers, from −13.9‰ to 8.1‰. Spatial trends in DIC differed between the two rivers (i.e., the tributaries), in part because factors controlling pCO2, which strongly affected carbonate dissolution, differed between the two river basins. Transport of soil CO2 and organic carbon through hydrologic conduits predominately controlled the levels of pCO2 in the Nanpan River. However, pCO2 along the upper reaches of the Nanpan River also was controlled by the extent of urbanization and industrialization relative to agriculture. DIC concentrations in the highly urbanized upper reaches of the Nanpan River were typical higher than in other carbonate-dominated areas of the upper Xi River. Within the Beipan River, the oxidation of organic carbon is the primary process that maintains pCO2 levels. The pCO2 within the Beipan River was more affected by sulfuric acid from coal industries, inputs from a scenic spot, and groundwater than along the Nanpan River. With regards to PIC, the contents and δ13C values in the Nanpan River were generally lower than those in the Beipan River, indicating that chemical and physical weathering contributes more marine carbonate detritus to the PIC along the Beipan River. The CO2 evasion flux from the Nanpan River was higher than that in the Beipan River, and generally higher than along the middle and lower reaches of the Xi River, demonstrating that the Nanpan River is an important net source of atmospheric CO2 in Southwest China. PMID:27513939

  14. Frequencies of genes for coat colour and horns in Nordic cattle breeds

    PubMed Central

    Kantanen, Juha; Olsaker, Ingrid; Brusgaard, Klaus; Eythorsdottir, Emma; Holm, Lars-Erik; Lien, Sigbjørn; Danell, Birgitta; Adalsteinsson, Stefan

    2000-01-01

    Gene frequencies of coat colour and horn types were assessed in 22 Nordic cattle breeds in a project aimed at establishing genetic profiles of the breeds under study. The coat colour loci yielding information on genetic variation were: extension, agouti, spotting, brindle, dun dilution and colour sided. The polled locus was assessed for two alleles. A profound variation between breeds was observed in the frequencies of both colour and horn alleles, with the older breeds generally showing greater variation in observed colour, horn types and segregating alleles than the modern breeds. The correspondence between the present genetic distance matrix and previous molecular marker distance matrices was low (r = 0.08 – 0.12). The branching pattern of a neighbour-joining tree disagreed to some extent with the molecular data structure. The current data indicates that 70% of the total genetic variation could be explained by differences between the breeds, suggesting a much greater breed differentiation than typically found at protein and microsatellite loci. The marked differentiation of the cattle breeds and observed disagreements with the results from the previous molecular data in the topology of the phylogenetic trees are most likely a result of selection on phenotypic characters analysed in this study. PMID:14736370

  15. The allele frequency of two single nucleotide polymorphisms in the von Hippel-Lindau (VHL) tumor suppressor gene in the Taiwanese population.

    PubMed

    Wang, Wen-Chung; Chen, Hui-Ju; Shu, Wei-Pang; Tsai, Yi-Chang; Lai, Yen-Chein

    2011-10-01

    The von Hippel-Lindau (VHL) tumor suppressor gene located on chromosome 3p25-26 is implicated in VHL disease. Two informative single nucleotide polymorphisms are at positions 19 and 1149 on the nucleotide sequence from Gene Bank NM_000551. In this study we examined the allele frequencies at these two loci in the Taiwanese population and compared the results to those from European ethnic populations. The allele frequency was examined in 616 healthy individuals including 301 university students and 315 neonates. Both A/G polymorphisms were investigated using restriction fragment length polymorphism analysis created by restriction enzymes, BsaJ I and Acc I. Among these subjects, the allele frequencies at 19 SNP and 1149 SNP for variant G were 0.130 and 0.133, respectively. And these results were significant differences from those of the Caucasian populations. In addition, 90% of the tested subjects had identical genotypes at these two loci suggesting the existence of nonrandom association of alleles. We found that the G allele frequency at these two loci in the Taiwanese population is much lower than that in people from Western countries. This phenomenon may be attributed to ethnic effects. Copyright © 2011. Published by Elsevier B.V.

  16. Decoding the principles underlying the frequency of association with nucleoli for RNA polymerase III–transcribed genes in budding yeast

    PubMed Central

    Belagal, Praveen; Normand, Christophe; Shukla, Ashutosh; Wang, Renjie; Léger-Silvestre, Isabelle; Dez, Christophe; Bhargava, Purnima; Gadal, Olivier

    2016-01-01

    The association of RNA polymerase III (Pol III)–transcribed genes with nucleoli seems to be an evolutionarily conserved property of the spatial organization of eukaryotic genomes. However, recent studies of global chromosome architecture in budding yeast have challenged this view. We used live-cell imaging to determine the intranuclear positions of 13 Pol III–transcribed genes. The frequency of association with nucleolus and nuclear periphery depends on linear genomic distance from the tethering elements—centromeres or telomeres. Releasing the hold of the tethering elements by inactivating centromere attachment to the spindle pole body or changing the position of ribosomal DNA arrays resulted in the association of Pol III–transcribed genes with nucleoli. Conversely, ectopic insertion of a Pol III–transcribed gene in the vicinity of a centromere prevented its association with nucleolus. Pol III–dependent transcription was independent of the intranuclear position of the gene, but the nucleolar recruitment of Pol III–transcribed genes required active transcription. We conclude that the association of Pol III–transcribed genes with the nucleolus, when permitted by global chromosome architecture, provides nucleolar and/or nuclear peripheral anchoring points contributing locally to intranuclear chromosome organization. PMID:27559135

  17. Mutation frequencies of the cytochrome CYP2D6 gene in Parkinson disease patients and in families

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

    Lucotte, G.; Turpin, J.C.; Gerard, N.

    1996-07-26

    The frequencies of five mutations of the debrisoquine 4-hydroxylase (CYP2D6) gene (mutations D6-A, B, C, D, and T), corresponding to poor metabolizer (PM) phenotypes, were determined by restriction fragment length polymorphism (RFLP) and polymerase chain reaction (PCR) in 47 patients with Parkinson disease, and compared with the findings in 47 healthy controls. These mutant alleles were about twice as frequent among patients as in controls, with an approximate relative risk ratio of 2.12 (95% confidence interval, 1.41-2.62). There seem to be no significant differences in frequencies of mutant genotypes in patients among gender and modalities of response with levodopa therapy;more » but frequency of the mutations was slightly enhanced after age-at-onset of 60 years. Mutations D6-B, D, and T were detected in 7 patients belonging to 10 Parkinson pedigrees. 25 refs., 1 fig., 2 tabs.« less

  18. Effects of AC/DC magnetic fields, frequency, and nanoparticle aspect ratio on cellular transfection of gene vectors

    NASA Astrophysics Data System (ADS)

    Ford, Kris; Mair, Lamar; Fisher, Mike; Rowshon Alam, Md.; Juliano, Rudolph; Superfine, Richard

    2008-10-01

    In order to make non-viral gene delivery a useful tool in the study and treatment of genetic disorders, it is imperative that these methodologies be further refined to yield optimal results. Transfection of magnetic nanoparticles and nanorods are used as non-viral gene vectors to transfect HeLa EGFP-654 cells that stably express a mutated enhanced green fluorescent protein (EGFP) gene. We deliver antisense oligonucleotides to these cells designed to correct the aberrant splicing caused by the mutation in the EGFP gene. We also transfect human bronchial endothelial cells and immortalized WI-38 lung cells with pEGFP-N1 vectors. To achieve this we bind the genes to magnetic nanoparticles and nanorods and introduce magnetic fields to effect transfection. We wish to examine the effects of magnetic fields on the transfection of these particles and the benefits of using alternating (AC) magnetic fields in improving transfection rates over direct (DC) magnetic fields. We specifically look at the frequency dependence of the AC field and particle aspect ratio as it pertains to influencing transfection rate. We posit that the increase in angular momentum brought about by the AC field and the high aspect ratio of the nanorod particles, is vital to generating the force needed to move the particle through the cell membrane.

  19. 77 FR 21813 - Changes to the Generic Aging Lessons Learned (GALL) Report Revision 2 AMP XI.M41, “Buried and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-11

    ... NUCLEAR REGULATORY COMMISSION [NRC-2012-0055] Changes to the Generic Aging Lessons Learned (GALL) Report Revision 2 AMP XI.M41, ``Buried and Underground Piping and Tanks'' AGENCY: Nuclear Regulatory... NUREG-1801, Revision 2, ``Generic Aging Lessons Learned (GALL) Report,'' and the NRC staff's aging...

  20. High frequency of EBV association and 30-bp deletion in the LMP-1 gene in CD56 lymphomas of the upper aerodigestive tract.

    PubMed

    Tai, Yan-Chin; Kim, Lian-Hua; Peh, Suat-Cheng

    2004-03-01

    Natural killer (NK)/T-cell lymphomas are frequently associated with Epstein-Barr virus (EBV), and usually lack TCR gene rearrangement. Studies from Asia have reported frequent deletion in the LMP-1 gene in EBV-associated nasopharyngeal carcinoma (NPC). The present study aims to investigate LMP-1 and TCRgamma gene status in upper aerodigestive tract lymphomas. A total of 43 cases were classified into T-, B-, and NK/T-cell tumors based on the phenotype expressions of CD3(+)/CD20(-)/CD56(-), CD3(-)/CD20(+)/CD56(-), and CD3(+)/CD20(-)/CD56(+), respectively. The presence of EBV in the tumor was confirmed by EBV early RNA-in situ hybridization. LMP-1 gene deletion and TCR gamma gene rearrangement were analyzed by polymerase chain reaction on paraffin-embedded tissues. There were 20 NK/T-, eight T-, and 15 B-cell phenotype lymphomas in the present series, and EBV was detected in 19 (95%), two (25%), and three (20%) cases in the respective groups. All EBV+ cases carried 30-bp deletion in the LMP-1 gene, and two of the NK/T-cell cases were infected by both the wild type and deleted strains. Five (25%) of the NK/T-cell phenotype lymphomas showed rearranged TCR gamma gene. The present study revealed a high frequency of EBV association, and a high frequency of 30-bp deletion in the LMP-1 gene in the virus in the present series of lymphoma. The NK/T-phenotype lymphomas are comprised of both NK-cell and cytotoxic T-lymphocyte-derived tumors.

  1. Efficacy of the treatments used for the control of Caligus rogercresseyi infecting Atlantic salmon, Salmo salar L., in a new fish-farming location in Region XI, Chile.

    PubMed

    Bravo, S; Nuñez, M; Silva, M T

    2013-03-01

    Caligus rogercresseyi is the most important parasite affecting Atlantic salmon and rainbow trout farming in sea water in Chile. After the outbreaks of the infectious salmon anaemia recorded in Region X from 2007, the salmon industry has expanded southwards to Region XI, where 60% of Atlantic salmon in Chile is now produced. In parallel with the relocation of salmon production, sea lice infestation has also spread to Region XI, and today C. rogercresseyi is the most serious threat to the salmon-farming industry in this region. The results obtained through a year of monitoring between September 2007 and August 2008 on a farm located in the 'Las Guaitecas Archipelago' in Region XI (44°S; 74°W) showed that treatments with emamectin benzoate and deltamethrin did not give the expected control of Caligus. Failures of the treatments were associated with the loss of sensitivity recorded for C. rogercresseyi to emamectin benzoate in Region X. In addition, a major influence was the lack of delousing coordination measures with the neighbouring farms sharing the same area in that period. © 2013 Blackwell Publishing Ltd.

  2. Cutaneous gene expression of plasmid DNA in excised human skin following delivery via microchannels created by radio frequency ablation.

    PubMed

    Birchall, James; Coulman, Sion; Anstey, Alexander; Gateley, Chris; Sweetland, Helen; Gershonowitz, Amikam; Neville, Lewis; Levin, Galit

    2006-04-07

    The skin is a valuable organ for the development and exploitation of gene medicines. Delivering genes to skin is restricted however by the physico-chemical properties of DNA and the stratum corneum (SC) barrier. In this study, we demonstrate the utility of an innovative technology that creates transient microconduits in human skin, allowing DNA delivery and resultant gene expression within the epidermis and dermis layers. The radio frequency (RF)-generated microchannels were of sufficient morphology and depth to permit the epidermal delivery of 100 nm diameter nanoparticles. Model fluorescent nanoparticles were used to confirm the capacity of the channels for augmenting diffusion of macromolecules through the SC. An ex vivo human organ culture model was used to establish the gene expression efficiency of a beta-galactosidase reporter plasmid DNA applied to ViaDerm treated skin. Skin treated with ViaDerm using 50 microm electrode arrays promoted intense levels of gene expression in the viable epidermis. The intensity and extent of gene expression was superior when ViaDerm was used following a prior surface application of the DNA formulation. In conclusion, the RF-microchannel generator (ViaDerm) creates microchannels amenable for delivery of nanoparticles and gene therapy vectors to the viable region of skin.

  3. Caesarean section rate and cost control effectiveness of case payment reform in the new cooperative medical scheme for delivery: evidence from Xi County, China.

    PubMed

    Liu, Shuang; Wang, Jing; Zhang, Liang; Zhang, Xiang

    2018-03-09

    In China, increases in both the caesarean section (CS) rates and delivery costs have raised questions regarding the reform of the medical insurance payment system. Case payment is useful for regulating the behaviour of health providers and for controlling the CS rates and excessive increases in medical expenses. New Cooperative Medical Scheme (NCMS) agencies in Xi County in Henan Province piloted a case payment reform (CPR) in delivery for inpatients. We aimed to observe the changes in the CS rates, compare the changes in delivery-related variables, and identify variables related to delivery costs before and after the CPR in Xi County. Overall, 28,314 cases were selected from the Xi County NCMS agency from 2009 to 2010 and from 2014 to 2015. One-way ANOVA and chi-square tests were used to compare the distributions of CS and vaginal delivery (VD) before and after the CPR under different indicators. We applied multivariate linear regressions for the total medical cost of the VD and CS groups and total samples to identify the relationships between medical expenses and variables. The CS rates in Xi County increased from 26.1% to 32.5% after the CPR. The length of stay (LOS), total medical cost, and proportion of county hospitals increased in the CS and VD groups after the CPR, which had significant differences. The total medical cost in the CS and VD groups as well as the total samples was significantly influenced by inpatient age, LOS, and hospital type, and had a significant correlation with the CPR in the VD group and the total samples. The CPR might fail to control the growth of unreasonable medical expenses and regulate the behaviour of providers, which possibly resulted from the unreasonable compensation standard of case payments, prolonged LOS, and the increasing proportion of county hospitals. The NCMS should modify the case payment standard of delivery to inhibit providers' motivation to render CS services. The LOS should be controlled by implementing clinical

  4. Structural organization of the inactive X chromosome in the mouse

    PubMed Central

    Giorgetti, Luca; Lajoie, Bryan R.; Carter, Ava C.; Attia, Mikael; Zhan, Ye; Xu, Jin; Chen, Chong Jian; Kaplan, Noam; Chang, Howard Y.; Heard, Edith; Dekker, Job

    2017-01-01

    X-chromosome inactivation (XCI) involves major reorganization of the X chromosome as it becomes silent and heterochromatic. During female mammalian development, XCI is triggered by upregulation of the non-coding Xist RNA from one of the two X chromosomes. Xist coats the chromosome in cis and induces silencing of almost all genes via its A-repeat region1,2, although some genes (constitutive escapees) avoid silencing in most cell types, and others (facultative escapees) escape XCI only in specific contexts3. A role for Xist in organizing the inactive X (Xi) chromosome has been proposed4–6. Recent chromosome conformation capture approaches have revealed global loss of local structure on the Xi chromosome and formation of large mega-domains, separated by a region containing the DXZ4 macrosatellite7–10. However, the molecular architecture of the Xi chromosome, in both the silent and expressed regions, remains unclear. Here we investigate the structure, chromatin accessibility and expression status of the mouse Xi chromosome in highly polymorphic clonal neural progenitors (NPCs) and embryonic stem cells. We demonstrate a crucial role for Xist and the DXZ4-containing boundary in shaping Xi chromosome structure using allele-specific genome-wide chromosome conformation capture (Hi-C) analysis, an assay for transposase-accessible chromatin with high throughput sequencing (ATAC–seq) and RNA sequencing. Deletion of the boundary disrupts mega-domain formation, and induction of Xist RNA initiates formation of the boundary and the loss of DNA accessibility. We also show that in NPCs, the Xi chromosome lacks active/inactive compartments and topologically associating domains (TADs), except around genes that escape XCI. Escapee gene clusters display TAD-like structures and retain DNA accessibility at promoter-proximal and CTCF-binding sites. Furthermore, altered patterns of facultative escape genes in different neural progenitor clones are associated with the presence of

  5. Bloom's syndrome. VI. The disorder in Israel and an estimation of the gene frequency in the Ashkenazim.

    PubMed Central

    German, J; Bloom, D; Passarge, E; Fried, K; Goodman, R M; Katzenellenbogen, I; Laron, Z; Legum, C; Levin, S; Wahrman

    1977-01-01

    An effort was made to identify all individuals with Bloom's syndrome living in Israel between September 1971 and September 1972. Each of the eight individuals located were Jewish and could readily be classified Ashkenazic. The frequency of the Bloom's syndrome gene in Ashkenazim was estimated to be .0042 (minimum), implying a heterozygote frequency greater than 1 in 120. A striking distortion of the sex ratio (M/F = 7.0) may have been due to underascertainment of affected females. One of the affected individuals ascertained during the survey subsequently has died from cancer, which is in keeping with the recognized cancer proneness of this condition. Four of the affected have married, but no conception is known to have occurred, which suggests that sub- or infertility is a feature of the syndrome. PMID:930922

  6. C677T (RS1801133 ) MTHFR gene polymorphism frequency in a colombian population.

    PubMed

    Romero-Sánchez, Consuelo; Gómez-Gutierrez, Alberto; Gómez, Piedad Elena; Casas-Gomez, Maria Consuelo; Briceño, Ignacio

    2015-01-01

    Abnormal levels of the enzyme methylenetetrahydrofolate reductase (MTHFR) are associated with an increased risk of both cardiovascular and cerebrovascular disease and higher concentrations of homocysteine. Abnormal levels are also related to birth defects, pregnancy complications, cancer and toxicity to methotrexate (MTX). Polymorphisms of MTHFR affect the activity of the enzyme. Genetic associations have been related to treatment efficacy. To establish the frequency of the C> T polymorphism at nucleotide 677 of the MTHFR gene in a group of Colombian individuals. Data from pharmacogenetic microarrays that include MTX sensibility-associated polymorphisms were retrospectively collected (Pathway Genomics(®)). The frequency of the C> T MTHFR rs1801133 marker polymorphism was analyzed. Microarray data from 68 men and 84 women were analyzed. Comparisons of genotype C/C vs. C/T and T/T were statistically significantly different (p= 0.00, p= 0.026, respectively), as were C/T and T / T (p= 0.0001). Results for the C/C and C/T genotypes in a Colombian population are similar to other previously studied groups of healthy subjects. Subjects from our population might be at risk of developing diseases associated with MTHFR polymorphisms and might present toxicity and adverse effects if treated with MTX, which suggests the need to evaluate therapeutic alternatives based on individual pharmacogenetic studies.

  7. Subjective well-being of the elderly in Xi Cheng District, Beijing

    PubMed Central

    Li, Shuo; Xie, Zhaohui; Shao, Jun; Xiao, Cunli; Tian, Liang; Zhao, Rongfeng; Gong, Jiakai; Han, Jinxiang; Wang, Yue; Han, Chao; Dang, Liping; Zhang, Yushi; Chen, Bo; Luo, Xiaojing; Guo, Wei

    2012-01-01

    Background In 2010 the Beijing Municipal Government promulgated a policy aimed at improving the quality of life and subjective well-being of elderly residents that included a component focused on mental health. Aim Identify factors associated with subjective well-being in a representative sample of elderly residents of Xi Cheng District in Beijing. Methods This cross-sectional study administered a self-completion survey to a stratified random sample of 2342 residents of Xi Cheng District who were 60 to 80 years of age. The level of well-being was assessed using a validated Chinese version of the Memorial University of Newfoundland Scale of Happiness (MUNSH). Detailed socioeconomic variables were obtained using a questionnaire developed by the authors. Social support, anxiety, and depression were assessed using validated Chinese versions of the Social Support Rating Scale (SSRS), Self-rating Anxiety Scale (SAS), and Self-rating Depression Scale (SDS). Results Among the 2342 respondents, 1616 (69.0%) had a total MUNSH score of 32 or above, indicating a high level of happiness; 423 (18.1%) has a total SSRS score 32 or below, indicating poor social support; 201 (8.6%) had a total SDS score of 53 or above, indicating significant depression; and 126 (5.3%) had a total SAS score of 50 or above, indicating significant anxiety. In the multivariate regression analysis the self-reported level of depression was the most important factor related to well-being. Anxiety, social support, income level, the quality of family relationships, the ability to self-regulate emotions, and regular exercise were also significantly related to well-being; but gender, marital status, age and educational level were not associated with well-being. Conclusion Among elderly urban residents in Beijing, self-reports of poor subjective well-being are closely associated with self-reports of depressive and anxiety symptoms and also associated with social factors such as social support, income level and

  8. The Settings, Pros and Cons of the New Surgical Robot da Vinci Xi System for Transoral Robotic Surgery (TORS): A Comparison With the Popular da Vinci Si System.

    PubMed

    Kim, Da Hee; Kim, Hwan; Kwak, Sanghyun; Baek, Kwangha; Na, Gina; Kim, Ji Hoon; Kim, Se Heon

    2016-10-01

    The da Vinci system (da Vinci Surgical System; Intuitive Surgical Inc.) has rapidly developed in several years from the S system to the Si system and now the Xi System. To investigate the surgical feasibility and to provide workflow guidance for the newly released system, we used the new da Vinci Xi system for transoral robotic surgery (TORS) on a cadaveric specimen. Bilateral supraglottic partial laryngectomy, hypopharyngectomy, lateral oropharyngectomy, and base of the tongue resection were serially performed in search of the optimal procedures with the new system. The new surgical robotic system has been upgraded in all respects. The telescope and camera were incorporated into one system, with a digital end-mounted camera. Overhead boom rotation allows multiquadrant access without axis limitation, the arms are now thinner and longer with grabbing movements for easy adjustments. The patient clearance button dramatically reduces external collisions. The new surgical robotic system has been optimized for improved anatomic access, with better-equipped appurtenances. This cadaveric study of TORS offers guidance on the best protocol for surgical workflow with the new Xi system leading to improvements in the functional results of TORS.

  9. Characteristics of bacterial and fungal aerosols during the autumn haze days in Xi'an, China

    NASA Astrophysics Data System (ADS)

    Li, Yanpeng; Fu, Honglei; Wang, Wei; Liu, Jun; Meng, Qinglong; Wang, Wenke

    2015-12-01

    In recent years, haze pollution has become one of the most critical environmental issues in Xi'an, China, with particular matter (PM) being one of the top pollutants. As an important fraction of PM, bioaerosols may have adverse effects on air quality and human health. In this study, to better understand the characteristics of such biological aerosols, airborne microbial samples were collected by using an Andersen six-stage sampler in Xi'an from October 8th to 22nd, 2014. The concentration, size distribution and genera of airborne viable bacteria and fungi were comparably investigated during the haze days and non-haze days. Correlations of bioaerosol levels with meteorological parameters and PM concentrations were also examined. The results showed that the daily average concentrations of airborne viable bacteria and fungi during the haze days, 1102.4-1736.5 and 1466.2-1703.9 CFU/m3, respectively, were not only much higher than those during the non-haze days, but also exceeded the recommended permissible limit values. Comparing to size distributions during the non-haze days, slightly different patterns for bacterial aerosols and similar single-peak distribution pattern for fungal aerosols were observed during the haze days. Moreover, more allergic and infectious genera (e.g. Neisseria, Aspergillus, and Paecilomyces) in bioaerosols were identified during the haze days than during non-haze days. The present results reveal that bioaerosols may have more significant effects on public health and urban air quality during the haze days than during non-haze days.

  10. Rare Frequency of Mutations in Pituitary Transcription Factor Genes in Combined Pituitary Hormone or Isolated Growth Hormone Deficiencies in Korea.

    PubMed

    Choi, Jin Ho; Jung, Chang Woo; Kang, Eungu; Kim, Yoon Myung; Heo, Sun Hee; Lee, Beom Hee; Kim, Gu Hwan; Yoo, Han Wook

    2017-05-01

    Congenital hypopituitarism is caused by mutations in pituitary transcription factors involved in the development of the hypothalamic-pituitary axis. Mutation frequencies of genes involved in congenital hypopituitarism are extremely low and vary substantially between ethnicities. This study was undertaken to compare the clinical, endocrinological, and radiological features of patients with an isolated growth hormone deficiency (IGHD) or combined pituitary hormone deficiency (CPHD). This study included 27 patients with sporadic IGHD and CPHD. A mutation analysis of the POU1F1, PROP1, LHX3, LHX4, and HESX1 genes was performed using genomic DNA from peripheral blood leukocytes. IGHD and CPHD were observed in 4 and 23 patients, respectively. Mean age at diagnosis was 8.28±7.25 years for IGHD and 13.48±10.46 years for CPHD (p=0.37). Serum insulin-like growth factor-1 and peak growth hormone (GH) levels following GH stimulation tests were significantly lower in patients with CPHD than in those with IGHD (p<0.05). Sellar MRI findings revealed structural abnormalities in 3 patients with IGHD (75%) and 21 patients with CPHD (91.3%) (p=0.62). A mutation analysis identified homozygous p.R109Q mutations in HESX1 in a patient with CPHD. Patients with CPHD had more severe GHD than those with IGHD. The frequency of defects in the genes encoding pituitary transcription factors was extremely low in Korean patients with congenital hypopituitarism. Environmental factors and the impact of other causative genes may contribute to this clinical phenotype. © Copyright: Yonsei University College of Medicine 2017

  11. Rare Frequency of Mutations in Pituitary Transcription Factor Genes in Combined Pituitary Hormone or Isolated Growth Hormone Deficiencies in Korea

    PubMed Central

    Choi, Jin-Ho; Jung, Chang-Woo; Kang, Eungu; Kim, Yoon-Myung; Heo, Sun Hee; Lee, Beom Hee; Kim, Gu-Hwan

    2017-01-01

    Purpose Congenital hypopituitarism is caused by mutations in pituitary transcription factors involved in the development of the hypothalamic-pituitary axis. Mutation frequencies of genes involved in congenital hypopituitarism are extremely low and vary substantially between ethnicities. This study was undertaken to compare the clinical, endocrinological, and radiological features of patients with an isolated growth hormone deficiency (IGHD) or combined pituitary hormone deficiency (CPHD). Materials and Methods This study included 27 patients with sporadic IGHD and CPHD. A mutation analysis of the POU1F1, PROP1, LHX3, LHX4, and HESX1 genes was performed using genomic DNA from peripheral blood leukocytes. Results IGHD and CPHD were observed in 4 and 23 patients, respectively. Mean age at diagnosis was 8.28±7.25 years for IGHD and 13.48±10.46 years for CPHD (p=0.37). Serum insulin-like growth factor-1 and peak growth hormone (GH) levels following GH stimulation tests were significantly lower in patients with CPHD than in those with IGHD (p<0.05). Sellar MRI findings revealed structural abnormalities in 3 patients with IGHD (75%) and 21 patients with CPHD (91.3%) (p=0.62). A mutation analysis identified homozygous p.R109Q mutations in HESX1 in a patient with CPHD. Patients with CPHD had more severe GHD than those with IGHD. Conclusion The frequency of defects in the genes encoding pituitary transcription factors was extremely low in Korean patients with congenital hypopituitarism. Environmental factors and the impact of other causative genes may contribute to this clinical phenotype. PMID:28332357

  12. Net accumulation rates derived from ice core stable isotope records of Pío XI glacier, Southern Patagonia Icefield

    NASA Astrophysics Data System (ADS)

    Schwikowski, M.; Schläppi, M.; Santibañez, P.; Rivera, A.; Casassa, G.

    2012-12-01

    Pío XI, the largest glacier of the Southern Patagonia Icefield, reached its neoglacial maximum extent in 1994 and is one of the few glaciers in that area which is not retreating. In view of the recent warming it is important to understand glacier responses to climate changes. Due to its remoteness and the harsh conditions in Patagonia, no systematic mass balance studies have been performed. In this study we derived net accumulation rates for the period 2000 to 2006 from a 50 m (33.2 4 m weq) ice core collected in the accumulation area of Pío XI (2600 m a.s.l., 49°16´40´´ S, 73°21´14´´ W). Borehole temperatures indicate near temperate ice, but the average melt percent is only 16% ± 14%. Records of stable isotopes are well preserved and were used for identification of annual layers. Net accumulation rates range from 3.4 to 7.1 water equivalent (m weq) with an average of 5.8 m weq, comparable to precipitation amounts at the Chilean coast, but not as high as expected for the Icefield. Ice core stable isotope data correlate well with upper air temperatures and may be used as temperature proxy.

  13. Frequencies of VNTR and RFLP polymorphisms associated with factor VIII gene in Singapore

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

    Fong, I.; Lai, P.S.; Ouah, T.C.

    1994-09-01

    The allelic frequency of any polymorphism within a population determines its usefulness for genetic counselling. This is important in populations of non-Caucasian origin as RFLPs may significantly differ among ethnic groups. We report a study of five intragenic polymorphisms in factor VIII gene carried out in Singapore. The three PCR-based RFLP markers studied were Intron 18/Bcl I, Intron 19/Hind III and Intron 22/Xba I. In an analysis of 148 unrelated normal X chromosomes, the allele frequencies were found to be A1 = 0.18, A2 = 0.82 (Bcl I RFLP), A1 = 0.80, A2 = 0.20 (Hind III RFLP) and A1more » = 0.58, and A2 = 0.42 (Xba I RFLP). The heterozygosity rates of 74 females analyzed separately were 31%, 32% and 84.2%, respectively. Linkage disequilibrium was also observed to some degree between Bcl I and Hind III polymorphism in our population. We have also analyzed a sequence polymorphism in Intron 7 using hybridization with radioactive-labelled {sup 32}P allele-specific oligonucleotide probes. This polymorphism was not very polymorphic in our population with only 2% of 117 individuals analyzed being informative. However, the use of a hypervariable dinucleotide repeat sequence (VNTR) in Intron 13 showed that 25 of our of 27 (93%) females were heterozygous. Allele frequencies ranged from 1 to 55 %. We conclude that a viable strategy for molecular analysis of Hemophilia A families in our population should include the use of Intron 18/Bcl I and Intron 22/Xba I RFLP markers and the Intron 13 VNTR marker.« less

  14. Frequency of 3' VNTR Polymorphism in the Dopamine Transporter Gene SLC6A3 in Humans Predisposed to Antisocial Behavior.

    PubMed

    Cherepkova, E V; Aftanas, L I; Maksimov, N; Menshanov, P N

    2016-11-01

    Predisposition to antisocial behavior can be related to the presence of certain polymorphic variants of genes encoding dopaminergic system proteins. We studied the frequencies of allele variants and genotypes of variable number tandem repeat polymorphism in 3' untranslated region (3' VTNR) of the dopaminergic transporter SLC6A3 gene in Caucasian men committed socially dangerous violent and non-violent crimes. Alleles with 9 and 10 repeats were most frequent in both the control group and group of men predisposed to antisocial behavior. At the same time, the 10/10 genotype was more frequently observed in the group of men prone to antisocial non-violent behavior. Hence, the presence of certain variants of 3' VTNR polymorphism of SLC6A3 gene in men is associated with predisposition to certain forms of antisocial behavior.

  15. Bilirubin UDP-Glucuronosyltransferase 1A1 (UGT1A1) Gene Promoter Polymorphisms and HPRT, Glycophorin A, and Micronuclei Mutant Frequencies in Human Blood

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

    Grant, D; Hall, I J; Eastmond, D

    2004-10-06

    A dinucleotide repeat polymorphism (5-, 6-, 7-, or 8-TA units) has been identified within the promoter region of UDP-glucuronosyltransferase 1A1 gene (UGT1A1). The 7-TA repeat allele has been associated with elevated serum bilirubin levels that cause a mild hyperbilirubinemia (Gilbert's syndrome). Studies suggest that promoter transcriptional activity of UGT1A1 is inversely related to the number of TA repeats and that unconjugated bilirubin concentration increases directly with the number of TA repeat elements. Because bilirubin is a known antioxidant, we hypothesized that UGT1A1 repeats associated with higher bilirubin may be protective against oxidative damage. We examined the effect of UGT1A1 genotypemore » on somatic mutant frequency in the hypoxanthine-guanine phosphoribosyl-transferase (HPRT) gene in human lymphocytes and the glycophorin A (GPA) gene of red blood cells (both N0, NN mutants), and the frequency of lymphocyte micronuclei (both kinetochore (K) positive or micronuclei K negative) in 101 healthy smoking and nonsmoking individuals. As hypothesized, genotypes containing 7-TA and 8-TA displayed marginally lower GPA{_}NN mutant frequency relative to 5/5, 5/6, 6/6 genotypes (p<0.05). In contrast, our analysis showed that lower expressing UGT1A1 alleles (7-TA and 8-TA) were associated with modestly increased HPRT mutation frequency (p<0.05) while the same low expression genotypes were not significantly associated with micronuclei frequencies (K-positive or K-negative) when compared to high expression genotypes (5-TA and 6-TA). We found weak evidence that UGT1A1 genotypes containing 7-TA and 8-TA were associated with increased GPA{_}N0 mutant frequency relative to 5/5, 5/6, 6/6 genotypes (p<0.05). These data suggest that UGT1A1 genotype may modulate somatic mutation of some types, in some cell lineages, by a mechanism not involving bilirubin antioxidant activity. More detailed studies examining UGT1A1 promoter variation, oxidant/antioxidant balance and

  16. A distributed network of low-cost continuous reading sensors to measure spatiotemporal variations of PM2.5 in Xi'an, China.

    PubMed

    Gao, Meiling; Cao, Junji; Seto, Edmund

    2015-04-01

    Fine particulate matter (PM2.5) is a growing public health concern especially in industrializing countries but existing monitoring networks are unable to properly characterize human exposures due to low resolution spatiotemporal data. Low-cost portable monitors can supplement existing networks in both developed and industrializing regions to increase density of sites and data. This study tests the performance of a low-cost sensor in high concentration urban environments. Seven Portable University of Washington Particle (PUWP) monitors were calibrated with optical and gravimetric PM2.5 reference monitors in Xi'an, China in December 2013. Pairwise correlations between the raw PUWP and the reference monitors were high (R(2) = 0.86-0.89). PUWP monitors were also simultaneously deployed at eight sites across Xi'an alongside gravimetric PM2.5 monitors (R(2) = 0.53). The PUWP monitors were able to identify the High-technology Zone site as a potential PM2.5 hotspot with sustained high concentrations compared to the city average throughout the day. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

  17. High frequency of genes' promoter methylation, but lack of BRAF V600E mutation among Iranian colorectal cancer patients.

    PubMed

    Naghibalhossaini, Fakhraddin; Hosseini, Hamideh Mahmoodzadeh; Mokarram, Pooneh; Zamani, Mozhdeh

    2011-12-01

    Gene silencing due to DNA hypermethylation is a major mechanism for loss of tumor suppressor genes function in colorectal cancer. Activating V600E mutation in BRAF gene has been linked with widespread methylation of CpG islands in sporadic colorectal cancers. The aim of the present study was to evaluate the methylation status of three cancer-related genes, APC2, p14ARF, and ECAD in colorectal carcinogenesis and their association with the mutational status of BRAF and KRAS among Iranian colorectal cancer patients. DNA from 110 unselected series of sporadic colorectal cancer patients was examined for BRAF V600E mutation by PCR-RFLP. Promoter methylation of genes in tumors was determined by methylation specific PCR. The frequency of APC2, E-CAD, and p14 methylation was 92.6%, 40.4% and 16.7%, respectively. But, no V600E mutation was identified in the BRAF gene in any sample. No association was found in cases showing epigenetic APC, ECAD, and p14 abnormality with the clinicopathological parameters under study. The association between KRAS mutations and the so called methylator phenotype was previously reported. Therefore, we also analyzed the association between the hot spot KRAS gene mutations in codons of 12 and 13 with genes' promoter hypermethylation in a subset of this group of patients. Out of 86 tumors, KRAS was mutated in 24 (28%) of tumors, the majority occurring in codon 12. KRAS mutations were not associated with genes' methylation in this tumor series. These findings suggest a distinct molecular pathway for methylation of APC2, p14, and ECAD genes from those previously described for colorectal cancers with BRAF or KRAS mutations.

  18. ISOLEUCINE AND VALINE METABOLISM IN ESCHERICHIA COLI XI. K-12

    PubMed Central

    Leavitt, Richard I.; Umbarger, H. E.

    1962-01-01

    Leavitt, Richard I. (Harvard Medical School, Boston, Mass.) and H. E. Umbarger. Isoleucine and valine metabolism in Escherichia coli. XI. Valine inhibition of the growth of Escherichia coli strain K-12. J. Bacteriol. 83:624–630. 1962.—The inhibition of the growth of Escherichia coli strain K-12 by valine was shown to be due to the sensitivity of the acetohydroxybutyrate-forming system to valine. It was demonstrated that both E. coli strain W, a strain whose growth is unaffected by valine, and a valine-resistant mutant of strain K-12 have acetolactate- and acetohydroxybutyrate-forming systems which are less sensitive to valine than that of strain K-12. It was further shown that α-aminobutyrate accumulates in the culture fluid of the valine-sensitive strain when incubated in the presence of valine. The levels of valine in the “free amino acid pool” were examined and found to be related to the differences in valine sensitivity of the acetolactate-forming systems of the three strains. PMID:14463257

  19. Frequency sensitive mechanism in low-intensity ultrasound enhanced bioeffects

    PubMed Central

    Chama, Abdoulkadri; Subramanian, Anuradha; Viljoen, Hendrik J.

    2017-01-01

    This study presents two novel theoretical models to elucidate frequency sensitive nuclear mechanisms in low-intensity ultrasound enhanced bioeffects. In contrast to the typical 1.5 MHz pulsed ultrasound regime, our group previously experimentally confirmed that ultrasound stimulation of anchored chondrocytes at resonant frequency maximized gene expression of load inducible genes which are regulatory markers for cellular response to external stimuli. However, ERK phosphorylation displayed no frequency dependency, suggesting that the biochemical mechanisms involved in enhanced gene expression is downstream of ERK phosphorylation. To elucidate such underlying mechanisms, this study presents a theoretical model of an anchored cell, representing an in vitro chondrocyte, in an ultrasound field. The model results showed that the mechanical energy storage is maximized at the chondrocyte’s resonant frequency and the energy density in the nucleus is almost twice as high as in the cytoplasm. Next, a mechanochemical model was developed to link the mechanical stimulation of ultrasound and the increased mechanical energy density in the nucleus to the downstream targets of the ERK pathway. This study showed for the first time that ultrasound stimulation induces frequency dependent gene expression as a result of altered rates of transcription factors binding to chromatin. PMID:28763448

  20. C677T (RS1801133 ) MTHFR gene polymorphism frequency in a colombian population

    PubMed Central

    Gómez-Gutierrez, Alberto; Gómez, Piedad Elena; Casas-Gomez, Maria Consuelo; Briceño, Ignacio

    2015-01-01

    Introduction: Abnormal levels of the enzyme methylenetetrahydrofolate reductase (MTHFR) are associated with an increased risk of both cardiovascular and cerebrovascular disease and higher concentrations of homocysteine. Abnormal levels are also related to birth defects, pregnancy complications, cancer and toxicity to methotrexate (MTX). Polymorphisms of MTHFR affect the activity of the enzyme. Genetic associations have been related to treatment efficacy. Objective: To establish the frequency of the C> T polymorphism at nucleotide 677 of the MTHFR gene in a group of Colombian individuals. Methods: Data from pharmacogenetic microarrays that include MTX sensibility-associated polymorphisms were retrospectively collected (Pathway Genomics®). The frequency of the C> T MTHFR rs1801133 marker polymorphism was analyzed. Results: Microarray data from 68 men and 84 women were analyzed. Comparisons of genotype C/C vs. C/T and T/T were statistically significantly different (p= 0.00, p= 0.026, respectively), as were C/T and T / T (p= 0.0001). Conclusions: Results for the C/C and C/T genotypes in a Colombian population are similar to other previously studied groups of healthy subjects. Subjects from our population might be at risk of developing diseases associated with MTHFR polymorphisms and might present toxicity and adverse effects if treated with MTX, which suggests the need to evaluate therapeutic alternatives based on individual pharmacogenetic studies. PMID:26309343

  1. Prevalence and Correlates of School Bullying Victimization in Xi'an, China.

    PubMed

    Zhu, Yuhong; Chan, Ko Ling

    2015-01-01

    This study used the data from a representative sample to estimate the prevalence of child bullying victimization in Xi'an, China. Data on social demographic information and the experiences of different types of bullying victimization were collected from a randomly selected sample with 3,175 middle school students aged 15-17 years by self-administrated questionnaires. t Test, χ2 test, and multiple logistic regression analyses were used to test group differences and examine the correlates of bullying victimization. Results show that 54.9% and 44.6% of Chinese children have been bullied in a lifetime and in the preceding year, respectively. Correlates for direct and relational bullying victimization includes male participants, father's lower education level, father's unemployment, having one or more siblings, smoking, depression, borderline personality trait, posttraumatic stress disorder, and from rural schools. Overall, the prevalence of child bullying victimization in China is substantial. The multiple correlates suggest prevention and intervention of bullying victimization in a holistic and comprehensive way.

  2. Decoding the principles underlying the frequency of association with nucleoli for RNA polymerase III-transcribed genes in budding yeast.

    PubMed

    Belagal, Praveen; Normand, Christophe; Shukla, Ashutosh; Wang, Renjie; Léger-Silvestre, Isabelle; Dez, Christophe; Bhargava, Purnima; Gadal, Olivier

    2016-10-15

    The association of RNA polymerase III (Pol III)-transcribed genes with nucleoli seems to be an evolutionarily conserved property of the spatial organization of eukaryotic genomes. However, recent studies of global chromosome architecture in budding yeast have challenged this view. We used live-cell imaging to determine the intranuclear positions of 13 Pol III-transcribed genes. The frequency of association with nucleolus and nuclear periphery depends on linear genomic distance from the tethering elements-centromeres or telomeres. Releasing the hold of the tethering elements by inactivating centromere attachment to the spindle pole body or changing the position of ribosomal DNA arrays resulted in the association of Pol III-transcribed genes with nucleoli. Conversely, ectopic insertion of a Pol III-transcribed gene in the vicinity of a centromere prevented its association with nucleolus. Pol III-dependent transcription was independent of the intranuclear position of the gene, but the nucleolar recruitment of Pol III-transcribed genes required active transcription. We conclude that the association of Pol III-transcribed genes with the nucleolus, when permitted by global chromosome architecture, provides nucleolar and/or nuclear peripheral anchoring points contributing locally to intranuclear chromosome organization. © 2016 Belagal et al. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  3. The frequency of previously undetectable deletions involving 3' Exons of the PMS2 gene.

    PubMed

    Vaughn, Cecily P; Baker, Christine L; Samowitz, Wade S; Swensen, Jeffrey J

    2013-01-01

    Lynch syndrome is characterized by mutations in one of four mismatch repair genes, MLH1, MSH2, MSH6, or PMS2. Clinical mutation analysis of these genes includes sequencing of exonic regions and deletion/duplication analysis. However, detection of deletions and duplications in PMS2 has previously been confined to Exons 1-11 due to gene conversion between PMS2 and the pseudogene PMS2CL in the remaining 3' exons (Exons 12-15). We have recently described an MLPA-based method that permits detection of deletions of PMS2 Exons 12-15; however, the frequency of such deletions has not yet been determined. To address this question, we tested for 3' deletions in 58 samples that were reported to be negative for PMS2 mutations using previously available methods. All samples were from individuals whose tumors exhibited loss of PMS2 immunohistochemical staining without concomitant loss of MLH1 immunostaining. We identified seven samples in this cohort with deletions in the 3' region of PMS2, including three previously reported samples with deletions of Exons 13-15 (two samples) and Exons 14-15. Also detected were deletions of Exons 12-15, Exon 13, and Exon 14 (two samples). Breakpoint analysis of the intragenic deletions suggests they occurred through Alu-mediated recombination. Our results indicate that ∼12% of samples suspected of harboring a PMS2 mutation based on immunohistochemical staining, for which mutations have not yet been identified, would benefit from testing using the new methodology. Copyright © 2012 Wiley Periodicals, Inc.

  4. VizieR Online Data Catalog: xi Tau UBV and MOST light curves (Nemravova+, 2016)

    NASA Astrophysics Data System (ADS)

    Nemravova, J. A.; Harmanec, P.; Broz, M.; Vokrouhlicky, D.; Mourard, D.; Hummel, C. A.; Cameron, C.; Matthews, J. M.; Bolton, C. T.; Bozic, H.; Chini, R.; Dembsky, T.; Engle, S.; Farrington, C.; Grunhut, J. H.; Guenther, D. B.; Guinan, E. F.; Korcakova, D.; Koubsky, P.; Kiek, R.; Kuschnig, R.; Mayer, P.; McCook, G. P.; Moffat, A. F. J.; Nardetto, N.; Pra, A.; Ribeiro, J.; Rowe, J.; Rucinski, S.; Skoda, P.; Slechta, M.; Tallon-Bosc, I.; Votruba, V.; Weiss, W. W.; Wolf, M.; Zasche, P.; Zavala, R. T.

    2016-05-01

    We present reduced observations, that were used in study of the quadruple hierarchical binary xi Tauri. The observational material consists of radial-velocity measurements (tabled1.dat), photometric measurements in the MOST filter (tabled2.dat), and Johnson's U (tabled3.dat), B (tabled4.dat), and V (tabled5.dat), and spectro-interferometric measurements represented by squared visibility moduli (tabled6.dat), and closure phases (tabled7.dat). The~description of the reductions is given in Appendices A (the spectroscopy), B (the photometry), and C (the spectro-interferometry). The procedure of radial-velocity measuring is described in Sect. 3.1. Headers of Tables D.1-D.7 published electronically are also given in Appendix D. (7 data files).

  5. Heterologous expression of Spathaspora passalidarum xylose reductase and xylitol dehydrogenase genes improved xylose fermentation ability of Aureobasidium pullulans.

    PubMed

    Guo, Jian; Huang, Siyao; Chen, Yefu; Guo, Xuewu; Xiao, Dongguang

    2018-04-30

    Aureobasidium pullulans is a yeast-like fungus that can ferment xylose to generate high-value-added products, such as pullulan, heavy oil, and melanin. The combinatorial expression of two xylose reductase (XR) genes and two xylitol dehydrogenase (XDH) genes from Spathaspora passalidarum and the heterologous expression of the Piromyces sp. xylose isomerase (XI) gene were induced in A. pullulans to increase the consumption capability of A. pullulans on xylose. The overexpression of XYL1.2 (encoding XR) and XYL2.2 (encoding XDH) was the most beneficial for xylose utilization, resulting in a 17.76% increase in consumed xylose compared with the parent strain, whereas the introduction of the Piromyces sp. XI pathway failed to enhance xylose utilization efficiency. Mutants with superior xylose fermentation performance exhibited increased intracellular reducing equivalents. The fermentation performance of all recombinant strains was not affected when glucose or sucrose was utilized as the carbon source. The strain with overexpression of XYL1.2 and XYL2.2 exhibited excellent fermentation performance with mimicked hydrolysate, and pullulan production increased by 97.72% compared with that of the parent strain. The present work indicates that the P4 mutant (using the XR/XDH pathway) with overexpressed XYL1.2 and XYL2.2 exhibited the best xylose fermentation performance. The P4 strain showed the highest intracellular reducing equivalents and XR and XDH activity, with consequently improved pullulan productivity and reduced melanin production. This valuable development in aerobic fermentation by the P4 strain may provide guidance for the biotransformation of xylose to high-value products by A. pullulans through genetic approach.

  6. Bacterial xylose isomerases from the mammal gut Bacteroidetes cluster function in Saccharomyces cerevisiae for effective xylose fermentation.

    PubMed

    Peng, Bingyin; Huang, Shuangcheng; Liu, Tingting; Geng, Anli

    2015-05-17

    Xylose isomerase (XI) catalyzes the conversion of xylose to xylulose, which is the key step for anaerobic ethanolic fermentation of xylose. Very few bacterial XIs can function actively in Saccharomyces cerevisiae. Here, we illustrate a group of XIs that would function for xylose fermentation in S. cerevisiae through phylogenetic analysis, recombinant yeast strain construction, and xylose fermentation. Phylogenetic analysis of deposited XI sequences showed that XI evolutionary relationship was highly consistent with the bacterial taxonomic orders and quite a few functional XIs in S. cerevisiae were clustered with XIs from mammal gut Bacteroidetes group. An XI from Bacteroides valgutus in this cluster was actively expressed in S. cerevisiae with an activity comparable to the fungal XI from Piromyces sp. Two XI genes were isolated from the environmental metagenome and they were clustered with XIs from environmental Bacteroidetes group. These two XIs could not be expressed in yeast with activity. With the XI from B. valgutus expressed in S. cerevisiae, background yeast strains were optimized by pentose metabolizing pathway enhancement and adaptive evolution in xylose medium. Afterwards, more XIs from the mammal gut Bacteroidetes group, including those from B. vulgatus, Tannerella sp. 6_1_58FAA_CT1, Paraprevotella xylaniphila and Alistipes sp. HGB5, were individually transformed into S. cerevisiae. The known functional XI from Orpinomyces sp. ukk1, a mammal gut fungus, was used as the control. All the resulting recombinant yeast strains were able to ferment xylose. The respiration-deficient strains harboring B. vulgatus and Alistipes sp. HGB5 XI genes respectively obtained specific xylose consumption rate of 0.662 and 0.704 g xylose gcdw(-1) h(-1), and ethanol specific productivity of 0.277 and 0.283 g ethanol gcdw(-1) h(-1), much comparable to those obtained by the control strain carrying Orpinomyces sp. ukk1 XI gene. This study demonstrated that XIs clustered in the

  7. Avirulence (AVR) Gene-Based Diagnosis Complements Existing Pathogen Surveillance Tools for Effective Deployment of Resistance (R) Genes Against Rice Blast Disease.

    PubMed

    Selisana, S M; Yanoria, M J; Quime, B; Chaipanya, C; Lu, G; Opulencia, R; Wang, G-L; Mitchell, T; Correll, J; Talbot, N J; Leung, H; Zhou, B

    2017-06-01

    Avirulence (AVR) genes in Magnaporthe oryzae, the fungal pathogen that causes the devastating rice blast disease, have been documented to be major targets subject to mutations to avoid recognition by resistance (R) genes. In this study, an AVR-gene-based diagnosis tool for determining the virulence spectrum of a rice blast pathogen population was developed and validated. A set of 77 single-spore field isolates was subjected to pathotype analysis using differential lines, each containing a single R gene, and classified into 20 virulent pathotypes, except for 4 isolates that lost pathogenicity. In all, 10 differential lines showed low frequency (<24%) of resistance whereas 8 lines showed a high frequency (>95%), inferring the effectiveness of R genes present in the respective differential lines. In addition, the haplotypes of seven AVR genes were determined by polymerase chain reaction amplification and sequencing, if applicable. The calculated frequency of different AVR genes displayed significant variations in the population. AVRPiz-t and AVR-Pii were detected in 100 and 84.9% of the isolates, respectively. Five AVR genes such as AVR-Pik-D (20.5%) and AVR-Pik-E (1.4%), AVRPiz-t (2.7%), AVR-Pita (0%), AVR-Pia (0%), and AVR1-CO39 (0%) displayed low or even zero frequency. The frequency of AVR genes correlated almost perfectly with the resistance frequency of the cognate R genes in differential lines, except for International Rice Research Institute-bred blast-resistant lines IRBLzt-T, IRBLta-K1, and IRBLkp-K60. Both genetic analysis and molecular marker validation revealed an additional R gene, most likely Pi19 or its allele, in these three differential lines. This can explain the spuriously higher resistance frequency of each target R gene based on conventional pathotyping. This study demonstrates that AVR-gene-based diagnosis provides a precise, R-gene-specific, and differential line-free assessment method that can be used for determining the virulence spectrum of

  8. Frequency of V1016I and F1534C mutations in the voltage-gated sodium channel gene in Aedes aegypti in Venezuela.

    PubMed

    Alvarez, Leslie C; Ponce, Gustavo; Saavedra-Rodriguez, Karla; Lopez, Beatriz; Flores, Adriana E

    2015-06-01

    The V1016I and F1534C mutations in the voltage-gated sodium channel gene have been associated with resistance to pyrethroids and DDT in Aedes aegypti mosquitoes. A study was carried out to determine the frequency of I1016 and C1534 by real-time PCR in five natural populations of Ae. aegypti in Venezuela during 2008, 2010 and 2012, as well as in a strain selected with 0.14 µg of deltamethrin for 15 generations. In natural populations, frequencies of I1016 varied between 0.01 and 0.37, and frequencies of C1534 between 0.35 and 1.0. In the Pampanito strain, the frequency of I1016 increased from 0.02 in F1 up to 0.5 in F15 and from 0.35 up to fixation for C1534 after selection with deltamethrin. The results showed that C1534 frequencies are higher than I1016 frequencies in natural populations of Ae. aegypti in Venezuela, and that deltamethrin selected the C1534 more rapidly than I1016. © 2014 Society of Chemical Industry.

  9. Comparison of oxidative stress and the frequency of polymorphisms in the HFE gene between hemoglobin S trait blood donors and sickle cell disease patients.

    PubMed

    Viana-Baracioli, L M S; Tukamoto Junior, N C; Ricci Junior, O; Mattos, L C; Ângulo, I L; Bonini-Domingos, C R

    2011-12-08

    It is well documented that Hb S and iron affect blood cells, and trigger oxidative processes and generation of free radicals with potential for lipid peroxidation. We evaluated the frequency of polymorphisms in the HFE gene in Hb AS blood donors and how these polymorphisms influenced lipid peroxidation and antioxidant capacity. Blood samples were collected from 211 Hb AS blood donors, 119 Hb AA blood donors as a control group, and 28 sickle cell disease patients (Hb SS). The H63D allele was found at a frequency of 10.5% in the Hb AS samples, and the C282Y allele frequency was 0.7%. In the control group, the frequencies of the H63D and C282Y alleles were 13.4 and 2.1%, respectively. In the sickle-cell disease patients, the H63D and the C282Y allele frequencies were 10.7 and 3.5%, respectively. The frequencies of the C282Y and H63D polymorphisms in Hb AS blood donors are similar to those reported for the Brazilian population. Serum malondialdehyde values, indicative of lipid peroxidation, were highest in sickle cell patients, independent of the polymorphisms in the HFE gene, with significant differences, showing the influence of Hb S allele in the levels of lipid peroxidation. However, the trolox equivalent antioxidant capacity average levels, indicative of the antioxidant capacity, were reduced with significant differences, indicating that in spite of a lipid peroxidation raise, this is not followed by the increased of the antioxidant capacity, leading to oxidative stress.

  10. Indoor phthalate concentration and exposure in residential and office buildings in Xi'an, China

    NASA Astrophysics Data System (ADS)

    Wang, Xinke; Tao, Wei; Xu, Ying; Feng, Jiangtao; Wang, Fenghao

    2014-04-01

    Indoor phthalate levels were investigated in 28 buildings, including 14 office and 14 residential buildings in Xi'an, China. Phthalate esters in the gas-, particle-, and dust- phase were measured separately. Four phthalates including dimethyl phthalate (DMP), diisobutyl phthalate (DiBP), di-n-butyl phthalate (DnBP) and di(2-ethylhexyl) phthalate (DEHP) were detected. The detection frequency of DnBP and DEHP was more than 90%. The concentrations of total phthalate esters ranged from 0.20 to 8.29 μg m-3 for the gas- phase, from 0.09 to 14.77 μg m-3 for the particle- phase and from 123 to 9504 μg g-1 for the dust- phase. The individual phthalate with the highest concentrations of 6.17 μg m-3, 7.97 μg m-3 and 7228 μg g-1 respectively for gas-, particle- and dust- phase in all investigated rooms is all DiBP. The median concentration of the gas- and particle-phase DiBP (0.52 and 0.72 μg m-3) and dust-phase DEHP (582 μg g-1) were the highest. It was also found that the average concentrations of individual phthalates in residential buildings were often higher than in office buildings, and correlation analysis indicated that DiBP, DnBP and DEHP might come from the same sources. Based on the gas- and particle-phase concentrations measured, the particle-air partition coefficients of phthalates were estimated, and their logarithm values were found to be linearly correlated with the logarithm values of their octanol-air partition coefficients. Finally, the total daily exposure to indoor phthalates in air and dust was calculated, and ranged from 2.6 μg kg-1 day-1 (for adults) to 7.4 μg kg-1 day-1 (for toddlers).

  11. Neurotic disorders of general medical outpatients in Xi'an, China: knowledge, attitudes, and help-seeking preferences.

    PubMed

    Ni, Chunping; Ma, Lihua; Wang, Bo; Yan, Yongping; Huang, Yueqin; Wallen, Gwenyth R; Li, Lu; Lang, Hongjuan; Hua, Qianzhen

    2014-08-01

    This study assessed knowledge of neurotic disorders, and attitudes and preferences toward professional help and treatment for them, among general medical outpatients in general hospitals in Xi'an, China. General medical outpatients (N=372) from general hospitals in China were recruited by using a stratified cluster sampling method between June and September 2010. In face-to-face interviews, participants age 16 years or older were assessed for their knowledge, attitudes, and help-seeking preferences in regard to neurotic disorders (obsessive-compulsive disorder, social phobia, and panic disorder). Demographic data were also collected. Lack of insight into neurotic disorders was common among medical outpatients in general hospitals of Xi'an, China. Twenty-four percent to 58% of the outpatients had some knowledge of the symptoms and treatment of neurotic disorders. Only 11% of the outpatients would reveal to others that they or a family member suffered from neurotic disorders. When faced with the problem of neurotic disorders, the preference of the respondents was to visit a psychiatrist in a general hospital (44%), and only 17% would visit a physician in a psychiatric hospital. Major ways for the outpatients to obtain knowledge regarding neurotic disorders were via radio and television (36%), and only 18%-23% of outpatients obtained knowledge about neurotic disorders through printed public health materials and by attending lectures. Study results underscore the need for information campaigns aimed at improving the mental health literacy of general medical outpatients. Such campaigns must consider culturally relevant beliefs to facilitate the development of specific educational programs.

  12. Optical properties and possible sources of brown carbon in PM2.5 over Xi'an, China

    NASA Astrophysics Data System (ADS)

    Shen, Zhenxing; Zhang, Qian; Cao, Junji; Zhang, Leiming; Lei, Yali; Huang, Yu; Huang, R.-J.; Gao, Jinjin; Zhao, Zhuzi; Zhu, Chongshu; Yin, Xiuli; Zheng, Chunli; Xu, Hongmei; Liu, Suixin

    2017-02-01

    To quantify optical and chemical properties of PM2.5 brown carbon (BrC) in Xi'an, 58 high-volume ambient PM2.5 samples were collected during 2 November 2009 to 13 October 2010. Mass concentrations of chemical components were determined, including water-soluble ions, water-soluble organic carbon, levoglucosan, organic carbon (OC), and element carbon (EC). BrC, as an unidentified and wavelength-dependent organic compound, was also measured from water-soluble carbon (WSOC) at 340 nm using UV-vis spectrometer. The wavelength-dependent absorption coefficient (babs) and mass absorption coefficient (MAC) were much abundant at 340 nm, and the high Absorption Ångström coefficient (AAC) values were observed around 5.4, corresponding to the existence of BrC in ambient PM2.5, especially in winter. Good correlations (R > 0.60) between babs and biomass burning markers, such as levoglucosan and K+, in winter indicated significant amounts of primary BrC from biomass burning emissions. Secondary organic carbon BrC (SOCsbnd BrC) was more abundant in winter than in summer. SOCsbnd BrC in winter was mainly fresh SOC formed from aqueous phase reactions while in summer, aged SOC from photo-chemical formation. Source profiles of BrC optical parameters were detected, which verified sources of BrC from biomass burning and coal burning emissions in areas surrounding Xi'an. The rapidly decreasing babs-340nm values from biomass burning smoldering to straw pellet burning suggested that burning straw pellet instead of burning straw directly is an effective measure for reducing BrC emissions.

  13. Microscale spatial distribution and health assessment of PM2.5-bound polycyclic aromatic hydrocarbons (PAHs) at nine communities in Xi'an, China.

    PubMed

    Xu, Hongmei; Ho, Steven Sai Hang; Gao, Meiling; Cao, Junji; Guinot, Benjamin; Ho, Kin Fai; Long, Xin; Wang, Jingzhi; Shen, Zhenxing; Liu, Suixin; Zheng, Chunli; Zhang, Qian

    2016-11-01

    Spatial variability of polycyclic aromatic hydrocarbons (PAHs) associated with fine particulate matter (PM 2.5 ) was investigated in Xi'an, China, in summer of 2013. Sixteen priority PAHs were quantified in 24-h integrated air samples collected simultaneously at nine urban and suburban communities. The total quantified PAHs mass concentrations ranged from 32.4 to 104.7 ng m -3 , with an average value of 57.1 ± 23.0 ng m -3 . PAHs were observed higher concentrations at suburban communities (average: 86.3 ng m -3 ) than at urban ones (average: 48.8 ng m -3 ) due to a better enforcement of the pollution control policies at the urban scale, and meanwhile the disorganized management of motor vehicles and massive building constructions in the suburbs. Elevated PAH levels were observed in the industrialized regions (west and northwest of Xi'an) from Kriging interpolation analysis. Satellite-based visual interpretations of land use were also applied for the supporting the spatial distribution of PAHs among the communities. The average benzo[a]pyrene-equivalent toxicity (Σ[BaP] eq ) at the nine communities was 6.9 ± 2.2 ng m -3 during the sampling period, showing a generally similar spatial distribution to PAHs levels. On average, the excess inhalation lifetime cancer risk derived from Σ[BaP] eq indicated that eight persons per million of community residents would develop cancer due to PM 2.5 -bound PAHs exposure in Xi'an. The great in-city spatial variability of PAHs confirmed the importance of multiple points sampling to conduct exposure health risk assessment. Copyright © 2016 Elsevier Ltd. All rights reserved.

  14. Comparison of CpG island methylator phenotype (CIMP) frequency in colon cancer using different probe- and gene-specific scoring alternatives on recommended multi-gene panels.

    PubMed

    Berg, Marianne; Hagland, Hanne R; Søreide, Kjetil

    2014-01-01

    In colorectal cancer a distinct subgroup of tumours demonstrate the CpG island methylator phenotype (CIMP). However, a consensus of how to score CIMP is not reached, and variation in definition may influence the reported CIMP prevalence in tumours. Thus, we sought to compare currently suggested definitions and cut-offs for methylation markers and how they influence CIMP classification in colon cancer. Methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA), with subsequent fragment analysis, was used to investigate methylation of tumour samples. In total, 31 CpG sites, located in 8 different genes (RUNX3, MLH1, NEUROG1, CDKN2A, IGF2, CRABP1, SOCS1 and CACNA1G) were investigated in 64 distinct colon cancers and 2 colon cancer cell lines. The Ogino gene panel includes all 8 genes, in addition to the Weisenberger panel of which only 5 of the 8 genes included were investigated. In total, 18 alternative combinations of scoring of CIMP positivity on probe-, gene-, and panel-level were analysed and compared. For 47 samples (71%), the CIMP status was constant and independent of criteria used for scoring; 34 samples were constantly scored as CIMP negative, and 13 (20%) consistently scored as CIMP positive. Only four of 31 probes (13%) investigated showed no difference in the numbers of positive samples using the different cut-offs. Within the panels a trend was observed that increasing the gene-level stringency resulted in a larger difference in CIMP positive samples than increasing the probe-level stringency. A significant difference between positive samples using 'the most stringent' as compared to 'the least stringent' criteria (20% vs 46%, respectively; p<0.005) was demonstrated. A statistical significant variation in the frequency of CIMP depending on the cut-offs and genes included in a panel was found, with twice as many positives samples by least compared to most stringent definition used.

  15. Next generation sequencing to dissect the genetic architecture of KNG1 and F11 loci using factor XI levels as an intermediate phenotype of thrombosis.

    PubMed

    Martin-Fernandez, Laura; Gavidia-Bovadilla, Giovana; Corrales, Irene; Brunel, Helena; Ramírez, Lorena; López, Sonia; Souto, Juan Carlos; Vidal, Francisco; Soria, José Manuel

    2017-01-01

    Venous thromboembolism is a complex disease with a high heritability. There are significant associations among Factor XI (FXI) levels and SNPs in the KNG1 and F11 loci. Our aim was to identify the genetic variation of KNG1 and F11 that might account for the variability of FXI levels. The KNG1 and F11 loci were sequenced completely in 110 unrelated individuals from the GAIT-2 (Genetic Analysis of Idiopathic Thrombophilia 2) Project using Next Generation Sequencing on an Illumina MiSeq. The GAIT-2 Project is a study of 935 individuals in 35 extended Spanish families selected through a proband with idiopathic thrombophilia. Among the 110 individuals, a subset of 40 individuals was chosen as a discovery sample for identifying variants. A total of 762 genetic variants were detected. Several significant associations were established among common variants and low-frequency variants sets in KNG1 and F11 with FXI levels using the PLINK and SKAT packages. Among these associations, those of rs710446 and five low-frequency variant sets in KNG1 with FXI level variation were significant after multiple testing correction and permutation. Also, two putative pathogenic mutations related to high and low FXI levels were identified by data filtering and in silico predictions. This study of KNG1 and F11 loci should help to understand the connection between genotypic variation and variation in FXI levels. The functional genetic variants should be useful as markers of thromboembolic risk.

  16. Asymmetry Studies in the Production of $$\\Lambda^0/\\bar \\Lambda^0$$, $$\\Xi^-/\\bar{\\Xi}^+$$ and $$\\Omega^-/\\bar{\\Omega}^+$$ Hyperons in 500 GeV/c $$\\pi^-$$ - Nucleon Interactions (in Portuguese)

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

    Solano Salinas, Carlos Javier

    Using data from fprmilab fixed-target experiment E791, we have measmed for the first time particle/antiparticle production asymmetries formore » $$\\Lambda^0 \\Xi^-$$ and $$\\Omega^-$$ hyperons in $$\\pi^-$$nucleon interactions at 500 GeV /c as joint functions of $$x_F$$ and $$p^2_{\\tau}$$ over the ranges $$-0.12 \\le x_F \\le 0.12$$ and $$0 \\le p^2_{\\tau} \\le 4 (GeV/c)^2$$. There is now direct evidence of a basic asymmetry, even at $$x_F$$ = 0.0, which may be due to associated production. In addition, there are leading-particle-type effects which are qualitativrly like what one would expect from rrcmnbination models or their alternatives. WP used the Dnal Parton Model (DPM) to cakulate the asymmetry for the $$\\Lambda^0$$ and compared with the Lund model (PYTHIA /JETSET) predictions and with om experimental results.« less

  17. blaOXA-23-like and blaTEM rather than blaOXA-51-like contributed to a high level of carbapenem resistance in Acinetobacter baumannii strains from a teaching hospital in Xi'an, China.

    PubMed

    Han, Lei; Lei, Jine; Xu, Jiru; Han, Shaoshan

    2017-12-01

    Acinetobacter baumannii is one of the major threats in clinical infections due to its antibiotic resistance ability. It shows increasing resistance to carbapenems, mainly due to β-lactamase mediated mechanisms. The aim of this study was to investigate carbapenem resistance (CR) profiles and analyze β-lactamases genes composition of clinical A. baumannii strains from a teaching hospital in Xi'an. The resistance patterns to imipenem and meropenem were checked for 51 clinical A. baumannii strains. The existence of 15 β-lactamases genes was detected by polymerase chain reaction (PCR), and the positive genes were sequenced. The correlation between PCR-positive genes and CR phenotype was analyzed using Chi-square test and contingency coefficient. The expressions of PCR-positive genes were investigated. Forty-five out of 51 strains were resistant to imipenem and meropenem. blaTEM, blaOXA-23-like, and blaOXA-51-like were positive among 15 β-lactamases genes, and TEM-1, OXA-23, and OXA-66/69 were their subtypes. TEM and OXA-23-like only showed up in CR isolates, with the occurrence rate of 91.1% and 97.8%, respectively, whereas OXA-51-like appeared in all strains. ISAba1 was present in the upstream of OXA-23-like, but absent from that of OXA-51-like in our strains. OXA-23-like had highest relationship with CR, followed by TEM, but OXA-51-like had no correlation. This was verified by RT-qPCR that the expression was positive for OXA-23 and TEM-1, but negative for OXA-66/-69. A high rate of CR A. baumannii was detected in this study. Coexistence of TEM, OXA-23-like, and OXA-51-like was the primary resistance profile. The expressions of OXA-23-like and TEM genes were closely related with CR, while OXA-51-like had no contribution to the CR phenotype.

  18. Spectrum and Frequency of the GJB2 Gene Pathogenic Variants in a Large Cohort of Patients with Hearing Impairment Living in a Subarctic Region of Russia (the Sakha Republic)

    PubMed Central

    Posukh, Olga L.; Teryutin, Fedor M.; Solovyev, Aisen V.; Klarov, Leonid A.; Romanov, Georgii P.; Gotovtsev, Nyurgun N.; Kozhevnikov, Andrey A.; Kirillina, Elena V.; Sidorova, Oksana G.; Vasilyevа, Lena M.; Fedotova, Elvira E.; Morozov, Igor V.; Bondar, Alexander A.; Solovyevа, Natalya A.; Kononova, Sardana K.; Rafailov, Adyum M.; Sazonov, Nikolay N.; Alekseev, Anatoliy N.; Tomsky, Mikhail I.; Dzhemileva, Lilya U.; Khusnutdinova, Elza K.; Fedorova, Sardana A.

    2016-01-01

    Pathogenic variants in the GJB2 gene, encoding connexin 26, are known to be a major cause of hearing impairment (HI). More than 300 allelic variants have been identified in the GJB2 gene. Spectrum and allelic frequencies of the GJB2 gene vary significantly among different ethnic groups worldwide. Until now, the spectrum and frequency of the pathogenic variants in exon 1, exon 2 and the flanking intronic regions of the GJB2 gene have not been described thoroughly in the Sakha Republic (Yakutia), which is located in a subarctic region in Russia. The complete sequencing of the non-coding and coding regions of the GJB2 gene was performed in 393 patients with HI (Yakuts—296, Russians—51, mixed and other ethnicities—46) and in 187 normal hearing individuals of Yakut (n = 107) and Russian (n = 80) populations. In the total sample (n = 580), we revealed 12 allelic variants of the GJB2 gene, 8 of which were recessive pathogenic variants. Ten genotypes with biallelic recessive pathogenic variants in the GJB2 gene (in a homozygous or a compound heterozygous state) were found in 192 out of 393 patients (48.85%). We found that the most frequent GJB2 pathogenic variant in the Yakut patients was c.-23+1G>A (51.82%) and that the second most frequent was c.109G>A (2.37%), followed by c.35delG (1.64%). Pathogenic variants с.35delG (22.34%), c.-23+1G>A (5.31%), and c.313_326del14 (2.12%) were found to be the most frequent among the Russian patients. The carrier frequencies of the c.-23+1G>A and с.109G>A pathogenic variants in the Yakut control group were 10.20% and 2.80%, respectively. The carrier frequencies of с.35delG and c.101T>C were identical (2.5%) in the Russian control group. We found that the contribution of the GJB2 gene pathogenic variants in HI in the population of the Sakha Republic (48.85%) was the highest among all of the previously studied regions of Asia. We suggest that extensive accumulation of the c.-23+1G>A pathogenic variant in the indigenous Yakut

  19. 77 FR 29633 - Alta Wind VII, LLC, Alta Wind IX, LLC, Alta Wind X, LLC, Alta Wind XI, LLC, Alta Wind XII, LLC...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-18

    ... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Docket No. EL12-68-000] Alta Wind VII, LLC, Alta Wind IX, LLC, Alta Wind X, LLC, Alta Wind XI, LLC, Alta Wind XII, LLC, Alta Wind XIII, LLC, Alta Wind XIV, LLC, Alta Wind XV, LLC, Alta Windpower Development, LLC, TGP Development Company, LLC...

  20. Lung Cancer Workshop XI: Tobacco-Induced Disease: Advances in Policy, Early Detection and Management.

    PubMed

    Mulshine, James L; Avila, Rick; Yankelevitz, David; Baer, Thomas M; Estépar, Raul San Jose; Ambrose, Laurie Fenton; Aldigé, Carolyn R

    2015-05-01

    The Prevent Cancer Foundation Lung Cancer Workshop XI: Tobacco-Induced Disease: Advances in Policy, Early Detection and Management was held in New York, NY on May 16 and 17, 2014. The two goals of the Workshop were to define strategies to drive innovation in precompetitive quantitative research on the use of imaging to assess new therapies for management of early lung cancer and to discuss a process to implement a national program to provide high quality computed tomography imaging for lung cancer and other tobacco-induced disease. With the central importance of computed tomography imaging for both early detection and volumetric lung cancer assessment, strategic issues around the development of imaging and ensuring its quality are critical to ensure continued progress against this most lethal cancer.

  1. The Number of Overlapping AID Hotspots in Germline IGHV Genes Is Inversely Correlated with Mutation Frequency in Chronic Lymphocytic Leukemia.

    PubMed

    Yuan, Chaohui; Chu, Charles C; Yan, Xiao-Jie; Bagnara, Davide; Chiorazzi, Nicholas; MacCarthy, Thomas

    2017-01-01

    The targeting of mutations by Activation-Induced Deaminase (AID) is a key step in generating antibody diversity at the Immunoglobulin (Ig) loci but is also implicated in B-cell malignancies such as chronic lymphocytic leukemia (CLL). AID has previously been shown to preferentially deaminate WRC (W = A/T, R = A/G) hotspots. WGCW sites, which contain an overlapping WRC hotspot on both DNA strands, mutate at much higher frequency than single hotspots. Human Ig heavy chain (IGHV) genes differ in terms of WGCW numbers, ranging from 4 for IGHV3-48*03 to as many as 12 in IGHV1-69*01. An absence of V-region mutations in CLL patients ("IGHV unmutated", or U-CLL) is associated with a poorer prognosis compared to "IGHV mutated" (M-CLL) patients. The reasons for this difference are still unclear, but it has been noted that particular IGHV genes associate with U-CLL vs M-CLL. For example, patients with IGHV1-69 clones tend to be U-CLL with a poor prognosis, whereas patients with IGHV3-30 tend to be M-CLL and have a better prognosis. Another distinctive feature of CLL is that ~30% of (mostly poor prognosis) patients can be classified into "stereotyped" subsets, each defined by HCDR3 similarity, suggesting selection, possibly for a self-antigen. We analyzed >1000 IGHV genes from CLL patients and found a highly significant statistical relationship between the number of WGCW hotspots in the germline V-region and the observed mutation frequency in patients. However, paradoxically, this correlation was inverse, with V-regions with more WGCW hotspots being less likely to be mutated, i.e., more likely to be U-CLL. The number of WGCW hotspots in particular, are more strongly correlated with mutation frequency than either non-overlapping (WRC) hotspots or more general models of mutability derived from somatic hypermutation data. Furthermore, this correlation is not observed in sequences from the B cell repertoires of normal individuals and those with autoimmune diseases.

  2. The Number of Overlapping AID Hotspots in Germline IGHV Genes Is Inversely Correlated with Mutation Frequency in Chronic Lymphocytic Leukemia

    PubMed Central

    Yuan, Chaohui; Chu, Charles C.; Yan, Xiao-Jie; Bagnara, Davide; Chiorazzi, Nicholas

    2017-01-01

    The targeting of mutations by Activation-Induced Deaminase (AID) is a key step in generating antibody diversity at the Immunoglobulin (Ig) loci but is also implicated in B-cell malignancies such as chronic lymphocytic leukemia (CLL). AID has previously been shown to preferentially deaminate WRC (W = A/T, R = A/G) hotspots. WGCW sites, which contain an overlapping WRC hotspot on both DNA strands, mutate at much higher frequency than single hotspots. Human Ig heavy chain (IGHV) genes differ in terms of WGCW numbers, ranging from 4 for IGHV3-48*03 to as many as 12 in IGHV1-69*01. An absence of V-region mutations in CLL patients (“IGHV unmutated”, or U-CLL) is associated with a poorer prognosis compared to “IGHV mutated” (M-CLL) patients. The reasons for this difference are still unclear, but it has been noted that particular IGHV genes associate with U-CLL vs M-CLL. For example, patients with IGHV1-69 clones tend to be U-CLL with a poor prognosis, whereas patients with IGHV3-30 tend to be M-CLL and have a better prognosis. Another distinctive feature of CLL is that ~30% of (mostly poor prognosis) patients can be classified into “stereotyped” subsets, each defined by HCDR3 similarity, suggesting selection, possibly for a self-antigen. We analyzed >1000 IGHV genes from CLL patients and found a highly significant statistical relationship between the number of WGCW hotspots in the germline V-region and the observed mutation frequency in patients. However, paradoxically, this correlation was inverse, with V-regions with more WGCW hotspots being less likely to be mutated, i.e., more likely to be U-CLL. The number of WGCW hotspots in particular, are more strongly correlated with mutation frequency than either non-overlapping (WRC) hotspots or more general models of mutability derived from somatic hypermutation data. Furthermore, this correlation is not observed in sequences from the B cell repertoires of normal individuals and those with autoimmune diseases. PMID

  3. Emerging Use of Gene Expression Microarrays in Plant Physiology

    DOE PAGES

    Wullschleger, Stan D.; Difazio, Stephen P.

    2003-01-01

    Microarrays have become an important technology for the global analysis of gene expression in humans, animals, plants, and microbes. Implemented in the context of a well-designed experiment, cDNA and oligonucleotide arrays can provide highthroughput, simultaneous analysis of transcript abundance for hundreds, if not thousands, of genes. However, despite widespread acceptance, the use of microarrays as a tool to better understand processes of interest to the plant physiologist is still being explored. To help illustrate current uses of microarrays in the plant sciences, several case studies that we believe demonstrate the emerging application of gene expression arrays in plant physiology weremore » selected from among the many posters and presentations at the 2003 Plant and Animal Genome XI Conference. Based on this survey, microarrays are being used to assess gene expression in plants exposed to the experimental manipulation of air temperature, soil water content and aluminium concentration in the root zone. Analysis often includes characterizing transcript profiles for multiple post-treatment sampling periods and categorizing genes with common patterns of response using hierarchical clustering techniques. In addition, microarrays are also providing insights into developmental changes in gene expression associated with fibre and root elongation in cotton and maize, respectively. Technical and analytical limitations of microarrays are discussed and projects attempting to advance areas of microarray design and data analysis are highlighted. Finally, although much work remains, we conclude that microarrays are a valuable tool for the plant physiologist interested in the characterization and identification of individual genes and gene families with potential application in the fields of agriculture, horticulture and forestry.« less

  4. Detection of maltose fermentation genes in the baking yeast strains of Saccharomyces cerevisiae.

    PubMed

    Oda, Y; Tonomura, K

    1996-10-01

    The presence of any one of the five unlinked MAL loci (MAL1, MAL2, MAL3, MAL4 and MAL6) confers the ability to ferment maltose on the yeast Saccharomyces cerevisiae. Each locus is composed of three genes encoding maltose permease, alpha-glucosidase and MAL activator. Chromosomal DNA of seven representative baking strains has been separated by pulse-field gel electrophoresis and probed with three genes in MAL6 locus. The DNA bands to which all of the three MAL-derived probes simultaneously hybridized were chromosome VII carrying MAL1 in all of the strains tested, chromosome XI carrying MAL4 in six strains, chromosome III carrying MAL2 in three strains and chromosomes II and VIII carrying MAL3 and MAL6, respectively, in the one strain. The number of MAL loci in baking strains was comparable to those of brewing strains.

  5. Allele frequency and genotype distribution of polymorphisms within disease-related genes is influenced by ethnic population sub-structuring in Sudan.

    PubMed

    Bereir, R E H; Mohamed, H S; Seielstad, M; El Hassani, A M; Khalil, E A G; Peacock, C S; Blackwell, J M; Ibrahim, M E

    2003-09-01

    Four single nucleotide polymorphisms (SNPs) and a variable number of tandem repeats (VNTR) polymorphism located within disease associated/causing genes were typed in four populations of different tribal and ethnic affiliation from the Sudan. The genotype and allele frequencies were compared with those of other groups from published and unpublished data of world populations. The combined Sudanese sample conformed with Hardy-Weinberg equilibrium (HWE) expectation. However, population sub-structuring according to ethnic/linguistic group indicated at least two SNPs in departure from HWE. Differences in allele frequencies and genotype distribution between groups was also noted in three of the four SNPs. The other loci were distributed homogeneously within the populations studied with genotype frequencies in agreement with HWE expectation. These results highlight the importance of inter-population stratification for polymorphic markers, as well as the potential influence of evolutionary history and ethnic variation of loci, in the general distribution of SNPs and other polymorphisms.

  6. l-Arabinose Isomerase and d-Xylose Isomerase from Lactobacillus reuteri: Characterization, Coexpression in the Food Grade Host Lactobacillus plantarum, and Application in the Conversion of d-Galactose and d-Glucose

    PubMed Central

    2014-01-01

    The l-arabinose isomerase (l-AI) and the d-xylose isomerase (d-XI) encoding genes from Lactobacillus reuteri (DSMZ 17509) were cloned and overexpressed in Escherichia coli BL21 (DE3). The proteins were purified to homogeneity by one-step affinity chromatography and characterized biochemically. l-AI displayed maximum activity at 65 °C and pH 6.0, whereas d-XI showed maximum activity at 65 °C and pH 5.0. Both enzymes require divalent metal ions. The genes were also ligated into the inducible lactobacillal expression vectors pSIP409 and pSIP609, the latter containing a food grade auxotrophy marker instead of an antibiotic resistance marker, and the l-AI- and d-XI-encoding sequences/genes were coexpressed in the food grade host Lactobacillus plantarum. The recombinant enzymes were tested for applications in carbohydrate conversion reactions of industrial relevance. The purified l-AI converted d-galactose to d-tagatose with a maximum conversion rate of 35%, and the d-XI isomerized d-glucose to d-fructose with a maximum conversion rate of 48% at 60 °C. PMID:24443973

  7. Novel mutation of FKBP10 in a pediatric patient with osteogenesis imperfecta type XI identified by clinical exome sequencing

    PubMed Central

    Velasco, Harvy Mauricio; Morales, Jessica L

    2017-01-01

    Osteogenesis imperfecta (OI) is a hereditary disease characterized by bone fragility caused by mutations in the proteins that support the formation of the extracellular matrix in the bone. The diagnosis of OI begins with clinical suspicion, from phenotypic findings at birth, low-impact fractures during childhood or family history that may lead to it. However, the variability in the semiology of the disease does not allow establishing an early diagnosis in all cases, and unfortunately, specific clinical data provided by the literature only report 28 patients with OI type XI. This information is limited and heterogeneous, and therefore, detailed information on the natural history of this disease is not yet available. This paper reports the case of a male patient who, despite undergoing multidisciplinary management, did not have a diagnosis for a long period of time, and could only be given one with the use of whole-exome sequencing. The use of the next-generation sequencing in patients with ultrarare genetic diseases, including skeletal dysplasias, should be justified when clear clinical criteria and an improvement in the quality of life of the patients and their families are intended while reducing economic and time costs. Thus, this case report corresponds to the 29th patient affected with OI type XI, and the 18th mutation in FKBP10, causative of this pathology. PMID:29158687

  8. High-frequency expression of a conserved kappa light-chain variable-region gene in chronic lymphocytic leukemia

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

    Kipps, T.J.; Fong, S.; Tomhave, E.

    Malignant B lymphocytes from several patients with chronic lymphocytic leukemia (CLL) were examined for reactivity with murine monoclonal antibody 17.109. This antibody, prepared against the rheumatoid factor (RF) paraprotein Sie, recognizes a cross reactive idiotype on 48% of human IgM RF paraproteins, but does not react with IgM paraproteins without RF activity or substantially with normal pooled immunoglobulin. The 17.109-reactive idiotype is a marker for a kappa III variable-region gene, designated V/sub kappa/RF, that is conserved in outbred human populations. In a limited study of 31 CLL patients, the leukemic cells from 5 of 20 patients with kappa light chain-expressingmore » CLL were recognized by the 17.109 monoclonal antibody. Despite having malignant cells specifically reactive with this antibody, patients with 17.109-positive CLL did not have elevated serum levels of circulating antibody bearing 17.109-reactive determinants. Total RNAs isolated from the CLL B lymphocytes, or from hybridomas produced by fusing the CLL cells with the WI-L2-729-HF/sub 2/ cell line, were fractionated electrophoretically and examined by blot hybridization. Under stringent hybridization conditions capable of discerning a single base-pair mismatch, RNA from the 17.109-idiotype-positive CLL cells hybridized to synthetic oligonucleotide probes corresponding to framework and complementary-determining regions in the V/sub kappa/RF gene. The high frequency of the 17.109-associated idiotype and the V/sub kappa/RF gene in CLL suggests that the disease may arise from B lymphocytes that express a restricted set of inherited immunoglobulin variable-region genes with little or no somatic mutation.« less

  9. Assessment of compatibility among Armillaria cepistipes, A. sinapina, and North American biological species X and XI, using culture morphology and molecular biology

    Treesearch

    Mark T. Banik; Harold H. Burdsall

    1998-01-01

    Ten single-spore isolates each of Armillaria sinapina, A. cepistipes, and North American biological species (NABS)X and XI were paired in all combinations. A second set of ten single-spore isolates of each species was likewise paired. Each pairing was duplicated for a total of 3280 pairs. Using the standard morphological criteria (e.g., fluffy, crustose) to assess the...

  10. Broken SU(3) antidecuplet for {Theta}{sup +} and {Xi}{sub 3/2}

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

    Pakvasa, Sandip; Suzuki, Mahiko

    2004-05-05

    If the narrow exotic baryon resonances {Theta}{sup +}(1540) and {Xi}{sub 3/2} are members of the J{sup P} = 1/2{sup +} antidecuplet with N*(1710), the octet-antidecuplet mixing is required not only by the mass spectrum but also by the decay pattern of N*(1710). This casts doubt on validity of the {Theta}{sup +} mass prediction by the chiral soliton model. While all pieces of the existing experimental information point to a small octet-decuplet mixing, the magnitude of mixing required by the mass spectrum is not consistent with the value needed to account for the hadronic decay rates. The discrepancy is not resolvedmore » even after the large experimental uncertainty is taken into consideration. We fail to find an alternative SU(3) assignment even with different spin-parity assignment. When we extend the analysis to mixing with a higher SU(3) multiplet, we find one experimentally testable scenario in the case of mixing with a 27-plet.« less

  11. Loss of Xist RNA from the inactive X during B cell development is restored in a dynamic YY1-dependent two-step process in activated B cells

    PubMed Central

    Syrett, Camille M.; Sindhava, Vishal; Hodawadekar, Suchita; Myles, Arpita; Liang, Guanxiang; Zhang, Yue; Nandi, Satabdi; Cancro, Michael; Atchison, Michael

    2017-01-01

    X-chromosome inactivation (XCI) in female lymphocytes is uniquely regulated, as the inactive X (Xi) chromosome lacks localized Xist RNA and heterochromatin modifications. Epigenetic profiling reveals that Xist RNA is lost from the Xi at the pro-B cell stage and that additional heterochromatic modifications are gradually lost during B cell development. Activation of mature B cells restores Xist RNA and heterochromatin to the Xi in a dynamic two-step process that differs in timing and pattern, depending on the method of B cell stimulation. Finally, we find that DNA binding domain of YY1 is necessary for XCI in activated B cells, as ex-vivo YY1 deletion results in loss of Xi heterochromatin marks and up-regulation of X-linked genes. Ectopic expression of the YY1 zinc finger domain is sufficient to restore Xist RNA localization during B cell activation. Together, our results indicate that Xist RNA localization is critical for maintaining XCI in female lymphocytes, and that chromatin changes on the Xi during B cell development and the dynamic nature of YY1-dependent XCI maintenance in mature B cells predisposes X-linked immunity genes to reactivation. PMID:28991910

  12. PREFACE: XI Latin American Workshop on Nonlinear Phenomena

    NASA Astrophysics Data System (ADS)

    Anteneodo, Celia; da Luz, Marcos G. E.

    2010-09-01

    The XI Latin American Workshop on Nonlinear Phenomena (LAWNP) has been held in Búzios-RJ, Brazil, from 5-9 October 2009. This international conference is one in a series that have gathered biennially, over the past 21 years, physicists and other scientists who direct their work towards several aspects of nonlinear phenomena and complex systems. The main purpose of LAWNP meetings is to create a friendly and motivating environment, such that researchers from Latin America and from other parts of the globe can discuss not only their own latest results but also the trends and perspectives in this very interdisciplinary field of investigation. Hence, it constitutes a forum for promoting scientific collaboration and fomenting the emergence of new ideas, helping to advance the field. The XI edition (LAWNP'09) has gathered more than 230 scientists and students (most from Latin America), covering all of the world (27 different countries from North and South America, Asia, Europe, and Oceania). In total there were 18 plenary lectures, 80 parallel talks, and 140 poster contributions. A stimulating round-table discussion also took place devoted to the present and future of the Latin American Institutions in Complex Phenomena (a summary can be found at http://lawnp09.fis.puc-rio.br, in the Round-Table report link). The 2009 workshop was devoted to a wide scope of themes and points of view, pursuing to include the latest trends and developments in the science of nonlinearity. In this way, we have a great pleasure in publishing this Proceedings volume based on the high quality scientific works presented at LAWNP'09, covering already established methods as well as new approaches, discussing both theoretical and practical aspects, and addressing paradigmatic systems and also completely new problems, in nonlinearity and complexity. In fact, the present volume may be a very valuable reference for those interested in an overview on how nonlinear interactions can affect different

  13. Frequencies of Functional Polymorphisms in Three Pharmacokinetic Genes of Clinical Interest within the Admixed Puerto Rican Population

    PubMed Central

    Orengo-Mercado, Carmelo; Nieves, Bianca; López, Lizbeth; Vallés-Ortiz, Nabila; Renta, Jessicca Y.; Santiago-Borrero, Pedro J.; Cadilla, Carmen L.; Duconge, Jorge

    2013-01-01

    Objective This cross-sectional study was aimed at determining the allele frequencies for the CYP2C19*2, CYP2C19*3, CYP2D6*10 and PON1 (rs662) polymorphisms in the Puerto Rican population. The CYP2C19, CYP2D6 and PON1 genes are known to be associated with functional changes in drug metabolism and activation. Individuals carrying the aforementioned polymorphisms are at a higher risk of suffering from drug-induced adverse events and/ or unresponsiveness from a variety of drugs that includes antidepressants, atypical antipsychotics and antiplatelet compounds. Information on the frequency of these polymorphisms is more commonly found on homogeneous populations, but is scarce in highly heterogeneous populations like Hispanics, as in the case of Puerto Ricans. Method Genotyping was carried out in 100 genomic DNA samples from dried blood spots supplied by the Puerto Rican Newborn Screening program using Taqman® Genotyping Assays. Results The Minor Allele Frequencies (MAF) obtained were 9% for CYP2C19*2 and CYP2D6*10, 50% for PON1 (rs662), while the CYP2C19*3 variant was not detected in our study. Furthermore, Hardy Weinberg equilibrium analysis was assessed as well as a comparison between Puerto Rico and other reference populations using a Z-test for proportions. Conclusion The observed allele and genotype frequencies on these relevant pharmacogenes in Puerto Ricans were more closely related to those early reported in two other reference populations of Americans (Mexicans and Colombians). PMID:24040574

  14. Frequencies of Functional Polymorphisms in Three Pharmacokinetic Genes of Clinical Interest within the Admixed Puerto Rican Population.

    PubMed

    Orengo-Mercado, Carmelo; Nieves, Bianca; López, Lizbeth; Vallés-Ortiz, Nabila; Renta, Jessicca Y; Santiago-Borrero, Pedro J; Cadilla, Carmen L; Duconge, Jorge

    2013-03-27

    This cross-sectional study was aimed at determining the allele frequencies for the CYP2C19*2, CYP2C19*3, CYP2D6*10 and PON1 (rs662) polymorphisms in the Puerto Rican population. The CYP2C19, CYP2D6 and PON1 genes are known to be associated with functional changes in drug metabolism and activation. Individuals carrying the aforementioned polymorphisms are at a higher risk of suffering from drug-induced adverse events and/ or unresponsiveness from a variety of drugs that includes antidepressants, atypical antipsychotics and antiplatelet compounds. Information on the frequency of these polymorphisms is more commonly found on homogeneous populations, but is scarce in highly heterogeneous populations like Hispanics, as in the case of Puerto Ricans. Genotyping was carried out in 100 genomic DNA samples from dried blood spots supplied by the Puerto Rican Newborn Screening program using Taqman® Genotyping Assays. The Minor Allele Frequencies (MAF) obtained were 9% for CYP2C19*2 and CYP2D6*10, 50% for PON1 (rs662), while the CYP2C19*3 variant was not detected in our study. Furthermore, Hardy Weinberg equilibrium analysis was assessed as well as a comparison between Puerto Rico and other reference populations using a Z-test for proportions. The observed allele and genotype frequencies on these relevant pharmacogenes in Puerto Ricans were more closely related to those early reported in two other reference populations of Americans (Mexicans and Colombians).

  15. Synthesis, structural and optical characterization of APbX{sub 3} (A=methylammonium, dimethylammonium, trimethylammonium; X=I, Br, Cl) hybrid organic-inorganic materials

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

    Mancini, Alessandro; Quadrelli, Paolo; Amoroso, Giuseppe

    2016-08-15

    In this paper we report the synthesis, the crystal structure and the optical response of APbX{sub 3} (A=MA, DMA, and TMA; X=I, Br) hybrid organic-inorganic materials including some new phases. We observe that as the cation group increases in size, the optical absorption edge shifts to higher energies with energy steps which are systematic and independent on the anion. A linear correlation between the optical bad gap and the tolerance factor has been shown for the series of samples investigated. - Graphical abstract: The crystal structure and the optical response of the two series of hybrid organic-inorganic materials APbX{sub 3}more » (A=MA, DMA, and TMA; X=I, Br), which include some new phases, are reported. A dependence of crystal structure and band-gap with tolerance factor is shown. Display Omitted - Highlights: • DMAPbI{sub 3}, TMAPbI{sub 3} and TMAPbBr{sub 3} are reported as new hybrid organic-inorganic compounds. • Crystal structure and optical properties as a function of the number of methyl groups are provided. • Correlation between structure and optical properties are given as a function of tolerance factor.« less

  16. A Review of Selected Genes with Known Effects on Performance and Health of Cattle

    PubMed Central

    Casas, Eduardo; Kehrli, Marcus E.

    2016-01-01

    There are genetic conditions that influence production in dairy and beef cattle. The objective of this review was to describe relevant genetic conditions that have been associated with productivity and health in cattle. Genes or genomic regions that have been identified as a candidate for the condition will be included, and the genetic basis of the condition will be defined. Genes and genetic conditions included in this review are bovine leukocyte adhesion deficiency, deficiency of the uridine monophosphate synthase, bovine chronic interstitial nephritis, horn development, myostatin, complex vertebral malformation, leptin, osteopetrosis, apoptosis peptide activating factor 1, chondrodysplastic dwarfism, caseins, calpastatin, umbilical hernia, lactoglobulin, citrullinemia, cholesterol deficiency, prions, thyroglobulin, diacylglycerol acyltransferase, syndactyly, maple syrup urine disease, slick hair, Factor XI deficiency, and μ-Calpain. This review is not meant to be comprehensive, and relevant information is provided to ascertain genetic markers associated with the conditions. PMID:28018909

  17. Renin Gene Polymorphisms in Bangladeshi Hypertensive Population

    PubMed Central

    Afruza, Rownock; Islam, Laila N; Banerjee, Sajal; Hassan, Md. Mahbub; Suzuki, Fumiaki; Nabi, AHM Nurun

    2014-01-01

    Objective: Linkages of renin gene polymorphisms with hypertension have been implicated in several populations with contrasting results. Present study aims to assess the pattern of renin gene polymorphisms in Bangladeshi hypertensive individuals. Methodology: Introns 1, 9 of renin gene and 4063 bases upstream of promoter sequence of renin gene were amplified from the genomic DNA of the total 124 (hypertensive and normotensive) subjects using respective primers. Polymerase chain reaction-based restriction fragment length polymorphisms were performed using BglI, MboI and TaqI restriction enzymes. Results: Homozygosity was common in renin gene regarding BglI (bb=48.4%, Bb=37.9%, BB=13.7%, χ2 =1.91, P>0.05), TaqI (TT=81.5%, Tt=14.5%, tt=4.0%, χ2 =7.50, P<0.01) and MboI (mm=63.7%, Mm=32.3%, MM=4.0%, χ2=0.00, P>0.05) polymorphisms among total study population. For BglI and TaqI genotype distribution, hypertensive subjects (BglI: χ2 =6.66, P<0.05; TaqI: χ2 = 10.28, P<0.005) significantly deviate from Hardy-Weinberg Equilibrium law compared to normotensive subjects (BglI: χ2=0.51, P>0.05; TaqI: χ2=0.20, P>0.05). On the other hand, with respect to MboI polymorphisms of renin gene, only normotensive subjects deviate from the law (patients: χ2=1.28, P>0.05; vs controls: χ2=6.81, P<0.01). In the context of allelic frequency, common T allele was clearly prevalent (T frequency=0.86, t frequency = 0.14) for TaqI, but rare alleles b and m were more frequent for both BglI (b frequency=0.69, B frequency=0.31) and MboI (m frequency=0.80 M frequency=0.20) polymorphisms, respectively. Conclusion: Thus, we report that Bangladeshi hypertensive subjects did not show any distinct pattern of renin gene polymorphisms compared to their healthy control subjects with regard to their genotypic and allelic frequencies. PMID:25057323

  18. Culture-gene coevolution of individualism-collectivism and the serotonin transporter gene.

    PubMed

    Chiao, Joan Y; Blizinsky, Katherine D

    2010-02-22

    Culture-gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism-collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture-gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism-collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture-gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism-collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture-gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed.

  19. Culture–gene coevolution of individualism–collectivism and the serotonin transporter gene

    PubMed Central

    Chiao, Joan Y.; Blizinsky, Katherine D.

    2010-01-01

    Culture–gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism–collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture–gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism–collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture–gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism–collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture–gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed. PMID:19864286

  20. Association between lower frequency of R381Q variant (rs11209026) in IL-23 receptor gene and increased risk of recurrent spontaneous abortion (RSA).

    PubMed

    Abdollahi, Elham; Tavasolian, Fataneh; Ghasemi, Nasrin; Mirghanizadeh, Seyed Ali; Azizi, Mohammdareza; Ghoryani, Mohsen; Samadi, Morteza

    2015-01-01

    Recurrent spontaneous abortion (RSA) is defined as three or more consecutive spontaneous abortions before the 20th week of gestation. The purpose of the present study was to investigate the association between a functional single nucleotide polymorphism (SNP) in the interleukin (IL)-23 receptor gene (IL-23R; rs11209026, 1142 G wild type → A reduced function, Arg381Gln, R381Q) and RSA. For the study, 200 RSA patients (confirmed using established diagnostic criteria) and 200 normal individuals in fertility and infertility centers in the cities of Yazd and Isfahan were recruited during a period from 2012-2013. Using PCR-RFLP, the R381Q variant was screened for in the IL-23R gene of the patients and controls. The results indicated there were significant differences in the frequency of this genetic variant in the patients versus the healthy controls, i.e. 2% and 7.5%, respectively (p value = 0.01; odds ratio = 0.25; CI = 95%). No significant difference was found for the G allelic frequency in patients with RSA and in the control group (p = 0.60). The A allelic frequency was significantly different between the two groups (p = 0.01). Based on these findings, it is concluded that the frequency of single nucleotide polymorphism in the IL-23 receptor (R381Q) in patients with recurrent spontaneous abortion (RSA) is less than that found in normal control women.

  1. The lower cranial nerves: IX, X, XI, XII.

    PubMed

    Sarrazin, J-L; Toulgoat, F; Benoudiba, F

    2013-10-01

    The lower cranial nerves innervate the pharynx and larynx by the glossopharyngeal (CN IX) and vagus (CN X) (mixed) nerves, and provide motor innervation of the muscles of the neck by the accessory nerve (CN XI) and the tongue by the hypoglossal nerve (CN XII). The symptomatology provoked by an anomaly is often discrete and rarely in the forefront. As with all cranial nerves, the context and clinical examinations, in case of suspicion of impairment of the lower cranial nerves, are determinant in guiding the imaging. In fact, the impairment may be located in the brain stem, in the peribulbar cisterns, in the foramens or even in the deep spaces of the face. The clinical localization of the probable seat of the lesion helps in choosing the adapted protocol in MRI and eventually completes it with a CT-scan. In the bulb, the intra-axial pathology is dominated by brain ischemia (in particular, with Wallenberg syndrome) and multiple sclerosis. Cisternal pathology is tumoral with two tumors, schwannoma and meningioma. The occurrence is much lower than in the cochleovestibular nerves as well as the leptomeningeal nerves (infectious, inflammatory or tumoral). Finally, foramen pathology is tumoral with, outside of the usual schwannomas and meningiomas, paragangliomas. For radiologists, fairly hesitant to explore these lower cranial pairs, it is necessary to be familiar with (or relearn) the anatomy, master the exploratory technique and be aware of the diagnostic possibilities. Copyright © 2013 Éditions françaises de radiologie. Published by Elsevier Masson SAS. All rights reserved.

  2. Application of mathematical expectation (ME) strategy for detecting low frequency mutations: An example for evaluating 14-bp insertion/deletion (indel) within the bovine PRNP gene.

    PubMed

    Yang, Qing; Zhang, Sihuan; Liu, Liangliang; Cao, Xiukai; Lei, Chuzhao; Qi, Xinglei; Lin, Fengpeng; Qu, Weidong; Qi, Xingshan; Liu, Jiming; Wang, Rongmin; Chen, Hong; Lan, Xianyong

    2016-09-02

    The detection method based on the mathematical expectation (ME) strategy is fast and accuracy for low frequency mutation screening in large samples. Previous studies have found that the 14-bp insertion/deletion (indel) variants of the 3' untranslated region (3' UTR) within bovine PRNP gene have been characterized with low frequency (≤5%) in global breeds outside China, which has not been determined in Chinese cattle breeds yet. Therefore, this study aimed to identify the 14-bp indel within PRNP gene in 5 major Chinese indigenous cattle breeds and to evaluate its associations with phenotypic traits. It was the first time to use ME strategy to detect low frequency indel polymorphisms and found that minor allele frequency was 0.038 (Qinchuan), 0.033 (Xianan), 0.013 (Nanyang), 0.003 (Jiaxian), and zero (Ji'an), respectively. Compared to the traditional detection method by which the sample was screened one by one, the reaction time by using the ME method was decreased 62.5%, 64.9%, 77.6%, 88.9% and 66.4%, respectively. In addition, the 14-bp indel was significantly associated with the growth traits in 2 cattle breeds, with the body length of Qinchuan cattle as well as the body weight and waistline of Xianan cattle. Our results have uncovered that the method based on ME strategy is rapid, reliable, and cost-effective for detecting the low frequency mutation as well as our findings provide a potential valuable theoretical basis for the marker-assisted selection (MAS) in beef cattle.

  3. Application of mathematical expectation (ME) strategy for detecting low frequency mutations: An example for evaluating 14-bp insertion/deletion (indel) within the bovine PRNP gene

    PubMed Central

    Yang, Qing; Zhang, Sihuan; Liu, Liangliang; Cao, Xiukai; Lei, Chuzhao; Qi, Xinglei; Lin, Fengpeng; Qu, Weidong; Qi, Xingshan; Liu, Jiming; Wang, Rongmin; Chen, Hong; Lan, Xianyong

    2016-01-01

    ABSTRACT The detection method based on the mathematical expectation (ME) strategy is fast and accuracy for low frequency mutation screening in large samples. Previous studies have found that the 14-bp insertion/deletion (indel) variants of the 3′ untranslated region (3′ UTR) within bovine PRNP gene have been characterized with low frequency (≤5%) in global breeds outside China, which has not been determined in Chinese cattle breeds yet. Therefore, this study aimed to identify the 14-bp indel within PRNP gene in 5 major Chinese indigenous cattle breeds and to evaluate its associations with phenotypic traits. It was the first time to use ME strategy to detect low frequency indel polymorphisms and found that minor allele frequency was 0.038 (Qinchuan), 0.033 (Xianan), 0.013 (Nanyang), 0.003 (Jiaxian), and zero (Ji'an), respectively. Compared to the traditional detection method by which the sample was screened one by one, the reaction time by using the ME method was decreased 62.5%, 64.9%, 77.6%, 88.9% and 66.4%, respectively. In addition, the 14-bp indel was significantly associated with the growth traits in 2 cattle breeds, with the body length of Qinchuan cattle as well as the body weight and waistline of Xianan cattle. Our results have uncovered that the method based on ME strategy is rapid, reliable, and cost-effective for detecting the low frequency mutation as well as our findings provide a potential valuable theoretical basis for the marker-assisted selection (MAS) in beef cattle. PMID:27580010

  4. [The polymorphism of catechol-O-methyltransferase (COMT) and hemochromatosis (HFE) genes in the radiocontaminated regions residents with different chromosome aberration frequency].

    PubMed

    Ivanova, T I; Kondrashova, T V; Krikunova, L I; Smirnova, I A; Shentereva, N I; Sychenkova, N I; Rykova, E V; Zharikova, I A; Khorokhorina, V A; Riabchenko, N I; Zamulaeva, I A

    2010-01-01

    The association between polymorphisms in genes COMT, HFE that takes part in oxidative stress regulation, and chromosome aberration frequency in lymphocytes was assessed in 278 female residents of radiation polluted regions of Central Russia: Bryansk (322 kBk/m2) and Tula Districts (137Cs - 171 kBk/m2). The C187G, G845A genotyping of HFE and G1947A (H/L) of COMT was done by means of polymerase chain reaction-restriction fragment length polymorphism. Studied population was divided into 3 subgroups by level of chromosome aberrations per cell (0-2, 3-4, >5). There was shown statistically significant difference in distribution of COMTand HFE genotypes between the groups. The high frequency of chromosome aberrations (> or = 5%) was associated with homozygotes of the high activity COMT G/G and HFE CC. Heterozygotes for G1947A COMT and C187G HFE reveal negative association with the high frequency of chromosome aberrations and correspond to "resistance factors".

  5. High prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carrying the mecC gene in a semi-extensive red deer (Cervus elaphus hispanicus) farm in Southern Spain.

    PubMed

    Gómez, Paula; Lozano, Carmen; González-Barrio, David; Zarazaga, Myriam; Ruiz-Fons, Francisco; Torres, Carmen

    2015-06-12

    The objective was to determine the prevalence of Staphylococcus aureus nasal carriage in red deer of a semi-extensive farm and in humans in contact with the estate animals, and to characterize obtained isolates. Nasal swabs of 65 deer and 15 humans were seeded on mannitol-salt-agar and oxacillin-resistance-screening-agar-base. Isolates were identified by microbiological and molecular methods. Antimicrobial susceptibility profile was determined for 16 antibiotics by disk-diffusion and the presence of eight antibiotic resistance genes, seven virulence genes and genes of immune-evasion-cluster (IEC) was analyzed by PCR. S. aureus was typed by PFGE-SmaI, spa, agr, SCCmec and MLST. Isolates were detected in 16 deer (24.6%). Eleven S. aureus isolates were methicillin-resistant (MRSA), and five were methicillin-susceptible (MSSA). All MRSA harbored mecC gene and were agr-III/SCCmecXI/ST1945 (four spa-t843 and seven spa-t1535). All mecC-MRSA carried blaZ-SCCmecXI and etd2, were IEC-type-E, and belonged to the same PFGE pattern. The five MSSA were typed as spa-t2420/agr-I/ST133. Regarding humans, S. aureus was recovered from six samples (40%). The isolates were MSSA and were typed as spa-t002/agr-II, spa-t012/agr-III or spa-t822/agr-III and showed different IEC types (A, B, D and F). blaZ and erm(A) genes were detected, as well as cna and tst genes. As conclusion, red deer analyzed in this study are frequent carriers of mecC-MRSA CC130 (16.9%), they are characterized by few resistance and virulence determinants, and by the presence of IEC type-E. Deer could be a source of mecC-MRSA which could potentially be transmitted to other animals, or even to humans. Copyright © 2015 Elsevier B.V. All rights reserved.

  6. Mechanotransduction of Ultrasound is Frequency Dependent Below the Cavitation Threshold

    PubMed Central

    Louw, Tobias M.; Budhiraja, Gaurav; Viljoen, Hendrik J.; Subramanian, Anuradha

    2013-01-01

    This study provides evidence that low-intensity ultrasound directly affects nuclear processes, and the magnitude of the effect varies with frequency. In particular, we show that the transcriptional induction of first load-inducible genes, which is independent of new protein synthesis, is frequency dependent. Bovine chondrocytes were exposed to low-intensity below the cavitational threshold) ultrasound at 2,5 and 8 MHz. Ultrasound elevated the expression of early response genes c-Fos, c-Jun and c-Myc, maximized at 5 MHz. The phosphorylated ERK inhibitor PD98059 abrogated any increase in c-series gene expression, suggesting that signaling occurs via the MAPPK/ERK pathway. However, phosphorylated ERK levels did not change with ultrasound frequency, indicating that processes downstream of ERK phosphorylation (such as nuclear transport and chromatin reorganization) respond to ultrasound with frequency dependence. A quantitative, biphasic mathematical model based on Biot theory predicted that cytoplasmic and nuclear stress is maximized at 5.2 ± 0.8 MHz for a chondrocyte, confirming experimental measurements. PMID:23562015

  7. Oversight Hearings on the Implementation of Title XI, Public Law 95-561: Problems in the BIA Portland Area. Hearings before the Subcommittee on Elementary, Secondary, and Vocational Education of the Committee on Education and Labor, House of Representatives, Ninety-Sixth Congress, Second Session (July 28-29, 1980).

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. House Committee on Education and Labor.

    The Subcommittee on Elementary, Secondary, and XI, Public Law 95-561: Problems in the BIA Portland Area. issue of administrative funds (Element 10, Title XI, Basic Indian Education Act) to be allotted to the Portland area of the Bureau of Indian Affairs (BIA). Maxine Edmo, president of the Advocates for Indian Education educational arm of the…

  8. Inter-annual variability of wintertime PM2.5 chemical composition in Xi'an, China: Evidences of changing source emissions.

    PubMed

    Xu, Hongmei; Cao, Junji; Chow, Judith C; Huang, R-J; Shen, Zhenxing; Chen, L W Antony; Ho, Kin Fai; Watson, John G

    2016-03-01

    Chemical characteristics of PM2.5 in Xi'an in wintertime of 2006, 2008, and 2010 were investigated. Markers of OC2, EC1, and NO3(-)/SO4(2-) ratio were calculated to investigate the changes in PM2.5 emission sources over the 5-year period. Positive matrix factorization (PMF) model was used to identify and quantify the main sources of PM2.5 and their contributions. The results showed that coal combustion, motor vehicular emissions, fugitive dust, and secondary inorganic aerosol accounted for more than 80% of PM2.5 mass. The importance of these major sources to the PM2.5 mass varied yearly: coal combustion was the largest contributor (31.2% ± 5.2%), followed by secondary inorganic aerosol (20.9% ± 5.2%) and motor vehicular emissions (19.3% ± 4.8%) in 2006; the order was still coal combustion emissions (27.6% ± 3.4%), secondary inorganic aerosol (23.2% ± 6.9%), and motor vehicular emissions (20.9% ± 4.6%) in 2008; while coal combustion emission further decreased (24.1% ± 3.1%) with fugitive dust (19.4% ± 5.5%) increasing in 2010. The changes in PM2.5 chemical compositions and source contributions can be attributed to the social and economic developments in Xi'an, China, including energy structure adjustment, energy consumption, the expansion of civil vehicles, and the increase of urban construction activities. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. Gene Prioritization of Resistant Rice Gene against Xanthomas oryzae pv. oryzae by Using Text Mining Technologies

    PubMed Central

    Xia, Jingbo; Zhang, Xing; Yuan, Daojun; Chen, Lingling; Webster, Jonathan; Fang, Alex Chengyu

    2013-01-01

    To effectively assess the possibility of the unknown rice protein resistant to Xanthomonas oryzae pv. oryzae, a hybrid strategy is proposed to enhance gene prioritization by combining text mining technologies with a sequence-based approach. The text mining technique of term frequency inverse document frequency is used to measure the importance of distinguished terms which reflect biomedical activity in rice before candidate genes are screened and vital terms are produced. Afterwards, a built-in classifier under the chaos games representation algorithm is used to sieve the best possible candidate gene. Our experiment results show that the combination of these two methods achieves enhanced gene prioritization. PMID:24371834

  10. Gene prioritization of resistant rice gene against Xanthomas oryzae pv. oryzae by using text mining technologies.

    PubMed

    Xia, Jingbo; Zhang, Xing; Yuan, Daojun; Chen, Lingling; Webster, Jonathan; Fang, Alex Chengyu

    2013-01-01

    To effectively assess the possibility of the unknown rice protein resistant to Xanthomonas oryzae pv. oryzae, a hybrid strategy is proposed to enhance gene prioritization by combining text mining technologies with a sequence-based approach. The text mining technique of term frequency inverse document frequency is used to measure the importance of distinguished terms which reflect biomedical activity in rice before candidate genes are screened and vital terms are produced. Afterwards, a built-in classifier under the chaos games representation algorithm is used to sieve the best possible candidate gene. Our experiment results show that the combination of these two methods achieves enhanced gene prioritization.

  11. Failure of a new protocol to improve treatment results in paediatric lymphoblastic leukaemia: lessons from the UK Medical Research Council trials UKALL X and UKALL XI.

    PubMed

    Chessells, Judith M; Harrison, Georgina; Richards, Susan M; Gibson, Brenda E; Bailey, Clifford C; Hill, Frank G H; Hann, Ian M

    2002-08-01

    The impact of various types of intensification therapy was examined in a cohort of 3617 children aged 1-14 years with acute lymphoblastic leukaemia (ALL) enrolled in the Medical Research Council (MRC) UKALL X (1985-90) and UKALL XI (1990-97) trials. UKALL XI was modified in 1992 to incorporate the "best arm" of UKALL X with two 5-d intensification blocks at 5 and 20 weeks, and an additional randomization in respect of a third intensification at 35 weeks but omission of two consecutive injections of daunorubicin during induction. All children were eligible for randomization irrespective of risk group. The impact of the various types of intensification therapy was examined in a stratified analysis. At a median follow up of 102 months, both trials had an identical event-free survival of 61% (95% CI 58-63%) at 8 years. Survival at 8 years in UKALL XI was significantly better in than in UKALL X, 81% (79-83%) compared with 74% (72-76%) (P = < 0.001), owing to improved management of relapse. There was a highly significant trend in reduction of the number of relapses and deaths with increased intensity of therapy both for children with initial leucocyte count < 50 x 10(9)/l (P = < 0.001) and > or = 50 x 10(9)/l (P = 0.002). Introduction of a third late intensification block compensated for omission of anthracyclines during induction but produced little additional benefit. These results show, in a large cohort of patients, that minor modifications of therapy may influence relapse rate and obviate the benefit of previous randomized trials. The failure to adapt treatment for higher risk children contributed to these disappointing results.

  12. Consensus Report of the XI Congress of the Spanish Society of Odontology for the Handicapped and Special Patients

    PubMed Central

    Cabrerizo-Merino, Carmen; Cutando-Soriano, Antonio; Giménez-Prats, María J.; Silvestre-Donat, Farncisco J.; Tomás-Carmona, Inmaculada

    2014-01-01

    This article summarizes the findings of consensus of the XI congress of the SEOEME. All of these conclusions are referring to the review articles responsible to the general rapporteurs in order to bringing up to date knowledge with regard to the use of implants in patients medically compromised and with special needs and, in the dental management of autism and cerebral palsy, in the dental treatment of patients with genetic and adquired haematological disorders, the dental implications of cardiovascular disease and hospital dentistry. Key words:Autism, cardiovascular diseases, cerebral palsy, dental implants, disabled patients, haematological disorders, hospital dentistry. PMID:24608224

  13. Identification of KIF3A as a Novel Candidate Gene for Childhood Asthma Using RNA Expression and Population Allelic Frequencies Differences

    PubMed Central

    Butsch Kovacic, Melinda; Biagini Myers, Jocelyn M.; Wang, Ning; Martin, Lisa J.; Lindsey, Mark; Ericksen, Mark B.; He, Hua; Patterson, Tia L.; Baye, Tesfaye M.; Torgerson, Dara; Roth, Lindsey A.; Gupta, Jayanta; Sivaprasad, Umasundari; Gibson, Aaron M.; Tsoras, Anna M.; Hu, Donglei; Eng, Celeste; Chapela, Rocío; Rodríguez-Santana, José R.; Rodríguez-Cintrón, William; Avila, Pedro C.; Beckman, Kenneth; Seibold, Max A.; Gignoux, Chris; Musaad, Salma M.; Chen, Weiguo; Burchard, Esteban González; Khurana Hershey, Gurjit K.

    2011-01-01

    Background Asthma is a chronic inflammatory disease with a strong genetic predisposition. A major challenge for candidate gene association studies in asthma is the selection of biologically relevant genes. Methodology/Principal Findings Using epithelial RNA expression arrays, HapMap allele frequency variation, and the literature, we identified six possible candidate susceptibility genes for childhood asthma including ADCY2, DNAH5, KIF3A, PDE4B, PLAU, SPRR2B. To evaluate these genes, we compared the genotypes of 194 predominantly tagging SNPs in 790 asthmatic, allergic and non-allergic children. We found that SNPs in all six genes were nominally associated with asthma (p<0.05) in our discovery cohort and in three independent cohorts at either the SNP or gene level (p<0.05). Further, we determined that our selection approach was superior to random selection of genes either differentially expressed in asthmatics compared to controls (p = 0.0049) or selected based on the literature alone (p = 0.0049), substantiating the validity of our gene selection approach. Importantly, we observed that 7 of 9 SNPs in the KIF3A gene more than doubled the odds of asthma (OR = 2.3, p<0.0001) and increased the odds of allergic disease (OR = 1.8, p<0.008). Our data indicate that KIF3A rs7737031 (T-allele) has an asthma population attributable risk of 18.5%. The association between KIF3A rs7737031 and asthma was validated in 3 independent populations, further substantiating the validity of our gene selection approach. Conclusions/Significance Our study demonstrates that KIF3A, a member of the kinesin superfamily of microtubule associated motors that are important in the transport of protein complexes within cilia, is a novel candidate gene for childhood asthma. Polymorphisms in KIF3A may in part be responsible for poor mucus and/or allergen clearance from the airways. Furthermore, our study provides a promising framework for the identification and evaluation of novel

  14. Frequency of distribution of leptin receptor gene polymorphism in obstructive sleep apnea patients.

    PubMed

    Popko, K; Gorska, E; Wasik, M; Stoklosa, A; Pływaczewski, R; Winiarska, M; Gorecka, D; Sliwinski, P; Demkow, U

    2007-11-01

    Leptin is an adipocyte-derived hormone regulating energy homeostasis and body weight. Leptin concentration is increased in patients with the obstructive sleep apnea syndrome (OSAS). Leptin receptor (LEPR) is a single transmembrane protein belonging to the superfamily of cytokine receptors related by a structure to the hemopoietin receptor family. The aim of the present study was to evaluate the frequency of distribution of leptin receptor gene polymorphism GLN223ARG in OSAS patients compared with healthy controls. The examined group included 179 subjects: 102 OSAS patients (74 men and 28 women) and 77 non-apneic controls (39 men and 38 women). Genomic DNA was isolated with the use of a column method and genotyping of DNA sequence variation was carried out by restriction enzyme analysis of PCR-amplified DNA. The results revealed a significant correlation between the polymorphism of LEPR and OSAS. Carriers of Arg allele in homozygotic genotype Arg/Arg and heterozygotic genotype Gln/Arg were more often obese and developed OSAS than the group of carriers of homozygotic Gln/Gln genotype. This tendency was observed in the whole examined population and in the group of obese women. We also found the highest levels of total cholesterol, LDL, HDL, and triglycerides in the group of homozygotic Arg/Arg genotype carriers, lower in heterozygotic Gln/Arg genotype carriers, and the lowest in the group of persons carring homozygotic Gln/Gln genotype. The presence of Arg allel seems linked to a higher risk of obesity and higher lipid levels in OSAS patients. OSAS may have a strong genetic basis due to the effects from a variety of genes including those for leptin receptor.

  15. Can the starpatch on Xi Bootis A be explained by using tangential flows?

    NASA Technical Reports Server (NTRS)

    Toner, Clifford G.; Labonte, Barry J.

    1991-01-01

    It is demonstrated that a modification of the starpatch model of Toner and Gray (1988), using tangential flows instead of an enhanced granulation velocity dispersion within the patch, is very successful at reproducing both the observed line asymmetry and the line broadening variations observed in the G8 dwarf Xi Boo A. Areal coverage of 10 percent + or - 3 percent of the visible disk, latitude 30 deg + or - 4 deg, mean brightness 0.85 + or - 0.05 relative to the 'quiet' photosphere, mean tangential flow velocities of 8.0 + or - 1.5 km/s, and dispersions about the mean of 8/0 + or - 2.0 km/s are inferred for the patch. A feature at a latitude of about 30 deg is inferred which covers about 10 percent of the visible disk and is 10-20 percent fainter than the rest of the photosphere. It is inferred that 70-80 percent of the patch is penumbra.

  16. Human X chromosome inactivation and reactivation: implications for cell reprogramming and disease.

    PubMed

    Cantone, Irene; Fisher, Amanda G

    2017-11-05

    X-chromosome inactivation (XCI) is an exemplar of epigenetic regulation that is set up as pluripotent cells differentiate. Once established, XCI is stably propagated, but can be reversed in vivo or by pluripotent reprogramming in vitro Although reprogramming provides a useful model for inactive X (Xi) reactivation in mouse, the relative instability and heterogeneity of human embryonic stem (ES) cells and induced pluripotent stem cells hampers comparable progress in human. Here we review studies aimed at reactivating the human Xi using different reprogramming strategies. We outline our recent results using mouse ES cells to reprogramme female human fibroblasts by cell-cell fusion. We show that pluripotent reprogramming induces widespread and rapid chromatin remodelling in which the human Xi loses XIST and H3K27m3 enrichment and selected Xi genes become reactivated, ahead of mitotic division. Using RNA sequencing to map the extent of human Xi reactivation, and chromatin-modifying drugs to potentiate reactivation, we outline how this approach could be used to better design strategies to re-express human X-linked loci. As cell fusion induces the expression of human pluripotency genes that represent both the 'primed' and 'naive' states, this approach may also offer a fresh opportunity to segregate human pluripotent states with distinct Xi expression profiles, using single-cell-based approaches.This article is part of the themed issue 'X-chromosome inactivation: a tribute to Mary Lyon'. © 2017 The Author(s).

  17. Mutation Frequency of the Major Frontotemporal Dementia Genes, MAPT, GRN and C9ORF72 in a Turkish Cohort of Dementia Patients.

    PubMed

    Guven, Gamze; Lohmann, Ebba; Bras, Jose; Gibbs, J Raphael; Gurvit, Hakan; Bilgic, Basar; Hanagasi, Hasmet; Rizzu, Patrizia; Heutink, Peter; Emre, Murat; Erginel-Unaltuna, Nihan; Just, Walter; Hardy, John; Singleton, Andrew; Guerreiro, Rita

    2016-01-01

    'Microtubule-associated protein tau' (MAPT), 'granulin' (GRN) and 'chromosome 9 open reading frame72' (C9ORF72) gene mutations are the major known genetic causes of frontotemporal dementia (FTD). Recent studies suggest that mutations in these genes may also be associated with other forms of dementia. Therefore we investigated whether MAPT, GRN and C9ORF72 gene mutations are major contributors to dementia in a random, unselected Turkish cohort of dementia patients. A combination of whole-exome sequencing, Sanger sequencing and fragment analysis/Southern blot was performed in order to identify pathogenic mutations and novel variants in these genes as well as other FTD-related genes such as the 'charged multivesicular body protein 2B' (CHMP2B), the 'FUS RNA binding protein' (FUS), the 'TAR DNA binding protein' (TARDBP), the 'sequestosome1' (SQSTM1), and the 'valosin containing protein' (VCP). We determined one pathogenic MAPT mutation (c.1906C>T, p.P636L) and one novel missense variant (c.38A>G, p.D13G). In GRN we identified a probably pathogenic TGAG deletion in the splice donor site of exon 6. Three patients were found to carry the GGGGCC expansions in the non-coding region of the C9ORF72 gene. In summary, a complete screening for mutations in MAPT, GRN and C9ORF72 genes revealed a frequency of 5.4% of pathogenic mutations in a random cohort of 93 Turkish index patients with dementia.

  18. Medea genes, handedness and other traits

    USGS Publications Warehouse

    Hatfield, Jeffrey

    2015-01-01

    Medea factors or genes are maternal-effects mechanisms, found in many species, in which the mother's body selectively kills embryos of a certain genotype.Humans have a similar genetic mechanism, the gene RHD which produces Rh-factor involved in blood type.Recently I proposed that RHD acts as a maternal-effects gene that determines handedness (i.e., right handed or non-right handed) in individuals of our species. Here, I argue that RHD functions as a Medea gene as well.The handedness gene (and also RHD itself in some cases) has been implicated in autism spectrum disorders (ASD), bipolar disorder, cerebral laterality (i.e., right-brained or left-brained speech laterality), hair-whorl rotation, schizophrenia, sexual orientation, and speech dyslexia.Identifying the gene or genes that determine handedness or cerebral laterality may help uncover the mechanisms underlying these behavioral phenotypes in our species.A relatively simple test of the handedness hypothesis has been proposed:In a sample of humans for whom handedness has been evaluated, we would need to genotype for RHD by determining whether Rh+ individuals have one or two copies of the dominant allele. If RHD and perhaps also an interaction with RHCE are involved in sexual orientation, it explains how selection could favor a gene or genes which cause some people to become non-heterosexual.The literature on Medea genes provides the explanation:A Medea allele must increase in frequency, sometimes to fixation (i.e., 100% frequency) even if it reduces fecundity (e.g., birth rate).In addition, treatment for RHD maternal-fetal genotype incompatibility, which allows more fetuses to survive to term now, may be one explanation for why ASD appears to be increasing in frequency in some populations, if RHD is indeed the handedness gene, although many other mechanisms have also been suggested. One wonders if bipolar disorder and the other alternative phenotypes are also increasing in frequency.

  19. Heart failure and endothelial nitric oxide synthase G894T gene polymorphism frequency variations within ancestries.

    PubMed

    Oliveira, Romulo V M; Albuquerque, Felipe N; Duque, Gustavo S; Freitas, Rossana G A; Carvalho, Elizeu F; Brandão, Andrea A; Silva, Dayse A; Mourilhe-Rocha, Ricardo; Albuquerque, Denilson C

    2018-02-28

    The G894T polymorphism in endothelial nitric oxide synthase enzyme gene plays an important role in heart failure (HF) and its frequency varies among populations. We investigated this association in highly admixed samples in terms of ancestry. The cohort included 210 HF patients and 106 healthy individuals. Self-reported race and NYHA class were analyzed for HF patients. G894T polymorphism was analyzed by polymerase chain reaction (PCR) and by restriction fragment length polymorphism technique. Ancestry was estimated using a PCR reaction containing 46 autosomal ancestry informative markers and an analysis by capillary electrophoresis. The GG homozygous genotype had a higher frequency in HF patients (63.8%) than in healthy individuals (48.1%), showing an increased chance (odds ratio 1.90, 95% confidence interval 1.18-3.05). The ancestry profiles in patients and controls were similar, with a major European contribution (57.1% and 63.2%), followed by African (30.2% and 24.0%) and Native American (12.7% and 12.8%), without a significant difference between both samples (p = 0.28). The GG genotype is associated to HF prognosis, and this association remains present in highly admixed sample groups. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. Evaluation of androgen receptor gene as a candidate gene in female androgenetic alopecia.

    PubMed

    el-Samahy, May H; Shaheen, Maha A; Saddik, Dina E B; Abdel-Fattah, Nermeen S A; el-Sawi, Mohammad A; Mahran, Manal Z; Shehab, Abeer A A

    2009-06-01

    Genetic polymorphisms of the androgen receptor (AR) gene have been studied in male androgenetic alopecia (AGA); however, little is known about gene polymorphism and female AGA. To evaluate the AR gene as a candidate gene for female AGA. Thirty premenopausal Egyptian female patients with AGA (mean age, 32.3 +/- 7 years) and 11 age- and sex-matched controls were included. All subjects underwent laboratory and pelvic ultrasound evaluation to exclude other precipitating cause(s) of hair loss. Scalp biopsy was taken and the AR gene was evaluated using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). According to Ludwig's classification, all patients had type II AGA. Statistical analysis showed no statistically significant difference in genotype (chi(2) = 5.513, P > or = 0.05) or allele frequency (chi(2) = 1.312, P > or = 0.05) between patients and controls. There was also no statistically significant difference between the genotype and allele frequency with disease duration. In contrast with male AGA, no association was found between type II AGA in Egyptian women and the AR gene. Therefore, the genetic study of this gene does not serve as a biomarker for the identification of women with a predisposition to AGA.

  1. High Resolution Frequency Swept Imaging.

    DTIC Science & Technology

    1983-09-30

    Appendix XI). Preliminary ex- perimental results obtained using ultrasound are extremely encouraging. These -12- ’!" , ,a, -’ ’- : "--’ .,"U...of broad-band nature. They are either In the form of relatively long chirps ( whistles ), impulse like pings or clicks of less than lmsec duration and...Bottlenose Porpoise: A Study of Whistles and Clicks", Zoologica, Vol. 47, 1962, pp. 121-128. L 2 I ._ 4! i APPENDIX II " HBOLOCRAPHY, WAVE-ILE GTH DIVERSITY

  2. First series of total robotic hysterectomy (TRH) using new integrated table motion for the da Vinci Xi: feasibility, safety and efficacy.

    PubMed

    Giannini, Andrea; Russo, Eleonora; Mannella, Paolo; Palla, Giulia; Pisaneschi, Silvia; Cecchi, Elena; Maremmani, Michele; Morelli, Luca; Perutelli, Alessandra; Cela, Vito; Melfi, Franca; Simoncini, Tommaso

    2017-08-01

    To present the first case series of total robotic hysterectomy (TRH), using integrated table motion (ITM), which is a new feature comprising a unique operating table by Trumpf Medical that communicates wirelessly with the da Vinci Xi surgical system. ITM has been specifically developed to improve multiquadrant robotic surgery such as that conducted in colorectal surgery. Between May and October 2015, a prospective post-market study was conducted on ITM in the EU in 40 cases from different specialties. The gynecological study group comprised 12 patients. Primary endpoints were ITM feasibility, safety and efficacy. Ten patients underwent TRH. Mean number of ITM moves was three during TRH; there were 31 instances of table moves in the ten procedures. Twenty-eight of 31 ITM moves were made to gain internal exposure. The endoscope remained inserted during 29 of the 31 table movements (94%), while the instruments remained inserted during 27 of the 31 moves (87%). No external instrument collisions or other problems related to the operating table were noted. There were no ITM safety-related observations and no adverse events. This preliminary study demonstrated the feasibility, safety and efficacy of ITM for the da Vinci Xi surgical system in TRH. ITM was safe, with no adverse events related to its use. Further studies will be useful to define the real role and potential benefit of ITM in gynecological surgery.

  3. Effects of single and combined low frequency electromagnetic fields and simulated microgravity on gene expression of human mesenchymal stem cells during chondrogenesis

    PubMed Central

    Hammerschmid, Florian; Blum, Helmut; Krebs, Stefan; Redeker, Julia I.; Holzapfel, Boris M.; Jansson, Volkmar; Müller, Peter E.

    2016-01-01

    Introduction Low frequency electromagnetic fields (LF-EMF) and simulated microgravity (SMG) have been observed to affect chondrogenesis. A controlled bioreactor system was developed to apply LF-EMF and SMG singly or combined during chondrogenic differentiation of human mesenchymal stem cells (hMSCs) in 3D culture. Material and methods An external motor gear SMG bioreactor was combined with magnetic Helmholtz coils for EMF (5 mT; 15 Hz). Pellets of hMSCs (±TGF-β3) were cultured (P5) under SMG, LF-EMF, LF-EMF/SMG and control (1 g) conditions for 3 weeks. Sections were stained with safranin-O and collagen type II. Gene expression was evaluated by microarray and real-time polymerase chain reaction analysis. Results Simulated microgravity application significantly changed gene expression; specifically, COLXA1 but also COL2A1, which represents the chondrogenic potential, were reduced (p < 0.05). Low frequency electromagnetic fields application showed no gene expression changes on a microarray basis. LF-EMF/SMG application obtained significant different expression values from cultures obtained under SMG conditions with a re-increase of COL2A1, therefore rescuing the chondrogenic potential, which had been lowered by SMG. Conclusions Simulated microgravity lowered hypertrophy but also the chondrogenic potential of hMSCs. Combined LF-EMF/SMG provided a rescue effect of the chondrogenic potential of hMSCs although no LF-EMF effect was observed under optimal conditions. The study provides new insights into how LF-EMF and SMG affect chondrogenesis of hMSCs and how they generate interdependent effects. PMID:29765449

  4. PREFACE: The XI Mexican School on Particles and Fields

    NASA Astrophysics Data System (ADS)

    2005-01-01

    The XI Mexican School on Particles and Fields took place on 2-13 August 2004, in the city of Xalapa, Veracruz, México. The School continued with the tradition of promoting High Energy Physics among the younger generation in Mexico. Thus, it was aimed specifically at graduate students and postdocs. The School consisted of several courses delivered by international experts on subjects of current interest to the scientific community. The length of each course was of six to eight hours, English being the language of instruction. A novelty in this edition of the School was its total duration (two weeks as opposed to one), the number of hours assigned to one subject, and the addition of some experimental courses for the students to overcome their inhibitions of a direct encounter with the equipment and its usage. There were also a few overview talks delivered by local experts on the current status of some of the research fields actively pursued in Mexico. The XI-MSPF was organized by the Particles and Fields Division of the Mexican Physical Society. It was generously sponsored by several institutions: Universidad de Veracruz, Universidad Nacional Autónoma de México, Universidad Michoacana de San Nicolás de Hidalgo, Centro de Investigaciones y Estudios Avanzados del IPN (CINVESTAV) and Consejo Nacional de Ciencia y Tecnología (CONACyT). We are very grateful to Dr Raúl Arias Lovillo, Dr Víctor Manuel Alcaráz Romero, Dr Asdrúbal Flóres López and Mtro Walter Saiz González, head of the Academic Secretariat, Director and Subdirector of the Office of Scientific Research and Director of the Division of Exact Sciences of the University of Veracruz, respectively, for their invaluable support in all senses to our Summer School. We also appreciate the important and useful assistance provided by Dr Rubén Bernardo Morante López, Director of the Museum of Anthropology of Xalapa, and Dr Héctor Coronel Brizio of the Secretariat of Education and Culture of the state of

  5. Myosin XI-dependent formation of tubular structures from endoplasmic reticulum isolated from tobacco cultured BY-2 cells.

    PubMed

    Yokota, Etsuo; Ueda, Haruko; Hashimoto, Kohsuke; Orii, Hidefumi; Shimada, Tomoo; Hara-Nishimura, Ikuko; Shimmen, Teruo

    2011-05-01

    The reticular network of the endoplasmic reticulum (ER) consists of tubular and lamellar elements and is arranged in the cortical region of plant cells. This network constantly shows shape change and remodeling motion. Tubular ER structures were formed when GTP was added to the ER vesicles isolated from tobacco (Nicotiana tabacum) cultured BY-2 cells expressing ER-localized green fluorescent protein. The hydrolysis of GTP during ER tubule formation was higher than that under conditions in which ER tubule formation was not induced. Furthermore, a shearing force, such as the flow of liquid, was needed for the elongation/extension of the ER tubule. The shearing force was assumed to correspond to the force generated by the actomyosin system in vivo. To confirm this hypothesis, the S12 fraction was prepared, which contained both cytosol and microsome fractions, including two classes of myosins, XI (175-kD myosin) and VIII (BY-2 myosin VIII-1), and ER-localized green fluorescent protein vesicles. The ER tubules and their mesh-like structures were arranged in the S12 fraction efficiently by the addition of ATP, GTP, and exogenous filamentous actin. The tubule formation was significantly inhibited by the depletion of 175-kD myosin from the S12 fraction but not BY-2 myosin VIII-1. Furthermore, a recombinant carboxyl-terminal tail region of 175-kD myosin also suppressed ER tubule formation. The tips of tubules moved along filamentous actin during tubule elongation. These results indicated that the motive force generated by the actomyosin system contributes to the formation of ER tubules, suggesting that myosin XI is responsible not only for the transport of ER in cytoplasm but also for the reticular organization of cortical ER.

  6. [Sources and potential risk of heavy metals in roadside soils of Xi' an City].

    PubMed

    Chen, Jing-hui; Lu, Xin-wei; Zhai, Meng

    2011-07-01

    Based on the X-Ray fluorescence spectroscopic measurement of heavy metals concentration in roadside soil samples from Xi' an City, and by the methods of principal component analysis, cluster analysis, and correlation analysis, this paper approached the possible sources of heavy metals in the roadside soils of the City. In the meantime, potential ecological risk index was used to assess the ecological risk of the heavy metals. In the roadside soils, the mean concentrations of Co, Cr, Cu, Mn, Ni, Pb, and Zn were higher than those of the Shaanxi soil background values. The As, Mn and Ni in roadside soils mainly came from natural source and transportation source, the Cu, Pb, and Zn mainly came from transportation source, and the Co and Cr mainly came from industry source. These heavy metals in the roadside soils belonged to medium pollution, and had medium potential ecological risk.

  7. 10-year prospective cohort follow-up of immediately restored XiVE implants.

    PubMed

    Degidi, Marco; Nardi, Diego; Piattelli, Adriano

    2016-06-01

    The aim of this prospective cohort study was to assess the ten-year performance of the condensing thread, self-tapping apex and internal hexagonal connection XiVE implant supporting partial fixed prostheses placed with an immediate restoration approach. All patients received a fixed two- to four-unit partial provisional restoration supported by immediately loaded implants. The final gold alloy/ceramic restorations were cemented approximately 28 weeks after implant insertion. Marginal bone level, pocket probing depth and percentage of bleeding on probing, biological or technical complications and any other adverse events were measured annually up to ten years after surgery. The overall success and survival rates at implant level were evaluated following the International Congress of Oral Implantologists (ICOI) Pisa Consensus Conference criteria. Implant placement in post-extractive or healed sites, smoking and a history of periodontal treatment were evaluated to assess whether they had an influence on bone resorption or on implant survival. Of 114 patients, for a total of 284 implants, fulfilled all the inclusion criteria and were enrolled in the study. 78 (27.5%) implants placed in 30 (26.3%) patients were lost to follow-up. Eight of 284 (2.8%) implants failed in 8 of 114 (7.0%) patients: one (12.5% of losses) due to failure to achieve osseointegration and seven (87.5% of losses) due to peri-implantitis. No cluster implant failures were assessed. The failure of the implant caused the failure of the prosthesis due to the strategic position of the implant in four patients. At the final ten-year follow-up, 121 (61.4%) implants exhibited a "full success" status with an optimal health condition, 21 (10.9%) implants scored a "satisfactory survival" condition, while 49 (25.49%) of the implants were classified as "compromised survival" status (Misch et al. 2008). Smoking was found to be statistically associated with "implant failure" (P = 0.010), while no association

  8. Charters, Constitutions and By-Laws of the Indian Tribes of North America. Part XI: The Basin-Plateau Tribes. Occasional Publications in Anthropology, Ethnology Series, No. 12.

    ERIC Educational Resources Information Center

    Fay, George E., Comp.

    The Museum of Anthropology, University of Northern Colorado at Greeley, has assembled various American Indian tribal charters, constitutions, and by-laws to comprise a series of publications. The present volume, Part XI of the series, deals with the Indian tribes of Nevada: The Moapa Band of Paiute Indians, the Pyramid Lake Paiute Tribe, the…

  9. Frequency of antimicrobial resistance and integron gene cassettes in Escherichia coli isolated from giant pandas (Ailuropoda melanoleuca) in China.

    PubMed

    Zou, Wencheng; Li, Caiwu; Yang, Xin; Wang, Yongxiang; Cheng, Guangyang; Zeng, Jinxin; Zhang, Xiuzhong; Chen, Yanpeng; Cai, Run; Huang, Qianru; Feng, Lan; Wang, Hongning; Li, Desheng; Zhang, Guiquan; Chen, Yanxi; Zhang, Zhizhong; Zhang, Heming

    2018-03-01

    Escherichia coli (E. coli) is considered as a common opportunistic pathogen, which causes seriously intestinal infections to giant pandas (Ailuropoda melanoleuca) and other animals. The aim of this investigation was to characterize the antimicrobial resistance and integron gene cassettes in E. coli isolated from the faeces of giant pandas in China. A total of 89 E. coli were isolated, after diagnosis of isolates and genomes were extracted. All the isolates were screened for the presence of related drug-resistance genes and integron gene cassettes through the Polymerase Chain Reaction (PCR) and sequencing. In addition, antimicrobial resistance testing was performed according to the standard disk diffusion method (CLSI 2013). The results demonstrated that all the isolates were multi-drug resistance (MDR). High resistance proportions of the E. coli isolates were to streptomycin (93%), cefazolin (90%), amikacin (75%), tetracycline (65%), ampicillin (62%), cefotaxime and trimethoprim-sulfamethoxazole (54%, each). With respect to the various resistance genes; bla CTX-M , sul1, ant (3')-Ia, tetA, qnrB, tetE, floR, aac (6')-Ib, sul2, rmtA, cmlA, rmtB and tetC were identified with the respective frequencies of 44%, 45%, 38%, 37%, 35%, 27%, 26%, 20%, 18%, 15%, 10%, 7% and 4%. None of the isolates was positive for qnrA and cfr genes. Moreover, a further investigation of integron revealed that the emergence of class 1 and 2 integrons were in 47% and 8% isolates, respectively. While class 3 integron was not screened. Six types of containing in class 1 integron specific gene cassettes (dfrA12-orfF-aadA2, dfrA17-aadA5, aadA1, aadA5, dfrA1 and dfrA7) were identified. However, only one gene cassette (dfrA1-sat2-aadA1) was detected in class 2 integron. These finding emphasize that a high level of E. coli isolates harbored antibiotics resistance and integron gene cassettes, which may bring so many potential threats to the health of giant pandas. Copyright © 2018 Elsevier Ltd. All

  10. Field Observation of Heterogeneous Formation of Dicarboxylic acids, Keto-carboxylic acids, α-Dicarbonyls and Nitrate in Xi'an, China during Asian dust storm periods

    NASA Astrophysics Data System (ADS)

    Wang, G.; Wang, J.; Ren, Y.; Li, J.

    2015-12-01

    To understand the formation mechanism of secondary organic aerosols (SOA) on dust surfaces, this study investigated the concentrations and compositions of dicarboxylic acids (C2-C11), keto-carboxylic acids (C3-C7), α-dicarbonyls and inorganic ions in size-segregated aerosols (9-stages) collected in Xi'an, China during the nondust storm and dust storm periods of 2009 and 2011. During the events the ambient particulate dicarboxylic acids were 932-2240 ng m-3, which are comparable and even higher than those in nondust periods. Molecular compositions of the above SOA are similar to those in nondust periods with oxalic acid being the leading species. In the presence of the dust storms, all the above mentioned SOA species in Xi'an were predominantly enriched on the coarse particles (>2.1μm), and oxalic acid well correlated with NO3- (R2=0.72, p<0.001) rather than SO42-.This phenomenon differs greatly from the SOA in any other nondust period that is characterized by an enrichment of oxalic acid in fine particles and a strong correlation of oxalic acid with SO42-. Our results further demonstrate that NO3- in the dust periods in Xi'an was mostly derived from secondary oxidation, whereas SO42- during the events was largely derived from surface soil of Gobi deserts. We propose a formation pathway to explain these observations, in which nitric acid and/or nitrogen oxides react with dust to produce Ca(NO3)2 and form a liquid phase on the surface of dust aerosols via water vapor-absorption of Ca(NO3)2, followed by a partitioning of the gas-phase water-soluble organic precursors (e.g.,glyoxal and methylglyoxal) into the aqueous-phase and a subsequent oxidation into oxalic acid. To the best of our knowledge, we found for the first time the enrichment of glyoxal and methylglyoxal on dust surface. Our data suggest an important role of nitrate in the heterogeneous formation process of SOA on the surface of Asian dust.

  11. Content of Heavy Metal in the Dust of Leisure Squares and Its Health Risk Assessment-A Case Study of Yanta District in Xi'an.

    PubMed

    Shao, Tianjie; Pan, Lihuan; Chen, Zhiqing; Wang, Ruiyuan; Li, Wenjing; Qin, Qing; He, Yuran

    2018-02-25

    Taking Yanta District in Xi'an as the research object, the present study measures the contents of Cadmium (Cd), Lead (Pb), Copper (Cu), Nickel (Ni), and Chromium (Cr) in dust samples and further assesses the health risk of heavy metals intake through dust based on the assessment method of human exposure risk proposed by U.S. EPA, with an aim to investigate the content of heavy metal in the dust of leisure squares and its exposure risk. As the results indicate, the average contents of five heavy metals are obviously higher than the soil background value in Shaanxi Province. Therefore, Cd, Ni, Cu, Pb, and Cr are obviously enriched in urban surface dust in Shaanxi Province, due to the influence of human activities. In addition, it can also be found that the non-carcinogen exposure risk in children is significantly higher than that in adults with the risk values of these five heavy metals all one order of magnitude higher than those of adults. Irrespective of whether addressing the results for children or adults, the non-carcinogen exposure doses of five heavy metals are sorted as Cr > Pb > Cu > Ni > Cd. According to the present situation, for a child, the total non-carcinogenic risk values of five heavy metals have exceeded the safety limit in 11 of the 20 leisure squares in Yanta District of Xi'an. That means the leisure squares are no longer suitable for physical and recreational activities. For the five heavy metals, the average non-carcinogenic risk value of Cr is largest, and causes the largest threat to health in Yanta District, Xi'an. The carcinogenic exposure doses of the heavy metals Cr, Cd, and Ni are very low in respiratory pathways and there is no carcinogenic health risk. In general, the Cr content in dust in domestic cities is higher than that of foreign cities; however, the Pb content is much lower.

  12. Polycyclic Aromatic Hydrocarbons in Urban Soil in the Semi-arid City of Xi'an, Northwest China: Composition, Distribution, Sources, and Relationships with Soil Properties.

    PubMed

    Wang, Lijun; Zhang, Panqing; Wang, Li; Zhang, Wenjuan; Shi, Xingmin; Lu, Xinwei; Li, Xiaoping; Li, Xiaoyun

    2018-03-27

    Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the environment. This study collected a total of 62 urban soil samples from the typical semi-arid city of Xi'an in Northwest. They were analyzed for the composition, distribution, and sources of PAHs as well as the relationships with soil properties. The sum of 16 individual PAHs (∑16PAHs) ranged from 390.6 to 10,652.8 μg/kg with a mean of 2052.6 μg/kg. The average ∑16PAHs decreased in the order of the third ring road (2321.1 μg/kg) > the first ring road (1893.7 μg/kg) > the second ring road (1610.0 μg/kg), and in the order of industrial areas (3125.6 μg/kg) > traffic areas (2551.6 μg/kg) > educational areas (2414.4 μg/kg) > parks (1649.5 μg/kg) > mixed commercial and traffic areas (1332.8 μg/kg) > residential areas (1031.0 μg/kg). The most abundant PAHs in the urban soil were 3- to 5-ring PAHs. Elevated levels of PAHs were found in industrial and traffic areas from the east and west suburbs and the northwest corner of Xi'an as well as the northeast corner in the urban district of Xi'an. PAHs in the urban soil were mainly related to the combustion of fossil fuel (i.e., coal, gasoline, diesel, and natural gas) and biomass (i.e., grass and wood) (variance contribution 57.2%) as well as the emissions of petroleum and its products (variance contribution 29.9%). Soil texture and magnetic susceptibility were the main factors affecting the concentration of PAHs in urban soil. Meanwhile, this study suggested that the single, rapid, and nondeductive magnetic measurements can be an indicator of soil pollution by PAHs.

  13. Multiple α-Glucoside Transporter Genes in Brewer’s Yeast

    PubMed Central

    Jespersen, Lene; Cesar, Lene B.; Meaden, Philip G.; Jakobsen, Mogens

    1999-01-01

    Maltose and maltotriose are the two most abundant fermentable sugars in brewer’s wort, and the rate of uptake of these sugars by brewer’s yeast can have a major impact on fermentation performance. In spite of this, no information is currently available on the genetics of maltose and maltotriose uptake in brewing strains of yeast. In this work, we studied 30 brewing strains of yeast (5 ale strains and 25 lager strains) with the aim of examining the alleles of maltose and maltotriose transporter genes contained by them. To do this, we hybridized gene probes to chromosome blots. Studies performed with laboratory strains have shown that maltose utilization is conferred by any one of five unlinked but highly homologous MAL loci (MAL1 to MAL4 and MAL6). Gene 1 at each locus encodes a maltose transporter. All of the strains of brewer’s yeast examined except two were found to contain MAL11 and MAL31 sequences, and only one of these strains lacked MAL41. MAL21 was not present in the five ale strains and 12 of the lager strains. MAL61 was not found in any of the yeast strains. In three of the lager strains, there was evidence that MAL transporter gene sequences occurred on chromosomes other than those known to carry MAL loci. Sequences corresponding to the AGT1 gene, which encodes a transporter of several α-glucosides, including maltose and maltotriose, were detected in all but one of the yeast strains. Homologues of AGT1 were identified in three of the lager strains, and two of these homologues were mapped, one to chromosome II and the other to chromosome XI. AGT1 appears to be a member of a family of closely related genes, which may have arisen in brewer’s yeast in response to selective pressure. PMID:9925567

  14. Analysis of Polymorphism of Angiotensin System Genes (ACE, AGTR1, and AGT) and Gene ITGB3 in Patients with Arterial Hypertension in Combination with Metabolic Syndrome.

    PubMed

    Zotova, T Yu; Kubanova, A P; Azova, M M; Aissa, A Ait; Gigani, O O; Frolov, V A

    2016-07-01

    Changes in the frequencies of genotypes and mutant alleles of ACE, AGTR1, AGT, and ITGB3 genes were analyzed in patients with arterial hypertension coupled with metabolic syndrome (N=15) and compared with population data and corresponding parameters in patients with isolated hypertension (N=15). Increased frequency of genotype ID of ACE gene (hypertension predictor) was confirmed for both groups. In case of isolated hypertension, M235M genotype (gene AGT) was more frequent, in case of hypertension combined with metabolic syndrome, the frequency of genotypes A1166C and C1166C of the gene AGTR1 was higher in comparison with population data. Comparison of mutant allele frequencies in the two groups showed that at the 90% significance level allele T of the AGT gene was more frequent in hypertension coupled with metabolic syndrome (OR=1.26) and genotype A1166A of the AGTR1 gene was more frequent in the group with isolated hypertension.

  15. Effects of Experiment Learning Strategy versus Expository and Cognitive Style for Physical Learning Result for Senior High School Student at Class XI of Senior High School

    ERIC Educational Resources Information Center

    Prayekti

    2016-01-01

    The research was aimed to know Effects of Experiment Learning Strategy versus Expository and Cognitive Style for Physical Learning Result of Senior High School Student at Class XI of Senior High School. Data was collected by test and observation. It is processed by ANCOVA and different test (t-test). (1) The result showed that all learning system…

  16. Impact of grid size on uniform scanning and IMPT plans in XiO treatment planning system for brain cancer

    PubMed Central

    Zheng, Yuanshui

    2015-01-01

    The main purposes of this study are to: 1) evaluate the accuracy of XiO treatment planning system (TPS) for different dose calculation grid size based on head phantom measurements in uniform scanning proton therapy (USPT); and 2) compare the dosimetric results for various dose calculation grid sizes based on real computed tomography (CT) dataset of pediatric brain cancer treatment plans generated by USPT and intensity‐modulated proton therapy (IMPT) techniques. For phantom study, we have utilized the anthropomorphic head proton phantom provided by Imaging and Radiation Oncology Core (IROC). The imaging, treatment planning, and beam delivery were carried out following the guidelines provided by the IROC. The USPT proton plan was generated in the XiO TPS, and dose calculations were performed for grid size ranged from 1 to 3 mm. The phantom containing thermoluminescent dosimeter (TLDs) and films was irradiated using uniform scanning proton beam. The irradiated TLDs were read by the IROC. The calculated doses from the XiO for different grid sizes were compared to the measured TLD doses provided by the IROC. Gamma evaluation was done by comparing calculated planar dose distribution of 3 mm grid size with measured planar dose distribution. Additionally, IMPT plan was generated based on the same CT dataset of the IROC phantom, and IMPT dose calculations were performed for grid size ranged from 1 to 3 mm. For comparative purpose, additional gamma analysis was done by comparing the planar dose distributions of standard grid size (3 mm) with that of other grid sizes (1, 1.5, 2, and 2.5 mm) for both the USPT and IMPT plans. For patient study, USPT plans of three pediatric brain cancer cases were selected. IMPT plans were generated for each of three pediatric cases. All patient treatment plans (USPT and IMPT) were generated in the XiO TPS for a total dose of 54 Gy (relative biological effectiveness [RBE]). Treatment plans (USPT and IMPT) of each case was recalculated for

  17. Family planning management of the floating population in Xi'an city.

    PubMed

    1996-12-01

    This article describes the population of migrants living in Xincheng District of Xi'an City, China. Xincheng district is a commercial center that includes the largest wholesale market in northwest China, Kangfulu Market in Sanfuwan village. The resident population of the district amounts to about 450,000 people. 72,000 additional population are the floating population of migrants, of whom about 50% are women of childbearing age. The district established stringent family planning policies in order to limit unplanned childbearing. Family planning policies were the collaborative work among staff members from departments of industry and commerce, labor, education, finance, public health, civil affairs, family planning, and other related agencies. Management of family planning is based on subdistrict committees, resident committees, and local permanent population. These individuals and groups provide registration for temporary residence, verify birth certificates, establish contraceptive status, and encourage landlords to disseminate birth control information among their tenants. The population around Kangfulu Market includes about 800 permanent residents and about 3000- 6000 migrants. The village authorities provide family planning and medical services free of charge to migrants. Villagers register migrant children in schools and offer business help to the newcomers. These efforts have contributed to fewer births among migrants.

  18. Extreme assay sensitivity in molecular diagnostics further unveils intratumour heterogeneity in metastatic colorectal cancer as well as artifactual low-frequency mutations in the KRAS gene.

    PubMed

    Mariani, Sara; Bertero, Luca; Osella-Abate, Simona; Di Bello, Cristiana; Francia di Celle, Paola; Coppola, Vittoria; Sapino, Anna; Cassoni, Paola; Marchiò, Caterina

    2017-07-25

    Gene mutations in the RAS family rule out metastatic colorectal carcinomas (mCRCs) from anti-EGFR therapies. We report a retrospective analysis by Sequenom Massarray and fast COLD-PCR followed by Sanger sequencing on 240 mCRCs. By Sequenom, KRAS and NRAS exons 2-3-4 were mutated in 52.9% (127/240) of tumours, while BRAF codon 600 mutations reached 5% (12/240). Fast COLD-PCR found extra mutations at KRAS exon 2 in 15/166 (9%) of samples, previously diagnosed by Sequenom as wild-type or mutated at RAS (exons 3-4) or BRAF genes. After UDG digestion results were reproduced in 2/12 analysable subclonally mutated samples leading to a frequency of true subclonal KRAS mutations of 1.2% (2.1% of the previous Sequenom wild-type subgroup). In 10 out of 12 samples, the subclonal KRAS mutations disappeared (9 out of 12) or turned to a different sequence variant (1 out of 12). mCRC can harbour coexisting multiple gene mutations. High sensitivity assays allow the detection of a small subset of patients harbouring true subclonal KRAS mutations. However, DNA changes with mutant allele frequencies <3% detected in formalin-fixed paraffin-embedded samples may be artifactual in a non-negligible fraction of cases. UDG pre-treatment of DNA is mandatory to identify true DNA changes in archival samples and avoid misinterpretation due to artifacts.

  19. Magnesium Increases Homoeologous Crossover Frequency During Meiosis in ZIP4 (Ph1 Gene) Mutant Wheat-Wild Relative Hybrids.

    PubMed

    Rey, María-Dolores; Martín, Azahara C; Smedley, Mark; Hayta, Sadiye; Harwood, Wendy; Shaw, Peter; Moore, Graham

    2018-01-01

    Wild relatives provide an important source of useful traits in wheat breeding. Wheat and wild relative hybrids have been widely used in breeding programs to introduce such traits into wheat. However, successful introgression is limited by the low frequency of homoeologous crossover (CO) between wheat and wild relative chromosomes. Hybrids between wheat carrying a 70 Mb deletion on chromosome 5B ( ph1b ) and wild relatives, have been exploited to increase the level of homoeologous CO, allowing chromosome exchange between their chromosomes. In ph1b -rye hybrids, CO number increases from a mean of 1 CO to 7 COs per cell. CO number can be further increased up to a mean of 12 COs per cell in these ph1b hybrids by treating the plants with Hoagland solution. More recently, it was shown that the major meiotic crossover gene ZIP4 on chromosome 5B ( TaZIP4-B2 ) within the 70 Mb deletion, was responsible for the restriction of homoeologous COs in wheat-wild relative hybrids, confirming the ph1b phenotype as a complete Tazip4-B2 deletion mutant ( Tazip4-B2 ph1b) . In this study, we have identified the particular Hoagland solution constituent responsible for the increased chiasma frequency in Tazip4-B2 ph1b mutant-rye hybrids and extended the analysis to Tazip4-B2 TILLING and CRISPR mutant- Ae variabilis hybrids. Chiasma frequency at meiotic metaphase I, in the absence of each Hoagland solution macronutrient (NH 4 H 2 PO 4 , KNO 3 , Ca (NO 3 )2·4H 2 O or Mg SO 4 ·7H 2 O) was analyzed. A significant decrease in homoeologous CO frequency was observed when the Mg 2+ ion was absent. A significant increase of homoeologous CO frequency was observed in all analyzed hybrids, when plants were irrigated with a 1 mM Mg 2+ solution. These observations suggest a role for magnesium supplementation in improving the success of genetic material introgression from wild relatives into wheat.

  20. Supplement: Proceedings XIth Latin American Congress of Surface Science and Its Applications (XI CLACSA)

    NASA Astrophysics Data System (ADS)

    Häberle, Patricio; Fuenzalida, Victor

    2004-07-01

    The 2003 Congreso Latinoamericano de Ciencia de Superficies y sus Aplicaciones (Latin American Congress of Surface Science and Its Applications) was held in Pucón, Chile, 7-12 December 2003. XI CLACSA is the continuation of a series of events that started in 1980. Until 1992, this series was called Simposio Latinoamericano de Física de Superficies (SLAFS). In recognition of the interdisciplinary nature of the field, starting in 1994 the meeting became CLACSA. The conference was organized by the Sociedad Latinoamericana de Ciencia de Superficies (SLACS) with the purpose of becoming a forum for the exchange of information associated with scientific research carried out in Latin America in the field of surface physics, systems of low dimensionality and areas related to condensed matter physics and science of materials. This scientific event has enjoyed a large participation from Latin American scientists, and has helped to stimulate the collaboration between researchers from Europe, Latin America and the United States.

  1. A Printed Xi-Shaped Left-Handed Metamaterial on Low-Cost Flexible Photo Paper.

    PubMed

    Ashraf, Farhad Bin; Alam, Touhidul; Islam, Mohammad Tariqul

    2017-07-05

    A Xi-shaped meta structure, has been introduced in this paper. A modified split-ring resonator (MSRR) and a capacitive loaded strip (CLS) were used to achieve the left-handed property of the metamaterial. The structure was printed using silver metallic nanoparticle ink, using a very low-cost photo paper as a substrate material. Resonators were inkjet-printed using silver nanoparticle metallic ink on paper to make this metamaterial flexible. It is also free from any kind of chemical waste, which makes it eco-friendly. A double negative region from 8.72 GHz to 10.91 GHz (bandwidth of 2.19 GHz) in the X-band microwave spectra was been found. Figure of merit was also obtained to measure any loss in the double negative region. The simulated result was verified by the performance of the fabricated prototype. The total dimensions of the proposed structure were 0.29 λ × 0.29 λ × 0.007 λ . It is a promising unit cell because of its simplicity, cost-effectiveness, and easy fabrication process.

  2. Metal contamination in campus dust of Xi'an, China: a study based on multivariate statistics and spatial distribution.

    PubMed

    Chen, Hao; Lu, Xinwei; Li, Loretta Y; Gao, Tianning; Chang, Yuyu

    2014-06-15

    The concentrations of As, Ba, Co, Cr, Cu, Mn, Ni, Pb, V and Zn in campus dust from kindergartens, elementary schools, middle schools and universities of Xi'an, China were determined by X-ray fluorescence spectrometry. Correlation coefficient analysis, principal component analysis (PCA) and cluster analysis (CA) were used to analyze the data and to identify possible sources of these metals in the dust. The spatial distributions of metals in urban dust of Xi'an were analyzed based on the metal concentrations in campus dusts using the geostatistics method. The results indicate that dust samples from campuses have elevated metal concentrations, especially for Pb, Zn, Co, Cu, Cr and Ba, with the mean values of 7.1, 5.6, 3.7, 2.9, 2.5 and 1.9 times the background values for Shaanxi soil, respectively. The enrichment factor results indicate that Mn, Ni, V, As and Ba in the campus dust were deficiently to minimally enriched, mainly affected by nature and partly by anthropogenic sources, while Co, Cr, Cu, Pb and Zn in the campus dust and especially Pb and Zn were mostly affected by human activities. As and Cu, Mn and Ni, Ba and V, and Pb and Zn had similar distribution patterns. The southwest high-tech industrial area and south commercial and residential areas have relatively high levels of most metals. Three main sources were identified based on correlation coefficient analysis, PCA, CA, as well as spatial distribution characteristics. As, Ni, Cu, Mn, Pb, Zn and Cr have mixed sources - nature, traffic, as well as fossil fuel combustion and weathering of materials. Ba and V are mainly derived from nature, but partly also from industrial emissions, as well as construction sources, while Co principally originates from construction. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. Frequency-dependent ultrasound-induced transformation in E. coli.

    PubMed

    Deeks, Jeremy; Windmill, James; Agbeze-Onuma, Maduka; Kalin, Robert M; Argondizza, Peter; Knapp, Charles W

    2014-12-01

    Ultrasound-enhanced gene transfer (UEGT) is continuing to gain interest across many disciplines; however, very few studies investigate UEGT efficiency across a range of frequencies. Using a variable frequency generator, UEGT was tested in E. coli at six ultrasonic frequencies. Results indicate frequency can significantly influence UEGT efficiency positively and negatively. A frequency of 61 kHz improved UEGT efficiency by ~70 % higher, but 99 kHz impeded UEGT to an extent worse than no ultrasound exposure. The other four frequencies (26, 133, 174, and 190 kHz) enhanced transformation compared to no ultrasound, but efficiencies did not vary. The influence of frequency on UEGT efficiency was observed across a range of operating frequencies. It is plausible that frequency-dependent dynamics of mechanical and chemical energies released during cavitational-bubble collapse (CBC) are responsible for observed UEGT efficiencies.

  4. Plasminogen Activator Inhibitor-1 (PAI-1) gene 4G/5G alleles frequency distribution in the Lebanese population.

    PubMed

    Shammaa, Dina M R; Sabbagh, Amira S; Taher, Ali T; Zaatari, Ghazi S; Mahfouz, Rami A R

    2008-09-01

    Plasminogen activator inhibitor-1 (PAI-1) is an inhibitor of fibrinolysis. Increased plasma PAI-1 levels play an essential role in the pathogenesis of cardiovascular risk and other diseases associated with thrombosis. The 4G/5G polymorphism of the PAI-1 promoter region has been extensively studied in different populations. We studied 160 healthy unrelated Lebanese individuals using a reverse hybridization PCR assay to detect the 5G/5G, 4G/5G and, 4G/4G genotypes of the PAI-1 gene and the frequencies of the 4G and 5G alleles. We found that 4G/5G genotype was the most prevalent (45.6%) followed by 5G/5G (36.9%) and 4G/4G (17.5%). The frequencies of the 4G and 5G alleles were calculated to be 0.403 and 0.597, respectively. Compared to other ethnic communities, the Lebanese population was found to harbour a relatively high prevalence of the rare 4G allele. This, in turn, may predispose this population to develop cardiovascular diseases and other thrombotic clinical conditions. This study aids to enhance our understanding of the genetic features of the Lebanese population.

  5. Adaptive aneuploidy protects against thiol peroxidase deficiency by increasing respiration via key mitochondrial proteins.

    PubMed

    Kaya, Alaattin; Gerashchenko, Maxim V; Seim, Inge; Labarre, Jean; Toledano, Michel B; Gladyshev, Vadim N

    2015-08-25

    Aerobic respiration is a fundamental energy-generating process; however, there is cost associated with living in an oxygen-rich environment, because partially reduced oxygen species can damage cellular components. Organisms evolved enzymes that alleviate this damage and protect the intracellular milieu, most notably thiol peroxidases, which are abundant and conserved enzymes that mediate hydrogen peroxide signaling and act as the first line of defense against oxidants in nearly all living organisms. Deletion of all eight thiol peroxidase genes in yeast (∆8 strain) is not lethal, but results in slow growth and a high mutation rate. Here we characterized mechanisms that allow yeast cells to survive under conditions of thiol peroxidase deficiency. Two independent ∆8 strains increased mitochondrial content, altered mitochondrial distribution, and became dependent on respiration for growth but they were not hypersensitive to H2O2. In addition, both strains independently acquired a second copy of chromosome XI and increased expression of genes encoded by it. Survival of ∆8 cells was dependent on mitochondrial cytochrome-c peroxidase (CCP1) and UTH1, present on chromosome XI. Coexpression of these genes in ∆8 cells led to the elimination of the extra copy of chromosome XI and improved cell growth, whereas deletion of either gene was lethal. Thus, thiol peroxidase deficiency requires dosage compensation of CCP1 and UTH1 via chromosome XI aneuploidy, wherein these proteins support hydroperoxide removal with the reducing equivalents generated by the electron transport chain. To our knowledge, this is the first evidence of adaptive aneuploidy counteracting oxidative stress.

  6. Implementation of ASME Code, Section XI, Code Case N-770, on Alternative Examination Requirements for Class 1 Butt Welds Fabricated with Alloy 82/182

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

    Sullivan, Edmund J.; Anderson, Michael T.

    In May 2010, the NRC issued a proposed notice of rulemaking that includes a provision to add a new section to its rules to require licensees to implement ASME Code Case N-770, ‘‘Alternative Examination Requirements and Acceptance Standards for Class 1 PWR Piping and Vessel Nozzle Butt Welds Fabricated with UNS N06082 or UNS W86182 Weld Filler Material With or Without the Application of Listed Mitigation Activities, Section XI, Division 1,’’ with 15 conditions. Code Case N-770 contains baseline and inservice inspection (ISI) requirements for unmitigated butt welds fabricated with Alloy 82/182 material and preservice and ISI requirements for mitigatedmore » butt welds. The NRC stated that application of ASME Code Case N-770 is necessary because the inspections currently required by the ASME Code, Section XI, were not written to address stress corrosion cracking Alloy 82/182 butt welds, and the safety consequences of inadequate inspections can be significant. The NRC expects to issue the final rule incorporating this code case into its regulations in the spring 2011 time frame. This paper discusses the new examination requirements, the conditions that NRC is imposing , and the major concerns with implementation of the new Code Case.« less

  7. Helicusin E, isochromophilone X and isochromophilone XI: new chloroazaphilones produced by the fungus Bartalinia robillardoides strain LF550.

    PubMed

    Jansen, Nils; Ohlendorf, Birgit; Erhard, Arlette; Bruhn, Torsten; Bringmann, Gerhard; Imhoff, Johannes F

    2013-03-12

    Microbial studies of the Mediterranean sponge Tethya aurantium led to the isolation of the fungus Bartalinia robillardoides strain LF550. The strain produced a number of secondary metabolites belonging to the chloroazaphilones. This is the first report on the isolation of chloroazaphilones of a fungal strain belonging to the genus Bartalinia. Besides some known compounds (helicusin A (1) and deacetylsclerotiorin (2)), three new chloroazaphilones (helicusin E (3); isochromophilone X (4) and isochromophilone XI (5)) and one new pentaketide (bartanolide (6)) were isolated. The structure elucidations were based on spectroscopic analyses. All isolated compounds revealed different biological activity spectra against a test panel of four bacteria: three fungi; two tumor cell lines and two enzymes.

  8. Rapid genotyping assays for the 4-base pair deletion of canine MDR1/ABCB1 gene and low frequency of the mutant allele in Border Collie dogs.

    PubMed

    Mizukami, Keijiro; Chang, Hye-Sook; Yabuki, Akira; Kawamichi, Takuji; Hossain, Mohammad A; Rahman, Mohammad M; Uddin, Mohammad M; Yamato, Osamu

    2012-01-01

    P-glycoprotein, encoded by the MDR1 or ABCB1 gene, is an integral component of the blood-brain barrier as an efflux pump for xenobiotics crucial in limiting drug uptake into the central nervous system. Dogs homozygous for a 4-base pair deletion of the canine MDR1 gene show altered expression or function of P-glycoprotein, resulting in neurotoxicosis after administration of the substrate drugs. In the present study, the usefulness of microchip electrophoresis for genotyping assays detecting this deletion mutation was evaluated. Mutagenically separated polymerase chain reaction (MS-PCR) and real-time PCR assays were newly developed and evaluated. Furthermore, a genotyping survey was carried out in a population of Border Collies dogs in Japan to determine the allele frequency in this breed. Microchip electrophoresis showed advantages in detection sensitivity and time saving over other modes of electrophoresis. The MS-PCR assay clearly discriminated all genotypes. Real-time PCR assay was most suitable for a large-scale survey due to its high throughput and rapidity. The genotyping survey demonstrated that the carrier and mutant allele frequencies were 0.49% and 0.25%, respectively, suggesting that the mutant allele frequency in Border Collies is markedly low compared to that in the susceptible dog breeds such as rough and smooth Collies.

  9. Ab initio gene identification in metagenomic sequences

    PubMed Central

    Zhu, Wenhan; Lomsadze, Alexandre; Borodovsky, Mark

    2010-01-01

    We describe an algorithm for gene identification in DNA sequences derived from shotgun sequencing of microbial communities. Accurate ab initio gene prediction in a short nucleotide sequence of anonymous origin is hampered by uncertainty in model parameters. While several machine learning approaches could be proposed to bypass this difficulty, one effective method is to estimate parameters from dependencies, formed in evolution, between frequencies of oligonucleotides in protein-coding regions and genome nucleotide composition. Original version of the method was proposed in 1999 and has been used since for (i) reconstructing codon frequency vector needed for gene finding in viral genomes and (ii) initializing parameters of self-training gene finding algorithms. With advent of new prokaryotic genomes en masse it became possible to enhance the original approach by using direct polynomial and logistic approximations of oligonucleotide frequencies, as well as by separating models for bacteria and archaea. These advances have increased the accuracy of model reconstruction and, subsequently, gene prediction. We describe the refined method and assess its accuracy on known prokaryotic genomes split into short sequences. Also, we show that as a result of application of the new method, several thousands of new genes could be added to existing annotations of several human and mouse gut metagenomes. PMID:20403810

  10. Medicinal Flowers. XXXII. Structures of oleanane-type triterpene saponins, perennisosides VIII, IX, X, XI, and XII, from the flowers of Bellis perennis.

    PubMed

    Morikawa, Toshio; Li, Xuezheng; Nishida, Eriko; Nakamura, Seikou; Ninomiya, Kiyofumi; Matsuda, Hisashi; Hamao, Makoto; Muraoka, Osamu; Hayakawa, Takao; Yoshikawa, Masayuki

    2011-01-01

    Five new triterpene saponins perennisosides VIII (1), IX (2), X (3), XI (4), and XII (5) were isolated from the MeOH-eluated fraction of the methanolic extract from the flowers of Bellis perennis. The MeOH-eluted fraction of the methanolic extract from the flowers of B. perennis was found to inhibit gastric emptying in olive oil-loaded mice at a dose of 200 mg/kg, per os (p.o.). The stereostructures of 1-5 were elucidated on the basis of chemical and spectroscopic evidence.

  11. Haplotype diversity in 11 candidate genes across four populations.

    PubMed

    Beaty, T H; Fallin, M D; Hetmanski, J B; McIntosh, I; Chong, S S; Ingersoll, R; Sheng, X; Chakraborty, R; Scott, A F

    2005-09-01

    Analysis of haplotypes based on multiple single-nucleotide polymorphisms (SNP) is becoming common for both candidate gene and fine-mapping studies. Before embarking on studies of haplotypes from genetically distinct populations, however, it is important to consider variation both in linkage disequilibrium (LD) and in haplotype frequencies within and across populations, as both vary. Such diversity will influence the choice of "tagging" SNPs for candidate gene or whole-genome association studies because some markers will not be polymorphic in all samples and some haplotypes will be poorly represented or completely absent. Here we analyze 11 genes, originally chosen as candidate genes for oral clefts, where multiple markers were genotyped on individuals from four populations. Estimated haplotype frequencies, measures of pairwise LD, and genetic diversity were computed for 135 European-Americans, 57 Chinese-Singaporeans, 45 Malay-Singaporeans, and 46 Indian-Singaporeans. Patterns of pairwise LD were compared across these four populations and haplotype frequencies were used to assess genetic variation. Although these populations are fairly similar in allele frequencies and overall patterns of LD, both haplotype frequencies and genetic diversity varied significantly across populations. Such haplotype diversity has implications for designing studies of association involving samples from genetically distinct populations.

  12. Extreme Ultraviolet Emission Lines of Iron Fe XI-XIII

    NASA Astrophysics Data System (ADS)

    Lepson, Jaan; Beiersdorfer, P.; Brown, G. V.; Liedahl, D. A.; Brickhouse, N. S.; Dupree, A. K.

    2013-04-01

    The extreme ultraviolet (EUV) spectral region (ca. 20--300 Å) is rich in emission lines from low- to mid-Z ions, particularly from the middle charge states of iron. Many of these emission lines are important diagnostics for astrophysical plasmas, providing information on properties such as elemental abundance, temperature, density, and even magnetic field strength. In recent years, strides have been made to understand the complexity of the atomic levels of the ions that emit the lines that contribute to the richness of the EUV region. Laboratory measurements have been made to verify and benchmark the lines. Here, we present laboratory measurements of Fe XI, Fe XII, and Fe XIII between 40-140 Å. The measurements were made at the Lawrence Livermore electron beam ion trap (EBIT) facility, which has been optimized for laboratory astrophysics, and which allows us to select specific charge states of iron to help line identification. We also present new calculations by the Hebrew University - Lawrence Livermore Atomic Code (HULLAC), which we also utilized for line identification. We found that HULLAC does a creditable job of reproducing the forest of lines we observed in the EBIT spectra, although line positions are in need of adjustment, and line intensities often differed from those observed. We identify or confirm a number of new lines for these charge states. This work was supported by the NASA Solar and Heliospheric Program under Contract NNH10AN31I and the DOE General Plasma Science program. Work was performed in part under the auspices of the Department of Energy by Lawrence Livermore National Laboratory under Contract DEAC52-07NA27344.

  13. Staphylococcus aureus Isolates Carrying Panton-Valentine Leucocidin Genes: Their Frequency, Antimicrobial Patterns, and Association With Infectious Disease in Shahrekord City, Southwest Iran

    PubMed Central

    Shariati, Laleh; Validi, Majid; Hasheminia, Ali Mohammad; Ghasemikhah, Reza; Kianpour, Fariborz; Karimi, Ali; Nafisi, Mohammad Reza; Tabatabaiefar, Mohammad Amin

    2016-01-01

    Background: A diversity of virulence factors work together to create the pathogenicity of Staphylococcus aureus. These factors include cell surface components that promote adherence to surfaces as well as exoproteins such as Panton-Valentine leukocidin (PVL), encoded by the luk-PV genes, that invade or bypass the immune system and are toxic to the host, thereby enhancing the severity of infections caused by methicillin-resistant Staphylococcus aureus (MRSA). Objectives: The aim of this study was to determine the frequency of PVL-positive MRSA strains by real-time PCR and their antibiotic susceptibility patterns by phenotypic test. Materials and Methods: In total, 284 Staphylococcus isolates, identified by phenotypic methods from clinical samples of Shahrekord University Hospitals, Shahrekord, Iran, were tested for nuc, mecA, and PVL genes by TaqMan real-time PCR. The antibiotic susceptibility patterns of PVL-containing MRSA strains were determined via the disk diffusion method. Results: In total, 196 isolates (69%) were nuc positive (i.e., S. aureus); of those isolates, 96 (49%) were mecA positive (MRSA). Eighteen (18.8%) of the 96 MRSA positive and 3 (3%) of the 100 methicillin-susceptible Staphylococcus aureus (MSSA) strains were PVL positive. PVL-positive MRSA strains were mostly recovered from tracheal specimens. Eight PVL-positive MRSA strains were resistant to all the tested antibiotics except vancomycin. A significant correlation (P = 0.001) was found between the mecA positivity and the presence of luk-PV genes. Conclusions: Community acquired (CA)-MRSA is becoming a public health concern in many parts of the world, including Asian countries. The variable prevalence of luk-PV-positive MRSA isolates in different regions and their rather high frequency in pneumonia necessitate the application of rapid diagnostic methods such as real-time PCR to improve treatment effectiveness. PMID:27099685

  14. Staphylococcus aureus Isolates Carrying Panton-Valentine Leucocidin Genes: Their Frequency, Antimicrobial Patterns, and Association With Infectious Disease in Shahrekord City, Southwest Iran.

    PubMed

    Shariati, Laleh; Validi, Majid; Hasheminia, Ali Mohammad; Ghasemikhah, Reza; Kianpour, Fariborz; Karimi, Ali; Nafisi, Mohammad Reza; Tabatabaiefar, Mohammad Amin

    2016-01-01

    A diversity of virulence factors work together to create the pathogenicity of Staphylococcus aureus. These factors include cell surface components that promote adherence to surfaces as well as exoproteins such as Panton-Valentine leukocidin (PVL), encoded by the luk-PV genes, that invade or bypass the immune system and are toxic to the host, thereby enhancing the severity of infections caused by methicillin-resistant Staphylococcus aureus (MRSA). The aim of this study was to determine the frequency of PVL-positive MRSA strains by real-time PCR and their antibiotic susceptibility patterns by phenotypic test. In total, 284 Staphylococcus isolates, identified by phenotypic methods from clinical samples of Shahrekord University Hospitals, Shahrekord, Iran, were tested for nuc, mecA, and PVL genes by TaqMan real-time PCR. The antibiotic susceptibility patterns of PVL-containing MRSA strains were determined via the disk diffusion method. In total, 196 isolates (69%) were nuc positive (i.e., S. aureus); of those isolates, 96 (49%) were mecA positive (MRSA). Eighteen (18.8%) of the 96 MRSA positive and 3 (3%) of the 100 methicillin-susceptible Staphylococcus aureus (MSSA) strains were PVL positive. PVL-positive MRSA strains were mostly recovered from tracheal specimens. Eight PVL-positive MRSA strains were resistant to all the tested antibiotics except vancomycin. A significant correlation (P = 0.001) was found between the mecA positivity and the presence of luk-PV genes. Community acquired (CA)-MRSA is becoming a public health concern in many parts of the world, including Asian countries. The variable prevalence of luk-PV-positive MRSA isolates in different regions and their rather high frequency in pneumonia necessitate the application of rapid diagnostic methods such as real-time PCR to improve treatment effectiveness.

  15. Frequency of common polymorphisms in Caveolin 1 (CAV1 ) gene in adults with high serum triglycerides from Colombian Caribbean Coast

    PubMed Central

    Ruiz-Diaz, Maria Stephany; Gomez-Camargo, Doris Esther; Gomez-Alegria, Claudio Jaime

    2017-01-01

    Abstract Background: Caveolin 1 gene (CAV1) has been associated with insulin resistance, metabolic syndrome and hypertension in humans. Also, it has been related to high serum triglycerides in rodents, however there is little evidence of this relation in humans. Aim: To describe frequencies of common variations in CAV1 in adults with high serum triglycerides. Methods: A case-control study was carried out with adults from Colombian Caribbean Coast. A whole blood sample was employed to measure serum concentrations of triglycerides, glucose, total cholesterol and HDLc. Six common Single Nucleotide Polymorphism (SNP) in CAV1 were genotyped (rs926198, rs3779512, rs10270569, rs11773845, rs7804372 and rs1049337). Allelic and genotypic frequencies were determined by direct count and Hardy-Weinberg Equilibrium (HWE) was assessed. Case and control groups were compared with null-hypothesis tests. Results: A total of 220 cases and 220 controls were included. For rs3779512 an excess in homozygotes frequency was found within case group (40.4% (GG), 41.3% (GT) and 18.1% (TT); Fis=0.13, p=0.03). Another homozygotes excess among case group was found in rs7804372 (59.5% (TT), 32.3% (TA) and 8.2% (AA); Fis= 0.12, p= 0.04). In rs1049337, cases also showed an excess in homozygotes frequency (52.7% (CC), 35.0% (CT) and 12.3% (TT); Fis= 0.16, p= 0.01). Finally, for rs1049337 there were differences in genotype distribution between case and control groups (p <0.05). Conclusion: An increased frequency of homozygote genotypes was found in subjects with high serum triglycerides. These findings suggest that minor alleles for SNPs rs3779512, rs7804372 and rs1049337 might be associated to higher risk of hypertriglyceridemia. PMID:29662258

  16. TNF-alpha SNP haplotype frequencies in equidae.

    PubMed

    Brown, J J; Ollier, W E R; Thomson, W; Matthews, J B; Carter, S D; Binns, M; Pinchbeck, G; Clegg, P D

    2006-05-01

    Tumour necrosis factor alpha (TNF-alpha) is a pro-inflammatory cytokine that plays a crucial role in the regulation of inflammatory and immune responses. In all vertebrate species the genes encoding TNF-alpha are located within the major histocompatability complex. In the horse TNF-alpha has been ascribed a role in a variety of important disease processes. Previously two single nucleotide polymorphisms (SNPs) have been reported within the 5' un-translated region of the equine TNF-alpha gene. We have examined the equine TNF-alpha promoter region further for additional SNPs by analysing DNA from 131 horses (Equus caballus), 19 donkeys (E. asinus), 2 Grant's zebras (E. burchellii boehmi) and one onager (E. hemionus). Two further SNPs were identified at nucleotide positions 24 (T/G) and 452 (T/C) relative to the first nucleotide of the 522 bp polymerase chain reaction product. A sequence variant at position 51 was observed between equidae. SNaPSHOT genotyping assays for these and the two previously reported SNPs were performed on 457 horses comprising seven different breeds and 23 donkeys to determine the gene frequencies. SNP frequencies varied considerably between different horse breeds and also between the equine species. In total, nine different TNF-alpha promoter SNP haplotypes and their frequencies were established amongst the various equidae examined, with some haplotypes being found only in horses and others only in donkeys or zebras. The haplotype frequencies observed varied greatly between different horse breeds. Such haplotypes may relate to levels of TNF-alpha production and disease susceptibility and further investigation is required to identify associations between particular haplotypes and altered risk of disease.

  17. Extreme assay sensitivity in molecular diagnostics further unveils intratumour heterogeneity in metastatic colorectal cancer as well as artifactual low-frequency mutations in the KRAS gene

    PubMed Central

    Mariani, Sara; Bertero, Luca; Osella-Abate, Simona; Di Bello, Cristiana; Francia di Celle, Paola; Coppola, Vittoria; Sapino, Anna; Cassoni, Paola; Marchiò, Caterina

    2017-01-01

    Background: Gene mutations in the RAS family rule out metastatic colorectal carcinomas (mCRCs) from anti-EGFR therapies. Methods: We report a retrospective analysis by Sequenom Massarray and fast COLD-PCR followed by Sanger sequencing on 240 mCRCs. Results: By Sequenom, KRAS and NRAS exons 2-3-4 were mutated in 52.9% (127/240) of tumours, while BRAF codon 600 mutations reached 5% (12/240). Fast COLD-PCR found extra mutations at KRAS exon 2 in 15/166 (9%) of samples, previously diagnosed by Sequenom as wild-type or mutated at RAS (exons 3-4) or BRAF genes. After UDG digestion results were reproduced in 2/12 analysable subclonally mutated samples leading to a frequency of true subclonal KRAS mutations of 1.2% (2.1% of the previous Sequenom wild-type subgroup). In 10 out of 12 samples, the subclonal KRAS mutations disappeared (9 out of 12) or turned to a different sequence variant (1 out of 12). Conclusions: mCRC can harbour coexisting multiple gene mutations. High sensitivity assays allow the detection of a small subset of patients harbouring true subclonal KRAS mutations. However, DNA changes with mutant allele frequencies <3% detected in formalin-fixed paraffin-embedded samples may be artifactual in a non-negligible fraction of cases. UDG pre-treatment of DNA is mandatory to identify true DNA changes in archival samples and avoid misinterpretation due to artifacts. PMID:28618430

  18. Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species.

    PubMed

    Bowman, Larry L; Kondrateva, Elizaveta S; Timofeyev, Maxim A; Yampolsky, Lev Y

    2018-06-01

    Local adaptation and phenotypic plasticity are main mechanisms of organisms' resilience in changing environments. Both are affected by gene flow and are expected to be weak in zooplankton populations inhabiting large continuous water bodies and strongly affected by currents. Lake Baikal, the deepest and one of the coldest lakes on Earth, experienced epilimnion temperature increase during the last 100 years, exposing Baikal's zooplankton to novel selective pressures. We obtained a partial transcriptome of Epischura baikalensis (Copepoda: Calanoida), the dominant component of Baikal's zooplankton, and estimated SNP allele frequencies and transcript abundances in samples from regions of Baikal that differ in multiyear average surface temperatures. The strongest signal in both SNP and transcript abundance differentiation is the SW-NE gradient along the 600+ km long axis of the lake, suggesting isolation by distance. SNP differentiation is stronger for nonsynonymous than synonymous SNPs and is paralleled by differential survival during a laboratory exposure to increased temperature, indicating directional selection operating on the temperature gradient. Transcript abundance, generally collinear with the SNP differentiation, shows samples from the warmest, less deep location clustering together with the southernmost samples. Differential expression is more frequent among transcripts orthologous to candidate thermal response genes previously identified in model arthropods, including genes encoding cytoskeleton proteins, heat-shock proteins, proteases, enzymes of central energy metabolism, lipid and antioxidant pathways. We conclude that the pivotal endemic zooplankton species in Lake Baikal exists under temperature-mediated selection and possesses both genetic variation and plasticity to respond to novel temperature-related environmental pressures. © 2018 John Wiley & Sons Ltd.

  19. [Operation and interaction peculiarities of diagnostic laboratories involved in providing protection from infectious diseases during the XXII Olympic Winter Games and XI Paralympic Winter Games 2014 in Sochi].

    PubMed

    Onishenko, G G; Popova, A Iu; Bragina, I V; Kuz'kin, B P; Ezhlova, E B; Demina, Iu V; Gus'kov, A S; Ivanov, G E; Chikina, L V; Klindukhova, V P; Grechanaia, T V; Tesheva, S Ch; Kulichenko, A N; Efremenko, D B; Manin, E A; Kuznetsova, I V; Parkhomenko, V V; Kulichenko, O A; Rafeenko, G K; Shcherbina, L I; Zavora, D L; Briukhanov, A F; Eldinova, V E; Iunicheva, Iu V; Derliatko, S K; Komarov, N S

    2015-01-01

    The experience of the organization and functioning of the laboratory network during the XXII Olympic Winter Games and XI Paralympic Winter Games of 2014 in Sochi is considered. Efforts to establish an effective system of laboratory support, the order of work and interaction of diagnostic laboratories involved in diseases control of population during the Olympic Games are analyzed.

  20. 3-D Acoustic Scattering from 2-D Rough Surfaces Using A Parabolic Equation Model

    DTIC Science & Technology

    2013-12-01

    Frequency Acoustic Propagation in Shallow Water.” Journal of Oceanic Engineering, September 2011: 1–10. Liu, Jin Yuan, Chen Fen Huang, and Ping Chang...loss values at a constant depth. .............................52  xi LIST OF ACRONYMS AND ABBREVIATIONS FD Finite Difference MMPE Monterey...2013). First, at each range step ( xi ), the 3-D field is transformed from cross-range spatial variable (y) to cross-range wavenumber variable (ky

  1. Detection of virulence-associated genes in pathogenic and commensal avian Escherichia coli isolates.

    PubMed

    Paixão, A C; Ferreira, A C; Fontes, M; Themudo, P; Albuquerque, T; Soares, M C; Fevereiro, M; Martins, L; Corrêa de Sá, M I

    2016-07-01

    Poultry colibacillosis due to Avian Pathogenic Escherichia coli (APEC) is responsible for several extra-intestinal pathological conditions, leading to serious economic damage in poultry production. The most commonly associated pathologies are airsacculitis, colisepticemia, and cellulitis in broiler chickens, and salpingitis and peritonitis in broiler breeders. In this work a total of 66 strains isolated from dead broiler breeders affected with colibacillosis and 61 strains from healthy broilers were studied. Strains from broiler breeders were typified with serogroups O2, O18, and O78, which are mainly associated with disease. The serogroup O78 was the most prevalent (58%). All the strains were checked for the presence of 11 virulence genes: 1) arginine succinyltransferase A (astA); ii) E.coli hemeutilization protein A (chuA); iii) colicin V A/B (cvaA/B); iv) fimbriae mannose-binding type 1 (fimC); v) ferric yersiniabactin uptake A (fyuA); vi) iron-repressible high-molecular-weight proteins 2 (irp2); vii) increased serum survival (iss); viii) iron-uptake systems of E.coli D (iucD); ix) pielonefritis associated to pili C (papC); x) temperature sensitive haemaglutinin (tsh), and xi) vacuolating autotransporter toxin (vat), by Multiplex-PCR. The results showed that all genes are present in both commensal and pathogenic E. coli strains. The iron uptake-related genes and the serum survival gene were more prevalent among APEC. The adhesin genes, except tsh, and the toxin genes, except astA, were also more prevalent among APEC isolates. Except for astA and tsh, APEC strains harbored the majority of the virulence-associated genes studied and fimC was the most prevalent gene, detected in 96.97 and 88.52% of APEC and AFEC strains, respectively. Possession of more than one iron transport system seems to play an important role on APEC survival. © 2016 Poultry Science Association Inc.

  2. Optimization of the photoelectric properties and photo-stability of CH3NH3PbBrXI3-X films for efficient planar perovskite solar cells

    NASA Astrophysics Data System (ADS)

    Jiang, Zhaoyi; Zhang, Weijia; Ma, Denghao; Liu, Haixu; Yu, Wei; Fan, Zhiqiang; Zhang, Yulong; Lu, Chaoqun; Li, Yun

    2018-01-01

    In this paper, the CH3NH3PbBrXI3-X films were prepared by introducing CH3NH3Br into CH3NH3I precursor solution, after which the microstructure and photoelectric properties of the films were thoroughly investigated. Due to Br incorporation in the perovskite films, the band gap increased and the light absorption was slightly reduced while the charge carrier lifetime was prolonged due to the enhanced crystallinity. For the films with higher bromine content, the red shift of the photoluminescence peaks indicated that the phase segregation appeared in the films under illumination, which led to the formation of the iodine-rich domains in this process and the reduced carrier lifetime. On the contrary, for films with lower bromine content, the red shift of the photoluminescence peaks was negligible, which revealed that instability of the perovskite films under illumination can be suppressed by adjusting the bromine content of the films. Consequently, by moderate Br incorporation (CH3NH3Br/CH3NH3I mole ratio = 3:7), the CH3NH3PbBrXI3-X films with optimal photoelectric properties and photo-stability were achieved, and the stable photoelectric conversion efficiency of corresponding device under illumination can reach 13.8%.

  3. [Study of androgen receptor and phosphoglycerate kinase gene polymorphism in major cellular components of the so-called pulmonary sclerosing hemangioma].

    PubMed

    Qi, Feng-jie; Zhang, Xiu-wei; Zhang, Yong-xing; Dai, Shun-dong; Wang, En-hua

    2006-05-01

    To study the clonality of polygonal cells and surface cuboidal cells in the so-called pulmonary sclerosing hemangioma (PSH). 17 female surgically resected PSH were found. The polygonal cells and surface cuboidal cells of the 17 PSH cases were microdissected from routine hematoxylin and eosin-stained sections. Genomic DNA was extracted, pretreated through incubation with methylation-sensitive restrictive endonuclease HhaI or HpaII, and amplified by nested polymerase chain reaction for X chromosome-linked androgen receptor (AR) and phosphoglycerate kinase (PGK) genes. The length polymorphism of AR gene was demonstrated by denaturing polyacrylamide gel electrophoresis and silver staining. The PGK gene products were treated with Bst XI and resolved on agarose gel. Amongst the 17 female cases of PSH, 15 samples were successfully amplified for AR and PGK genes. The rates of polymorphism were 53% (8/15) and 27% (4/15) for AR and PGK genes respectively. Polygonal cells and surface cuboidal cells of 10 cases which were suitable for clonality study, showed the same loss of alleles (clonality ratio = 0) or unbalanced methylation pattern (clonality ratio < 0.25). The polygonal cells and surface cuboidal cells in PSH demonstrate patterns of monoclonal proliferation, indicating that both represent true neoplastic cells.

  4. Population-specific documentation of pharmacogenomic markers and their allelic frequencies in FINDbase.

    PubMed

    Georgitsi, Marianthi; Viennas, Emmanouil; Gkantouna, Vassiliki; Christodoulopoulou, Elena; Zagoriti, Zoi; Tafrali, Christina; Ntellos, Fotios; Giannakopoulou, Olga; Boulakou, Athanassia; Vlahopoulou, Panagiota; Kyriacou, Eva; Tsaknakis, John; Tsakalidis, Athanassios; Poulas, Konstantinos; Tzimas, Giannis; Patrinos, George P

    2011-01-01

    Population and ethnic group-specific allele frequencies of pharmacogenomic markers are poorly documented and not systematically collected in structured data repositories. We developed the Frequency of Inherited Disorders Pharmacogenomics database (FINDbase-PGx), a separate module of the FINDbase, aiming to systematically document pharmacogenomic allele frequencies in various populations and ethnic groups worldwide. We critically collected and curated 214 scientific articles reporting pharmacogenomic markers allele frequencies in various populations and ethnic groups worldwide. Subsequently, in order to host the curated data, support data visualization and data mining, we developed a website application, utilizing Microsoft™ PivotViewer software. Curated allelic frequency data pertaining to 144 pharmacogenomic markers across 14 genes, representing approximately 87,000 individuals from 150 populations worldwide, are currently included in FINDbase-PGx. A user-friendly query interface allows for easy data querying, based on numerous content criteria, such as population, ethnic group, geographical region, gene, drug and rare allele frequency. FINDbase-PGx is a comprehensive database, which, unlike other pharmacogenomic knowledgebases, fulfills the much needed requirement to systematically document pharmacogenomic allelic frequencies in various populations and ethnic groups worldwide.

  5. Genetics Home Reference: factor XI deficiency

    MedlinePlus

    ... with this disorder can have heavy or prolonged menstrual bleeding (menorrhagia) or prolonged bleeding after childbirth. In ... the particular mutation and whether one or both copies of the F11 gene in each cell have ...

  6. Effect of feeding frequency on growth, body composition, antioxidant status and mRNA expression of immunodependent genes before or after ammonia-N stress in juvenile oriental river prawn, Macrobrachium nipponense.

    PubMed

    Ding, Zhili; Kong, Youqin; Zhang, Yixiang; Li, Jingfen; Cao, Fang; Zhou, Junbo; Ye, Jinyun

    2017-09-01

    Feeding frequency is important for the improvement of growth performance and immunity of aquatic animals. In this study, the effect of feeding frequency on growth, body composition, antioxidant status and mRNA expression of immunodependent genes before or after ammonia-N stress was examined in Macrobrachium nipponense. Prawns were randomly assigned to one of five feeding frequencies (1, 2, 3, 4 and 6 times/day) following the same ration size over an 8-week growth trial. After the feeding trial, prawns were challenged by ammonia-N. The weight gain of prawns fed with 3-6 times/day was significantly higher than that of prawns fed with 1 time/day. The best feed conversion ratio was obtained from prawns fed with 3-6 times/day. Body crude lipid with feeding frequency of 3, 4 or 6 times/day was quite lower than that with 1 time/day. High feeding frequency (6 times/day) induced significantly elevated hepatopancreas super oxide dismutase and catalase activities. The malondialdehyde level in prawns fed with 6 times/day was also significantly increased, which was higher than that of prawns fed with other feeding frequency. mRNA expression of toll like receptor 3 and myeloid differentiation primary response protein MyD88 was promoted by feeding frequency from 3 to 4 time/day but inhibited by high or low feeding frequency. Similar mRNA expression variation trends of the two genes were observed in prawns after ammonia-N stress. After ammonia-N challenge, the highest cumulative mortality was observed in prawns fed with 6 times/day, which was significantly higher than that of prawns fed with 2-4 times/day. These findings demonstrate that (1) too high feeding frequency induced oxidative stress and malondialdehyde accumulation, negatively affecting the health status of prawns and reduced its resistance to ammonia-N stress; (2) the optimal feeding frequency to improve growth and immune response of this species at juvenile stage is 3-4 times/day; (3) considering costs of labour, a

  7. Absence of FKBP10 in Recessive Type XI Osteogenesis Imperfecta Leads to Diminished Collagen Cross-Linking and Reduced Collagen Deposition in Extracellular Matrix

    PubMed Central

    Barnes, Aileen M.; Cabral, Wayne A.; Weis, MaryAnn; Makareeva, Elena; Mertz, Edward L.; Leikin, Sergey; Eyre, David; Trujillo, Carlos; Marini, Joan C.

    2012-01-01

    Recessive osteogenesis imperfecta (OI) is caused by defects in genes whose products interact with type I collagen for modification and/or folding. We identified a Palestinian pedigree with moderate and lethal forms of recessive OI caused by mutations in FKBP10 or PPIB, which encode endoplasmic reticulum resident chaperone/isomerases FKBP65 and CyPB, respectively. In one pedigree branch, both parents carry a deletion in PPIB (c.563_566delACAG), causing lethal type IX OI in their two children. In another branch, a child with moderate type XI OI has a homozygous FKBP10 mutation (c.1271_1272delCCinsA). Proband FKBP10 transcripts are 4% of control and FKBP65 protein is absent from proband cells. Proband collagen electrophoresis reveals slight band broadening, compatible with ≈10% overmodification. Normal chain incorporation, helix folding, and collagen Tm support a minimal general collagen chaperone role for FKBP65. However, there is a dramatic decrease in collagen deposited in culture despite normal collagen secretion. Mass spectrometry reveals absence of hydroxylation of the collagen telopeptide lysine involved in cross-linking, suggesting that FKBP65 is required for lysyl hydroxylase activity or access to type I collagen telopeptide lysines, perhaps through its function as a peptidylprolyl isomerase. Proband collagen to organics ratio in matrix is approximately 30% of normal in Raman spectra. Immunofluorescence shows sparse, disorganized collagen fibrils in proband matrix. PMID:22718341

  8. Micronuclei in cord blood lymphocytes and associations with biomarkers of exposure to carcinogens and hormonally active factors, gene polymorphisms, and gene expression: the NewGeneris cohort.

    PubMed

    Merlo, Domenico Franco; Agramunt, Silvia; Anna, Lívia; Besselink, Harrie; Botsivali, Maria; Brady, Nigel J; Ceppi, Marcello; Chatzi, Leda; Chen, Bowang; Decordier, Ilse; Farmer, Peter B; Fleming, Sarah; Fontana, Vincenzo; Försti, Asta; Fthenou, Eleni; Gallo, Fabio; Georgiadis, Panagiotis; Gmuender, Hans; Godschalk, Roger W; Granum, Berit; Hardie, Laura J; Hemminki, Kari; Hochstenbach, Kevin; Knudsen, Lisbeth E; Kogevinas, Manolis; Kovács, Katalin; Kyrtopoulos, Soterios A; Løvik, Martinus; Nielsen, Jeanette K; Nygaard, Unni Cecilie; Pedersen, Marie; Rydberg, Per; Schoket, Bernadette; Segerbäck, Dan; Singh, Rajinder; Sunyer, Jordi; Törnqvist, Margareta; van Loveren, Henk; van Schooten, Frederik J; Vande Loock, Kim; von Stedingk, Hans; Wright, John; Kleinjans, Jos C; Kirsch-Volders, Micheline; van Delft, Joost H M

    2014-02-01

    Leukemia incidence has increased in recent decades among European children, suggesting that early-life environmental exposures play an important role in disease development. We investigated the hypothesis that childhood susceptibility may increase as a result of in utero exposure to carcinogens and hormonally acting factors. Using cord blood samples from the NewGeneris cohort, we examined associations between a range of biomarkers of carcinogen exposure and hormonally acting factors with micronuclei (MN) frequency as a proxy measure of cancer risk. Associations with gene expression and genotype were also explored. DNA and protein adducts, gene expression profiles, circulating hormonally acting factors, and GWAS (genome-wide association study) data were investigated in relation to genomic damage measured by MN frequency in lymphocytes from 623 newborns enrolled between 2006 and 2010 across Europe. Malondialdehyde DNA adducts (M1dG) were associated with increased MN frequency in binucleated lymphocytes (MNBN), and exposure to androgenic, estrogenic, and dioxin-like compounds was associated with MN frequency in mononucleated lymphocytes (MNMONO), although no monotonic exposure-outcome relationship was observed. Lower frequencies of MNBN were associated with a 1-unit increase expression of PDCD11, LATS2, TRIM13, CD28, SMC1A, IL7R, and NIPBL genes. Gene expression was significantly higher in association with the highest versus lowest category of bulky and M1dG-DNA adducts for five and six genes, respectively. Gene expression levels were significantly lower for 11 genes in association with the highest versus lowest category of plasma AR CALUX® (chemically activated luciferase expression for androgens) (8 genes), ERα CALUX® (for estrogens) (2 genes), and DR CALUX® (for dioxins). Several SNPs (single-nucleotide polymorphisms) on chromosome 11 near FOLH1 significantly modified associations between androgen activity and MNBN frequency. Polymorphisms in EPHX1/2 and CYP2E1

  9. [Models for biomass estimation of four shrub species planted in urban area of Xi'an city, Northwest China].

    PubMed

    Yao, Zheng-Yang; Liu, Jian-Jun

    2014-01-01

    Four common greening shrub species (i. e. Ligustrum quihoui, Buxus bodinieri, Berberis xinganensis and Buxus megistophylla) in Xi'an City were selected to develop the highest correlation and best-fit estimation models for the organ (branch, leaf and root) and total biomass against different independent variables. The results indicated that the organ and total biomass optimal models of the four shrubs were power functional model (CAR model) except for the leaf biomass model of B. megistophylla which was logarithmic functional model (VAR model). The independent variables included basal diameter, crown diameter, crown diameter multiplied by height, canopy area and canopy volume. B. megistophylla significantly differed from the other three shrub species in the independent variable selection, which were basal diameter and crown-related factors, respectively.

  10. The kinetic temperature in the interior of the Xi Ophiuchi cloud from Copernicus observations of interstellar C2

    NASA Technical Reports Server (NTRS)

    Snow, T. P., Jr.

    1978-01-01

    Satellite observations of transitions of C2 at 2312 Angstroms in the spectrum of Xi Ophiuchi were carried out to evaluate the kinetic temperature of the interior cloud. A column density of 1.22 x 10 to the 12th per sq cm is derived from an absorption feature at the 4 sigma level of significance at the position of the R(0) line. This would imply a rotational temperature of not more than 22 K, with a more probable value of less than 16 K. Since total column density (3.2 x 10 to the 12th per sq cm) is found to be lower by a factor of approximately 4 than that which had been previously reported, substantial photo-dissociation of C2 is assumed.

  11. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses.

    PubMed

    Chen, Chih-Yu; Shi, Wenqiang; Balaton, Bradley P; Matthews, Allison M; Li, Yifeng; Arenillas, David J; Mathelier, Anthony; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Brown, Carolyn J; Wasserman, Wyeth W

    2016-11-18

    Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors.

  12. Genotypic and allelic frequencies of gene polymorphisms associated with meat tenderness in Nellore beef cattle.

    PubMed

    Carvalho, M E; Eler, J P; Bonin, M N; Rezende, F M; Biase, F H; Meirelles, F V; Regitano, L C A; Coutinho, L L; Balieiro, J C C; Ferraz, J B S

    2017-02-16

    The objectives of this study were to characterize the allelic and genotypic frequencies of polymorphisms in the µ-calpain and calpastatin genes, and to assess their association with meat tenderness and animal growth in Nellore cattle. We evaluated 605 Nellore animals at 24 months of age, on average, at slaughter. The polymorphisms were determined for the molecular markers CAPN316, CAPN530, CAPN4751, CAPN4753, and UOGACAST1. Analyses of meat tenderness at 7, 14, and 21 days of maturation were performed in samples of longissimus thoracis obtained between the 12th and 13th rib and sheared using a Warner Bratzler Shear Force. Significant effects were observed for meat tenderness at days 7, 14, and 21 of maturation for the marker CAPN4751, at day 21 for the marker CAPN4753, and at days 14 and 21 for the marker UOGCAST1. For genotypic combinations of markers, the results were significant for the combination CAPN4751/UOGCAST1 in the three maturation periods and CAPN4753/UOGCAST1 at days 14 and 21 of maturation.

  13. Polymorphism of the bovine POU1F1 gene: allele frequencies and effects on milk production in three Iranian native breeds and Holstein cattle of Iran.

    PubMed

    Zakizadeh, S; Reissmann, M; Rahimi, G; Javaremi, A Nejati; Reinecke, P; Mirae-Ashtiani, S R; Shahrbabak, M Moradi

    2007-08-01

    The aim of this study was to estimate the allele frequencies in polymorphic site of exon six of POU1F1 gene in three Iranian native and Holstein cattle. Genomic DNA was extracted from 3 Iranian native cattle breeds, including 97 Mazandarani, 87 Sarabi, 112 Golpaygani and also 110 Holstein cattle. A 451 bp fragment of intron 5 and exon 6 were amplified and digested with HinfI restriction enzyme. Frequencies of allele A were 0.37, 0.27, 0.34 and 0.21 for Mazandarani, Sarabi, Golpaygani and Holstein cattle, respectively. Significant differences in genotype frequencies were found between Mazandarani or Golpaygani and Holstein cattle. No significant differences in genotype frequencies were found between Sarabi and Holstein cattle. Transition A to G in nucleotide 1256 is responsible for HinfI(-) allele. No significant association was observed between POU1F1 polymorphism and milk production. Differences in allelic frequency between native Bos indicus breeds (Mazandarani, Golpaygani) and Holstein at the present study might be due to differences in origin breeds, low number of samples and/or as the effect of natural selection in native breeds.

  14. The functional spectrum of low-frequency coding variation.

    PubMed

    Marth, Gabor T; Yu, Fuli; Indap, Amit R; Garimella, Kiran; Gravel, Simon; Leong, Wen Fung; Tyler-Smith, Chris; Bainbridge, Matthew; Blackwell, Tom; Zheng-Bradley, Xiangqun; Chen, Yuan; Challis, Danny; Clarke, Laura; Ball, Edward V; Cibulskis, Kristian; Cooper, David N; Fulton, Bob; Hartl, Chris; Koboldt, Dan; Muzny, Donna; Smith, Richard; Sougnez, Carrie; Stewart, Chip; Ward, Alistair; Yu, Jin; Xue, Yali; Altshuler, David; Bustamante, Carlos D; Clark, Andrew G; Daly, Mark; DePristo, Mark; Flicek, Paul; Gabriel, Stacey; Mardis, Elaine; Palotie, Aarno; Gibbs, Richard

    2011-09-14

    Rare coding variants constitute an important class of human genetic variation, but are underrepresented in current databases that are based on small population samples. Recent studies show that variants altering amino acid sequence and protein function are enriched at low variant allele frequency, 2 to 5%, but because of insufficient sample size it is not clear if the same trend holds for rare variants below 1% allele frequency. The 1000 Genomes Exon Pilot Project has collected deep-coverage exon-capture data in roughly 1,000 human genes, for nearly 700 samples. Although medical whole-exome projects are currently afoot, this is still the deepest reported sampling of a large number of human genes with next-generation technologies. According to the goals of the 1000 Genomes Project, we created effective informatics pipelines to process and analyze the data, and discovered 12,758 exonic SNPs, 70% of them novel, and 74% below 1% allele frequency in the seven population samples we examined. Our analysis confirms that coding variants below 1% allele frequency show increased population-specificity and are enriched for functional variants. This study represents a large step toward detecting and interpreting low frequency coding variation, clearly lays out technical steps for effective analysis of DNA capture data, and articulates functional and population properties of this important class of genetic variation.

  15. An allosteric disulfide bond is involved in enhanced activation of factor XI by protein disulfide isomerase.

    PubMed

    Zucker, M; Seligsohn, U; Yeheskel, A; Mor-Cohen, R

    2016-11-01

    Essentials Reduction of three disulfide bonds in factor (F) XI enhances chromogenic substrate cleavage. We measured FXI activity upon reduction and identified a bond involved in the enhanced activity. Reduction of FXI augments FIX cleavage, probably by faster conversion of FXI to FXIa. The Cys362-Cys482 disulfide bond is responsible for FXI enhanced activation upon its reduction. Background Reduction of factor (F) XI by protein disulfide isomerase (PDI) has been shown to enhance the ability of FXI to cleave its chromogenic substrate. Three disulfide bonds in FXI (Cys118-Cys147, Cys362-Cys482, and Cys321-Cys321) are involved in this augmented activation. Objectives To characterize the mechanisms by which PDI enhances FXI activity. Methods FXI activity was measured following PDI reduction. Thiols that were exposed in FXI after PDI reduction were labeled with 3-(N-maleimidopropionyl)-biocytin (MPB) and detected with avidin. The rate of conversion of FXI to activated FXI (FXIa) following thrombin activation was assessed with western blotting. FXI molecules harboring mutations that disrupt the three disulfide bonds (C147S, C321S, and C482S) were expressed in cells. The antigenicity of secreted FXI was measured with ELISA, and its activity was assessed by the use of a chromogenic substrate. The effect of disulfide bond reduction was analyzed by the use of molecular dynamics. Results Reduction of FXI by PDI enhanced cleavage of both its chromogenic substrate, S2366, and its physiologic substrate, FIX, and resulted in opening of the Cys362-Cys482 bond. The rate of conversion of FXI to FXIa was increased following its reduction by PDI. C482S-FXI showed enhanced activity as compared with both wild-type FXI and C321S-FXI. MD showed that disruption of the Cys362-Cys482 bond leads to a broader thrombin-binding site in FXI. Conclusions Reduction of FXI by PDI enhances its ability to cleave FIX, probably by causing faster conversion of FXI to FXIa. The Cys362-Cys482 disulfide

  16. Quantitative study on spatio-temporal change of urban landscape pattern based on RS/GIS: a case of Xi'an metropolitan area in China

    NASA Astrophysics Data System (ADS)

    Chen, Meiwu; Zong, Yueguang; Ma, Qiang; Li, Jian

    2007-06-01

    The study on landscape pattern is an important field of urban land use and ecological change. Since 1990s, the widely accepted Patch-Corridor-Matrix model is generally used in qualitative description of landscape pattern. In recent years, quantitative evaluation on urban landscape dynamics is becoming hot in research. By making a critical review on existing research methods of landscape pattern, a new approach based on RS/GIS is put forward in this paper, comprising three steps, "General pattern characteristics - Gradient differentiation feature- Directional signature of the landscape", and we call it GGD. This method is applied to the case study of Xi'an metropolitan area in China. The result shows that the method is effective on quantitative study of urban landscape. The preparation of the method GGD is setting up research platform based on RS and GIS. By using the software of Geographical Information System (Arcgis9.0 & Erdas), the authors got the interpretation of remote sensing images of different years, and carried on the division of the landscape type of the research region. By calculating various index of landscape level with software Fragstats3.3 as an assistant tool and adopting three steps of GGD combined with landscape index, this paper can assesses the landscape spatial pattern of urban area: 1) General pattern characteristics analysis is to get transition probability of various landscape through Markov chain and to predict the landscape transformation by introducing CA model. The analysis emphasizes on total landscape structure and its change over time; 2) Gradient characteristic analysis, which makes gradient zone by taking city as a center outwardly with certain distance and contrastively analyzes the landscape index of each subarea, stresses the spatial character of landscape pattern, verifies urban morphology theories and provides the quantitative warranty for establishment of urban modality. Therefore, the analysis is useful for supervising urban

  17. Frequency of enterotoxins, toxic shock syndrome toxin-1, and biofilm formation genes in Staphylococcus aureus isolates from cows with mastitis in the Northeast of Brazil.

    PubMed

    Costa, F N; Belo, N O; Costa, E A; Andrade, G I; Pereira, L S; Carvalho, I A; Santos, R L

    2018-06-01

    Staphylococcus aureus is among the microorganisms more frequently associated with subclinical bovine mastitis. S. aureus may produce several virulence factors. This study aimed at determining the frequency of virulence factors such as enterotoxins, toxic shock syndrome toxin 1, and ica adhesion genes. In addition, we assessed antimicrobial drug resistance in S. aureus isolated from clinical and subclinical cases of mastitis. A total of 88 cows with clinical or subclinical mastitis were sampled, resulting in 38 S. aureus isolates, from which 25 (65.78%) carried toxin genes, including seb, sec, sed, tst, and icaD adhesion gene. These S. aureus isolates belong to 21 ribotypes and three S. aureus strains belonged to the same ribotype producing ica adhesion gene. Approximately 90% of S. aureus strains obtained in our study demonstrated multiple resistance to different antimicrobial agents. The most efficacious antimicrobial agents against the isolates were gentamicin, amoxicillin, and norfloxacin. Gentamicin was the most efficacious agent inhibiting 78.95% of the S. aureus isolates. The least efficacious were penicillin, streptomycin, and ampicillin. Our results can help in understanding the relationship between virulence factors and subclinical mastitis caused by S. aureus. Further research about diversity of S. aureus isolates and genes responsible for the pathogenicity of subclinical mastitis is essential.

  18. Gene-for-genes interactions between cotton R genes and Xanthomonas campestris pv. malvacearum avr genes.

    PubMed

    De Feyter, R; Yang, Y; Gabriel, D W

    1993-01-01

    Six plasmid-borne avirulence (avr) genes were previously cloned from strain XcmH of the cotton pathogen, Xanthomonas campestris pv. malvacearum. We have now localized all six avr genes on the cloned fragments by subcloning and Tn5-gusA insertional mutagenesis. None of these avr genes appeared to exhibit exclusively gene-for-gene patterns of interactions with cotton R genes, and avrB4 was demonstrated to confer avr gene-for-R genes (plural) avirulence to X. c. pv. malvacearum on congenic cotton lines carrying either of two different resistance loci, B1 or B4. Furthermore, the B1 locus appeared to confer R gene-for-avr genes resistance to cotton against isogenic X. c. pv. malvacearum strains carrying any one of three avr genes: avrB4, avrb6, or avrB102. Restriction enzyme, Southern blot hybridization, and DNA sequence analyses showed that the XcmH avr genes are all highly similar to each other, to avrBs3 and avrBsP from the pepper pathogen X. c. pv. vesicatoria, and to the host-specific virulence gene pthA from the citrus pathogen X. citri. The XcmH avr genes differed primarily in the multiplicity of a tandemly repeated 102-base pair motif within the central portions of the genes, repeated from 14 to 23 times in members of this gene family. The complete nucleotide sequence of avrb6 revealed that it is 97% identical in DNA sequence to avrB4, avrBs3, avrBsP, and pthA and that 62-bp inverted terminal repeats mark the boundaries of homology between avrb6 and all members of this Xanthomonas virulence/avirulence gene family sequenced to date. The terminal 38 bp of both inverted repeats are highly similar to the 38-bp consensus terminal sequence of the Tn3 family of transposons. Up to 11 members of the avr gene family appear to be present in North American strains of X. c. pv. malvacearum, including XcmH. The high level of homology observed among these avr genes and their presence in multiple copies may explain the gene-for-genes interactions and also the observed high

  19. Outcrossed sex allows a selfish gene to invade yeast populations.

    PubMed

    Goddard, M R; Greig, D; Burt, A

    2001-12-22

    Homing endonuclease genes (HEGs) in eukaryotes are optional genes that have no obvious effect on host phenotype except for causing chromosomes not containing a copy of the gene to be cut, thus causing them to be inherited at a greater than Mendelian rate via gene conversion. These genes are therefore expected to increase in frequency in outcrossed populations, but not in obligately selfed populations. In order to test this idea, we compared the dynamics of the VDE HEG in six replicate outcrossed and inbred populations of yeast (Saccharomyces cerevisiae). VDE increased in frequency from 0.21 to 0.55 in four outcrossed generations, but showed no change in frequency in the inbred populations. The absence of change in the inbred populations indicates that any effect of VDE on mitotic replication rates is less than 1%. The data from the outcrossed populations best fit a model in which 82% of individuals are derived from outcrossing and VDE is inherited by 74% of the meiotic products from heterozygotes (as compared with 50% for Mendelian genes). These results empirically demonstrate how a host mating system plays a key role in determining the population dynamics of a selfish gene.

  20. Outcrossed sex allows a selfish gene to invade yeast populations.

    PubMed Central

    Goddard, M. R.; Greig, D.; Burt, A.

    2001-01-01

    Homing endonuclease genes (HEGs) in eukaryotes are optional genes that have no obvious effect on host phenotype except for causing chromosomes not containing a copy of the gene to be cut, thus causing them to be inherited at a greater than Mendelian rate via gene conversion. These genes are therefore expected to increase in frequency in outcrossed populations, but not in obligately selfed populations. In order to test this idea, we compared the dynamics of the VDE HEG in six replicate outcrossed and inbred populations of yeast (Saccharomyces cerevisiae). VDE increased in frequency from 0.21 to 0.55 in four outcrossed generations, but showed no change in frequency in the inbred populations. The absence of change in the inbred populations indicates that any effect of VDE on mitotic replication rates is less than 1%. The data from the outcrossed populations best fit a model in which 82% of individuals are derived from outcrossing and VDE is inherited by 74% of the meiotic products from heterozygotes (as compared with 50% for Mendelian genes). These results empirically demonstrate how a host mating system plays a key role in determining the population dynamics of a selfish gene. PMID:11749707

  1. Population-based analysis of the frequency of HFE gene polymorphisms: Correlation with the susceptibility to develop hereditary hemochromatosis.

    PubMed

    Katsarou, Martha-Spyridoula; Latsi, Rosana; Papasavva, Maria; Demertzis, Nikolaos; Kalogridis, Thodoris; Tsatsakis, Aristides M; Spandidos, Demetrios A; Drakoulis, Nikolaos

    2016-07-01

    Hereditary hemochromatosis (HH) is an autosomal recessive genetic disease, characterized by increased dietary iron absorption. Due to the absence of an effective excretory mechanism, the excess iron in the body may accumulate resulting in toxic effects. The HFE gene also affects the activity of hepcidin, a hormone which acts as a negative regulator of iron metabolism. In this study, we performed a population-based analysis of the distribution of three hemochromatosis-related polymorphisms in the HFE gene (rs1800562, rs1799945 and rs1800730). DNA from 1,446 non‑related individuals of Greek ethnicity was collected and analyzed, either from whole blood or buccal swabs. The frequency distribution of these HFE gene polymorphisms was then determined. The results revealed that in our Greek population cohort (gr) the frequencies of each polymorphism were as follows: rs1800562: GG (wild‑type)=97.0%, GA=1.5%, AA=1.5%; rs1799945: CC (wild‑type)=74.4%, CG=23.4%, GG=2.2%; rs1800730: AA (wild‑type)=98.1%, AT=1.5% and TT=0.4%. No association between the HFE polymorphisms rs1800562, rs1799945 and rs1800730 and gender could be established. As regards the rs1800562 polymorphism, the A allele (mutant) was ~1.8‑fold more frequent in the European population (eur) than in the Greek population [(gr)=2,3%<(eur)=4%]. As for the rs1799945 polymorphism, the G allele (mutant) was 1.2‑fold more frequent in the European population than in the Greek population [(gr)=13,9%<(eur)=17%]. As regards the rs1800730 polymorphism, the T allele (mutant) was ~1.7‑fold more frequent in the European population than in the Greek population [(gr)=1.2%<(eur)=2%]. However, these pathogenic mutations were found more frequently in the Greek population compared to the global population (gl) [rs1800562: (gl)=1%<(gr)=2,3%; rs1799945: (gl)=7%<(gr)=13,9%; rs1800730: (gl)=<1%<(gr)=1.2%]. This suggests that the Greek population may differ genetically from the northern European population

  2. Evaluation of ACE gene I/D polymorphism in Iranian elite athletes.

    PubMed

    Shahmoradi, Somayeh; Ahmadalipour, Ali; Salehi, Mansoor

    2014-01-01

    Angiotensin converting enzyme (ACE) is an important gene, which is associated with the successful physical activity. The ACE gene has a major polymorphism (I/D) in intron 16 that determines its plasma and tissue levels. In this study, we aimed to determine whether there is an association between this polymorphism and sports performance in our studied population including elite athletes of different sports disciplines. We investigated allele frequency and genotype distribution of the ACE gene in 156 Iranian elite athletes compared to 163 healthy individuals. We also investigated this allele frequency between elite athletes in three functional groups of endurance, power, and mixed sports performances. DNA was extracted from peripheral blood, and polymerase chain reaction (PCR) method was performed on intron 16 of the ACE gene. The ACE genotype was determined for each subject. Statistical analysis was performed by SPSS 15, and results were analyzed by Chi-Square test. There was a significant difference in genotype distribution and allele frequency of the ACE gene in athletes and control group (P = 0.05, P = 0.03, respectively). There was also a significant difference in allele frequency of the ACE gene in 3 groups of athletes with different sports disciplines (P = 0.045). Proportion of the ACE gene D allele was greater in elite endurance athletes (37 high-distance cyclists) than two other groups. Findings of the present study demonstrated that there is an association between the ACE gene I/D polymorphism and sports performance in Iranian elite athletes.

  3. Trends in gastrectomy and ADH1B and ALDH2 genotypes in Japanese alcoholic men and their gene-gastrectomy, gene-gene and gene-age interactions for risk of alcoholism.

    PubMed

    Yokoyama, Akira; Yokoyama, Tetsuji; Matsui, Toshifumi; Mizukami, Takeshi; Kimura, Mitsuru; Matsushita, Sachio; Higuchi, Susumu; Maruyama, Katsuya

    2013-01-01

    The life-time drinking profiles of Japanese alcoholics have shown that gastrectomy increases susceptibility to alcoholism. We investigated the trends in gastrectomy and alcohol dehydrogenase-1B (ADH1B) and aldehyde dehydrogenase-2 (ALDH2) genotypes and their interactions in alcoholics. This survey was conducted on 4879 Japanese alcoholic men 40 years of age or older who underwent routine gastrointestinal endoscopic screening during the period 1996-2010. ADH1B/ALDH2 genotyping was performed in 3702 patients. A history of gastrectomy was found in 508 (10.4%) patients. The reason for the gastrectomy was peptic ulcer in 317 patients and gastric cancer in 187 patients. The frequency of gastrectomy had gradually decreased from 13.3% in 1996-2000 to 10.5% in 2001-2005 and to 7.8% in 2006-2010 (P < 0.0001). ADH1B*1/*1 was less frequent in the gastrectomy group than in the non-gastrectomy group (age-adjusted prevalence: 20.4 vs. 27.6%, P = 0.006). ALDH2 genotype distribution did not differ between the two groups. The frequency of inactive ALDH2*1/*2 heterozygotes increased slightly from 13.0% in 1996-2000 to 14.0% in 2001-2005 and to 15.4% in 2006-2010 (P < 0.08). Two alcoholism-susceptibility genotypes, ADH1B*1/*1 and ALDH2*1/*1, modestly but significantly tended not to occur in the same individual (P = 0.026). The frequency of ADH1B*1/*1 decreased with ascending age groups. The high frequency of history of gastrectomy suggested that gastrectomy is still a risk factor for alcoholism, although the percentage decreased during the period. The alcoholism-susceptibility genotype ADH1B*1/*1 was less frequent in the gastrectomy group, suggesting a competitive gene-gastrectomy interaction for alcoholism. A gene-gene interaction and gene-age interactions regarding the ADH1B genotype were observed.

  4. Myosin XI-Dependent Formation of Tubular Structures from Endoplasmic Reticulum Isolated from Tobacco Cultured BY-2 Cells1[W][OA

    PubMed Central

    Yokota, Etsuo; Ueda, Haruko; Hashimoto, Kohsuke; Orii, Hidefumi; Shimada, Tomoo; Hara-Nishimura, Ikuko; Shimmen, Teruo

    2011-01-01

    The reticular network of the endoplasmic reticulum (ER) consists of tubular and lamellar elements and is arranged in the cortical region of plant cells. This network constantly shows shape change and remodeling motion. Tubular ER structures were formed when GTP was added to the ER vesicles isolated from tobacco (Nicotiana tabacum) cultured BY-2 cells expressing ER-localized green fluorescent protein. The hydrolysis of GTP during ER tubule formation was higher than that under conditions in which ER tubule formation was not induced. Furthermore, a shearing force, such as the flow of liquid, was needed for the elongation/extension of the ER tubule. The shearing force was assumed to correspond to the force generated by the actomyosin system in vivo. To confirm this hypothesis, the S12 fraction was prepared, which contained both cytosol and microsome fractions, including two classes of myosins, XI (175-kD myosin) and VIII (BY-2 myosin VIII-1), and ER-localized green fluorescent protein vesicles. The ER tubules and their mesh-like structures were arranged in the S12 fraction efficiently by the addition of ATP, GTP, and exogenous filamentous actin. The tubule formation was significantly inhibited by the depletion of 175-kD myosin from the S12 fraction but not BY-2 myosin VIII-1. Furthermore, a recombinant carboxyl-terminal tail region of 175-kD myosin also suppressed ER tubule formation. The tips of tubules moved along filamentous actin during tubule elongation. These results indicated that the motive force generated by the actomyosin system contributes to the formation of ER tubules, suggesting that myosin XI is responsible not only for the transport of ER in cytoplasm but also for the reticular organization of cortical ER. PMID:21427277

  5. Contamination and ecological risk assessment of toxic trace elements in the Xi River, an urban river of Shenyang city, China.

    PubMed

    Lin, Chunye; He, Mengchang; Liu, Xitao; Guo, Wei; Liu, Shaoqing

    2013-05-01

    The objectives of this study were to assess the enrichment, contamination, and ecological risk posed by toxic trace elements in the sediments of the Xi River in the industrialized city of Shenyang, China. Surface sediment and sediment core were collected; analyzed for toxic trace elements; and assessed with an index of geoaccumulation (Igeo), enrichment factor (EF) value, potential ecological risk factor (Er), ecological risk index (RI), and probable effect concentration quotient (PECQ). Elemental concentrations (milligram per kilogram) were 8.5-637.9 for As, 6.5-103.9 for Cd, 12.2-21.9 for Co, 90.6-516.0 for Cr, 258.1-1,791.5 for Cu, 2.6-19.0 for Hg, 70.5-174.5 for Ni, 126.9-1,405.8 for Pb, 3.7-260.0 for Sb, 38.4-100.4 for V, and 503-4,929 for Zn. The Igeo, EF, Er, and PECQ indices showed that the contamination of Cd and Hg was more serious than that of As, Cr, Cu, Ni, Pb, Sb, and Zn, whereas the presence of Co and V might be primarily from natural sources. The Igeo index for Cr and Ni might underestimate the degree of contamination, potentially as a result of high concentrations of these elements in the shale. The RI index was higher than 600, indicating a notably high ecological risk of sediment for the river. The average PECQ for As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn ranged from 1.4 to 4.1 for surface sediment and from 5.2 to 9.6 in the sediment cores, indicating a high potential for an adverse biological effect. It was concluded that the sediment in the Xi River was severely contaminated and should be remediated as a hazardous material.

  6. BRAF Gene Copy Number and Mutant Allele Frequency Correlate with Time to Progression in Metastatic Melanoma Patients Treated with MAPK Inhibitors.

    PubMed

    Stagni, Camilla; Zamuner, Carolina; Elefanti, Lisa; Zanin, Tiziana; Bianco, Paola Del; Sommariva, Antonio; Fabozzi, Alessio; Pigozzo, Jacopo; Mocellin, Simone; Montesco, Maria Cristina; Chiarion-Sileni, Vanna; De Nicolo, Arcangela; Menin, Chiara

    2018-06-01

    Metastatic melanoma is characterized by complex genomic alterations, including a high rate of mutations in driver genes and widespread deletions and amplifications encompassing various chromosome regions. Among them, chromosome 7 is frequently gained in BRAF -mutant melanoma, inducing a mutant allele-specific imbalance. Although BRAF amplification is a known mechanism of acquired resistance to therapy with MAPK inhibitors, it is still unclear if BRAF copy-number variation and BRAF mutant allele imbalance at baseline can be associated with response to treatment. In this study, we used a multimodal approach to assess BRAF copy number and mutant allele frequency in pretreatment melanoma samples from 46 patients who received MAPK inhibitor-based therapy, and we analyzed the association with progression-free survival. We found that 65% patients displayed BRAF gains, often supported by chromosome 7 polysomy. In addition, we observed that 64% patients had a balanced BRAF -mutant/wild-type allele ratio, whereas 14% and 23% patients had low and high BRAF mutant allele frequency, respectively. Notably, a significantly higher risk of progression was observed in patients with a diploid BRAF status versus those with BRAF gains [HR, 2.86; 95% confidence interval (CI), 1.29-6.35; P = 0.01] and in patients with low percentage versus those with a balanced BRAF mutant allele percentage (HR, 4.54; 95% CI, 1.33-15.53; P = 0.016). Our data suggest that quantitative analysis of the BRAF gene could be useful to select the melanoma patients who are most likely to benefit from therapy with MAPK inhibitors. Mol Cancer Ther; 17(6); 1332-40. ©2018 AACR . ©2018 American Association for Cancer Research.

  7. A functional polymorphism of the microRNA-146a gene is associated with susceptibility to drug-resistant epilepsy and seizures frequency.

    PubMed

    Cui, Lili; Tao, Hua; Wang, Yan; Liu, Zhou; Xu, Zhien; Zhou, Haihong; Cai, Yujie; Yao, Lifen; Chen, Beichu; Liang, Wandong; Liu, Yu; Cheng, Wanwen; Liu, Tingting; Ma, Guoda; Li, You; Zhao, Bin; Li, Keshen

    2015-04-01

    Epilepsy is the third most common chronic brain disorder and is characterized by an enduring predisposition for seizures. Recently, a growing body of evidence has suggested that microRNA-146a (miR-146a) is upregulated in the brains of epilepsy patients and of mouse models; furthermore, miR-146a may be involved in the development and progression of seizures through the regulation of inflammation and immune responses. In this report, we performed a case-control study to analyze the relationship between the two potentially functional single nucleotide polymorphisms (SNPs) of the miR-146a gene (rs2910464 and rs57095329) and the risk of epilepsy in a Chinese population comprising 249 cases and 249 healthy controls. Our study comprised 249 epilepsy patients and 249 healthy controls in two regions of China. The DNA was genotyped using the ABI PRISM SNapShot method. The statistical analysis was estimated using the chi-square test or Fisher's exact test. Our results indicated a significant association between the rs57095329 SNP of the miR-146a gene and the risk of drug resistant epilepsy (DRE) (genotypes, p = 0.0258 and alleles, p = 0.0108). Moreover, the rs57095329 A allele was found to be associated with a reduced risk of seizures frequency in DRE patients (all p < 0.001). However, the rs2910164 variant was not associated with epilepsy. Our data indicate that the rs57095329 polymorphism in the promoter region of miR-146a is involved in the genetic susceptibility to DRE and the seizures frequency. Copyright © 2015 British Epilepsy Association. Published by Elsevier Ltd. All rights reserved.

  8. Plasma thromboplastin antecedent (PTA, factor XI): a specific and sensitive radioimmunoassay. [/sup 125/I tracer technique

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

    Saito, H.; Goldsmith, G.H. Jr.

    A specific, sensitive, and reproducible radioimmunoassay for human plasma thromboplastin antecedent (PTA, factor XI) has been developed with purified PTA and monospecific rabbit antiserum. Precise measurements of PTA antigen were possible for concentrations as low as 0.3% of that in normal pooled plasma. Normal plasma contained approximately 6 ..mu..g PTA/ml. A good correlation (correlation coefficient 0.68) existed between the PTA procoagulant assays and radioimmunoassays among 50 normal adults (25 males and 25 females). PTA antigen was markedly reduced in plasma of 13 patients with congenital homozygous PTA deficiency (range <0.003-0.128 U/ml) and 9 patients with hepatic cirrhosis (0.35 +- 0.17more » U/ml), but was normal in those of 9 patients under treatment with warfarin, 8 patients with disseminated intravascular coagulation and 16 patients with other congenital clotting factor abnormalities, including prekallikrein deficiency (Fletcher trait) and high molecular weight kininogen deficiency (Fitzgerald trait).« less

  9. Microsporidia, amitochondrial protists, possess a 70-kDa heat shock protein gene of mitochondrial evolutionary origin.

    PubMed

    Peyretaillade, E; Broussolle, V; Peyret, P; Méténier, G; Gouy, M; Vivarès, C P

    1998-06-01

    An intronless gene encoding a protein of 592 amino acid residues with similarity to 70-kDa heat shock proteins (HSP70s) has been cloned and sequenced from the amitochondrial protist Encephalitozoon cuniculi (phylum Microsporidia). Southern blot analyses show the presence of a single gene copy located on chromosome XI. The encoded protein exhibits an N-terminal hydrophobic leader sequence and two motifs shared by proteobacterial and mitochondrially expressed HSP70 homologs. Phylogenetic analysis using maximum likelihood and evolutionary distances place the E. cuniculi sequence in the cluster of mitochondrially expressed HSP70s, with a higher evolutionary rate than those of homologous sequences. Similar results were obtained after cloning a fragment of the homologous gene in the closely related species E. hellem. The presence of a nuclear targeting signal-like sequence supports a role of the Encephalitozoon HSP70 as a molecular chaperone of nuclear proteins. No evidence for cytosolic or endoplasmic reticulum forms of HSP70 was obtained through PCR amplification. These data suggest that Encephalitozoon species have evolved from an ancestor bearing mitochondria, which is in disagreement with the postulated presymbiotic origin of Microsporidia. The specific role and intracellular localization of the mitochondrial HSP70-like protein remain to be elucidated.

  10. Association of polymorphisms in nicotinic acetylcholine receptor alpha 4 subunit gene (CHRNA4), mu-opioid receptor gene (OPRM1), and ethanol-metabolizing enzyme genes with alcoholism in Korean patients.

    PubMed

    Kim, Soon Ae; Kim, Jong-Woo; Song, Ji-Young; Park, Sunny; Lee, Hee Jae; Chung, Joo-Ho

    2004-01-01

    Findings obtained from several studies indicate that ethanol enhances the activity of alpha4beta2 neuronal nicotinic acetylcholine receptor and support the possibility that a polymorphism of the nicotinic acetylcholine receptor alpha4 subunit gene (CHRNA4) modulates enhancement of nicotinic receptor function by ethanol. To identify the association between the CfoI polymorphism of the CHRNA4 and alcoholism, we examined distribution of genotypes and allele frequencies in Korean patients diagnosed with alcoholism (n = 127) and Korean control subjects without alcoholism (n = 185) with polymerase chain reaction-restriction fragment length polymorphism methods. We were able to detect the association between the CfoI polymorphism of the CHRNA4 and alcoholism in Korean patients (genotype P = .023; allele frequency P = .047). The genotypes and allele frequencies of known polymorphisms in other alcoholism candidate genes, such as alcohol metabolism-related genes [alcohol dehydrogenase 2 (ADH2), aldehyde dehydrogenase 2 (ALDH2), alcohol dehydrogenase 3 (ADH3), and cytochrome P450 2E1 (CYP2E1)] and mu-opioid receptor gene (OPRM1), were studied. The polymorphisms of ADH2, ALDH2, and CYP2E1 were significantly different in Korean patients with alcoholism and Korean control subjects without alcoholism, but ADH3 and OPRM1 did not differ between the two groups.

  11. High frequency of a single nucleotide substitution (c.-6-180T>G) of the canine MDR1/ABCB1 gene associated with phenobarbital-resistant idiopathic epilepsy in Border Collie dogs.

    PubMed

    Mizukami, Keijiro; Yabuki, Akira; Chang, Hye-Sook; Uddin, Mohammad Mejbah; Rahman, Mohammad Mahbubur; Kushida, Kazuya; Kohyama, Moeko; Yamato, Osamu

    2013-01-01

    A single nucleotide substitution (c.-6-180T>G) associated with resistance to phenobarbital therapy has been found in the canine MDR1/ABCB1 gene in Border Collies with idiopathic epilepsy. In the present study, a PCR-restriction fragment length polymorphism assay was developed for genotyping this mutation, and a genotyping survey was carried out in a population of 472 Border Collies in Japan to determine the current allele frequency. The survey demonstrated the frequencies of the T/T wild type, T/G heterozygote, and G/G mutant homozygote to be 60.0%, 30.3%, and 9.8%, respectively, indicating that the frequency of the mutant G allele is extremely high (24.9%) in Border Collies. The results suggest that this high mutation frequency of the mutation is likely to cause a high prevalence of phenobarbital-resistant epilepsy in Border Collies.

  12. Estimating Exceptionally Rare Germline and Somatic Mutation Frequencies via Next Generation Sequencing

    PubMed Central

    Yoon, Song-Ro; Arnheim, Norman; Calabrese, Peter

    2016-01-01

    We used targeted next generation deep-sequencing (Safe Sequencing System) to measure ultra-rare de novo mutation frequencies in the human male germline by attaching a unique identifier code to each target DNA molecule. Segments from three different human genes (FGFR3, MECP2 and PTPN11) were studied. Regardless of the gene segment, the particular testis donor or the 73 different testis pieces used, the frequencies for any one of the six different mutation types were consistent. Averaging over the C>T/G>A and G>T/C>A mutation types the background mutation frequency was 2.6x10-5 per base pair, while for the four other mutation types the average background frequency was lower at 1.5x10-6 per base pair. These rates far exceed the well documented human genome average frequency per base pair (~10−8) suggesting a non-biological explanation for our data. By computational modeling and a new experimental procedure to distinguish between pre-mutagenic lesion base mismatches and a fully mutated base pair in the original DNA molecule, we argue that most of the base-dependent variation in background frequency is due to a mixture of deamination and oxidation during the first two PCR cycles. Finally, we looked at a previously studied disease mutation in the PTPN11 gene and could easily distinguish true mutations from the SSS background. We also discuss the limits and possibilities of this and other methods to measure exceptionally rare mutation frequencies, and we present calculations for other scientists seeking to design their own such experiments. PMID:27341568

  13. Genome-wide association study identifies common and low-frequency variants at the AMH gene locus that strongly predict serum AMH levels in males.

    PubMed

    Perry, John R B; McMahon, George; Day, Felix R; Ring, Susan M; Nelson, Scott M; Lawlor, Debbie A

    2016-01-15

    Anti-Müllerian hormone (AMH) is an essential messenger of sexual differentiation in the foetus and is an emerging biomarker of postnatal reproductive function in females. Due to a paucity of adequately sized studies, the genetic determinants of circulating AMH levels are poorly characterized. In samples from 2815 adolescents aged 15 from the ALSPAC study, we performed the first genome-wide association study of serum AMH levels across a set of ∼9 m '1000 Genomes Reference Panel' imputed genetic variants. Genetic variants at the AMH protein-coding gene showed considerable allelic heterogeneity, with both common variants [rs4807216 (P(Male) = 2 × 10(-49), Beta: ∼0.9 SDs per allele), rs8112524 (P(Male) = 3 × 10(-8), Beta: ∼0.25)] and low-frequency variants [rs2385821 (P(Male) = 6 × 10(-31), Beta: ∼1.2, frequency 3.6%)] independently associated with apparently large effect sizes in males, but not females. For all three SNPs, we highlight mechanistic links to AMH gene function and demonstrate highly significant sex interactions (P(Het) 0.0003-6.3 × 10(-12)), culminating in contrasting estimates of trait variance explained (24.5% in males versus 0.8% in females). Using these SNPs as a genetic proxy for AMH levels, we found no evidence in additional datasets to support a biological role for AMH in complex traits and diseases in men. © The Author 2015. Published by Oxford University Press.

  14. Frequency of pathogenic germline mutations in cancer susceptibility genes in breast cancer patients.

    PubMed

    Kaur, Raman Preet; Shafi, Gowhar; Benipal, Raja Paramjeet Singh; Munshi, Anjana

    2018-04-26

    In this study, we evaluated the incidence of pathogenic germline mutations in 30 breast cancer susceptibility genes in breast cancer patients. Our aim was to understand the involvement of the inherited mutations in these genes in a breast cancer cohort. Two hundred ninety-six female breast cancer patients including 4.5% of familial breast cancer cases were included in the study. 200 ng of genomic DNA was used to evaluate the pathogenic mutations, detected using Global Screening Array (GSA) microchip (Illumina Inc.) according to the manufacturer's instructions. The pathogenic frameshift and nonsense mutations were observed in BRCA2 (10.9%), MLH1 (58.6%), MTHFR (50%), MSH2 (14.2%), and CYTB (52%) genes. Familial breast cancer patients (4.5%) had variations in BRCA2, MLH1, MSH2, and CYTB genes. 28% of patients with metastasis, recurrence, and death harbored mono/biallelic alterations in MSH2, MLH1, and BRCA2 genes. The results of this study can guide to develop a panel to test the breast cancer patients for pathogenic mutations, from Malwa region of Punjab. The screening of MSH2, MLH1, and BRCA2 should be carried in individuals with or without family history of breast cancer as these genes have been reported to increase the cancer risk by tenfold.

  15. Variations in the water vapor distribution and the associated effects on fog and haze events over Xi'an based on Raman lidar data and back trajectories.

    PubMed

    Wang, Yufeng; Zhang, Jing; Fu, Qiang; Song, Yuehui; Di, Huige; Li, Bo; Hua, Dengxin

    2017-10-01

    A combination of more than two years of water vapor lidar data with back trajectory analysis using the hybrid single-particle Lagrangian integrated trajectory (HYSPLIT) model was used to study the long-range transport of air masses and the water vapor distribution characteristics and variations over Xi'an, China (34.233° N, 108.911° E), which is a typical city in Northwest China. High-quality profiles of the water vapor density were derived from a multifunction Raman lidar system built in Xi'an, and more than 2000 sets of profiles with >400 nighttime observations from October 2013 to July 2016 were collected and used for statistical and quantitative analyses. The vertical variations in the water vapor content were discussed. A mutation height of the water vapor exists at 2-4 km with a high occurrence rate of ∼60% during the autumn and winter seasons. This height reflects a distinct stratification in the water vapor content. Additionally, the atmospheric water vapor content was mainly concentrated in the lower troposphere, and the proportion of the water vapor content at 0.5-5 km accounted for 80%-90% of the total water vapor below 10 km. Obvious seasonal variations were observed, including large water vapor content during the spring and summer and small content during the autumn and winter. Combined with back trajectory analysis, the results showed that markedly different water vapor transport pathways contribute to seasonal variations in the water vapor content. South and southeast airflows dominated during the summer, with 30% of the 84 trajectories originating from these areas; however, the air masses during the winter originated from the north and local regions (64.3%) and from the northwest (27%). In addition, we discussed variations in the water vapor during fog and haze weather conditions during the winter. A considerable enhancement in the mean water vapor density at 0.5-3 km exhibited a clear positive correlation (correlation coefficient >0.8) with

  16. Genetic structure of Quechua-speakers of the Central Andes and geographic patterns of gene frequencies in South Amerindian populations.

    PubMed

    Luiselli, D; Simoni, L; Tarazona-Santos, E; Pastor, S; Pettener, D

    2000-09-01

    A sample of 141 Quechua-speaking individuals of the population of Tayacaja, in the Peruvian Central Andes, was typed for the following 16 genetic systems: ABO, Rh, MNSs, P, Duffy, AcP1, EsD, GLOI, PGM1, AK, 6-PGD, Hp, Gc, Pi, C3, and Bf. The genetic structure of the population was analyzed in relation to the allele frequencies available for other South Amerindian populations, using a combination of multivariate and multivariable techniques. Spatial autocorrelation analysis was performed independently for 13 alleles to identify patterns of gene flow in South America as a whole and in more specific geographic regions. We found a longitudinal cline for the AcP1*a and EsD*1 alleles which we interpreted as the result of an ancient longitudinal expansion of a putative ancestral population of modern Amerindians. Monmonnier's algorithm, used to identify areas of sharp genetic discontinuity, suggested a clear east-west differentiation of native South American populations, which was confirmed by analysis of the distribution of genetic distances. We suggest that this pattern of genetic structures is the consequence of the independent peopling of western and eastern South America or to low levels of gene flow between these regions, related to different environmental and demographic histories. Copyright 2000 Wiley-Liss, Inc.

  17. Mutation of Surface Residues to Promote Crystallization of Activated Factor XI as a Complex with Benzamidine: an Essential Step for the Iterative Structure-Based Design of Factor XI Inhibitors

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

    Jin,L.; Pandey, P.; Babine, R.

    Activated factor XI (FXIa) is a key enzyme in the amplification phase of the blood-coagulation cascade. Thus, a selective FXIa inhibitor may have lesser bleeding liabilities and provide a safe alternative for antithrombosis therapy to available drugs on the market. In a previous report, the crystal structures of the catalytic domain of FXIa (rhFXI370-607) in complex with various ecotin mutants have been described [Jin et al. (2005), Journal of Biological Chemistry 280, 4704-4712]. However, ecotin forms a matrix-like interaction with rhFXI370-607 and is impossible to displace with small-molecule inhibitors; ecotin crystals are therefore not suitable for iterative structure-based ligand design.more » In addition, rhFXI370-607 did not crystallize in the presence of small-molecule ligands. In order to obtain the crystal structure of rhFXI370-607 with a weak small-molecule ligand, namely benzamidine, several rounds of surface-residue mutation were implemented to promote crystal formation of rhFXI370-607. A quadruple mutant of rhFXI370-607 (rhFXI370-607-S434A, T475A, C482S, K437A) readily crystallized in the presence of benzamidine. The benzamidine in the preformed crystals was easily exchanged with other FXIa small-molecule inhibitors. These crystals have facilitated the structure-based design of small-molecule FXIa inhibitors.« less

  18. Association of gene polymorphisms in ABO blood group chromosomal regions and menstrual disorders

    PubMed Central

    SU, YONG; KONG, GUI-LIAN; SU, YA-LI; ZHOU, YAN; LV, LI-FANG; WANG, QIONG; HUANG, BAO-PING; ZHENG, RUI-ZHI; LI, QUAN-ZHONG; YUAN, HUI-JUAN; ZHAO, ZHI-GANG

    2015-01-01

    This study aimed to investigate whether single nucleotide polymorphisms (SNPs) located near the gene of the ABO blood group play an important role in the genetic aetiology of menstrual disorders (MDs). Polymerase chain reaction-ligase detection reaction technology was used to detect eight SNPs near the ABO gene location on the chromosomes in 250 cases of MD and 250 cases of normal menstruation. The differences in the distribution of each genotype, as well as the allele frequency in the normal and control groups, were analysed using Pearson's χ2 test to search for disease-associated loci. SHEsis software was used to analyse the linkage disequilibrium and haplotype frequencies and to inspect the correlation between haplotypes and the disease. Compared with the control group, the experimental group exhibited statistically significant differences in the genotype distribution frequencies of the rs657152 locus of the ABO blood group gene and the rs17250673 locus of the tumour necrosis factor cofactor 2 (TRAF2) gene, which is located downstream of the ABO gene. The allele distribution frequencies of rs657152 and rs495828 loci in the ABO blood group gene exhibited significant differences between the groups. Dominant and recessive genetic model analysis of each locus revealed that the experimental group exhibited statistically significant differences from the control group in the genotype distribution frequencies of rs657152 and rs495828 loci, respectively. These results indicate that the ABO blood group gene and TRAF2 gene may be a cause of MDs. PMID:26136981

  19. Absence of FKBP10 in recessive type XI osteogenesis imperfecta leads to diminished collagen cross-linking and reduced collagen deposition in extracellular matrix.

    PubMed

    Barnes, Aileen M; Cabral, Wayne A; Weis, MaryAnn; Makareeva, Elena; Mertz, Edward L; Leikin, Sergey; Eyre, David; Trujillo, Carlos; Marini, Joan C

    2012-11-01

    Recessive osteogenesis imperfecta (OI) is caused by defects in genes whose products interact with type I collagen for modification and/or folding. We identified a Palestinian pedigree with moderate and lethal forms of recessive OI caused by mutations in FKBP10 or PPIB, which encode endoplasmic reticulum resident chaperone/isomerases FKBP65 and CyPB, respectively. In one pedigree branch, both parents carry a deletion in PPIB (c.563_566delACAG), causing lethal type IX OI in their two children. In another branch, a child with moderate type XI OI has a homozygous FKBP10 mutation (c.1271_1272delCCinsA). Proband FKBP10 transcripts are 4% of control and FKBP65 protein is absent from proband cells. Proband collagen electrophoresis reveals slight band broadening, compatible with ≈10% over-modification. Normal chain incorporation, helix folding, and collagen T(m) support a minimal general collagen chaperone role for FKBP65. However, there is a dramatic decrease in collagen deposited in culture despite normal collagen secretion. Mass spectrometry reveals absence of hydroxylation of the collagen telopeptide lysine involved in cross-linking, suggesting that FKBP65 is required for lysyl hydroxylase activity or access to type I collagen telopeptide lysines, perhaps through its function as a peptidylprolyl isomerase. Proband collagen to organics ratio in matrix is approximately 30% of normal in Raman spectra. Immunofluorescence shows sparse, disorganized collagen fibrils in proband matrix. Published 2012 Wiley Periodicals, Inc.*This article is a US Government work and, as such, is in the public domain of the United States of America.

  20. C-5A Cargo Deck Low-Frequency Vibration Environment

    DTIC Science & Technology

    1975-02-01

    SAMPLE VIBRATION CALCULATIONS 13 1. Normal Distribution 13 2. Binomial Distribution 15 IV CONCLUSIONS 17 -! V REFERENCES 18 t: FEiCENDIJJ PAGS 2LANKNOT...Calculation for Binomial Distribution 108 (Vertical Acceleration, Right Rear Cargo Deck) xi I. INTRODUCTION The availability of large transport...the end of taxi. These peaks could then be used directly to compile the probability of occurrence of specific values of acceleration using the binomial

  1. Induced change of formative processes in pepper (Capsicum annuum L. ). I. Effect of mutagenic treatment on the crossingover frequency of the linked and recombination of unlinked marker genes

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

    Samovol, A.P.

    The effect of mutagenic treatment of the F/sub 1/ seeds of pepper on the crossingover frequency in the al/sub 2/-b segment, monohybrid and dihybrid segregation for the unlinked marker genes al/sub 2/ and pi was studied. It has been demonstrated that treatment leads to a significant reduction in the crossover frequency in the al/sub 2/-b zone. Highly significant differences between the control and individual treatment of the hybrid seeds indicated reduction in recombinations due to the mutagens used. A case of induced deviation in independent segregation of al/sub 2/ and pi, i.e., quasilinkage has been recorded.

  2. Improved synthesis of 3 alpha, 7 alpha, 12 alpha, 24 = xi-tetrahydroxy-5 beta-cholestan-26-oic acid.

    PubMed

    Batta, A K; Tint, G S; Dayal, B; Shefer, S; Salen, G

    1982-06-01

    This paper describes three simple and short methods for the conversion of cholic acid into cholylaldehyde with protected hydroxyl groups. The first method involves lithium aluminum hydride reduction of the tetrahydropyranyl ether of methyl cholate and oxidation of the resulting primary alcohol with pyridinium chlorochromate. The second method employs diborane for the reduction of the -COOH group to the -CH2OH group, while the third method involves the reduction of 3 alpha, 7 alpha, 12 alpha-triformyloxy-5 beta-cholan-24-oic acid (as the acid chloride) directly into 3 alpha, 7 alpha, 12 alpha-triformyloxy-5 beta-cholan-24-al with TMA-ferride (tetramethylammonium hydridoirontetracarbonyl). The aldehyde obtained by any of the above methods underwent smooth Reformatsky reaction with ethyl alpha-bromopropionate to yield 3 alpha, 7 alpha, 12 alpha, 24 xi-tetrahydroxy-5 beta-cholestan-26-oic acid.

  3. Estimating PM2.5 Concentrations in Xi'an City Using a Generalized Additive Model with Multi-Source Monitoring Data

    PubMed Central

    Song, Yong-Ze; Yang, Hong-Lei; Peng, Jun-Huan; Song, Yi-Rong; Sun, Qian; Li, Yuan

    2015-01-01

    Particulate matter with an aerodynamic diameter <2.5 μm (PM2.5) represents a severe environmental problem and is of negative impact on human health. Xi'an City, with a population of 6.5 million, is among the highest concentrations of PM2.5 in China. In 2013, in total, there were 191 days in Xi’an City on which PM2.5 concentrations were greater than 100 μg/m3. Recently, a few studies have explored the potential causes of high PM2.5 concentration using remote sensing data such as the MODIS aerosol optical thickness (AOT) product. Linear regression is a commonly used method to find statistical relationships among PM2.5 concentrations and other pollutants, including CO, NO2, SO2, and O3, which can be indicative of emission sources. The relationships of these variables, however, are usually complicated and non-linear. Therefore, a generalized additive model (GAM) is used to estimate the statistical relationships between potential variables and PM2.5 concentrations. This model contains linear functions of SO2 and CO, univariate smoothing non-linear functions of NO2, O3, AOT and temperature, and bivariate smoothing non-linear functions of location and wind variables. The model can explain 69.50% of PM2.5 concentrations, with R2 = 0.691, which improves the result of a stepwise linear regression (R2 = 0.582) by 18.73%. The two most significant variables, CO concentration and AOT, represent 20.65% and 19.54% of the deviance, respectively, while the three other gas-phase concentrations, SO2, NO2, and O3 account for 10.88% of the total deviance. These results show that in Xi'an City, the traffic and other industrial emissions are the primary source of PM2.5. Temperature, location, and wind variables also non-linearly related with PM2.5. PMID:26540446

  4. [Frequency of intron 1 inversion of factor VIII gene in Chinese hemophilia A patients with case report of a female patient with heterozygous intron 1 inversion].

    PubMed

    Yan, Zhen-yu; Liang, Yan; Yan, Mei; Fan, Lian-kai; Xiao, Bai; Hua, Bao-lai; Liu, Jing-zhong; Zhao, Yong-qiang

    2008-10-21

    To investigate the frequency of intron 1 inversion (inv1) in FVIII gene in Chinese hemophilia A (HA) patients and to investigate the mechanism of pathogenesis. Peripheral blood samples were collected from 158 unrelated HA patients, aged 20 (1 - 73), including one female HA patient, aged 5, and several family members of a patient positive in inv1. One-stage method was used to assay the FVIII activity (FVIII:C). Long distance PCR and multiple PCR in duplex reactions were used to screen for the intron 22 inversion (inv22) and inv1 of the FVIII coding gene (F8). The F8 coding sequence was amplified with PCR and sequenced with an automatic sequencer. Two unrelated patients (pedigrees) were detected as inv1 positive with a positive rate of 1.26%. A rare female HA patient with inv1 was also discovered in a positive family (3 HA cases were found in this family and regarded as one case in calculating the total detection rate). The full length of FVIII was sequenced, and no other mutation was detected. There frequency of FVIII inv1 is low in Chinese HA patients compared with other populations. Female HA patients are heterozygous for FVIII inv1 and that may be resulted from nonrandom inactivation of X chromosome.

  5. High Frequency of a Single Nucleotide Substitution (c.-6-180T>G) of the Canine MDR1/ABCB1 Gene Associated with Phenobarbital-Resistant Idiopathic Epilepsy in Border Collie Dogs

    PubMed Central

    Mizukami, Keijiro; Yabuki, Akira; Chang, Hye-Sook; Uddin, Mohammad Mejbah; Rahman, Mohammad Mahbubur; Kushida, Kazuya; Kohyama, Moeko

    2013-01-01

    A single nucleotide substitution (c.-6-180T>G) associated with resistance to phenobarbital therapy has been found in the canine MDR1/ABCB1 gene in Border Collies with idiopathic epilepsy. In the present study, a PCR-restriction fragment length polymorphism assay was developed for genotyping this mutation, and a genotyping survey was carried out in a population of 472 Border Collies in Japan to determine the current allele frequency. The survey demonstrated the frequencies of the T/T wild type, T/G heterozygote, and G/G mutant homozygote to be 60.0%, 30.3%, and 9.8%, respectively, indicating that the frequency of the mutant G allele is extremely high (24.9%) in Border Collies. The results suggest that this high mutation frequency of the mutation is likely to cause a high prevalence of phenobarbital-resistant epilepsy in Border Collies. PMID:24302812

  6. YY1 binding association with sex-biased transcription revealed through X-linked transcript levels and allelic binding analyses

    PubMed Central

    Chen, Chih-yu; Shi, Wenqiang; Balaton, Bradley P.; Matthews, Allison M.; Li, Yifeng; Arenillas, David J.; Mathelier, Anthony; Itoh, Masayoshi; Kawaji, Hideya; Lassmann, Timo; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R. R.; Brown, Carolyn J.; Wasserman, Wyeth W.

    2016-01-01

    Sex differences in susceptibility and progression have been reported in numerous diseases. Female cells have two copies of the X chromosome with X-chromosome inactivation imparting mono-allelic gene silencing for dosage compensation. However, a subset of genes, named escapees, escape silencing and are transcribed bi-allelically resulting in sexual dimorphism. Here we conducted in silico analyses of the sexes using human datasets to gain perspectives into such regulation. We identified transcription start sites of escapees (escTSSs) based on higher transcription levels in female cells using FANTOM5 CAGE data. Significant over-representations of YY1 transcription factor binding motif and ChIP-seq peaks around escTSSs highlighted its positive association with escapees. Furthermore, YY1 occupancy is significantly biased towards the inactive X (Xi) at long non-coding RNA loci that are frequent contacts of Xi-specific superloops. Our study suggests a role for YY1 in transcriptional activity on Xi in general through sequence-specific binding, and its involvement at superloop anchors. PMID:27857184

  7. Investigating into composition, distribution, sources and health risk of phthalic acid esters in street dust of Xi'an City, Northwest China.

    PubMed

    Wang, Lijun; Zhang, Wenjuan; Tao, Wendong; Wang, Li; Shi, Xingmin; Lu, Xinwei

    2017-08-01

    Phthalic acid esters (PAEs) are widely used as plasticizers and in consumer products, which may enter the environment and present risks to human health. U.S. EPA classifies six PAEs as priority pollutants, which could be accumulated in street dust at the interface of atmosphere, biosphere and geosphere. This study collected a total of 58 street dust samples from Xi'an City in Northwest China and analyzed for concentrations of the priority PAEs. Composition, distribution, sources and health risk of the PAEs were further examined. All the priority PAEs were detected in the street dust. The concentrations of individual PAEs varied between not detected and 183.19 mg/kg. The sum of the 6 priority PAEs (∑6PAEs) ranged from 0.87 to 250.30 mg/kg with a mean of 40.48 mg/kg. The most abundant PAEs in the street dust were di-n-butyl phthalate and di (2-ethylhexyl) phthalate (DEHP). Higher concentrations of ∑6PAEs in the street dust were found in the south and west parts of Xi'an City as well as its urban center, which were possibly attributed to the prevailing northerly Asian winter monsoon. The PAEs in the street dust originated mainly from wide application of plasticizers as well as cosmetics and personal care products. The main pathways of human exposure to PAEs in the street dust were ingestion and dermal adsorption of dust particles. The non-cancer risk of human exposure to PAEs in the street dust was relatively low, while the risk to children was higher than that to adults. The cancer risk of human exposure to DEHP in the street dust was lower than the standard limit value of 10 -6 .

  8. Sentinel Node Mapping Using Indocyanine Green and Near-infrared Fluorescence Imaging Technology for Uterine Malignancies: Preliminary Experience With the Da Vinci Xi System.

    PubMed

    Siesto, Gabriele; Romano, Fabrizio; Fiamengo, Barbara; Vitobello, Domenico

    2016-01-01

    Sentinel lymph node (SLN) mapping has emerged as the new frontier for the surgical staging of apparently early-stage cervical and endometrial cancer. Different colorimetric and radioactive tracers, alone and in combination, have been proposed with encouraging results. Fluorometric mapping using indocyanine green (ICG) appears to be a suitable and attractive alternative to provide reliable staging [1-4]. In this video, we present the technique of SLN mapping in 2 cases (1 endometrial and 1 cervical cancer, respectively) using ICG and the near-infrared technology provided by the newest Da Vinci Xi robotic system (Intuitive Surgical Inc., Sunnyvale, CA). Together we report the results of our preliminary experience on the first 20 cases performed. The new robotic Da Vinci Xi system was available at our institution since May 2015. Upon institutional review board/ethical committee approval, all consecutive patients with early-stage endometrial and cervical cancer who were judged suitable for robotic surgery have been enrolled for SLN mapping with ICG. We adopted the Memorial Sloan Kettering Cancer Center SLN algorithm; the tracer was delivered into the cervix in all cases. Four milliliters (1.25 mg/mL) of ICG was injected divided into the 3- and 9-o'clock positions of the cervix alone, with 1 mL deep into the stroma and 1 mL submucosally at the skin incision. Sentinel lymph nodes were examined with a protocol including both ultrastaging with immunohistochemistry [3] and 1-step nucleic acid amplification assay [5,6] under a parallel protocol of study. During the study period, 20 cases were managed; 14 and 6 patients had endometrial and cervical cancer, respectively. SLN was detected in all cases (20/20, 100%). Bilateral SLNs were detected in 17 of 20 (85.0%) cases. Based on preoperative and intraoperative findings, 13 (65.0%) patients received systematic pelvic lymphadenectomy after SLN mapping. Three (15.0%) patients had microscopic nodal metastases on SLN. No

  9. Occurrence of tetracycline-resistant fecal coliforms and their resistance genes in an urban river impacted by municipal wastewater treatment plant discharges.

    PubMed

    Zhang, Chong-Miao; Du, Cong; Xu, Huan; Miao, Yan-Hui; Cheng, Yan-Yan; Tang, Hao; Zhou, Jin-Hong; Wang, Xiao-Chang

    2015-01-01

    Antibiotic resistance of fecal coliforms in an urban river poses great threats to both human health and the environment. To investigate the occurrence and distribution of antibiotic resistant bacteria in an urban river, water samples were collected from the Chanhe River in Xi'an, China. After membrane filtration of water samples, the tetracycline resistance rate of fecal coliforms and their resistance genes were detected by plating and polymerase chain reaction (PCR), respectively. We found that fecal coliforms were generally resistant to tetracycline and saw average resistance rates of 44.7%. The genes tetA and tetB were widely detected, and their positive rate was 60%-100% and 40%-90%, respectively. We found few strains containing tetC, tetK, tetQ and tetX, and we did not identify any strains containing tetG, tetM or tetO. The prevalence of tetA and tetB over other genes indicated that the main mechanism for resistance to tetracycline is by changes to the efflux pump. Our analysis of the types and proportion of tetracycline resistance genes in the Chanhe River at locations upstream and downstream of the urban center suggests that the increased number of tetracycline-resistant fecal coliforms and spatial variation of tetracycline resistance genes diversity were related to municipal wastewater treatment plant discharge.

  10. [Catering for client groups during the XXII Olympic winter games and XI Paralympic winter games of 2014 in Sochi].

    PubMed

    Popova, A Yu; Gus'kov, A S; Ivanov, G E; Chikina, L V; Klindukhov, V P; Nikolaevich, P N; Grechanaya, T V; Balaeva, M I; Vechernyaya, L S; Vechernyaya, E A; Bozhko, I I; Parkhomenko, V V; Kulichenko, O A; Tushina, O V; Manin, E A; Taran, T V

    2016-01-01

    The problems of catering control various client groups during the XXII Olympic Winter Games and XI Paralympic Winter Games of 2014 in Sochi is one of the priorities of the sanitary and epidemiological welfare of the population during mass events. The data on the order of nutrition of guests and participants of the games, control of food items, sanitary and microbiological monitoring of drinking water, food raw materials and products are presented. It is noted that the ongoing supervisory activities contributed to the sanitary and epidemiological well-being during the Games. The purpose of this study was to lighting modern achievements in the field of nutrition and food microbiology in the period of the Olympic Games and the determination of their value to the further improvement and use at when conducting mass gatherings.

  11. Comparative study of polymorphism frequencies of the CYP2D6, CYP3A5, CYP2C8 and IL-10 genes in Mexican and Spanish women with breast cancer.

    PubMed

    Alcazar-González, Gregorio Antonio; Calderón-Garcidueñas, Ana Laura; Garza-Rodríguez, María Lourdes; Rubio-Hernández, Gabriela; Escorza-Treviño, Sergio; Olano-Martin, Estibaliz; Cerda-Flores, Ricardo Martín; Castruita-Avila, Ana Lilia; González-Guerrero, Juan Francisco; le Brun, Stéphane; Simon-Buela, Laureano; Barrera-Saldaña, Hugo Alberto

    2013-10-01

    Pharmacogenetic studies in breast cancer (BC) may predict the efficacy of tamoxifen and the toxicity of paclitaxel and capecitabine. We determined the frequency of polymorphisms in the CYP2D6 gene associated with activation of tamoxifen, and those of the genes CYP2C8, CYP3A5 and DPYD associated with toxicity of paclitaxel and capecitabine. We also included a IL-10 gene polymorphism associated with advanced tumor stage at diagnosis. Genomic DNAs from 241 BC patients from northeast Mexico were genotyped using DNA microarray technology. For tamoxifen processing, CYP2D6 genotyping predicted that 90.8% of patients were normal metabolizers, 4.2% ultrarapid, 2.1% intermediate and 2.9% poor metabolizers. For paclitaxel and the CYP2C8 gene, 75.3% were normal, 23.4% intermediate and 1.3% poor metabolizers. Regarding the DPYD gene, only one patient was a poor metabolizer. For the IL-10 gene, 47.1% were poor metabolizers. These results contribute valuable information towards personalizing BC chemotherapy in Mexican women.

  12. Protective Low-Frequency Variants for Preeclampsia in the Fms Related Tyrosine Kinase 1 Gene in the Finnish Population.

    PubMed

    Lokki, A Inkeri; Daly, Emma; Triebwasser, Michael; Kurki, Mitja I; Roberson, Elisha D O; Häppölä, Paavo; Auro, Kirsi; Perola, Markus; Heinonen, Seppo; Kajantie, Eero; Kere, Juha; Kivinen, Katja; Pouta, Anneli; Salmon, Jane E; Meri, Seppo; Daly, Mark; Atkinson, John P; Laivuori, Hannele

    2017-08-01

    Preeclampsia is a common pregnancy-specific vascular disorder characterized by new-onset hypertension and proteinuria during the second half of pregnancy. Predisposition to preeclampsia is in part heritable. It is associated with an increased risk of cardiovascular disease later in life. We have sequenced 124 candidate genes implicated in preeclampsia to pinpoint genetic variants contributing to predisposition to or protection from preeclampsia. First, targeted exomic sequencing was performed in 500 preeclamptic women and 190 controls from the FINNPEC cohort (Finnish Genetics of Preeclampsia Consortium). Then 122 women with a history of preeclampsia and 1905 parous women with no such history from the National FINRISK Study (a large Finnish population survey on risk factors of chronic, noncommunicable diseases) were included in the analyses. We tested 146 rare and low-frequency variants and found an excess (observed 13 versus expected 7.3) nominally associated with preeclampsia ( P <0.05). The most significantly associated sequence variants were protective variants rs35832528 (E982A; P =2.49E-4; odds ratio=0.387) and rs141440705 (R54S; P =0.003; odds ratio=0.442) in Fms related tyrosine kinase 1. These variants are enriched in the Finnish population with minor allele frequencies 0.026 and 0.017, respectively. They may also be associated with a lower risk of heart failure in 11 257 FINRISK women. This study provides the first evidence of maternal protective genetic variants in preeclampsia. © 2017 American Heart Association, Inc.

  13. Allele frequencies for 12 autosomal short tandem repeat loci in two Bolivian populations.

    PubMed

    Cifuentes, L; Jorquera, H; Acuña, M; Ordóñez, J; Sierra, A L

    2008-03-18

    Two hundred and sixty unrelated subjects who asked for paternity testing at two Bolivian Laboratories in La Paz and Santa Cruz were studied. The loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, TH01, TPOX, and CSF1PO were typed from blood samples, amplifying DNA by polymerase chain reactions and electrophoresis. Allele frequencies were estimated by simple counting and the unbiased heterozygosity was calculated. Hardy-Weinberg equilibrium was studied and gene frequencies were compared between the two samples. All loci conformed to the Hardy-Weinberg law and allele frequencies were similar in samples from the two cities. The Bolivian gene frequencies estimated were significantly different from those described for Chile and the United States Hispanic-Americans for most of the loci.

  14. [Cytosine deaminase and thymidine kinase double suicide gene system driven by carcinoembryonic antigen promoter for the treatment of colorectal carcinoma xenograft in nude mice].

    PubMed

    Huang, Zheng-jie; Feng, Qing-zhao; You, Jun; Xu, Lin; Luo, Wei-yuan; Yi, Wen-cheng; Zeng, Yue-yue; Luo, Qi

    2013-07-23

    To explore the therapeutic efficacy of double suicide gene system driven by carcinoembryonic antigen (CEA) promoter (Cp-CDglyTK) on colorectal carcinoma xenograft in nude mice. The plasmid pcDNA3.1(-)Cp-CDglyTK was transfected into the CEA-positive SW480 and CEA-negative HeLa cells respectively. The expression of suicide gene was detected by RT-PCR. And the transfected cells were treated with 5-fluorocytosine (5-FC) and ganciclovir (GCV) at different concentrations and the cell-killing and bystander effects assayed by methyl thiazolyl tetrazolium (MTT). By a transplantation of cultivated cells, SW480 or HeLa cell lines were injected subcutaneously into right axillary of nude mice to establish 96 SW480 and 72 HeLa tumor animal models. Nude mice were completely randomized with statistical software according to tumor volume. For prodrug therapy, 48 SW480-bearing mice were divided equally into 4 groups of I-IV. At the same time, 48 HeLa-bearing mice were divided equally into 4 groups of V-VIII. Groups I & V received an intratumoral injection of PBS, groups II & VIGCV and 5-FC intratumorally, groups III & VII PBS intraperitoneally and groups IV & VIII GCV and 5-FC intraperitoneally. Forty-eight SW480-bearing mice were divided equally into 4 groups of IX∼XII and 24 Hela-bearing ones into groups of & in therapy experiment by suicide gene plus prodrug. Six groups received an intratumoral injection of liposome Lipofectamine and plasmid CP-CDglyTK and then an intraperitoneal injection of drug. The groups of IX and received an injection of PBS, group X GCV, group XI 5-FC and groups XII & GCV and 5-FC. The observation parameters included tumor bulk, tumor weight, survival time and treatment effect in each group. SW480 cells transfected by plasmid pcDNA3.1(-)Cp- CDglyTK expressed CDglyTK gene. The inhibition rates of GCV and 5-FC were significantly higher than those of HeLa cells (59.87% ± 0.21% vs 9.90% ± 0.09%, P < 0.01). And higher inhibition rates and stronger bystander

  15. Micronuclei in Cord Blood Lymphocytes and Associations with Biomarkers of Exposure to Carcinogens and Hormonally Active Factors, Gene Polymorphisms, and Gene Expression: The NewGeneris Cohort

    PubMed Central

    Merlo, Domenico Franco; Agramunt, Silvia; Anna, Lívia; Besselink, Harrie; Botsivali, Maria; Brady, Nigel J.; Ceppi, Marcello; Chatzi, Leda; Chen, Bowang; Decordier, Ilse; Farmer, Peter B.; Fleming, Sarah; Fontana, Vincenzo; Försti, Asta; Fthenou, Eleni; Gallo, Fabio; Georgiadis, Panagiotis; Gmuender, Hans; Godschalk, Roger W.; Granum, Berit; Hardie, Laura J.; Hemminki, Kari; Hochstenbach, Kevin; Knudsen, Lisbeth E.; Kogevinas, Manolis; Kovács, Katalin; Kyrtopoulos, Soterios A.; Løvik, Martinus; Nielsen, Jeanette K; Nygaard, Unni Cecilie; Pedersen, Marie; Rydberg, Per; Schoket, Bernadette; Segerbäck, Dan; Singh, Rajinder; Sunyer, Jordi; Törnqvist, Margareta; van Loveren, Henk; van Schooten, Frederik J.; Vande Loock, Kim; von Stedingk, Hans; Wright, John; Kirsch-Volders, Micheline; van Delft, Joost H.M.

    2013-01-01

    Background: Leukemia incidence has increased in recent decades among European children, suggesting that early-life environmental exposures play an important role in disease development. Objectives: We investigated the hypothesis that childhood susceptibility may increase as a result of in utero exposure to carcinogens and hormonally acting factors. Using cord blood samples from the NewGeneris cohort, we examined associations between a range of biomarkers of carcinogen exposure and hormonally acting factors with micronuclei (MN) frequency as a proxy measure of cancer risk. Associations with gene expression and genotype were also explored. Methods: DNA and protein adducts, gene expression profiles, circulating hormonally acting factors, and GWAS (genome-wide association study) data were investigated in relation to genomic damage measured by MN frequency in lymphocytes from 623 newborns enrolled between 2006 and 2010 across Europe. Results: Malondialdehyde DNA adducts (M1dG) were associated with increased MN frequency in binucleated lymphocytes (MNBN), and exposure to androgenic, estrogenic, and dioxin-like compounds was associated with MN frequency in mononucleated lymphocytes (MNMONO), although no monotonic exposure–outcome relationship was observed. Lower frequencies of MNBN were associated with a 1-unit increase expression of PDCD11, LATS2, TRIM13, CD28, SMC1A, IL7R, and NIPBL genes. Gene expression was significantly higher in association with the highest versus lowest category of bulky and M1dG–DNA adducts for five and six genes, respectively. Gene expression levels were significantly lower for 11 genes in association with the highest versus lowest category of plasma AR CALUX® (chemically activated luciferase expression for androgens) (8 genes), ERα CALUX® (for estrogens) (2 genes), and DR CALUX® (for dioxins). Several SNPs (single-nucleotide polymorphisms) on chromosome 11 near FOLH1 significantly modified associations between androgen activity and MNBN

  16. Frequency Standards and Metrology

    NASA Astrophysics Data System (ADS)

    Maleki, Lute

    2009-04-01

    over 172 KM of installed fiber / S. Crane -- pt. X. Miniature systems. Chip-scale atomic devices: precision atomic instruments based on MEMS (Invited) / J. Kitching ... [et al.]. CSAC - the chip-scale atomic clock (Invited) / R. Lutwak ... [et al.]. Reaching a few 10[symbol] stability level with a compact cold atom clock / F. X. Esnault ... [et al.]. Evaluation of Lin||Lin CPT for compact and high performance frequency standard / E. Breschi ... [et al.] -- pt. XI. Time scales. Atomic time scales TAI and TI(BIPM): present status and prospects (Invited) / G. Petit. Weight functions for biases in atomic frequency standards / J. H. Shirley -- pt. XII. Interferometers. Definition and construction of noise budget in atom interferometry (Invited) / E. D'Ambriosio. Characterization of a cold atom gyroscope (Invited) / A. Landragin ... [et al.]. A mobile atom interferometer for high precision measurements of local gravity / M. Schmidt ... [et al.]. Demonstration of atom interferometer comprised of geometric beam splitters / Hiromitsu Imai and Atsuo Morinaga -- pt. XIII. New directions. Active optical clocks (Invited) / J. Chen. Prospects for a nuclear optical frequency standard based on Thorium-229 (Invited) / E. Peik ... [et al.]. Whispering gallery mode oscillators and optical comb generators (Invited) / A. B. Matsko ... [et al.]. Frequency comparison using energy-time entangled photons / A. Stefanov -- List of participants.

  17. Gene Introgression in Weeds Depends on Initial Gene Location in the Crop: Brassica napus-Raphanus raphanistrum Model.

    PubMed

    Adamczyk-Chauvat, Katarzyna; Delaunay, Sabrina; Vannier, Anne; François, Caroline; Thomas, Gwenaëlle; Eber, Frédérique; Lodé, Maryse; Gilet, Marie; Huteau, Virginie; Morice, Jérôme; Nègre, Sylvie; Falentin, Cyril; Coriton, Olivier; Darmency, Henri; Alrustom, Bachar; Jenczewski, Eric; Rousseau-Gueutin, Mathieu; Chèvre, Anne-Marie

    2017-07-01

    The effect of gene location within a crop genome on its transfer to a weed genome remains an open question for gene flow assessment. To elucidate this question, we analyzed advanced generations of intergeneric hybrids, derived from an initial pollination of known oilseed rape varieties ( Brassica napus , AACC, 2 n  = 38) by a local population of wild radish ( Raphanus raphanistrum , RrRr, 2 n  = 18). After five generations of recurrent pollination, 307 G5 plants with a chromosome number similar to wild radish were genotyped using 105 B. napus specific markers well distributed along the chromosomes. They revealed that 49.8% of G5 plants carried at least one B. napus genomic region. According to the frequency of B. napus markers (0-28%), four classes were defined: Class 1 (near zero frequency), with 75 markers covering ∼70% of oilseed rape genome; Class 2 (low frequency), with 20 markers located on 11 genomic regions; Class 3 (high frequency), with eight markers on three genomic regions; and Class 4 (higher frequency), with two adjacent markers detected on A10. Therefore, some regions of the oilseed rape genome are more prone than others to be introgressed into wild radish. Inheritance and growth of plant progeny revealed that genomic regions of oilseed rape could be stably introduced into wild radish and variably impact the plant fitness (plant height and seed number). Our results pinpoint that novel technologies enabling the targeted insertion of transgenes should select genomic regions that are less likely to be introgressed into the weed genome, thereby reducing gene flow. Copyright © 2017 by the Genetics Society of America.

  18. Glucose-6-phosphate dehydrogenase deficiency and sickle cell genes in Bisha.

    PubMed

    el-Hazmi, M A; al-Swailem, A; Warsy, A S

    1995-08-01

    This study was conducted on 820 Saudi males and females from Bisha in the western province of Saudi Arabia. Blood samples were analysed to determine the frequency of glucose-6-phosphate dehydrogenase deficiency and haemoglobin S (Hb S) genes, and to investigate interactions between the two genes. Severe G-6-PD deficiency in this population was due to G-6-PD-Mediterranean; the African variant G-6-PD-A- was not detected. The normal and common form of the enzyme was G-6-PD-B+, occurring at a frequency of 0.8444 and 0.8177 in males and females, respectively. Variants included G-6-PD-A+, G-6-PD-Mediterranean, and G-6-PD-Mediterranean-like at frequencies of 0.0043, 0.0767, and 0.0746, respectively, in males and 0.0057, 0.05413, and 0.0855, respectively, in females. Sickle cell haemoglobin (Hb S) was encountered in the homozygous (4 per cent) and heterozygous (10 per cent) states at a gene frequency of 0.0860. No interaction between G-6-PD deficiency and Hb S gene was observed. A severe haematological and clinical presentation of the Hb SS disease was encountered in the children from Bisha.

  19. Frequency of genetic defects in combined pituitary hormone deficiency: a systematic review and analysis of a multicentre Italian cohort.

    PubMed

    De Rienzo, Francesca; Mellone, Simona; Bellone, Simonetta; Babu, Deepak; Fusco, Ileana; Prodam, Flavia; Petri, Antonella; Muniswamy, Ranjith; De Luca, Filippo; Salerno, Mariacarolina; Momigliano-Richardi, Patricia; Bona, Gianni; Giordano, Mara

    2015-12-01

    Combined pituitary hormonal deficiency (CPHD) can result from mutations within genes that encode transcription factors. This study evaluated the frequency of mutations in these genes in a cohort of 144 unrelated Italian patients with CPHD and estimated the overall prevalence of mutations across different populations using a systematic literature review. A multicentre study of adult and paediatric patients with CPHD was performed. The PROP1, POU1F1, HESX1, LHX3 and LHX4 genes were analysed for the presence of mutations using direct sequencing. We systematically searched PubMed with no date restrictions for studies that reported genetic screening of CPHD cohorts. We only considered genetic screenings with at least 10 individuals. Data extraction was conducted in accordance with the guidelines set by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). Global mutation frequency in Italian patients with CPHD was 2·9% (4/136) in sporadic cases and 12·5% (1/8) in familial cases. The worldwide mutation frequency for the five genes calculated from 21 studies was 12·4%, which ranged from 11·2% in sporadic to 63% in familial cases. PROP1 was the most frequently mutated gene in sporadic (6·7%) and familial cases (48·5%). The frequency of defects in genes encoding pituitary transcription factors is quite low in Italian patients with CPHD and other western European countries, especially in sporadic patients. The decision of which genes should be tested and in which order should be guided by hormonal and imaging phenotype, the presence of extrapituitary abnormalities and the frequency of mutation for each gene in the patient-referring population. © 2015 John Wiley & Sons Ltd.

  20. The red-green visual pigment gene region in adrenoleukodystrophy.

    PubMed Central

    Aubourg, P; Feil, R; Guidoux, S; Kaplan, J C; Moser, H; Kahn, A; Mandel, J L

    1990-01-01

    Although recent data established that a specific very-long-chain fatty acyl-CoA synthetase is defective in X-linked adrenoleukodystrophy (ALD), the ALD gene is still unidentified. The ALD locus has been mapped to Xq28, like the red and green color pigment genes. Abnormal color vision has been observed in 12 of 27 patients with adrenomyeloneuropathy (AMN), a milder form of ALD. Furthermore, rearrangements of the color vision gene cluster were found in four of eight ALD kindreds. This led us to propose that a single DNA rearrangement could underlie both ALD and abnormal color vision in these patients. Study of 34 French ALD patients failed to reveal a higher than expected frequency of green/red visual pigment rearrangements 3' to the red/green color vision gene complex. The previous report of such rearrangements was based on small numbers and lack of knowledge that the frequency of "abnormal" color vision arrays on molecular analysis was twice as high as expected on the basis of the frequency of phenotypic color vision defects. The red/green color pigment (R/GCP) region was studied by pulsed-field gel electrophoresis in 14 of these patients, and we did not find any fragment size difference between the patients and normal individuals who have the same number of pigment genes. The R/GCP region was also analyzed in 29 French and seven North American ALD patients by using six genomic DNA probes, isolated from a cosmid walk, that flank the color vision genes. No deletions were found with probes that lie 3' of the green pigment genes. One of the eight previously reported ALD individuals has a long deletion 5' of the red pigment gene, a deletion causing blue cone monochromacy. This finding and the previous findings of a 45% frequency of phenotypic color vision defects in patients with AMN may suggest that the ALD/AMN gene lies 5' to the red pigment gene and that the frequent phenotypic color vision anomalies owe their origin to deleted DNA that includes regulatory genes for

  1. Frequency distribution of polymorphisms of CYP2C19, CYP2C9, VKORC1 and SLCO1B1 genes in the Yakut population.

    PubMed

    Vasilyev, Filipp Filippovich; Danilova, Diana Aleksandrovna; Kaimonov, Vladimir Sergeevich; Chertovskih, Yana Valerievna; Maksimova, Nadezda Romanovna

    2016-01-01

    Allele frequencies of single nucleotide polymorphisms (SNPs) are variable among different populations; therefore the study of SNPs in ethnic groups is important for establishing the clinical significance of the screening of these polymorphisms. The main goal of the research is to study the polymorphisms of CYP2C9, CYP2C19, VKORC1, and SLCO1B1 in Yakuts. Genomic DNA from 229 Yakut subjects were analyzed by real-time polymerase chain reaction (PCR) (SLCO1B1 +521T > C, VKORC1 -1639G>A, CYP2C19 +681G>A, +636G>A, CYP2C9 +430С>T, +1075A>C). Genotype frequencies of polymorphisms in the population of the Yakuts were more characteristic of the Asian population. The results have been included in the software application "Lekgen" that we developed for the interpretation of pharmacogenetic testing. The data of our study obtained on frequency carriers of polymorphisms of genes SLCO1B1, CYP2C19, CYP2C9, VKORC1 among the Yakuts may be useful in developing recommendations for a personalized therapy.

  2. Frequency distribution of polymorphisms of CYP2C19, CYP2C9, VKORC1 and SLCO1B1 genes in the Yakut population

    PubMed Central

    Vasilyev, Filipp Filippovich; Danilova, Diana Aleksandrovna; Kaimonov, Vladimir Sergeevich; Chertovskih, Yana Valerievna; Maksimova, Nadezda Romanovna

    2016-01-01

    Allele frequencies of single nucleotide polymorphisms (SNPs) are variable among different populations; therefore the study of SNPs in ethnic groups is important for establishing the clinical significance of the screening of these polymorphisms. The main goal of the research is to study the polymorphisms of CYP2C9, CYP2C19, VKORC1, and SLCO1B1 in Yakuts. Genomic DNA from 229 Yakut subjects were analyzed by real-time polymerase chain reaction (PCR) (SLCO1B1 +521T > C, VKORC1 -1639G>A, CYP2C19 +681G>A, +636G>A, CYP2C9 +430С>T, +1075A>C). Genotype frequencies of polymorphisms in the population of the Yakuts were more characteristic of the Asian population. The results have been included in the software application “Lekgen” that we developed for the interpretation of pharmacogenetic testing. The data of our study obtained on frequency carriers of polymorphisms of genes SLCO1B1, CYP2C19, CYP2C9, VKORC1 among the Yakuts may be useful in developing recommendations for a personalized therapy. PMID:27499796

  3. Non-alcoholic fatty liver disease predicts type 2 diabetes mellitus, but not prediabetes, in Xi'an, China: a five-year cohort study.

    PubMed

    Ming, Jie; Xu, Shaoyong; Gao, Bin; Liu, Guocai; Ji, Yufei; Yang, Fan; Jia, Yunan; Fang, Yujie; Ji, Qiuhe

    2015-11-01

    Emerging studies have focused the association between non-alcoholic fatty liver disease (NAFLD) and the risk of type 2 diabetes mellitus (T2DM) but the results were inconsistent. In addition, few studies have put focus on the association between NAFLD and the risk of prediabetes. We aimed to investigate whether NAFLD diagnosed by ultrasonography could predict the risk of future T2DM and prediabetes in Chinese population. The population-based cohort study held in Xi'an, Northwestern China, was based on China National Diabetes and Metabolic Disorders Survey. During a follow-up of 5 years, 508 healthy subjects were included as study sample. NAFLD was determined by abdominal ultrasonography. T2DM and prediabetes were diagnosed based on oral glucose tolerance test. Of 508 subjects, 97 (19.1%) were diagnosed as NAFLD and 411 (80.9%) were as non-NAFLD; 20 (3.9%) developed diabetes and 85 (16.7%) developed prediabetes during follow-up. The incidence of diabetes and prediabetes in the NAFLD group was 20.6 and 51.6 per 1000 person-years, respectively, whereas that in non-NAFLD group was 4.9 and 29.2 per 1000 person-years respectively. Cox proportional hazard regression showed that the multivariable-adjusted relative risk (RR) of T2DM and prediabetes in the NAFLD group was 4.462 [95% confidence interval (CI): 1.855-10.734, P < 0.001] and 1.642 (95% CI: 0.965-2.793, P = 0.067), respectively, compared with non-NAFLD group. Non-alcoholic fatty liver disease was a significant predictor for future diabetes, but not for prediabetes, in Xi'an, China. More cohort studies are needed to confirm our findings. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  4. Metacognitive skills and students' motivation toward chemical equilibrium problem solving ability: A correlational study on students of XI IPA SMAN 2 Banjarmasin

    NASA Astrophysics Data System (ADS)

    Muna, Khairiatul; Sanjaya, Rahmat Eko; Syahmani, Bakti, Iriani

    2017-12-01

    The demand for students to have metacognitive skills and problem solving ability can be seen in the core competencies of the 2013 curriculum. Metacognitive skills are the skills which affect students' success in solving problems depending on students' motivation. This explains the possibility of the relationship between metacognition and motivation in affecting students' achievement including problem solving. Due to the importance of metacognitive skills to solve problems and the possible relationship between metacognition and motivation, a study to find the relationship among the variables is necessary to conduct, particularly on chemistry problem solving. This one shot case study using quantitative method aimed to investigate the correlation between metacognitive skills and motivation toward problem solving ability focusing on chemical equilibrium. The research population was students of grade XI of majoring Science of Banjarmasin Public High Scool 2 (XI IPA SMAN 2 Banjarmasin) with the samples of 33 students obtained by using purposive sampling technique. The research data were collected using test and non-test and analyzed using multiple regression in SPSS 21. The results of this study showed that (1) the students' metacognitive skills and motivation correlated positively with coefficient of +0.450 to problem solving ability on chemical equilibrium: (2) inter-variables of students' motivation (self-efficacy, active learning strategies, science/chemistry learning value, performance goal, achievement goal, and learning environment stimulations) correlated positively to metacognitive skills with the correlation coefficients of +0.580, +0.537, +0.363, +0.241, +0.516, and +0.271, respectively. Based on the results, it is necessary for teachers to implement learning which develops students' metacognitive skills and motivation, such as learning with scientific approach. The implementation of the learning is also supposed to be complemented with the use of learning

  5. Level and source of 129I of environmental samples in Xi'an region, China.

    PubMed

    Zhang, Luyuan; Zhou, Weijian; Hou, Xiaolin; Chen, Ning; Liu, Qi; He, Chaohui; Fan, Yukun; Luo, Maoyi; Wang, Zhiwen; Fu, Yunchong

    2011-09-01

    Iodine-129 is widely used as a tracer in various environmental practices such as monitoring of nuclear environmental safety, seawater exchange and transport, geochemical cycle of stable iodine and dating of geological events. The spatial distribution of (129)I concentration varies significantly on global scale because of anthropogenic input from nuclear activities coupled with scarcity of data on environmental (129)I variability in many parts of the world including Asia. Here we report new data on (129)I and (127)I concentrations in soil, vegetation, river water and precipitation collected from Xi'an area, China. The results indicate values for environmental (129)I/(127)I ratios in the investigated area range from 1.1×10(-10) to 43.5×10(-10) with a mean of 20.6×10(-10), which is 1-3 orders of magnitude lower than the ratios observed in Europe, but comparable with those observed in the locations far from direct effect of point release sources and at similar latitude. The main source of (129)I in the investigated area is attributed to the global fallout of both atmospheric nuclear weapons testing and long distance dispersion of fuel reprocessing releases. Copyright © 2011 Elsevier B.V. All rights reserved.

  6. Progress report on new antiepileptic drugs: a summary of the Eleventh Eilat Conference (EILAT XI).

    PubMed

    Bialer, Meir; Johannessen, Svein I; Levy, René H; Perucca, Emilio; Tomson, Torbjörn; White, H Steve

    2013-01-01

    The Eleventh Eilat Conference on New Antiepileptic Drugs (AEDs)-EILAT XI, took place in Eilat, Israel from the 6th to 10th of May 2012. About 100 basic scientists, clinical pharmacologists and neurologists from 20 countries attended the conference, whose main themes included "Indications overlapping with epilepsy" and "Securing the successful development of an investigational antiepileptic drug in the current environment". Consistent with previous formats of this conference, a large part of the program was devoted to a review of AEDs in development, as well as updates on AEDs introduced since 1994. Like the EILAT X report, the current manuscript focuses only on the preclinical and clinical pharmacology of AEDs that are currently in development. These include brivaracetam, 2-deoxy-glucose, ganaxolone, ICA-105665, imepitoin, NAX 801-2, perampanel and other AMPA receptor antagonists, tonabersat, valnoctamide and its homologue sec-propylbutylacetamide (SPD), VX-765 and YK3089. Since the previous Eilat conference, retigabine (ezogabine) has been marketed and four newer AEDs in development (NAX 810-2, SPD, tonabersat and VX-765) are included in this manuscript. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. Inferring Allele Frequency Trajectories from Ancient DNA Indicates That Selection on a Chicken Gene Coincided with Changes in Medieval Husbandry Practices.

    PubMed

    Loog, Liisa; Thomas, Mark G; Barnett, Ross; Allen, Richard; Sykes, Naomi; Paxinos, Ptolemaios D; Lebrasseur, Ophélie; Dobney, Keith; Peters, Joris; Manica, Andrea; Larson, Greger; Eriksson, Anders

    2017-08-01

    Ancient DNA provides an opportunity to infer the drivers of natural selection by linking allele frequency changes to temporal shifts in environment or cultural practices. However, analyses have often been hampered by uneven sampling and uncertainties in sample dating, as well as being confounded by demographic processes. Here, we present a Bayesian statistical framework for quantifying the timing and strength of selection using ancient DNA that explicitly addresses these challenges. We applied this method to time series data for two loci: TSHR and BCDO2, both hypothesised to have undergone strong and recent selection in domestic chickens. The derived variant in TSHR, associated with reduced aggression to conspecifics and faster onset of egg laying, shows strong selection beginning around 1,100 years ago, coincident with archaeological evidence for intensified chicken production and documented changes in egg and chicken consumption. To our knowledge, this is the first example of preindustrial domesticate trait selection in response to a historically attested cultural shift in food preference. For BCDO2, we find support for selection, but demonstrate that the recent rise in allele frequency could also have been driven by gene flow from imported Asian chickens during more recent breed formations. Our findings highlight that traits found ubiquitously in modern domestic species may not necessarily have originated during the early stages of domestication. In addition, our results demonstrate the importance of precise estimation of allele frequency trajectories through time for understanding the drivers of selection. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  8. Low-Magnitude, High-Frequency Vibration Fails to Accelerate Ligament Healing but Stimulates Collagen Synthesis in the Achilles Tendon.

    PubMed

    Thompson, William R; Keller, Benjamin V; Davis, Matthew L; Dahners, Laurence E; Weinhold, Paul S

    2015-05-01

    Low-magnitude, high-frequency vibration accelerates fracture and wound healing and prevents disuse atrophy in musculoskeletal tissues. To investigate the role of low-magnitude, high-frequency vibration as a treatment to accelerate healing of an acute ligament injury and to examine gene expression in the intact Achilles tendon of the injured limb after low-magnitude, high-frequency vibration. Controlled laboratory study. Complete surgical transection of the medial collateral ligament (MCL) was performed in 32 Sprague-Dawley rats, divided into control and low-magnitude, high-frequency vibration groups. Low-magnitude, high-frequency vibration started on postoperative day 2, and rats received vibration for 30 minutes a day for 12 days. All rats were sacrificed 2 weeks after the operation, and their intact and injured MCLs were biomechanically tested or used for histological analysis. Intact Achilles tendons from the injured limb were evaluated for differences in gene expression. Mechanical testing revealed no differences in the ultimate tensile load or the structural stiffness between the control and vibration groups for either the injured or intact MCL. Vibration exposure increased gene expression of collagen 1 alpha (3-fold), interleukin 6 (7-fold), cyclooxygenase 2 (5-fold), and bone morphogenetic protein 12 (4-fold) in the intact Achilles tendon when compared with control tendons ( P < .05). While no differences were observed in the mechanical or histological properties of the fully transected MCL after low-magnitude, high-frequency vibration treatment, significant enhancements in gene expression were observed in the intact Achilles tendon. These included collagen, several inflammatory cytokines, and growth factors critical for tendons. As low-magnitude, high-frequency vibration had no negative effects on ligament healing, vibration therapy may be a useful tool to accelerate healing of other tissues (bone) in multitrauma injuries without inhibiting ligament healing

  9. LGscore: A method to identify disease-related genes using biological literature and Google data.

    PubMed

    Kim, Jeongwoo; Kim, Hyunjin; Yoon, Youngmi; Park, Sanghyun

    2015-04-01

    Since the genome project in 1990s, a number of studies associated with genes have been conducted and researchers have confirmed that genes are involved in disease. For this reason, the identification of the relationships between diseases and genes is important in biology. We propose a method called LGscore, which identifies disease-related genes using Google data and literature data. To implement this method, first, we construct a disease-related gene network using text-mining results. We then extract gene-gene interactions based on co-occurrences in abstract data obtained from PubMed, and calculate the weights of edges in the gene network by means of Z-scoring. The weights contain two values: the frequency and the Google search results. The frequency value is extracted from literature data, and the Google search result is obtained using Google. We assign a score to each gene through a network analysis. We assume that genes with a large number of links and numerous Google search results and frequency values are more likely to be involved in disease. For validation, we investigated the top 20 inferred genes for five different diseases using answer sets. The answer sets comprised six databases that contain information on disease-gene relationships. We identified a significant number of disease-related genes as well as candidate genes for Alzheimer's disease, diabetes, colon cancer, lung cancer, and prostate cancer. Our method was up to 40% more accurate than existing methods. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Targeted Resequencing and Functional Testing Identifies Low-Frequency Missense Variants in the Gene Encoding GARP as Significant Contributors to Atopic Dermatitis Risk.

    PubMed

    Manz, Judith; Rodríguez, Elke; ElSharawy, Abdou; Oesau, Eva-Maria; Petersen, Britt-Sabina; Baurecht, Hansjörg; Mayr, Gabriele; Weber, Susanne; Harder, Jürgen; Reischl, Eva; Schwarz, Agatha; Novak, Natalija; Franke, Andre; Weidinger, Stephan

    2016-12-01

    Gene-mapping studies have consistently identified a susceptibility locus for atopic dermatitis and other inflammatory diseases on chromosome band 11q13.5, with the strongest association observed for a common variant located in an intergenic region between the two annotated genes C11orf30 and LRRC32. Using a targeted resequencing approach we identified low-frequency and rare missense mutations within the LRRC32 gene encoding the protein GARP, a receptor on activated regulatory T cells that binds latent transforming growth factor-β. Subsequent association testing in more than 2,000 atopic dermatitis patients and 2,000 control subjects showed a significant excess of these LRRC32 variants in individuals with atopic dermatitis. Structural protein modeling and bioinformatic analysis predicted a disruption of protein transport upon these variants, and overexpression assays in CD4 + CD25 - T cells showed a significant reduction in surface expression of the mutated protein. Consistently, flow cytometric (FACS) analyses of different T-cell subtypes obtained from atopic dermatitis patients showed a significantly reduced surface expression of GARP and a reduced conversion of CD4 + CD25 - T cells into regulatory T cells, along with lower expression of latency-associated protein upon stimulation in carriers of the LRRC32 A407T variant. These results link inherited disturbances of transforming growth factor-β signaling with atopic dermatitis risk. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  11. Deletion of a target gene in Indica rice via CRISPR/Cas9.

    PubMed

    Wang, Ying; Geng, Lizhao; Yuan, Menglong; Wei, Juan; Jin, Chen; Li, Min; Yu, Kun; Zhang, Ya; Jin, Huaibing; Wang, Eric; Chai, Zhijian; Fu, Xiangdong; Li, Xianggan

    2017-08-01

    Using CRISPR/Cas9, we successfully deleted large fragments of the yield-related gene DENSE AND ERECT PANICLE1 in Indica rice at relatively high frequency and generated gain-of-function dep1 mutants. CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a rapidly developing technology used to produce gene-specific modifications in both mammalian and plant systems. Most CRISPR-induced modifications in plants reported to date have been small insertions or deletions. Few large target gene deletions have thus far been reported, especially for Indica rice. In this study, we designed multiple CRISPR sgRNAs and successfully deleted DNA fragments in the gene DENSE AND ERECT PANICLE1 (DEP1) in the elite Indica rice line IR58025B. We achieved deletion frequencies of up to 21% for a 430 bp target and 9% for a 10 kb target among T0 events. Constructs with four sgRNAs did not generate higher full-length deletion frequencies than constructs with two sgRNAs. The multiple mutagenesis frequency reached 93% for four targets, and the homozygous mutation frequency reached 21% at the T0 stage. Important yield-related trait characteristics, such as dense and erect panicles and reduced plant height, were observed in dep1 homozygous T0 mutant plants produced by CRISPR/Cas9. Therefore, we successfully obtained deletions in DEP1 in the Indica background using the CRISPR/Cas9 editing tool at relatively high frequency.

  12. Construction of a Schizosaccharomyces pombe gene bank in a yeast bacterial shuttle vector and its use to isolate genes by complementation.

    PubMed

    Beach, D; Piper, M; Nurse, P

    1982-01-01

    A gene bank of partial Sau3A restriction fragments of S. pombe DNA has been constructed in the plasmid vector, pDB248', which is capable of high frequency transformation of S. pombe. Procedures are described which enable plasmids to be recovered from S. pombe by their reintroduction into E. coli. These methods have been used to detect the S. pombe genes lys 1+, ade 6+ and his 2+ in the gene bank by complementation of mutant gene functions, and to physically isolate the lys 1+ gene.

  13. Compositional gene landscapes in vertebrates.

    PubMed

    Cruveiller, Stéphane; Jabbari, Kamel; Clay, Oliver; Bernardi, Giorgio

    2004-05-01

    The existence of a well conserved linear relationship between GC levels of genes' second and third codon positions (GC2, GC3) prompted us to focus on the landscape, or joint distribution, spanned by these two variables. In human, well curated coding sequences now cover at least 15%-30% of the estimated total gene set. Our analysis of the landscape defined by this gene set revealed not only the well documented linear crest, but also the presence of several peaks and valleys along that crest, a property that was also indicated in two other warm-blooded vertebrates represented by large gene databases, that is, mouse and chicken. GC2 is the sum of eight amino acid frequencies, whereas GC3 is linearly related to the GC level of the chromosomal region containing the gene. The landscapes therefore portray relations between proteins and the DNA environments of the genes that encode them.

  14. Mutagenesis of diploid mammalian genes by gene entrapment

    PubMed Central

    Lin, Qing; Donahue, Sarah L.; Moore-Jarrett, Tracy; Cao, Shang; Osipovich, Anna B.; Ruley, H. Earl

    2006-01-01

    The present study describes a genome-wide method for biallelic mutagenesis in mammalian cells. Novel poly(A) gene trap vectors, which contain features for direct cloning vector–cell fusion transcripts and for post-entrapment genome engineering, were used to generate a library of 979 mutant ES cells. The entrapment mutations generally disrupted gene expression and were readily transmitted through the germline, establishing the library as a resource for constructing mutant mice. Cells homozygous for most entrapment loci could be isolated by selecting for enhanced expression of an inserted neomycin-resistance gene that resulted from losses of heterozygosity (LOH). The frequencies of LOH measured at 37 sites in the genome ranged from 1.3 × 10−5 to 1.2 × 10−4 per cell and increased with increasing distance from the centromere, implicating mitotic recombination in the process. The ease and efficiency of obtaining homozygous mutations will (i) facilitate genetic studies of gene function in cultured cells, (ii) permit genome-wide studies of recombination events that result in LOH and mediate a type of chromosomal instability important in carcinogenesis, and (iii) provide new strategies for phenotype-driven mutagenesis screens in mammalian cells. PMID:17062627

  15. Aerosol size distribution and new particle formation events in the suburb of Xi'an, northwest China

    NASA Astrophysics Data System (ADS)

    Peng, Yan; Liu, Xiaodong; Dai, Jin; Wang, Zhao; Dong, Zipeng; Dong, Yan; Chen, Chuang; Li, Xingmin; Zhao, Na; Fan, Chao

    2017-03-01

    Particle number concentration and size distribution are important for better understanding the characteristics of aerosols. However, their measurements are scarce in western China. Based on the first measurement of particle number size distribution (10-487 nm) in the suburb of Xi'an, northwest China from November 2013 to December 2014, the seasonal, monthly and diurnal average particle number concentrations were investigated, and the characteristics of new particle formation (NPF) events and their dependencies on meteorological parameters also discussed. The results showed that the annual average particle number concentrations in the nucleation (NNUC), Aitken (NAIT), and Accumulation (NACC) size ranges were 960 cm-3, 4457 cm-3, 3548 cm-3, respectively. The mean total particle number concentration (NTOT) was 8965 cm-3 and largely dominated by particles in Aitken mode. The number concentration was dominated by particles around 67.3 nm in spring, summer and fall, while about 89.8 nm in winter. The percentage of the ultrafine size range (UFP, particles of diameter below 100 nm) to total particle number concentration was 63.2%, 69.6%, 62.2% and 58.1% in four seasons. The diurnal variation of the nucleation mode particles was mainly influenced by NPF events in summer, while by both traffic densities and NPF events in spring, fall and winter. The diurnal variation of the number concentration of Aitken mode particles correlated with the traffic emission in spring, fall and winter, while in summer it more correlated with contribution of the growth of the nucleation mode particles. The burst of nucleation mode particles typically started in the daytime (08:15-16:05, LST). The growth rates of nucleated particles ranged from 2.8 to 10.7 nm h-1 with an average of 5.0 ± 1.9 nm h-1. Among observed 66 NPF events from 347 effective measurement days, 85 percent of their air masses came from north or northwest China, resulting in a low concentration of pre-existing particles, and

  16. Frequency of a FAS ligand gene variant associated with inherited feline autoimmune lymphoproliferative syndrome in British shorthair cats in New Zealand.

    PubMed

    Aberdein, D; Munday, J S; Dittmer, K E; Heathcott, R W; Lyons, L A

    2017-11-01

    AIMS To determine the frequency of the FAS-ligand gene (FASLG) variant associated with feline autoimmune lymphoproliferative syndrome (FALPS) and the proportion of carriers of the variant in three British shorthair (BSH) breeding catteries in New Zealand. METHODS Buccal swabs were collected from all cats in two BSH breeding catteries from the South Island and one from the North Island of New Zealand. DNA was extracted and was tested for the presence of the FASLG variant using PCR. Cats with the FASLG variant were identified and the frequency of the FASLG variant allele calculated. Pedigree analysis was performed and inbreeding coefficients were calculated for cats with the FASLG variant. RESULTS Of 32 BSH cats successfully tested for the presence of the FASLG variant, one kitten (3%) was homozygous (FALPS-affected), and seven (22%) cats were heterozygous (carriers) for the FASLG variant allele, and 24 (75%) cats were homozygous for the wild type allele. The overall frequency of the FASLG variant allele in these 32 cats was 0.14. Cats carrying the FASLG variant were from all three breeding catteries sampled, including two catteries that had not previously reported cases of FALPS. Pedigree analysis revealed common ancestry of FALPS-affected and carrier cats within six generations, as well as frequent inbreeding, with inbreeding coefficients >0.12 for five cats with the FASLG variant. CONCLUSIONS AND CLINICAL RELEVANCE There was a high frequency of the FASLG variant allele (0.14) in this small sample of BSH cats, with 22% of healthy cats identified as carriers of the FASLG variant. For an inherited disease, lethal at a young age, in a small population in which inbreeding is common, these results are significant. To prevent future cases of disease and stop further spread of the FASLG variant allele within the BSH population in New Zealand, it is recommended that all BSH and BSH-cross cats be tested for the presence of the FASLG variant before mating. Cats identified as

  17. Genetic and pharmacological reactivation of the mammalian inactive X chromosome

    PubMed Central

    Bhatnagar, Sanchita; Zhu, Xiaochun; Ou, Jianhong; Lin, Ling; Chamberlain, Lynn; Zhu, Lihua J.; Wajapeyee, Narendra; Green, Michael R.

    2014-01-01

    X-chromosome inactivation (XCI), the random transcriptional silencing of one X chromosome in somatic cells of female mammals, is a mechanism that ensures equal expression of X-linked genes in both sexes. XCI is initiated in cis by the noncoding Xist RNA, which coats the inactive X chromosome (Xi) from which it is produced. However, trans-acting factors that mediate XCI remain largely unknown. Here, we perform a large-scale RNA interference screen to identify trans-acting XCI factors (XCIFs) that comprise regulators of cell signaling and transcription, including the DNA methyltransferase, DNMT1. The expression pattern of the XCIFs explains the selective onset of XCI following differentiation. The XCIFs function, at least in part, by promoting expression and/or localization of Xist to the Xi. Surprisingly, we find that DNMT1, which is generally a transcriptional repressor, is an activator of Xist transcription. Small-molecule inhibitors of two of the XCIFs can reversibly reactivate the Xi, which has implications for treatment of Rett syndrome and other dominant X-linked diseases. A homozygous mouse knockout of one of the XCIFs, stanniocalcin 1 (STC1), has an expected XCI defect but surprisingly is phenotypically normal. Remarkably, X-linked genes are not overexpressed in female Stc1−/− mice, revealing the existence of a mechanism(s) that can compensate for a persistent XCI deficiency to regulate X-linked gene expression. PMID:25136103

  18. Splicing defect in FKBP10 gene causes autosomal recessive osteogenesis imperfecta disease: a case report.

    PubMed

    Maghami, Fatemeh; Tabei, Seyed Mohammad Bagher; Moravej, Hossein; Dastsooz, Hassan; Modarresi, Farzaneh; Silawi, Mohammad; Faghihi, Mohammad Ali

    2018-05-25

    Osteogenesis imperfecta (OI) is a group of connective tissue disorder caused by mutations of genes involved in the production of collagen and its supporting proteins. Although the majority of reported OI variants are in COL1A1 and COL1A2 genes, recent reports have shown problems in other non-collagenous genes involved in the post translational modifications, folding and transport, transcription and proliferation of osteoblasts, bone mineralization, and cell signaling. Up to now, 17 types of OI have been reported in which types I to IV are the most frequent cases with autosomal dominant pattern of inheritance. Here we report an 8- year- old boy with OI who has had multiple fractures since birth and now he is wheelchair-dependent. To identify genetic cause of OI in our patient, whole exome sequencing (WES) was carried out and it revealed a novel deleterious homozygote splice acceptor site mutation (c.1257-2A > G, IVS7-2A > G) in FKBP10 gene in the patient. Then, the identified mutation was confirmed using Sanger sequencing in the proband as homozygous and in his parents as heterozygous, indicating its autosomal recessive pattern of inheritance. In addition, we performed RT-PCR on RNA transcripts originated from skin fibroblast of the proband to analyze the functional effect of the mutation on splicing pattern of FKBP10 gene and it showed skipping of the exon 8 of this gene. Moreover, Real-Time PCR was carried out to quantify the expression level of FKBP10 in the proband and his family members in which it revealed nearly the full decrease in the level of FKBP10 expression in the proband and around 75% decrease in its level in the carriers of the mutation, strongly suggesting the pathogenicity of the mutation. Our study identified, for the first time, a private pathogenic splice site mutation in FKBP10 gene and further prove the involvement of this gene in the rare cases of autosomal recessive OI type XI with distinguished clinical manifestations.

  19. Frequency Evaluation of T6235C (m1) and A4889G (m2) Polymorphisms of CYP1A1 Gene in a Healthy Population from the west of Mazandaran Province, Iran.

    PubMed

    Ahangar, N; Alizadeh, B; Tousi, A

    2016-06-30

    CYP1A1 is an important phase I xenobiotic metabolizing enzyme involved in the metabolism of numbers of toxins, endogenous hormones and drugs. Polymorphisms in this phase I gene can alter enzyme activity and induction, also are known to be associated with cancer susceptibility related to environmental toxins and hormone exposure. The present study was aimed to determine the frequencies of commonly known functional polymorphismsof CYP1A1 gene including CYP1A1 m1 (MspI), and CYP1A1 m2 (Ile-Val) in a healthy population from the west of Mazandaran province, Iran. A total of 200 unrelated healthy subjects from Mazandaran province, residing in Tonekabon city, coming for blood donating at Tonekabon Blood Transfusion Center were enrolled. Genomic DNA was extracted from peripheral blood lymphocytes of each subject. All subjects were genotyped for CYP1A1 m1 (T>C) and m2 (A>G) by polymerase chain reaction-restriction fragment length polymorphism method. The frequencies of the TT(wt/wt), TC(wt/mt) and CC(mt/mt) genotypes were as 65.5%, 32.0% and 2.5% respectively for m1 and frequencies of the AA(wt/wt), AG(wt/mt) and GG(mt/mt) genotypes were as 84.5%, 15% and 0.5% respectively for the m2. The frequencies of T and C alleles in the population were 81.5% and 18.5% respectively and the frequencies of A and G alleles were 92% and 8% respectively. Results of the present study might be important in understanding the distribution of CYP1A1 (m1) and CYP1A1 (m2) polymorphisms in Mazandaran province of Iran. Moreover, these results may determine the susceptibilities of individuals towards environmental procarcinogens that result in several cancers.

  20. Efficient strategy for detecting gene × gene joint action and its application in schizophrenia.

    PubMed

    Won, Sungho; Kwon, Min-Seok; Mattheisen, Manuel; Park, Suyeon; Park, Changsoon; Kihara, Daisuke; Cichon, Sven; Ophoff, Roel; Nöthen, Markus M; Rietschel, Marcella; Baur, Max; Uitterlinden, Andre G; Hofmann, A; Lange, Christoph

    2014-01-01

    We propose a new approach to detect gene × gene joint action in genome-wide association studies (GWASs) for case-control designs. This approach offers an exhaustive search for all two-way joint action (including, as a special case, single gene action) that is computationally feasible at the genome-wide level and has reasonable statistical power under most genetic models. We found that the presence of any gene × gene joint action may imply differences in three types of genetic components: the minor allele frequencies and the amounts of Hardy-Weinberg disequilibrium may differ between cases and controls, and between the two genetic loci the degree of linkage disequilibrium may differ between cases and controls. Using Fisher's method, it is possible to combine the different sources of genetic information in an overall test for detecting gene × gene joint action. The proposed statistical analysis is efficient and its simplicity makes it applicable to GWASs. In the current study, we applied the proposed approach to a GWAS on schizophrenia and found several potential gene × gene interactions. Our application illustrates the practical advantage of the proposed method. © 2013 WILEY PERIODICALS, INC.

  1. Transcription of detoxification genes following permethrin selection in the mosquito Aedes aegypti

    PubMed Central

    Saavedra-Rodriguez, Karla; Suarez, Adriana Flores; Salas, Ildefonso Fernandez; Strode, Clare; Ranson, Hilary; Hemingway, Janet; Black, William C.

    2011-01-01

    Changes in gene expression before, during and after five generations of permethrin laboratory selection were monitored in six strains of Aedes aegypti: five F2 – F3 collections from the Yucatán Peninsula of México and one F2 from Iquitos, Perú. Three biological replicate lines were generated for each strain. The response to selection was measured as changes in the lethal and knockdown permethrin concentrations (LC50, KC50) and in the frequency of the Ile1,016 substitution in the voltage gated sodium channel (para) gene. Changes in expression of 290 metabolic detoxification genes were measured using the “Aedes Detox” microarray. Selection simultaneously increased the LC50, KC50 and Ile1,016 frequency. There was an inverse relationship between Ile1,016 frequency and the numbers of differentially transcribed genes. The Iquitos strain lacked the Ile1,016 allele and 51 genes were differentially transcribed following selection as compared to 10–18 genes in the Mexican strains. Very few of the same genes were differentially transcribed among field strains but ten cytochrome P450 genes were upregulated in more than one strain. Laboratory adaptation to permethrin in Ae. aegypti is genetically complex and largely conditioned by geographic origin and preexisting target site insensitivity in the para gene. The lack of uniformity in the genes that responded to artificial selection as well as differences in the direction of their responses challenges the assumption that one or a few genes control permethrin metabolic resistance. Attempts to identify one or a few metabolic genes that are predictably associated with permethrin adaptation may be futile. PMID:22032702

  2. Mid-Latitude Mobile Wideband HF- NVIS Channel Analysis: Part 1

    DTIC Science & Technology

    2017-09-14

    Division EXECUTIVE SUMMARY High frequency (HF) links (2 to 30 MHz) are an alternative to the cost and tactical fragility of commercial satellite...43 4.5 HIGH -LATITUDE HF AND HF-NVIS MODELS...ionosphere without vehicle speed..................... B-6 xi 1. REPORT OUTLINE This report analyzes a mid-latitude wideband high frequency nearly vertical

  3. High frequency of exon 15 deletion in the FANCA gene in Tunisian patients affected with Fanconi anemia disease: implication for diagnosis.

    PubMed

    Amouri, Ahlem; Talmoudi, Faten; Messaoud, Olfa; d'Enghien, Catherine D; Rekaya, Mariem B; Allegui, Ines; Azaiez, Héla; Kefi, Rym; Abdelhak, Ahlem; Meseddi, Sondes H; Torjemane, Lamia; Ouederni, Monia; Mellouli, Fethi; Abid, Héla B; Aissaoui, Lamia; Bejaoui, Mohamed; Othmen, Tarek B; Lyonnet, Dominique S; Soulier, Jean; Hachicha, Mongia; Dellagi, Koussay; Abdelhak, Sonia; Fanconi, Tunisian

    2014-03-01

    Tunisian population is characterized by its heterogeneous ethnic background and high rate of consanguinity. In consequence, there is an increase in the frequency of recessive genetic disorders including Fanconi anemia (FA). The aim of this study was to confirm the existence of a founder haplotype among FA Tunisian patients and to identify the associated mutation in order to develop a simple tool for FA diagnosis. Seventy-four unrelated families with a total of 95 FA patients were investigated. All available family members were genotyped with four microsatellite markers flanking FANCA gene. Haplotype analysis and homozygosity mapping assigned 83 patients belonging to 62 families to the FA-A group. A common haplotype was shared by 42 patients from 26 families at a homozygous state while five patients from five families were heterozygous. Among them, 85% were from southern Tunisia suggesting a founder effect. Using multiplex ligation-dependent probe amplification (MLPA) technique, we have also demonstrated that this haplotype is associated with a total deletion of exon 15 in FANCA gene. Identification of a founder mutation allowed genetic counseling in relatives of these families, better bone marrow graft donor selection and prenatal diagnosis. This mutation should be investigated in priority for patients originating from North Africa and Middle East.

  4. High frequency of exon 15 deletion in the FANCA gene in Tunisian patients affected with Fanconi anemia disease: implication for diagnosis

    PubMed Central

    Amouri, Ahlem; Talmoudi, Faten; Messaoud, Olfa; d'Enghien, Catherine D; Rekaya, Mariem B; Allegui, Ines; Azaiez, Héla; Kefi, Rym; Abdelhak, Ahlem; Meseddi, Sondes H; Torjemane, Lamia; Ouederni, Monia; Mellouli, Fethi; Abid, Héla B; Aissaoui, Lamia; Bejaoui, Mohamed; Othmen, Tarek B; Lyonnet, Dominique S; Soulier, Jean; Hachicha, Mongia; Dellagi, Koussay; Abdelhak, Sonia; Fanconi, Tunisian

    2014-01-01

    Tunisian population is characterized by its heterogeneous ethnic background and high rate of consanguinity. In consequence, there is an increase in the frequency of recessive genetic disorders including Fanconi anemia (FA). The aim of this study was to confirm the existence of a founder haplotype among FA Tunisian patients and to identify the associated mutation in order to develop a simple tool for FA diagnosis. Seventy-four unrelated families with a total of 95 FA patients were investigated. All available family members were genotyped with four microsatellite markers flanking FANCA gene. Haplotype analysis and homozygosity mapping assigned 83 patients belonging to 62 families to the FA-A group. A common haplotype was shared by 42 patients from 26 families at a homozygous state while five patients from five families were heterozygous. Among them, 85% were from southern Tunisia suggesting a founder effect. Using multiplex ligation-dependent probe amplification (MLPA) technique, we have also demonstrated that this haplotype is associated with a total deletion of exon 15 in FANCA gene. Identification of a founder mutation allowed genetic counseling in relatives of these families, better bone marrow graft donor selection and prenatal diagnosis. This mutation should be investigated in priority for patients originating from North Africa and Middle East. PMID:24689079

  5. Lhx2 Determines Odorant Receptor Expression Frequency in Mature Olfactory Sensory Neurons

    PubMed Central

    Zhang, Guangfan; Titlow, William B.; Biecker, Stephanie M.; Stromberg, Arnold J.

    2016-01-01

    Abstract A developmental program of epigenetic repression prepares each mammalian olfactory sensory neuron (OSN) to strongly express one allele from just one of hundreds of odorant receptor (OR) genes, but what completes this process of OR gene choice by driving the expression of this allele is incompletely understood. Conditional deletion experiments in mice demonstrate that Lhx2 is necessary for normal expression frequencies of nearly all ORs and all trace amine-associated receptors, irrespective of whether the deletion of Lhx2 is initiated in immature or mature OSNs. Given previous evidence that Lhx2 binds OR gene control elements, these findings indicate that Lhx2 is directly involved in driving OR expression. The data also support the conclusion that OR expression is necessary to allow immature OSNs to complete differentiation and become mature. In contrast to the robust effects of conditional deletion of Lhx2, the loss of Emx2 has much smaller effects and more often causes increased expression frequencies. Lhx2:Emx2 double mutants show opposing effects on Olfr15 expression that reveal independent effects of these two transcription factors. While Lhx2 is necessary for OR expression that supports OR gene choice, Emx2 can act differently; perhaps by helping to control the availability of OR genes for expression. PMID:27822500

  6. Association of -330 interleukin-2 gene polymorphism with oral cancer.

    PubMed

    Singh, Prithvi Kumar; Kumar, Vijay; Ahmad, Mohammad Kaleem; Gupta, Rajni; Mahdi, Abbas Ali; Jain, Amita; Bogra, Jaishri; Chandra, Girish

    2017-12-01

    Cytokines play an important role in the development of cancer. Several single-nucleotide polymorphisms (SNPs) of cytokine genes have been reported to be associated with the development and severity of inflammatory diseases and cancer predisposition. This study was undertaken to evaluate a possible association of interleukin 2 (IL-2) (- 330A>C) gene polymorphisms with the susceptibility to oral cancer. The SNP in IL-2 (-330A>C) gene was genotyped in 300 oral cancer patients and in similar number of healthy volunteers by polymerase chain reaction (PCR)-restriction fragment length polymorphism and the association of the gene with the disease was evaluated. IL-2 (-330A>C) gene polymorphism was significantly associated with oral cancer whereas it was neither associated with clinicopathological status nor with cancer pain. The AC heterozygous genotype was significantly associated with oral cancer patients as compared to controls [odds ratio (OR): 3.0; confidence interval (CI): 2.14-4.20; P<0.001]. The C allele frequency was also significantly associated with oral cancer (OR: 1.80; CI: 1.39-2.33; P<0.001). IL-2 (-330A>C) gene polymorphism was also associated with oral cancer in tobacco smokers and chewers. Our results showed that oral cancer patients had significantly higher frequency of AA genotype but significantly lower frequency of AC genotype and C allele compared to controls. The IL-2 AC genotype and C allele of IL-2 (-330A>C) gene polymorphisms could be potential protective factors and might reduce the risk of oral cancer in Indian population.

  7. Characterization of parent and oxygenated-polycyclic aromatic hydrocarbons (PAHs) in Xi'an, China during heating period: An investigation of spatial distribution and transformation.

    PubMed

    Wang, Jingzhi; Hang Ho, Steven Sai; Huang, Rujin; Gao, Meiling; Liu, Suixin; Zhao, Shuyu; Cao, Junji; Wang, Gehui; Shen, Zhenxing; Han, Yongming

    2016-09-01

    Polycyclic aromatic hydrocarbons (PAHs) and its oxygenated derivatives (OPAHs) are toxins in PM2.5. Little information has been known for their transformation in the ambient airs. In this study, PM2.5 samples were collected at 19 sampling sites in Xi'an, China during the heating period, which is classified into: urban residential, university, commercial area, suburban region, and industry. Organic compounds including PAHs, OPAHs, hopanes and cholestanes were quantified. The average of total quantified PAHs and OPAHs concentrations were 196.5 ng/m(3) and 29.4 ng/m(3), respectively, which were consistent with other northern cities in China. Statistical analyses showed that there were significant differences on the distributions of PAHs between urban and suburban regions. The industry also had distinguishable profiles compared with urban residential and commercial area for OPAHs. The greater diversity of OPAHs than PAHs might be due to different primary emission sources and transformation and degradation pathways. The ratios of OPAHs to the corresponding parent PAHs, including 9-fluorenone/fluorene, anthraquinone/anthracene, benz[a]anthracene-7,12-dione/benzo[a]anthracene were 6.2, 12.7, and 1.4, respectively, which were much higher than those for the fresh emissions from coal combustion and biomass burning. These prove the importance of secondary formation and transformation of OPAHs in the ambient airs. Biomarkers such as retene, cyclopenta[CD]pyrene and αα-homohopane were characterized for the source apportionment. With Positive Matrix Factorization (PMF) model analysis, biomass burning was recognized as the most dominant pollution sources for PAHs during the heading period, which accounted for a contribution of 37.1%. Vehicle emission (22.8%) and coal combustion (22.6%) were also contributors in Xi'an. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. The Saccharomyces cerevisiae LOS1 gene involved in pre-tRNA splicing encodes a nuclear protein that behaves as a component of the nuclear matrix.

    PubMed

    Shen, W C; Selvakumar, D; Stanford, D R; Hopper, A K

    1993-09-15

    Mutations of the Saccharomyces cerevisiae LOS1 gene cause the accumulation of end matured intron-containing pre-tRNAs at elevated temperatures. In an effort to decipher the role of the LOS1 protein in pre-tRNA splicing, we have analyzed the LOS1 gene and its protein product. The LOS1 gene is located on the left arm of chromosome XI and the order of genes in this area of the chromosome is .... URA1 ... SAC1 TRP3 UBA1 STE6 LOS1 .... FAS1..... The LOS1 open reading frame encodes a putative protein of 1100 amino acids that shows no significant homology to other genes. The LOS1 open reading frame was tagged with the influenza virus hemagglutinin epitope recognized by the 12CA5 antibody. The 12CA5 antibody recognizes an epitope-tagged protein of the size predicted by the LOS1 open reading frame. Using this antibody for indirect immunofluorescence and cell fractionation studies we show that the LOS1 protein is located in nuclei. Los1p cannot be extracted from nuclei by treatment with nucleases, salts, or Triton X-100. This insolubility suggests that Los1p is a component of the nucleoskeleton. We propose that LOS1 mutations may affect pre-tRNA processing via alteration of the nuclear matrix.

  9. Prostate cancer and polymorphism D85Y in gene for dihydrotestosterone degrading enzyme UGT2B15: Frequency of DD homozygotes increases with Gleason Score.

    PubMed

    Hajdinjak, Tine; Zagradisnik, Boris

    2004-06-01

    Although, a functional rationale for influence of polymorphism D85Y in gene UGT2B15 on prostate cancer (PCa) exists (different V(max) of enzyme), conflicting results have been reported. DNA from 178 controls and 206 PCa patients with known Gleason score were genotyped using a newly developed RFLP assay, which allowed the detection of both alleles in an individual after single PCR amplification. 16% DD, 52% DY; PCa patients: 23% DD, 49% DY. Subgroups of PCa: well differentiated: 11% DD, 37% DY; moderately differentiated: 22% DD, 50% DY; poorly differentiated: 34% DD, 50% DY. Correlation was confirmed between Gleason score and number of D alleles (P = 0.018) and persisted after age adjustment. When comparing controls to patients with a Gleason score of 7 or more, difference for the frequency of homozygosity DD was significant between the groups (P = 0.032, OR = 2.04). Polymorphism D85Y in gene UGT2B15 correlates with differentiation of PCa. Copyright 2004 Wiley-Liss, Inc.

  10. [Improving prevention activities of infectious diseases during preparation and holding of the XXII Olympic Winter Games and XI Paralympic Winter Games 2014 in Sochi].

    PubMed

    Onishchenko, G G; Bragina, I V; Ezhlova, E B; Demina, Iu V; Grechanaia, T V; Nikolaevich, P N; Balaeva, M I; Tesheva, S Ch; Biriukov, V A; Kulichenko, A N; Vasilenko, N F; Maletskaia, O V; Manin, E A; Orobeĭ, V G

    2015-01-01

    The article presents data on the implementation of a set of preventive activities to ensure sanitation and epidemiological welfare during the XXII Olympic Winter Games and XI Paralympic Winter Games 2014 in Sochi. The importance of monitoring and evaluation of epidemiological risk, as the basis of formation of preventive measures is noticed. The questions of specific, and nonspecific prevention of infectious diseases, especially the work done during the pre-Olympic period are considered. The importance of specifically developed regulatory basis, and health education are emphasized. The conclusion about the effectiveness of the measures taken, which led to a significant reduction of infectious diseases in the region is made.

  11. Effects of Amplitude and Frequency of Mechanical Vibration Stimulation on Cultured Osteoblasts

    NASA Astrophysics Data System (ADS)

    Shikata, Tetsuo; Shiraishi, Toshihiko; Morishita, Shin; Takeuchi, Ryohei; Saito, Tomoyuki

    Mechanical stimulation to bones affects bone formation such as decrease of bone mass of astronauts under zero gravity, walking rehabilitation to bone fracture and fracture repair with ultrasound devices. Bone cells have been reported to sense and response to mechanical stimulation at cellular level morphologically and metabolically. In the view of mechanical vibrations, bone cells are deformed according to mechanical stimulation and their mechanical characteristics. In this study, sinusoidal inertia force was applied to cultured osteoblasts, which are a kind of bone cells, and effects of frequency and acceleration amplitude of mechanical vibration on the cells were investigated in respect of the cell proliferation, bone matrix generation and alkaline phosphatase (ALP) gene expression. The results to be obtained are as follows. The significant difference of cell density and bone mass generation between the non-vibrating and vibrating groups is found. ALP gene expression shows a peak to frequency at 50 Hz and the value of it is approximately 4.5 times as high as that of the non-vibrating group in the case of the acceleration amplitude of 0.5 G. ALP gene expression at 0.5 G is significantly larger than at 0, 0.125 or 0.25 G in the case of the frequency of 50 Hz.

  12. Compositional Gene Landscapes in Vertebrates

    PubMed Central

    Cruveiller, Stéphane; Jabbari, Kamel; Clay, Oliver; Bernardi, Giorgio

    2004-01-01

    The existence of a well conserved linear relationship between GC levels of genes' second and third codon positions (GC2, GC3) prompted us to focus on the landscape, or joint distribution, spanned by these two variables. In human, well curated coding sequences now cover at least 15%–30% of the estimated total gene set. Our analysis of the landscape defined by this gene set revealed not only the well documented linear crest, but also the presence of several peaks and valleys along that crest, a property that was also indicated in two other warm-blooded vertebrates represented by large gene databases, that is, mouse and chicken. GC2 is the sum of eight amino acid frequencies, whereas GC3 is linearly related to the GC level of the chromosomal region containing the gene. The landscapes therefore portray relations between proteins and the DNA environments of the genes that encode them. PMID:15123586

  13. Impact on air quality of measures to reduce CO2 emissions from road traffic in Basel, Rotterdam, Xi'an and Suzhou

    NASA Astrophysics Data System (ADS)

    Keuken, M. P.; Jonkers, S.; Verhagen, H. L. M.; Perez, L.; Trüeb, S.; Okkerse, W.-J.; Liu, J.; Pan, X. C.; Zheng, L.; Wang, H.; Xu, R.; Sabel, C. E.

    2014-12-01

    Two traffic scenarios to reduce CO2 emissions from road traffic in two European cities (Basel and Rotterdam) and two Chinese cities (Xi'an and Suzhou) were evaluated in terms of their impact on air quality. The two scenarios, one modelling a reduction of private vehicle kilometres driven by 10% on urban streets and the other modelling the introduction of 50% electric-powered private vehicle kilometres on urban streets, were both compared to a scenario following “business-as-usual”: 2020-BAU. The annual average concentrations of NO2, PM2.5, PM10 and elemental carbon (EC) were modelled separately in busy street canyons, near urban motorways and in the remainder of the urban area. It was concluded that traffic-related CO2 emissions in 2020-BAU could be expected to remain at the levels of 2010 in Basel and Rotterdam, while in Xi'an and Suzhou to increase 30-50% due to growth in the traffic volume. Traffic-related CO2 emissions may be reduced by up to 5% and 25%, respectively using the first and second scenarios. Air pollution in the Chinese cities is a factor 3 to 5 higher than in the European cities in 2010 and 2020-BAU. The impact of both CO2 reduction scenarios on air quality in 2020-BAU is limited. In Europe, due to implementation of stringent emission standards in all sectors, air quality is expected to improve at both the urban background and near busy road traffic. In China, the regional background is expected to improve for EC, stabilize for PM2.5 and PM10, and decrease for NO2. The urban background follows this regional trend, while near busy road traffic, air pollution will remain elevated due to the considerable growth in traffic volume. A major constraint for modelling air quality in China is access to the input data required and lack of measurements at ground level for validation.

  14. Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African Buffalo: a plausible new mechanism for a high frequency anomaly.

    PubMed

    van Hooft, Pim; Greyling, Ben J; Getz, Wayne M; van Helden, Paul D; Zwaan, Bas J; Bastos, Armanda D S

    2014-01-01

    Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite being associated with low body condition, appears to impart a relative reproductive advantage, and which is stably maintained through a sex-ratio suppressor. Apparently, this sex-ratio suppressor prevents fertility reduction that generally accompanies sex-ratio distortion. We hypothesize that this body-condition-associated reproductive advantage increases the fitness of alleles that negatively affect male body condition, causing genome-wide positive selection of these alleles. To investigate this we genotyped 459 buffalo using 17 autosomal microsatellites. By correlating heterozygosity with body condition (heterozygosity-fitness correlations), we found that most microsatellites were associated with one of two gene types: one with elevated frequencies of deleterious alleles that have a negative effect on body condition, irrespective of sex; the other with elevated frequencies of sexually antagonistic alleles that are negative for male body condition but positive for female body condition. Positive selection and a direct association with a Y-chromosomal sex-ratio suppressor are indicated, respectively, by allele clines and by relatively high numbers of homozygous deleterious alleles among sex-ratio suppressor carriers. This study, which employs novel statistical techniques to analyse heterozygosity-fitness correlations, is the first to demonstrate the abundance of sexually-antagonistic genes in a natural mammal population. It also has important

  15. Measurements of density dependent intensity ratios of extreme ultraviolet line emission from Fe X, XI, and XII

    NASA Astrophysics Data System (ADS)

    Shimizu, Erina; Ali, Safdar; Tsuda, Takashi; Sakaue, Hiroyuki A.; Kato, Daiji; Murakami, Izumi; Hara, Hirohisa; Watanabe, Tetsuya; Nakamura, Nobuyuki

    2017-05-01

    We report high-resolution density dependent intensity ratio measurements for middle charge states of iron in the extreme ultraviolet (EUV) spectral wavelength range of 160-200 Å. The measurements were performed at the Tokyo EBIT laboratory by employing a flat-field grazing incidence spectrometer installed on a low energy compact electron beam ion trap. The intensity ratios for several line pairs stemming from Fe X, Fe XI and Fe XII were extracted from spectra collected at the electron beam energies of 340 and 400 eV by varying the beam current between 7.5 and 12 mA at each energy. In addition, the effective electron densities were obtained experimentally by imaging the electron beam profile and ion cloud size with a pinhole camera and visible spectrometer, respectively. In this paper, the experimental results are compared with previous data from the literature and with the present calculations performed using a collisional-radiative model. Our experimental results show a rather good agreement with the calculations and previous reported results.

  16. Determination of frequencies of alleles, associated with the pseudodeficiency of lysosomal hydrolases, in population of Ukraine.

    PubMed

    Olkhovych, N V; Gorovenko, N G

    2016-01-01

    The pseudodeficiency of lysosomal hydrolases described as a significant reduction in enzyme activi­ty in vitro in clinically healthy individuals, can lead to diagnostic errors in the process of biochemical analysis of lysosomal storage disease in case of its combination with pathology of another origin. Pseudodeficiency is mostly caused by some non-pathogenic changes in the corresponding gene. These changes lead to the in vitro lability of the enzyme molecule, whereas in vivo the enzyme retains its functional activity. To assess the prevalence of the most common lysosomal hydrolases pseudodeficiency alleles in Ukraine, we have determined the frequency of alleles c.1055A>G and c.* 96A>G in the ARSA gene, substitutions c.739C>T (R247W) and c.745C>T (R249W) in the HEXA gene, c.1726G>A (G576S) and c.2065G>A (E689K) in the GAA gene, c.937G>T (D313Y) in the GLA1 gene and c.898G>A (A300T) in the IDUA gene in a group of 117 healthy individuals from different regions of the country and 14 heterozygous carriers of pathogenic mutations in the HEXA gene (parents of children with confirmed diagnosis of Tay-Sachs disease). The total frequency of haplotypes, associated with arylsulfatase A pseudodeficiency, in healthy people in Ukraine (c.1055G/c.*96G and c.1055G/c.*96A haplotypes) was 10.3%. The frequency of c.739C>T (R247W) allele, associated with hexo­saminidase A pseudodeficiency, among Tay-Sachs carriers from Ukraine was 7.1%. The total frequency of α-glucosidase pseudodeficiency haplotypes in healthy individuals in Ukraine (c.1726A/c.2065A and c.1726G/c.2065A haplotypes) was 2.6%. No person among examined individuals with the substitution c.937G>T (D313Y) in the GLA1 gene and c.898G>A (A300T) in the IDUA gene was found. The differential diagnostics of lysosomal storage diseases requires obligatory determination of the presence of the pseudodeficiency alleles, particularly the ones with high incidence in the total population. Ignoring phenomenon of pseudodeficiency may

  17. Duplication polymorphisms in exon 4 of κ-casein gene in yak breeds/populations.

    PubMed

    Pingcuo, S; Gao, J; Jiang, Z R; Jin, S Y; Fu, C Y; Liu, X; Huang, L; Zheng, Y C

    2015-08-28

    The objective of this study was to compare 12 bp-duplication polymorphisms in exon 4 of the κ-casein gene among 3 breeds/populations of yak (Bos grunniens). Genomic DNA was extracted from yak blood or muscle samples (N = 211) and a partial sequence of exon 4 of κ-casein gene was amplified by polymerase chain reaction. A polyacrylamide gel electrophoresis assay of the products (169 bp) revealed 2 variants. These variants differed in a 12-bp duplication of the nucleotide sequence corresponding to amino acids 147-150 (Glu-Ala-Ser-Pro) or 148-151 (Ala-Ser-Pro-Glu). The genotype frequency and gene frequency of the 2 κ-casein variants differed among the 3 yak breeds/populations. The long form of the κ-casein gene was the predominant allele, and the Jiulong yak showed the highest frequency of the short form variant of the κ-casein gene. In addition, 2 nucleotide differences resulting in amino acid substitutions were also identified in yaks. These results are significant for designing a breeding strategy to improve the genetic makeup of yak herds.

  18. Mutation frequency in 15 common cancer genes in high-risk head and neck squamous cell carcinoma.

    PubMed

    McBride, Sean M; Rothenberg, S Michael; Faquin, William C; Chan, Annie W; Clark, John R; Ellisen, Leif W; Wirth, Lori J

    2014-08-01

    With prior studies having looked at unselected cohorts, we sought to explore the mutational landscape in a high-risk group of head and neck squamous cell carcinoma (HNSCC) tumors. A multiplexed polymerase chain reaction (PCR) assay evaluating 68 loci in 15 genes was performed on 64 patients with high-risk HNSCC. Because of the frequent PIK3CA and AKT1 mutations in patients with oropharyngeal carcinoma, we evaluated the relationship between mutation status and both clinical/pathologic variables and tumor control in this subgroup. Seventeen of 64 patients harbored mutations in the assayed loci: 16% in PIK3CA, 9% in TP53, 2% in AKT1, and 2% in epidermal growth factor receptor (EGFR). The frequency of PIK3CA/AKT1 mutations in oropharyngeal and sinonasal primaries was increased compared to other primary sites (35% vs 6%; p = .005). There was no relationship between mutation status and overall survival (OS), disease-specific death, or progression in the oropharyngeal cohort. We identified frequent PIK3CA mutations in patients with high-risk HNSCC confined predominantly to the oropharyngeal and sinonasal subsites; for the first time, mutation in AKT1 has been identified in HNSCC. Copyright © 2014 Wiley Periodicals, Inc.

  19. [Liver cirrhosis patogenetics: polymorphism of glutation S-transferase genes].

    PubMed

    Goncharova, I A; Rachkovskiĭ, M I; Beloborodova, E V; Gamal' Abd El'-Aziz Nasar, Kh; Puzyrev, V P

    2010-01-01

    Association of deletion polymorphism in GSTT1 and GSTM1 genes and polymorphic variant A313G of GSTP1 gene with cirrhosis diseases and 4-year survival rate for the Tomsk region (West Siberia) patients were tested. Homozygous deletion of GSTM1 gene (null genotype) was a protective factor for alcoholic and mixed (HCV, HBV and alcohol) liver cirrhosis development. The patients from the joint group (all etiology forms) as well as having alcoholic and mixed cirrhosis had lower frequency of GSTM1 null genotype (39.2, 39.0, and 34.2%, respectively) in comparison with the control group (64.6%). The GSTM1 null genotype and GSTP1 gene A313G polymorphic variant correlated with the patients' survival rate. The patients survived in comparison with the dead had higher frequency of a GSTM1 null genotype (46.6 vs. 30.2%) and GSTP1 AA genotype (63.1 vs. 40.5%), and lower frequency of GSTP1 AG (A313G) genotype (31.1 vs. 51.2%). A survival rate was 2.5 times higher for patients having GSTP1 AA genotype in comparison with the GG and AG genotype carriers and 2 times higher for patients having GSTM1 null genotype than the gene carriers. A 4-year fatal case probability was 2.3 times higher among the patients having heterozygous AG GSTP1 genotype in comparison with homozygous AA and GG genotype carriers.

  20. Polymorphisms and allele frequencies of the ABO blood group gene among the Jomon, Epi-Jomon and Okhotsk people in Hokkaido, northern Japan, revealed by ancient DNA analysis.

    PubMed

    Sato, Takehiro; Kazuta, Hisako; Amano, Tetsuya; Ono, Hiroko; Ishida, Hajime; Kodera, Haruto; Matsumura, Hirofumi; Yoneda, Minoru; Dodo, Yukio; Masuda, Ryuichi

    2010-10-01

    To investigate the genetic characteristics of the ancient populations of Hokkaido, northern Japan, polymorphisms of the ABO blood group gene were analyzed for 17 Jomon/Epi-Jomon specimens and 15 Okhotsk specimens using amplified product-length polymorphism and restriction fragment length polymorphism analyses. Five ABO alleles were identified from the Jomon/ Epi-Jomon and Okhotsk people. Allele frequencies of the Jomon/Epi-Jomon and Okhotsk people were compared with those of the modern Asian, European and Oceanic populations. The genetic relationships inferred from principal component analyses indicated that both Jomon/Epi-Jomon and Okhotsk people are included in the same group as modern Asian populations. However, the genetic characteristics of these ancient populations in Hokkaido were significantly different from each other, which is in agreement with the conclusions from mitochondrial DNA and ABCC11 gene analyses that were previously reported.

  1. Inherited DNA-Repair Gene Mutations in Men with Metastatic Prostate Cancer.

    PubMed

    Pritchard, Colin C; Mateo, Joaquin; Walsh, Michael F; De Sarkar, Navonil; Abida, Wassim; Beltran, Himisha; Garofalo, Andrea; Gulati, Roman; Carreira, Suzanne; Eeles, Rosalind; Elemento, Olivier; Rubin, Mark A; Robinson, Dan; Lonigro, Robert; Hussain, Maha; Chinnaiyan, Arul; Vinson, Jake; Filipenko, Julie; Garraway, Levi; Taplin, Mary-Ellen; AlDubayan, Saud; Han, G Celine; Beightol, Mallory; Morrissey, Colm; Nghiem, Belinda; Cheng, Heather H; Montgomery, Bruce; Walsh, Tom; Casadei, Silvia; Berger, Michael; Zhang, Liying; Zehir, Ahmet; Vijai, Joseph; Scher, Howard I; Sawyers, Charles; Schultz, Nikolaus; Kantoff, Philip W; Solit, David; Robson, Mark; Van Allen, Eliezer M; Offit, Kenneth; de Bono, Johann; Nelson, Peter S

    2016-08-04

    Inherited mutations in DNA-repair genes such as BRCA2 are associated with increased risks of lethal prostate cancer. Although the prevalence of germline mutations in DNA-repair genes among men with localized prostate cancer who are unselected for family predisposition is insufficient to warrant routine testing, the frequency of such mutations in patients with metastatic prostate cancer has not been established. We recruited 692 men with documented metastatic prostate cancer who were unselected for family history of cancer or age at diagnosis. We isolated germline DNA and used multiplex sequencing assays to assess mutations in 20 DNA-repair genes associated with autosomal dominant cancer-predisposition syndromes. A total of 84 germline DNA-repair gene mutations that were presumed to be deleterious were identified in 82 men (11.8%); mutations were found in 16 genes, including BRCA2 (37 men [5.3%]), ATM (11 [1.6%]), CHEK2 (10 [1.9% of 534 men with data]), BRCA1 (6 [0.9%]), RAD51D (3 [0.4%]), and PALB2 (3 [0.4%]). Mutation frequencies did not differ according to whether a family history of prostate cancer was present or according to age at diagnosis. Overall, the frequency of germline mutations in DNA-repair genes among men with metastatic prostate cancer significantly exceeded the prevalence of 4.6% among 499 men with localized prostate cancer (P<0.001), including men with high-risk disease, and the prevalence of 2.7% in the Exome Aggregation Consortium, which includes 53,105 persons without a known cancer diagnosis (P<0.001). In our multicenter study, the incidence of germline mutations in genes mediating DNA-repair processes among men with metastatic prostate cancer was 11.8%, which was significantly higher than the incidence among men with localized prostate cancer. The frequencies of germline mutations in DNA-repair genes among men with metastatic disease did not differ significantly according to age at diagnosis or family history of prostate cancer. (Funded by

  2. Screening and correlates of neurotic disorders among general medical outpatients in Xi'an China.

    PubMed

    Ni, Chunping; Ma, Lihua; Wang, Bo; Hua, Yan; Hua, Qianzhen; Wallen, Gwenyth R; Gao, Bo; Yan, Yongping; Huang, Yueqin

    2015-04-01

    Little is known about the distribution and correlates of neurotic disorders among general medical outpatients. The aim was to identify the population distribution and associated factors of neurotic disorders among general medical outpatients. A cross-sectional design was used. Computer-assisted interviews of 372 general outpatients aged 16 years or older in Xi'an China were conducted using a Chinese version of the World Health Organization Composite International Diagnostic Interview version 3.0 (CIDI-3.0). The estimated lifetime prevalence of any ICD-10 neurotic disorder among general medical outpatients was 10.8%. The most prevalent subtype of neurotic disorders was specific phobias (5.7%) followed by obsessive-compulsive disorders (3.8%) and social phobias (1.3%). General outpatients who visited the department of internal medicine (OR = 6.55, 95% CI 1.51-28.38), who were under 40 years old (OR = 4.44, 95% CI 2.05-9.62), had less than high school education (OR = 4.19, 95% CI 1.79-9.79), and were female (OR = 2.25, 95% CI 1.14-4.47) were most likely to report neurotic disorders. Effective identification of neurotic disorders is crucial for its early detection and targeted intervention among general medical outpatients. Those outpatients who had younger age and lower education level, and were female and had visited internal medicine departments require additional attention. © 2014 Wiley Periodicals, Inc.

  3. Multiple phenological responses to climate change among 42 plant species in Xi'an, China.

    PubMed

    Dai, Junhu; Wang, Huanjiong; Ge, Quansheng

    2013-09-01

    Phenological data of 42 woody plants in a temperate deciduous forest from the Chinese Phenological Observation Network (CPON) and the corresponding meteorological data from 1963 to 2011 in Xi'an, Shaanxi Province, China were collected and analyzed. The first leaf date (FLD), leaf coloring date (LCD) and first flower date (FFD) are revealed as strong biological signals of climatic change. The FLD, LCD and FFD of most species are sensitive to average temperature during a certain period before phenophase onset. Regional precipitation also has a significant impact on phenophases of about half of the species investigated. Affected by climate change, the FLD and FFD of these species have advanced by 5.54 days and 10.20 days on average during 2003-2011 compared with the period 1963-1996, respectively. Meanwhile, the LCD has delayed by 10.59 days, and growing season length has extended 16.13 days. Diverse responses of phenology commonly exist among different species and functional groups during the study period. Especially for FFD, the deviations between the above two periods ranged from -20.68 to -2.79 days; biotic pollination species showed a significantly greater advance than abiotic pollination species. These results were conducive to the understanding of possible changes in both the structure of plant communities and interspecific relationships in the context of climate change.

  4. High frequency of silver resistance genes in invasive isolates of Enterobacter and Klebsiella species.

    PubMed

    Sütterlin, S; Dahlö, M; Tellgren-Roth, C; Schaal, W; Melhus, Å

    2017-07-01

    Silver-based products have been marketed as an alternative to antibiotics, and their consumption has increased. Bacteria may, however, develop resistance to silver. To study the presence of genes encoding silver resistance (silE, silP, silS) over time in three clinically important Enterobacteriaceae genera. Using polymerase chain reaction (PCR), 752 bloodstream isolates from the years 1990-2010 were investigated. Age, gender, and ward of patients were registered, and the susceptibility to antibiotics and silver nitrate was tested. Clonality and single nucleotide polymorphism were assessed with repetitive element sequence-based PCR, multi-locus sequence typing, and whole-genome sequencing. Genes encoding silver resistance were detected most frequently in Enterobacter spp. (48%), followed by Klebsiella spp. (41%) and Escherichia coli 4%. Phenotypical resistance to silver nitrate was found in Enterobacter (13%) and Klebsiella (3%) isolates. The lowest carriage rate of sil genes was observed in blood isolates from the neonatology ward (24%), and the highest in blood isolates from the oncology/haematology wards (66%). Presence of sil genes was observed in international high-risk clones. Sequences of the sil and pco clusters indicated that a single mutational event in the silS gene could have caused the phenotypic resistance. Despite a restricted consumption of silver-based products in Swedish health care, silver resistance genes are widely represented in clinical isolates of Enterobacter and Klebsiella species. To avoid further selection and spread of silver-resistant bacteria with a high potential for healthcare-associated infections, the use of silver-based products needs to be controlled and the silver resistance monitored. Copyright © 2017 The Healthcare Infection Society. Published by Elsevier Ltd. All rights reserved.

  5. A Dynamical Model Reveals Gene Co-Localizations in Nucleus

    PubMed Central

    Yao, Ye; Lin, Wei; Hennessy, Conor; Fraser, Peter; Feng, Jianfeng

    2011-01-01

    Co-localization of networks of genes in the nucleus is thought to play an important role in determining gene expression patterns. Based upon experimental data, we built a dynamical model to test whether pure diffusion could account for the observed co-localization of genes within a defined subnuclear region. A simple standard Brownian motion model in two and three dimensions shows that preferential co-localization is possible for co-regulated genes without any direct interaction, and suggests the occurrence may be due to a limitation in the number of available transcription factors. Experimental data of chromatin movements demonstrates that fractional rather than standard Brownian motion is more appropriate to model gene mobilizations, and we tested our dynamical model against recent static experimental data, using a sub-diffusion process by which the genes tend to colocalize more easily. Moreover, in order to compare our model with recently obtained experimental data, we studied the association level between genes and factors, and presented data supporting the validation of this dynamic model. As further applications of our model, we applied it to test against more biological observations. We found that increasing transcription factor number, rather than factory number and nucleus size, might be the reason for decreasing gene co-localization. In the scenario of frequency- or amplitude-modulation of transcription factors, our model predicted that frequency-modulation may increase the co-localization between its targeted genes. PMID:21760760

  6. Factor IX gene haplotypes in Amerindians.

    PubMed

    Franco, R F; Araújo, A G; Zago, M A; Guerreiro, J F; Figueiredo, M S

    1997-02-01

    We have determined the haplotypes of the factor IX gene for 95 Indians from 5 Brazilian Amazon tribes: Wayampí, Wayana-Apalaí, Kayapó, Arára, and Yanomámi. Eight polymorphisms linked to the factor IX gene were investigated: MseI (at 5', nt -698), BamHI (at 5', nt -561), DdeI (intron 1), BamHI (intron 2), XmnI (intron 3), TaqI (intron 4), MspI (intron 4), and HhaI (at 3', approximately 8 kb). The results of the haplotype distribution and the allele frequencies for each of the factor IX gene polymorphisms in Amerindians were similar to the results reported for Asian populations but differed from results for other ethnic groups. Only five haplotypes were identified within the entire Amerindian study population, and the haplotype distribution was significantly different among the five tribes, with one (Arára) to four (Wayampí) haplotypes being found per tribe. These findings indicate a significant heterogeneity among the Indian tribes and contrast with the homogeneous distribution of the beta-globin gene cluster haplotypes but agree with our recent findings on the distribution of alpha-globin gene cluster haplotypes and the allele frequencies for six VNTRs in the same Amerindian tribes. Our data represent the first study of factor IX-associated polymorphisms in Amerindian populations and emphasizes the applicability of these genetic markers for population and human evolution studies.

  7. Triglyceride associated polymorphisms of the APOA5 gene have very different allele frequencies in Pune, India compared to Europeans

    PubMed Central

    Chandak, Giriraj R; Ward, Kirsten J; Yajnik, Chittaranjan S; Pandit, Anand N; Bavdekar, Ashish; Joglekar, Charu V; Fall, Caroline HD; Mohankrishna, P; Wilkin, Terence J; Metcalf, Bradley S; Weedon, Michael N; Frayling, Timothy M; Hattersley, Andrew T

    2006-01-01

    Background The APOA5 gene variants, -1131T>C and S19W, are associated with altered triglyceride concentrations in studies of subjects of Caucasian and East Asian descent. There are few studies of these variants in South Asians. We investigated whether the two APOA5 variants also show similar association with various lipid parameters in Indian population as in the UK white subjects. Methods We genotyped 557 Indian adults from Pune, India, and 237 UK white adults for -1131T>C and S19W variants in the APOA5 gene, compared their allelic and genotype frequency and determined their association with fasting serum triglycerides, total cholesterol, HDL and LDL cholesterol levels using univariate general linear analysis. APOC3 SstI polymorphism was also analyzed in 175 Pune Indian subjects for analysis of linkage disequilibrium with the APOA5 variants. Results The APOA5 -1131C allele was more prevalent in Indians from Pune (Pune Indians) compared to UK white subjects (allele frequency 20% vs. 4%, p = 0.00001), whereas the 19W allele was less prevalent (3% vs. 6% p = 0.0015). Patterns of linkage disequilibrium between the two variants were similar between the two populations and confirmed that they occur on two different haplotypes. In Pune Indians, the presence of -1131C allele and the 19W allele was associated with a 19% and 15% increase respectively in triglyceride concentrations although only -1131C was significant (p = 0.0003). This effect size was similar to that seen in the UK white subjects. Analysis of the APOC3 SstI polymorphism in 175 Pune Indian subjects showed that this variant is not in appreciable linkage disequilibrium with the APOA5 -1131T>C variant (r2 = 0.07). Conclusion This is the first study to look at the role of APOA5 in Asian Indian subjects that reside in India. The -1131C allele is more prevalent and the 19W allele is less prevalent in Pune Indians compared to UK Caucasians. We confirm that the APOA5 variants are associated with triglyceride levels

  8. Impact of karyotype organization on interlocus recombination between T cell receptor genes in Equidae.

    PubMed

    Drbalova, Jitka; Musilova, Petra; Kubickova, Svatava; Sebestova, Hana; Vahala, Jiri; Rubes, Jiri

    2014-01-01

    The T cell receptor (TCR) genes (TRA, TRB, TRD and TRG) reside in 3 different chromosomal regions. During the maturation of T lymphocytes, the TCR genes are rearranged by site-specific recombination, a process that also predisposes T cells to aberrant rearrangements. Illegitimate recombination between the TCR genes occurs at a low level in healthy individuals, but this frequency may correlate with the risk of lymphoma. The aim of this work was to investigate interlocus recombination in equids. Illegitimate rearrangements were studied in peripheral blood lymphocytes by FISH with painting and BAC probes and by sequencing of PCR products, and the frequencies of recombination were assessed in horses and 4 other equids. The presence of several trans-rearrangement products between the TRA and TRG genes was verified by PCR in all investigated equids. Frequencies of trans-rearrangements in horses are higher than in humans, and colocalization of the TCR genes on the same chromosome increases the incidence of trans-rearrangements between them. The orientation of the TCR genes does not impact interlocus recombination itself but does affect the viability of cells carrying its products and consequently the number of trans-rearrangements observed in lymphocytes.

  9. The Relationship Between Gene Polymorphism of Leptin and Leptin Receptor and Growth Hormone Deficiency.

    PubMed

    He, Jinshui; Fang, Yanling; Lin, Xinfu; Zhou, Huowang; Zhu, Shaobo; Zhang, Yugui; Yang, Huicong; Ye, Xiaoling

    2016-02-26

    BACKGROUND Growth hormone deficiency (GHD) is a major cause of congenital short stature. GHD patients have significantly decreased serum leptin levels, which are regulated by gene polymorphism of leptin and leptin receptor. This study thus investigated the relationship between gene polymorphism and susceptibility to GHD. MATERIAL AND METHODS A case-control study was performed using 180 GHD children in addition to 160 healthy controls. After the extraction of whole genomic DNA, the genotypes of leptin and leptin receptor gene loci were analyzed by sequencing for single-nucleotide polymorphism. RESULTS The frequency distribution of all alleles identified in leptin gene (loci rs7799039) and leptin receptor gene (loci rs1137100 and rs1137101) fit Hardy-Weinberg equilibrium. There was a significant difference in allele frequency at loci rs7799039 or rs1137101, as individuals with heterozygous GA allele had lower (rs7799039) or higher (rs1137101) GHD risk. No significant difference in allele frequency was discovered at loci rs1137100 (p>0.05), which was unrelated to GHD susceptibility. CONCLUSIONS Gene polymorphism of leptin (loci rs7799039) and leptin receptor (loci rs1137101) are correlated with GHD susceptibility.

  10. Robotic-Assisted Sleeve Lobectomy Using the Four-Arm Technique in the DaVinci Si® and Xi® Systems.

    PubMed

    Egberts, Jan-Hendrik; Möller, Thorben; Becker, Thomas

    2018-06-16

    Sleeve lobectomy (SL) makes it possible to resect centrally located lung carcinoma oncological correct while protecting healthy lung tissue. However, this procedure is often limited with conventional video-assisted thoracoscopic surgery, due to the limited mobility of the rigid and long instruments and the limited visualization. Therefore, these interventions are often still performed in the open conventional technique with the well-known disadvantages. Particularly in the reconstruction of the respiratory tract, precise sewing must be performed in a small space to avoid stenosis of the different diameter of the lumina. Robotic surgery offers several advantages through an enlarged three-dimensional view and flexibility of the robotic instruments, which are particularly evident when sewing. So far, there are only a few reports of robotic SL. Here, we describe our experience of performing robotic SL with four arms on both, the currently available DaVinci Xi ® and Si ® systems. Georg Thieme Verlag KG Stuttgart · New York.

  11. Low frequency of c-MPL gene mutations in Iranian patients with Philadelphia-negative myeloproliferative disorders.

    PubMed

    Ghotaslou, A; Nadali, F; Chahardouli, B; Alizad Ghandforosh, N; Rostami, S H; Alimoghaddam, K; Ghavamzadeh, A

    2015-01-01

    Myeloproliferative disorders are a group of diseases characterized by increased proliferation of myeloid lineage. In addition to JAK2V617F mutation, several mutations in the c-MPL gene have been reported in patients with philadelphia-negative chronic myeloproliferative disorders that could be important in the pathogenesis of diseases. The aim of the present study was to investigate the frequency of c-MPL and JAK2V617F mutations in Iranian patients with Philadelphia-negativemyeloproliferative disorders. Peripheral blood samples were collected from 60 patients with Philadelphia-negative MPD) Subgroups ET and PMF) and 25 healthy subjects as control group. The mutation status of c-MPL and Jak2V617F were investigated by using Amplification-refractory mutation system (ARMS) and Allele-Specific PCR (AS-PCR), respectively. The results were confirmed by sequencing. Among 60 patients, 34 (56.6%) and 1(1.7%) had Jak2V617F and c-MPL mutation, respectively. Patients with Jak2V617F mutation had higher WBC counts and hemoglobin concentration than those without the mutation (p= 0.005, p=0.003). In addition, for all healthy subjects in control group, mutations were negative. The present study revealed that the c-MPL mutations unlike the Jak2V617F mutations are rare in Iranian patients with Ph-negative MPNs and the low mutation rate should be considered in the design of screening strategies of MPD patients.

  12. Low frequency of c-MPL gene mutations in Iranian patients with Philadelphia-negative myeloproliferative disorders

    PubMed Central

    Ghotaslou, A; Nadali, F; Chahardouli, B; Alizad Ghandforosh, N; Rostami, SH; Alimoghaddam, K; Ghavamzadeh, A

    2015-01-01

    Background Myeloproliferative disorders are a group of diseases characterized by increased proliferation of myeloid lineage. In addition to JAK2V617F mutation, several mutations in the c-MPL gene have been reported in patients with philadelphia-negative chronic myeloproliferative disorders that could be important in the pathogenesis of diseases. The aim of the present study was to investigate the frequency of c-MPL and JAK2V617F mutations in Iranian patients with Philadelphia-negativemyeloproliferative disorders. Material and Methods Peripheral blood samples were collected from 60 patients with Philadelphia-negative MPD) Subgroups ET and PMF) and 25 healthy subjects as control group. The mutation status of c-MPL and Jak2V617F were investigated by using Amplification-refractory mutation system (ARMS) and Allele-Specific PCR (AS-PCR), respectively. The results were confirmed by sequencing. Results Among 60 patients, 34 (56.6%) and 1(1.7%) had Jak2V617F and c-MPL mutation, respectively. Patients with Jak2V617F mutation had higher WBC counts and hemoglobin concentration than those without the mutation (p= 0.005, p=0.003). In addition, for all healthy subjects in control group, mutations were negative. Conclusions The present study revealed that the c-MPL mutations unlike the Jak2V617F mutations are rare in Iranian patients with Ph-negative MPNs and the low mutation rate should be considered in the design of screening strategies of MPD patients. PMID:25914801

  13. Text analysis of MEDLINE for discovering functional relationships among genes: evaluation of keyword extraction weighting schemes.

    PubMed

    Liu, Ying; Navathe, Shamkant B; Pivoshenko, Alex; Dasigi, Venu G; Dingledine, Ray; Ciliax, Brian J

    2006-01-01

    One of the key challenges of microarray studies is to derive biological insights from the gene-expression patterns. Clustering genes by functional keyword association can provide direct information about the functional links among genes. However, the quality of the keyword lists significantly affects the clustering results. We compared two keyword weighting schemes: normalised z-score and term frequency-inverse document frequency (TFIDF). Two gene sets were tested to evaluate the effectiveness of the weighting schemes for keyword extraction for gene clustering. Using established measures of cluster quality, the results produced from TFIDF-weighted keywords outperformed those produced from normalised z-score weighted keywords. The optimised algorithms should be useful for partitioning genes from microarray lists into functionally discrete clusters.

  14. [Influence of extremely low-frequency magnetic field on circadian rhythm of cryptochrome in mouse embryonic fibroblasts].

    PubMed

    Sun, Z Y; Geng, D Y; Chen, C F; Wang, P P; Song, T

    2017-06-20

    Objective: To investigate the influence of extremely low-frequency magnetic field on periodical expression of cryptochrome ( Cry ) gene in mouse embryonic fibroblast NIH3T3 cells. Methods: The NIH3T3 cells were divided into magnetic field group and sham-exposure group. The NIH3T3 cells in the magnetic field group were stimulated by horse serum and then exposed to an extremely low-frequency magnetic field (50 Hz and 0.3 mT) for 48 hours, and those in the sham-exposure group were also stimulated by horse serum and then exposed to a coil for 48 hours. The NIH3T3 cells were collected, total RNA was extracted, and cDNA was obtained via reverse transcription. Real-time fluorescent quantitative RT-PCR was used to measure the changes in transcription cycles of Cry and Period genes in both groups. Results: There was no significant difference in the proliferation rate at 0, 12, 24, and 48 hours of exposure between the two groups ( P >0.05) . Both sham-exposure group and magnetic field group showed a rhythmic change in the expression of Cry gene, and compared with the sham-exposure group, the magnetic field group had a significantly shortened circadian rhythm of Cry gene in NIH3T3 cells ( t =2.57, P <0.05) . Both groups had rhythmic and periodical expression of Period gene and there was no significant difference between the two groups ( t =0.70, P >0.05) . Conclusion: Extremely low-frequency magnetic field can significantly shorten the circadian rhythm of Cry gene in mouse embryonic fibroblasts, while there is no significant change in the circadian rhythm of Period gene.

  15. Comparison of gene expression profiles between dental pulp and periodontal ligament tissues in humans

    PubMed Central

    Gong, Ai-Xiu; Zhang, Jing-Han; Li, Jing; Wu, Jun; Wang, Lin; Miao, Deng-Shun

    2017-01-01

    There are anatomical and functional differences between human dental pulp (DP) and periodontal ligament (PDL). However, the molecular biological differences and function of these tissues are poorly understood. In the present study, we employed a cDNA microarray array to screen for differentially expressed genes (DEGs) between human DP and PDL tissues, and used the online software WebGestalt to perform the functional analysis of the DEGs. In addition, the STRING database and KEGG pathway analysis were applied for interaction network and pathway analysis of the DEGs. DP and PDL samples were obtained from permanent premolars (n=16) extracted for orthodontic purposes. The results of the microarray assay were confirmed by RT-qPCR. The DEGs were found to be significantly associated with the extracellular matrix and focal adhesion. A total of 10 genes were selected to confirm the results. The mRNA levels of integrin alpha 4 (ITGA4), integrin alpha 8 (ITGA8), neurexin 1 (NRXN1) and contactin 1 (CNTN1) were significantly higher in the DP than in the PDL tissues. However, the levels of collagen type XI alpha 1 (COL11A1), aggrecan (ACAN), collagen type VI alpha 1 (COL6A1), chondroadherin (CHAD), laminin gamma 2 (LAMC2) and laminin alpha 3 (LAMA3) were higher in the PDL than in the DP samples. The gene expression profiles provide novel insight into the characterization of DP and PDL tissues, and contribute to our understanding of the potential molecular mechanisms of dental tissue mineralization and regeneration. PMID:28713908

  16. Flamenco, a gene controlling the gypsy retrovirus of drosophila melanogaster

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

    Prud`homme, N.; Gans, M.; Masson, M.

    1995-02-01

    Gypsy is an endogenous retrovirus of Drosophila melanogaster. It is table and does not transpose with detectable frequencies in most Drosophila strains. However, we have characterized unstable strains, known as MG, in which it transposes at high frequency. These stocks contain more copies of gypsy than usual stocks. Transposition results in mutations in several genes such as ovo and cut. They are stable and are due to gypsy insertions. Integrations into the ovo{sup D1} female sterile-dominant mutation result in a null allele of the gene and occurrence of fertile females. This phenomenon, known as the ovo{sup D1} reversion assay, canmore » be used to quantitate gypsy activity. We have shown that the properties of MG strains result from mutation of a host gene that we called flamenco (flam). It has a strict maternal effect on gypsy mobilization: transposition occurs at high frequency only in the germ line of the progeny of females homozygous for mutations of the gene. It is located at position 65.9 (20A1-3) on the X chromosome. The mutant allele present in MG strains is essentially recessive. Flamenco seems to control the infective properties of gypsy. 40 refs., 10 figs., 6 tabs.« less

  17. Methylation of miRNA genes and oncogenesis.

    PubMed

    Loginov, V I; Rykov, S V; Fridman, M V; Braga, E A

    2015-02-01

    Interaction between microRNA (miRNA) and messenger RNA of target genes at the posttranscriptional level provides fine-tuned dynamic regulation of cell signaling pathways. Each miRNA can be involved in regulating hundreds of protein-coding genes, and, conversely, a number of different miRNAs usually target a structural gene. Epigenetic gene inactivation associated with methylation of promoter CpG-islands is common to both protein-coding genes and miRNA genes. Here, data on functions of miRNAs in development of tumor-cell phenotype are reviewed. Genomic organization of promoter CpG-islands of the miRNA genes located in inter- and intragenic areas is discussed. The literature and our own results on frequency of CpG-island methylation in miRNA genes from tumors are summarized, and data regarding a link between such modification and changed activity of miRNA genes and, consequently, protein-coding target genes are presented. Moreover, the impact of miRNA gene methylation on key oncogenetic processes as well as affected signaling pathways is discussed.

  18. [Inheritance of bc1 gene in intersubspecific hybrids of rice (Oryza sativa L.)].

    PubMed

    Lü, Chuan-Gen; Zong, Shou-Yu; Zhao, Ling; Qi, Qing-Ming; Zou, Jiang-Shi; Ikehashi, Hiroshi

    2004-10-01

    Distorted segregation of the brittle culm-1 gene (bc1) on rice chromosome 3 was found with greatly increased or decreased frequency of bc1 bc1 genotype in inter-subspecific hybrids, although the gene normally transmitted to its offspring following the Mendelian Law in intra-subspecific hybrids. In a combination of Kamairazu//Ketan Nangka/Kamairazu,an increased frequency of bc1 bc1 in F1, normal segregation in F2, and increased and decreased frequency in a few F3 and F4 lines were observed. In a cross of IR36/Kamairazu, decreased frequency in F2, both normal and decreased segregations in F3 and F4, and a few lines of increased ratio in F4 were found. In F2 of Ketan Nangka/IR36//Kamairazu, increased and decreased and normal segregations were all observed. There was no significant correlation between the frequency of bc1 bc1 and pollen fertility. It implied that distorted segregation of bc1 was caused by selective fertilization of male gametes, which were governed by gametophyte genes of ga2, ga3 and ga14 on chromosome 3.

  19. Frequency of iss and irp2 genes by PCR method in Escherichia coli isolated from poultry with colibacillosis in comparison with healthy chicken in poultry farms of Zabol, South East of Iran.

    PubMed

    Sadeghi Bonjar, M S; Salari, S; Jahantigh, M; Rashki, A

    2017-03-01

    There is no special trait for differentiation of Avian Pathogenic Escherichia coli from Avian Fecal Escherichia coli. This investigation is aimed, as a case control study, to evaluate and compare the frequency of iss and irp2 in 43 AFEC strains and also 40 and 56 E. coli strains isolated from the liver and kidney of chickens with colibacillosis, respectively, farmed in Zabol, as a border region of Iran, by PCR. 86.9% and 37.2% of isolates collected from chickens with colibacillosis and feces samples obtained from healthy chickens were positive for iss gene, respectively (P<0.05). On average, 59.3% of E. coli strains isolated from colibacillosis have irp2 gene while 27.9% of isolates from the feces of healthy birds were positive (P<0.05). 52.15% of isolates from colibacillosis and 19.62% of isolates from healthy chicken feces were positive for both genes, with statistical significant difference (p<0.05). This marked difference in the distribution of iss and irp2 genes makes these two genes good markers to differentiate AFEC and APEC strains especially in Sistan region to improve colibacillosis control measurements.

  20. Extensive Copy-Number Variation of Young Genes across Stickleback Populations

    PubMed Central

    Eizaguirre, Christophe; Samonte, Irene E.; Kalbe, Martin; Lenz, Tobias L.; Stoll, Monika; Bornberg-Bauer, Erich; Milinski, Manfred; Reusch, Thorsten B. H.

    2014-01-01

    Duplicate genes emerge as copy-number variations (CNVs) at the population level, and remain copy-number polymorphic until they are fixed or lost. The successful establishment of such structural polymorphisms in the genome plays an important role in evolution by promoting genetic diversity, complexity and innovation. To characterize the early evolutionary stages of duplicate genes and their potential adaptive benefits, we combine comparative genomics with population genomics analyses to evaluate the distribution and impact of CNVs across natural populations of an eco-genomic model, the three-spined stickleback. With whole genome sequences of 66 individuals from populations inhabiting three distinct habitats, we find that CNVs generally occur at low frequencies and are often only found in one of the 11 populations surveyed. A subset of CNVs, however, displays copy-number differentiation between populations, showing elevated within-population frequencies consistent with local adaptation. By comparing teleost genomes to identify lineage-specific genes and duplications in sticklebacks, we highlight rampant gene content differences among individuals in which over 30% of young duplicate genes are CNVs. These CNV genes are evolving rapidly at the molecular level and are enriched with functional categories associated with environmental interactions, depicting the dynamic early copy-number polymorphic stage of genes during population differentiation. PMID:25474574

  1. Analysis of common deafness gene mutations in deaf people from unique ethnic groups in Gansu Province, China.

    PubMed

    Xu, Bai-Cheng; Bian, Pan-Pan; Liu, Xiao-Wen; Zhu, Yi-Ming; Yang, Xiao-Long; Ma, Jian-Li; Chen, Xing-Jian; Wang, Yan-Li; Guo, Yu-Fen

    2014-09-01

    The GJB2 gene mutation characteristic of Dongxiang was the interaction result of ethnic background and geographical environment, and Yugur exhibited the typical founder effect. The SLC26A4 gene mutation characteristic of Dongxiang was related to caucasian backgrounds and selection of purpose exons, i.e. ethnic background and the penetrance of ethnic specificity caused the low mtDNA1555A>G mutation frequency in Dongxiang. To determine the prevalence of GJB2 and SLC26A4 genes and mtDNA1555A>G mutations and analyze the ethnic specificity in the non-syndromic sensorineural hearing loss (NSHL) of unique ethnic groups in Gansu Province. Peripheral blood samples were obtained from Dongxiang, Yugur, Bonan, and ethnic Han groups with moderately severe to profound NSHL in Gansu Province. Bidirectional sequencing (or enzyme digestion) was applied to identify the sequence variations. The pathogenic allele frequency of the three gene mutations was different. The frequency of the GJB2 gene among the Dongxiang, Yugur, Bonan, and ethnic Han groups was 9.03%, 12.5%, 5.88%, and 12.17%, respectively. No difference was found between the ethnic groups. The frequencies of the SLC26A4 genes were 3.23%, 8.33%, 0%, and 9.81%, respectively. The mutation frequency of mtDNA1555A>G was 0%, 0%, 0%, and 6.03%, respectively. No difference was found between the ethnic groups, except for the Dongxiang and ethnic Han groups, both in SLC26A4 gene and mtDNA1555A>G.

  2. Occurrence of tetracycline resistance genes in aquaculture facilities with varying use of oxytetracycline

    PubMed Central

    Seyfried, Erin E.; Newton, Ryan J.; Rubert, Kennedy F.; Pedersen, Joel A.; McMahon, Katherine D.

    2014-01-01

    The contribution of human activities to environmental reservoirs of antibiotic resistance is poorly understood. The purpose of this study was to determine if oxytetracycline (OTC) use in aquaculture facilities increased the detection frequency (i.e. prevalence) of tetracycline resistance genes relative to facilities with no recent OTC treatment. We used PCR to screen water and sediment from four non-commercial fish farms in northwestern Wisconsin for the presence of ten tetracycline resistance determinants (tetR): tet(A), tet(B), tet(D), tet(E), tet(G), tet(M), tet(O), tet(Q), tet(S) and tet(W). Water from farms with recent OTC use had significantly higher tetR detection frequencies than did water from farms without recent OTC use, with prevalence in raceways and rearing ponds of farms with recent OTC use exceeded by more than two-fold that of farms not using OTC. Effluent from all farms, regardless of treatment regime, had higher tetR detection frequencies than their corresponding influent for all genes, but the specific combinations of tetR genes detected in a sample were not different from their corresponding influent. Although OTC use was associated with the increased occurrence and diversity of tetR genes in water samples, it was not found to relate to tetR gene occurrence in sediment samples. Sediment samples from facilities with no recent OTC use had significantly higher frequencies of tetR gene detection than did samples from facilities with recent OTC use. All of the tetR genes were detected in both the medicated and non-medicated feed samples analyzed in this study. These findings suggest that both OTC treatment in aquaculture facilities, and the farms themselves, may be sources of tetR gene introduction to the environment. To our knowledge, this is the first study to use genotypic and cultivation-independent methods to examine tetR gene occurrence associated with OTC use in aquaculture. PMID:20217406

  3. Same-sex sexual behaviors among male migrants in a context of male "marriage squeeze": results from an exploratory survey in urban Xi'an, China.

    PubMed

    Yang, Xueyan; Attané, Isabelle; Li, Shuzhuo; Yang, Bo

    2012-11-01

    The male marriage squeeze in China may increase the prevalence of male same-sex sexual behaviors among unmarried male migrants who lack stable female sexual partners. The same-sex sexual behaviors among unmarried male migrants appear to be at high risk of transmission of human immunodeficiency virus (HIV) and sexually transmitted infections (STIs), mainly because of a lack of knowledge of these diseases. Using data from the "Survey on Reproductive Health and Family Life of Migrant Male Bachelors in Urban Areas" conducted in Xi'an City, Shaanxi Province, in December 2009 and January 2010, this study compares same-sex sexual behaviors of unmarried with that of married male migrants (including married but separated men who are migrating without their spouse or partner and cohabitating men who are migrating with their spouse or partner). It is reported that the prevalence of same-sex sexual behaviors among unmarried males reaches 11%, more than twice the 5.1% reported by married but separated men and thrice the 3.8% reported by cohabitating men. It also appears that the same-sex sexual behaviors is significantly associated with men's attitudes toward same-sex sexual behaviors (odds ratio = 1.59, p < .001), toward life-long bachelorhood (odds ratio = 1.35, p < .01), and with marital status (odds ratio = 0.37, p < .01). The frequency of condom use appears to be higher among unmarried men than among men who are married, whether or not they migrated with their wives, and is significantly associated with scores on knowledge about HIV/AIDS (estimated coefficient = .12, p < .001) and STIs (estimated coefficient = .22, p < .01). It is also associated with the likelihood of same-sex sexual behaviors (estimated coefficients = .83, p < .01) and marital status (estimated coefficients for married but separated = -.50, p < .05; estimated coefficients for cohabitating = -.77, p < .001).

  4. Frequency of APOE, MTHFR and ACE polymorphisms in the Zambian population

    PubMed Central

    2014-01-01

    Background Polymorphisms within the apolipoprotein-E (APOE), Methylenetetrahydrofolate reductase (MTHFR) and Angiotensin I-converting enzyme (ACE) genes has been associated with cardiovascular and cerebrovascular disorders, Alzheimer’s disease and other complex diseases in various populations. The aim of the study was to analyze the allelic and genotypic frequencies of APOE, MTHFR C677T and ACE I/D gene polymorphisms in the Zambian population. Results The allele frequencies of APOE polymorphism in the Zambian populations were 13.8%, 59.5% and 26.7% for the ε2, ε3 and ε4 alleles respectively. MTHFR C677T and ACE I/D allele frequencies were 8.6% and 13.8% for the T and D minor alleles respectively. The ε2ε2 genotype and TT genotype were absent in the Zambian population. The genetic distances between Zambian and other African and non-African major populations revealed an independent variability of these polymorphisms. Conclusion We found that the APOE ε3 allele and the I allele of the ACE were significantly high in our study population while there were low frequencies observed for the MTHFR 677 T and ACE D alleles. Our analysis of the APOE, MTHFR and ACE polymorphisms may provide valuable insight into the understanding of the disease risk in the Zambian population. PMID:24679048

  5. Crystal Structure of Saccharomyces cerevisiae ECM4, a Xi-Class Glutathione Transferase that Reacts with Glutathionyl-(hydro)quinones

    PubMed Central

    Schwartz, Mathieu; Didierjean, Claude; Hecker, Arnaud; Girardet, Jean-Michel; Morel-Rouhier, Mélanie; Gelhaye, Eric; Favier, Frédérique

    2016-01-01

    Glutathionyl-hydroquinone reductases (GHRs) belong to the recently characterized Xi-class of glutathione transferases (GSTXs) according to unique structural properties and are present in all but animal kingdoms. The GHR ScECM4 from the yeast Saccharomyces cerevisiae has been studied since 1997 when it was found to be potentially involved in cell-wall biosynthesis. Up to now and in spite of biological studies made on this enzyme, its physiological role remains challenging. The work here reports its crystallographic study. In addition to exhibiting the general GSTX structural features, ScECM4 shows extensions including a huge loop which contributes to the quaternary assembly. These structural extensions are probably specific to Saccharomycetaceae. Soaking of ScECM4 crystals with GS-menadione results in a structure where glutathione forms a mixed disulfide bond with the cysteine 46. Solution studies confirm that ScECM4 has reductase activity for GS-menadione in presence of glutathione. Moreover, the high resolution structures allowed us to propose new roles of conserved residues of the active site to assist the cysteine 46 during the catalytic act. PMID:27736955

  6. [Thrombophlebitis in the central vein catheter (AVA3Xi) custody to the internal jugular vein: a case report].

    PubMed

    Morohashi, Toru; Ogura, Takahiro; Inamura, Rie; Kazama, Tomiei

    2012-06-01

    The central vein catheter-related infection and thrombosis are comparatively frequent and may cause a serious complication. AVA3Xi was taken into custody to the internal jugular vein, and the patient suffured from thrombophlebitis on the seventh day after the operation. A 73-year-old woman 151 cm tall and weighing 50 kg was scheduled for pancreatoduodenectomy under propofol-remifentanil anesthesia combined with epidural anesthesia (operating time 9 hours and 21 minutes, anesthetizing time 12 hours and 1 minute). The past history of the thrombosis was not present, and it was especially unquestionable for the trap including the preoperative testing and the central venous catheter insertion. The time course after the operation was also good. But the patient claimed the stiffness of the cervix on the postoperative seventh day; fever and shivering were also accompanied. S. epidermidis was identified by the blood culture. Thrombophlebitis was diagnosed with CT. It is necessary to choose an appropriate catheter and endeavor for the prevention and early detection of the blood clot formation to prevent catheter-related infection and thrombosis with cooperation with the surgeon.

  7. The effects of 2.45 GHz radio frequency energy on neurological tissue genes using an unrestrained murine model in vivo

    NASA Astrophysics Data System (ADS)

    Stevens, Brandon William

    The effects that radio frequency (RF) energy has on the body is currently an inconclusive and controversial topic. This is in part due to the differences and issues that can be found in previous studies. This thesis describes a study on the effect of continuous RF energy on the genome of in vivo mouse brain tissue for a duration of 31 days. To address the issues found in previous studies a new standardized procedure was followed. The genome of the brain tissue was quantified using RNA-seq and then analyzed using statistical combinations and empirical p-values. Transcripts with their respective p-values were uploaded into Integrity Pathway Analysis® to determine genes associated disease and function within the brain tissue. The results from this study provided evidence that supports RF energy induces changes in the genome. Additionally, the results provided evidence of the first reported case of a potential RF-controlled genetic transistor.

  8. Maintenance of genetic variation with a frequency-dependent selection model as compared to the overdominant model.

    PubMed

    Hedrick, P W

    1972-12-01

    A frequency-dependent selection model proposed by Huang, Singh and Kojima (1971) was found to be more effective at maintaining genetic variation in a finite population than the overdominant model. The fourth moment parameter of the distribution of unfixed states showed that there was a more platykurtic distribution for the frequency-dependent model. This agreed well with the expected gene frequency change found for an infinite population.

  9. Increased frequency of angiotensin-converting enzyme DD genotype in patients with type 2 diabetes in Taiwan.

    PubMed

    Hsieh, M C; Lin, S R; Hsieh, T J; Hsu, C H; Chen, H C; Shin, S J; Tsai, J H

    2000-07-01

    Diabetes is one of the major causes of end-stage renal failure in the Taiwanese population. Previous studies have shown that angiotensin-converting enzyme (ACE) inhibitor can improve glucose utilization and suppress hepatic glucose production and the renin-angiotensin system may play an important role in the initiation and progression of diabetic nephropathy. Thus, ACE gene polymorphism may be associated with type 2 diabetes and diabetic nephropathy. To investigate the distribution of ACE-I/D genotype in type 2 diabetes and diabetic nephropathy, we examined 336 patients with type 2 diabetes (157 without nephropathy and 179 with nephropathy) and 263 age-matched normal controls. The diagnosis of nephropathy was made when daily protein loss exceeded 500 mg. ACE gene polymorphism was analysed by use of polymerase chain reaction. Our study revealed that the frequency of the D allele of the ACE gene was 29.3% in normal controls. The frequency of ACE DD genotype was significantly higher in type 2 diabetics compared with normal controls (18.2 vs 9.1%, P<0.01). The frequency of ACE DD genotype in patients with diabetic nephropathy was significantly higher than in patients without nephropathy (22.3 vs 13.4%, P<0.05). To determine whether ACE gene polymorphism was associated with the severity of diabetic nephropathy, we divided patients with diabetic nephropathy into dialysis and non-dialysis groups. The frequency of ACE DD genotype in the dialysis group was significantly higher than in non-dialysis group (28.7 vs 15.3%, P<0.05). Our results indicate that the frequency of ACE DD genotype is markedly higher in patients with type 2 diabetes, and the ACE DD genotype is significantly associated with diabetic nephropathy.

  10. [From Science to Law: Findings of Reha XI Project on Ascertaining the Need for Rehabilitation in Medical Service Assessments].

    PubMed

    Kalwitzki, T; Huter, K; Runte, R; Breuninger, K; Janatzek, S; Gronemeyer, S; Gansweid, B; Rothgang, H

    2017-03-01

    Introduction: In the broad-based consortium project "Reha XI - Identifying rehabilitative requirements in medical service assessments: evaluation and implementation", a comprehensive analysis of the corresponding procedures was carried out by the medical services of the German Health Insurance Funds (MDK). On the basis of this analysis, a Good Practice Standard (GPS) for assessments was drawn up and scientifically evaluated. This article discusses the findings and applicability of the GPS as the basis for a nationwide standardized procedure in Germany as required by the Second Act to Strengthen Long-Term Care (PSG II) under Vol. XI Para. 18 (6) of the German Social Welfare Code. Method: The consortium project comprised four project phases: 1. Qualitative and quantitative situation analysis of the procedures for ascertaining rehabilitative needs in care assessments carried out by the MDK; 2. Development of a Good Practice Standard (GPS) in a structured, consensus-based procedure; 3. Scientific evaluation of the validity, reliability and practicability of the assessment procedure according to the GPS in the MDK's operational practice; 4. Survey of long-term care insurance funds with respect to the appropriateness of the rehabilitation recommendations drawn up by care assessors in line with the GPS for providing a qualified recommendation for the applicant. The evaluation carried out in the third project phase was subject to methodological limitations that may have given rise to distortions in the findings. Findings: On the basis of the situation analysis, 7 major thematic areas were identified in which improvements were implemented by applying the GPS. For the evaluation of the GPS, a total of 3 247 applicants were assessed in line with the GPS; in 6.3% of the applicants, an indication for medical rehabilitation was determined. The GPS procedure showed a high degree of reliability and practicability, but the values for the validity of the assessment procedure were

  11. [Study on the content and carbon isotopic composition of water dissolved inorganic carbon from rivers around Xi'an City].

    PubMed

    Guo, Wei; Li, Xiang-Zhong; Liu, Wei-Guo

    2013-04-01

    In this study, the content and isotopic compositions of water dissolved inorganic carbon (DIC) from four typical rivers (Chanhe, Bahe, Laohe and Heihe) around Xi'an City were studied to trace the possible sources of DIC. The results of this study showed that the content of DIC in the four rivers varied from 0.34 to 5.66 mmol x L(-1) with an average value of 1.23 mmol x L(-1). In general, the content of DIC increased from the headstream to the river mouth. The delta13C(DIC) of four rivers ranged from -13.3 per thousand to -7.2 per thousand, with an average value of -10.1 per thousand. The delta13C(DIC) values of river water were all negative (average value of -12.6 per thousand) at the headstream of four rivers, but the delta13C(DIC) values of downstream water were more positive (with an average value of -9.4 per thousand). In addition, delta13C(DIC) of river water showed relatively negative values (the average value of delta13C(DIC) was -10.5 per thousand) near the estuary of the rivers. The variation of the DIC content and its carbon isotope suggested that the DIC sources of the rivers varied from the headstream to the river mouth. The negative delta13C(DIC) value indicated that the DIC may originate from the soil CO2 at the headstream of the rivers. On the other hand, the delta13C(DIC) values of river water at the middle and lower reaches of rivers were more positive, and it showed that soil CO2 produced by respiration of the C4 plants (like corn) and soil carbonates with positive delta13C values may be imported into river water. Meanwhile, the input of pollutants with low delta13C(DIC) values may result in a decrease of delta13C(DIC) values in the rivers. The study indicated that the DIC content and carbon isotope may be used to trace the sources of DIC in rivers around Xi'an City. Our study may provide some basic information for tracing the sources of DIC of rivers in the small watershed area in the Loess Plateau of China.

  12. Frequency and genetic characterization of V(DD)J recombinants in the human peripheral blood antibody repertoire.

    PubMed

    Briney, Bryan S; Willis, Jordan R; Hicar, Mark D; Thomas, James W; Crowe, James E

    2012-09-01

    Antibody heavy-chain recombination that results in the incorporation of multiple diversity (D) genes, although uncommon, contributes substantially to the diversity of the human antibody repertoire. Such recombination allows the generation of heavy chain complementarity determining region 3 (HCDR3) regions of extreme length and enables junctional regions that, because of the nucleotide bias of N-addition regions, are difficult to produce through normal V(D)J recombination. Although this non-classical recombination process has been observed infrequently, comprehensive analysis of the frequency and genetic characteristics of such events in the human peripheral blood antibody repertoire has not been possible because of the rarity of such recombinants and the limitations of traditional sequencing technologies. Here, through the use of high-throughput sequencing of the normal human peripheral blood antibody repertoire, we analysed the frequency and genetic characteristics of V(DD)J recombinants. We found that these recombinations were present in approximately 1 in 800 circulating B cells, and that the frequency was severely reduced in memory cell subsets. We also found that V(DD)J recombination can occur across the spectrum of diversity genes, indicating that virtually all recombination signal sequences that flank diversity genes are amenable to V(DD)J recombination. Finally, we observed a repertoire bias in the diversity gene repertoire at the upstream (5') position, and discovered that this bias was primarily attributable to the order of diversity genes in the genomic locus. © 2012 The Authors. Immunology © 2012 Blackwell Publishing Ltd.

  13. Systematic study of association of four GABAergic genes: glutamic acid decarboxylase 1 gene, glutamic acid decarboxylase 2 gene, GABA(B) receptor 1 gene and GABA(A) receptor subunit beta2 gene, with schizophrenia using a universal DNA microarray.

    PubMed

    Zhao, Xu; Qin, Shengying; Shi, Yongyong; Zhang, Aiping; Zhang, Jing; Bian, Li; Wan, Chunling; Feng, Guoyin; Gu, Niufan; Zhang, Guangqi; He, Guang; He, Lin

    2007-07-01

    Several studies have suggested the dysfunction of the GABAergic system as a risk factor in the pathogenesis of schizophrenia. In the present study, case-control association analysis was conducted in four GABAergic genes: two glutamic acid decarboxylase genes (GAD1 and GAD2), a GABA(A) receptor subunit beta2 gene (GABRB2) and a GABA(B) receptor 1 gene (GABBR1). Using a universal DNA microarray procedure we genotyped a total of 20 SNPs on the above four genes in a study involving 292 patients and 286 controls of Chinese descent. Statistically significant differences were observed in the allelic frequencies of the rs187269C/T polymorphism in the GABRB2 gene (P=0.0450, chi(2)=12.40, OR=1.65) and the -292A/C polymorphism in the GAD1 gene (P=0.0450, chi(2)=14.64 OR=1.77). In addition, using an electrophoretic mobility shift assay (EMSA), we discovered differences in the U251 nuclear protein binding to oligonucleotides representing the -292 SNP on the GAD1 gene, which suggests that the -292C allele has reduced transcription factor binding efficiency compared with the 292A allele. Using the multifactor-dimensionality reduction method (MDR), we found that the interactions among the rs187269C/T polymorphism in the GABRB2 gene, the -243A/G polymorphism in the GAD2 gene and the 27379C/T and 661C/T polymorphisms in the GAD1 gene revealed a significant association with schizophrenia (P<0.001). These findings suggest that the GABRB2 and GAD1 genes alone and the combined effects of the polymorphisms in the four GABAergic system genes may confer susceptibility to the development of schizophrenia in the Chinese population.

  14. Models of stochastic gene expression

    NASA Astrophysics Data System (ADS)

    Paulsson, Johan

    2005-06-01

    Gene expression is an inherently stochastic process: Genes are activated and inactivated by random association and dissociation events, transcription is typically rare, and many proteins are present in low numbers per cell. The last few years have seen an explosion in the stochastic modeling of these processes, predicting protein fluctuations in terms of the frequencies of the probabilistic events. Here I discuss commonalities between theoretical descriptions, focusing on a gene-mRNA-protein model that includes most published studies as special cases. I also show how expression bursts can be explained as simplistic time-averaging, and how generic approximations can allow for concrete interpretations without requiring concrete assumptions. Measures and nomenclature are discussed to some extent and the modeling literature is briefly reviewed.

  15. Molecular genetic techniques for gene manipulation in Candida albicans.

    PubMed

    Xu, Qiu-Rong; Yan, Lan; Lv, Quan-Zhen; Zhou, Mi; Sui, Xue; Cao, Yong-Bing; Jiang, Yuan-Ying

    2014-05-15

    Candida albicans is one of the most common fungal pathogen in humans due to its high frequency as an opportunistic and pathogenic fungus causing superficial as well as invasive infections in immunocompromised patients. An understanding of gene function in C. albicans is necessary to study the molecular basis of its pathogenesis, virulence and drug resistance. Several manipulation techniques have been used for investigation of gene function in C. albicans, including gene disruption, controlled gene expression, protein tagging, gene reintegration, and overexpression. In this review, the main cassettes containing selectable markers used for gene manipulation in C. albicans are summarized; the advantages and limitations of these cassettes are discussed concerning the influences on the target gene expression and the virulence of the mutant strains.

  16. Mutation intolerant genes and targets of FMRP are enriched for nonsynonymous alleles in schizophrenia.

    PubMed

    Leonenko, Ganna; Richards, Alexander L; Walters, James T; Pocklington, Andrew; Chambert, Kimberly; Al Eissa, Mariam M; Sharp, Sally I; O'Brien, Niamh L; Curtis, David; Bass, Nicholas J; McQuillin, Andrew; Hultman, Christina; Moran, Jennifer L; McCarroll, Steven A; Sklar, Pamela; Neale, Benjamin M; Holmans, Peter A; Owen, Michael J; Sullivan, Patrick F; O'Donovan, Michael C

    2017-10-01

    Risk of schizophrenia is conferred by alleles occurring across the full spectrum of frequencies from common SNPs of weak effect through to ultra rare alleles, some of which may be moderately to highly penetrant. Previous studies have suggested that some of the risk of schizophrenia is attributable to uncommon alleles represented on Illumina exome arrays. Here, we present the largest study of exomic variation in schizophrenia to date, using samples from the United Kingdom and Sweden (10,011 schizophrenia cases and 13,791 controls). Single variants, genes, and gene sets were analyzed for association with schizophrenia. No single variant or gene reached genome-wide significance. Among candidate gene sets, we found significant enrichment for rare alleles (minor allele frequency [MAF] < 0.001) in genes intolerant of loss-of-function (LoF) variation and in genes whose messenger RNAs bind to fragile X mental retardation protein (FMRP). We further delineate the genetic architecture of schizophrenia by excluding a role for uncommon exomic variants (0.01 ≤ MAF ≥ 0.001) that confer a relatively large effect (odds ratio [OR] > 4). We also show risk alleles within this frequency range exist, but confer smaller effects and should be identified by larger studies. © 2017 Wiley Periodicals, Inc.

  17. The in vivo Pig-a gene mutation assay, a potential tool for regulatory safety assessment.

    PubMed

    Dobrovolsky, Vasily N; Miura, Daishiro; Heflich, Robert H; Dertinger, Stephen D

    2010-01-01

    The Pig-a (phosphatidylinositol glycan, Class A) gene codes for a catalytic subunit of the N-acetylglucosamine transferase complex involved in an early step of glycosylphosphatidyl inositol (GPI) cell surface anchor synthesis. Pig-a is the only gene involved in GPI anchor synthesis that is on the X-chromosome, and research into the origins of an acquired genetic disease involving GPI anchor deficiency (paroxysmal nocturnal hemoglobinuria) indicates that cells lacking GPI anchors, or GPI-anchored cell surface proteins, almost always have mutations in the Pig-a gene. These properties of the Pig-a gene and the GPI anchor system have been exploited in a series of assays for measuring in vivo gene mutation in blood cells from humans, rats, mice, and monkeys. In rats, flow cytometric measurement of Pig-a mutation in red blood cells requires microliter volumes of blood and data can be generated in hours. Spontaneous mutant frequencies are relatively low (<5 × 10(-6)) and rats treated with multiple doses of the potent mutagen, N-ethyl-N-nitrosourea, display Pig-a mutant frequencies that are close to the sum of the frequencies produced by the individual exposures. A general observation is that induced mutant frequencies are manifested earlier in reticulocytes (about 2 weeks after treatment) than in total red blood cells (about 2 months after exposure). Based on data from a limited number of test agents, the assay shows promise for regulatory applications, including integration of gene mutation measurement into repeat-dose toxicology studies.

  18. [Study on pollution characteristics of carbonaceous aerosols in Xi'an City during the spring festival].

    PubMed

    Zhou, Bian-Hong; Zhang, Cheng-Zhong; Wang, Ge-Hui

    2013-02-01

    The samples of PM2.5 with 8 times periods were collected using Automated Cartridge Collection Unit (ACCU) of Rupprecht& Patashnick (R&P)Corporation, and monitored by R&P1400a instrument of TEOM series online during 2011 Spring Festival in Xi'an city. The organic carbon (OC), elemental carbon (EC), water-soluble organic carbon (WSOC) and water-insoluble organic carbon (WIOC) contents of 3 h integrated PM2.5 were analyzed to evaluate the influence of firework display on the carbonaceous components in urban air. The mass concentration of PM2.5 was found increased significantly from 00:00 A. M. to 02:59 A. M. at the Chinese Lunar New Year's Eve than the non-firework periods, reaching 1514.8 microg.m-3 at 01:00 A. M. The mass concentrations of OC, EC, WSOC, and WIOC during the same time period were 123.3 microg.m-3, 18.6 microg.m-3, 66.7 microg.m-3, and 56.6 microg.m-3, about 1.7, 1.2, 1.4, and 2.2 times higher than the average in normal days, respectively. Correlation analysis among WSOC, OC, and EC contents in PM25 showed that firework emission was an obvious source of carbonaceous aerosol in the Spring Festival vacation. However, it only contributes to 9. 4% for aerosol in fireworks emission.

  19. Polymorphic human somatostatin gene is located on chromosome 3.

    PubMed Central

    Naylor, S L; Sakaguchi, A Y; Shen, L P; Bell, G I; Rutter, W J; Shows, T B

    1983-01-01

    Somatostatin is a 14-amino-acid neuropeptide and hormone that inhibits the secretion of several peptide hormones. The human gene for somatostatin SST has been cloned, and the sequence has been determined. This clone was used as a probe in chromosome mapping studies to detect the human somatostatin sequence in human-rodent hybrids. Southern blot analysis of 41 hybrids, including some containing translocations of human chromosomes, placed SST in the q21 leads to qter region of chromosome 3. Human DNAs from unrelated individuals were screened for restriction fragment polymorphisms detectable by the somatostatin gene probe. Two polymorphisms were found: (i) an EcoRI variant located at the 3' end of the gene, found in Caucasian, U.S. Black, and Asian populations with a frequency of approximately 0.10 and (ii) a BamHI variant in the intron, which occurs in Caucasians at a frequency of 0.13. Images PMID:6133281

  20. Digital sorting of complex tissues for cell type-specific gene expression profiles.

    PubMed

    Zhong, Yi; Wan, Ying-Wooi; Pang, Kaifang; Chow, Lionel M L; Liu, Zhandong

    2013-03-07

    Cellular heterogeneity is present in almost all gene expression profiles. However, transcriptome analysis of tissue specimens often ignores the cellular heterogeneity present in these samples. Standard deconvolution algorithms require prior knowledge of the cell type frequencies within a tissue or their in vitro expression profiles. Furthermore, these algorithms tend to report biased estimations. Here, we describe a Digital Sorting Algorithm (DSA) for extracting cell-type specific gene expression profiles from mixed tissue samples that is unbiased and does not require prior knowledge of cell type frequencies. The results suggest that DSA is a specific and sensitivity algorithm in gene expression profile deconvolution and will be useful in studying individual cell types of complex tissues.